Gut microbe may challenge textbook on complex cells

A gut microbe collected from chinchilla droppings might be the first complex life form to lack even a shred of a supposedly universal organelle.

Monocercomonoides, a one-celled gut microbe collected from a pet chinchilla in Prague decades ago, apparently has no mitochondria, the organelles known as the cell’s power plants. Cataloging DNA in the microbe turns up none of the known genes for mitochondrial proteins. But stealing genetic material from bacteria — which survive without mitochondria — allowed the microbe to do without them, too, researchers report May 12 in Current Biology.
Mitochondria are tiny capsules that speckle the insides of all complex cells from pond scum to people, or so textbooks have said for decades. Some complex (or eukaryotic) cells look as if they have no mitochondria; so far, though, further searches have eventually detected mitochondrial remnants.

But Monocercomonoides appears to have completely done away with mitochondria and the genes to make them, says study coauthor Anna Karnkowska, an evolutionary biologist now at the University of British Columbia in Vancouver.

This discovery marks “the most extreme mitochondrial reduction observed,” says Vladimír Hampl of Charles University in Prague, also a coauthor of the study.

The new work also supports the idea that there really is no single core function that defines mitochondria. Although commonly described as cell powerhouses, mitochondria don’t have much to do with supplying energy for cells that live in low-oxygen or no-oxygen environments, Karnkowska says. For these anaerobic cells, mitochondria can serve as more of a building studio. One supposedly essential mitochondrial function, scientists have proposed, is assembling clusters of iron and sulfur that activate a class of widely useful cell compounds.

Bacteria and other simple (prokaryotic) cells have their own assembly systems, and they don’t need to wall off the construction of iron-sulfur clusters. The newly studied Monocercomonoides carry the genes for an assembly system that looks as if it was taken from bacteria, the researchers conclude.
Researchers discovered the lack of mitochondrial genes and the bacterial substitute while working out the DNA components that encode instructions for all the proteins in the whole organism. There were notably no signs of chaperone proteins for conveying other proteins through membranes, something mitochondria do. Nor did other signature mitochondrial proteins show up.

“Pretty amazing story,” says Roland Lill of Philipps University of Marburg in Germany, who studies the way cells use iron. The new paper doesn’t change the basic idea that complex cells need very special conditions, usually created only inside mitochondria, to build their iron-sulfur clusters. “But the beauty of biology,” he says, “is that there are always amazing exceptions to basic biological rules.”

Zapping clouds with lasers could tweak planet’s temperature

Laser blasts might help scientists tweak Earth’s thermostat by shattering the ice crystals found in cirrus clouds.

Zapping tiny ice particles in the lab forms new, smaller bits of ice, researchers report May 20 in Science Advances. Since clouds with more numerous, smaller ice particles reflect more light, the technique could combat global warming by causing the clouds to reflect more sunlight back into space, the scientists say.

Scientists from the University of Geneva and from Karlsruhe Institute of Technology in Germany injected water drops into a chilled chamber that mimics the frigid conditions high in the atmosphere, where wispy cirrus clouds live. The water froze into spherical ice particles, which the scientists walloped with short, intense bursts of laser light.
When the laser hits an ice particle, ultrahot plasma forms at its center, producing a shock wave that breaks the particle apart and vaporizes much of the ice. The excess water vapor left in the aftermath then condenses and freezes into new, smaller ice particles.
Applying this technique to clouds is “a long, long, long way in the future,” says physicist Mary Matthews of the University of Geneva, a coauthor of the study. Current laser technology is not up to the task of cloud zapping — yet. “What we are hoping for is that the advances in laser technology, which are moving faster and faster all the time, will enable high-powered, mobile lasers,” Matthews says.

But tinkering with cirrus clouds could backfire if scientists aren’t careful, says atmospheric scientist Trude Storelvmo of Yale University. The clouds also trap heat, through the greenhouse effect, so breaking up their ice particles could actually warm the Earth. The method“could potentially work, but only if you target certain types of cirrus clouds,” she says, such as those that are very thick.

