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Scientists have discovered a new species of fish that glides gently through the water on white, translucent wings 5 miles beneath the ocean surface. The newly discovered species is now the world’s deepest known fish recorded at 8,143 m depth. The fish has a novel body form that has not been seen before. It stunned scientists because in other trenches, there is only one fish species at this depth--a snailfish; this fish is really different from any other deep-sea fish that scientists have ever seen.
"We were just blown away when we saw it," said Paul Yancey, a biology professor at Whitman College, Washington who studies how animals adapt to life in the deep sea. "Someone on the ship said it looks like a cross between a puppy, an angel and an eel." The fish was first spotted in November during an international research cruise to the Mariana Trench -- the deepest place on Earth.
The new fish, which has not yet been named, was discovered by accident. In the video above you can see it swimming around a series of tubes that were part of an instrument collecting mud samples from the sea floor. The camera was supposed to be filming the core collecting, when suddenly this ghostly fish swam into view. It is about 10 inches in length, and almost entirely transparent. The dense white part you can see is actually its skull, visible through its skin, Yancey said. It's lengthy, mostly see-through tail is probably made of gelatin.
"It's moving very slowly so it's not clear how well it can swim," he said. "But there has to be some muscle in there somewhere." The Mariana Trench is located in the Western Pacific, just off the coast of Guam. It starts about 3 miles beneath the ocean surface and stretches to an ultimate depth of 6.8 miles. Humans couldn't survive even at the top rim of the trench. At that depth, the proteins and cells in our membranes would collapse. And at the bottom of the trench, the pressure is so immense it would be like having 100 elephants standing on your head.
One way deep sea animals survive even under the weight of all that water is with a molecule called trimethylamine N-oxide (TMAO) that protects their proteins from being crushed. "It's the molecule that makes marine animals like fish and shrimp smell 'fishy,' " said Yancey, "and in deep sea animals there is a lot more of it."
The Marshall Islands is experiencing its worst-ever coral bleaching as global warming threatens reefs across the entire northern Pacific, scientists found in a recent study.
Marine researchers said an El Nino weather pattern had been developing in recent months, raising ocean temperatures and stressing delicate coral reefs. "The worst coral bleaching event ever recorded for the Marshall Islands has been occurring since mid-September," Karl Fellenius, a Majuro-based marine scientist with the University of Hawaii told AFP.
C. Mark Eakin, manager of the US National Oceanic and Atmospheric Administration's Coral Reef Watch programme, said recent observations showed the problem was widespread across the vast waters of the northern Pacific. "Major bleaching was seen in Guam and the Commonwealth of the Northern Marianas Islands, the northwestern Hawaiian Islands (NWHI), the Marshall Islands, and Kiribati," he said.
"Thermal stress levels set new record highs in CNMI and the NWHI and we saw the first widespread bleaching event in the main Hawaiian Islands." Fellenius said coral bleaching was a naturally occurring phenomenon but not on the scale currently being seen. "While bleaching can occur on very hot days in pools of water with little circulation (such as) very low tides on reef flats, it has become a global problem due to greenhouse gas emissions causing elevated temperatures under climate change."
He said sea surface temperatures had been on average half to a full degree Celsius higher than normal for months, adding: "This does not seem like a lot but it makes a big difference to corals." Fellenius said the last major bleaching event was in 1997, when an exceptionally strong El Nino system affected about a quarter of the world's coral reefs.
A Yale University lab has crafted the first synthetic molecules that have both the targeting and response functions of antibodies. The new molecules — synthetic antibody mimics (SyAMs) — attach themselves simultaneously to disease cells and disease-fighting cells. The result is a highly targeted immune response, similar to the action of natural human antibodies.
“Unlike antibodies, however, our molecules are synthetic organic compounds that are approximately one-twentieth the size of antibodies,” said David A. Spiegel, a professor of chemistry at Yale whose lab developed the molecules. “They are unlikely to cause unwanted immune reactions due to their structure, are thermally stable, and have the potential to be administered orally, just like traditional, small-molecule drugs.”
Spiegel and his team describe the research in a paper published online Dec. 16 by the Journal of the American Chemical Society. The paper looks specifically at SyAM molecules used to attack prostate cancer. Called SyAM-Ps, they work first by recognizing cancer cells and binding with a specific protein on their surface. Next, they also bind with a receptor on an immune cell. This induces a targeted response that leads to the destruction of the cancer cell.
Spiegel said the process of synthesizing and optimizing the structure of the molecules required considerable time and effort. “We now know that synthetic molecules of intermediate size possess perhaps the most important functional properties of antibodies — targeting and stimulation of immune cells,” he said.
“It’s also noteworthy that molecules of such a small size can bring together two objects as enormous as cells, and trigger a specific functional response, entirely as a result of specific receptor interactions,” Spiegel added. Beyond their potential for treating prostate cancer, SyAMs may have applications for treating other forms of cancer, HIV and various bacterial diseases.
Computers aren't best suited to visual object recognition. Our brains are hardwired to quickly see and match patterns in everything, with great leaps of intuition, while the processing center of a computer is more akin to a very powerful calculator. But that hasn't stopped neuroscientists and computer scientists from trying over the past 40 years to design computer networks that mimic our visual skills. Recent advances in computing power and deep learning algorithms have accelerated that process to the point where a group of MIT neuroscientists has found a network design that compares favorably to the brain of our primate cousins.
