Thursday, February 10, 2011


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Researchers funded by BBSRC have developed chickens that are genetically modified to prevent them from spreading bird flu to other chickens. If this genetic modification is introduced into poultry flocks in the future it has the potential to protect the health of the birds and so increase the production of meat and eggs. It could also reduce the risk of bird flu epidemics that can lead to new flu outbreaks in the human population.

The study, which the researchers say is the first step in developing chickens that are completely resistant to avian flu, was published last night in the journal Science. The work was carried out by teams based in The Roslin Institute, an institute of BBSRC, at the University of Edinburgh and in the University of Cambridge Department of Veterinary Medicine.

Professor Helen Sang, who led the team at The Roslin Institute said that as well as improving welfare and sustainability in the poultry industry, "this work could also form the basis for improving economic and food security in many regions of the world where bird flu is a significant problem."

Meat production and consumption worldwide is increasing in general and poultry makes up a significant proportion of that increase. There appears to be a trend towards eating chicken as a major source of protein and as the global population is predicted to hit 9 billion in 2050, "infectious diseases of livestock represent a significant threat to global food security," says Professor Douglas Kell, BBSRC Chief Executive.

There is also the potential, Professor Kell added, for infectious diseases of livestock to "jump to humans and become pandemic". This, he says, "has been identified by the Government as a top level national security risk."

Dr Laurence Tiley, Senior Lecturer in Virology who led the team that developed the inhibitory transgene at the University of Cambridge said "Chickens are potential bridging hosts that can enable new strains of flu to be transmitted to humans. Preventing virus transmission in chickens should reduce the risk posed to people exposed to infected birds."

To produce these chickens, the scientists introduced a new gene that manufactures a small "decoy" molecule. In this case, it is a short length of a type of molecule called ribonucleic acid, or RNA. Dr Tiley explained that "the decoy mimics an essential part of the flu virus genome that is identical for all strains of influenza A. The replication machinery of the virus is tricked into recognising the decoy molecule instead of the viral genome and this interferes with the replication cycle of the virus".

The decoy is expected to work against all strains of bird flu and will not need updating for each season.

"The virus will find it difficult to evolve to escape the effects of the decoy. This is quite different from conventional flu vaccines, which need to be updated in the face of virus evolution as they tend only to protect against closely matching strains of virus and do not always prevent spread within a flock," Dr Tiley concluded.

Biotechnology and Biological Sciences Research Council


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A new way to calculate the age of the Earth’s crust has been developed by researchers from the University of Bristol and the University of St Andrews.

The continental crust is the principal record of conditions on the Earth for the last 4.4 billion years. Its formation modified the composition of the mantle and the atmosphere, it supports life, and it remains a sink for carbon dioxide through weathering and erosion. The continental crust therefore has had a key role in the evolution of the Earth, and yet the timing of its generation remains the topic of considerable debate.

It is widely believed that the juvenile continental crust has grown from the depleted upper mantle. One common way to assess when new crust was formed is to determine the radiogenic isotope composition of any crustal sample, and to compare its isotope signature with that of the depleted mantle. In other words, radiogenic isotopes can be used to calculate ‘model ages’ of crust formation, which represent the time since a crustal sample was separated from its mantle source.

The concept of ‘model age’ has been widely used in crustal evolution studies for the last three decades. However it is increasingly clear that using the isotope composition of the depleted mantle as a reference for the calculation of model ages of continental crust generation can lead to incomplete interpretations.

In a paper published today in Science, Dr Bruno Dhuime of Bristol’s School of Earth Sciences and colleagues describe a new methodology for the calculation of model ages, based on the isotope composition of the average new continental crust.

Dr Dhuime said: “Ages calculated this way are significantly younger than model ages calculated from the isotope composition of the depleted mantle. New ages obtained are more consistent with the geological record, which opens new perspectives in crustal evolution studies based on radiogenic isotopes.”

(Photo: NASA)

University of Bristol


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We know that people tend to be attracted to, date, and marry other people who resemble themselves in terms of personality, values, and physical appearance. However, these features only skim the surface of what makes a relationship work. The ways that people talk are also important. A new study published in Psychological Science, a journal of the Association for Psychological Science, finds that people who speak in similar styles are more compatible.

