Excerpts from Recent Articles from 2008

2008 Back Issues

A snail's sting - December 2008
Despite their apparent slothfulness, some snails know how to put a predator on its knees. Intuitively, we are inclined to believe that defence involves not only speed but liveliness – two qualities which would not be those that spring to mind when describing a snail. So there is more to a snail than meets the eye. Indeed. Though the snails themselves may be the very image of idleness, they can produce molecules which can kill. Fast. This is nothing new. What is new, however, is that scientists have just found a toxin in a snail known as the apple snail, which is not only a protein but is also found in the snail’s eggs. So, long before a snail has actually developed into a mature mollusc, it is outfitted with a means of defence. (PDF version - 120K bytes)
Swiss-Prot cross references
Perivitellin-2 67 kDa subunit, Pomacea canaliculata, (Golden apple snail) : P0C8G6
Perivitellin-2 31 kDa subunit, Pomacea canaliculata, (Golden apple snail) : P0C8G7
Hidden powers - November 2008
We all take advantage of each other, one way or another. Cats hunt mice for food. Humans keep dogs for company. Flowers give off a scent to attract pollinators. Viruses use organisms to multiply. And ticks suck animal blood to stay alive. The tricks we use to these ends are varied and subtle. Flowers have put much effort into developing perfumes which are perceived by specific pollinators. Ticks have found ways of keeping blood fluid to be able to sip it. But it hasn’t been easy. Adaptation has taken its time to fine-tune ways of making good use of another organism. Ticks, for instance, have thought up the finest of strategies not only to recognise an organism from which they can feed but also to land on it, fix itself to it and feed from it. Each step is crucial to a tick’s survival. Understanding how a tick manages to shun its host’s immune system – let alone keep its blood from coagulating – can be very informative for the development of therapeutic drugs. (PDF version - 48K bytes)
Swiss-Prot cross references
Evasin-1, Rhipicephalus sanguineus : P0C8E7
Evasin-3, Rhipicephalus sanguineus : P0C8E8
Evasin-4, Rhipicephalus sanguineus : P0C8E9
The juice of life - October 2008
There is no life without blood. Pumped through us by the heart, blood carries the oxygen we breathe and relays it to every part of our body to keep us going. If too much of it leaves us, life leaves us too. As a consequence, this rich red fluid has become a powerful social, religious and literary symbol. Our bodies also know how vital it is and produce red blood cells continuously to replace those that have gone past their use-by date. However, there are instances – an accident, an illness or surgery for example – when the amount of blood required exceeds the amount that a body can produce on its own. And the only way to solve the problem is by pouring fresh blood into the body which needs it. It sounds simple but it is not. Today we know that blood can only be transfused if both the donor’s and the recipient’s blood match. If they don’t, our immune system will eventually kill us. Blood is always difficult to come by so years of research have been dedicated to finding ways of making it. Recently, a couple of bacterial enzymes were discovered, which could ‘clean’ red blood cells so that they could be transfused to any patient regardless of the blood group. (PDF version - 182K bytes)
Swiss-Prot cross references
Alpha-N-acetylgalactosaminidase, Flavobacterium meningosepticum : A4Q8F7
Alpha-1,3-galactosidase A, Streptomyces griseoplanus : B1V8K7
The queen's perfume - September 2008
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. (PDF version - 63K bytes)
Swiss-Prot cross references
Pheromone-binding protein Gp-9, Solenopsis invicta (Red imported fire ant) : Q8WP90
Take a walk on the genome - August 2008
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. (PDF version - 73K bytes)
Going unnoticed - June 2008
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. (PDF version - 452K bytes)
Swiss-Prot cross references
Urease subunit alpha, Helicobacter pylori : P14916
Urease subunit beta, Helicobacter pylori : P69996
The selfish smell - May 2008
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. (PDF version - 251K bytes)
Swiss-Prot cross references
Olfactory receptor 7D4, Homo sapiens (Human): Q8NG98
Molecular chastity - April 2008
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. (PDF version - 99K bytes)
Swiss-Prot cross references
Zona pellucida sperm-binding protein 3, Homo sapiens (Human): P21754
Zona pellucida sperm-binding protein 3, Mus musculus (Mouse): P10761
Zona pellucida sperm-binding protein 3, Rattus norvegicus (Rat): P97708

A dog's life - March 2008
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. (PDF version - 72K bytes)
Swiss-Prot cross references
Insulin-like growth factor 1, Canis familiaris (Dog): P33712

The hands to say it - February 2008
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. (PDF version - 65K bytes)
Swiss-Prot cross references
Leucine-rich repeat transmembrane neuronal protein 1, Homo sapiens (Human): Q96DN1

I'll have you for supper - January 2008
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. (PDF version - 49K bytes)
Swiss-Prot cross references
Sporulation killing factor skfA, Bacillus subtilis : O31422
Killing factor sdpC, Bacillus subtilis : O34344
Immunity protein sdpI, Bacillus subtilis : O32241


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