The results : The most striking result is the very high estimated probability of winning when batting second in Dubai (where Australia triumphed in the tournament’s final). Even when the batting-second team was ranked lower than its opponent, there still was a high estimated probability of victory.

The analysis revealed some evidence that it was beneficial to bat second in this world cup, but this is likely to depend greatly on the conditions. If we assume a match is played on a randomly selected pitch from the four venues used, and there is a 50% chance the higher-ranked team bats second, my model estimates the probability of winning when batting second is around 0.6, with a 95% confidence interval of 0.48 to 0.71.

So there is a likely benefit to batting second, but it’s far from a foregone conclusion.

https://theconversation.com/does-batting-second-in-t20-world-cup-cr...

Part 4

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Researchers find the finger snap to have the highest acceleration the human body produces

Snapping of fingers: Using an intermediate amount of friction, not too high and not too low, a snap of the finger produces the highest rotational accelerations observed in humans, even faster than the arm of a professional baseball pitcher. The results were published Nov. 17 in the Journal of the Royal Society Interface.

 In earlier work researc

hers had developed a general framework for explaining the surprisingly powerful and ultrafast motions observed in living organisms. The framework seemed to naturally apply to the snap. It posits that organisms depend on the use of a spring and latching mechanism to store up energy, which they can then quickly release.

Using high-speed imaging, automated image processing, and dynamic force sensors, the researchers analyzed a variety of finger snaps. They explored the role of friction by covering fingers with different materials, including metallic thimbles to simulate the effects of trying to snap while wearing a metallic gauntlet, much like Thanos.

For an ordinary snap with bare fingers, the researchers measured maximal rotational velocities of 7,800 degrees per second and rotational accelerations of 1.6 million degrees per second squared. The rotational velocity is less than that measured for the fastest rotational motions observed in humans, which come from the arms of professional baseball players during the act of pitching. However, the snap acceleration is the fastest human angular acceleration yet measured, almost three times faster than the rotational acceleration of a professional baseball pitcher's arm.

The finger snap occurs in only seven milliseconds, more than twenty times faster than the blink of an eye, which takes more than 150 milliseconds.

When the fingertips of the subjects were covered with metal thimbles, their maximal rotational velocities decreased dramatically, confirming the researchers' imaginations.

Reducing both the compressibility and friction of the skin by using things like metal armours make it a lot harder to build up enough force in your fingers to actually snap.

Surprisingly, increasing the friction of the fingertips with rubber coverings also reduce speed and acceleration. The researchers concluded that a Goldilocks zone of friction was necessary—too little friction and not enough energy was stored to power the snap, and too much friction led to energy dissipation as the fingers took longer to slide past each other, wasting the stored energy into heat.

The ultrafast snap of a finger is mediated by skin friction, Journal of the Royal Society Interface (2021). DOI: 10.1098/rsif.2021.0672. rsif.royalsocietypublishing.or … .1098/rsif.2021.0672

https://phys.org/news/2021-11-art-finger-snap-highest-human.html?ut...

Understanding how proteins are broken down in cells using advanced microscopes

How do organisms break down proteins when they are finished doing their job?

Protein degradation is a carefully orchestrated process. Proteins are marked for disposal with a molecular label called ubiquitin, and then fed into proteasomes, a kind of cellular paper shredder that chops up the proteins into small pieces. This process of ubiquitination, or labeling proteins with ubiquitin, is involved in a wide range of cellular processes, including cell division, DNA repair, and immune responses.

In a new study published in Nature on November 17, 2021, researchers used advanced electron microscopes to delve deeper into the process of protein degradation. They described the structure of a key enzyme that helps mediate ubiquitination in yeast, part of a cellular process called the N-degron pathway that may be responsible for determining the rate of degradation for up to 80% of equivalent proteins in humans. Malfunctions in this pathway can lead to accumulation of damaged or misfolded proteins, which underlies the aging process, neurodegeneration, and some rare autosomal recessive disorders, so understanding it better provides an opportunity to develop treatments.

Researchers were able to describe the structure of several intermediate enzyme complexes involved in the pathway, which will help researchers looking for ways to target proteins with drugs or intervene in a malfunctioning protein degradation process.

 Minglei Zhao, Structural insights into Ubr1-mediated N-degron polyubiquitination, Nature (2021). DOI: 10.1038/s41586-021-04097-8. www.nature.com/articles/s41586-021-04097-8

https://phys.org/news/2021-11-advanced-microscopes-scientists-cells...

**

Using nematodes to sniff out cancer

 A screening test using tiny worms to detect early signs of pancreatic cancer in urine has been developed by a  biotech firm, which hopes it could help boost routine screening.

Scientists have long known that the bodily fluids of cancer patients smell different to those of healthy people, with dogs trained to detect the disease in breath or urine samples.

But Hirotsu Bio Science has genetically modified a type of worm called "C. elegans" -- around one millimetre long, with an acute sense of smell -- to react to the urine of people with pancreatic cancer, which is notoriously difficult to detect early.

The  firm has already used the worms to detect cancer in screening tests, though without specifying which type.

The new test is not meant to diagnose pancreatic cancer, but could help boost routine screening as urine samples can be collected at home without the need for a hospital visit.

 If the worms raise the alarm, the patient would then be referred to a doctor for further testing. In separate tests conducted by the firm, the worms correctly identified all 22 urine samples from pancreatic cancer patients, including people with early stages of the disease.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0...

https://researchnews.cc/news/10038/What-a-worm--Japan-firm-uses-nem...

Seaweed-Like Device Generates Electricity Underwater

Energizer atoms: Physicists find new way to keep atoms excited

Researchers have tricked nature by tuning a dense quantum gas of atoms to make a congested "Fermi sea," thus keeping atoms in a high-energy state, or excited, for about 10% longer than usual by delaying their normal return to the lowest-energy state. The technique might be used to improve quantum communication networks and atomic clocks.

Quantum systems such as atoms that are excited above their resting state naturally calm down, or decay, by releasing light in quantized portions called photons. This common process is evident in the glow of fireflies and emission from LEDs. The rate of decay can be engineered by modifying the environment or the internal properties of the atoms. Previous research has modified the electromagnetic environment; the new work focuses on the atoms.

The new  method relies on a rule of the quantum world known as the Pauli exclusion principle, which says identical fermions (a category of particles) can't share the same quantum states at the same time. Therefore, if enough fermions are in a crowd—creating a Fermi sea—an excited fermion might not be able to fling out a photon as usual, because it would need to then recoil. That recoil could land it in the same quantum state of motion as one of its neighbors, which is forbidden due to a mechanism called Pauli blocking.

The blocking achievement is described in the Nov. 19 issue of Science. 

Pauli blocking uses well-organized quantum motional states of a Fermi sea to block the recoil of an atom that wants to decay, thus prohibiting spontaneous decay. It is a profound quantum effect for the control of matter's properties that was previously deemed unchangeable.

Christian Sanner et al, Pauli blocking of atom-light scattering, Science (2021). DOI: 10.1126/science.abh3483. www.science.org/doi/10.1126/science.abh3483

https://phys.org/news/2021-11-energizer-atoms-physicists.html?utm_s...

Host immunity drives viral evolution of dengue

New research by a team of investigators, provides evidence that host immunity drives evolution of the dengue virus. The work, published recently in Science, retrospectively analyzes two decades of dengue virus genetic variation from Thailand, alongside population-level measures of infection and immunity.

There are four types of dengue virus, and all four have co-circulated in Thailand since the early 1960s. This provides an opportunity to study how the viruses compete against each other for human hosts.

