September 2009 – David Bradley

Nervous, Monopolar, Solvents

Full Metal Alchemist Superfast fluorescent sensor molecules that detect and destroy nerve agent, chemical weapons, caught The Alchemist’s eye this week, as did new insights into the ancient oxygen levels of the early earth.

A very alchemical notion emerges from Austria suggesting that life elsewhere in the universe may use sulfuric acid instead of water as its vital solvent.

Spin ice reveals the existence of magnetic monopoles, the norths without the souths, so to speak.

Meanwhile, a graphene-semiconductor mashup shows us the way to future molecular electronics.

More on these and the links in this week’s Alchemist.

microRNAs

Until 2001, few people had heard the term micro ribonucleic acids, but these little chunks of nucleic acid, just 21 to 23 bases long, have been conserved throughout evolution. They don’t code for proteins, but they do seem to be involved in the regulation of immunity, the development and differentiation of immune cells, antibody production and the release of chemicals involved in the inflammatory response. So micro by name, but not by nature, you might say.

Indeed, microRNA, or miRNA, represent something of a new paradigm in the regulation of a vast array of responses of physiological and hence medical importance. They play a key role in diverse such diverse areas as virology, embryogenesis, differentiation of stem cells, cholesterol and fat metabolism, inflammation and (of course) cancer.

Victor Ambros, Rosalind Lee and Rhonda Feinbaum, at Harvard University, first revealed the existence of miRNA through studies with the lin-4 gene, an essential component of normal developmental in the lab technician’s favourite nematode Caenorhabditis elegans. They demonstrated that the lin-4 gene sequence from four species of nematode worm does not encode for a protein. That was an odd finding because nucleic acid sequences generally do. Instead it seemed that lin-4 regulates a so-called antisense RNA to RNA interaction. That was way back in 1993.

By 2001, the year the term miRNA was coined, these little chunks of RNA were becoming much more well known as the controls for post-transcriptional regulatory mechanisms. Since then it has been recognised that miRNAs are involved in the development of cardiovascular disease, hepatitis C, Alzheimer’s, and various forms of cancer. Wherever an important molecule emerges in biological research you can bet the notion of targeting that molecule with other molecules, pharmaceuticals, will be the next stage in the research.

Bioinformatics specialists Virendra Gomase and and Akshay Parundekar of the Padmashree Dr. D.Y. Patil University, in Mumbai, India, recently reported that miRNAs having been implicated in a range of diseases are now attractive targets for the development of new drugs. They explain that one approach to silencing miRNAs and so inhibiting the progression of various diseases is through the use of antagomirs.

Antagomirs are small molecules that resemble the oligonucleotides used to build RNA, but they are modified chemically so that they are not simply incorporated into working miRNA but block it by distorting it structurally or chemically. These compounds are, of course, related to the drugs used to treat RNA viruses, such as acyclovir, which is an analogue of the RNA oligonucleotide guanosine.

Studies have already demonstrated that antagomirs administered intravenously against various miRNAs – miR-16, miR-122, miR-192, and miR-194 – result in a marked reduction in levels of each miRNA in liver, lung, kidney, heart, intestine, fat, skin, bone marrow, muscle, ovaries and kidneys. Apparently, this method of silencing miRNAs in the body is specific (meaning fewer side-effects) and long-lasting (which means efficacious). But, the approach is still in its infancy, Gomase and Parundekar point out.

Indeed, they explain that in order to understand the enigma of gene expression as regulated by miRNA, there is a triangle of three parameters that must be unravelled:

Regulation (if any) of a gene at transcriptional level
Regulation of the transcript of that gene by microRNA
Regulation of that microRNA itself

Once that happens…

“The evolution of microRNA-omics will open up the possibility of potent future diagnostics and therapeutics for serious diseases,” the team concludes.

