Permafrost bacteria may slow down ageing: scientists

The species of bacteria -- given the name Bacillius F -- was found in laboratory tests to have shown signs of slowing down the process of ageing on mice, the Russian Academy of Sciences (RAN) said.

The Siberian branch of the RAN said Bacillius F lags 3 million years behind similar bacteria in evolutionary terms, according to the characteristics of proteins and some other factors.

"Taking into consideration the unusual living environment, one can only marvel at the resilience of these bacteria," it said.

It added that the organisms found in Russia's northern region of Yakutia -- home to the coldest inhabited area on the planet -- reproduce at just 5 degrees Celsius.

"We just thought: since the bacteria were found in the permafrost where they were successfully preserved they will possibly have mechanisms of retaining viability," added Nadezhda Mironova, senior research scientist at the Institute of Chemical Biology and Fundamental Medicine of the Russian Academy of Sciences.

"This is what happened," she was quoted as saying.

Injections of the bacteria into mice have helped boost the natural defences of the animals as they grew older.

"Bacillius F injections have favourably affected the quality of being of the aging animals," the Russian scientists said.

"First and foremost, this concerns immunity and the speed of its activation."

Experiments have shown that metabolism in the tested mice have increased by 20 to 30 percent, the scientists said, adding that the bacterium may also reduce instances of senile blindness but not the emergence of tumours.

The Russian Academy of Sciences did not say how many mice were tested, adding more animals were needed for the experiments to be more reliable. The mice from a test group lived longer than those in a control group however, it said, calling the results "impressive."

(c) 2012 AFP

Japanese company develops silver ink that requires no heat to harden

Everyone knows that silver is a pretty soft metal, but it’s also amazingly conductive, and that’s why it’s used so much in electronics. The problem is, using heat to harden the silver reduces the number of materials on which it can be applied because it would cause them to melt. Thus, a new process that uses ultraviolet light at room temperature to harden the silver would allow silver ink to be printed and hardened onto virtually any surface, which might mean, the electronics industry is finally on the path to creating flexible and other exotic-material based electronic devices.

Product sample. Image: Tanaka Kikinzoku Kogyo K.K.

To print silver onto a surface, it first must be made into an ink of sorts, which typically involves making a resin (liquid material that hardens under certain conditions) that will not only stick to the surface to which it’s being applied but allow for the ink to exist in a liquid state so that it can be squirted or squeezed out of a nozzle. And that apparently is the key to new ink, it’s in the materials used in making the resin, though of course the company isn’t divulging just what they’ve done to make that ink, as they prefer to reap some profits from their work. But the bottom line is, once the silver ink is laid or sprayed onto a surface, they shoot it with an ultraviolet light and it hardens in just 0.3 seconds. And because a manufacturing process that uses ultraviolet light would be much cheaper and simpler than one that relies on heat, prices for such circuit boards should go down resulting in lowered prices for consumer products that use them.

More information: Press release

? 2011 PhysOrg.com

The great gas hydrate escape

The analysis is the first time researchers have accurately quantified the molecular-scale interactions between the gases -- either hydrogen or methane, aka natural gas -- and the water molecules that form cages around them. A team of researchers from the Department of Energy's Pacific Northwest National Laboratory published the results in Chemical Physics Letters online December 22, 2011.

The results could also provide insight into the process of replacing methane with carbon dioxide in the naturally abundant "water-based reservoirs," according to the lead author, PNNL chemist Sotiris Xantheas.

"Current thinking is that you need large amounts of energy to push the methane out, which destroys the scaffold in the process," said Xantheas. "But the computer modeling shows that there is an alternative low energy pathway. All you need to do is break a single hydrogen bond between water molecules forming the cage -- the methane comes out, and then the hydrate reseals itself."

Cagey Ice

Gas hydrates -- especially methane hydrates, which store natural gas -- look like ice but actually hold burnable fuel. Naturally found deep in the ocean, water and gas interweave in the hydrates, but little is known about their chemical structure and processes occurring at the molecular level. They have been known to cause problems for the petroleum industry because they tend to clog pipes and can explode. A methane hydrate produced the bubble of methane gas that contributed to 2010's Gulf of Mexico oil spill.

