Learning to read Chinese might seem daunting to Westerners used to an alphabetic script, but brain scans of French and Chinese native speakers show that people harness the same brain centers for reading across cultures.
Via Sakis Koukouvis
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Genetic residue from ancient viral infections has been repurposed to play a vital role in acquiring pluripotency, the developmental state that allows a fertilized human egg to become all the cells in the body.
Genetic material from ancient viral infections is critical to human development, according to researchers at the Stanford University School of Medicine. They’ve identified several noncoding RNA molecules of viral origins that are necessary for a fertilized human egg to acquire the ability in early development to become all the cells and tissues of the body. Blocking the production of this RNA molecule stops development in its tracks, they found.
The discovery comes on the heels of a Stanford study earlier this year showing that early human embryos are packed full of what appear to be viral particles arising from similar left-behind genetic material. “We’re starting to accumulate evidence that these viral sequences, which originally may have threatened the survival of our species, were co-opted by our genomes for their own benefit,” said Vittorio Sebastiano, PhD, an assistant professor of obstetrics and gynecology. “In this manner, they may even have contributed species-specific characteristics and fundamental cell processes, even in humans.”
Sebastiano is a co-lead and co-senior author of the study, published online Nov. 23 in Nature Genetics.Postdoctoral scholar Jens Durruthy-Durruthy, PhD, is the other lead author. The other senior author of the paper is Renee Reijo Pera, PhD, a former professor of obstetrics and gynecology at Stanford who is now on the faculty of Montana State University.
Sebastiano and his colleagues were interested in learning how cells become pluripotent, or able to become any tissue in the body. A human egg becomes pluripotent after fertilization, for example. And scientists have learned how to induce other, fully developed human cells to become pluripotent by exposing them to proteins known to be present in the very early human embryo. But the nitty-gritty molecular details of this transformative process are not well understood in either case.
The researchers knew that a type of RNA molecules called long-intergenic noncoding, or lincRNAs, have been implicated in many important biological processes, including the acquisition of pluripotency. These molecules are made from DNA in the genome, but they don’t go on to make proteins. Instead they function as RNA molecules to affect the expression of other genes.
Sebastiano and Durruthy-Durruthy used recently developed RNA sequencing techniques to examine which lincRNAs are highly expressed in human embryonic stem cells. Previously, this type of analysis was stymied by the fact that many of the molecules contain highly similar, very repetitive regions that are difficult to sequence accurately.
They identified more than 2,000 previously unknown RNA sequences, and found that 146 are specifically expressed in embryonic stem cells. They homed in on the 23 most highly expressed sequences, which they termed HPAT1-23, for further study. Thirteen of these, they found, were made up almost entirely of genetic material left behind after an eons-ago infection by a virus called HERV-H.
HERV-H is what’s known as a retrovirus. These viruses spread by inserting their genetic material into the genome of an infected cell. In this way, the virus can use the cell’s protein-making machinery to generate viral proteins for assembly into a new viral particle. That particle then goes on to infect other cells. If the infected cell is a sperm or an egg, the retroviral sequence can also be passed to future generations.
HIV is one common retrovirus that currently causes disease in humans. But our genomes are also littered with sequences left behind from long-ago retroviral infections. Unlike HIV, which can go on to infect new cells, these retroviral sequences are thought to be relatively inert; millions of years of evolution and accumulated mutations mean that few maintain the capacity to give instructions for functional proteins.
After identifying HPAT1-23 in embryonic stem cells, Sebastiano and his colleagues studied their expression in human blastocysts — the hollow clump of cells that arises from the egg in the first days after fertilization. They found that HPAT2, HPAT3 and HPAT5 were expressed only in the inner cell mass of the blastocyst, which becomes the developing fetus. Blocking their expression in one cell of a two-celled embryo stopped the affected cell from contributing to the embryo’s inner cell mass. Further studies showed that the expression of the three genes is also required for efficient reprogramming of adult cells into induced pluripotent stem cells.
The wired rose leaf can be darkened or lightened with a zap of electricity.
Scientists have just taken a surprising leap toward actually integrating living plants into human electronics and power systems: A team of Swedish botanists and electrical engineers unveiled a fascinating method of growing and powering conductive wires inside living plants. Led by Eleni Stavrinidou—a bioelectronic engingeer at Linköping University in Linköping, Sweden—the scientists employed a transparent, conductive gel that cut roses could naturally soak up into their stems and leaves.
After a few hours, the gel material would harden and form flexible wires inside the plants' stems. Thanks to the fantastic properties of the plant-embedded wires, electric current could even be run through the wired stems, without (as far as the scientists could tell) damaging the plants.
"Although many attempts have been made to augment plant function with electroactive materials, [until now] plants' 'circuitry' has never been directly merged with electronics," writes the reseach team. The scientists describe their curious, bionic vegetation today in a remarkably titled science paper —"Electronic plants"—in the journal Science Advances.
Stavrinidou's research team tested countless conductive materials before they came across a winner. Their aim was to get plants to soak up materials that could later harden into wires through the plants xylem, the vein-like system a plant uses to transport water and nutrients. However, most materials (for example, two molecules called pyrrole and aniline) either simply wouldn't uptake, proved toxic when it came down to the hardening phase, or would clog the xylem. In the end, the winning material was a transparent, organic polymer that basically acts like conductive plastic. It's a flavor of a material called PEDOT—short for poly(3,4-ethylenedioxythiophene).
Via Neelima Sinha
Scientists from the University of Leicester have for the first time created a detailed image of a toxin - called pneumolysin - associated with deadly infections such as bacterial pneumonia, meningitis and septicaemia.
he three-year study involving four research groups from across the University has been described as an exciting advance because it points to the possibility of creating therapeutics that block assembly of pneumolysin pores to treat people with pneumococcal disease. The University has recently set up a company Axendos Therapeutics to pursue this aim.
