3-D protein modeling suggests why COVID-19 infects some animals, but not others

3D protein modeling suggests why COVID-19 infects some animals, but not others
3D structure model of the receptor-binding domain of SARS-CoV-2 (in blue) interacting with the human ACE2 receptor (in gray). Amino acids important to the interaction, which are present only in COVID-susceptible animal species are highlighted in yellow. Sugars bound to the proteins are shown in pink. Credit: Rodrigues et al. 2020 (CC-BY 2.0)

Some animals are more susceptible to COVID-19 infection than others, and new research suggests this may be due to distinctive structural features of a protein found on the surface of animal cells. João Rodrigues of Stanford University, California, and colleagues present these findings in the open-access journal PLOS Computational Biology.

Previous research suggests that the current pandemic began when the virus that causes COVID-19, SARS-CoV-2, jumped from bats or pangolins to humans. Certain other animals, such as cattle and cats, appear to be susceptible to COVID-19, while others, such as pigs and chickens, are not. One zoo even reported infections in tigers. However, it was unclear why some animals are immune and others are not.

To address this question, Rodrigues and colleagues looked for clues in the first step of infection, when SARS-CoV-2’s “spike” protein binds to an “ACE2” receptor protein on the surface of an animal cell. They used computers to simulate the proteins’ 3-D structures and investigate how the spike protein interacts with different animals’ ACE2 receptors—similar to checking which locks fit a certain key.

The researchers found that certain animals’ ACE2 “locks” fit the viral “key” better, and that these animals, including humans, are susceptible to infection. Despite being approximations, the simulations pinpointed certain structural features unique to the ACE2 receptors of these susceptible species. The analysis suggest that other species are immune because their ACE2 receptors lack these features, leading to weaker interactions with spike proteins.

These findings could aid development of antiviral strategies that use artificial “locks” to trap the virus and prevent it from interacting with human receptors. They could also help improve models to monitor animal hosts from which a virus could potentially jump to humans, ultimately preventing future outbreaks.

“Thanks to open-access data, preprints, and freely available academic software, we went from wondering if tigers could catch COVID-19 to having 3-D models of protein structures offering a possible explanation as to why that is the case in just a few weeks,” Rodrigues says.

His team plans to continue refining the computational tools used in this study.

Dozens of mammals could be susceptible to SARS-CoV-2

More information:
Rodrigues JPGLM, Barrera-Vilarmau S, M. C. Teixeira J, Sorokina M, Seckel E, Kastritis PL, et al. (2020) Insights on cross-species transmission of SARS-CoV-2 from structural modeling. PLoS Comput Biol 16(12): e1008449. doi.org/10.1371/journal.pcbi.1008449
Provided by
Public Library of Science

3-D protein modeling suggests why COVID-19 infects some animals, but not others (2020, December 3)
retrieved 3 December 2020
from https://phys.org/news/2020-12-d-protein-covid-infects-animals.html

This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no
part may be reproduced without the written permission. The content is

Read more

Deep Space Might Not Be Completely Dark, New Study Suggests

When we look out at the darkest night skies available on Earth, even the emptiest abyss we can find isn’t completely dark. We can look between the individual stars in the Milky Way, seeing out into the Universe beyond. We can look at the space between the myriad of galaxies populating the Universe, finding many regions without identifiable light sources of any type. But even when we do, the light from our own backyard still gets in our way.

From the Sun, the Earth, the Moon, and the tiny, light-reflecting dust grains found within our Solar System, even the greatest space telescopes of all must contend with this extraneous light from all directions: zodiacal light. From the individual atoms, ions, and molecules present within the Milky Way, a faint galactic glow always appears, as well. But if there were a way to subtract all these excess light sources away, would space appear completely dark, or would there be some light left over: a cosmic optical background? In a fascinating new study, a team from NASA’s New Horizons mission claims to have done this for the first time, claiming that deep space might not be entirely dark, after all. Here’s what they found.

When you think of the abyss of deep space, you probably think of the deepest images ever taken: images like the Hubble eXtreme Deep Field, which have revealed some of the faintest, farthest galaxies ever seen by humanity. These images were constructed brilliantly, by:

  • locating a region of space with no known bright stars or galaxies,
  • away from the plane of the zodiacal light in the Solar System,
  • away from the plane of the Milky Way galaxy,
  • that would be consistently visible by the telescope over a long period of time,
  • and by gathering many long-exposure images across a variety of wavelength ranges.