This video is not supported by your browser at this time.

This is a computer simulation of methane, also known as natural gas, escaping from a methane hydrate. Many of these methane hydrate subunits combine to form a chunk of ice that burns, and this simulation shows how methane can get out without collapsing the entire structure. Red-and-silver water molecules form a cage around two blue-and-silver methane molecules. Two methane molecules are too tight a fit, so a low-energy hydrogen bond -- the red dotted lines -- between two water molecules breaks. This allows the water molecule to swing open like a gate as the methane makes a dash for it. The water molecule swings back into place, the hydrogen bond re-forms, and the methane hydrate remains stable. Credit: Sotiris Xantheas, PNNL

In previous work, Xantheas and colleagues used computer algorithms and models to examine the water-based, ice-like scaffold that holds the gas. Water molecules form individual cages made with 20 or 24 molecules. Multiple cages join together in large lattices. But those scaffolds were empty in the earlier analysis.

To find out how fuels can be accommodated inside the water cages, Xantheas and PNNL colleague Soohaeng Yoo Willow built computer models of the cages with either hydrogen gas -- in which two hydrogen atoms are bound together -- or methane gas, a small molecule made with one carbon and four hydrogen atoms.

In the hydrogen hydrates, which could potentially be used as materials for hydrogen fuel storage, a small hollow cage made from 20 water molecules could hold up to a maximum of five hydrogen molecules and a larger cage made from 24 water molecules could hold up to seven.

The maximum storage capacity equates to about 10 weight-percent, or the percentage of hydrogen by mass in the chunks of ice, although packing hydrogen in that tight puts undue strain on the system. The Department of Energy's goal for hydrogen storage -- to make the fuel practical -- is above 5.5 weight-percent.

Experimentally, hydrogen storage researchers typically measure much less storage capacities. The computer model showed them why: The hydrogen molecules tended to leak out of the cages, reducing the amount of hydrogen that could be stored.

The researchers found that adding a methane molecule to the larger cages in the pure hydrogen hydrate, however, prevented the hydrogen gas from leaking out. The computer model showed the researchers that they could store the hydrogen at high pressure and practical temperatures, and release it by reducing the pressure, which melts it.

Water Gates

Understanding how the gas interacts and moves through the cages can help chemists or engineers store gas and remove it at will. Willow and Xantheas' computer simulations showed that hydrogen molecules could migrate through the cages by passing between the figurative bars of the water cages. However, the cages also had gates: Sometimes a low-energy bond between two water molecules broke, causing a water molecule to swing open and let the hydrogen molecule drift out. The "gate" closed right after the molecule passed through to reform the lattice.

With methane hydrates, some fuel producers want to remove the gas safely to use it. Others see the emptied cages as potential storage sites for carbon dioxide, which could theoretically keep it out of the atmosphere and ocean, where it warms the earth and acidifies the sea. So, Willow and Xantheas tested how methane could migrate through the cages.

The water cages were only big enough to comfortably hold one methane molecule, so the chemists stuffed two methanes inside and watched what happened. Quickly, one of the water molecules forming the cage swung open like a gate, allowing one methane molecule to escape. The gate then slammed shut as the remaining methane scooted into the middle of the cage.

"This process is important because it can happen with natural gas. It shows how methane can move in the natural world," said Xantheas. "We hope this analysis will help with the technical issues that need to be addressed with gas hydrate research and development."

Xantheas said performing computer simulations with carbon dioxide instead of methane might help determine whether it's chemically feasible to store carbon dioxide in hydrates.

More information: Soohaeng Yoo Willow and Sotiris S. Xantheas, 2011/12. Enhancement of Hydrogen Storage capacity in Hydrate Lattices, Chem. Phys. Lett. Dec. 22, 2011, doi: 10.1016/j.cplett.2011.12.036

Provided by Pacific Northwest National Laboratory (news : web)

Designing chemical catalysts: There's an app for that

Five scientists from the SUNCAT Center for Interface Science and Catalysis, at SLAC National Accelerator Laboratory and Stanford's Department of Chemical Engineering, have a solution for those who design new chemical catalysts: They made an app.