There could also be warming if fossil fuels are burned to power the laser, says David Mitchell of the Desert Research Institute in Reno, Nev. “I think it’s really interesting research, but I’m just not seeing how it’s going to make the world a cooler place.”

Animals get safe spots to cross the road — and car collisions drop

U.S. 191 is one of the driving options for people headed to Grand Teton or Yellowstone National Parks. But the road also cuts through prime territory for mule deer and pronghorns. And cars and large wildlife don’t usually mix well. When they do tangle, the cars end up heavily damaged, and the animals end up dead.

In an effort to reduce this conflict, the Wyoming Department of Transportation spent nearly $10 million to install two overpasses and six underpasses, along with deer-proof fencing, on sections of the highway near Daniel Junction in 2012. The sites for the passes were chosen based, in part, on the migration patterns of mule deer and pronghorns through the area.

Shortly after the installation, the animals were seen using the crossings, and vehicle collisions appeared to decline. The project was labeled a success. Now, an analysis of the project finds just how successful it has been: Car collisions with pronghorn have disappeared entirely and those with mule deer have dropped by 79 percent, Hall Sawyer of Western Ecosystems Technology Inc., and colleagues report May 16 in the Wildlife Society Bulletin.

Two digital cameras were installed at each overpass and one at each underpass to monitor wildlife using the crossings during the spring and fall migration periods in 2012 through 2015. Thousands of animals started using the pathways, and each year, more and more animals crossed the highway using these safe paths. Over the years, 40,251 mule deer and 19,290 pronghorn made their way through the passages.

Of the mule deer passing through, 79 percent used the underpasses. But among pronghorns, 92 percent took the overpasses. This confirms something that researchers had thought would be true but never really had any data to back up. They figured that ungulates such as pronghorns that live in open areas and are heavily reliant on vision to detect predators should prefer overpasses, because the structures would allow the animals to have better vision and movement. The new finding supports this, at least for pronghorns, and shows that building overpasses, which are more expensive than paths beneath highways, really is necessary for some animals.

This area of U.S. 191 was one of the worst for wildlife vehicle collisions before the crossings were built, averaging 85 per year from 2005 to 2012. By the third year after the installation, though, collisions had dropped to just 16 per year.

When the crossings were put in place, the Department of Transportation claimed that, by preventing vehicle collisions, the project would essentially pay for itself in 20 years. But this project has been so successful, the team calculates, that a crossing could pay for itself in just 4 years. And then, of course, there’s the benefit for the wildlife itself, which can now more easily and safely move through the landscape.
The team does note that Wyoming did have to make a few adjustments to the project to accommodate human behavior. The overpasses are edged with high berms to prevent animals from seeing the highway, but those berms proved tempting to ATV users and motorcyclists. Because this activity is damaging to vegetation and could reduce effectiveness of the crossings, the Bureau of Land Management had to post signs warning people away.

And when the crossings first went up, some canny hunters figured that the overpasses were good spots to find hundreds of pronghorn; hunting is now banned within 800 meters of a wildlife overpass.

Scary tomato appears to bleed

A newly discovered species of tomato belongs in a haunted house, not on a sandwich.

Fruit from the bush tomato plant Solanum ossicruentum bears little resemblance to its cultivated cousins. The Australian tomato, about a couple centimeters wide, grows enclosed in a shell of spikes. These burrs probably help the fruit latch on to the fur of passing mammals, which then spread the tomato’s seeds elsewhere, researchers at Bucknell University in Lewisburg, Pa., report May 3 in PhytoKeys.

Slice open the fearsome fruit and within five minutes, its sticky white-green flesh appears to bleed, flushing bright red to dark maroon in response to air exposure. One brave researcher tasted an unripe fruit and deemed it salty. The bush tomato becomes no more appetizing with time: Mature fruits harden into dry, bony nuggets.

