Share robotic frogs help turn a boring mating call into a serenade

July 15, 2013 — With the help of a robotic frog, biologists at The University of Texas at Austin and Salisbury University have discovered that two wrong mating calls can make a right for female túngara frogs.The “rather bizarre” result may be evidence not of a defect in the frog brain, but of how well frogs have evolved to extract meaning from noise, much the way humans have. The research, which was published last month in Science, may also provide insight into how complex traits evolve by hooking together much simpler traits.When choosing a potential mate, female túngara frogs listen to the sounds of the male calls, which are based on a pattern of “whines” and “chucks.” If visible, the sight of the male frogs inflating their vocal sacs adds to the appeal of the calls. It makes a whine more attractive, though still less attractive than a whine-chuck, and it makes a whine-chuck more attractive still.In an innovative experiment, biologists Michael Ryan and Ryan Taylor played around with those visual and auditory signals. They took a recording of a basic whine, then added a robotic frog that inflated its vocal sac late. They ran a parallel experiment with a chuck that arrived late relative to the whine.On their own neither the late vocal sac expansion or the sluggish chuck added to the sex appeal of the whine. In both cases it was as if the frog had just whined.When the late cues were strung together, however, something extraordinary happened. The vocal sac “perceptually rescued” the chuck and bound it together with the first part of the whine-chuck call. The resulting signal was as attractive to the female túngara frogs as a well-timed “whine-chuck.””It never would happen in nature, but it’s evidence of how much jury-rigging there is in evolution, that the female can be tricked in this way,” said Ryan, the Clark Hubbs Regents Professor of Zoology in the College of Natural Sciences at The University of Texas at Austin.Ryan compared the phenomenon to what’s called a “continuity illusion” in humans. If loud enough white noise is played in between a pair of beeps, humans will begin to perceive the beeps as a continuous tone. It’s not fully understood why this happens, but it’s probably a byproduct of our brains’ useful ability to filter out background noise.Túngara frogs are challenged by an auditory world similar to what confronts humans in noisy environments (what’s called the “cocktail party problem” by cognitive scientists). …

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Where do muscles get their power? Fifty-year-old assumptions about strength muscled aside

July 12, 2013 — Doctors have a new way of thinking about how to treat heart and skeletal muscle diseases. Body builders have a new way of thinking about how they maximize their power. Both owe their new insight to high-energy X-rays, a moth and cloud computing.The understanding of how muscles get their power has been greatly expanded with new results published online July 10 in the Royal Society journal Proceedings of the Royal Society B. The Royal Society is the U.K.’s national academy of sciences.The basics of how a muscle generates power remain the same: Filaments of myosin tugging on filaments of actin shorten, or contract, the muscle — but the power doesn’t just come from what’s happening straight up and down the length of the muscle, as has been assumed for 50 years.Instead, University of Washington-led research shows that as muscles bulge, the filaments are drawn apart from each other, the myosin tugs at sharper angles over greater distances, and it’s that action that deserves credit for half the change in muscle force scientists have been measuring.Researchers made this discovery when using computer modeling to test the geometry and physics of the 50-year-old understanding of how muscles work. The computer results of the force trends were validated through X-ray diffraction experiments on moth flight muscle, which is very similar to human cardiac muscle. The X-ray work was led by co-author Thomas Irving, an Illinois Institute of Technology professor and director of the Biophysics Collaborative Access Team (Bio-CAT) beamline at the Advanced Photon Source, which is housed at the U.S. Department of Energy’s Argonne National Laboratory.A previous lack of readily available access to computational power and X-ray diffraction facilities are two reasons that this is the first time these findings have been documented, speculated lead-author C. David Williams, who earned his doctorate at the UW while conducting the research, and now is a postdoctoral researcher at Harvard University. Currently, X-ray lightsources have a waiting list of about three researchers for every one active experiment. The APS is undergoing an upgrade that will greatly increase access and research power and expedite data collection.The new understanding of muscle dynamics derived from this study has implications for the research and use of all muscles, including organs.”In the heart especially, because the muscle surrounds the chambers that fill with blood, being able to account for forces that are generated in several directions during muscle contraction allows for much more accurate and realistic study of how pressure is generated to eject blood from the heart,” said co-author Michael Regnier, a UW bioengineering professor. …

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Low levels of toxic proteins linked to brain diseases, study suggests

