These giant viruses have more protein-making gear than any known virus

Two newly discovered giant viruses have the most comprehensive toolkit for assembling proteins found in any known virus. In a host cell, the viruses have the enzymes needed to wrangle all 20 standard amino acids, the building blocks of life.

Researchers dubbed the viruses Tupanvirus deep ocean and Tupanvirus soda lake, combining the name of the indigenous South American god of thunder, Tupan, with the extreme environment where each type of virus was found. The giant viruses are among the largest of their kind — up to 2.3 micrometers in length — which is about 23 times as long as a particle of HIV, the scientists report February 27 in Nature Communications.
Tupanviruses can infect a wide range of hosts, such as protists and amoebas, but pose no threat to humans, the researchers say.

Viruses are considered nonliving, but the genetic complexity of giant viruses has some scientists questioning that categorization. Each Tupanvirus, for example, has a massive genetic instruction book with roughly 1.5 million base pairs of DNA, more than what some bacteria have, says coauthor Bernard La Scola, a virologist at Aix-Marseille University in France.

But other scientists say giant viruses aren’t so different from their smaller kin. Research by Frederik Schulz, with the Department of Energy Joint Genome Institute in Walnut Creek, Calif., suggests these microscopic behemoths are regular viruses that acquired extra genes from hosts and should not be classified as life.

Tupanviruses don’t settle the controversy, but they do challenge our preconceptions of what life is, La Scola says.

Pollution regulations help Chesapeake Bay seagrass rebound

Underwater grasses are growing back in the Chesapeake Bay. The plants now carpet three times as much real estate as in 1984, thanks to more than 30 years of efforts to reduce nitrogen pollution. This environmental success story shows that regulations put in place to protect the bay’s health have made a difference, researchers report the week of March 5 in Proceedings of the National Academy of Sciences.

Rules limiting nutrient runoff from farms and wastewater treatment plants helped to decrease nitrogen concentrations in the bay by 23 percent since 1984. That decline in nitrogen has allowed the recovery of 17,000 hectares of grasses, the new study shows — enough to cover roughly 32,000 football fields.
“This is one of the best examples we have of linking long-term research data with management to show how important that is in restoring this critical habitat,” says Karen McGlathery, an environmental scientist at the University of Virginia in Charlottesville who wasn’t involved in the research. ”I don’t know of any other system that’s so large and so complicated where these connections have been made.”

The bay’s aquatic vegetation, including seagrasses and freshwater grasses, is an important part of coastal ecosystems, says study coauthor Jonathan Lefcheck, a marine ecologist at the Bigelow Laboratory for Ocean Sciences in East Boothbay, Maine. Beds of underwater grasses act as nurseries that shelter young fish and aquatic invertebrates. The plants clean the water by trapping particulates, and stabilize shorelines by preventing erosion. But the once-lush grasses began dying off in the 1950s when the region’s human population boomed, and cities and farms dumped increasing amounts of nitrogen and other nutrients into the bay.

In the late 1970s and early 1980s, state and federal agencies took action, limiting the amount of nutrients that could enter the bay from farms, water treatment facilities and other sources. Those groups also instituted programs to monitor the bay’s health, building up the stockpile of information that Lefcheck and his colleagues have now analyzed.

The researchers looked at aerial surveys of the bay, data on water temperature and nutrient levels, as well as land and fertilizer use. Using mathematical equations to test which variables had the biggest impact on seagrass regrowth, the team pinned down nitrogen reduction as the driving force. That makes sense: Too much nitrogen in water promotes the growth of plankton, which can block sunlight, and algae, which can settle on the grass blades and smother them.
Now, though, researchers are seeing just the opposite. Grasses need clean water to get a foothold, but once they settle in, they “modify their own environment and make it better,” Lefcheck says. “Once you get a little bit established, it can take off.”

Hospital admissions show the opioid crisis affects kids, too

As I’ve been reporting a story about the opioid epidemic, I’ve sorted through a lot of tragic numbers that make the astronomical spike in deaths and injuries related to the drugs feel more real.

