Hey robot, shimmy like a centipede

Centipedes move quickly. And when one is coming directly at you, you might not care to spend a moment pondering its agility.

So perhaps our lack of understanding about just why centipedes move with such dexterity, even over obstacles, has been related to fear. But undeterred, researchers at Kyoto University have asked precisely this question, and have turned to computer simulations and ultimately robotics to find an answer.

What they have uncovered is a surprising insight into the mechanics of locomotion itself, namely that taming instability -- a factor that might be a disadvantage -- is a key to the centipede's success.

"During their locomotion, many legs are in contact with the ground to support the body against gravity and produce propulsive and decelerating forces," explains lead scientist Shinya Aoi. "These many legs are physically constrained on the ground, and this constraint can impede their locomotion maneuverability."

Centipedes overcome these constraints by harnessing instability, producing the creature's characteristic undulating movement.

"Our group developed a mathematical model of centipedes and found that the straight walk becomes unstable and body undulations appear through a supercritical Hopf bifurcation by changing the locomotion speed and body axis flexibility," continues Aoi, referring to a mathematical description of the walking system's tipping point from stable to unstable.

First with computer models and then with segmented, multi-legged robots, the team was able to replicate the centipede's movement, including the wave-like body motion, as described in a paper in the online journal Scientific Reports.

But Aoi and his colleagues are not satisfied with merely taming creepy crawlies.

"This study provides clues to unresolved issues of intelligent motor functions of animals, and meaningful insight for biological sciences," he says, pointing out that much remains unknown about the exact mechanics of animal locomotion.

And further down the line, such knowledge could lead to better motion for robots -- no matter how many legs they may have.

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The above post is reprinted from materials provided by Kyoto University.Note: Materials may be edited for content and length.

Why architects should let the microbes in

Architectural design is often concerned with energy efficiency or aesthetics, not microbial exposure. But, in a Science & Society article published July 7 in Trends in Microbiology, Yale environmental engineers make a case for assessing the benefits of having these unseen organisms in our homes. Maybe, they say, instead of pushing all of them out, we should let the right ones in.

"It's a common misconception that all microbes found in one's home are hazardous to your health," says Yale Professor of Chemical and Environmental Engineering Jordan Peccia (@jordan_peccia), co-author of the review with PhD student Sarah Kwan. "Many have no impact on health, while some may even be beneficial."

Past studies have shown that children growing up on a farm (or even in a home close to a rural area), are exposed to such beneficial microbes, and are less likely to develop allergies as a result. In one example, children from a Bavarian family (a population known for their agrarian lifestyle, such as working the fields, using horses for transport, and drinking unpasteurized milk) had less than half the levels of asthma compared to a suburban European family (5.2% versus 19.1%). This effect was found to persist into adulthood. This is likely because some microbes in the body send signals to white blood cells known as T cells to form T regulatory cells, which prevent unnecessary immune responses.

"One big question becomes how building design (e.g., the geographical layout, the building materials, occupancy, and ventilation) modulates microbial exposure, and our own microbiomes," says Peccia. "As more and more beneficial microbes are identified, we--architects, engineers, and the general public--need to think about how we can facilitate our exposure to them."

"There are certainly trade-offs we need to better understand and circumvent," he adds. "Indoor air quality is often worse than outdoor air quality, so building ventilation with outdoor air makes a lot of sense. However, in cities with very poor outdoor air quality, increased ventilation results may result in unhealthy exposures to outdoor air contaminants."

Short of working on a farm, one way we can "train" our immune system is through exposure to animals, especially cats and dogs. Aside from carrying their own families of microbes, they also can track in common bacteria and fungi from the outdoors, further contributing to the aforementioned "beneficial diversity" of indoor microbes. These can then be easily inhaled or swallowed when trapped in a tightly enclosed space, such as a home or office building, where we inhale gallons of air each day and sometimes ingest floor dust.

Although this field is still in its infancy, Peccia does have some advice for building occupants, namely, that there is not a "one size fits all" approach to improving the microbiome in one's home. "Not everyone should run out and get a dog, of course," he says, "but we can work to develop new, quantitative approaches for solving these problems--something better than our portable air filters and inhalers."

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The above post is reprinted from materials provided by Cell Press. Note: Materials may be edited for content and length.

Messaging by flow in the brain

We have all bumped our heads at some point, and such incidents are usually harmless. This is thanks to fluid-filled chambers in our brain that offset minor knocks and jolts and provide padding for sensitive components of our nervous system. Cerebral fluid, however, has more than just a protective function: It removes cellular waste, supplies our nervous tissue with nutrients, and transports important messenger substances. How these messenger substances are actually being delivered to their destination in the brain, however, was unclear until now.

Göttingen-based Max Planck researchers have now discovered that tiny cilia on the surface of specialized cells could lead the way. Through synchronized beating movements, they create a complex network of dynamic flows that act like conveyor belts transporting molecular "freight." The results obtained by the scientists suggest that these flows send messenger substances directly to where they are needed.

Millions of cilia on the surface of specialized cells inside our body literally make this a hairy affair. Cilia free our airways of dust, mucus, and pathogens, transport egg cells through the fallopian tubes, and help sperm to move forward. The four chambers in our brain, so-called cerebral ventricles, are also lined with a layer of highly specialized cells covered with bundles of cilia on their surface. Although each one is just a few thousandths of a millimeter in size, hundreds of them beating in unison can generate powerful flows.

