Few people today could recite the scientific accomplishments of 19th century physician Julius Petri. But almost everybody has heard of his dish.

For more than a century, microbiologists have studied bacteria by isolating, growing and observing them in a petri dish. That palm-sized plate has revealed the microbial universe — but only a fraction, the easy stuff, the scientific equivalent of looking for keys under the lamppost.

But in the light — that is, the greenhouse-like conditions of a laboratory — most bacteria won’t grow. By one estimate, a staggering 99 percent of all microbial species on Earth have yet to be discovered, remaining in the shadows. They’re known as “microbial dark matter,” a reference to astronomers’ description of the vast invisible matter in space that makes up most of the mass in the cosmos.
In the last decade or so, though, scientists have developed new tools for growing bacteria and collecting genetic data, allowing faster and better identifications of microbes without ever removing them from natural conditions. A device called the iChip, for instance, encourages bacteria to grow in their home turf. (That device led to the discovery of a potential new antibiotic, in a time when infections are fast outwitting all the old drugs.) Recent genetic explorations of land, water and the human body have raised the prospect of finding hundreds of thousands of new bacterial species.

Already, the detection of these newfound organisms is challenging what scientists thought they knew about the chemical processes of biology, the tree of life and the manner in which microbes live and grow. The secrets of microbial dark matter may redefine how life evolved and exists, and even improve the understanding of, and treatments, for many diseases.

“Everything is changing,” says Kelly Wrighton, a microbiologist at Ohio State University in Columbus. “The whole field is full of enthusiasm and discovery.”
Counter culture
Microbiologists have in the past discovered new organisms without petri dishes, but those experiments were slow going. In one of her first projects, Tanja Woyke analyzed the bacterial community huddled inside a worm that lives in the Mediterranean Sea. Woyke, a microbiologist at the U.S. Department of Energy’s Joint Genome Institute in Walnut Creek, Calif., and colleagues published the report in Nature in 2006. It was two years in the making.

They relied on metagenomics, which involves gathering a sample of DNA from the environment — in soil, water or, in this case, worm insides. After extracting the genetic material of every microbe the worm contained, Woyke and colleagues determined the order, or sequences, of all the DNA units, or bases. Analyzing that sequence data allowed the researchers to infer the existence of four previously unknown microbes. It was a bit like obtaining boxes of jigsaw puzzle pieces that need assembly without knowing what the pictures look like or how many different puzzles they belong to, she says. The project involved 300 million bases and cost more than $100,000, using the time-consuming methods available at the time.
Just as Woyke was wrapping up the worm endeavor, new technology came online that gave genetic analysis a turbo boost. Sequencing a genome — the entirety of an organism’s DNA — became faster and cheaper than most scientists ever predicted. With next-generation sequencing, Woyke can analyze more than 100 billion bases in the time it takes to turn around an Amazon order, she says, and for just a few thousand dollars. By scooping up random environmental samples and searching for DNA with next-generation sequencing, scientists have turned up entirely new phyla of bacteria in practically every place they look. In 2013 in Nature, Woyke and her colleagues described more than 200 members of almost 30 previously unknown phyla. Finding so many phyla, the first big groupings within a kingdom, tells biologists that there’s a mind-boggling amount of uncharted diversity.

Woyke has shifted from these broad genetic fishing expeditions to working on individual bacterial cells. Gently breaking them open, she catalogs the DNA inside. Many of the organisms she has found defy previous rules of biological chemistry. Two genomes taken from a hydrothermal vent in the Pacific Ocean, for example, contained the code UGA, which stands for the bases uracil, guanine and adenine in a strand of RNA. UGA normally separates the genes that code for different proteins, acting like a period at the end of a sentence. In most other known species of animal or microbe, UGA means “stop.” But in these organisms, and one found about the same time in a human mouth, instead of “stop,” the sequence codes for the amino acid glycine. “That was something we had never seen before,” Woyke says. “The genetic code is not as rigid as we thought.”

Other recent finds also defy long-held notions of how life works. This year in the ISME Journal, Ohio State’s Wrighton reported a study of the enzyme RubisCO taken from a new microbial species that had never been grown in a laboratory. RubisCO, considered the most abundant protein on Earth, is key to photosynthesis; it helps convert carbon from the atmosphere into a form useful to living things. Because the majority of life on the planet would not exist without it, RubisCO is a familiar molecule — so familiar that most scientists thought they had found all the forms it could take. Yet, Wrighton says, “we found so many new versions of this protein that were entirely different from anything we had seen before.”