The rise in the abuse of opioids — powerfully addictive painkillers — is driven by adults. But kids are also swept up in the current, a new study makes clear. The number of children admitted to pediatric intensive care units at hospitals for opioid-related trouble nearly doubled between 2004 and 2015, researchers report in the March Pediatrics.
Researchers combed through medical records from 46 hospitals around the United States, looking for opioid-related reasons for admission to the hospital. When the researchers looked at children who landed in pediatric intensive care units for opioid-related crises, the numbers were grim, nearly doubling. In the period including 2004 to 2007, 367 children landed in the PICU for opioid-related trouble. In the period including 2012 to 2015, that number was 643. (From 2008 to 2011, 554 kids were admitted to the PICU for opioid-related illnesses.)
Most opioid-related hospital admissions were for children ages 12 to 17, the researchers found. The available stats couldn’t say how many of those events were accidental ingestions versus intentional drug use. (Though for older kids, there’s a sliver of good news from elsewhere: Prescription opioid use among teenagers is actually down, a recent survey suggests.)
But about a third of the hospitalizations were for children younger than 6. And among these young kids, about 20 percent of the poisonings involved methadone, a drug that’s used to treat opioid addiction. That means that these young kids are getting into adults’ drugs (illicit or prescribed) and accidentally ingesting them.

Lots of parents don’t store their prescription opioid painkillers safely away from their young children, a survey last year suggests. Drugs, prescription or otherwise, should be kept out of sight and out of reach, ideally locked away. Some kids are great climbers, and some are crafty bottle openers who can, with persistence, work around supposedly child-resistant packaging.

These are tips for everyone living with small kids — not just those who may have opioids in the house. Children are curious, persistent and, sadly, extra vulnerable to powerful drugs, which means that we should all do our best to keep them away from these potentially dangerous drugs.

Earwigs take origami to extremes to fold their wings

To quickly unfurl and refold their wings, earwigs stretch the rules of origami.

Yes, those garden pests that scurry out from under overturned flowerpots can also fly. Because earwigs spend most of their time underground and only occasionally take to the air, they pack their wings into packages with a surface area more than 10 times smaller than when unfurled, using an origami-like series of folds. Springy wing joints let the insects bypass some of the mathematical constraints that normally limit the way a rigid two-dimensional material can be folded, researchers report March 23 in Science.
Earwig wings’ folding pattern should be impossible according to mathematical equations that predict the three-dimensional designs that can be made by folding a two-dimensional material like a sheet of paper, says study coauthor Andres Arrieta, a mechanical engineer at Purdue University in West Lafayette, Ind.

Origami theory assumes that the material being folded is perfectly rigid. But the joints of earwigs’ wings — where creases form — are rich in a rubbery polymer called resilin. This little bit of stretch lets earwig wings do what a regular origami structure can’t: lock into two different conformations, open or folded up, and transition between the two.
It’s an example of a bistable structure — something like the slap bracelets, popular in the 1980s and 1990s, which switch from a flat conformation to a curved one when whacked against a wrist, says study coauthor André Studart, a materials scientist at ETH Zürich. When locked open, earwig wings store energy in the springy resilin joints. When that strain is released, the wings rapidly crumple back to their folded position.
Such constructions can inform robotics design. Inspired by the wings, the researchers created a prototype gripper. Its rigid pieces are held together by rubbery, strategically placed joints. Within fractions of a second, the structure can snap from its mostly flat conformation to one that can grip a small object and hold it without constant external force.
While other materials scientists have pushed the limits of origami by making flat pieces bendable, this design instead stretches the hinges, says Jesse Silverberg, a physicist at Harvard University who wasn’t part of the study. Such a design has been observed and discussed, but never before been implemented in this way.

The earwig “is a beautiful example of how nature uses slight extensions to ideal mathematical origami to do something amazing,” says Itai Cohen, a physicist at Cornell University who wasn’t part of the study.

Perhaps that’s a slight redemption for the much-maligned insect.

Umbilical cord banking gets a lot of buzz. Why all the excitement?

When you’re pregnant, especially for the first time, you have to make a lot of decisions. Will coffee remain a part of your life? Where are you going to give birth? What are you going to name the baby? What values will you teach him? Do you really need a baby spa bathtub?

