research (62)

RNA and Covid-19...

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NIST researcher Megan Cleveland uses a PCR machine to amplify DNA sequences by copying them numerous times through a series of chemical reactions.
Credit: M. Cleveland/NIST

Topics: Biology, Biotechnology, COVID-19, Diversity in Science, NIST, Research, Women in Science

Scientists track and monitor the circulation of SARS-CoV-2, the virus that causes COVID-19, using methods based on a laboratory technique called polymerase chain reaction (PCR). Also used as the “gold standard” test to diagnose COVID-19 in individuals, PCR amplifies pieces of DNA by copying them numerous times through a series of chemical reactions. The number of cycles it takes to amplify DNA sequences of interest so that they are detectable by the PCR machine, known as the cycle threshold (Ct), is what researchers and medical professionals look at to detect the virus.

However, not all labs get the same Ct values (sometimes also called “Cq” values). In efforts to make the results more comparable between labs, the National Institute of Standards and Technology (NIST) contributed to a multiorganizational study that looked at anchoring these Ct values to a reference sample with known amounts of the virus.

Researchers published their findings in the journal PLOS One.

SARS-CoV-2 is an RNA virus: Its genetic material is single-stranded instead of double-stranded like DNA and contains some different molecular building blocks, namely uracil in place of thymine. But the PCR test only works with DNA, and labs first must convert the RNA to DNA to screen for COVID-19. For the test, RNA is isolated from a patient’s sample and combined with other ingredients, including short DNA sequences are known as primers, to transform the RNA into DNA.

RNA Reference Materials Are Useful for Standardizing COVID-19 Tests, Study Shows, NIST

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OIPCs and Janus...

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Topics: Battery, Energy, Green Tech, Research, Solid-State Physics

Janus, in Roman religion, the animistic spirit of doorways (januae) and archways (Jani). Janus and the nymph Camasene were the parents of Tiberinus, whose death in or by the river Albula caused it to be renamed Tiber. Source: Encylopedia Britannica

Over the past decade, lithium-ion batteries have seen stunning improvements in their size, weight, cost, and overall performance. (See Physics Today, December 2019, page 20.) But they haven’t yet reached their full potential. One of the biggest remaining hurdles has to do with the electrolyte, the material that conducts Li+ ions from anode to cathode inside the battery to drive the equal and opposite flow of charge in the external circuit.

Most commercial lithium-ion batteries use organic liquid electrolytes. The liquids are excellent conductors of Li+ ions, but they’re volatile and flammable, and they offer no defense against the whisker-like Li-metal dendrites that can build up between the electrodes and eventually short-circuit the battery. Because safety comes first, battery designers must sacrifice some performance in favor of not having their batteries catch fire.

A solid-state electrolyte could solve those problems. But what kind of solid conducts ions? An ordered crystal won’t do—when every site is filled in a crystalline lattice, Li+ ions have nowhere to move to. A solid electrolyte, therefore, needs to have a disordered, defect-riddled structure. It must also provide a polar environment to welcome the Li+ ions, but with no negative charges so strong that the Li+ ions stick to them and don’t let go.

For several years, Jenny PringleMaria Forsyth, and colleagues at Deakin University in Australia have been exploring a class of materials, called organic ionic plastic crystals (OIPCs), that could fit the bill. As a mix of positive and negative ions, an OIPC offers the necessary polar environment for conducting Li+. And because the constituent ions are organic, the researchers have lots of chemical leeways to design their shapes so they can’t easily fit together into a regular lattice but are forced to adopt a disordered, Li+-permeable structure.

Two-faced ions form a promising battery material, Johanna L. Miller, Physics Today

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ACE2 Gum and Covid...

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Visual Abstract

Topics: Biology, Biotechnology, COVID-19, Research

To advance a novel concept of debulking virus in the oral cavity, the primary site of viral replication, virus-trapping proteins CTB-ACE2 were expressed in chloroplasts and clinical-grade plant material was developed to meet FDA requirements. Chewing gum (2 g) containing plant cells expressed CTB-ACE2 up to 17.2 mg ACE2/g dry weight (11.7% leaf protein), have physical characteristics and taste/flavor like conventional gums, and no protein was lost during gum compression. CTB-ACE2 gum efficiently (>95%) inhibited entry of lentivirus spike or VSV-spike pseudovirus into Vero/CHO cells when quantified by luciferase or red fluorescence. Incubation of CTB-ACE2 microparticles reduced SARS-CoV-2 virus count in COVID-19 swab/saliva samples by >95% when evaluated by microbubbles (femtomolar concentration) or qPCR, demonstrating both virus trapping and blocking of cellular entry. COVID-19 saliva samples showed low or undetectable ACE2 activity when compared with healthy individuals (2,582 versus 50,126 ΔRFU; 27 versus 225 enzyme units), confirming greater susceptibility of infected patients for viral entry. CTB-ACE2 activity was completely inhibited by pre-incubation with SARS-CoV-2 receptor-binding domain, offering an explanation for reduced saliva ACE2 activity among COVID-19 patients. Chewing gum with virus-trapping proteins offers a generally affordable strategy to protect patients from most oral virus re-infections through debulking or minimizing transmission to others.