Dengue virus types are grouped according to how their surface proteins, or antigens, interact with infection-fighting antibodies in human blood. The four types, also called serotypes, are noted as DENV1 through DENV4. Although there is genetic variation between each dengue virus type, there is also variation within each dengue virus type.

Part 1

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The new study used 1,944 archival blood samples from Bangkok. The samples were preserved from people known to be ill with dengue and they represent all four dengue virus strains from every year between 1994 and 2014. The team genetically sequenced more than 2,000 virus samples.

The researchers then performed tests on a smaller subset of samples that represented a time series of each strain. From this, they then characterized the antigenic relationship of the strains to each other through time. Antigenic relationships characterize how well an immune response to one virus protects against other viruses.

Researchers  found that there is a pattern like influenza, where you get different viruses every year that are driven by natural selection for viruses that evade the human immune response to the population.  This work shown that that this is also happening with dengue.

The team used a process called antigenic cartography which makes a map to visualize the relatedness of viruses.

"When two viruses are close on that map, then that means immune responses 'sees' the viruses as similar," Katzelnick says. "For example, if you are infected with one virus, then an immune response to that virus would protect you against another virus that is nearby on the map."

The team found an overall pattern of dengue virus strains evolving away from each other over the 20-year study timeframe. While the serotypes at times oscillated closer, in general they grew further apart.

Part 2

the results also show a clear inverse relationship between the level of antigenic diversity in a given year and epidemic levels. When Thailand experienced large epidemic outbreaks, antigenic diversity was low. But in years when epidemic levels were lower than average, the antigenic diversity was higher.

"In general, it's been thought that if you get infected with one serotype of DENV then you are immune to that serotype for the rest of your life. But there have been observations where that seems to not be strictly true."

One explanation for re-infections is that dengue viruses may be subject to natural selective forces to evade the immune system of previously infected individuals. In essence, they must change just enough to avoid immune detection in a host where another serotype has already caused an infection.

These findings suggest that the dengue viruses are moving away from the viruses that generated immunity in the population in the past. It's sort of like the flu story, dengue is evolving to escape the immunity that is in the population at any particular time. But it seems to be happening at a slower pace with dengue than influenza.

Researchers already knew that there is a complex interplay between immunity and the dengue virus. When someone is exposed to a serotype of this virus, they will typically experience a mild infection that results in partial infection. But when they are exposed again, the partial immunity can trigger an overreaction that can lead to serious outcomes. The dengue virus appears, in these cases, to not only evade the immune response, but use it to its advantage to potentially increase its rate of growth.

Ninety to 95% of the people showing up at a hospital in Bangkok with dengue are having their second infection. "And most people who live their whole lives in Bangkok are getting infected multiple times."

This enhanced infection phenomenon may also contribute to the evolution of the pathogen, selecting for viruses that are similar enough to take advantage of the Immune response.

Overall, viruses were growing more different from each other over time, but scientists also observed that they grew closer together during some periods of time, particularly early in the time series. This indicates a tradeoff between evading immunity and taking advantage of partial immunity.

This paper is suggesting that the dengue viruses are changing and we need to update how we do surveillance to better understand immunity in populations and to ultimately reduce the number of people who get sick.

Leah Katzelnick et al, Antigenic evolution of dengue viruses over 20 years, Science (2021). DOI: 10.1126/science.abk0058. www.science.org/doi/10.1126/science.abk0058

https://phys.org/news/2021-11-host-immunity-viral-evolution-dengue....

Part 3

Cancer cells use 'tiny tentacles' to suppress the immune system

To grow and spread, cancer cells must evade the immune system. Investigators from Brigham and Women's Hospital and MIT used the power of nanotechnology to discover a new way that cancer can disarm its would-be cellular attackers by extending out nanoscale tentacles that can reach into an immune cell and pull out its powerpack. Slurping out the immune cell's mitochondria powers up the cancer cell and depletes the immune cell. The new findings, published in Nature Nanotechnology, could lead to new targets for developing the next generation of immunotherapy against cancer.

Cancer kills when the immune system is suppressed and cancer cells are able to metastasize, and it appears that nanotubes can help them do both. This is a completely new mechanism by which cancer cells evade the immune system and it gives us a new target to go after.

To investigate how cancer cells and immune cells interact at the nanoscale level, researchers set up experiments in which they co-cultured breast cancer cells and immune cells, such as T cells. Using field-emission scanning electron microscopy, they caught a glimpse of something unusual: Cancer cells and immune cells appeared to be physically connected by tiny tendrils, with widths mostly in the 100-1000 nanometer range. (For comparison, a human hair is approximately 80,000 to 100,000 nanometers). In some cases, the nanotubes came together to form thicker tubes. The team then stained mitochondria—which provide energy for cells—from the T cells with a fluorescent dye and watched as bright green mitochondria were pulled out of the immune cells, through the nanotubes, and into the cancer cells.

By carefully preserving the cell culture condition and observing intracellular structures, researchers saw these delicate nanotubes and they were stealing the immune cells' energy source. It was very exciting because this kind of behavior had never been observed before in cancer cells. The researchers then looked to see what would happen if they prevented the cancer cells from hijacking mitochondria. When they injected an inhibitor of nanotube formation into mouse models used for studying lung cancer and breast cancer, they saw a significant reduction in tumor growth.

Hae Jang, Intercellular nanotubes mediate mitochondrial trafficking between cancer and immune cells, Nature Nanotechnology (2021). DOI: 10.1038/s41565-021-01000-4. www.nature.com/articles/s41565-021-01000-4

https://phys.org/news/2021-11-cancer-cells-tiny-tentacles-suppress....

Warmer soil stores less carbon: study

Global warming will cause the world's soil to release carbon, new research shows.

Scientists used data on more than 9,000 soil samples from around the world, and found that carbon storage "declines strongly" as average temperatures increase.

This is an example of a "positive feedback", where global warming causes more carbon to be released into the atmosphere, further accelerating climate change.

Importantly, the amount of carbon that could be released depends on the soil type, with coarse-textured (low-clay) soils losing three times as much carbon as fine-textured (clay-rich) soils.

The researchers  say their findings help to identify vulnerable carbon stocks and provide an opportunity to improve Earth System Models (ESMs) that simulate future climate change.

Because there is more carbon stored in soils than there is in the atmosphere and all the trees on the planet combined, releasing even a small percentage could have a significant impact on our climate.

This analysis identified the carbon stores in coarse-textured soils at high-latitudes (far from the Equator) as likely to be the most vulnerable to climate change.

Such stores, therefore, may require particular attention given the high rates of warming taking place in cooler regions.

In contrast, researchers found carbon stores in fine-textured soils in tropical areas to be less vulnerable to climate warming.

By comparing carbon storage in places with different average temperatures, the researchers estimated the likely impact of global warming.

For every 10°C of increase in temperature, average carbon storage (across all soils) fell by more than 25%.

These results make it clear that, as temperatures rise, more and more carbon is release from soil.

The differences in carbon storage based on soil texture occur because finer soils provide more mineral surface area for carbon-based organic material to bond to, reducing the ability of microbes to access and decompose it.

Temperature effects on carbon storage are controlled by soil stabilisation capacities, Nature Communications (2021). DOI: 10.1038/s41467-021-27101-1

https://phys.org/news/2021-11-warmer-soil-carbon.html?utm_source=nw...

Severe spinal cord injuries repaired with 'dancing molecules'

https://www.youtube.com/watch?v=Q_xvCE904YU&t=184s

The Birth of Microbiology

Dengue antibodies can knock out Zika—and vice versa

Cross-protective antibodies from dengue and Zika last far longer than previously thought, scientists have found in a massive study involving more than 4,000 children in Nicaragua.