Virendra S. Gomase, & and Akshay N. Parundekar (2009). microRNA: human disease and development Int. J. Bioinformatics Research and Applications, 5 (5), 479-500

Organic Compost Chemistry

Okay…so I was kind of joking about doing a regular weekly gardening column, but having spent rather longer weeding and feeding this week than I intended to, I need to get something written for Sciencebase today that wouldn’t be too demanding. So here’s a quick guide to composting your kitchen and garden waste.

These are the fast-rotting greens that should definitely be in your compost heap. These all provide moisture and the all important organic matter and nitrogen for your compost. They also quickly accumulate bacteria and fungi that start the rotting process – the aerobic decomposition process – and generate necessary heat to get the compost heap going and produce rich humus from the break down of plant cellulose and the other complex molecules
in your kitchen and garden waste.

Grass clippings
Tea bags
Egg shells
Raw vegetable peelings
Fruit skins
Unused salad leaves
Dead flowers
Nettles
Rhubarb leaves
Spent bedding plants and annuals

You must also add materials such as cardboard and fallen leaves, sawdust, twigs, bark, and crumpled or shredded paper as much more slow-to-rot materials to build up air spaces in the compost heap and to add fibrous bulk to the compost. A good balance of these so-called green and brown waste products in your compost bin, will produce nice crumbly, but moist compost that earthworms love within 9-12 months. Speaking of earthworms red wigglers (Eisenia foetida or E. andrei) are great composters.

Get the balance badly wrong (too much grass, too many banana skins) or to much leaf waste and you’ll end up with either a dry pile of leaves and twigs or a smelly sticky mass, that is rotting but on the whole anaerobically. 50:50 green to brown is about right and don’t forget to fork it occasionally, but try to keep it nice and warm too. A good compost heap will get up to 77 Celsius through the heat generated by aerobic activity. Cornell University has the figures on carbon and nitrogen content of particular waste products.

The plant remains (including any that have passed through an animal gut) contain organic compounds: sugars, starches, proteins, carbohydrates, lignins, waxes, resins and organic acids. The process of organic matter decay in the soil begins with the decomposition of sugars and starches from carbohydrates, which break down easily, while the remaining cellulose and lignin break down more slowly.

The overall humification process leads to humus, which is a stable organic substance that essentially decays no further but fertilises soil with which it is mixed and provides nutrients for the next generation of plant growth.

There are some things you should not add to a compost heap or bin, partly because they reduce the quality of the compost, lead to the spread of weeds, or attract rats, foxes, and cats:

Meat
Cooked vegetables
Dairy products, particularly lumps of cheese
Animal and human waste
Perennial weeds and seed heads
Sanitary and infant hygiene products

Of course, if you have chickens or goats to feed (we don’t…yet) then most of your kitchen scraps can be used to augment their growth rather than feeding the soil. Chicken guano is great for compost heaps by the way, full of nitrogen and phosphorus and minerals. As too is fairly well-rotted horse manure, but don’t add too a high a proportion.

Finally, a compost heap needs potassium and trace minerals, such as calcium, iron, boron, and copper. These are all essential to microbial metabolism and are usually present in sufficient quantities in the waste materials you add to your heap.

Compost also needs phosphorus and adding a source can help the composting process considerably. It’s a very good idea to make sure there’s a good supply of this essential element being added regularly to your compost bin. There’s no need to rush out to the garden centre to pick up a bottle of “phosphorus”, you release adequate quantities at just the right concentration, together with nitrogen in your urine. I don’t need to spell it out do I? Just make sure the neighbours don’t get a nasty surprise and if you’re a female gardener perhaps invest in a SheWee…

Treating the Obesity Epidemic

Drugmaker Vivus saw its experimental weight-loss medication, Qnexa, pass two Phase III clinical trials C&EN reported on September 10, and the company’s share price skyrocketed.

The rewards of developing a safe and effective anti-obesity medication will be in the tens of billions of dollars, according to Bloomberg. Of course, such apparent breakthroughs are going to hit the headlines, big time. After all, who wants to reduce calorie intake and increase exercise levels when popping a pill could solve one’s weight problems?

