Monday, 30 September 2013
Sep. 25, 2013 — Oxygen appeared in the atmosphere up to 700 million years earlier than we previously thought, according to research published today in the journal Nature, raising new questions about the evolution of early life.Researchers from the University of Copenhagen and University of British Columbia examined the chemical composition of three-billion-year-old soils from South Africa -- the oldest soils on Earth -- and found evidence for low concentrations of atmospheric oxygen. Previous research indicated that oxygen began accumulating in the atmosphere only about 2.3 billion years ago during a dynamic period in Earth's history referred to as the Great Oxygenation Event.
"We've always known that oxygen production by photosynthesis led to the eventual oxygenation of the atmosphere and the evolution of aerobic life," says Sean Crowe, co-lead author of the study and an assistant professor in the Departments of Microbiology and Immunology, and Earth, Ocean and Atmospheric Sciences at UBC.
"This study now suggests that the process began very early in Earth's history, supporting a much greater antiquity for oxygen producing photosynthesis and aerobic life," says Crowe, who conducted the research while a post-doctoral fellow at Nordic Center for Earth Evolution at the University of Southern Denmark in partnership with the centre's director Donald Canfield.
There was no oxygen in the atmosphere for at least hundreds of millions of years after Earth formed. Today, Earth's atmosphere is 20 per cent oxygen thanks to photosynthetic bacteria that, like trees and other plants, consume carbon dioxide and release oxygen. The bacteria laid the foundation for oxygen breathing organisms to evolve and inhabit the planet.
"These findings imply that it took a very long time for geological and biological processes to conspire and produce the oxygen rich atmosphere we now enjoy," says Lasse Døssing, the other lead scientist on the study, from the University of Copenhagen
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Sep. 25, 2013 — A team of Stanford engineers has built a basic computer using carbon nanotubes, a semiconductor material that has the potential to launch a new generation of electronic devices that run faster, while using less energy, than those made from silicon chipsThis unprecedented feat culminates years of efforts by scientists around the world to harness this promising material.
The achievement is reported today in an article on the cover of Nature Magazine written by Max Shulaker and other doctoral students in electrical engineering. The research was led by Stanford professors Subhasish Mitra and H.S. Philip Wong.
"People have been talking about a new era of carbon nanotube electronics moving beyond silicon," said Mitra, an electrical engineer and computer scientist and Chambers Faculty Scholar of Engineering. "But there have been few demonstrations of complete digital systems using this exciting technology. Here is the proof."
Experts say the Stanford achievement will galvanize efforts to find successors to silicon chips, which could soon encounter physical limits that might prevent them from delivering smaller, faster, cheaper electronic devices.
"Carbon nanotubes (CNTs) have long been considered as a potential successor to the silicon transistor," said Professor Jan Rabaey, a world expert on electronic circuits and systems at UC Berkeley.
But until now it hasn't been clear that CNTs could fulfill those expectations.
"There is no question that this will get the attention of researchers in the semiconductor community and entice them to explore how this technology can lead to smaller, more energy-efficient processors in the next decade," Rabaey said.
Mihail Roco, senior advisor for Nanotechnology at the National Science Foundation, called the Stanford work "an important, scientific breakthrough."
Max Shulaker, doctoral student in electrical engineering at Stanford University, holds a wafer filled with carbon nanotube computers (CNTs). To his left, a basic CNT computer utilizing this technology is sandwiched beneath a probe card to input and output signals. (Norbert von der Groeben)
It was roughly 15 years ago that carbon nanotubes were first fashioned into transistors, the on-off switches at the heart of digital electronic systems.
But a bedeviling array of imperfections in these carbon nanotubes has long frustrated efforts to build complex circuits using CNTs.
Professor Giovanni De Micheli, director of the Institute of Electrical Engineering at École Polytechnique Fédérale de Lausanne in Switzerland, highlighted two key contributions the Stanford team has made to this worldwide effort.
"First, they put in place a process for fabricating CNT-based circuits," De Micheli said. "Second, they built a simple but effective circuit that shows that computation is doable using CNTs."
As Mitra said: "It's not just about the CNT computer. It's about a change in directions that shows you can build something real using nanotechnologies that move beyond silicon and its cousins."
Why worry about a successor to silicon?
Such concerns arise from the demands that designers place upon semiconductors and their fundamental workhorse unit, those on-off switches known as transistors.
For decades, progress in electronics has meant shrinking the size of each transistor to pack more transistors on a chip. But as transistors become tinier they waste more power and generate more heat -- all in a smaller and smaller space, as evidenced by the warmth emanating from the bottom of a laptop.
Many researchers believe that this power-wasting phenomenon could spell the end of Moore's Law, named for Intel Corp. co-founder Gordon Moore, who predicted in 1965 that the density of transistors would double roughly every two years, leading to smaller, faster and, as it turned out, cheaper electronics.
But smaller, faster and cheaper has also meant smaller, faster and hotter.
"Energy dissipation of silicon-based systems has been a major concern," said Anantha Chandrakasan, head of electrical engineering and computer science at MIT and a world leader in chip research. He called the Stanford work "a major benchmark" in moving CNTs toward practical use.
CNTs are long chains of carbon atoms that are extremely efficient at conducting and controlling electricity. They are so thin -- thousands of CNTs could fit side by side in a human hair -- that it takes very little energy to switch them off, according to Wong, co-author of the paper and the Williard R. and Inez Kerr Bell Professor at Stanford.
"Think of it as stepping on a garden hose," Wong said. "The thinner the hose, the easier it is to shut off the flow."
In theory, this combination of efficient conductivity and low-power switching make carbon nanotubes excellent candidates to serve as electronic transistors.
"CNTs could take us at least an order of magnitude in performance beyond where you can project silicon could take us," Wong said.
But inherent imperfections have stood in the way of putting this promising material to practical use.
First, CNTs do not necessarily grow in neat parallel lines, as chipmakers would like.
Over time, researchers have devised tricks to grow 99.5 percent of CNTs in straight lines. But with billions of nanotubes on a chip, even a tiny degree of misaligned tubes could cause errors, so that problem remained.
A second type of imperfection has also stymied CNT technology.
Depending on how the CNTs grow, a fraction of these carbon nanotubes can end up behaving like metallic wires that always conduct electricity, instead of acting like semiconductors that can be switched off.
Since mass production is the eventual goal, researchers had to find ways to deal with misaligned and/or metallic CNTs without having to hunt for them like needles in a haystack.
"We needed a way to design circuits without having to look for imperfections or even know where they were," Mitra said.
The Stanford paper describes a two-pronged approach that the authors call an "imperfection-immune design."
To eliminate the wire-like or metallic nanotubes, the Stanford team switched off all the good CNTs. Then they pumped the semiconductor circuit full of electricity. All of that electricity concentrated in the metallic nanotubes, which grew so hot that they burned up and literally vaporized into tiny puffs of carbon dioxide. This sophisticated technique was able to eliminate virtually all of the metallic CNTs in the circuit at once.
Bypassing the misaligned nanotubes required even greater subtlety.
So the Stanford researchers created a powerful algorithm that maps out a circuit layout that is guaranteed to work no matter whether or where CNTs might be askew.
"This 'imperfections-immune design' (technique) makes this discovery truly exemplary," said Sankar Basu, a program director at the National Science Foundation.
The Stanford team used this imperfection-immune design to assemble a basic computer with 178 transistors, a limit imposed by the fact that they used the university's chip-making facilities rather than an industrial fabrication process.
Their CNT computer performed tasks such as counting and number sorting. It runs a basic operating system that allows it to swap between these processes. In a demonstration of its potential, the researchers also showed that the CNT computer could run MIPS, a commercial instruction set developed in the early 1980s by then Stanford engineering professor and now university President John Hennessy.
Though it could take years to mature, the Stanford approach points toward the possibility of industrial-scale production of carbon nanotube semiconductors, according to Naresh Shanbhag, a professor at the University of Illinois at Urbana-Champaign and director of SONIC, a consortium for next-generation chip design research.