Debulking SARS-CoV-2 in saliva using angiotensin-converting enzyme 2 in chewing gum to decrease oral virus transmission and infection, Molecular Therapy: Cell.com

Henry Daniell, Smruti K. Nair, Nardana Esmaeili, Geetanjali Wakade, Naila Shahid, Prem Kumar Ganesan, Md Reyazul Islam, Ariel Shepley-McTaggart, Sheng Feng, Ebony N. Gary, Ali R. Ali, Manunya Nuth, Selene Nunez Cruz, Jevon Graham-Wooten, Stephen J. Streatfield, Ruben Montoya-Lopez, Paul Kaznica, Margaret Mawson, Brian J. Green, Robert Ricciardi, Michael Milone, Ronald N. Harty, Ping Wang, David B. Weiner, Kenneth B. Margulies, Ronald G. Collman

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Time...

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GIF source: article link below

Topics: Applied Physics, Education, Research, Thermodynamics

Also note the Hyper Physics link on the Second Law of Thermodynamics, particularly "Time's Arrow."

"The two most powerful warriors are patience and time," Leo Tolstoy, War, and Peace

The short answer

We can measure time intervals — the duration between two events — most accurately with atomic clocks. These clocks produce electromagnetic radiation, such as microwaves, with a precise frequency that causes atoms in the clock to jump from one energy level to another. Cesium atoms make such quantum jumps by absorbing microwaves with a frequency of 9,192,631,770 cycles per second, which then defines the international scientific unit for time, the second.

The answer to how we measure time may seem obvious. We do so with clocks. However, when we say we’re measuring time, we are speaking loosely. Time has no physical properties to measure. What we are really measuring is time intervals, the duration separating two events.

Throughout history, people have recorded the passage of time in many ways, such as using sunrise and sunset and the phases of the moon. Clocks evolved from sundials and water wheels to more accurate pendulums and quartz crystals. Nowadays when we need to know the current time, we look at our wristwatch or the digital clock on our computer or phone. 

The digital clocks on our computers and phones get their time from atomic clocks, including the ones developed and operated by the National Institute of Standards and Technology (NIST).

How Do We Measure Time? NIST

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Your Brain on Covid...

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Credit: Getty Images

Topics: Biology, COVID-19, DNA, Research

Note: I have friends who thankfully survived infection now affected by this phenomenon. The article thus grabbed my attention.

SARS-CoV-2 appears to travel widely across the cerebral cortex

“Brain fog” is not a formal medical descriptor. But it aptly describes an inability to think clearly that can turn up in multiple sclerosis, cancer, or chronic fatigue. Recently, the condition has grabbed headlines because of reports that it afflicts those recovering from COVID-19.

COVID’s brain-related symptoms go beyond mere mental fuzziness. They range across a spectrum that encompasses headaches, anxiety, depression, hallucinations, and vivid dreams, not to mention well-known smell and taste anomalies. Strokes and seizures are also on the list. One study showed that more than 80 percent of COVID patients encountered neurological complications.

The mystery of how the virus enters and then inhabits the brain’s protected no-fly zone is under intensive investigation. At the 50th annual meeting of the Society for Neuroscience, or SFN (held in virtual form this month after a pandemic hiatus in 2020), a set of yet-to-be-published research reports chronicle aspects of the COVID-causing SARS-COV-2 virus’s full trek in the brain—from cell penetration to dispersion among brain regions, to disruption of neural functioning.

How COVID Might Sow Chaos in the Brain, Gary Stix, Scientific American

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Vapor Ragnarok...

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Credit: Mark Ross

Topics: Climate Change, Existentialism, Global Warming, Research

More moisture in a warmer atmosphere is fueling intense hurricanes and flooding rains.

The summer of 2021 was a glaring example of what disruptive weather will look like in a warming world. In mid-July, storms in western Germany and Belgium dropped up to eight inches of rain in two days. Floodwaters ripped buildings apart and propelled them through village streets. A week later a year’s worth of rain—more than two feet—fell in China’s Henan province in just three days. Hundreds of thousands of people fled rivers that had burst their banks. In the capital city of Zhengzhou, commuters posted videos showing passengers trapped inside flooding subway cars, straining their heads toward the ceiling to reach the last pocket of air above the quickly rising water. In mid-August a sharp kink in the jet stream brought torrential storms to Tennessee that dropped an incredible 17 inches of rain in just 24 hours; catastrophic flooding killed at least 20 people. None of these storm systems were hurricanes or tropical depressions.

Soon enough, though, Hurricane Ida swirled into the Gulf of Mexico, the ninth named tropical storm in the year’s busy North Atlantic season. On August 28 it was a Category 1 storm with sustained winds of 85 miles per hour. Less than 24 hours later Ida exploded to Category 4, whipped up at nearly twice the rate that the National Hurricane Center uses to define a rapidly intensifying storm. It hit the Louisiana coast with winds of 150 miles an hour, leaving more than a million people without power and more than 600,000 without water for days. Ida’s wrath continued into the Northeast, where it delivered a record-breaking 3.15 inches of rain in one hour in New York City. The storm killed at least 80 people and devastated a swath of communities in the eastern U.S.

