David Bradley – Page 252

Sperm, Discharge, Heroin, and Alzheimers

alkaline-batteries Batteries are included (unfortunately) – A chemical cocktail of toxic gases is released when you burn alkaline batteries, according to the latest research from Spain. The investigating team highlights the issue with respect to municipal waste incineration, which is used as an alternative to landfill and suggests that recycling is perhaps the only environmentally viable alternative.

Today, UK government departments BERR and Defra, in conjunction with the Devolved Administrations,
today published a Consultation Document containing draft Regulations setting out proposed systems for the collection, treatment and recycling of waste portable, industrial and automotive batteries.

Cutting heroin analysis – Analysing samples of street heroin just got easier as researchers have developed a statistical method for removing uninformative signals from their near-infra-red spectra of seized samples.

Sperm and eggs – Scientists in Sweden have determined the precise molecular structure of a protein, ZP3, essential to the interaction of the mammalian egg coat and sperm. The work could eventually lead to improved contraceptives, has implications for fertility studies, and might, in some sense, explain how new species arise.

Untangling Alzheimer molecules – Magnetic resonance spectroscopy provides new clues about how a dipeptide molecule blocks the formation of the toxic amyloid beta-peptide aggregates in the mouse brain. The discovery could put paid to the theory that amyloid beta-peptide causes Alzheimer’s disease and suggest a therapeutic lead that focus on the real culprit at an earlier stage.

Alchemy Under the Spotlight

atlantic-bathymetry This week, The Alchemist is digging in the dirt to find out about the carbon cycle and climate change, taking his whisky (or is it whiskey) with or without water, and discovering how to juggle molecules, on the other hand. Also in biochemical news this week, the crystal structure of a plant hormone receptor is revealed while researchers in Israel focus on blocking the protein misfolding that occurs in Alzheimer’s disease.

And, under the December physical sciences Spotlight

It’s all in the marine mix – Mixing of surface waters in the Atlantic Ocean seems to have reverted in the winter of 2007/2008 to “normal” levels for the first time in almost a decade…

Well, wooden you know? – New materials that look and behave like plastics can be produced from a renewable raw material known as liquid wood. The bioplastics promise to displace petroleum as a feedstock for certain applications…

Running with knives – Stabbing is the most common form of murder in the UK and Ireland. However, while forensic scientists understand the basics of the process…

Rx Reviews Redux

A new(ish) website has launched that aims to provide unbiased patient-generated data on the benefits of 7000 prescription medications and their side-effects.

Rateadrug.com hopes to do for pharma products what dooyoo and ciao do for gadgets by bringing the crowd to the debate. Patients can anonymously rate and review any of the prescription drugs they take and view other people’s experiences for free.

“All information on this site is unique, community data that is not biased by pharmaceutical or corporate objectives,” says spokesman Jack Dowd. He adds that, “The site provides patients with truly independent survey results about the risks and benefits of their medications. The more people that start using the site to rate their prescription medications (a quick 5-minute survey), the greater this resource will become.”

Using a prescription drug appropriate to your condition and your genetics can have significant, and often life-saving benefits, but with physicians particularly in the UK and a few other places emphasising how patients should help manage their own illness it is important to know what problems may arise or whether asking for a different prescription might actually be better for them.

Not all medications hit everyone in the same way, because of various factors including your SNPs (single nucleotide polymorphisms), that affect your body’s enzyme and receptor activity. “What’s effective and side-effect free for one person might not be the best drug for someone else, yet most harried doctors prescribe the same drug for 90% of their patients with similar conditions – regardless of individual sensitivities,” the site’s developers say. They hope that Rateadrug will prevent the next Vioxx from happening.

A side project of Rateadrug is involving pre-med students through the PreMed Prescription Rating and Experience Program (PREPP) where the students help senior citizens become more proactive with their drug intake by reporting their experiences through Rateadrug.com.