The tomato’s gruesome qualities inspired its name, courtesy of a group of Pennsylvanian seventh-grade science students: “Ossicruentum” combines the Latin words for “bone” and “bloody.”

Monitoring online groups offers insight into ISIS attacks

Social media supporters of the Islamic State, or ISIS, form online groups that may provide clues crucial to predicting when terrorist attacks will take place, a new analysis finds.

These virtual communities drive ISIS activity on a Facebook-like site called VKontakte, say physicist Neil Johnson of the University of Miami in Coral Gables, Fla., and colleagues. VKontakte, a social networking service based in Russia with more than 350 million users, allows messaging in many languages and is used worldwide.
In the June 17 Science, Johnson’s team describes a mathematical model that predicts online groups of ISIS supporters will proliferate days before real-world Islamic State attacks. That’s just what happened in September 2014, researchers say. Pro-ISIS groups on VKontakte mushroomed the day before Islamic State forces overran Kobane, a small Syrian town.

The researchers refer to groups of followers of an online page that form spontaneously as aggregates. “Our work suggests that, to manage and monitor online ISIS activity, we need to focus on aggregates rather than individuals,” Johnson says.

Pro-ISIS aggregates on VKontakte exchanged information on issues such as recruiting fighters to Syria and how to survive drone attacks.

The new model suggests that authorities need to shut down online pro-ISIS groups in their early stages. Small-scale aggregates favoring the same cause gradually expand when left alone and eventually merge into a much larger online community that’s more difficult to break up, Johnson’s model forecasts.

“This is the first serious, large-scale, data-driven study that shows how online support develops for terrorist groups such as ISIS,” says computer scientist V.S. Subrahmanian of the University of Maryland in College Park, who builds computational models of terror networks. But it remains to be seen whether the new model can predict when and possibly where future Islamic State attacks will occur, Subrahmanian cautions.
Johnson’s team identified 196 pro-ISIS aggregates, consisting of 108,086 individual followers, which operated between January 1 and August 31, 2015. Intelligence agencies, hackers and website moderators work to shut down these online groups, but to a lesser extent on VKontakte than on Facebook.

Pro-ISIS aggregates rapidly adapted to these survival threats in several ways, the researchers say. Fifteen percent of aggregates changed their online names; 7 percent flipped back and forth between opening their content to any VKontakte user or to current aggregate followers only; and 4 percent engaged in a digital form of reincarnation. Pro-ISIS aggregates under unusually intense attack by hackers and others opted for reincarnation, Johnson says.

Reincarnating aggregates disappeared and then returned, often within weeks, with new names and at least 60 percent of the same followers as before. Aggregates that vanished appear to have reassembled without any direction or urging from one or a few members, Johnson says. New names of reincarnated groups often resembled original names enough to alert former members but not enough to trigger VKontakte’s automated system for identifying names of probable pro-militant groups, he points out.

As with predictions of terror attacks based on the expansion of pro-ISIS aggregates, the new model shows promise in predicting when mass public protests will occur based on sudden jumps in numbers of pro-protest aggregates, the scientists say. There is a difference: Reincarnation did not appear within the last three years among Facebook aggregates consisting of civil protesters in Brazil and several other Latin American countries, the researchers found. Those online groups experienced fewer pressures to shut down than pro-ISIS aggregates on VKontakte did.

Johnson’s analysis moves the study of online militant groups forward, says terrorism analyst J.M. Berger of George Washington University in Washington, D.C. But it’s likely that considerably fewer members of pro-ISIS aggregates than the total studied in the new analysis were actually hard-core Islamic State supporters, Berger contends. Concerted efforts to shut down online terrorist networks have depressed numbers of committed ISIS supporters using social media, in his view. Berger and a colleague have found that English-language Twitter use has declined sharply among ISIS supporters over the last two years, due to suspensions of their accounts by the social media site.

Johnson suspects most pro-ISIS aggregate members were staunch supporters, since aggregates aggressively weed out those deemed unserious or hostile.