The list of oddities goes on. Some newly discovered organisms are so small that they barely qualify as bacteria at all. Jillian Banfield, a microbiologist at the University of California, Berkeley, has long studied the microorganisms in the groundwater pumped out of an aquifer in Rifle, Colo. To filter this water, she and her colleagues used a mesh with openings 0.2 micrometers wide — tiny enough that the water coming out the other side is considered bacteria-free. Out of curiosity, Banfield’s team decided to use next-generation sequencing to identify cells that might have slipped through. Sure enough, the water contained extremely minuscule sets of genes.
“We realized these genomes were really, really tiny,” Banfield says. “So we speculated if something has a tiny genome, the cells are probably pretty tiny, too.” And she has pictures to prove it. Last year in Nature Communications, she and her team published the first images (taken with an electron microscope) and detailed description of these ultrasmall microbes (see, right). They are probably difficult to isolate in a petri dish, Banfield says, because they are slow-growing and must scavenge many of the essential nutrients they need from the environment around them. Part of the price of a minigenome is that you don’t have room for the DNA to make everything you need to live.

Relationship status: It’s complicated
Banfield predicts that an “unimaginably large number” of species await in every cranny of the globe — soil, rocks, air, water, plants and animals. The human microbiome alone is probably teeming with unfamiliar microbial swarms. As a collection of organisms that live on and in the body, the human microbiome affects health in ways that science is just beginning to comprehend (SN: 2/6/16, p. 6).

Scientists from UCLA, the University of Washington in Seattle and colleagues recently offered the most detailed descriptions yet of a human mouth bacterium belonging to a new phylum: TM7. (TM stands for “Torf, mittlere Schicht,” German for a middle layer of peat; organisms in this phylum were first detected in the mid-1990s in a bog in northern Germany.) German scientists found TM7 by sifting through soil samples, using a test that’s specific for the genetic information in bacteria. In the last decade, TM7 species have been found throughout the human body. An overabundance of TM7 appears to be correlated with inflammatory bowel disease and gum disease, plus other conditions.

Until recently, members of TM7 have stubbornly resisted scientists’ efforts to study them. In 2015, Jeff McLean, a microbiologist at the University of Washington, and his collaborators finally isolated a TM7 species in a lab and deciphered its full genome. To do so, the team combined the best of old and new technology: First the researchers figured out how to grow most known oral bacteria together, and then they gradually thinned down the population until only two species remained: TM7 and a larger organism.

“The really remarkable thing is we finally found out how it lives,” McLean says, and why it wouldn’t grow in the lab. They discovered that this species of TM7, like the miniature bacteria in Colorado groundwater, doesn’t have the cellular machinery to get by on its own. Even more unusual, these bacteria pilfer missing amino acids and whatever else they need by latching on, like parasites, to a larger bacterium. Eventually they can kill their host. “We think this is the first example of a bacterium that lives in this manner,” McLean says.

He expects to see more unusual relationships among microbes as the dark matter comes to light. Many have evaded detection, he suspects, because of their small size (sometimes perhaps mistaken for bacterial debris) and dependence on other organisms for survival. In 2013 in the Proceedings of the National Academy of Sciences, McLean and colleagues were the first to describe a member of another uncultivated phylum, TM6. They found this group growing in the slime in a hospital sink drain. Later studies determined that the organism lives by tucking itself inside an amoeba.
One of the greatest hopes for microbial dark matter exploration is that newly found microbes might provide desperately needed antibiotics. From the 1940s to the 1960s, scientists discovered 10 new classes of drugs by testing chemicals found in soil and elsewhere for action against common infections. But only two classes of medically important antibiotics have been discovered in the last 30 years, and none since 1997. Some major infections are at the brink of being unstoppable because they’ve become resistant to most existing drugs (SN Online: 5/27/16). Many experts think that natural sources of antibiotics have been exhausted.

Maybe not. In 2015, a research team led by scientists from Northeastern University in Boston captured headlines after describing in Nature a new chemical extracted from a ground-dwelling bacterium in Maine. The scientists isolated the organism using the iChip, a thumb-sized tool that contains almost 400 separate wells, each large enough to hold only an individual bacterial cell plus a smidgen of its home dirt. The bacteria grow on this scaffold in part because they never leave their natural surroundings. In lauding the discovery, Francis Collins, director of the National Institutes of Health, called the iChip “an ingenious approach that enhances our ability to search one of nature’s richest sources of potential antibiotics: soil.” So far, the research team has discovered about 50,000 new strains of bacteria.

One strain held an antibiotic, named teixobactin (SN: 2/7/15, p. 10). In laboratory experiments, it killed two major pathogens in a way that did not appear easily vulnerable to the development of resistance. Most antibiotics work by disrupting a microbe’s survival mechanism. Over time, the bacteria genetically adapt, find a work-around and overcome the threat. This new antibiotic, however, prevents a microbe from assembling the molecules it needs to form an outer wall. Since the antibiotic interrupts a mechanical process and not just a specific chemical reaction, “there’s no obvious molecular target” for resistance, says Kim Lewis, a microbiologist at Northeastern.
Everything is illuminated
Some microbiologists feel like astronomers who, after years of staring up into the dark, were just handed the Hubble Space Telescope. Billions of galaxies are coming into view. Banfield expects this new microbial universe to be mapped over the next few years. Then, she says, an even more exciting era begins, as science explores how these dark matter bacteria make a living. “They are doing a lot of things, and we have no idea what,” she says.