Using a technique called X-ray crystallography at Diamond Light Source, the UK's national synchrotron science facility, the Leicester team was able to see the individual atoms of the toxin. The structure not only reveals what the toxin looks like, but also shows how it assembles on the surface of cells to form lethal pores.
Professor Wallis said: "Our research is about a toxin called pneumolysin produced by a bacterium called pneumococcus (aka Streptococcus pneumoniae). Pneumococcal infections are the leading cause of bacterial pneumonia as well as the cause of a range of other life-threatening diseases such as meningitis and septicaemia. Pneumolysin is instrumental in the ability of pneumococcus to cause disease. The World Health Organization (WHO) estimated that more than 1.6 million people die every year from pneumococcal infections, including more than 800,000 children under 5 years old.
"The aim of the research was to find out how pneumolysin kills our cells, thereby causing tissue damage and contributing to disease. In particular we wanted to find out how multiple copies of the toxin assemble on the surface of cells. "We managed to determine the structure of pneumolysin using a technique called X-ray crystallography, which enables us to see the individual atoms of the toxin. The structure not only reveals what the toxin looks like, but also shows how it assembles to form lethal pores.
"Ours is the first detailed structure of pneumolysin. This level of detail is important and useful because it enables us to begin to understand how the toxin works. For example, we can see which parts of the toxin come together during pore assembly. When we disrupt these contacts, the toxin becomes inactivated so can no longer kill cells. "The mode of action of pneumolysin action revealed by our work appears to be conserved in related toxins from other disease-causing bacteria e.g. toxins produced by pathogenic species of Listeria."
The Top 500 supercomputer rankings are a fun way to gauge which countries boast the most powerful rigs in the world. And, perhaps unsurprisingly, China has won the top spot for the sixth time in a row.
Not only that, but the nation has nearly tripled its supercomputer count from 37 to 109 in only six months. Although the US still maintains a healthy 201 supercomputers, first place in terms of quantity, that’s actually a record low for the nation in the Top 500, which was conceived back in 1993.
Produced by its National University of Defense Technology, China’s Tianhe-2 bolsters a whopping 3,120,000 cores with the ability to achieve 33.86 quadrillion floating point operations (flops) per second. As if that information alone wasn’t intimidating enough, those numbers are almost double that of the US energy department’s still powerful, but not quite as monumental, Titan Cray XK7, apparently capable of 17.59 petaflops, according to the Linpack benchmark.
A United States-owned rig also occupies the third place position, that is, IBM’s Sequoia, custom-built for the National Nuclear Security Administration and housed in the Lawrence Livermore National Lab. The Sequoia, which claimed the top spot in 2012, has since been surpassed by both the Tianhe-2 and the Titan Cray XK7.
Among the top 10 of the Top 500, only the Trinity and Hazel Hen are fresh faces to the list, positioned at numbers 6 and 8, respectively. While the Trinity was conceived for the US Department of Energy, the Hazel Hen rests in Stuttgart, Germany.
In an interview with the BBC, Rajnish Arora, vice president of enterprise computing at IDC Asia Pacific, explained to the network that China’s domination in the supercomputer space is less reflective of the United States’ inability to compete and more representative of China’s economic growth.
“When China started off appearing on the center stage of the global economy in the 80s and 90s, it was predominately a manufacturing hub,” Arora said. “All the IP or design work would happen in Europe or the US and the companies would just send manufacturing or production jobs to China. Now as these companies become bigger, they want to invest in technical research capabilities, so that they can create a lot more innovation and do basic design and engineering work.”
Via Ben van Lier
For decades, bacteria have served society by producing antibiotics – the chemical compounds that can cure infectious diseases. However, it is possible that many natural microorganisms carry the recipes for the medicines of the future hidden in their genetic material, without this part of their genetic code being activated or “switched on”.
But now, biotechnologists from SINTEF and NTNU are developing technology that will make it easier to find – and exploit – these hidden and unutilized medicine factories in bacteria that exist in the natural environment. The hunt will concentrate on marine bacteria, and is one of the projects run by the new Norwegian Centre for Digital Life.
“Our aim is to identify novel compounds that are capable, for example, of killing cancer cells or antibiotic-resistant bacteria. The technology that we are developing will reduce the time taken to search for these and to make the production process more efficient,” says Alexander Wentzel, a senior scientist at SINTEF.
As a strategy, scientists will clip out genetic material from a large number of microorganisms before they transfer their DNA to cultivable bacteria; organisms whose characteristics have already been studied and will be optimized by the researchers in the INBioPharm project. The alterations will enable these organisms to switch on production of new substances that cannot be produced in the microorganism from which the DNA has been extracted.
With the aid of systems biology and synthetic biology (see fact-box), the project will develop the microorganisms in a way which, when they are cultivated, will produce small test quantities of all the possible products, and later, enable mass-production of the most promising substances.
Twist Bioscience dramatically scaled down the equipment for synthesizing DNA in a lab, making the process cheaper and faster. The stamp-sized wafers contain 100 microwells. Each of these contains 100 nanowells in which DNA can be synthesized.
AT TWIST BIOSCIENCE’S office in San Francisco, CEO Emily Leproust pulled out of her tote bag two things she carries around everywhere: a standard 96-well plastic plate ubiquitous in biology labs and her company’s invention, a silicon wafer studded with a similar number of nanowells.
Twist’s pitch is that it has dramatically scaled down the equipment for synthesizing DNA in a lab, making the process cheaper and faster. As Leproust gave her spiel, I looked from the jankety plastic plate, the size of two decks of cards side by side, to the sleek stamp-sized silicon wafer and politely nodded along. Then she handed me a magnifying lens to look down the wafer’s nanowells. Inside each nanowell was another 100 microscope holes.
That’s when I actually got it. The 96-well plate was not equivalent to the wafer, the entire plate was equivalent toone nanowell on the wafer. To put a number on it, traditional DNA synthesis machines can make one gene per 96-well plate; Twist’s machine can make 10,000 genes on a silicon wafer set the same size as the plate.
