Excerpts from Recent Articles from 2009

2009 Back Issues

String of intrusion - December 2009
When I was little, I used to wear little cotton shirts that were knitted by my grandmother. So? Well, onto them she sewed tiny nacre buttons you could never get hold of and which mesmerized me because of the different colours that shone off them depending on how you oriented them in the light. You can still find these buttons today but plastic ones have almost completely replaced them – and some even try to copy the lustre which is so particular to mother of pearl. What is it that makes pearl what it is known for? Aragonite. Aragonite is a calcium carbonate mineral and, very recently, scientists discovered a complex of three proteins in the pearl oyster Pinctada fucata, which seems to be at the heart of aragonite formation and orientation, and hence the famous sheen. (PDF version - 274K bytes)
UniProt cross references
Pearlin, Pinctada fucata, (Pearl oyster) : O97048
Pif80, Pinctada fucata, (Pearl oyster) : C7G0B5
Pif97, Pinctada fucata, (Pearl oyster) : C7G0B5
Darwin's dessert - November 2009
Charles Darwin has been resting in Westminster Abbey since April 1882 and scientists have been wondering ever since what it was that he suffered from for most of his adult life. It is a well-known fact that the famous naturalist steered clear of many official gatherings and was barely able to defend his theory of evolution because of chronic ailments of all sorts which kept him from being the sociable man he may otherwise have been. Many have thought that the origin of his various complaints – which were as diverse as vomiting, severe headaches, palpitations, eczema and flatulence – were purely psychosomatic. Others have suggested that Darwin must have been afflicted by some kind of illness such as Chagas’ disease or, more recently, Crohn’s disease. What everyone seems to agree upon though is that Darwin was definitely suffering from a form of gastrointestinal disorder which may well have involved an inherited lactose intolerance. Lactose intolerance is brought about by the lack of the enzyme lactase which breaks down lactose, thus making it digestible. (PDF version - 60K bytes)
UniProt cross references
Lactase-phlorizin hydrolase, Homo sapiens, (Human) : P09848
in like a shot - October 2009
Making use of a tubular structure to inject something into something else is a widespread practice. Doctors use syringes to inject medicine into patients. Mammals use their reproductive organ to supply their female counterparts with semen. Wasps use their sting to insert venom into their enemy. And Encephalitozoon cuniculi uses a polar tube as a means to infect. E.cuniculi infects species throughout the animal kingdom. It does this by inserting a long tube into the host cell’s membrane and injecting directly into the cytoplasm what it needs to proliferate. E.cuniculi is a parasitic unicellular eukaryote and thus cannot survive on its own. But the pathogen has to be able to recognise its host first. Scientists have discovered one protein – known as ‘spore wall and anchoring disk complex protein EnP1’ – which is found in the area from where the polar tube is thrust, and which is capable of binding to surface molecules on the host cell’s membrane. Thus creating the cell to cell contact needed to trigger off infection. (PDF version - 42K bytes)
UniProt cross references
Spore wall and anchoring disk complex protein EnP1, Encephalitozoon cuniculi, (Microsporidian parasite) : Q8SWL3
another dark horse - September 2009
Life is sustained thanks to a continuous flow of chemistry within cells and between cells. Molecules of all shapes and sizes are being scooped up, modified, and released – albeit in a different form – to produce fuel, trigger off a metabolic process or indeed put an end to one, act as a messenger or simply become waste product. Until fairly recently, lactate was thought to be just that: a dead-end by-product following muscular effort for example. And for many a year, it was stashed away in the backs of minds as something which had no future. But it does. In the past decade or so, scientists have discovered that lactate has a life after all; it is not only being shuttled inside a cell but also from cell to cell, and may well have a role in telling our brain when a muscle is tired, or helping us to perceive muscular pain. As for most chemical entities, there are always proteins involved in binding to them, breaking them down or adding something onto them. One enzyme in particular is directly involved in lactate’s career: lactate dehydrogenase, or LDH. (PDF version - 57K bytes)