The 11-year longitudinal analysis unexpectedly revealed that antibodies from either dengue or Zika—which naturally protect against infections caused by either virus—remain stable for years and do not precipitously wane.

Solving scientific mysteries about old foes such as dengue, and an emerging infection like Zika, helps lay the scientific groundwork for better responding to future outbreaks.

It has been previously thought that initial infection with dengue or Zika [viruses] leads to antibodies that are initially protective but wane over time to a point where they become enhancing and drive severe disease.

Cross-reactive antibody protection became abundantly clear during the Zika epidemic of 2015, which swept through multiple Caribbean, Central and South American countries. Stunningly, the incidence of dengue disease dropped dramatically in the midst of the surging Zika outbreak. Dengue and Zika are members of the same family of flaviviruses, so patients who had recovered from dengue infections had cross-protective antibodies capable of neutralizing dengue and Zika. Both viruses are carried by Aedes aegypti mosquitoes.

Yet, previous studies had suggested that the cross-reactive antibodies lasted only two years before dropping to levels that actually made future dengue infections more likely. Scientists in 2015 also had recognized—at least anecdotally—that some people surprisingly had immune protection against the newly emerged Zika virus.

So scientists designed a new study to understand this that allowed them to track antibody responses to initial and secondary dengue as well as to Zika infections. The team focused on community-based and hospital cohorts of children in Nicaragua. To their surprise, instead of diminishing, the antibody kenetics research allowed the scientists to conclude that cross-protective antibodies remained stable for as long as 11 years.

They found that t overall dengue virus iELISA titers stabilized by eight months after primary dengue infection to a half-life longer than a human life and [then] waned.

The half-life, which is longer than a human life, was estimated at 130,000 years, according to the team's research.

The team also observed cross-protective antibodies that were similarly stable in children who were infected with Zika virus. However, the amount of cross-protective antibodies differed across children, which suggests that the quantity of antibodies determines the degree of protection.

Leah C. Katzelnick et al, Dengue and Zika virus infections in children elicit cross-reactive protective and enhancing antibodies that persist long term, Science Translational Medicine (2021). DOI: 10.1126/scitranslmed.abg9478

https://medicalxpress.com/news/2021-11-secrets-antibodies-dengue-zi...

Scientists develop promising vaccine method against recurrent UTI

Researchers are investigating the use of whole-cell vaccines to fight urinary tract infection (UTI), part of an effort to tackle the increasingly serious issue of antibiotic-resistant bacteria. They  recently demonstrated the use of metal-organic frameworks (MOFs) to encapsulate and inactivate whole bacterial cells to create a "depot" that allows the vaccines to last longer in the body.

The resulting study, published online Sept. 21 in the American Chemical Society's journal ACS Nano, showed that in mice this method produced substantially enhanced antibody production and significantly higher survival rates compared to standard whole-cell vaccine preparation methods.

Vaccination as a therapeutic route for recurrent UTIs is being explored because antibiotics aren't working anymore. Patients are losing their bladders to save their lives because the bacteria cannot be killed by antibiotics or because of an extreme allergy to antibiotics, which is more common in the older population than people may realize. If not successfully treated, a UTI can lead to sepsis, which can be fatal. Even if you clear the bacteria from the bladder, populations persist elsewhere and usually become resistant to the antibiotic used. When patients accumulate antibiotic resistances, they're eventually going to run out of options.

Vaccines work by introducing a small amount of killed or weakened disease-causing germs, or some of their components, to the body. These antigens prompt the immune system to produce antibodies against a particular disease. Building vaccines against pathogenic bacteria is inherently difficult because bacteria are significantly larger and more complex than viruses. Selecting which biological components to use to create antigens has been a major challenge.

Consequently, using the entire cell is preferable to choosing just a piece of a bacterium

part 1

Vaccines using whole-cell dead bacteria haven't succeeded because the cells typically don't last long enough in the body to produce long-term, durable immune responses.

That's the reason for  this new MOF antigen depot: It allows an intact, dead pathogen to exist in tissue longer, as if it were an infection, in order to trigger a full-scale immune system response.

The metal-organic framework Gassensmith's team developed encapsulates and immobilizes an individual bacterium cell in a crystalline polymeric matrix that not only kills the bacterium but also preserves and stabilizes the dead cell against high temperature, moisture and organic solvents.

In their experiments, the researchers used a strain of Escherichia coli. There are no vaccines against any pathogenic strain of this bacterium. Uropathogenic E. coli causes about 80% of all community-acquired UTIs.

"When we challenged these mice with a lethal injection of bacteria, after they were vaccinated, almost all of our animals survived, which is a much better performance than with traditional vaccine approaches," Gassensmith said. "This result was repeated multiple times, and we're quite impressed with how reliable it is."

Although the method has not yet been tested in humans, De Nisco said it has the potential to help millions of patients.

part 2

This study on UTI was a proof of concept that whole-cell vaccines are more effective in this extreme, lethal-sepsis model. Showing that this works against recurrent UTI would be a significant breakthrough.

Beyond recurrent UTI or urosepsis, researchers think the antigen depot method could be applied broadly to bacterial infections, including endocarditis and tuberculosis.

Michael A. Luzuriaga et al, Metal–Organic Framework Encapsulated Whole-Cell Vaccines Enhance Humoral Immunity against Bacterial Infection, ACS Nano (2021). DOI: 10.1021/acsnano.1c03092

https://phys.org/news/2021-11-scientists-vaccine-method-recurrent-u...

Part 3

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Why do frozen turkeys explode when deep-fried?

Deep-frying a turkey is a great way to get a delicious, moist meal for Thanksgiving. But this method of cooking can be a very dangerous undertaking.

Every fall, millions of dollars of damage, trips to the ER and even deaths result from attempts to deep-fry turkeys. The vast majority of these accidents happen because people put frozen turkeys into boiling oil. If you are considering deep-frying this year, do not forget to thaw and dry your turkey before placing it in the pot. Failure to do so may lead to an explosive disaster.

What is so dangerous about putting even a partially frozen turkey in a deep-fryer?

The reason frozen turkeys explode, at its core, has to do with differences in density. Density is how much an object weighs given a specific volume. There is a difference in density between oil and water and differences in the density of water between its solid, liquid and gas states. When these density differences interact in just the right way, you get an explosion.

The first important density difference when it comes to frying is that water is more dense than oil. This has to do with how tightly the molecules of each substance pack together and how heavy the atoms are that make up each liquid.

Water molecules are small and pack tightly together. Oil molecules are much larger and don't pack together as well by comparison. Additionally, water is composed of oxygen and hydrogen atoms, while oils are predominantly carbon and hydrogen. Oxygen is heavier than carbon. This means that, for example, one cup of water has more atoms than one cup of oil, and those individuals atoms are heavier. This is why oil floats on top of water. It is less dense.

Part 1

While different materials have different densities, liquids, solids and gases of a single material can have different densities as well. You observe this every time you place an ice cube in a glass of water: The ice floats to the top because it is less dense than water.

When water absorbs heat, it changes to its gas phase, steam. Steam occupies 1,700 times the volume as the same number of liquid water molecules. You observe this effect when you boil water in a tea kettle. The force of expanding gas pushes steam out of the kettle through the whistle, causing the squealing noise.

Part 2

Frozen turkeys—or any kind of frozen meats, for that matter—contain a lot of ice. Raw meat can be anywhere from 56% to 73% water. If you have ever thawed a frozen piece of meat, you have probably seen all the liquid that comes out.

For deep-frying, cooking oil is heated to around 350 degrees Fahrenheit (175 C). This is much hotter than the boiling point of water, which is 212 F (100 C). So when the ice in a frozen turkey comes in contact with the hot oil, the surface ice quickly turns to steam.