But who wants to order 10,000 genes? Until recently, that question might have been met with silence. “It was a lonely time,” says Leproust of her early fundraising efforts for Twist. Fast forward a couple years, though, and Twist has just signed a deal to sell at least 100 million letters of DNA—equivalent to tens of thousands of genes—to Ginkgo Bioworks, a synthetic biology outfit that inserts genes into yeast to make scents like rose oil or flavors like vanillin. Ginkgo is at the forefront of a wave of synthetic biology companies, bolstered by new gene-editing technologies likeCrispr and investor interest.
“We’re Intel and Ginkgo is Microsoft,” says Leproust, which sounds exactly the kind of rhetoric you hear all the time in startupland. But her words reveal Twist’s specific ambition to be the driver behind synthetic biology innovations. Synthesizing genes in a lab allows biologists to design—down to the letter—the ones they want to test. Companies out there are already tinkering with DNA in various cells to create spider silk, cancer treatments, biodegradable plastic, diesel fuel—and Twist’s founders thinks the company can become the driving technology behind that new world.
Via Marko Dolinar
For nearly 400 years, Thanksgiving has been a time in North America when families come together to celebrate food and agriculture. As we reflect on yet another year, agricultural scientists at USDA continue to keep a wary eye on the future. At the end of what may be the hottest year on record, a period of drought has threatened the heart of one of the most important agricultural production zones in the United States. Water demands are increasing, and disease and pest pressures are continually evolving. This challenges our farmers’ ability to raise livestock and crops. How are science and technology going to address the problems facing our food supply?
To find answers, agricultural scientists turn to data—big data. Genomics, the field of science responsible for cataloging billions of DNA base pairs that encode thousands of genes in an organism, is fundamentally changing our understanding of plants and animals. USDA has already helped to fund and collect genomes for 25 crop plant species, important livestock and fish species, and numerous bacteria, fungi, and insect species related to agricultural production. Other USDA-supported research projects expanding these efforts are currently underway, including genome sequencing of 1,000 breeds of bulls and 5,000 insect species in the i5K initiative. But classifying and understanding DNA is only part of the story.
Even if neighboring farmers were to raise identical varieties of tomato, small variations in the environment can reduce crop performance and/or increase pests and disease. So, scientists and farmers are increasingly using technology like satellites, drones, sensors, and laser-guided tractors to collect thousands of data points about the environmental conditions in a field, such as temperature, humidity, soil composition, or slope of the land. Using these “precision agriculture” techniques, farmers could reduce their environmental footprint by matching land management practices to the unique environments on their farm.
In the long term, USDA researchers are hoping to combine precision agriculture and genomics in a remarkable way—to develop crops with combinations of genes that lead to the best performance in specific environments. To support this goal, USDA continues to lead the way in collecting and maintaining open access to these types of agriculture data. As a result, your local farmer’s market or grocery store may one day have even more varieties of produce to choose from on Thanksgiving, with each optimized for the farm or field on which it was grown.
Via Integrated DNA Technologies
Australian and Italian researchers have developed a smart sensor that can detect single molecules in chemical and biological compounds – a highly valued function in medicine, security and defence.
The researchers from the University of New South Wales, Swinburne University of Technology, Monash University and the University of Parma in Italy used a chemical and biochemical sensing technique called surface-enhanced Raman spectroscopy (SERS), which is used to understand more about the make-up of materials.
They were able to greatly amplify the technique's performance by taking advantage of metal nanostructures, which help generate 'hotspots' in close proximity to the metal surfaces.
The sensor was created using gold nanoparticles which self-assemble onto a gold- and silica-coated silicon base. This approach means the nanoparticles find the perfect spacing to achieve lots of uniformly distributed hotspots on the surface.
The hotspots also used a heat responsive polymer which acted as a gate to trap molecules, but importantly also allow them to be released down the track. "The sensor shows not only a good SERS reproducibility but also the ability to repetitively catch and release molecules for single-molecular sensing," postdoctoral fellow at Swinburne's Centre for Micro-Photonics, Dr Lorenzo Rosa, said.
"This reversible trapping process makes it possible to detect an abundance of analytes in one measurement, but also to reuse the SERS substrate multiple times." The technique used in this work has various applications for other measurement and detection systems sensitive to humidity, pH and light.
QBI researchers have uncovered an entirely new form of secret light communication used by mantis shrimp.
The findings may have applications in satellite remote sensing, biomedical imaging, cancer detection, and computer data storage.
Dr Yakir Gagnon, Professor Justin Marshall and colleagues previously showed that mantis shrimp (Gonodactylaceus falcatus) can reflect and detect circular polarising light, an ability extremely rare in nature. Until now, no-one has known what they use it for.
The new study shows the shrimp use circular polarisation as a means to covertly advertise their presence to aggressive competitors. “In birds, colour is what we’re familiar with and in the ocean, reef fish display with colour – this is a form of communication we understand. What we’re now discovering is there’s a completely new language of communication,” said Professor Marshall.
Linear polarised light is seen only in one plane, whereas circular polarised light travels in a spiral – clockwise or anti-clockwise – direction. Humans cannot perceive polarised light without the help of special lenses, often found in sunglasses.
"We've determined that a mantis shrimp displays circular polarised patterns on its body, particularly on its legs, head and heavily armoured tail," he said. "These are the regions most visible when it curls up during conflict."
“These shrimps live in holes in the reef,” said Professor Marshall. “They like to hide away; they’re secretive and don’t like to be in the open.” They are also “very violent”, Professor Marshall adds. “They’re nasty animals. They’re called mantis shrimps because they have a pair of legs at the front used to catch their prey, but 40 times faster than the preying mantis. They can pack a punch like a .22 calibre bullet and can break aquarium glass. Other mantis shrimp know this and are very cautious on the reef.”
Researchers dropped a mantis shrimp into a tank with two burrows to hide in: one reflecting unpolarised light and the other, circular polarised light. The shrimps chose the unpolarised burrow 68 per cent of the time – suggesting the circular polarised burrow was perceived as being occupied by another mantis shrimp.
