Culture

Scientists have discovered hundreds of unusually large, bacteria-killing viruses with capabilities normally associated with living organisms, blurring the line between living microbes and viral machines.

These phages -- short for bacteriophages, so-called because they "eat" bacteria -- are of a size and complexity considered typical of life, carry numerous genes normally found in bacteria and use these genes against their bacterial hosts.

University of California, Berkeley, researchers and their collaborators found these huge phages by scouring a large database of DNA that they generated from nearly 30 different Earth environments, ranging from the guts of premature infants and pregnant women to a Tibetan hot spring, a South African bioreactor, hospital rooms, oceans, lakes and deep underground.

Altogether they identified 351 different huge phages, all with genomes four or more times larger than the average genomes of viruses that prey on single-celled bacteria.

Among these is the largest bacteriophage discovered to date: Its genome, 735,000 base-pairs long, is nearly 15 times larger than the average phage. This largest known phage genome is much larger than the genomes of many bacteria.

"We are exploring Earth's microbiomes, and sometimes unexpected things turn up. These viruses of bacteria are a part of biology, of replicating entities, that we know very little about," said Jill Banfield, a UC Berkeley professor of earth and planetary science and of environmental science, policy and management, and senior author of a paper about the findings appearing Feb 12 in the journal Nature. "These huge phages bridge the gap between non-living bacteriophages, on the one hand, and bacteria and Archaea. There definitely seem to be successful strategies of existence that are hybrids between what we think of as traditional viruses and traditional living organisms."

Ironically, within the DNA that these huge phages lug around are parts of the CRISPR system that bacteria use to fight viruses. It's likely that once these phages inject their DNA into bacteria, the viral CRISPR system augments the CRISPR system of the host bacteria, probably mostly to target other viruses.

"It is fascinating how these phages have repurposed this system we thought of as bacterial or archaeal to use for their own benefit against their competition, to fuel warfare between these viruses," said UC Berkeley graduate student Basem Al-Shayeb. Al-Shayeb and research associate Rohan Sachdeva are co-first authors of the Nature paper.

New Cas protein

One of the huge phages also is able to make a protein analogous to the Cas9 protein that is part of the revolutionary tool CRISPR-Cas9 that Jennifer Doudna of UC Berkeley and her European colleague, Emmanuelle Charpentier, adapted for gene-editing. The team dubbed this tiny protein CasØ, because the Greek letter Ø, or phi, has traditionally been used to denote bacteriophage.

"In these huge phages, there is a lot of potential for finding new tools for genome engineering," Sachdeva said. "A lot of the genes we found are unknown, they don't have a putative function and may be a source of new proteins for industrial, medical or agricultural applications."

Aside from providing new insight into the constant warfare between phages and bacteria, the new findings also have implications for human disease. Viruses, in general, carry genes between cells, including genes that confer resistance to antibiotics. And since phages occur wherever bacteria and Archaea live, including the human gut microbiome, they can carry damaging genes into the bacteria that colonize humans.

"Some diseases are caused indirectly by phages, because phages move around genes involved in pathogenesis and antibiotic resistance," said Banfield, who is also director of microbial research at the Innovative Genomics Institute (IGI) and a CZ Biohub investigator. "And the larger the genome, the larger the capacity you have to move around those sorts of genes, and the higher the probability that you will be able to deliver undesirable genes to bacteria in human microbiomes."

Sequencing Earth's biomes

For more than 15 years, Banfield has been exploring the diversity of bacteria, Archaea -- which, she says, are fascinating cousins of bacteria -- and phages in different environments around the planet. She does this by sequencing all the DNA in a sample and then piecing the fragments together to assemble draft genomes or, in some cases, fully curated genomes of never-before-seen microbes.

In the process, she has found that many of the new microbes have extremely tiny genomes, seemingly insufficient to sustain independent life. Instead, they appear to depend on other bacteria and archaea to survive.

One year ago, she reported that some of the largest phages, a group she called Lak phages, can be found in our guts and mouths, where they prey on gut and saliva microbiomes.

The new Nature paper came out of a more thorough search for huge phages within all the metagenomic sequences Banfield has accumulated, plus new metagenomes provided by research collaborators around the globe. The metagenomes came from baboons, pigs, Alaskan moose, soil samples, oceans, rivers, lakes and groundwater, and included Bangladeshis who had been drinking arsenic-tainted water.

The team identified 351 phage genomes that were more than 200 kilobases long, four times the average phage genome length of 50 kilobytes (kb). They were able to establish the exact length of 175 phage genomes; the others could be much larger than 200 kb. One of the complete genomes, 735,000 base-pairs long, is now the largest known phage genome.

While most of the genes in these huge phages code for unknown proteins, the researchers were able to identify genes that code for proteins critical to the machinery, called the ribosome, that translates messenger RNA into protein. Such genes are not typically found in viruses, only in bacteria or archaea.

The researchers found many genes for transfer RNAs, which carry amino acids to the ribosome to be incorporated into new proteins; genes for proteins that load and regulate tRNAs; genes for proteins that turn on translation and even pieces of the ribosome itself.

"Typically, what separates life from non-life is to have ribosomes and the ability to do translation; that is one of the major defining features that separate viruses and bacteria, non-life and life," Sachdeva said. "Some large phages have a lot of this translational machinery, so they are blurring the line a bit."