What all these destructive events have in common is water vapor—lots of it. Water vapor—the gaseous form of H2O—is playing an outsized role in fueling destructive storms and accelerating climate change. As the oceans and atmosphere warm, additional water evaporates into the air. Warmer air, in turn, can hold more of that vapor before it condenses into cloud droplets that can create flooding rains. The amount of vapor in the atmosphere has increased about 4 percent globally just since the mid-1990s. That may not sound like much, but it is a big deal to the climate system. A juicier atmosphere provides extra energy and moisture for storms of all kinds, including summertime thunderstorms, nor’easters along the U.S. Eastern Seaboard, hurricanes, and even snowstorms. Additional vapor helps tropical storms like Ida intensify faster, too, leaving precious little time for safety officials to warn people in the crosshairs.

Vapor Storms Are Threatening People and Property, Jennifer A. Francis, Scientific American

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Alvarez, and Apocalypse...

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Luis Walter Alvarez co-developed the theory that the extinction of the dinosaurs was caused by an asteroid impact (Courtesy: iStock/estt)

Topics: Dinosaurs, Nobel Prize, Research

In the run-up to the announcement of the 2021 Nobel Prize for Physics on 5 October, we’re running a series of blog posts looking at previous recipients and what they did after their Nobel-prize-winning work. In this first installment, Laura Hiscott explores the wide-ranging research of Luis Walter Alvarez, who won the prize for developing the hydrogen bubble chamber, but also investigated the Egyptian pyramids and dinosaur extinction.

I don’t remember the first time I heard the theory that the dinosaurs were wiped out by an asteroid crashing into the Earth. It’s a dramatic story that gets told to wide-eyed children in classrooms and natural history museums at an earlier age than many can remember, so it feels more like absorbed knowledge. What is less commonly known, however, is that one of the originators of this proposal was Luis Walter Alvarez, who won the 1968 Nobel Prize for Physics for his work on the hydrogen bubble chamber.

But it wasn’t just dinosaurs and asteroids that Alvarez got excited about. Throughout his long and varied career, Alvarez was also involved in sending particle detectors into the sky in high-altitude balloons and searching for hidden chambers inside ancient Egyptian pyramids. It appears that his innate curiosity and experimental creativity, which were so vital for winning the Nobel prize, also led him to investigate many more questions both within physics and beyond.

Life beyond the Nobel: how Luis Alvarez deduced the disappearance of the dinosaurs, Laura Hiscott, Physics World

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Foxes, Minks, Racoon Dogs...

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Topics: Biology, COVID-19, Education, Research

During the first year of the COVID-19 pandemic, the “[lab] leak” theory gained little traction. Sure, U.S. President Donald Trump suggested SARS-CoV-2 originated in a laboratory in Wuhan, China—and called it “the China virus”—but he never presented evidence, and few in the scientific community took him seriously. In fact, early in the pandemic, a group of prominent researchers dismissed lab-origin notions as “conspiracy theories” in a letter in The Lancet. A report from a World Health Organization (WHO) “joint mission,” which sent a scientific team to China in January to explore possible origins with Chinese colleagues, described a lab accident as “extremely unlikely.”

But this spring, views began to shift. Suddenly it seemed that the lab-leak hypothesis had been too blithely dismissed. In a widely read piece, fueled by a “smoking gun” quote from a Nobel laureate, a veteran science journalist accused scientists and the mainstream media of ignoring “substantial evidence” for the scenario. The head of WHO openly pushed back against the joint mission’s conclusion, and U.S. President Joe Biden ordered the intelligence community to reassess the lab-leak possibility. Eighteen scientists, including leaders in virology and evolutionary biology, signed a letter published in Science in May that called for a more balanced appraisal of the “laboratory incident” hypothesis.

Yet behind the clamor, little had changed. No breakthrough studies have been published. The highly anticipated U.S. intelligence review, delivered to Biden on 24 August, reached no firm conclusions but leaned toward the theory that the virus has a natural origin.

Fresh evidence that would resolve the question may not emerge anytime soon. China remains the best place to hunt for clues, but its relative openness to collaboration during the joint mission seems to have evaporated. Chinese officials have scoffed at calls from Biden and WHO Director-General Tedros Adhanom Ghebreyesus for an independent audit of key Wuhan labs, which some say should include an investigation of notebooks, computers, and freezers. Chinese vice health minister Zeng Yixin said such demands show “disrespect toward common sense and arrogance toward science.” In response to the increasing pressure, China has also blocked the “phase 2” studies outlined in the joint mission’s March report, which could reveal a natural jump between species.

Despite the impasse, many scientists say the existing evidence—including early epidemiological patterns, SARS-CoV-2’s genomic makeup, and a recent paper about animal markets in Wuhan—makes it far more probable that the virus, like many emerging pathogens, made a natural “zoonotic” jump from animals to humans.

Virologist Robert Garry of Tulane University finds it improbable that a Wuhan lab worker picked up SARS-CoV-2 from a bat and then brought it back to the city, sparking the pandemic. As the WIV study of people living near bat caves shows, the transmission of related bat coronaviruses occurs routinely. “Why would the virus first have infected a few dozen lab researchers?” he asks. The virus may also have moved from bats into other species before jumping to humans, as happened with SARS. But again, why would it have infected a lab worker first? “There are hundreds of millions of people who come in contact with wildlife.”

