Share:Freshwater fish, amphibians supercharge their ability to see infrared light

Date:November 5, 2015

Source:Washington University in St. Louis

Summary:Salmon migrating from the open ocean to inland waters do more than swim upstream. To navigate the murkier freshwater streams and reach a spot to spawn, the fish have evolved a means to enhance their ability to see infrared light.

Salmon and other freshwater fish and amphibians supercharge their ability to see red and infrared light. Scientists at Washington University School of Medicine in St. Louis have shown that this evolutionary adaptation hinges on the activity of an enzyme that converts vitamin A1 to vitamin A2, enabling the aquatic creatures to more easily navigate murky waters.
Credit: National Park Service

Salmon migrating from the open ocean to inland waters do more than swim upstream. To navigate the murkier freshwater streams and reach a spot to spawn, the fish have evolved a means to enhance their ability to see infrared light. Humans lack this evolutionary adaptation.

For nearly a century, scientists have puzzled over how salmon as well as other freshwater fish and amphibians, including frogs, easily shift their vision from marine or terrestrial environments — where the light environment is blue-green — to the waters of inland steams. In such streams, mud, algae and other particles filter out light from the blue end of the visual spectrum, creating a light environment that shifts to the red and infrared end of the spectrum.

Now, scientists at Washington University School of Medicine in St. Louis report in the journal Current Biology that they have solved the mystery.

“We’ve discovered an enzyme that switches the visual systems of some fish and amphibians and supercharges their ability to see infrared light,” said senior author Joseph Corbo, MD, PhD, associate professor of pathology and immunology. “For example, when salmon migrate from the ocean to inland streams, they turn on this enzyme, activating a chemical reaction that shifts the visual system, helping the fish peer more deeply into murky water.”

As it turns out, the enzyme — called Cyp27c1 — is closely linked to vitamin A, long known to promote good vision, especially in low light. The enzyme converts vitamin A1 to vitamin A2; the latter has remarkable properties to enhance the ability to see longer wavelength light such as red and infrared light.

The findings could lead to advances in biomedical research, particularly in optogenetics, a hot, new field in which light is used to control the firing of neurons in the brain. Optogenetic applications currently are limited to visible light, which penetrates only the top layer of neural tissue.

But if scientists are able to incorporate the newly discovered enzyme, they may be able to activate photosensitive neurons with infrared light, which penetrates much deeper. “Just as the enzyme helps fish peer into murky water, it could help us peer deeper into the brain,” said Corbo.

Corbo and his team made the enzyme discovery in zebrafish — tiny, transparent freshwater fish that remain a staple of laboratory research. They confirmed their findings in bullfrogs, whose eyes are uniquely designed for the light environments of both air and freshwater.

Bullfrogs sit with their eyes at the water’s surface so that they can look up into the air and down into the water at the same time. The researchers found vitamin A2 and the enzyme Cyp27c1 right where they expected: in the upper half of the bullfrog’s eyes that peer down into the water, but not in the lower half which looks upward into the air.

Furthermore, the scientists showed that zebrafish with normal copies of the cyp27c1 gene move toward infrared light shined into a dark aquarium. But fish with disabled cyp27c1 genes continue to behave like they are in the dark, whether or not the infrared light is on.

Humans have a form of the same gene, but it is not turned on in the eye. Thus, people are not able enhance their infrared vision in the same way fish can. To do so, they must wear night-vision goggles. “We don’t know yet how this enzyme is utilized in the human body,” Corbo said.

“But just because our eyes don’t make vitamin A2 doesn’t mean we can’t use it,” he said. Research on medical students in the 1940s showed that people who consume vitamin A2 have an enhanced ability to detect red and infrared light. In 2013, a group of “biohackers” successfully crowdfunded an experiment to try to extend their vision into the near-infrared spectrum by eating a diet supplemented with vitamin A2.

“I wouldn’t necessarily recommend following their dietary advice, but the concept is sound,” Corbo said.

Story Source:

The above post is reprinted from materials provided by Washington University in St. Louis. The original item was written by Tamara Bhandari.Note: Materials may be edited for content and length.