"The Wong/Mitra paper demonstrates the promise of CNTs in designing complex computing systems," Shanbhag said, adding that this "will motivate researchers elsewhere" toward greater efforts in chip design beyond silicon.
"These are initial necessary steps in taking carbon nanotubes from the chemistry lab to a real environment," said Supratik Guha, director of physical sciences for IBM's Thomas J. Watson Research Center and a world leader in CNT research.
Professor Georges Gielen, Vice Rector of Science, Engineering and Technology at the Katholieke Universiteit in Leuven, Belgium, said the next generation of electronics, including wireless sensor networks and other tiny devices envisioned as part of the "Internet of things," require low-power, high performance chips.
"A big challenge for the massive deployment of such systems is the powering: wire line supply is impossible, batteries often not practical or affordable," Gielen said, adding: "CNTs are an emerging technology that offer the potential to cut down significantly, by orders of magnitude, on the power consumption of electronics compared to today's state-of-the-art technologies. If this materializes, this will be a major breakthrough for all the mentioned and future applications.
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Sep. 25, 2013 — Astronomers have uncovered the strange case of a neutron star with the peculiar ability to transform from a radio pulsar into an X-ray pulsar and back again. This star's capricious behavior appears to be fueled by a nearby companion star and may give new insights into the birth of millisecond pulsars.
"What we're seeing is a star that is the cosmic equivalent of 'Dr. Jekyll and Mr. Hyde,' with the ability to change from one form to its more intense counterpart with startling speed," said Scott Ransom, an astronomer at the National Radio Astronomy Observatory (NRAO) in Charlottesville, Va. "Though we have known that X-ray binaries -- some of which are observed as X-ray pulsars -- can evolve over millions of years to become rapidly spinning radio pulsars, we were surprised to find one that seemed to swing so quickly between the two."
Neutron stars are the superdense remains of massive stars that have exploded as supernovas. This particular neutron star, dubbed IGR J18245-2452, is located about 18,000 light-years from Earth in the constellation Sagittarius in a cluster of stars known as M28. It was first identified as a millisecond radio pulsar in 2005 with the National Science Foundation's Robert C. Byrd Green Bank Telescope (GBT) and then later rediscovered as an X-ray pulsar by another team of astronomers in 2013. The two teams eventually realized they were observing the same object, even though it was behaving very differently depending on when it was observed. Additional observations and archival data from other telescopes confirmed the on-again, off-again cycle of X-ray and radio pulsations.
"Various observations of one particular star over the years and with different telescopes have revealed vastly different things -- at one time a pulsar and the other an X-ray binary," said Alessandro Papitto of the Institute of Space Sciences (Consejo Superior de Investigaciones Cientificas -- Institut d'Estudis Espacials de Catalunya) in Barcelona, Spain, and lead author of a paper published in the journal Nature. "This was particularly intriguing because radio pulses don't come from an X-ray binary and the X-ray source has to be long gone before radio signals can emerge."
The answer to this puzzle was found in the complex interplay between the neutron star and its nearby companion.
X-ray binaries, as their name implies, occur in a two-star system in which a neutron star is accompanied by a more normal, low-mass star. The smaller but considerably more massive neutron star can draw off material from its companion, forming a flattened disk of gas around the neutron star. Gradually, as this material swirls down to the surface of the neutron star, it becomes superheated and generates intense X-rays.
Astronomers believed that this process of accretion continued, mostly unabated, for millions of years. Eventually, the material would run out and the accretion would stop, along with the X-ray emission.
Without the influx of new material, the neutron star's powerful magnetic fields are able to generate beams of radio waves that sweep across space as the star rotates, giving the pulsar its characteristic lighthouse-like appearance.
Most radio pulsars rotate a few tens of times each second and -- if left to their own devices -- will slow down over many thousands of years. If the neutron star begins life as an X-ray binary, however, the matter accumulating on its surface causes the neutron star to "spin up," increasing its rate of rotation until it spins hundreds of times each second. When this accretion process stops, the result is a millisecond pulsar.
During their observations, the researchers detected outbursts of X-ray pulsations that went on for approximately one month and then abruptly stopped. Within a few days, the radio pulses once again emerged. These wild swings indicated that the material from the accretion disk was falling onto the neutron star in fits and starts, rather than in a long and constant stream as astronomers theorized.
An earlier study of another system with the GBT detected the first evidence of an accretion disk around a neutron star, which helped establish the link between low-mass X-ray binaries and pulsars.
The new data support this link but also show for the first time that the evolution process, which was thought to take perhaps millions of years, is actually more complex and can occur in episodic bursts that can last just a few days or weeks. "This not only demonstrates the evolutionary link between accretion and rotation-powered millisecond pulsars," said Ransom, "but also that some systems can swing between the two states on very short timescales."
The X-ray source was discovered by the International Gamma-Ray Astrophysics Laboratory (INTEGRAL) and follow-up X-ray observations were performed by the XMM-Newton, Swift, and Chandra satellites. Radio observations were made by the GBT, the Parkes radio telescope, the Australia Telescope Compact Array, and the Westerbork Synthesis Radio Telescope.
The National Radio Astronomy Observatory is a facility of the National Science Foundation, operated under cooperative agreement by Associated Universities, Inc.
Sep. 24, 2013 — The fossilised remains of a reptile closely related to lizards are the oldest yet to be discovered.Two new fossil jaws discovered in Vellberg, Germany provide the first direct evidence that the ancestors of lizards, snakes and tuatara (known collectively as lepidosaurs) were alive during the Middle Triassic period -- around 240 million years ago.
The new fossil finds predate all other lepidosaur records by 12 million years. The findings are published in BMC Evolutionary Biology.
The international team of scientists who dated the fossil jaws have provided evidence that lepidosaurs first appeared after the end-Permian mass extinction event, a period when fauna began to recover and thrive in the more humid climate.
Lead author Dr Marc Jones, who conducted the research at UCL, explained: "The Middle Triassic represents a time when the world has recovered from the Permian mass extinction but is not yet dominated by dinosaurs. This is also when familiar groups, such as frogs and lizards, may have first appeared."
The small teeth and lightly built jaws suggest that the extinct animal preyed on small insects. The new fossils are most closely related to the tuatara, a lizard-like reptile.
Tuatara can be found on 35 islands lying off the coast of New Zealand and were recently reintroduced to the mainland. However, they are the sole survivors of a group that was once as globally widespread as lizards are today. Tuatara feed on beetles, spiders, crickets and small lizards, also enjoying the occasional sea bird.
Today, there are over 9,000 species of lizards, snakes and tuatara. Knowing when the common ancestor of this grouping first appeared is crucial for understanding the ecological context in which it first evolved as well as its subsequent diversification.
To establish the age of the fossil remains, biologists use a dating technique known as a "molecular clock." This method compares the amount of genetic divergence between living animals, caused by changes in their DNA sequences that have accumulated since they split from a common ancestor. These mutations occur fairly regularly, ticking along at a clock-like rate. However, for the clock to convert genetic differences into geological time, it has to be calibrated using one or more fossils of known relationship and time.
Molecular clocks have been used by biologists to answer questions as important as when the first modern humans emerged, and when humans and chimpanzees shared a common ancestor. The new fossil jaws can improve molecular dating estimates of when reptiles began to diversify into snakes, lizard and tuatara, and when the first modern lizards inhabited the earth. Previous estimates have varied over a range of 64 million years and the team are keen to help narrow this down.
"Some previous estimates based on molecular data suggested that lizards first evolved 290 million years ago," said second author Cajsa Lisa Anderson, University of Gothenburg. "To a palaeontologist this seems way too old and our revised molecular analysis agrees with the fossils."
Revised molecular dating in light of this new fossil find now suggests lizards began to diversify into most of the modern groups we recognise today, such as geckos and skinks, less than 150 million years ago in the Cretaceous period, following continental fragmentation.