This is important beyond the needs of automated digital information processing like Google's image search. Computer-based neural networks that work like the human brain will further our understanding of how the brain works, and any attempts to create them will test that understanding. Essentially, the fact that these networks work to a level comparable to primates suggests that neuroscientists now have a solid grasp of how object recognition works in the brain.
To see how current networks hold up, the MIT scientists started by testing primates. They implanted arrays of electrodes in the inferior temporal (IT) cortex and area V4 (a part of the visual system that feeds into the IT cortex) of the primates' brains. This allowed them to see how neurons related to object recognition responded when the animals looked at various objects in 1,960 images. The viewing time per image was a mere 100 milliseconds, which is long enough for humans to recognize an object.
They then compared these results with those of the latest deep neural networks. These networks produce arrays of numbers when fed an image – different numbers for different images. If it groups similar objects into similar clusters in this number matrix representation, it's deemed accurate. "Through each of these computational transformations, through each of these layers of networks, certain objects or images get closer together, while others get further apart," explains lead author Charles Cadieu.
The best network, developed by researchers at New York University, classified objects as well as the macaque - a medium-sized Old World monkey - brain. That's the good news. The bad is that they don't know why. Neural networks are learning from massive datasets containing millions or billions of images, churning through the information with help from the high-performance graphical processing units that power the latest video games. But nobody knows quite what is going on in there as the networks refine their own algorithms.
Quantum computers will someday perform calculations impossible for conventional digital computers. But for that to happen, the core quantum information must be preserved against contamination from the environment. In other words, decoherence of qubits must be forestalled. Coherence, the ability of a system to retain quantum integrity—-meaning that one part of the system can be used to predict the behavior of other parts—-is an important consideration.
Over the past dozen years, remarkable experiments have shown how the coherence of a Bose condensate loaded into optical lattices can collapse and later return. New theoretical work by JQI scientists provides a detailed explanation for this quantum revival. The heart of their theory are interactions involving three atoms simultaneously.
In Bose Einstein condensates (BECs) typically a million atoms are chilled until their respective waves overlap. In effect, they become a single coherent object. If furthermore the BEC is lined up into a series of zones in space using the powerful electric fields of crisscrossing laser beams—-a configuration called an optical lattice—-then the BEC atoms become a sort of crystal.
The effect of the optical lattice is to encase the atoms in stacks of egg-carton-like confinements. Typically about 100x100x100 (one million) egg-carton slots are filled by a BEC cloud. For a million-BEC atom BEC this corresponds to about one atom per lattice site. The atoms in this artificial crystal are spaced much farther apart than the atoms in a natural crystal but still close enough for them to interact in interesting ways.
If suddenly the strength of the lasers is increased, the depth of the well becomes deeper, and the atoms are less likely to tunnel from one compartment to another, and consequently more likely to interact with its partners within that well. What happens to the coherence of the BEC ensemble when atoms are encouraged to interact with each other at close range in the lattice sites? This is what scientists at the Max Planck Institute for Quantum Physics in Garching, Germany set out to explore in an experiment conducted a dozen years ago.
In May 2013, the mathematician Yitang Zhang launched what has proven to be a banner year and a half for the study of prime numbers, those numbers that aren’t divisible by any smaller number except 1. Zhang, of the University of New Hampshire, showed for the first time that even though primes get increasingly rare as you go further out along the number line, you will never stop finding pairs of primes that are a bounded distance apart — within 70 million, he proved. Dozens ofmathematicians then put their heads together to improve on Zhang’s 70 million bound, bringing it down to 246 — within striking range of the celebrated twin primes conjecture, which posits that there are infinitely many pairs of primes that differ by only 2.
Now, mathematicians have made the first substantial progress in 76 years on the reverse question: How far apart can consecutive primes be? The average spacing between primes approaches infinity as you travel up the number line, but in any finite list of numbers, the biggest prime gap could be much larger than the average. No one has been able to establish how large these gaps can be. This past August, two different groups of mathematicians released papers proving a long-standing conjecture by the mathematician Paul Erdős about how large prime gaps can get. The two teams have joined forces to strengthen their result on the spacing of primes still further, and expect to release a new paper later this month.
Many mathematicians believe that the true size of large prime gaps is probably considerably larger — more on the order of (log X)2, an idea first put forth by the Swedish mathematician Harald Cramér in 1936. Gaps of size (log X)2 are what would occur if the prime numbers behaved like a collection of random numbers, which in many respects they appear to do. But no one can come close to proving Cramér’s conjecture, Tao said. “We just don’t understand prime numbers very well.” Erdős made a more modest conjecture: It should be possible, he said, to replace the 1/3 in Rankin’s formula by as large a number as you like, provided you go out far enough along the number line. That would mean that prime gaps can get much larger than in Rankin’s formula, though still smaller than in Cramér’s.
The two new proofs of Erdős’ conjecture are both based on a simple way to construct large prime gaps. A large prime gap is the same thing as a long list of non-prime, or “composite,” numbers between two prime numbers. Here’s one easy way to construct a list of, say, 100 composite numbers in a row: Start with the numbers 2, 3, 4, … , 101, and add to each of these the number 101 factorial (the product of the first 101 numbers, written 101!). The list then becomes 101! + 2, 101! + 3, 101! + 4, … , 101! + 101. Since 101! is divisible by all the numbers from 2 to 101, each of the numbers in the new list is composite: 101! + 2 is divisible by 2, 101! + 3 is divisible by 3, and so on. “All the proofs about large prime gaps use only slight variations on this high school construction,” said James Maynard of Oxford, who wrote the second of the two papers.