Journal Reference:

  1. Jennifer M. Enright, Matthew B. Toomey, Shin-ya Sato, Shelby E. Temple, James R. Allen, Rina Fujiwara, Valerie M. Kramlinger, Leslie D. Nagy, Kevin M. Johnson, Yi Xiao, Martin J. How, Stephen L. Johnson, Nicholas W. Roberts, Vladimir J. Kefalov, F. Peter Guengerich, Joseph C. Corbo. Cyp27c1 Red-Shifts the Spectral Sensitivity of Photoreceptors by Converting Vitamin A1 into A2. Current Biology, 2015; DOI: 10.1016/j.cub.2015.10.018

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Share Video: Giant guitarfish eye gymnastics

Like sharks, the giant guitarfish doesn’t have eyelids that close all the way, so it can’t blink. That might guarantee a win in a staring contest, but it does pose problems for eye protection in the sandy, tropical waters where the creature lives. So when thrashing prey kick sand or bits of coral its way, the guitarfish protects itself with an eye-catching method: retracting its eyes almost completely into its head, leaving a craterlike depression. Now, new research shows that guitarfish can thank a specialized eye muscle for that ability. Using high-speed video, researchers found a guitarfish could sink its eye nearly 40 mm. That’s almost as much as the diameter of the eyeball itself and likely more than any other vertebrate, the researchers reported online before print in Zoology. A muscle known as the obliquus inferior appears to be key; when the researchers electrically stimulated the muscle in a dissected guitarfish, the eyeball sank. Other animals, including frogs, bottlenose dolphins, and mudskippers, also retract their eyes, but employ a different mechanism. Some rays and skates, however, have the same muscle arrangement as guitarfish, so researchers are eyeing them for future studies.

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Science News-Latest experiment at Large Hadron Collider reports first results

Source:Massachusetts Institute of Technology

Summary:After a two-year hiatus, the Large Hadron Collider, the largest and most powerful particle accelerator in the world, began its second run of experiments in June, smashing together subatomic particles at 13 teraelectronvolts (TeV) — the highest energy ever achieved in a laboratory. Physicists hope that such high-energy collisions may produce completely new particles, and potentially simulate the conditions that were seen in the early universe.

Particles created from the proton collision stream out from the center of the Compact Muon Solenoid detector. They are first detected by the Silicon Tracker, whose data can be used to reconstruct the particle trajectories, indicated by yellow lines. An Electromagnetic Calorimeter detects energy deposited by electrons and photons, indicated by green boxes. The energy detected by the Hadronic Calorimeter, the primary component of jets, is indicated by blue boxes. Particles reaching the outermost parts of the detector are indicated in red.
Credit: CERN

After a two-year hiatus, the Large Hadron Collider, the largest and most powerful particle accelerator in the world, began its second run of experiments in June, smashing together subatomic particles at 13 teraelectronvolts (TeV) — the highest energy ever achieved in a laboratory. Physicists hope that such high-energy collisions may produce completely new particles, and potentially simulate the conditions that were seen in the early universe.

In a paper to appear in the journal Physics Letters B, the Compact Muon Solenoid (CMS) collaboration at the European Organization for Nuclear Research (CERN) reports on the run’s very first particle collisions, and describes what an average collision between two protons looks like at 13 TeV. One of the study leaders is MIT assistant professor of physics Yen-Jie Lee, who leads MIT’s Relativistic Heavy Ion Group, together with physics professors Gunther Roland and Bolek Wyslouch.

In the experimental run, researchers sent two proton beams hurtling in opposite directions around the collider at close to the speed of light. Each beam contained 476 bunches of 100 billion protons, with collisions between protons occurring every 50 nanoseconds. The team analyzed 20 million “snapshots” of the interacting proton beams, and identified 150,000 events containing proton-proton collisions.

For each collision that the researchers identified, they determined the number and angle of particles scattered from the colliding protons. The average proton collision produced about 22 charged particles known as hadrons, which were mainly scattered along the transverse plane, immediately around the main collision point.

Compared with the collider’s first run, at an energy intensity of 7 TeV, the recent experiment at 13 TeV produced 30 percent more particles per collision.