“If you essentially label holes with circular polarising light, by shining circular polarising light out of them, shrimps won’t go near it,” said Professor Marshall. “They know – or they think they know – there’s another shrimp there.
An ancient, 3-foot-tall (0.9 meters) human whose diminutive stature has earned it the nickname "hobbit" has puzzled evolutionary scientists since its little bones were discovered on the Indonesian island of Flores. Some have suggested the individual was a Homo sapiens with some miniaturizing disorder.
Now, teeth from the hobbit suggest it belonged to a unique species rather than a modern human with a growth disorder. The new research also suggests hobbits may share a direct ancestor with modern humans.
Via Kathy Bosiak
Physicists from the University of Würzburg have managed to use an electric current to emit light from a nanoantenna only 250 nanometres in size. They present their breakthrough in the magazine "Nature Photonics".
Electrically driven miniature light sources are of potential use, for example, in smartphone displays, where the integration of 3D techniques will require pixel densities far beyond nowadays standards. Nano light sources could also be used in computer chips for low-loss data exchange between processor cores at the speed of light.
How do optical antennas work? "In fact, they work in a similar way as their much larger radio-frequency counterparts," Bert Hecht explains: There an AC voltage is applied that causes electrons in the antenna to oscillate. As a result, the antenna emits electromagnetic waves of a well-defined wavelength and spatial pattern determined by the antenna geometry. However, in the optical frequency regime the alternating current concept cannot be applied anymore.
It’s a quantum mechanical effect that led to the Würzburg breakthrough. The optical antenna they developed has two arms each fitted with a contact wire, their ends almost touching. The tiny space between the arms is filled with a gold nanoparticle which touches the one arm and leaves a gap of about one nanometre to the other arm. The gap is so small that electrons can bridge it due to the quantum mechanical tunnel effect when applying voltage, directly causing oscillations at optical frequencies.
The antenna thus constructed emits electromagnetic waves in the form of visible light. The colour of the light is determined by the length of the antenna arms. "This enables us to build extremely compact light sources and we can tune their properties simply by adjusting the antenna geometry," says Hecht.
Graphene has been hailed as a wonder material since it was first isolated from graphite in 2004. Graphene is just a single atom thick but it is flexible, stronger than steel, and capable of efficiently conducting heat and electricity.
However, widespread industrial adoption of graphene has so far been limited by the expense of producing it. Affordable graphene production could lead to a wide range of new technologies reaching the market, including synthetic skin capable of providing sensory feedback to people with limb prostheses.
Researchers at the University of Glasgow have now found a way to produce large sheets of graphene using the same cheap type of copper used to manufacture lithium-ion batteries found in many household devices.
In a new paper published today in the journal Scientific Reports, a team led by Dr Ravinder Dahiya explain how they have been able to produce large-area graphene around 100 times cheaper than ever before. Graphene is often produced by a process known as chemical vapour deposition, or CVD, which turns gaseous reactants into a film of graphene on a special surface known as a substrate.
The research team used a similar process to create high-quality graphene across the surface of commercially-available copper foils of the type often used as the negative electrodes in lithium-ion batteries. The ultra-smooth surface of the copper provided an excellent bed for the graphene to form upon.
They found that the graphene they produced offered a stark improvement in the electrical and optical performance of transistors which they made compared to similar materials produced from the older process.
Dr Dahiya, of the University of Glasgow's School of Engineering, said: "The commercially-available copper we used in our process retails for around one dollar per square metre, compared to around $115 for a similar amount of the copper currently used in graphene production. This more expensive form of copper often required preparation before it can be used, adding further to the cost of the process.
Mathematical modeling enables $100 depth sensor to approximate the measurements of a $100,000 piece of lab equipment.
The system uses a technique called fluorescence lifetime imaging, which has applications in DNA sequencing and cancer diagnosis, among other things. So the new work could have implications for both biological research and clinical practice.
“The theme of our work is to take the electronic and optical precision of this big expensive microscope and replace it with sophistication in mathematical modeling,” says Ayush Bhandari, a graduate student at the MIT Media Lab and one of the system’s developers. “We show that you can use something in consumer imaging, like the Microsoft Kinect, to do bioimaging in much the same way that the microscope is doing.”
The MIT researchers reported the new work in the Nov. 20 issue of the journal Optica. Bhandari is the first author on the paper, and he’s joined by associate professor of media arts and sciences Ramesh Raskar and Christopher Barsi, a former research scientist in Raskar’s group who now teaches physics at the Commonwealth School in Boston.
Fluorescence lifetime imaging, as its name implies, depends on fluorescence, or the tendency of materials known as fluorophores to absorb light and then re-emit it a short time later. For a given fluorophore, interactions with other chemicals will shorten the interval between the absorption and emission of light in a predictable way. Measuring that interval — the “lifetime” of the fluorescence — in a biological sample treated with a fluorescent dye can reveal information about the sample’s chemical composition.
In traditional fluorescence lifetime imaging, the imaging system emits a burst of light, much of which is absorbed by the sample, and then measures how long it takes for returning light particles, or photons, to strike an array of detectors. To make the measurement as precise as possible, the light bursts are extremely short.
The fluorescence lifetimes pertinent to biomedical imaging are in the nanosecond range. So traditional fluorescence lifetime imaging uses light bursts that last just picoseconds, or thousandths of nanoseconds.
A new study finds that while the human brain can distinguish between millions of colors, it has difficulty remembering specific shades. For example, most people can easily tell the difference between azure, navy and ultramarine, but when it comes to remembering these shades, people tend to label them all as blue, the study found. This tendency to lump colors together could explain why it's so hard to match the color of house paint based on memory alone, the researchers said. [Eye Tricks: Gallery of Visual Illusions].
Many cultures have the same color words or categories, said Jonathan Flombaum, a cognitive psychologist at Johns Hopkins University in Baltimore. "But at the same time, there's a lot of debate around the role those categories play in the perception of color," he said.
