Sunday, February 28, 2021

SARS-CoV-2 Mutations in Competition

SARS-CoV-2 mutations in competition

How dangerous are new mutations of the SARS-CoV-2 virus? An international team involving researchers from the Institute of Virology and Immunology (IVI) of the Federal Food Safety and Veterinary Office BLV and the University of Bern (Switzerland), the Centers for Disease Control and Prevention (USA), and the Friedrich-Loeffler Institute (Germany), has developed an approach that can accurately assess the transmissibility of new virus mutants.


Credit: University of Bern 

Prior to the emergence of new mutants of the coronavirus, such as the British variant B.1.1.7, the SARS-CoV-2 variant named D614G had already mutated from the original SARS-CoV-2 pathogen that triggered the pandemic. D614G has rapidly spread to become the most abundant variant worldwide and this D614G mutation remains in all the new emerging variants. An international team including researchers from Bern has now been able to demonstrate in both the laboratory and in animal models why the D614G variant was able to gain the upper hand over the original SARS-CoV-2 virus. "Our approach also allows us to characterize emerging mutations such as the British variant B.1.1.7 better and quicker," says Volker Thiel of the Institute of Virology and Immunology (IVI), one of the four lead authors of the study.

The findings are extremely important for assessing the risk of new mutants running rampant, as they show how a fitness advantage of virus variants can lead to higher transmission. First results were released earlier allowing for scientific discussion on what is known as a preprint server. The results of the study have now been published in full in Nature. The D614G variant carries a mutation in the spike protein that makes it easier for the virus to dock onto human cells.

The researchers at IVI and in David E. Wentworth’s laboratory at the Centers for Disease Control and Prevention in Atlanta (USA) first demonstrated in human cell cultures from the upper respiratory tract, as well as from the nose, that the D614G variant binds more strongly and also replicates faster than the original virus. The increased replication of the D614G variant was also confirmed in vivo, in a new mouse model first described in this study. These experiments were also carried out at the IVI in Charaf Benarafa’s group.

The new mutation clearly prevails

The spread of SARS-CoV-2 viruses can be studied better in other animals rather than mice. Hamsters and ferrets are well established in infection research and are especially suitable animal models. To compare the two variants, a mixture of equal parts of the original version of the SARS-CoV-2 virus and the D614G variant was applied into the nose of each animal under light anesthesia. After one day, experimentally infected animals were rehoused with another healthy sentinel animal of the same species, to evaluate the transmission of the two variants in direct competition with each other. The experiment was repeated with six pairs of animals in total. In virtually all sentinel animals, the proportion of transmitted SARS-CoV-2 viruses was massively dominated by the D614G variant early on.

The differentiation of the variants was carried out using the latest sequencing technology and PCR techniques by Martin Beer's team at the Friedrich Loeffler Institute, Federal Research Institute for Animal Health, in Greifswald-Insel Riems (D). "Our study stands out because we were able to clearly discern the more efficient transmission of the mutated variant in direct comparison with the original variant," says Volker Thiel.

A fitness test for further mutations

This approach can even be used to test any single mutation or a specific combination of mutations that are present in a number of currently circulating viral variants. The IVI relies on a cloning technique developed in Bern a year ago, in which SARS-CoV-2 viruses can be exactly reproduced in the laboratory. The British virus, for example, is known to have not just one but often more than 14 mutations, eight of which occur in the spike protein. Thus, with the help of the cloning technique, any number of mutations of variants can be reproduced and used to compete against each other in the established cell cultures and animal models. The results show how single mutations affect the fitness and transmissibility of new variants. "Our testing strategy allows us to rapidly examine why other, newly emerging virus variants have become established," says Volker Thiel.

Similar research projects on infectious pathogens could also be carried out in the future at the newly established Multidisciplinary Center for Infectious Diseases and Immunity (MCIDI) at the University of Bern.

The study was financially supported by the Swiss National Science Foundation SNF, the European Commission, the German Federal Ministry of Education and Research, and the U.S. Department of Health & Human Services, National Institutes of Health (NIH) / Institute of Allergy and Infectious Diseases (NIAID).

Institute of Virology and Immunology IVI

The Institute of Virology and Immunology (IVI) with locations in Mittelhäusern and Bern is a research institution affiliated with the Federal Food Safety and Veterinary Office FSVO with participation of the University of Bern. It is the only high-security laboratory in Switzerland where highly contagious animal diseases (such as foot-and-mouth disease or swine fever) can be diagnosed and researched. In line with the "one health" concept, one research focus is on viral infections that pose a threat to animals and humans (zoonoses).Further information
 



Contacts and sources:
University of Bern



Publication: SARS-CoV-2 spike 614G variant confers enhanced replication and transmission. Bin Zhou, Tran Thi Nhu Thao, Donata Hoffmann, Adriano Taddeo et al.: Nature, 26 February 2021, https://www.nature.com/articles/s41586-021-033






Prehistoric Landscape Reconstruction Reveals Early Dinosaurs Lived on Tropical Islands

A new study using leading edge technology has shed surprising light on the ancient habitat where some of the first dinosaurs roamed in the UK around 200 million years ago.

The research, led by the University of Bristol, examined hundreds of pieces of old and new data including historic literature vividly describing the landscape as a “landscape of limestone islands like the Florida Everglades” swept by storms powerful enough to “scatter pebbles, roll fragments of marl, break bones and teeth.”

Map of the Triassic palaeo-islands of the Bristol area. Includes silhouettes of the animals that lived on the islands and swam in the sea surrounding them


Produced by paper authors. Thecodontosaurus silhouette based on the Bob Nicholls/palaeocreation 2013 sculpture

The evidence was carefully compiled and digitised so it could be used to generate for the first time a 3D map showing the evolution of a Caribbean-style environment, which played host to small dinosaurs, lizard-like animals, and some of the first mammals.

“No one has ever gathered all this data before. It was often thought that these small dinosaurs and lizard-like animals lived in a desert landscape, but this provides the first standardised evidence supporting the theory that they lived alongside each other on flooded tropical islands,” said Jack Lovegrove, lead author of the study published today in Journal of the Geological Society.

The Bristol dinosaur. Thecodontos aurus, standing on one of the palaeo-island's beaches.

Credit: Artwork by Fabio Pastori, pixel-shack.com; © University of Bristol


The study amassed all the data about the geological succession as measured all round Bristol through the last 200 years, from quarries, road sections, cliffs, and boreholes, and generated a 3D topographic model of the area to show the landscape before the Rhaetian flood, and through the next 5 million years as sea levels rose.

At the end of the Triassic period the UK was close to the Equator and enjoyed a warm Mediterranean climate. Sea levels were high, as a great sea, the Rhaetian Ocean, flooded most of the land. The Atlantic Ocean began to open up between Europe and North America causing the land level to fall. In the Bristol Channel area, sea levels were 100 metres higher than today.

High areas, such as the Mendip Hills, a ridge across the Clifton Downs in Bristol, and the hills of South Wales poked through the water, forming an archipelago of 20 to 30 islands. The islands were made from limestone which became fissured and cracked with rainfall, forming cave systems.

“The process was more complicated than simply drawing the ancient coastlines around the present-day 100-metre contour line because as sea levels rose, there was all kinds of small-scale faulting. The coastlines dropped in many places as sea levels rose,” said Jack, who is studying Palaeontology and Evolution.

The findings have provided greater insight into the type of surroundings inhabited by the Thecodontosaurus, a small dinosaur the size of a medium-sized dog with a long tail also known as the Bristol dinosaur.

Co-author Professor Michael Benton, Professor of Vertebrate Palaeontology at the University of Bristol, said: “I was keen we did this work to try to resolve just what the ancient landscape looked like in the Late Triassic. The Thecodontosaurus lived on several of these islands including the one that cut across the Clifton Downs, and we wanted to understand the world it occupied and why the dinosaurs on different islands show some differences. Perhaps they couldn’t swim too well.”


3D model used to generate maps of the palaeo-island chain. Showing the palaeozoic strata surface in green relative to the Triassic strata surface in blue. Short version: 3D model used to generate maps of the palaeo-island chain

Credit: Produced by paper authors

“We also wanted to see whether these early island-dwellers showed any of the effects of island life,” said co-author Dr David Whiteside, Research Associate at the University of Bristol.

“On islands today, middle-sized animals are often dwarfed because there are fewer resources, and we found that in the case of the Bristol archipelago. Also, we found evidence that the small islands were occupied by small numbers of species, whereas larger islands, such as the Mendip Island, could support many more.”

The study, carried out with the British Geological Survey, demonstrates the level of detail that can be drawn from geological information using modern analytical tools. The new map even shows how the Mendip Island was flooded step-by-step, with sea level rising a few metres every million years, until it became nearly completely flooded 100 million years later, in the Cretaceous.