Gregor Eichele and Regina Faubel at the Max Planck Institute for Biophysical Chemistry, together with Eberhard Bodenschatz and Christian Westendorf at the Max Planck Institute for Dynamics and Self-Organization, have now succeeded in making the complex network of these flows visible in an isolated cerebral ventricle tissue. For their experiments, the researchers in Göttingen concentrated on the third cerebral ventricle, which is embedded in the hypothalamus. "The hypothalamus is a very important control center, regulating functions like the circulatory system, body temperature, sexual behavior, food intake, and hormonal balance. To our surprise, there is a sophisticated transport system to and from the hypothalamus for distributing messenger substances via cerebral fluid," explains Gregor Eichele, Head of the Department of Genes and Behavior at the Max Planck Institute for Biophysical Chemistry.

Fluorescent spheres under the microscope

The movement of the fluid, however, cannot be directly observed under a microscope. To visualize the movement, Regina Faubel of Eichele's Department developed a new experimental approach using isolated cerebral ventricle tissue from the mouse. In a culture dish, the scientist injected the nerve tissue with tiny fluorescent particles that subsequently moved with the culture medium as tracer. She then recorded the path of each particle within the nerve tissue under the microscope. With the aid of a computer program specially developed by her colleague Christian Westendorf, the researchers finally combined the extensive data to create a picture that could be scientifically analyzed.

"In these images, we can see a complex network of fluid paths inside the cerebral ventricle. However, in contrast to the blood which flows through our blood vessels, these paths are not confined by walls. The exciting question for us was therefore: Is the flow pattern created solely by the synchronized beating of the cilia?" reports Regina Faubel, first author of the study. The researchers then filmed the cilia live in action, thus determining the direction of the beating as well as the resulting flows. "Our experiments have shown that the flows are actually generated solely by the movements of the cilia. These act like conveyor belts and would therefore be an ideal means of transporting messenger substances to the right place in the brain," says Eberhard Bodenschatz, Head of the Department of Fluid Dynamics, Pattern Formation and Biocomplexity at the Max Planck Institute for Dynamics and Self-Organization. "These flows could also help to restrict substances locally, in that the fluid paths flowing against one another could act like barriers," adds Christian Westendorf, second author of the study.

Changing flow directions

However, in contrast to the road networks that we travel on daily by car or bicycle, these fluid paths are by no means rigid. To the researchers' surprise, the cilia changed the direction of beating in a temporal rhythm. This came as a big surprise as according to the prevalent school of thought the direction of cilia beating cannot be changed.

"In the cerebral fluid of humans, there are hundreds -- if not thousands -- of physiologically active substances," Eichele explains. "We are assuming that the network of flows we discovered plays an important role in distributing these substances. In other experiments, we would like to look at which messenger substances are transported via the flows, and where these are ultimately deposited in the tissue." "But the understanding of the physics of fluid dynamics of cilia is also itself a research objective," adds Bodenschatz.

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Robot helps study how first land animals moved 360 million years ago

When early terrestrial animals began moving about on mud and sand 360 million years ago, the powerful tails they used as fish may have been more important than scientists previously realized. That's one conclusion from a new study of African mudskipper fish and a robot modeled on the animal.

Animals analogous to the mudskipper would have used modified fins to move around on flat surfaces, but for climbing sandy slopes, the animals could have benefitted from using their tails to propel themselves forward, the researchers found. Results of the study, reported this week in the journalScience, could help designers create amphibious robots able to move across granular surfaces more efficiently -- and with less likelihood of getting stuck in the mud.

Sponsored by the National Science Foundation, the Army Research Office and the Army Research Laboratory, the project involved a multidisciplinary team of physicists, biologists and roboticists from the Georgia Institute of Technology, Clemson University and Carnegie Mellon University. In addition to a detailed study of the mudskipper and development of a robot model that used the animal's locomotion techniques, the study also examined flow and drag conditions in representative granular materials, and applied a mathematical model incorporating new physics based on the drag research.

"Most robots have trouble moving on terrain that includes sandy slopes," said Dan Goldman, an associate professor in the Georgia Tech School of Physics. "We noted that not only did the mudskippers use their limbs to propel themselves in a kind of crutching motion on sand and sandy slopes, but that when the going got tough, they used their tails in concert with limb propulsion to ascend a slope. Our robot model was only able to climb sandy slopes when it similarly used its tail in coordination with its appendages."

Based on fossil records, scientists have long studied how early land animals may have gotten around, and the new study suggests their tails -- which played a key role in swimming as fish -- may have helped supplement the work of fins, especially on sloping granular surfaces such as beaches and mudflats.

"We were interested in examining one of the most important evolutionary events in our history as animals: the transition from living in water to living on land," said Richard Blob, alumni distinguished professor of biological sciences at Clemson University. "Because of the focus on limbs, the role of the tail may not have been considered very strongly in the past. In some ways, it was hiding in plain sight. Some of the features that the animals used were new, such as limbs, but some of them were existing features that they simply co-opted to allow them to move into a new habitat."

With Ph.D. student Sandy Kawano, now a researcher at the National Institute of Mathematical and Biological Synthesis, Blob's lab recorded how the mudskippers (Periopthalmus barbaratus) moved on a variety of loose surfaces, providing data and video to Goldman's laboratory. The small fish, which uses its front fins and tail to move on land, lives in tidal areas near shore, spending time in the water and on sandy and muddy surfaces.