The earliest official announcement about the pandemic came on 31 December 2019, when Wuhan’s Municipal Health Commission reported a cluster of unexplained pneumonia cases linked to the city’s Huanan seafood market. The WHO report devotes much attention to details about Huanan and other Wuhan markets but also cautions that their role remains “unclear” because several early cases had no link to any market. But after reading the report, Andersen became more convinced that the Huanan market played a critical role.

One specific finding bolsters that case, Wang says. The report describes how scientists took many samples from floors, walls, and other surfaces at Wuhan markets and were able to culture two viruses isolated from Huanan. That shows the market was bursting with a virus, Wang says: “In my career, I have never been able to isolate a coronavirus from an environmental sample.”

The report also contained a major error: It claimed there were “no verified reports of live mammals being sold around 2019” at Huanan and other markets linked to early cases. A surprising study published in June by Zhou Zhao-Min of China West Normal University and colleagues challenged that view. It found nearly 50,000 animals from 38 species, most alive, for sale at 17 shops at Huanan and three other Wuhan markets between May 2017 and November 2019. (The researchers had surveyed the markets as part of a study of a tick-borne disease afflicting animals.)

Live animals can more easily transmit a respiratory virus than meat from a butchered one, and the animals included masked palm civets, the main species that transmitted SARS-CoV to humans, and raccoon dogs, which also naturally harbored that virus and have been infected with SARS-CoV-2 in lab experiments. Minks—a species farmed for fur that has acquired SARS-CoV-2 infections from humans in many countries— were also abundant. “None of the 17 shops posted an origin certificate or quarantine certificate, so all wildlife trade was fundamentally illegal,” Zhou and his colleagues wrote in their paper. (Zhou did not respond to emails from Science.)

Call of the Wild: Why many scientists say it’s unlikely that SARS-CoV-2 originated from a “lab leak,” Jon Cohen, Science Magazine

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Cold Atmospheric Plasmas...

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FIG. 1. Schematic of the motivation and the method for this paper.

Topics: Applied Physics, Chemistry, Physics, Plasma, Research

ABSTRACT

Cold atmospheric plasmas have great application potential due to their production of diverse types of reactive species, so understanding the production mechanism and then improving the production efficiency of the key reactive species are very important. However, plasma chemistry typically comprises a complex network of chemical species and reactions, which greatly hinders the identification of the main production/reduction reactions of the reactive species. Previous studies have identified the main reactions of some plasmas via human experience, but since plasma chemistry is sensitive to discharge conditions, which are much different for different plasmas, widespread application of the experience-dependent method is difficult. In this paper, a method based on graph theory, namely, vital nodes identification, is used for the simplification of plasma chemistry in two ways: (1) holistically identifying the main reactions for all the key reactive species and (2) extracting the main reactions relevant to one key reactive species of interest. This simplification is applied to He + air plasma as a representative, chemically complex plasma, which contains 59 species and 866 chemical reactions, as reported previously. Simplified global models are then developed with the key reactive species and main reactions, and the simulation results are compared with those of the full global model, in which all species and reactions are incorporated. It was found that this simplification reduces the number of reactions by a factor of 8–20 while providing simulation results of the simplified global models, i.e., densities of the key reactive species, which are within a factor of two of the full global model. This finding suggests that the vital nodes identification method can capture the main chemical profile from a chemically complex plasma while greatly reducing the computational load for simulation.

Simplification of plasma chemistry by means of vital nodes identification

Bowen Sun, Dingxin Liu, Yifan Liu, Santu Luo, Mingyan Zhang, Jishen Zhang, Aijun Yang, Xiaohua Wang, and Mingzhe Rong, Journal of Applied Physics

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ARPA-E, and Emission-Free Metal...

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Australian metals mining wastes (top) and the metal hyperaccumulator plants Alyssum murale and Berkheya coddii (bottom). The former plant can take up 1–3% of its weight in nickel. It has demonstrated yields of up to 400 kg of nickel per hectare annually, worth around $7000 at current prices, excluding processing and production costs. (Images adapted from A. van der Ent, A. Parbhakar-Fox, P. D. Erskine, Sci. Total Environ. 758, 143673, 2021, doi:10.1016/j.scitotenv.2020.143673.)

 

Topics: Climate Change, Green Tech, Materials Science, Research

 

When it comes to making steel greener, “only the laws of physics limit our imagination,” says Christina Chang of the Advanced Research Projects Agency-Energy (ARPA–E). Chang, an ARPA–E fellow, is seeking public input on a potential new agency program titled Steel Made via Emissions-Less Technologies. During her two-year tenure, she will guide program creation, agency strategy, and outreach. Steelmaking currently accounts for about 7% of the world’s carbon dioxide emissions, and demand for steel is expected to double by 2050 as low-income countries’ economies grow, according to the International Energy Agency.

