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"We live in the post-genomic era, when DNA sequence data is growing exponentially", says Miami University (Ohio) computational biologist Iddo Friedberg. "But for most of the genes that we identify, we have no idea of their biological functions. They are like words in a foreign language, waiting to be deciphered." Understanding the function of genes is a problem that has emerged at the forefront of molecular biology. Many groups develop and employ sophisticated algorithms to decipher these "words". However, until now there was no comprehensive picture of how well these methods perform, "To use the information in our genes to our advantage, we first need to take stock of how well we are doing in interpreting these data". To do so, Friedberg and his colleagues, Predrag Radivojac, of Indiana University, Bloomington IN and Sean Mooney, Buck Institute for Research on Aging, Novato CA organized the Critical Assessment of protein Function Annotation, or CAFA. CAFA is a community-wide experiment to assess the performance of the many methods used today to predict the functions of proteins, the workhorses of the cell coded by our genes. Thirty research groups comprising 102 scientists and students participated in CAFA, presented a total of 54 methods. The participating groups came from leading universities in North America, Europe, Asia and Australia. The groups participated in blind-test experiments in which they predicted the function of protein sequences for which the functions are already known but haven't yet been made publicly available. Independent assessors then judged their performance. The results are published in this month's issue of Nature Methods co-authored by members of all the participating groups, with Friedberg and Radivojac as lead authors. Fifteen companion papers have been published in a special issue of BMC Bioinformatics detailing the methods "We have discovered a great enthusiasm and community spirit", said Friedberg, who since 2005 has been organizing Automated Function Prediction (AFP) meetings internationally. This, despite the competitive environment in which research groups want their methods to perform better than their peers' methods. Overall, throughout CAFA there was a highly collegial spirit, and a willingness to share information and science. "Everyone recognized that this is an important endeavor, and that only by a group effort can we move the field forward and learn to harness the deluge of genomic data, turning it into useful information." "For the first time we have broad insight into what works, where improvement is needed, and how we should move the field forward. We will continue running CAFA in the future, as we are confident it will only help generate better methods to understand the information locked in our genomes, and those of other organisms," Friedberg said. The initial analysis suggests that algorithms combining disparate prediction clues taken from different knowledge-bases provide more accurate predictions. The lead methods combined data from phylogenetic, gene-expression and protein-protein interaction data to provide predictions.
Scientists at the U.S. Department of Energy's Brookhaven National Laboratory have discovered that DNA "linker" strands coax nano-sized rods to line up in way unlike any other spontaneous arrangement of rod-shaped objects. The arrangement -- with the rods forming "rungs" on ladder-like ribbons linked by multiple DNA strands -- results from the collective interactions of the flexible DNA tethers and may be unique to the nanoscale.
"This is a completely new mechanism of self-assembly that does not have direct analogs in the realm of molecular or microscale systems," said Brookhaven physicist Oleg Gang, lead author on the paper, who conducted the bulk of the research at the Lab's Center for Functional Nanomaterials. Broad classes of rod-like objects, ranging from molecules to viruses, often exhibit typical liquid-crystal-like behavior, where the rods align with a directional dependence, sometimes with the aligned crystals forming two-dimensional planes over a given area. Rod shaped objects with strong directionality and attractive forces between their ends-resulting, for example, from polarized charge distribution-may also sometimes line up end-to-end forming linear one-dimensional chains.
Using synthetic DNA as a form of molecular glue to guide nanoparticle assembly has been a central approach of Gang's research at the CFN. His previous work has shown that strands of this molecule-better known for carrying the genetic code of living things-can pull nanoparticles together when strands bearing complementary sequences of nucleotide bases (known by the letters A, T, G, and C) are used as tethers, or inhibit binding when unmatched strands are used. Carefully controlling those attractive and inhibitory forces can lead to fine-tuned nanoscale engineering. In the current study, the scientists used gold nanorods and single strands of DNA to explore arrangements made with complementary tethers attached to adjacent rods. They also examined the effects of using linker strands of varying lengths to serve as the tethering glue. After mixing the various combinations, they studied the resulting arrangements using ultraviolet-visible spectroscopy at the CFN, and also with small-angle x-ray scattering at Brookhaven's National Synchrotron Light Source (NSLS,http://www.bnl.gov/ps/nsls/about-NSLS.asp). They also used techniques to "freeze" the action at various points during assembly and observed those static phases using scanning electron microscopy to get a better understanding of how the process progressed over time. The various analysis methods confirmed the side-by-side arrangement of the nanorods arrayed like rungs on a ladder-like ribbon during the early stages of assembly, followed later by stacking of the ribbons and finally larger-scale three-dimensional aggregation due to the formation of DNA bridges between the ribbons. This staged assembly process, called hierarchical, is reminiscent of self-assembly in many biological systems, for example, the linking of amino acids into chains followed by the subsequent folding of these chains to form functional proteins. The stepwise nature of the assembly suggested to the team that the process could be stopped at the intermediate stages. Using "blocker" strands of DNA to bind up the remaining free tethers on the linear ribbon-like structures, they demonstrated their ability to prevent the later-stage interactions that form aggregate structures. "Stopping the assembly process at the ladder-like ribbon stage could potentially be applied for the fabrication of linear structures with engineered properties," Gang said. "For example by controlling plasmonic or fluorescent properties-the materials' responses to light-we might be able to make nanoscale light concentrators or light guides, and be able to switch them on demand."