Benjamin McInroe was a Georgia Tech undergraduate who analyzed the mudskipper data provided by the Clemson team. He applied the principles to a robot model known as MuddyBot that has two limbs and a powerful tail, with motion provided by electric motors. Information from both the mudskipper and robotic studies were also factored into a mathematical model provided by researchers at Carnegie Mellon University.

"We used three complementary approaches," said McInroe, who is a now a Ph.D. student at the University of California Berkeley. "The fish provided a morphological, functional model of these early walkers. With the robot, we are able to simplify the complexity of the mudskipper and by varying the parameters, understand the physical mechanisms of what was happening. With the mathematical model and its simulations, we were able to understand the physics behind what was going on."

Both the mudskippers and the robot moved by lifting themselves up to reduce drag on their bodies, and both needed a kick from their tails to climb 20-degree sandy slopes. Using their "fins" alone, both struggled to climb slopes and often slid backward if they didn't use their tails, McInroe noted. Early land animals likely didn't have precise control over their limbs, and the tail may have compensated for that limitation, helping the animals ascend sandy slopes.

The Carnegie Mellon University researchers, who have worked with Goldman on relating the locomotion of other animals to robots, demonstrated that theoretical models developed to describe the complex motion of robots can also be used to understand locomotion in the natural world.

"Our computer modeling tools allow us to visualize, and therefore better understand, how the mudskipper incorporates its tail and flipper motions to locomote," said Howie Choset, a professor in the Robotics Institute at Carnegie Mellon University. "This work also will advance robotics in those cases where a robot needs to surmount challenging terrains with various inclinations."

The model was based on a framework proposed to broadly understand locomotion by physicist Frank Wilczek -- a Nobel Prize winner -- and his then student Alfred Shapere in the 1980s. The so-called "geometric mechanics" approach to locomotion of human-made devices (like satellites) was largely developed by engineers, including those in Choset's group. To provide force relationships as inputs to the mudskipper robot model, Georgia Tech postdoctoral fellow Jennifer Rieser and Georgia Tech graduate student Perrin Schiebel measured drag in inclined granular materials.

Information from the study could help in the design of robots that may need to move on surfaces such as sand that flows around limbs, said Goldman. Such flow of the substrate can impede motion, depending on the shape of the appendage entering the sand and the type of motion.

But the study's most significant impact may be to provide new insights into how vertebrates made the transition from water to land.

"We want to ultimately know how natural selection can act to modify structures already present in organisms to allow for locomotion in a fundamentally different environment," Goldman said. "Swimming and walking on land are fundamentally different, yet these early animals had to make the transition."

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The above post is reprinted from materials provided by Georgia Institute of Technology. The original item was written by John Toon. Note: Materials may be edited for content and length.

Surprising planet with three suns discovered

A team of astronomers have used the SPHERE instrument on ESO's Very Large Telescope to image the first planet ever found in a wide orbit inside a triple-star system. The orbit of such a planet had been expected to be unstable, probably resulting in the planet being quickly ejected from the system. But somehow this one survives. This unexpected observation suggests that such systems may actually be more common than previously thought. The results will be published online in the journal Science on 7 July 2016.

Luke Skywalker's home planet, Tatooine, in the Star Wars saga, was a strange world with two suns in the sky, but astronomers have now found a planet in an even more exotic system, where an observer would either experience constant daylight or enjoy triple sunrises and sunsets each day, depending on the seasons, which last longer than human lifetimes.

This world has been discovered by a team of astronomers led by the University of Arizona, USA, using direct imaging at ESO's Very Large Telescope (VLT) in Chile. The planet, HD 131399Ab, is unlike any other known world -- its orbit around the brightest of the three stars is by far the widest known within a multi-star system. Such orbits are often unstable, because of the complex and changing gravitational attraction from the other two stars in the system, and planets in stable orbits were thought to be very unlikely.

Located about 320 light-years from Earth in the constellation of Centaurus (The Centaur), HD 131399Ab is about 16 million years old, making it also one of the youngest exoplanets discovered to date, and one of very few directly imaged planets. With a temperature of around 580 degrees Celsius and an estimated mass of four Jupiter masses, it is also one of the coldest and least massive directly-imaged exoplanets.

"HD 131399Ab is one of the few exoplanets that have been directly imaged, and it's the first one in such an interesting dynamical configuration," said Daniel Apai, from the University of Arizona, USA, and one of the co-authors of the new paper.

"For about half of the planet's orbit, which lasts 550 Earth-years, three stars are visible in the sky; the fainter two are always much closer together, and change in apparent separation from the brightest star throughout the year," adds Kevin Wagner, the paper's first author and discoverer of HD 131399Ab.

Kevin Wagner, who is a PhD student at the University of Arizona, identified the planet among hundreds of candidate planets and led the follow-up observations to verify its nature.

The planet also marks the first discovery of an exoplanet made with the SPHERE instrument on the VLT. SPHERE is sensitive to infrared light, allowing it to detect the heat signatures of young planets, along with sophisticated features correcting for atmospheric disturbances and blocking out the otherwise blinding light of their host stars.

Although repeated and long-term observations will be needed to precisely determine the planet's trajectory among its host stars, observations and simulations seem to suggest the following scenario: the brightest star is estimated to be eighty percent more massive than the Sun and dubbed HD 131399A, which itself is orbited by the less massive stars, B and C, at about 300 au (one au, or astronomical unit, equals the average distance between Earth and the Sun). All the while, B and C twirl around each other like a spinning dumbbell, separated by a distance roughly equal to that between the Sun and Saturn (10 au).