Co-author Dr Andy Newell, of the British Geological Survey, said: “It was great working on this project because 3D models of the Earth’s crust can help us understand so much about the history of the landscape, and also where to find water resources. In the UK we have this rich resource of historical data from mining and other development, and we now have the computational tools to make complex, but accurate, models.”

 
Contacts and sources:
University of Bristol


Publication: Testing the relationship between marine transgression and evolving island palaeogeography using 3D GIS: an example from the Late Triassic of SW England
Jack Lovegrove, Andrew J. Newell, David I. Whiteside, Michael J. Benton..  Journal of the Geological Society l Society, 2021; jgs2020-158 DOI: 10.1144/jgs2020-158








Parker Solar Probe Offers Stunning View of Venus



NASA’s Parker Solar Probe captured stunning views of Venus during its close flyby of the planet in July 2020.

Though Parker Solar Probe’s focus is the Sun, Venus plays a critical role in the mission: The spacecraft whips by Venus a total of seven times over the course of its seven-year mission, using the planet’s gravity to bend the spacecraft’s orbit. These Venus gravity assists allow Parker Solar Probe to fly closer and closer to the Sun on its mission to study the dynamics of the solar wind close to its source.

But — along with the orbital dynamics — these passes can also yield some unique and even unexpected views of the inner solar system. During the mission’s third Venus gravity assist on July 11, 2020, the onboard Wide-field Imager for Parker Solar Probe, or WISPR, captured a striking image of the planet’s nightside from 7,693 miles away.

When flying past Venus in July 2020, Parker Solar Probe’s WISPR instrument, short for Wide-field Imager for Parker Solar Probe, detected a bright rim around the edge of the planet that may be nightglow — light emitted by oxygen atoms high in the atmosphere that recombine into molecules in the nightside. The prominent dark feature in the center of the image is Aphrodite Terra, the largest highland region on the Venusian surface. Bright streaks in WISPR, such as the ones seen here, are typically caused by a combination of charged particles — called cosmic rays — sunlight reflected by grains of space dust, and particles of material expelled from the spacecraft’s structures after impact with those dust grains. The number of streaks varies along the orbit or when the spacecraft is traveling at different speeds, and scientists are still in discussion about the specific origins of the streaks here. The dark spot appearing on the lower portion of Venus is an artifact from the WISPR instrument.  

Credits: NASA/Johns Hopkins APL/Naval Research Laboratory/Guillermo Stenborg and Brendan Gallagher

WISPR is designed to take images of the solar corona and inner heliosphere in visible light, as well as images of the solar wind and its structures as they approach and fly by the spacecraft. At Venus, the camera detected a bright rim around the edge of the planet that may be nightglow — light emitted by oxygen atoms high in the atmosphere that recombine into molecules in the nightside. The prominent dark feature in the center of the image is Aphrodite Terra, the largest highland region on the Venusian surface. The feature appears dark because of its lower temperature, about 85 degrees Fahrenheit (30 degrees Celsius) cooler than its surroundings.

That aspect of the image took the team by surprise, said Angelos Vourlidas, the WISPR project scientist from the Johns Hopkins Applied Physics Laboratory (APL) in Laurel, Maryland, who coordinated a WISPR imaging campaign with Japan’s Venus-orbiting Akatsuki mission. “WISPR is tailored and tested for visible light observations. We expected to see clouds, but the camera peered right through to the surface.”

NASA’s Parker Solar Probe had an up-close view of Venus when it flew by the planet in July 2020. Some of the features seen by scientists are labeled in this annotated image. The dark spot appearing on the lower portion of Venus is an artifact from the WISPR instrument. 

Credits: NASA/Johns Hopkins APL/Naval Research Laboratory/Guillermo Stenborg and Brendan Gallagher


“WISPR effectively captured the thermal emission of the Venusian surface,” said Brian Wood, an astrophysicist and WISPR team member from the U.S. Naval Research Laboratory in Washington, D.C. “It’s very similar to images acquired by the Akatsuki spacecraft at near-infrared wavelengths.”

This surprising observation sent the WISPR team back to the lab to measure the instrument’s sensitivity to infrared light. If WISPR can indeed pick up near-infrared wavelengths of light, the unforeseen capability would provide new opportunities to study dust around the Sun and in the inner solar system. If it can’t pick up extra infrared wavelengths, then these images — showing signatures of features on Venus’ surface — may have revealed a previously unknown “window” through the Venusian atmosphere.

“Either way,” Vourlidas said, “some exciting science opportunities await us.”

For more insight into the July 2020 images, the WISPR team planned a set of similar observations of the Venusian nightside during Parker Solar Probe’s latest Venus flyby on Feb. 20, 2021. Mission team scientists expect to receive and process that data for analysis by the end of April.

“We are really looking forward to these new images,” said Javier Peralta, a planetary scientist from the Akatsuki team, who first suggested a Parker Solar Probe campaign with Akatsuki, which has been in orbiting Venus since 2015. “If WISPR can sense the thermal emission from the surface of Venus and nightglow — most likely from oxygen — at the limb of the planet, it can make valuable contributions to studies of the Venusian surface.”

Parker Solar Probe is part of NASA’s Living with a Star program to explore aspects of the Sun-Earth system that directly affect life and society. The Living with a Star program is managed by the agency’s Goddard Space Flight Center in Greenbelt, Maryland, for NASA’s Science Mission Directorate in Washington. Johns Hopkins APL designed, built and operates the spacecraft.



Contacts and sources:
By Michael Buckley
Johns Hopkins University Applied Physics Laboratory, Laurel, Md.

Karen Fox
NASA's Goddard Space Flight Center, Greenbelt, Md.









Signs of Burnout Can Be Detected in Sweat

EPFL engineers, working in association with startup Xsensio, have developed a wearable sensing chip that can measure the concentration of cortisol – the stress hormone – in human sweat. Enabling future quasi-continuous monitoring, their device can eventually help doctors better understand and treat stress-related conditions like burnout and obesity.

Credit: EPFL


We’ve all felt stressed at some point, whether in our personal or professional lives or in response to exceptional circumstances like the COVID-19 pandemic. But until now there has been no way to quantify stress levels in an objective manner.

That could soon change thanks to a small wearable sensor developed by engineers at EPFL’s Nanoelectronic Devices Laboratory (Nanolab) and Xsensio. The device has the potential to be placed directly on a patient’s skin in a wearable patch and, in the future, to quasi-continually measure the concentration of cortisol, the main stress biomarker, in the patient’s sweat.

Cortisol: A double-edged sword

Cortisol is a steroid hormone made by our adrenal glands out of cholesterol. Its secretion is controlled by the adrenocorticotropic hormone (ACTH), which is produced by the pituitary gland. Cortisol carries out essential functions in our bodies, such as regulating metabolism, blood sugar levels and blood pressure; it also affects the immune system and cardiovascular functions.

When we’re in a stressful situation, whether life-threatening or mundane, cortisol is the hormone that takes over. It instructs our bodies to direct the required energy to our brain, muscles and heart. “Cortisol can be secreted on impulse – you feel fine and suddenly something happens that puts you under stress, and your body starts producing more of the hormone,” says Adrian Ionescu, head of Nanolab.

While cortisol helps our bodies respond to stressful situations, it’s actually a double-edged sword. It’s usually secreted throughout the day according to a circadian rhythm, peaking between 6am and 8am and then gradually decreasing into the afternoon and evening. “But in people who suffer from stress-related diseases, this circadian rhythm is completely thrown off,” says Ionescu. “And if the body makes too much or not enough cortisol, that can seriously damage an individual’s health, potentially leading to obesity, cardiovascular disease, depression or burnout.”

Qualitative depiction of regular and irregular circadian levels throughout the day
. © Credit: Nanolab, EPFL

Capturing the hormone to measure it

Blood tests can be used to take snapshot measurements of patients’ cortisol levels. However, detectable amounts of cortisol can also be found in saliva, urine and sweat. Ionescu’s team at Nanolab decided to focus on sweat as the detection fluid and developed a wearable smart patch with a miniaturized sensor.

The patch contains a transistor and an electrode made from graphene which, due to its unique proprieties, offers high sensitivity and very low detection limits. The graphene is functionalized through aptamers, which are short fragments of single-stranded DNA or RNA that can bind to specific compounds. The aptamer in the EPFL patch carries a negative charge; when it comes into contact with cortisol, it immediately captures the hormone, causing the strands to fold onto themselves and bringing the charge closer to the electrode surface. The device then detects the charge, and is consequently able to measure the cortisol concentration in the wearer’s sweat.

Process flow for capturing cortisol with the graphene electrode and aptamers

 Credit: . © Nanolab, EPFL

So far, no other system has been developed for monitoring cortisol concentrations continuously throughout the circadian cycle. “That’s the key advantage and innovative feature of our device. Because it can be worn, scientists can collect quantitative, objective data on certain stress-related diseases. And they can do so in a non-invasive, precise and instantaneous manner over the full range of cortisol concentrations in human sweat,” says Ionescu.

