. Scientific Frontline

Sunday, September 5, 2021

Coronavirus Epidemics first hit more than 21,000 years ago


Sarbecoviruses have crossed into humans twice in the last decade, leading to the deadly SARS-CoV-1 outbreak in 2002-04 and the current COVID-19 pandemic, caused by the SARS-CoV-2 virus.  A new Oxford University Study, published today, shows that the most recent common ancestor of these viruses existed more than 21,000 years ago, nearly 30 times older than previous estimates.

‘Finding the evolutionary origins of pandemic viral infections such as COVID-19 help us understand how long humanity may have been exposed to these viruses, how frequently they might have caused disease outbreaks in the past, and how likely they might be to cause novel outbreaks in future.’ Said Prof Katzourakis, who led the work.

Despite having a very rapid rate of evolution over short timescales, to survive, viruses must remain highly adapted to their hosts - this imposes severe restrictions on their freedom to accumulate mutations without reducing their fitness. This causes the apparent rate of evolution of viruses to slow down over time. The new research, for the first time, successfully recreates the patterns of this observed rate decay in viruses. 

‘We developed a new method that can recover the age of viruses over longer timescales and correct for a kind of ‘evolutionary relativity’, where the apparent rate of evolution depends on the timescale of measurement. Our estimate based on viral sequence data, of more than 21,000 years ago, is in remarkable concordance with a recent analysis on human genomic dataset that suggests infection with an ancient coronavirus around the same time.’ Said Mahan Ghafari, from Oxford University.

The study also demonstrates that while existing evolutionary models have often failed to measure the divergence between virus species over periods - from a few hundred to a few thousands of years - the evolutionary framework developed in this study will enable the reliable estimation of virus divergence across vast timescales, potentially over the entire course of animal and plant evolution. 

The new model enables us to not only reconstruct the evolutionary history of viruses related to SARS-CoV-2, but also a much wider range of RNA and DNA viruses during more remote periods in the past. 

The model predictions for hepatitis C virus - a leading global cause of liver disease - are consistent with the idea that it has circulated for nearly a half a million years. HCV may thus have spread worldwide as an intrinsic part of the “Out-of-Africa” migration of modern humans around 150,000 years ago. 

The different genotypes of HCV indigenous to human populations in South and South-East Asia and Central Africa may have originated over this prolonged period and this revised timescale may resolve the longstanding riddle of their global distributions. 

‘With this new technique we can look much more widely at other viruses; re-evaluate the timescales of their deeper evolution and gain insights into host relationships that are key to understanding their ability to cause disease.’ Prof Simmonds, Oxford University

Source / Credit: University of Oxford


Friday, September 3, 2021

Birds and mammals evolve faster if their home is rising


Wild Kea, New Zealand  Credit: Pablo Heimplatz
Researchers at the University of Cambridge have combined reconstructions of the Earth’s changing surface elevations over the past three million years with data on climate change over this timeframe, and with bird and mammal species’ locations. Their results reveal how species evolved into new ones as land elevation changed - and disentangle the effects of elevation from the effects of climate.

The study found that the effect of elevation increase is greater than that of historical climate change, and of present-day elevation and temperature, in driving the formation of new species – ‘or speciation’.

In contrast to areas where land elevation is increasing, elevation loss was not found to be an important predictor of where speciation happens. Instead, present-day temperature is a better indicator of speciation in these areas.

The results are published in the journal Nature Ecology and Evolution.

“Often at the tops of mountains there are many more unique species that aren’t found elsewhere. Whereas previously the formation of new species was thought to be driven by climate, we’ve found that elevation change has a greater effect at a global scale,” said Dr Andrew Tanentzap in the University of Cambridge’s Department of Plant Sciences, senior author of the paper.

As land elevation increases, temperature generally decreases and habitat complexity increases. In some cases, for example where mountains form, increasing elevation creates a barrier that prevents species moving and mixing, so populations become reproductively isolated. This is the first step towards the formation of new species.

