Research Highlights

Our pick of the latest scientific literature

Micrograph of lung tissue affected by cancer

Lung tissue (brown) is invaded by cells (purple) of a type of cancer called adenocarcinoma, which can be detected by a machine-learning model. Credit: Eye of Science/SPL

Cancer

Pathologists meet their match in tumour-spotting algorithm

Deep-learning model picks out two kinds of lung cancer by studying images of tissue.

Artificial-intelligence technology that examines images of lung tissue can identify two common lung cancers just as well as pathologists do.

A team led by Narges Razavian and Aristotelis Tsirigos at the New York University School of Medicine trained and tested a convolutional neural network — a deep-learning algorithm that is adept at processing images — on 1,634 images of cancerous and healthy lung tissue. The algorithm identified healthy cases and distinguished as accurately as three pathologists between two common types of lung cancer: adenocarcinoma and squamous-cell carcinoma.

The researchers also trained the network on adenocarcinoma images that had been labelled with the mutations underlying the cancer. After this training, the algorithm was able to accurately predict the mutations associated with some unlabelled images.

If the algorithm were trained on further labelled images, it might be able to identify adenocarcinomas’ mutations with greater accuracy, the researchers say. That could improve this tumour’s treatment, which is often tailored to the underlying mutation.

Short looping clip of a red toy boat bobbing on waves in the centre of the 86cm prototype of the wave concentrator device

A toy boat bobs inside a structure designed to raise the height of water waves in its centre. Credit: C. Li <i>et al.</i> <i>Phys. Rev. Lett.</i> <b>121</b>, 104501 (2018)/APS

Fluid dynamics

Water waves grow tall with help from a trick of light

Ring-shaped invention channels waves to triple their height — a potential boon to wave energy.

A ring-shaped device can concentrate waves in water into a relatively small space without reflecting them — a technique that could make harvesting wave energy more efficient.

Structures that boost the height of water waves in a confined area can increase energy harvest from the sea. But these structures often end up reflecting waves, which dissipates some of their energy.

Inspired by their previous work using optical devices to control light waves, Huanyang Chen at Xiamen University in China, Zhenyu Wang at Zhejiang University in Hangzhou, China, and their colleagues created a ring of thin metal sheets, arranged like slides in a projector’s carousel. The structure channelled incoming waves towards the ring’s centre. By tailoring the length and depth of the gaps between sheets, the team created cavities that also caused reflected waves of a set frequency to interfere and cancel each other out, preventing reflections.

Tests in a tank showed that a prototype device that is 86 centimetres across could triple the height of waves at the ring’s centre, while leaving waves outside the ring undisturbed.

A nepalese man can be seen through a doorway of a collapsed house in Bhaktapur. Broken timber beams are in foreground

An earthquake centred in Nepal in 2015 killed about 10,000 people, but the toll could be much higher if the region experienced a repeat of powerful quakes that hit the Himalayas centuries ago. Credit: Prakash Mathema/AFP/Getty

Geophysics

The devastating death toll forecast for Himalayan quakes

Hundreds of thousands of lives are at risk as a result of population boom in seismic zone.

An earthquake similar to one that struck the Himalayas five centuries ago could kill almost 600,000 people in the region today, most of them in India.

The Indian plate of Earth’s crust rams into the Eurasian plate, pushing the Himalayas upwards and raising the risk of large earthquakes, such as the magnitude-7.8 quake in Nepal that killed about 10,000 people in 2015.

A team led by Max Wyss at the International Centre for Earth Simulation Foundation in Geneva, Switzerland, analysed what might happen if either of two massive historical Himalayan earthquakes was to occur today. Many more people live in the region now than when those quakes struck.

A quake in the western Himalayas in 1555 may have been as large as magnitude 8. Today, a quake of this magnitude could kill 221,000 people and injure 884,000. Meanwhile, the 1505 earthquake that struck the central Himalayas may have measured as much as magnitude 8.7. A repeat could kill 599,000 people and injure more than one million.

Understanding the scope of possible disasters helps society to better prepare for such events, the team says.

