Alchemy bonus

AlchemistThe Alchemist this week discovers how a bodybuilders’ supplement might help treat Parkinson’s disease, the route taken by mercury from groundwater to coast, and how to boost your storage space with fullerenes. Also this week, physical condensation problems solved and how Raman spectroscopy is laying it on thin to help scientists understand carbon sheets. And, this week’s award goes to Perry McCarty for his pioneering work in understanding waste water chemistry and microbiology. Alchemical happenings on ChemWeb

If you missed the previous instalment, we discovered proof positive that Asian pollution could affect global weather, how to scratch fatty acids from the surface of stone buildings, and discovered hundreds of new drug targets for the battle against cancer. We also did a spot of spring cleaning with a new type of duster for mopping up even the tiniest toxic particles and found out how filling up in the UK became more expensive than ever thanks to an inadvertent silicon injection into fuel. Find out more in the older Alchemist

Cool cats make heavy metal fallout

Catalytic converterThe rapid adoption by the car industry of catalytic converters for petrol engines to reduce NOx and other pollutants has significantly improved the quality of air in busy towns and cities. However, Italian scientists says this improvement has comes at a significant price as they are finding rapidly rising levels of heavy metal fallout that could have serious implications for health.

Claudio Botr̬ of the University of Rome and Alessandro Alimonti of the Italian National Institute of Health in Rome and their colleagues explain that the increasing numbers of catalytic converters on the road has led to rising environmental levels of the metals used as the catalysts in these devices Рplatinum, rhodium, palladium, and iridium. The team has published their detailed findings in the International Journal of Environment and Health.

More on this in a media release on AlphaGalileo

Hey good looking, what you got cooking, in those genes?

Attractive peopleHere’s a puzzle. If evolution ensures that ‘good’ genes spread through a population, then why are individuals so different? Why don’t people get better and better looking through each generation to the detriment of ugliness and lead to a population of real lookers?

The problem with current evolutionary theory is that it would seem that if females select the most attractive mates, then the genes responsible for their attractive features would spread quickly, leading to all males becoming equally attractive (think peacock tails). Ultimately, further sexual selection would then no longer take place and evolution would stop in its tracks.

This is the so-called lek paradox and it has remained a foil in the weaponry of the intelligent design advocate’s arsenal for many years. Until now.

Thanks to research at Newcastle University, England, this apparent fundamental flaw in Darwin’s theory of evolution, latched on to by creationists can be explained quite effectively by evolution itself. The findings of Newcastle’s Marion Petrie and Gilbert Roberts research suggests that sexual selection leads to increased genetic diversity by a mechanism not previously understood.

Petrie reasoned that as genetic mutations occur naturally anywhere in the genome, some will actually affect those used to produce the DNA repair kit enzymes found in all cells. This would lead to those individuals with a malfunctioning or inefficient repair kit, having more mutations left unrepaired and so greater variation in their genome.

Usually, damaged DNA leads to an unviable organism that either dies quickly of the effects or is otherwise unable to reproduce. However, if those variations are present in sections of the genome responsible for disease defence, then variation can actually be beneficial as greater variation in the genome at these points means more chance of warding of bacteria and viruses.

Petrie modelled the spread of genes in a population and demonstrated that the tendency towards reduction in genetic diversity caused by sexual selection is outweighed by the maintenance in greater genetic diversity generated by mutations affecting genome repair.

The researchers began this research a decade ago and their model genes are now a great fit for the observations of variations. “We find that sexual selection can promote genetic diversity despite expectations to the contrary,” Petrie says. The team publishes details of their findings today in the journal Heredity.

With this Ring

Bishnu Khanal and Eugene Zubarev of Rice University in Houston, Texas have found that nanoscopic gold roads coated with polymer can spontaneously self-assemble into rings within seconds of water droplets condensing on to the surface of a solution of the rods in dichloromethane solvent.

Nanoscale objects organized into superstructures are interesting because the properties of such tiny particles depend not only on their composition, shape, and size, but also to a large extent on their spatial distribution and the degree of their ordering within a superstructure.

Images obtained with an electron microscope show that the nanorods in the rings are oriented randomly when their concentration in the original solution is high. However, at lower concentrations the result is truly amazing: The nanorods are oriented in a head-to-tail sequence along the edge of the ring.

