French Fries, Wild Mushrooms and Ouzo

Alchemist ChemWebA mixed bag this week in my Alchemist column on ChemWeb.com this week. First up, news that US$1 million is to be ploughed into biofuels research that could circumvent some of the serious environmental concerns associated with this renewable energy source.

In the world of pharmaceuticals we discover that there might be yet another string to the bow of aspirin-like drugs, this time in the fight against breast cancer. There’s good chemical news for those hoping to save Gulf Coast Wetlands from the rampages of the coypu with the discovery of a chemical lure, The Alchemist also hears of a novel system of surfactants and gelating agents that can form separate compartmentalized structures resembling the organelles in a living cell. You might care to have a drink with The Alchemist this week in celebration of a clearer understanding of why some drinks, such as ouzo, form cloudy emulsions with water. There’s more on the ouzo effect in my SpectroscopyNOW story on the subject where an independent team working in parallel have used NMR to take a look at these rare and peculiar emulsions.

Finally, a little kitchen chemistry could give your French fries a little je ne c’est quoi.

Edible wild mushrooms

Speaking of haute cuisine…also on this week’s SpectroscopyNOW, I report on how Portuguese scientists have identified a whole range of smelly molecules found in wild edible mushrooms. It’s pioneering work that will allow the food industry to ensure it is not being fobbed off with cheap mushrooms when a more expensive variety is what they ordered. The results could also be used by biotechnologists to engineer specific flavours into easily cultivatable varieties of mushroom. Two points arose as I was writing the item: The first is that overall mushrooms smell of nothing more complex than 1-octen-3-ol, which the researchers describe helpfully as having a mushroom-like odour. Secondly, the notion of cultivating wild things is at odds with the whole ethos of wild mushrooms, surely?

Either way, it’s hopefully an interesting read. Now, pass the ketchup for my mushrooms and fries, would ya?

Girly Games

My latest science news write-ups on the SpectroscopyNOW portal are now up for grabs. This week, I cover the apparent gender gap when it comes to computer games, how Japanese researchers are using near-infrared light to probe young women’s brains to find out if they can reduce stress and potentially acne with pleasant fragrances, and the discovery that cancer cells seem to be stuffed full of the dreaded trans fats. You can find my other spec news from this week linked in the Sciencebase Geeky Bits column.

Perfect skinHowever, I want to step back a little with respect to that video games research. The team used the apparently powerful technique of functional MRI (basically a brain scan that can spot changes and lights up active regions of the brain). The researchers devised a very simple computer game, a kind of cross between Tetris and Pong (without the bats). To win you had to gain territory. The researchers scanned the brains of males and females while they played this game. Their results showed that men and women got the game, but the men were sharper when it came to realising you had to use a particular strategy to gain the most territory.

What was most interesting to Allan Reiss and colleagues at Stanford University School of Medicine who carried out the research was that the region of the brain associated with rewarding feelings lit up the most in the males than in the females. This, the researchers say, suggests a possible explanation as to why males enjoy, and even become addicted to, video games more commonly than females. “These gender differences may help explain why males are more attracted to, and more likely to become ‘hooked’ on video games than females,” Reiss explains in the Journal of Psychiatric Research.

Now, I take issue with the fundamental assumption that Reiss and his colleagues make regarding video games. While historically video games have been aimed almost squarely at boys, the manufacturers over the last few years have recognised that they only corner half the potential market with such a biased aim. As such, they have developed dozens of new types of games that are not of the familiar war and killing fantasy type. They have also remodelled their hardware to offer colours and skins that will appeal to females, the pink and white Nintendos, for instance, generally appeal to the female market more than the blue.

More to the point though, my ten-year old daughter and dozens, if not all, of her friends have taken to Nintendos, Wiis, Playstations, Tamagotchi, just as addictively as their male counterparts, fighting for screen time on their various devices and computers. Admittedly, the games they play are more frequently of the SingStar, Petz, and Sims kind as opposed to Halo, World of Warcraft etc. They also network with each other online in various online games with small furry animals rather than three-eyed aliens with vast armaments. Like I say, though, they are just as addicted to these games as the boys.

So, while Reiss’s work is fascinating and does hint vaguely at latent aspects of how territorialism evolved in the male brain. One has to wonder whether if he and his colleagues created a different type of game, a more “feminine” type game, like a pet simulation, for instance, they would see those reward centres lighting up more brightly in the female brain. Perhaps if the experiment had had an intrinsic bias towards a feminine type of game and they’d seen such activity in their fMRI, they would have come to a very different conclusion about video game addiction.