Lee says the results support the theory that higher-energy collisions may increase the chance of finding new particles. The results also provide a precise picture of a typical proton collision — a picture that may help scientists sift through average events looking for atypical particles.

“At this high intensity, we will observe hundreds of millions of collisions each second,” Lee says. “But the problem is, almost all of these collisions are typical background events. You really need to understand the background well, so you can separate it from the signals for new physics effects. Now we’ve prepared ourselves for the potential discovery of new particles.”

Shrinking the uncertainty of tiny collisions

Normally, 13 TeV is not a large amount of energy — about that expended by a flying mosquito. But when that energy is packed into a single proton, less than a trillionth the size of a mosquito, that particle’s energy density becomes enormous. When two such energy-packed protons smash into each other, they can knock off constituents from each proton — either quarks or gluons — that may, in turn, interact to produce entirely new particles.

Predicting the number of particles produced by a proton collision could help scientists determine the probability of detecting a new particle. However, existing models generate predictions with an uncertainty of 30 to 40 percent. That means that for high-energy collisions that produce a large number of particles, the uncertainty of detecting rare particles can be a considerable problem.

“For high-luminosity runs, you might have up to 100 collisions, and the uncertainty of the background level, based on existing models, would be very big,” Lee says.

To shrink this uncertainty and more precisely count the number of particles produced in an average proton collision, Lee and his team used the Large Hadron Collider’s CMS detector. The detector is built around a massive magnet that can generate a field that’s 100,000 times stronger than Earth’s magnetic field.

Typically, a magnetic field acts to bend charged particles that are produced by proton collisions. This bending allows scientists to measure a particle’s momentum. However, an average collision typically produces lightweight particles with very low momentum — particles that, in a magnetic field, end up coiling their way toward the main collider’s beam pipe, instead of bending toward the CMS detector.

To count these charged, lightweight particles, the scientists analyzed the data with the detector’s magnet off. While they couldn’t measure the particles’ momentum, they could precisely count the number of charged particles, and measure the angles at which they arrived at the detector. The measurements, Lee says, give a more accurate picture of an average proton collision, compared with existing theoretical models.

“Our measurement actually shrinks the uncertainty dramatically, to just a few percent,” Lee says.

Simulating the early universe

Knowing what a typical proton collision looks like will help scientists set the collider to essentially see through the background of average events, to more efficiently detect rare particles.

Lee says the new results may also have a significant impact on the study of the hot and dense medium from the early universe. In addition to proton collisions, scientists also plan to study the highest-energy collisions of lead ions, each of which contain 208 protons and neutrons. When accelerated in a collider, lead ions flatten into disks due to a force called the Lorentz contraction. When smashed together, lead ions can generate hundreds of interactions between protons and produce an extremely dense medium that is thought to mimic the conditions of space just after the Big Bang. In this way, the Large Hadron Collider experiment could potentially simulate the condition of the very first moments of the early universe.

“One microsecond after the Big Bang, the universe was very dense and hot — about 1 trillion degrees,” Lee says. “With lead ion collisions, we can reproduce the early universe in a ‘small bang.’ If we can understand what one proton collision looks like, we may be able to get some more insights about what will happen when hundreds of them occur at the same time. Then we can see what we can learn about the early universe.”

This research was funded, in part, by the U.S. Department of Energy.

Story Source:

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

Journal Reference:

  1. CMS Collaboration. Pseudorapidity distribution of charged hadrons in proton–proton collisions at √s=13 TeV. Physics Letters B, 2015; DOI: 10.1016/j.physletb.2015.10.004

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News:Wolves beat dogs at problem-solving test

Facing a treat-filled puzzle, wolves proved less willing than dogs to give

7:00AM, OCTOBER 12, 2015
dogs looking

Humans may be a bad influence on their best friends — at least when it comes to problem-solving. In a task that wasn’t very tough, wolves outperformed dogs. All any of the animals had to do was tug the lid off of a food container.

