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...

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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.

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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.

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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

quantified the entropy produced by a system evolving in quantum superposition of processes with opposite time arrows. We found this most often results in projecting the system onto a well-defined time's direction, corresponding to the most likely process of the two. And yet, when small amounts of entropy are involved (for instance, when there is so little toothpaste spilled that one could see it being reabsorbed into the tube), then one can physically observe the consequences of the system having evolved along the forward and backward temporal directions at the same time.

Aside from the fundamental feature that time itself might not be well-defined, the work also has practical implications in quantum thermodynamics. Placing a quantum system in a superposition of alternative time's arrows could offer advantages in the performance of thermal machines and refrigerators.

Although time is often treated as a continuously increasing parameter, this study shows the laws governing its flow in quantum mechanical contexts are much more complex. This may suggest that we need to rethink the way we represent this quantity in all those contexts where quantum laws play a crucial role.

Quantum superposition of thermodynamic evolutions with opposing time's arrows, Communications Physics (2021). DOI: 10.1038/s42005-021-00759-1

https://phys.org/news/2021-11-quantum-realm.html?utm_source=nwlette...

Part 2

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COVID-19 : Measuring viral RNA to predict which patients will die

The amount of a SARS-CoV-2 genetic material—viral RNA—in the blood is a reliable indicator in detecting which patients will die of the disease, a team  of researchers has found.

In this study, scientists were able to determine which biomarkers are predictors of mortality in the 60 days following the onset of symptoms. They have successfully developed and validated a statistical model based on one blood biomarker, viral RNA.  Several biomarkers have been identified in other studies, but juggling the profusion of parameters is not possible in a clinical setting and hinders doctors' ability to make quick medical decisions.

Using blood samples collected from 279 patients during their hospitalization for COVID-19, ranging in degrees of severity from moderate to critical, the  team measured amounts of inflammatory proteins, looking for any that stood out.

At the same time, they measured the amounts of viral RNA and  the levels of antibodies targeting the virus. Samples were collected 11 days after the onset of symptoms and patients were monitored for a minimum of 60 days after that.

The goal: to test the hypothesis that immunological indicators were associated with increased mortality. Among all of the biomarkers they evaluated, they showed that the amount of viral RNA in the blood was directly associated with mortality and provided the best predictive response, once their model was adjusted for the age and sex of the patient. They even found that including additional biomarkers did not improve predictive quality.

It made no difference which hospital the patients were treated at, nor which period of the pandemic they fell into: in all cases, the predictive model worked. Now the researchers  want to put it to practical use.

Elsa Brunet-Ratnasingham et al, Integrated immunovirological profiling validates plasma SARS-CoV-2 RNA as an early predictor of COVID-19 mortality, Science Advances (2021). DOI: 10.1126/sciadv.abj5629. www.science.org/doi/10.1126/sciadv.abj5629

https://medicalxpress.com/news/2021-11-covid-viral-rna-patients-die...

Using molecules and atoms to conduct the double-slit experiment

A team of researchers  has developed a way to conduct the famous double-slit experiment at the molecular level. In their paper published in the journal Science, the group describes their technique and suggest that it could be used to assist with other molecular experiments.

In 1801, Thomas Young conducted what has come to be known as the double-slit experiment. At the time, he used it as a means to prove that light behaves as a wave. Since that time, light has been found to also behave as a particle of course, and the double-slit experiment has since been conducted in various ways under various conditions. Others have shown that electrons and atoms and molecules exhibit the same type of behavior. In this new effort, the researchers have taken the experiment to a new level by using nothing but molecules, single atoms and lasers. In the original double-slit experiment, the light passed through both slits in a superposition of trajectories. In this new method, there is only one slit, but it is in a superposition of positions.

Part 1

The experiment by the team involved creating a beam of deuterium and helium molecules in a chamber cooled to –272°C. They then used pairs of polarized laser bursts to push deuterium molecules into a certain vibrational and rotational state with different orientations—at right angles to one another. These served as the slits for the experiment. The team also forced other deuterium molecules into a state where they were suppositions of both of the orientations of the slits. As helium atoms scattered off the superposed molecules (along different paths that interfered with one another), the deuterium could in a sense "feel" them both at the same time. And as the helium atoms collided with the molecules, the deuterium atoms were released back to their original state at which point, they were ionized and studied by the research team.