Part of the excitement comes from knowing that microbes have a history of granting unexpected solutions to problems that scientists never expected to solve. Consider that the enzyme that makes the laboratory technique PCR possible came from organisms that live inside the thermal vents at Yellowstone National Park. PCR, which works like a photocopier to make multiple copies of DNA segments, is now used across a range of situations, from diagnosing cancer to paternity testing. CRISPR, a powerful gene-editing technology, relies on “molecular scissors” that were found in bacteria (SN: 9/3/16, p. 22).

Banfield estimates that 30 to 50 percent of newly discovered organisms contain proteins that never met a petri dish. Their function in the chemistry of life is an obscure mystery. Since microbes are the world’s most abundant organism, Banfield says, “the vast majority of life consists of biochemistry we don’t understand.” But once we do, the future could be very bright.

For chickens, a dip in the sandbox is good hygiene.

Cage-free flocks that “bathe” by flapping around in diatomaceous earth (a fine dust of fossilized algae) and sand prevent serious mite infections, researchers report September 14 in the Journal of Economic Entomology. Major infections of more than 100 mites per bird make hens lay 2 to 4 percent fewer eggs on average. So access to boxes filled with dust, which look like tiny sandboxes, makes sense for birds’ health and for farmers’ wallets.

Dust baths damage mites’ waxy outer coating and kill the pests by drying them out. Scientists already knew dust can help manage mites in badly infested birds but weren’t sure if it could also be preventative.

Researchers from the University of California, Riverside kept cage-free chickens in poultry houses with dust boxes. The scientists infected clean chickens with 20 to 30 mites each, for two consecutive weeks, and then monitored the size of each bird’s infestation. Over six to 10 weeks, each dust-bathing hen carried 100 or fewer mites, on average. When the dust baths were removed, mite populations skyrocketed. The new results point to dust boxes as an alternative to pesticides for cage-free and organic farms, the researchers say.

A star that mysteriously disappeared might be the first confirmed case of a failed supernova, a star that tried to explode but couldn’t finish the job. A newborn black hole appears to have been left behind to snack on the star’s remains.

In 2009, a star in the galaxy NGC 6946 flared up over several months to become over 1 million times as bright as the sun. Then, it seemed to vanish. While the star could just be hiding behind a wall of dust, new observations with the Hubble Space Telescope, reported online September 6 at arXiv.org, strongly suggest that the star did not survive. A faint trickle of infrared light, however, emanates from where the star used to be. The remnant glow probably comes from debris falling onto a black hole that formed when the star died, write Caltech astronomer Scott Adams and colleagues.
Black holes are typically thought to form in the aftermath of a supernova, the explosive death of a massive star. But multiple lines of evidence have recently hinted that not all heavyweights go out with a bang. Some stars might skip the supernova and collapse into a black hole. Until now, though, evidence that this happens has been either spotty or indirect.

“This is the first really solid observational evidence for a failed supernova,” says Elizabeth Lovegrove, an astronomer at the University of California, Santa Cruz. “Some supernovas really do fail and this is what they look like.”

This attempt at a supernova, first observed with the Large Binocular Telescope in Arizona, occurred about 19 million light-years away in the constellation Cygnus. Only one other known star — a yellow supergiant that faded away in 2010 — is suspected to be a failed supernova, though there’s not enough data to say for certain.

When a star at least eight times as heavy as the sun runs out of thermonuclear fuel, it can no longer support its own weight. Gas crashes down on the star’s core, bounces and sends a shock wave racing back toward the surface that tears the star apart. Some stars might be so massive that the shock wave doesn’t have enough oomph to push against the onrush of collapsing star stuff. The shock fizzles, the supernova fails and the core gathers enough mass to collapse into a black hole, possibly taking the rest of the star down with it.

If the dying star is a red supergiant — a ruddy orb that can be over 1,000 times as wide as the sun — it might give a signal before vanishing. As the core collapses, it releases an enormous amount of gravitational energy. A second shock wave ripples up through the star — not powerful enough for an explosion, but enough to burp off the loosely held outer layers of the supergiant and expose the feeding black hole.
That’s exactly what Adams and colleagues think they saw. Hubble images from before 2009 reveal a star about 25 to 30 times as massive as the sun sitting where the flash of light came from. The star doesn’t show up in images taken since the eruption. Neither the brightness of the flash, the rate at which the brightness evolved nor the amount of light coming from there now fully matches other types of stellar incidents, such as a collision between a pair of stars or the violent outbursts that accompany some aging supermassive stars.

If the star did give birth to a black hole, X-rays may be radiating from debris spiraling down its gravitational throat. Adams and collaborators are waiting on observations from the space-based Chandra X-ray Observatory to check that idea. They also continue to monitor what’s left of the star. The star might still be there, hiding within a shell of dust expelled during the 2009 eruption. If that’s the case, it should become visible again in the coming years as the cloak dissipates.