The Hubble Space Telescope’s first attempt to do this created the original Hubble Deep Field, while upgraded cameras, wider wavelength ranges, superior instrumentation and data processing, and longer observing times wound up creating even deeper images.

Read more

Extreme Life Thrived in Hot Asteroid Pit After Dinosaur Extinction, Evidence Suggests

An asteroid struck the Yucatan Peninsula, seen here from the International Space Station, 66 million years ago, sparking a mass extinction event.

An asteroid struck the Yucatan Peninsula, seen here from the International Space Station, 66 million years ago, sparking a mass extinction event.
Photo: Tim Peake/ESA/NASA

A gigantic pool of magma emerged beneath Earth’s surface following the impact event that wiped out all non-avian dinosaurs. New research suggests this hellish subterranean chamber hosted a biological ecosystem, a finding that could give clues as to how life emerged during Earth’s tumultuous early days.

When the asteroid struck our unfortunate planet some 66 million years ago, it created a 110-mile-wide (180-kilometer) impact crater in what is now the Yucatan Peninsula. Evidence presented earlier this year showed the impact also produced a gigantic subterranean magma chamber, which persisted for hundreds of thousands of years, possibly even millions of years. Incredibly, this hydrothermal system supported an entire microbial ecosystem, according to new research published today in Astrobiology.

David Kring, the lead author of both studies and a geologist at the Lunar and Planetary Institute (LPI), believes the Chicxulub hydrothermal system is a possible glimpse into the early conditions on Earth, when life was starting to emerge. Kring’s co-authors are Martin Whitehouse from the Swedish Museum of Natural History and Martin Schmieder from Neu-Ulm University in Germany.

During its peak, the Chicxulub magma chamber was around 1.86 miles (3 km) thick and encompassed 33,500 cubic miles (140,000 cubic kilometers) of Earth’s crust. By comparison, the caldera at Yellowstone National Park is nine times smaller.

Kring and his colleagues discovered evidence of this hydrothermal system in a rock core pulled from the crater’s peak ring, which is basically the jagged ring found inside some impact craters (good examples here). Approximately 33,000 pounds (15,000 kg) of rock was pulled from a depth of 0.81 miles (1.3 km), in an expedition supported by the International Continental Scientific Drilling Program and the International Ocean Discovery Program.

Delving once again into the Chicxulub sample material, the scientists spotted tiny spheres of pyrite, called framboids. Sulfur isotope analysis of these fromboids, which measure just 10 millionths of a meter in diameter, pointed to the presence of “thermophilic colonies of sulfate-reducing organisms,” in other words, clumps of heat-loving microscopic organisms with an appetite for sulfates. These microorganisms lived in the “porous, permeable rock beneath the floor of the crater and fed on sulfate transported through the rock,” which was made available by the impact-generated hydrothermal system, according to the study.

As the authors point out, these subterranean microbes made a living by taking advantage of chemical reactions happening inside the hydrothermal system, namely inside mineral-rich waters warmed by the magma. During this process, sulphate converted into sulfide, which was preserved as pyrite. These organisms are not unlike some heat-loving bacteria and archaea found at Yellowstone today.

Illustration for article titled Extreme Life Thrived in Hot Asteroid Pit After Dinosaur Extinction, Evidence Suggests

This finding is super interesting in its own right, but it potentially speaks to the conditions found on early Earth, specifically during the Late Heavy Bombardment (LHB) period, which ended some 3.8 billion

Read more

India Has Good Reason to Give Up Its No-First-Strike Nuclear Doctrine. But the State of Its Arsenal Suggests That It Won’t.

In a statement to the Conference on Disarmament on Oct. 14, Indian Ambassador Pankaj Sharma reiterated that—even as tensions with neighboring China heat up—his country remains committed to its doctrine that it will not use its nuclear weapons against an adversary unless first attacked with them.

India’s adherence to a no-first-use principle is long-standing. Ever since 1998, when the country went nuclear, New Delhi has rejected the idea of initiating the use of such weapons in any conflict scenario. Nukes, in Indian strategy, are purely retaliatory. And that stance has made good military and diplomatic sense. The relatively small size of India’s arsenal ruled out a first strike anyway, and the country’s commitment to restraint, meanwhile, built its image as a responsible nuclear stakeholder and helped ease New Delhi’s accommodation in the international nuclear order.