Terrorists use chains of social and messaging sites online to achieve their ends, Subrahmanian says. How that works, and whether the same aggregate operates under different guises from one site to the next, has yet to be studied.

Tight spaces cause spreading cancer cells to divide improperly

Scientists have found a new way to study how cancer cells divide and thrive in difficult-to-reach crannies of the body.

Transparent artificial membranes — just nanometers thick — can be rolled into tubes to mimic capillaries that host spreading cancer cells, researchers report in the June ACS Nano. Cells squished inside such tubes didn’t organize their internal components the way they normally do before splitting. As a result, the cells divided unevenly, potentially introducing new mutations.
Inside the body, cancer cells fight for space. Sometimes they’ll spread, or metastasize, to other organs via tight blood vessels. Although cancer cells are more likely to kill once they spread, scientists still don’t understand how the abnormal cells divide inside such tiny tubes. These cells are difficult to study in the body because they’re tucked away in hard-to-reach places. They’re challenging to study in the lab, too, because they behave differently in a petri dish than in their natural environment.

By replicating that environment more closely, this experiment gives “an appreciation for what it’s like to be a cell in a body,” says Buzz Baum, a biologist at University College London who was not involved in the work.

Other researchers have looked at cells constrained in other ways. But the nanotubes are round, just like blood vessels. They’re transparent, making it easier to visualize what’s happening inside. And it’s possible to study many cells at once by growing nearly a thousand tubes, all exactly the same size, on a chip slightly larger than a postage stamp.

When watching single human cancer cells inside the tubes through high-powered microscopes, the team noticed that the squished cells didn’t divide symmetrically. Instead of sending half the chromosomes to each new cell, some of those cells got extra genetic instructions, while others were shortchanged.

The squished cells also took longer to divide. And the protein structures that help guide the chromosomes and organelles into place before division didn’t develop correctly, says study coauthor Wang Xi, a materials scientist who did the work at the Leibniz Institute for Solid State and Materials Research Dresden in Germany.
Cancer cells succeed by mutating enough that they can evade capture, without becoming too mutated to keep replicating.

“A cell that makes too many mistakes will just die,” says Baum.

When cells are trapped inside blood vessels, “they become misshapen but they’re still able to divide,” says Xi, now at the National University of Singapore.

Xi and his colleagues think that a bulging of the cell membrane in response to pressure, called blebbing, might help the trapped cells divide in a slightly less distorted way. When the researchers prevented the cells from blebbing, the division was even more uneven. But because the team can’t yet explain why this would be the case, it’s too soon to say whether blebbing itself is responsible for the improved division.

Baum says he has shown similar deformities in cancer cells dividing under other types of constraints. But, he adds, it’s important to have systems that more closely replicate the body’s internal environment. Otherwise, it can be a big jump between doing tests in a petri dish and in a live animal.

Study coauthor Christine Schmidt, a biochemist at the University of Cambridge, says understanding how cancer cells manage to divide in tight quarters could eventually inspire ways to kill spreading cancer cells without hurting healthy cells.

Mini ‘wind farm’ could capture energy from microbes in motion

Fluid filled with lively, churning bacteria could one day become a small-scale power source.

New computer simulations indicate that a miniature wind farm‒like device could harvest the energy of chaotically swirling bacteria. That energy could be used to power micromachines or pump fluids through tiny channels. In the simulations, bacteria tended to spontaneously swim in an orderly fashion around an array of cylindrical turbines. These turbines then rotated steadily like windmills in a breeze, scientists report July 8 in Science Advances.
Previous research has harnessed the energy of the motion in such chaotic fluids using tiny, asymmetric gears, which spin as bacteria bump into their teeth. But the new result shows that a very simple system can serve the same purpose — a result that could make such devices easier to construct. “You don’t have to muck around with getting the teeth right; you just have a nice smooth cylinder,” says biophysicist and study coauthor Tyler Shendruk of the University of Oxford. The technique would sidestep the need to manufacture complicated microscopic gears.