The study focused on words called “function words.” These aren’t nouns and verbs; they’re the words that show how those words relate. They’re hard to explicitly define, but we use them all the time—words like the, a, be, anything, that, will, him, and and. How we use these words constitutes our writing and speaking style, says study coauthor James Pennebaker of the University of Texas at Austin.

“Function words are highly social and they require social skills to use,” he says. “For example, if I’m talking about the article that’s coming out, and in a few minutes I make some reference to ‘the article,’ you and I both know what the article means.” But someone who wasn’t part of that conversation wouldn’t understand.

Pennebaker, Molly Ireland, and their colleagues examined whether the speaking and writing styles couples adopt during conversation with each other predict future dating behavior and the long-term strength of relationships. They conducted two experiments in which a computer program compared partners’ language styles.

In the first study, pairs of college students had four-minute speed dates while their conversations were recorded. Almost every pair covered the same topics: What’s your major? Where are you from? How do you like college? Every conversation sounded more or less the same to the naked ear, but text analysis revealed stark differences in language synchrony. The pairs whose language style matching scores were above average were almost four times as likely to want future contact as pairs whose speaking styles were out of sync.

A second study revealed the same pattern in everyday online chats between dating couples over the course of 10 days. Almost 80 percent of the couples whose writing style matched were still dating three months later, compared with approximately 54 percent of the couples who didn’t match as well.

What people are saying to each other is important, but how they are saying it may be even more telling. People aren’t consciously synchronizing their speech, Pennebaker says. “What’s wonderful about this is we don’t really make that decision; it just comes out of our mouths.”

Association for Psychological Science


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As people age, things fall apart. You can’t read without glasses—or even with them. Bones weaken. You can’t find your keys. And yet, people tend to become happier as they age. A new paper published in Current Directions in Psychological Science, a journal of the Association for Psychological Science, suggests that this could be because older people are better at regulating their emotions.

“Older age gives us this really interesting so-called paradox: physically, you’re falling apart, and yet people are doing well,” says Heather L. Urry of Tufts University, who cowrote the paper with James J. Gross of Stanford University. Scientists have suggested several reasons why older people might seem to be happier than we would think. One possibility is changes in the brain. Another is that we just aren’t very good at guessing what will affect our happiness.

In this paper, Urry and Gross look at a third possibility: that older adults are better at emotion regulation. “I think a lot of people think that your emotional responses are just there and there’s nothing you can do about it,” Urry says. But this is wrong; there are things we can do to change how we feel.

One way to change emotions is to change your situation. For example, if you are unhappy at work, you could figure out what is making you unsatisfied and change it—ask for a cubicle away from an annoying coworker, for example. Another is to think about your situation and reappraise it. “Let’s say you get fired. If you were to interpret that as the end of the world, and you must be a failure, that would be one way of interpreting it,” Urry says. But you could also see it as a new opportunity or your employer’s mistake. “You might still feel bad, but you wouldn’t probably feel as bad.”

People seem to develop better skills for regulating their emotions as they age. For example, older people often have smaller and closer social networks than younger people; this may show that they’re choosing to put themselves in pleasant situations with people they like. Studies have found that older adults pay more attention to positive information than to negative information, which may improve mood. Also, some evidence suggests that older people are better at predicting how a certain situation will make them feel, which gives them a better chance of choosing enjoyable situations and avoiding unpleasantness.

Urry and Gross propose that people may shift how they regulate their emotions over the course of their lifetime, perhaps by shifting to strategies that don’t require as much quick thinking. Psychological scientists have yet to determine which mental resources are used to regulate emotion, Urry says; future research should focus on figuring out how people regulate their emotions and how that changes with age.

Association for Psychological Science


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There’s a reason why Hollywood makes movies like Arachnophobia and Snakes on a Plane: Most people are afraid of spiders and snakes. A new paper published in Current Directions in Psychological Science, a journal of the Association for Psychological Science, reviews research with infants and toddlers and finds that we aren’t born afraid of spiders and snakes, but we can learn these fears very quickly.