Green coloured SEM of rod shaped C.difficile bacteria

The bacterium Clostridium difficile (yellow), which frequently causes diarrhoea in people who have been on antibiotics, produces a compound that smothers the growth of other gut microbes. Credit: SPL

Microbiology

The chemical weapon that helps bacterium wreak havoc in the gut

Microbe’s attack on the competition allows it to overrun the intestinal tract after antibiotic treatment.

A diarrhoea-causing bacterium does its dirty work by emitting a compound that harms certain bacteria residing in the human gut.

The bacterium Clostridium difficile is the leading cause of diarrhoea in people who have been taking antibiotics, which upset the gut’s natural microbial balance. Lisa Dawson at the London School of Hygiene and Tropical Medicine and her colleagues examined the effects of para-cresol, a compound made by C. difficile, on microbes growing in lab dishes. They found that the compound blocks the growth of many species of gut bacterium but leaves C. difficile itself relatively unscathed.

The team dosed mice with antibiotics and then infected the rodents with C. difficile. Numerous species of gut bacterium struggled to grow in mice infected with ordinary C. difficile. But those same bacteria thrived in mice infected with mutant C. difficile that does not make para-cresol, suggesting that the compound gives the pathogen a survival edge.

Reconstruction of the Etruscan Tomb of the Leopards. At centre are 4 lit statues of female mourners in different poses.

Statues of mourning women stand in a reconstruction of a tomb built by the Etruscans, who conquered Tuscany. Credit: Prisma/UIG via Getty

Anthropology

Tuscans’ roots in their corner of western Italy date back five millennia

Prehistoric genetic lineages have lasted to the present day, despite waves of conquerors and immigrants.

Some Tuscans can trace their heritage to female ancestors who lived in the same region 5,000 years ago.

Such genetic continuity has been reported in isolated human populations but has rarely been shown in such highly trafficked areas as Tuscany. The region, a corridor of cultural exchange between central Italy and the western Mediterranean coast throughout history, has hosted conquerors from the Romans to Napoleon.

Michela Leonardi at the University of Cambridge, UK, and her colleagues studied mitochondrial DNA, which is inherited only through the maternal line, from modern individuals in northwestern Tuscany. Their analyses identified genetic continuity between modern mitochondrial DNA and remains dating to the region’s prehistoric, Etruscan, Roman and Renaissance eras.

The authors used computer simulations to model evolution of the historical populations involved, estimating population sizes at key times. The simulations compared the effects of genetic continuity and discontinuity for each pair of periods. In each era, genealogical continuity better accounted for the genetic diversity of data the ancient and modern samples.

The authors suggest that the various conquerors might not have brought their womenfolk.

Illustration of Cas9 binding to DNA

The Cas9 enzyme (purple; artist's impression) is stymied if it tries to access DNA (blue, white and black strands) that is wound around nucleosome proteins (green). Credit: Janet Iwasa/Univ. Utah

Biological techniques

How DNA fends off a favourite gene-editing tool

Protein–DNA bundles thwart enzymes in the widely used CRISPR–Cas9 gene-editing technology.

The popular genome-editing system CRISPR–Cas9 is a powerful tool for altering DNA sequences. But experiments show that this system cannot edit target sites in DNA wrapped tightly around a protein, which might limit CRISPR’s usefulness.

Many cells store their DNA by winding it around proteins to create structures called nucleosomes. These structures must move or unwind their DNA before enzymes can either copy it or read it to make proteins.

To alter a genome, the CRISPR system cuts a DNA strand at a target site selected by researchers. Dana Carroll at the University of Utah School of Medicine in Salt Lake City and his colleagues found that removing nucleosomes from yeast DNA allowed CRISPR–Cas9 to bind and cut more of its targets. But the CRISPR machinery had difficulty doing so after the researchers inserted DNA mutations that encouraged the formation of nucleosomes.

CRISPR might work well in dividing cells, which unwind their DNA, the authors say. But editing DNA in cells that aren’t dividing might require researchers to remove nucleosomes from CRISPR targets — or to select more-accessible targets.

Little Corella parrot with an advanced case of Psittacine Beak and Feather Disease

A type of cockatoo called a little corella (Cacatua sanguinea) infected with beak and feather disease virus, which has spread through the pet trade. Credit: cbstockfoto/Alamy

Conservation biology

Virus that robs parrots of their plumage has spread around the globe

Beak and feather disease virus has appeared in eight countries where it had been unknown.

