Month: May 2007

Windows cause pollution

Windows Cause
Pollution  This is not another terrible advertisement for an alternative computer operating system to the eponymous installation mentioned in the title, but an environmental analysis that reveals how dirty windows are a major contributor to urban pollution.

A Scent for
Explosives  A new type of biosensor based on yeast, jellyfish
proteins, and a rat’s sense of smell could sniff out explosives, landmines, and agents, such as sarin gas, according to researchers at Temple University.

The Long and the
Short of It  A new composite material that acts as a catalyst to
speed up chemical reactions has been developed to create arrays of the
world’s longest carbon nanotubes.

Meeting of Molecular Movie Stars  A clandestine meeting between molecules, a chemical handshake, and an exchange of energy have all been recorded on camera by scientists in the UK and Germany.

Read the full stories in Reactive Reports, the chemistry webzine from David Bradley Science Writer and ACD/Labs. Next month, we have a profile of Berkeley nuclear chemist and Sciencebase regular commentator Mitch Garcia.

Join the Mile High Club, Cure Jet Lag

Sildenafil, ViagraViagra could be the cure mile-high clubbers have been waiting for. Apparently, not only can the drug help men keep up appearances at any altitude, new research could lead to its extension to other areas of medicine, such as the treatment of jet lag.

Apparently, researchers in Brazil simulated jet lag in hamsters by exposing them to light out of phase with their natural body clock, giving the little beasts the feeling of having flown from Paris to New York on the red-eye day after day. The result was that the hamsters’ circadian cycle got so skewed that they would mount their wheels and run 14 hours before they should each night.

However, Diego Golombek and colleagues from the Quilmes National University in Buenos Aires, figured that a quick shot of Viagra (sildenafil citrate, sildenafil without its counter ion is shown) might work wonders for the hardy little creatures. In fact a 70 mg dose of the ED drug, reduced the jet lag recover period for the animals to just over a week, compared with the two weeks it took the Viagra-free hamsters to recover. What a relief.

Circadian clocks regulate the timing of biological functions in almost all higher organisms, say Cornell University and Dartmouth College researchers writing independently in the journal Science, this week. Anyone who has flown through several time zones knows the jet lag that can result when this timing is disrupted, they say.

Now, the Cornell and Dartmouth scientists believe they can explain the biological mechanism behind how circadian clocks sense light through a process that transfers energy from light to chemical reactions in cells. Whether or not this research tells us if you should keep your eyes closed during or after entry into the mile-high club or how to disguise why you are not suffering jet lag after a long trip is a different matter.

InChI=1/C22H30N6O4S/c1-5-7-17-19-20(27(4)25-17)22(29)24-21(23-19)16-14-15(8-9-18(16)32-6-2)33(30,31)28-12-10-26(3)11-13-28/h8-9,14H,5-7,10-13H2,1-4H3,(H,23,24,29)/f/h23H

Nanotechnology Used to Enter Plant Cells

US scientists are using nanotechnology to penetrate plant cell walls and deliver a gene and a chemical triggers with great precision. The work could lead to a powerful new tool for targeted delivery into plant cells.

The research is highlighted in the May issue of Nature Nanotechnology. Kan Wang of Iowa State University and his colleagues point out that introducing a gene into a plant cell is possible but chemical activation usuall involves an imprecise and separate process that may be toxic to the plant.

“With the mesoporous nanoparticles, we can deliver two biogenic species at the same time,” Wang said. “We can bring in a gene and induce it in a controlled manner at the same time and at the same location. That’s never been done before.”

The controlled release will improve the ability to study gene function in plants. And in the future, scientists could use the new technology to deliver imaging agents or chemicals inside cell walls. This would provide plant biologists with a window into intracellular events.

Lin’s porous, silica nanosphere system has arrays of independent porous channels, which form a honeycomb-like structure that can be filled with chemicals. “One gram of this kind of material can have a total surface area of a football field, making it possible to carry a large payload,” Trewyn said.

Organic Lectures Reach Drexel Island

Jean-Claude Bradley at Drexel University has taken his second life persona to his professional bosom and is now providing organic chemistry students not only with obelisks on the dragon-shaped island of Drexel (Drexopia, perhaps?), but they can now see organic chemistry lectures there too. It is an incredibly innovative use of SL, but I wonder whether students are going to feel like they are being monitored not only in the real world of university lecture rooms and study areas, but in the escapist virtual spaces of SL too. Scary thought.

Heavy metal plants in the spectral news

Over on SpectroscopNOW.com David Bradley reports on the usual eclectic mix of science news with a hint of the spectral. This week:

Heavy metal plants – Herbal medicine is a global phenomenon, a multibillion dollar industry, and its raw materials phytochemicals are widely used as the precursors for regulated pharmaceutical products. One problematic area on both sides is in product purity, with contamination by toxic heavy metals one of the most common complaints. Now, researchers in Argentina have developed a way to “digest” herbal medicines to improve the detection limits of heavy metal contaminants, such as lead and cadmium, for quality control of these products.