Full Spectrum Science News

Musical molecules

Musical molecules, bright fibres, polarised brain chemistry, and cholesterol regulation, all feature in my SpectroscopyNOW column this week.

Musical molecules – What do Schroedinger’s equation and Schoenberg’s expressionism have in common? Not a lot you might think. However, researchers in Germany and the US have now modelled the hydrogen molecule, the archetypal subject of molecular modelling, using a theory of behaviour that emerges from music. The study demonstrates how a hydrogen molecule responds to laser pulses as if the molecule’s vibrational motions, its quantum states, were the notes making up a changing musical chord and offers the opportunity of laser-controlled chemical reactions.

Fibre, fibre burning bright – A European research team has developed novel strategies for the rapid trace element analysis of metals in polyamide synthetic fibres by graphite furnace atomic absorption spectrometry and inductively coupled plasma mass spectrometry. Their method allows the accurate determination for quality control of polyamide products containing titanium dioxide as an optical brightener.

Bad cholesterol regulator – US researchers have discovered exactly how a destructive protein binds to and interferes with one of the molecules involved in removing low-density lipoproteins (LDL), the so-called “bad” cholesterol, from the blood.

Bipolar disorder – Spectroscopic studies of post mortem brain chemistry reveals that sufferers of bipolar disorder (often referred to as manic depression) have a distinct chemical signature linked to this mental illness. A collaboration between researchers in the UK and US also suggests a possible mode of action for the mood stabilisers used to treat the disorder and how they counteract changes in brain chemistry.

Brain Scan Reveals Cultural Differences

Magnetic resonance imaging

I’ve just finished writing a news article for the SpectroscopyNOW.com MRI ezine and wanted to expand on some of the implications of the work here. The item describes the results of recent research that purportedly show differences in how born-and-bred Americans differed from immigrant East Asians tackling a simple visual test based on displayed sequences of boxes and lines.

The functional magnetic resonance imaging (fMRI) study looked at differences in activity between 10 Americans and 10 East Asians while they carried out that task. Apparently, they found significant differences depending on whether or not the volunteers were working out the solution to the task based on individual lines or the lines in the context of others. The volunteers were also asked to complete a questionnaire about their cultural attitudes. The research doesn’t intend to imply that either group did better or worse than the other, this is simply about different regions of the brain lighting up during the task and whether that might be correlated with differences in cultural heritage.

It’s interesting work and the researchers claim to have shown for the first time that a person’s cultural upbringing and the extent to which one identifies with those cultural influences can affect brain activity patterns when faced with a specific task.

In the current study, however, the researchers seem to make the rather sweeping generalisation that American culture values the individual and so emphasizes the independence of objects from their context, while East Asian culture tends to emphasize the collective and the interdependence of objects based on context. This, they say, explains why they see such a big difference in brain activity between the two groups of volunteers, the Americans focusing on the individual aspects of the task and the East Asians seeing the collectiveness of the boxes and sticks in the sequence.

My first thought while writing the news item, was whether or not their initial assumptions about cultural stereotypes remains valid in an increasingly globalised world. Do Americans focus on the individual and do East Asians think more in terms of society as a whole? More to the point the study was carried out with just ten individuals from each culture. Yes, those two groups may have different attitudes and aptitudes, but are those results statistically significant?

How random was the choice of the ten East Asians. Apparently, they were people coming to the USA to live! Does that make them “typical” of their fellow countrymen? I would suggest not at all. People who leave their home country are often very different from their stay-at-home counterparts in attitude and outlook . Perhaps these ten individuals had a very different cultural attitude to their former countrymen. Indeed, what if by virtue of their wishing to emigrate to the USA had coloured their whole outlook and notions of their own culture. Maybe they carried out the task in a way they hoped would be more American, or conversely, maybe they tried to be more East Asian to help the researchers. Similarly, who’s to say anyone taking part in such experiments behaves as they normally would given that they’re stuck in a noisy MRI machine being put under pressure to perform.

fMRI is a powerful tool. The burgeoning list of results it generates grows day by day and I will continue to report them for the ezine assuming they are worthy of reporting. The present results are intriguing, but I do feel that they are stretching the perceived prowess of fMRI a little too far. To my mind, there is an enormous gulf between demonstrating some difference in brain activity while a a few individuals carry out an esoteric task and correlating that with alleged cultural differences, especially given the circumstances of those who are supposed to have essentially polarised outlooks.

Nature’s Missing Crystal – Found It!

K4 crystal

Diamond is not unique! Nature’s missing crystal discovered! A crystal as beautiful as diamond! Those were the themes running through dozens of articles in the media about a discovery made by Japanese mathematician Toshi Sunada of Meiji University. The original press release proclaimed that he had discovered a theoretical crystal structure with the same symmetry properties as diamond but with handedness, or chirality, and that this knocked the crown from diamond’s uniqueness.