A virus that can inflict feather loss and severe beak deformities on infected parrots is widespread in the wild.

Infections with beak and feather disease virus, which can cause lethal illness, are common in captive cockatoos, parakeets and other types of parrot. But how far the virus, which originated in Australasia, has spread in wild bird populations has been a mystery.

Deborah Fogell at the University of Kent in Canterbury, UK, and her colleagues screened wild and captive parakeets and parrots from five species. The testing revealed viral DNA in birds from eight countries where the virus had not previously been recorded, including nations home to threatened parrot species.

In some cases, viruses isolated from one bird population were closely related to viruses found in populations of a separate species living thousands of kilometres away, suggesting that the virus had been recently introduced by the pet trade. The team also found the first evidence of infection in wild rose-ringed parakeets (Psittacula krameri) — an invasive species that continues to spread globally — living in their native range.

Molecular knots

The arrangement of the two most complex molecular knots yet made — a composite knot (left) and a catenane — is depicted by this diagram. Credit: Adapted from L. Zhang <i>et al.</i>/<i>Nature Chem.</i>

Chemistry

The world’s most complex molecular knot ties up a record

Metal framework allows triple knot to be created in the lab.

Researchers have tied strings of molecules into a complicated knot whose strands cross one another nine times — an unprecedented feat.

In nature, a DNA molecule often takes the form of one large knot composed of smaller knots. But in the lab, such ‘composite knots’ are difficult to produce in a specific configuration.

To create a composite knot, David Leigh and his colleagues at the University of Manchester, UK, used six iron atoms as scaffolding. Around those atoms, the researchers wove six molecular strands that, between them, contained 324 atoms. The team carefully designed the strands to control their connections with the iron atoms.

This allowed the authors to join the strands’ 12 loose ends to form one of two different patterns. One was a composite knot made of three identical tangles; the second was a structure known as a catenane, which was composed of three twisted loops linked to each other. In both cases, the strands crossed each other nine times.

Synthesizing complex knots could aid in the study of processes such as the part knotted DNA plays in the spread of viruses, the authors write.

Adelie penguin on ice floe

Adélie penguins in East Antarctica died in large numbers roughly 200 and 750 years ago, probably as a result of heavy precipitation. Credit: Cultura RF/Brett Phibbs/Getty

Ecology

Caches of mummified penguins warn of climate-change impacts

Two die-offs of Adélie penguins are traced to climatic episodes similar to those expected as Earth warms.

A throng of mummified penguins in Antarctica has been linked to long stretches of abnormally heavy precipitation, which caused the birds' deaths centuries ago.

Long Peninsula in East Antarctica is currently home to about 100,000 Adélie penguins (Pygoscelis adeliae), as well as numerous abandoned penguin colonies. Zhouqing Xie and Liguang Sun at the University of Science and Technology of China in Hefei sampled tissue from 14 penguin carcasses found at several abandoned colonies to determine the birds’ cause of death.

Carbon dating revealed that the penguins perished in two die-offs that each lasted a decade or longer: one 750 years ago and another 200 years ago. Analysis of the sediment around the carcasses suggested that it was deposited over the course of several decades of unusually heavy rain or snow.

This precipitation pattern is becoming more common as a result of global climate change, the researchers say, which could cause more mass penguin die-offs in the future.

Piglet drinking in a stall

Diets focused on pork and other types of meat place more stress on water resources than the plant-rich meals recommended by health authorities. Credit: Carsten Koall/Getty

Water resources

The foods that could save Europe’s water and boost Europeans’ health

A plant-rich diet has a smaller ‘water footprint’ than one based on meat feasts.

The amount of water required to produce food across large swathes of Europe could fall significantly if local people improved their diets.

Vegetarian diets, with or without seafood, require substantially less water to produce than diets containing fresh meat and meat products such as sausages. Davy Vanham and his colleagues at the European Commission’s Joint Research Centre in Ispra, Italy, determined the amount of water needed to produce the food and alcoholic beverages consumed in each of some 44,000 administrative districts across the United Kingdom, France and Germany.

The authors found that if people adhered to national dietary guidelines — which generally recommend balanced meals rich in fruit, vegetables and grains — each district’s dietary ‘water footprint’ would fall by 11–55%, depending on regional eating habits.