Before my first daughter arrived, an instructor at a birth class threw me a curveball: Was I planning on banking my baby’s umbilical cord blood?
For much of pregnancy, the umbilical cord is the lifeline of a fetus, tethering it to the placenta. Snaking through the nearly 2-feet-long cord, there’s a vein ferrying nutrients and oxygen from mom’s blood (via the placenta), plus two arteries carrying oxygen- and nutrient-depleted blood from the fetus back to mom. Because mother’s blood and fetal blood don’t actually mix much, the blood in the placenta and umbilical cord at birth belongs mainly to the fetus.

That fetal blood holds all sorts of interesting — and potentially therapeutic — cells and molecules. This realization has, in some cases, changed the way the umbilical cord and placenta are handled during birth. Instead of tossing it aside, some doctors, scientists and parents are choosing to bank this fetal blood — harvesting it from the baby’s umbilical cord and placenta, freezing it and storing it away for later.

Proponents of cord blood banking are convinced that instead of being medical waste, the fetal cells within are biological gold. In this post, and the two that follow, I’ll take a look at the evidence for those claims, and sort through some of the questions that arise as parents consider whether to bank their baby’s cord blood.

Back in the 1980s, umbilical cord blood caught the attention of researchers who suspected that the often-discarded tissue could be a valuable source of shape-shifting stem cells. These cells, which can become several different types of blood cells, are similar to the specialized stem cells found in bone marrow that can churn out new blood cells. Such stem cells are found in adult blood, too, but not as abundantly.
In 1988, a 5-year-old named Matthew with a rare type of anemia received umbilical cord blood cells from his newborn sister, who didn’t have the disease. That transfer, called an umbilical cord blood transplant, worked, and the boy was soon free of the disease.

At the time, researchers didn’t know much about the properties of the cells found in umbilical cord blood. But research has zoomed forward, illuminating more about the contents of this young blood.

Of particular interest are the flexible hematopoietic stem cells important in that initial transplant. In certain cases, transplanting these cells might be able to reboot a person’s body and get rid of a disease-related defect. Cord blood transplants are similar to bone marrow transplants. A person with leukemia, for instance, might have his own cancerous blood cells wiped out with chemotherapy and radiation. Healthy, non-cancerous stem cells from a donor can then repopulate the blood.

Extracting stem cells from bone marrow requires surgery under anesthesia; extracting them from the blood requires taking a drug to stimulate their production. And in order to work, these stem cell donations need to come from a person who carries a similar pattern of proteins on the outsides of his or her cells, a molecular calling card known as HLA type. Stem cells found in cord blood don’t need to be as closely matched to work. Because these cells are so flexible, there’s more wiggle room between donor and recipient. That’s particularly good news for people of certain ethnic minorities who often have trouble finding matched stem cell transplant donors.

Hard numbers are tricky to pin down, but between that first transplant in 1988 and 2015, an estimated 35,000 umbilical cord blood transplants had been performed globally. That number includes people treated for leukemia and other types of cancer, blood disorders and immune diseases. And the utility of umbilical cord cells may stretch well beyond the disorders that the cells are currently being used for. “If you read the literature, it’s pretty exciting,” says pediatrician and immunologist William Shearer of Baylor College of Medicine and Texas Children’s Hospital.

Some researchers suspect that umbilical cord blood contains other cells that may have therapeutic effects beyond the blood. Specialized immune cells may be able to tweak brain function, for instance. Trials around the world are studying umbilical cord blood’s capabilities in a wide range of diseases (see Table 2 here): Cerebral palsy, autism, diabetes and lupus are currently under investigation. The cells are even being tested for an ameliorating role in Alzheimer’s disease and other neurodegenerative conditions.

After injections with their own umbilical cord blood, 63 children with cerebral palsy improved on motor skills, on average. And a clinical trial to see whether cord blood transplants improve symptoms of children with autism spectrum disorder should wrap up in the summer of 2018, says pediatric researcher and clinician Joanne Kurtzberg of Duke University, who helped establish a not-for-profit umbilical cord bank in North Carolina. (A small but optimistic pilot study has already been completed.)

