http://www.expasy.org/spotlight/ one month, one protein en-us Vivienne.Gerritsen@isb-sib.ch 2008-09-30T14:45:29+01:00 hourly 1 2000-01-01T12:00+00:00 http://www.expasy.org/spotlight/back_issues/sptlt097.shtml Can a smell affect social behaviour? Without a doubt. Let off an unpleasant one and those closest to you will move somewhere else. Likewise, an agreeable scent will keep them hovering in your vicinity. It’s an old trick. Flowers and animals have been using smells for millions of years to ward off predators or to attract individuals for the sake of reproduction. So it does not come as a surprise to learn that ants use the same kind of technique as a means of communication and social interaction. However, it is not so much the odour but the capacity to detect it that is at the basis of two types of social behaviour in a species of red fire ant, Solenopsis invicta – the ecological pest. This particular ant either belongs to a colony that has only one queen (monogyne) reigning over it or to a far larger colony which is ruled by several queens (polygyne). In the 1990s, scientists discovered that the basis of a monogyne or a polygyne colony amounted to the existence of only one protein: pheromone-binding protein. 619@http://www.expasy.org/spotlight/ Article 2008-09-30T14:45:29+01:00 http://www.expasy.org/spotlight/back_issues/sptlt096.shtml What? No issue in July? A number of our regular readers may have noticed that – for the first time in a short decade – no article appeared during the month of July. And time has only just given us the opportunity to squeeze one into a month of August about to end. What happened? 2008 marks the 10th anniversary of the Institute. About a year ago, we pondered on the idea of conceiving an exhibition which would not only celebrate this little milestone but would also present the world of bioinformatics in as attractive a way as possible to non-scientists. It was not an easy task. For many, the word ‘bioinformatics’ is as sexy as the word ‘pots’, and the work carried out is as attractive as the bottom of a cake tin. Despite this and thanks to a year’s collaboration with scientists, writers and graphic designers – and the financial support of a few sponsors – our exhibition ‘Chromosome Walk, a saunter along the human genome’ is about to celebrate its opening, on September 1st in Geneva’s botanical gardens. 616@http://www.expasy.org/spotlight/ Article 2008-08-27T21:39:03+01:00 http://www.expasy.org/spotlight/back_issues/sptlt095.shtml There are people who saunter through life unnoticed until something happens and reveals that they are far less ordinary than they appeared to be. The same goes for Heliobacter pylori. H. pylori is a bacterium which was discovered in the late 1800s but was forgotten for the best part of a century simply because no one had succeeded in cultivating it. Its role in causing gastric diseases was also discussed at the turn of the 19th century, only as the results were published in Polish they met with very little recognition outside Poland. And while H.pylori was being ignored, attempts were being made to study an enzyme which helps it to survive in the organisms it infects: urease. Like H.pylori, urease had to wade through waves of short-sightedness. Not only was it a common belief in those days that enzymes could not be proteins, but enzymes were also thought to exist in excessively low concentrations in plants and animals… Despite these barriers, H.pylori and urease finally triumphed at the end of the 20th century and both turned out to be singular entities. 615@http://www.expasy.org/spotlight/ Article 2008-06-29T11:20:28+01:00 http://www.expasy.org/spotlight/back_issues/sptlt094.shtml We are surrounded by smells. Pleasant ones and not so pleasant ones, hard to distinguish ones, mild ones and strong ones. Smells are not part of our everyday life for the simple sake of pleasure. They are there for a purpose. The perfume of a flower can be used as an attractant for a potential pollinator, for instance. The scent given off by a poisonous mushroom is a way of warding off a predator and, by the same token, can be instantly recognised as toxic by an animal, thereby saving both species. Special scents are also given off by males and females when mating is in the air, and no wine grower will ever argue that a wine’s fragrance is not for the sole purpose of seduction. But what is a smell? More often than not, a scent is made up of a mixture of odorant molecules which, together, will trigger off a complex olfactory system that will ultimately let us perceive it and, if we wish to, put words to it. The very first step in such a system involves an odorant receptor to which an odorant molecule binds. Recently, a new human odorant receptor – OR7D4 – was discovered. OR7D4 is special in that it is the first receptor known to respond to a specific odorant molecule. 612@http://www.expasy.org/spotlight/ Article 2008-05-22T15:06:48+01:00 http://www.expasy.org/spotlight/back_issues/sptlt093.shtml Triggering off the making of a baby may seem a pretty straightforward process. Which it is, from a certain point of view. Yet, before any decisive action is undertaken by a woman and a man in order to unite their gametes, sperm – like ovules – have already been through a very complex series of developmental transformations. Such transformations ensure that only sperm and ovules of the same species get involved with one another, for example, or that once a couple of gametes has united no one else is allowed in. Properties of this sort are expressed on the molecular level both on the sperm’s and the ovule’s surface. One such molecule is a receptor known as zp3 found in mammals. Zp3 is expressed on the ovule’s surface and, though it is just one of many molecules, it is an essential one. Without it, sperm would not only be incapable of binding to the ovule’s membrane but they would also most probably miss their target altogether. 