Engineering improved healthcare

The engineers tested their device on Xsensio’s proprietary Lab-on-SkinTM platform; the next step will be to place it in the hands of healthcare workers. Esmeralda Megally, CEO of Xsensio, says: “The joint R&D team at EPFL and Xsensio reached an important R&D milestone in the detection of the cortisol hormone. We look forward to testing this new sensor in a hospital setting and unlocking new insight into how our body works.” The team has set up a bridge project with Prof. Nelly Pitteloud, chief of endocrinology, diabetes and metabolism at the Lausanne University Hospital (CHUV), for her staff to try out the continuous cortisol-monitoring system on human patients. These trials will involve healthy individuals as well as people suffering from Cushing’s syndrome (when the body produces too much cortisol), Addison’s disease (when the body doesn’t produce enough) and stress-related obesity. The engineers believe their sensor can make a major contribution to the study of the physiological and pathological rhythms of cortisol secretion.

So what about psychological diseases caused by too much stress? “For now, they are assessed based only on patients’ perceptions and states of mind, which are often subjective,” says Ionescu. “So having a reliable, wearable sensor can help doctors objectively quantify whether a patient is suffering from depression or burnout, for example, and whether their treatment is effective. What’s more, doctors would have that information in real time. That would mark a major step forward in the understanding of these diseases.” And who knows, maybe one day this technology will be incorporated into smart bracelets. “The next phase will focus on product development to turn this exciting invention into a key part of our Lab-on-SkinTM sensing platform, and bring stress monitoring to next-generation wearables,” says Megally.
 



Contacts and sources:
 Julie Haffner
Ecole Polytechnique Federale de Lausanne (EPFL)




Publication: “Extended gate field-effect-transistor for sensing cortisol stress hormone.”
Sheibani, S., Capua, L., Kamaei, S., Akbari S. S. A., Zhang J., Guerin H. and Ionescu A. M.
Communications Materials 2, Article number 10 (2021).




Like Wine, Environmental Conditions Impact Flavor of Whiskey, Study Finds

Flavor differences in whiskey can be discerned based solely on the environment in which the barley used to make the whiskey is grown, a new study co-authored by an Oregon State University researcher found.

Credit: OSU

This is first scientific study that found the environmental conditions, or terroir, of where the barley is grown impacts the flavor of whiskey, said Dustin Herb, an author of the study and a courtesy faculty member in the Department of Crop and Soil Science at Oregon State University.

“Terroir is increasingly being used to differentiate and market agricultural products, most commonly wine, as consumers grow more interested in the origins of their food,” Herb said. “Understanding terroir is something that involves a lot of research, a lot of time and a lot of dedication. Our research shows that environmental conditions in which the barley is grown have a significant impact.”

Herb, who is originally from Lebanon, Oregon, and earned his undergraduate and doctoral degrees from Oregon State, is the only American author of the study, which was published in the journal Foods. The other authors are all from Ireland, where the study was conducted.

Herb’s doctoral research at Oregon State with Pat Hayes, a barley breeder in the College of Agricultural Sciences, focused on the contributions of barley to beer flavor. Their research found notable differences in the taste of beers malted from barley varieties reputed to have flavor qualities.

That research caught the attention of Waterford Distillery. The Irish distillery reached out to Herb, flew him to Ireland and asked him if he could design a study that would attempt to answer the question of whether terroir exists in whiskey. They dubbed it The Whisky Terroir Project. (Whiskey can be spelled with and without an “e.”)



Credit: OSU

Herb designed a study that involved planting two common commercial varieties of barley in Ireland – Olympus and Laureate – in two distinct environments: Athy, Co. Kildare and Buncloudy, Co. Wexford in 2017 and 2018. Athy is an inland site and Buncloudy is a coastal site. They were selected in part because they have different soil types and different temperature ranges and rainfall levels during the barley growing season.

The crops of each barley variety at each site in each year were harvested, stored, malted and distilled in a standardized way. Once distilled, the product is called “new make spirit.” (It isn’t called whiskey until it is matured in a wooden cask for at least three years.)

The researchers used gas chromatography mass spectrometry and the noses of a six-person trained sensory panel to determine which compounds in the barley most contributed to the aroma of the new make spirit.

That analysis, along with further mathematical and statistical analysis, found that the environment in which the barley was grown had a greater contribution to the aroma of the whiskey than the variety of the barley. That was the clear indication of the impact terroir has on the new make spirit.

Furthermore, the sensory analysis found distinct differences in the aroma characteristics of the new make spirit from the barley grown in each location. In Athy, it was more positively associated with sweet, cereal/grainy, feinty/earthy, oily finish, soapy, sour, stale and mouldy sensory attributes and in Bunclody it was more associated with dried fruit and solventy attributes.

“What this does is actually make the farmer and the producer come to the forefront of the product,” Herb said. “It gets to the point where we might have more choices and it might provide an opportunity for a smaller brewer or a smaller distiller or a smaller baker to capitalize on their terroir, like we see in the wine industry with a Napa Valley wine, or Willamette Valley wine or a French Bordeaux.”



Credit: OSU

The sensory analysis also found differences in the aromatic profiles between the 2017 and 2018 seasons that were studied.

“This makes us think there might be a vintage aspect to the whiskey like wine, where you buy a 2019 or a 2020 or a 2016,” Herb said. “Could the whiskey industry operate in a similar way, where someone is going to seek out a certain vintage of a certain year?”

To answer that question, more research needs to be done, Herb said. That is a project the Whisky Terroir Project plans to tackle: examining flavor changes in the spirits as they mature in casks and to see what happens with the terroir impact.

The team is also scaling up the research to study terroir in commercial-scale barley fields over a five-year period.

In addition to Herb, who also works full-time as a plant breeder at Albany, Oregon-based OreGro, which develops turf and forage products, other authors of the paper are: Maria Kyraleou and Kieran Kilcawley of the Teagasc Food Research Park; Grace O’Reilly and Neil Conway of Waterford Distillery; and Tom Bryan of Boormalt.

The research was funded by Enterprise Ireland Commercialization Fund in collaboration with Waterford Distillery.

Contacts and sources:
Sean Nealon
Oregon State University

 





Engineering the Boundary between 2D and 3D Materials Atom by Atom

In recent years, engineers have found ways to modify the properties of some “two- dimensional” materials, which are just one or a few atoms thick, by stacking two layers together and rotating one slightly in relation to the other. This creates what are known as moiré patterns, where tiny shifts in the alignment of atoms between the two sheets create larger-scale patterns. It also changes the way electrons move through the material, in potentially useful ways.

But for practical applications, such two-dimensional materials must at some point connect with the ordinary world of 3D materials. An international team led by MIT researchers has now come up with a way of imaging what goes on at these interfaces, down to the level of individual atoms, and of correlating the moiré patterns at the 2D-3D boundary with the resulting changes in the material’s properties.
ese images of "islands" of gold atoms deposited on a layer of two-dimensional molybdenum sulfide were produced by two different modes, using a new scanning tunneling electron microscope (STEM) in the new MIT.nano facility. By combining the data from the two different modes the researchers were able to figure out the three-dimensional arrangement of atoms where the two materials meet.

Credits: Image courtesy of the researchers

The new findings are described today in the journal Nature Communications, in a paper by MIT graduate students Kate Reidy and Georgios Varnavides, professors of materials science and engineering Frances Ross, Jim LeBeau, and Polina Anikeeva, and five others at MIT, Harvard University, and the University of Victoria in Canada.

Pairs of two-dimensional materials such as graphene or hexagonal boron nitride can exhibit amazing variations in their behavior when the two sheets are just slightly twisted relative to each other. That causes the chicken-wire-like atomic lattices to form moiré patterns, the kinds of odd bands and blobs that sometimes appear when taking a picture of a printed image, or through a window screen. In the case of 2D materials, “it seems like anything, every interesting materials property you can think of, you can somehow modulate or change by twisting the 2D materials with respect to each other,” says Ross, who is the Ellen Swallow Richards Professor at MIT.

While these 2D pairings have attracted scientific attention worldwide, she says, little has been known about what happens where 2D materials meet regular 3D solids. “What got us interested in this topic,” Ross says, was “what happens when a 2D material and a 3D material are put together. Firstly, how do you measure the atomic positions at, and near, the interface? Secondly, what are the differences between a 3D-2D and a 2D-2D interface? And thirdly, how you might control it — is there a way to deliberately design the interfacial structure” to produce desired properties?

Figuring out exactly what happens at such 2D-3D interfaces was a daunting challenge because electron microscopes produce an image of the sample in projection, and they’re limited in their ability to extract depth information needed to analyze details of the interface structure. But the team figured out a set of algorithms that allowed them to extrapolate back from images of the sample, which look somewhat like a set of overlapping shadows, to figure out which configuration of stacked layers would yield that complex “shadow.”