Huge phages likely use these genes to redirect the ribosomes to make more copies of their own proteins at the expense of bacterial proteins. Some huge phages also have alternative genetic codes, the nucleic acid triplets that code for a specific amino acid, which could confuse the bacterial ribosome that decodes RNA.

In addition, some of the newly discovered huge phages carry genes for variants of the Cas proteins found in a variety of bacterial CRISPR systems, such as the Cas9, Cas12, CasX and CasY families. CasØ is a variant of the Cas12 family. Some of the huge phages also have CRISPR arrays, which are areas of the bacterial genome where snippets of viral DNA are stored for future reference, allowing bacteria to recognize returning phages and to mobilize their Cas proteins to target and cut them up.

"The high-level conclusion is that phages with large genomes are quite prominent across Earth's ecosystems, they are not a peculiarity of one ecosystem," Banfield said. "And phages which have large genomes are related, which means that these are established lineages with a long history of large genome size. Having large genomes is one successful strategy for existence, and a strategy we know very little about."

The researchers divided the 351 megaphages into 10 new groups, or clades, named after words for "big" in the languages of the paper's co-authors: Mahaphage (Sanskrit), Kabirphage, Dakhmphage and Jabbarphage (Arabic); Kyodaiphage (Japanese); Biggiephage (Australian), Whopperphage (American); Judaphage (Chinese), Enormephage (French); and Kaempephage (Danish).

HOUSTON -- Loss of an important tumor-suppressing gene allows head and neck cancer to spin off signals to nearby nerves, changing their function and recruiting them to the tumor, where they fuel growth and cancer progression, researchers from The University of Texas MD Anderson Cancer Center report in the journal Nature today.

By cracking the mechanism that launches neuronal invasion of tumors, a known marker of poor prognosis for patients, the team has uncovered possible avenues to block the process, including the use of drugs commonly used to treat blood pressure and irregular heartbeat.

"Tons of studies show that patients who have lots of nerves in their tumor are doing worse - recurrence rates are higher, survival is shorter," says co-first author Moran Amit, M.D., Ph.D., assistant professor of Head and Neck Surgery. "Nerve endings found in surgically removed tumors can't be easily characterized or tracked back to their source, so it's been a neglected field, a neglected hallmark of cancer."

"When surgeons remove head and neck cancers and find a high degree of nerve invasion, post-surgical radiation sometimes is effective," said co-senior author Jeffrey Myers, M.D., Ph.D., chair of Head and Neck Surgery. "But we really haven't understood whether the tumor was growing into the nerves or the nerve growing into the tumor and what signaling drove those interactions."

Co-senior author George Calin, M.D., Ph.D., professor of Experimental Therapeutics and an expert on non-coding RNAs added that the paper "puts together for the first time the mechanism of involvement of neurons in tumor generation, a new hallmark of cancer."

The team found that the neurons that invade the tumor are adrenergic nerves, which are involved in stress response. These nerves' neurotransmitters - adrenaline (epinephrine) and noradrenaline (norepinephrine) - are susceptible to drugs known as alpha and beta blockers, long used to treat high blood pressure and irregular heartbeats.

In the study, mice with oral cancer treated with the adrenergic blocker carvedilol had sharply lower tumor growth and cancer cell proliferation. Myers says the team is working to develop clinical trials of adrenergic blockers, most likely in combination with other drugs.

"We used to think that nerves are just randomly growing into the tumor, and that's completely wrong," Amit says.

Loss of p53 flips a microRNA switch to re-program neurons

Damage to the p53 gene is a major characteristic of head and neck cancers. A tumor-suppressing master transcriptional gene that governs the expression of many other genes, p53 is also mutated in a variety of cancers.

The team found high density of neurons in p53-deficient mouse models and human xenograft tumors of oral cavity squamous cell carcinoma (OCSCC) as well as increased neural growth in clusters of nerves exposed to p53-deficient OCSCC.

The researchers also discovered that oral cancer communicates with nerves by launching extracellular vesicles - membrane balls that carry various molecules - packed with microRNAs to connect with the nerves. The miRNA cargo varied depending on p53 status of the tumors.

"When you have intact p53, you have specific types of microRNAs that keep neurons in a quiescent state," Amit says. "Once you lose p53, the micro RNA population within the exosomes changes and then you get positive signals to induce nerve growth."

Investigators identified adrenergic nerves extending into the tumors and suspected they were extensions of pre-existing nerves. However, when they cut adrenergic nerves before inducing tumors in mice, adrenergic nerves still appeared in the tumor and the tumors still grew.

Subsequent experiments showed the miRNAs in vesicles from p53-deficient tumors were connecting instead with existing sensory nerves, a different nerve type, and actually changing them into the adrenergic type. These neo-adrenergic nerves then invaded the tumor.

To confirm this finding, they cut sensory nerves ahead of inducing p53-deficient tumors in mice. Without the sensory nerve targets for the vesicles, the tumor shrank.

Impact of adrenergic nerve density on patients

To validate the impact of their findings on people with OCSCC, the researchers analyzed the presence of adrenergic nerves in the tumors of 70 patients who were treated at MD Anderson. Adrenergic nerve density in the tumors was associated with lower recurrence-free survival and overall survival.

