Chemistry – Page 35 – David Bradley

Reactive chemistry

Macrocycle The latest issue of Reactive Reports (#63) is now online featuring a selection of the hottest science news and our interview with the new Managing Director of the Royal Society of Chemistry, Dr Robert Parker.

Also in this issue:

Cocoa Has Beans One of the natural compounds found in cocoa, teas, wine, and some fruit and vegetables could lead to a breakthrough in health and nutrition, according to US researchers.

Chemists Go Round the Bend Chemists often think of molecular wires as “shape-persistent” rods with limited flexibility, so says Oxford University’s Harry Anderson, and he should know, having worked with the inflexible nanoscopic objects known as molecules since the early 1990s.

Natural Copy Cat Green plants can extract carbon dioxide gas from the air and turn it into sugar molecules using sunlight and give off oxygen. Now, a catalyst could help us do the same.

Waste Not, Want Not A fungus that can convert waste paper into an antibacterial and super-absorbent material has been discovered by researchers at BorÃ¥s University College in Sweden.

Chemical pipe works

Chemical pipe works Mitch Garcia of UC Berkeley seems to be far more expert with the latest web 2.0 tool that lets you produce your own search algorithms than I, so I asked him to look into creating a Yahoo Pipe to allow anyone to search as many chemistry journals as possible that offer ASAP and in press papers online. And, much kudos to him, he has done just that. Here’s chemistry journals search pipe. He explains the process and the limitations in a little more detail on his own blog.

Give it a try and let us know what you think. What makes this tool totally tubular is that once you’ve run a search using a pipe, the results are their own RSS feed, which means you can subscribe to the results with your news reader (My Yahoo, Bloglines, Google Reader etc). Even more intriguing is the idea that you could presumably then use that feed as the basis for creating an even more sophisticated Pipe of your own.

For instance, this feed displays the results from Mitch’s Pipe searching all those chemistry journals for the word greenhouse. It’s quite unlikely that there will be any gardening papers in the ACS, RSC or Wiley chemistry journals, so you can be fairly sure that this feed will bring you the latest papers on greenhouse gases and their effects. Combine that with a feed for global warming, and one for climate change, and you should have the niche covered.

Intelligent materials protect sports lovers

An intelligent plastic that is so flexible when left to its own devices while flow like a very slow moving liquid, but hit it with a hammer and the intelligent molecules form which it is made stiffen up instantaneously and absorb the energy of the blow. Such a polymer has been incorporated into textiles and clothing to create lightweight and flexible body armour for high-impact sports and other activities to save users from serious impact injuries. The polymer and textile-embedded material was the brainchild of UK company d3o, which has recently worked with a sports clothing manufacturer to develop a range of protective gear.

There was a video that demonstrated how to protect a falling egg using this material. This would make an excellent science fair project: compare different packaging materials for protecting eggs – cardboard, polycarbonate, d30 intelligent material. Unfortunately, the vid is no longer available.

The smart material is made up of a matrix of polymers with tiny pockets filled with a fluid. In normal wear, the material moves freely with your body movements but if you take a dive, the intelligent molecules in the fluid stiffen in less than a thousandth of a second, which makes them absorb the energy of the impact It works because under normal conditions, the polymer molecules move and slide across each other, but when they are put under rapid shear stress in an impact, for instance, the polymer molecules immediately form cross-links with one another and the material stiffens to take the brunt of the impact. Once the force is removed, the polymer cross-links are disengaged by further low force movements and the material reverts to its flexible state.

Power up your genome with chemistry

Post-genomic science Researchers have developed several tools to help them exploit the underlying chemistry of genomics, while novel chemistry has enabled faster, parallel sequencing methods that not only accelerate genomic research but also cut costs. The very same techniques allow sex chromosomes and complete genomes to be decoded faster and more cheaply than ever before.

Concomitantly, microfluidics technology is improving the way conventional fluorescence chemistry can be exploited in sequencing. Improved understanding of nanoscale channels – both synthetic and protein channels offers the possibility of studying individual biological macromolecules and microfabricated microarrays are opening up massively parallel opportunities. Novel chemical technologies are also opening up locked nucleic acids as well as non-DNA molecules such as microRNAs.

The so-called post-genomic era put the molecular smack in the middle of the biological quarter. Now, as cross-disciplinary communication matures, research at the intersection of chemistry and biology is working harder than ever to solve fundamental questions in science and medicine.

You can read the complete feature on the subject of chemistry in the post-genomic era from David Bradley in Science magazine today. It is the lead article on the Science Products page.

Anorexia and Kidney Disease

Anorexia nervosa is a serious and potentially fatal eating disorder usually characterized by a severely reduced appetite and often a total aversion to food. In the mainstream media, it is most commonly associated with teenage girls and the celebrity quest for a “size zero” figure. However, it is a serious and life-threatening disorder that goes far beyond the realm of body image and extreme dieting. Important clues as to the underlying causes of this disorder may be found in its association with chronic kidney disease.

According to Peter Stenvinkel of the Division of Renal Medicine, Karolinska University Hospital at Huddinge, Sweden, anorexia is observed frequently in kidney dialysis patients. The condition worsens as kidney disease progresses leading to severe muscle wasting and malnutrition, with all its associated health problems. Scientists had suggested a link to defective central nervous system control of appetite, so Stenvinkel and his colleagues have done an analysis of various biomolecules, including natural inflammatory compounds and sex hormones. Their results suggest that inflammation is closely linked to the development of anorexia in kidney patients and is more common in men than women.