The part of the brain that tells us the direction to travel when we navigate has been identified by UCL scientists, and the strength of its signal predicts how well people can navigate.
It has long been known that some people are better at navigating than others, but until now it has been unclear why. The latest study, funded by the Wellcome Trust and published in Current Biology, shows that the strength and reliability of ‘homing signals’ in the human brain vary among people and can predict navigational ability.
In order to successfully navigate to a destination, you need to know which direction you are currently facing and which direction to travel in. For example, ‘I am facing north and want to head east’. It is already known that mammals have brain cells that signal the direction that they are currently facing, a discovery that formed part of the 2014 Nobel Prize in Physiology or Medicine to UCL Professor John O’Keefe.
The latest research reveals that the part of the brain that signals which direction you are facing, called the entorhinal region, is also used to signal the direction in which you need to travel to reach your destination. This part of the brain tells you not only which direction you are currently facing, but also which direction you should be facing in the future. In other words, the researchers have found where our ‘sense of direction’ comes from in the brain and worked out a way to measure it using functional magnetic resonance imaging (fMRI).
In the study, 16 healthy volunteers were asked to navigate a simple square environment simulated on a computer. Each wall had a picture of a different landscape, and each corner contained a different object. Participants were placed in a corner of the environment, facing a certain direction and asked how to navigate to an object in another corner.
Dr Martin Chadwick (UCL Experimental Psychology), lead author of the study, said: “Our results provide evidence to support the idea that your internal ‘compass’ readjusts as you move through the environment. For example, if you turn left then your entorhinal region should process this to shift your facing direction and goal direction accordingly. If you get lost after taking too many turns, this may be because your brain could not keep up and failed to adjust your facing and goal directions.”
Interferometers capture a basic mystery of quantum mechanics: a single particle can exhibit wave behaviour, yet that wave behaviour disappears when one tries to determine the particle’s path inside the interferometer. This idea has been formulated quantitatively as an inequality, for example, by Englert and Jaeger, Shimony and Vaidman, which upper bounds the sum of the interference visibility and the path distinguishability. Such wave–particle duality relations (WPDRs) are often thought to be conceptually inequivalent to Heisenberg’s uncertainty principle, although this has been debated in the past. A group of physicists now shows that WPDRs correspond precisely to a modern formulation of the uncertainty principle in terms of entropies, namely, the min- and max-entropies. This observation unifies two fundamental concepts in quantum mechanics. Furthermore, it leads to a robust framework for deriving novel WPDRs by applying entropic uncertainty relations to interferometric models.
Contrary to intuition, adding pockets of water to solids can actually make them stronger. This finding, the result of research by Yale scientists, offers “a new knob to turn” for engineers, the researchers say. Engineers will be able to add exciting new properties to composite materials–such as electromagnetism–by embedding droplets of liquid, and, on a purely scientific level, the research provides valuable insight into the nature of the material properties at small and large scales–how the relative strengths of a material at one size can be opposite to that at another size.
“This is a great example of how different types of physics emerge at different scales,” Dr. Eric Dufresne, associate professor of mechanical engineering and materials science at Yale and principle investigator of the study, told The Speaker. “Shrinking the scale of an object can really change how it behaves.”
“Surface tension is a force that tries to reduce the surface area of a material,” Dufresne told us. “It is familiar in fluids–it’s the force that pulls water into a sponge, makes wet hair clump together and lets insects walk on water. Solids have surface tension too, but usually the ‘elastic force’ of the solid is so strong that surface tension doesn’t have much of an effect. The ‘elastic force’ of a solid is what makes a solid spring back to its original shape after you stop pushing on it. “As the solid gets stiffer, the liquid droplets need to be smaller in order to have this stiffening or cloaking effect. By embedding the solid with droplets of different materials, one can give it new electrical, optical or mechanical properties.
“It turns out that the importance of surface tension is inversely proportional to the size,” Dufresne said of the study. “So what’s just a negligible force for big things becomes a strong force for very small things–which in turn can strongly affect the material as a whole.”
The report, “Stiffening solids with liquid inclusions,” was completed by Drs. W. Style, Rostislav Boltyanskiy, Benjamin Allen, Katharine E.Jensen, Henry P. Foote, John S. Wettlaufer, and Eric R. Dufresne, and was published in December’s Nature Physics.
NASA's Systems Analysis and Concepts Directorate has issued a report outlining a possible way for humans to visit Venus, rather than Mars—by hovering in the atmosphere instead of landing on the surface. The hovering vehicle, which they call a High Altitude Venus Operational Concept (HAVOC), would resemble a blimp with solar panels on top, and would allow people to do research just 50 kilometers above the surface of the planet.
Most everyone knows that NASA wants to send people to Mars—that planet also gets most of the press. Mars is attractive because it looks more like Earth and is relatively close to us. The surface of Venus on the other hand, though slightly closer, is not so attractive, with temperatures that can melt lead and atmospheric pressure 92 times that of Earth. There's also that thick carbon dioxide atmosphere with sulfuric acid clouds, lots of earthquakes, volcanoes going off and terrifying lightning bolts. So, why would anyone rather go to Venus than Mars? Because of far lower radiation and much better solar energy.