The statistical significance of the adrenergic nerve densities held up in multivariable analysis after adjustment for other variables, such as age, sex, cancer stage, surgical margin status, overall neuronal invasion and treatment type. They suggest nerve density measurements merit exploration as a predictive marker of oral cancer aggressiveness. Myers, Calin, Amit and colleagues believe the paper opens up a new area for cancer researchers.

"Neurons control everything that we do in everyday life," Amit says. "They control our voluntary and involuntary bodily functions, so it's intuitive that they are involved in cancer."

A large proportion of highly active men watch more television than their low-active peers do. In contrast, highly active women watch less television than low-active women do.

revious studies have found prolonged television time to be more harmful to health than other domains of sedentariness. A recent longitudinal study with a ten-year follow-up examined how the television viewing time of Finnish adults was associated with their physical activity level during leisure-time.

The results showed that maintaining a high level of leisure-time physical activity was accompanied by less television viewing time for women. High television time (3 hours or more per day) especially was more prevalent among low-active women than it was among highly active women.

Surprisingly, highly active men tended to watch more television (approximately 2 hours per day) than did their low-active peers, who tended to watch television one hour or less a day. Highly active men seemed to have time for physical activity as well as television viewing.

The researchers thought about the reasons behind the differences between genders.

"One reason might be the different motivations men and women have for participating in physical activities," says Senior Researcher Xiaolin Yang from the LIKES Research Centre for Physical Activity and Health: "According to a previous study, men have more intrinsic orientation, meaning mastery and competition, whereas women have more extrinsic orientation, for example appearance and physical condition. Additionally, women are usually more health-conscious than men are. Thus, the health consciousness of physically active women may have an additive effect on their decision-making regarding television viewing as well."

Irinja Lounassalo, a PhD student at the Faculty of Sport and Health Sciences at the University of Jyväskylä, adds another point of view to the previous one: "The differences between genders may also be related to the use of leisure-time. According to time use studies, Finnish women spend nearly an hour more on household work on an average day than Finnish men do. Thus, those women devoting more time to physical activity might take the time for it from television time - not, for example, from housework."

Researchers at North Carolina State University have developed a new technique for shielding electronics in military and space exploration technology from ionizing radiation. The new approach is more cost effective than existing techniques, and the secret ingredient is...rust.

"Our approach can be used to maintain the same level of radiation shielding and reduce the weight by 30% or more, or you could maintain the same weight and improve shielding by 30% or more - compared to the most widely used shielding techniques," says Rob Hayes, co-author of a paper on the work and an associate professor of nuclear engineering at NC State. "Either way, our approach reduces the volume of space taken up by shielding."

Ionizing radiation can cause significant problems for electronic devices. To protect against this, devices that may be exposed to radiation - such as devices used in spacecraft - incorporate radiation shielding.

Weight is a significant factor in designing aerospace technologies, and the shielding most commonly found in aerospace devices consists of putting an aluminum box around any sensitive technologies. This has been viewed as providing the best tradeoff between a shield's weight and the protection it provides.

The new technique relies on mixing oxidized metal powder - rust - into a polymer, and then incorporating it into a common conformal coating on the relevant electronics.

"Metal oxide powder offers less shielding than metal powder would, but oxides are less toxic and don't pose electromagnetic challenges that could interfere with a device's operation," Hayes says.

"Radiation transport calculations show that inclusion of the metal oxide powder provides shielding comparable to a conventional shield," says Mike DeVanzo, a former graduate student at NC State and first author on the work. "At low energies, the metal oxide powder reduces both gamma radiation to the electronics by a factor of 300 and the neutron radiation damage by 225%."

"At the same time, the coating is less bulky than a shielding box," Hayes says. "And in computational simulations, the worst performance of the oxide coating still absorbed 30% more radiation than a conventional shield of the same weight.

"On top of that, the oxide particulate is much less expensive than the same amount of the pure metal," Hayes says.

"This could potentially reduce the need for conventional shielding materials on space-based electronics," adds DeVanzo, who works at Lockheed Martin Space.

The researchers are continuing to test and fine-tune their shielding technique for use in various applications.

"We're now looking for industry partners to help us develop the technology for commercial use," Hayes says.

By creating neatly spaced slits in a clay mineral, University of Groningen Professor of Experimental Solid State Physics Petra Rudolf was able to filter water to remove a toxic herbicide. After removing the pollutant by heating the material, the clay can be reused. Together with colleagues from Greece, Rudolf presents this proof of principle study in the journal Environmental Science Nano.

In the Netherlands, a lot of sugar beets are grown. On these fields, the herbicide chloridazon is widely used. This compound is toxic to humans, does not break down in nature and will eventually seep into the groundwater. Chloridazon concentrations in groundwater are currently below the safety threshold but as it is persistent in the environment, they are expected to increase. 'Water purification plants can break down chloridazon using UV light - but the breakdown products of chloridazon are also toxic,' explains Rudolf.

Pillars

Rudolf has acquired a technique to make well-defined nanocavities in clay, which she adapted to trap the herbicide. 'Clay is a layered mineral,' Rudolf explains. 'The layers have a negative charge and are separated by positive ions. We can replace those with molecular pillars of our own design.' The natural clays are first washed and then treated with sodium salts. The sodium replaces the natural positive ions between the layers. 'These sodium ions are surrounded by a water mantle, which pushes the layers slightly further apart. By simply adding the pillar molecules to the water, they will replace the sodium.'