The team made use of two unique transmission electron microscopes at MIT that enable a combination of capabilities that is unrivalled in the world. In one of these instruments, a microscope is connected directly to a fabrication system so that samples can be produced onsite by deposition processes and immediately fed straight into the imaging system. This is one of only a few such facilities worldwide, which use an ultrahigh vacuum system that prevents even the tiniest of impurities from contaminating the sample as the 2D-3D interface is being prepared. The second instrument is a scanning transmission electron microscope located in MIT’s new research facility, MIT.nano. This microscope has outstanding stability for high-resolution imaging, as well as multiple imaging modes for collecting information about the sample.

Unlike stacked 2D materials, whose orientations can be relatively easily changed by simply picking up one layer, twisting it slightly, and placing it down again, the bonds holding 3D materials together are much stronger, so the team had to develop new ways of obtaining aligned layers. To do this, they added the 3D material onto the 2D material in ultrahigh vacuum, choosing growth conditions where the layers self-assembled in a reproducible orientation with specific degrees of twist. “We had to grow a structure that was going to be aligned in a certain way,” Reidy says.


Having grown the materials, they then had to figure out how to reveal the atomic configurations and orientations of the different layers. A scanning transmission electron microscope actually produces more information than is apparent in a flat image; in fact, every point in the image contains details of the paths along which the electrons arrived and departed (the process of diffraction), as well as any energy that the electrons lost in the process. All these data can be separated out so that the information at all points in an image can be used to decode the actual solid structure. This process is only possible for state-of-the-art microscopes, such as that in MIT.nano, which generates a probe of electrons that is unusually narrow and precise.

The researchers used a combination of techniques called 4D STEM and integrated differential phase contrast to achieve that process of extracting the full structure at the interface from the image. Then, Varnavides says, they asked, “Now that we can image the full structure at the interface, what does this mean for our understanding of the properties of this interface?” The researchers showed through modeling that electronic properties are expected to be modified in a way that can only be understood if the full structure of the interface is included in the physical theory. “What we found is that indeed this stacking, the way the atoms are stacked out-of-plane, does modulate the electronic and charge density properties,” he says.

Ross says the findings could help lead to improved kinds of junctions in some microchips, for example. “Every 2D material that’s used in a device has to exist in the 3D world, and so it has to have a junction somehow with three-dimensional materials,” she says. So, with this better understanding of those interfaces, and new ways to study them in action, “we’re in good shape for making structures with desirable properties in a kind of planned rather than ad hoc way.”

“The present work opens a field by itself, allowing the application of this methodology to the growing research line of moiré engineering, highly important in fields such as quantum physics or even in catalysis,” says Jordi Arbiol of the Catalan Institute of Nanoscience and Nanotechnology in Spain, who was not associated with this work.

“The methodology used has the potential to calculate from the acquired local diffraction patterns the modulation of the local electron momentum,” he says, addingthat “the methodology and research shown here has an outstanding future and high interest for the materials science community.”



Contacts and sources:
David L. Chandler
Massachusetts Institute of Technology




Publication: . Direct imaging and electronic structure modulation of moiré superlattices at the 2D/3D interface.
Kate Reidy, Georgios Varnavides, Joachim Dahl Thomsen, Abinash Kumar, Thang Pham, Arthur M. Blackburn, Polina Anikeeva, Prineha Narang, James M. LeBeau, Frances M. Ross Nature Communications, 2021; 12 (1) DOI: 10.1038/s41467-021-21363-5



Investigating the Diet of Ancient Dogs

Coprolites, or fossilized dog feces, are often used to understand the dietary preferences of ancient civilizations. However, the samples are often contaminated, making the analysis difficult. A new study, published in Scientific Reports, uses different techniques to improve the investigation of coprolites.

Coprolites are found at archeological sites and they provide dietary insight

Credit: University of Illinois at Urbana-Champaign


“We have been interested in analyzing coprolites for many years. We have attempted to extract DNA and look at the microbiome before, but the tools were not as robust,” said Ripan Malhi (GNDP/GSP/IGOH), a professor of anthropology. “As far as I know, this is the first time anyone has used multiple approaches to provide a snapshot of the daily diet, health, and the long-term trends in ancient dogs of the Americas, all in one study.”

The samples were recovered from Cahokia, near modern St. Louis, Missouri. At its peak, Cahokia was a large urban center with a population greater than London or Paris. Several other investigations have shown that there is an overlap between the diet of dogs and humans, either because the dogs were fed the same food or because they ate human food scraps. Therefore, investigating coprolites also provides an insight into human health and diet.

“Initially, the residents were growing crops such as squash and sunflowers. As the city got bigger, it is believed that the diet shifted to maize. Our analysis suggests the same since we saw that some of the dogs were also eating maize,” said Kelsey Witt, a postdoctoral researcher at Brown University and former PhD student in the Malhi lab.

The maize samples were examined using stable isotope analysis, which is used to measure different forms of carbon in a sample. Depending on the carbon concentrations, one can identify what kind of plant was consumed. The researchers also investigated the animal and plant remains in the coprolites to show that walnuts, grapes, a variety of fish, and duck were a part of the dogs’ diet.

The researchers also used DNA sequencing to determine the microbiome—the community of microbes—of the coprolites. “The technique we used came out in 2020. It helped us verify whether the samples were from dogs or humans, as well as confirm general aspects of diet which can only be done by comparing the microbiomes,” said Karthik Yarlagadda, a PhD student in the Malhi lab.

Although the techniques are novel and more sensitive, coprolites are still challenging to study for a number of reasons. The DNA has already passed through the digestive process in the dogs and has therefore been broken down. Furthermore, since the samples are ancient, the extracted DNA is degraded to a large extent due to weathering.

“One of the biggest challenges we faced was dealing with sample contamination,” Yarlagadda said. “These samples were deposited a thousand years ago. After that, the environment changed, certain microbes died off, and new microbes took over. All these factors complicate the analysis.”

The researchers are working with the Indigenous communities to further understand what the diets looked like in their ancestors. “Since there are a lot of limitations to our research, talking to community members about what their ancestors ate and how they interacted with dogs helps us understand our results better,” Witt said.

The study “Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet” can be found at https://doi.org/10.1038/s41598-021-82362-6. The work was sponsored by the Vice Chancellor of Research, University of Illinois, and the Illinois State Archaeological Survey.

Contacts and sources:
Ananya Sen
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign


Publication: Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet.
Kelsey E. Witt, Karthik Yarlagadda, Julie M. Allen, Alyssa C. Bader, Mary L. Simon, Steven R. Kuehn, Kelly S. Swanson, Tzu-Wen L. Cross, Kristin M. Hedman, Stanley H. Ambrose, Ripan S. Malhi. Scientific Reports, 2021; 11 (1) DOI: 10.1038/s41598-021-82362-6




Allergy Season Starts Earlier Each Year Due to Climate Change and Pollen Transport

Scientists in Munich study how pollen from far distances -- sometimes hundreds of kilometers away -- affects the length of allergy seasons in Germany

Allergy sufferers are no strangers to problems with pollen. But now - due to climate change - the pollen season is lasting longer and starting earlier than ever before, meaning more days of itchy eyes and runny noses. Warmer temperatures cause flowers to bloom earlier, while higher CO2 levels cause more pollen to be produced.

Grass pollen grains under light microscope 
Credit: A. Menzel and Y. Yuan, Technical University of Munich

The effects of climate change on the pollen season have been studied at-length, and according to some scientists, has grown by as much as 20 days in the past 30 years, at least in the US and Canada. But one important element is often overlooked - "Pollen is meant to fly," says Dr Annette Menzel, Professor of ecoclimatology at the Technical University of Munich. "Transport phenomena have to be taken into account."

Along with her colleagues, she studied the transport of pollen in Bavaria, Germany, in order to better understand how the pollen season has changed over time. "The transport of pollen has important implications for the length, timing, and severity of the allergenic pollen season," says Dr Ye Yuan, a coauthor on the study.

Menzel and her team focused on Bavaria - a state in southeast Germany - and used six pollen monitoring stations scattered around the region to analyze data. Their results were recently published in Frontiers in Allergy. They found that certain species of pollen, such as from hazel shrubs and alder trees, advanced the start of their seasons by up to 2 days per year, over a period of 30 years (between 1987 and 2017). Other species, which tend to bloom later in the year, such as birch and ash trees, moved their seasons 0.5 days earlier on average each year, across that same time period.

Pollen can travel hundreds of kilometers and, with changing weather patterns and altered species distributions, it's possible that people are becoming exposed to "new" pollen species - meaning pollen that our bodies are unaccustomed to encountering each year.