In the study, Flombaum and his colleagues conducted four experiments on four different groups of people. In the first experiment, they asked people to look at a color wheel with 180 different hues, and asked them to find the best name for each color. The exercise was designed to find the perceived boundaries between colors, the researchers said. In a second experiment, the scientists showed different people the same colors, but this time they asked them to find the "best example" of a particular color.
For a third experiment, the researchers showed participants colored squares, and asked them to select the best match on the color wheel. In a fourth experiment, another group of participants completed the same task, but there was a delay of 90 milliseconds between when each color square was displayed and when they were asked to select the best match on the color wheel.
The results revealed that categories are indeed important in how people identify and remember colors. The participants who were asked to name the colors reliably saw five hues: blue, yellow, pink, purple and green. Most of the colors were given one name, butambiguous colors got two labels, such as blue and green. "Where that fuzzy naming happened, those are the boundaries" between colors, Flombaum told Live Science
But what was really striking was how the people in the memory experiment remembered the colors they saw, the scientists said. The researchers expected that the participants' responses for what colors they had seen would reflect a bell curve centered on the correct color. But instead, they found that the distribution of responses was skewed toward the "best example" of the color they had seen, not the true color.
The findings suggest that the brain remembers colors as discrete categories as well as a continuum of shades, and combines these representations to produce a memory. There could be many reasons for this, but it likely boils down to efficiency, Flombaum said. "Most of the time, what we care about is the category," he said.
Via Levin Chin
Sequencing reveals that the genome of the Tardigrade has been published, revealing approximately 6,000 genes of foreign origin.
The tardigrade, also known as the water bear, is renowned for many reasons. The nearly indestructible micro-organism is known to have the capacity to survive extreme temperatures (-272C to 151C), and is the only animal able to survive in the vacuum of space.
Today, with the publication of its genome in PNAS, the humble water bear can add another item to its exhaustive list of superlatives. Sequencing of the genome, performed by a team of researchers at the University of North Carolina at Chapel Hill, has revealed that a massive portion of the tiny organism’s genome is of foreign origin. Indeed, nearly 17.5% of the water bear’s genome is comprised of foreign DNA, translating to a genetic complement of approximately 6,000 genes. These genes are primarily of bacterial origin, though genes from fungi and plants have also been identified.
Horizontal gene transfer, defined as the shifting of genetic material materially (thus horizontally) between organisms is widespread in the microscopic world. In humans, however, the process does occur, but in a limited fashion, and via transposons and viruses. Other microscopic animals are also known to have large complements of foreign genes.
The authors of the newly published work have proposed a method by which this extremely extensive gene transfer may have occurred. Tardigrades have long been known to undergo, and survive, the process of desiccation (extreme drying out). The authors therefore postulated that during this drying out process and the subsequent rehydration, the tardigrade’s genome may have undergone significant sheering and breakage, resulting in a general loss of integrity and leakiness experienced by the water bear’s nucleus. In turn, this compromised nuclear integrity may have enabled foreign genetic material to readily integrate the genome, in much the same way as scientists perform gene transfer through the process of electroporation.
For now, the tardigrade has a dual claim to fame, being the only known animal to survive the vacuum of space, and being the animal with the largest genetic complement. Only with the study of other micro-organisms will we be able to validate if the humble tardigrade maintains its two, current, great claims to fame.
"Animals that can survive extreme stresses may be particularly prone to acquiring foreign genes—and bacterial genes might be better able to withstand stresses than animal ones," said Boothby, a postdoctoral fellow in Goldstein's lab. After all, bacteria have survived the Earth's most extreme environments for billions of years.
The team speculates that the DNA is getting into the genome randomly but what is being kept is what allows tardigrades to survive the harshest of environments, e.g. stick a tardigrade in a - 80 celsius freezer for a year or 10 and it starts running around in 20 minutes after thawing.
This is what the team thinks happens: when tardigrades are under conditions of extreme stress such as desiccation - or a state of extreme dryness—Boothby and Goldstein believe that the tardigrade's DNA breaks into tiny pieces. When the cell rehydrates, the cell's membrane and nucleus, where the DNA resides, becomes temporarily leaky and DNA and other large molecules can pass through easily. Tardigrades not only can repair their own damaged DNA as the cell rehydrates but also stitch in the foreign DNA in the process, creating a mosaic of genes that come from different species.
Army ants build living bridges by linking their bodies to span gaps and create shortcuts across rainforests in Central and South America. An international team of researchers has now discovered these bridges can move from their original building point to span large gaps and change position as required.
The bridges stop moving when they become so long that the increasing costs incurred by locking workers into the structure outweigh the benefit that the colony gains from further shortening their trail. Bridges dismantle when the ants in the structure sense the traffic walking over them slows down below a critical threshold.
Co-lead author Dr Christopher Reid, a postdoctoral researcher at the University of Sydney's Insect Behaviour and Ecology Lab and formerly with the New Jersey Institute of Technology, said the findings could be applied to develop swarm robotics for exploration and rescue operations. By analysing how ants optimise utility, researchers may be able to create simple control algorithms to allow swarms of robots to behave in similar ways to an ant colony.
The team of researchers - from the Max Planck Institute for Ornithology (Konstanz, Germany), University of Konstanz, and the United States's New Jersey Institute of Technology, Princeton University and George Washington University - found the bridges can assemble and disassemble in seconds. They can also change their position in response to the immediate environment.
The dynamic nature of the bridges has been found to facilitate travel by the colony at maximum speed, across unknown and potentially dangerous terrains. Prior to the study it was assumed that, once they had been built, the bridges were relatively static structures.
The paper, 'Army ants dynamically adjust living bridges in response to a cost-benefit trade-off', is being published in the journal Proceedings of the National Academy of Sciences (PNAS).
A Northeastern University research team has found “extensive” leakage of users’ information — device and user identifiers, locations, and passwords — into network traffic from apps on mobile devices, including iOS, Android, and Windows phones. The researchers have also devised a way to stop the flow.