First predicted by American physicist Douglas Hofstadter in 1976, the butterfly pattern emerges when electrons are confined to a two-dimensional plane and subjected to both a periodic potential energy and a strong magnetic field. The Hofstadter butterfly is a fractal pattern—meaning that it contains shapes that repeat on smaller and smaller size scales. Fractals are common in systems such as fluid mechanics, but rare in the quantum mechanical world. The Hofstadter butterfly is one of the first quantum fractals theoretically discovered in physics but, until now, there has been no direct experimental proof of this spectrum. Columbia University led the study and also involved scientists from the City University of New York, Tohoku University and the National Institute for Materials Science in Japan. Columbia prepared the sample and the UCF team measured the regular recurrence of the high-fidelity periodic pattern, engineered by inducing nanoscale ripples on graphene, a carbon material. The measured recurrence served as the essential proof that the measured spectrum was indeed the Hofstadter butterfly. The image that captured the evidence was taken in UCF Assistant Professor Masa Ishigami’s laboratory. Jyoti Katoch, Ishigami’s graduate student, used a non-contact atomic force high-resolution microscope to image the ripples, which have the height of only 0.2 angstroms (twenty trillionth of a meter), to confirm that the observed Hofstadter butterfly spectrum indeed matched the theoretical prediction. “The arrangement of individual atoms, even just one atom can drastically alter properties of nanoscale materials. That is the basis for nanotechnology,” Ishigami said. “Atomic structures must be resolved to understand the properties of nanoscale materials. What we do here at UCF is to explain why nanoscale materials behave so different by resolving their atomic structures. Only when we understand the origin of the extraordinary properties of nanoscale materials, we can propel nanoscience and technology forward. What Jyoti has done here is to image how graphene is rippled to explain the observed Hofstadter spectrum.” UCF’s laboratory utilizes a novel, the state-of-the-art microscopy technique to simultaneously determine the atomic structure and electronic properties of nanoscale materials such as graphene. Katoch has been working with Ishigami since 2008, when Ishigami joined UCF. Katoch helped build the laboratory and developed the atomic-resolution capability critical to capturing the picture proof for this study. Ishigami has a Ph.D. in physics from the University of California at Berkeley and a bachelor’s degree in physics from the Massachusetts Institute of Technology. He has won multiple awards, including the Intelligence Community postdoctoral fellowship and the Hertz graduate fellowship, and has published more than 30 papers in journals including Science.
Just after the Big Bang, the Universe's dimensions may have been completely different to the four-dimensional space-time we know and love today. Shortly after the Big Bang, the Universe possessed only one dimension of space and one dimension of time. It was basically a straight line. As the Universe began to cool, and expanded, this one dimension of space became “wrapped up” in such a way to create two dimensions of space and one of time — a plane, like a sheet of flat paper. The transition from one to two dimensions of space was calculated by the researchers to occur when the Universe “cooled” to an energy level of 100 TeV (tera-electron volts, a measurement of energy commonly used in particle physics). A period of time after that, the Universe continued to expand and cool until it reached an energy of 1 TeV. At this point, the Universe got promoted to a higher dimension; three dimensions of space and one dimension of time, i.e., the Universe we live in today. Mureika and Stojkovic think the Universe will eventually be promoted again, to a five-dimensional state, at some point in the future.
Scouring the caves of Southwest Oregon, scientists have made the incredible discovery of a fearsome apex predator with massive, sickle claws. No, it's not the Velociraptor fromJurassic Park: it's a large spider that is so unique scientists were forced to create a new taxonomic family for it. This is the first new spider family to be discovered in North America in over 130 years.
"This is something completely new," lead author of a paper on the species, Charles Griswold with the California Academy of Sciences, told SFGate. "It's a historic event."
The discoverers, who published their description paper in the open-access journalZoo Keyshave named thenew speciesTrogloraptor, which translates loosely to "cave robber," and they have dubbed a new spider family—Trogloraptoridae—to accommodate what they believe is a primitive spider. The full species name is Trogloraptor marchingtoniafter one of its discoverers.
Thanks to a little serendipity, Rice University scientists have created a tiny coaxial cable that is about a thousand times smaller than a human hair and has higher capacitance than previously reported microcapacitors. This nanocable was produced with techniques pioneered in the nascent graphene research field and could be used to build next-generation energy-storage systems. It could also find use in wiring up components of lab-on-a-chip processors, but its discovery is owed partly to chance. “We didn’t expect to create this when we started,” said study co-author Jun Lou, associate professor of mechanical engineering and materials science at Rice. “At the outset, we were just curious to see what would happen electrically and mechanically if we took small copper wires known as interconnects and covered them with a thin layer of carbon.”
The tiny coaxial cable is remarkably similar in makeup to the ones that carry cable television signals into millions of homes and offices. The heart of the cable is a solid copper wire that is surrounded by a thin sheath of insulating copper oxide. A third layer, another conductor, surrounds that. In the case of TV cables, the third layer is copper again, but in the nanocable it is a thin layer of carbon measuring just a few atoms thick. The coax nanocable is about 100 nanometers, or 100 billionths of a meter, wide. While the coaxial cable is a mainstay of broadband telecommunications, the three-layer, metal-insulator-metal structure can also be used to build energy-storage devices called capacitors. Unlike batteries, which rely on chemical reactions to both store and supply electricity, capacitors use electrical fields. A capacitor contains two electrical conductors, one negative and the other positive, that are separated by thin layer of insulation. Separating the oppositely charged conductors creates an electrical potential, and that potential increases as the separated charges increase and as the distance between them – occupied by the insulating layer — decreases. The proportion between the charge density and the separating distance is known as capacitance, and it’s the standard measure of efficiency of a capacitor.