The effect of increasing elevation on that rate of new species formation over time was more pronounced for mammals than for birds; the researchers think this is because birds can fly across barriers to find mates in other areas. Birds were affected more by present-day temperatures; in birds, variation in temperature creates differences in the timing and extent of mating, risking reproductive isolation from populations of the same species elsewhere.

Until now, most large-scale studies into the importance of topography in generating new species have only considered present-day land elevation, or elevation changes in specific mountain ranges.

“It’s surprising just how much effect historical elevation change had on generating the world’s biodiversity – it has been much more important than traditionally studied variables like temperature. The rate at which species evolved in different places on Earth is tightly linked to topography changes over millions of years,” said Dr Javier Igea in the University of Cambridge’s Department of Plant Sciences, first author of the paper.

He added: “This work highlights important arenas for evolution to play out. From a conservation perspective these are the places we might want to protect, especially given climate change. Although climate change is happening over decades, not millions of years, our study points to areas that can harbor species with greater potential to evolve.”

The researchers say that as the Earth’s surface continues to rise and fall, topography will remain an important driver of evolutionary change.

This research was funded by Wellcome, the Gatsby Charitable Foundation and the Isaac Newton Trust.

Source/Credit: University of Cambridge


Warming Atlantic forces whales into new habitats, danger


Source: Pexels
Warming oceans have driven the critically endangered North Atlantic right whale population from its traditional and protected habitat, exposing the animals to more lethal ship strikes, disastrous commercial fishing entanglements and greatly reduced calving rates.

Without improving its management, the right whale populations will decline and potentially become extinct in the coming decades, according to a Cornell- and University of South Carolina-led report in the Sept. 1 journal Oceanography.

“Most of the warming in the Gulf of Maine is not coming from the atmosphere or ocean surface, as one may think,” said senior author Charles Greene, professor emeritus in the Department of Earth and Atmospheric Sciences in the College of Agriculture and Life Sciences. “It is coming from invading slope water many hundreds of feet below the ocean surface, forcing the right whales to abandon their traditional habitat.”

Since 2010, the calving rate has declined and the right whale population has dropped by an estimated 26%, according to the paper. At the beginning of the decade, the North Atlantic right whale population had numbered over 500. Now, the North Atlantic Right Whale Consortium estimates the population at just 356 whales.

The species is considered critically endangered by the International Union for Conservation of Nature Red List of Threatened Species.

Individual whales are not interchangeable; each right whale has its own name and personality, and scientists know them quite well. The whales have been given monikers including Tux, Popcorn, Arrow and Sundog. When scientists spot the right whales, they log the sighting into an international catalog for a perpetually updated census.

“Right whales are one of the best studied, best understood populations in the ocean,” said Greene., a faculty fellow at the Cornell Atkinson Center for Sustainability. “We basically know every individual. It’s very rare that you can study a population where you know everybody.”

And when the right whales have run-ins with humans, such as large ships or commercial fishing lines, scientists can easily identify their carcasses.

The warm slope water entering the Gulf of Maine at depth derives its heat from the Gulf Stream. As the tail end of the Atlantic Meridional Overturning Circulation, the Gulf Stream has changed its trajectory dramatically during the past ten years.

“Due to a warming climate, the Atlantic Meridional Overturning Circulation is slowing down, causing the Gulf Stream to move North, injecting warmer and saltier slope water into the Gulf of Maine,” Greene said.

The warming Gulf of Maine has reduced the abundance of copepods, the tiny crustaceans that serve as the right whales’ favorite snack. This has reduced right whale calving rates and forced the whales to abandon their mid-summer feeding grounds in the Gulf of Maine. Instead, the whales have headed north to the cooler waters of the Gulf of St. Lawrence.

Since 2015, scientists have witnessed an increased number of right whales feeding in the Gulf of St. Lawrence, where there were no protections in place to prevent ship strikes and fishing gear entanglement. This has led to an Unusual Mortality Event declared by NOAA in 2017, when 17 right whale deaths were confirmed, mostly in the Gulf of St. Lawrence. Ten right whales were found dead in 2019, while for 2020 and 2021, four deaths have occurred thus far.