 

Founded in 2009, ARPA–E is a tiny, imaginative office within the Department of Energy. SMELT is one part of a three-pronged thrust by ARPA–E to green up processes involved in producing steel and nonferrous metals, from the mine through to the finished products. Another program seeks ways to make use of the vast volumes of wastes that accumulate from mining operations around the globe—and reduce the amounts generated in the future. The agency is also exploring the feasibility of deploying plants that suck up from soils elements such as cobalt, nickel, and rare earths. Despite being essential ingredients in electric vehicles, batteries, and wind turbines, the US has little or no domestic production of them. (See Physics TodayFebruary 2021, page 20.)

 

Steelmaking

 

The first step in steelmaking is separating iron ore into oxygen and iron metal, which produces CO2 through both the reduction process and the fossil-fuel burning necessary to create high heat. An ARPA–E solicitation for ideas to clean up that process closed on 14 June. The agency is looking to replace the centuries-old blast furnace with greener technology that can work at the scale of 2 gigatons of steel production annually. It may or may not follow up with a request for research proposals to fund.

 

ARPA–E explores paths to emissions-free metal making, Physics Today

 

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The Anatomy of Delta...

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A computer simulation of the structure of the coronavirus SARS-CoV-2.Credit: Janet Iwasa, University of Utah

Topics: Biology, Biotechnology, COVID-19, DNA, Existentialism, Research

The coronavirus sports a luxurious sugar coat. “It’s striking,” thought Rommie Amaro, staring at her computer simulation of one of the trademark spike proteins of SARS-CoV-2, which stick out from the virus’s surface. It was swathed in sugar molecules, known as glycans.

“When you see it with all the glycans, it’s almost unrecognizable,” says Amaro, a computational biophysical chemist at the University of California, San Diego.

Many viruses have glycans covering their outer proteins, camouflaging them from the human immune system like a wolf in sheep’s clothing. But last year, Amaro’s laboratory group and collaborators created the most detailed visualization yet of this coat, based on structural and genetic data and rendered atom-by-atom by a supercomputer. On 22 March 2020, she posted the simulation to Twitter. Within an hour, one researcher asked in a comment: what was the naked, uncoated loop sticking out of the top of the protein?

Amaro had no idea. But ten minutes later, structural biologist Jason McLellan at the University of Texas at Austin chimed in: the uncoated loop was a receptor-binding domain (RBD), one of three sections of the spike that bind to receptors on human cells (see ‘A hidden spike’).

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Source: Structural image from Lorenzo Casalino, Univ. California, San Diego (Ref. 1); Graphic: Nik Spencer/Nature

How the coronavirus infects cells — and why Delta is so dangerous, Megan Scudellari, Nature

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COVID, and Fieldwork...

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Image Source: Link Below

Topics: Climate Change, COVID-19, Research, STEM

Just before dawn in the Jama-Coaque Ecological Reserve, a patch of Ecuador’s lush coastal forest, Abhimanyu Lele unfurls a tall net between two poles, then retreats out of sight. A half-hour later, he and a local assistant reappear and smile: Their catch—10 birds that collided with the net and tumbled into a pocket along its length—was a good one. The pair records species, measures and photographs the captives, and pricks wings for blood that can yield DNA before releasing the birds back into the forest. The data, Lele hopes, will shed light on how Ecuadorean songbirds adapt to different altitudes and other conditions.

The third-year graduate student at the University of Chicago (UC), who returns next week from a 10-week field season, was delighted to have made it to his destination. In a typical year, thousands of graduate students and faculty fan out across the world to tackle important research in climate change, fragile ecosystems, animal populations, and more. But the pandemic shut down travel, and fieldwork can’t be done via Zoom, depriving young scientists like Lele of the data and publications they need to climb the academic ladder and help advance science. Now, he and a few others are venturing out—into a very different world.

They are the exceptions. “Most folks have never been able to get back out there,” because COVID-19 continues to spread in much of the world, says Benjamin Halpern, an ecologist with the National Center for Ecological Analysis and Synthesis at the University of California, Santa Barbara. “They are just waiting.”

At the American Museum of Natural History, which mounts about 100 international expeditions a year, “Travel to countries still having trouble [is] just not going to happen,” says Frank Burbrink, a herpetologist there. “This is the longest I’ve ever gone without catching snakes since I was 12 years old.” The Smithsonian Institution’s National Museum of Natural History likewise “is not putting people overseas,” says Director Kirk Johnson.

How COVID-19 has transformed scientific fieldwork, Elisabeth Pennisi, Science Magazine

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Collider Neutrinos...

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New territory Two candidate collider-neutrino events from the FASERν pilot detector in the plane longitudinal to (top) and transverse to (bottom) the beam direction. The different lines in each event show charged-particle tracks originating from the neutrino interaction point. Credit: FASER Collaboration.

Topics: CERN, High Energy Physics, Particle Physics, Research

Think “neutrino detector” and images of giant installations come to mind, necessary to compensate for the vanishingly small interaction probability of neutrinos with matter. The extreme luminosity of proton-proton collisions at the LHC, however, produces a large neutrino flux in the forward direction, with energies leading to cross-sections high enough for neutrinos to be detected using a much more compact apparatus.