David Choffnes, an assistant professor in the College of Computer and Information Science, and his colleagues developed a simple, efficient cloud-based system called ReCon. It detects leaks of “personally identifiable information,” alerts users to those breaches, and enables users to control the leaks by specifying what information they want blocked and from whom.
The team’s study followed 31 mobile device users with iOS devices and Android devices who used ReCon for a period of one week to 101 days and then monitored their personal leakages through a ReCon secure webpage. The results were alarming. “Depressingly, even in our small user study we found 165 cases of credentials being leaked in plaintext,” the researchers wrote.
Of the top 100 apps in each operating system’s app store that participants were using, more than 50 percent leaked device identifiers, more than 14 percent leaked actual names or other user identifiers, 14–26 percent leaked locations, and three leaked passwords in plaintext. In addition to those top apps, the study found similar password leaks from 10 additional apps that participants had installed and used.
The password-leaking apps included MapMyRun, the language app Duolingo, and the Indian digital music app Gaana. All three developers have since fixed the leaks. Several other apps continue to send plaintext passwords into traffic, including a popular dating app.
“What’s really troubling is that we even see significant numbers of apps sending your password, in plaintext readable form, when you log in,” says Choffnes. In a public-WiFi setting, that means anyone running “some pretty simple software” could nab it.
Computed-tomography reconstruction obtained from the transmitted intensity using standard filtered backprojection. b, Orientation of bone ultrastructure as determined using SAS tensor tomography.
The mechanical properties of many materials are based on the macroscopic arrangement and orientation of their nanostructure. This nanostructure can be ordered over a range of length scales. In biology, the principle of hierarchical ordering is often used to maximize functionality, such as strength and robustness of the material, while minimizing weight and energy cost.
Methods for nanoscale imaging provide direct visual access to the ultrastructure (nanoscale structure that is too small to be imaged using light microscopy), but the field of view is limited and does not easily allow a full correlative study of changes in the ultrastructure over a macroscopic sample. Other methods of probing ultrastructure ordering, such as small-angle scattering of X-rays or neutrons, can be applied to macroscopic samples; however, these scattering methods remain constrained to two-dimensional specimens1, 2, 3, 4 or to isotropically oriented ultrastructures5, 6, 7. These constraints limit the use of these methods for studying nanostructures with more complex orientation patterns, which are abundant in nature and materials science.
Now, a team of scientists introduce an imaging method that combines small-angle scattering with tensor tomography to probe nanoscale structures in three-dimensional macroscopic samples in a non-destructive way. They demonstrate the method by measuring the main orientation and the degree of orientation of nanoscale mineralized collagen fibrils in a human trabecula bone sample with a spatial resolution of 25 micrometres. Symmetries within the sample, such as the cylindrical symmetry commonly observed for mineralized collagen fibrils in bone8, 9, 10, allow for tractable sampling requirements and numerical efficiency.
Small-angle scattering tensor tomography is applicable to both biological and materials science specimens, and may be useful for understanding and characterizing smart or bio-inspired materials. Moreover, because the method is non-destructive, it is appropriate for in situ measurements and allows, for example, the role of ultrastructure in the mechanical response of a biological tissue or manufactured material to be studied.
Via Ath Godelitsas
Technology is allowing researchers to generate vast amounts of information about tumors. The next step is to use this genomic data to transform patient care.
Adrian Lee has dedicated his career to studying breast cancer, which is to say he is actually tackling many different diseases at once. “No two breast cancers are the same,” says Lee, a pharmacologist and chemical biologist at the University of Pittsburgh in Pennsylvania. “Cancer is way more complex than we know.”
Lee is using genomic technology to fully describe cancers of the breast and apply that knowledge to guide treatment decisions for individual patients. “We can now analyse multiple variables from a single specimen, such as changes in DNA, changes in RNA and changes in methylation,” he says. “Genome-wide scans allow for better systems biology and allow us to learn what's gone wrong in a particular tumor.”
Sequencing tumors is faster, cheaper and easier than ever. With many researchers collecting sequence data and uploading these to public databases such as the The Cancer Genome Atlas (TCGA), opportunities to describe the many different cancers that arise in breast tissue are upon us. “The challenge used to be generating the data,” says Nicholas Navin, a geneticist at The University of Texas MD Anderson Cancer Center in Houston. “Those issues have been resolved. Now the challenge is data processing and data analysing — interpreting the mutations and communicating those to oncologists.”
At the University of Pittsburgh, researchers are working to link the molecular signatures of people with breast cancer to a host of clinical data, including demographic information associated with risk such as age, ethnicity and body weight. They are mining electronic health records for clinical correlates, treatment interactions and outcomes. “We've got a big haystack and we're trying to find the needle,” says Lee. “But we're also trying to incriminate the needle, by linking it to lots of things.” Collecting all that data from patients' electronic records adds up, Lee says. It takes infrastructure — Pittsburgh has already accumulated 5 petabytes, or 5 million gigabytes, which is enough data to overload around 40,000 new iPhone 6 devices.
Making the connection between the reams of data coming out of sequencing laboratories and the individual women fighting breast cancer takes big-time computing power. Big data needs researchers who are comfortable with statistical noise and those who are old hands at the iterative process required to create flexible computer programs.
Big-data researchers take a large data set and look for patterns. The idea is to identify mutations that can be targeted with drug treatment. It is the essence of personalized medicine: screen a patient's tumour for a set of biomarkers to choose the best treatment to fight the cancer. Big-data researchers believe that analysing the data of the thousands of tumours that have come before will reveal patterns that can improve screening and diagnosis, and inform treatment.
Lee and his colleagues have illustrated how big-data science led to a rethink of breast cancer1. They used two public databases — TCGA and METABRIC (Molecular Taxonomy of Breast Cancer International Consortium), which contain data on the entire set of genes, RNA transcripts and proteins of thousands of breast-cancer tumours — to parse out potential differences in the molecular signatures of breast tumours in younger compared with older women. Women who are diagnosed before the age of 40 tend to have worse disease: they are more likely to have later-stage cancers, poorer prognoses and worse survival outcomes than older women.