Their creation, called CatApp, displays reaction and activation energies for reactions occurring on catalytic metal surfaces. These factors are important in predicting how fast and completely a catalyzed reaction will proceed.

Catalysts are substances that promote chemical reactions without being altered or consumed themselves. They are essential for making many products, such as gasoline and other liquid fuels.

Making catalysts is a big business at the heart of a huge business. SRI Consulting reported in September 2010 that companies worldwide spend about $13 billion per year on catalysts used to produce some $500 to $600 billion worth of chemicals and refined petrochemicals.

Companies are always looking for new catalysts that are more selective and efficient, require less energy and produce fewer waste products. The quest at the heart of SUNCAT – finding ways to use solar energy to make new fuels and chemicals from biomass and other non-fossil sources – also requires novel catalysts.

“CatApp is accessible to any phone, tablet or computer with Internet access,” said theoretical-physicist-turned-programmer Jens S. Hummelshoj, who spearheaded its development. “Moreover, the entire app and database is a compact 150-kilobyte download, so users can also run the app offline.”

CatApp’s database contains calculated reaction energies for 1,054 catalytic reaction combinations involving reactant molecules having up to three carbon, nitrogen or oxygen atoms on 53 single-crystal surface types of 18 metallic elements. Users first choose a metal surface and reactant.

Then with just one screen tap, CatApp displays a simple diagram showing the corresponding activation energy and reaction-energy difference. The user can also easily explore how favorably the reaction would occur on other metal surfaces. The database includes references to source publications.

The development team – Hummelshoj, Frank Abild-Pedersen, Felix Studt, Thomas Bligaard and SUNCAT Director Jens K. Norskov – described CatApp in a technical paper published in the Jan. 2 edition of the Germany-based chemistry journal Angewantde Chemie.

“We expect this to be of interest both to academics and to industrial researchers and catalyst developers,” said Bligaard, who leads the Materials Informatics efforts at SUNCAT. “Imagine being able to make a simple, first test of new ideas before going into the laboratory to make new catalysts and characterize them.“

“In the near future, we will open the CatApp database so all researchers can submit their own data upon publication,” said Hummelshoj, who designed CatApp with future expansion in mind. “We will also add many more catalytic surface types and structures, including oxide, carbide, nitride, sulfide, alloy and nanoparticle surfaces; calculation uncertainties, and higher-temperature reactions. I could add a million reactions.”

Further enhancements include adding experimental surface reaction data, creating a desktop version with more functionality and linking to the National Institute of Science and Technology’s Chemistry WebBook, which contains a wide variety of chemical properties data.

CatApp is the first published element of the Quantum Materials Informatics Project, a joint initiative between SUNCAT, Argonne National Laboratory, University of Chicago and the Technical University of Denmark to establish a common framework for storing and sharing electronic structure calculations.

QMIP is aligned with the country’s future Materials Genome Initiative, which aims to create computational tools for researchers to use in rapidly discovering and developing new materials. One early such effort – The Materials Project collaboration between MIT and Lawrence Berkeley National Laboratory – is concentrating primarily on bulk materials.

“It will be highly desirable to couple these and other databases together, leading to a universal web-based materials data warehouse,” said Bligaard. 

Provided by SLAC National Accelerator Laboratory (news : web)

Powerful fungal infection drug amphotericin kills yeast by simply binding ergosterol

Led by chemistry professor and Howard Hughes Medical Institute early career scientist Martin Burke, the researchers demonstrated that the top drug for treating systemic fungal infections works by simply binding to a lipid molecule essential to yeast's physiology, a finding that could change the direction of drug development endeavors and could lead to better treatment not only for microbial infections but also for diseases caused by ion channel deficiencies.