One theory about why we fear spiders and snakes is because so many are poisonous; natural selection may have favored people who stayed away from these dangerous critters. Indeed, several studies have found that it’s easier for both humans and monkeys to learn to fear evolutionarily threatening things than non-threatening things. For example, research by Arne Ohman at the Karolinska Institute in Sweden, you can teach people to associate an electric shock with either photos of snakes and spiders or photos of flowers and mushrooms—but the effect lasts a lot longer with the snakes and spiders. Similarly, Susan Mineka’s research (from Northwestern University) shows that monkeys that are raised in the lab aren’t afraid of snakes, but they’ll learn to fear snakes much more readily than flowers or rabbits.

The authors of the Current Directions in Psychological Science paper have studied how infants and toddlers react to scary objects. In one set of experiments, they showed infants as young as 7 months old two videos side by side—one of a snake and one of something non-threatening, such as an elephant. At the same time, the researchers played either a fearful voice or a happy voice. The babies spent more time looking at the snake videos when listening to the fearful voices, but showed no signs of fear themselves.

“What we’re suggesting is that we have these biases to detect things like snakes and spiders really quickly, and to associate them with things that are yucky or bad, like a fearful voice,” says Vanessa LoBue of Rutgers University, who cowrote the paper with David H. Rakison of Carnegie Mellon University and Judy S. DeLoache of the University of Virginia.

In another study, three-year-olds were shown a screen of nine photographs and told to pick out some target item. They identified snakes more quickly than flowers and more quickly than other animals that look similar to snakes, such as frogs and caterpillars. Children who were afraid of snakes were just as fast at picking them out than children who hadn’t developed that fear.

“The original research by Ohman and Mineka with monkeys and adults suggested two important things that make snakes and spiders different,” LoBue says. “One is that we detect them quickly. The other is that we learn to be afraid of them really quickly.” Her research on infants and young children suggests that this is true early in life, too—but not innate, since small children aren’t necessarily afraid of snakes and spiders.

Association for Psychological Science


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In an effort to better understand the dynamics of complex networks, scientists have developed a mathematical model to describe interactions within ecological food webs. This research, performed by Northwestern University physics professor Adilson Motter and his student, Sagar Sahasrabudhe, is published in the January 25 issue of Nature Communications. The work illustrates how human intervention may effectively aid species conservation efforts.

"Our study provides a theoretical basis for management efforts that would aim to mitigate extinction cascades in food web networks. There is evidence that a significant fraction of all extinctions are caused not by a primary perturbation but instead by the propagation of a cascade," said Motter.

Extinction cascades are often observed following the loss of a key species within an ecosystem. As the system changes to compensate for the loss, availability of food, territory and other resources to each of the remaining members can fluctuate wildly, creating a boom-or-bust environment that can lead to even more extinctions. According to the study, more than 70 percent of these extinctions are preventable, assuming that the system can be brought into balance using only available resources--no new factors may be introduced.

Motter explained further, "We find that extinction cascades can often be mitigated by suppressing--rather than enhancing--the populations of specific species. In numerous cases, it is predicted that even the proactive removal of a species that would otherwise be extinct by a cascade can prevent the extinction of other species."

The finding may seem counterintuitive to conservationists because the compensatory actions seem to inflict further damage to the system. However, when the entire ecosystem is considered, the effect is beneficial. This news holds promise for those charged with maintaining Earth's biodiversity and natural resources--the health of which can counteract many of the causes of climate change, and some man-made disasters such as the Gulf of Mexico oil spill.

The dodo bird, Raphus cucullatus, is one example of extinction due to human activity. The dodo was a large, flightless bird that became extinct in the 1600s. It is likely that a combination of factors including hunting, loss of habitat, and perhaps even a flash flood, stressed the ecosystem on the island of Mauritius, home of the dodo. Some researchers think that human introduction of non-native species, such as dogs, pigs, cats and rats to the island, is what ultimately lead to the demise of the dodo.

In any case, in the future, it may be possible to avoid extinction of some species in stressed ecosystems by applying the new method of analysis developed by Motter.

