Bacteria’s amyloids display surprising structure

Clusters of a toxic bacterial protein have a surprising structure, differing from similar clumps associated with Alzheimer’s and Parkinson’s in humans, scientists report in the Feb. 24 Science.

These clusters, called amyloids, are defined in part by their structure: straight regions of protein chains called beta strands, folded accordion-style into flat beta sheets, which then stack up to form a fiber. That definition might now need to be broadened.

“All the amyloids that have been structurally looked at so far have certain characteristics,” says Matthew Chapman, a biologist at the University of Michigan in Ann Arbor who wasn’t part of the work. “This is the odd amyloid out right now.”
In the human brain, misfolded proteins can form amyloids that trigger neurodegenerative diseases. But amyloids aren’t always a sign of something gone wrong — some bacteria make amyloids to help defend their turf.

In Staphylococcus aureus, for example, the PSMα3 protein assembles into amyloids that help the bacteria kill other cells. Previous research suggested that PSMα3 clusters were like any other amyloid. But researchers using X-ray crystallography found that instead of straight beta strands, the PSMα3 fiber was made up of curly structures called alpha helices that resemble an old-fashioned phone cord. The helices still formed a familiar fiber shape just like the beta strands did, but the sheets making up that fiber were rippled instead of flat.
“From the outside, it looks exactly the same. But zooming in, it looks completely different in its fundamental units,” says study coauthor Meytal Landau, a biologist at the Technion–Israel Institute of Technology in Haifa. “It’s something that really threw me off.”

Chapman first thought the finding must have been a mistake. Alpha helices are a very common protein structure, but “they don’t typically stack on each other to form a sheet,” he says. “That’s a really rare structure in nature.” Now, he says, it’s quite clear that alpha helices are building this amyloid.

Getting such a detailed picture of an amyloid is a challenge, so Landau isn’t sure whether PSMα3 is truly an exception or whether other proteins can make similar amyloid-like clusters.

Either way, knowing the structure can be useful. When Landau and her colleagues prevented the PSMα3 from forming an amyloid-like structure, the bacteria weren’t as good at attacking human immune cells. Rather than hunting for strong drugs that target the hard-to-kill bacteria themselves, Landau suggests, scientists might eventually be able to develop drugs that target the proteins controlling the bacteria’s aggression.

Fleets of drones could pollinate future crops

Eijiro Miyako gets emotional about the decline of honeybees.

“We need pollination,” he says. “If that system is collapsed, it’s terrible.”

Insects, especially bees, help pollinate both food crops and wild plants. But pollinators are declining worldwide due to habitat loss, disease and exposure to pesticides, among other factors (SN: 1/23/16, p. 16).

Miyako, a chemist at the National Institute of Advanced Industrial Science and Technology in Tsukuba, Japan, became passionate about the loss of pollinators after watching a TV documentary. He remembers thinking: “I need to create something to solve this problem.”
His answer was in an 8-year-old jar in his lab.

In 2007, he had tried to make a gel that conducts electricity, but it was “a complete failure,” he says. So he poured the liquid into a jar, put it in a drawer and forgot about it. Cleaning out his lab in 2015, he accidentally dropped and broke the jar.
Surprisingly, the gel was still sticky and picked up dust from the floor. Miyako realized that the gel’s ability to capture the tiny particles was similar to how honeybee body hairs trap pollen. His thoughts jumped to artificial pollination.

First, he investigated whether non-pollinating insects could help do the job. He dabbed his gel onto ants and set them loose in a box of tulips. The ants were coated with pollen after three days.

Still, Miyako worried that predators would snack on his insect pollinators. To give them camouflage, he mixed four light-reactive compounds into the gel. He tested the new concoction on flies, placing a droplet on their backs and setting the insects in front of blue paper. Under ultraviolet light, the gel changed from clear to blue, mimicking the color of the backdrop.

Though this chemical invisibility cloak might protect the insects, Miyako wanted a pollinator that could be controlled and wouldn’t wander off at the first scent of a picnic.