In the developed world, overweight and obesity (BMI > 30) and other diet-related problems, such as cardiovascular disease, diabetes, and metabolic syndrome, are on the increase. And, while it might be assumed that the billions of people who live in abject poverty with the daily threat of acutely lethal diseases, such as malaria, have other things to worry about, the diseases we commonly associate with the “Western” lifestyle are emerging across the globe. The WHO says that, perhaps with the exception of sub-Saharan Africa, deaths caused by chronic diseases dominate the mortality statistics.

Astoundingly, WHO figures from 2005 suggested that there are more people suffering from overweight-related problems than malnutrition. At the time, globally there were more than 1.6 billion people aged over 15 years who were overweight and 400 million of those were clinically obese, while around 800 million suffered from malnutrition. Those numbers are already changing. The WHO predicts that by 2015, approximately 2.3 billion adults will be overweight and more than 700 million will be obese.

The costs in terms of loss of quality of life and impact on healthcare providers in the developed world are likely to be unsustainable in terms of demands on surgical and drug treatments.

While much of the focus on the obesity epidemic is aimed at the US, high rates of cardiovascular disease associated with poor nutritional choices, dietary trends, and exercise issues ring just as true in the UK.

Andreas Anastasiou of the Department of Agricultural and Food Economics at the University of Reading, and a quantitative risk analyst at the Bank of Santander, London, UK and Athanasios Anastasiou a lecturer at the Technological Education Institute of Patras, Greece and an economist at the University of Patras, recently highlighted the sorry state of the British diet and the burden the growing obesity problem will ultimately have on the economy and society as a whole.

Here are just a few of the UK obesity facts and figures cited by the authors:

30,000 – deaths a year
9 years – average life reduction
18 million – working days lost
£1 billion – cost to National Health Service
£2.5 billion – cost to the economy

Obesity and associated chronic diseases are a serious threat to a nation’s health and well-being, the researchers say. “Their impact on the economy and society as a whole is tremendous exhibiting enormous healthcare costs and losses in working hours and years of life.” They suggest that improvements will happen if long-term changes to food choices and dietary habits are made, whether this should come top down from government and healthcare providers is difficult to say. How ever it is achieved, you can be almost certain that popping a pill will not be the cure all, despite what pharmaceutical share prices might suggest.

Andreas G. Anastasiou, & Athanasios Anastasiou (2009). The effects of current dietary trends and consumption patterns on health: evidence from the UK Int. J. Behavioural and Healthcare Research, 1 (3), 318-333

Dental Lead, Lung Cancer and Monopoles

This week’s ezines on SpectroscopyNOW are now live, featuring a breath test for lung cancer, magnetic monopoles, a way to boost fuel cells, and reducing toxic waste from dental surgeries.

Extracting the dental lead – Lead contamination in the black paper used to mask dental X-ray paper has been determined for the first time using AAS. The worrying results suggest that the used material represents an environmental waste problem requiring pre-treatment before disposal.

I asked the researchers to outline the importance of their study. Team leader Debora Guedes told me that, “There are still more than 600 million packets of intraoral film exposed each year in the USA alone, and much more elsewhere in the world. The volume of potential waste materials is significant,” she says.

She pointed out that while attention has previously been given to the disposal of the lead foil used against backscatter radiation that can fog an X-ray image and also to avoiding lead-lined boxes to store intraoral dental X-ray film, lead contamination of the black paper used to help exclude light from the film, or the paper or plastic wrapping of the film and lead foil has been ignored entirely, she adds. “This study is an important public health contribution as it indicates that this neglect is of potential importance,” Guedes told me.

A breather for lung cancer suspects – Researchers in Israel have used cheminformatics methods to “train” an array of gold-nanoparticle sensors to rapidly distinguish between the out breath of lung cancer patients and that of healthy individuals.