Via Integrated DNA Technologies
Cardiologists from the Institute of Cardiology, Warsaw, Poland have used Google Glass in a challenging surgical procedure, successfully clearing a blockage in the right coronary artery of a 49-year-old male patient and restoring blood flow, reports the Canadian Journal of Cardiology.
Chronic total occlusion, a complete blockage of the coronary artery, sometimes referred to as the “final frontier in interventional cardiology,” represents a major challenge for catheter-based percutaneous coronary intervention (PCI), according to the cardiologists.
That’s because of the difficulty of recanalizing (forming new blood vessels through an obstruction) combined with poor visualization of the occluded coronary arteries.
Coronary computed tomography angiography (CTA) is increasingly used to provide physicians with guidance when performing PCI for this procedure. The 3-D CTA data can be projected on monitors, but this technique is expensive and technically difficult, the cardiologists say.
So a team of physicists from the Interdisciplinary Centre for Mathematical and Computational Modelling of the University of Warsaw developed a way to use Google Glass to clearly visualize the distal coronary vessel and verify the direction of the guide-wire advancement relative to the course of the blocked vessel segment.
So a team of physicists from the Interdisciplinary Centre for Mathematical and Computational Modelling of the University of Warsaw developed a way to use Google Glass to clearly visualize the distal coronary vessel and verify the direction of the guide-wire advancement relative to the course of the blocked vessel segment.
The procedure was completed successfully, including implantation of two drug-eluting stents. “This case demonstrates the novel application of wearable devices for display of CTA data sets in the catheterization laboratory that can be used for better planning and guidance of interventional procedures, and provides proof of concept that wearable devices can improve operator comfort and procedure efficiency in interventional cardiology,” said lead investigator Maksymilian P. Opolski, MD, PhD, of the Department of Interventional Cardiology and Angiology at the Institute of Cardiology, Warsaw, Poland.
“We believe wearable computers have a great potential to optimize percutaneous revascularization, and thus favorably affect interventional cardiologists in their daily clinical activities,” he said. He also advised that “wearable devices might be potentially equipped with filter lenses that provide protection against X-radiation.
From fiber optic cables delivering high-speed internet to laser eye surgery, scientists' ability to manipulate fundamental particles of light (photons) is revolutionizing our world. New developments in photonic devices rely on fundamental physics and complex chemistry to extract the maximum efficiency and sensitivity to particles of light.
It's at the nanoscale that researchers from UOW's School of Physics have discovered a new method of constructing nanowires for use as semiconductors—the foundation of all modern electronics. PhD student Julian Steele said the precision assembly of semiconductors at the nanoscale was undergoing an explosion of interest in scientific circles, due to their promise for building advanced electronic and photonic devices.
"Control over these tiny structures is important in determining their final applications," Julian said. "The more control we have over a wider range of materials, the more we extend the palette of functional design options available to engineers." Silicon-based devices are currently the most widely used for telecommunications and circuit elements. Much further down the periodic table of elements is an exotic element called bismuth.
When added to the elements gallium and arsenide, the heavier bismuth resists entering the gallium-arsenide crystal and gathers on the surface in small droplets. "These droplets act as a catalyst for the growth of nanostructures, which in this case turned out to self-assemble in the form of tracks," Julian explained. "The nanotracks themselves were grown by our collaborators at in the UK and the US, who were actually trying to grow solid thin-film materials.
"We were able to add to the work in understanding what we were seeing and why the tracks formed. The problem with trying to understand how the nanotrack shape is formed is the fact that only a handful of theoretical models exist to describe how they grow, and none that explains our unusual shapes."
"Our work also proposes a new type of growth model in detail. A simulation based on the model has fantastic agreement with our experiment and yields insights into the psychical origins of some of the more exotic features observed in these nanotracks."
The curtain at the edge of the universe may be rippling, hinting that there’s more backstage. Data from the European Space Agency’s Planck telescope could be giving us our first glimpse of another universe, with different physics, bumping up against our own.
That’s the tentative conclusion of an analysis by Ranga-Ram Chary, a researcher at Planck’s US data centre in California. Armed with Planck’s painstaking map of the cosmic microwave background (CMB) – light lingering from the hot, soupy state of the early universe – Chary revealed an eerie glow that could be due to matter from aneighbouring universe leaking into ours.
This sort of collision should be possible, according to modern cosmological theories that suggest the universe we see is just one bubble among many. Such a multiverse may be a consequence of cosmic inflation, the widely accepted idea that the early universe expanded exponentially in the slimmest fraction of a second after the big bang.
Once it starts, inflation never quite stops, so a multitude of universes becomes nearly inevitable. “I would say most versions of inflation in fact lead to eternal inflation, producing a number of pocket universes,” says Alan Guth of the Massachusetts Institute of Technology, an architect of the theory.
Energy hidden in empty space drives inflation, and the amount that’s around could vary from place to place, so some regions would eventually settle down and stop expanding at such a manic pace. But the spots where inflation is going gangbusters would spawn inflating universes. And even areas within these new bubbles could balloon into pocket universes themselves.
Like compositions on the same theme, each universe produced this way would be likely to have its own spin on physics. The matter in some bubbles – the boring ones – would fly apart within 10-40 seconds of their creation. Others would be full of particles and rules similar to ours, or even exactly like ours. In the multiverse of eternal inflation, everything that can happen has happened – and will probably happen again. That notion could explain why the physical constants of our universe seem to be so exquisitely tuned to allow for galaxies, stars, planets and life (see “Just right for life?“).
Sadly, if they do exist, other bubbles are nigh on impossible to learn about. With the space between them and us always expanding, light is too slow to carry any information between different regions. “They could never even know about each other’s existence,” says Matthew Johnson of York University in Toronto, Canada. “It sounds like a fun idea but it seems like there’s no way to test it.”
