Friday, June 10, 2011

Green cats eye up new kitty litter

Scratching around in the kitty tray could soon be a greener experience for cats in the UK and world-wide, thanks to a new type of low-cost cat litter developed by researchers at Imperial College London, in partnership with a leading supplier of pet products.

Currently, the biggest selling types of cat litter products are low-cost brands that are primarily made from such as bentonite and sepiolite, which are mined and imported from quarries in Mediterranean countries. However, these products have a significant and high product miles because they have to be transported over .

Now, the Imperial team, working with the pet products company Bob Martin, has developed a new type of low-cost cat litter that is made from waste material already available in UK quarries, making the cat litter more sustainable. The new cat litter does not have to be transported far to be either processed or sold, reducing its impact on the environment. It is expected to be available in leading supermarkets from 2012.

One of the challenges for the team was to develop cat litter with the absorbent qualities of the minerals used in imported cat litter products.

The researchers had to augment the quarry waste material, which primarily consists of limestone fines, so that it could become more absorbent. The team mixed the with an organic binder and a small amount of absorbent used in nappies to soak up waste. The ingredients were then mixed and dried to produce a granular cat litter product.

Dr. Chris Cheeseman, Department of Civil and Environmental Engineering at Imperial College London, who worked on the project, says:

“Most people would not realise all the stringent tests that all products have to go through before they reach the consumer. Even humble cat litter! We had to develop a product that was absorbent and robust enough so that it didn’t end up as pulverised dust when tipped out of a packet. We even had to make sure that cat litter did not stick to pussy paws and leave cat tracks throughout the house. On a more serious note, it was great working with Bob Martin on this project. We have developed a potentially world leading product that could be manufactured and marketed anywhere in the world where people keep cats.”

The team behind the new cat litter also believes that the engineered granule technology they have created could be adapted for use in a range of other applications including new engineered de-icing grits for roads, soil supplements to increase the efficiency of water irrigation and speciality horticultural products.

Provided by Imperial College London (news : web)

Biochemist David Deamer explores how life began in new book, 'First Life'

David Deamer began studying the origin of life in the early 1980s, and his research over the past 30 years has had a major influence on scientific understanding of how life on Earth got started. In his new book, First Life (UC Press, June 2011), Deamer presents a personal history of his work in this field, while also providing an engaging and accessible overview of research into life's beginnings.

The book describes this research within the framework of a new scientific discipline called astrobiology, which studies the origin and evolution of in a broader cosmic context. " is a narrative that encompasses our understanding of , the formation of our solar system, the environment, and how behave in such a way that they are driven toward increasing complexity of structures and interactions," said Deamer, a research professor of biomolecular engineering in the Baskin School of Engineering at UC Santa Cruz.

The main focus of his research has been the role of membranes in the . He began his career studying the biophysics of cell membranes, which are made of molecules called lipids. In the 1980s, he demonstrated that meteorites contain lipid-like molecules capable of forming stable membranes. More recently, research in Deamer's lab has shown that lipid membranes have an organizing effect on other molecules that helps small molecules join together to form longer polymers similar to the RNA and DNA, which are essential to all known forms of life.

This organizing effect of membranes is seen when chemical mixtures go through cycles of wetting and drying, as would occur along the margins of pools of hot water on volcanic sites. Such sites would have been a common environment on the early Earth. Wetting and drying promotes chemical reactions and also causes lipid membranes to form compartments that encapsulate different mixtures of compounds. According to Deamer, the first life emerged from the natural production of vast numbers of these membrane-bound "protocells."

"The first life was not just replicating molecules, it was an encapsulated system of molecules--a cell," he said.

The most recent findings from Deamer's lab, published in the January issue of the journal Biochimie, showed that wet-dry cycles in a system including membrane-forming lipids can drive the replication of a DNA molecule without any need for the polymerase enzyme that performs this function in living cells today.

"Some people are still skeptical--I think the new results have to soak in for awhile, and the experiment needs to be repeated by others. I've had this idea for the past 20 years that lipids could have an organizing effect that helps polymerization occur and then encapsulate the resulting polymers to produce simple cellular structures," Deamer said.