“Right whales continue to die each year,” said lead author Erin Meyer-Gutbrod, Ph.D. ’16, assistant professor at the University of South Carolina. “Protective policies must be strengthened immediately before this species declines past the point of no-return.”

Ocean scientists are hoping for new policies on rope-free fishing gear, vessel speed limit enforcement and money for monitoring and ecosystem forecasting.

“Right whale populations can shift quickly and unexpectedly in our changing climate,” Meyer-Gutbrod said. “There is no time to waste.”

In addition to Greene and Meyer-Gutbrod, co-authors on the research, “Ocean Regime Shift is Driving Collapse of the North Atlantic Right Whale Population,” are Kimberley T.A. Davies, assistant professor, University of New Brunswick, Canada; and David G. Johns, head of the Continuous Plankton Recorder Survey, Marine Biological Association of the United Kingdom, Plymouth, United Kingdom.

Funding for this research was provided by the Lenfest Ocean Program.

Source/Credit: Cornell University / Blaine Friedlander


Thursday, September 2, 2021

Discovery paves way for improved quantum devices


Schematic of a superconducting circuit [thin black lines] on a silicon chip [yellow base], being imaged using terahertz scanning near-field microscopy [red beam focused into yellow tip].

Physicists and engineers have found a way to identify and address imperfections in materials for one of the most promising technologies in commercial quantum computing.

The University of Queensland team was able to develop treatments and optimize fabrication protocols in common techniques for building superconducting circuits on silicon chips.

Dr Peter Jacobson, who co-led the research, said the team had identified that imperfections introduced during fabrication reduced the effectiveness of the circuits.

"Superconducting quantum circuits are attracting interest from industry giants such as Google and IBM, but widespread application is hindered by ‘decoherence’, a phenomenon which causes information to be lost,” he said.

“Decoherence is primarily due to interactions between the superconducting circuit and the silicon chip – a physics problem – and to material imperfections introduced during fabrication – an engineering problem.

“So we needed input from physicists and engineers to find a solution.”

 The team used a method called terahertz scanning near-field optical microscopy (THz SNOM) – an atomic force microscope combined with a THz light source and detector.

This provided a combination of high spatial resolution – seeing down to the size of viruses – and local spectroscopic measurements.

Professor Aleksandar Rakić said the technique enabled probing at the nanoscale rather than the macroscale by focusing light onto a metallic tip.  

“This provides new access for us to understand where imperfections are located so we can reduce decoherence and help reduce losses in superconducting quantum devices,” Professor Rakić said.

“We found that commonly used fabrication recipes unintentionally introduce imperfections into the silicon chips, which contribute to decoherence.

“And we also showed that surface treatments reduce these imperfections, which in turn reduces losses in the superconducting quantum circuits.”

Associate Professor Arkady Fedorov said this allowed the team to determine where in the process defects were introduced and optimize fabrication protocols to address them.

“Our method allows the same device to be probed multiple times, in contrast to other   methods that often require the devices to be cut up before being probed,” Dr Fedorov said.

“The team’s results provide a path towards improving superconducting devices for use in quantum computing applications.”

In future, THz SNOM could be used to define new ways to improve the operation of quantum devices and their integration into a viable quantum computer.

The results are published in Applied Physics Letters

News Release
Source/Credit: University of Queensland


A Black Hole Triggers a Premature Supernova


Dillon Dong, with a 27-meter radio dish at
Caltech's Owens Valley Radio Observatory in the background.
In 2017, a particularly luminous and unusual source of radio waves was discovered in data taken by the Very Large Array (VLA) Sky Survey, a project that scans the night sky in radio wavelengths. Now, led by Caltech graduate student Dillon Dong (MS '18), a team of astronomers has established that the bright radio flare was caused by a black hole or neutron star crashing into its companion star in a never-before-seen process.

"Massive stars usually explode as supernovae when they run out of nuclear fuel," says Gregg Hallinan, professor of astronomy at Caltech. "But in this case, an invading black hole or neutron star has prematurely triggered its companion star to explode." This is the first time a merger-triggered supernova has ever been confirmed.