In March, the CERN research board approved the Scattering and Neutrino Detector (SND@LHC) for installation in an unused tunnel that links the LHC to the SPS, 480 m downstream from the ATLAS experiment. Designed to detect neutrinos produced in a hitherto unexplored pseudo-rapidity range (7.2 < 𝜂 < 8.6), the experiment will complement and extend the physics reach of the other LHC experiments — in particular FASERν, which was approved last year. Construction of FASERν, which is located in an unused service tunnel on the opposite side of ATLAS along the LHC beamline (covering |𝜂|>9.1), was completed in March, while installation of SND@LHC is about to begin.

Both experiments will be able to detect neutrinos of all types, with SND@LHC positioned off the beamline to detect neutrinos produced at slightly larger angles. Expected to commence data-taking during LHC Run 3 in spring 2022, these latest additions to the LHC experiment family are poised to make the first observations of collider neutrinos while opening new searches for feebly interacting particles and other new physics.

Collider neutrinos on the horizon, Matthew Chalmers, CERN Courier

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Every Tank Has Its Limits...

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Topics: Biology, Planetary Science, Research, Tardigrades

They can survive temperatures close to absolute zero. They can withstand heat beyond the boiling point of water. They can shrug off the vacuum of space and doses of radiation that would be lethal to humans. Now, researchers have subjected tardigrades, microscopic creatures affectionately known as water bears, to impacts as fast as a flying bullet. And the animals survive them, too—but only up to a point. The test places new limits on their ability to survive impacts in space—and potentially seed life on other planets.

The research was inspired by a 2019 Israeli mission called Beresheet, which attempted to land on the Moon. The probe infamously included tardigrades on board that mission managers had not disclosed to the public, and the lander crashed with its passengers in tow, raising concerns about contamination. “I was very curious,” says Alejandra Traspas, a Ph.D. student at Queen Mary University of London who led the study. “I wanted to know if they were alive.”

Traspas and her supervisor, Mark Burchell, a planetary scientist at the University of Kent, wanted to find out whether tardigrades could survive such an impact—and they wanted to conduct their experiment ethically. So after feeding about 20 tardigrades moss and mineral water, they put them into hibernation, a so-called “tun” state in which their metabolism decreases to 0.1% of their normal activity, by freezing them for 48 hours.</em>

They then placed two to four at a time in a hollow nylon bullet and fired them at increasing speeds using a two-stage light gas gun, a tool in physics experiments that can achieve muzzle velocities far higher than any conventional gun. When shooting the bullets into a sand target several meters away, the researchers found the creatures could survive impacts up to about 900 meters per second (or about 3000 kilometers per hour), and momentary shock pressures up to a limit of 1.14 gigapascals (GPa), they report this month in Astrobiology. “Above [those speeds], they just mush,” Traspas says.</em>

Hardy water bears survive bullet impacts—up to a point, Jonathan O'Callaghan, Science Magazine

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Elephants, Mice, and Clocks...

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Topics: Biology, DNA, Evolution, Research

In her laboratory in Barcelona, Spain, Miki Ebisuya has built a clock without cogs, springs, or numbers. This clock doesn’t tick. It is made of genes and proteins, and it keeps time in a layer of cells that Ebisuya’s team has grown in its lab. This biological clock is tiny, but it could help to explain some of the most conspicuous differences between animal species.

Animal cells bustle with activity, and the pace varies between species. In all observed instances, mouse cells run faster than human cells, which tick faster than whale cells. These differences affect how big an animal gets, how its parts are arranged, and perhaps even how long it will live. But biologists have long wondered what cellular timekeepers control these speeds, and why they vary.

A wave of research is starting to yield answers for one of the many clocks that control the workings of cells. There is a clock in early embryos that beats out a regular rhythm by activating and deactivating genes. This ‘segmentation clock’ creates repeating body segments such as the vertebrae in our spines. This is the timepiece that Ebisuya has made in her lab.

“I’m interested in biological time,” says Ebisuya, a developmental biologist at the European Molecular Biology Laboratory Barcelona. “But lifespan or gestation period, they are too long for me to study.” The swift speed of the segmentation clock makes it an ideal model system, she says.

These cellular clocks help explain why elephants are bigger than mice, Michael Marshall, Nature

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VOC...

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Inside the B.1.1.7 Coronavirus Variant, By Jonathan Corum and Carl ZimmerJan, The New York Times, January 18, 2021

Topics: Biology, COVID-19, DNA, Research

VariantReported cases in the USNumber of Jurisdictions Reporting
B.1.1.716,27552
B.1.35138636
P.135625
Source: CDC

Download Accessible Data [XLS – 738 B]

CDC is closely monitoring these variants of concern (VOC). These variants have mutations in the virus genome that alter the characteristics and cause the virus to act differently in ways that are significant to public health (e.g., causes more severe disease, spreads more easily between humans, requires different treatments, changes the effectiveness of current vaccines).

CDC: US COVID-19 Cases Caused by Variants

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Weather Prediction...

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Observations of clouds, sunbeams, and birds—like those seen in this photo taken in Salisbury, UK—were important elements of classical weather forecasting. (Image courtesy of Peter Lawrence.)