This quick transition is not a problem when it happens at the very surface of the oil. The steam escapes harmlessly into the air.

However, when you submerge a turkey into the oil, the ice inside the turkey absorbs the heat and melts, forming liquid water. Here is where the density comes into play.

This liquid water is more dense than the oil, so it falls the bottom of the pot. The water molecules continue to absorb heat and energy and eventually they change phases and become steam. The water molecules then rapidly spread far apart from one another and the volume expands by 1,700 times. This expansion causes the density of the water to drop to a fraction of a percent of the density of the oil, so the gas wants to quickly rise to the surface.

Combine the fast change in density together with the expansion of volume and you get an explosion. The steam expands and rises, blowing the boiling oil out the pot. If that weren't dangerous enough, as the displaced oil comes into contact with a burner or flame, it can catch fire. Once some droplets of oil catch on fire, the flames will quickly ignite nearby oil molecules, resulting in a fast-moving and often catastrophic fire.

Every year, thousands of accidents like this happen. So, should you decide to deep-fry a turkey for this year's Thanksgiving, be sure to thoroughly thaw it and pat it dry. And next time you add a bit of liquid to an oil-filled pan and end up with oil all over the stove, you'll know the science of why.

https://theconversation.com/why-do-frozen-turkeys-explode-when-deep...

Part 3

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Artificial lights are disrupting firefly mating, putting them on the road to extinction

Light pollution impacts mating success and courtship behavior in fireflies, says recent study.

According to a 2019 study, artificial light impacts fireflies in a big way. Fireflies find mates through a courtship process that involves flashing their “lights.” And not just any light: the courting process involves a series of flashes, which are unique to each male and female. Females will choose their mate based on their unique flashing patterns. The females, in turn, will start a flashing “dialogue” with the mate of their choosing. It’s an amazing sight to see.

So how does this courtship process clash with the lights we keep on at night? Fireflies rely on light to communicate, which has led scientists to wonder if light pollution impacts them in some way. Prior studies by the researchers confirmed this, as well as a substantial body of research. So the next logical question, and the one that the researchers tackled, was how this lighting impacts fireflies at the most basic level: courtship.

In these lighted zones, the fireflies were less likely to engage in courtship flashes, and mating success was reduced. The researchers also investigated whether light pollution affected predator-prey relationships, but no significant impact was found.

Outdoor LED lighting spaces, like the one used in this study, can also act as demographic traps, say the researchers. That means that immigration (or the amount of fireflies coming into the area) far exceeds emigration (the amount of fireflies leaving the area) – meaning that fireflies, barring other circumstances, will stay in the lit areas. While the fireflies may be loving the bright LED lights, the lighting affects courtship behaviors, which are significantly reduced, and also likely reduces mating success.

Fireflies are attracted to light but this light “sucks” them in. It’s like how a warm, cozy house is where you want to be on a cold winter day. It attracts you and you don’t want to leave. In the same way, fireflies are attracted to our bright LEDs and don’t want to leave the light. More fireflies enter the area, and then leave. They are attracted to it like a trap. But, like how it’s not healthy for us to stay home all the time, it’s not healthy for fireflies to stay attracted to this light. Fireflies rely on ambient light cues to know when to start courtship flashing, but when the environment is always lit, there is a problem. Courtship behaviors go down and breeding success is also likely to go down.

This is a huge problem – light pollution is one of the fastest growing types of environmental degradation

https://next.massivesci.com/articles/artificial-light-led-impacts-f...

**

Probing the mystery of how stem cells age

The intestinal microbiota shapes gut physiology and regulates enteric neurons and glia

Brief period of 'blindness' is essential for vision

 Fixational eye movements are tiny movements of the eye—so small we humans aren’t even aware of them. Yet they play a large role in our ability to see letters, numbers, and objects at a distance.

In a new paper published in Proceedings of the National Academy of Sciences, researchers  further cement the evidence for the important role of these tiny movements. By studying how a type of fixational eye movement called a microsaccade affects the foveola, a small region at the center of the retina, the researchers provide important foundational information that can lead to improved treatments and therapies for vision impairments.

Although the foveola is tiny, it is essential for seeing fine details and conducting everyday tasks such as searching for a friend in a crowd or reading distant road signs while driving. Because the region is so small, however, we need to constantly shift our gaze to allow the foveola to get a full view of the world, similar to rotating a telescope to get a full view of a scene. Unlike when we might rotate a telescope, however, our eyes make most of these gaze shifts, especially the smallest ones, on their own, often beneath our awareness. But the gaze shifts are critical for vision. How well we see at any given moment is tightly linked to how and when we shift our gaze.

The researchers focused on microsaccades, tiny rapid gaze shifts that frequently occur when we’re examining fine details. It’s long been known that vision is transiently impaired during larger gaze shifts, such as those we are aware of making, for instance looking back and forth between two computer screens. This phenomenon of transiently impaired vision is known as saccadic suppression. Until now, however, it was unknown whether a suppression also occurs during microsaccades and whether that would affect visibility in the foveola.

The researchers recorded microsaccades in human observers who were engaged in a computer task— searching on the screen for “fleas” jumping in a patch of “fur,” a task that resembles social grooming in primates.

What the researchers found was surprising. 
Immediately before and immediately after participants’ gaze shifted, the participants could not see the fleas, even when they were looking directly at them.

Researchers observed that microsaccades are accompanied by brief periods of visual suppression during which people are essentially blind. However, the researchers found that vision recovered rapidly at the center of the gaze and continued to improve, so that vision was overall transiently enhanced in this region after the saccade.

The results show that the very center of gaze undergoes drastic and rapid modulations every time we redirect our gaze. This brief loss of vision likely occurs so that we do not see the image of the world shifting around whenever we move our eyes. By suppressing perception during saccades, our visual system is able to create a stable percept.

Future research will determine more about this phenomenon and how humans control eye movements to balance the saccadic suppression with the visual enhancement that follows.

https://www.pnas.org/content/118/37/e2101259118

https://www.rochester.edu/newscenter/brief-period-of-blindness-is-e...

https://researchnews.cc/news/10116/Brief-period-of--blindness--is-e...

How sugar-loving microbes could help power future cars

It sounds like modern-day alchemy: Transforming sugar into hydrocarbons found in gasoline.

But that's exactly what scientists have done.

In a forthcoming study in Nature Chemistry, researchers report harnessing the wonders of biology and chemistry to turn glucose (a type of sugar) into olefins (a type of hydrocarbon, and one of several types of molecules that make up gasoline).

Olefins comprise a small percentage of the molecules in gasoline as it's currently produced, but the process the team developed could likely be adjusted in the future to generate other types of hydrocarbons as well, including some of the other components of gasoline. Olefins have non-fuel applications, as they are used in industrial lubricants and as precursors for making plastics.

To complete the study, the researchers began by feeding glucose to strains of E. coli that don't pose a danger to human health. These microbes are sugar junkies. 

The E. coli in the experiments were genetically engineered to produce a suite of four enzymes that convert glucose into compounds called 3-hydroxy fatty acids. As the bacteria consumed the glucose, they also started to make the fatty acids.

To complete the transformation, the team used a catalyst called niobium pentoxide (Nb2O5) to chop off unwanted parts of the fatty acids in a chemical process, generating the final product: the olefins.

The scientists identified the enzymes and catalyst through trial and error, testing different molecules with properties that lent themselves to the tasks at hand. Using this method, they were able to make olefins directly from glucose.