These pillars are usually made of silicon oxide, with an added chemical group that defines the affinity of the cavities. Rudolf: 'In this case, we added copper ions to attract the chloridazon and its breakdown products.' The functionalized clay absorbed the herbicide in significant amounts: nearly 900 milligrams per kilogram of clay. 'This is a good result and we see scope to further increase the absorption.' Furthermore, Rudolf and her colleagues have shown that the herbicide is removed by heating the clay, which can then be used again.

Groundwater

The first results were obtained using 10 times the highest concentration of chloridazon measured in the environment. Furthermore, the experiments were performed in clean water. 'So, we need to repeat this in real groundwater, to see if other compounds affect the absorption.' If all these tests yield positive results, the next question is how to make this clay into a product that can be used in water treatment. 'The options are to add the clay to water and then retrieve it by filtration, or to build the clay into a membrane,' explains Rudolf.

By altering the width of the slits and changing the affinity of the pillars, different chemical compounds could be caught by the functionalized clay. 'We are testing systems to remove two other compounds from water,' says Rudolf. 'Furthermore, a similar system could be created using other layered materials, such as graphene oxide.'

Radiation from cell phones is associated with higher rates of thyroid cancer among people with genetic variations in specific genes, a new study led by the Yale School of Public Health finds.

The researchers examined over 900 people in Connecticut and found that those with certain single nucleotide polymorphisms (genetic variations commonly referred to as SNPs and pronounced as "snips") were significantly more likely to develop cancer in their thyroid, a gland in the throat that controls metabolism.

Cell phone users with SNPs in four of the genes studied were more than two times likely to develop cancer. The researchers examined a total of 176 genes and identified 10 SNPs that appear to increase the risk of thyroid cancer among cell phone users.

Published in the journal Environmental Research, the study is believed to be the first to examine the combined influence of genetic susceptibility and cell phone use in relation to thyroid cancer.

"Our study provides evidence that genetic susceptibility influences the relationship between cell phone use and thyroid cancer," said Yawei Zhang, M.D., Ph.D., a professor in the Department of Environmental Health Sciences at the Yale School of Public Health. "More studies are needed to identify populations who are susceptible to radiofrequency radiation (RFR) and understand exposure to RFR by different using patterns of cell phones."

The findings suggest that genetic susceptibilities play an important role in cell phone use and the risk of developing thyroid cancer and could help to identify subgroups who are potentially at risk. Further research is needed to confirm the findings and to better understand the interaction between cell phone radiation and SNPs within specific genes.

The rates of thyroid cancer have been steadily increasing in the United States and in many other parts of the world, Zhang said.

According to the American Cancer Society's most recent report, there were nearly 53,000 new cases of thyroid cancer in the United States, resulting in 2,180 deaths. Thyroid cancer is three times more common in women and is diagnosed at a younger age than most other cancers.

Zhang noted that the study relied on data collected from 2010 to 2011 when smartphones were first being introduced to the market. At the time, only a small proportion of people had smart phones. Therefore, if cell phone use increased the risk of thyroid cancer, it was possibly due to the use of earlier generation cell phones that were more commonly used when the data was collected.

Additionally, the transition to smartphones has also seen a major change in how cell phones are used (e.g., texting vs. phone calls). As a result, findings from this current study warrant a further evaluation in future studies, she said.

RESEARCH TRIANGLE PARK, N.C. -- Researchers working on an Army project developed nanoscale thermal switches that are key to thermal management of nanoscale devices, refrigeration, data storage, thermal computing and heat management of buildings.

The journal Nature Nanotechnology published an Army-funded study from University of Michigan researchers that showed for the first time how a nanoscale thermal switch can be built by employing nanoscale effects that arise when heat is transferred between a hot and cold nanoscale-thick membrane via thermal radiation.

In comparison to the vast array of devices, such as transistors and diodes that are available to control the flow of electricity, there exists currently very few proposals for controlling the flow of heat, especially at the nanoscale. To overcome this challenge researchers have been exploring nanoscale phenomena that may enable novel functional thermal devices.

"It's exciting to see Army investments in basic research leading to the discovery of new effects and proof of concept demonstrations of novel thermal devices," said Dr. Chakrapani Varanasi, a program manager at the Army Research Office, an element of the U.S. Army Combat Capabilities Development Command's Army Research Laboratory. "These findings can have a strong impact on thermal management for next generation computing for the military."

The Army's network modernization strategy is designed to enable the Army to fight tonight while also actively seeking next-generation solutions to stay ahead of potential adversaries.

A 2018 discovery by the research team, which highlighted how heat is transported in preferential directions from nanoscale membranes, led Dr. Dakotah Thompson, the lead author of the 2018 study, to begin exploring potential applications.

"After some thought it became apparent to us that we could potentially create a thermal switch by controlling the emission properties of the nanomembranes by bringing a third object into close proximity of the nanomembrane," said Dr. Edgar Meyhofer, a professor of mechanical engineering at the University of Michigan.

In order to test this hypothesis, Thompson developed a scheme where a planar object can be brought into close proximity (microns) of two co-planar membranes that were exchanging heat.

"In order to accomplish this challenging goal, I nanofabricated both suspended calorimetric devices that had unprecedented calorimetric resolution and a planar mesa-shaped object, and controlled the separation between them using a custom developed nanopositioner," Thompson said.