The goal of this project, funded by the National Science Foundation's Division of Mathematical Sciences, is to develop mathematical methods to study dynamical processes in complex networks. Although the specific application mentioned here may be useful in management of ecosystems, the mathematical foundation underlying the analysis is much more universal. The broad concept is innovative in the area of complex networks because it concludes that large-scale failures can be avoided by focusing on preventing the waves of failure that follow the initial event.

This approach could be used to stabilize a wide array of complex networks. It can apply to biochemical networks in order to slow or stop progression of diseases caused by variations inside individual cells. It can also be used to manage technological networks such as the smart grid to prevent blackouts. It can even apply to regulation of complicated financial networks by identifying key factors in the early stages of a financial downturn, which, when met with human intervention, could potentially save billions of dollars.

The world is a complicated place that gets even trickier when trying to mathematically explain a complex network, especially when the network evolves within an environment that is itself changing. But, Motter says his mathematical model is promising for the study of changing environments.

"Uncertainty itself is not a problem," he quipped. "The problem comes when you cannot estimate uncertainty."

(Photo: Zina Deretsky, National Science Foundation)

National Science Foundation


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The Consumer Electronics Show in Las Vegas in January 2010 was abuzz about a slew of prototype 3-D TVs, but if new research from the MIT Media Lab is any indication, holographic TVs could be close behind. At the Society of Photo-Optical Instrumentation Engineers’ (SPIE) Practical Holography conference in San Francisco the weekend of Jan. 23, members of Michael Bove’s Object-Based Media Group presented a new system that can capture visual information using off-the-shelf electronics, send it over the Internet to a holographic display, and update the image at rates approaching those of feature films.

In November, researchers at the University of Arizona made headlines with an experimental holographic-video transmission system that used 16 cameras to capture data and whose display refreshed every two seconds. The new MIT system uses only one data-capture device — the new Kinect camera designed for Microsoft’s Xbox gaming system — and averages about 15 frames per second. Moreover, the MIT researchers didn’t get their hands on a Kinect until the end of December, and only in the week before the conference did they double the system’s frame rate from seven to 15 frames per second. They’re confident that with a little more time, they can boost the rate even higher, to the 24 frames per second of feature films or the 30 frames per second of TV — rates that create the illusion of continuous motion.

The difference between holograms and the type of 3-D images becoming common in movie theaters is frequently overlooked, Bove says. During a screening of, say, the 3-D version of Avatar, viewers on the far-left aisle of the theater see the same image that viewers on the far-right aisle do. That image may have depth, but it’s filmed from a single perspective. As a viewer moves around a hologram, however, his or her perspective on the depicted object changes continuously, just as it would if the object were real.

A standard 3-D movie camera captures light bouncing off of an object at two different angles, one for each eye. But in the real world, light bounces off of objects at an infinite number of angles. Holographic video systems use devices that produce so-called diffraction fringes, fine patterns of light and dark that can bend the light passing through them in predictable ways. A dense enough array of fringe patterns, each bending light in a different direction, can simulate the effect of light bouncing off of a three-dimensional object.

The challenge with real-time holographic video is taking video data — in the case of the Kinect, the light intensity of image pixels and, for each of them, a measure of distance from the camera — and, on the fly, converting that data into a set of fringe patterns. Bove and his grad students — James Barabas, David Cranor, Sundeep Jolly and Dan Smalley — have made that challenge even tougher by limiting themselves to off-the-shelf hardware.

“Really, the focus of our work in digital holography — and I think this makes us pretty much unique among the very small community of people in the world even doing holovideo — is that we’re trying to make a consumer product,” Bove says. “So we’ve been saying, ‘How do you make it as cheap as possible — take advantage of hardware and standards and software and everything else that already exists?’ Because that’s the quickest way to bring it to market.”

In the group’s lab setup, the Kinect feeds data to an ordinary laptop, which relays it over the Internet. At the receiving end, a PC with three commercial graphics processing units — GPUs — computes the diffraction patterns.

GPUs differ from ordinary computer chips — CPUs — in that their circuitry has been tailored to a cluster of computationally intensive tasks that arise frequently during the processing of large graphics files. Much of the work that went into the new system involved re-describing the problem of computing diffraction patterns in a way that takes advantage of GPUs’ strengths.