Zhen Wang, A dual cellular–heterogeneous catalyst strategy for the production of olefins from glucose, Nature Chemistry (2021). DOI: 10.1038/s41557-021-00820-0. www.nature.com/articles/s41557-021-00820-0

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Scientists are also interested in increasing the yield. Currently, it takes 100 glucose molecules to produce about 8 olefin molecules, Wang says. She would like to improve that ratio, with a focus on coaxing the E. coli to produce more of the 3-hydroxy fatty acids for every gram of glucose consumed.

https://phys.org/news/2021-11-sugar-loving-microbes-power-future-ca...

 How longer lives are tied to physical activity: evolutionary explanation for why lack of physical activity as humans age increases disease risk and reduces longevity.

You know exercise is good for you. Some people can even rattle off reasons it keeps your muscles and joints strong, and how it fights off certain diseases. But  can  you tell the story of why and how physical activity was built into human biology?

A team of evolutionary biologists and biomedical researchers from Harvard are taking a run at it (sometimes literally) in a new study published in PNAS. The work lays out evolutionary and biomedical evidence showing that humans, who evolved to live many decades after they stopped reproducing, also evolved to be relatively active in their later years.

The researchers say that physical activity later in life shifts energy away from processes that can compromise health and toward mechanisms in the body that extend it. They hypothesize that humans evolved to remain physically active as they age—and in doing so to allocate energy to physiological processes that slow the body's gradual deterioration over the years. This guards against chronic illnesses such as cardiovascular disease, type 2 diabetes, and even some cancers.

Researchers examined two pathways by which lifelong physical activity reallocates energy to improve health. The first involves dealing excess energy away from potentially harmful mechanisms, like excess fat storage. The team also identified how physical activity allocates energy to repair and maintenance processes. The paper shows that besides burning calories, physical activity is physiologically stressful, causing damage to the body at the molecular, cellular, and tissue levels. The body's response to this damage, however, is essentially to build back stronger.

This includes repairing tears in muscle fibers, repairing cartilage damage, and healing microfractures. The response also causes the release of exercise-related antioxidants and anti-inflammatories, and enhances blood flow. In the absence of physical activity, these responses are activated less. The cellular and DNA repair processes have been shown to lower the risk of diabetes, obesity, cancer, osteoporosis, Alzheimer's, and depression.

The key take-home point is that because we evolved to be active throughout our lives, our bodies need physical activity to age well. In the past, daily physical activity was necessary in order to survive, but today we have to choose to exercise, that is do voluntary physical activity for the sake of health and fitness.

The active grandparent hypothesis: Physical activity and the evolution of extended human healthspans and lifespans, PNAS (2021). DOI: 10.1073/pnas.2107621118

https://phys.org/news/2021-11-outlines-longer-tied-physical.html?ut...

Crazy plan  to give Mars an artificial magnetosphere

Terraforming Mars is one of the great dreams of humanity. Mars has a lot going for it. Its day is about the same length as Earth's, it has plenty of frozen water just under its surface, and it likely could be given a reasonably breathable atmosphere in time. But one of the things it lacks is a strong magnetic field. So if we want to make Mars a second Earth, we'll have to give it an artificial one.

The reason magnetic fields are so important is that they shield a planet from solar wind and ionizing particles. Earth's magnetic field prevents most high-energy charged particles from reaching the surface. Instead, they are deflected from Earth, keeping us safe. The magnetic field also prevents solar winds from stripping Earth's atmosphere over time. Early Mars had a thick, water-rich atmosphere, but it was gradually depleted without the protection of a strong magnetic field.

Unfortunately, we can't just recreate Earth's magnetic field on Mars. Our field is generated by a dynamo effect in Earth's core, where the convection of iron alloys generates Earth's geomagnetic field. The interior of Mars is smaller and cooler, and we can't simply "start it up" to create a magnetic dynamo. But there are a few ways we can create an artificial magnetic field, as a recent study shows.

As the study points out, if you want a good planetary magnetic field, what you really need is a strong flow of charged particles, either within the planet or around the planet. Since the former isn't a great option for Mars, the team looks at the latter. It turns out you can create a ring of charged particles around Mars, thanks to its moon Phobos.

Phobos is the larger of the two Martian moons, and it orbits the planet quite closely—so closely that it makes a trip around Mars every eight hours. So the team proposes using Phobos by ionizing particles from its surface, then accelerating them so they create a plasma torus along the orbit of Phobos. This would create a magnetic field strong enough to protect a terraformed Mars.

It's a bold plan, and while it seems achievable, the engineering hurdles would be significant. But as the authors point out, this is the time for ideas. Start thinking about the problems we need to solve, and how we can solve them, so when humanity does reach Mars, we will be ready to put the best ideas to the test.

R.A. Bamford et al, How to create an artificial magnetosphere for Mars, Acta Astronautica (2021). DOI: 10.1016/j.actaastro.2021.09.023

https://phys.org/news/2021-11-absolutely-bonkers-mars-artificial-ma...

COVIDisAirborne: Multiscale ComputationalMicroscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

When bees get a taste for dead things: Meat-eating 'vulture bees'

A little-known species of tropical bee has evolved an extra tooth for biting flesh and a gut that more closely resembles that of vultures rather than other bees.

Bees don't eat meat. However, a species of stingless bee in the tropics has evolved the ability to do so, presumably due to intense competition for nectar.

These are the only bees in the world that have evolved to use food sources not produced by plants, which is a pretty remarkable change in dietary habits.

Honeybees, bumblebees, and stingless bees have guts that are colonized by the same five core microbes. Unlike humans, whose guts change with every meal, most bee species have retained these same bacteria over roughly 80 million years of evolution. Given their radical change in food choice, a team of UCR scientists wondered whether the vulture bees'  gut bacteria differed from those of a typical vegetarian bee. They differed quite dramatically, according to a study the team published today in the American Society of Microbiologists' journal mBio.

To track these changes, the researchers went to Costa Rica, where these bees are known to reside. They set up baits—fresh pieces of raw chicken suspended from branches and smeared with petroleum jelly to deter ants.

The baits successfully attracted vulture bees and related species that opportunistically feed on meat for their protein. Normally, stingless bees have baskets on their hind legs for collecting pollen. However, the team observed carrion-feeding bees using those same structures to collect the bait.

For comparison, the team also collected stingless bees that feed both on meat and flowers, and some that feed only on pollen. On analyzing the microbiomes of all three bee types, they found the most extreme changes among exclusive meat-feeders.

The vulture bee microbiome is enriched in acid-loving bacteria, which are novel bacteria that their relatives don't have. These bacteria are similar to ones found in actual vultures, as well as hyenas and other carrion-feeders, presumably to help protect them from pathogens that show up on carrion.

Laura L. Figueroa et al, Why Did the Bee Eat the Chicken? Symbiont Gain, Loss, and Retention in the Vulture Bee Microbiome, mBio (2021). DOI: 10.1128/mBio.02317-21

https://phys.org/news/2021-11-bees-dead-meat-eating-vulture-sport.h...

How bacteria makes copper into an antibiotic

Copper in small quantities is an essential nutrient but can also be toxic. Human immune cells use copper to fight invading pathogens. Some microorganisms, in turn, have evolved ways to take up copper and incorporate it into biological molecules, either as a way to absorb copper for nutrition or to neutralize its toxic effects.

One of these organisms is the soil bacterium Pseudomonas aeruginosa, which can cause infections in hospital patients. A new study from researchers published Nov. 19 in Science, shows how P. aeruginosa uses copper to make an antibiotic called fluopsin C.

This finding helps us understand how this pathogenic bacterium resists copper and out competes our natural microbiota during infection and will drive the discovery of new treatments. Fluopsin C was discovered in 1970. It is a broad-spectrum antibiotic that kills a wide range of bacteria and fungi, including strains resistant to other drugs.