Bright Flares in the Night Sky

Hallinan and his team look for so-called radio transients—short-lived sources of radio waves that flare
brightly and burn out quickly like a match lit in a dark room. Radio transients are an excellent way to identify unusual astronomical events, such as massive stars that explode and blast out energetic jets or the mergers of neutron stars.

As Dong sifted through the VLA's massive dataset, he singled out an extremely luminous source of radio waves from the VLA survey called VT 1210+4956. This source is tied for the brightest radio transient ever associated with a supernova.

Dong determined that the bright radio energy was originally a star surrounded by a thick and dense shell of gas. This gas shell had been cast off the star a few hundred years before the present day. VT 1210+4956, the radio transient, occurred when the star finally exploded in a supernova and the material ejected from the explosion interacted with the gas shell. Yet, the gas shell itself, and the timescale on which it was cast off from the star, were unusual, so Dong suspected that there might be more to the story of this explosion.

Two Unusual Events

Following Dong's discovery, Caltech graduate student Anna Ho (PhD '20) suggested that this radio transient be compared with a different catalog of brief bright events in the X-ray spectrum. Some of these X-ray events were so short-lived that they were only present in the sky for a few seconds of Earth time. By examining this other catalog, Dong discovered a source of X-rays that originated from the same spot in the sky as VT 1210+4956. Through careful analysis, Dong established that the X-rays and the radio waves were likely coming from the same event.

Gregg Hallinan

"The X-ray transient was an unusual event—it signaled that a relativistic jet was launched at the time of the explosion," says Dong. "And the luminous radio glow indicated that the material from that explosion later crashed into a massive torus of dense gas that had been ejected from the star centuries earlier. These two events have never been associated with each other, and on their own they're very rare."

A Mystery Solved

So, what happened? After careful modeling, the team determined the most likely explanation—an event that involved some of the same cosmic players that are known to generate gravitational waves.

They speculated that a leftover compact remnant of a star that had previously exploded—that is, a black hole or a neutron star—had been closely orbiting around a star. Over time, the black hole had begun siphoning away the atmosphere of its companion star and ejecting it into space, forming the torus of gas. This process dragged the two objects ever closer until the black hole plunged into the star, causing the star to collapse and explode as a supernova.

The X-rays were produced by a jet launched from the core of the star at the moment of its collapse. The radio waves, by contrast, were produced years later as the exploding star reached the torus of gas that had been ejected by the inspiraling compact object.

Astronomers know that a massive star and a companion compact object can form what is called a stable orbit, in which the two bodies gradually spiral closer and closer over an extremely long period of time. This process forms a binary system that is stable for millions to billions of years but that will eventually collide and emit the kind of gravitational waves that were discovered by LIGO in 2015 and 2017.

However, in the case of VT 1210+4956, the two objects instead collided immediately and catastrophically, producing the blasts of X-rays and radio waves observed. Although collisions such as this have been predicted theoretically, VT 1210+4956 provides the first concrete evidence that it happens.

Serendipitous Surveying

The VLA Sky Survey produces enormous amounts of data about radio signals from the night sky, but sifting through that data to discover a bright and interesting event such as VT 1210+4956 is like finding a needle in a haystack. Finding this particular needle, Dong says, was, in a way, serendipitous.

"We had ideas of what we might find in the VLA survey, but we were open to the possibility of finding things we didn't expect," explains Dong. "We created the conditions to discover something interesting by conducting loosely constrained, open-minded searches of large data sets and then taking into account all of the contextual clues we could assemble about the objects that we found. During this process you find yourself pulled in different directions by different explanations, and you simply let nature tell you what's out there."