The specimens were collected and initially identified by Professor Rainer Schoch from the Staatliches Museum für Naturkunde in Stuttgart, where the specimens are now registered.
Scientists anticipate that the Vellberg site will yield yet more fossil discoveries in the future, broadening our knowledge of the vertebrate fossil record.
Co-Author Professor Susan Evans, from the UCL Department of Cell and Developmental Biology, said: "The fossil record of small animals such as lizards and frogs is very patchy. Hopefully, this new fossil site in Germany will eventually give us a broader understanding of what was going on at this time.
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Tuesday, 24 September 2013
Sep. 23, 2013 — More than 83,000 volunteer citizen scientists. Over 16 million galaxy classifications. Information on more than 300,000 galaxies. This is what you get when you ask the public for help in learning more about our universe.
The project, named Galaxy Zoo 2, is the second phase of a crowdsourcing effort to categorize galaxies in our universe. Researchers say computers are good at automatically measuring properties such as size and color of galaxies, but more challenging characteristics, such as shape and structure, can currently only be determined by the human eye.
An international group of researchers, led by the University of Minnesota, has just produced a catalog of this new galaxy data. This catalog is 10 times larger than any previous catalog of its kind.
View examples of images categorized by citizen scientists athttp://z.umn.edu/galaxyimages.
"This catalog is the first time we've been able to gather this much information about a population of galaxies," said Kyle Willett, a physics and astronomy postdoctoral researcher in the University of Minnesota's College of Science and Engineering and the paper's lead author. "People all over the world are beginning to examine the data to gain a more detailed understanding of galaxy types."
Between Feb. 2009 and April 2010, more than 83,000 Galaxy Zoo 2 volunteers from around the world looked at images online gathered from the Sloan Digital Sky Survey. They answered questions about the galaxy, including whether it had spirals, the number of spiral arms present, or if it had galactic bars, which are long extended features that represent a concentration of stars. Each image was classified an average of 40-45 times to ensure accuracy. More than 16 million classifications of more than 300,000 galaxies were gathered representing about 57 million computer clicks.
When volunteers were asked why they got involved in the project, the most common answer was because they enjoyed contributing to science. Researchers estimate that the effort of the volunteers on this project represents about 30 years of full-time work by one researcher.
"With today's high-powered telescopes, we are gathering so many new images that astronomers just can't keep up with detailed classifications," said Lucy Fortson, a professor of physics and astronomy in the University of Minnesota's College of Science and Engineering and one of the co-authors of the research paper. "We could never have produced a data catalog like this without crowdsourcing help from the public."
Fortson said Galaxy Zoo 2 is similar to a census of the galaxies. With this new catalog, researchers now have a snapshot of the different types of galaxies as they are today. The next catalog will tell us about galaxies in the distant past. The catalogs together will let us understand how our universe is changing.
To help create the next catalog, volunteer citizen scientists continue to be needed for the project. To participate, visitwww.galaxyzoo.org. No special skills are needed, and volunteers can start classifying galaxies and helping the scientists within minutes of going to the website.
In addition to Fortson and Willett, other authors of the research paper include Chris Lintott, Oxford Astrophysics and Adler Planetarium; Steven Bamford, University of Nottingham; Karen Masters, Robert Nichol and Daniel Thomas, University of Portsmouth and South East Physics Network; Brooke Simmons and Robert Simpson, Oxford Astrophysics; Kevin Casteels, University of Barcelona; Edward Edmondson and Thomas Melvin, University of Portsmouth; Sugata Kaviraj, Oxford Astrophysics and University of Hertfordshire; William Keel, University of Alabama; M. Jordan Raddick, Johns Hopkins University; Kevin Schawinski, ETH Zurich; Ramin Skibba, University of California, San Diego; and Arfon Smith, Adler Planetarium.
The research was funded primarily by the National Science Foundation and the Leverhulme Trust.
Sep. 23, 2013 — The Fraunhofer Institute for Solar Energy Systems ISE, Soitec, CEA-Leti and the Helmholtz Center Berlin jointly announced today having achieved a new world record for the conversion of sunlight into electricity using a new solar cell structure with four solar subcells. Surpassing competition after only over three years of research, and entering the roadmap at world class level, a new record efficiency of 44.7% was measured at a concentration of 297 suns. This indicates that 44.7% of the solar spectrum's energy, from ultraviolet through to the infrared, is converted into electrical energy. This is a major step towards reducing further the costs of solar electricity and continues to pave the way to the 50% efficiency roadmap.Back in May 2013, the German-French team of Fraunhofer ISE, Soitec, CEA-Leti and the Helmholtz Center Berlin had already announced a solar cell with 43.6% efficiency. Building on this result, further intensive research work and optimization steps led to the present efficiency of 44.7%.
These solar cells are used in concentrator photovoltaics (CPV), a technology which achieves more than twice the efficiency of conventional PV power plants in sun-rich locations. The terrestrial use of so-called III-V multi-junction solar cells, which originally came from space technology, has prevailed to realize highest efficiencies for the conversion of sunlight to electricity. In this multi-junction solar cell, several cells made out of different III-V semiconductor materials are stacked on top of each other. The single subcells absorb different wavelength ranges of the solar spectrum.
"We are incredibly proud of our team which has been working now for three years on this four-junction solar cell," says Frank Dimroth, Department Head and Project Leader in charge of this development work at Fraunhofer ISE. "This four-junction solar cell contains our collected expertise in this area over many years. Besides improved materials and optimization of the structure, a new procedure called wafer bonding plays a central role. With this technology, we are able to connect two semiconductor crystals, which otherwise cannot be grown on top of each other with high crystal quality. In this way we can produce the optimal semiconductor combination to create the highest efficiency solar cells."
"This world record increasing our efficiency level by more than 1 point in less than 4 months demonstrates the extreme potential of our four-junction solar cell design which relies on Soitec bonding techniques and expertise," says André-Jacques Auberton-Hervé, Soitec's Chairman and CEO. "It confirms the acceleration of the roadmap towards higher efficiencies which represents a key contributor to competitiveness of our own CPV systems. We are very proud of this achievement, a demonstration of a very successful collaboration."
"This new record value reinforces the credibility of the direct semiconductor bonding approaches that is developed in the frame of our collaboration with Soitec and Fraunhofer ISE. We are very proud of this new result, confirming the broad path that exists in solar technologies for advanced III-V semiconductor processing," said Leti CEO Laurent Malier. Concentrator modules are produced by Soitec (started in 2005 under the name Concentrix Solar, a spin-off of Fraunhofer ISE). This particularly efficient technology is employed in solar power plants located in sun-rich regions with a high percentage of direct radiation. Presently Soitec has CPV installations in 18 different countries including Italy, France, South Africa and California
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Sep. 23, 2013 — The question of how human societies evolve from small groups to the huge, anonymous and complex societies of today has been answered mathematically, accurately matching the historical record on the emergence of complex states in the ancient world.Intense warfare is the evolutionary driver of large complex societies, according to new research from a trans-disciplinary team at the University of Connecticut, the University of Exeter in England, and the National Institute for Mathematical and Biological Synthesis (NIMBioS). The study appears this week as an open-access article in the journal Proceedings of the National Academy of Sciences.
The study's cultural evolutionary model predicts where and when the largest-scale complex societies arose in human history.
Simulated within a realistic landscape of the Afro-Eurasian landmass during 1,500 BCE to 1,500 CE, the mathematical model was tested against the historical record. During the time period, horse-related military innovations, such as chariots and cavalry, dominated warfare within Afro-Eurasia. Geography also mattered, as nomads living in the Eurasian Steppe influenced nearby agrarian societies, thereby spreading intense forms of offensive warfare out from the steppe belt.
The study focuses on the interaction of ecology and geography as well as the spread of military innovations and predicts that selection for ultra-social institutions that allow for cooperation in huge groups of genetically unrelated individuals and large-scale complex states, is greater where warfare is more intense.