609@http://www.expasy.org/spotlight/ Article 2008-04-24T12:57:58+01:00 http://www.expasy.org/spotlight/back_issues/sptlt092.shtml Dogs were not meant to fit into a bag. Yet, some do. Consequently, instead of enjoying a healthy walk in the countryside they can go shopping with their owners. Convenience – both for humans and dogs – has trimmed down canine size in the past few hundred years. It is easier for dogs to be part of a household if they are medium-sized and more practical for humans to keep them if they are not too large. As such, natural selection coupled with selective breeding has supplied us with dogs ranging from barely twenty centimetres to giant samples which measure over one metre. And the stakes that a cross between a large poodle and a tiny Chihuahua will produce a medium-sized mongrel are high. So there must be a straightforward mechanism which is involved in their size. IGF1 – or insulin growth factor 1 – seems to be at the heart of such a mechanism. Indeed, scientists have discovered that small dogs all carry a certain variant of IGF1 while large dogs do not – or very few. This would suggest that the IGF1 variant has the power to reduce the size of a dog. 603@http://www.expasy.org/spotlight/ Article 2008-03-20T09:49:45+01:00 http://www.expasy.org/spotlight/back_issues/sptlt091.shtml When I was a little girl, I thought that my left-handed classmates were special. I envied their difference. And I used to marvel at the way they crouched over their desk, embracing something invisible as they did their best to avoid smudging ink all over their sheet of paper. Left-handedness is special. But so is right-handedness. Humans are not the only animals to make use of their hands – or claws, or paws, or hooves - but they are the only ones who show a marked preference for either the left one, or the right one. If this is so, there must be a reason for it. And not only must there be a reason but it must translate a certain structure of our brain: an asymmetry somewhere. Indeed, our brain is divided into two hemispheres which are dedicated to processing different activities. One side looks after our dreams, while the other is far more down to earth. LRRTM1 is the first protein to have been discovered which seems to be directly involved in this brain asymmetry. Consequently, it influences the handedness of a human-being and, more astonishingly, may also predispose individuals to psychotic troubles such as schizophrenia. 600@http://www.expasy.org/spotlight/ Article 2008-02-22T13:00:48+01:00 http://www.expasy.org/spotlight/back_issues/sptlt090.shtml When there is nothing left to eat, we do not eat our parents or our children. We go down to the closest supermarket for food. Supermarkets, however, are not an option for bacteria. When they are short of nutrients, they are faced with a number of fates amongst which are sporulation, starvation or, for some, cannibalism. Indeed, Bacillus subtilis – a sporulating bacterium – has devised a way to feed on its sister cells in order to prolong its non-spore life. It does this by way of toxins which it produces itself and from which it must be protected to avoid committing suicide inadvertently… Needless to say, the molecular pathway is intricate and still obscure. However, hosts of proteins are being discovered, two of which are known as SkfA and SpdC whose actions result in B.subtilis sister cell lysis, from which the non-lysed cells will feed. 597@http://www.expasy.org/spotlight/ Article 2008-01-17T11:43:16+01:00 http://www.expasy.org/spotlight/back_issues/sptlt089.shtml 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. 593@http://www.expasy.org/spotlight/ Article 2007-12-17T11:16:28+01:00 http://www.expasy.org/spotlight/back_issues/sptlt088.shtml 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. 590@http://www.expasy.org/spotlight/ Article 2007-11-22T15:32:13+01:00 http://www.expasy.org/spotlight/back_issues/sptlt087.shtml There is more to RNA than meets the eye. In the 1980s, students in biology were told that this molecule’s raison d’ętre 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. 586@http://www.expasy.org/spotlight/ Article 2007-10-23T08:50:33+01:00 http://www.expasy.org/spotlight/back_issues/sptlt086.shtml 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. 585@http://www.expasy.org/spotlight/ Article 2007-09-27T16:38:24+01:00 http://www.expasy.org/spotlight/back_issues/sptlt085.shtml 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. 582@http://www.expasy.org/spotlight/ Article 2007-08-31T10:41:26+01:00 http://www.expasy.org/spotlight/back_issues/sptlt084.shtml 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. 576@http://www.expasy.org/spotlight/ Article 2007-07-16T12:46:03+01:00 http://www.expasy.org/spotlight/back_issues/sptlt083.shtml 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. 573@http://www.expasy.org/spotlight/ Article 2007-06-15T18:04:48+01:00