David Bradley – Page 296

Spinneret Secret Unraveled

Spider silk is “pound for pound” stronger than steel and has a greater elasticity than rubber. Such properties would make it a rather useful material for a large variety of medical and engineering applications if only it could be made in large enough quantities and with a useful thickness and consistency.

Thomas Scheibel at the Technical University of Munich has now taken a step towards understanding the spider’s secret with a view to creating an artificial spinneret for producing unlimited quantities of spider silk. Writing in in Angewandte, the team explain how they have discovered that the interaction between the hydrophilic and lipophilic properties of the silk proteins plays an important role in the spinning process.

Fundamentally, the spinning of spider silk represents a phase change from a solution into a solid thread. The silk used by orb weaver spiders to spin the edges and spokes of their webs and to make a quick escape when attacked is composed of two different proteins. The Munich team has now successfully used genetic engineering to produce one of the spider silk proteins of the European garden spider (Araneus daidematus).

While purifying the protein by dialysis, the researchers observed the separation of two different fluid phases. Whereas one phase consisted of protein dimers, the second consisted of oligomers. After adding potassium phosphate, a natural initiator of silk aggregation, the liquid could be pulled into threads. “It is clearly not a structural change in the protein, but rather the degree of oligomerization that is crucial for thread formation,” concludes Scheibel.

Five times faster than BitTorrent

Anyone who has dared to download, a large file using the Bit Torrent system in which chunks of the file are pulled from other BT users in a form of distributed file sharing will know how slow (and sometimes how fast) the method can be. Although much of the BT system is exploited to share pirated movies and music it has a serious, legitimate side that also allows scientists, engineers and programmers to share the burden of huge database and ISO image downloads. Now, thousands of US tax dollars (in the form of an NSF CAREER grant) have been spent on improving on the Bit Torrent system.

David Andersen and colleagues at Carnegie Mellon University spotted the fatal flaw in torrents that often leads to the file sharing system grinding to a halt if the number of users with the complete or almost complete file are offline.

In conventional BT downloads, the files being shared must match exactly across the distributed sharing network or else they are ignored for download purposes. Anderson realized that identifying relevant chunks of files that may not be identical but are similar to a desired file could speed up Bit Torrent downloads. Anderson and his colleagues have designed Similarity-Enhanced Transfer (SET) to exploit this concept.

Anderson claims SET could make some transfers five times faster. “This is a technique that I would like people to steal,” Andersen said. Though he and his colleagues hope to implement SET in a service for sharing software or academic papers, they have no intention of applying it themselves to movie- or music-sharing services. “But it would make P2P transfers faster and more efficient,” he added, “and developers should just take the idea and use it in their own systems.”

SET works in a similar way to BitTorrent. Once a download is started, the source file is broken down into unique chunks. These chunks are downloaded simultaneously from accessible sources on the sharing network and then reassembled on the user’s computer. While this is underway, the SET program continues to search for similar files using a process called handprinting. In this method, sampling of non-identical files is used to find chunks that match the required chunks. Relevant chunks can then be downloaded from the similar files identified by this method, making the overall process much faster.

Although the researchers hope to use the SET approach for legitimate academic file sharing, they tested it on more common music and movie downloads. They saw a more than 70% improvement in downloading an mp3 file. A larger 55 Mb movie trailer was 30% faster when it could pull chunks from movie trailers that were 47 percent similar.

The researchers hope that such efficiency improvements will make SET part of the next generation of high-speed online multimedia delivery. “We believe that handprinting strikes an attractive balance for multi-source transfers. It efficiently locates the sources of exploitable similarity that have the most chunks to contribute to a receiver, and it does so using only a small, constant number of lookups. For these reasons, we believe that this technique is an attractive one to use in any multi-source file transfer system,” say the researchers.

R&R leads to molecular recovery

Mark Kuzyk is at it again. The physicist continues to explore a range of novel, light-sensitive compounds and has found one that degrades over time…but if kept in the dark for a short period of time, spontaneously heals itself. This amazing property could be exploited in industrial processes such as optical data storage and photolithography, which could use the recyclable material instead of having to replace the expensive stuff for every turn over.

Kuzyk and colleagues at Washington State University have found a molecule that loses its ability to fluoresce when bathed with laser light but regains this talent if it gets plenty of rest in the dark. Recovery starts during a half hour power nap and is complete after a good eight hours R&R, say the resarchers.

“It’s almost as if you have a piece of paper that’s yellowed over time, and you put it in a dark room for a day, and it comes back brand-new,” enthuses Kuzyk. Previously, I discussed Kuzyk’s work on Sciencebase and Intute Spotlight.

Kuzyk and students Ye Zhu and Juefei Zhou discovered the “self-healing” property of the dye AF455, which excels at two-photon absorption, an important property in optical data storage and in producing microelectronics for photolithography. The team will report details in the April 15 issue of the journal Optics Letters.

I received a follow-up email to this from Kuzyk: I’ve reproduced the Mark Kuzyk email here.