No one wants to go the surface of Venus, at least not anytime soon, instead, researchers at NASA are looking into the possibility of sending people to hover in the sky above the planet, conducting research in a far less dangerous place than even on the surface of Mars. At 50 kilometers up, an HAVOC would experience just one atmosphere of atmospheric pressure and temperatures averaging just 75 degrees Celsius, with radiation levels equivalent to those in Canada. Astronauts on Mars, on the other hand would experience 40 times the amount of radiation typically faced back here on Earth, which suggests they'd have to live deep underground to survive—a problem that scientists have not yet solved. Some are even beginning to wonder about the feasibility of sending humans to the surface of Mars.
The mass extinction event was thought to have paved the way for mammals to dominate, but researchers say many of them died out alongside the dinosaurs. During the Cretaceous period, extinct relatives of living marsupials – such as possums and kangaroos – thrived.
An international team of experts on mammal evolution and mass extinctions has shown that the once-abundant animals – known as metatherian mammals – came close to extinction. A 10-km-wide asteroid struck what is now Mexico at the end of the Cretaceous period, unleashing a global cataclysm of environmental destruction which led to the demise of the dinosaurs.
The study, including the University of Edinburgh scientists, shows that two-thirds of all metatherians living in North America also perished. This included more than 90 per cent of species living in the northern Great Plains of the US, which is the best area in the world for finding latest Cretaceous mammal fossils, researchers said.
Metatherians never recovered their previous diversity, which explains why marsupials are rare today and largely restricted to unusual environments in Australia and South America.
Species that give birth to well-developed live young – known as placental mammals – took full advantage of the metatherians’ demise. Placental mammals – which include many species from mice to men – are ubiquitous across the globe today, researchers said.
“This is a new twist on a classic story. It wasn’t only that dinosaurs died out, providing an opportunity for mammals to reign, but that many types of mammals, such as most metatherians, died out too – this allowed advanced placental mammals to rise to dominance,” said Dr Thomas Williamson from the New Mexico Museum of Natural History and Science.
Researchers reviewed the evolutionary history of metatherians and constructed the most up-to-date family tree for the mammals based on the latest fossil records, allowing them to study extinction patterns in unprecedented detail.
Electrons may be seen as small magnets that also carry a negative electrical charge. On a fundamental level, these two properties are indivisible. However, in certain materials where the electrons are constrained in a quasi one-dimensional world, they appear to split into a magnet and an electrical charge, which can move freely and independently of each other. A longstanding question has been whether or not similar phenomenon can happen in more than one dimension. A team lead by EPFL scientists now has uncovered new evidence showing that this can happen in quasi two-dimensional magnetic materials. Their work is published in Nature Physics.
A strange phenomenon occurs with electrons in materials that are so thin that they can be thought of as being one-dimensional, e.g. nanowires. Under certain conditions, the electrons in these materials can actually split into an electrical charge and a magnet, which are referred to as "fractional particles". An important but still unresolved question in fundamental particle physics is whether this phenomenon could arise and be observed in more dimensions, like two- or three-dimensional systems.
Under temperatures close to absolute zero, electrons bind together to form an exotic liquid that can flow with exactly no friction. While this was previously observed at near-absolute zero temperatures in other materials, this electron liquid can form in cuprates at much higher temperatures that can be reached using liquid nitrogen alone. Consequently, there is currently an effort to find new materials displaying high-temperature superconductivity at room temperature. But understanding how it arises on a fundamental level has proven challenging, which limits the development of materials that can be used in applications. The advances brought by the EPFL scientists now bring support for the theory of superconductivity as postulated by Anderson.
"This work marks a new level of understanding in one of the most fundamental models in physics," says Henrik M. Rønnow. "It also lends new support for Anderson's theory of high-temperature superconductivity, which, despite twenty-five years of intense research, remains one of the greatest mysteries in the discovery of modern materials."
Paleontologists have documented the evolutionary adaptations necessary for ancient lobe-finned fish to transform pectoral fins used underwater into strong, bony structures, such as those of Tiktaalik roseae. This enabled these emerging tetrapods, animals with limbs, to crawl in shallow water or on land. But evolutionary biologists have wondered why the modern structure called the autopod—comprising wrists and fingers or ankles and toes—has no obvious morphological counterpart in the fins of living fishes.
In the Dec. 22, 2014, issue of the Proceedings of the National Academy of Sciences, researchers argue previous efforts to connect fin and fingers fell short because they focused on the wrong fish. Instead, they found the rudimentary genetic machinery for mammalian autopod assembly in a non-model fish, the spotted gar, whose genome was recently sequenced.
"Fossils show that the wrist and digits clearly have an aquatic origin," said Neil Shubin, PhD, the Robert R. Bensley Professor of organismal biology and anatomy at the University of Chicago and a leader of the team that discovered Tiktaalik in 2004. "But fins and limbs have different purposes. They have evolved in different directions since they diverged. We wanted to explore, and better understand, their connections by adding genetic and molecular data to what we already know from the fossil record."