Building entire multiple-component devices on single nanowires is a promising strategy for miniaturizing electronic applications. Here we demonstrate a single nanowire capacitor with a coaxial asymmetric Cu-Cu2O-C structure, fabricated using a two-step chemical reaction and vapour deposition method. The capacitance measured from a single nanowire device corresponds to ~140 μF cm−2, exceeding previous reported values for metal–insulator–metal micro-capacitors and is more than one order of magnitude higher than what is predicted by classical electrostatics. Quantum mechanical calculations indicate that this unusually high capacitance may be attributed to a negative quantum capacitance of the dielectric–metal interface, enhanced significantly at the nanoscale.
Social animals usually congregate for protection or mating or to capture bigger prey, but a University of California, Berkeley, biologist has found that the terrestrial hermit crab has a more self-serving social agenda: to kick another crab out of its shell and move into a larger home. All hermit crabs appropriate abandoned snail shells for their homes, but the dozen or so species of land-based hermit crabs – popular terrarium pets – are the only ones that hollow out and remodel their shells, sometimes doubling the internal volume. This provides more room to grow, more room for eggs – sometimes a thousand more eggs – and a lighter home to lug around as they forage.
But empty snail shells are rare on land, so the best hope of moving to a new home is to kick others out of their remodeled shells, said Mark Laidre, a UC Berkeley Miller Post-Doctoral Fellow. When three or more terrestrial hermit crabs congregate, they quickly attract dozens of others eager to trade up. They typically form a conga line, smallest to largest, each holding onto the crab in front of it, and, once a hapless crab is wrenched from its shell, simultaneously move into larger shells. “The one that gets yanked out of its shell is often left with the smallest shell, which it can’t really protect itself with,” said Laidre, who is in the Department of Integrative Biology. “Then it’s liable to be eaten by anything. For hermit crabs, it’s really their sociality that drives predation.”
Laidre says the crabs’ unusual behavior is a rare example of how evolving to take advantage of a specialized niche – in this case, land versus ocean – led to an unexpected byproduct: socialization in a typically solitary animal.
China and India are some of the world's top polluters, with countless cars, factories, and households belching more than 2 million metric tons of carbon soot and other dark pollutants into the air every year. These pollutants aren't just bad news for the countries themselves. A new study reveals that they can affect climate thousands of kilometers away, warming the United States by up to 0.4°C by 2024, while cooling other countries. Some forms of pollution—especially light-colored aerosols such as sulfates that spew from power plants and volcanoes—scatter light back into space, cooling Earth. But dark aerosols, such as soot from diesel engines and power plants, absorb more sunlight than they scatter, gaining heat and warming the air around them. Rapidly developing countries, especially China, India, and those in southeastern Asia, are prolific sources of such aerosols. Over the past few decades, the pall hanging over the region has come to be known as "the Asian brown cloud." Previous studies have shown that even though layers of air polluted with carbon aerosols become substantially warmer, the cloud slightly cools temperatures at ground level, by some estimates reducing the amount of sunlight reaching the surface by between 10% and 15%. The brown cloud also weakens winds during the Asian summer monsoon and changes the timing and location of monsoon rainfall. The cloud has dramatically thickened in recent decades, with some studies showing that dark aerosol emissions from China alone doubled between 2000 and 2006. To gauge the impact of this thickening, Haiyan Teng, a climate scientist at the National Center for Atmospheric Research in Boulder, Colorado, and colleagues used a detailed climate model that evaluated the interactions among land, sea, atmosphere, and sea ice. In three different scenarios, the team boosted dark, carbon-rich emissions from the equator to 50°N and from 70°E to 150°E, a region that covers India and much of China and southeastern Asia. The scenarios simulated what would happen if dark aerosol emissions doubled between 2005 and 2024, increased to six times current rates, and jumped to 10 times current rates. Increasing the emissions to six and 10 times current rates over the course of 20 years seems extreme, says Teng. But the team used these values because the climate model somewhat underestimates the atmospheric warming caused by dark aerosols. Such tweaking of a climate model "is not unusual," says Yi Ming, a climate scientist with the National Oceanic and Atmospheric Administration in Princeton, New Jersey, who was not involved in the study. "It makes sense to increase the [dark aerosol] emissions to produce the right amount of heating, and to better match observations," he says. The sixfold and 10-fold increases in dark aerosol emissions would cause global average temperatures at ground level to rise 0.1°C by 2024, the researchers report in a forthcoming issue of Geophysical Research Letters. But possibly more important, the thickening brown cloud would trigger significant changes in long-term weather patterns that would affect areas thousands of kilometers away. The effect would be somewhat like a human-made El Niño, the climate phenomenon in which sea-surface warming in the tropical Pacific alters temperature and precipitation in the United States and elsewhere. Although scientists have long studied the effects of pollutants on cloud formation and other small-scale phenomena, determining their effects on climate in distant regions is a relatively new field, says Chien Wang, an atmospheric scientist at the Massachusetts Institute of Technology in Cambridge, who wasn't involved in the research. The new findings "are not surprising at all," he notes. However, he adds, the team's new study "is a highly idealized experiment," so the results are probably more accurate in terms of capturing the overall pattern of changes than they are at estimating the precise amount of warming or cooling in a particular locale.