The paper is titled "A transient radio source consistent with a merger-triggered core collapse supernova." Dillon Dong is the first author. In addition to Hallinan and Ho, additional co-authors are Ehud Nakar, Andrew Hughes, Kenta Hotokezaka, Steve Myers (PhD '90), Kishalay De (MS '18, PHD '21), Kunal Mooley (PhD '15), Vikram Ravi, Assaf Horesh, Mansi Kasliwal (MS '07, PhD '11), and Shri Kulkarni. Funding was provided by the National Science Foundation, the United States–Israel Binational Science Foundation, the I-Core Program of the Planning and Budgeting Committee and the Israel Science Foundation, Canada's Natural Sciences and Engineering Research Council, the Miller Institute for Basic Research in Science at the UC Berkeley, the Japan Society for the Promotion of Science Early-Career Scientists Program, the National Radio Astronomy Observatory, and the Heising-Simons Foundation.

A paper about the findings will appear in the journal Science on September 3.

Source/Credit: California Institute of Technology / Lori Dajose


Z Turns Twenty-five Years Old


An open-shutter photo showing electrical energy coursing through the
transmission line sections of Sandia National Laboratories’ Z machine.
(Photo by Randy Montoya)
Sandia National Laboratories is celebrating 25 years of research conducted at its Z Pulsed Power Facility — a gymnasium-sized accelerator commonly referred to as Z or the Z machine.

Z began with a simple idea — running large pulsed electrical currents through targets at the center of the machine — that has resulted in startling science even after 25 years.

“We have seen continuous innovation over the history of Z, and we still have about another decade of exciting research lined up,” says Dan Sinars, Sandia’s pulsed power sciences director.

The adventure began 25 years ago, said former director Don Cook, when Sandia researchers modified a machine built in 1985 called the Particle Beam Fusion Accelerator. That machine — Z’s ancestor, in a sense — employed a very high voltage and smaller current to make lithium-ion beams for fusion research. The experimental output was powerful, about 15 terawatts, but had hardly increased in a decade of testing.

So, trying a different approach, the machine was restructured to deliver very high currents and lower voltages. Currents 100 times larger than those in a bolt of lightning efficiently vaporized arrays of tiny wires into clouds of ions. Then the powerful magnetic field accompanying the electric current slammed the ions into each other, a process that emitted copious X-rays that could be used for fusion research and other applications.

The new method, attempted first on a smaller Sandia machine called Saturn, immediately increased the output to 40 terawatts, and led to many experiments to improve the number, size, material choice and placement of succeeding arrays.

“Once it was confirmed in experiments in 1996 on a machine temporarily called PBFA II-Z that enormous pressures (millions of atmospheres) and very high temperatures (millions of degrees Celsius) could be produced by z-pinches, we renamed the machine simply Z in 1996. So, 2021 is the 25th anniversary of Z,” said Cook.

Researchers around the world marveled at the huge output increase, which quickly reached more than 200 terawatts, said former Sandia vice president and early Z leader Gerry Yonas. The Z-pinch work — called Z because the operation occurs along the Z axis in three-dimensional graphs — generated data for the U.S. nuclear stockpile.

Z hasn’t yet created fusion ignition, though the effort to increase its fusion output continues. “Achieving nuclear fusion in the lab isn’t for people who give up easily,” said Sandia fellow Keith Matzen, Z director from 2005-2013 and again from 2015-2019, who cautions it will take a bigger version of Z to demonstrate that the fusion energy emitted by the process is equal to the electrical energy stored in the facility, a milestone known as break-even.

Meanwhile Z researchers have delved into other areas, including determining where life elsewhere in our galaxy may have evolved; investigating the existence of diamonds on Neptune and liquid helium on Saturn; determining the age of white dwarf stars and the behavior of black holes in space; and the amount of water in the universe and its age, said Sinars.

To achieve these unusual capabilities, he said, researchers over decades reimagined work on Z so that the huge magnetic fields naturally accompanying Z’s powerful electrical discharges became instruments in their own right, testing materials by creating pressures exceeding those at Earth’s core or aiding in the effort to create breakeven nuclear fusion by pre-compressing the target fuel environs.

“In the meantime,” said Cook, “Z has become the most energetic source of X-rays for fusion research and for stockpile stewardship on the planet. Its capabilities as a pre-eminent research facility for high energy density sciences are known and appreciated worldwide.”