In this scenario, planet HD 131399Ab travels around the star A in an orbit with a radius of about 80 au, about twice as large as Pluto's in the Solar System, and brings the planet to about one third of the separation between star A and the B/C star pair. The authors point out that a range of orbital scenarios is possible, and the verdict on the long-term stability of the system will have to wait for planned follow-up observations that will better constrain the planet's orbit.

"If the planet was further away from the most massive star in the system, it would be kicked out of the system," Apai explained. "Our computer simulations have shown that this type of orbit can be stable, but if you change things around just a little bit, it can become unstable very quickly."

Planets in multi-star systems are of special interest to astronomers and planetary scientists because they provide an example of how the mechanism of planetary formation functions in these more extreme scenarios. While multi-star systems seem exotic to us in our orbit around our solitary star, multi-star systems are in fact just as common as single stars.

"It is not clear how this planet ended up on its wide orbit in this extreme system, and we can't say yet what this means for our broader understanding of the types of planetary systems, but it shows that there is more variety out there than many would have deemed possible," concludes Kevin Wagner. "What we do know is that planets in multi-star systems have been studied far less often, but are potentially just as numerous as planets in single-star systems."

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The above post is reprinted from materials provided by ESO. Note: Materials may be edited for content and length.

Watery roadblock in the pathway to biofuels

In creating fuels from agricultural waste and other biomass, water slows a solid acid catalyst's ability to get the job done, costing time and energy. But scientists didn't know how the adverse reactions occurred. A team from Pacific Northwest National Laboratory and a major German university delved into the mystery.

Because removing oxygen is crucial for biofuel production, the team focused on how water interferes with two oxygen-removal paths driven by a zeolite catalyst. Water blocks both pathways. The team demonstrated unequivocally that water helps create a highly stable intermediate. Turning this intermediate into the desired product is like pushing a boulder uphill. It takes far more energy than if the water hadn't interfered. And when it comes to producing fuels, adding energy is expensive in economic and environmental terms.

"Water is ubiquitous and abundant in biomass-derived feedstocks," said Dr. Hui Shi, a postdoctorate fellow who has worked for 3 years at PNNL and participated in this joint research. "Understanding water's impact is crucial to the design and synthesis of catalytic materials that are less or not negatively affected by water."

To upgrade renewable biomass sources into liquid fuels requires removing oxygen atoms, often from intermediately formed alcohols. When catalyzed by acids, this process is known as dehydrating an alcohol. The team's detailed analysis of two model dehydration pathways could aid others in engineering subtle adjustments to reduce biofuel production's costs.

The team's work shows how to gather the needed information. "Researchers really need to combine experiments and theory to build models that fully describe the entire reaction, however simple it may seem," said Dr. Donald Camaioni, who is mentoring Shi as part of the postdoctoral program. "It pays off when it comes to rational catalyst and process design, which ought to be more knowledge based than empirical."

To achieve a molecular-level understanding of the two pathways, known as the "monomer path" and the "dimer path," they used rigorous kinetic, calorimetric, and spectroscopic techniques. They combined the resulting measurements with complex calculations. Their results show how molecules move, bind, form, and release in both pathways and the amount of energy involved. "We would not have succeeded without using this integrated approach," said Shi.

They performed experiments with two key techniques. Infrared spectroscopy provides details by exploiting how molecules absorb light in the infrared region. Thermogravimetry-differential scanning calorimetry characterizes the physical and chemical properties of the molecules as a function of increasing temperature. The team designed experiments with a significantly wider range of conditions, including higher pressures, compared to literature precedents. In the experiments, they used a clean sample that lacked interfering structural factors.

Their results established the relative population, as well as the energetics, of the key surface intermediates under the reaction conditions. For the monomer pathway, one propanol molecule enters the catalyst's active site. It binds to the active site, picking up a proton. Water is broken off, but it enables an intermediate to form. It leads to a nonsymmetrical molecule that's got a proton bridge to the catalyst. The catalyst's active site is inoperative until the intermediate is untethered, forming the desired propene.

For the dimer pathway, two propanol molecules enter the active site. This leads to a charged two-part, or dimer, species. This dimer is very stable and energy must be added to cleave the right bonds to form an intermediate that returns protons to the catalyst and releases both water and propanol. This intermediate is different from that created in the monomer path. The energy needs are also different.

"The team did not cut corners by assuming that conclusions reached in one catalytic system would necessarily hold true for another," said Camaioni.

In this study, the water was in the gas phase. In the next study, the team will be working with liquid water rather than steam. This research is part of an ongoing program, funded by the Office of Science at the U.S. Department of Energy. The program's goal is to overcome the fundamental questions that are holding us back from designing faster, cheaper, more efficient ways to create biofuels.

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Missing link in epigenetics could explain conundrum of disease inheritance

The process by which a mother's diet during pregnancy can permanently affect her offspring's attributes, such as weight, could be strongly influenced by genetic variation in an unexpected part of the genome, according to research led by Queen Mary University of London (QMUL). The discovery could shed light on why many human genetic studies have previously not been able to fully explain how certain diseases, such as type 2 diabetes and obesity, are inherited.

The study, published in Science and co-authored by University of Cambridge and King's College London, shows that the genetic variation of ribosomal DNA (rDNA) could be driving how the environment within the womb determines an offspring's attributes. rDNA is the genetic material that forms ribosomes -- the protein building machines within the cell.