He bought 10 kiwi-sized drones and taught himself to fly them, breaking all but one in the process. Miyako covered the bottom of the surviving drone with short horsehair, using electricity to make the hair stand up. Adding his gel made the horsehair work like bee fuzz.
In tests so far, the drone has successfully pollinated Japanese lilies more than a third of the time, brushing up against one flower to collect pollen, then flying into another to knock the grains off, his team reports in the Feb. 9 Chem.
Glad he saved that failed gel, Miyako thinks it is possible to automate a fleet of 100 drones, using GPS and artificial intelligence, to pollinate alongside bees and other insects. “It’s not science fiction,” he says.

Remnants of Earth’s original crust preserve time before plate tectonics

Not all of the newborn Earth’s surface has been lost to time. Transformed bits of this rocky material remain embedded in the hearts of continents, new research suggests. These lingering remnants hint that full-fledged plate tectonics, the movements of large plates of Earth’s outer shell, began relatively late in the planet’s history, researchers report in the March 17 Science.

These revelations come from ancient continental rock in Canada that preserves geochemical traces of the even older, 4.2-billion-year-old rock from which it formed. “For the first time, we can say something about what kind of rock was a precursor to the first continental crust,” says study coauthor Jonathan O’Neil, a geochemist at the University of Ottawa.
Earth began as a molten ball around 4.54 billion years ago, and over the next tens of millions of years, its surface cooled and solidified. Almost all of Earth’s early rocky surface has been destroyed and recycled by geologic processes such as plate tectonics. The oldest known unaltered bits of the planet aren’t rocks but tiny zircon crystals formed nearly 4.4 billion years ago (SN Online: 2/23/14). The oldest actual rocks date back to only about 4 billion years. “We’re missing a lot of Earth’s history,” O’Neil says.

The new discovery fills in some of that history. In northeastern Canada, along the eastern shore of the Hudson Bay, O’Neil and geochemist Richard Carlson of the Carnegie Institution for Science in Washington, D.C., discovered 2.7-billion-year-old continental rocks that hinted at something much older. The rocks contain an unusually large abundance of an isotope of neodymium that formed only during the first few hundred million years of Earth’s history. To have so much of this neodymium, the rocks must have formed from material that was first created more than 4.2 billion years ago, the researchers calculate. That’s far older than the oldest rocks ever studied.

Based on the composition of the Canadian rocks, the researchers think that the precursor material was similar to the crust that underlies modern oceans. The finding affirms previous studies that suggested that the first continental crust arose from the partial melting of oceanic crust (SN Online: 9/20/16).

But unlike modern oceanic crust, which typically lingers for less than 200 million years before getting recycled into Earth’s interior by plate tectonics, the precursor crust survived for more than a billion years before being reworked into continental crust 2.7 billion years ago. Plate tectonics during the precursor crust’s life span must have therefore been nonexistent, sluggish or limited to certain regions, O’Neil concludes.

“If you ask five geologists the simple question of when did plate tectonics start, you’ll have answers from 4.3 billion years ago to 1 billion years ago,” he says. The new finding seems to rule out the idea that full-blown, global plate tectonics began early in Earth’s history.

The new work is exciting and sheds light on the processes that set the scene for Earth’s subsequent evolution and habitability, says geologist Tony Kemp of the University of Western Australia in Crawley. Other vestiges of early crust may lurk undiscovered elsewhere on Earth as well, he says. “It will be intriguing to see how this [research] unfolds with future studies of this type.”

Anatomy analysis suggests new dinosaur family tree

The standard dinosaur family tree may soon be just a relic.

After examining more than 400 anatomical traits, scientists have proposed a radical reshuffling of the major dinosaur groups. The rewrite, reported in the March 23 Nature, upsets century-old ideas about dinosaur evolution. It lends support to the accepted idea that the earliest dinosaurs were smallish, two-legged creatures. But contrary to current thinking, the new tree suggests that these early dinosaurs had grasping hands and were omnivores, snapping up meat and plant matter alike.
“This is a novel proposal and a really interesting hypothesis,” says Randall Irmis, a paleontologist at the Natural History Museum of Utah and the University of Utah in Salt Lake City. Irmis, who was not involved with the work, says it’s “a possibility” that the new family tree reflects actual dinosaur relationships. But, he says, “It goes against our ideas of the general relationships of dinosaurs. It’s certainly going to generate a lot of discussion.”