A recent report complied by environmental experts stated an alarming find: The rapid rate in which the Arctic Ocean's ice caps are melting may mean that the sea ice will cease to exist within the next 20-25 years. Scientists from the National Snow and Ice Data Center (NSIDC) released preliminary figures last week, suggesting that Arctic sea ice has reached it lowest level in recorded history. The Arctic sea ice has been monitored since 1979, and according to the data on September 16th Arctic ice extent noted drop of at least 45% since records began and measured at 3.41 million sq. km. The previous record low for Arctic sea ice extent, set on September 18, 2007 with a 4.17-million sq.-km. ice cap, was already shattered by the end of August this year when it had melted to below 4-million sq. km. The depleting ice cover would have serious ramifications for the planet, as Arctic ice acts as a reflector of sunlight, helping regulate the Earth’s temperature and cooling the climate. “When there’s no longer that sea ice below the air mass and it’s just open ocean, that’s when more moisture off the ocean’s surface gets into the atmosphere and the water vapor in the atmosphere makes for more violent storms,” John Yackel, a sea ice geophysicist and climatologist with the Cryosphere Climate Research Group, explained. “We can also expect to see an increase in storm frequency and storm intensity for most of the world’s populated places as the Arctic and Earth continues to warm,” he added.
Sperm pairing is an unusual phenomenon that occurs in New World, but not Australian or New Guinean, marsupial mammals. Newly formed spermatozoa join up precisely along the sides of their heads, leaving their tails to move freely, thus apparently improving their ability to navigate the fluids contained in the female reproductive tract. The mechanism that causes the sperm to pair in the male reproductive tract and, later in the female tract, to separate, is not fully understood.
We are surrounded by tiny, intelligent devices that capture data about how we live and what we do. Soon we'll be able to choreograph them to respond to our needs, solve our problems, and even save our lives. Imagine a factory where every machine, every room, feeds back information to solve problems on the production line. Imagine a hotel room (like the ones at the Aria in Las Vegas) where the lights, the stereo, and the window shade are not just controlled from a central station but adjust to your preferences before you even walk in. Think of a gym where the machines know your workout as soon as you arrive, or a medical device that can point toward the closest defibrillator when you have a heart attack. Consider a hybrid car—like the new Ford Fusion—that can maximize energy efficiency by drawing down the battery as it nears a charging station. There are few more appropriate guides to this impending future than Hawkinson, whose DC-based startup, SmartThings, has built what’s arguably the most advanced hub to tie connected objects together. At his house, more than 200 objects, from the garage door to the coffeemaker to his daughter’s trampoline, are all connected to his SmartThings system. His office can automatically text his wife when he leaves and tell his home A/C system to start powering up. In this future, the intelligence once locked in our devices now flows into the universe of physical objects. Technologists have struggled to name this emerging phenomenon. Some have called it the Internet of Things or the Internet of Everything or the Industrial Internet—despite the fact that most of these devices aren’t actually on the Internet directly but instead communicate through simple wireless protocols. Other observers, paying homage to the stripped-down tech embedded in so many smart devices, are calling it the Sensor Revolution. But here’s a better way to think about what we’re building: It’s the Programmable World. After all, what’s remarkable about this future isn’t the sensors, nor is it that all our sensors and objects and devices are linked together. It’s the fact that once we get enough of these objects onto our networks, they’re no longer one-off novelties or data sources but instead become a coherent system, a vast ensemble that can be choreographed, a body that can dance. Really, it’s the opposite of an “Internet,” a term that even today—in the era of the cloud and the app and the walled garden—connotes a peer-to-peer system in which each node is equally empowered. By contrast, these connected objects will act more like a swarm of drones, a distributed legion of bots, far-flung and sometimes even hidden from view but nevertheless coordinated as if they were a single giant machine. For the Programmable World to reach its full potential, we need to pass through three stages. The first is simply the act of getting more devices onto the network—more sensors, more processors in everyday objects, more wireless hookups to extract data from the processors that already exist. The second is to make those devices rely on one another, coordinating their actions to carry out simple tasks without any human intervention. The third and final stage, once connected things become ubiquitous, is to understand them as a system to be programmed, a bona fide platform that can run software in much the same manner that a computer or smartphone can. Once we get there, that system will transform the world of everyday objects into a designable environment, a playground for coders and engineers. It will change the whole way we think about the division between the virtual and the physical. This might sound like a scary encroachment of technology, but the Programmable World could actually let us put more of our gadgets away, automating activities we normally do by hand and putting intelligence from the cloud into everything we touch.
The way in which radio spectrum is currently allocated to different wireless technologies can lead to gross inefficiencies. In some regions, for instance, the frequencies used by cellphones can be desperately congested, while large swaths of the broadcast-television spectrum stand idle.
One solution to that problem is the 15-year-old idea of “cognitive radio,” in which wireless devices would scan their environments for vacant frequencies and use these for transmissions. Different proposals for cognitive radio place different emphases on hardware and software, but the chief component of many hardware approaches is a bank of filters that can isolate any frequency in a wide band.
Researchers at MIT’s Microsystems Technology Laboratory (MTL) have developed a new method for manufacturing such filters that should improve their performance while enabling 14 times as many of them to be crammed on a single chip. That’s a vital consideration in handheld devices where space is tight. But just as important, the new method uses techniques already common in the production of signal-processing chips, so it should be easy for manufacturers to adopt. There are two main approaches to hardware-based radio-signal filtration: one is to perform the filtration electronically; the other is to convert the radio signal to an acoustic signal — a physical vibration — and then convert it back to an electrical signal.