In a recent poll, more than four-fifths of U.S. adults could not name a living scientist. Of those who could, the plurality (40 percent) named Stephen Hawking. (The next highest response was Neil deGrasse Tyson, followed by Jane Goodall.) No offense to the rightfully famous Hawking, but at Science News we would like to change these results. Why aren’t more scientists, particularly those who are young and accomplished, household names? Where, we want to know, are the Taylor Swifts of science?

You’ll find some of them below. For the second year in a row, Science News is highlighting 10 early- and mid-career scientists on their way to widespread acclaim. The SN 10: Scientists to Watch includes a laser physicist with laserlike focus, a materials scientist challenging what it means to be alive and a computational biologist willing to get personal with his microbiome, among many others who are making important advances in their chosen fields.

Though none of these scientists have recorded hit singles — at least not that our reporting uncovered — all were nominated by a Nobel laureate or recently elected member of the National Academy of Sciences. And all were age 40 or younger at the time of nomination.

These remarkable individuals have diverse personalities and talents: They are tenacious and creative, practical-minded and dreamers. They are lab animals and data heads. Some seek simplicity, others complexity. If there is one unifying trait, though, it would have to be their passion — a quality so cliché among successful scientists that it has to be true. As Marie Curie famously wrote in a letter to her sister, “Sometimes my courage fails me and I think I ought to stop working…. But I am held by a thousand bonds.” She did not know, she confessed, whether she could live without the laboratory.

After a year caring for patients at the heart of Brazil’s Zika epidemic, pediatric neurologist Vanessa van der Linden has seen some of the worst cases.

She was one of the first researchers to link Zika virus to microcephaly, a now well-known birth defect marked by a small, misshapen head and, sometimes, a forehead that slopes backward. Babies with the defect can have other symptoms, too: Van der Linden has seen 24-hour crying bouts, spasms, extreme irritability and difficulty swallowing.
But microcephaly is just the tip of the Zika iceberg, she said September 22 at a workshop hosted by the National Institutes of Health in North Bethesda, Md. That’s something public health officials have been warning about for months. Now, scientists have begun to describe a head-to-toe assortment of health problems linked to Zika virus infection in utero; they’re calling it congenital Zika syndrome.

Still, the full scope of the problem, including the threat of more subtle neurologic disorders such as learning disabilities or developmental delays, remains murky, says Peter Hotez, a pediatrician and microbiologist at Baylor College of Medicine in Houston.

“That’s the big unknown: There’s probably a spectrum of illness,” similar to autism, he says. And it could take years for scientists to sort it all out.

It’s a problem that Brazil is facing now, and one that Puerto Rico has just begun grappling with.

As of September 23, the U.S. territory had reported 22,358 confirmed cases of Zika infection. Of these cases, 1,871 are pregnant women. Carmen Zorrilla, an obstetrician-gynecologist at the University of Puerto Rico’s Maternal-Infant Studies Center who has examined some of these women and their babies, emphasizes the importance of following up on all babies exposed to Zika in the womb — even those without apparent birth defects.
“Even if they are born normal,” she said, “it doesn’t mean they’ll be OK.”

Insidious problems
At the workshop, Zorrilla described the case of one of the first Puerto Rican babies born to a mother diagnosed with Zika. The baby didn’t have microcephaly, but she did have another unusual problem: She couldn’t open her eyes. A bad case of conjunctivitis (pinkeye) left her needing help opening her eyelids every morning — even 27 days after birth.
Zorrilla can’t say for sure whether the problem was related to Zika, but “it really concerned me,” she said. “This is the first baby I’ve seen with conjunctivitis that lasted for so long.”

The case may be another clue that Zika’s assaults on the body are widespread. And Zorrilla can expect to see more cases soon. Ultrasound examinations of 228 women in Puerto Rico with confirmed Zika infection have spotted brain abnormalities in 13 fetuses, including one with microcephaly.

Another observation could hint at problems yet to come: Most of the Zika-exposed fetuses tended to have slightly smaller heads than average, although “still within the normal limits,” Zorrilla said. But measurements of leg bones and stomach size indicate that the rest of the body is growing normally. Implications remain unclear, but the findings — preliminary results from Alberto de la Vega, also an obstetrician-gynecologist at the University of Puerto Rico — are the latest in a litany of anomalies linked to Zika.

Long-term problems aren’t unusual in babies infected with a different kind of virus that causes microcephaly. Like Zika, cytomegalovirus can infect babies in the womb. Most CMV-infected babies don’t have any obvious symptoms, but asymptomatic kids may have problems as they grow, including intellectual disabilities, hearing loss or cerebral palsy, researchers suggested in the October Brain and Development.