From these experiments the authors could show that heat transfer between nanoscale membranes can be turned on and off by simply modifying the separation between the membranes and the planar mesa.

In order to make precise numerical predictions of the experimental observations, Dr. Linxiao Zhu, a post-doctoral fellow at Michigan, and Thompson performed detailed calculations that showed how the observations can be quantitatively related to how the propagation of light, which is the carrier of heat, from one membrane to the other is impeded by the planar mesa which can either absorb the light propagating between the membranes or reflect it away from the membranes.

Scientists at the CCDC Army Research Laboratory are closely following this research to use these developments to create novel Army relevant devices.

One of the most controversial hypotheses for the origin of human language faculty is the evolutionary conjecture that language arose instantaneously in humans through a single gene mutation. `

Two recent publications by researchers at the University of Barcelona (UB), led by Cedric Boeckx, ICREA Research professor from the Section of General Linguistics and member of the Institute of Complex Systems of the UB (UBICS), question this hypothesis, advocated among others by linguist Noam Chomsky, and suggest that it is more likely that language evolved gradually.

Merge, the cognitive operation key to human language

For decades, several scholars such as Chomsky have proposed that modern humans are genetically equipped with a unique cognitive capacity that specifically allows us to implement computations over hierarchically structured symbolic representations. This capacity is enabled by a formally simple cognitive operation known as Merge, which is the basis of our ability to represent complex grammars in a way that other species cannot. "Merge is claimed to be sufficient to yield grammatical structure. Put it simple, Merge takes two linguistic units (say, words) and combines them into a set that can then be combined further with other linguistic units, effectively creating unbounded linguistic expressions. These, in turn, are claimed to form the basis for our cognitive creativity and flexibility, setting us aside from other species," said Cedric Boeckx.

"The strongest version of this hypothesis --Cedric Boeckx continued -- suggests that the biological foundation of our modern language capacity is a single genetic mutation, a macromutation, that emerged instantaneously in a single hominin individual who is an ancestor of all modern humans, and spread through the population."

Modeling the single gene mutation hypothesis

In the first paper, published in Scientific Reports -with participation of Cedric Boeckx and researchers from the Free University of Brussels (Belgium) and the Max Plank Institute of Psycholinguistics (Netherlands), they examine this hypothesis by modeling the evolutionary dynamics of such a scenario, taking into account different parameters such as how long ago this mutation would have happened and the population size at the time. "We examine the dynamics of a single, critical, mutation spreading rapidly through a population in a given time window, combining this theoretical proposal with contemporary genetic and demographic findings", said Cedric Boeckx.

In this case, researchers have applied a variety of techniques from theoretical biology to the question of how to quantify the probability of a complex trait like language evolving in a single step, in many small steps, or in a limited number of intermediate steps, within a specific time window and population size.

Researchers concluded that, instead of a single mutation with an extremely large fitness advantage, the most likely scenario is one where higher number of mutations, each with moderate fitness advantages, accumulate. "A scenario in which the genetic bases of our linguistic ability evolved through a gradual accumulation of smaller biological changes. This scenario can be articulated in many different ways, for instance as syntax evolving from phonological form, from rapid manual actions or from much simple pragmatic sequencing of words", said Boeckx.

Challenging the logic of the hypothesis

In the other study, published in PLoS Biology, UB graduate student Pedro Tiago Martins and Cedric Boeckx question this evolutionary hypothesis from a different angle: by going over its logic. Defendants of the single hypothesis claim that Merge, being such a simple operation had to be the result of a single genetic mutation that endowed one individual with the necessary biological equipment for language. In addition, because Merge is either fully present or fully absent --in other words, there cannot be such a thing as half-Merge--, the human language faculty had to emerge suddenly, as the result of this single mutation.

"From the formal properties of Merge, it is not possible to derive of number of evolutionary steps that led to the emergence of Merge. The computational simplicity of Merge does not correlate in any meaningful way to biological simplicity, and that once different levels of organization are taken into account there is no way to derive such simplistic evolutionary scenarios for any complex trait.",said Pedro Tiago Martins. The study highlights that even if a trait, such as the Merge operation, does not manifest itself in intermediate steps, its evolution may very well be gradual.

Researchers explained that the evolution of something as complex as human language deserves integration of results and insights from different corners of the research landscape, namely the fields of neurobiology, genetics, cognitive science, comparative biology, archaeology, psychology, and linguistics. "This is hard because it requires compatible levels of granularity between all fields involved, but it is the only way of achieving meaningful understanding," said Pedro Tiago Martins.

Together, these studies suggest that evolutionary reasoning does not warrant a scenario of sudden emergence of human language by means of a single mutation, and that it is more likely instead that language evolved gradually.

In a new short paper in the journal Nature Machine Intelligence, Roger A. Søraa from Norwegian University of Science and Technology (NTNU) and co-authors Eduard Fosch-Villaronga from Leiden University in the Netherlands, and Adam Poulsen from Charles Sturt University in Australia discuss what a queering of robots might entail.

"It is imperative that we construct mechanisms and policies that acknowledge the importance of inclusivity, diversity, and non-discrimination, also for the LGBTQ+ community in the development and use of robots and AI," the researchers wrote.

They point out that technology is not developed in a vacuum, but instead reflects biases and reproduces societal values and beliefs.