Initial attempts to confirm the link based on shape comparisons of fin and limb bones were unsuccessful. The autopod differs from most fins. The wrist is composed of a series of small nodular bones, followed by longer thin bones that make up the digits. The bones of living fish fins look much different, with a set of longer bones ending in small circular bones called radials. The primary genes that shape the bones, known as the HoxD and HoxA clusters, also differ. The researchers first tested the ability of genetic "switches" that control HoxD and HoxA genes from teleosts—bony, ray-finned fish—to shape the limbs of developing transgenic mice. The fish control switches, however, did not trigger any activity in the autopod.
When the research team compared Hox gene switches from the spotted gar with tetrapods, they found "an unprecedented and previously undescribed level of deep conservation of the vertebrate autopod regulatory apparatus." This suggests, they note, a high degree of similarity between "distal radials of bony fish and the autopod of tetrapods."
They tested this by inserting gar gene switches related to fin development into developing mice. This evoked patterns of activity that were "nearly indistinguishable," the authors note, from those driven by the mouse genome. "Overall," the researchers conclude, "our results provide regulatory support for an ancient origin of the 'late' phase of Hox expression that is responsible for building the autopod."
Mars is a very harsh and hostile environment for future human explorers and like any other known planet it has no breathable air. That could change someday, and it may be soon enough for our generation to witness it, as the student team from Germany has a bold vision to make a first step to terraform the Red Planet, turning it more Earth-like. The plan is to send cyanobacteria to Mars to generate oxygen out of carbon dioxide which is the main component of Martian atmosphere (nearly 96%). "Cyanobacteria do live in conditions on Earth where no life would be expected. You find them everywhere on our planet!" team leader Robert P. Schröder told astrowatch.net. "It is the first step on Mars to test microorganisms." The project is participating in the Mars One University Competition and if it wins, it will be send as a payload to Mars, onboard the Dutch company's mission to the Red Planet. Now everyone can vote to help make it happen by visiting the CyanoKnights.bio webpage.
The team behind the initiative is composed of a voluntary and interdisciplinary group of students and scientists, from the University of Applied Science and Technical University, both located in Darmstadt, Germany. Cyanobacteria will deliver oxygen made of their photosynthesis, reducing carbon dioxide and produce an environment for living organisms. Furthermore, they can supply food and important vitamins for a healthy nutrition. The team is already testing cyanobacteria with different environmental conditions in quarantined photobioreactors and monitoring their activities to determine the best working solution on Mars.
Schröder reveals that the idea was born in August this year. But why cyanobacteria? "Initial ideas were of a technical nature, but that was too boring for me. In school I liked biotechnology and that have not changed very much. Once I heard of cyanobacteria and how they can survive in harsh conditions on earth and at this special night I had a flashback which grabbed me and convinced me completely," he explains.
So what amount of this bacteria will be needed to fully terraform Mars? "As for now we don't know that really, because we need to find out the best habitable conditions for each strain to cultivate them and then we have references and can calculate it," Schröder says. "We need to test Mars-like conditions and analyze how much energy we have to put into the photobioreactor. So it's a lot work to do."
Mars One will take one project to Mars along with its unmanned lander mission in 2018. Voting submission will be accepted until Dec. 31, 2014. The winning university payload will be announced on Jan. 5, 2015.
Scientists have discovered a fossilized fish so well preserved that the rods and cones in its 300-million-year-old eyeballs are still visible under a scanning electron microscope.
It is the first time that fossilized photoreceptors from a vertebrate eye have ever been found, according to a paper published Tuesday in Nature Communications. The researchers say the discovery also suggests that fish have been seeing the world in color for at least 300 million years. Rods and cones are cells that line the retina in our eyes. Rods are long and thin, and more sensitive to light than cones. However, cones, which are triangular, allow us to see in color. Both these cells rely on pigments to absorb light. Using chemical analysis, the scientists found evidence of one of these pigments -- melanin -- in the fossilized eye as well.
The fish pictured above is about 10 centimeters long. It was found in the Hamilton Quarry in Kansas, which was once a shallow lagoon. Fossils from this area are remarkably well preserved because they were buried very quickly in sediments in the lagoon, said Gengo Tanaka of Kumamoto University in Japan, the lead author of the paper. In the case of this fish, an extinct species called Acanthodes bridgei, the preservation process probably also got some help from bacterial activity that left a thin film of phosphate over the eyes before it was buried. Tanaka said that gills and pigments on other parts of the fish were also preserved. However, he had not looked to see whether organs and nerves were intact as well.
The so-called “streetlight effect” has often fettered scientists who study complex hereditary diseases. The term refers to an old joke about a drunk searching for his lost keys under a streetlight. A cop asks, "Are you sure this is where you lost them?" The drunk says, "No, I lost them in the park, but the light is better here."
For researchers who study the genetic roots of human diseases, most of the light has shone down on the 2 percent of the human genome that includes protein-coding DNA sequences. “That’s fine. Lots of diseases are caused by mutations there, but those mutations are low-hanging fruit,” says University of Toronto (U.T.) professor Brendan Frey who studies genetic networks. “They’re easy to find because the mutation actually changes one amino acid to another one, and that very much changes the protein.”
The trouble is, many disease-related mutations also happen in noncoding regions of the genome—the parts that do not directly make proteins but that still regulate how genes behave. Scientists have long been aware of how valuable it would be to analyze the other 98 percent but there has not been a practical way to do it.