Beyond microcephaly, scientists have recently described other symptoms linked to Zika infection. In some babies, for example, Zika seems to damage hearing. Of 70 Zika-exposed infants born with microcephaly, 10 percent had some hearing loss, researchers noted in a Sept. 2 report published by the U.S. Centers for Disease Control and Prevention.
Zika can leave a mark on the eyes, too. More than a third of 29 babies with microcephaly had some sort of eye oddity, including mottled pigmenting and withered tissue, researchers reported in May in JAMA Ophthalmology.

Van der Linden has also observed a link between Zika and a deformity called arthrogryposis, where a child’s joints can be stuck in contorted positions — even in babies without microcephaly. The condition might stem from problems with infected babies’ motor neurons, the nerve cells that relay messages from the brain to the muscles, van der Linden and colleagues suggested August 9 in BMJ.

She has even seen babies born with normal head circumferences who later develop microcephaly or other brain defects. One mother, she says, came in five months after giving birth because she thought her baby wasn’t developing normally. Like children with congenital Zika syndrome, the baby’s head scans revealed “the same pattern of brain damage,” van der Linden says. This pattern includes a malformed cerebral cortex, the wrinkled outer layer of the brain, and calcifications, strange lumps of calcium deposited within the tissue.

Infiltrating the brain
Scientists still don’t know exactly how Zika damages the brain, but they have some ideas.

One recent report found that the virus can infiltrate and kill both neuroepithelial stem cells, which give rise to all sorts of brain cells, and radial glial cells, which can generate newborn neurons and help guide them to their proper place in the brain.

Zika also hinders these cells’ ability to split into new cells, Yale University neuroscientist Marco Onorati and colleagues reported September 6 in Cell Reports.
Stem cells at work in the fetal brain eventually give rise to structures responsible for thought and memory and learning, raising concerns of a cascade of problems down the road. “This is a virus that blocks the development of the fetal brain,” Hotez says. “That’s about the worst thing you can possibly imagine.”

And fetuses might not be the only ones at risk, he points out. “Kids in the first years of life also have growing, developing brains,” he says. “What if they get infected with Zika?”

It’s not an easy question to answer. But another disease could offer clues.

Malaria, for example, can cause severe neurological problems. In children, a condition called cerebral malaria may be linked to mental health disorders such as attention-deficit/hyperactivity disorder, antisocial behavior and depression, researchers reported in March in Malaria Journal.

Researchers will also need to watch out for long-term troubles in Zika-exposed babies born with no obvious symptoms, says the CDC’s Sonja Rasmussen. “We don’t want to make families too scared,” she says. “But we do recognize the possibility of later-on seizures or developmental delay.”

Since most people don’t show signs of Zika infection, pinpointing the total number of pregnant women (and babies) exposed to the virus may be impossible.

In the Americas, at least, the number is probably enormous. Tens of thousands of children may eventually suffer some sort of neurologic or psychiatric illness triggered by Zika, Hotez predicted in a paper published in JAMA Pediatrics in August.

Van der Linden can’t say whether the babies she has seen have learning disabilities or psychiatric illnesses, or other more subtle cognitive problems — most of her patients are between 9 months and 1 year old.

But she plans to follow these patients, and the babies who appeared normal at birth, for years. “We need time to better understand the disease,” she says.

Hotez agrees: “It’s going to take a generation of pediatric neurologists and infectious disease experts to figure this out.”

Figuring out the nuts and bolts of the cell’s recycling machinery has earned the 2016 Nobel Prize in physiology or medicine. Cell biologist Yoshinori Ohsumi of the Tokyo Institute of Technology has received the prize for his work on autophagy, a method for breaking down and recycling large pieces of cellular junk, such as clusters of damaged proteins or worn-out organelles.

Keeping this recycling machinery in good working condition is crucial for cells’ health (SN: 3/26/11, p. 18). Not enough recycling can cause cellular trash to build up and lead to neurological diseases such as Alzheimer’s and Parkinson’s. Too much recycling, on the other hand, has been linked to cancer.
“It’s so exciting that Ohsumi has received the Nobel Prize, which he no question deserved,” says biologist Jennifer Lippincott-Schwartz of Howard Hughes Medical Institute’s Janelia Research Campus in Ashburn, Va. “He set the framework for an entire new field in cell biology.”

Ohsumi‘s discoveries helped reveal the mechanism and significance of a fundamental physiological process, biologist Maria Masucci of the Karolinska Institute in Sweden said in a news briefing October 3. “There is growing hope that this knowledge will lead to the development of new strategies for the treatment of many human diseases.”

Scientists got their first glimpse of autophagy in the 1960s, not long after the discovery of the lysosome, a pouch within cells that acts as a garbage disposal, grinding fats and proteins and sugars into their basic building blocks. (That discovery won Belgian scientist Christian de Duve a share of the Nobel Prize in 1974.) Researchers had observed lysosomes stuffed with big chunks of cellular material — like the bulk waste of the cellular world — as well as another, mysterious pouch that carried the waste to the lysosome.