Swiss-Prot cross references
L-lactate dehydrogenase B (LDH heart subunit), Homo sapiens, (Human) : P07195
L-lactate dehydrogenase A (LDH muscle subunit), Homo sapiens, (Human) : P00338
paint my thoughts - August 2009
Drawing is probably not a talent the layman would normally associate with Science. Yet it has been an essential ingredient in the life of many scientists for the advancement of their field of research, among them, the Spanish neurobiologist Santiago Ramón y Cajal (1852-1934). Cajal contributed greatly to our understanding of the brain, not only in his writings but also by way of the fine drawings of his observations, which have always been heralded as a key element in conveying the evidence necessary to establish the neuron theory of the anatomy and physiology of the brain. Almost a century later, the world of brain research has gone one step further. Thanks to genetic recombination, scientists are getting proteins to draw for them. What is more, in colour and 3D… The artist’s name is GFP – green fluorescent protein – a protein whose fluorescent properties have inspired many a researcher since its chance discovery in the 1960s. (PDF version - 468K bytes)
Swiss-Prot cross references
Green fluorescent protein, Aequoria victoria, (Jellyfish) : P42212
the beetle's brothel - July 2009
It’s nice to have a warm place to mate. You may think this applies only to mammals. But it doesn’t. Insects also love to breed in a cosy setting – in particular some beetles that have taken to coupling in large lilies which provide them with heat, as long as they stick around long enough to carry some pollen away. It’s a clever invention, based on ‘give and take’ and a way-of-living largely put into practice by plants since they are stricken with immobility. They’re ready to give insects a little of their nectar but they’ll also make sure some of their pollen flies off with them for dissemination. How do lilies warm the place for beetles? By way of one of two respiratory pathways – known as the alternative one – which turns the energy produced into heat. A key enzyme involved in this alternative respiratory pathway has the sexy name of ‘alternative oxidase’. (PDF version - 56K bytes)
Swiss-Prot cross references
Alternative oxidase, Sauromatum guttatum , (Voodoo lily) : P22185
when tough is soft - June 2009
The way to fertility can be a long one. When a bee innocently drops a grain of pollen in a flower, there is no guarantee that the ovary is close by. Mother Nature has not given pollen the means to walk but she has armed it with a built-in system – the pollen tube – which grows longer and longer until it reaches the ovary. The procedure is simple and effective, and in some respects not so different from our own reproductive system. Needless to say, such a structure needs to be both rigid and supple in order to preserve its shape while it elongates. How does it do this? At the end of the tube is a budding tip – the only part which grows. Here, a host of enzymes are hard at work either solidifying or softening the cell wall as the pollen tube germinates. Amongst these enzymes are the pectin methylesterases which are capable of turning the cell wall polysaccharide pectin into a rigid frame or soft jelly… (PDF version - 37K bytes)
Swiss-Prot cross references
Pectinesterase 5, Arabidopsis thaliana , (Mouse-ear cress) : Q5MFV8
a question of length - May 2009
When Charles Darwin accepted the invitation to accompany Captain Fitzroy on HMS Beagle as the ship’s naturalist, little did he know that he would bring back with him material that was to haunt him – one way or another - until the end of his days. Amongst the many mineral, plant and animal specimens which were unloaded from the ship on its return in October 1836, there were a number of preserved finches which Darwin had found on the Galapagos Islands. It was the study of these finches, which later became known as ‘Darwin’s finches’, that helped to forge the notion of the transmutation of species. In other words, any given species had the capacity to adapt, evolve and undergo transformations – and it turned out to be in the name of survival. With regards to finches, their beaks were different depending on the kind of diet they had. Charles Darwin had no idea how such changes could occur within a species. Today, we are getting closer and closer to understanding how it happens on the molecular level. And it seems that a protein known as calmodulin has a major role. (PDF version - 45K bytes)
Swiss-Prot cross references