But India’s steadfast rhetorical adherence to its no-first-use principle has been facing challenges on multiple fronts.

First, there is a growing consensus in the Western nonproliferation community that, in practice, New Delhi has already nearly relinquished the policy. In fact, experts believe that should India and Pakistan go to war, India would ready its nuclear force for preemptive strikes. And it has acquired the capability—nuclear arsenal, delivery systems, and ISR (intelligence, surveillance, and reconnaissance) systems—to do so. Moreover, having already been granted recognition of its right to a nuclear program through the 2005 Indo-U.S. nuclear deal, New Delhi has less incentive for caution.

Second, China and India are embroiled in military scuffling in the Western Himalayas, where the Chinese army has sliced off significant chunks of Indian territory. Given the disparity between New Delhi’s conventional military power and Beijing’s, publicly adopting a first-use doctrine would communicate both power and resolve on India’s part. In other words, this would be an opportune time for India to align its stated policy with its apparent intentions.

Sharma’s message, though, amounts to a categorical rejection of both facts. The essential puzzle in India’s nuclear policy, therefore, boils down to the following: If Indian intentions and capability to initiate first use of nuclear weapons have indeed shifted, why is New Delhi hesitant about leveraging this shift where it may matter most—against China?

States do have an incentive to hide new military capabilities; the no-first-use doctrine may simply be a public lie to hide private intentions. However, backing away from the principle would also signal strength and perhaps make it less likely that India would need to use its new military capabilities to begin with.

Another explanation is that India doesn’t think it needs the added deterrence. So far, New Delhi has opted for a conventional buildup along the border with China. But that has put enormous strain on its underequipped and overstretched armed forces, as well as its underperforming economy. Diplomatically, too, building up conventional deterrence has been costly. Measures such as inviting Australia to joint naval exercises in Malabar and initiating official trade talks with Taiwan rattle Beijing, but not much more. Meanwhile, they entrap New Delhi into expensive

Read more

A Broadly Used Indicator Suggests That Stocks Are Fairly Valued

With the U.S. economy struggling to emerge from one of the worst recessions in history, it seems reasonable to ask why the S&P 500 is up 7% for the year. Are stocks wildly overvalued?

A measure that is often used to answer this question is CAPE – the ten-year average of the S&P 500 price/earnings ratio. According to it, stocks don’t seem to be overpriced at all.

In a recent paper published by the Federal Reserve Bank of San Francisco, economist Kevin Lansing notes that CAPE was at 30.9 at the end of the third quarter of 2020, or about 50% above its 60-year average of 20.5. A naïve conclusion from this observation would be that stocks are enormously overvalued. However, CAPE was higher two years ago, at 32.6 at the end of 3Q18. Yet, stocks climbed 20% since then and CAPE is now lower. How, then, can we use CAPE to know whether stocks are expensive or cheap?

Many pundits compare CAPE to its long-term average and, if it is significantly above it, conclude that stocks are overvalued. The obvious problem with this approach is that a long-term average is a value that only exists today: comparing stocks five years ago with a ratio that includes the then-unknown values of the following five years makes little sense. Yet, some insist on using CAPE this way. A slight improvement would be to use a moving average, for example.

Lansing from the San Francisco Fed uses a different approach. He notes that some economic indicators can account for fluctuations on the CAPE ratio, and he chooses three: interest rates, the growth potential of the economy, and uncertainty.

Interest rates, as we discussed in a previous post, are important determinants of the value of stocks (Warren Buffett said that they are “the most important” determinant) because lower rates increase the value of future dividends, and therefore of equities, even if earnings do not change.

The growth rate of potential economic output (a measure computed by the Congressional Budget Office) also influences the value of equities relative to earnings because if the economy has the potential of growing faster, so do future corporate earnings.

Economic uncertainty can be measured as the forecast error of various gauges of the economy, and is in fact tabulated in an index created by academics at Columbia and NYU. The idea is to measure the forecast error of various macroeconomic indicators. If it is true that “the market hates uncertainty” as we often hear, more uncertainty should bring down equity values because it puts future earnings in doubt.