The site blurb suggests you use the reviews together with your doctor’s advice and FDA disclosures to achieve the best possible outcome for your (or your loved ones) medical condition. Of course, spammers and corporate shills will be readying themselves to distort the results in their favour, unless preventative measures are put in place. “To prevent spam and ensure a real person is taking each survey we require email verification where the user has to click on a link that we email to them,” Dowd told Sciencebase, “We also flag accounts that submit more than one rating for a specific drug. We’re committed to providing quality, real-user data and will continue to ensure that our results are not skewed by spam or anyone trying to influence the results of a specific drug.”

The site also drops a cookie on to your machine so that it knows how many people log in from a specific computer or IP address. If it looks like there are a lot of ratings for the same drug from the same IP address, they will flag those ratings for manual checking.

I asked Dowd to expand on how they are addressing security and validity issues. “At the moment we receive 20 or fewer ratings per day, and carefully review each one,” adds Dowd, “As the volume increases significantly it will become more difficult to impact and distort results – real ratings should outweigh any attempts to skew ratings. But, we will do our best to prevent this type of tampering.”

“Right now, we have a database of over 7000 drugs, but only about 300 have been rated and reviewed by users/patients,” he adds. Dowd and his colleagues hope that as more people find out about this site, the numbers will grow. “Our intention is to provide real ratings by real people and will do everything we can to assure this as we progress,” he told me.

According to CEO Mark Deuitch, RateADrug is currently hoping to get large numbers of patients to review the cholesterol-lowering statin drugs Lipitor, Lescol, Mevacor, Pravachol, and Zocar, anti-depressants such as Lexapro, Prozac, Effexor, Paxil, Zoloft, and Pristiq, and drugs used to treat insomnia including Ambien, Lunesta, Sonata, Rozerem, and Benzodiazepines.

In related news from the UK’s National Health Service: Drug reference information in the British National Formulary will become a key element of the new NHS Evidence portal due to be launched in April 2009. As a result, responsibility for provision of this information for the NHS will transfer from the Department of Health to the National Institute for Health and Clinical Excellence (NICE), as part of the development of NHS Evidence.

Melamine Detector

A fast and inexpensive melamine detector is reported in the RSC’s journal ChemComm this week. The research follows hot on the heels of the melamine in milk scandal of 2008 and the petfood contamination in 2007 and earlier. The two techniques are based on mass spectrometry and could be adapted to provide on-site kits that would require little training to use.

Melamine, commonly used as a fire retardant and polymerized to a plastic resin, was added to milk during processing to artificially boost its apparent protein content.

David Muddiman, professor of mass spectrometry at North Carolina State University, Raleigh, US, describes the techniques as “marvellous examples of how innovative, direct analysis ionisation methods, when coupled with mass spectrometry have the ability to address contemporary problems facing the world. The [researchers have removed all the major obstacles allowing for mass spectrometry not only to compete, but to take the lead in these types of analyses.”

More details here.

Social Media for Science Librarians

roddy-macleod I’m still following the social media for scientists trail and asked my good friend Roddy MacLeod of Heriot-Watt University, Edinburgh, who runs the Internet Resources Newsletter whether he had any thoughts on gathering up social media resources and scientists into a directory or other online resource. It would be useful, for instance, to know which scientists are on Twitter, who is using Ning sites and who can be poked, with a testtube, on Facebook.

I asked MacLeod what he thought of the idea of collating all the scientists on Twitter, Facebook, LinkedIn etc. “The question maybe is whether all the scientists would like to be gathered up. After all, it’s the individual who is in control of his/her own environment in these general social networks, and maybe that’s the way it should be.”

“I did a wee post on some social networking services on the spineless blog, but mostly leave that to SciTechNet and Brian Kelly et al,” he told me. “One thing I reckon is that as social networking sites like IET Discover and 2collab, and others multiply, it’s going to get more difficult for librarians. They can’t be expected to join and participate in all the possible specialised social networks, unless they specialise in a very particular subject, so they’ll end up missing a lot of potentially useful stuff. “There are so many, I can barely keep up,” he confessed, “Some interoperability between them would be great, because otherwise you have to spend time creating a brand-new profile for each one.”