Calmodulin, Homo sapiens, (Human) : P62158
the making of crooked - April 2009
Moving any one of our limbs is not something most of us have to think twice about. Rising from a chair to make a cup of coffee or picking your nose is usually a piece of cake. Yet the natural mobility of our legs – for instance – can be dependent on the existence or not of molecular loops. Nature can tease us with very little. Any one of our movements is made possible thanks not only to the existence of motor neurons but their growth and differentiation. Growth and differentiation are, in turn, dependent on many cellular activities, in particular the trafficking of entities from one end of a nerve cell to another. If the trafficking is checked for any given reason, the neuron does not react the way it should and whatever limb it activates will suffer the consequences. Spastin is an enzyme which has a central role in the building of highways for neuron traffic and we now know that it is also guilty of causing a neurodegenerative disease in the lower limbs, known as hereditary spastic paraplegia. (PDF version - 83K bytes)
Swiss-Prot cross references
Spastin, Homo sapiens, (Human) : Q9UBP0
about the blues - March 2009
Every living being has devised a way to protect its embryos. Humans lodge them in wombs. Fungi protect them in spores. Butterflies keep them in cocoons. Nature’s imagination has no limits. In order to keep life going, she has thought up hundreds – if not thousands – of ways of protecting her little ones. Some of her inventions are colourful indeed. Certain species of frog are capable of whipping up bright pink or orange foams in which are embedded their eggs, thereby hidden from predators or sheltered from challenging weather. A certain type of Malaysian tree frog, known as Polypedates leucomystax or the Java whipping frog, whisks up foam while it is mating, which gradually turns into a greenish blue on its surface. To what end? No one really knows. But we do know what it is that makes the foam blue: ranasmurfin. (PDF version - 225K bytes)
Swiss-Prot cross references
Ranasmurfin, Polypedates leucomystax, (Java whipping frog) : P85511
Silent pain - February 2009
Is there really a point to pain? Yes, argue most. Pain warns you that something is not right. It teaches children not to put their hands on a hot plate because they know heat hurts. It urges you to consult your doctor when pain persists in any part of your body. Yes, but what about pain that accompanies something which has already been diagnosed? What about the persistent pain that frequently escorts chronic conditions, such as a sore back or cancer? Who can see the good in that kind of pain? Though there may be instances when it seems superfluous and even cruel, the sensation of pain is more necessary than it is not. It is a clear indicator that there is something wrong, and that it needs to be seen to. In the absence of pain, no alert signals are given off – which could ultimately put your life in danger. It is a complex sensation with many a meaning and many a pathway. One particular pathway was discovered when members of a family were incapable of feeling pain – a singular and rare condition due to the loss of function of a protein known as SCN9A or Nav1.7. (PDF version - 46K bytes)
Swiss-Prot cross references
Sodium channel protein type IX subunit alpha, Homo sapiens, (Human) : Q15858
Sleepless nights - January 2009
Everyone knows what it feels like to lack sleep. The usual drive to get on with life is diminished. Problems are difficult to cope with. The urge to do any physical exercise is low. Short temper is just around the corner and the desire for a nap becomes greater as the hours tick by. Intuitively, everyone knows that you need to sleep to recharge the battery. It sounds simple enough because we know we feel restored after some rest and we’ve been living with it ever since we were born. But – like any physiological process – the act of sleeping is not so straightforward. Something inside us has to tell us: ‘it’s time to sleep’. And something else has to say: ‘you need to sleep’. Our quality of sleep is driven by these two notions. Since the 1960s, scientists have been searching for genes which are at the heart of such processes. Recently, one protein named ‘Sleepless’ was discovered. Sleepless seems to be directly involved in telling us that all activity is to be put on hold for the space of a rest. (PDF version - 67K bytes)
Swiss-Prot cross references
Sleepless, Drosophila melanogaster , (Fruit fly) : B5A5T4


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