Monique Udell studies animal behavior at Oregon State University in Corvallis. In recent tests, canine were given a closed, plastic storage box containing a sausage treat. Eight of the 10 wolves successfully gnawed, pawed and ripped their way into the container — then gobbled up the treat. In contrast, just one in 20 dogs succeeded at the same challenge.

The social tendencies of dogs may be getting in the way of persistent, independent struggling that would have freed the treat, Udell now suggests.

She tested 10 pet dogs and another 10 dogs from an animal shelter (that had each had some history of pethood). In one set of tests, a person was nearby but did not encourage or discourage the dogs. Those dogs typically spent 10 to 15 percent of their time gazing at the person. They spent a mere 5 percent of their time or less touching the container.

Udell offered the same challenge to wolves. These animals had been raised and fed by people but still lived outdoors. Here, the wolves barely looked at a nearby person. Instead, they devoted about 90 percent of each two-minute trial to grappling with the box holding a treat.

When someone hovered over the dogs and actively encouraged them to keep trying to open the box, the dogs did spend more time tackling the problem. A few more even managed to open the box. But their success rate still did not match the wolves.  The dogs and wolves also were tested when no one was present. But even now, the dogs didn’t paw or mouth the box much more than they did when a human was present.

Udell published her findings September 16 in Biology Letters.


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Share Video: Caterpillars head-butt intruders during turf battles

Fat, fuzzy caterpillars might not seem like the aggressive type. But new research reveals that some of the insects aren’t above using their heads to push and pummel other caterpillars out of their home territory. The study, published in the Journal of Insect Behavior, looked at four types of “leaf-tying” caterpillars, which fashion shelters from silk and feces between pairs of overlapping leaves. After allowing unsuspecting caterpillars to set up house in an artificial leaf tie, the researcher staged confrontations between the resident insects and would-be intruders. When a challenger approached, the headstrong rivals battled it out by pushing or even walloping one another with their heads, as seen in this video, until one retreated. In more than half of all interactions, the defender won. In 24% of the confrontations, the usurper emerged victorious, whereas in another 24%, the former fighters established an uneasy peace, sharing the same space they had been battling over. Defenders may be more successful at fending off aspiring shelter crashers because they have more to lose, having expended the energy to build the protective structures in the first place, the paper says. Although such humble poop and silk digs may not look like much to us, for these caterpillars, home is where the crap is—and they’ll spare no head-butt to defend it.

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Share:How Sheep Are like an Avalanche


Sheep are rarely dangerous to skiers, but otherwise they have a lot in common with avalanches. That’s what physicists say after mathematically modeling the ungulates’ behavior (and staying well out of their path).

Francesco Ginelli, who researches complex systems at the University of Aberdeen in Scotland, had already studied flocks of birds and schools of fish. But he was curious to learn what was different about the movement of sheep or other grazers. Animals like these have a simple goal, Ginelli says: “They need to eat without being eaten.” 

Ginelli and his colleagues started their investigation by simply watching some merino sheep. At an experimental farm in the south of France, the researchers led herds of 100 female sheep into square enclosures 80 meters on each side. For up to 3.5 hours at a time, they let the sheep roam around their pastures. Meanwhile a camera snapped high-resolution photos from overhead, one picture per second.

Then researchers digitized this footage, going frame-by-frame and marking each sheep’s position by hand. The herd’s movements looked strikingly like an avalanche, Ginelli says.

Most of the time, a herd of sheep spreads slowly across an open area. The animals eat as they go. But every once in a while, a sheep near the periphery notices that it’s too isolated from the rest of the group. It suddenly sprints back toward the center, where it will be safer from predators. There’s no event that seems to trigger this movement, no “Baa!” of alarm; it comes out of nowhere. As the first sheep runs, others start to follow it, gathering mass like cascading pile of snow. Then, all at once—and again with no discernible signal—the animals stop moving. They continue grazing as before, now in a densely packed herd. (You can watch this behavior here.)

The researchers tried to build a computer model that would make a digital herd unpack and re-pack itself just like a real one does. They succeeded by creating a set of rules for a digital sheep, Ginelli says:

First, graze. You may either walk slowly or stand still while you eat grass. Try to align yourself with your close neighbors.