The team reports details of their results in Angewandte

Beating Heart Disease with Vitamin B Drugs

Niacin vitamin BNiacin is involved in the metabolism or carbohydrates, fats and proteins, but at high dosage it can increase HDL more than a third and reduce levels of “artery-clogging” triglycerides by half.

Graeme Semple of Arena Pharmaceuticals, San Diego, reports how new drugs that raise high-density lipoproteins, so-called good cholesterol might be developed by following the lead of familiar B vitamin, niacin.

Researchers at Arena and elsewhere are trying to develop new drugs that are even more effective than niacin and so could have greater potential to protect at-risk people against heart attacks and stroke. Semple discusses the latest developments at the ACS annual meeting today.

You can read more about the biochemistry of niacin and LDL cholesterol in Sciencebase.

InChI=1/C6H5NO2/c8-6(9)5-2-1-3-7-4-5/h1-4H,(H,8,9)/f/h8H

Free software shows how drugs work

Partition coefficientIf you are already a user of free chemistry drawing package ACD/ChemSketch but need a little more physical information from your tools than simple structure drawing, then ACD/Labs’ latest freebie might be right up your street. They just released ACD/LogP, which can be used to extract a lipophilicity prediction from your structures with a few mouse clicks.

For those not in the know, logP, is the octanol-water partition coefficient and is a useful value assessing how a putative drug might partition between cell membranes and cellular fluids. It gives you an indication of potential oral availability in other words. This allows drug designers to find out early on whether they will need to do additional work to make a compound available by mouth.

logP isn’t only about drugs though, agrochemists can use it to help them predict how their experimental compounds might partition between different species. This allows them to see whether a compound might target particular pests in preference to beneficial insects, for example.

This property is also useful to flavour and fragrance scientists who can judge in silico how a new compound might behave when added to food or dabbed on the skin as perfume.

ACD’s physical chemisty products manager Greg Pearl explains that making logP available to the community for free will not only support research but will help students and educators get to grips with this important property. ‘Freeware is especially valuable to educators and students with limited resources,” he says. “For example, during a lecture, an educator can interactively demonstrate how subtle changes to a molecule changes it physical properties – much more compelling than discussing a table of numerical results. It also gives students a chance to use the types of tools they will encounter in the workplace.’

“Through this release of ACD/LogP freeware to scientists worldwide we continue our tradition of advancing chemical research by making critical physicochemical properties available to scientists in an open-access environment,” Pearl adds. “Users will benefit from over a decade of algorithm refinement resulting in accurate and reliable predictions.”

Just for the record, ACD/Labs hosts the Reactive Reports chemistry webzine. There’s more information about logP on their site here

Power Your iPod With a Cola

SucroseGot an iPod? Sick of having to charge it up at the electric outlet? Then try maple syrup or cola!

Researchers at Saint Louis University in Missouri have developed a fuel cell that uses sugar from almost any source from soft drinks (although not lite or diet versions though, so Coke Zero is out) to tree sap or even honey. They reckon their fuel cell could run three times longer than a conventional rechargeable lithium battery on a single charge. Better still, the fuel cell is itself biodegradable so at end of life it does not become a toxic burden on the environment like lithium or nickel-cadmium batteries.

“This study shows that renewable fuels can be directly employed in batteries at room temperature to lead to more energy-efficient battery technology than metal-based approaches,” explains team leader Shelley Minteer, an electrochemist at SLU. “It demonstrates that by bridging biology and chemistry, we can build a better battery that’s also cleaner for the environment.” Minteer reports her findings this week at the 233rd national meeting of the ACS in Chicago.

For more on how fuel cells might be improved, check out this recent item in Reactive Reports

InChI=1/C12H22O11/c13-1-4-6(16)8(18)9(19)11(21-4)23-12(3-15)10(20)7(17)5(2-14)22-12/h4-11,13-20H,1-3H2

Magnetizing a Baby

It is possible to magnetize a baby with a few drops of water, some ordinary sugar and a teether. It’s all down to changes that take place in the brain when the baby tastes the sugar.

