Thursday, April 14, 2011

Antibiotic progress for disease that causes half a million deaths a year

Scientists are making progress in their quest to find an improved antibiotic for a strain of meningitis that results in over half a million deaths a year worldwide. The fungal disease Cryptococcal Meningitis is especially rife in AIDS patients and there are fears that if new drugs cannot be found, it could become untreatable. The results are published in one of the most respected journals in the field of membrane biology - Biochimica et Biophysica Acta – Biomembranes. Further experiments will be carried out at STFC’s ISIS neutron source this week.

Cryptococcal Meningitis is diagnosed in nearly a million people a year worldwide, mainly in patients but also in others with defects in their cell mediated-immunity. More than 600,000 of these cases lead to fatalities. Currently, there is no vaccine for Cryptococcal Meningitis. Unlike most other strains of the disease, it is not passed from person to person, but is actually acquired from the environment, possibly by exposure to birds. The disease is most prominent in Sub-Saharan Africa but is also known to be on the increase in areas such as Thailand and India.

With funding from the Engineering and Physical Sciences Research Council, scientists from King’s College London have been using neutrons to look at the effects of the antibiotic Amphotericin which is currently used to treat Cryptococcal Meningitis. They hope this will help them devise new and more effective treatments, in particular for the disease-causing fungi that have developed a resistance to the drug.

“Such an approach, of course, requires that we fully understand how Amphotericin works, and unfortunately this is not the case”, said David Barlow – the lead researcher from King’s College London.

“We do know that the drug has little effect on the cells in a human because these cells are surrounded by membranes containing cholesterol. We also know that the drug exerts its effects on fungi because their cells do not contain cholesterol, but instead have a related steroid, ergosterol. However it is quite unclear how this difference between human and fungal cell membranes matters to the workings of Amphotericin.”

Research published in the journal Biochimica et Biophysica Acta – Biomembranes shows that Amphotericin can insert itself into cell membranes regardless of whether they contain cholesterol, ergosterol, or no sterol at all, and the resulting changes in the structure of the membrane seem to be the same for all three systems. This means the reason for the drug having less impact on human cells than fungal cells cannot purely be down to the fact that human cells contain cholesterol – other factors must be at play.

What seems more likely is that the drug interacts more rapidly with fungal cells than human cells, or that the structures it forms after inserting in to their membranes are different for the two types of cell.

“We're now going on to investigate the first of these possibilities, and during our next experiments at ISIS, we plan to look for differences in the speed with which the drug enters human and fungal cell membranes”, said David Barlow. “The more information we can gather about how this complex system works, the more likely we are to be able to develop a new antibiotic that will be as effective as Amphotericin has been until recently”.

In addition to Cryptococcal , Amphotericin is also used to treat infections such as the tropical disease Visceral Leishmaniasis.

More information: Download the full scientific paper.

Provided by Science & Technology Facilities Council

New test for germs: Fluorescing DNAzymes detect metabolic products from bacteria

Germs in food, bioterrorism, drug-resistant bacteria and viruses—these are the problems of our time that make early detection of pathogens particularly important. Whereas conventional methods are either slow or require complex instruments, Yingfu Li and a team at McMaster University in Hamilton (Ontario, Canada), additionally supported by the Sentinel Bioactive Paper Network, have now developed an especially simple, universal fluorescence test system that specifically and rapidly detects germs by means of their metabolic products. As the researchers report in the journal Angewandte Chemie, It isn’t even necessary to know which substance the test is reacting to.

Traditionally have been detected through microbiological methods, which are very precise but can take days or weeks. PCR- or antibody-based methods are rapid but require many steps and special equipment. “We were motivated to develop an especially simple, but very rapid and precise method,” says Li. “It must also be universal, meaning that it should be possible to develop tests for any desired germ using the same principle.”

“When a pathogen is metabolically active and multiplying in a given medium, it releases many substances into this environment. These are what we want to use,” says Li. The idea is to produce DNAzymes that react to a pathogen-specific product. A DNAzyme is a synthetic one-stranded DNA molecule with catalytic activity. Making a large pool of DNA molecules with random sequences and subjecting these to repeated selection and amplification steps allows for the development of molecules with the desired property.

At the core of the conceptual DNAzyme is a single RNA nucleotide. To its right and left are a fluorescing dye and a quencher. A quencher is a molecule that switches off the fluorescence of a dye when it is nearby. The researchers developed a DNAzyme that binds to a specific metabolic product from E. coli bacteria, which causes the DNAzyme to change its shape. In this altered form, the DNAzyme has RNA-splitting capability and cuts its own strand at the location of the RNA nucleotide. This separates the quencher from the dye, which begins to fluoresce. The fluorescence indicates that E. coli is present in the sample. This DNAzyme does not react to other bacteria.

