Month: November 2006

Eradicating polio

Researchers hope to revise the vaccine strategy for inocculating people in certain parts of the world against the crippling disease polio. Their approach could eradicate this endemic disease once and for all, they report, in this week’s Science magazine.

The new study, by researchers from Imperial College London and
international collaborators explains why the disease continues to afflict people in northern India. Poor sanitation and overcrowded living
conditions in Uttar Pradesh and Bihar pose a dual challenge to the
eradication effort because they encourage poliovirus to spread via infected faeces contaminating drinking water, they explain. This coupled with other infections and diarrhoea interfere with the efficacy of the
oral polio vaccine.

The researchers argue that the simple measure of using a ‘monovalent’
form of the polio vaccine alongside the standard ‘trivalent’ form in
these areas could sufficiently increase the effectiveness of vaccination
programmes to wipe out the poliovirus where it persists.

The trivalent vaccine currently in use contains weakened strains of all
three types of poliovirus, unlike monovalent vaccines, which are
strain-specific. The trivalent vaccine is typically used when more than
one strain of the poliovirus is at large in the population. The problem
with trivalent vaccines is that the three strains can interfere with
each other inside the body, producing immunity to one strain but not
another.

The researchers argue that as the type 1 strain of the virus is now the
dominant one in India, it would be more effective to focus on the
monovalent form of the vaccine.

Lead author Nick Grassly says, “The global polio eradication programme has achieved a great deal. As expected, the last remaining pockets of transmission are the biggest challenge. These pockets of transmission act as sources for all the outbreaks we see around the world today. Our research shows that in northern India the efficacy of the trivalent vaccine is compromised.”

Unaccepted Medline

Last week, I discussed how to get free research papers online without having to hack into any publisher’s database.

Now, my Google Alert for Journal of Biological Chemistry has raised an interesting issue on the MEDLIB-L list from Thomas B. Craig, Assistant Director of Library Services at The University of Texas Health Center at Tyler.

Craig points out that he gets a lot of eprint requests from users after JBC papers that simply don’t show up in his library system as yet being available.

As Sciencebase readers know, JBC puts its “Papers in Press” free online. There can be a few dozen of over a thousand available at its website at any one time. The journal indexing system Medline, automatically indexes these “in press” papers and so as Craig explained some time ago on MEDLIB-L, “we get Docline requests for them when a library does not recognize a citation as coming from JBC Papers in Press.”

The requests contain an ID number but no page or issue number, just an annotation to say: “e-pub ahead of print”.

The JBC papers are essentially preprints, they go live on the site even before they’re edited or accepted officially for publication.

Craig thus asked: “Does this type of paper belong in MEDLINE, and what is its usefulness when it has yet to be accepted and is subject to change?”

Early awareness of research in a particular area would be one reason, but this issue makes a mockery of the out-dated and pointless system of artificial media embargoes that journals such as JACS, Nature, PNAS, Science, and others slap on their papers to help them coordinate the press response to a particular paper’s publication. Moreover, given that a paper published ahead of acceptance and seen by more peers might lead to flaws being spotted that were missed by the official referees, before it goes to press, might help the review process and prevent dubious papers ever making it to the Table of Contents.

The recent suspected research fraud being investigated at the University of Missouri is just the most recent example in a string of problems associated with fabricated and massaged data stretching back decades.

Don’t judge a lemur by its cover

If you’re ever out lemur spotting, and thing you’ve seen an entirely new species, you may wish to refer back to US research published today in the journal BMC Evolutionary Biology wherein you will find a study that claims that different coat colour does not necessarily correspond to a different species for nocturnal lemurs. In fact, as with cats and dogs, coat colour does not mean an awful lot when trying to distinguish new species. Genetically speaking whatever the fur, it’s the genes that matter.

Kellie Heckman of Yale University and colleagues sequenced the mitochondrial gene for cytochrome b in seventy mouse lemurs. Originally, these lemurs were thought to belong to up to three different species because they live in different forest habitats and have distinctive coat colouration.

However, Heckman’s phylogenetic analysis came to the rather surprising result that all seventy specimens are actually identical genetically, to all intents and purposes; making them all Microcebus griseorufus.

While, the press release on this says the results are surprising, it then goes on to explain that these nocturnal animals use auditory cues and smell to recognise each other rather than judging who’s who on the basis of the coat they’re wearing. So, it’s not really surprising at all, when you think about it like that. After all, an extra wing stripe can separate to otherwise identical bird species, but birds are generally diurnal and have great day sight. Colours are pretty much a secondary thing at night no matter how good your eyes.