Monopoles apart – Four research papers, two of which were published in the journal Science, this week, and two submitted to the physics preprint archive, suggest that a long-sought icon of fundamental physics has finally been discovered – the magnetic monopole. This fundamental research could have enormous potential in materials research, nanotechnology, and eventually instrumentation.

Fuelling nanotube potential – X-ray diffraction and X-ray photoelectron spectroscopy have been used to analyse semimetallic titanium dioxide nanotubes with potential in fuel cell technology.

Chemical-free Gardening

David Bradley It may come as a shock to anyone thinking of taking up gardening as a hobby or as a way to beat back the credit crunch by doing a little grow-your-own that gardening is based entirely on chemistry. There is no escaping this simple truth. Chemicals grow in the garden. There is no such thing as chemical-free gardening.

Now I’m not talking about the manufactured pesticides, herbicides, and fertilisers that your local garden centre stocks in abundance, whether those are labelled organic, all-natural, or otherwise, those are all chemicals, and some of them are essential for success. Incidentally, even all-natural pesticides are made from chemicals shock, horror. No, I’m talking fundamentals from the humus that brings life to soil to the best initiator you can add to your compost heap – urine. All chemicals.

There are four main chemical ingredients that make up everything in the garden (with the exception of any cast-iron furniture you may have): – carbon, nitrogen, oxygen, and hydrogen – as organic molecules from humic acids to the proteins that comprise earthworms to nitrates and water, and the potassium and phosphorus that plants simply cannot live without.

This autumn, I made the life-affirming decision to tidy up our garden, to weed and feed the lawn, to dig a vegetable patch and to plant some bulbs in the border to bring a little colour to the Spring. So, for the last few weeks, I’ve been hanging with my hoes and developing serious backache from getting down and dirty. I’ll let you know in March whether the colour came and whether I’ve got a crop of winter greens. Actually, I planted purple brocolli, onions, garlic, and am readying a patch for early potatoes, and a mini portable greenhouse is ready for tomato plants in the Spring.

Incidentally, the only thing you can put into your garden that will have a positive effect and isn’t chemical is effort. Well, that’s my story and I’m sticking to it.

Find out a little about the chemistry of compost next Friday (September 25).

File Sharing for Scientists

In the olden days, scientists used to send out paper reprints of their research papers to colleagues…maybe they still do. I get the occasional request for such an archaic entity for the items I have had published in Science, PNAS, and other journals.

These days, you’re more likely to simply ask for an eprint of a scientific paper, probably a PDF, possibly a doc file, or some other electronic format. But, even that’s really only a front to making contact with the author as it ever was. However, these days journal copyright clauses usually allow individual researchers to republish their individual papers on their personal website, which opens up a whole new way of accessing single research papers for free.

Dr Ijad Madisch CEO of ResearchGate calls this the “green route” to Open Access. ResearchGate has around 140,000 scientist members after just a year online and each member has their own personal web page within the scientific social network…you see where this is leading, I presume?

ResearchGate today launches its Self-archiving Repository, which could provide members with free access to potentially millions of research papers without the obstacle of library subscriptions or the financial barrier of pay-per-view. It’s almost like ResearchGate is set to do for journal article what Spotify, Last.fm, and Pandora have done for music – a quick search and you can access the content you want instantly without a fee.

“Our publication index, containing metadata for 35 million publications, will be automatically matched with the SHERPA RoMEO (http://www.sherpa.ac.uk/romeo) data set of journal and publisher’s selfarchiving agreements,” explains Madisch, “As a result, authors will know which versions of their articles they can legally upload. Since nine out of ten journals allow self-archiving, this project could give thousands of researchers immediate access to articles that are not yet freely available.”

ResearchGate says that by using this approach its SelfArchiving Repository does not infringe copyright because each profile page within ResearchGATE is legally considered the personal website of the user.

It’s a neat idea, and one that could open the floodgates to other similar systems. I suspect, however, that once it becomes more well-known, the journal publishers will start looking more closely at their author copyright agreements and adjust them accordingly to preclude uploading to sites that are considered external to the authors’ own company or institution.