The accepted tree of dinosaur relationships has three dominant branches, each containing critters familiar even to the non–dinosaur obsessed. One branch leads to the “bird-hipped” ornithischians, which include the plant-eating duckbills, stegosaurs and Triceratops and its bony-frilled kin. Another branch contains the “reptile-hipped” saurischians, which are further divided into two groups: the plant-eating sauropods (typically four-legged, like Brontosaurus) and the meat-eating theropods (typically two-legged, like Tyrannosaurus rex and modern birds).
This split between the bird-hipped and reptile-hipped dinos was first proposed in 1887 by British paleontologist Harry Seeley, who had noticed the two strikingly different kinds of pelvic anatomy. That hypothesis of dinosaur relationships was formalized and strengthened in the 1980s and has been accepted since then.

The new tree yields four groups atop two main branches. The bird-hipped ornithischians, which used to live on their own lone branch, now share a main branch with the reptile-hipped theropods like T. rex. This placement suggests these once-distant cousins are actually closely related. It also underscores existing questions about the bird-hipped dinos, an oddball group with murky origins; they appear late in the dinosaur fossil record and then are everywhere. Some scientists have suggested that they evolved from an existing group of dinosaurs, perhaps similarly herbivorous sauropods. But by placing the bird-hipped dinos next to the theropods, the tree hints that the late-to-the-party vegetarian weirdos could have evolved from their now close relatives, the meat-eating theropods.

Sauropods (like Brontosaurus) are no longer next to the theropods but now reside on a branch with the meat-eating herrerasaurids. Herrerasaurids are a confusing group of creatures that some scientists think belong near the other meat eaters, the theropods, while others say the herrerasaurids are not quite dinosaurs at all.

The new hypothesis of relationships came about when researchers led by Matthew Baron, a paleontologist at the University of Cambridge and Natural History Museum in London, decided to do a wholesale examination of dinosaur anatomy with fresh eyes. Using a mix of fossils, photographs and descriptions from the scientific literature, Baron and colleagues surveyed the anatomy of more than 70 different dinosaurs and non-dino close relatives, examining 457 anatomical features. The presence, absence and types of features, which include the shape of a hole on the snout, a cheekbone ridge and braincase anatomy, were fed into a computer program, generating a family tree that groups animals that share specialized features.

In this new interpretation of dinosaur anatomy and the resulting tree, many of the earliest dinosaurs have grasping hands and a mix of meat-eating and plant-eating teeth. If the earliest dinos were really omnivores, given the relationships in the new four-pronged tree, the evolution of specialized diets (vegetarians and meat eaters) each happened twice in the dinosaur lineage.

When the researchers saw the resulting tree, “We were very surprised — and cautious,” Baron says. “It’s a big change that flies in the face of 130 years of thinking.”

The arrangement of the new tree stuck even when the researchers fiddled around with their descriptions of various features, Baron says. The close relationship between the bird-hipped, plant-eating ornithischians and the reptile-hipped, meat-eating theropods, for example, isn’t based on one or two distinctive traits but on 21 small details.

“The lesson is that dinosaur groups aren’t characterized by radical new inventions,” says paleontologist Kevin Padian of the University of California, Berkeley. “The relationships are read in the minutiae, not big horns and frills.” That said, Padian, whose assessment of the research also appears in Nature, isn’t certain that the new tree reflects reality. Such trees are constructed based on how scientists interpret particular anatomical features, decisions that will surely be quibbled with. “The devil is in the details,” Padian says. “These guys have done their homework and now everyone’s going to have to roll up their sleeves and start checking their work.”

Asteroid in Jupiter’s orbit goes its own way

One of Jupiter’s companions is a bit of a nonconformist.