Lead researcher Professor Vardhman Rakyan from QMUL said: "The fact that genetic variation of ribosomal DNA seems to play such a major role suggests that many human genetics studies could be missing a key part of the puzzle. These studies only looked at a single copy part of individuals' genomes and never at ribosomal DNA.

"This could be the reason why we've only so far been able to explain a small fraction of the heritability of many health conditions, which makes a lot of sense in the context of metabolic diseases, such as type 2 diabetes."

The environmental factors that play a role alongside genetic factors in determining a person's attributes are also present in the in-utero environment. When offspring are in the womb, what their mothers experience environmentally (for example, diet, stress, smoking), influences the attributes of offspring when they are adults. This 'developmental programming' is understood to be a large contributor to the obesity epidemic seen today.

A major contributor to this process is 'epigenetics'. This describes naturally-occurring modifications to genes that control how they are expressed. One such modification involves tagging DNA with chemical compounds called methyl groups. These epigenetic markers determine which genes are expressed or not expressed. Liver cells and kidney cells are genetically identical apart from their epigenetic marks. It has been proposed that in response to a poor in-utero environment, an offspring's epigenetic profile will change.

The team compared the offspring of pregnant mice when given a low protein diet (8 per cent protein) and a normal diet (20 per cent protein). After they were weaned, all offspring were given a normal diet, and the team then looked at the difference in the offspring's DNA methylation, from mothers exposed to low protein and those that were not.

Professor Rakyan said: "Initially, we found nothing, so that was a big surprise, but then we looked at the data in a different way. We looked at the ribosomal DNA data and found huge epigenetic differences.

"When cells are stressed, for example when nutrient levels are low, they alter protein production as a survival strategy. In our low protein mice mothers, we saw that their offspring had methylated rDNA. This slowed the expression of their rDNA, which could be influencing the function of ribosomes, and resulted in smaller offspring -- as much as 25 per cent lighter."

These epigenetic effects occur in a critical developmental window while the offspring is in-utero but is a permanent effect that remains into adulthood. A mother's low protein diet while pregnant is therefore likely to have more severe consequence on the offspring's epigenetic state and weight than an offspring's own diet after it has been weaned.

Professor Rakyan added: "Looking beyond the epigenetic markers, when we looked at the basic genetic sequence of the rDNA, we found an even bigger surprise. Even though all the mice in the study were bred to be genetically identical, we found that the rDNA between the individual mice was not genetically identical, and that even within an individual mouse, different copies of rDNA were genetically distinct. So there is huge variation in rDNA which is also playing a big role in determining the attributes of offspring."

In any given genome, there are many copies of rDNA, and Professor Rakyan and colleagues found that not all copies of the rDNA were responding epigenetically. In offspring from mothers who were fed on low protein diets, it was only one form of rDNA -- the 'A-variant' -- that appeared to undergo methylation and affect weight.

This means that the epigenetic response of a given mouse is determined by the genetic variation of the rDNA -- those who have more A-variant rDNA end up being smaller.

Heritability (how much the risk of a disease is explained by genetic factors) of type 2 diabetes has been estimated to be between 25 and 80 per cent in different studies. However, only about 20 per cent of the heritability of type 2 diabetes has been explained by genome studies of people with the disease. The major role that genetic variation of rDNA appears to have and the fact that rDNA analysis would not have been included in these studies could explain some of this missing heritability.

The findings also complement other studies that have found that mice that are put on high fat diets have offspring who show increased rDNA methylation. This suggests that methylation is a general stress response and may also explain the rise in obesity that is happening across the world.

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The above post is reprinted from materials provided by Queen Mary University of London. Note: Materials may be edited for content and length.

Tiny bacteria-powered 'windfarm' for your phone?

A team of scientists from Oxford University has shown how the natural movement of bacteria could be harnessed to assemble and power microscopic 'windfarms' -- or other human-made micromachines such as smartphone components.

The study, published in the journal Science Advances, uses computer simulations to demonstrate that the chaotic swarming effect of dense active matter such as bacteria can be organised to turn cylindrical rotors and provide a steady power source.

Researchers say these biologically driven power plants could someday be the microscopic engines for tiny, human-made devices that are self-assembled and self-powered -- everything from optical switches to smartphone microphones.

Co-author Dr Tyler Shendruk, from Oxford University's Department of Physics, said: 'Many of society's energy challenges are on the gigawatt scale, but some are downright microscopic. One potential way to generate tiny amounts of power for micromachines might be to harvest it directly from biological systems such as bacteria suspensions.'

Dense bacterial suspensions are the quintessential example of active fluids that flow spontaneously. While swimming bacteria are capable of swarming and driving disorganised living flows, they are normally too disordered to extract any useful power from.

But when the Oxford team immersed a lattice of 64 symmetric microrotors into this active fluid, the scientists found that the bacteria spontaneously organised itself in such a way that neighbouring rotors began to spin in opposite directions -- a simple structural organisation reminiscent of a windfarm.

Dr Shendruk added: 'The amazing thing is that we didn't have to pre-design microscopic gear-shaped turbines. The rotors just self-assembled into a sort of bacterial windfarm.

'When we did the simulation with a single rotor in the bacterial turbulence, it just got kicked around randomly. But when we put an array of rotors in the living fluid, they suddenly formed a regular pattern, with neighbouring rotors spinning in opposite directions.'