Meanwhile, the authors of the study offer a cautionary word for those searching for new species. They say that looks aren’t everything and that size, shape, geography, ecological, and most importantly genetic differences have to be taken into account to provide an accurate picture of species diversity.

More than a flash in the pan

x-ray diffractionA 25 femtosecond snapshot of a stick man is all that was needed to prove that a new free-electron laser technique would work. Unfortunately, the poor old stick man evaporated within that split second into a 60,000 degree plasma.

Theory suggested that researchers might be able to obtain a single diffraction pattern from a large macromolecule, a virus, or even a cell using a suitably short and bright burst of X-rays from such a free-electron laser. Only a single set of data would be possible because the sample would be fried by this pulse. Now an international team has demonstrated that the technique works. Their results will mean that biologists might be able to obtain crystal structures from complex molecules, such as proteins, without even having to crystallise them first. They can just blast a sample with an X-ray pulse and get almost all the data they need.

You can grab the full story in my regular techy news round-up on SpectroscopyNOW.com

Read on…

Painkiller in saliva

PainkillerA natural analgesic (painkiller) that is six times stronger than the opiate morphine has been found in human saliva.

In 2003, Catherine Rougeot and her colleagues at the Pasteur Institute identified a potent pain sensation inhibitor in rats they called sialorphin. The present work confirms the presence of a related compound in humans. The compound inhibits the same class of proteins as sialorphin.

The analgesic, termed opiorphin (someone not related to the research team registered domain name opiorphin.com yesterday!) is a peptide with the amino acid sequence: tyrosine glutamine arginine phenylalanine serine arginine.

In rat studies, injections of opiorphin suppressed pain sensation for both chemical-induced inflammation and acute physical pain. In both cases, the administered dose of 1 mg/kg opiorphin provided the same painkilling power as 3-6 mg/kg of morphine.

The authors hope to next identify which physiological conditions trigger the natural release of opiorphin, but also note that the strong analgesic properties of opiorphin warrants potential exploration for clinical pain management. However, Rougeot cautions that it might not be developable as a conventional painkiller as the compound may also have anti-depressant activity.

I’m curious though, if spit has this potent painkiller why does it hurt so much when you accidentally bite your tongue?

The work is reported in this week’s issue of PNAS.

What are molecular sieves

As the name might suggest these are molecules that can sieve out other molecules, acting like a filter but on the molecular scale. They are usually composed of a highly porous mineral or organometallic compound, the tiny pores of which are usually of uniform size and shape.

Clays, porous glasses, microporous charcoals, active carbons, aluminosilicate minerals, zeolites, and various synthetic compounds which we’ve discussed in Elemental Discoveries in the past allow much smaller molecules to enter and either pass through or be adsorbed on to the inside surface of the molecular sieve. As such. molecular sieves can be used to absorb liquids and gases. For instance, water molecules are often small enough to enter such porous materials while larger molecules are not, making molecular sieves useful as drying agents, or desiccants. A molecular sieve can absorb water up to 22% of its own weight. The petroleum industry makes wide use of molecular sieves for purifying gas streams. You can find out more here.

For more on molecular sieves research check out the Elemental Discoveries archive and the Reactive Reports website.

Brainy pictures

It always surprises me what visitors to the site are searching for when they hit these pages. A common search this month is for brain pictures. Now, from the search keywords it’s not possible to tell whether it’s a photo of the brain, an MRI scan, or a schematic that the searchers are looking for. So, to cover all bases, here are a few links that might help:

All these images are hosted under the US government domain (.gov) and so should be copyright free, but don’t take my word for it if you plan to use them in your science project or for anything other than personal use. Google Images, of course, would have been my first port of call for finding brain pictures.

Play real air guitar

Air guitar shirtBB King had his Lucille, old slowhand his well-worn Strat, and who could forget Jimmy Page with his Gibson SG twin-neck? You too could join the greats and learn how to play guitar, thanks to new technology from Australia’s science research centre – CSIRO. And, all you have to do is put on their new designer shirt and start strumming…the air.

Engineer Richard Helmer in the Textiles and Fibre Technology section in Geelong has created a ‘wearable instrument shirt’ (WIS) which enables users to play ‘air guitar’ and make real sounds simply by moving one arm to pick chords and the other to strum the imaginary instrument’s strings.