The potential powers of these cells have researchers excited. But what that scientific hope means for expectant parents facing decisions about cord blood banking is far from clear. For all of the promise, there are lots of reasons why umbilical cord cells may turn out to be less useful than thought. Read my next post for more about these potential drawbacks.

Seafloor map shows why Greenland’s glaciers melt at different rates

Greenland is melting rapidly, but some glaciers are disappearing faster than others. A new map of the surrounding seafloor helps explain why: Many of the fastest-melting glaciers sit atop deep fjords that allow Atlantic Ocean water to melt them from below.

Researchers led by glaciologist Romain Millan of the University of California, Irvine analyzed new oceanographic and topographic data for 20 major glaciers within 10 fjords in southeast Greenland. The mapping revealed that some fjords are several hundred meters deeper than simulations of the bathymetry suggested, the researchers report online March 25 in Geophysical Research Letters. These troughs allow warmer and saltier waters from deeper in the ocean to reach the glaciers and erode them.
Other glaciers are protected by shallow sills, or raised seafloor ledges. These sills act as barriers to the deep, warm water, the new seafloor maps show. The researchers compared their findings with observations of glacier melt from 1930 to 2017, and found that the fastest-melting glaciers tended to be those more exposed to melting from below.
The study uses data from two NASA missions — Operation IceBridge, which measures ice thickness and gravity from aircraft, and Oceans Melting Greenland, or OMG, which uses sonar and gravity instruments to map the shape and depth of the seafloor close to the ice front. The OMG mission also involves dropping hundreds of probes into the ocean each year to measure temperature and salinity at different depths.
Scientists have long suspected Greenland’s melting may be accelerated by the ocean (SN Online: 7/6/11), but needed data on fjord depth and glacier thickness to prove it.

The high-resolution OMG datasets, in particular, reveal bumps and troughs in the seafloor that were previously unknown, says glaciologist Andy Aschwanden at the University of Alaska Fairbanks, who was not involved with the study. “Those small details can make quite a difference to when a glacier will retreat.”

This plastic-gobbling enzyme just got an upgrade

Just a few tweaks to a bacterial enzyme make it a lean, mean plastic-destroying machine.

One type of plastic, polyethylene terephthalate, or PET, is widely used in polyester clothing and disposable bottles and is notoriously persistent in landfills. In 2016, Japanese scientists identified a new species of bacteria, Ideonella sakaiensis, which has a specialized enzyme that can naturally break down PET.

Now, an international team of researchers studying the enzyme’s structure has created a variant that’s even more efficient at gobbling plastic, the team reports April 17 in Proceedings of the National Academy of Sciences.

The scientists used a technique called X-ray crystallography to examine the enzyme’s structure for clues to its plastic-killing abilities. Then, they genetically tweaked the enzyme to create small variations in the structure, and tested those versions for PET-degrading performance. Some changes made the enzyme work even better. Both the original version and the mutated versions could break down both PET and another, newer bio-based plastic called PEF, short for polyethylene-2,5-furandicarboxylate. With a little more engineering, these enzymes could someday feast at landfills.

A hole in an ancient cow’s skull could have been surgery practice

Ancient surgeons may have practiced dangerous skull-opening procedures on cows before operating on people.

A previously excavated cow skull from a roughly 5,400- to 5,000-year-old settlement in France contains a surgically created hole on the right side, a new study finds. No signs of bone healing, which start several days after an injury, appear around the opening. One or more people may have rehearsed surgical techniques on a dead cow, or may have tried unsuccessfully to save a sick cow’s life in what would be the oldest known case of veterinary surgery, researchers conclude online April 19 in Scientific Reports.

Evidence of skull surgery on humans, whether for medical or ritual reasons, goes back about 11,000 years (SN: 5/28/16, p. 12). Ancient surgeons needed to know how and where to scrape away bone without harming brain tissue and blood vessels. So practicing bone removal on cows or other animals is plausible.