While existing theories on why there is so much variation in the ability of different human populations to construct viable states are usually formulated verbally, by contrast, the authors' work leads to sharply defined quantitative predictions, which can be tested empirically.
The model-predicted spread of large-scale societies was very similar to the observed one; the model was able to explain two-thirds of the variation in determining the rise of large-scale societies.
"What's so exciting about this area of research is that instead of just telling stories or describing what occurred, we can now explain general historical patterns with quantitative accuracy. Explaining historical events helps us better understand the present, and ultimately may help us predict the future," said the study's co-author Sergey Gavrilets, NIMBioS director for scientific activities
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Sep. 22, 2013 — Scientists have moved closer to developing a universal flu vaccine after using the 2009 pandemic as a natural experiment to study why some people seem to resist severe illness.Researchers at Imperial College London asked volunteers to donate blood samples just as the swine flu pandemic was getting underway and report any symptoms they experienced over the next two flu seasons.
They found that those who avoided severe illness had more CD8 T cells, a type of virus-killing immune cell, in their blood at the start of the pandemic.
They believe a vaccine that stimulates the body to produce more of these cells could be effective at preventing flu viruses, including new strains that cross into humans from birds and pigs, from causing serious disease.
The findings are published in Nature Medicine.
Professor Ajit Lalvani from the National Heart and Lung Institute at Imperial College London, who led the study, said: "New strains of flu are continuously emerging, some of which are deadly, and so the Holy Grail is to create a universal vaccine that would be effective against all strains of flu."
Today's flu vaccines make the immune system produce antibodies that recognise structures on the surface of the virus to prevent infection with the most prevalent circulating strains. But they are usually one step behind as they have to be changed each year as new viruses with different surface structures evolve.
Previously, experimental models had suggested that T cells may protect against flu symptoms but until now this idea has not been tested in humans during a pandemic.
Professor Lalvani's team rapidly recruited 342 staff and students at Imperial to take part in their study in autumn 2009. The volunteers donated blood samples and were given nasal swabs. They were sent emails every three weeks asking them to fill in a survey about their health. If they experienced flu symptoms, they took a nasal swab and sent it back to the lab.
They found that those who fell more severely ill with flu had fewer CD8 T cells in their blood, and those who caught flu but had no symptoms or only mild symptoms had more of these cells.
Professor Lalvani said, "The immune system produces these CD8 T cells in response to usual seasonal flu. Unlike antibodies, they target the core of the virus, which doesn't change, even in new pandemic strains. The 2009 pandemic provided a unique natural experiment to test whether T cells could recognise, and protect us against, new strains that we haven't encountered before and to which we lack antibodies.
"Our findings suggest that by making the body produce more of this specific type of CD8 T cell, you can protect people against symptomatic illness. This provides the blueprint for developing a universal flu vaccine.
"We already know how to stimulate the immune system to make CD8 T cells by vaccination. Now that we know these T cells may protect, we can design a vaccine to prevent people getting symptoms and transmitting infection to others. This could curb seasonal flu annually and protect people against future pandemics.
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Sep. 23, 2013 — According to researchers from ETH Zurich and the University of Miami, some of the largest ocean eddies on Earth are mathematically equivalent to the mysterious black holes of space. These eddies are so tightly shielded by circular water paths that nothing caught up in them escapes.
The mild winters experienced in Northern Europe are thanks to the Gulf Stream, which makes up part of those ocean currents spanning the globe that impact on the climate. However, our climate is also influenced by huge eddies of over 150 kilometres in diameter that rotate and drift across the ocean. Their number is reportedly on the rise in the Southern Ocean, increasing the northward transport of warm and salty water. Intriguingly, this could moderate the negative impact of melting sea ice in a warming climate.
However, scientists have been unable to quantify this impact so far, because the exact boundaries of these swirling water bodies have remained undetectable. George Haller, Professor of Nonlinear Dynamics at ETH Zurich, and Francisco Beron-Vera, Research Professor of Oceanography at the University of Miami, have now come up with a solution to this problem. In a paper just published in the Journal of Fluid Mechanics, they develop a new mathematical technique to find water-transporting eddies with coherent boundaries.
The challenge in finding such eddies is to pinpoint coherent water islands in a turbulent ocean. The rotating and drifting fluid motion appears chaotic to the observer both inside and outside an eddy. Haller and Beron-Vera were able to restore order in this chaos by isolating coherent water islands from a sequence of satellite observations. To their surprise, such coherent eddies turned out to be mathematically equivalent to black holes.
No escape from the vortex
Black holes are objects in space with a mass so great that they attract everything that comes within a certain distance of them. Nothing that comes too close can escape, not even light. But at a critical distance, a light beam no longer spirals into the black hole. Rather, it dramatically bends and comes back to its original position, forming a circular orbit. A barrier surface formed by closed light orbits is called a photon sphere in Einstein's theory of relativity.
Haller and Beron-Vera discovered similar closed barriers around select ocean eddies. In these barriers, fluid particles move around in closed loops -- similar to the path of light in a photon sphere. And as in a black hole, nothing can escape from the inside of these loops, not even water.
It is precisely these barriers that help to identify coherent ocean eddies in the vast amount of observational data available. According to Haller, the very fact that such coherent water orbits exist amidst complex ocean currents is surprising.
Eddies as water taxis
Because black-hole-type ocean eddies are stable, they function in the same way as a transportation vehicle -- not only for micro-organisms such as plankton or foreign bodies like plastic waste or oil, but also for water with a heat and salt content that can differ from the surrounding water. Haller and Beron-Vera have verified this observation for the Agulhas Rings, a group of ocean eddies that emerge regularly in the Southern Ocean off the southern tip of Africa and transport warm, salty water northwest. The researchers identified seven Agulhas Rings of the black-hole type, which transported the same body of water without leaking for almost a year.
Haller points out that similar coherent vortices exist in other complex flows outside of the ocean. In this sense, many whirlwinds are likely to be similar to black holes as well. Even the Great Red Spot -- a stationary storm -- on the planet Jupiter could just be the most spectacular example of a black-hole type vortex . "Mathematicians have been trying to understand such peculiarly coherent vortices in turbulent flows for a very long time," explains Haller.
Notably, the first person to describe ocean eddies as coherent water islands may well have been the American writer, Edgar Allan Poe. In his story "A Descent into the Maelstrom," he envisioned a stable belt of foam around a maelstrom. This served as inspiration for Haller and Beron-Vera, who went on to find these belts -- the oceanic equivalent to photon spheres -- using sophisticated mathematical formulas. Their results are expected to help in resolving a number of oceanic puzzles, ranging from climate-related questions to the spread of environmental pollution patterns.
Eddy in the Gulf of Mexico
Just after the publication of Haller's and Beron-Vera's results, Josefina Olascoaga, also a Professor of Oceanography in Miami, tested their new mathematical method. She unexpectedly found a large, black-hole type eddy in the Gulf of Mexico. Olascoaga now uses her finding to assess the coherent transport of contamination from a possible future oil spill.
Sep. 23, 2013 — Using low-frequency laser pulses, a team of researchers has carried out the first measurements that reveal the detailed characteristics of a unique kind of magnetism found in a mineral called herbertsmithite.In this material, the magnetic elements constantly fluctuate, leading to an exotic state of fluid magnetism called a "quantum spin liquid." This is in contrast to conventional magnetism, found in materials called ferromagnets -- where all of the magnetic forces align in the same direction, reinforcing each other -- or antiferromagnets, where adjacent magnetic elements align in opposite directions, leading to complete cancellation of the material's overall magnetic field.
Although a spin-liquid state has previously been observed in herbertsmithite, there has never been a detailed analysis of how the material's electrons respond to light -- a key to determining which of several competing theories about the material is correct.
Now a team at MIT, Boston College and Harvard University has successfully carried out these measurements. The new analysis is reported in a paper in Physical Review Letters, co-authored by Nuh Gedik, the Biedenharn Career Development Associate Professor of Physics at MIT, graduate student Daniel Pilon, postdoc Chun Hung Lui and four others.