Somehow, the cell had devised a way to consume large parts of itself. De Duve dubbed the process autophagy, from the Greek words for “self” and “to eat.” But over the next 30 years, little more became known about the process.
“The machinery was unknown, and how the system was working was unknown, and whether or not it was involved in disease was also unknown,” said physiologist Juleen Zierath, also of the Karolinska Institute, in an interview after the prize’s announcement.

That all changed in the 1990s when Ohsumi decided to study autophagy in a single-celled organism called baker’s yeast, microbes known for making bread rise. The process was tricky to catch in action, partly because it happened so fast. So Ohsumi bred special strains of yeast that couldn’t break down proteins in their cellular garbage disposals (called vacuoles in yeast).

“He reasoned that if he could stop the degradation process, he could see an accumulation of the autophagy machinery in these cells,” Zierath said.

And that’s just what Ohsumi saw. When he starved the yeast cells, the “self-eating” machinery kicked into gear (presumably to scrounge up food for the cells). But because the garbage disposals were defective, the machinery piled up in the vacuoles, which swelled like balloons stuffed with sand. Ohsumi could see the bulging, packed bags clearly under a light microscope. He published the work in a 1992 paper in the Journal of Cell Biology.
Finding the autophagy machinery let Ohsumi study it in detail. A year later, he discovered as many as 15 genes needed for the machinery to work. In the following years, Ohsumi and other scientists examined the proteins encoded by these genes and began to figure out how the components of the “bulk waste” bag, or autophagosome, came together, and then fused with the lysosome.

The work revealed something new about the cell’s garbage centers, Zierath said. “Before Ohsumi came on the scene, people understood that the waste dump was in the cell,” she said. “But what he showed was that it wasn’t a waste dump. It was a recycling plant.”

Later, Ohsumi and his colleagues studied autophagy in mammalian cells and realized that the process played a key maintenance role in all kinds of cells, breaking down materials for reuse. Ohsumi “found a pathway that has its counterparts in all cells that have a nucleus,” says 2013 Nobel laureate Randy Schekman, a cell biologist at the University of California, Berkeley. “Virtually every corner of the cell is touched by the autophagic process.”

Since Ohsumi’s discoveries, research on autophagy has exploded, says Lippincott-Schwartz. “It’s an amazing system that every year becomes more and more fascinating.”

Ohsumi, 71, remains an active researcher today. He received the call from the Nobel committee at his lab in Japan. The prize includes an award of 8 million Swedish kronor (equivalent to about $934,000). About his work, he said: “It was lucky. Yeast was a very good system, and autophagy was a very good topic.”

Still, he added in an interview with a Nobel representative, “we have so many questions. Even now we have more questions than when I started.”

A satellite of Saturn joins the club of moons with possible oceans. A subsurface sea of water might hide beneath the icy crust of Dione, one of Saturn’s moons, researchers report online October 9 in Geophysical Research Letters. That puts Dione in good company alongside Enceladus (another moon of Saturn) and several moons of Jupiter, as well as possibly Pluto (SN Online: 9/23/16).

Dione’s ocean is about 100 kilometers below the surface and roughly 65 kilometers deep, Mikael Beuthe, a planetary scientist at the Royal Observatory of Belgium in Brussels, and colleagues report. They inferred the ocean’s presence from measurements of Dione’s gravity made by the Cassini spacecraft.

When babies are ready for solid foods, the meal usually arrives on a spoon. Parents scoop up pureed carrots, liquefied banana or soupy rice cereal and deliver it straight to their baby’s mouth (or forehead). But a different way of introducing solids is gaining ground. Called baby-led weaning, the approach is based on letting the baby feed herself whole foods such as a soft pear or a spear of cooked broccoli — no spoon required.

Advocates say that by having control over what goes in their mouths, babies learn to regulate their food intake, refine motor skills and perhaps even become more adventurous eaters. But critics fret that inexperienced eaters may be more likely to choke on solid foods that they feed themselves. A new study of about 200 Australian babies has some reassuring news: Provided that certain risky foods were avoided, babies who fed themselves solid foods were no more likely to choke than spoon-fed babies.

Half of the babies started solid food the traditional way, with parents spoon-feeding them purees and other mushy foods. The other half were given solid foods on their trays and encouraged to feed themselves. Parents were told that babies ought to be sitting up and in the presence of a caregiver while eating. And parents also received a list of risky foods to avoid: hard crackers, diced or hard meat, raw vegetables and popcorn made the list. (A general rule of thumb for checking whether the food is safe: If you can squish the food against the roof of your mouth, then it’s probably OK for your baby to try.)

Spoon-fed babies choked just as much as babies who fed themselves, the researchers report in the September Pediatrics. At 6 months of age, about 22 percent of spoon-fed babies had choked at least once. In the baby-led weaning group, about 18 percent of babies had choked at least once. Choking rates between the two groups were on par as the babies grew older.