Topics: History, Meteorology, Research

In August 1861 the London-based newspaper The Times published the world’s first “daily weather forecast.” The term itself was created by the enterprising meteorologist Robert FitzRoy, who wanted to distance his work from astrological “prognostications.” That story has led to a widespread assumption that weather forecasting is an entirely modern phenomenon and that in earlier periods only quackery or folklore-based weather signs were available.

However, more recent research has demonstrated that astronomers and astrologers in the medieval Islamic world drew widely on Greek, Indian, Persian, and Roman knowledge to create a new science termed astrometeorology. Central to the new science was the universal belief that the planets and their movements around Earth affected atmospheric conditions and weather. It was enthusiastically received in Christian Latin Europe and was further developed by Tycho Brahe, Johannes Kepler, and other astronomers. The drive to produce reliable weather forecasts led scientists to believe that astrometeorological forecasting could be more accurate if they used precise observations and records of weather to refine predictions for specific localities. Such records were kept across Europe beginning in the 13th century and were correlated with astronomical data, which paved the way for the data-driven forecasts produced by FitzRoy.1

Islamicate astrometeorologists were the first to replace the ancient practice of observing only short-term signs, such as clouds and the flight of birds, to predict the weather. They based their action on the hypothesis that weather is caused by the movements of planets and mediated by regional and seasonal climate conditions. Improved calculations of planetary orbits and updated geographical and meteorological information made the new science possible and compelling.

The prospect of acquiring reliable weather forecasts, closely linked to predictions of coming trends in human health and agricultural production, made the new meteorology attractive in Christian Europe too. Considerable pride shines through medieval Christian accounts of the weather questions that they could now start to answer. Central among them was one that classical meteorologists had failed to figure out: How can weather vary so much from one year to the next when the seasons are caused by regular, repeating patterns produced by Earth’s spherical shape and its interactions with the Sun?

Medieval weather prediction, Anne Lawrence-Mathers is a professor of history at the University of Reading in the UK. Physics Today

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Women's History Month, and CRISPR...

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Topics: Biology, Chemistry, DNA, Nobel Prize, Research, Women in Science

This year’s (2020) Nobel Prize in Chemistry has been awarded to two scientists who transformed an obscure bacterial immune mechanism, commonly called CRISPR, into a tool that can simply and cheaply edit the genomes of everything from wheat to mosquitoes to humans. 

The award went jointly to Emmanuelle Charpentier of the Max Planck Unit for the Science of Pathogens and Jennifer Doudna of the University of California, Berkeley, “for the development of a method for genome editing.” They first showed that CRISPR—which stands for clustered regularly interspaced short palindromic repeats—could edit DNA in an in vitro system in a paper published in the 28 June 2012 issue of Science. Their discovery was rapidly expanded on by many others and soon made CRISPR a common tool in labs around the world. The genome editor spawned industries working on making new medicines, agricultural products, and ways to control pests.

Many scientists anticipated that Feng Zhang of the Broad Institute, who showed 6 months later that CRISPR worked in mammalian cells, would share the prize. The institutions of the three scientists are locked in a fierce patent battle over who deserves the intellectual property rights to CRISPR’s discovery, which some estimate could be worth billions of dollars.

“The ability to cut DNA where you want has revolutionized the life sciences. The genetic scissors were discovered 8 years ago, but have already benefited humankind greatly,” Pernilla Wittung Stafshede, a chemical biologist at the Chalmers University of Technology, said at the prize briefing.

CRISPR was also used in one of the most controversial biomedical experiments of the past decade, when a Chinese scientist edited the genomes of human embryos, resulting in the birth of three babies with altered genes. He was widely condemned and eventually sentenced to jail in China, a country that has become a leader in other areas of CRISPR research.

Although scientists were not surprised Doudna and Charpentier won the prize, Charpentier was stunned. “As much as I have been awarded a number of prizes, it’s something you hear, but you don’t completely connect,” she said in a phone call with the Nobel Prize officials. “I was told a number of times that when it happens, you’re very surprised and feel that it’s not real.”

At a press briefing today, Doudna noted she was asleep and missed the initial calls from Sweden, only waking up to answer the phone finally when a Nature reporter called. "She wanted to know if I could comment on the Nobel and I said, Well, who won it? And she was shocked that she was the person to tell me."

CRISPR, the revolutionary genetic ‘scissors,’ honored by Chemistry Nobel, Jon Cohen, Science Magazine, AAAS

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Our Flexible Molecule...

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1 Soap, shampoo, and worm-like micelles Soaps and shampoos are made from amphiphilic molecules with water-loving (red) and water-hating (blue) parts that arrange themselves to form long tubes known as “worm-like micelles”. Entanglements between the tubes give these materials their pleasant, sticky feel. b The micelles can, however, disentangle themselves, just as entangled long-chain polymer molecules can slide apart too. In polymers, this process can be modeled by imagining the molecule sliding, like a snake, out of an imaginary tube formed by the surrounding spatial constraints. c Worm-like micelles can also morph their architecture by performing reconnections (left), breakages (down), and fusions (right). These operations occur randomly along the backbone, are in thermal equilibrium, and reversible. (Courtesy: Davide Michieletto)

Topics: Biology, DNA, Physics, Polymer Science, Research

DNA molecules are not fixed objects – they are constantly getting broken up and glued back together to adopt new shapes. Davide Michieletto explains how this process can be harnessed to create a new generation of “topologically active” materials.