Unfortunately, he soon discovered just how embarrassing press attention can be as chemists and crystallographers began filling his email inbox with messages alerting him to the existence of the exact same structure he was “predicting” already having been found. I asked Sunada about what happened.

“After my article appeared [in Notices of the American Mathematical Society; PDF file] a few people pointed out the oversight,” he told me, “They were rather sympathetic to that the difference of culture between mathematics and other sciences that leads to such ignorance.” He adds that although he hadn’t been aware of the known crystal structure until his modelling constructed it before his eyes, the people who contacted him were unaware of the history of his work in this area stretching back a decade. The original work that led to the discovery of the structure was done by AF Wells in the mid-1970s.

It highlights just how far apart different fields in mathematics and the sciences are despite efforts by various agencies and funding bodies to attempt to build multidisciplinary bridges. The debacle reminded me of how it took a mathematician colleague to point out to Harry Kroto and his colleagues that the structure of the all-carbon molecule buckminsterfullerene and the symmetry laid bare by their spectra was suggestive of a truncated icosahedron, a soccerball, in other words!

It makes me wonder what other discoveries have we missed because the sciences are no longer as joined up as they were in the heyday of the nineteenth century polymaths like Faraday. Put another way how much money is wasted re-inventing the wheel. Without wishing to criticise Sunada or the referees of the original paper, but if a chemical colleague happened to have seen his structural simulations they might have spotted th fatal flaw in the argument that much sooner. Perhaps the Scandinavian idea of hot-desking should be introduced into labs, hot-benching you might call it, to boost the potentially innovative cross fertilisation of ideas. Or, how about a cross-disciplinary approach to peer review, send to two experts and an additional referee in another field entirely if the paper claims true novelty.

Anyway, back to Sunada’s work. It may at first seem that here was merely a mathematician modelling something that chemists and materials scientists already knew, but although one half of his discovery was not a discovery at all because the structure was already known, one aspect of his work could save chemists a lot of searching in vain. “My result pins down that there are only two crystals having these properties,” he told me.

You can read more about Sunada’s discovery in my SpectroscopyNOW column this week.

Composting Chitosan Cat-litter Composite

Spectroscopy Now

That has to be the oddest blog headline I’ve come up with this week, but it’s not in fact that esoteric once you get down to it. Basically, researchers in China have created a new material based on dolomite (porous kitty litter material) and the crab shell derivative chitosan.

The new composite material not only absorbs water it can release an NPK (nitrogen, phosphorus, potassium) fertiliser over a prolonged period for use in agriculture and horticulture. Advantages are, improved irrigation efficiency and less run off into waterways together with improved crop yields. More on this, in my SpectroscopyNOW column this week and you get a chance to see a photo of my kitty too. What more could you want? Other than links to the rest of this week’s news in SpecNOW, of course.

In NMR news, a brainy approach to using microNMR coils could allow scientists to probe the activity of cerebral compounds, such as choline, without having to worry about NMR’s relatively low sensitivity. In the X-ray ezine, I report on how British scientists have demonstrated that it is possible to predict the crystal structures of small organic molecules using software, winning them accolades at this year’s Blind Test in Crystal Structure Prediction, organised by the University of Cambridge and hosted by the Cambridge Crystallographic Data Centre.

Finally, new informatics evidence suggests that the land-bridge which is currently the Bering Strait was the sole route into the Americas for humans tens of thousands of years.

Sciencebase Top Ten Molecules of 2007

Graphene

Everyone loves a list. (Don’t they?) Well, as we’re approaching the end of the year and some of us are well into the panto and party season already, I thought it would be a good idea to run down a hit parade of this year’s molecules. So, here’s the Sciencebase Top Ten Molecules of 2007:

  • 10 – Graphene – chicken wire carbon sheets hit the headlines this year and will continue to do so as researchers learn more about this unique material’s optical and electrical properties. One day, carbon may even replace silicon as the elemental of choice in computing.
  • 9 – Helium – at the time of writing physicists in Canada had taken an important step towards understanding supersolidity in helium, stretching it a bit to include this in a list of molecules. This new state of matter forms at very low temperature and under extreme pressure and now it has been found that cooling makes supersolid helium even stiffer.
  • 8 – DNA – deoxyribonucleic acid, and more specifically, the deoxyribonucleic acid that resides in every cell of genomics pioneer Craig Venter. The J Craig Venter Institute claims that this “Independent sequence and assembly of the six billion base pairs from the genome of one person ushers in the era of individualized genome-based medicine”.
  • 7 – Water – Good old H2O continues to confound those scientists hoping to explain its anomalous properties, as supplies of the fresh stuff will dwindle as the century moves on, it’s heartening to know that close to absolute zero, water exists in yet another phase.
  • 6 – Ethanol – a seasonal favourite, of course, the active ingredient in so many beverages. As with a certain other molecule in this Top Ten, this year there has been a lot of hot breath resulting from various and conflicting health studies on the effects of ethanol on human health, expectant mothers and their unborn children, and others. So…raise your glasses to ethanol!
  • 5 – Rotaxane – 140 years ago, Scottish physicist James Clerk Maxwell devised a thought experiment that might help scientists break the law. An entirely legal, molecular version of Maxwell’s Demon made its debut this year, thanks to chemists at Edinburgh University.
  • 4 – Azadirachtin – After decades of trying and countless post-doc and grad students have come and gone Steve Ley at Cambridge University finally published a total synthesis for the natural insecticide azadirachtin.
  • 3 – Epothilone – could the anticancer drugs produced by soil microbes finally have come of age with the announcement from pharma giant Bristol Myers Squibb that it has obtained approval in the US for semi-synthetic analogue of epothilone B against drug-resistant metastatic breast cancer.
  • 2 – Carbon dioxide – this year, there has been more hot air produced around this greenhouse gas and climate change than I care to cite.
  • 1 – Hydrogen sulfide – yet another small molecule with a big impact. Scientists recently discovered that H2S could be the key to longevity, at least if you’re a nematode worm. A study published in PNAS in December demonstrated that the “rotten egg” molecule increases heat tolerance and lifespan in the molecular biologist’s favourite, Caenorhabditis elegans
  • Well, those are my choices, I deliberately avoided looking at Science to see what they’d come up with for their Molecule of the Year, before I put this post together. If anyone has their own Top Ten or even just a Number 1 let me know.

Sweet Proteins, Crystallised Proteins

Brazzein sweet protein

A new naturally derived artificial sweetener could soon hit the market, thanks to the development of a mass production technique devised by University of Wisconsin-Madison research Fariba Assadi-Porter. The sweetener, known as brazzein, is a 54 amino acid protein derived from an extract of the fruit of the tropical plant Pentadiplandra brazzeana Baillon. It has been eaten in West Africa across the millennia, but only recently caught the attention of the West because of its incredible sweetness. The protein extract tastes sweet only to humans and old-world monkeys and is is 2000 times sweeter than sucrose when compared to a 2% solution of sugar.

Assadi-Porter and her colleagues are using spectroscopy to help them understand the relationship between the structure of this protein and its sweetness. They have recently devised a new approach to fermenting it on a large scale and startup company Natur Research is now seeking FDA approval to commercialise the protein as a food stuff for the low-calorie drinks and food industries. A paper detailing the production process has now been accepted by Protein Expression and Purification Journal, and you can read more about the story in the NMR channel on SpectroscopyNOW.

More on proteins in this week’s issue: Roderick MacKinnon and his colleagues at Rockerfeller U have come up with a novel technique, lipid-detergent-mediated crystallization, that allows them to crystallise membrane proteins, such as the voltage-dependent potassium ion channel, in as near as natural state as possible. The approach could open the door to countless studies of membrane proteins using crystallography that have not previously been possible. More on that in the SpectroscopyNOW X-ray ezine, here

Also in this week’s round up, news not related directly to proteins and molecular biology. Researchers in Canada and the US have used MRI to demonstrate that there is something like a three-year delay in the development of certain regions of the brain in children with ADHD. The most obvious delay is seen in the front cortex, a region important in thinking, concentration, and planning. Rather than worrying parents, the discovery should be reassuring to parents and sufferers, says Philip Shaw of the NIMH Child Psychiatry Branch who led the research because although there is a delay, brain development is otherwise normal. “Finding a normal pattern of cortex maturation, albeit delayed, in children with ADHD should be reassuring to families and could help to explain why many youth eventually seem to grow out of the disorder,” he says.

The research also revealed that the regions affected by the developmental delay are coincident with the regions that develop precociously in children with autism. More on the scan results, again in SpectroscopyNOW.

Taking the P out of Urine Testing

Blood pressure hormone

A new approach to testing urine samples without having to purify them first has led to the discovery of a new hormone that controls sodium excretion and so could be involved in controlling high blood pressure. Too much sodium equates to raised bp. The discovery solves a riddle that confronted medical scientists for more than four decades and could lead to new approaches to treating high blood pressure.