There’s an important distinction here between gagging and true choking. Gagging is common among babies as their mouths learn to handle new textures and flavors. The throat slams shut and the mouth tries to get the offending food out. A gagging baby may have watery eyes, push his tongue out of his mouth and make retching movements. He may even puke. This can be hard for parents to watch, but gagging isn’t dangerous.

True choking is. This is when the airway becomes partially or fully blocked. The baby may cough or sputter in an attempt to dislodge the food. He may make a raspy, squeaky whisper as he tries to communicate distress. Or he may go silent. It’s always good to be up on infant CPR, particularly if you’ve got a new eater.

The babies who fed themselves seemed to quickly hone their skills. Initially, self-feeding babies gagged more often than spoon-fed babies at 6 months of age. But by 8 months old, self-feeders had become experts, gagging less than spoon-fed babies.
Although the news seems good for parents who want to try baby-led weaning, the research also turned up something concerning: Lots of babies were given risky foods, regardless of feeding style. At seven months of age, just over half of babies were given something from the no-feed list. By 12 months, almost all the babies had been given riskier foods that can lead to choking. Hard crackers, meat and whole grapes topped the list.

The results suggest that whether you feed your baby or you let your baby feed herself, it’s still important to pay attention to the type of food that’s going into her cute little mouth.

PASADENA, Calif. — NASA’s Juno spacecraft, in orbit around Jupiter since July 4, is lying low after entering an unexpected “safe mode” early on October 19. A misbehaving valve in the fuel system, not necessarily related to the safe mode, has also led to a delay in a planned engine burn that would have shortened the probe’s orbit.

Juno turned off its science instruments and some other nonessential components this morning at 1:47 a.m. EDT after computers detected some unexpected situation, mission head Scott Bolton reported at an October 19 news conference. The spacecraft was hurtling toward its second close approach to the planet, soaring about 5,000 kilometers from the cloud tops. It has now passed that point and is moving back away from the planet with all science instruments switched off.

The rocket firing was intended to take Juno from a 53.5-day orbit to a 14-day orbit. Juno can stay in its current orbit indefinitely without any impact on the science goals, Bolton said. The goal of the mission — to peer deep beneath Jupiter’s clouds — depends on the close approaches that it makes with every orbit, not how quickly it loops around. “We changed to a 14-day orbit primarily because we wanted the science faster,” he said. “But there’s no requirement to do that.”

For now, mission scientists are trying to figure what happened with the fuel valve and what triggered the safe mode before proceeding with further instructions to the probe.

Scientists have lost their latest round of hide-and-seek with dark matter, but they’re not out of the game.

Despite overwhelming evidence that an exotic form of matter lurks unseen in the cosmos, decades of searches have failed to definitively detect a single particle of dark matter. While some scientists continue down the road of increasingly larger detectors designed to catch the particles, others are beginning to consider a broader landscape of possibilities for what dark matter might be.

“We’ve been looking where our best guess told us to look for all these years, and we’re starting to wonder if we maybe guessed wrong,” says theoretical astrophysicist Dan Hooper of Fermilab in Batavia, Ill. “People are just opening their minds to a wider range of options.”

Dark matter permeates the cosmos: The material keeps galaxies from flying apart and has left its imprints in the oldest light in the universe, the cosmic microwave background, which dates back to just 380,000 years after the Big Bang. Indirect evidence from dark matter’s gravitational influences shows that it makes up the bulk of the mass in the universe. But scientists can’t pin down what dark matter is without detecting it directly.
In new results published in August and September, three teams of scientists have come up empty-handed, finding no hints of dark matter. The trio of experiments searched for one particular variety of dark matter — hypothetical particles known as WIMPs, or weakly interacting massive particles, with a range of possible masses that starts at several times that of a proton. WIMPs, despite their name, are dark matter bigwigs — they have long been the favorite explanation for the universe’s missing mass. WIMPs are thought to interact with normal matter only via the weak nuclear force and gravity.

Part of WIMPs’ appeal comes from a prominent but unverified theory, supersymmetry, which independently predicts such particles. Supersymmetry posits that each known elementary particle has a heavier partner; the lightest partner particle could be a dark matter WIMP. But evidence for supersymmetry hasn’t materialized in particle collisions at the Large Hadron Collider in Geneva, so supersymmetry’s favored status is eroding (SN: 10/1/16, p. 12). Supersymmetry arguments for WIMPs are thus becoming shakier — especially since WIMPs aren’t showing up in detectors.

Scientists typically search for WIMPs by looking for interactions with normal matter inside a detector. Several current experiments use tanks of liquefied xenon, an element found in trace amounts in Earth’s atmosphere, in hopes of detecting the tiny amounts of light and electric charge that would be released when a WIMP strikes a xenon nucleus and causes it to recoil.