While it can sometimes be difficult to differentiate between local and transported pollen, the researchers focused on pre-season transports. So, for example, if pollen from birch trees was present at the monitoring station, but local birch trees would not flower for at least another 10 days, that pollen was considered to be transported from far away.

"We were surprised that pre-season pollen transport is a quite common phenomenon being observed in two-thirds of the cases," says Menzel. As for why it's important to understand how much pollen is from far away, Yuan says that: "Especially for light-weight allergenic [pollen], long distance transport could seriously influence local human health."

Perennial perenne, whose pollen is an important cause of allergic rhinitis 
Credit: A. Menzel and Y. Yuan, Technical University of Munich

By examining another element besides simple pollen concentration, scientists can delve deeper into how exactly the pollen season is being affected by climate change. For example, Menzel says that the pollen season may be even longer than estimated based on flowering observations by "taking into account pollen transport, as it has been done in our current study."

While the Munich study did not track how far pollen was transported, and only differentiated between local and long-range transport (meaning pollen coming from outside Bavaria), it provides a crucial key in our understanding of annual pollen patterns. Yuan says that future studies should account for "climate change scenarios [and] land use/land cover changes." He also adds that citizen scientists may be able to contribute to pollen studies, who can help collect local observations and contribute to data collection.

It doesn't look like the pollen season will shorten any time soon, but more research on the subject can provide a better understanding of global patterns and changes so that we can better address these issues in the future.

 
Contacts and sources:
Mischa Dijkstra
Frontiers



Publication: A First Pre-season Pollen Transport Climatology to Bavaria, Germany Annette Menzel1,2, Homa Ghasemifard1, Ye Yuan1* and Nicole Estrella1 1Department of Life Science Systems, TUM School of Life Sciences, Technical University of Munich (TUM), Freising, Germany 2Institute for Advanced Study, Technical University of Munich (TUM), Garching, Germany https://www.frontiersin.org/articles/10.3389/falgy.2021.627863/full  http://dx.doi.org/10.3389/falgy.2021.627863




Changing the Silkworm's Diet to Spin Stronger Silk


Tohoku University researchers have produced cellulose nanofiber (CNF) synthesized silk naturally through a simple tweak to silkworms' diet. Mixing CNF with commercially available food and feeding the silkworms resulted in a stronger and more tensile silk.

Credit: Tohoku University


The results of their research were published in the journal Materials and Design on February 1, 2021.

"The idea for our research came to us when we realized the flow-focusing method by which silkworms produce silk is optimal for the nanofibril alignment of CNF," said Tohoku University materials engineer Fumio Narita and co-author of the study.

The silk worm and its CNF containing feed . 
Credit: ©Tohoku University

Silk is usually associated with clothes. But its usage is incredibly diverse thanks to its strength and elastic properties. Its biocompatibility makes it even safe to use inside the human body.

Because of this, researchers have been investigating ways to further strengthen silk. Processes investigated thus far, however, require the use of toxic chemicals that are harmful to humans and the environment.

Cellulose nanofibers--plant derived fibers that have been refined to the micro-level-- show promise in synthesizing low-cost, lightweight, high strength, and sustainable nanocomposites such as silk.

However, previous CNF based synthesized materials have demonstrated few mechanical improvements even with the benefit of expensive equipment due to the lack of nanofibril alignment.

In contrast, silkworms produce silk in a flow-focused method. Silk is dispersed via their salivary glands, orientating the fibrils along the flow direction and thus enabling better nanofibril alignment.

The resultant cocoons with different CNF wt% (0,5, and 10 wt% from left to right). 

Credit: ©Tohoku University

In the present study, silkworm larvae were divided into three groups and reared on food containing differing amounts of CNF content. The research group performed strength tests on the drawn silk fibers which were found to be about 2.0 times stronger than the silk from non-CNF fed silkworms.

An illustration showing the sustainable cycle of CNF synthesized silk production based on the current study. 

Credit: ©Tohoku University


 "Our findings demonstrate an environmentally friendly way to produce sustainable biomaterials by simply using the CNF as bait," said Narita.







Contacts and sources:
Fumio Narita (Profile)
Graduate School of Environmental Studies, Tohoku University


Publication: Nanocellulose Reinforced Silkworm Silk Fibers for Application to Biodegradable Polymers
Authors: C. Wu, S. Egawa, T. Kanno, H. Kurita, Z. Wang, E. Iida and F. Narita
Journal: Materials & Design
DOI: 10.1016/j.matdes.2021.109537
 




Wednesday, February 24, 2021

Viruses Most Numerous Biological Entities on Planet and Your Gut Is Home to 140,000 Different Virus Species

Viruses are the most numerous biological entities on the planet. Now researchers at the Wellcome Sanger Institute and EMBL’s European Bioinformatics Institute (EMBL-EBI) have identified over 140,000 viral species living in the human gut, more than half of which have never been seen before.

The results form the basis of the highly-curated Gut Phage Database (GPD) which will be an invaluable resource for those studying bacteriophages and the role they play on regulating the health of both our gut bacteria and ourselves

Credit: Wellcome Sanger Institute

The paper, published today (18 February 2021) in Cell, contains an analysis of over 28,000 gut microbiome samples collected in different parts of the world. The number and diversity of the viruses the researchers found was surprisingly high, and the data opens up new research avenues for understanding how viruses living in the gut affect human health.

The human gut is an incredibly biodiverse environment. In addition to bacteria, hundreds of thousands of viruses called bacteriophages, which can infect bacteria, also live in the human gut.

It is known that imbalances in our gut microbiome can contribute to diseases and complex conditions such as Inflammatory Bowel Disease, allergies and obesity. But relatively little is known about the role our gut bacteria, and the bacteriophages that infect them, play in human health and disease.

Using a DNA-sequencing method called metagenomics*, researchers at the Wellcome Sanger Institute and EMBL’s European Bioinformatics Institute (EMBL-EBI) explored and catalogued the biodiversity of the viral species found in 28,060 public human gut metagenomes and 2,898 bacterial isolate genomes cultured from the human gut.

The analysis identified over 140,000 viral species living in the human gut, more than half of which have never been seen before.

“It’s important to remember that not all viruses are harmful, but represent an integral component of the gut ecosystem. For one thing, most of the viruses we found have DNA as their genetic material, which is different from the pathogens most people know, such as SARS-CoV-2 or Zika, which are RNA viruses. Secondly, these samples came mainly from healthy individuals who didn’t share any specific diseases. It’s fascinating to see how many unknown species live in our gut, and to try and unravel the link between them and human health.” said Dr Alexandre Almeida,Postdoctoral Fellow at EMBL-EBI and the Wellcome Sanger Institute

Among the tens of thousands of viruses discovered, a new highly prevalent clade – or group of viruses believed to have a common ancestor – was identified, which the authors refer to as the Gubaphage. This was found to be the second most prevalent virus clade in the human gut, after the crAssphage, which was discovered in 2014.

Both of these viruses seem to infect similar types of human gut bacteria, but without further research it’s very difficult to know the exact functions of the newly discovered Gubaphage.


“An important aspect of our work was to ensure that the reconstructed viral genomes were of the highest quality. A stringent quality control pipeline coupled with a machine learning approach enabled us to mitigate contamination and obtain highly complete viral genomes. High-quality viral genomes pave the way to better understand what role viruses play in our gut microbiome, including the discovery of new treatments such as antimicrobials from bacteriophage origin.” said  Dr Luis F. Camarillo-Guerrero, first author of the study from the Wellcome Sanger Institute

The results of the study form the basis of the Gut Phage Database (GPD), a highly curated database containing 142,809 non-redundant phage genomes that will be an invaluable resource for those studying bacteriophages and the role they play on regulating the health of both our gut bacteria and ourselves.

“Bacteriophage research is currently experiencing a renaissance. This high-quality, large-scale catalogue of human gut viruses comes at the right time to serve as a blueprint to guide ecological and evolutionary analysis in future virome studies.” said Dr Trevor Lawley, senior author of the study from the Wellcome Sanger Institute.


Contacts and sources:
Wellcome Trust Sanger Institute


Publication: Massive expansion of human gut bacteriophage diversity.
Luis F. Camarillo-Guerrero, Alexandre Almeida, Guillermo Rangel-Pineros, Robert D. Finn, Trevor D. Lawley.Cell, 2021; 184 (4): 1098 DOI: 10.1016/j.cell.2021.01.029






COVID-19 Data Suggests that the Disease Deteriorates Men’s Testosterone Levels.





COVID-19 infection may deplete testosterone, helping to explain male patients’ poorer prognosis – new study shows


Over half of male patients studied were found to have lower than their normal testosterone levels

For the first time, data from a study with patients hospitalized due to COVID-19 suggest that the disease might deteriorate men’s testosterone levels.