The researchers followed the uptake of copper by cultured P. aeruginosa and showed that the copper atoms were incorporated into fluopsin C. 

The researchers found that two small sulfur-containing molecules bind to each copper atom in a mix of cis and trans isomers.

The study shows how Fluopsin C could be synthesized by an enzymatic process instead of using hazardous chemicals. Repurposing copper  into an antibiotic in this way is a different response from processes in most organisms, which either sequester or export the metal from the cell.

Jon B. Patteson et al, Biosynthesis of fluopsin C, a copper-containing antibiotic from Pseudomonas aeruginosa, Science (2021). DOI: 10.1126/science.abj6749

https://phys.org/news/2021-11-bacteria-copper-antibiotic.html?utm_s...

Scientists finally detected a quantum effect that blocks atoms from scattering light

When all available quantum states are full, ultracold atom clouds become more transparent

A cloud of ultracold atoms is like a motel with a neon “no vacancy” sign.

If a guest at the motel wants to switch rooms, they’re out of luck. No vacant rooms means there’s no choice but to stay put. Likewise, in new experiments, atoms boxed in by crowded conditions have no way to switch up their quantum states. That constraint means the atoms don’t scatter light as they normally would, three teams of researchers report in the Nov. 19 Science. Predicted more than three decades ago, this effect has now been seen for the first time.

Under normal circumstances, atoms interact readily with light. Shine a beam of light on a cloud of atoms, and they’ll scatter some of that light in all directions. This type of light scattering is a common phenomenon: It happens in Earth’s atmosphere. “We see the sky as blue because of scattered radiation from the sun,” says Yair Margalit, who was part of the team at MIT that performed one of the experiments.

But quantum physics comes to the fore in ultracold, dense atom clouds. “The way they interact with light or scatter light is different.

According to a rule called the Pauli exclusion principle, atoms in the experiments can’t take on the same quantum state — namely, they can’t have the same momentum as another atom in the experiment (SN: 5/19/20). If atoms are packed together in a dense cloud and cooled to near absolute zero, they’ll settle into the lowest-energy quantum states. Those low-energy states will be entirely filled, like a motel with no open rooms.

When an atom scatters light, it gets a kick of momentum, changing its quantum state, as it sends light off in another direction. But if the atom can’t change its state due to the crowded conditions, it won’t scatter the light. The atom cloud becomes more transparent, letting light through instead of scattering it.  

Part 1

To observe the effect, Margalit and colleagues beamed light through a cloud of lithium atoms, measuring the amount of light it scattered. Then, the team decreased the temperature to make the atoms fill up the lowest energy states, suppressing the scattering of light. As the temperature dropped, the atoms scattered 37 percent less light, indicating that many atoms were prevented from scattering light. (Some atoms can still scatter light, for example if they get kicked into higher-energy quantum states that are unoccupied.)

In another experiment, physicist Christian Sanner of the research institute JILA in Boulder, Colo., and colleagues studied a cloud of ultracold strontium atoms. The researchers measured how much light was scattered at small angles, for which the atoms are jostled less by the light and therefore are even less likely to be able to find an unoccupied quantum state. At lower temperatures, the atoms scattered half as much light as at higher temperatures.

The third experiment, performed by Deb and physicist Niels Kjærgaard, also of the University of Otago, measured a similar scattering drop in an ultracold potassium atom cloud and a corresponding increase in how much light was transmitted through the cloud.

Because the Pauli exclusion principle also governs how electrons, protons and neutrons behave, it is responsible for the structure of atoms and matter as we know it. These new results reveal the wide-ranging principle in a new context, says Sanner. “It’s fascinating because it shows a very fundamental principle in nature at work.”

The work also suggests new ways to control light and atoms. “One could imagine a lot of interesting applications,” says theoretical physicist Peter Zoller of the University of Innsbruck in Austria, who was not involved with the research. In particular, light scattering is closely related to a process called spontaneous emission, in which an atom in a high-energy state decays to a lower energy by emitting light. The results suggest that decay could be blocked, increasing the lifetime of the energetic state. Such a technique might be useful for storing quantum information for a lengthier period of time than is normally possible, for example in a quantum computer.

So far, these applications are still theoretical, Zoller says. “How realistic they are is something to be explored in the future.”

https://www.sciencenews.org/article/quantum-physics-atom-light-paul...

Part 2

CITATIONS

C. Sanner et al. Pauli blocking of atom-light scattering. Science. Vol. 374, November, 19 2021, p. 979. doi: 10.1126/science.abh3483.

A.B. Deb and N. Kjærgaard. Observation of Pauli blocking in light scattering from quantum dege.... Science. Vol. 374, November 19, 2021, p. 972. doi: 10.1126/science.abh3470.

Y. Margalit et al. Pauli blocking of light scattering in degenerate fermions. Science. Vol. 374, November 19, 2021, p. 976. doi: 10.1126/science.abi6153

Part 3

We might not know half of what's in our cells, new AI technique reveals

Most human diseases can be traced to malfunctioning parts of a cell—a tumor is able to grow because a gene wasn't accurately translated into a particular protein or a metabolic disease arises because mitochondria aren't firing properly, for example. But to understand what parts of a cell can go wrong in a disease, scientists first need to have a complete list of parts.

By combining microscopy, biochemistry techniques and artificial intelligence, researchers have taken what they think may turn out to be a significant leap forward in the understanding of human cells. The technique, known as Multi-Scale Integrated Cell (MuSIC), is described November 24, 2021 in Nature.

Scientists have long realized there's more that we don't know than we know, but now we finally have a way to look deeper. In the pilot study, MuSIC revealed approximately 70 components contained within a human kidney cell line, half of which had never been seen before. In one example, the researchers spotted a group of proteins forming an unfamiliar structure.

Part 1

they eventually determined the structure to be a new complex of proteins that binds RNA. The complex is likely involved in splicing, an important cellular event that enables the translation of genes to proteins, and helps determine which genes are activated at which times.

The insides of cells—and the many proteins found there—are typically studied using one of two techniques: microscope imaging or biophysical association. With imaging, researchers add florescent tags of various colors to proteins of interest and track their movements and associations across the microscope's field of view. To look at biophysical associations, researchers might use an antibody specific to a protein to pull it out of the cell and see what else is attached to it.

The team has been interested in mapping the inner workings of cells for many years. What's different about this study  is the use of deep learning to map the cell directly from cellular microscopy images. The combination of these technologies is unique and powerful because it's the first time measurements at vastly different scales have been brought together.

part 2

Microscopes allow scientists to see down to the level of a single micron, about the size of some organelles, such as mitochondria. Smaller elements, such as individual proteins and protein complexes, can't be seen through a microscope. Biochemistry techniques, which start with a single protein, allow scientists to get down to the nanometer scale.

"But how do you bridge that gap from nanometer to micron scale? That has long been a big hurdle in the biological sciences. Turns out you can do it with artificial intelligence—looking at data from multiple sources and asking the system to assemble it into a model of a cell.

The team trained the MuSIC artificial intelligence platform to look at all the data and construct a model of the cell. The system doesn't yet map the cell contents to specific locations, like a textbook diagram, in part because their locations aren't necessarily fixed. Instead, component locations are fluid and change depending on cell type and situation.

The clear next step is to blow through the entire human cell," Ideker said, "and then move to different cell types, people and species. Eventually we might be able to better understand the molecular basis of many diseases by comparing what's different between healthy and diseased cells.

Trey Ideker, A multi-scale map of cell structure fusing protein images and interactions, Nature (2021). DOI: 10.1038/s41586-021-04115-9. www.nature.com/articles/s41586-021-04115-9

https://phys.org/news/2021-11-cells-ai-technique-reveals.html?utm_s...

