Bottled seaside air

Seaside Beach HutsBottled seaside air! It almost sounds like a scam from the Victorian era when the bracing “ozone” of fresh air at the British seaside was said to cure all kinds of ailments and led to a boom in seaside resorts and continues to ebb and flow.

But, it’s not a scam. Researchers at the University of East Anglia have been plucking bacteria from the North Norfolk coast at a little village called Stiffkey (pronounced Stoo-Kee) and fermenting them to reproduce the marshy smell of the seaside in the laboratory.

Andrew Johnston and his team isolated the bacterium from the mud at Stiffkey saltmarsh and have identified the single gene responsible for the emission of the strong-smelling gas, dimethyl sulfide (DMS).

“On bracing childhood visits to the seaside we were always told to “breathe in that ozone, it’s good for you’,” said Prof Johnston. “But we were misled, twice over,” he adds, “First, that distinctive smell is not ozone [a highly toxic allotrope of oxygen], it is dimethyl sulfide. And secondly, inhaling it is not necessarily good for you.”

DMS is a little known but important gas. Across the world’s oceans, seas and coasts, tens of millions of tonnes are released by microbes that live near plankton and marine plants, including seaweeds and some salt-marsh plants. The gas plays an important role in the formation of cloud cover over the oceans, with major effects on climate.

Intriguingly, DMS acts as a homing scent for seabirds, almost like the odour of Brussels sprouts at a festive dinner table – it helps birds sniff out food in the lonely oceans, even at astonishingly low concentrations. Understanding the role of microbes in producing this key chemical is important in understanding a whole range of ecosystems.

The discovery adds to the diverse list of Stiffkey’s claims to fame. The small coastal village is renowned for its ‘Stewkey Blue’ cockles and was also the home of Henry Williamson, author of “Tarka the Otter”. It’s also known for its infamous rector, Reverend Harold Davidson, who was defrocked in 1932 after allegedly “cavorting with” London prostitutes. The pronunciation of the village’s name itself is even controversial with the older locals preferring the archaic Stoo-Kee, while the incomers often prefer the posher sounding and phonetic Stiff-Key. (Incidentally, my photograph of beachhuts at the head of this article was taken along the coast at Wells-next-the-Sea.

Viruses Versus Bacteria

bacteriophageIn 1919, long before antibiotics were commonplace and long before the notion of drug resistance had emerged, a doctor in the east European state of what is now Georgia, Felix d’Herelle, gave a patient suffering from severe dysentery a seemingly lethal concoction of viruses. You might think such a drink would kill the patient, but these were no ordinary viruses, they were bacteriophages, the nemesis of bacteria.

The patient was well again within a week.

Thus was heralded in the age of phage therapy. Different viral strains were selected for almost every bacterial infection. Diseases were cured. What’s more, because bacteriophages are themselves in some sense alive, they can evolve to keep up with any resistance efforts mounted by the bacteria.

So what happened to bacteriophages? Why are the news headlines filled with stories of new deadly bacteria, such as MRSA, and the newly re-emerged forms of tuberculosis? Why are we so worried about outbreaks of E coli, salmonella, and other bacteria. Surely, we have a whole armoury of trusty phages to turn to that can wipe out the rank and file of resistance microbes quickly?

Well, we don’t, somewhere between the discovery of penicillin and the second world war, chemical antibiotics fell in to pharmaceutical line as the treatment of choice to deal with bacterial infections. Never mind the fact that within months of the first dose of penicillin being given doctors were already seeing resistance. Today, there are thousands of antibiotics on the market, some are even available over-the-counter in southern Europe. Moreover, in countries that cannot really afford to use them, individuals receive short dose regimens that don’t cure their illness and provide new opportunities for bacteria to develop resistant genes.

Swiss science editor Thomas Häusler tells the story of bacteriophages and phage therapy from its humble roots to its dimly recalled heyday of the 1920s and 1930s in his book Viruses vs. Superbugs. He tells a tale of rancidity and disease that were all but eradicated by bacteriophages but that is gradually returning as hospital wards succumb to the resistant hoards and various sectors of society, such as drug users and the homeless are dealt a deadly blow as TB and other “old” diseases crawl the streets.

In the USA alone some 90000 people die each year from these so-called superbugs. The likes of the World Health Organization and other official bodies agree that things can only get worse. Perhaps a discovery from the middle of the Great War of 1914-1918 could take the place of the dozens of obsolete antibiotics stacked on pharmacy shelves and provide a final cure for the bacterial infections that until the 1960s the medical profession had all but consigned to the history books.

