Excerpts from Recent Articles from 2002

2002 Back Issues

Platypus poison - December 2002
Platypuses (Ornithorhynchus anatinus) are the only mammals that squirt venom. They do this from a mobile calcaneus spur situated on the inside of each hind limb. It is a sophisticated system. The spur itself is attached at its base to a small bone which can articulate; when needed it moves at a right angle to the limb ready to fire. Strangely, only male platypuses have spurs; female platypuses lose theirs during development. Platypus venom has been under close scrutiny since 1895 when two naturalists Charles J. Martin and Frank Tidswell made their first account. We know today that platypus venom is a cocktail of toxins, most of which is a mixture of proteins which resemble no other to date. These have been named the defensin-like proteins, or DLPs, because their three dimensional structure resembles that of an antimicrobial peptide known as beta-defensin. (PDF version - 46K bytes)
Swiss-Prot cross references
Defensin-like peptide 1, Ornithorhynchus anatinus (Duckbill platypus): P82172
Defensin-like peptide 2, Ornithorhynchus anatinus (Duckbill platypus): P82140
Defensin-like peptide 3, Ornithorhynchus anatinus (Duckbill platypus): P82141
No LFS, no cry - November 2002
While for many, shedding a few tears as they cut an onion is a fair price to pay considering the improvement it can make to a dish, there are some who would gladly do without. Cooks for one. Until recently, it was thought that what made the distinct flavour and aroma of onions was also what made you cry. So if you tampered with the lachrymatory factor, the onion’s flavour and aroma would be dulled - which would not do. A small revolution has occurred, however. A team of Japanese scientists discovered, quite by chance, an enzyme which catalyses only the lachrymatory factor, and has been named lachrymatory factor synthase (LFS). Tampering with LFS may allow us to dry up the tears while preserving the taste. (PDF version - 126K bytes)
Swiss-Prot cross references
Lachrymatory factor synthase, Allium cepa (Onion): P59082
Nature's junkie - October 2002
Humans are not the only mammals to indulge in cocaine. A particular strain of the bacterium Rhodococcus does too. In fact, it thrives on it. Not for the same reasons however. For this drug-consuming Rhodococcus, cocaine is the sole source of carbon and nitrogen. Scientists were led to it whilst rummaging in the soil, which surrounded the roots of coca plants, in their pursuit for a subtle drug detector. The bacterium revealed an enzyme – cocaine esterase – which is at the heart of cocaine metabolism. Cocaine esterase may well offer cocaine trackers a very fine drug sensor and could be used in emergency cases for cocaine overdose. (PDF version - 449K bytes)
Swiss-Prot cross references
Cocaine esterase, Rhodococcus sp. : Q9L9d7
Squeeze me - September 2002
Boil a lobster and its colour will go from blue to red. It is a known fact. And a fact that has been known for ages. What has not, however, is how a lobster’s outside – which is blue – can turn red. Astaxanthin is the chromophore which lends a lobster its boiled orangey-red hue, as it does to many sea animals such as the pink flesh of salmon, the exoskeletons of crayfish – from where it was first identified – and shrimps, for instance. Surprisingly, astaxanthin is also the chromophore which gives lobsters their initial ‘pre-boiled’ blue-green colour. Why lobsters turn red in boiling water in the first place is a question which the American biologist George Wald (1906-1997) raised over half a century ago, and to which we now have an answer. What is more, as research progresses, it appears that astaxanthin could have beneficial effects on our health and that the structure of crustacyanin itself could be particularly interesting in the field of drug design. (PDF version - 801K bytes)
Swiss-Prot cross references
Crustacyanin A1 subunit, Homarus gammarus (European lobster): P58989
Crustacyanin A2 subunit, Homarus gammarus (European lobster): P80007
Crustacyanin C1 subunit, Homarus gammarus (European lobster): P80029
Life's jokers - August 2002
T here is more to the genetic code than meets the eye. We are acquainted with the dogma: ‘One codon, one amino acid’. Life, however, has found a way of wriggling out of this straight jacket by using its stop codons as jokers. One example is given by our own mitochondrial DNA where the translational machinery recognises the UGA stop codon as tryptophan, and not as the classical stop codon as in the nucleus. Tryptophan though is an old-timer. As are the great majority of the now classical twenty amino acids which have been on the scene for over a century. Threonine was the last of the classics to be discovered in 1936. 1986, though, was another scoop year, when it was discovered that the UGA codon could produce a new amino acid altogether: selenocysteine. Selenocysteine, the 21st amino acid, is found in archaea, eubacteria and animals. Selenocysteine may just sound like a modified cysteine, but it is not because it has its own tRNA which is like granting it a passport. Similarly, in May 2002, the existence of a 22nd amino acid was reported: pyrrolysine. (PDF version - 37K bytes)
Swiss-Prot cross references
Monomethylamine methyltransferase, Methanosarcina barkeri : O30642
The tiptoe of an airbus - July 2002
In the 1900s, the Swiss physicist Auguste Piccard invented the bathyscaph, a submersible vessel for deep-sea observation. Long before though, spiders had already thought up a way of carrying out deep-pond observations using the same kind of strategy. A species of spider that lives in freshwater ponds throughout Europe weaves its own bathyscaph with silk. Bubbles of air keep the contraption afloat and a silk thread tethers it to a plant. Spiders use their silk for a number of purposes: besides catching their dinner by way of a woven web, some male spiders deposit sperm onto it and then offer the parcel to a female’s genital opening. Silk is also used to wrap eggs in a silken cocoon or to hold offspring by means of a silk lifeline. (PDF version - 41K bytes)
Swiss-Prot cross references
Dragline silk fibroin 1, Nephila clavipes (Orb spider): P19837
Dragline silk fibroin 2, Nephila clavipes (Orb spider): P46804