Now Frey has developed a “deep-learning” machine algorithm that effectively shines a light on the entire genome. A paper appearing December 18 in Science describes how this algorithm can identify patterns of mutation across coding and noncoding DNA alike. The algorithm can also predict how likely each variant is to contribute to a given disease. “Our method works very differently from existing methods,” says Frey, the study’s lead author. “GWAS-, QTL- and ENCODE-type approaches can't figure out causal relationships. They can only correlate. Our system can predict whether or not a mutation will cause a change in RNA splicing that could lead to a disease phenotype.”
RNA splicing is one of the major steps in turning genetic blueprints into living organisms. Splicing determines which bits of DNA code get included in the messenger-RNA strings that build proteins. Different configurations yield different proteins. Misregulated splicing contributes to an estimated 15 to 60 percent of human genetic diseases.
The combination of whole-genome analysis and predictive models for RNA splicing makes Frey’s method a major contribution to the field, according to Stephan Sanders, an assistant professor at the University of California, San Francisco, School of Medicine. “I’m looking forward to using this tool in larger data sets and really getting sense of how important splicing is,” he says. Sanders, who researches the genetic causes of diseases, notes Frey’s approach complements, rather than replaces, other methods of genetic analysis. “I think any genomist [sic] would agree that noncoding [areas of the genome] are hugely important. This method is a really novel way of getting at that,” he says.
Synthetic two-dimensional materials based on metal chalcogenide compounds could be the basis for superthin devices, according to Rice researchers. One such material, molybdenum disulfide, is being widely studied for its light-detecting properties, but copper indium selenide (CIS) also shows extraordinary promise.
Sidong Lei, a graduate student in the Rice lab of materials scientist Pulickel Ajayan, synthesized CIS, a single-layer matrix of copper, indium and selenium atoms. Lei also built a prototype—a three-pixel, charge-coupled device (CCD)—to prove the material's ability to capture an image.
The details appear this month in the American Chemical Society journal Nano Letters. Lei said the optoelectronic memory material could be an important component in two-dimensional electronics that capture images. "Traditional CCDs are thick and rigid, and it would not make sense to combine them with 2-D elements," he said. "CIS-based CCDs would be ultrathin, transparent and flexible, and are the missing piece for things like 2-D imaging devices."
The device traps electrons formed when light hits the material and holds them until released for storage, Lei said. CIS pixels are highly sensitive to light because the trapped electrons dissipate so slowly, said Robert Vajtai, a senior faculty fellow in Rice's Department of Materials Science and NanoEngineering. "There are many two-dimensional materials that can sense light, but none are as efficient as this material," he said. "This material is 10 times more efficient than the best we've seen before."
A new study predicts that large-scale power plants based on thermoelectric effects, such as small temperature differences in ocean water, could generate electricity at a lower cost than photovoltaic power plants.
Liping Liu, Associate Professor at Rutgers University, envisions that thermoelectric power plants would look like giant barges sitting in the tropical ocean, where electricity is generated by heating cold, deep water with warm, shallow water heated by the sun. Liu has published a paper in the New Journal of Physics in which he analyzes the feasibility of such power plants.
"This work is about the new idea of large-scale green power plants that make economic use of the largest accessible and sustainable energy reservoir on the earth," Liu told Phys.org, speaking of the oceans. This is because the sun heats the surface water to a temperature that, in tropical regions, is about 20 K higher than water 600 m deep. Essentially, the surface water acts as a giant storage tank of solar energy.
As Liu explains, thermoelectric power plants would work by harvesting the energy of ocean waves to pump cold water from a few hundred meters deep up through a long channel. As the cold water nears the surface, it enters a heat exchanger where it is heated by surface water on the outside. The heat exchanger acts as an electric generator, as its tubes are made of thermoelectric materials that can transfer heat through their walls and directly convert temperature differences into electricity.
Large-scale, ocean-based thermoelectric power plants would have many advantages. For one, the "fuel" or temperature differences are free, unlimited, and easily accessible. Also, the plants do not take up space on land. Because they have no moving solid parts, they would have low maintenance costs. In addition, the power output does not depend on the time of day or season. And finally, the method is green, as it does not release emissions.
As the West African Ebola epidemic enters its second year small batches of experimental vaccines are on the cusp of reaching people in the affected countries. Nature magazine tackles the questions that will determine whether vaccines play a role in ending the current epidemic — and can prevent future flare-ups. Two vaccines are leading contenders to be deployed in West Africa early next year. The furthest along is one co-developed by London-based drug firm GlaxoSmithKline (GSK) and the US National Institute for Allergy and Infectious Disease (NIAID) in Bethesda, Maryland. Their vaccine is made of an inactivated chimpanzee cold-causing adenovirus (called ChAd3) that has been engineered to produce an Ebola protein.
Only efficacy trials — slated for next year in Liberia and Sierra Leone — can determine whether a vaccine can prevent Ebola infection. But researchers are scouring data from safety trials to identify the doses and regimens that offer the best chances of working. Those decisions will be made by mid-January, according to Ballou.
The Liberia trial will probably enrol around 30,000 people living in Monrovia. The plan is for volunteers to be randomly assigned to receive either the GSK–NIAID vaccine, the NewLink–Merck vaccine or a saline-solution injection that will serve as a placebo control. But it is unclear how the suspension of the NewLink–Merck safety trial in Geneva will affect those plans. “If that means it is not going forward rapidly for safety reasons, it would impact on plans for the efficacy trial in Liberia,” Hill says. One possibility is to delay this arm of the trial until additional safety tests are completed.