Both types of filtration use devices called resonators, and acoustic resonators have a couple of clear advantages over electronic ones. One is that their filtration is more precise.
“If I pluck a guitar string — that’s the easiest resonator to think of — it’s going to resonate at some frequency, and it’s going to die down due to losses,” Weinstein explains. “That loss is related to, basically, energy leaked away from that resonance mode into all other frequencies. Less loss means better frequency selectivity, and mechanical acoustic resonators have less loss than electrical resonators.”
Commercial adoption of cognitive radio has been slow for a number of reasons. “Part of it is being able to get the frequency-agile components and do it in a cost-effective manner,” says Thomas Kazior, a principal engineering fellow at Raytheon. “Plus the size constraint: Filters tend to be big to begin with, and banks of tunable filters just make things even bigger.”
The MTL researchers’ work could help with both problems, Kazior says. “We’re talking about making filters that are directly integrated onto, say, a receiver chip, because the little resonator devices are literally the size of a transistor,” he says. “These are all on a tiny scale.”
“They can help with the cost problem because these resonator-type structures almost come for free,” Kazior adds. “Building them is part of the semiconductor fabrication process, using pretty much the existing fabrication steps that you’re using to build the transistor and the rest of the circuits. You just may need to add one, or two at the most, additional steps — out of 100 or more steps."
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Looks like this 100-million-year old spider didn’t get to enjoy its final meal. Trapped in a piece of amber, the juvenile spider appears to be on the cusp of devouring a male wasp that was caught in its web. Such a grisly scene between spider and prey has never before been found in the fossil record. The amazing snapshot shows an event that occurred in the Early Cretaceous period, about 97 to 110 million years ago, in the Hukawng Valley of Myanmar, “almost certainly with dinosaurs wandering nearby,” as the press release about this discovery reports. The spider is a social orb-weaver spider, formally known asGeratonephila burmanica, and its victim is a wasp of the species Cascoscelio incassus. Both species are extinct today but the fossil suggests that insect behavior from the past is not too different from the present. Related wasp species are known to parasitize spider eggs, so there is some poetic justice in the spider’s attack. “This was the wasp’s worst nightmare, and it never ended. The wasp was watching the spider just as it was about to be attacked, when tree resin flowed over and captured both of them,” said entomologist George Poinar Jr. of Oregon State University in the release. This latest fossil doesn’t just capture the dramatic spider attack but also evidence of spider social life in the Early Cretaceous. Another spider, an adult male, is captured some distance away in the amber, co-habiting on the same web as the juvenile. Males of modern-day social orb-weavers are typically found living on female-constructed webs, where they assist in capturing insects and maintaining the web.
Physicists may have created the smallest drops of liquid ever made in the lab. That possibility has been raised by the results of a recent experiment conducted by Vanderbilt physicist Julia Velkovska and her colleagues at the Large Hadron Collider, the world's largest and most powerful particle collider located at the European Laboratory for Nuclear and Particle Physics (CERN) in Switzerland. Evidence of the minuscule droplets was extracted from the results of colliding protons with lead ions at velocities approaching the speed of light. According to the scientists' calculations, these short-lived droplets are the size of three to five protons. To provide a sense of scale, that is about one-100,000th the size of a hydrogen atom or one-100,000,000th the size of a virus. "With this discovery, we seem to be seeing the very origin of collective behavior," said Velkovska, professor of physics at Vanderbilt who serves as a co-convener of the heavy ion program of the CMS detector, the LHC instrument that made the unexpected discovery. "Regardless of the material that we are using, collisions have to be violent enough to produce about 50 sub-atomic particles before we begin to see collective, flow-like behavior." These tiny droplets "flow" in a manner similar to the behavior of the quark-gluon plasma, a state of matter that is a mixture of the sub-atomic particles that makes up protons and neutrons and only exists at extreme temperatures and densities. Cosmologists propose that the entire universe once consisted of this strongly interacting elixir for fractions of a second after the Big Bang when conditions were dramatically hotter and denser than they are today. Now that the universe has spent billions of years expanding and cooling, the only way scientists can reproduce this primordial plasma is to bang atomic nuclei together with tremendous energy.
Despite decades of study, scientists remained unsure as to how insulin binds to the insulin receptor on the surface of cells to allow them to take up sugar from the blood and transform it into energy. Now, a definitive answer has now been found with a team of scientists capturing the first three-dimensional images of insulin “docking” to its receptor. It is hoped that the new knowledge can be exploited to develop new and improved insulin medications to treat type 1 and type 2 diabetes. The international research team was led by scientists from the Walter and Eliza Hall Institute (WEHI) in Melbourne, with collaborators from La Trobe University, the University of Melbourne, Case Western Reserve University, the University of Chicago, the University of York and the Institute of Organic Chemistry and Biochemistry in Prague. Using the MX2 microcrystallography beamline at Australia’s Synchrotron, the researchers were able to obtain highly detailed, three-dimensional x-ray images of insulin and the insulin receptor to reveal how the two interact. “We have now found that the insulin hormone engages its receptor in a very unusual way,” Associate Professor Mike Lawrence from the WEHI said. “Both insulin and its receptor undergo rearrangement as they interact – a piece of insulin folds out and key pieces within the receptor move to engage the insulin hormone. You might call it a 'molecular handshake'.”