A mix of approaches, including health-information campaigns and regulatory measures, may be needed to stimulate dietary shifts beneficial for both human health and the environment, the authors say.

Cross section of membrane

Passing an organic vapour over a membrane formed by layering zinc (green) onto an aluminium-based substrate (red) makes the membrane permeable to small molecules. Credit: Prashant Kumar

Chemistry

‘Molecular sieve’ offers inexpensive way to sift plastic’s raw materials

A membrane with minuscule pores could help to replace bulky, energy-hungry infrastructure.

Low-cost membranes pierced with pores so small that they admit only certain molecules could serve as environmentally friendly filters.

The industrial technology used to separate many chemical mixtures into their constituents is energy-intensive, and membranes that can perform such separations have so far proved expensive to produce.

To make a modestly priced membrane, Xiaoli Ma, Michael Tsapatsis and their colleagues at the University of Minnesota in Minneapolis added an impervious layer of zinc oxide to an aluminium-oxide base. The researchers then wafted an organic vapour over the zinc. The zinc and vapour combined to create a type of porous material called a zeolitic imidazolate framework (ZIF).

The team passed a mixture of propylene — a feedstock for plastics — and propane over the ZIF face of the membrane. Large amounts of propylene passed through the ZIF’s pores, but propane could not do the same.

The process could also be used to produce other types of industrial membrane, the authors say.

Abdominal aortic aneurysm

An abdominal aortic aneurysm (green), a bulge in the lower aorta, can rupture catastrophically at a moment's notice. Credit: Ronald L. Dalman

Technology

How to warn of a pulsating artery that could burst any time

A genomic test predicts whether a crucial artery has become enlarged and weakened.

Genome sequences and electronic health records have been combined to help identify those at risk of a life-threatening rupture of the aorta.

Genetic factors are known to contribute to the risk of abdominal aortic aneurysm, a fragile bulge in the lower section of the aorta, the body’s main artery. But the condition is complex and difficult to study.

Philip Tsao and Michael Snyder at Stanford University in California and their colleagues sequenced the full genomes of 268 people with the condition, and 133 controls. They then used a machine-learning method to analyse the genetic data, and built a machine-learning model based on information from electronic health records, such as cholesterol levels. Finally, the team designed a model based on both genetic data and health records that made highly accurate predictions of which samples came from people with the disease.

The genetic analysis singled out 60 genes that were more likely to carry mutations in individuals with abdominal aortic aneurysms than in the controls. These genes tended to be expressed at higher levels in tissue taken from people with the disease, compared to those without it.

Correction: A previous version of this story attributed the work to only the corresponding authors.

Artist's concept showing planet KELT-9b orbiting its host star, KELT-9.

The exoplanet KELT-9b is a ‘hot Jupiter’ at risk of destruction by its star (artist’s impression). Credit: NASA/JPL-Caltech

Planetary science

The stars that team up to push planets to their death

One member of a stellar pair nudges planets towards its partner, which rips apart or swallows its victims.

Stars of a certain kind destroy most of their Jupiter-sized planets, simulations suggest.

Stars classified as A-type stars are roughly 1.6–2.4 times the mass of the Sun and are often gravitationally bound to a second star, known as a stellar ‘companion’. Towards the end of their lives, A-type stars swell to form enormous bodies called red giants.

Alexander Stephan at the University of California, Los Angeles, and his colleagues carried out several thousand simulations of systems that included an A-type star, a stellar companion and an orbiting Jupiter-sized planet. In 61% of cases, the companion star’s presence influenced the orbit of Jupiter-sized planets, which moved close enough to the A-type stars to eventually be destroyed — either ripped apart by the star’s gravity, or swallowed up by the star in its bloated later years.

Across the Milky Way, tens of thousands of red giants are probably feasting on such planets at any given time, the authors write.

Influenza A Virus

Influenza viruses are thwarted by a drug that targets a viral enzyme. Credit: Dennis Kunkel Microscopy/SPL

Medical research

Meagre ranks of anti-flu drugs look set to grow

A compound thwarts the influenza virus by blocking viral replication.

Large-scale trials of a new compound show that it quickly beats back the influenza virus — results that could admit this compound to the small club of effective antiviral flu drugs.