The ancient cow’s skull opening, shaped almost in a square and framed by scrape marks, resembles two instances of human skull surgery from around the same time in France, say biological anthropologists Fernando Ramirez Rozzi of CNRS in Montrouge, France, and Alain Froment of IRD-Museum of Man in Paris. Microscopic and X-ray analyses found no fractures or splintered bone that would have resulted from goring by another cow’s horn. No damage typical of someone having struck the cow’s head with a club or other weapon appeared, either.

Clues to an Iron Age massacre lie in what the assailants left behind

Club-wielding assailants struck the Scandinavian settlement with devastating violence, slaughtering at least 26 people and leaving the bodies where they fell. There, the bodies lay for 1,500 years until recovered recently by archaeologists analyzing clues about the Iron Age massacre.

It’s unclear why the seaside ringfort of Sandby borg, on the Baltic Sea island of Ӧland, was targeted at a time of political turmoil following the Roman Empire’s fall in Western Europe. Adults, teenagers and children died suddenly and brutally — their skeletons showing bones fractured by clubs, but no defensive wounds, say archaeologist Clara Alfsdotter of Bohuslӓns Museum in Udevalla, Sweden, and her colleagues. When the slaughter was over, the attackers left the sheep and other animals to starve and the valuables untouched, the scientists report in the April Antiquity. No one came back to bury the dead.
That’s somewhat unusual: At most other excavated battlefield and massacre sites in Europe, bodies have been found in mass graves ( SN: 1/23/16, p. 7). However, 67 farming villagers slaughtered around 7,200 years ago at Austria’s Asparn-Schletz site were also left in place. Circumstances surrounding the attacks on Asparn-Schletz and Sandby borg are poorly understood, making it difficult to compare the two events, says anthropologist Bruno Boulestin of the University of Bordeaux in France, who did not participate in the excavation.
The bones from Sandby borg have yet to undergo radiocarbon dating, making it impossible to say precisely when the massacre occurred, says archaeologist Ian Armit of the University of Bradford in England, who did not participate in the Sandby borg research. But the researchers suspect the killing happened after 476, when the fall of the Western Roman Empire left a power vacuum and power struggles broke out across parts of Europe and southern Scandinavia. Sandby borg’s attackers may have installed themselves as the new local rulers, the team suggests.

“It was not the killing that was the point, but the statement toward those witnessing it from a distance that ‘if you mess with us, this is what happens,’” says study coauthor Ludvig Papmehl-Dufay of Kalmar County Museum in Sweden.

Sandby borg, spanning roughly 5,000 square meters contained by an eroded oval stone wall, has been a center for archaeological excavations since 2011. Aerial photographs and ground surveys have revealed stone structures buried inside the ringfort off Sweden’s southeast coast. Investigators have located 53 houses, some within a central block circled by a street. By 2016, two houses had been fully excavated and seven others had undergone some investigation. Inside, researchers found gilded silver brooches, glass beads and silver bell pendants, in styles suggesting the fort was occupied in the late 400s.
In one house, the skeletons of nine individuals of various ages were found. Their positions suggested they had been surprised by the attack, say Alfsdotter, Papmehl-Dufay and coauthor Helena Victor, also of Kalmar County Museum. One teenage boy appears to have fallen backward over an adult victim. Two corpses showed evidence of being partially burned, suggesting the attackers tried unsuccessfully to set the structure on fire or that a fire accidentally broke out. A tiny half skeleton from a herring lay next to the fireplace, adding support to the theory that the attackers left quickly without touching or eating anything. A pile of lamb skeletons stacked in the corner and showing signs of recent slaughter suggests the attack occurred sometime between late spring and early fall, the researchers say.

Scientists are working on radiocarbon dating the Sandby borg skeletons as the annual excavations continue, Papmehl-Dufay says. With more than 90 percent of the ringfort settlement yet to be excavated, there are likely more clues to the killing to be found.

A celebration of curiosity for Feynman’s 100th birthday

Richard Feynman was a curious character.

He advertised as much in the subtitle of his autobiography, Surely You’re Joking, Mr. Feynman!: Adventures of a Curious Character. Everybody knew that, in many respects, Feynman was an oddball.