An international team of scientists announced today that for the first time ever, they were able to create new human stem cells by cloning older, fully mature human cells. The process cannot be used to create full human clones, as the scientists involved were quick to point out, but it does allow for cells to be grown to fit specific functions within an individual's body — resulting in new, patient-specific liver cells or heart cells that actually pulse on their own, for example. Eventually, scientists hope to refine the process to the point it could be used to help treat disease and even create whole custom organs, but that is likely to be several years away at the earliest. "While there is much work to be done in developing safe and effective stem cell treatments, we believe this is a significant step forward in developing the cells that could be used in regenerative medicine," said Shoukhrat Mitalipov, the leader of the research team and a senior scientist at the Oregon National Primate Research Center (ONPRC), in a news release. The research team was led by scientists at the Oregon Health & Science University, who used a technique similar to the one that created Dolly the sheep, the first mammal cloned from adult cells, back in 1996. In a basic sense, this method involves taking an adult cell from a patient's body, sucking out the central portion containing DNA (the nucleus), then injecting this material into an empty egg cell donated by another human volunteer. The genetic material from the adult cell tells the empty egg cell what type it should mature into.
‘Hijacking’ cells that normally attack common infections to target cancer instead could offer the body a ready-made army against the killer disease University researchers and Oxford-based biotech company, Immunocore Limited have uncovered. The Immunocore team engineered a range of TCRs to bind very tightly to cancer cells and equipped them with the ability to activate non-cancer specific T cells. This new class of drug, named ‘ImmTACs’ (Immune Mobilising mTCR against Cancer), can be used to ‘hi-jack’ the body’s existing T cells that normally kill viruses and redirect them to kill cancer cells instead. The team included Nat Liddy and Katy Adams, Immunocore employees and PhD students at Cardiff University, as well as Professors Andy Sewell and David Price, School of Medicine. Nat Liddy said: "With Immuncore’s novel ImmTAC drugs we found we could effectively target cancer cells and mark them for destruction by the killer T cells that might normally fight common infections. "Our initial studies and findings show that administration of ImmTAC could, potentially, result in the regression of established tumours". The Immunocore team engineered a range of TCRs to bind very tightly to cancer cells and equipped them with the ability to activate non-cancer specific T cells. Recent advances have enabled molecular targeting of disease using immune molecules called antigen receptors. There are two main classes of antigen receptor: antibodies and T cell receptors. Therapeutic application of antibodies has been a huge medical success over the last decade and over 40% of the new drugs on the market in 2011 were based on these molecules. Exploitation of T cell receptors (TCRs) has so far lagged behind, but research led by Immunocore Ltd, with help from Cardiff University’s Institute of Infection and Immunity, is set to close the gap and open up an entirely new field of medical treatments. Professor Andy Sewell, School of Medicine, said: "T cell receptors have advantages over antibodies as these molecules can see inside cells and tell if they are abnormal. Similar technology based around antibodies has shown great promise in clinical trials. This new TCR-based research technology extends this potential as it could possibly be applied to any form of cancer." The most advanced of Immunocore’s ImmTACs, a drug called IMCgp100, is already in clinical trials in the UK and US for the treatment of melanoma. A second oncology ImmTAC, IMCmage1, is set to enter the clinic in both countries later this year and is applicable to the treatment of a large number of poorly served cancer indications. James Noble, Immunocore’s CEO, said: "The power of this new technology lies in its ability to be used for a host of cancers that are currently very difficult to treat. We look forward to building on the emerging clinical data and generating a robust pipeline of products over the coming years".
Scientists have mapped the evolutionary relationships among all 9,993 of the world's known living bird species. The study is an ambitious project that uses DNA-sequence data to create a phylogenetic tree — a branching map of evolutionary relationships among species — that also links global bird speciation rates across space and time. “This is the first dated tree of life for a class of species this size to be put on a global map,” says study co-author Walter Jetz, an evolutionary biologist at Yale University in New Haven, Connecticut. But the endeavour is also controversial, owing to the large number of species for which no sequence data are available. “This is a conceptually brilliant attempt to link space with time while crafting a complete phylogeny,” says Trevor Price, an evolutionary biologist at the University of Chicago in Illinois. “But there are almost certainly introduced artefacts by lacking one-third of the sequences used to create it.” Jetz and his colleagues built on an extensive phylogenomic study, published in 2008, to divide bird species into 158 clades, well-established groups believed to have evolved from a common ancestor2. Using ten fossils, the researchers dated and anchored that backbone, and placed all the living species on the tree, starting with the roughly 6,600 for which genetic information was available. For the remaining 3,330 species for which no genetic data were available, the researchers used specific constraints — such as membership in the same genus — to identify where species would most likely be placed in the tree. They then created thousands of possible tree configurations and modeled estimates of speciation and extinction rates for each one to account for the uncertainty. The researchers found that although rapid radiations have occurred throughout time and space, the rate of speciation has sharply increased over the past 40 million years.
Some scientists question the finding. “For a tree this size, any small systematic biases in assumptions, integrated over 10,000 species, may result in the detection of trends that simply didn’t exist,” says Mark Pagel, an evolutionary biologist at the University of Reading, UK. But when the researchers repeated the analysis using only species for which genetic data exists, they saw roughly the same pattern.