The gas giant shares its orbit around the sun with a slew of asteroids, but scientists have now discovered one that goes against the flow. It journeys around the solar system in reverse — in the opposite direction of Jupiter and all the other planets. Asteroid 2015 BZ509 is the first object found that orbits in the same region as a planet but travels backward, researchers from Canada and the United States report March 30 in Nature.
The asteroid was discovered with the Pan-STARRS observatory in Hawaii in 2015, and the researchers made additional observations with the Large Binocular Telescope Observatory in Arizona.

Backward-going asteroids are rare — only 0.01 percent of known asteroids are in retrograde orbits. Until now, none were known to share a planet’s orbit. It was thought that asteroids going in reverse couldn’t coexist with a planet because interactions with the celestial body, twice each orbit, would knock the asteroid off track. But because 2015 BZ509 passes on alternating sides of Jupiter, the interactions cancel each other out, the researchers say. The first flyby in orbit pulls the asteroid outward, and the next tugs it inward — keeping the maverick asteroid in line.

The asteroid’s relationship with Jupiter is no short-term fling: The researchers determined that the two have shared an orbit for a million years.

When coal replaces a cleaner energy source, health is on the line

Where I grew up in Tennessee, a coal-fired power plant perches by the river, just down from the bridge that my wild brothers and their friends would jump off in the summer. Despite the proximity, I never thought too much about the power plant and the energy it was churning out.

But then I read an April 3 Nature Energy paper on coal-fired energy production that used my town — and others in the Tennessee Valley Authority area — as a natural experiment. The story the data tell is simultaneously fascinating and frustrating, and arrives at a politically prescient time. In recent weeks, the Trump administration has signaled a shift in energy policy back toward the fossil fuel.

The roots of this story were planted in the 1930s, when the TVA was created as a New Deal project to help haul America out of the Great Depression. The organization soon got into the power business, relying on a mix of energy sources: hydropower, coal and nuclear. After the 1979 accident at Three Mile Island — a nuclear power plant in Pennsylvania — stricter regulations driven by public fear prompted TVA to shut down its two nuclear reactors. Those temporary closures in 1985 left a gaping hole in the region’s energy production, a need immediately filled by coal.

Economist Edson Severnini realized that this dramatic shift from nuclear to coal offered a chance to study the effects of coal-fired power on health. He analyzed power production, particle pollution and medical records of babies born near coal plants. One in particular picked up the most slack: Paradise Fossil Plant in Paradise, Ky. (Incidentally, that town is the same coal-ravaged one John Prine sings about in arguably the best song ever written.) The plant’s power production increased by about 27 percent, replacing about a quarter of the missing nuclear energy.

Not surprisingly, air pollution near the Paradise plant rose, Severnini found. The levels of an air pollution indicator called total suspended particulate fell below the Environmental Protection Agency’s limit at the time (but wouldn’t have passed today’s tougher standards, Severnini says). Still, babies born near the plant in the 18 months after the nuclear shutdowns in 1985 were about 5 percent smaller than babies born in the 18 months before. No difference in birth weight showed up in babies born near other power plants that didn’t change their output (including my town’s).
That 5 percent difference was “really, really surprising,” says Severnini, of Carnegie Mellon University in Pittsburgh. Studies have linked low birth weight to trouble later in life, including a lower IQ, lower earnings and health problems, particularly heart disease.
UCLA environmental epidemiologist Beate Ritz puts that 5 percent drop in context. “These coal-fired power plants coming online can be compared with a pregnant woman smoking one pack of cigarettes a day,” she says. “That’s pretty bad.”

Ritz, who studies the hazards of air pollution in Los Angeles, points out that it’s not just the lowest birth weight babies affected. The whole curve of birth weights shifted, so that in all likelihood, most babies born there were impacted in some way. “There’s only a small percent in the upper end of the curve that is unaffected,” she says. “Everybody else has probably some kind of subtle effect that you can’t measure on their brain development, on their lung development, on their immune system.”

The study compares nuclear energy to coal. But the issue is far more complex than that, Severnini says. He hopes the example he found will serve as a reminder of how all energy decisions come with complex trade-offs. “Any energy production choice we make has costs and benefits, and we need to weigh them fully.”

The TVA case study fits with many other examples of how coal pollution can harm health, says Bernard Goldstein, a physician and environmental public health expert at University of Pittsburgh. “We should get rid of particulates, and coal contributes to that,” he says.