“Through targeted selection, it should be possible to find a specific DNAzyme for any desired germ,” says Li. “It is not necessary to know what the metabolic product is, or to isolate it from the sample.” By using a common cell culture step, it is possible for the pathogens in a sample to multiply before the test, which allows for detection of a single original cell.

More information: Yingfu Li, Fluorogenic DNAzyme Probes as Bacterial Indicators, Angewandte Chemie International Edition 2011, 50, No. 16, 3751–3754, … ie.201100477

Provided by Wiley (news : web)

Powerful optical centrifuge created to study dynamics of fast spinning molecules

High-energy molecules play a major role in the chemistry of combustion, plasmas and the atmosphere. Scientists have been able to generate and investigate molecules with large amounts of vibrational, electronic or translational energy, but methods for producing and studying molecules with large amounts of rotational energy have remained elusive. In the April 5 issue of the Proceedings of the National Academies of Science, University of Maryland Chemistry Professor Amy S. Mullin and her research team introduce a new instrument that can both impart extremely large amounts of rotational energy to molecules and study how they subsequently transfer their energy to other molecules.

"The difficulty in generating molecules with extreme amounts of rotational energy," explains Mullin, "is that the energy must be added bit by bit. It's like pushing children on a merry-go-round: you start off slowly, and then each push gets the merry-go-round spinning faster and faster. The trick is finding a method to do the same thing with molecules, and to be able to generate enough of these spinning molecules to study their behavior."

Mullin and her team employed an approach called an optical centrifuge to get the molecules spinning. This method, which was developed by Paul Corkum and co-workers at the National Research Council in Canada, uses a strong to align molecules and then rotationally accelerate molecules. Mullin's team developed a new optical centrifuge that is a hundred times more powerful than the original instrument. As a result of the added power, they are able to create large enough populations of molecules in extreme rotational states that it is possible for the first time to use spectroscopy to observe their fate.

"We used high-resolution spectroscopy to study how the rotational energy is redistributed into other forms of energy through collisions," continues Mullin. "These studies took advantage of time-resolved optical methods to identify the major energy-flow pathways that cause the rotational energy to dissipate into translation, vibration and rotation of other molecules."

The amount of rotational energy that the optical centrifuge imparts to molecules is on the order of the strength of a chemical bond. New types of chemical behavior are therefore likely to occur at such large rotational energies. "The allows us to apply large amounts of torque at the molecular level," says Mullin, "and we are now in a position to determine how such torques affect chemical bonds. Practically nothing is known about in this environment, and we are excited to be investigating this new frontier in chemistry."

More information: Dynamics of Molecules in Extreme Rotational States, http://www.pnas.or … ull.pdf+html

Provided by University of Maryland (news : web)

Polymer-reinforced aerogel found resilient for space missions

Polymer-reinforced aerogels could soon go on a space mission. Modifying the mechanical properties of aerogels with a polymer reinforcement creates a durable thermal insulator primed for aerospace, according to recently published research by Dr. Sadhan C. Jana, University of Akron Department of Polymer Engineering chair and professor, UA Ph.D. graduate Jason Randall and NASA Glenn Research Center collaborator Dr. Mary Ann Meador.

"Tailoring of Aerogels for Aerospace Application," featured as a spotlight article in the March 23, 2011, edition of the American Chemical Society's Applied Material & Interfaces describes how polymer-strengthened silica aerogels maintain their effectiveness as thermal insulators under supercritical conditions of outer space, including temperature and pressure extremes.

Polymer improves strength and flexibility

Low thermal conductivity and low density make silica aerogels ideal insulators, according to Jana, yet their fragility often counters their prospective effectiveness, particularly in aerospace applications. Comprised of approximately 95 percent air and 5 percent silica, the delicate aerogels typically break down under relatively low stresses. However, a polymer conformal coating on the nanoskeleton not only improves the strength of aerogels, but their elasticity and flexibility as well.

"Consequently, you now have a material capable of withstanding compression and bending stresses as well as temperature extremes, making it a candidate for use on space rovers, inflatable decelerators and EVA suits," says Jana, whose team research examined density, pore structure, modulus and elastic recovery of epoxy-reinforced aerogels.

Subsequent research could lead to streamlined methods for applying the polymer reinforcement to aerosol articles and expanding their use and configuration. As flexible thin sheets, for example, aerogel insulation material can be wrapped easily around pipes or tanks, using shape memory properties of the polymer reinforcement, or can be produced in net shapes obviating secondary processing or secondary handling, according to Jana.