“We don’t know how publishers will respond to this,” Madisch told me, “but we are definitely not looking for confrontation. Our primary goal when developing this tool was to serve the entire scientific community.”

Aside from the fact that the green route to Open Access is bound to be welcomed by authors, it’s not going to be music to the ears of the journal publishing industry.

Organic, Nano, Pharma

Challenging natural products succumb to radical synthetic prowess, the Alchemist hears this week, while US researchers find a way to construct macroscopic crystals from tiny DNA triangles.

The growing problem of obesity drug abuse in the UK is highlighted in the British Journal of Clinical Pharmacology and Bayer Cropscience is going underground with storage for safety reasons.

Also this week, Korean chemists have developed a scrubber for cleaning up the greenhouse.

Finally, this week’s award is represented by big NSF grants to Rutgers University for sustainable energy developed using nanotechnology and biotechnology.

Get the details and the links in the current issue of The Alchemist on ChemWeb.com

Fun Science Games

It’s Friday, our kids have been back at school a week now, so with the ever-present prospect of a wet weekend ahead of us, how to distract them from Youtube and Facebook with some educational that might help them next week in school…

…so, how about a quick trawl for fun science games. It seems there are millions of sites on the web offering games and virtual toys with a scientific underpinning. Science Review Games lets you play basketball, soccer and “deal or no deal” while reviewing science topics, for instance.

The site looks a bit kludgy and quite 90s, so I suspect my kids will not be persuaded with this one, although younger children might take a look. That said, they apparently have astronomy, biology, chemistry, earth science and geology, living environment, meteorology, nature of science, and physics.

CSUN’s site, which is a sourcebook for teaching science looks even more flat and 90s styled, but provides templates for “printing off” (remember that?) that let you play science taboo, science jeopardy, science bingo, science…you get the picture.

The Science Museum in London brings the web styling almost up to date with their online games. These include the apparently popular Launchball, which has you bouncing a ping-pong around obstacles, presumably with some underlying mechanics controlling the ball’s behaviour. Building Bonanza, Cracker, Energy Flows and Energy Ninjas, Hungry Mice, and ID-fit, and half a dozen more might also provide a little wet-afternoon distraction.

The BBC has always been around for science revision and offers games for youngsters, high schoolers, and those readying themselves for curriculum-based exams. Apparently, mathematics, science, and English skills are needed for almost all their games. ELEMENTAL has the coolest logo, but it’s basically a quiz…

Speaking of which, NT Science has a whole range of crossword puzzles to entertain the scientifically minded word fan.

Given Darwin’s prominence this year, it’s no surprise that there are games around that promise to let you follow in his footsteps. This award-winning game for little kids is from Rolls Royce.

Finally, we’re big fans of ubergeek show /Bang in our house. It’s the BBC’s re-entry into the edutainment science arena without the crassness of Brainiac and without being so overbearing as some myth-busting shows. This week, there’s been a /Bang initiated test to see whether you can train your brain, which might be fun to take part in and perhaps even scientifically useful…

Babies, Smokestacks, and Kudzu Vine

Tears and smiles bond secure mothers to baby – The sight of her baby’s smile or even its tears cause the reward centres in a mother’s brain to light up, according to an international functional magnetic resonance imaging (fMRI) study, but only if the mother herself had a secure attachment to her own parent.

Smokestack scrubber – Korean researchers have developed a new, highly porous material that can soak up carbon dioxide efficiently and highly selectively. The material, characterised by X-ray diffraction and other techniques might one day be used to “scrub” out the greenhouse gas from power stations and factories that burn fossil fuels for energy

One from the vine – Kudzu is a weedy vine that has overgrown almost 10 million acres in the southeastern United States. However, it could one day sprout into a dietary supplement to helpe reduce metabolic syndrome in millions of people. Mass spectrometry and UV spectroscopy have now been used to identify and quantify the putatively active isoflavones in extracts of the vine by US scientists.