Søraa is active in robot and cyborg research through the newly started Immersive Technology and Social Robots Lab at NTNU, and has been active in queer and gender debates, including starting the NTNU LGBTQ+ networks for employees.

Søraa and his co-authors highlight the lack in the inclusion of queer perspectives on robots and machines. This, they argue, should be better recognized in both the research and design of the robots of the future, and should prod developers and designers to be more inclusive in how they build and create the machines that increasingly walk, talk and act among us.

Scientists and engineers from Nanyang Technological University, Singapore (NTU Singapore) and the University of Leeds in the UK have created the first electrically-driven 'topological' laser, which has the ability to route light particles around corners - and to cope with defects in the manufacture of the device.

Electrically-driven semiconductor lasers are the most common type of laser device today. They are used in products such as barcode readers and laser printers, for fibre optic communications, and in emerging applications such as laser ranging sensors for self-driving cars.

However, their manufacture is an exacting process and current laser designs do not work well if any defects are introduced into the structure of the laser during these processes.

The Singapore-UK advance reported in Nature today (12 February) overcomes this long-standing problem and promises to lead to more efficient and less wasteful manufacturing using existing semiconductor technologies. This is accomplished by harnessing a concept from theoretical physics known as the topological states, in order to make a 'topological laser'.

In the 1980s scientists found that electrons flowing in certain materials have 'topological features' - meaning that they can flow around corners or imperfections without scattering or leaking. The 2016 Nobel Prize in Physics was awarded to three theoretical physicists who pioneered the study of such topological states of electrons.

Now, an interdisciplinary team of engineers and physicists from NTU Singapore in collaboration with material scientists from the University of Leeds, have applied this topological approach to light particles, known as photons.

"Every batch of manufactured laser devices has some fraction that fails to emit laser light due to imperfections introduced during fabrication and packaging," said Professor Qi Jie Wang, the lead scientist from NTU Singapore's School of Electrical and Electronic Engineering. "This was one of our motivations for exploring topological states of light, which are much more robust than ordinary light waves."

In the present study, the researchers worked with a type of electrically-driven laser called a quantum cascade laser, based on advanced semiconductor wafers developed at the University of Leeds.

A senior author of the study, Professor Giles Davies FREng, Pro-Dean for Research and Innovation in the Faculty of Engineering and Physical Sciences at the University of Leeds, said: "The topological laser is a great example of a fascinating fundamental scientific phenomenon being applied to a practical electronic device, and as our study shows, it has the potential to improve the performance of laser systems."

To achieve topological states on a laser platform, the NTU and Leeds team developed a new design containing a valley photonic crystal, which was inspired by electronic topological materials known as two-dimensional valleytronic insulators.

The design consists of hexagonal holes arranged in a triangular lattice, etched into a semiconductor wafer, making it extremely compact.

Within the microstructure, the topological states of light circulate within a triangular loop of 1.2 millimetre circumference, acting as an optical resonator to accumulate the light energy required to form a laser beam.

"The fact that light circulates in this loop, including going around the sharp corners of the triangle, is due to the special features of topological states," says Associate Professor Yi Dong Chong, a theoretical physicist in NTU Singapore's School of Physical and Mathematical Sciences and co-lead investigator of the project. "Ordinary light waves would be disrupted by the sharp corners, preventing them from circulating smoothly."

The researchers note that an interesting feature of the new topological quantum cascade laser is that the light it emits is at terahertz frequencies between the microwave and infrared regions of the electromagnetic spectrum. Terahertz light has been identified as one of the principal realms from which future technological applications in sensing, illumination, and wireless communications may emerge.

This research project spanned two years, and involved an interdisciplinary team of twelve researchers. Team members also include NTU physicists: Associate Professor Baile Zhang, postdoctoral research fellow and first author of the paper, Dr Yongquan Zeng; as well as Professor Edmund Linfield, Professor of Terahertz Electronics, and Dr Lianhe Li, Senior Research Fellow, both at Leeds.

Looking ahead, the joint team is working on lasers that make use of other types of topological states.

"The design we used in this project, called a valley photonic crystal, is not the only way to create topological states," Professor Wang said. "There are many different types of topological states, imparting protection against different kinds of imperfections. We think it will be possible to tailor the design to the needs of different devices and applications."

In 2018, a team at the Technion - Israel Institute of Technology and the University of Central Florida in the USA developed a topological laser made from an array of connected optical resonators. The researchers showed that the topological states of light could travel efficiently around corners and defects in the laser array. However, this prototype laser had the drawback of being much larger than most semiconductor lasers, as well as being 'optically driven', meaning that it was powered by another laser.

In Brazil there is a plant so strange that researchers predicted - and 27 years later, proved - that opossums are key to its pollination. The findings are published in the Ecological Society of America's journal Ecology.

The plant Scybalium fungiforme, a little-known fungus-like species of the family Balanophoraceae, has bunches of tiny pale flowers that are surrounded and housed by a hard surface of bracts - like on an artichoke. Because of their scale-like shape, the bracts must be opened or peeled back to expose the flowers and nectar to pollinators such as bees.

While most species in the Balanophoraceae plant family are primarily pollinated by bees and wasps, researchers at São Paulo State University in Botucatu, Brazil hypothesized something different. They thought that opossums, with their opposable thumbs, would be a key pollinator for S. fungiforme due to the challenging bracts covering the flowers.

