Friday, 27 March 2009

Jingo jargon

BELOW you will notice a short scientific highlight, entitled When autumn falls, published in this month's issue of Nature Reviews Molecular Cell Biology. I include it for one very simple reason: I wrote it. But in preparing it for this site, I realized quite how high the assumed understanding of the piece is, and so offer this as a short lesson in the jargon of science. What is with all those italics? What is a transcript, and what is a gene? What the devil is a microRNA?

Much like starch (that wonderful carbohydrate in our staple foodstuff, the potato), which is a string of individual glucose sugars (a polymer of glucose monomers), DNA is a string of individual nucleic acids. Each nucleic acid is a little more complicated than glucose molecules - comprising a sugar, a phosphate and a nitrogenous 'base'. Cleverly, there are two strings wound around each other (the famed 'double helix'), which provides a cunning mechanism for the DNA to copy itself - you see, there are four common types of nucleic acid, identical except for the nitrogenous bases. The four different bases are called adenine, cytosine, guanine and thymine, or, for simplicity, A, C, G and T. Owing to their chemical structures, the bases 'pair' up across the helix, with A aligning with T, and C with G:

Strand 1 Strand 2
| |
A = T
C = G
| |
(diagram for illustrative purposes only: at ease, scientific pedants)

So, all you need to copy a strand of DNA is a plentiful supply of free nucleic acids and a way to unzip the double strand. Once unwound, the exposed single strand becomes a template: A binds to T, and C binds to G in the order of the complete strand, and then some enzymes come in, work their magic, and seal the monomers into second strand.

But, we hear that DNA is the 'information' in a cell. Packaged in the nucleus of every cell in the body (well, almost), DNA is the source of those elusive entities: genes. But how can a string of four types of acid be responsible for building you, hedgehogs and eyes of newt?

Contrary to common understanding, proteins are much more than a dietary requirement for making muscles. They are an enormously complicated family of molecules that do everything that makes you you - they are the enzymes that break down your food, they help to make hormones, they assist the division of your cells and, yes, they are structural components too.

DNA makes proteins. Specifically, it encodes them. First, a messenger molecule is made in the same way as DNA is replicated: the double-strand unzips and free nucleic acids align with their counterparts to form a copy. The nucleic acids in this circumstance are RNA, not DNA, monomers. These differ chemically, and are more transient, but work in the same way - although RNA does not have thymine (it uses uracil (U) instead). This messenger (a transcript) is called a messenger RNA, or mRNA, and is single stranded. Second, the mRNA leaves the nucleus (as DNA cannot) and feeds into a complex structure called a ribosome, which is, to all intents and purposes, a protein factory. And here's the clever bit:

Proteins are made of 20 or so amino acids. To turn a genetic code of 4 letters into a 20-letter amino acid alphabet, the mRNA molecule is 'read' by the ribosome three letters at a time. So, for example, GGU equates to a glycine amino acid. The amino acids attach to another specific RNA molecule, a transfer RNA (tRNA), which exposes three specific RNA nucleic acids to pair up with the mRNA in the ribosome, thereby aligning the amino acids in the correct order, as specified by the original DNA in the nucleus.

These are the fundamentals of genetics: DNA encodes mRNA, which leaves the nucleus and uses ribosomal wizardry to pair up with amino acid-carrying tRNAs, allowing the ribosome to combine the amino acids in the order aseembled, thereby making a protein. A gene? Well, this is the stretch of DNA of the correct length to make a specific protein*.

In scientific literature, gene symbols are denoted by italics and proteins in roman. The use of capitals depends on the species involved.

In my article, I talk about Arabidopsis thaliana, a plant species from the brassica family that is used as a model organism - that is, it is the standard and best-characterized species for study. The authors uncovered a genetic loop of two genes - EIN2 and ORE1 (note italics) - and a microRNA called miR164. A microRNA is encoded by DNA but is never translated into a protein; instead, in RNA form, it suppresses the mRNA of other genes. How this works is not known with any certainty. It follows, based on the nomenclature stated above, that miR164 is the actual microRNA, and MIR164 is the gene that encodes it. Lastly, the article mentions ore1 and ein2 mutants - these are plants in which ORE1 and EIN2 have been altered in some way to function differently or not at all (the lower case is a specific style for Arabidopsis).

With all this in mind, hopefully my highlight now makes some kind of sense!

*Definitions vary.

Friday, 13 March 2009

Days gone by

SAT next to me, at our shared house group social, was Eamonn. A retired member of the Irish diaspora, he spends his winters watching classic films, eager for the warm weather to return so that he can get out and about. He especially likes The Cider House Rules.

Eamonn comes from a forgotten world.