Their measurements, using laser pulses lasting just a trillionth of a second, reveal a signature in the optical conductivity of the spin-liquid state that reflects the influence of magnetism on the motion of electrons. This observation supports a set of theoretical predictions that have not previously been demonstrated experimentally. "We think this is good evidence," Gedik says, "and it can help to settle what has been a pretty big debate in spin-liquid research."
"Theorists have provided a number of theories on how a spin-liquid state could be formed in herbertsmithite," Pilon explains. "But to date there has been no experiment that directly distinguishes among them. We believe that our experiment has provided the first direct evidence for the realization of one of these theoretical models in herbertsmithite."
The concept of quantum spin liquids was first proposed in 1973, but the first direct evidence for such a material was only found within the last few years. The new measurements help to clarify the fundamental characteristics of this exotic system, which is thought to be closely related to the origins of high-temperature superconductivity.
Gedik says, "Although it is hard to predict any potential applications at this stage, basic research on this unusual phase of matter could help us to solve some very complicated problems in physics, particularly high-temperature superconductivity, which might eventually lead to important applications." In addition, Pilon says, "This work might also be useful for the development of quantum computing."
Leon Balents, a professor of physics at the University of California at Santa Barbara who was not involved in this work, says, "If the observed optical conductivity in these measurements is truly intrinsic, it is an important and exciting result, which will be very important in understanding the nature of the spin-liquid state."
Balents adds that further work is needed to confirm this result, but says "this is clearly an exciting and important measurement, which I hope will be pursued further by extending the frequency and magnetic field range in the future."
The work was supported by the U.S. Department of Energy, and also included Young Lee and Tian-Heng Han of MIT, David Shrekenhamer and Willie J. Padilla of Boston College, and graduate student Alex J. Frenzel of MIT and Harvard
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Sep. 22, 2013 — Data from NASA's Curiosity rover has revealed the Martian environment lacks methane. This is a surprise to researchers because previous data reported by U.S. and international scientists indicated positive detections.The roving laboratory performed extensive tests to search for traces of Martian methane. Whether the Martian atmosphere contains traces of the gas has been a question of high interest for years because methane could be a potential sign of life, although it also can be produced without biology.
"This important result will help direct our efforts to examine the possibility of life on Mars," said Michael Meyer, NASA's lead scientist for Mars exploration. "It reduces the probability of current methane-producing Martian microbes, but this addresses only one type of microbial metabolism. As we know, there are many types of terrestrial microbes that don't generate methane."
Curiosity analyzed samples of the Martian atmosphere for methane six times from October 2012 through June and detected none. Given the sensitivity of the instrument used, the Tunable Laser Spectrometer, and not detecting the gas, scientists calculate the amount of methane in the Martian atmosphere today must be no more than 1.3 parts per billion. That is about one-sixth as much as some earlier estimates. Details of the findings appear in the Thursday edition of Science Express.
"It would have been exciting to find methane, but we have high confidence in our measurements, and the progress in expanding knowledge is what's really important," said the report's lead author, Chris Webster of NASA's Jet Propulsion Laboratory in Pasadena, Calif. "We measured repeatedly from Martian spring to late summer, but with no detection of methane."
Webster is the lead scientist for spectrometer, which is part of Curiosity's Sample Analysis at Mars (SAM) laboratory. It can be tuned specifically for detection of trace methane. The laboratory also can concentrate any methane to increase the gas' ability to be detected. The rover team will use this method to check for methane at concentrations well below 1 part per billion.
Methane, the most abundant hydrocarbon in our solar system, has one carbon atom bound to four hydrogen atoms in each molecule. Previous reports of localized methane concentrations up to 45 parts per billion on Mars, which sparked interest in the possibility of a biological source on Mars, were based on observations from Earth and from orbit around Mars. However, the measurements from Curiosity are not consistent with such concentrations, even if the methane had dispersed globally.
"There's no known way for methane to disappear quickly from the atmosphere," said one of the paper's co-authors, Sushil Atreya of the University of Michigan, Ann Arbor. "Methane is persistent. It would last for hundreds of years in the Martian atmosphere. Without a way to take it out of the atmosphere quicker, our measurements indicate there cannot be much methane being put into the atmosphere by any mechanism, whether biology, geology, or by ultraviolet degradation of organics delivered by the fall of meteorites or interplanetary dust particles."
The highest concentration of methane that could be present without being detected by Curiosity's measurements so far would amount to no more than 10 to 20 tons per year of methane entering the Martian atmosphere, Atreya estimated. That is about 50 million times less than the rate of methane entering Earth's atmosphere.
Curiosity landed inside Gale Crater on Mars in August 2012 and is investigating evidence about habitable environments there. JPL manages the mission and built the rover for NASA's Science Mission Directorate in Washington. The rover's Sample Analysis at Mars suite of instruments was developed at NASA's Goddard Space Flight Center in Greenbelt, Md., with instrument contributions from Goddard, JPL and the University of Paris in France
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Sep. 22, 2013 — Since the discovery of the Van Allen radiation belts in 1958, space scientists have believed these belts encircling Earth consist of two doughnut-shaped rings of highly charged particles -- an inner ring of high-energy electrons and energetic positive ions and an outer ring of high-energy electrons.
In February of this year, a team of scientists reported the surprising discovery of a previously unknown third radiation ring -- a narrow one that briefly appeared between the inner and outer rings in September 2012 and persisted for a month.
In new research, UCLA space scientists have successfully modeled and explained the unprecedented behavior of this third ring, showing that the extremely energetic particles that made up this ring, known as ultra-relativistic electrons, are driven by very different physics than typically observed Van Allen radiation belt particles. The region the belts occupy -- ranging from about 1,000 to 50,000 kilometers above Earth's surface -- is filled with electrons so energetic they move close to the speed of light.
"In the past, scientists thought that all the electrons in the radiation belts around the Earth obeyed the same physics," said Yuri Shprits, a research geophysicist with the UCLA Department of Earth and Space Sciences. "We are finding now that radiation belts consist of different populations that are driven by very different physical processes."
Shprits, who is also an associate professor at Russia's Skolkovo Institute of Science and Technology, a new university co-organized by MIT, led the study, which is published Sept. 22 in the journalNature Physics.
The Van Allen belts can pose a severe danger to satellites and spacecraft, with hazards ranging from minor anomalies to the complete failure of critical satellites. A better understanding of the radiation in space is instrumental to protecting people and equipment, Shprits said.
Ultra-relativistic electrons -- which made up the third ring and are present in both the outer and inner belts -- are especially hazardous and can penetrate through the shielding of the most protected and most valuable satellites in space, noted Shprits and Adam Kellerman, a staff research associate in Shprits' group.
"Their velocity is very close to the speed of light, and the energy of their motion is several times larger than the energy contained in their mass when they are at rest," Kellerman said. "The distinction between the behavior of the ultra-relativistic electrons and those at lower energies was key to this study." Shprits and his team found that on Sept. 1, 2012, plasma waves produced by ions that do not typically affect energetic electrons "whipped out ultra-relativistic electrons in the outer belt almost down to the inner edge of the outer belt." Only a narrow ring of ultra-relativistic electrons survived this storm. This remnant formed the third ring.
After the storm, a cold bubble of plasma around Earth expanded to protect the particles in the narrow ring from ion waves, allowing the ring to persist. Shprits' group also found that very low-frequency electromagnetic pulsations that were thought to be dominant in accelerating and losing radiation belt electrons did not influence the ultra-relativistic electrons.
The Van Allen radiation belts "can no longer be considered as one consistent mass of electrons. They behave according to their energies and react in various ways to the disturbances in space," said Shprits, who was honored by President Obama last July with a Presidential Early Career Award for Scientists and Engineers.