In addition to laboratory experiments, Deamer has conducted field experiments at volcanic sites in Russia, Hawaii, and California. "I think we need to be bolder in testing our ideas," he said. "There has to be sufficient complexity in our experiments to match the complex conditions of the . That's one reason I started doing experiments in real-world environments."

Deamer's long involvement in research on life's origins and his personal relationships with other leading scientists in the field has enabled him to give readers of the new book a "behind-the-scenes" look at this exciting scientific quest.

"In First , Deamer offers a delightful synthesis of research into life's dawn with his own vision for how it came to be," wrote science writer Carl Zimmer.

Provided by University of California - Santa Cruz (news : web)

Finding answers century-old questions about platinum's catalytic properties

Researchers now understand more about why platinum is so efficient at producing power in hydrogen fuel cells.

"Understanding platinum's properties for speeding up chemical reactions will potentially enable scientists to create significantly cheaper synthetic or metal alloy alternatives for use in sustainable devices like fuel cells," says Gregory Jerkiewicz, a professor in the Department of Chemistry who led the groundbreaking study.

Dr. Jerkiewicz's research team has found that when platinum is used in reactions involving hydrogen it develops an embedded layer of hydrogen just one atom thick. This gives the platinum hydrophobic or water-repelling qualities, meaning that stray water molecules inside the fuel cell cannot bond strongly with the surface of the platinum.

The water-repelling nature of the modified platinum means that incoming can easily attach to the surface of the platinum and separate into smaller particles without requiring additional energy to displace any that are in the way.

The reduction in the energy required for hydrogen molecules to attach to the surface of the platinum means that the process is fast and efficient and the fuel cell can deliver a lot of power.

Provided by Queen's University (news : web)

Bacterial protein caught in the act of secreting sticky appendages

New atomic-level "snapshots" published in the June 2, 2011, issue of Nature reveal details of how bacteria such as E. coli produce and secrete sticky appendages called pili, which help the microbes attach to and infect human cells. "These crystal structures unravel a complex choreography of protein-protein interactions that will aid in the design of new antibacterial drugs," said Huilin Li, a biophysicist at the U.S. Department of Energy's Brookhaven National Laboratory and a professor at Stony Brook University, who participated in the research with a number of collaborators in the U.S. and in Europe.

Many E. coli strains live harmlessly in our guts, but when they find their way into the urinary tract, they produce pili with sticky ends that allow them to attach to bladder cells and cause infection. Finding ways to interfere with pili formation could help thwart , which affect millions of women around the world each year.

Previously, Li's group at Brookhaven/Stony Brook and colleagues at Washington University School of Medicine and University College London solved individual pieces of the puzzle. In 2008, they combined their efforts to publish the first complete structure of the pore-like protein complex that traverses the bacterial membrane and transports pili components from the microbe cell's interior to its outer surface.

But the scientists were still not sure how the transporter protein's various parts worked to "recruit" and bring together the many subunits that make up the pili - or how it assembled and moved these structures through the membrane to the bacterial cell's surface. The new work, again combining efforts from the two teams, uses a range of imaging techniques and computer modeling to arrive at a more complete picture of the assembly process and transport mechanism.

"This is the first view of a protein transporter in the act of secreting its substrate," said Li.

At the European Synchrotron Radiation Facility in Grenoble, France, the Washington University/UK group determined the crystal structure of the entire transporter protein, known as an "usher," bound to the sticky adhesin subunit that forms the end of a pilus and another helper protein, called a chaperone, that shuttles the pilus subunits to the usher one at a time. Meanwhile, Li's group worked at the National Synchrotron Light Source at Brookhaven to produce new images of the unbound usher protein in its closed, inactive state.

"Each group's work tells only part of the story, but when combined, the results provide unique insights into how the transporter works," said Li. "By comparing the same transporter in the closed and open state, we've determined how the gate should open, and exactly how the structure of the channel changes in response to the gate opening so the growing pilus can reach the exterior of the membrane," Li said.

When no subunits are bound to the usher, the barrel like pore remains plugged, completely sealed off. But when the first chaperoned subunit, the adhesin, arrives, it causes a dramatic conformational change that unplugs the pore and changes its shape from an oval to nearly circular.