A phase 3 trial of around 6,000 health-care workers in Sierra Leone is also in the planning stages. The current strategy is for all the volunteers to receive a vaccine (yet to be selected) in a phased roll-out. Researchers will determine whether the vaccine works by comparing infection rates among vaccinated and unvaccinated people.
Officials are also discussing the possibility of a third efficacy trial to test whether a strategy known as ring vaccination can quell the epidemic. In this approach, patients living around a newly diagnosed case are vaccinated, in an attempt to prevent transmission.
Infrasound may have alerted warblers to the approaching storm, prompting them to fly more than a thousand kilometers to avoid it.
A group of songbirds may have avoided a devastating storm by fleeing their US breeding grounds after detecting telltale infrasound waves.
Researchers noticed the behaviour after analysing trackers attached to the birds to study their migration patterns. They believe it is the first documented case of birds making detours to avoid destructive weather systems on the basis of infrasound.
The golden-winged warblers had just returned from South America to their breeding grounds in the mountains of Tennessee in 2013 when a massive storm was edging closer. Although the birds had just completed a migration of more than 2,500km, they still had the energy to evade the danger.
The storm, which spawned more than 80 tornadoes across the US and killed 35 people, was 900km away when the birds, apparently acting independently of one another, fled south, with one bird embarking on a 1,500km flight to Cuba before making the return trip once the storm had passed.
“We looked at barometric pressure, wind speeds on the ground and at low elevations, and the precipitation, but none of these things that typically trigger birds to move had changed,” said David Andersen at the University of Minnesota. “What we’re left with is something that allows them to detect a storm from a long distance, and the one thing that seems to be the most obvious is infrasound from tornadoes, which travels through the ground.”
The scientists cannot be sure that the birds picked up infrasound waves from the storm, but previous work in pigeons has suggested that birds might use infrasound to help them navigate. Infrasound waves range from about 0.5Hz to 18Hz, below the audible range of humans.
The discovery of the evasive action could be good news, said Andersen. “With climate change increasing the frequency and severity of storms, this suggests that birds may have some ability to cope that we hadn’t previously realised. These birds seemed to be capable of making really dramatic movements at short notice, even just after returning on their northwards migration,” he said.
Had the storm arrived a couple of weeks later, the birds may not have taken flight. By that time, they would have been nesting, and females especially may have been less likely to flee. “It’s hard to say what would happen. It may be more advantageous to survive than stay with a nest that is going to be destroyed anyway,” Andersen said.
Crows have the brain power to solve higher-order, relational-matching tasks, and they can do so spontaneously, according to new research. That means crows join humans, apes and monkeys in exhibiting advanced relational thinking, according to the research.
Crows have long been heralded for their high intelligence -- they can remember faces, use tools and communicate in sophisticated ways.
But a newly published study finds crows also have the brain power to solve higher-order, relational-matching tasks, and they can do so spontaneously. That means crows join humans, apes and monkeys in exhibiting advanced relational thinking, according to the research.
Russian researcher Anna Smirnova studies a crow making the correct selection during a relational matching trial.
"What the crows have done is a phenomenal feat," says Ed Wasserman, a psychology professor at the University of Iowa and corresponding author of the study. "That's the marvel of the results. It's been done before with apes and monkeys, but now we're dealing with a bird; but not just any bird, a bird with a brain as special to birds as the brain of an apes is special to mammals."
Here is how it worked: the birds were placed into a wire mesh cage into which a plastic tray containing three small cups was occasionally inserted. The sample cup in the middle was covered with a small card on which was pictured a color, shape or number of items. The other two cups were also covered with cards -- one that matched the sample and one that did not. During this initial training period, the cup with the matching card contained two mealworms; the crows were rewarded with these food items when they chose the matching card, but they received no food when they chose the other card.
Once the crows has been trained on identity matching-to-sample, the researchers moved to the second phase of the experiment. This time, the birds were assessed with relational matching pairs of items.
These relational matching trials were arranged in such a way that neither test pairs precisely matched the sample pair, thereby eliminating control by physical identity. For example, the crows might have to choose two same-sized circles rather than two different-sized circles when the sample card displayed two same-sized squares.
What surprised the researchers was not only that the crows could correctly perform the relational matches, but that they did so spontaneously--without explicit training. "That is the crux of the discovery," Wasserman says. "Honestly, if it was only by brute force that the crows showed this learning, then it would have been an impressive result. But this feat was spontaneous."
Anna Smirnova, Zoya Zorina, Tanya Obozova, Edward Wasserman. Crows Spontaneously Exhibit Analogical Reasoning. Current Biology, 2014 DOI: 10.1016/j.cub.2014.11.063
The prolific spacecraft has spotted its first newalien planet since being hobbled by a malfunction in May 2013, researchers announced today (Dec. 18). The newly discovered world, called HIP 116454b, is a "super Earth" about 2.5 times larger than our home planet. It lies 180 light-years from Earth, in the constellation Pisces — close enough to be studied by other instruments, scientists said.
"Like a phoenix rising from the ashes, Kepler has been reborn and is continuing to make discoveries," study lead author Andrew Vanderburg, of the Harvard-Smithsonian Center for Astrophysics (CfA), said in a statement. "Even better, the planet it found is ripe for follow-up studies."