I asked team leader Frank Schroeder about the work and discuss it in detail in this week’s SpectroscopyNOW. One issue that must be addressed before such a discovery can be applied realistically to the develop of new therapies for high blood pressure, or even low blood pressure, is to find out whether the hormone is involved in other control systems in the body. This is somewhat likely given that most other known hormones multitask. I asked Schroeder about this aspect of the research:

“At this point, it is difficult to speculate about what other biological processes might be influenced by the newly identified compounds, and the next step will be to find the receptor(s) that the [hormonal] xanthurenic acid derivatives bind to,” he told me. “From our analyses, it appears that the two xanthurenic acid derivatives represent the actual signalling molecules – the activity is very well-defined and the compounds are of high specific potency. Furthermore, a closely related metabolite, xanthurenic acid itself, is not active.”

Also, in this week’s issue, in the field of atomic spectroscopy, Jordanian scientists have found that garlic extract can reduce the levels of the toxic heavy metals, cadmium and lead, in vital organs, such as the liver, heart, and kidneys. You can read more about that here.

In pure chemistry, it has been a record-breaking year for coordination chemists Klaus Theopold and Kevin Kreisel of the University of Delaware and their colleagues who have synthesised an organometallic chromium compound with the shortest Cr-Cr bond ever. Not since the 1978 work of F. Albert Cotton and his team at Texas A&M University has such a short one been seen. Theopold told me that he does not think it will be too long before this new record is broken. “I don’t think it will be another 30 years, although I’d like to hold on to the record for a while,” he said, “As to who, there are three possibilities: somebody who is not trying for it, and discovers it accidentally (like us), Phil Power, or myself, because I am now interested and have some ideas.”

Finally, the rather delicate subject of turning raw sewage into compost for farms. Remy Albrecht of the Paul Cézanne University in Aix-Marseille and colleagues have developed an infra-red technique that could be used to monitor how well the composting process is going for biological wastes, such as sewage sludge. Obviously, compost quality for land application must be monitored and controlled closely, but there are so many benefits, such as quickly raising nutrient levels and improving soil quality that it is worth the effort. An analytical approach to near infrared reflectance spectroscopy can provide an inexpensive way to monitor the composting process, Albrecht told me.

“NIRS is a highly reproducible technique able to draw a precise chemical fingerprint of an organic material Moreover, NIRS is rapid and makes it possible to analyse a large number of samples in a practical and timely manner. Control of maturation can be easily simplified with good calibrations and a data bank in reference,” he said.

I do worry about the accumulation of heavy metals from such biological sources as with each iteration from crop/livestock, to dinner table, to sewage plant, back to farm, they could increase in concentration. There is also the issue of pathogens. I’d be interested to learn what safeguards are in place to prevent their circulation.

Virtualizing the Lab Book

I am a lab-note-freak who loves to write extremely detailed, organized lab notes, so organized that I really want to see the design of a really effective computer-based lab book software system.

With such a system, I’d want to be able to divide my lab work into several categories: Synthesis, Measurement, and other Manipulations. I’d also want to be able to create new categories by selecting and combining from a set of basic operations provided by the software.

Each type of lab work requires a unique form to fill in.Some fields are universal among all types of lab work such as Date, Title, Purpose, Results, Discussion, etc. But some fields depend on the type of lab work you are noting. For example Observations in the progress of a Synthesis lab work are important, but you don’t have any if you are doing NMR (a Measurement lab work) because you cannot see the sample.

With the help of database techniques your software labnotes could be searched, tagged, and, if online, shared! You could search people’s lab notes with “broadening” in Discussion field and “NMR” in Title field, for instance to learn from others’ experiences in the peak-broadening effects of an NMR study. And, of course, the digital chemical noting techniques (Smiles, InChI KEY etc.) connected to search engines could be incorporated into the software, too. I believe this is not very difficult technically speaking.

When I first heard of the online Open Notebook idea I thought it would be like the above-mentioned ideas, but now it seems that the current open notebook instances are essentially mere wikis and blogs. Wikis may be nice if you manually organize them into a labnote database but that’s much more tedious than directly using a database with a user-friendly shell. Blogs can be of some help with their datestamp format. Combined with tags you could make a blog-based lab notebook searchable, but it would still not be as good as specialized software designed for the purpose.

Perhaps I am missing the point of Open Notebook. Maybe it does encompass all my desires. I hope to learn more in the follow-up comments to this post.

— Guest blog post by PhD chemist Andrew Sun who is based in Guangzhou, southern China. You can find Andrew Sun via his Nature Networks blog where he discusses his life in chemistry.