He arrived in London shortly after the war. Work in Ireland was becoming hard to come by, so, by recommendation, he moved to London. Reeling from the Blitz, London was the place to be if you were in the building industry, and Eamonn was a carpenter by trade.

Throughout his time in the working world he moved from the construction trade to shop window design and construction to the building of exhibition spaces. He didn't just stay in London, moving up and down the country from Torquay to Yorkshire. Along the way he learnt to discern international accents, as the country was far more culturally diverse than you might assume. Even now, he can expertly distinguish South African from Kiwi.

But this is not what makes Eamonn's tale spectacular.

He told us of the time when London was big but not busy. Crime happened, but you didn't hear about it, and you certainly weren't paranoid about it. Life felt safer. Nobody would be found out and about after 10.30pm. You worked and then you went to the pub to laugh about the day. Or, you went to the dance.

This is where the boys met the girls, and a man would be picked from the boys on account of his quick-stepping, his jive and his ability to lead in the foxtrot. No drinking to boost false confidence, no teeny bopping and self-conscious feelings. This was entertainment. The boys watch the girls who watch the boys, who watch the girls go by, eye to eye.

He met his lovely wife at a dance. Many of his peers met their partners there too. You went to the dance to court. The world was a simpler, less panicked, happier place.

I can't be the only one who longs for days gone by, can I?

Thursday, 12 March 2009

Been there. Done that. Ate a pig.

MONDAY's commute was a little longer than usual, arriving (on time) at work in King's Cross, London, having awoken in Selly Oak, Birmingham, 100 miles away. I spend a lot of my time there these days. I rather miss it.

The peculiar thing about Birmingham is that it's a very topsy turvy city. There is no centre from which everything else radiates. There is, of course, a city centre, but everything is hidden below and above each other. You need to know where to find it. One moment you'll be in a state-of-the-art shopping centre, then suddenly China town will be below you, or the brick work of a railway embankment or canal bridge will ascend high above you. There is everything in a very small space. It is no less diverse as you travel across it: jump on a train from student-central Selly Oak, with its rows upon rows of terraces, and on your way to the centre you'll pass allotments, the Botanic Gardens and the leafy loveliness that is Edgbaston and then descend beneath a mass of roads and warehouses. Keep going and you'll pass the deprived yet captivating areas of Duddeston and Aston, canals and flyovers, and suddenly find affluence all over again. Then Birmingham ends, there are fields (of brussel sprouts) and then... Lichfield.

On Sunday, Rachel and I went to Lichfield for an adventure. We knew little about the place, other than that it lies at the end of the invaluable Selly Oak to Birmingham New Street train line. Turns out, it's quite the gem.

Formerly more important than Birmingham, Lichfield is a small city steeped in history - it is, for example, the birthplace of Dr Samuel Johnson, author of the first dictionary - quietly tucked away in the Midlands. We arrived at about 1.30, finding first a shopping centre that felt oddly reminiscent of Exeter years ago. There was an Adams. I suspect if we'd have looked closely enough there would have been a QS and a Peacocks too. Rachel was keenly looking out for a C&A. Then suddenly the brick work ages dramatically, the pedestrianised streets become paved, the tudor houses come out in force, and there are cloisters. It is the type of place that can get away with having a hat shop.

The world is a better place because hat shops still thrive in places like this.

But, in truth, it took us several hours to find all of this, despite being just minutes walk from the train station. This is because it was lunchtime, and no adventure would be complete without a good sit down meal. Fortunately for us, there is the Kaspico cafe, which, you see, serves fantastic food at bargain prices. A roast, for example, will set you back £4. So will a Honey Roast Pork Shank with lots of lovely vegetables.

Guess what I had?

The shank was so large that the couple next to us felt inclined to wish me luck before I started, and we are fairly sure that the staff behind the counter took bets as to whether I could polish it off. It was enormous; but I was not defeated. On leaving, the cafe owner even asked me if I had managed it. I like to think that I left them in awe.

On we went (slowly), through the market square to the cathedral, a truly inspiring piece of architecture. And on, to the house of Erasmus Darwin, now a museum to the doctor, inventor, poet and influential evolutionist. His house looks out on his herb garden and, behind it, the giant cathedral. We tried to do the museum as quickly as possible. Running out of time but genuinely interested, we desperately tried not to let down the man at the welcome desk, who had valiantly put so much effort into explaining what we could see and learn, how best to structure our visit, and how to use our audio guides. All we had really wanted was to pop in and look around in a few minutes, but he had seemed so happy that we'd picked up the audio guides. The look on his face as we left was one of genuine hurt and crushing disappointment. I promise here and now to go back and do his museum justice.

Anyway, then we had to go home: back to the train station and back to studentville.

(Via the fudge shop.)