Lansing runs a simple regression with these three indicators and comes up with a CAPE estimation that fits rather well with the observed values, especially in the last 20 or 30 years. A clear takeaway is that comparing CAPE to a fixed multi-decade average value not only does not make much sense but also

Read more

SpaceX’s Elon Musk Suggests Alien Life May Be Hiding In These 2 Spots


  • Elon Musk responded to a young fan who sent a letter asking if he believes there is life on other planets
  • The SpaceX founder suggested Mars or Europa may harbor extraterrestrial life
  • NASA is aiming to send its Europa Clipper spacecraft to the Jupiter moon by 2023

Is there life on other planets? Elon Musk suggested that it may be possible to find extraterrestrial life if space missions look in certain places.

On Thursday, the SpaceX and Tesla founder shared the two most likely spots where humans may be able to find extraterrestrial life in response to a letter sent to him by a 13-year old boy, who asked if Musk believes there is life on other planets. The two places he mentioned? Earth’s neighbor, Mars, and Jupiter’s moon, Europa.

“Doesn’t seem to be any life in this solar system. Maybe under the ice of Europa or extremophile bacteria below the surface of Mars,” he tweeted

Musk added a link that leads to the Wikipedia page of the Drake equation — a probabilistic equation that is used by scientists to estimate the possible number of communicating extraterrestrial civilizations in the Milky Way galaxy.

This is not the first time Musk has been asked about alien life. 

“As far as we know, we’re the only consciousness or the only life that’s out there,” Musk said last year during the unveiling of Starship Mk1, a prototype for SpaceX’s massive reusable launch system, Space.com reported. “There might be other life, but we’ve seen no signs of it.”

“People often ask me,” he shared. “‘What do you know about the aliens?’ and I’m like, ‘Man, I tell you, pretty sure I’d know if there were aliens. I’ve not seen any sign of aliens.'”

Meanwhile, NASA announced last year that it is sending the Europa Clipper spacecraft to Jupiter’s mysterious and icy moon, targeting a launch date between 2023 and 2025. The mission aims to study the conditions of Europa’s environment and determine whether it is suitable for supporting life.

Jupiter’s sixth-largest moon is said to have a surface temperature roughly 238 degrees below zero and is believed to have oceans underneath its icy surface, according to NASA. 

Mars, on the other hand, has displayed shreds of evidence of conditions that could have supported life. Due to dry riverbeds, ancient shorelines, and salty surface chemistry discovered by orbiters and rovers at Mars, it is believed that the red planet once had liquid water and even lakes. Scientists also found evidence of organic compounds, or the chemical building blocks of life, on Mars using data from NASA’s Curiosity Rover.

In July, NASA sent off the Mars 2020 Perseverance Rover to the red planet with the goal of finding signs of past microbial life.

Both places mentioned, Mars and Europa, are still largely unexplored. However, the space missions to these locations may soon unlock more of their secrets and determine whether or not extraterrestrial life had once lurked, or are lurking, on Mars and

Read more

Modern aircraft ventilation systems aren’t spreading viruses, DoD study suggests

A new study released Thursday suggests that people don’t need to worry about circulating air spreading coronavirus on airplanes.

a large passenger jet flying through a cloudy blue sky: TOPSHOT - Fleecy clouds are seen in the sky as an airplane prepares to land at the airport in Frankfurt am Main, western Germany, on November 5, 2018. (Photo by Silas Stein / dpa / AFP) / Germany OUT    (Photo credit should read SILAS STEIN/DPA/AFP via Getty Images)

© SILAS STEIN/DPA/DPA/AFP via Getty Images
TOPSHOT – Fleecy clouds are seen in the sky as an airplane prepares to land at the airport in Frankfurt am Main, western Germany, on November 5, 2018. (Photo by Silas Stein / dpa / AFP) / Germany OUT (Photo credit should read SILAS STEIN/DPA/AFP via Getty Images)

The US Department of Defense study supports earlier research showing the ventilation systems on aircraft filter the air efficiently and take out particles that could transmit viruses.

The study, which was released without peer review, did not take into account other ways that people could catch the virus on aircraft — including from others coughing or breathing directly on them, from surfaces or from confined spaces such as restrooms.

The US Transportation Command, The Defense Advanced Research Project Agency (DARPA) and the Air Mobility Command used Boeing 777-200 and 767-300 aircraft loaded up with sensors meant to duplicate the effect of a fully loaded passenger flight.

A dummy wearing a surgical mask simulated a coughing passenger infected with a respiratory virus.

The team used fluorescent aerosol tracers to see where particles emitted from the coughing “passenger” went. They were sucked quickly into the ventilation system, the team concluded, and were unlikely to contaminate nearby surfaces or blow into the breathing zones of people seated nearby.