Co-author Dr Amin Doostmohammadi, from Oxford University's Department of Physics, said: 'The ability to get even a tiny amount of mechanical work from these biological systems is valuable because they do not need an input power and use internal biochemical processes to move around.

'At micro scales, our simulations show that the flow generated by biological assemblies is capable of reorganising itself in such a way as to generate a persistent mechanical power for rotating an array of microrotors.'

Senior author Professor Julia Yeomans, from Oxford University's Department of Physics, added: 'Nature is brilliant at creating tiny engines, and there is enormous potential if we can understand how to exploit similar designs.'

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Injectable biomaterial could be used to manipulate organ behavior

In the campy 1966 science fiction movie "Fantastic Voyage," scientists miniaturize a submarine with themselves inside and travel through the body of a colleague to break up a potentially fatal blood clot. Right. Micro-humans aside, imagine the inflammation that metal sub would cause.

Ideally, injectable or implantable medical devices should not only be small and electrically functional, they should be soft, like the body tissues with which they interact. Scientists from two UChicago labs set out to see if they could design a material with all three of those properties.

The material they came up with, published online June 27, 2016, in Nature Materials, forms the basis of an ingenious light-activated injectable device that could eventually be used to stimulate nerve cells and manipulate the behavior of muscles and organs.

"Most traditional materials for implants are very rigid and bulky, especially if you want to do electrical stimulation," said Bozhi Tian, an assistant professor in chemistry whose lab collaborated with that of neuroscientist Francisco Bezanilla on the research.

The new material, in contrast, is soft and tiny -- particles just a few micrometers in diameter (far less than the width of a human hair) that disperse easily in a saline solution so they can be injected. The particles also degrade naturally inside the body after a few months, so no surgery would be needed to remove them.

Nanoscale 'sponge'

Each particle is built of two types of silicon that together form a structure full of nano-scale pores, like a tiny sponge. And like a sponge, it is squishy -- a hundred to a thousand times less rigid than the familiar crystalline silicon used in transistors and solar cells. "It is comparable to the rigidity of the collagen fibers in our bodies," said Yuanwen Jiang, Tian's graduate student. "So we're creating a material that matches the rigidity of real tissue."

The material constitutes half of an electrical device that creates itself spontaneously when one of the silicon particles is injected into a cell culture, or, eventually, a human body. The particle attaches to a cell, making an interface with the cell's plasma membrane. Those two elements together -- cell membrane plus particle -- form a unit that generates current when light is shined on the silicon particle.

"You don't need to inject the entire device; you just need to inject one component," João L. Carvalho-de-Souza , Bezanilla's postdoc said. "This single particle connection with the cell membrane allows sufficient generation of current that could be used to stimulate the cell and change its activity. After you achieve your therapeutic goal, the material degrades naturally. And if you want to do therapy again, you do another injection."

The scientists built the particles using a process they call nano-casting. They fabricate a silicon dioxide mold composed of tiny channels -- "nano-wires" -- about seven nanometers in diameter (less than 10,000 times smaller than the width of a human hair) connected by much smaller "micro-bridges." Into the mold they inject silane gas, which fills the pores and channels and decomposes into silicon.

And this is where things get particularly cunning. The scientists exploit the fact the smaller an object is, the more the atoms on its surface dominate its reactions to what is around it. The micro-bridges are minute, so most of their atoms are on the surface. These interact with oxygen that is present in the silicon dioxide mold, creating micro-bridges made of oxidized silicon gleaned from materials at hand. The much larger nano-wires have proportionately fewer surface atoms, are much less interactive, and remain mostly pure silicon.

"This is the beauty of nanoscience," Jiang said. "It allows you to engineer chemical compositions just by manipulating the size of things."

Web-like nanostructure

Finally, the mold is dissolved. What remains is a web-like structure of silicon nano-wires connected by micro-bridges of oxidized silicon that can absorb water and help increase the structure's softness. The pure silicon retains its ability to absorb light.

The scientists have added the particles onto neurons in culture in the lab, shone light on the particles, and seen current flow into the neurons which activates the cells. The next step is to see what happens in living animals. They are particularly interested in stimulating nerves in the peripheral nervous system that connect to organs. These nerves are relatively close to the surface of the body, so near-infra-red wavelength light can reach them through the skin.

Tian imagines using the light-activated devices to engineer human tissue and create artificial organs to replace damaged ones. Currently, scientists can make engineered organs with the correct form but not the ideal function.

To get a lab-built organ to function properly, they will need to be able to manipulate individual cells in the engineered tissue. The injectable device would allow a scientist to do that, tweaking an individual cell using a tightly focused beam of light like a mechanic reaching into an engine and turning a single bolt. The possibility of doing this kind of synthetic biology without genetic engineering is enticing.

"No one wants their genetics to be altered," Tian said. "It can be risky. There's a need for a non-genetic system that can still manipulate cell behavior. This could be that kind of system."

Tian's graduate student Yuanwen Jiang did the material development and characterization on the project. The biological part of the collaboration was done in the lab of Francisco Bezanilla, the Lillian Eichelberger Cannon Professor of Biochemistry and Molecular Biology, by postdoc João L. Carvalho-de-Souza. They were, said Tian, the "heroes" of the work.