We believe quantum computing may help solve some of the most challenging computer science problems, particularly in machine learning. Machine learning is all about building better models of the world to make more accurate predictions. If we want to cure diseases, we need better models of how they develop. If we want to create effective environmental policies, we need better models of what’s happening to our climate. And if we want to build a more useful search engine, we need to better understand spoken questions and what’s on the web so you get the best answer.
So today we’re launching the Quantum Artificial Intelligence Lab. NASA’s Ames Research Center will host the lab, which will house a quantum computer from D-Wave Systems, and the USRA (Universities Space Research Association) will invite researchers from around the world to share time on it. Our goal: to study how quantum computing might advance machine learning.
Machine learning is highly difficult. It’s what mathematicians call an “NP-hard” problem. That’s because building a good model is really a creative act. As an analogy, consider what it takes to architect a house. You’re balancing lots of constraints -- budget, usage requirements, space limitations, etc. -- but still trying to create the most beautiful house you can. A creative architect will find a great solution. Mathematically speaking the architect is solving an optimization problem and creativity can be thought of as the ability to come up with a good solution given an objective and constraints.
Classical computers aren’t well suited to these types of creative problems. Solving such problems can be imagined as trying to find the lowest point on a surface covered in hills and valleys. Classical computing might use what’s called “gradient descent”: start at a random spot on the surface, look around for a lower spot to walk down to, and repeat until you can’t walk downhill anymore. But all too often that gets you stuck in a “local minimum” -- a valley that isn’t the very lowest point on the surface.
That’s where quantum computing comes in. It lets you cheat a little, giving you some chance to “tunnel” through a ridge to see if there’s a lower valley hidden beyond it. This gives you a much better shot at finding the true lowest point -- the optimal solution.
We’ve already developed some quantum machine learning algorithms. One produces very compact, efficient recognizers -- very useful when you’re short on power, as on a mobile device. Another can handle highly polluted training data, where a high percentage of the examples are mislabeled, as they often are in the real world. And we’ve learned some useful principles: e.g., you get the best results not with pure quantum computing, but by mixing quantum and classical computing.
Can we move these ideas from theory to practice, building real solutions on quantum hardware? Answering this question is what the Quantum Artificial Intelligence Lab is for. We hope it helps researchers construct more efficient and more accurate models for everything from speech recognition, to web search, to protein folding. We actually think quantum machine learning may provide the most creative problem-solving process under the known laws of physics. We’re excited to get started with NASA Ames, D-Wave, the USRA, and scientists from around the world.
Deregulated phosphatidylinositol 3-kinase pathway signaling through AGC kinases including AKT, p70S6 kinase, PKA, SGK and Rho kinase is a key driver of multiple cancers. The simultaneous inhibition of multiple AGC kinases may increase antitumor activity and minimize clinical resistance compared with a single pathway component. A research team from the UK investigated the detailed pharmacology and antitumor activity of the novel clinical drug candidate AT13148, an oral ATP-competitive multi-AGC kinase inhibitor. Gene expression microarray studies were undertaken to characterize the molecular mechanisms of action of AT13148. Their results show that AT13148 caused a substantial blockade of AKT, p70S6K, PKA, ROCK, and SGK substrate phosphorylation and induced apoptosis in a concentration and time-dependent manner in cancer cells with clinically relevant genetic defects in vitro and in vivo. Antitumor efficacy in HER2-positive, PIK3CA-mutant BT474 breast, PTEN-deficient PC3 human prostate cancer, and PTEN-deficient MES-SA uterine tumor xenografts was shown. These experiments demonstrate for the first time that induction of AKT phosphorylation at serine 473 by AT13148, as reported for other ATP-competitive inhibitors of AKT, is not the therapeutically relevant reactivation step. Gene expression studies showed that AT13148 has a predominant effect on apoptosis genes, whereas the selective AKT inhibitor CCT128930 modulates cell-cycle genes. Induction of upstream regulators including IRS2 and PIK3IP1 as a result of compensatory feedback loops was observed.
Thus, the clinical candidate AT13148 is a novel oral multi-AGC kinase inhibitor with potent pharmacodynamic and antitumor activity, which shows a distinct mechanism of action from other AKT inhibitors. AT13148 will now be assessed in a first-in-human phase I trial.
Another innovative feature has been added to the world's first practical "artificial leaf," making the device even more suitable for providing people in developing countries and remote areas with electricity, scientists reported in New Orleans on April 8. It gives the leaf the ability to self-heal damage that occurs during production of energy. Daniel G. Nocera, Ph.D., described the advance during the "Kavli Foundation Innovations in Chemistry Lecture" at the 245th National Meeting & Exposition of the American Chemical Society. Nocera, leader of the research team, explained that the "leaf" mimics the ability of real leaves to produce energy from sunlight and water. The device, however, actually is a simple catalyst-coated wafer of silicon, rather than a complicated reproduction of the photosynthesis mechanism in real leaves. Dropped into a jar of water and exposed to sunlight, catalysts in the device break water down into its components, hydrogen and oxygen. Those gases bubble up and can be collected and used as fuel to produce electricity in fuel cells. "Surprisingly, some of the catalysts we've developed for use in the artificial leaf device actually heal themselves," Nocera said. "They are a kind of 'living catalyst.' This is an important innovation that eases one of the concerns about initial use of the leaf in developing countries and other remote areas." Nocera, who is the Patterson Rockwood Professor of Energy at Harvard University, explained that the artificial leaf likely would find its first uses in providing "personalized" electricity to individual homes in areas that lack traditional electric power generating stations and electric transmission lines. Less than one quart of drinking water, for instance, would be enough to provide about 100 watts of electricity 24 hours a day. Earlier versions of the leaf required pure water, because bacteria eventually formed biofilms on the leaf's surface, shutting down production. "Self-healing enables the artificial leaf to run on the impure, bacteria-contaminated water found in nature," Nocera said. "We figured out a way to tweak the conditions so that part of the catalyst falls apart, denying bacteria the smooth surface needed to form a biofilm. Then the catalyst can heal and re-assemble." Nocera said that about 3 billion people today live in areas that lack access to traditional electric production and distribution systems. That population will grow by billions in the decades ahead. About 1 billion people in the developing world already lack reliable access to clean water. Thus, a clear need exists for a simple device like the artificial leaf that's compatible with local conditions.