For the 2017–18 flu season, the US Centers for Disease Control and Prevention endorsed only three antiviral drugs for treating flu. Unlike those treatments, the compound baloxavir inhibits the virus’s machinery for making genetic information that it needs to replicate itself.

Frederick Hayden at the University of Virginia School of Medicine in Charlottesville and his colleagues performed two clinical trials of baloxavir in people with flu. One trial compared baloxavir to a placebo; the second compared the compound to both a placebo and oseltamivir (Tamiflu), a standard antiviral drug.

In both trials, participants’ viral concentrations dropped steeply after one day of treatment with baloxavir. The same decrease took three days to achieve in participants treated with Tamiflu and longer still in participants who took a placebo. Baloxavir did not relieve flu symptoms faster than Tamiflu, but the researchers say that the compound could provide an alternative for people who are unresponsive to other treatments.

Bonnethead Shark in the shallows

The bonnethead shark supplements its diet of invertebrates with seagrass, making it the first known omnivorous shark. Credit: Jay Fleming/Getty

Animal behaviour

The world’s first flexitarian shark grazes like a cow

A member of the hammerhead family munches on seagrass meadows as well as guzzling squid.

Sharks are notorious carnivores, but one small hammerhead shark also feels the need to eat its greens.

Bonnethead sharks (Sphyrna tiburo) live in seagrass meadows in the shallow waters off the coasts of the Americas. In addition to consuming invertebrates such as squid, they have been observed eating large amounts of seagrass. But whether the animals digest this dietary plant matter has been a mystery.

Samantha Leigh at the University of California, Irvine, and her colleagues fed five captive bonnetheads on seagrass grown in water containing carbon-13, an uncommon form of carbon. After several weeks on this regimen, the sharks’ blood contained high levels of carbon-13, which must have come from the seagrass in their diet. The team also found that the creatures’ guts host enzymes capable of breaking down cellulose and other carbohydrates found in grasses.

This makes the bonnethead the first omnivorous shark ever recorded. Because they are both predators and grazers, bonnetheads play an important part in seagrass ecosystems, the authors say.

Staphylococcus epidermidis bacteria

The bacterium Staphylococcus epidermidis has developed resistance to multiple antibiotics, complicating the treatment of people infected with the common microbe. Credit: Eye of Science/SPL

Antibiotics

Skin bacterium learns to shrug off antibiotic of last resort

Microbes that are part of the normal human flora have given rise to drug-resistant strains that are now found in healthcare facilities worldwide.

Antibiotic-resistant strains of a bacterium that can cause hospital-acquired infections have spread around the globe.

The bacterium Staphylococcus epidermidis lives on human skin and is normally harmless to its host. But when the skin is breached, the bacterium can cause infections, particularly among people with medical implants, such as long-term catheters, or prosthetics, such as artificial heart valves.

Benjamin Howden at the Peter Doherty Institute for Infection and Immunity in Melbourne, Australia, and his colleagues looked at hundreds of samples of S. epidermidis collected from 96 hospitals and research centres across 24 countries. They found that three bacterial lineages that are resistant to almost all antibiotics have spread around the world during the past few decades.

The researchers also found that some of the genetic mutations identified in these lineages confer resistance not only to an antibiotic called rifampicin but also to last-resort antibiotics such as vancomycin. Clinical guidelines often recommend co-administering both rifampicin and vancomycin for the treatment of Staphylococcus infections to prevent the development of drug resistance. But the authors’ findings suggest that the combination may instead fuel resistance in S. epidermidis.

Restoration of dystrophin in diaphragm treated with CRISPR

Muscle from a healthy dog (left panel) includes the protein dystrophin (green); this is missing (centre) in tissue from a dog with a muscle-wasting disease but can be restored (right) by a gene-editing regimen. Credit: UT Southwestern

Medical research

Canine CRISPR trial raises hopes for humans with deadly disease

Dogs with a disorder similar to Duchenne muscular dystrophy improve after gene-editing treatment.

A powerful gene-editing technique can stimulate dogs’ production of an important muscle protein, a finding that takes researchers a step closer to trying the technology in humans who have a fatal deficit in the same molecule.