“Testing assumes that mask wearing is continuous, and that the number of infected personnel is low,” the research team wrote. “Contamination of surfaces via non-aerosol routes (large droplets or fecal contamination) is more likely in lavatories and other common areas and is not tested here,” they added.

“These alternative routes of exposure are more challenging to predict because of uncertainty in human behavior.”

Other reports have found people became infected with coronavirus on flights, perhaps when they took off masks to use restrooms.

“Testing did not include substantial movement throughout the plane or in the airport, lounge or jetway, where air change rates and human interactions will vary,” the researchers added.

“Similarly, the mannequin remained facing forward, uncertainty in human behavior with conversations and behavior may change the risk and directionality in the closest seats to an index patient, especially for large droplets.”

A lot left to learn

Much is still unknown about Covid-19 transmission aboard planes. Two previous studies documented real-life cases of suspected transmission aboard flights.

Both studies involved cases connected to long flights early in the pandemic, before airlines began requiring face masks.

Another study documenting a case of suspected coronavirus transmission aboard a flight involved a woman who wore an N95 mask throughout her flight except when she used the lavatory.

The lavatory was shared by an asymptomatic patient who was seated three rows away.

The US Centers for Disease Control and Prevention notes that “most viruses and other germs do not spread easily on flights because of how air circulates and is filtered on airplanes,” adding

Read more

Scimitar-Toothed Cats Hunted Prey to Exhaustion, DNA Study Suggests

Artist’s depiction of scimitar-toothed cats chasing down an ancient horse.

Artist’s depiction of scimitar-toothed cats chasing down an ancient horse.
Illustration: Velizar Simeonovski/University of Copenhagen

Scientists have mapped the entire nuclear genome of a saber-toothed cat species known as Homotherium latidens, also called the scimitar-toothed cat. The resulting DNA analysis suggests these Pleistocene predators were fearsome pack hunters capable of running for long distances as they chased their prey to exhaustion.

Smilodon, with its impossibly long fangs, is probably the most famous saber-toothed cat, but new research published today in Current Biology suggests another saber-toothed cat, a species known as Homotherium latidens, is equally worthy of our attention.

Oh, in case you’re wondering, “saber-toothed cats” is a kind of colloquial catch-all term used to describe extinct predatory felids with long canines that protruded from their mouths even when their jaws were closed. The more technical term for this group is Machairodontinae, a now-extinct subfamily of Felidae. And no, we don’t call them “saber-toothed tigers” anymore, because they weren’t actually tigers.

Homotherium, also known as the scimitar-toothed cat, may not have sprouted maxillary canines on the scale of Smilodon, but these predators had a lot going for them. They were built for long-distance running and were more slender than Smilodon and modern lions. Homotherium’s limb proportions are reminiscent of those seen on modern hyenas, as they featured longer forelimbs relative to their hindlimbs, according to Michael Westbury, the lead author of the new study and a geneticist at the University of Copenhagen.

Reconstruction of Homotherium latidens.

Reconstruction of Homotherium latidens.
Image: R. Barnett et al., 2020/Current Biology

Sitting comfortably atop the food web, Homotherium preyed on large Pleistocene herd animals, such as giant ground sloths and mammoths. They used their long incisors and lower canines for puncturing and gripping, as well as picking up and relocating dead prey.

These traits and behaviors were primarily inferred from fossil evidence, but many questions about Homotherium remained unanswered, such as the specific genetic adaptations that allowed them to thrive and survive and whether these animals interbred with other saber-toothed cat species.

To learn more about scimitar-toothed cats, Westbury and his colleagues recovered and analyzed DNA from a Homotherium latidens specimen found in Canada’s Yukon Territory. The specimen, pulled from frozen sediment, was too old for radiocarbon dating, so it’s at least 47,500 years old, according to the new study. The researchers mapped its entire nuclear genome—a first for a saber-toothed cat—and compared it to those of modern cats, like lions and tigers.

“The quality of this data allowed us to do a lot of interesting analyses that are normally limited to high-quality genomes from living species,” explained Westbury in an email, saying he was surprised to obtain such good quality DNA from a specimen so old.

The scientists found no less than 31 genes in Homotherium that were subject to positive selection. Of note, the genetic makeup of their nervous system points to complex social behaviors, which meshes nicely with our understanding

Read more