He adds, that we [information scientists and librarians] are in a similar situation as they were with the burgeoning spread of trade journals, but at least librarians could scan those occasionally, so keeping up was easier. Many of the thousands of trade journals are free.

MacLeod echoes a commentator in my previous SM post regarding financing of these sites: “I reckon that only the well-supported social networking services will survive (those backed up by large professional societies or major publishers),” he told me, “Some of the smaller ones may end up like those discussion forums on some sites where no-one actually discusses anything.” There already are plenty of cob-webs on the net. “Yes, there are the very general all-subject ones, the well-supported general ones such as IET Discover and 2collab, some niche ones which are likely to survive,” adds MacLeod, “and some chancer ones that are trying to jump on the bandwagon. This means some wasted effort as we wait to see which ones will take off and survive, but there is no other way.”

MacLeod will soon be busy promoting ticTOCs, which will potentially help all researchers, including those unaware of RSS newsfeeds or who don’t care for that technology and keen RSS aggregators alike. “ticTOCs will serve both types of user in different ways allowing them to keep up-to-date with the research literature.”

To use ticTOCs as a current awareness service, you don’t need to know anything at all about RSS. ticTOCs ingests RSS feeds behind the scenes, but it’s perfectly possible, using ticTOCs to find, display, expand and then save (to the MyTOCs feature in ticTOCs) tables of contents to keep current without any mention or knowledge of RSS. “To me, this is the main use of ticTOCs because,” adds MacLeod, “as a Forrester report recently pointed out many people don’t understand/use/can’t be bothered with RSS. However, for the minority who are happy to use RSS, ticTOCs can be used as a tool to find relevant table of contents feeds, and then export them to the person’s favourite feed reader.”

The important point about RSS and TOCs is described in Lisa Rogers’ article in FUMSI. What librarians and every researcher needs is RSS feeds for journal TOCs. Moreover, publishers must produce TOC feeds in a standardised way, says MacLeod. This will allow both individuals, and services such as ticTOCs and others (see 6 mentioned in IRN) to better utilise feeds, and this in turn will help get current journals better exploited. “What ticTOCs has found is that publishers currently don’t produce journal TOC RSS feeds in a standard way,” MacLeod says, “they insert all sorts of things in various fields, they put the authors in various fields, they often don’t include abstracts, often don’t include the DOI, often don’t cite authors in a standard way, etc.

Rogers’ article goes some way to explaining what publishers should do, and CrossRef will be coming out with more Recommendations for publishers with respect to tables of contents RSS feeds in the future. “This is also very important for publishers because of the increasing emphasis on papers being deposited in Institutional Repositories after 6 months of being published,” adds MacLeod, “So, the publishers need to exploit their current content as soon as possible after publication as possible.”

Water of Life

A while back, I visited the Bushmills whiskey distillery (it was my second visit in as many decades) always a pleasure, especially the tasting panel at the end of the tour just before you spend all your money on, ahem, souvenirs.

Whisky is a broad category of distilled drinks made from fermented grain mash and aged in wooden casks. Different grains are used for different varieties, including barley, malted barley, rye, malted rye, wheat, and maize (corn), certainly a favourite at holiday time and the subject of many a New Year’s Resolution. The fermentation liquid is distilled, sometimes several times, to produce neat spirit, which is then aged in casks. Different barrels, virgin oak barrels, pine barrels, used sherry casks, charred barrels, are used to produce different flavours.

It’s quite ironic that there are some 200 to 300 chemicals in the finished product including carbonyl compounds, alcohols, carboxylic acids and their esters, nitrogen- and sulfur-containing compounds, tannins and other polyphenolic compounds, terpenes, and oxygen-containing heterocyclic compounds, and esters of fatty acids any one of which would probably be banned under health and safety rules if you were inventing whisky as a product today. Indeed, the nitrogen compounds include pyridines, picolines and pyrazines, carcinogens on the rocks, any one?