“Our air guitar consists of a wearable sensor interface embedded in a conventional ‘shirt’ which uses custom software to map gestures with audio samples. ‘It’s an easy-to-use, virtual instrument that allows real-time music making — even by players without significant musical or computing skills. It allows you to jump around and the sound generated.”

The WIS works by recognising and interpreting arm movements and relaying this wirelessly to a computer for audio generation. There are no trailing cables to get in the way and no risk of electrocution when you’re getting all hot and sweaty thrashing away in front of your bedroom mirror.

The real advantage of the wear-guitar is that when you reach the climax of the gig you can smash your guitar against the imaginary stack of Marshall 4x12s without wrecking thousands of dollars of equipment. Just remember, once you’re done, to ask your mom not to add it to the regular laundry.

Performance enhancing steroids

Most sports stars know that injecting steroids to boost performance is plain stupid. But, some do it anyway, because the potential gains, they reason, outweigh the risks to health and the chances of being stripped of glory are much smaller than their chances of winning the medal without them.

Not all steroids are purely about enhancement. Another group of steroids, known as corticosteroids, are used to reduce inflammation and pain following injury. Alarmingly high doses are often used to speed up the recovery process but with potentially serious side effects on the tissues into which they are injected. As such corticosteroids injections are also banned in sports.

However, there is a drug produect available to errant sports people that can stimulate the body’s own production of corticosteroids, it’s a protein known by the tradename of Synacthen. It was essentially undetectable as only tiny quantities are needed to cause the desired stimulation and such small concentrations are easily lost in the background noise of other more abundant proteins in a blood sample.

Now, researchers writing in the journal Rapid Communications in Mass Spectrometry have developed an analytical separation and detection technique, based on chromatography and mass spec, that can pin down this elusive drug and render the cheats visible even if the compound is present only in incredibly low concentrations in a blood sample; even at 10,000,000 times lower concentration than other proteins in the blood plasma.

‘If the drug testing authorities adopt this new test it will close a gap in the current drug testing system, and mean that athletes will no longer be able to get away with this form of cheating,’ says lead author Mario Thevis, who works in the Center for Preventive Doping Research — Institute of Biochemistry, at the German Sport University Cologne in Germany.

Looks like a few well known sports celebs will have to start using RICE for their injuries again…

Get research papers free

Wouldn’t it be great if you could get all those research papers you need for free without having to wait for the publishers to all convert to open access?

Well you can, kind of.

Most of the time when you scroll through the ToCs (table of contents) pages at a publisher’s site, you’ll see a little red “free” symbol next to the abstract. Click for “full paper” or “pdf” and you’re usually taken to a login page where you have to enter your subscriber username or password. That’s fine if you’re at an institution with a site-wide licence for the content, but what if you’re away from your lab and don’t have a remote login?

Well, not everyone has noticed but some of the major journals do make their content free after a set time period. Papers in PNAS, for instance, are free after six months, no login required. But, six months is a long time in research and may be too late if you’re after the most cutting edge info.

Physicists of all flavours are fairly well served with preprints courtesy of the LANL preprint server, just head on over type in your keywords and pull up papers that haven’t even been published by the journals (yet). You can read the most recent physics preprints here. Physicists after IOP journals are also well served, this publisher gives free access to papers for the first 30 days after publication, which is rather unusual.

Biological chemists are fairly well served too, at least when it comes to the Journal of Biological Chemistry, which offers pre-edited papers that have been accepted, so-called “pips” (papers in press) for free. Once the papers go live, they’re pay as you go, but until then you can grab them for nothing more than a few mouseclicks as long as you don’t mind that some t’s may not have been dotted and a few i’s may have been left uncrossed. Set yourself a Google Alert to tell you when that page changes, export it as a newsfeed or have it emailed and you’ll be able to grab the papers as soon as they appear at zero cost. Same goes for Biol Reprod and several other journals. Also in biomedical is PubMedCentral, but that’s one of those OA systems, rather than freebies by the back door. More OA journals can be found at DOAJ.

For scientists who publish in Springer journals they can make a one-off payment of $3000 at the time of writing to allow their paper to be made available to readers for free. It’s like paying for infinite digital reprints, which works out at a very small cost per reprint and is probably well within the reach of only the most prominent labs, or multi-author papers where everyone chips in a few bucks to get the word out as far and wide as possible.

Crystallographers are well served too – one source of OA crystallography material can be found here.

For chemists a quite comprehensive list of free chemistry journals can be found here and there is also Chemrefer, which we have mentioned previously which lets you search by keyword for freebie papers.