Friday, April 15, 2011

Finding may end a 30-year scientific 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 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 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 of an AFP from an Antarctic , 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 via hydrogen bonds. Not until the ordered waters are anchored to the AFP is it able to bond to ice.

More information: This research will be published today in the Proceedings of the National Academy of Sciences.

Provided by Queen's University (news : web)

New technique tracks viral infections, aids development of antiviral drugs

 Scientists at the Naval Research Laboratory Center for Bio-Molecular Science and Engineering have developed a method to detect the presence of viruses in cells and to study their growth. Targeting a virus that has ribonucleic acid (RNA) as its genetic makeup, the new technique referred to as locked nucleic acid (LNA) flow cytometry-fluorescence in situ hybridization (flow-FISH), involves the binding of an LNA probe to viral RNA.

While individual parts of the technique have been developed previously, Drs. Kelly Robertson and Eddie Chang, in collaboration with researchers at the NRL Lab for Biosensors and Biomaterials, demonstrate for the first time that the combination of LNA probes with flow-FISH can be used to quantify in infected cells. This also allows the scientists to monitor the changes in viral RNA accompanying treatment.

Once the probe is bound to the viral RNA inside , it is tagged with a , then thousands of these tagged cells are measured rapidly by "flow cytometry" — a method for counting and examining microscopic particles, such as cells and chromosomes, by suspending them in a stream of fluid and passing them by an electronic detection apparatus.

"The ability to rapidly measure thousands of cells for the presence of virus, sets this technique apart from currently used methods to monitor viral replication," said Robertson.

Traditionally, antibodies used to detect viruses must be produced and calibrated for each specific strain and are highly susceptible to viral mutations. Assays commonly used for quantifying viral loads and for drug development can be time consuming and rely on visible signs of cell damage, which is not produced in all viruses and can take long periods of time to occur.

Techniques such as quantitative reverse transcription-polymerase chain reaction (qRT-PCR), microarrays, and enzyme-linked immunosorbent assays (ELISAs), while highly sensitive, involve the lysis [the breaking down] of cells prior to measurement and are therefore unable to provide information about cellular viability, infected cell phenotypes, percentage of infected cells or the variation in infection among a cell population. The LNA probe differs from traditional nucleotide probes by binding more tightly to its target RNA.

LNA-flow FISH presents a fast and easy way to screen for compounds with antiviral activity and could be adapted for monitoring infections in the blood for vaccine therapy and development. This method adds a necessary tool for several emerging areas in cell biology that enables the use of high throughput measurements for entire populations and improves statistical analyses.

"This method can be expanded by adding more than one kind of LNA probe to enable multiple detection of different viral and host RNA," adds Robertson. "The multiplexing enhancement can be used to better understand infectious agents, allowing this technique to be used to aid in the development of antiviral drugs for a variety of viruses."

LNA flow-FISH offers an advantage over other techniques due to its simplicity and superiority. Methods involving genetic recombination of the virus to express a fluorescent protein as a means to mark the presence of virus can utilize flow cytometry for large-batch analysis of infected cells. However, an exception to this approach is viral strains that have not acquired genetic mutations, known as wild-type viruses (such as strains of Human Immunodeficiency Virus-HIV), which would require a large initial investment of labor for engineering each of interest.

Provided by Naval Research Laboratory (news : web)

Future fuels for everyone powered by the sun

New scheme would use only sunlight, air and water to supply energy for cars, laptops, GPS systems.

"At the California Institute of Technology, they're developing a way to turn sunlight and water into fuel for our cars."--President , Jan. 25, 2011

The Sun is Earth's primary energy source and harnessing its abundant light is the Holy Grail of renewable energy

Now, a group of scientists has demonstrated a new way to use sunlight, water (H2O) and (CO2)--some of the cheapest and most commonplace stuff on Earth--to make unlimited amounts of fuel to power almost anything, anywhere.

The method uses concentrated heat from the sun to convert water and carbon dioxide into hydrogen (H2) or carbon monoxide (CO). Large amounts of these two gases could be combined to make that fits into America's existing energy economy.

"Alternatively, you could use the H2 and CO to make methane (natural gas) for a gas-fired electricity generator," said Sossina Haile, professor of and of Chemical Engineering at California Institute of Technology in Pasadena. "Or, because the fuels we produce are so pure, they could be easily used to run fuel cells, which generate power very efficiently."

The researchers say one of the most exciting things about the discovery is its versatility. "We are not dictating to the user what the should be," Haile said. "We are making solar energy easy to use by putting it into a form that our industry is used to seeing and making it available on demand."