Anyway, one aspect of the whole process from grain to bottled liquor that fascinates me is that the distilled liquid, the spirit, is an almost pure ethanol-water mix (an azeotrope). In fact, the tourguide at Bushmills told us that this was so and that the flavour is then all to be found in the aging process in the barrel. But, if that’s so, then it doesn’t explain the wide range of flavours of whiskys matured in similar casks, nor does it explain how the peaty fireside phenols of some Scotch whiskys, the Islay type for instance, are carried into the bottle.

As is my current wont, I twurned to Twitter to ask about this and hooked up there with Michelle Jones of justaddbourbon.com who asked some of her friends in the bourbon trade about the spirit of the water of life, so we’ve got a Stateside answer.

“Look at it this way, distillation provides the palette by which aging can work its magic. There is no doubt that American Whiskey was once a very harsh tipple. Once aging was introduced, it mellowed the whiskey considerably. But even that doesn’t wholly answer the question. Aging contributes differently based on time. Short aging might contribute a little more sweetness whereas long aging contributes smokiness and oakiness. But most people pick out mintiness and a long finish from Heaven Hill whiskeys. That is a result of the distillation process.”

Whisky lactone (3-methyl-4-octanolide) is present in oak, which is the most commonly used barrel material and endows whiskies with an essence of coconut aroma, while the diketone diacetyl (2,3-butanedione) gives the buttery aroma of most spirits. Commercially charred oaks used for aging barrels are particularly rich in phenols, with some 40 different phenolic compounds, having been revealed in charred oak barrels, each one of which can add to the flavour. The coumarin scopoletin is also present in whisky.

Oh, and just in case you thought I was being inconsistent with the whiskey/whisky spelling, it’s impossible to know which one should be used whiskey is often for Irish and American, and whisky for Scotch and Canadian, but it’s Maker’s Mark Bourbon Whisky (original distillers were Scottish) and Woodford Reserve Bourbon Whiskey (waiting on an answer as to whether they have Irish origins), and they’re made just 80 miles apart in Kentucky.

Dioxins in Pork

dioxin-pig Dioxins Before Swine – Irish pork is off the menu, according to the BBC.

The UK’s Food Standards Agency is monitoring pork products in the Irish Republic because of fears of contamination with dioxins. “Tests showed some pork products contained up to 200 times more dioxins than the recognised safety limit.” Interestingly, dioxin levels in soil have been declining in recent years, according to another BBC report from 2007. The alert over dioxins followed an alert after PCBs (polychlorinated biphenyls) were reported to have been found in Irish pork on 1st December after samples were taken 19th November.

There is some hint that machine lubricating oils contaminated with PCBs (stable polychlorinated biphenyls) may have degraded to release dioxins which somehow found their way into the pig feed. But, more likely is that non-feed grade oil is being used at some point in the cycle to dry biscuit meal (out of date biscuits and bakery goods from the food industry). Such non-feed oils obviously do not have the same quality controls as extra virgin olive oil and so could very easily have higher than food-safe levels of contaminants, including PCBs and dioxins. This suggestion hints once again, as did the ongoing melamine scandal, at how easy it seems to be for unscrupulous sectors of the food industry to use non-food materials in their products, allegedly.

So, what are dioxins and should we be worried about them?

Dioxin Dioxins are organic compounds formed when a huge range of materials, particularly chlorinated polymers (PVC plastics) burn and in some industrial processes. They are ubiquitous in the environment and became the focus of environmental activism because of their reputation for being among the most toxic compounds known. Colloquially “dioxin” is talked of as if it were a single compound rather than a class of compounds, but the most usual reference is to the chlorine-containing compound 2,3,6,7-tetrachlorodibenzodioxin. Dioxins should not be confused with the compound 1,2-dioxin and 1,4-dioxin, which are heterocyclic, organic, antiaromatic compounds.