Tubeless and hyphenated – Slightly more esoteric, but equally important for analytical science is the development of a new software algorithm for getting the most out nuclear magnetic resonance (NMR) experiments. According the Gary Martin of Schering-Plough, the software developed with ACD/Labs collaboration, means that even if a sample of product has been lost, the spectroscopist can retrieve latent information from the initial NMR runs without having to find a new sample and spend a week record experimental spectra. Martin confesses that this new approach to sophisticated NMR is not without its critics. He gave an ENC invited lecture on the subject of this new technique, known as Unsymmetrical Indirect Covariance, and told me that his talk raised a few eyebrows, to say the least.

Super plat cats – A new form of platinum, 24-facet nanocrystals, have been produced by an international collaboration. The novel tetrahexahedral particles are four times as effective a catalyst as the industrially important commercial platinum available for oxidising formic acid and ethanol. The work could lead to a more efficient process of catalytic oxidation for the production of hydrogen for fuel cells. “If we are going to have a hydrogen economy, we will need better catalysts,” says Zhong Lin Wang of the Georgia Institute of Technology, “This new shape for platinum catalyst nanoparticles greatly improves their activity.” Discussion continues elsewhere on Sciencebase regarding the putative folly of a hydrogen economy. Hopefully, if such an approach to alternative energy does not come to pass, Wang will find numerous other industrial applications for these super plat cats.

Consolidated database – US researchers have exploited a new technique to identify almost all the chemical changes nature makes by adding phosphate groups to human proteins. They have now hooked up this data to the publicly accessible PhosphoMotif Finder system in an effort to stimulate further biomedical research into the vital process of phosphorylation.

Possums, horses, and pigs do it

Brushtail possums, photo by wollombi http://www.flickr.com/photos/wollombi/I just received an early publication alert from the Australian research organisation CSIRO announcing the imminent publication of volume 19 of their journal on reproductive science, fascinating I thought as I opened the attachment.

First up in the list of contents was a paper that sounded rather intriguing from FC Molinia and colleagues entitled: “Uterine and vaginal insemination optimised in brushtail possums (Trichosurus vulpecula) superovulated with pregnant mare serum gonadotrophin and porcine luteinising hormone”.

So, let us just dissect what that convoluted title actually means. Basically, they stimulated brushtail possums with hormones from a horse and a pig to make it produce more eggs than normal and then artificially inseminated the females, with brushtail possum sperm, obviously. I am pretty sure it is all standard procedure for getting those little brushtails up the duff, and it is not so odd that they used horse hormones in the process, after all, one form of human hormone replacement therapy uses equine estrogen.

Something worries me a lot about this particular EarlyAlert. The abstract says that artificial insemination of brushtail possums (Trichosurus vulpecula) is being developed as an assisted breeding model for endangered marsupials, as well as a bioassay for testing fertility control vaccines to manage overabundant populations.

Hmmm…humans do not have a strong record on “assisting” animals in this way, and particularly not in Australia, I am thinking rabbits and mixomatosis, feral camels, and the infamous cane toad, to name but three. Why is it that we feel we can intervene and manage ecosystems in this way? The end results are usually disastrous and given the purportedly fragile nature of Australia’s ecosystems, should we not leave well alone?

The full paper can be accessed here.

Smog masks at the ready

Smog mask by zoonabarThe gist of a recent press release regarding research into alternative fuels for reducing the environmental impact of transport and helping us head towards a sustainable transport system said that there is basically no single alternative fuel that could provide all the answers. The research in question, published in the International Journal of Alternative Propulsion drew up a league table of alternative fuels that placed petrol (gasoline) and diesel at the bottom in terms of their negative environmental impact, closely followed by hybrid liquid gas driven vehicles. Surprisingly, at the top of the league table was the use of hydrogen fuel cells running on hydrogen obtained from converted methane. Surprising because one would assume that the use of methane, or natural gas, would have such an environmental impact as to push it down the league table and moreover be unsustainable.

The study’s authors, Karl Høyer of Oslo University College, Norway and Erling Holden of the Western Norway Research Institute, do concede, as is mentioned in the press release, that there is no alternative fuel that is 100% sustainable and has a zero carbon footprint. That is perhaps inevitable. However, there is research being undertaken that would suggest that natural gas is not the limited fossil fuel we might think. Indeed, there are vast reserves that are apparently produced by bacterial activity that might feed the league-topping fuel cells mentioned in Høyer and Holden’s paper.

One commentator, John Zerbe of the USDA Forest Service, in Madison, Wisconsin, was not convinced that the Høyer and Holden league table was valid at all. This is what he had to say on the matter:

“I think the most significant conclusion from the Norwegian scientists’ work is that currently there is no consensus regarding sustainable transport development. They obviously considered the relative importance of energy use, carbon dioxide emissions, and nitrogen oxide pollution differently than I would have. There is no way that I would rank fuel cell powered vehicles using hydrogen gas obtained from natural gas methane at the head of the list.”