Provided by University of Akron

New research advances understanding of lead selenide nanowires

The advancements of our electronic age rests on our ability to control how electric charge moves, from point A to point B, through circuitry. Doing so requires particular precision, for applications ranging from computers, image sensors and solar cells, and that task falls to semiconductors.

Now, a research team at the University of Pennsylvania's schools of Engineering and Applied Science and Arts and Sciences has shown how to control the characteristics of semiconductor nanowires made of a promising material: lead selenide.

Led by Cherie Kagan, professor in the departments of Electrical and Systems Engineering, Materials Science and Engineering and Chemistry and co-director of Pennergy, Penn's center focused on developing alternative energy technologies, the team's research was primarily conducted by David Kim, a graduate student in the Materials Science and Engineering program.

The team's work was published online in the journal ACS Nano and will be featured in the Journal's April podcast.

The key contribution of the team's work has to do with controlling the conductive properties of lead selenide nanowires in circuitry. Semiconductors come in two types, n and p, referring to the negative or positive charge they can carry. The ones that move electrons, which have a negative charge, are called "n-type." Their "p-type" counterparts don't move protons but rather the absenceof an electron -- a "hole" -- which is the equivalent of moving a positive charge.

Before they are integrated into circuitry, the semiconductor nanowire must be "wired up" into a device. Metal electrodes must be placed on both ends to allow electricity to flow in and out; however, the "wiring" may influence the observed electrical characteristics of the nanowires, whether the device appears to be n-type or p-type. Contamination, even from air, can also influence the device type. Through rigorous air-free synthesis, purification and analysis, they kept the nanowires clean, allowing them to discover the unique properties of these lead selenide nanomaterials.

Researchers designed experiments allowing them to separate the influence of the metal "wiring" on the motion of electrons and holes from that of the behavior intrinsic to the lead selenide nanowires. By controlling the exposure of the semiconductor nanowire device to oxygen or the chemical hydrazine, they were able to change the conductive properties between p-type and n-type. Altering the duration and concentration of the exposure, the nanowire device type could be flipped back and forth.

"If you expose the surfaces of these structures, which are unique to nanoscale materials, you can make them p-type, you can make them n-type, and you can make them somewhere in between, where it can conduct both electrons and holes," Kagan said. "This is what we call 'ambipolar.'"

Devices combining one n-type and one p-type semiconductor are used in many high-tech applications, ranging from the circuits of everyday electronics, to solar cells and thermoelectrics, which can convert heat into electricity.

"Thinking about how we can build these things and take advantage of the characteristics of nanoscale materials is really what this new understanding allows," Kagan said.

Figuring out the characteristics of nanoscale materials and their behavior in device structures are the first steps in looking forward to their applications.

These lead selenide nanowires are attractive because they may be synthesized by low-cost methods in large quantities.

"Compared to the big machinery you need to make other semiconductor devices, it's significantly cheaper," Kagan said. "It doesn't look much more complicated than the hoods people would recognize from when they had to take chemistry lab."

In addition to the low cost, the manufacturing process for lead selenide nanowires is relatively easy and consistent.

"You don't have to go to high temperatures to get mass quantities of these high-quality lead selenide nanowires," Kim said. "The techniques we use are high yield and high purity; we can use all of them."

And because the conductive qualities of the lead selenide nanowires can be changed while they are situated in a device, they have a wider range of functionality, unlike traditional silicon semiconductors, which must first be "doped" with other elements to make them "p" or "n."

The Penn team's work is a step toward integrating these nanomaterials in a range of electronic and optoelectronic devices, such as photo sensors.

The research was conducted by Kim and Kagan, along with Materials Science and Engineering undergraduate and graduate students Tarun R. Vemulkar and Soong Ju Oh; Weon-Kyu Koh, a graduate student in Chemistry; and Christopher B. Murray, a professor in Chemistry and in Materials Science and Engineering.

This work was supported with funding from the National Science Foundation Division of Materials Research, the National Science Foundation Solar Program and the National Science Foundation Nano-Bio Interface Center.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by University of Pennsylvania.

Journal Reference:

David K. Kim, Tarun R. Vemulkar, Soong Ju Oh, Weon-Kyu Koh, Christopher B. Murray, Cherie R. Kagan. Ambipolar and Unipolar PbSe Nanowire Field-Effect Transistors. ACS Nano, 2011; 110321110927018 DOI: 10.1021/nn200348p


How antifreeze proteins bind to surface of ice crystals: Finding may end 30-year debate

A chance observation by a Queen's researcher might have ended a decades-old debate about the precise way antifreeze proteins (AFP) bind to the surface of ice crystals.