Kepler launched in March 2009, on a 3.5-year mission to determine how frequently Earth-like planets occur around the Milky Way galaxy. The spacecraft has been incredibly successful to date, finding nearly 1,000 confirmed planets — more than half of all known alien worlds — along with about 3,200 other "candidates," the vast majority of which should turn out to be the real deal.
HIP 116454b is about 20,000 miles (32,000 kilometers) wide and is 12 times more massive than Earth, scientists said. The planet's density suggests that it is either primarily covered by water or is a "mini Neptune" with a large, thick atmosphere. HIP 116454b lies just 8.4 million miles (13.5 million km) from its host star, an "orange dwarf" slightly smaller and cooler than the sun, and completes one orbit every 9.1 days. The close-orbiting planet is too hot to host life as we know it, researchers said. The planet's relative proximity to Earth means it will likely attract further attention in the future.
Members of Genlisea, a genus of carnivorous plants, possess the smallest genomes known in plants. To elucidate genomic evolution in the group as a whole, researchers have now surveyed a wider range of species, and found a new record-holder.
The genus Genlisea (corkscrew plants) belongs to the bladderwort family (Lentubulariaceae), a family of carnivorous plants. Some of the 29 species of Genlisea that have been described possess tiny genome sizes. Indeed, the smallest genome yet discovered among flowering plants belongs to a member of the group. The term 'genome' here refers to all genetic material arranged in a set of individual chromosomes present in each cell of a given species. An international team of researchers, led by Professor Günther Heubl of LMU's Department of Biology, has now explored, for the first time, the evolution of genome size and chromosome number in the genus. Heubl and his collaborators studied just over half the known species of Genlisea, and their findings are reported in the latest issue of the journal Annals of Botany.
"During the evolution of the genus, the genomes of some Genlisea species must have undergone a drastic reduction in size, which was accompanied by miniaturization of chromosomes, but an increase in chromosome number," says Dr. Andreas Fleischmann, a member of Heubl's research group. Indeed, the chromosomes of the corkscrew plants are so minute that they can only just be resolved by conventional light microscopy. With the aid of an ingenious preparation technique, Dr. Aretuza Sousa, a specialist in cytogenetics and cytology at the Institute of Systematic Botany at LMU, was able to visualize the ultrasmall chromosomes of Genlisea species by fluorescence microscopy. Thanks to this methodology, the researchers were able to identify individual chromosomes and determine their number, as well as measuring the total DNA content of the nuclear genomes of selected representatives of the genus.
The LMU researchers also discovered a new record-holder. Genlisea tuberosa, a species that was discovered only recently from Brazil, and was first described by Andreas Fleischmann in collaboration with Brazilian botanists, turns out to have a genome that encompasses only 61 million base pairs (= Mbp; the genome size is expressed as the total number of nucleotide bases found on each of the paired strands of the DNA double helix) Thus G. tuberosa possesses now the smallest plant genome known, beating the previous record by 3 Mbp. Moreover, genome sizes vary widely between different Genlisea species, spanning the range from ~60 to 1700 Mbp.
In a development that holds promise for future magnetic memory and logic devices, researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) and Cornell University successfully used an electric field to reverse the magnetization direction in a multiferroic spintronic device at room temperature. This demonstration, which runs counter to conventional scientific wisdom, points a new way towards spintronics and smaller, faster and cheaper ways of storing and processing data.
“Our work shows that 180-degree magnetization switching in the multiferroic bismuth ferrite can be achieved at room temperature with an external electric field when the kinetics of the switching involves a two-step process,” says Ramamoorthy Ramesh, Berkeley Lab’s Associate Laboratory Director for Energy Technologies, who led this research. “We exploited this multi-step switching process to demonstrate energy-efficient control of a spintronic device.”
Ramesh, who also holds the Purnendu Chatterjee Endowed Chair in Energy Technologies at the University of California (UC) Berkeley, is the senior author of a paper describing this research in Nature. The paper is titled “Deterministic switching of ferromagnetism at room temperature using an electric field.” John Heron, now with Cornell University, is the lead and corresponding author.
“The electrical currents that today’s memory and logic devices rely on to generate a magnetic field are the primary source of power consumption and heating in these devices,” he says. “This has triggered significant interest in multiferroics for their potential to reduce energy consumption while also adding functionality to devices.” To demonstrate the potential technological applicability of their technique, Ramesh, Heron and their co-authors used heterostructures of bismuth ferrite and cobalt iron to fabricate a spin-valve, a spintronic device consisting of a non-magnetic material sandwiched between two ferromagnets whose electrical resistance can be readily changed. X-ray magnetic circular dichroism photoemission electron microscopy (XMCD-PEEM) images showed a clear correlation between magnetization switching and the switching from high-to-low electrical resistance in the spin-valve. The XMCD-PEEM measurements were completed at PEEM-3, an aberration corrected photoemission electron microscope at beamline 11.0.1 of Berkeley Lab’s Advanced Light Source.
Phen-Gen is the first computer analysis software that cross-references a patient’s symptoms and a person’s genome sequence, to better aid doctors in diagnosing diseases. The software was created by a team of scientists at A*STAR’s Genome Institute of Singapore (GIS), led by Dr. Pauline Ng. Results from the research were published in the prestigious journal Nature Methods on 4th August 2014.