Granted, fuel cell powered vehicles should be efficient. Chevron has stations that dispense hydrogen made, mostly, from natural gas. So, energy use with the fuel cell vehicle powered by hydrogen should be good and there is probably no nitrogen oxide pollution.

However, until Chevron has some experience, it is hard to know what the hang-ups will be. Use of fossil natural gas will certainly be bad for global warming. It is already conceded that hydrogen isn’t amenable to long distance transportation. So Chevron makes hydrogen close to where it is being used. Imagine the difficulties in filling a fuel tank on a vehicle with 5000 psi hydrogen. It seems impossible that they could prevent all leaks, and hydrogen at 5000 psi is probably more prone to explosion than gasoline or diesel at atmospheric pressure.”

Zerbe suggests that the best well-to-wheel evaluation would have to take into account a complete lifecycle analysis. Energy use would certainly be important in such an analysis, but a lifecycle analysis could be weighted so that generally more acceptable limitations, such as the unsustainable nature of fossil fuel natural gas is considered a more negative factor.

Bioethanol Boom or Bust

Ethanol structureBioethanol, or strictly speaking cellulose-derived ethanol is fast becoming the front-runner in efforts to reduce our reliance on oil. There are problems associated with its production, not least issues of water supply and the environmental impact. The high production cost remains one of the biggest obstacles.

Now, researchers at Baylor University have identified forty different compounds formed in the pre-treatment step when making cellulosic ethanol that could be responsible for inhibiting the fermentation process, their elimination might reduce overall production costs and make this form of biofuel more economically viable.

“We screened for forty compounds, like phenols and organic acids, and they were all present,” said Kevin Chambliss, “We chose these particular compounds because they are believed to be inhibitory, but other compounds could be involved too.”

While conventional ethanol and cellulosic ethanol are essentially the same product, the two are made from different feedstocks. Conventional ethanol is produced from grains such as corn and wheat. Cellulosic ethanol is made from the non-food portion of many agricultural wastes. One of the more common wastes used is corn stover, which are the stalks and residue left over after harvest. Researchers said there has been a recent emphasis on learning more about cellulosic ethanol because agricultural wastes are mostly an untapped resource.

“If you can identify a pre-treatment condition that maximizes sugar production, yet minimizes inhibitor production, that could increase efficiency better than just removing the compound,” adds team member Peter van Walsum. The team will be testing softwood feedstocks, such as Dougas fir trees next.

InChI=1/C2H6O/c1-2-3/h3H,2H2,1H3

Matrix recharged

Matrix rechargedOne of the big problems facing society in its search for sustainable alternative energy sources is not how to harness wind, solar, or wave power, but how to store the electricity produced using these elements at times of low demand. Capacitors could be the answer. These devices can be charged up very quickly, store electrical energy for long periods, and then be discharged rapidly for a range of applications. Such capacitors are on the horizon but their small-scale cousins are developing even more rapidly for portable applications. Find out more in the May issue of Intute Spotlight.

Also under the Spotlight this month, Norwegian scientists have drawn up a league table of alternative fuels for cars based on what they call a “well-to-wheel” analysis. Their approach takes into account the energy costs in manufacturing, total energy use, and overall pollution included greenhouse gas emissions. Unsurprisingly, petrol and diesel vehicles foot the table, closely followed by hybrid vehicles. In contrast, the greenest way to power a vehicle turns out to be to use an electric fuel cell powered by hydrogen made from natural gas, methane.

Finally, in the 1950s, the atomic clock was the pinnacle of split-second time-keeping. Today, physicists use its successors based on energy transitions in rubidium atoms that gives them 100 times more accuracy. These clocks currently operate at their theoretical limit but nevertheless are accurate to one second every 50 million years. Quantum noise, the random fluctuations of atoms and ions and the grim truth of Heisenberg’s Uncertainty Principle would probably mean no improvements for the next 50 million years.

DBPedia for Chemists

Taxol Total Synthesis Color

Cambridge chemist Peter Murray-Rust recently alerted me to the DBpedia service. DBpedia.org is a community effort to extract structured information (semantics) from Wikipedia and to make this information available on the Web. DBpedia allows you to ask sophisticated questions of Wikipedia rather than carrying out simple searches. “DBPedia is a semantic distillate of Wikipedia and soon all the chemistry will be in semantic form,” asserts Murray-Rust, “It will then be possible to ask questions like: “find compounds which were discovered by a Russian chemist in the 19th Century”. That is a simplistic example, of course. He believes that such efforts form part of a new information philosophy of linked data and points out that Open chemical resources, such as Pubchem, DBPedia, CrystalEye, ChEBI, etc. will soon become part of that philosophy.