Publishing their results in the peer-reviewed journal The Aging Male, experts from the University of Mersin and the Mersin City Education And Research Hospital in Turkey found as men’s testosterone level at baseline decreases, the probability for them to be in the intensive care unit (ICU) significantly increases.





Lead author Selahittin Çayan, Professor of Urology, states that while it has already been reported that low testosterone levels could be a cause for poor prognosis following a positive SARS-CoV-2 test, this is the first study to show that COVID-19 itself depletes testosterone.

It is hoped that the development could help to explain why so many studies have found that male prognosis is worse than those females with COVID-19, and therefore to discover possible improvement in clinical outcomes using testosterone-based treatments.

“Testosterone is associated with the immune system of respiratory organs, and low levels of testosterone might increase the risk of respiratory infections. Low testosterone is also associated with infection-related hospitalisation and all-cause mortality in male in ICU patients, so testosterone treatment may also have benefits beyond improving outcomes for COVID-19,” Professor Çayan explains.

“In our study, the mean total testosterone decreased, as the severity of the COVID-19 increased. The mean total testosterone level was significantly lower in the ICU group than in the asymptomatic group. In addition, the mean total testosterone level was significantly lower in the ICU group than in the Intermediate Care Unit group. The mean serum follicle stimulating hormone level was significantly higher in the ICU group than in the asymptomatic group.

“We found, Hypogonadism – a condition in which the body doesn’t produce enough testosterone –in 113 (51.1%) of the male patients.

“The patients who died, had significantly lower mean total testosterone than the patients who were alive.

“However, even 65.2% of the 46 male patients who were asymptomatic had a loss of loss of libido.”

The research team looked at a total of 438 patients. This included 232 males, each with laboratory confirmed SARS-CoV-2. All data were prospectively collected. A detailed clinical history, complete physical examination, laboratory and radiological imaging studies were performed in every patient. All data of the patients were checked and reviewed by the two physicians.

The cohort study was divided into three groups: asymptomatic patients (n: 46), symptomatic patients who were hospitalized in the internal medicine unit (IMU) (n: 129), and patients who were hospitalized in the intensive care unit (ICU) (n: 46).

In the patients who had pre-COVID-19 serum gonadal hormones test (n: 24), serum total testosterone level significantly decreased from pre-COVID-19 level of 458 ± 198 ng/dl to 315 ± 120 ng/dl at the time of COVID-19 in the patients (p = 0.003).

Death was observed in 11 of the male adult patients (4.97%) and 7 of the female patients (3.55%), revealing no significance between the two genders (p > 0.05).

Commenting on the results of the study, Professor Çayan added: “It could be recommended that at the time of COVID-19 diagnosis, testosterone levels are also tested. In men with low levels of sex hormones who test positive for COVID-19, testosterone treatment could improve their prognosis. More research is needed on this.”

The limitations of this study include it not including a control group of patients with conditions other than COVID-19, this was due to the restrictions placed on the hospital that they were monitoring the patients in.

The authors state future studies should look at the concentration levels of ACE2 (Angiotensin-converting enzyme 2) – an enzyme attached to the cell membranes of cells located in the intestines –, in relationship with the total testosterone levels.


FURTHER INFORMATION

For more information, please contact:
Simon Wesson,

Contacts and sources:
Taylor & Francis Group




Publication: Effect of serum total testosterone and its relationship with other laboratory parameters on the prognosis of coronavirus disease 2019 (COVID-19) in SARS-CoV-2 infected male patients: a cohort study
Selahittin Çayan, Mustafa Uğuz, Barış Saylam, Erdem Akbay. . The Aging Male, 2020; 1 DOI: 10.1080/13685538.2020.1807930



Toward a Disease-Sniffing Device to Rival a Dog’s Nose

Trained dogs can detect cancer and other diseases by smell. A miniaturized detector can analyze trace molecules to mimic the process.

Caption:
Andreas Mershin visits with one of the trained disease-sniffing dogs in his office at MIT. The dogs are trained and handled in the UK by the organization Medical Detection Dogs.

Credits: Photo: Medical Diagnostic Dogs

Numerous studies have shown that trained dogs can detect many kinds of disease — including lung, breast, ovarian, bladder, and prostate cancers, and possibly Covid-19 — simply through smell. In some cases, involving prostate cancer for example, the dogs had a 99 percent success rate in detecting the disease by sniffing patients’ urine samples.

But it takes time to train such dogs, and their availability and time is limited. Scientists have been hunting for ways of automating the amazing olfactory capabilities of the canine nose and brain, in a compact device. Now, a team of researchers at MIT and other institutions has come up with a system that can detect the chemical and microbial content of an air sample with even greater sensitivity than a dog’s nose. They coupled this to a machine-learning process that can identify the distinctive characteristics of the disease-bearing samples.

The findings, which the researchers say could someday lead to an automated odor-detection system small enough to be incorporated into a cellphone, are being published today in the journal PLOS One, in a paper by Claire Guest of Medical Detection Dogs in the U.K., Research Scientist Andreas Mershin of MIT, and 18 others at Johns Hopkins University, the Prostate Cancer Foundation, and several other universities and organizations.

“Dogs, for now 15 years or so, have been shown to be the earliest, most accurate disease detectors for anything that we’ve ever tried,” Mershin says. And their performance in controlled tests has in some cases exceeded that of the best current lab tests, he says. “So far, many different types of cancer have been detected earlier by dogs than any other technology.”

What’s more, the dogs apparently pick up connections that have so far eluded human researchers: When trained to respond to samples from patients with one type of cancer, some dogs have then identified several other types of cancer — even though the similarities between the samples weren’t evident to humans.

These dogs can identify “cancers that don’t have any identical biomolecular signatures in common, nothing in the odorants,” Mershin says. Using powerful analytical tools including gas chromatography mass spectrometry (GCMS) and microbial profiling, “if you analyze the samples from, let’s say, skin cancer and bladder cancer and breast cancer and lung cancer — all things that the dog has been shown to be able to detect — they have nothing in common.” Yet the dog can somehow generalize from one kind of cancer to be able to identify the others.

Mershin and the team over the last few years have developed, and continued to improve on, a miniaturized detector system that incorporates mammalian olfactory receptors stabilized to act as sensors, whose data streams can be handled in real-time by a typical smartphone’s capabilities. He envisions a day when every phone will have a scent detector built in, just as cameras are now ubiquitous in phones. Such detectors, equipped with advanced algorithms developed through machine learning, could potentially pick up early signs of disease far sooner than typical screening regimes, he says — and could even warn of smoke or a gas leak as well.

In the latest tests, the team tested 50 samples of urine from confirmed cases of prostate cancer and controls known to be free of the disease, using both dogs trained and handled by Medical Detection Dogs in the U.K. and the miniaturized detection system. They then applied a machine-learning program to tease out any similarities and differences between the samples that could help the sensor-based system to identify the disease. In testing the same samples, the artificial system was able to match the success rates of the dogs, with both methods scoring more than 70 percent.

The miniaturized detection system, Mershin says, is actually 200 times more sensitive than a dog’s nose in terms of being able to detect and identify tiny traces of different molecules, as confirmed through controlled tests mandated by DARPA. But in terms of interpreting those molecules, “it’s 100 percent dumber.” That’s where the machine learning comes in, to try to find the elusive patterns that dogs can infer from the scent, but humans haven’t been able to grasp from a chemical analysis.

“The dogs don’t know any chemistry,” Mershin says. “They don’t see a list of molecules appear in their head. When you smell a cup of coffee, you don’t see a list of names and concentrations, you feel an integrated sensation. That sensation of scent character is what the dogs can mine.”

While the physical apparatus for detecting and analyzing the molecules in air has been under development for several years, with much of the focus on reducing its size, until now the analysis was lacking. “We knew that the sensors are already better than what the dogs can do in terms of the limit of detection, but what we haven’t shown before is that we can train an artificial intelligence to mimic the dogs,” he says. “And now we’ve shown that we can do this. We’ve shown that what the dog does can be replicated to a certain extent.”

This achievement, the researchers say, provides a solid framework for further research to develop the technology to a level suitable for clinical use. Mershin hopes to be able to test a far larger set of samples, perhaps 5,000, to pinpoint in greater detail the significant indicators of disease. But such testing doesn’t come cheap: It costs about $1,000 per sample for clinically tested and certified samples of disease-carrying and disease-free urine to be collected, documented, shipped, and analyzed he says.

Reflecting on how he became involved in this research, Mershin recalled a study of bladder cancer detection, in which a dog kept misidentifying one member of the control group as being positive for the disease, even though he had been specifically selected based on hospital tests as being disease free. The patient, who knew about the dog’s test, opted to have further tests, and a few months later was found to have the disease at a very early stage. “Even though it’s just one case, I have to admit that did sway me,” Mershin says.