“I think it’s quite surprising because previous work showed that you need to have a certain nonsymmetry in the system” to generate rotation, says physicist Igor Aronson of Argonne National Laboratory in Illinois, who was not involved with the new work.

The researchers studied simulations of a liquid filled with many self-propelled particles, called a dense active fluid. These fluids can be made up of swimming bacteria or biological motors found inside cells — for instance, the proteins myosin and actin, which cause muscles to contract. Such fluids are normally turbulent, with swarms of particles generating rapidly and unpredictably changing flows. That makes it a challenge to harvest energy from the fluid. “It’s chaotic, so you can’t use it to do anything useful because it’s a random flow,” Shendruk says.
But when Shendruk and colleagues added a grid of cylindrical rotors, each a few hundredths of a millimeter in diameter, into their simulated fluid, they found that bacteria would spontaneously organize, like sailors all rowing in the same direction. The swimming bacteria produced a circular fluid flow that spun the rotors. That rotation could be used to generate electrical power in the same manner as windmills do, but in much smaller amounts that might be used to power tiny electronics. Each rotor might produce around a quadrillionth of a watt of electrical power, Shendruk estimates.
A single rotor on its own didn’t work as well: Its spin changed direction periodically as the chaotic fluid swirled around it. But with an array of rotors close together, the bacteria became steady synchronized swimmers squeezing through gaps between the rotors — and making each rotor consistently spin in the direction opposite to that of its neighbors.

The system should translate well from simulation to the real world, says Shendruk, and the researchers are already discussing the possibilities for constructing it. But, says applied mathematician Jörn Dunkel of MIT, the details of the real world are important. Whether the rotors would behave the same way in a real-life system where the rotors experience friction is uncertain. “The effect is there — I don’t doubt that. The question is how strong.”

Scientists throw a curve at knuckleball explanation

Knuckleballs baffle baseball players with their unpredictable swerves. A new study suggests a possible cause of the pitch’s erratic flight — sudden changes in the drag force on a ball, due to a phenomenon called a drag crisis.

The result is at odds with previous research that attributed the zigzags to the effect of airflow over the baseball’s seams. Scientists report the finding July 13 in the New Journal of Physics.

Knuckleballs are well known in baseball, but similar phenomena also confound players in soccer and volleyball. Knuckleballs occur when balls sail through the air with very little spin, producing unstable flight.
In drag crisis, the thin layer of air surrounding the ball flips between turbulent and smooth flow, abruptly changing the drag forces on the ball. If the transition occurs asymmetrically, it can push the ball to one side. “This phenomenon is intermittent” and hard to predict, says study coauthor Caroline Cohen, a physicist at École Polytechnique in Palaiseau, France. “We can’t know in advance [to] which side it will go.” Balls must move at a certain speed to experience a drag crisis, which may be why knuckleballs tend to be thrown slower than other pitches, the researchers suggest. While the fastest pitches can top 100 miles per hour, knuckleballs are usually closer to 60 or 70 miles per hour.

The scientists built a knuckleball machine, designed to launch a beach ball without any spin, and measured how much the ball veered off course. Then they calculated the ball’s expected motion based on the physics of the drag crisis and found that the predicted trajectories matched the experiments. The scientists’ calculations also correctly predict knuckleball-like phenomena in soccer, volleyball, cricket and baseball — but not in sports like tennis or basketball, where knuckleballs aren’t seen due to the properties of the ball, including texture, typical speed and how far it flies.

“It’s a fine piece of work,” says Alan Nathan of the University of Illinois at Urbana-Champaign, who studies the physics of baseball (SN: 3/23/13, p.32). But he is not entirely convinced by the explanation of knuckleballs. “Wind tunnel experiments seem to strongly suggest that it’s associated with the seams on the ball,” Nathan says, which can create turbulence that causes the ball to swerve.

So knuckleballs may remain as much of a challenge to explain as it is to hit them.