Next, freak out (maybe). Run, especially if you see a close neighbor running. This will get the whole herd back into its tightly packed state. In the model, the switch to freak-out mode is partly random, and partly influenced by how close a sheep’s neighbors are and what they’re doing.

This model works “fairly well” at creating artificial sheep herds that move like real ones, Ginelli says. It matters to researchers who are trying to understand how groups of animals behave, and how those behaviors evolved. “The origin of cooperative behavior in social groups is a very important question in evolutionary biology,” Ginelli says.

Merino sheep, it turns out, organize themselves pretty much like an avalanche does. This knowledge might help scientists grasp how other communities of grazers operate. Soon they may discover cow tsunamis or goatquakes—but probably not sharknados.

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Share:New treasures discovered from ancient Greek shipwreck

New treasures discovered from ancient Greek shipwreck

Marine archaeologists have recovered more than 50 luxurious remnants from the ancient Greek Antikythera shipwreck, first discovered in 1900, the Woods Hole Oceanographic Institution reports. This excavation is the first scientifically driven dive and has sparked the first comprehensive study of the artifacts. Scientists hope that the uncovered treasures will provide hints to how the “1%” lived in ancient Greece.

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Share video:Should you flush those ‘flushable wipes?’

A new video from Chemical & Engineering News’s (C&EN’s) Speaking of Chemistry series examines the chemistry underpinning what makes so-called flushable wipes actually flushable. In theory, chemical binders that help hold some wipes together are designed to “deactivate” once the wipes are removed from the wetting solution they come in, they say. As a result, the wipes—sometimes made of synthetic fibers and sometimes of plant-based cellulose ones—should fall apart as they make their way through the sewer system, but a growing number of water and sewer managers disagree. They have alleged in recent years the wipes don’t actually fall apart once they’re flushed—as the companies that make the products claim—leading to pipe clogs that interrupt sewer service and cost money to fix, C&EN reports.
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Share: Wartime Germans weren’t that close to developing atomic bomb

Wartime Germans weren’t that close to developing atomic bomb

In the midst of World War II, fears that Germany might be on the cusp of developing an atomic bomb fueled the United States’s nuclear research. But how close were the Germans to actually developing such a weapon? A new study argues not that close, Forbes reports. In research published online before print in Angewandte Chemie, the scientists investigated uranium samples from 1940s German nuclear projects and found no evidence of a self-sustained nuclear chain reaction—the chemical foundations of an atomic bomb. Specifically, the team measured amounts of uranium-236 and plutonium-239—isotopes that occur in small amounts naturally but can be produced in nuclear reactors—and found only minor amounts, the researchers say.

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Share:Specific fatty acids may worsen Crohn’s disease

Source:Duke University

Summary:Some research has suggested that omega-3 fatty acids, abundant in fish oils, can relieve inflammation in the digestive tracts of people with Crohn’s disease. But a new study hints that we should be paying closer attention to what the other omegas — namely, omega-6 and omega-7 — and are doing to improve or worsen the disease.

A new software tool allows scientists to link different human diseases and traits through the genetic variations they share.
Credit: Liuyang Wang, Dennis Ko lab

Some research has suggested that omega-3 fatty acids, abundant in fish oils, can relieve inflammation in Crohn’s disease. But a new study using software developed by Duke scientists hints that we should be paying closer attention to what the other omegas — namely, omega-6 and omega-7 — are doing to improve or worsen the disease.

Crohn’s disease is an inflammatory disease of the digestive tract that causes abdominal pain, diarrhea, fever and weight loss. Although it is thought to stem from an interplay between environmental and genetic factors, the exact causes are unclear. There is no cure, but people with the disease can avoid flare-ups by taking anti-inflammatory drugs and altering diet.

“Dietary therapies for Crohn’s disease should be examined more systematically, and this study provides a good first step,” said Dennis Ko, an assistant professor of molecular genetics and microbiology in the Duke School of Medicine.

Published September 15 in Genome Biology, the study relied on new software for researchers that identifies connections between seemingly unrelated human diseases and traits through the tiny, risk-conferring genetic variations they have in common.

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