"This large conformational rearrangement in the translocation channel upon activation by adhesin-chaperone is unprecedented for these barrel proteins, which until now were considered rigid structures," Li said.

The research also reveals that the usher protein has two binding sites for chaperone-subunit complexes. From the imaging studies and bioassays, it appears that the two operate in concert: While one chaperone-subunit complex remains bound as it moves through the translocation channel, the other site is available to recruit the next chaperone-subunit complex and add it to the growing pilus. Computer models show that the next incoming subunit is positioned in an ideal orientation for addition to the growing pilus structure via a "zip-in-zip-out" binding mechanism.

Blocking or removing either of the two binding sites may therefore be a way to inhibit pilus formation, and this idea is already being explored in new drug-development investigations. The other details of pilus assembly revealed by this study may suggest additional targets for new drugs.

More information: Crystal structure of the FimDusher bound to its cognate FimC-FimH substrate, Nature, DOI:10.1038/nature10109

Provided by Brookhaven National Laboratory (news : web)

Scientists discover new direction in Alzheimer's research

In what they are calling a new direction in the study of Alzheimer's disease, UC Santa Barbara scientists have made an important finding about what happens to brain cells that are destroyed in Alzheimer's disease and related dementias. The results are published in the online version of The Journal of Biological Chemistry.

Stuart Feinstein, professor of Molecular, Cellular and Developmental Biology, senior author, and co-director of UCSB's Neuroscience Research Institute, explained: "With dementia, the , or , that you need for are no longer working properly. Then, they're not even there anymore because they die. That's what leads to dementia; you're losing neuronal capacity."

Feinstein has studied the protein called "tau" for about 30 years, using biochemistry and a variety of as models. Under normal conditions, tau is found in the long of neurons that serve to connect neurons with their targets, often far from the cell body itself. Among tau's major functions is to stabilize microtubules, which are an integral part of the cellular cytoskeleton that is essential for many aspects of neuronal cell structure and function.

It has been known for many years that a small peptide named amyloid beta can cause and Alzheimer's disease, although the mechanism for how it works has been poorly understood. Recently, has demonstrated that the ability of amyloid beta to kill neurons requires tau; however, what it does to tau has been enigmatic. "We know amyloid beta is a bad guy," said Feinstein. "Amyloid beta causes disease; amyloid beta causes Alzheimer's. The question is how does it do it?"

He explained that most Alzheimer's researchers would argue that amyloid beta causes tau to become abnormally and excessively phosphorylated. This means that the tau proteins get inappropriately chemically modified with phosphate groups. "Many of our proteins get phosphorylated," said Feinstein. "It can be done properly or improperly."

Feinstein added that he and his students wanted to determine the precise details of the presumed abnormal phosphorylation of tau in order to gain a better understanding of what goes wrong. "That would provide clues for drug companies; they would have a more precise target to work on," said Feinstein. "The more precisely they understand the biochemistry of the target, the better attack a pharmaceutical company can make on a problem."

Feinstein said that the team's initial hypothesis suggesting that amyloid beta leads to extensive abnormal tau phosphorylation turned out not to be true. "We all like to get a curve ball tossed our way once in a while, right?" said Feinstein. "You like to see something different and unexpected."

The research team found that when they added amyloid beta to neuronal cells, the tau in those cells did not get massively phosphorylated, as predicted. Rather, the surprising observation was the complete fragmentation of tau within one to two hours of exposure of the cells to amyloid beta. Within 24 hours, the cells were dead.

Feinstein explained that tau has many jobs, but its best-understood job is to regulate the cellular cytoskeleton. Cells have a skeleton much like humans have a skeleton. The major difference is that human skeletons don't change shape very abruptly, whereas a cell's skeleton is constantly growing, shortening, and moving. It does this in order to help the cell perform many of its essential functions. The cytoskeleton is especially important to neurons because of their great length.

Feinstein argues that neurons die in Alzheimer's disease because their cytoskeleton is not working properly. "If you destroy tau, which is an important regulator of the , one could easily see how that could also cause cell death," said Feinstein. "We know from cancer drugs that if you treat cells with drugs that disrupt the , the cells die," he said. "In my mind, the same thing could be happening here."