July 2, 2013 — Neurodegenerative diseases such as Alzheimer’s could be better understood thanks to insight into proteins linked to such conditions, a study suggests.Scientists studying thread-like chains of protein — called amyloid fibres — have found that low levels of these proteins may cause more harm to health than high levels.These rarely formed protein chains, which have been linked with dozens of diseases, are produced as a result of a genetic flaw or changes in body chemistry brought about by ageing.When this happens, short fibres are formed which become sticky and attract copies of themselves, forming an endless chain. These chains spontaneously break, creating more filament ends to which more proteins attach.In the context of neurodegenerative diseases, it is these short, broken pieces that seem to be most harmful, scientists say.Researchers have found that when protein levels are low, lots of short protein threads are formed. But when protein levels are high, this spontaneous breakage stops and most protein filaments remain long.Compared with harmful short protein fibres, long fibres do not appear to be damaging in the case of neurodegenerative diseases. Researchers therefore believe that high levels of the protein — which lead to these longer chains — may actually be protective.In addition to shedding light on disease, this insight into the protein chains may help scientists develop useful biomaterials, such as cell scaffolds, which are used for tissue engineering or to make artificial silk.Cait MacPhee, Professor of Biological Physics at the University of Edinburgh’s School of Physics and Astronomy, said; “We would expect that the higher the level of toxins, the worse the disease. However, in this study we found that the lower the level of the protein, the more of these damaging short fibres we see. Understanding how these protein chains form offers us insight not only into how diseases progress, but how we can produce controlled biomaterials for tissue engineering.”

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Link between fear and sound perception discovered

June 30, 2013 — Anyone who’s ever heard a Beethoven sonata or a Beatles song knows how powerfully sound can affect our emotions. But it can work the other way as well — our emotions can actually affect how we hear and process sound. When certain types of sounds become associated in our brains with strong emotions, hearing similar sounds can evoke those same feelings, even far removed from their original context. It’s a phenomenon commonly seen in combat veterans suffering from post-traumatic stress disorder (PTSD), in whom harrowing memories of the battlefield can be triggered by something as common as the sound of thunder. But the brain mechanisms responsible for creating those troubling associations remain unknown. Now, a pair of researchers from the Perelman School of Medicine at the University of Pennsylvania has discovered how fear can actually increase or decrease the ability to discriminate among sounds depending on context, providing new insight into the distorted perceptions of victims of PTSD.Their study is published in Nature Neuroscience.”Emotions are closely linked to perception and very often our emotional response really helps us deal with reality,” says senior study author Maria N. Geffen, PhD, assistant professor of Otorhinolaryngology: Head and Neck Surgery and Neuroscience at Penn. “For example, a fear response helps you escape potentially dangerous situations and react quickly. But there are also situations where things can go wrong in the way the fear response develops. That’s what happens in anxiety and also in PTSD — the emotional response to the events is generalized to the point where the fear response starts getting developed to a very broad range of stimuli.”Geffen and the first author of the study, Mark Aizenberg, PhD, a postdoctoral researcher in her laboratory, used emotional conditioning in mice to investigate how hearing acuity (the ability to distinguish between tones of different frequencies) can change following a traumatic event, known as emotional learning. …

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How fish swim: Researchers examine mechanical bases for the emergence of undulatory swimmers

June 24, 2013 — How do fish swim? It is a simple question, but there is no simple answer.Researchers at Northwestern University have revealed some of the mechanical properties that allow fish to perform their complex movements. Their findings, published on June 13 in the journal PLOS Computational Biology, could provide insights in evolutionary biology and lead to an understanding of the neural control of movement and development of bio-inspired underwater vehicles.”If we could play God and create an undulatory swimmer, how stiff should its body be? At what wave frequency should its body undulate so it moves at its top speed? How does its brain control those movements?” said Neelesh Patankar, professor of mechanical engineering at Northwestern’s McCormick School of Engineering and Applied Science. “Millennia ago, undulatory swimmers like eels that had the right mechanical properties are the ones that would have survived.”The researchers used computational methods to test assumptions about the preferred evolutionary characteristics. For example, species with low muscle activation frequency and high body stiffness are the most successful; the researchers found the optimal values for each property.”The stiffness that we predict for good swimming characteristics is, in fact, the same as the experimentally determined stiffness of undulatory swimmers with a backbone,” said Amneet Bhalla, graduate student in mechanical engineering at McCormick and one of the paper’s authors.”Thus, our results suggest that precursors of a backbone would have given rise to animals with the appropriate body stiffness,” added Patankar. “We hypothesize that this would have been mechanically beneficial to the evolutionary emergence of swimming vertebrates.”In addition, species must be resilient to small changes in physical characteristics from one generation to the next. The researchers confirmed that the ability to swim, while dependent upon mechanical parameters, is not sensitive to minor generational changes; as long as the body stiffness is above a certain value, the ability to swim quickly is insensitive to the value of the stiffness, the researchers found.Finally, making a connection to the neural control of movement, the researchers analyzed the curvature of its undulations to determine if it was the result of a single bending torque, or if precise bending torques were necessary at every point along its body. They learned that a simple movement pattern gives rise to the complicated-looking deformation.”This suggests that the animal does not need precise control of its movements,” Patankar said.To make these determinations, the researchers applied a common physics concept known as “spring mass damper” — a model, applied to everything from car suspension to Slinkies, that determines movement in systems that are losing energy — to the body of the fish.This novel approach for the first time unified the concepts of active and passive swimming — swimming in which forcing comes from within the fish (active) or from the surrounding water (passive) — by calculating the conditions necessary for the fish to swim both actively and passively.

