Excerpts from Recent Articles from 2007

2007 Back Issues

Ear of stone - December 2007
The end of December is a time of year when many lose their balance. This, however, is usually due to the numbing of the senses by an exaggerated consumption of alcohol. There are many other ways of losing your balance, and one of them can be caused by an altered architecture of the inner ear. Besides bearing the intricate machinery which allows animals to perceive sound, the inner ear is also responsible for our sense of movement. Those who are stricken with sea-sickness know all too well what this means. Very small regions known as the saccule and the utricle detect both gravity and acceleration, two forces we spend our time dealing with. Deprived of the capacity to perceive them, the simple act of moving our head would prove to be an awesome experience. At the heart of this perception are small stones. And one protein, otopetrin 1, is proving to be essential for their formation. (PDF version - 79K bytes)
Swiss-Prot cross references
Otopetrin 1, Danio rerio (Zebrafish): Q7ZWK8
Otopetrin 1, Homo sapiens (Human): Q7RTM1
Otopetrin 1a, Mus musculus (Mouse): Q80VM9

An unexpected place - November 2007
Life has its ways. We are given opportunities to make choices. We are even given opportunities to nudge life onto a path we wish. And yet, there seems to be an invisible force lurking beneath which leads you to the most unexpected places…an unexpected place which, in time, turns out to be the place where you should be. Call it destiny, perhaps. Today, fifty years after the day he was born, Amos is sitting in an office in Geneva at the head of a project which has travelled around the world and for which many people work. From a cramped attic to a large open space office, Swiss-Prot continues to grow both in work force and in use. Amos has won prizes for it. He has been praised for it. He has put much of his soul and his heart into it. And despite this, far from him was the desire of ever having really wanted it. (PDF version - 41K bytes)
Swiss-Prot cross references
Amos is behind each one of them. The first ever entered was P00001, now renamed: P99999
The dark side of RNA - October 2007
There is more to RNA than meets the eye. In the 1980s, students in biology were told that this molecule’s raison d’être was to be a template for the making of a protein. RNA, like DNA, was made out of nucleotides and had no particular function other than that of being a text that was to be read. Today, almost 30 years later, there is growing evidence that little bits of single-stranded RNA are just as crafty as many transcription factors and can regulate the expression of a gene, and hence a protein. However, they cannot do it without the help of enzymes, two of which are known as Drosha and Dicer. Drosha and Dicer are ribonucleases which work in unison to sculpt RNA strands that in turn acquire the ability to bind to specific parts of mRNA, which they subsequently silence. As a result, the mRNA’s product is not translated. (PDF version - 55K bytes)
Swiss-Prot cross references
Drosha, Homo sapiens (Human): Q9NRR4
Dicer, Homo sapiens (Human): Q9UPY3
Red velvet - September 2007
Autumn has come. So have the hunters. And stags have finished fashioning their antlers in their quest to seduce a partner, and fight off rivals. Besides copulation, antlers are one of nature’s many wonders. Not only are they beautiful and sculptural but they are a rare example of an organ which regenerates, rapidly and on a yearly basis. Consequently, it is hardly surprising that scientists are spending a lot of time trying to unravel the underlying mechanisms which participate in the growth of an antler. Annexin 2 is just one of the proteins involved in antler regeneration, and more specifically in cartilage mineralization. (PDF version - 64K bytes)
Swiss-Prot cross references
Annexin A2, Cervus elaphus (Red deer): Q2Q1M6
Of fidgets and food - August 2007
When you’re hungry, your thoughts go towards food. Without the urge to get up and find some, you’re in trouble. It’s a basic rule. Yet when transgressed one way or another, you can end up either overweight or underweight. It may sound silly because we feel – as humans – that we can decide for ourselves when to open the fridge or not. As it happens, we tend to an awful lot because eating is one of our pleasures. Consequently, we gather a surplus of energy which we stock around our buttocks and stomachs. However, given a little thought, moving for a meal is not so straightforward. Imagine a chicken whose organism needs fuel. If deprived of the sense of hunger, it may well do nothing about it, and starve. So there must be some underlying mechanism which pushes it to hunt down a grain or two; a mechanism which actually drives it to move elsewhere in pursuit of the calories it needs. Naturally, such a mechanism is always very complex. Yet scientists have discovered a protein – known as Bsx protein – which seems to be at the heart of both fidgeting and food intake, and hence of the propensity to be either stout or slim. (PDF version - 44K bytes)
Swiss-Prot cross references
Brain-specific homeobox protein, Homo sapiens (Human): Q3C1V8
Brain-specific homeobox protein, Mus musculus (Mouse): Q810B3
Brain-specific homeobox protein, Gallus gallus (Chicken): Q6RFL5