Provided by University of California - Santa Barbara (news : web)

New drugs target delay of Huntington's symptoms

McMaster researchers have discovered a new drug target that may be effective at preventing the onset of Huntington's disease, working much the same way heart medications slow the progression of heart disease and reduce heart attacks.

Their landmark research discovered a family of kinase inhibitor drugs - that all target one enzyme called IKK beta kinase - as effective for Huntington's.

The drug restores a critical chemical change that should occur in the huntingtin protein, but does not occur in people with Huntington's disease.

The research appears in the May 29 online edition of Nature Chemical Biology.

"It is the first time anyone has identified drugs that affect how the huntingtin protein gets modified at one critical site, and through what pathway," said Ray Truant, professor in the Department of Biochemistry and Biomedical Sciences of the Michael G. DeGroote School of Medicine at McMaster.

Huntington's disease, which impacts one in 4,000 Canadians, is an inherited disease that causes certain in the brain to waste away. People are born with a , but symptoms usually don't appear until middle age. Early symptoms include depression and , with later symptoms including uncontrolled movements, clumsiness and . At some point patients may have difficulty walking, talking or swallowing. There is no specific treatment for the disease.

Currently kinase inhibitor drugs form a family of successful, new generation drugs that are coming on the market or have been approved for a wide range of diseases including stroke, arthritis and cancer.

The McMaster researchers are currently looking at inhibitors that can cross the blood to brain barrier, before starting preliminary trials. If successful, human clinical trials are five or more years away.

Truant and Randy Singh Atwal, a PhD graduate, discovered the huntintin protein has an essential role in chemical stresses relating to human aging and the protein is not properly modified in response to these stresses during Huntington's Disease.

"This is one explanation as to why it takes until middle age for Huntington's to develop in most patients, because the role of the is more critical as a person ages," said Truant.

The research is supported by the Canadian Institutes of Health Research, the not-for- profit Cure for Huntington's Disease Initiative Inc., and the Toronto-based Krembil Family Foundation. Truant is chair of the Huntington Society of Canada's scientific advisory board.

"These new results are extremely important because they may help to delay the progression of ," said Dr. Anthony Phillips, scientific director of the Canadian Institutes of Health Research (CIHR) Institute of Neurosciences, Mental Health and Addiction. "CIHR is proud to support researchers who devote their time to look into this genetic brain disorder that has such challenging effects on individuals and their families in Canada."

More information: Kinase inhibitors modulate huntingtin cell localization and toxicity, Nature Chemical Biology (2011) doi:10.1038/nchembio.582

Two serine residues within the first 17 amino acid residues of huntingtin (N17) are crucial for modulation of mutant huntingtin toxicity in cell and mouse genetic models of Huntington's disease. Here we show that the stress-dependent phosphorylation of huntingtin at Ser13 and Ser16 affects N17 conformation and targets full-length huntingtin to chromatin-dependent subregions of the nucleus, the mitotic spindle and cleavage furrow during cell division. Polyglutamine-expanded mutant huntingtin is hypophosphorylated in N17 in both homozygous and heterozygous cell contexts. By high-content screening in live cells, we identified kinase inhibitors that modulated N17 phosphorylation and hence huntingtin subcellular localization. N17 phosphorylation was reduced by casein kinase-2 inhibitors. Paradoxically, IKKß kinase inhibition increased N17 phosphorylation, affecting huntingtin nuclear and subnuclear localization. These data indicate that huntingtin phosphorylation at Ser13 and Ser16 can be modulated by small-molecule drugs, which may have therapeutic potential in Huntington's disease.

Provided by McMaster University (news : web)

Scientists identify how major biological sensor in the body works

A biological sensor is a critical part of a human cell's control system that is able to trigger a number of cell activities. A type of sensor known as the "gating ring" can open a channel that allows a flow of potassium ions through the cell's wall or membrane — similar to the way a subway turnstile allows people into a station. This flow of ions, in turn, is involved in the regulation of crucial bodily activities like blood pressure, insulin secretion and brain signaling.

But the biophysical functioning of the gating ring sensor has not been clearly understood. Now, UCLA researchers have uncovered for the first time the sensor's molecular mechanism, shedding new light on the complexity of cells' control systems.