"Ultra-relativistic particles move very fast and cannot be at the right frequency with waves when they are close to the equatorial plane," said Ksenia Orlova, a UCLA postdoctoral scholar in Shprits' group who is funded by NASA's Jack Eddy Fellowship. "This is the main reason the acceleration and scattering into the atmosphere of ultra-relativistic electrons by these waves is less efficient."
"This study shows that completely different populations of particles exist in space that change on different timescales, are driven by different physics and show very different spatial structures," Shprits said.
The team performed simulations with a model of Earth's radiation belts for the period from late August 2012 to early October 2012. The simulation, conducted using the physics of ultra-relativistic electrons and space weather conditions monitored by ground stations, matched the observations from NASA's Van Allen Probes mission extraordinarily well, confirming the team's theory about the new ring.
"We have a remarkable agreement between our model and observations, both encompassing a wide range of energies," said Dmitriy Subbotin, a former graduate student of Shprits and current UCLA staff research associate.
"I believe that, with this study, we have uncovered the tip of the iceberg," Shprits said. "We still need to fully understand how these electrons are accelerated, where they originate and how the dynamics of the belts is different for different storms."
Earth's radiation belts were discovered in 1958 by Explorer I, the first U.S. satellite that traveled to space
Friday, 20 September 2013
Sep. 18, 2013 — A team of researchers led by King's College London has for the first time identified a new gene which may have the ability to prevent HIV, the virus that causes AIDS, from spreading after it enters the body.Published in Nature today, the study is the first to identify a role for the human MX2 gene in inhibiting HIV. Researchers say this gene could be a new target for effective, less toxic treatments where the body's own natural defence system is mobilised against the virus.
The work was funded by the Medical Research Council and the National Institute for Health Research (NIHR) Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London. The study was also supported by the Wellcome Trust and European Commission.
Scientists carried out experiments on human cells in the lab, introducing the virus to two different cell lines and observing the effects. In one cell line the MX2 gene was expressed or 'switched on', and in the other it was not, or 'silenced'. They saw that in the cells where MX2 was silenced, the virus replicated and spread. In the cells where the MX2 gene was expressed, the virus was not able to replicate and new viruses were not produced.
The work was led by Dr Caroline Goujon and Professor Mike Malim at the Department of Infectious Diseases, King's College London. Professor Malim said: 'This is an extremely exciting finding which advances our understanding of how HIV virus interacts with the immune system and opens up opportunities to develop new therapies to treat the disease. Until now we knew very little about the MX2 gene, but now we recognise both its potent anti-viral function and a key point of vulnerability in the life cycle of HIV.
'Developing drugs to stimulate the body's natural inhibitors is a very important approach because you are triggering a natural process and therefore won't have the problem of drug resistance. There are two possible routes -- it may be possible to develop either a molecule that mimics the role of MX2 or a drug which activates the gene's natural capabilities.
'Although people with HIV are living longer, healthier lives with the virus thanks to current effective treatments, they can often be toxic for the body and drug resistance can become an issue with long-term use. It is important to continue to find new ways of mobilising the body's natural defence systems and this gene appears to be a key player in establishing viral control in people with HIV.
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Sep. 18, 2013 — Physicists have created a crystal-like arrangement of ultracold gas molecules that can swap quantum "spin" properties with nearby and distant partners. The novel structure might be used to simulate or even invent new materials that derive exotic properties from quantum spin behavior, for electronics or other practical applications.Described in a Nature paper posted online on Sept. 18, 2013, the JILA* experiment is the first to record ultracold gas molecules exchanging spins at a distance, a behavior that may be similar to that of intriguing solids such as "frustrated" magnets with competing internal forces, or high-temperature superconductors, which transmit electricity without resistance. The new results build on the same JILA team's prior creation of the first molecular quantum gases and demonstrations of ultracold chemistry.
"One of the main thrusts for our cold molecules research was to realize this interaction, so this is a major breakthrough," NIST/JILA Fellow Jun Ye says. "We can now explore very exotic new phases of quantum systems." NIST/JILA Fellow Deborah Jin points out that "these interactions are advantageous for creating models of quantum magnetism because they do not require the molecules to move around" the crystal structure.
The new JILA crystal has advantages over other experimental quantum simulators, which typically use atoms. Molecules, made of two or more atoms, have a broader range of properties, and thus, might be used to simulate more complex materials. Jin and Ye are especially interested in using the structure to create new materials not found in nature. An example might be topological insulators -- a hot topic in physics -- which might transmit data encoded in various spin patterns in future transistors, sensors or quantum computers.
The molecules used in the JILA experiments are made of one potassium atom bonded to one rubidium atom. The molecules are polar, with a positive electric charge at the rubidium end and a negative charge at the potassium end. This feature means the molecules can interact strongly and can be controlled with electric fields.
In the latest experiment, about 20,000 molecules were trapped in an optical lattice, an ordered pattern that looks like a stack of egg cartons created by intersecting laser beams. The lattice was only partly filled, with about one molecule per every 10 lattice wells. The lattice suppressed the molecules' travel and chemical reactions, allowing their internal properties to guide interactions.
The JILA team used microwave pulses to manipulate the molecules' spins, or natural rotations around an axis -- similar to a spinning top -- to create a "superposition" of two opposite spins at the same time. Scientists then observed oscillating patterns in the average spin of all the molecules, as well as a falloff or decay in the spin signal over time, indicating the molecules were swapping spins.
Scientists calculated the interaction energy that each molecule experiences with all other molecules in the lattice, with the energy intensity depending on the distance and angle between pairs (see graphic). JILA theorist Ana Maria Ray's modeling of spin oscillations and time periods agreed with the experimental measurements. Ye says the spin-swapping interactions "entangle" the molecules, a signature feature of the quantum world that links the properties of physically separated particles.
The results are expected to open up a new field in which scientists create customized molecular spin models in solid-like structures held in place by the lattice. JILA scientists plan to fill the lattice more fully and add an external electric field to increase the variety of spin models that can be created.
*JILA is a joint institute of the National Institute of Standards and Technology (NIST) and the University of Colorado Boulder. The research was funded by NIST, the National Science Foundation, the Air Force Office of Scientific Research, the Army Research Office, the Department of Energy and the Defense Advanced Research Projects Agency
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Sep. 18, 2013 — Embryonic stem cells have the enormous potential to treat and cure many medical problems. That is why the discovery that induced embryonic-like stem cells can be created from skin cells (iPS cells) was rewarded with a Nobel Prize in 2012. But the process has remained frustratingly slow and inefficient, and the resulting stem cells are not yet ready for medical use. Research in the lab of the Weizmann Institute's Dr. Yaqub Hanna, which appears today in Nature, dramatically changes that: He and his group revealed the "brake" that holds back the production of stem cells, and found that releasing this brake can both synchronize the process and increase its efficiency from around 1% or less today to 100%. These findings may help facilitate the production of stem cells for medical use, as well as advancing our understanding of the mysterious process by which adult cells can revert back into their original, embryonic state.Embryonic stem cells are those that have not undergone any "specialization"; thus they can give rise to any type of cell in the body. This is what makes them so valuable: They can be used, among other things, to repair damaged tissue, treat autoimmune disease and even grow transplant organs. Using stem cells taken from embryos is problematic because of availability and ethical concerns, but the hopes for their use were renewed in 2006, when a team led by Shinya Yamanaka of Kyoto University discovered that it is possible to "reprogram" adult cells. The resulting cells, called "induced pluripotent stem cells" (iPSCs), are created by inserting four genes into their DNA. Despite this breakthrough, the reprograming process is fraught with difficulty: It can take up to four weeks; the timing is not coordinated among the cells; and less than one percent of the treated cells actually end up becoming stem cells.
Hanna and his team asked: What is the main obstacle -- or obstacles -- that prevent successful reprograming in the majority of cells? In his postdoctoral research, Hanna had employed mathematical models to show that a single obstacle was responsible. Of course in biology, Hanna is the first to admit, experimental proof is required to back up the models. The present study not only provides the proof, it reveals the identity of that single obstacle and shows that removing it can dramatically improve reprograming.