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The above post is reprinted from materials provided by University of Chicago. Note: Materials may be edited for content and length

Parkinson's Disease biomarker found in patient urine samples

For more than five years, urine and cerebral-spinal fluid samples from patients with Parkinson's disease have been locked in freezers in the NINDS National Repository, stored with the expectation they might someday help unravel the still-hidden course of this slow-acting neurodegenerative disease.

Now, research by Andrew West, Ph.D., and colleagues at the University of Alabama at Birmingham has revealed that the tubes hold a brand-new type of biomarker -- a phosphorylated protein that correlates with the presence and severity of Parkinson's disease. West and colleagues, with support from the National Institutes of Health, the Michael J. Fox Foundation for Parkinson's Disease Research and the Parkinson's Disease Foundation, are digging deeper into these biobanked samples, to validate the biomarker as a possible guide for future clinical treatments and a monitor of the efficacy of potential new Parkinson's drugs in real time during treatment.

"Nobody thought we'd be able to measure the activity of this huge protein called LRRK2 (pronounced lark two) in biofluids since it is usually found inside neurons in the brain," said West, co-director of the Center for Neurodegeneration and Experimental Therapeutics, and the John A. and Ruth R. Jurenko Professor of Neurology at UAB. "New biochemical markers like the one we've discovered together with new neuroimaging approaches are going to be the key to successfully stopping Parkinson's disease in its tracks. I think the days of blindly testing new therapies for complex diseases like Parkinson's without having active feedback both for 'on-target' drug effects and for effectiveness in patients are thankfully coming to an end."

A biomarker helps physicians predict, diagnose or monitor disease, because the biomarker corresponds to the presence or risk of disease, and its levels may change as the disease progresses. Validated biomarkers can aid both preclinical trial work in the laboratory and future clinical trials of drugs to treat Parkinson's. West and others are paving the way for an inhibitor drug that prevented neuroinflammation and neurodegeneration in an animal model of the disease, as reported last year by West and colleagues.

The new biomarker findings were published in Neurology in March andMovement Disorders in June. The biomarker, LRRK2, has been shown to play a role in hereditary Parkinson's, and the most common of these mutations -- called G2019S -- causes the LRRK2 kinase to add too many phosphates to itself and other proteins. Why this leads to Parkinson's disease is not yet clear.

The key to West's biomarker approach was the recognition that LRRK2 can be purified from a new type of vesicle called exosomes found in all human biofluids, like urine and saliva. Cells in the body continually release exosomes that contain a mixture of proteins, RNA and DNA derived from different kinds of cells. West and colleagues were able to purify exosomes from 3- or 4-ounce urine samples donated by patients, and then measure phosphorylated LRRK2 in those exosomes.

The findings

In the Neurology study, they found that elevated phosphorylated LRRK2 predicted the risk for onset of Parkinson's disease for people carrying a mutation in LRRK2, which is about 2-3 percent of all Parkinson's disease patients. These findings were first tested with a preliminary, 14-person cohort of urine samples from the Columbia University Movement Disorders Center. That was followed by a larger replication study of 72 biobanked urine samples from the Michael J. Fox Foundation LRRK2 Cohort Consortium. All samples were provided to UAB in a blinded fashion to ensure the approach was rigorous.

The follow-up Movement Disorders paper -- the first study of its type -- expanded the scope to people without LRRK2 mutations, which is most Parkinson's disease patients. Using 158 urine samples from Parkinson's disease patients and healthy controls enrolled in the UAB Movement Disorder Clinic as part of the NIH Parkinson's Disease Biomarker Program, West and colleagues found that approximately 20 percent of people without LRRK2 mutations but with Parkinson's disease also showed highly elevated phosphorylated LRRK2 similar to people with LRRK2 mutations, and this was not present in healthy controls. The study speculates that people with elevated phosphorylated LRRK2 may be particularly good candidates for future drugs that reduce phosphorylated LRRK2.

Next steps

Questions remain for this evidence of biochemical changes in LRRK2 in idiopathic Parkinson's disease. One is finding out where the urinary exosomes come from. Given a suspected role for inflammation in Parkinson's disease, it is interesting that LRRK2 is highly expressed in cells of the innate immune system. A possible explanation for the phosphorylated LRRK2 in patients with more severe disease may be an increased inflammation in those patients who have aggressive progression of disease.

In May, West was awarded a new U01 collaborative grant from the National Institute of Neurological Disorders and Stroke to further explore urinary exosomes and extend the observations to cerebral-spinal fluid as a marker for disease prediction and prognosis.

Besides West, authors of the Neurology paper, "Urinary LRRK2 phosphorylation predicts parkinsonian phenotypes in G2019S LRRK2 carriers," are Kyle B. Fraser and Mark S. Moehle, of the Center for Neurodegeneration and Experimental Therapeutics and Department of Neurology, UAB School of Medicine; and Roy N. Alcalay, M.D., Columbia University Department of Neurology.

Besides West, authors of the Movement Disorders paper, "Ser(P)-1292 LRRK2 in urinary exosomes is elevated in idiopathic Parkinson's disease," are Fraser, Ashlee B. Rawlins, Rachel G. Clark and David G. Standaert, M.D., Ph.D., of the UAB Center for Neurodegeneration and Experimental Therapeutics and Department of Neurology; Alcalay; and Nianjun Liu, Ph.D., Department of Biostatistics, UAB School of Public Health.

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The above post is reprinted from materials provided by University of Alabama at Birmingham. The original item was written by Jeff Hansen.Note: Materials may be edited for content and length.