The findings, published in the June 10 issue of the and featured as a "Paper of the Week," could lead to the development of specific therapies against diseases such as hypertension and genetic epilepsy.

Just as a smoke detector senses its environment and responds by emitting a sound signal, cells control their intracellular environment through molecular sensors that assess changes and trigger a response.

In this case, when calcium ions bind to the gating ring — which constitutes the intracellular part of an ionic channel known as the BK channel — the cell responds by allowing the flow of potassium ions across the cell membrane, with a wide range of consequences for the body.

BK channels are present in most cells in the body and regulate fundamental biological processes such as blood pressure, electrical signaling in the brain and nervous system, inner ear hair-tuning that impacts hearing, muscle contractions in the bladder, and insulin secretion from the pancreas, to name a few.

The UCLA researchers were able to identify for the first time how the gating ring is activated and how it rearranges itself to open the gateway that the ions flow through. Using state-of-the-art electrophysiological, biochemical and spectroscopic techniques in the laboratory, the team demonstrated that when calcium ions bind to the gating ring, its structure changes — that is, it converts the chemical energy of the calcium binding into mechanical work that facilitates the opening of the BK channel.

"We were able to resolve the biophysical changes occurring in the sensor, under conditions resembling those present inside a living cell, so we believe that these transformations reflect the molecular events occurring when BK channels operate in the body," said research team leader Riccardo Olcese, an associate professor in the department of anesthesiology's division of molecular medicine and a member of both the Cardiovascular Research Laboratory and Brain Research Institute at the David Geffen School of Medicine at UCLA.

"This is an exciting field of study and we hope that these findings will lead to a greater understanding of how this complex operates," said study author Anoosh D. Javaherian, a research associate in the department of anesthesiology's division of molecular medicine division at the Geffen School of Medicine.

Javaherian added that only last year were the structures involved in the BK sensor even identified. This is the first study to demonstrate its function.

Since the BK channel and its sensor are involved in so many aspects of normal physiological function, researchers believe that it is likely the process could be implicated in many aspects of disease as well.

"This molecular and dynamic view of the BK intracellular sensor helps us understand how signaling molecules are sensed, providing new ideas on how to fight disease," said Taleh Yusifov, a research associate in the department of anesthesiology's division of molecular medicine at the Geffen School of Medicine.

For example, Yusifov noted, the malfunction of this BK channel's sensor has been associated with genetic epilepsy.

The next step in the research will assess if the BK gating ring sensor and channel are involved in sensing small molecules — other than calcium ions — which also have great biological significance in the workings of the human body.

Provided by University of California - Los Angeles

Researchers create nanoscale waveguide for future photonics

The creation of a new quasiparticle called the "hybrid plasmon polariton" may throw open the doors to integrated photonic circuits and optical computing for the 21st century. Researchers with the U.S. Department of Energy (DOE)'s Lawrence Berkeley National Laboratory (Berkeley Lab) have demonstrated the first true nanoscale waveguides for next generation on-chip optical communication systems.

"We have directly demonstrated the nanoscale waveguiding of light at visible and near infrared frequencies in a metal-insulator-semiconductor device featuring low loss and broadband operation," says Xiang Zhang, the leader of this research. "The novel mode design of our nanoscale waveguide holds great potential for nanoscale photonic applications, such as intra-chip optical communication, signal modulation, nanoscale lasers and bio-medical sensing."

Zhang, a principal investigator with Berkeley Lab's Materials Sciences Division and director of the University of California at Berkeley's Nano-scale Science and Engineering Center (SINAM), is the corresponding author of a paper published by Nature Communications that describes this work titled "Experimental Demonstration of Low-Loss Optical Waveguiding at Deep Sub-wavelength Scales." Co-authoring the paper with Zhang were Volker Sorger, Ziliang Ye, Rupert Oulton, Yuan Wang, Guy Bartal and Xiaobo Yin.

In this paper, Zhang and his co-authors describe the use of the hybrid plasmon polariton, a quasi-particle they conceptualized and created, in a nanoscale waveguide system that is capable of shepherding light waves along a metal-dielectric nanostructure interface over sufficient distances for the routing of optical communication signals in photonic devices. The key is the insertion of a thin low-dielectric layer between the metal and a semiconductor strip.