Hanna's group, led by Dr. Noa Novershtern, Yoach Rais, Asaf Zviran and Shay Geula of the Molecular Genetics Department, together with members of the genomics unit of the Institute's Israel Structural Proteomics Center, looked at a certain protein, called MBD3, whose function was unknown. MBD3 had caught their attention because it is expressed in every cell in the body, at every stage of development. This is quite rare: In general, most types of proteins are produced in specific cells, at specific times, for specific functions. The team found that there is one exception to the rule of universal expression of this protein: the first three days after conception. These are exactly the three days in which the fertilized egg begins dividing, and the nascent embryo is a growing ball of pluripotent stem cells that will eventually supply all the cell types in the body. Starting on the fourth day, differentiation begins and the cells already start to lose their pluripotent status. And that is just when the MBD3 proteins first appear.
This finding has significant implications for the producing iPSCs for medical use. Yamanaka used viruses to insert the four genes but, for safety reasons, these are not used in reprograming cells to be used in patients. This gives the process an even lower success rate of only around a tenth of a percent. The researchers showed that removing MBD3 from the adult cells can improve efficiency and speed the process by several orders of magnitude. The time needed to produce the stem cells was shortened from four weeks to eight days. As an added bonus, since the cells all underwent the reprograming at the same rate, the scientists will now be able, for the first time, to actually follow it step by step and reveal its mechanisms of operation. Hanna points out that his team's achievement was based on research into the natural pathways of embryonic development: "Scientists investigating reprograming can benefit from a deeper understanding of how embryonic stem cells are produced in nature. After all, nature still makes them best, in the most efficient manner.
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Sep. 18, 2013 — California biologists have discovered four new species of reclusive legless lizards living in some of the most marginal habitat in the state: a vacant lot in downtown Bakersfield, among oil derricks in the lower San Joaquin Valley, on the margins of the Mojave desert, and at the end of one of the runways at LAX."This shows that there is a lot of undocumented biodiversity within California," said Theodore Papenfuss, a reptile and amphibian expert, or herpetologist, with UC Berkeley's Museum of Vertebrate Zoology, who discovered and identified the new species with James Parham of California State University, Fullerton. The discoveries raise the number of California legless lizard species from one to five.
The herpetologists named the new snake-like lizards after four legendary UC Berkeley scientists: museum founder Joseph Grinnell, paleontologist Charles Camp, philanthropist and amateur scientist Annie Alexander and herpetologist Robert C. Stebbins, at 98 the only one of the group still alive.
"These are animals that have existed in the San Joaquin Valley, separate from any other species, for millions of years, completely unknown," said Parham, who obtained his doctorate from Berkeley and is now curator of paleontology at the John D. Cooper Archaeology and Paleontology Center. "If you want to preserve biodiversity, it is the really distinct species like these that you want to preserve."
Papenfuss and Parham reported their discovery this month in the journal Breviora, a publication of the Museum of Comparative Zoology at Harvard University.
Legless lizards, represented by more than 200 species worldwide, are well-adapted to life in loose soil, Papenfuss said. Millions of years ago, lizards on five continents independently lost their limbs in order to burrow more quickly into sand or soil, wriggling like snakes. Some still have vestigial legs. Though up to eight inches in length, the creatures are seldom seen because they live mostly underground, eating insects and larvae, and may spend their lives within an area the size of a dining table. Most are discovered in moist areas when people overturn logs or rocks.
Herping the Central Valley
For the past 15 years, Papenfuss and Parham have scoured the state for new species, suspecting that the fairly common California legless lizard (Anniella pulchra), the only legless lizard in the U.S. West, had at least some relatives. They discovered one new species -- yellow-bellied like its common cousin -- under leaf litter in protected dunes west of Los Angeles International Airport. They named that species A. stebbinsi, because Stebbins grew up and developed an early interest in natural history in the nearby Santa Monica Mountains.
Because many sandy, loamy areas, including dunes and desert areas, offer little cover for lizards if they emerge, Papenfuss distributed thousands of pieces of cardboard throughout the state in areas likely to host the lizard. He returned year after year to see if lizards were using the moist, cool areas under the cardboard as resting or hunting grounds.
This led to the discovery of a silver-bellied species near Fellows in the oil fields around Taft, which they named A. alexanderae after Annie Alexander, who endowed the UC Berkeley museum in 1908 and added 20,000 specimens to its collections. The herpetologists found another species in three isolated, arid canyons on the edge of the Mojave Desert just below and east of Walker Pass in the Sierra Nevada and named it A. campi after Charles Camp, because of his early-career discovery of the Mt. Lyell salamander in the Sierra. The purple-bellied fourth was found in three vacant lots in downtown Bakersfield, though only one of those lots remains: the others have been bulldozed and developed. The biologists named that speciesA. grinnelli after Joseph Grinnell, who in 1912 first noted habitat destruction around Bakersfield from agriculture and oil drilling.
Interestingly, all these species had been collected before and were in collections around California, but when preserved in alcohol, the lizards lose their distinctive color and look identical. Papenfuss and Parham identified the species through genetic profiling, but they subsequently found ways to distinguish them from one another via belly color, number and arrangement of scales, and number of vertebrae. However, two species -- the previously known common legless lizard of Northern California and the newly named southern species found at LAX and apparently broadly distributed south of the Tehachapi Mountains -- remain indistinguishable except by genetic tests or, now, the location where they are found.
Species of special concern
Papenfuss and Parham are working with the California Department of Fish and Wildlife (CDFW) to determine whether the lizards need protected status. Currently, the common legless lizard is listed by the state as a species of special concern.
"These species definitely warrant attention, but we need to do a lot more surveys in California before we can know whether they need higher listing," Parham said.
Papenfuss noted that two of the species are within the range of the blunt-nosed leopard lizard, which is listed as an endangered species by both the federal and state governments.
"On one hand, there are fewer legless lizards than leopard lizards, so maybe these two new species should be given special protection," he said. "On the other hand, there may be ways to protect their habitat without establishing legal status. They don't need a lot of habitat, so as long as we have some protected sites, they are probably OK."
Papenfuss says they are not yet in danger of going extinct, since he has found some of the lizards in protected reserves operated by the CDFW, the U.S. Bureau of Land Management and a private water reserve outside Bakersfield, in addition to the El Segundo Dunes near LAX
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Sep. 19, 2013 — A team of astronomers has discovered enormous arms of hot gas in the Coma cluster of galaxies by using NASA's Chandra X-ray Observatory and ESA's XMM-Newton. These features, which span at least half a million light years, provide insight into how the Coma cluster has grown through mergers of smaller groups and clusters of galaxies to become one of the largest structures in the Universe held together by gravity.A new composite image, with Chandra data in pink and optical data from the Sloan Digital Sky Survey appearing in white and blue, features these spectacular arms. In this image, the Chandra data have been processed so extra detail can be seen.
The X-ray emission is from multimillion-degree gas and the optical data shows galaxies in the Coma Cluster, which contain only about one-sixth the mass in hot gas. Only the brightest X-ray emission is shown here, to emphasize the arms, but the hot gas is present over the entire field of view.
Researchers think that these arms were most likely formed when smaller galaxy clusters had their gas stripped away by the head wind created by the motion of the cluster through the hot gas, in much the same way that the headwind created by a roller coaster blows the hats off riders.
Coma is an unusual galaxy cluster because it contains not one, but two giant elliptical galaxies near its center. These two giant elliptical galaxies are probably the vestiges from each of the two largest clusters that merged with Coma in the past. The researchers also uncovered other signs of past collisions and mergers in the data.
From their length, and the speed of sound in the hot gas (about 4 million km/hr), the newly discovered X-ray arms are estimated to be about 300 million years old, and they appear to have a rather smooth shape. This gives researchers some clues about the conditions of the hot gas in Coma. Most theoretical models expect that mergers between clusters like those in Coma will produce strong turbulence, like ocean water that has been churned by many passing ships. Instead, the smooth shape of these lengthy arms points to a rather calm setting for the hot gas in the Coma cluster, even after many mergers.