Sandia National Laboratories is a multimission laboratory operated by National Technology and Engineering Solutions of Sandia LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration. Sandia Labs has major research and development responsibilities in nuclear deterrence, global security, defense, energy technologies and economic competitiveness, with main facilities in Albuquerque, New Mexico, and Livermore, California.

Press Release
Source/Credit: Sandia National Laboratories


What's Up September 2021


Source/Credit: NASA/JPL

Wednesday, September 1, 2021

Physicists find ‘magnon’ origins in 2D magnet


Rice University physicists Pengcheng Dai (left) and Lebing Chen have discovered that unusual magnetic features they previously noticed in 2D chromium triiodide arise from topological features. (Photo by Jeff Fitlow/Rice University)

Rice physicists have confirmed the topological origins of magnons, magnetic features they discovered three years ago in a 2D material that could prove useful for encoding information in the spins of electrons.

The discovery, described in a study published online this week in the American Physical Society journal PRX, provides a new understanding of topology-driven spin excitations in materials known as in 2D van der Waals magnets. The materials are of growing interest for spintronics, a movement in the solid-state electronics community toward technologies that use electron spins to encode information for computation, storage and communications.

Spin is an intrinsic feature of quantum objects and the spins of electrons play a key role in bringing about magnetism.

Rice physicist Pengcheng Dai, co-corresponding author of the PRX study, said inelastic neutron-scattering experiments on the 2D material chromium triiodine confirmed the origin of the topological nature of spin excitations, called magnons, that his group and others discovered in the material in 2018.

The group’s latest experiments at Oak Ridge National Laboratory’s (ORNL) Spallation Neutron Source showed “spin-orbit coupling induces asymmetric interactions between spins” of electrons in chromium triiodine, Dai said. “As a result, the electron spins feel the magnetic field of moving nuclei differently, and this affects their topological excitations.”

In van der Waals materials, atomically thin 2D layers are stacked like pages in a book. The atoms

Graduate student Lebing Chen displays chromium triiodide crystals
 he made in a Rice University laboratory.
(Photo by Jeff Fitlow/Rice University)

within layers are tightly bonded, but the bonds between layers are weak. The materials are useful for exploring unusual electronic and magnetic behaviors. For example, a single 2D sheet of chromium triiodine has the same sort of magnetic order that makes magnetic decals stick to a metal refrigerator. Stacks of three or more 2D layers also have that magnetic order, which physics call ferromagnetic. But two stacked sheets of chromium triiodine have an opposite order called antiferromagnetic.

That strange behavior led Dai and colleagues to study the material. Rice graduate student Lebing Chen, the lead author of this week’s PRX study and of the 2018 study in the same journal, developed methods for making and aligning sheets of chromium triiodide for experiments at ORNL. By bombarding these samples with neutrons and measuring the resulting spin excitations with neutron time-of-flight spectrometry, Chen, Dai and colleagues can discern unknown features and behaviors of the material.

In their previous study, the researchers showed chromium triiodine makes its own magnetic field thanks to magnons that move so fast they feel as if they are moving without resistance. Dai said the latest study explains why a stack of two 2D layers of chromium triiodide has antiferromagnetic order.

“We found evidence of a stacking-dependent magnetic order in the material,” Dai said. Discovering the origins and key features of the state is important because it could exist in other 2D van der Waals magnets.

Additional co-authors include Bin Gao of Rice, Jae-Ho Chung of Korea University, Matthew Stone, Alexander Kolesnikov, Barry Winn, Ovidiu Garlea and Douglas Abernathy of ORNL, and Mathias Augustin and Elton Santos of the University of Edinburgh.

The research was funded by the National Science Foundation (1700081), the Welch Foundation (C-1839), the National Research Foundation of Korea (2020R1A5A1016518, 2020K1A3A7A09077712), the United Kingdom’s Engineering and Physical Research Council and the University of Edinburgh and made use of facilities provided by the United Kingdom’s ARCHER National Supercomputing Service and the Department of Energy’s Office of Science.