"We reveal mode sizes down to 50-by-60 square nanometers using Near-field scanning optical microscopy (NSOM) at optical wavelengths," says Volker Sorger a graduate student in Zhang's research group and one of the two lead authors on the Nature Communications paper. "The propagation lengths were 10 times the vacuum wavelength of visible light and 20 times that of near infrared."

The high-technology world is eagerly anticipating the replacement of today's electronic circuits in microprocessors and other devices with circuits based on the transmission of light and other forms of electromagnetic waves. Photonic technology, or "photonics," promises to be superfast and ultrasensitive in comparison to electronic technology.

"To meet the ever-growing demand for higher data bandwidth and lower power consumption, we need to reduce the energy required to create, transmit and detect each bit of information," says Sorger. "This requires reducing physical photonic component sizes down beyond the diffraction limit of light while still providing integrated functionality."

Until recently, the size and performance of photonic devices was constrained by the interference that arises between closely spaced light waves. This diffraction limit results in weak photonic-electronic interactions that can only be avoided through the use of devices much larger in size than today's electronic circuits. A breakthrough came with the discovery that it is possible to couple photons with electrons by squeezing light waves through the interface between a metal/dielectric nanostructure whose dimensions are smaller than half the wavelengths of the incident photons in free space.

Directing waves of light across the surface of a metal nanostructure generates electronic surface waves -- called plasmons -- that roll through the metal's conduction electrons (those loosely attached to molecules and atoms). The resulting interaction between plasmons and photons creates a quasi-particle called a surface plasmon polariton(SPP) that can serve as a carrier of information. Hopes were high for SPPs in nanoscale photonic devices because their wavelengths can be scaled down below the diffraction limit, but problems arose because any light signal loses strength as it passes through the metal portion of a metal-dielectric interface.

"Until now, the direct experimental demonstration of low-loss propagation of deep sub-wavelength optical modes was not realized due to the huge propagation loss in the optical mode that resulted from the electromagnetic field being pushed into the metal," Zhang says. "With this trade-off between optical confinement and metallic losses, the use of plasmonics for integrated photonics, in particular for optical interconnects, has remained uncertain."

To solve the problem of optical signal loss, Zhang and his group proposed the hybrid plasmon polariton (HPP) concept. A semiconductor (high-dielectric) strip is placed on a metal interface, just barely separated by a thin oxide (low-dielectric) layer. This new metal-oxide-semiconductor design results in a redistribution of an incoming light wave's energy. Instead of being concentrated in the metal, where optical losses are high, some of the light wave's energy is squeezed into the low dielectric gap where optical losses are substantially less compared to the plasmonic metal.

"With this design, we create an HPP mode, a hybrid of the photonic and plasmonic modes that takes the best from both systems and gives us high confinement with low signal loss," says Ziliang Ye, the other lead authors of the Nature Communications paper who is also a graduate student in Zhang's research group. "The HPP mode is not only advantageous for down-scaling physical device sizes, but also for delivering novel physical effects at the device level that pave the way for nanolasers, as well as for quantum photonics and single-photon all-optical switches."

The HPP waveguide system is fully compatible with current semiconductor/CMOS processing techniques, as well as with the Silicon-on-Insulator (SOI) platform used today for photonic integration. This should make it easier to incorporate the technology into low-cost, large-scale integration and manufacturing schemes. Sorger believes that prototypes based on this technology could be ready within the next two years and the first actual products could be on the market within five years.

"We are already working on demonstrating an all-optical transistor and electro-optical modulator based on the HPP waveguide system," Sorger says. "We're also now looking into bio-medical applications, such as using the HPP waveguide to make a molecular sensor."

This research was supported by the National Science Foundation's Nano-Scale Science and Engineering Center.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by DOE/Lawrence Berkeley National Laboratory.

Journal Reference:

Volker J. Sorger, Ziliang Ye, Rupert F. Oulton, Yuan Wang, Guy Bartal, Xiaobo Yin, Xiang Zhang. Experimental demonstration of low-loss optical waveguiding at deep sub-wavelength scales. Nature Communications, 2011; 2: 331 DOI: 10.1038/ncomms1315