Problem: Synthetic biology has the potential to create new organisms that could do an infinite number of things. But the cost of synthesizing DNA is currently prohibitively expensive.
Solution: Austen has developed a new technique to synthesize DNA 10,000 times cheaper than existing technology.
Technology: One of the big challenges with DNA synthesis is error correction during fabrication, fabricating the correct sequence of A, T, G and Cs. Austen solves this problem by fabricating billions of strands at once, quickly (and cheaply) optically sequencing them and then selecting the correct DNA sequences using a fast moving laser.
WELCOME TO THE ECOSPHERE.
A real-time view of the global climate change discussion around the COP17 Conference.
Every tweet tagged with hashtag #COP17 will stimulate growth in a plant or tree in the ECOPSHERE that represents a certain topic (e.g. Sustainability). In this constantly evolving environment users are able to see the discussion develop as people talk on Twitter - a real-time visualisation of the global conversation.
The-state-of-the art ECOSPHERE microsite was produced by STINK DIGITAL LONDON/NEW YORK and developed and designed by MINIVEGAS Amsterdam/Los Angeles.
MINIVEGAS has developed a real-time infographic of sorts, treating the viewer to a stunning visual representation of the evolving global discussion. A lush 3D environment that allows the viewer to explore, view content up close or zoom out to observe the visualisation as a whole. At the core of the experience is a digital growth algorithm is based on actual organic growth in the plant world -- plants and trees grow organically with every #COP17 tweet and topics compete for space and light on the sphere.
The ECOSPHERE constantly listens to the global conversation on Twitter -- every new tweet tagged with hashtag #COP17 is brought into the environment, scanned for keywords and then grouped with similar contributions, connecting input from around the world - building conversations in a fascinating evolving environment.
CNN COVERAGE
CNN International will also use the ECOSPHERE Project in its live reporting about the summit. CNN correspondents Robyn Curnow and Diana Magnay will report and comment on events in and around the meeting, exploring what effect the decisions taken in Durban will have on the world, on business and on every individual person on the planet.
In addition, the ECOSPHERE Project will also be part of the December edition of "Road to Durban: A Green City Journey". In the months approaching the summit, CNN made the journey to Durban starting in the UK and travelling across Germany and Turkey reporting on local climate protection projects. In December "Road to Durban: A Green City Journey" will be dedicated to the themes of the 17th World Climate Summit. For more information please go to www.cnn.com/roadtodurban.
Recently, mid-air displays are attracting a lot of attention in the fields of digital signage and home TV, and many types of holographic displays have been proposed and developed. Although we can "see" holograhpic images as if they are really floating in front of us, we cannot "touch" them, because they are nothing but light. This project adds tactile feedback to the hovering image in 3D free space. Tactile sensation requires contact with objects, but including a stimulator in the work space dilutes the appearance of holographic images. The Airborne Ultrasound Tactile Display solves this problem by producing tactile sensation on a user's hand without any direct contact and without diluting the quality of the holographic projection.
MIT researchers find that the key to purple bacteria’s light-harvesting prowess lies in highly symmetrical molecules. Purple bacteria are among Earth’s oldest organisms, and among its most efficient in turning sunlight into usable chemical energy. Now, a key to their light-harvesting prowess has been explained through a detailed structural analysis by scientists at MIT.
A ring-shaped molecule with an unusual ninefold symmetry is critical, the researchers found. The circular symmetry accounts for its efficiency in converting sunlight, and for its mechanical durability and strength. The new analysis, carried out by professors of chemistry Jianshu Cao and the late Robert Silbey, postdoc Liam Cleary, and graduate students Hang Chen and Chern Chuang, has been published in Proceedings of the National Academy of Sciences.
“The symmetry makes the energy transfer much more robust,” Cao says. “Most biological systems are quite soft and disordered. You would not expect a regular structure, almost a perfect structure,” as is found in this primitive microbe, he says.
In these regular round complexes, Cao says, “nature only used certain symmetry numbers: mostly ninefold, some eightfold, very few tenfold. It’s very selective.” His group’s mathematical analysis shows there are good reasons for that, he says.
These ring-shaped molecules, in turn, are arranged in a hexagonal pattern on the spherical photosynthetic membrane of purple bacteria, Cao says.
“With these symmetry numbers, the interactions between all pairs of the symmetric rings are optimized at the same time. … We believe that nature found the most robust structures in terms of energy transfer,” Cao says. Both eightfold and tenfold symmetries also work, though not as well: Only a lattice made up of ninefold symmetric complexes can tolerate an error in either direction. “You want consecutive numbers so it can tolerate such mistakes,” Cao says.
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