But he was curious in every other sense of the word as well. His curiosity about nature, about how the world works, led to a Nobel Prize in physics and a legendary reputation, both among physicists and the public at large.
Feynman was born 100 years ago May 11. It’s an anniversary inspiring much celebration in the physics world. Feynman was one of the last great physicist celebrities, universally acknowledged as a genius who stood out even from other geniuses.

In 1997 I interviewed Nobel laureate Hans Bethe, a Cornell University physicist who worked with Feynman during World War II on the atomic bomb project at Los Alamos (and later on the Cornell faculty). “Normal” geniuses, Bethe said, did things much better than other people but you could figure out how they did it. And then there were magicians. “Feynman was a magician. I could not imagine how he got his ideas,” Bethe told me. “He was a phenomenon. Feynman certainly was the most original physicist I have seen in my life, and I have seen lots of them.”

Apart from his brilliance as a physicist, Feynman was also known for his skill at playing the bongo drums and cracking safes. Public acclaim came after he served on the presidential commission investigating the explosion of the space shuttle Challenger. In a dramatic moment during a hearing about that disaster, he dipped material from an O-ring (a crucial seal on the shuttle’s rockets) into icy water, demonstrating that an O-ring would not have remained flexible at the launch-time temperature.
His autobiography had already become a best seller, so Feynman was well-known when he died in February 1988.

When I heard of Feynman’s death, I called John Wheeler, Feynman’s doctoral adviser at Princeton University before World War II.

“I felt very lucky to have him as my graduate student,” said Wheeler, who died in 2008. “There was an immense vitality about Feynman. He was interested in all kinds of problems.”

Feynman’s curiosity was not satisfied merely by being told the solution to a problem, though.

“If you said you had the answer to something, he wouldn’t let you tell it,” Wheeler said. “He had to stand on his head and pace up and down and figure out the answer for himself. It was his way of keeping the ability to make headway into brand new frontiers.”

Feynman found fascination in all sorts of things, some profound, some trivial. In his autobiography, he revealed that he spent a lot of time analyzing ant trails. He sometimes entertained Wheeler’s children by tossing tin cans into the air and then explaining how the way the can turned revealed whether the contents were solid or liquid.

Curiosity of that type was instrumental in the work that led to his Nobel Prize. While eating in the Cornell cafeteria, Feynman noticed someone tossing a plate, kind of like a Frisbee. As the plate flew by, Feynman noticed that the Cornell medallion on the plate was rotating more rapidly than the plate was wobbling. He performed some calculations and showed that the medallion’s rotation rate should be precisely twice the rate of the wobbling. He then perceived an analogy to a problem he had been investigating relating to the motion of electrons. The wobbling plate turned out to provide the clue he needed to develop a new version of the theory of quantum electrodynamics.

“The whole business that I got the Nobel Prize for came from that piddling around with the wobbling plate,” he wrote in his autobiography.

It was not curiosity alone that made Feynman a legend. His approach to physics and life incorporated a willful disdain for authority. He regularly disregarded bureaucratic rules, ignored expert opinion and was willing to fearlessly criticize the most eminent of other scientists.

During his time at Los Alamos, for instance, he encountered Niels Bohr, the foremost atomic physicist of the era. Other physicists held Bohr in awe. “Even to the big shot guys,” Feynman recalled, “Bohr was a great god.” During a meeting in which the “big shots” deferred to Bohr, Feynman kept pestering him with questions. Before the next meeting, Bohr called Feynman in to talk without the big shots. Bohr’s son (and assistant) later explained why. “He’s the only guy who’s not afraid of me, and will say when I’ve got a crazy idea,” Niels had said to his son. “So next time when we want to discuss ideas, we’re not going to be able to do it with these guys who say everything is yes, yes, Dr. Bohr. Get that guy and we’ll talk with him first.”

Feynman knew that he sometimes made mistakes. Once he foolishly even read some papers by experts that turned out to be wrong, retarding his work on understanding the form of radioactivity known as beta decay. He vowed never to make the mistake of listening to “experts” again.

“Of course,” he ended one chapter of his autobiography, “you only live one life, and you make all your mistakes, and learn what not to do, and that’s the end of you.”