Doing the two-step

Scientists have long known how to convert water and carbon dioxide into hydrogen and carbon monoxide. But to do it cheaply and efficiently enough to make the process affordable on a wide scale has been the issue. Part of the problem was the need for expensive and rare elements, such as platinum or , to act as catalysts that encourage the conversion to happen.

So Haile and her team took a novel approach; they tried ceria, a material used in the walls of self-cleaning ovens. Ceria is the oxidized or "rust" form of the element cerium, which is more abundant, and therefore cheaper, than other metals that could do the same job.

The new method requires two steps, the first at high temperature using concentrated heat from the sun (about 3,000 degrees Fahrenheit), and the second at a much lower temperature.

Haile describes the process this way, "If we heat ceria up, the material 'naturally' releases some oxygen from its structure. If we then cool it back down, those oxygen vacancies want to be refilled. In other words, the ceria 'exhales' oxygen at high temperature and then 'inhales' it back when the temperature is lowered."

To make fuel, the second step requires the presence of water and carbon dioxide gases. "At lower temperatures, the cerium, the hydrogen and the carbon all want the oxygen, but the cerium wants it most," Haile said. "So the oxygen vacancies in the ceria are filled by stripping oxygen from H2O and CO2, leaving H2 and CO."

An international collaboration

Haile and her Caltech team, supported by an award from the National Science Foundation, recently published a paper describing the breakthrough in the journal Science. For this project, they collaborated with researchers led by Aldo Steinfeld, a renewable energy technology professor at the Swiss Federal Institute of Technology, also called ETH Zürich, in Switzerland. Steinfeld also leads the Solar Technology Laboratory at the Paul Scherrer Institute in Switzerland.


Two pieces of equipment were needed for the experiment. The first piece, built at Caltech, is a reactor "just a bit smaller than a gallon-jug," Haile said. The reactor is basically a cylindrical container lined with ceria that has input and output lines for the gases.

The second piece is a solar concentrator, which is the most difficult part to build. The concentrator is basically a set of giant curved mirrors that gather sunlight from a wide area. For this experiment, the researchers were able to use an existing solar concentrator located at the Paul Scherrer Institute.

The Caltech scientists took their reactor to Switzerland and attached it to the bottom of the concentrator, allowing the sunlight to heat up the ceria inside. Then they piped steam and carbon dioxide into the reactor and measured the hydrogen and gases flowing out.

Cheaper and more efficient

How far reaching could this new technology be and how much oil, gas or coal could it replace?

"The abundance of cerium means that this approach could have a significant impact on our national energy budget," Haile said. Because cerium is 100,000 times more abundant than the precious metal platinum, she said, the cost would be many orders of magnitude smaller.

For this experiment, the efficiency of the reactor at converting sunlight to usable energy measured just under one percent, which Haile said is comparable to other methods. However, this was a first cut, aimed at simply proving that the process is practical and could be done economically.

Before bringing the technology to market, Haile said, the reactor design needs to be much tighter to get better efficiency.

"As a second step, it will be important to develop materials with even better characteristics than ceria," she added.

"Ideally, one wants a material with a smaller temperature swing required as this will also increase efficiency," Haile said. "In addition, if both the high and low temperatures can be lowered, the overall system lifetime will be improved. Better materials could result in a better process."

Provided by National Science Foundation (news : web)

Positioning enzymes with ease

Virtually all processes in the human body rely on a unique class of proteins known as enzymes. To study them, scientists want to attach these molecules to surfaces and hold them fast, but this can often be a tricky undertaking.

Now Jinglin Fu and his colleagues at the Biodesign Institute at Arizona State University have developed a superior method for immobilizing enzymes on surfaces, deftly controlling their orientation, improving their efficiency and rendering them more stable. The group's results appear in today's advanced online issue of .

Enzymes are essential for the normal functioning of cells, and are involved in tasks including cell regulation, metabolism and signal transduction. They are also necessary for and the transport of ions and other materials throughout the cytoskeleton.

Enzymes like amylases and are central players in the digestive systems of many animals, breaking down starches and other large molecules into smaller parts that can be absorbed by the intestines. Herbivorous animals make use of the enzyme cellulose, to break down plant fiber. "No wonder has been a topic of longstanding concern for biochemistry and medicine," says Fu.

Like other proteins, enzymes are composed of linear chains of . They can range from tens to thousands of amino acids in length. The job of the enzyme is to increase the rate of the desired reaction, without increasing the rate of undesired reactions. Here, a molecule known as the substrate interacts with a given enzyme to produce a product. Without enzymes, many reactions essential to living things could not proceed.