In 2007, Johnson and his PhD adviser proposed that these clashing bubbles might show up as circular bruises on the CMB. They were looking for cosmic dance partners that resembled our own universe, but with more of everything. That would make a collision appear as a bright, hot ring of photons.
By 2011, they were able to search for them in data from NASA’s WMAP probe, the precursor to Planck. But they came up empty-handed. Now Chary thinks he may have spotted a different signature of a clash with a foreign universe. “There are two approaches, looking for different classes of pocket universes,” Johnson says. “They’re hunting for lions, and we’re hunting for polar bears.” Instead of looking at the CMB itself, Chary subtracted a model of the CMB from Planck’s picture of the entire sky. Then he took away everything else, too: the stars, gas and dust.
With our universe scrubbed away, nothing should be left except noise. But in a certain frequency range, scattered patches on the sky look far brighter than they should. If they check out, these anomalous clumps could be caused by cosmic fist-bumps: our universe colliding with another part of the multiverse (arxiv.org/abs/1510.00126). These patches look like they come from the era a few hundred thousand years after the big bang when electrons and protons first joined forces to create hydrogen, which emits light in a limited range of colours. We can see signs of that era, called recombination, in the light from that early hydrogen. Studying the light from recombination could be a unique signature of the matter in our universe – and potentially distinguish signs from beyond. “This signal is one of the fingerprints of our own universe,” says Jens Chluba of the University of Cambridge. “Other universes should leave a different mark.”
Juliano Pinto, a 29-year-old paraplegic, kicked off the 2014 World Cup in São Paulo with a robotic exoskeleton suit that he wore and controlled with his mind. The event was broadcast internationally and served as a symbol of the exciting possibilities of brain-controlled machines. Over the last few decades research into brain–computer interfaces (BCIs), which allow direct communication between the brain and an external device such a computer or prosthetic, has skyrocketed. Although these new developments are exciting, there are still major hurdles to overcome before people can easily use these devices as a part of daily life.
Via Wildcat2030, Jocelyn Stoller
The fundamental constants of nature—such as the speed of light, Planck's constant, and Newton's gravitational constant—are thought to be constant in time, as their name suggests. But scientists have questioned this assumption as far back as 1937, when Paul Dirac hypothesized that Newton's gravitational constant might decrease over time.
Now in a new paper published in Physical Review Letters, Yevgeny V. Stadnik and Victor V. Flambaum at the University of New South Wales in Sydney, Australia, have theoretically shown that dark matter can cause the fundamental constants of nature to slowly evolve as well as oscillate due to oscillations in the dark matter field. This idea requires that the weakly interacting dark matter particles be able to interact a small amount with standard model particles, which the scientists show is possible.
In their paper, the scientists considered a model in which dark matter is made of weakly interacting, low-mass particles. In the early Universe, according to the model, large numbers of such dark matter particles formed an oscillating field. Because these particles interact so weakly with standard model particles, they could have survived for billions of years and still exist today, forming what we know as dark matter.
Although these low-mass dark matter particles are weakly interacting, they are thought to still interact with standard model particles to some extent, but it's unclear exactly how much. By using data from experiments that have measured the amount of helium produced during big bang nucleosynthesis, as well as measurements of the rare element dysprosium and the cosmic microwave background, Stadnik and Flambaum have derived the most stringent limits to date on how strongly such dark matter particles interact with photons, electrons, and light quarks, improving on existing constraints by up to 15 orders of magnitude.
The new limits on the dark matter interaction strength allow for the possibility that an oscillating, low-mass dark matter field coupled to standard model particles causes variations in the fundamental constants. As the scientists explain, this could have important implications for understanding life's origins.
The fundamental constants are 'fine-tuned' to be consistent with the existence of life in the Universe. If the physical constants were even slightly different, life could not have appeared. The discovery of varying fundamental 'constants' may help shed important light on how the physical constants came to have their life-sustaining values today. We simply appeared in an area of the Universe where they are consistent with our existence. Whether or not the fundamental constants actually do vary due to dark matter is still an open question, but the scientists hope that future experiments with atomic clocks, laser interferometers, and other devices may help test out the new idea.
“Pigeons do just as well as humans in categorizing digitized slides and mammograms of benign and malignant human breast tissue,” said Richard Levenson, professor of pathology and laboratory medicine at UC Davis Health System and lead author of a new open-access study in PLoS One by researchers at the University of California, Davis and The University of Iowa.
“The pigeons were able to generalize what they had learned, so that when we showed them a completely new set of normal and cancerous digitized slides, they correctly identified them,” Levenson said. “The pigeons also learned to correctly identify cancer-relevant microcalcifications on mammograms, but they had a tougher time classifying suspicious masses on mammograms — a task that is extremely difficult, even for skilled human observers.”
Although a pigeon’s brain is no bigger than the tip of an index finger, the neural pathways involved operate in ways very similar to those at work in the human brain. “Research over the past 50 years has shown that pigeons can distinguish identities and emotional expressions on human faces, letters of the alphabet, misshapen pharmaceutical capsules, and even paintings by Monet vs. Picasso,” said Edward Wasserman, professor of psychological and brain sciences at The University of Iowa and co-author of the study. “Their visual memory is equally impressive, with a proven recall of more than 1,800 images.”
For the study, each pigeon learned to discriminate cancerous from non-cancerous images and slides using traditional “operant conditioning,” a technique in which a bird was rewarded only when a correct selection was made; incorrect selections were not rewarded and prompted correction trials. Training with stained pathology slides included a large set of benign and cancerous samples from routine cases at UC Davis Medical Center.
“The birds were remarkably adept at discriminating between benign and malignant breast cancer slides at all magnifications, a task that can perplex inexperienced human observers, who typically require considerable training to attain mastery,” Levenson said. He said the pigeons achieved nearly 85 percent correct within 15 days.
“When we showed a cohort of four birds a set of uncompressed images, an approach known as “flock-sourcing,” the group’s accuracy level reached an amazing 99 percent correct, higher than that achieved by any of the four individual birds.” Wasserman has conducted studies on pigeons for more than 40 years.