"We got a beautiful view of water bound to the ice-binding site on the protein," says Peter Davies, a professor in the Department of Biochemistry and a world leader in antifreeze protein research. "In a sense we got a lucky break."

AFPs are a class of proteins that bind to the surface of ice crystals and prevent further growth and recrystallization of ice. Fish, insects, bacteria and plants that live in sub-zero environments all rely on AFPs to survive. AFPs are also important to many industries, including ice cream and frozen yogurt production which relies on AFPs to control ice-crystal growth.

The implications of this finding reach far beyond creating low-fat, high water-content ice cream that maintains a rich, creamy texture. Having a clear idea of how AFPs bind to the surface of ice crystals would allow researchers and industries to engineer strong, versatile AFPs with countless commercial applications ranging from increasing the freeze tolerance of crops to enhancing the preservation of transplant organs and tissues.

While determining the crystal structure of an AFP from an Antarctic bacterium, biochemistry doctoral candidate Christopher Garnham was fortunate enough to see an exposed ice-binding site -- a rare find in the field of AFP crystallography that Mr. Garnham studies.

The ice binding surface of an AFP contains both hydrophobic or 'water repelling' groups as well as hydrophilic or 'water loving' groups. Until now, the exact function of these counter-acting forces with respect to ice-binding was unknown.

While the presence of water repellent sites can appear counterintuitive on a protein that bonds with ice, Mr. Garnham and Dr. Davies are hypothesizing that the function of these water repellent sites is to force water molecules near the surface of the protein into an ice-like cage that mirrors the pattern of water molecules on the surface of the ice crystal. The water-loving sites on the protein's surface then anchor this ice-like cage to the protein via hydrogen bonds. Not until the ordered waters are anchored to the AFP is it able to bond to ice.

This research is published in the Proceedings of the National Academy of Sciences.

Story Source:

The above story is reprinted (with editorial adaptations ) from materials provided by Queen's University.

Journal Reference:

Christopher P. Garnham, Robert L. Campbell, Peter L. Davies. Anchored clathrate waters bind antifreeze proteins to ice. Proceedings of the National Academy of Sciences, 2011; DOI: 10.1073/pnas.1100429108

Fracking controversy: Using water, sand and chemicals to extract natural gas from shale

The turmoil in oil-producing nations is triggering turmoil at home, as rising oil prices force Americans to pay more at the pump. Meanwhile, there's a growing industry that's promising jobs and access to cheaper energy resources on American soil, but it's not without its controversy.

Deborah Kittner, a University of Cincinnati doctoral student in geography, presents, "What's the Fracking Problem? Extraction Industry's Neglect of the Locals in the Pennsylvania Marcellus Region," at the annual meeting of the Association of American Geographers. Kittner will be presenting April 14 at the meeting in Seattle. She is part of a large contingent of UC researchers to be presenting at the conference.

Hydraulic fracturing, or fracking, involves using millions of gallons of water, sand and a chemical cocktail to break up organic-rich shale to release natural gas resources. Kittner's research examined the industry in Pennsylvania, known as the "sweet spot" for this resource, because of the abundance of natural gas. Pittsburgh has now outlawed fracking in its city limits as has Buffalo, N.Y., amid concerns that chemical leaks could contaminate groundwater, wells and other water resources.

The EPA is now doing additional study on the relationship of hydraulic fracturing and drinking water and groundwater after congress stated its concern about the potential adverse impact that the process may have on water quality and public health. Kittner attended an EPA hearing and also interviewed people in the hydraulic fracturing industry. She says billions of dollars from domestic as well as international sources have been invested in the industry.

The chemical cocktail used in the process is actually relatively small. The mixture is about 95-percent water, nearly five percent sand, and the rest chemical, yet, Kittner says some of those chemicals are known toxins and carcinogens, hence, the "not in my backyard" backlash from communities that can be prospects for drilling. The flow-back water from drilling is naturally a very salty brine, prone to bacterial growth, and potentially contaminated with heavy metals, Kittner says. In addition, there's the question of how to properly dispose of millions of gallons of contaminated water, as well as concerns about trucking it on winding, rural back roads.

Based on her research, Kittner says that many in the industry are "working to be environmentally responsible, and become frustrated at companies that do otherwise."

"I think that the study that the EPA is doing is going to be really helpful, and the industry -- however reluctant to new regulations -- is working with the EPA on this," Kittner says.

Kittner has lived in Ft. Thomas, Ky., for two decades, but is originally from Warren, Pa. Her research took her to an EPA public meeting in Canonsburg, Pa., where she audio-taped 114 people presenting public statements of what they wanted the EPA study to examine. That study is expected to be completed in 2012 and will include an examination of what to do with millions of gallons of contaminated flow-back water.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by University of Cincinnati.