Such has also been adapted and broadly applied in the biomedical arena (especially for various diagnostic testing), as well for industrial applications ranging from photography to the brewing of beer.

Enzymes are also critical for the study of disease. Given their central role in maintaining homeostasis, any single enzyme aberration, including mutation, overproduction, underproduction or deletion can have dire consequences for health. Phenylketonuria, for example, is a disease linked with a single amino acid mutation in the enzyme phenylalanine hydroxylase. If untreated, the condition can lead to mental retardation. Malfunctioning of DNA repair enzymes is associated with a number of forms of cancer.

To properly study enzymes, particularly their catalytic activity, it is necessary to fix them in place on a surface. While researchers have used several techniques for enzyme immobilization, existing methods suffer from several shortcomings. Enzymes need to be properly oriented on the surface with respect to the molecule they are catalyzing in order to work properly. The non-specific binding of proteins can contaminate the reaction and lower or block its efficient progress. Finally, proteins are prone to becoming unfolded and deactivated over time—a process known as denaturation.

In the current study, Fu first generated a high-density array of peptides on a glass slide, each peptide composed of 20 randomly assembled amino acids. A specific enzyme, ß galactosidase, was then screened against this array. This method identified two peptides that covalently bound to the enzyme with high affinity, and these were used for the subsequent experiments.

When compared with low-affinity binding peptides and with preexisting surface immobilization techniques, the group found that the high affinity peptides not only were more effective at holding the enzyme in its proper orientation on the slide, they also produced higher specific activity in the enzyme. The enzyme was also less subject to denaturation, compared with controls.

In a further refinement of the technique, the group created mutations of the high affinity peptides, by deleting a single amino acid along the peptide's length and replacing it with a different amino acid. This procedure was repeated with all 20 amino acids in the peptide chain, with the resulting mutations once more screened against the ß galactosidase enzyme. The technique, known as single-point variant screening, improved both the binding affinity and specific activity of the bound .

"This development gives us a new tool, both for enhancing the function of surface bound enzymes, which are of ever-increasing importance to industry, and also for studying the interactions between multiple enzymes in a metabolic pathway," said Neal Woodburry, a co-author of the PLoS ONE study.

Provided by Arizona State University (news : web)

Army pyrotechnic experts find safer alternative for green fireworks

For years, the U.S. army and many other agencies around the world have been using hand-held green light-emitting signal flares; flares which are very nearly indispensable under certain adverse conditions. The problem is, the flares contain barium, a toxic metal that can build up quickly on training grounds. Barium is also the ingredient used in fireworks to make them glow green, which creates a problem for places such as Disneyworld that shoot off fireworks every night.

Enter Jesse Sabatini and his colleagues at Picatinny Arsenal in New Jersey; they were tasked by the U.S. army with finding an alternative to barium that would work just as well but wouldn’t cost any more. After working first with the powdery form of the pure element boron, which they knew when burned would produce boron oxide and in the process green light, they began investigating other boric substances because of the high cost and tendency of the pure stuff to burn too quickly. Eventually, after some research they hit upon the idea of using a ceramic already widely used as a plating material due to its extreme hardness. They found that it could be burned in its pure state and would produce green light just as well as barium and at nearly the same cost and have published their findings in Angewandte Chemie International Edition.

The team’s findings come as a bit of a surprise to many in the chemistry field due to the fact that boron carbide has traditionally been considered highly inert (not chemically active).

In addition to eliminating the toxicity problem of using barium in flares, switching to boron carbide would also help reduce the dispersal of polychlorinated biphenyls since the current flares also contain a polyvinyl chloride (PVC) component, a very well known toxic agent that has been in the news as a pollutant for decades.
The U.S. army, which uses flares as both a means of illumination and to simulate battlefield explosions, stands to benefit dramatically by this new finding as it now spends a significant amount of money just cleaning up the toxic leftovers of its current flares.

It also seems likely based on the results of this new research that boron carbide will also soon replace in as well, making resorts all over the world safer places to visit.

More information: Boron Carbide as a Barium-Free Green Light Emitter and Burn-Rate Modifier in Pyrotechnics, Angewandte Chemie International Edition, Article first published online: 6 APR 2011 DOI:10.1002/anie.201007827
via Nature


Tandem catalysis in nanocrystal interfaces could be boon to green energy

In a development that holds intriguing possibilities for the future of industrial catalysis, as well as for such promising clean green energy technologies as artificial photosynthesis, researchers with the U.S. Department of Energy (DOE)'s Lawrence Berkeley National Laboratory (Berkeley Lab) have created bilayered nanocrystals of a metal-metal oxide that are the first to feature multiple catalytic sites on nanocrystal interfaces. These multiple catalytic sites allow for multiple, sequential catalytic reactions to be carried out selectively and in tandem.