"journey into a tiny world" - July 2007
In 2002, Sylvie Déthiollaz and I were asked to imagine something that could entertain young children within the framework of a science fair. The fair was to be held in the Museum of the History of Science in Geneva, a neoclassical 19th century villa on the edge of Lake Geneva, which sits in the middle of a beautiful park. We had been thinking up activities for children for a couple of years already, which invariably involved coloured beads which we threaded onto a bit of wire to illustrate a protein’s sequence of amino acids. We then folded the wire to give an idea of what a protein’s 3D structure could resemble. The activity was always very popular, although frequently used as a spot where parents could leave their children while they wandered off to see something else. Besides our growing distaste in being used as a nursery, we couldn’t face beads and wire anymore either and, quite naturally, we suggested writing up a tale for children instead. And “journey into a tiny world” was conceived. (PDF version - 48K bytes)
Swiss-Prot cross references
Name of protein characters, in order of appearance and in Lily, Homo sapiens (Human):
Poietin, Homo sapiens (Human): P01588
Pepsin, Homo sapiens (Human): P00790
Albumin, Homo sapiens (Human): P02768
Globin, Homo sapiens (Human): P69905
Insulin, Homo sapiens (Human): P01308
Actin, Homo sapiens (Human): P60709
Myosin, Homo sapiens (Human): P12883
Collagen, Homo sapiens (Human): P02452
Immunoglobulin, Homo sapiens (Human): P01591
Orexin, Homo sapiens (Human): O43612
Crystalline, Homo sapiens (Human): P02489

Tangled - June 2007
Dementia is a debilitating experience. For the afflicted, and for those who are close to them. Alzheimer’s disease (AD) is a form of dementia from which millions of people suffer worldwide. Besides the well-known symptom of memory decline, people with Alzheimer’s are progressively troubled by language impediments and peculiar visuospatial perception, for example, but also behavioural and psychiatric dysfunctions. Though the passing of the years is the main cause for what is known as sporadic AD, there is also a far more rare hereditary form. Rare or not, both types of AD are the result of irreversible neuron loss, brought on by protein deposits in the central nervous system. Detecting Alzheimer’s is not a trivial affair. The first symptoms are not different from the normal process of aging. And it takes years before serious handicaps emerge. However, there seems to be one protein – known as apoE4 – whose presence is proving to be a sure indicator of whether or not someone is prone to AD. (PDF version - 74K bytes)
Swiss-Prot cross references
Apolipoprotein E precursor, Homo sapiens (Human): P02649

The power behind pain - May 2007
We feel pain for a reason. Either to be informed of something that is likely to hurt us more unless we turn our backs on it, or of something that has gone wrong inside us. It is a sensation that has been evolving over millions of years, from yeast to man. Pain is multiple. Understanding its vocabulary and intricate syntax can shed light on what it is, why it is and how it could be countered. Detected by receptors, the sensation of pain can be kick-started from any part of our body. The TRP receptors are a family of such receptors, activated by an array of pain stimuli. They can detect hordes of different noxious chemical compounds but also environmental sensations such as extreme heat and cold. One particular TRP receptor – TRPA1 – comes as a surprise because, unlike many of the other TRP family members, it can detect multiple sensations leading to pain, as opposed to only one. (PDF version - 81K bytes)
Swiss-Prot cross references
Transient receptor potential cation channel, Mus musculus (Mouse): Q8BLA8
Transient receptor potential cation channel, Homo sapiens (Human) : O75762