U.S. dependence on coal is ebbing, in part because natural gas is cheap right now. But coal isn’t dead yet. “My administration is putting an end to the war on coal,” President Donald Trump said March 28, before he signed an executive order that lifted the ban on coal leases on federal land. He also aims to lift other restrictions that affect the coal industry. It’s not yet clear how — or whether —those policies will be enacted, or whether they’ll be enough to revive the coal industry. (Tellingly, the Paradise plant plans to shut down two of its three coal-burning units as it shifts to natural gas.)

“If the president gets his way, this would slow [coal’s descent] down,” says Goldstein, who coauthored a March 23 New England Journal of Medicine opinion piece on why the Trump administration should pay attention to environmental science. Goldstein likens the situation to government efforts to discourage teenage smoking, a trend that’s also decreasing. Just because the numbers are already falling doesn’t mean we shouldn’t hasten that drop, he says.

And unlike exposure to other pollutants like cigarette smoke, air isn’t optional. “You don’t have a choice,” Ritz notes. We are all breathing the air that’s around us, whether we are in Paradise or not.

Bedbugs bugged prehistoric humans, too

The oldest known specimens of bedbug relatives have been unearthed in an Oregon cave system where ancient humans once lived. The partial fossils from three different species in the bedbug family date back 5,000 to 11,000 years, predating a previous find from 3,500 years ago, researchers report April 4 in the Journal of Medical Entomology.

“The bedbugs that we know in modern times originated as bat parasites, and it’s believed that they became human parasites when humans lived in caves with bats,” says study coauthor Martin Adams of Paleoinsect Research in Portland, Ore. When humans moved elsewhere, bedbugs came along for the ride.

These three species (Cimix antennatus, Cimex latipennis and Cimex pilosellus) probably coexisted with humans in Oregon’s Paisley Five Mile Point Caves, and probably snacked on people at least occasionally, Adams says. Even though all three species are still around today, they still feast mostly on bats.

Archaeologists think that ancient humans lived in the Paisley Caves only seasonally, which could explain why these particular species of bedbugs didn’t switch to a human-centric diet.

Size matters to lizards, but numbers may not

The quantitative abilities of lizards may have their limits.

From horses to salamanders, lots of different species display some form of number sense, but the phenomenon hasn’t been investigated in reptiles. So a team of researchers in Italy set up two experiments for 27 ruin lizards (Podarcis sicula) collected from walls on the University of Ferrara’s campus. In the first test, the team served up two house fly larvae of varying sizes. Lizards consistently chose to scarf down bigger maggots.

Then in the second experiment, the researchers gave lizards a choice between different numbers of larvae that were all the same size. The lizards didn’t show a preference. While the data suggest that the reptiles do discriminate between larger and smaller prey, they don’t distinguish between higher and lower numbers of maggots in a meal, the scientists report April 12 in Biology Letters.

The researchers cite two potential explanations for the discrepancy. Selecting larger prey rather than more prey might sometimes be advantageous for a predator. Or reptiles simply lack the numerical know-how seen in vertebrate relatives, such as fish.

Editor’s note: This story was updated April 17, 2017, to replace the previous image of a Podarcis muralis lizard with one that shows P. sicula, the species used in the study.

No long, twisted tail trails the solar system

The solar system doesn’t have a long, twisted tail after all.

Data from the Cassini and Voyager spacecraft show that the bubble of particles surrounding the solar system is spherical, not comet-shaped. Observing a spherical bubble runs counter to 55 years of speculation on the shape of this solar system feature, says Tom Krimigis of the Johns Hopkins Applied Physics Laboratory in Laurel, Md. He and colleagues report the result online April 24 in Nature Astronomy.
“You can’t really argue with the new result,” says Merav Opher of Boston University, who was not involved in the study. “The data so loudly say that there is no tail.”

The bubble, called the heliosphere, is inflated by particles streaming from the sun and envelops all of the material in the solar system. Its shape is important because it provides clues about how the solar system interacts with interstellar space.