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Part 3

Morning exposure to deep red light improves declining eyesight

Just three minutes of exposure to deep red light once a week, when delivered in the morning, can significantly improve declining eyesight, finds a pioneering new study by UCL researchers.

Published in Scientific Reports, the study builds on the team's previous work, which showed daily three-minute exposure to longwave deep red light 'switched on' energy producing mitochondria cells in the human retina, helping boost naturally declining vision.

For this latest study, scientists wanted to establish what effect a single three-minute exposure would have, while also using much lower energy levels than their previous studies. Furthermore, building on separate UCL research in flies that found mitochondria display 'shifting workloads' depending on the time of day, the team compared morning exposure to afternoon exposure.

Researchers found there was, on average, a 17% improvement in participants' color contrast vision when exposed to three minutes of 670 nanometre (long wavelength) deep red light in the morning and the effects of this single exposure lasted for at least a week. However, when the same test was conducted in the afternoon, no improvement was seen.

Scientists say the benefits of deep red light, highlighted by the findings, mark a breakthrough for eye health and should lead to affordable home-based eye therapies, helping the millions of people globally with naturally declining vision.

Part 1

In humans around 40 years old, cells in the eye's retina begin to age, and the pace of this aging is caused, in part, when the cell's mitochondria, whose role is to produce energy (known as ATP) and boost cell function, also start to decline.

Mitochondrial density is greatest in the retina's photoreceptor cells, which have high energy demands. As a result, the retina ages faster than other organs, with a 70% ATP reduction over life, causing a significant decline in photoreceptor function as they lack the energy to perform their normal role.

In studying the effects of deep red light in humans, researchers built on their previous findings in mice, bumblebees and fruit flies, which all found significant improvements in the function of the retina's photoreceptors when their eyes were exposed to 670 nanometre (long wavelength) deep red light.

"Mitochondria have specific sensitivities to long wavelength light influencing their performance: longer wavelengths spanning 650 to 900nm improve mitochondrial performance to increase energy production.

part 2

The retina's photoreceptor population is formed of cones, which mediate color vision, and rods, which adapt vision in low/dim light. This study focused on cones and observed color contrast sensitivity, along the protan axis (measuring red-green contrast) and the tritan axis (blue-yellow).

All the participants were aged between 34 and 70, had no ocular disease, completed a questionnaire regarding eye health prior to testing, and had normal color vision (cone function). This was assessed using a 'Chroma Test': identifying colored letters that had very low contrast and appeared increasingly blurred, a process called color contrast.

Using a provided LED device all 20 participants (13 female and 7 male) were exposed to three minutes of 670nm deep red light in the morning between 8am and 9am. Their color vision was then tested again three hours post exposure and 10 of the participants were also tested one week post exposure.

On average there was a 'significant' 17% improvement in color vision, which lasted a week in tested participants; in some older participants there was a 20% improvement, also lasting a week.

A few months on from the first test (ensuring any positive effects of the deep red light had been 'washed out') six (three female, three male) of the 20 participants, carried out the same test in the afternoon, between 12pm to 1pm. When participants then had their color vision tested again, it showed zero improvement.

Morning exposure is absolutely key to achieving improvements in declining vision: as we have previously seen in flies, mitochondria have shifting work patterns and do not respond in the same way to light in the afternoon—this study confirms this.

Weeklong improved colour contrasts sensitivity after single 670nm exposures associated with enhanced mitochondrial function, Scientific Reports (2021). DOI: 10.1038/s41598-021-02311-1

https://medicalxpress.com/news/2021-11-morning-exposure-deep-red-de...

Part 3

Screen of 250,000 Species Reveals Tweaks to Genetic Code

A massive screen of bacterial and archaeal genomes revealed five previously unknown instances where an organism uses an alternate code to translate genetic blueprints into proteins.

he genetic code that dictates how genetic information is translated into specific proteins is less rigid than scientists have long assumed, according to research published today (November 9) in eLife. In the paper, scientists report screening the genomes of more than 250,000 species of bacteria and archaea and finding five organisms that rely on an alternate genetic code, signifying branches in evolutionary history that haven’t been fully explained.

The genetic code refers to how sequences of DNA nucleotide bases lead to specific chains of amino acids during the process of protein synthesis. To perform this synthesis, ribosomes read strands of mRNA—copies of bits of the organism’s genome—in chunks of three bases at a time. Each three-base sequence, known as a codon, binds to a specific transfer RNA (tRNA) that ferries a corresponding amino acid to the ribosome to the added to the protein chain. An organism with an alternate genetic code, like the five new instances that the study authors found, has codons that correspond to different amino acids than they would in the standard genetic code employed by the vast majority of known life forms.

The genetic code has been set in stone for 3 billion years. The fact that some organisms have found a way to change it is really fascinating . Changing the genetic code requires changing ancient, important molecules like tRNAs that are so fundamental to how biology works.

As such, the code was thought to be largely preserved across all forms of life, with scientists finding the occasional exception during the past several decades of research. In addition to finding five new alternate genetic codes, the team also verified seven others that had been discovered one-by-one in the past, bringing the total number of known exceptions in bacteria to 12.

Part of the reason changes do happen is that some bacterial genomes may have a low composition of certain nucleotides compared to others. That brings the usage of codons that rely on those nucleotides down to nearly zero, making it easier for an organism to survive shifts without altering too many proteins in a drastic way.

Part 1

Tracing down why these alternate genetic codes emerged during evolutionary history is difficult, multiple researchers tell The Scientist, in no small part because humans couldn’t watch it happen. But the authors do have some hypotheses.

 a bacterium that uses the same alternate code as a bacteriophage virus that infects it, indicating that the bacteria seemingly evolved an alternate code that prevented its cellular machinery from being hijacked—and that the phage may have then made the same adaptation to follow its host.

https://www.the-scientist.com/news-opinion/screen-of-250-000-specie...

‘Super jelly’ can survive being run over by a car

Researchers have developed a jelly-like material that can withstand the equivalent of an elephant standing on it, and completely recover to its original shape, even though it’s 80% water.

The soft-yet-strong material, developed by a team at the University of Cambridge, looks and feels like a squishy jelly, but acts like an ultra-hard, shatterproof glass when compressed, despite its high water content.

The non-water portion of the material is a network of polymers held together by reversible on/off interactions that control the material’s mechanical properties. This is the first time that such significant resistance to compression has been incorporated into a soft material.

The ‘super jelly’ could be used for a wide range of potential applications, including soft robotics, bioelectronics or even as a cartilage replacement for biomedical use. The results are reported in the journal Nature Materials.

https://www.nature.com/articles/s41563-021-01124-x

Antibodies mimicking the virus may explain long haul COVID-19, rare vaccine side effects

The COVID-19 pandemic has challenged scientists and those in the medical field. Researchers are working to find effective vaccines and therapies, as well as understand the long-term effects of the infection.

While the vaccines have been critical in pandemic control, researchers are still learning how and how well they work. This is especially true with the emergence of new viral variants and the rare vaccine side effects like allergic reactions, heart inflammation (myocarditis) and blood-clotting (thrombosis).

Critical questions about the infection itself also remain. Approximately one in four COVID-19 patients have lingering symptoms, even after recovering from the virus. These symptoms, known as "long COVID," and the vaccines' off-target side effects are thought to be due to a patient's immune response.

In an article published recently in The New England Journal of Medicine, scientists present a possible explanation to the diverse immune responses to the virus and the vaccines.

Part 1

Antibodies mimicking the virus

Drawing upon classic immunological concepts, Murphy and Longo suggest that the Network Hypothesis by Nobel Laureate Niels Jerne might offer insights.