Call me naïve, but until a few years ago I had never realized you can actually buy DNA. As a physicist, I’d been familiar with DNA as the “molecule of life” – something that carries genetic information and allows complex organisms, such as you and me, to be created. But I was surprised to find that biotech firms purify DNA from viruses and will ship concentrated solutions in the post. In fact, you can just go online and order DNA, which is exactly what I did. Only there was another surprise in store.

When the DNA solution arrived at my lab in Edinburgh, it came in a tube with about half a milligram of DNA per centimeter cube of water. Keen to experiment on it, I tried to pipette some of the solution out, but it didn’t run freely into my plastic tube. Instead, it was all gloopy and resisted the suction of my pipette. I rushed over to a colleague in my lab, eagerly announcing my amazing “discovery”. They just looked at me like I was an idiot. Of course, solutions of DNA are gloopy.

I should have known better. It’s easy to idealize DNA as some kind of magic material, but it’s essentially just a long-chain double-helical polymer consisting of four different types of monomers – the nucleotides A, T, C, and G, which stack together into base pairs. And like all polymers at high concentrations, the DNA chains can get entangled. In fact, they get so tied up that a single human cell can have up to 2 m of DNA crammed into an object just 10 μm in size. Scaled up, it’s like storing 20 km of hair-thin wire in a box no bigger than your mobile phone.

Make or break: building soft materials with DNA, Davide Michieletto is a Royal Society university research fellow in the School of Physics and Astronomy, University of Edinburgh

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Haplotypes and Neanderthals...

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a, Manhattan plot of a genome-wide association study of 3,199 hospitalized patients with COVID-19 and 897,488 population controls. The dashed line indicates genome-wide significance (P = 5 × 10−8). Data were modified from the COVID-19 Host Genetics Initiative2 (https://www.covid19hg.org/). b, Linkage disequilibrium between the index risk variant (rs35044562) and genetic variants in the 1000 Genomes Project. Red circles indicate genetic variants for which the alleles are correlated to the risk variant (r2 > 0.1) and the risk alleles match the Vindija 33.19 Neanderthal genome. The core Neanderthal haplotype (r2 > 0.98) is indicated by a black bar. Some individuals carry longer Neanderthal-like haplotypes. The location of the genes in the region is indicated below using standard gene symbols. The x-axis shows hg19 coordinates.

Topics: Biology, COVID-19, Genetics, Research

Abstract

A recent genetic association study1 identified a gene cluster on chromosome 3 as a risk locus for respiratory failure after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A separate study (COVID-19 Host Genetics Initiative)2 comprising 3,199 hospitalized patients with coronavirus disease 2019 (COVID-19) and control individuals showed that this cluster is the major genetic risk factor for severe symptoms after SARS-CoV-2 infection and hospitalization. Here we show that the risk is conferred by a genomic segment of around 50 kilobases in size that is inherited from Neanderthals and is carried by around 50% of people in South Asia and around 16% of people in Europe.

Main

The COVID-19 pandemic has caused considerable morbidity and mortality and has resulted in the death of over a million people to date3. The clinical manifestations of the disease caused by the virus, SARS-CoV-2, vary widely in severity, ranging from no or mild symptoms to rapid progression to respiratory failure4. Early in the pandemic, it became clear that advanced age is a major risk factor, as well as being male and some co-morbidities5. These risk factors, however, do not fully explain why some people have no or mild symptoms whereas others have severe symptoms. Thus, genetic risk factors may have a role in disease progression. A previous study1 identified two genomic regions that are associated with severe COVID-19: one region on chromosome 3, which contains six genes, and one region on chromosome 9 that determines ABO blood groups. Recently, a dataset was released by the COVID-19 Host Genetics Initiative in which the region on chromosome 3 is the only region that is significantly associated with severe COVID-19 at the genome-wide level (Fig. 1a). The risk variant in this region confers an odds ratio for requiring hospitalization of 1.6 (95% confidence interval, 1.42–1.79) (Extended Data Fig. 1).

The genetic variants that are most associated with severe COVID-19 on chromosome 3 (45,859,651–45,909,024 (hg19)) are all in high linkage disequilibrium (LD)—that is, they are all strongly associated with each other in the population (r2 > 0.98)—and span 49.4 thousand bases (kb) (Fig. 1b). This ‘core’ haplotype is furthermore in weaker linkage disequilibrium with longer haplotypes of up to 333.8 kb (r2 > 0.32) (Extended Data Fig. 2). Some such long haplotypes have entered the human population by gene flow from Neanderthals or Denisovans, extinct hominins that contributed genetic variants to the ancestors of present-day humans around 40,000–60,000 years ago6,7. We, therefore, investigated whether the haplotype may have come from Neanderthals or Denisovans.

The major genetic risk factor for severe COVID-19 is inherited from Neanderthals, Hugo Zeberg, & Svante Pääbo, Nature

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