It’s a dog’s life

Puppy dog Cutting out the French fries, burgers, chips, candy, beer, soda, and other delicious yet largely non-nutritious food and drink from your diet is generally a good idea. One of the reasons, health experts suspect, is that somehow a reduced-calorie diet leads to a longer life. Now, researchers at Imperial College London have looked at a dog’s life and discovered why dietary restriction could lead to a longer life.

Jeremy Nicholson and colleagues followed 12 “pairs” of dogs in which one partner in each pair was given 25% less food than the other. Nicholson and his colleagues found that the dogs who had less food lived almost 2 years longer (that perhaps equates to between 10 and 14 years). They also found that those dogs suffered less diabetes and osteoarthritis, and were older on average when plagued by the common diseases of old age.

But, why?

The scientists believe that differences in the populations of microbes in the dogs’ guts could partly explain the metabolic differences. The dogs that were not on a restricted diet had increased levels of potentially unhealthy aliphatic amines in their urine, the team found. The presence of higher levels of these compounds indicate reduced levels of choline, the compound essential for metabolizing fat. Such a microbial profile has, in other studies, been associated with the development of insulin resistance and obesity in humans.

Nicholson explains: “This fascinating study was primarily focused on trying to find optimized nutritional regimes to keep pet animals such as dogs healthy and as long-lived as possible. However these types of life-long studies can help us understand human diseases and aging as well, and that is the added bonus of being able to do long-term non-invasive metabolic monitoring.”

So, might this study be applicable to humans and should we too be cutting down on our doggy treats and Pedigree Chum? Potentially, yes. Despite superficial appearances and the sometimes disgusting things dogs choose to eat, the flora and fauna of our guts are very similar. It all depends on whether cutting your burger and soda intake by 25% is worth it for those extra 10 to 14 dog years.

Details of the study are published today in the Journal of Proteome Research. The paper is one in a special issue of the journal in “Metabolomics, Metabonomics, and Metabolic Profiling in Complex Organisms: The Portals to “Real-Life” Systems Biology”.

Choline chemical structure
InChI=1/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1

In totally, unrelated canine news, scientists from the University of Utah and seven other institutions have identified a piece of doggy DNA that reduces the activity of a growth gene, ensuring that small breeds stay small. More on that via Newswise.

Getting up close and graphic with graphene

Graphene recently hit the headlines as a potential replacement for silicon in a future world of molecular computing. However, until silicon technology has run its course and arrays of millions of transistors can be carved at will from this material, scientists will have to be content with investigating its properties and devising novel uses.

Nevertheless an international team led by scientists at MIT has turned the Raman spotlight on graphene and its chemical cousins to help them explain the materials’ unique physicochemical properties.

Mildred Dresselhaus of Massachusetts Institute of Technology, USA, and colleagues there and at the Federal University of Minas Gerais, Brazil, Tohoku University and CREST, Sendai, Japan, point out that Raman spectroscopy has played an important historical role in understanding graphitic materials. Most usefully, Raman can reveal information about defects and stacking of graphene sheets. The team has now used Raman to look at the modern counterparts of these materials, nanographites and individual graphene molecules.

You can read the whole story in this week’s SpectroscopyNOW news round-up from David Bradley.

A Tasty Approach to Flavanoids

The flavanone structure is a tough act to swallow, synthetically speaking. Its the common skeleton for flavonoids and other compounds in plant-derived food and drink, such as red wine, dark chocolate, green tea, soy, milk thistle, kosam root, and citrus fruits, and are thought to have positive effects on health via anti-tumor and anti-inflammatory behavior. There are literally hundreds scattered throughout nature, but until now chemists had no straightforward method of synthesizing them with enantiomeric purity.

Karl Scheidt of Northwestern University and his colleagues have developed a general route to ten different chiral flavanones and chromanones that relies on simple bifunctional thiourea catalysts. The team reports how decarboxylation of the beta-ketoester proceeds smoothly in a one-pot reaction with 80-94% enantiomeric excess for aryl and alkyl substrates.

The method sets the stage for a new range of potential anticancer drugs ripe for testing. Further details can be found in JACS.

InChI=1/C15H12O2/c16-13-10-15(11-6-2-1-3-7-11)17-14-9-5-4-8-12(13)14/h1-9,15H,10H2

Workout limits

Do you workout hard? Is “no pain, no gain” your exercise ethos? Do you feel like you are not getting the fitness results you expect? Your brain could be to blame.

Yagesh Bhambhani and Rohit Malik of the Faculty of Rehabilitation Medicine, at the University of Alberta, Edmonton, Canada and Swapan Mookerjee of Bloomsburg University, Bloomsburg, Pennsylvania, USA, have monitored the oxygen levels of blood flowing in the brains of healthy volunteers while they worked out using near infrared spectroscopy.

NIRS can evaluate changes in blood volume and oxygen levels in the brain while people exercise by measuring the absorption of this form of electromagnetic radiation by the blood, which varies depending on how much oxygen is present.

The team has found that even if you are healthy, there could be an upper limit on just how hard you can push yourself, because brain activity begins to be affected detrimentally as you push harder and harder.