In the early 1990s Patrícia Morellato, a professor at the university, first made the prediction. She and her colleagues studied the plant and they captured an opossum with nectar on its nose. There observations went unpublished because they did not record or obtain direct evidence of the opossums pollinating the flowers.

Felipe Amorim, assistant professor at the university and lead author on this study, did not encounter the plant until 2017, but hypothesized that a non-flying mammal is needed for pollination based on the flower morphology. In April 2019 his students independently hypothesized that perhaps rodents could act as the main pollinators of this species. "At that time, neither of us knew anything about the unpublished observations made by Patrícia in the '90s,'" he explains.

In May 2019 Amorim and a team of researchers went to Serra do Japi Biological Reserve, located about 50 km from the area studied by Morellato, and set up night-vision cameras to record the activity of nocturnal flower visitors. The cameras captured opossums removing bracts from the fungus-like plant and pushing their faces into the flowers to eat the nectar. It was the first direct evidence of opossums pollinating the plant.

Amorim sent his colleague Morellato the footage. "When she watched the videos," he says, "she sent me a voice message as excited as we were when we first saw the opossum visiting the flowers, because it was the first time she saw something she predicted two and a half-decades ago!"

The researchers had made the opossum prediction based on "pollination syndrome" - the concept that floral attributes such as color, morphology, scent, and size reflect the adaptation of a plant species to pollination by a certain group of animals. Opossums, having "hands" with opposable thumbs, are capable of peeling back the scale-like leafs covering the flowers of S. fungiforme. The plant does have other floral visitors that act as secondary pollinators once the bracts are removed - bees and wasps dominate the crowd, but a surprising additional visitor was several hummingbirds.

"Based on the flower morphology," Amorim says, "Morellato, my students, and I could safely predict that this plant should be pollinated by non-flying mammals, but the occurrence of hummingbirds coming to the ground to visit these flowers was something completely unexpected to me." Morellato had not seen any hummingbirds visiting this species at her study site during the '90s, but researchers have more recently obtained indirect evidence that hummingbirds visit the plant in both study locations.

The authors hope to continue studying the pollinators of S. fungiforme to assess the efficiency of each group of flower visitor (mammals, hummingbirds, and bees and wasps) in order to quantify their contribution to the fruit production of this plant. They also want to analyze the chemical compounds of nectar and floral scent, which can reveal much about the adaptation of a plant for a given group of pollinator.

Overall, the story is an interesting one to tell, the culmination of nearly three decades of prediction and observation based on the hard shell surrounding a bunch of tiny flowers. Amorim contemplates that "at the time that non-flying mammals were first predicted as the pollinators of this fungus-like plant, I was about 11 years old, and most of the authors of this study haven't even had born!"

Brain-eating amoebae can cause particularly harmful forms of encephalitis, and more than 95% of people who develop these rare but devastating infections die. Despite the high mortality rate, there is currently no single effective drug available to fight these microbes. Now, however, researchers have designed some new compounds that show promise in the laboratory as treatments, according to a report in ACS Chemical Neuroscience.

Naegleria fowleri and Balamuthia mandrillaris are two types of amoebae that can cause primary amoebic meningoencephalitis and granulomatous amoebic encephalitis. They are single-celled microorganisms that live in water and soil, and can enter the body through the nose or open wounds. These pathogens can then move to the central nervous system, where they destroy brain cells. In the very few cases that have been treated successfully, patients were given high doses of many different antimicrobials. However, these drugs generally lack specificity and can have toxic effects at high levels. To make progress toward a single drug, Ruqaiyyah Siddiqui and colleagues turned to quinazolinones. These compounds are effective against a wide spectrum of human foes, including bacteria, viruses, fungi, parasites and cancer, but they had never been tested against brain-eating amoebae.

The researchers synthesized 34 new quinazolinone derivatives and studied their effects on N. fowleri and B. mandrillaris. Some of the new compounds were effective at killing the microorganisms and limiting the harm the pathogens could do to human cells in a Petri dish. In some cases, attaching silver nanoparticles to the derivatives enhanced that activity. The most effective compounds contained chlorine, methyl or methoxy groups, and their toxicity for human cells was low. The researchers say their results show that quinazolinones are good candidates for drug development studies.

As a result of climate change, more frequent and longer drought periods are predicted in the future. Drought risks are suggested to decrease agricultural yield. Researchers at the University of Bayreuth and the Leibniz Centre for Agricultural Landscape Research (ZALF) have now discovered a way to mitigate this problem: Amorphous silica is able to significantly increase the amount of available water for plants. This offers an opportunity to enhance global food security despite climate change. The researchers presented their findings in the journal Scientific Reports. They suggest a soil management that ensures a higher amorphous silica content.

The new research results are the product of close collaboration between environmental geochemists and soil physicists. The scientists have systematically investigated how amorphous silica affects the ability of soils to absorb and store water, for the first time. The results are impressive: Even if the proportion of amorphous silica in soils increases by just one percent by weight, the amount of plant available water in soils increases by up to 40 percent - or even more", reports Dr. Jörg Schaller from the Department of Environmental Geochemistry at the University of Bayreuth and ZALF. This is because gels, which contain enormous amounts of water, form in the soil out of amorphous silica molecules. These water supplies are easily accessible to the roots of plants.