News Release
Source/Credit: Rice University / Jade Boyd


Glacial Ice Cores Reveal 15,000 Year Old Microbes


Extensive glaciation at high altitudes in the Tibetan Plateau.
Source: Reurinkjan
Known as the world’s “Third Pole”, the Tibetan Plateau holds a vast amount of Earth’s ice. Over 46,000 glaciers blanket the arid, elevated landscape, which is part of the expansive Hindu Kush Himalaya (HKH) mountain range. These mountains and their icefields collectively hold the largest volume of snow and ice outside the Arctic and Antarctic. One might easily assume that the ice is sterile and void of life beyond its inert composition, considering the ancient and inaccessible depths it descends to. However, a new investigation of Tibetan glacial ice cores reveals quite the opposite: these immense glaciers in fact hold a rich chronological record of frozen, unique microbial life.

Zhi-Ping Zhong is a postdoctoral paleoclimatology researcher at Ohio State University’s Byrd Polar and Climate Research Center, and the lead author of a new publication in the journal Microbiome outlining his team’s investigation of nearly 15,000-year-old microbes in Tibetan ice. Their innovation is in their methodology — it is notoriously difficult to isolate and preserve ancient microbial DNA well enough to resolve individual genomes, while simultaneously avoiding contamination or degradation of the sample. In addition, glacier ice contains very low levels of biomass, making contamination by today’s microbes and viruses an even more imposing risk. Zhong and his team pioneered a new approach that accomplished this difficult task with remarkable precision, permitting them to see right down to the ancient genes.

“We developed clean methods to remove the contaminants on glacier ice core surfaces,” Zhong explained in an interview with GlacierHub. “This helps guarantee we obtain the ‘real’ microbes and viruses that were archived in glacier ice, not contaminants.” The team’s methods involved meticulous shaving and disinfection of the cores down to their innermost ice, isolating relatively uncontaminated material for analysis. They expanded upon previous work by first validating their methods on artificial cores they had laced with known bacteria, allowing them to measure what amount of the mock contaminants remained. With more concrete data on the efficacy of their approach, they proceeded to clean and process the actual cores.

The ice cores used in the investigation were drilled by Lonnie Thompson and colleagues in 2015 from the Guliya Ice Cap. Thompson, a renowned paleoclimatologist and professor at Ohio State University since 1991, began (alongside Ellen Mosley-Thompson) building the Byrd Polar and Climate Research Center’s ice core collection several decades ago. Zhong emphasises that glacier ice does not only archive past climates and chemical information about Earth’s atmosphere — it also archives entire microbial ecosystems, providing a preserved biological record going back untold thousands of years. 

The research team’s meticulous contamination prevention and reduction methods both outside and inside the lab revealed certain groups of bacteria commonly found in glacier ice such as Janthinobacterium, Polaromonas, and Sphingomonas. However, investigation of viral genetic material uncovered entire genetic sequences which were unique to the study, revealing 28 novel genera. This rate of 88 percent novel genera found in the glacier ice is much higher than those found by viral analyses of ocean environments (52 percent unique genera) and soils (61 percent unique genera). Such discoveries at exceptional levels of detail are integral to Zhong’s goals for the study. He explains that he hopes to understand the mutation rates of microbes over long periods of time by comparing the frozen genomes with those of more current bacteria and viruses. “These efforts will provide us the possibility of using a sort of molecular clock to help date the ice.”

The potential applications of Zhong. et al’s methods don’t end on this planet, either. Extremophilic life on Earth (including hardy ice-dwelling bacteria and other microbes) are frequently studied as potential models for extraterrestrial life on other planets and moons. Numerous bodies in our solar system harbor water ice, albeit in more extreme climatic conditions, leading to the astrobiological assumption that such ice may be sufficient to provide habitable conditions for life. Because the team’s protocol was developed for microbial and viral extraction from high-elevation, cold, and dry environments on Earth, Zhong noted how similar techniques “may one day be applied in the search for life in the Martian polar regions as well in other icy worlds in our solar system.” 