The one component of the researchers’ experimental system that can’t be bought at an electronics store for a couple hundred dollars is the holographic display itself. It’s the result of decades of research that began with MIT’s Stephen Benton, who built the first holographic video display in the late 1980s. (When Benton died in 2003, Bove’s group inherited the holographic-video project.) The current project uses a display known as the Mark-II, a successor to Benton’s original display that both Benton’s and Bove’s groups helped design. But Bove says that his group is developing a new display that is much more compact, produces larger images, and should also be cheaper to manufacture. (Bove and his students reported on an early version of the display at the same SPIE conference four years ago.)

Mark Lucente, director of display products for Zebra Imaging in Austin, Texas, which is commercializing holographic displays for videoconferencing applications, says that his company’s prospective customers are often uncomfortable with the sheer computational intensity of holographic video. “It’s very daunting,” he says. “1.5 gigabytes per second are being generated on the fly.” By demonstrating that off-the-shelf components can keep up with the computational load, Lucente says, Bove’s group is “helping show that it’s within the realm of possibility.” Indeed, he says, “by taking a video game and using it as an input device, [Bove] shows that it’s a hop, skip and a jump away from reality.”

When the Media Lab researchers demonstrate their new technology at the conference in San Francisco, another grad student in Bove’s group, Edwina Portocarrero, sporting a cowled tunic and a wig with side buns, will re-enact the scene from the first Star Wars movie in which a hologram of Princess Leia implores Obi-Wan Kenobi to re-join the battle against the evil empire. The resolution of the real hologram won’t be nearly as high as that of the special-effects hologram in the movie, but as Bove points out, “Princess Leia wasn’t being transmitted in real time. She was stored.”

(Photo: James D. Barabas)



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Careful dating of new dinosaur fossils and volcanic ash around them by researchers from UC Davis and UC Berkeley casts doubt on the idea that dinosaurs appeared and opportunistically replaced other animals. Instead -- at least in one South American valley -- they seem to have existed side by side and gone through similar periods of extinction.

Geologists from Argentina and the United States announced earlier this month the discovery of a new dinosaur that roamed what is now South America 230 million years ago, at the beginning of the age of the dinosaurs. The newly discovered Eodramaeus, or "dawn runner," was a predatory dinosaur that walked (or ran) on two legs and weighed 10 to 15 pounds. The new fossil was described in a paper by Ricardo Martinez of the Universidad Nacional de San Juan, Argentina, and colleagues in the journal Science Jan. 14.

The fossils come from a valley in the foothills of the Andes in northwestern Argentina. More than 200 million years ago, it was a rift valley on the western edge of the supercontinent Pangaea, surrounded by volcanoes. It's one of the few places in the world where a piece of tectonically active continental margin has been preserved, said Isabel Montañez, a UC Davis geology professor and a co-author of the Science paper.

Montañez, with Brian Currie from Miami University, Ohio, and Paul Renne at UC Berkeley's Geochronology Center, have conducted earlier studies of the ancient soils from the valley, dating layers of ash and researching how the climate changed. Those climate studies have been published previously.

According to Montañez, there are two major temporal boundaries in the geology of the era: The Carnian-Norian boundary at 228 million years ago and the Triassic-Jurassic transition at about 210 million years ago. Geologists have long thought that dinosaurs jumped in number and variety at both points, opportunistically replacing other reptiles.

But the carefully aged fossils from South America show no such increase at the Carnian-Norian boundary, Montañez said. Rather, dinosaurs were as diverse and abundant before the transition as later in the Jurassic, although several species of both dinosaurs and other animals went extinct at the boundary.

At that time, the climate in the valley changed from semi-arid, like today's Mojave desert, to more humid. It's not clear whether that was a global phenomenon or local to that area, Montanez said.

"Those dinosaurs were perfectly happy before the Carnian-Norian transition," Montanez said. There's no indication that the dinosaurs appeared and wiped out other animals, which has been the prevailing hypothesis for the origin of dinosaurs based on fossils from North America and elsewhere in the world.