Neal Barnard MD, founder of the Physicians Committee for Responsible Medicine (PCRM), explains the process. Of course it’s not really magnetization, it’s the release of opiates in the brain, natural versions of morphine and heroin, that make us feel good. Barnard discusses the science underlying food addictions. Personal willpower is not necessarily to blame, chocolate, cheese, meat, and sugar all release these opioids. substances. Dr. Barnard also discusses how industry, aided by government, exploits these natural cravings, pushing us to eat more and more unhealthy foods. He suggests that a purely plant-based (vegan) diet is the solution to avoid many of these problems.

He points out how cheese and other dairy products contain natural compounds closely related to morphine, perhaps as a natural bonding chemical to ensure suckling mammals “enjoy” the suckling process. The presence of tiny quantities of these compounds in so many foods could explain why dairy products, chocolate, wheat, meat, nuts, onions, corn, tomatoes, onions, bananas, citrus fruits etc are common dietary triggers of migraine, for instance, users are simply overdosing on the opiates and then suffering withdrawal symptoms. And, as to cardiovascular disease, stroke, and heart attack…cardiologists know that if a man in his fifties presents with impotence, there is a one in four chance that he will have a heart attack or stroke within two years. Barnard blames our addiction to meat and even got cattle ranchers in the mid-west to prick up their ears when he relayed that fact and had them asking for his tofu recipes and tips on cooking brown rice.

Anyway, it’s a long video (40 minutes) but makes very interesting viewing.

<br /> Watch on Google Video

Blueberry Molecule Fights Colon Cancer

Pterostilbene, an antioxidant found in blueberries, has shown promise as a putative protective agent against colon cancer in animals, according researchers from Rutgers University and the US Department of Agriculture. Colon cancer is the second leading cause of cancer death in the United States and so a supplement or drug developed from this compound could potentially save many lives.

Rutgers’ Bandaru Reddy and colleagues reported their findings today at the 233rd national meeting of the American Chemical Society during National Colorectal Cancer Awareness Month.

“This study underscores the need to include more berries in the diet, especially blueberries,” says Reddy, “Although the blueberry compound won’t cure colon cancer, it represents a potential new and attractive strategy for preventing the disease naturally.”

Pterostilbene is also found in grapes a finding that was reported in Spinneret sibling webzine Reactive Reports in an item entitled Grape Expectations

InChI=1/C16H16O3/c1-18-15-9-13(10-16(11-15)19-2)4-3-12-5-7-14(17)8-6-12/h3-11,17H,1-2H3/b4-3+

No flies on this chemical web

ChemSpider logoThe latest, and potentially the greatest, in freely accessible chemistry database went live at midnight EST to coincide with the start of this year’s ACS Annual Meeting in Chicago. ChemSpider was built to aggregate and index chemical structures across the web together with their associated meta data and provide a single searchable repository available to everybody, for free. Structure identifiers such as SMILES, InChI, IUPAC and Index Names as well as numerous physicochemical properties are embedded with each database entry, of which there are 10 million at the moment. According to the site FAQ, “We intend ChemSpider to offer the fastest chemical structure searches available online and delivered with the flexibility and usability necessary to encourage repeat usage.” Chemists among the Sciencebase readership will no doubt already be clamouring to try out the beta release and to compare it with the likes of PubChem and ChEBI.

There are dozens and dozens of chemical structure databases across the web, but no simple way to search all of them. Some are curated from the research literature others are vendor catalogues, and yet others are molecular properties, environmental data, toxicity data, analytical data repositories. ChemSpider will aggregate all of these (even the commercial ones) into a single database, so providing pointers to virtually all the available information. Many of the end pages users will reach will be open access and free while others will require a paid login ultimately. Regardless, at least you will know whether or not information exists on those structures and you can then choose to subscribe or not to the external information.

Okay, so if this post is starting to sound a bit too much like an advertisement for ChemSpider, I have to confess something of a vested interest. As part of the launch, Sciencebase has collaborated with the good folks at ChemSpider to bring you the site’s very own webzine (all puns intended!) – Spinneret. And, in case you’re wondering what exactly a spinneret is, you can find out on the site’s About page. Don’t forget to subscribe to the Spinneret RSS to keep ahead of the game and find out how Spinneret is weaving the chemical web one molecule at a time (another of those puns, sorry).