Jupiter’s Great Red Spot is hot

On Jupiter, the Great Red Spot is the hottest thing going. Temperatures over the ruddy oval, a storm that could engulf Earth, are hundreds of degrees warmer than neighboring parcels of air and higher than anywhere else on the planet, researchers report online July 27 in Nature. Heat from the storm might help explain why Jupiter is unusually toasty given its distance from the sun.

Astronomers have known for over 40 years that Jupiter’s upper atmosphere is surprisingly hot. Mid-latitude temperatures are about 530° Celsius, roughly 600 degrees warmer than they would be if the sun was the only source of heat. Warmth must come from inside the planet, but until now, researchers had not come up with a satisfactory explanation for how.
Active storms all around Jupiter could be injecting heat into the atmosphere, suggest James O’Donoghue, an astrophysicist at Boston University, and colleagues. Using observations from NASA’s Infrared Telescope Facility in Hawaii, the researchers found that the temperature over the Great Red Spot is about 1,300° Celsius. Sound waves generated by turbulence might be heating the air above the storm, the researchers suggest. Similar heating (on a much smaller scale) has been seen on Earth, as air ripples over the Andes Mountains in South America.

New fossil suggests echolocation evolved early in whales

A roughly 27-million-year-old fossilized skull echoes growing evidence that ancient whales could navigate using high-frequency sound.

Discovered over a decade ago in a drainage ditch by an amateur fossil hunter on the South Carolina coast, the skull belongs to an early toothed whale. The fossil is so well-preserved that it includes rare inner ear bones similar to those found in modern whales and dolphins. Inspired by the Latin for “echo hunter,” scientists have now named the ancient whale Echovenator sandersi.
“It suggests that the earliest toothed whales could hear high-frequency sounds,” which is essential for echolocation, says Morgan Churchill, an anatomist at the New York Institute of Technology in Old Westbury. Churchill and his colleagues describe the specimen online August 4 in Current Biology.

Modern whales are divided on the sound spectrum. Toothed whales, such as orcas and porpoises, use high-frequency clicking sounds to sense predators and prey.

Filter-feeding baleen whales, on the other hand, use low-frequency sound for long-distance communication. Around 35 million years ago, the two groups split, and E. sandersi emerged soon after.

CT scans show that E. sandersi had a few features indicative of ultrasonic hearing in modern whales and dolphins. Most importantly, it had a spiraling inner ear bone with wide curves and a long bony support structure, both of which allow a greater sensitivity to higher-frequency sound. A small nerve canal probably transmitted sound signals to the brain.
“Scientists have long suspected that early toothed whales could produce the high-frequency sounds needed for echolocation based on features on their skulls,” says Travis Park of Monash University in Melbourne, Australia. Previous work points to early toothed whales sensing those high frequencies. Park and his colleagues reported in April in Biology Letters the discovery of a 26-million-year-old lone ear bone showing signs of high-frequency hearing. But it wasn’t connected to a skull and, thus, couldn’t be tied to a specific whale species.

Tracing inner ear features in CT scans of 24 ancient and modern whales, including E. sandersi, plus two hippos, whales’ closest living relatives, Churchill’s team ups the ante. Because primitive versions of the bony spiral and nerve canal appeared before the first known toothed whale, the researchers suggest that rudimentary high-frequency hearing might have emerged in the common ancestor of toothed and baleen whales at least 43 million years ago. If so, baleen whales lost their high-frequency hearing at some point. Determining whether that’s truly the case requires more analysis and a wider array of fossil data, says Park, who’s unconvinced.

But there is growing consensus that the first toothed whales could hear and produce sounds at high-frequency ranges. The skull of a 28-million-year-old toothed whale also suggests that such animals could make high-frequency calls (SN: 4/19/14, p. 6). “The next step is to look at when their brains got big enough to process echolocation signals,” says Nicholas Pyenson, a paleobiologist at the Smithsonian’s National Museum of Natural History who was not affiliated with the study. “This is great, but there’s more to be done.”