Lush Venus? Searing Earth? It could have happened

If conditions had been just a little different an eon ago, there might be plentiful life on Venus and none on Earth.

The idea isn't so far-fetched, according to a hypothesis by Rice University scientists and their colleagues who published their thoughts on life-sustaining planets, the planets' histories and the possibility of finding more inAstrobiology this month.

The researchers maintain that minor evolutionary changes could have altered the fates of both Earth and Venus in ways that scientists may soon be able to model through observation of other solar systems, particularly ones in the process of forming, according to Rice Earth scientist Adrian Lenardic.

The paper, he said, includes "a little bit about the philosophy of science as well as the science itself, and about how we might search in the future. It's a bit of a different spin because we haven't actually ­­­­done the work, in terms of searching for signs of life outside our solar system, yet. It's about how we go about doing the work."

Lenardic and his colleagues suggested that habitable planets may lie outside the "Goldilocks zone" in extra-solar systems, and that planets farther from or closer to their suns than Earth may harbor the conditions necessary for life.

The Goldilocks zone has long been defined as the band of space around a star that is not too warm, not too cold, rocky and with the right conditions for maintaining surface water and a breathable atmosphere. But that description, which to date scientists have only been able to calibrate using observations from our own solar system, may be too limiting, Lenardic said.

"For a long time we've been living, effectively, in one experiment, our solar system," he said, channeling his mentor, the late William Kaula. Kaula is considered the father of space geodetics, a system by which all the properties in a planetary system can be quantified. "Although the paper is about planets, in one way it's about old issues that scientists have: the balance between chance and necessity, laws and contingencies, strict determinism and probability.

"But in another way, it asks whether, if you could run the experiment again, would it turn out like this solar system or not? For a long time, it was a purely philosophical question. Now that we're observing solar systems and other planets around other stars, we can ask that as a scientific question.

"If we find a planet (in another solar system) sitting where Venus is that actually has signs of life, we'll know that what we see in our solar system is not universal," he said.

In expanding the notion of habitable zones, the researchers determined that life on Earth itself isn't necessarily a given based on the Goldilocks concept. A nudge this way or that in the conditions that existed early in the planet's formation may have made it inhospitable.

By extension, a similarly small variation could have changed the fortunes of Venus, Earth's closest neighbor, preventing it from becoming a burning desert with an atmosphere poisonous to terrestrials.

The paper also questions the idea that plate tectonics is a critical reason Earth harbors life. "There's debate about this, but the Earth in its earliest lifetimes, let's say 2-3 billion years ago, would have looked for all intents and purposes like an alien planet," Lenardic said. "We know the atmosphere was completely different, with no oxygen. There's a debate that plate tectonics might not have been operative.

"Yet there's no argument there was life then, even in this different a setting. The Earth itself could have transitioned between planetary states as it evolved. So we have to ask ourselves as we look at other planets, should we rule out an early Earth-like situation even if there's no sign of oxygen and potentially a tectonic mode distinctly different from the one that operates on our planet at present?

"Habitability is an evolutionary variable," he said. "Understanding how life and a planet co-evolve is something we need to think about."

Lenardic is kicking his ideas into action, spending time this summer at conferences with the engineers designing future space telescopes. The right instruments will greatly enhance the ability to find, characterize and build a database of distant solar systems and their planets, and perhaps even find signs of life.

"There are things that are on the horizon that, when I was a student, it was crazy to even think about," he said. "Our paper is in many ways about imagining, within the laws of physics, chemistry and biology, how things could be over a range of planets, not just the ones we currently have access to. Given that we will have access to more observations, it seems to me we should not limit our imagination as it leads to alternate hypothesis."

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Rice graduate student Matt Weller, now a postdoctoral fellow at the Lunar and Planetary Institute, is a co-author of the paper. Additional co-authors are John Crowley, a geodetic engineer at the Canadian Geodetic Survey of Natural Resources Canada and an adjunct professor in the Department of Earth and Environmental Sciences at the University of Ottawa, and Mark Jellinek, a professor of volcanology, geodynamics, planetary science and geological fluid mechanics at the University of British Columbia.

The National Science Foundation supported the research.

Read the abstract at http://online.liebertpub.com/doi/abs/10.1089/ast.2015.1378

This news release can be found online at http://news.rice.edu/2016/07/05/lush-venus-searing-earth-it-could-have-happened/

Follow Rice News and Media Relations via Twitter @RiceUNews.

Related materials:

Adrian Lenardic: http://earthscience.rice.edu/directory/user/18/

Mark Jellinek: https://www.eoas.ubc.ca/about/faculty/M.Jellinek.html

Rice Department of Earth Science: http://earthscience.rice.edu

Located on a 300-acre forested campus in Houston, Rice University is consistently ranked among the nation's top 20 universities by U.S. News & World Report. Rice has highly respected schools of Architecture, Business, Continuing Studies, Engineering, Humanities, Music, Natural Sciences and Social Sciences and is home to the Baker Institute for Public Policy. With 3,910 undergraduates and 2,809 graduate students, Rice's undergraduate student-to-faculty ratio is 6-to-1. Its residential college system builds close-knit communities and lifelong friendships, just one reason why Rice is ranked No. 1 for best quality of life and for lots of race/class interaction by the Princeton Review. Rice is also rated as a best value among private universities by Kiplinger's Personal Finance. To read "What they're saying about Rice," go to http://tinyurl.com/RiceUniversityoverview.

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