Read the full story in today’s SpectroscopyNOW.

Frogs legs and AMPs

Solid state NMR is unlocking the secrets of compounds found in natural membranes from frogs’ legs to human lungs that could lead to an entirely new class of antibiotic drugs. The compounds in question are antimicrobial peptides (AMPs) and they have been detected in every living creature studied so far. AMPs act as a first line chemical defence system in a huge range of organisms and could provide a novel approach to defeating drugs resistance in bacteria.

“Our overall mission is to use the kind of basic physical data we obtain from NMR to help interpret biological functions,” team leader Ayyalusamy Ramamoorthy of the University of Michigan explains. As with most discoveries of this nature, it will be several years before any clinical trials for specific health problems or diseases are complete. “How it works against viruses are under investigation in other labs,” Ramamoorthy told me.

You can find out more about AMPs as the front line defenders in the latest issue of SpectroscopyNOW.

Let’s Get Physical, Right Now

The latest issue of the monthly Spotlight column over on the physical sciences section of Intute is now online, this time featuring research from the earth sciences, the greening of chemistry in the developing world, and humans acquitted over Neanderthal extinction.

Cassava by David Monniaux Chemists go veggie

Chemists working on tight budgets in developing countries may be able to swap flasks of laboratory reagents for extracts of celery and potatoes, or cassava and carrots and other inexpensive, …

Neanderthals more than severely put out by bad weather

Climate change saw off the last of the Neanderthals from their final stronghold on the Iberian peninsula thousands of years ago, according to …

Slumbering Yellowstone snores

Beneath the beautiful Yellowstone National Park in Wyoming lies a slumbering giant, a supervolcano who wakes every few hundred thousand years and wreaks havoc across hundreds of …

Viruses Do Not Eat Spaghetti

The faint glow from a single molecule combined with a stretch from “magnetic tweezers” could help scientists get a grip on how viruses that infect bacteria, so-called bacteriophages pack up their DNA. The research could lead to a resurgence of interest in the West for a potent treatment for infection that uses bacteriophages instead of antibiotics to attack disease-causing bacteria. The treatment side-steps the problem of bacteria evolving resistance to antibiotics because the agent of bacterial death can evolve just as quickly to cope with any defences put up by the bacteria.

In the face of deadly emergent bacteria such as Escherichia coli O157, multiple-resistance Staphylococcus aureus (MRSA) and Clostridium difficile, there is renewed interest in this alternative to antibiotics. The same study might also lead to new insights into how to combat viruses that infect people too, including herpes and adenoma viruses.

Many viruses use a self-assembly stage in which a powerful molecular motor packs their genetic code into the viruses’ preformed protein shell, its capsid. Now, Carlos Bustamente and colleagues at the University of California, Berkeley, have demonstrated that the genetic code is not coiled up like so much spaghetti on a fork but is packed using a concertina type approach. You can find out more about the details of this work in the current news round-up on SpectroscopyNOW.com

Chemical Wedding Gifts

Fullerene Most people are well aware of the traditional materials offered to married couples to celebrate their wedding anniversary. You know the kinds of thing I mean – ruby for instance is the gem of choice for a 40th anniversary, although why a chunk of chromium infested aluminium oxide should have been chosen for this year in particular I don’t know. The noble elements silver and gold are 25th and 50th respectively, while the hardest allotrope of carbon, represents the 60th celebration (diamond, that is). If you want the complete list check out our traditional wedding anniversary gifts page, but if you want something a little different, a reference for Kevlar, zeolites, buckyballs, or PVC say, take a look at our chymical wedding round-up.

Acid test research project

This probably is not a project you could do for your school science project, unless you are really, really keen. Chemists at Queen’s University Belfast have developed a molecular system that acts like an ion-selective electrode across a pH range of 9. Prasanna de Silva and his colleagues, who featured in a special issue of Intute Spotlight recently, explain that their device has the advantage of operating on the nanoscale and so could be incorporated into microelectromechanical systems, or so-called lab-on-a-chip devices. The team used a set of four sensor molecules in relay to act as the quantitative version of universal indicator paper. One sensor does the hard work of sensitively responding to pH across approximately 2 pH units and then hands on the baton to the next, which in turn works hard over the next 2 pH units and so on covering 9.5 units on the pH scale. de Silva says that the molecular devices show an almost linear intensity-pH profile that is reminiscent of the response of a conventional glass pH electrode but a thousand times smaller than even micrometer-scale intracellular pH electrodes.

“Our research shows a simple and predictive way of greatly extending the sensing range of molecular sensors,” de Silva told Sciencebase, “We do it by using a set of four sensors to act somewhat like a 4×100 m relay team. One sensor does the hard work of sensitively responding to pH across approximately 2 pH units and then hands over the task to the next one, which in turn works hard over the next 2 pH units (approximately) and then hands over the task to the next one etc. In this way we get a range of 9.5 pH units whereas the normal range of a molecular sensors is only 2 (as you learn in high school science).”

Scientists have thought about this problem before (resulting in the famous universal indicator), there was no quantitative version of a molecular universal indicator until now. The nearly linear intensity-pH profile is reminiscent of the glass pH electrode’s response, even though the electrode is obviously a lot bigger in size (the smallest ones are micrometer-sized and used for intracellular pH measurements), de Silva told me.

You can get the full experimental details in their JACS paper on this: Analog Parallel Processing of Molecular Sensory Information