Slip sliding away - April 2007
Like us, bacteria have to move if they want to get somewhere. Or away from something. We take the bus, hop into a car, use our legs or climb onto a bicycle. Different bacteria have different means of locomotion that they have had ample time to perfect since their first appearance on earth millions of years ago. Some squirt slime to propel themselves forward. Or use flagella to swim in water. While others hitch a ride on a fellow cell, or project pili with which they heave themselves forward. Recently, researchers discovered yet another mechanism: gliding by way of minute anchors. Such motility systems always involve complex protein assemblies but one individual sticks out among the others: the adventurous gliding Z protein. AglZ is an essential part of the gliding mechanism some bacteria use to skim across solid surfaces. (PDF version - 47K bytes)
Swiss-Prot cross references
Adventurous-gliding motility protein Z, Myxococcus xanthus : Q6RW49

The tenuous nature of sex - March 2007
Everyone knows how to tell the difference between a boy and a girl. The exterior signals are obvious. And yet, despite such a clear statement on Nature’s behalf, the molecular pathways underlying our being either male or female are subtle and fragile. It takes very little to make a woman out of a man – at least as far as our chromosome makeup is involved. We were told that boys are XY, and girls XX. But it’s not so simple. Some girls are XY, and some boys are XX… So there must be something sophisticated involved. And we are only beginning to discover what. Because of its singular architecture, the male Y chromosome is distinctive under the microscope and it was not long before 19th century scientists caught on that it had a major role in the making of a man. A closer look at it led molecular biologists to a specific region on the Y chromosome and, in the 1990s, scientists announced the discovery of a protein – the Sex-determining region Y protein (Sry) – that had a major role in convincing a foetus to become a baby boy. (PDF version - 274K bytes)
Swiss-Prot cross references
Sex-determining region Y protein, Homo sapiens (Human) : Q05066
Sex-determining region Y protein, Mus musculus (Mouse) : Q05738

Heavy metal - February 2007
Our grandmothers used to make jam in huge copper pans. The same copper pans that you would see hanging over the stove, with that distinctive green patina lining the inside. The same green patina that children instinctively knew was poisonous. And yet copper is essential to life. Without traces of this heavy metal in most living beings, a lot can go wrong because many enzymes depend on it to carry out their function. As a result, an organism must know how to keep copper at a healthy level – neither too high, nor too low. And this is achieved by way of transmembrane pumps which taxi copper in and out of cells. One such copper pump is known as the Menkes disease-associated protein because an American neurologist, John Menkes, first described an illness associated with this pump. Indeed, when the protein is deficient, it creates havoc. (PDF version - 45K bytes)
Swiss-Prot cross references
Menkes disease-associated protein, Homo sapiens (Human) : Q04656
Menkes disease-associated protein, Mus musculus (Mouse) : Q64430
Menkes disease-associated protein, Rattus norvegicus (Rat) : P70705

Of froth and haze - January 2007
When we raise a glass of wine, rarely do we give a thought to what has been involved in its making. Yet a wine’s hue, its taste, its aroma, its sparkle and even the nature of its haze are given the same attention a mother would to her newborn. Many of the qualities of a wine are the doings not only of proteins inherent to the grapes, rice or any other product used to make it, but also to proteins which belong to yeast strains that are added for fermentation, and hence the production of alcohol. Consequently, it is hardly surprising that much time and effort is put into the identification and understanding of such proteins, in the quest to satisfy the palates and aesthetics of many. And the purses of others. Recently, two yeast proteins were discovered. The first is involved in the production of foam as the Japanese rice wine – sake – is brewed, and the second in the production of haze in white wine. Despite a difference in their functions, parts of their sequence are very similar, not to mention identical, and both belong to the cell wall of different strains of Saccharomyces cerevisiae. (PDF version - 52K bytes)
Swiss-Prot cross references
Cell wall protein AWA1, Saccharomyces cerevisiae (Baker's yeast) : Q8TGE1
Haze protective factor, Saccharomyces cerevisiae (Baker's yeast) : Q05164


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