"Dr. Burke's elegant approach to synthesizing amphotericin B, which has been used extensively as an antifungal for more than 50 years, has now allowed him to expose its elusive mode of action," said Miles Fabian, who oversees medicinal chemistry research grants at the National Institute of General Medical Sciences. The institute is part of the National Institutes of Health, which supported the work. "This work opens up avenues for improving upon current antifungals and developing novel approaches for the discovery of new agents."

Systemic fungal infections are a problem worldwide and affect patients whose immune systems have been compromised, such as the elderly, patients treated with chemotherapy or dialysis, and those with HIV or other immune disorders. A drug called amphotericin (pronounced AM-foe-TARE-uh-sin) has been medicine's best defense against fungal infections since its discovery in the 1950s. It effectively kills a broad spectrum of pathogenic fungi and yeast, and has eluded the resistance that has dogged other antibiotics despite its long history of use.

The downside? Amphotericin is highly toxic.

"When I was in my medical rotations, we called it 'ampho-terrible,' because it's an awful medicine for patients," said Burke, who has an M.D. in addition to a Ph.D. "But its capacity to form ion channels is fascinating. So my group asked, could we make it a better drug by making a derivative that's less toxic but still powerful? And what could it teach us about avoiding resistance in clinical medicine and possibly even replacing missing ion channels with small molecules? All of this depends upon understanding how it works, but up until now, it's been very enigmatic."

While amphotericin's efficacy is clear, the reasons for its remarkable infection-fighting ability remained uncertain. Doctors and researchers do know that amphotericin creates ion channels that permeate the cell membrane. Physicians have long assumed that this was the mechanism that killed the infection, and possibly the patient's cells as well. This widely accepted dogma appears in many scientific publications and textbooks.

However, several studies have shown that channel formation alone may not be the killing stroke. In fact, as Burke's group discovered, the mechanism is much simpler.

Amphotericin binds to a lipid molecule called ergosterol, prevalent in fungus and yeast cells, as the first step in forming the complexes that make ion channels. But Burke's group found that, to kill a cell, the drug doesn't need to create ion channels at all – it simply needs to bind up the cell's ergosterol.

Burke's group produced a derivative of amphotericin using a molecule synthesis method Burke pioneered called iterative cross-coupling (ICC), a way of building designer molecules using simple chemical "building blocks" called MIDA boronates joined together by one simple reaction. They created a derivative that could bind ergosterol but could not form ion channels, and tested it against the original amphotericin.

If the widely accepted model was true, and ion channel formation was the drug's primary antifungal action, then the derivative would not be able to wipe out a yeast colony. But the ergosterol-binding, non-channel-forming derivative was almost equally potent to natural amphotericin against both of the yeast cell lines the researchers tested, once of which is highly pathogenic in humans. The researchers detailed their findings in the journal Proceedings of the National Academy of Sciences.

"The results are all consistent with the same conclusion: In contrast to half a century of prior study and the textbook-classic model, amphotericin kills yeast by simply binding ergosterol," Burke said.

"The beauty is, because we now know this is the key mechanism, we can focus squarely on that goal. Now we can start to think about drug discovery programs targeting lipid binding."

The researchers currently are working to synthesize a derivative that will bind to ergosterol in yeast cells, but will not bind to cholesterol in human cells, to see if that could kill an infection without harming the patient. They also hope to explore other derivatives that would target lipids in fungi, bacteria and other microbes that are not present in human cells. Attacking these lipids could be a therapeutic strategy that may defy resistance.

In addition to exploiting amphotericin's lipid-binding properties for antimicrobial drugs, Burke and his group hope to harness its channel-creating ability to develop treatments for conditions caused by ion-channel deficiencies; for example, cystic fibrosis. These new findings suggest that the ion-channel mechanism could be decoupled from the cell-killing mechanism, thus enabling development of derivatives that could serve as "molecular prosthetics," replacing missing proteins in cell membranes with small-molecule surrogates.

"Now we have a road map to take ampho-terrible and turn it into ampho-terrific," Burke said.

More information: "Amphotericin Primarily Kills Yeast by Simply Binding Ergosterol," PNAS (2012).

Provided by University of Illinois at Urbana-Champaign (news : web)