Large-scale magnetic fields are likely responsible for the small amount of turbulence that is present in Coma. Estimating the amount of turbulence in a galaxy cluster has been a challenging problem for astrophysicists. Researchers have found a range of answers, some of them conflicting, and so observations of other clusters are needed.
Two of the arms appear to be connected to a group of galaxies located about two million light years from the center of Coma. One or both of these arms connects to a larger structure seen in the XMM-Newton data, and spans a distance or at least 1.5 million light years. A very thin tail also appears behind one of the galaxies in Coma. This is probably evidence of gas being stripped from a single galaxy, in addition to the groups or clusters that have merged there.
These new results on the Coma cluster, which incorporate over six days worth of Chandra observing time, will appear in the September 20, 2013, issue of the journal Science. The first author of the paper is Jeremy Sanders from the Max Planck Institute for Extraterrestrial Physics in Garching, Germany. The co-authors are Andy Fabian from Cambridge University in the UK; Eugene Churazov from the Max Planck Institute for Astrophysics in Garching, Germany; Alexander Schekochihin from University of Oxford in the UK; Aurora Simionescu from Stanford University in Stanford, CA; Stephen Walker from Cambridge University in the UK and Norbert Werner from Stanford University in Stanford, CA
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Sep. 19, 2013 — Scientists at the Stanford University School of Medicine have shown how a protein fragment known as beta-amyloid, strongly implicated in Alzheimer's disease, begins destroying synapses before it clumps into plaques that lead to nerve cell death.Key features of Alzheimer's, which affects about 5 million Americans, are wholesale loss of synapses -- contact points via which nerve cells relay signals to one another -- and a parallel deterioration in brain function, notably in the ability to remember.
"Our discovery suggests that Alzheimer's disease starts to manifest long before plaque formation becomes evident," said Carla Shatz, PhD, professor of neurobiology and of biology and senior author of a study that will be published Sept. 20 in Science.
Investigators at Harvard University also contributed to the study. The research, conducted in mice and in human brain tissue, may help to explain the failures in recent years of large-scale clinical trials attempting to slow the progression of Alzheimer's by pharmacologically ridding the brain of amyloid plaques. It may also point the way to better treatments at earlier stages of the disease.
Beta-amyloid begins life as a solitary molecule but tends to bunch up -- initially into small clusters that are still soluble and can travel freely in the brain, and finally into the plaques that are hallmarks of Alzheimer's. The study showed for the first time that in this clustered form, beta-amyloid can bind strongly to a receptor on nerve cells, setting in motion an intercellular process that erodes their synapses with other nerve cells.
Synapses are the connections between nerve cells. They are essential to storing memories, processing thoughts and emotions, and planning and ordering how we move our bodies. The relative strength of these connections, moreover, can change in response to new experiences.
Using an experimental mouse strain that is highly susceptible to the synaptic and cognitive impairments of Alzheimer's disease, Shatz and her colleagues showed that if these mice lacked a surface protein ordinarily situated very close to synapses, they were resistant to the memory breakdown and synapse loss associated with the disorder. The study demonstrated for the first time that this protein, called PirB, is a high-affinity receptor for beta-amyloid in its "soluble cluster" form, meaning that soluble beta-amyloid clusters stick to PirB quite powerfully. That trips off a cascade of biochemical activities culminating in the destruction of synapses.
Shatz is the Sapp Family Provostial Professor, as well as the director of Bio-X, a large Stanford interdisciplinary consortium drawing on medical, engineering and biology faculty. She has been studying PirB for many years, but in a different context. In earlier work, Shatz explored the role of PirB in the brain using genetically engineered mice that lacked it. She discovered that PirB, previously thought to be used only by cells in the immune system, is also found on nerve cells in the brain, where it slows the ability of synapses to strengthen in proportion to the extent to which they are engaged, and actually promotes their weakening. Such brakes are desirable in the brain because too-easy synaptic strength-shifting could trigger untoward consequences like epilepsy.
In the new study, Shatz's team employed a different genetically engineered mouse strain whose genome contained mutant copies of two separate human genes. Each of these mutations is known to predispose individuals to Alzheimer's disease. When both mutations are present in mice, which ordinarily never develop amyloid plaques, the result is abundant amyloid plaque deposition with advancing age, as well as an eventual decline in performance on various tests of memory.
"I've always found it strange that these mice -- and, in fact, all the mouse models for Alzheimer's disease that we and other people study -- seem not to have any problems with memory until they get old," Shatz said. "These mice's brains have high levels of beta-amyloid at a very early age."
Shatz found herself wondering if there might be a more sensitive measure of beta-amyloid's early effects on young brains. A study she co-authored in 2012 demonstrated that a particular mouse brain region, whose constituent synapses are normally quite nimble at shifting their relative strengths in response to early-life experiences, showed no such flexibility in young Alzheimer's-prone mice. This suggested that subtle Alzheimer's-related effects might appear far earlier than plaques or memory loss do.
Now, Shatz wondered whether eliminating PirB from the Alzheimer's mouse strain could restore that flexibility. So her team bred the Alzheimer's-genes-carrying strain with the PirB-lacking strain to create hybrids. Experimentation showed that the brains of young "Alzheimer's mice" in which PirB was absent retained as much synaptic-strength-shifting flexibility as those of normal mice. PirB-lacking Alzheimer's mice also performed as well in adulthood as normal mice did on well-established tests of memory, while their otherwise identical PirB-expressing peers suffered substantial synapse and memory loss.
"The PirB-lacking Alzheimer's mice were protected from the beta-amyloid-generating consequences of their mutations," Shatz said. The question now was, why?
Taeho Kim, PhD, a postdoctoral scholar in Shatz's lab and the lead author of the new study, advanced a hypothesis he had cooked up in 2011 while describing his research to a captive audience of one -- his then-4-year-old son, whom he was driving to the Monterey Bay Aquarium: Maybe PirB and beta-amyloid were binding. This might cause PirB to stomp on the brakes even more than it usually does, weakening synapses so much they could disappear altogether, taking memories with them.
Further experiments showed that, indeed, beta-amyloid binds strongly to PirB. While PirB is specifically a mouse protein, Kim also identified for the first time an analogous beta-amyloid receptor in the human brain: a protein called LilrB2.
In another experiment, Kim compared proteins in the brains of PirB-lacking Alzheimer's mice to those in the brains of PirB-expressing Alzheimer's mice. The latter showed significantly increased activity on the part of a few workhorse proteins, notably an enzyme called cofilin. Subsequent studies also found that cofilin activity in the brains of autopsied Alzheimer's patients is substantially higher than in the brains of people without the disorder.
Here the plot thickens: Cofilin works by breaking down actin, a building-block protein essential to maintaining synaptic structure. And, as the new study also showed, beta-amyloid's binding to PirB results in biochemical changes to cofilin that revs up its actin-busting, synapse-disassembling activity.
"No actin, no synapse," Shatz said.
Kim's hypothesis appears to have been correct. Beta-amyloid binds to PirB (and, the researchers proved, to its human analog, LilrB2), boosting cofilin activity and busting synapses' structural integrity.
Although there may be other avenues of destruction along which synapses are forced to walk, Shatz doubts there are very many. She said she thinks the direct participation of beta-amyloid -- as well as cofilin, so clearly implicated in synaptic breakdown -- suggests that this pathway is important. "We looked at human brains in this study, too, and we found that a similar derangement of cofilin activity is present in Alzheimer's brains but not healthy brains," she said.
Shatz suggested that drugs that block beta-amyloid's binding to PirB on nerve-cell surfaces -- for example, soluble PirB fragments containing portions of the molecule that could act as decoy -- might be able to exert a therapeutic effect. "I hope this finding will be enticing enough to pharmaceutical and biotechnology companies that someone will try pushing this idea forward," she said
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