People with the genetic disease Duchenne muscular dystrophy cannot synthesize dystrophin, a component of the scaffolding inside muscle cells. This deficiency results in muscle wasting and early death. The CRISPR–Cas9 gene-editing system has previously been used to trigger dystrophin production in mice, but Eric Olson at the University of Texas Southwestern Medical Center in Dallas and his colleagues sought to test the technique in a larger animal.

The researchers treated four dogs — all lacking dystrophin because of a genetic mutation — with the CRISPR–Cas9 system, which snipped out a short stretch of the animals’ DNA. This allowed the dogs’ cells to make dystrophin. Levels of the protein in one dog’s heart muscle reached 92% of normal.

Tiny silicon bowtie structure claims record photon confinement in time and space.

A newly designed photonic crystal traps light using a series of bow-tie-shaped gaps. Photon density (depicted in 3D for easy visualization) is highest at the centre of the bow tie’s knot (red) and dwindles (from yellow to green to purple) towards the knot’s outer edges. Credit: Ella Maru Studio

Optics and photonics

‘Bow ties’ break record for bottling up light

Similar designs could store information in circuits that carry light instead of electrical current.

Light can be trapped with unprecedented effectiveness inside a device smaller than a dust particle.

The device is a photonic crystal, a structure that can transmit specific wavelengths of light while blocking others. Such structures can be fashioned to include minuscule cavities, called resonators, that trap light. Future photonic circuits — which would carry light instead of electric current — could rely on resonators to store bits of information in the form of light pulses.

Sharon Weiss at Vanderbilt University in Nashville, Tennessee, and her collaborators carved a slab of silicon with bow-tie-shaped openings: two roughly triangular gaps connected by a 12-nanometre-wide silicon bridge. Together, the shapes trap light close to the ‘knots’ of the bow ties, concentrating photons at densities at least 60 times higher than achieved with previous photonic crystals.

Structures that concentrate light in this way could be useful for making efficient photonic transistors, which allow the passage of light through circuits to be switched on or off.

Cell sorting machine

Channels in a glass-and-silicon chip (clear vertical panel) carry cells past microscope lenses (silver and black barrels), which help sort the cells into categories. Credit: Keisuke Goda

Biological techniques

A ‘smart’ system could upend a decades-old method of cell analysis

Artificial intelligence is brought to bear on the complex job of sorting cells into subtypes.

Cell sorting, one of the most widely used procedures in biology, is based on technology invented decades ago. But a new method that separates cells on the basis of their shape and molecular make-up could improve the speed and accuracy of the task, which is used in biomedical tests as well as fundamental research.

Current sorting techniques require researchers to add fluorescent tags to key proteins that distinguish cell types. Automated instruments then sort the cells by detecting the presence of fluorescence.

Keisuke Goda at the University of Tokyo and his colleagues devised a new technique that uses imaging to refine the fluorescent-sorting process. A mixture of fluorescently tagged cells passes under a microscope, which photographs them in 2D. An artificial-intelligence system recognizes patterns in the cells’ physical and chemical structures and either counts or sorts them into tubes, processing up to 100 cells per second.

The researchers plan to adapt their system for more-complex cellular structures, including tissues and whole organisms.

TEM image of graphene

Flakes of graphene ‘snow’ are made by breaking apart methane. Credit: Yangyong Sun et al./Adv. Mater.

Graphene

How to make graphene ‘snow’ in a microwave

A simple method produces a high yield of graphene, which is difficult to manufacture in bulk.

A remarkable material called graphene can be produced in an ordinary microwave oven, through a process similar to how snowflakes form.

Graphene, which is formed of carbon sheets only one atom thick, is highly conductive and the strongest material ever tested. But large-scale production is difficult and expensive.

A team led by Jin Zhang at Peking University in Beijing and Yingying Zhang at Tsinghua University, also in Beijing, used a microwave to heat a tube containing silicon dioxide and silicon, creating plasma — a hot, electrically charged gas — of more than 700 ºC. When the researchers added methane, some of the plasma broke down, and the methane’s constituent carbon formed graphene.

These graphene bits accumulated into sheets, in a process similar to the growth of an ice crystal into a snowflake. As the plasma moved, the sheets drifted gently, like falling snowflakes.

Snow was allowed to pile up on a flexible surface and formed a graphene ‘snow bank’. From this, the team created a sensor, which measured the strain produced by a force applied to the surface.