Jerne's hypothesis details a means for the immune system to regulate antibodies. It describes a cascade in which the immune system initially launches protective antibody responses to an antigen (like a virus). These same protective antibodies later can trigger a new antibody response toward themselves, leading to their disappearance over time.

These secondary antibodies, called anti-idiotype antibodies, can bind to and deplete the initial protective antibody responses. They have the potential to mirror or act like the original antigen itself. This may result in adverse effects.

Coronavirus and the immune system

When SARS-CoV-2, the virus causing COVID-19, enters the body, its spike protein binds with the ACE2 receptor, gaining entry to the cell. The immune system responds by producing protective antibodies that bind to the invading virus, blocking or neutralizing its effects.

As a form of down-regulation, these protective antibodies can also cause immune responses with anti-idiotype antibodies. Over time, these anti-idiotype responses can clear the initial protective antibodies and potentially result in limited efficacy of antibody-based therapies.

"A fascinating aspect of the newly formed anti-idiotype antibodies is that some of their structures can be a mirror image of the original antigen and act like it in binding to the same receptors that the viral antigen binds. This binding can potentially lead to unwanted actions and pathology, particularly in the long term.

The authors suggest that the anti-idiotype antibodies can potentially target the same ACE2 receptors. In blocking or triggering these receptors, they could affect various normal ACE2 functions.

"Given the critical functions and wide distribution of ACE2 receptors on numerous cell types, it would be important to determine if these regulatory immune responses could be responsible for some of the off-target or long-lasting effects being reported. These responses may also explain why such long-term effects can occur long after the viral infection has passed.

Part 2

As for COVID-19 vaccines, the primary antigen used is the SARS-CoV-2 spike protein. According to Murphy and Longo, current research studies on antibody responses to these vaccines mainly focus on the initial protective responses and virus-neutralizing efficacy, rather than other long-term aspects.

"With the incredible impact of the pandemic and our reliance on vaccines as our primary weapon, there is an immense need for more basic science research to understand the complex immunological pathways at play. This need follows to what it takes to keep the protective responses going, as well as to the potential unwanted side effects of both the infection and the different SARS-CoV-2 vaccine types, especially as boosting is now applied. "The good news is that these are testable questions that can be partially addressed in the laboratory, and in fact, have been used with other viral models."

 William J. Murphy et al, A Possible Role for Anti-idiotype Antibodies in SARS-CoV-2 Infection and Vaccination, New England Journal of Medicine (2021). DOI: 10.1056/NEJMcibr2113694

https://medicalxpress.com/news/2021-11-antibodies-mimicking-virus-h...

Part 3

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Scientists produce new antibiotics by gene editing

Scientists have discovered a new route to produce complex antibiotics exploiting gene editing to re-program pathways to future medicines urgently required to combat antimicrobial resistance, treat neglected diseases and tackle future pandemics.

Researchers from The University of Manchester have discovered a new way of manipulating key assembly line enzymes in bacteria which could pave the way for a new generation of antibiotic treatments.

New research published today in Nature Communications, describes how CRISPR-Cas9 gene editing can be used to create new nonribosomal peptide synthetase (NRPS) enzymes that deliver clinically important antibiotics. NRPS enzymes are prolific producers of natural antibiotics such as penicillin. However, up until now, manipulating these complex enzymes to produce new and more effective antibiotics has been a major challenge.

 the gene editing process could be used to produce improved antibiotics and possibly lead to the development of new treatments helping in the fight against drug-resistant pathogens and illnesses in the future. 

The emergence of antibiotic-resistant pathogens is one of the biggest threats we face today.

The gene editing approach the researchers  developed now is a very efficient and rapid way to engineer complex assembly line enzymes that can produce new antibiotic structures with potentially improved properties.

Part 1

Microorganisms in our environment, such as soil dwelling bacteria, have evolved nonribosomal peptide synthetase enzymes (NRPS) that assemble building blocks called amino acids into peptide products which often have very potent antibiotic activity. Many of the most therapeutically important antibiotics, used in the clinic today, are derived from these NRPS enzymes (e.g. penicillin, vancomycin and daptomycin).

Unfortunately, deadly pathogens are emerging which are resistant to all of these existing antibiotic drugs. One solution could be to create new antibiotics with improved properties that can evade the resistance mechanisms of the pathogens. However, the nonribosomal peptide antibiotics are very complex structures which are difficult and expensive to produce by normal chemical methods. To address this, the research  team use gene editing to engineer the NRPS enzymes, swapping domains that recognize different amino acid building blocks, leading to new assembly lines that can deliver new peptide products.

Researchers are now able to use gene editing to introduce targeted changes to complex NRPS enzymes, enabling alternative amino acids precursors to be incorporated into the peptide structures. They are optimistic that this new approach could lead to new ways of making improved antibiotics which are urgently needed to combat emerging drug-resistant pathogens.

Wei Li Thong et al, Gene editing enables rapid engineering of complex antibiotic assembly lines, Nature Communications (2021). DOI: 10.1038/s41467-021-27139-1

https://phys.org/news/2021-11-scientists-antibiotics-gene.html?utm_...

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Physicists detect signs of neutrinos at Large Hadron Collider

The international Forward Search Experiment team has achieved the first-ever detection of neutrino candidates produced by the Large Hadron Collider at the CERN facility near Geneva, Switzerland.

In a paper published recently in the journal Physical Review D, the researchers describe how they observed six neutrino interactions during a pilot run of a compact emulsion detector installed at the LHC in 2018. This significant breakthrough is a step toward developing a deeper understanding of these elusive particles and the role they play in the universe.

 Henso Abreu et al, First neutrino interaction candidates at the LHC, Physical Review D (2021). DOI: 10.1103/PhysRevD.104.L091101

https://phys.org/news/2021-11-physicists-neutrinos-large-hadron-col...

In the quantum realm, not even time flows as you might expect

A team of physicists has shown how quantum systems can simultaneously evolve along two opposite time arrows—both forward and backward in time.

The study, published in the latest issue of Communications Physics, necessitates a rethink of how the flow of time is understood and represented in contexts where quantum laws play a crucial role.

For centuries, philosophers and physicists have been pondering the existence of time. Yet, in the classical world, our experience seems to extinguish any doubt that time exists and goes on. Indeed, in nature, processes tend to evolve spontaneously from states with less disorder to states with more disorder, and this propensity can be used to identify an arrow of time. In physics, this is described in terms of 'entropy', which is the physical quantity defining the amount of disorder in a system.

If a phenomenon produces a large amount of entropy, observing its time-reversal is so improbable as to become essentially impossible. However, when the entropy produced is small enough, there is a non-negligible probability of seeing the time-reversal of a phenomenon occur naturally.

An example. If we were shown our toothpaste moving from the toothbrush back into its tube, we would be in no doubt it was a rewinded recording of our day. However, if we squeezed the tube gently so only a small part of the toothpaste came out, it would not be so unlikely to observe it re-entering the tube, sucked in by the tube's decompression.

The authors of this study applied this idea to the quantum realm, one of whose peculiarities is the principle of quantum superposition, according to which if two states of a quantum system are both possible, then that system can also be in both states at the same time.

Extending this principle to time's arrows, it results that quantum systems evolving in one or the other temporal direction (the toothpaste coming out of or going back into the tube), can also find themselves evolving simultaneously along both temporal directions.

"Although this idea seems rather nonsensical when applied to our day-to-day experience, at its most fundamental level, the laws of the universe are based on quantum-mechanical principles. This begs the question of why we never encounter these superpositions of time flows in nature.

Part 1