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New research backs genetic ‘switches’ in human evolution

June 19, 2013 — A Cornell University study offers further proof that the divergence of humans from chimpanzees some 4 million to 6 million years ago was profoundly influenced by mutations to DNA sequences that play roles in turning genes on and off.The study, published June 9 in Nature Genetics, provides evidence for a 40-year-old hypothesis that regulation of genes must play an important role in evolution since there is little difference between humans and chimps in the proteins produced by genes. Indeed, human and chimpanzee proteins are more than 99 percent identical.The researchers showed that the number of evolutionary adaptations to the part of the machinery that regulates genes, called transcription factor binding sites, may be roughly equal to adaptations to the genes themselves.”This is the most comprehensive and most direct analysis to date of the evolution of gene regulatory sequences in humans,” said senior author Adam Siepel, Cornell associate professor of biological statistics and computational biology.”It’s taken these 40 years to get a clear picture of what’s going on in these sequences because we haven’t had the data until very recently,” said Leonardo Arbiza, a postdoctoral researcher in Siepel’s lab and the paper’s lead author.Less than 2 percent of the human genome — the complete set of genetic material — contains genes that code for proteins. In cells, these proteins are instrumental in biological pathways that affect an organism’s health, appearance and behavior. Much less is known about the remaining 98 percent of the genome; however, in the 1960s, scientists recognized that some of the non-protein coding DNA regulates when and where genes are turned on and off, and how much protein they produce. The regulatory machinery works when proteins called transcription factors bind to specific short sequences of DNA that flank the gene, called transcription factor binding sites, and by doing so, switch genes on and off.Among the findings, the study reports that when compared with protein coding genes, binding site DNA shows close to three times as many “weakly deleterious mutations,” that is, mutations that may weaken or make an individual more susceptible to disease, but are generally not severe. Weakly deleterious mutations exist in low frequencies in a population and are eventually weeded out over time. These mutations are responsible for many inherited human diseases.While genes generally tend to resist change, a mutation occasionally leads to a favorable trait and increases across a population; this is called positive selection. By contrast, “transcription factor binding sites show considerable amounts of positive selection,” said Arbiza, with evidence for adaptation in binding sites that regulate genes controlling blood cells, brain function and immunity, among others.”The overall picture shows more evolutionary flexibility in the binding sites than in protein coding genes,” said Siepel. “This has important implications for how we think about human evolution and disease.”This is one of the first studies to combine recent data that identifies transcription factor binding sites, data on human genetic variation and genome comparisons between humans and apes. A new computational method called INSIGHT (Inference of Natural Selection from Interspersed Genomically coHerent elemenTs), designed by Ilan Gronau, a postdoctoral researcher in Siepel’s lab and a co-author of the study, allowed the scientists to integrate these diverse data types and find evidence of natural selection in the regulatory DNA.”Transcription factor binding sites are probably the regulatory elements we know the most about,” said Arbiza. …

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Less oxygen triggers grasshopper molting, farmers could benefit

May 13, 2013 — Less oxygen = shorter time between molts = shorter life-span = fewer hungry grasshoppers. And for farmers, that’s very good news. A recent study conducted by Scott Kirkton, associate professor of biology at Union College, offers insight into the relationship between respiratory function and molting that could help farmers save more of their crops.

“These grasshoppers, Schistocerca americana, emerge as 10-milligram juveniles and become 2.5-gram adults in about six weeks,” Kirkton said. “That’s a 250-fold weight increase — the equivalent of an 8-pound baby being 2,000 pounds after six weeks.”

With each molt, grasshoppers shed their exoskeletons and emerge into new ones that provide room for growth. During the six stages of their lifecycle, they get progressively larger.

Using an x-ray video or synchrotron at Argonne National Laboratory’s Advanced Photon Source in Chicago, Kirkton and his collaborator, Kendra Greenlee, assistant professor of biology at North Dakota State University, visualized living grasshoppers at different stages within an instar — the time between molts. They found that grasshoppers’ insides are essentially too big for their outsides near the end of each stage, and organs for breathing (air sacs and tracheae) were compressed.

“We found that late-stage grasshoppers have trouble breathing and oxygen delivery is reduced, such that molting might occur sooner than expected to increase exoskeleton size and alleviate respiratory system compression,” said Kirkton.

And if oxygen availability does trigger molting, farmers could benefit.

“If crops were stored at lower oxygen levels, we might be able to reduce the effect of pests,” said Kirkton. “Less oxygen would decrease body size by forcing pests to complete life-stages faster, giving them less time to reach maximum adult size. Also, low oxygen may reduce metabolism, and therefore, insect appetite.”

The research was funded by the National Science Foundation and the U.S. Department of Energy.

Future work will examine how oxygen delivery varies with development in other crop pests, such as the tobacco hornworm caterpillar, Manduca sexta.

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