The three xenon experiments are the Large Underground Xenon, or LUX, experiment, located in the Sanford Underground Research Facility in Lead, S.D.; the PandaX-II experiment, located in China’s JinPing underground laboratory in Sichuan; and the XENON100 experiment, located in the Gran Sasso National Laboratory in Italy. Teams of scientists at the three locations each reported no signs of dark matter particles. The experiments are most sensitive to particles with masses around 40 or 50 times that of a proton. Scientists can’t completely rule out WIMPs of these masses, but the interactions would have to be exceedingly rare.
In initial searches, proponents of WIMPs expected that the particles would be easy to find. “It was thought to be like, ‘OK, we’ll run the detector for five minutes, discover dark matter, and we’re all done,’” says physicist Matthew Szydagis of the University at Albany in New York, a member of LUX. That has turned into decades of hard work. As WIMPs keep failing to turn up, some scientists are beginning to become less enamored with the particles and are considering other possibilities more closely.

One alternative dark matter contender now attracting more attention is the axion. This particle was originally proposed decades ago as part of the solution to a particle physics quandary known as the strong CP problem — the question of why the strong nuclear force, which holds particles together inside the nucleus, treats matter and antimatter equally. If dark matter consists of axions, the particle could therefore solve two problems at once.

Axions are small fry as dark matter goes — they can be as tiny as a millionth of a billionth the mass of a WIMP. The particles interact so feebly that they are extremely difficult to detect. If axions are dark matter, “you’re sitting in an enormous, dense sea of axions and you don’t even notice them,” says physicist Leslie Rosenberg of the University of Washington in Seattle, the leader of the Axion Dark Matter eXperiment. After a recent upgrade to the experiment, ADMX scientists are searching for dark matter axions using a magnetic field and special equipment to coax the particles to convert into photons, which can then be detected.
Although WIMPs and axions remain the front-runners, scientists are beginning to move beyond these two possibilities. In between the featherweight axions and hulking WIMPs lies a broad range of masses that hasn’t been well explored. Scientists’ favorite theories don’t predict dark matter particles with such intermediate masses, says theoretical physicist Kathryn Zurek of Lawrence Berkeley National Laboratory in California, but that doesn’t mean that dark matter couldn’t be found there. Zurek advocates a diverse search over a broad range of masses, instead of focusing on one particular theory. “Dark matter direct detection is not one-size-fits-all,” she says.
In two papers published in Physical Review Letters on January 7 and September 14, Zurek and colleagues proposed using superconductors — materials that allow electricity to flow without resistance — and superfluids, which allow fluids to flow without friction, to detect light dark matter particles. “We are trying to broaden as much as possible the tools to search for dark matter,” says Zurek. Likewise, scientists with the upcoming Super Cryogenic Dark Matter Search SNOLAB experiment, to be located in an underground lab in Sudbury, Canada, will use detectors made of germanium and silicon to search for dark matter with smaller masses than the xenon experiments can.

Scientists have not given up on xenon WIMP experiments. Soon some of those experiments will be scaling up — going from hundreds of kilograms of liquid xenon to tons — to improve their chances of catching a dark matter particle on the fly. The next version of XENON100, the XENON1T experiment (pronounced “XENON one ton”) is nearly ready to begin taking data. LUX’s next generation experiment, known as LUX-ZEPLIN or LZ, is scheduled to begin in 2020. PandaX-II scientists are also planning a sequel. Physicists are still optimistic that these detectors will finally find the elusive particles. “Maybe we will have some opportunity to see something nobody has seen,” says Xiangdong Ji of Shanghai Jiao Tong University, the leader of PandaX-II. “That’s what’s so exciting.”

In the sea of nondetections of dark matter, there is one glaring exception. For years, scientists with the DAMA/LIBRA experiment at Gran Sasso have claimed to see signs of dark matter, using crystals of sodium iodide. But other experiments have found no signs of DAMA’s dark matter. Many scientists believe that DAMA has been debunked. “I don’t know what generates the weird signal that DAMA sees,” says Hooper. “That being said, I don’t think it’s likely that it’s dark matter.”

But other experiments have not used the same technology as DAMA, says theoretical astrophysicist Katherine Freese of the University of Michigan in Ann Arbor. “There is no alternative explanation that anybody can think of, so that is why it is actually still very interesting.” Three upcoming experiments should soon close the door on the mystery, by searching for dark matter using sodium iodide, as DAMA does: the ANAIS experiment in the Canfranc Underground Laboratory in Spain, the COSINE-100 experiment at YangYang Underground Laboratory in South Korea, and the SABRE experiment, planned for the Stawell Underground Physics Laboratory in Australia.

Scientists’ efforts could still end up being for naught; dark matter may not be directly detectable at all. “It’s possible that gravity is the only lens with which we can view dark matter,” says Szydagis. Dark matter could interact only via gravity, not via the weak force or any other force. Or it could live in its own “hidden sector” of particles that interact among themselves, but mostly shun normal matter.

Even if no particles are detected anytime soon, most scientists remain convinced that an unseen form of matter exists. No alternative theory can explain all of scientists’ cosmological observations. “The human being is not going to give up for a long, long time to try to search for dark matter, because it’s such a big problem for us,” says Ji.