The study watched blood flow and volume as well as measuring carbon dioxide breathed out during an incremental exercise test. In the tests, exercise intensity is gradually stepped up until the volunteers reach exhaustion and must stop. The observed fall off in carbon dioxide levels coincided with decreased blood flow to the brain, which affects exercise capacity, the researchers say.

You can find out more about the science behind the exercise threshold here. Of course, if you are not pushing your exercise regime to the limits, then you probably have nothing to worry about. More to the point, the research is aimed at fine tuning finely tuned athletes and others, not providing the sedantary or mediocre with an excuse to give up half way through their treadmill cycle. (Ahem, mentioning no names…)

Magnetic control

MRI robot Think of MRI and most people think of medical scanning, the kind of analytical tool that can slice through your brain or other organs, virtually speaking, and produce a three-dimensiona view of your innards. But researchers in Canada are putting the magnetic in magnetic resonance imaging to a different. They hope to use it to control tiny robot devices that can be guided through blood vessels in an application reminiscent of 1960s sci-fi movie Fantastic Voyage.

The demonstration by Sylvain Martel of the NanoRobotics Laboratory at Montreal Polytechnic School could herald the emergence of a new form of surgery that uses MRI to control “untethered” devices within the body. The team has spent the last several years developing microelectrochemical systems (MEMS) that could be used in diagnostics and treatment and have now successfully guided, an inactive prototype device for the first time through an artery (see picture) using computer-controlled MRI. More details here.

A New Look at Neopentane’s Chirality

The absolute configuration of a subtly chiral molecule has been determined using Raman optical activity and quantum mechanics. Werner Hug and his colleagues at the University of Fribourg, Switzerland, obtained the configuration of (R)-[2H1, 2H2, 2H3]-neopentane a molecule in which the central carbon is surrounded by four methyl groups bearing differing numbers of hydrogen isotopes.

For those who don’t know, a molecule is chiral (or handed) by definition if the left and right hand forms cannot be superimposed on to each other (a pair of hands, or gloves, for that matter are archetypally chiral (which comes from the Greek for hand).

The left and right-handed forms, or enantiomers, of (R)-[2H1, 2H2, 2H3]-neopentane are so similar that chemists had consigned this oddity to the lab shelf having given up any hope of distinguishing between its enantiomers. But not Hug. He and his colleagues were determined to push the limits of Raman spectroscopy to take this molecule back off the shelf and provide us with new insights into the nature of chirality.

Chirality itself lies at the heart of life on earth, but understanding the origin of the homochirality seen in nature remains a serious challenge, the new insights from Hug et al provides an important clue as to how isotopes may have played a role.

Hug et al publish details of their work in Nature.

InChI=1/C5H12/c1-5(2,3)4/h1-4H3/i1D,2D,3D

How to produce static electricity with water

Yesterday, we ran a video showing you a water powered battery that can generate a 15kV spark using nothing more than some simple hardware and a professor who looks a bit like Einstein. Some readers may have worried that it was a spoof given the date (April 1) but this is a genuine piece of science based on the principles of static electricity.

Water is a polar molecule – there is a small difference in electric charge from one end to the other – but pure (deionized) water is also a very good insulator. As the droplets of water fall through the bottomless metal cans, their polarity induces a charge in the cans (which are by the way heavily insulated from earth (or ground). A positive charge builds up on the cans as the water molecules falling into the buckets become negative. This results in a charge separation or a potential difference between the paint cans and the buckets of water (which are also heavily insulated from earth).

Eventually the potential difference reaches a threshold at which point the insulating properties of the air between the two balls breaks down and a spark leaps across the gap. This spark, which has a temperature of several thousand degrees Celsius carries a voltage of between 10 and 15 thousand Volts, far more than you need to power even the biggest set of plugin speakers for your mp3 player.

Several questions remain. Where does the energy come from to create this enormous potential difference and could this form of electricity be tapped by building some kind of power station at the top of a waterfall and using two enormous cans and buckets? Well to answer the first question just look at the vertical arrangement of the equipment. The energy comes from gravity, from the potential energy of the water, which is above the paint cans. The second question is a little more complicated to answer. It would be possible to build a bigger generator, although insulating the components from earth would be tougher and the dissolved salts in river water would make it far less efficient than a generator using deionized water, but those are probably not the main issues.

Think about it, to make electricity generation useful we need a current to flow. How might you “tap” off a current from this type of generator when its product is effectively small-scale lightning? A capacitor in the spark zone, you say? But then isn’t the air acting as a capacitor, still doesn’t solve the problem of tapping off a current. Find an efficient and safe way to tap the power of lightning and you could make a fortune and solve the world’s energy needs. But, please don’t try those kinds of experiment at home!

Instead of generating static electricity, however, it is possible to use gravity’s power to move water to produce a current, much more readily…think water wheel, dynamo-type generator…think hydroelectric dam.

By the way, this experimental setup was originally devised by Lord Kelvin in the nineteenth century and is known as Kelvin’s Thunderstorm, it featured in Bill Beaty’s amateur scientist column in 1995, you can find a more detailed explanation there.