In the 1960s, researchers proposed that the heliosphere was either shaped like a comet or was spherical. Magnetic fields surrounding the sun and the planets look sort of like comets, with long tails extending behind them. So, scientists speculated that the heliosphere would have a tail, too. In 2013, data from the Interstellar Boundary Explorer, or IBEX, spacecraft found signs that the tail assumption was right. The probe counted the number of fast-moving atoms that are thought to be kicked inward from the edge of the solar system when they collide with charged particles from the sun. Detecting those atoms offers clues to the shape of the heliosphere, and the images suggested that solar system had a long, twisted tail that looked like a four-leaf clover (SN: 8/24/13, p. 9).

But it wasn’t clear from the data exactly how far away from the spacecraft the atoms were and therefore how far the heliosphere’s tail extended, Krimigis says. By combining more than a decade’s worth of data from the Voyager and Cassini probes, he and colleagues sought a clearer picture. The team specifically tracked how the abundance of the speedy atoms changed in different parts of the heliosphere as the intensity of charged particles streaming from the sun, the solar wind, waxed and waned.

At the front of the heliosphere, where the Voyager probes sit, when the intensity of the solar wind decreased, so did the abundance of speedy atoms. When it increased, the number went up, in lockstep. Looking at speedy atoms at the back of the heliosphere, the team saw the same changes. If there were a long tail, Krimigis says, the changes in the number of atoms wouldn’t be the same in both directions. Because the atoms would have farther to travel in a tail, it would take longer for their abundance to build up there again.

While the observational evidence now favors a spherical shape for the heliosphere, recent simulations suggest something more exotic. The bubble might actually be shaped like a croissant, Opher says. The simulations, which incorporate data from Voyager 1, show that the interaction of the magnetic fields from the sun and interstellar space squish the solar wind into two jets — what might be observed as two short tails. These jets haven’t been detected yet. But if they are, she says, they could give clues to other sets of jets seen in the universe such as those shooting from young stars or possibly even black holes.

How a dolphin eats an octopus without dying

Most people who eat octopus prefer it immobile, cut into pieces and nicely grilled or otherwise cooked. For some, though, the wiggly, sucker-covered arms of a live octopus are a treat — even though those arms can stick to the throat and suffocate the diner if they haven’t been chopped into small enough pieces.

Dolphins risk the same fate when eating octopus — and they can’t cook it or cut it up with a chef’s knife. “Octopus is a dangerous meal,” notes Kate Sprogis of Murdoch University in Australia. Even if a dolphin manages to remove an octopus’ head, it still has to deal with those sucker-covered tentacles. “The suckered arms would be difficult to handle considering dolphins don’t have hands to assist them,” Sprogis says.

A group of hungry dolphins off the coast of Western Australia have figured out a solution. They shake and toss their prey until the head falls off, the animal is in pieces and its arms are tender and not wiggling anymore, Sprogis and her colleagues report April 2 in Marine Mammal Science.

The behavior, never before reported, was discovered during observations between March 2007 and August 2013 of bottlenose dolphins living in the waters off Bunbury, Western Australia. During that time, researchers witnessed 33 events in which dolphins handled an octopus with two different methods.

In one technique, a dolphin held an octopus in its mouth and shook it, slamming its prey into the water’s surface until the meal was in pieces.
Each dolphin would repeat its preferred motion, or combine the two, usually around a dozen times, over several minutes until the octopus was safe to eat. (See video below.)

“If the dolphins haven’t prepared their meal enough, then this can cause problems,” Sprogis notes. There have been two dead dolphins found in this area with whole octopuses lodged in their throats. The researchers assume that the dolphins suffocated.

Dolphins have garnered a reputation for tackling difficult-to-eat foods in creative ways. Some have been spotted using cone-shaped sponges to flush out little fish from the sandy ocean floor. Others use a six-step process to prepare a cuttlefish meal.
The Bunbury dolphins eat both octopus and cuttlefish, and those meals appear to be more common in the winter and spring, when waters are cooler, Sprogis notes. That may be when the octopus and cuttlefish breed and lose some of their camouflage abilities — making them easy prey for dolphins brave or knowledgeable enough to take advantage of the potential meal.