However, it has been known for some time that conventional methods of agriculture lead to a steady decline of the content of amorphous silica in the soil. In combination with the expected consequences of climate change, this may lead to serve drought problems in e.g. agricultural systems in future, decreasing yield even more. This increases the risks to global food security. "Our new study shows a way to mitigate this risk. For this, soil management should be modified to increase the amorphous silica stocks in soils. Moreover, artificial produce amorphous silica - which has the same chemical properties as the biogenic silica - should be used as soil amendments. Such soil silica amendments may play an important role in global food security in the future," Schaller said.

St. Paul, MN (February 2020)--Transmitted by insects, especially the aster leafhopper, aster yellows (AY) outbreaks can cause severe production losses in many crops, including carrots, lettuce, and canola. Canola is a billion-dollar crop for Canada but the growing season in Western Canada is very short. Depending on the environmental conditions and number of infected leafhoppers, AY can be transmitted to canola in less than 24 hours and the leafhoppers can continue spreading the disease for the rest of their lives.

Scientists based in Saskatoon, Canada, developed a rapid, simple laboratory and field-adaptable DNA extraction method that allowed them to identify both plant pathogen and insect vector using molecular barcoding and gene sequencing. This method reduced the time from collection of insects to a positive identification of the presence of a pathogen from up to two weeks to less than one hour. They published their findings in Plant Health Progress.

"Using this methodology, we were able to go from DNA extraction to pathogen detection in less than one hour," according to lead author Karolina Pusz-Bochenska. "This rapid technique allows for same-day management decisions essential to preventing the spread of insect-transmitted pathogens."

To achieve this quick turnaround, Pusz-Bochenska and colleagues used DNA lysis paper to extract pathogen DNA, which was a novel choice that they combined with the rapid-detection potential of the sensitive and field-adaptable loop-mediated isothermal amplification (LAMP) assay. According to Pusz-Bochenska, this combination was groundbreaking.

"When the aster leafhoppers migrate into Canada in spring, they bring AY phytoplasmas that can cause devastating damage to canola crops, and we need a rapid-test to determine if these migrant leafhoppers are a threat or not. A rapid analysis of the leafhoppers allows us to estimate the infectivity of the population and forecast the risk to the crops, allowing the growers to make management decisions if the leafhoppers have arrived in their fields."

While this research focuses on agriculture, this techniques has potential applications to horticulture as well as animal and human health. For more details, read "A Rapid, Simple, Laboratory and Field-Adaptable DNA Extraction and Diagnostic Method Suitable for Insect-Transmitted Plant Pathogen and Insect Identification," which is freely available through the end of March.

New research spearheaded by McGill University has discovered that bacteriophages (viruses that infect bacteria) found in the intestinal tracts of children may play a role in childhood stunting, a significant impediment to growth that affects 22% of children under the age of five around the world.

The study, published today in Cell Host & Microbe, also suggests that because they affect the abundance and diversity of bacterial communities in the gastrointestinal tract, these viruses could also be used to improve health. The researchers believe this work offers hope of developing new cost efficient therapies for populations where nutritional interventions, which have been shown to work, are difficult to implement and sustain in vulnerable human populations.

Phages, bacteria and stunting

Earlier studies had suggested that the gut microbiome might play a role in stunting by showing that stunted children have increased numbers of disease-causing bacteria--associated with impaired digestive and absorption functions--living in their gastrointestinal tracts.

But while much research has focused on the bacteria present in our gut and the influence they can have on human health, little attention has thus far been paid to other very common residents of our gastrointestinal tract - bacteriophages.

"Phages or bacteriophages, which are bacterial viruses, are naturally found in every environment where bacteria are found, and the human gut is no exception," says Corinne Maurice, an assistant professor in McGill's Department of Microbiology and Immunology and senior author of the new study. "Because phages are as abundant as their hosts, they might be involved in regulating them in many ways by killing specific bacteria, transferring virulence or antibiotic resistance genes to them, for example, but we currently don't have a clear understanding of what they do and how they do it. This is a fairly new and exciting field of research."

Distinct viruses in healthy and stunted children

To understand how these viruses might play a role in stunting, Maurice's team, in collaboration with the International Centre for Diarrheal Disease Research in Bangladesh, collected fecal samples from 30 non-stunted and 30 unrelated stunted Bangladeshi children aged between 14 and 38 months.

Using a combination of microscopy, ribosomal gene sequencing, and metagenomics, they were able to determine that the phages found in the gut of non-stunted and stunted children are distinct. Furthermore, when gut bacteria from non-stunted children were exposed to phages from the guts of stunted children in vitro, they found that "bad" bacteria, suspected of being involved in stunting, proliferated.

"By showing that phages can change the bacterial community in children between 6 and 23 months, our work shows the potential of phages for reestablishing the gut bacterial community in stunting," says Mohammadali Khan Mirzaei, a former postdoctoral student in the Maurice lab and first author of the new study.

"Stunting has lifelong consequences (health/socioeconomic) and can be transferred from mother to child," says Maurice, who is also Canada Research Chair in Gut Microbial Physiology and a CIFAR Azrieli Global Scholar. "If phages can change bacterial communities in a specific way and long-term during child development, this could be a cheap treatment with no risk of antibiotic resistance."

Though the findings now need to be validated using a larger sample and in animal models, Maurice says that by understanding interactions between bacteria and viruses in the human gut, we might be able to one day manipulate them to improve human health.