Sex and diabetes

Approximately half of men with diabetes suffer at least one episode of erectile dysfunction and there are several strategies available to overcome what is in those cases usually a problem of body chemistry. According to a report in the Cochrane Review of clinical trials, the well-known drugs for treating erectile dysfunction really do improve sexual satisfaction for sufferers. The report covers the three main phosphodiesterase type 5 (PDE-5) inhibitors, sildenafil (Viagra), vardenafil (Levitra) and tadalafil (Cialis).

According to the study side-effects, such as headache and flushing, are common, but not sufficiently adverse as to dissuade users from abandoning the drug.

The Cochrane Review draws data from eight clinical trials (totalling almost 1800 participants) in which 976 men had been given a PDE-5 inhibitor, and 741 a placebo.

‘If taken as prescribed and when no contra-indications exist, PDE-5 inhibitors provide a useful option for men with diabetes who suffer from erectile dysfunction,’ says report author Moshe Vardi of the Carmel Medical Center, in Haifa, Israel.

You can read the abstract from the report at the Cochrane Library site. For more on the origins of Viagra and the other PDE-5 that followed in its wake, check out the Sciencebase archives.

Obesity and colon cancer link

Obesity is a major risk factor for colon cancer, but until now medical scientists were at a loss to explain why. Now, a study of on three human colon cancer cell-lines has demonstrated that the “fat hormone” leptin may enhance the growth of colonic cancer cells. The discovery not only offers an explanation as to the underlying cause of the increase colon cancer risk in obesity but could lead to a new approach to fighting this type of cancer.

The hormone leptin is released by fat cells, adipocytes, so the higher your body fat content (calculate your body fat now), the higher the concentration of leptin in your blood stream is likely to be. Leptin plays a key role in regulating metabolism, body weight and energy expenditure.

According to previous research, people who are obese are two to three times more likely to develop colon cancer than their leaner counterparts. Other research revealed that some colon cancer cells carry receptors for leptin.

Now, scientists at the University of California San Diego School of Medicine believe they have found the link.

“These results may explain why obesity increases a person’s risk of colonic cancer, and the fact that we have shown how leptin stimulates these cells means that drug companies may be in a better position to develop new treatments against the disease,’ says UCSD’s Kim Barrett.

The team grew cancer cells in the laboratory and found that leptin could stimulate their growth. In two out of three cell lines, leptin also blocked normal programmed cell death, apoptosis, which usually prevents runaway cell growth. When apoptosis fails normal cells can become cancerous.

The researchers explain that they have also found the complex chemical signalling pathways in the cell that are influenced by leptin, which reinforces their claim that leptin does indeed play a critical part in influencing cancer cell growth in the colon.

The results are published in detail in the journal BJS.

UK PubMed Central

A UK version of the free biomedical research server PubMed Central will provide free access to a permanent online archive of peer-reviewed research papers in medicine and the life sciences.

UK research funders, led by the Wellcome Trust, awarded the contract to develop UKPMC to a partnership between the British Library, The University of Manchester and the European Bioinformatics Institute (EMBL-EBI).

Members of this group now require that articles describing the results of research they support are made available in UKPMC with the aim of maximising its impact. The UKPMC service will ensure that articles resulting from research paid for by any member of the funding consortium will be freely available, fully searchable and extensively linked to other online resources.

The UKPMC essentially mirrors the US PubMed Central database but as of 8th January 2007, UK scientists will also be able to submit their research outputs for inclusion in UKPMC.

Mark Walport, Director of the Wellcome Trust commented: “Medical research is not complete until the results have been communicated. The development of UKPMC provides a great opportunity for this research to be made freely available, and I am very pleased that a first class partnership of the British Library, the University of Manchester, and the European Bioinformatics Institute will be running it.”

The British Library will run the service, promote it to researchers, as well as offering support for those who want to include their research papers in UKPMC. The University of Manchester hosts the service — on servers based at MIMAS (Manchester Information and Associated Services) — and will support the process of engaging with higher-education users. EBI, which is part of the European Molecular Biology Laboratory (EMBL), will contribute its biomedical domain knowledge and state-of-the-art text-mining tools to integrate the research literature with the underlying bioinformatics databases.

The launch of UKPMC brings into sharp relief once again the ethical debate surrounding scholarly publication. The Wellcome Trust has insisted that authors publish research arising from its funding in open access repositories since 1st October 2006.

Writing in PLoS Biology in 2005, Robert Terry (Senior Policy Adviser at the Wellcome Trust, Cambridge, United Kingdom), discussing the plans for UKPMC at the time said, “For a funder, having all its research in one format, ‘under one roof’, and searchable will improve the efficiency of strategy setting–for example, setting funding priorities–assessing the outputs of the funded research, and even gaining an insight into the impact of the work. As grants management becomes more electronic, there can be a direct link between original research proposals and the research outputs.”