The team included researchers at MIT, Johns Hopkins University in Maryland, Medical Detection Dogs in Milton Keynes, U.K., the Cambridge Polymer Group, the Prostate Cancer Foundation, the University of Texas at El Paso, Imagination Engines, and Harvard University. The research was supported by the Prostate Cancer Foundation, the National Cancer Institute, and the National Institutes of Health.


Contacts and sources:
David L. Chandler
Massachusetts Institute of Technology


Publication: Feasibility of integrating canine olfaction with chemical and microbial profiling of urine to detect lethal prostate cancer.
Claire Guest, Rob Harris, Karen S. Sfanos, Eva Shrestha, Alan W. Partin, Bruce Trock, Leslie Mangold, Rebecca Bader, Adam Kozak, Scott Mclean, Jonathan Simons, Howard Soule, Thomas Johnson, Wen-Yee Lee, Qin Gao, Sophie Aziz, Patritsia Maria Stathatou, Stephen Thaler, Simmie Foster, Andreas Mershin. PLOS ONE, 2021; 16 (2): e0245530 DOI: 10.1371/journal.pone.0245530





Reclusive Neutron Star Thought Found among Debris of Famous Supernova

Astronomers now have evidence from two X-ray telescopes (Chandra and NuSTAR) for a key component of a famous supernova remnant.

Supernova 1987A was discovered on Earth on February 24, 1987, making it the first such event witnessed during the telescopic age.

For decades, scientists have searched for a neutron star in SN 1987A, i.e. a dense collapsed core that should have been left behind by the explosion.

This latest study shows that a "pulsar wind nebula" created by such a neutron star may be present.

Credit: NASA's Chandra X-ray Observatory

Astronomers have recently found evidence for the existence of a neutron star at the center of Supernova 1987A (SN 1987A), which scientists have been seeking for over three decades. As reported in our latest press release, SN 1987A was discovered on February 24, 1987. The panel on the left contains a 3D computer simulation, based on Chandra data, of the supernova debris from SN 1987A crashing into a surrounding ring of material. The artist's illustration (right panel) depicts a so-called pulsar wind nebula, a web of particles and energy blown away from a pulsar, which is a rotating, highly magnetized neutron star. Data collected from NASA's Chandra X-ray Observatory and NuSTAR in a new study support the presence of a pulsar wind nebula at the center of the ring.

If this result is upheld by future observations, it would confirm the existence of a neutron star in SN 1987A, the collapsed core that astronomers expect would be present after the star exploded. The pulsar would also be the youngest one ever found.


NuSTAR and Chandra images of Supernova 1987A

When a star explodes, it collapses onto itself before the outer layers are blasted into space. The compression of the core turns it into an extraordinarily dense object, with the mass of the Sun squeezed into an object only about 10 miles across. Neutron stars, as they were dubbed because they are made nearly exclusively of densely packed neutrons, are laboratories of extreme physics that cannot be duplicated here on Earth. Some neutron stars have strong magnetic fields and rotate rapidly, producing a beam of light akin to a lighthouse. Astronomers call these objects "pulsars," and they sometimes blow winds of charged particles that can create pulsar wind nebulas.

With Chandra and NuSTAR, the team found relatively low-energy X-rays from the supernova debris crashing into surrounding material. The team also found evidence of high-energy particles, using NuSTAR's ability to detect higher-energy X-rays.

There are two likely explanations for this energetic X-ray emission: either a pulsar wind nebula, or particles being accelerated to high energies by blast wave of the explosion. The latter effect doesn't require the presence of a pulsar and occurs over much larger distances from the center of the explosion.

The latest X-ray study supports the case for the pulsar wind nebula on a couple of fronts. First, the brightness of the higher energy X-rays remained about the same between 2012 and 2014, while the radio emission increased. This goes against expectations in the scenario of energetic particles in the explosion debris. Next, authors estimate it would take almost 400 years to accelerate the electrons up to the highest energies seen in the NuSTAR data, which is over ten times older than the age of the remnant.

The Chandra and NuSTAR data also support a 2020 result from the Atacama Large Millimeter Array (ALMA) that provided possible evidence for the structure of a pulsar wind nebula in the radio band. While this "blob" had other potential explanations, its identification as a pulsar wind nebula could be substantiated with the new X-ray data.

The center of SN 1987A is surrounded by gas and dust. The authors used state-of-the-art simulations to understand how this material would absorb X-rays at different energies, enabling more accurate interpretation of the X-ray spectrum, that is, the spread of X-rays over wavelength. This enables them to estimate what the spectrum of the central regions of SN 1987A is without the obscuring material.

A paper describing these results is being published this week in The Astrophysical Journal and a preprint is available online. The authors of the paper are Emanuele Greco and Marco Miceli (University of Palermo in Italy), Salvatore Orlando, Barbara Olmi and Fabrizio Bocchino (Palermo Astronomical Observatory, a National Institute for Astrophysics, or INAF, research facility); Shigehiro Nagataki and Masaomi Ono (Astrophysical Big Bang Laboratory, RIKEN in Japan); Akira Dohi (Kyushu University in Japan), and Giovanni Peres (University of Palermo).

NASA's Marshall Space Flight Center manages the Chandra program. The Smithsonian Astrophysical Observatory's Chandra X-ray Center controls science from Cambridge Massachusetts and flight operations from Burlington, Massachusetts.

NuSTAR is a Small Explorer mission led by Caltech and managed by NASA's Jet Propulsion Laboratory for the agency's Science Mission Directorate in Washington. NuSTAR was developed in partnership with the Danish Technical University and the Italian Space Agency (ASI). The spacecraft was built by Orbital Sciences Corporation in Dulles, Virginia (now part of Northrop Grumman). NuSTAR's mission operations center is at UC Berkeley, and the official data archive is at NASA's High Energy Astrophysics Science Archive Research Center. ASI provides the mission's ground station and a mirror archive. JPL is a division of Caltech.
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Credit Chandra (X-ray): NASA/CXC/Univ. di Palermo/E. Greco; Illustration: INAF-Osservatorio Astronomico di Palermo/Salvatore Orlando


 




Contacts and sources:
Megan Watzke
NASA's Chandra X-ray Observatory


Publication: 




Tuesday, February 23, 2021

First Flight of an Aircraft on Another World.

This high-resolution still image is part of a video taken by several cameras as NASA’s Perseverance rover touched down on Mars on Feb. 18, 2021. A camera aboard the descent stage captured this shot. A key objective for Perseverance’s mission on Mars is astrobiology, including the search for signs of ancient microbial life. The rover will characterize the planet’s geology and past climate, pave the way for human exploration of the Red Planet, and be the first mission to collect and cache Martian rock and regolith (broken rock and dust). Subsequent NASA missions, in cooperation with ESA (the European Space Agency), would send spacecraft to Mars to collect these cached samples from the surface and return them to Earth for in-depth analysis. The Mars 2020 mission is part of a larger program that includes missions to the Moon as a way to prepare for human exploration of the Red Planet. JPL, which is managed for NASA by Caltech in Pasadena, California, built and manages operations of the Perseverance and Curiosity rovers.
Credits: NASA/JPL-Caltech

New video from NASA’s Mars 2020 Perseverance rover chronicles major milestones during the final minutes of its entry, descent, and landing (EDL) on the Red Planet on Feb. 18 as the spacecraft plummeted, parachuted, and rocketed toward the surface of Mars. A microphone on the rover also has provided the first audio recording of sounds from Mars.

From the moment of parachute inflation, the camera system covers the entirety of the descent process, showing some of the rover’s intense ride to Mars’ Jezero Crater. The footage from high-definition cameras aboard the spacecraft starts 7 miles (11 kilometers) above the surface, showing the supersonic deployment of the most massive parachute ever sent to another world, and ends with the rover’s touchdown in the crater.
Credit: NASA

A microphone attached to the rover did not collect usable data during the descent, but the commercial off-the-shelf device survived the highly dynamic descent to the surface and obtained sounds from Jezero Crater on Feb. 20. About 10 seconds into the 60-second recording, a Martian breeze is audible for a few seconds, as are mechanical sounds of the rover operating on the surface.

"For those who wonder how you land on Mars – or why it is so difficult – or how cool it would be to do so – you need look no further,” said acting NASA Administrator Steve Jurczyk. “Perseverance is just getting started, and already has provided some of the most iconic visuals in space exploration history. It reinforces the remarkable level of engineering and precision that is required to build and fly a vehicle to the Red Planet.”

NASA's Mars 2020 Perseverance mission captured thrilling footage of its rover landing in Mars' Jezero Crater on Feb. 18, 2021. The real footage in this video was captured by several cameras that are part of the rover's entry, descent, and landing suite. The views include a camera looking down from the spacecraft's descent stage (a kind of rocket-powered jet pack that helps fly the rover to its landing site), a camera on the rover looking up at the descent stage, a camera on the top of the aeroshell (a capsule protecting the rover) looking up at that parachute, and a camera on the bottom of the rover looking down at the Martian surface. The audio embedded in the video comes from the mission control call-outs during entry, descent, and landing.
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Credits: NASA/JPL-Caltech

Also released Monday was the mission’s first panorama of the rover’s landing location, taken by the two Navigation Cameras located on its mast. The six-wheeled robotic astrobiologist, the fifth rover the agency has landed on Mars, currently is undergoing an extensive checkout of all its systems and instruments.