"The demonstration of rationally designed and assembled nanocrystal bilayers with multiple built-in metal–metal oxide interfaces for tandem catalysis represents a powerful new approach towards designing high-performance, multifunctional nanostructured catalysts for multiple-step chemical reactions," says the leader of this research Peidong Yang, a chemist who holds joint appointments with Berkeley Lab's Materials Sciences Division, and the University of California Berkeley's Chemistry Department and Department of Materials Science and Engineering.

Yang is the corresponding author of a paper describing this research that appears in the journal Nature Chemistry. The paper is titled "Nanocrystal bilayer for tandem catalysis."

Co-authoring the paper were Yusuke Yamada, Chia-Kuang Tsung, Wenyu Huang, Ziyang Huo, Susan Habas, Tetsuro Soejima, Cesar Aliaga and leading authority on catalysis Gabor Somorjai.

Catalysts – substances that speed up the rates of chemical reactions without themselves being chemically changed – are used to initiate virtually every industrial manufacturing process that involves chemistry. Metal catalysts have been the traditional workhorses, but in recent years, with the advent of nano-sized catalysts, metal,oxide and their interface have surged in importance.

"High-performance metal-oxide nanocatalysts are central to the development of new-generation energy conversion and storage technologies," Yang says. "However, to significantly improve our capability of designing better catalysts, new concepts for the rational design and assembly of metal–metal oxide interfaces are needed."

Studies in recent years have shown that for nanocrystals, the size and shape – specifically surface faceting with well-defined atomic arrangements – can have an enormous impact on catalytic properties. This makes it easier to optimize nanocrystal catalysts for activity and selectivity than bulk-sized catalysts. Shape- and size-controlled metal oxide nanocrystal catalysts have shown particular promise.


In a unqiue new bilyaer nanocatalyst system, single layers of metal and metal oxide nanocubes are deposited to create two distinct metal-metal oxide interfaces that allow for multiple, sequential catalytic reactions to be carried out selectively and in tandem. Credit: Image courtesy of Yang group

"It is well-known that catalysis can be modulated by using different metal oxide supports, or metal oxide supports with different crystal surfaces," Yang says. "Precise selection and control of metal-metal oxide interfaces in nanocrystals should therefore yield better activity and selectivity for a desired reaction."

To determine whether the integration of two types of metal oxide interfaces on the surface of a single active metal nanocrystal could yield a novel tandem catalyst for multistep reactions, Yang and his coauthors used the Lamgnuir-Blodgett assembly technique to deposit nanocube monolayers of platinum and cerium oxide on a silica (silicon dioxide) substrate. The nanocube layers were each less than 10 nanometers thick and stacked one on top of the other to create two distinct metal–metal oxide interfaces – platinum-silica and cerium oxide-platinum. These two interfaces were then used to catalyze two separate and sequential reactions. First, the cerium oxide-platinum interface catalyzed methanol to produce carbon monoxide and hydrogen. These products then underwent ethylene hydroformylation through a reaction catalyzed by the platinum-silica interface. The final result of this tandem catalysis was propanal.

"The cubic shape of the nanocrystal layers is ideal for assembling metal–metal oxide interfaces with large contact areas," Yang says. "Integrating binary to form highly ordered superlattices is a new and highly effective way to form multiple interfaces with new functionalities."

Yang says that the concept of tandem catalysis through multiple interface design that he and his co-authors have developed should be especially valuable for applications in which multiple sequential reactions are required to produce chemicals in a highly active and selective manner. A prime example is , the effort to capture energy from the sun and transform it into electricity or chemical fuels. To this end, Yang leads the Berkeley component of the Joint Center for Artificial Photosynthesis, a new Energy Innovation Hub created by the U.S. Department of Energy that partners Berkeley Lab with the California Institute of Technology (Caltech).

"Artificial photosynthesis typically involves multiple chemical reactions in a sequential manner, including, for example, water reduction and oxidation, and carbon dioxide reduction," says Yang. "Our tandem catalysis approach should also be relevant to photoelectrochemical reactions, such as solar water splitting, again where sequential, multiple reaction steps are necessary. For this, however, we will need to explore new or other semiconductor supports, such as titanium dioxide, in our catalyst design."

Provided by Lawrence Berkeley National Laboratory (news : web)