These techniques hold great promise for expanding our understanding of microbial history and evolution, but alongside this field’s emergence comes the existential threat of climate change. A quarter of the Third Pole has melted since 1970, and according to a 2019 IPCC report, two-thirds of its glaciers are predicted to disappear within the next 80 years. These catastrophic trends are global to varying degrees, and with the melt comes the Earth-wide loss of a biological history going back hundreds of thousands of years, unsalvageable as these records transition to meltwater. 

Aware of this threat, the Byrd Polar and Climate Research Center has collected and preserved more than 7,000 meters of ice core sections over its 40 years of glacier ice analysis across the globe. The frozen room at the Byrd Center is a time capsule preserving histories of the world that soon may not be accessible anywhere else. Both the archived ice cores and Zhong’s methods may serve as a foundation for the next generation of researchers, working in a world where the only views of once magnificent and biology-rich glaciers are in shelved cylinders of ice, each four inches across and about a yard long. Scientists have barely begun to read the vast genetic tome that is contained in Earth’s glaciers — these new methods of recovering frozen genomes and preserving threatened ice are now facing a fruitful, fateful race against time.

Source/Credit: Columbia University Climate School / by Daniel Burgess


Using Liquid Metal to Turn Motion into Electricity


Photo credit: Veenasri Vallem
Researchers at North Carolina State University have created a soft and stretchable device that converts movement into electricity and can work in wet environments.

“Mechanical energy – such as the kinetic energy of wind, waves, body movement and vibrations from motors – is abundant,” says Michael Dickey, corresponding author of a paper on the work and Camille & Henry Dreyfus Professor of Chemical and Biomolecular Engineering at NC State. “We have created a device that can turn this type of mechanical motion into electricity. And one of its remarkable attributes is that it works perfectly well underwater.”

The heart of the energy harvester is a liquid metal alloy of gallium and indium. The alloy is encased in a hydrogel – a soft, elastic polymer swollen with water.

The water in the hydrogel contains dissolved salts called ions. The ions assemble at the surface of the metal, which can induce charge in the metal. Increasing the area of the metal provides more surface to attract charge. This generates electricity, which is captured by a wire attached to the device.

“Since the device is soft, any mechanical motion can cause it to deform, including squishing, stretching and twisting,” Dickey says. “This makes it versatile for harvesting mechanical energy. For example, the hydrogel is elastic enough to be stretched to five times its original length.”

In experiments, researchers found that deforming the device by only a few millimeters generates a power density of approximately 0.5 mW m-2. This amount of electricity is comparable to several popular classes of energy harvesting technologies.

“However, other technologies don’t work well, if at all, in wet environments,” Dickey says. “This unique feature may enable applications from biomedical settings to athletic wear to marine environments. Plus, the device is simple to make.

“There is a path to increase the power, so we consider the work we described here a proof-of-concept demonstration.”

The researchers already have two related projects under way.

One project is aimed at using the technology to power wearable devices by increasing the harvester’s power output. The second project evaluates how this technology could be used to harvest wave power from the ocean.

The paper, “A Soft Variable-Area Electrical-Double-Layer Energy Harvester,” is published in the journal Advanced Materials. First author of the paper is Veenasri Vallem, a Ph.D. student at NC State. Co-authors include Erin Roosa and Tyler Ledinh, who were undergrads at NC State when the work was done; Sahar Rashid-Nadimi and Abolfazl Kiani, who were visiting scholars at NC State and are now at California State University, Bakersfield; and Woojin Jung and Tae-il Kim of Sungkyunkwan University in South Korea, who worked on the project while visiting NC State.

The work was done with support from NC State’s ASSIST Center, which is funded by the National Science Foundation under grant EEC-1160483. Additional support came from the Coastal Studies Institute of North Carolina and the Fostering Global Talents for Innovative Growth Program supervised by the Korea Institute for Advancement of Technology.

Source/Credit: North Carolina State University


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Autism and ADHD are linked to disturbed gut flora very early in life

The researchers have found links between the gut flora in babies first year of life and future diagnoses. Photo Credit:  Cheryl Holt Disturb...

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