“This video of Perseverance’s descent is the closest you can get to landing on Mars without putting on a pressure suit,” said Thomas Zurbuchen, NASA associate administrator for science. “It should become mandatory viewing for young women and men who not only want to explore other worlds and build the spacecraft that will take them there, but also want to be part of the diverse teams achieving all the audacious goals in our future.”

The world’s most intimate view of a Mars landing begins about 230 seconds after the spacecraft entered the Red Planet’s upper atmosphere at 12,500 mph (20,100 kph). The video opens in black, with the camera lens still covered within the parachute compartment. Within less than a second, the spacecraft’s parachute deploys and transforms from a compressed 18-by-26 inch (46-by-66 centimeter) cylinder of nylon, Technora, and Kevlar into a fully inflated 70.5-foot-wide (21.5-meter-wide) canopy – the largest ever sent to Mars. The tens of thousands of pounds of force that the parachute generates in such a short period stresses both the parachute and the vehicle.

“Now we finally have a front-row view to what we call ‘the seven minutes of terror’ while landing on Mars,” said Michael Watkins, director of NASA’s Jet Propulsion Laboratory in Southern California, which manages the mission for the agency. “From the explosive opening of the parachute to the landing rockets’ plume sending dust and debris flying at touchdown, it’s absolutely awe-inspiring.”

The video also captures the heat shield dropping away after protecting Perseverance from scorching temperatures during its entry into the Martian atmosphere. The downward view from the rover sways gently like a pendulum as the descent stage, with Perseverance attached, hangs from the back shell and parachute. The Martian landscape quickly pitches as the descent stage – the rover’s free-flying “jetpack,” which decelerates using rocket engines and then lowers the rover on cables to the surface – breaks free, its eight thrusters engaging to put distance between it and the now-discarded back shell and the parachute.

Then, 80 seconds and 7,000 feet (2,130 meters) later, the cameras capture the descent stage performing the sky crane maneuver over the landing site – the plume of its rocket engines kicking up dust and small rocks that have likely been in place for billions of years.

“We put the EDL camera system onto the spacecraft not only for the opportunity to gain a better understanding of our spacecraft’s performance during entry, descent, and landing, but also because we wanted to take the public along for the ride of a lifetime – landing on the surface of Mars,” said Dave Gruel, lead engineer for Mars 2020 Perseverance’s EDL camera and microphone subsystem at JPL. “We know the public is fascinated with Mars exploration, so we added the EDL Cam microphone to the vehicle because we hoped it could enhance the experience, especially for visually-impaired space fans, and engage and inspire people around the world.”

The footage ends with Perseverance’s aluminum wheels making contact with the surface at 1.61 mph (2.6 kph), and then pyrotechnically fired blades sever the cables connecting it to the still-hovering descent stage. The descent stage then climbs and accelerates away in the preplanned flyaway maneuver.

“If this were an old Western movie, I’d say the descent stage was our hero riding slowly into the setting Sun, but the heroes are actually back here on Earth,” said Matt Wallace, Mars 2020 Perseverance deputy project manager at JPL. “I’ve been waiting 25 years for the opportunity to see a spacecraft land on Mars. It was worth the wait. Being able to share this with the world is a great moment for our team.”

Five commercial off-the-shelf cameras located on three different spacecraft components collected the imagery. Two cameras on the back shell, which encapsulated the rover on its journey, took pictures of the parachute inflating. A camera on the descent stage provided a downward view – including the top of the rover – while two on the rover chassis offered both upward and downward perspectives.

The rover team continues its initial inspection of Perseverance’s systems and its immediate surroundings. Monday, the team will check out five of the rover’s seven instruments and take the first weather observations with the Mars Environmental Dynamics Analyzer instrument. In the coming days, a 360-degree panorama of Jezero by the Mastcam-Z should be transmitted down, providing the highest resolution look at the road ahead.

More About the Mission

A key objective of Perseverance's mission on Mars is astrobiology, including the search for signs of ancient microbial life. The rover will characterize the planet’s geology and past climate, pave the way for human exploration of the Red Planet, and be the first mission to collect and cache Martian rock and regolith.

Subsequent NASA missions, in cooperation with ESA (European Space Agency), would send spacecraft to Mars to collect these sealed samples from the surface and return them to Earth for in-depth analysis.

The Mars 2020 Perseverance mission is part of NASA’s Moon to Mars exploration approach, which includes Artemis missions to the Moon that will help prepare for human exploration of the Red Planet.

JPL, which is managed for NASA by Caltech in Pasadena, California, built and manages operations of the Perseverance rover.



The technology demonstration has phoned home from where it is attached to the belly of NASA’s Perseverance rover.



Mission controllers at NASA’s Jet Propulsion Laboratory in Southern California have received the first status report from the Ingenuity Mars Helicopter, which landed Feb. 18, 2021, at Jezero Crater attached to the belly of the agency’s Mars 2020 Perseverance rover. The downlink, which arrived at 3:30 p.m. PST (6:30 p.m. EST) via a connection through the Mars Reconnaissance Orbiter, indicates that both the helicopter, which will remain attached to the rover for 30 to 60 days, and its base station (an electrical box on the rover that stores and routes communications between the rotorcraft and Earth) are operating as expected.



“There are two big-ticket items we are looking for in the data: the state of charge of Ingenuity’s batteries as well as confirmation the base station is operating as designed, commanding heaters to turn off and on to keep the helicopter’s electronics within an expected range,” said Tim Canham, Ingenuity Mars Helicopter operations lead at JPL. “Both appear to be working great. With this positive report, we will move forward with tomorrow’s charge of the helicopter’s batteries.”



Ensuring that Ingenuity has plenty of stored energy aboard to maintain heating and other vital functions while also maintaining optimal battery health is essential to the success of the Mars Helicopter. The one-hour power-up will boost the rotorcraft’s batteries to about 30% of its total capacity. A few days after that, they’ll be charged again to reach 35%, with future charging sessions planned weekly while the helicopter is attached to the rover. The data downlinked during tomorrow’s charge sessions will be compared to battery-charging sessions done during cruise to Mars to help the team plan future charging sessions.

In this illustration, NASA's Ingenuity Mars Helicopter stands on the Red Planet's surface as NASA's Perseverance rover (partially visible on the left) rolls away.
Credits: NASA/JPL-Caltech

Like much of the 4-pound (2-kilogram) rotorcraft, the six lithium-ion batteries are off-the-shelf. They currently receive recharges from the rover’s power supply. Once Ingenuity is deployed to Mars’ surface, the helicopter’s batteries will be charged solely by its own solar panel.

After Perseverance deploys Ingenuity to the surface, the helicopter will then have a 30-Martian-day (31-Earth-day) experimental flight test window. If Ingenuity survives its first bone-chilling Martian nights – where temperatures dip as low as minus 130 degrees Fahrenheit (minus 90 degrees Celsius) – the team will proceed with the first flight of an aircraft on another world.

If Ingenuity succeeds in taking off and hovering during its first flight, over 90% of the project’s goals will have been achieved. If the rotorcraft lands successfully and remains operable, up to four more flights could be attempted, each one building on the success of the last.

“We are in uncharted territory, but this team is used to that,” said MiMi Aung, project manager for the Ingenuity Mars Helicopter at JPL. “Just about every milestone from here through the end of our flight demonstration program will be a first, and each has to succeed for us to go on to the next. We’ll enjoy this good news for the moment, but then we have to get back to work.”

Next-generation rotorcraft, the descendants of Ingenuity, could add an aerial dimension to future exploration of the Red Planet. These advanced robotic flying vehicles would offer a unique viewpoint not provided by current orbiters high overhead or by rovers and landers on the ground, providing high-definition images and reconnaissance for robots or humans, and enable access to terrain that is difficult for rovers to reach.

More About Ingenuity

The Ingenuity Mars Helicopter was built by NASA’s Jet Propulsion Laboratory in Southern California which also manages the technology demonstration for NASA Headquarters in Washington. NASA’s Ames and Langley Research Centers provided significant flight performance analysis and technical assistance. AeroVironment Inc., Qualcomm, Snapdragon, and SolAero also provided design assistance and major vehicle components. The Mars Helicopter Delivery System was designed and manufactured by Lockheed Space Systems in Denver.



Contacts and sources:
DC Agle
Jet Propulsion Laboratory, Pasadena, Calif.

Alana Johnson / Grey Hautaluoma
NASA Headquarters, Washington