According to AJ Cann on MicrobiologyBytes recently, this widely adopted funding-body policy already means “publishers are over a barrel – sign up or sign out.”

Being particular about DNA

Surface-enhanced Raman spectra (SERS) of DNA and RNA mononucleotides can be detected with high sensitivity, according to UK researchers. Using citrate-reduced silver colloidal nanoparticles aggregated with magnesium sulfate instead of the more common halide ions, reduces inappropriate enhancements and produces spectra that are sufficiently different to allow each to be distinguished.

“The main advantage of our SERS approach is that it allows direct label-free identification of mononucleotides in aqueous solution,” Steven Bell, Director of the Innovative Molecular Materials Group, at Queen’s University Belfast, explains, “There is no requirement for labels because the Raman signals of each of the mononucleotides are intrinsically different due to the differences in their chemical structures.” He adds that spectra can be obtained at ten nanograms per millilitre. “We were working with large samples but reducing the sampling volume to a few microlitres would move the sample down to tens of picograms,” he says.

More…

Nervous scoop

An action shot of the protein Scp1, which plays a crucial role in the development of the nervous system has been obtained using crystallography by researchers in the US. Their structure could provide drug designers with a template for creating small molecule inhibitors of this protein that would be useful in neurological research.

Joseph Noel and Samuel Pfaff of the Salk Institute for Biological Studies and colleagues there and at the University of California, San Diego (UCSD) and The Scripps Research Institute, La Jolla explain that a network of signalling molecules controls embryonic stem cell differentiation. Controlling the controllers might allow scientists to nudge embryonic stem cells into becoming specific cell types, which would be useful in basic research and for potential therapies.

Read on…

Boxing Day Boredom and Monkey Proteins

Monkey proteinsIt’s Boxing Day and you’re probably seriously bored playing the “normal” game of Pick-up Monkeys. Rather than heading for the Wii or the PS3, how about adding a little monkey magic, or more seriously some wire binders and following Dr N. Michael Green, Division of Mathematical Biology, of the UK’s prestigious Medical Research Council (MRC) National Institute for Medical Research to do a little bit of science education with those colourful plastic monkeys.

“Pick up Monkeys’ was originally produced as a children’s game (1965) and they have proved very versatile,” Green explains, “I discovered in 1968 that they were ideal models for protein subunits, being asymmetric, having multiple interaction sites and available in several colours. This exhibition illustrates their use in modelling the geometry of multi—subunit protein structures.”

Stop monkeying around, take a look at Green’s site to get the hang [pun intended!] of proteins. It’s a great idea for a science fair project too.

Sniffing out our sense of smell

How we smellOur sense of smell is much better than we give it credit for. A report in Nature Neuroscience puts paid to the notion that the human reputation for having a poor sense of smell compared to other animals.

Noam Sobel and colleagues laid down scent trails in a grassy field, and asked human subjects to find the trail and track it to the end. Subjects were blindfolded and wore thick gloves and earplugs to force them to rely exclusively on smell. Contrary to expectations, the volunteers exhibited some of the same tracking strategies used by dogs and were certainly capable of following the trail.

In follow-up experiments, the authors also demonstrated that this ability partially depends on comparisons of odour information in each nostril, it’s almost like smelling in stereo.

When subjects had one nostril plugged their tracking performance was much worse.

Admittedly, the volunteers were much slower than dogs at following the scent trail, but with practice they got quicker.

the findings raise the intriguing possibility that our sense of smell is far better than we think and that using it more effectively is simply a skill we don’t teach our children so it gives us the impression that we don’t have it.

For more on a provocative theory of how we smell check out this page from the Sciencebase archives.

YAFSE – train your beady eye on EB-eye

The European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) this week launched its new website. Apparently, the web interface has been streamlined on the basis of user feedback. Nothing too exciting in that, except they have also upgraded their search engine and describe it as being at the centre of the site and exhaustive in its breadth.

Underpinning the new site is “EB-eye”, a trendy-sounding and powerful search engine allowing instant searches of all the EBI’s databases from a single query. “If you can use Google you can use this,” explains associate directory Graham Cameron, latching on to the “proper-verb” of the day.

Seriously though, the new site architecture should allow much swifter navigation between databases, so that you can get from genomes to genes, proteins to structures and biological functions from a single, simple interface.

Intriguingly for an organisation that goes by the monicker of EMBL-EBI acronyms (and jargo, allegedly) have been banished from the site wherever possible. You’re unlikely to hear scientists say, “I’ve just EB-eye’d it,” just yet. But, it might make more sense for specialists to do just that rather than “Googling” for their information needs.