Heterocyst or not heterocyst? - June 2002
What is it in a cell that drives it to become one type of cell rather than another? Or for that matter, what is it in a cell that summons it not to budge? It is the fascinating world of cell fate, one of the most intriguing questions developmental biologists have been asking themselves for centuries now. The blue-green algae cyanobacteria Anabaena is a perfect illustration of one model which has been on the scene for some time: cell differentiation occurs thanks to the diffusion of molecules, which creates a cell gradient. (PDF version - 52K bytes)
Swiss-Prot cross references
Heterocyst inhibition signaling peptide, Anabaena sp. : O52748
Pump up the volume - May 2002
There is not much we would hear without our cochlea. Our what? The cochlea is a part of our inner ear and looks remarkably like a snail’s shell. This minute masterpiece of mammal physiology - only a few millimetres large - acts as a sound amplifier and without it the noises which surround us would be mere fuzz. And how does it amplify sound? Amongst the many controversial theories, there is one which is based on the behaviour of quite a singular protein: prestin. Why singular? Because prestin is the only cellular motor to date which does not require biological energy – such as ATP – to function. (PDF version - 734K bytes)
Swiss-Prot cross references
Prestin, Homo sapiens (Human): P58743
Prestin, Rattus norvegicus (Rat): Q9EPH0
Prestin, Mus musculus (Mouse): Q99NH7
Prestin, Meriones unguiculatus (Mongolian gerbil): Q9JKQ2
The man behind the molecular lung - April 2002
Max Perutz (1914-2002) solved the molecular structure of haemoglobin in 1960. It had taken him the best part of 25 years. He arrived at the Cavendish laboratory in Cambridge in 1936 eager to start a PhD. In those days, there was marked excitement about the possibility that X-ray photography of protein crystals could deliver the atomic arrangement of proteins. Two crystals were presented to Perutz: one of chymotrypsin and another of haemoglobin. The chymotrypsin crystals grew in such a manner that they were too complex to decipher so Perutz turned to the haemoglobin crystals which he felt would be easier to solve. Haemoglobin was also a choice candidate: it has an important physiological role, supplies are never scarce and it forms crystals easily. And little did Perutz know that this macromolecule would keep him busy for the rest of his life. (PDF version - 68K bytes)
Swiss-Prot cross references
Hemoglobin alpha chain, Homo sapiens (Human): P01922
Hemoglobin beta chain, Homo sapiens (Human): P02023
Hemoglobin alpha chains, Equus callabus (Horse): P01958
Hemoglobin beta chain, Equus callabus (Horse): P02062
The protein with a topological twist - March 2002
Scientists discovered the use of Oldenlandia affinis as an oxitocic agent in Africa, in the 1960s. O. affinis is a perennial weed with a woody root and blue-violet flowers, and is found in the tropical zones of Africa and western Asia. There are 196 different species of Oldenlandia and their use in traditional medicine is as widespread as their geography. India uses many of the different species in as many different drugs. However, it was the uteroactive activity of a green brew, Kalata-Kalata, given to African women during labour that first triggered an interest. The decoction was made from a handful of dried O. affinis boiled in about a litre of water. Women about to give birth were either given the tea to sip or it was directly applied per vaginum; contractions became stronger and delivery was shortened. What was the nature of the uteroactive agent? The green potion was whipped to a laboratory and the main uteractive agent turned out to be a small protein named after the traditional medicine from which it was extracted: kalata B1. (PDF version - 100K bytes)
Swiss-Prot cross references
Kalata B1, Oldenlandia affinis : P56254
From sausages to wrinkles - February 2002
It was a bout of sausage poisoning which led to the discovery of a protein now known as botulinum toxin. During the Napeolonic Wars, the Dukedom of Würtemberg in Stuttgart observed an increase in human deaths due to food intoxication. Smoked sausages seemed to be at the heart of the problem and the poison was subsequently termed sausage poison. It was the medical officer and poet Justinus Kerner (1786-1862) who first suspected poison of biological origin. The clinical symptoms added to his own experimental observations – he had fed bad sausage to various animals as well as to himself – led him to believe that the poison interfered with the motor and autonomous nervous signal transmission system. ‘The nerve conduction is brought by the toxin into a condition in which its influence on the chemical process of life is interrupted.’ Indeed, patients experienced a progressive paralysis from the cranium down which would end in death by suffocation following progressive difficulties in breathing. Kerner, however, did not know what the nature of the toxin was. (PDF version - 34K bytes)
Swiss-Prot cross references
Botulinum neurotoxin type A, Clostridium botulinum : P10845
Smart sweat - January 2002
We all sweat. Which is just as well because, generally speaking, the loss of body fluids is essential to our well-being. It rids us of a certain number of physiological impurities. Our skin – the material through which we sweat – is an organ per se, the largest one we carry around and a particularly complex one. It is a spaghetti junction of blood vessels, a harbour for nerve endings, a workshop for pigmentation and a field of sweat glands, oil glands and hair follicles. And that is not all. Our skin has also been called our ‘third kidney’. Indeed, waste seeps through it daily: sodium, chloride, potassium, magnesium, calcium, urea, ammonia, uric acid – which is what tastes salty on the skin once all the water has evaporated – but also toxic metals such as copper, lead, zinc and mercury offered to us by way of environmental pollution. Amongst all this body garbage, however, is a protein known as dermcidin, which is not debris but an antibiotic peptide. Here is medicine we actually perspire. (PDF version - 114K bytes)
Swiss-Prot cross references
Dermcidin, Homo sapiens (Human): P81605


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