It may be that there are missing pieces from the fossil records elsewhere, Montanez said, noting that, "nowhere else is this well dated."

UC Davis


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A new scientific study shows that debris coverage –– pebbles, rocks, and debris from surrounding mountains –– may be a missing link in the understanding of the decline of glaciers. Debris is distinct from soot and dust, according to the scientists.

Melting of glaciers in the Himalayan Mountains affects water supplies for hundreds of millions of people living in South and Central Asia. Experts have stated that global warming is a key element in the melting of glaciers worldwide.

Bodo Bookhagen, assistant professor in the Department of Geography at UC Santa Barbara, co-authored a paper on this topic in Nature Geoscience, published this week. The first author is Dirk Scherler, Bookhagen's graduate student from Germany, who performed part of this research while studying at UCSB.

"With the aid of new remote-sensing methods and satellite images, we identified debris coverage to be an important contributor to glacial advance and retreat behaviors," said Bookhagen. "This parameter has been almost completely neglected in previous Himalayan and other mountainous region studies, although its impact has been known for some time."

The finding is one more element in a worldwide political controversy involving global warming. "Controversy about the current state and future evolution of Himalayan glaciers has been stirred up by erroneous reports by the Intergovernmental Panel on Climate Change (IPCC)," according to the paper.

"There is no ‘stereotypical' Himalayan glacier," said Bookhagen. "This is in clear contrast to the IPCC reports that lumps all Himalayan glaciers together."

Bookhagen noted that glaciers in the Karakoram region of Northwestern Himalaya are mostly stagnating. However, glaciers in the Western, Central, and Eastern Himalaya are retreating, with the highest retreat rates –– approximately 8 meters per year –– in the Western Himalayan Mountains. The authors found that half of the studied glaciers in the Karakoram region are stable or advancing, whereas about two-thirds are in retreat elsewhere throughout High Asia. This is in contrast to the prevailing notion that all glaciers in the tropics are retreating.

Bookhagen explained the difference between debris and coverage by soot and dust on glaciers: "The debris cover has the opposite effect of soot and dust on glaciers. Debris coverage thickness above 2 centimeters, or about a half an inch, ‘shields' the glacier and prevents melting. This is the case for many Himalayan glaciers that are surrounded by towering mountains that almost continuously shed pebbles, debris, and rocks onto the glacier."

Thus, glaciers in the steep Himalaya are not only affected by temperature and precipitation, but also by debris coverage, and have no uniform and less predictable response, explained the authors. The debris coverage may be one of the missing links to creating a more coherent picture of glacial behavior throughout all mountains. The scientists contrast this Himalayan glacial study with glaciers from the gently dipping, low-relief Tibetan Plateau that have no debris coverage. Those glaciers behave in a different way, and their frontal changes can be explained by temperature and precipitation changes.

Bookhagen described results of another of his recent studies on this topic. He said that one of the key findings was that the Western Himalaya, including the Indus catchment and regions in Northern Pakistan and Northwestern India, depend heavily on seasonal snow and glacial melt waters, while Central Himalayan regions –– Western India and Nepal –– mostly depend on monsoonal rainfall.

The smaller seasonal water storage space in the Central Himalaya, which has only steep glaciers and no large snow fields, makes this region much more vulnerable to shifts in monsoonal strength and to glacial melting, explained Bookhagen. River discharge in these regions is crucial to sustain agriculture, hydropower, and drinking water. If the Indian monsoon season is weaker because of global atmospheric changes such as El Niño, then Central Nepal must primarily rely on water coming from the seasonal melting of glaciers and the small amount of snowmelt that is available.

"Retreating glaciers, and thus a reduction of seasonal water storage in this region, have a large impact on hundreds of millions of people living in the downstream section of these rivers," said Bookhagen. "The mitigation and adaptation strategies in the Himalaya Mountains thus need to take into account the spatial climatic and topographic variability. There is no regional solution, but only different local strategies to the future water shortage. The geographic setting of High Asia poses political difficulties as future water treaties need to be carefully evaluated."

(Photo: Bodo Bookhagen, UCSB)





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