2,3,6,7-Tetrachlorodibenzodioxin can have some nasty effects such as irritation to the eyes, allergic dermatitis, chloracne, porphyria; gastrointestinal disturbance, possible reproductive, teratogenic effects, liver, kidney damage, haemorrhage, and occupational carcinogenicity. But, does that long list of problems mean anyone eating any of the food products from Ireland – bacon, ham, sausages, white pudding and pizzas with ham toppings – were or are in any danger. “The UK’s Food Standards Agency said it did not believe at this stage that UK consumers faced any ‘significant risk’,” reports the BBC. Seems like fair comment, only serious chronic exposure to low levels of dioxins or acute high-level exposure are of real concern.

No member of the public has ever died from dioxin poisoning, despite the fact that for several decades industry has been inadvertently releasing these materials into the environment as impurities in hundreds of products and that countless burning materials release the same supposedly deadly compounds across the globe continuously. Occupational exposure has led to probably at most four deaths from industrial accidents involving the release of dioxins, according to John Emsley writing in The Consumer’s Good Chemical Guide.

Flu Structure, Mp3s, and Magnetic Minestrone

You can read my latest science news updates in spectroscopynow.com:

One flu over – X-ray studies have revealed details of the structure of a protein used by the avian influenza, H5N1, that allows it to hide its RNA from the infected host’s immune system. The structure could provide a new target for the development of antiviral drugs against this potentially lethal virus

Minestrone and magnetic resonance – Researchers in the US and France may have overturned decades of theory in magnetic resonance studies by spotting a discrepancy in the way nuclear spins behave. Their new mathematical model of the process improves our understanding of atomic behaviour and could lead to better NMR spectra, sharper magnetic resonance images, and perhaps one day a fully portable MRI machine.

Organic soil matters – Could the earth beneath our feet hold the key to climate change? According to scientists at the University of Toronto Scarborough their NMR results show that global warming is changing the molecular structure of organic matter in soil.

Battery capacity is full of holes – Researchers in Korea have developed a novel material for the anode in rechargeable batteries, which they say could make them much more efficient and extend significantly the length of time between charges.

And on ChemWeb for science news with a chemical element:

First on the list in this week’s Alchemist, more on the new anode material, which is potentially good news for the iPod generation. In analytical research, HPLC has been used to spot dummy tequila and in medical chemistry US radiologists suggest that a dose of modified vitamin D could protect citizens from a dirty bomb attack. Next up, a new approach to addressing qubits allows for faster measurements that could take us a step closer to a quantum computer, while Yorkshire chemists are working out the best mix of starting materials to get the maximum height yield on their tasty products. Finally, this week’s award is a record breaker in the State where big is everything.

Top Ten Mutants

dna-test If you ever thought genetics was only about disease, then check out the popular SNPs list on SNPedia. A SNP (pronounced “snip”) is a single nucleotide polymorphism, which in BradSpeak(TM) is basically a difference in a bit of your DNA that makes you different from the rest.

Anyway, here’s the Top Five SNPs that might be described as having no obvious direct medical importance.

rs1815739 sprinters vs endurance athletes (I reckon I lack both)
rs7495174 green eye color and rs12913832 for blue eye color
rs6152 can prevent baldness (this was discovered far too late for me)
rs1805009 determines red hair (some “comedians” might suggest this be swapped to the second list below)
rs17822931 determines earwax (and presumably how well your ears stay clear of insect infestation)

And, here’s the more sober list of SNPs that could have serious medical implications should you happen to discover you have one of these when you have your genome read by the likes of 23andMe.

rs9939609 triggers obesity (not a genetic excuse for eating too much)
rs662799 prevents weight gain from high fat diets (ditto)
rs4420638 and rs429358 can raise the risk of Alzheimer’s disease by tenfold or more
rs7903146 and rs12255372 linked to type-2 diabetes, the latter also to breast cancer
rs324650 influences alcohol dependence, rs1799971 makes alcohol cravings stronger (it would not be funny to say, “Mine’s a pint, with a whisky chaser”, right now)

It was a twitter discussion between SNP experts mza and attilacsordas that led me to the SNP list.

Author: David Bradley