The researchers suggest that in addition to conducting the double-slit experiment in a new way, their work also lays the groundwork for studying quantum behavior in a new way—by preparing new types of matter. They conclude by suggesting that their techniques could also be adapted for use in studying decoherence.

Haowen Zhou et al, Quantum mechanical double slit for molecular scattering, Science (2021). DOI: 10.1126/science.abl4143

https://phys.org/news/2021-11-molecules-atoms-double-slit.html?utm_...

Part 2

**

Warm weather or bright lights can influence tree greening

How both global warming and bright city lights can impact phenology in trees (when they begin to grow leaves in the spring?

 In her paper published in the journal Science, Meng, the Science & SciLifeLab Prize  for young scientist's award winner, outlines her study of satellite data showing green areas in cities along with artificial light sources and also trees growing in the Alps.

Prior research has shown that higher temperatures in cities can impact vegetation growth. In this new effort, Meng wondered what city warming, combined with global warming might be doing to the times that trees "green up" in the spring each year. To find out, she obtained and analyzed satellite data that showed when trees begin producing leaves in the spring each year for 85 U.S. cities over the years 2001 to 2014.

She found that tree green-up happens on average 6 days earlier in urban areas compared to rural areas. She also found that trees in the city are responding to climate change faster than trees in rural areas.

Meng also wondered about the impact of bright lights on trees and whether they might make trees start growing their leaves earlier in the spring each year. She studied trees growing in the Alps in Europe—noting that it is a place with a rather uniform temperature distribution but also has changing lengths of daylight across latitudes. She found evidence of a reduction in an early green-up likely due to global warming. She then studied data from NASA's Black Marble satellite, which measures artificial light in cities and also phenology data from the USA National Phenology Network. This allowed her to compare conditions in cities both with and without artificial light in the U.S., and she found that artificial light pushed spring green-up by nine days in the most extreme cases.

Meng concludes by suggesting that artificial light, by supplementing day length, leads to additions of earlier spring greening in cities, adding to the impact of earlier greening due to global warming. 

Lin Meng, Green with phenology, Science (2021). DOI: 10.1126/science.abm8136

https://phys.org/news/2021-11-weather-bright-tree-greening.html?utm...

**

Supercomputer Simulations Test Star-destroying Black Holes

Water disinfection byproduct disrupts reproductive hormones, damages pituitary in female mice

 Chemical disinfection makes water from both natural sources and wastewater streams drinkable; however, the process also creates byproducts, not all of which are understood or regulated. A new study from University of Illinois Urbana-Champaign researchers has found that one byproduct disrupts hormones in the brain that regulate the female reproductive cycle in mice and also damages cells in the pituitary gland.

Iodoacetic acid, or IAA, is created when an oxidizing disinfectant such as chlorine reacts with the iodide naturally present in water, said study leader Lori Raetzman, a professor of molecular and integrative physiology. The new study’s findings of IAA’s effects on reproductive regulation in the brain complement previous work by study co-author Jodi Flaws, a professor of comparative biosciences, which found that IAA also disrupts function in and causes damage to ovary cells, indicating that the chemical could impact the entire reproductive system.

We know we need to disinfect water, but the water that’s coming out of our taps isn’t pure – regulators only screen for the things they know about. Water regulatory bodies have not been looking for IAA. This study is contributing to the growing body of evidence that suggests that IAA may impact reproduction, so it might be reasonable to have screening for this too, and to establish a safe level for it.

In the new study, published in the journal Toxological Sciences, the researchers gave mice drinking water containing IAA at levels comparable to possible human exposure, as well as a control group of mice that were given water with no IAA present, for 35-40 days. Then they measured the production of reproduction-regulating factors in two key parts of the neuroendocrine system – the hypothalamus and the pituitary.

“Mice are often used as models for the human reproductive system because they have estrous cycles that are similar to human menstrual cycles. The hypothalamus and the pituitary are the master regulators of the endocrine system. It’s a good foundation to say that a human exposed to a certain amount of IAA could potentially have similar effects.

The researchers found that, even at low levels, IAA disrupted production of a key reproduction-regulating factor in the hypothalamus. At higher levels, IAA reduced pituitary production of follicle stimulating hormone, a key hormone for promoting egg maturation in the ovaries leading up to ovulation. The hormone also is linked to estrogen production.

n addition, the researchers saw toxic effects, including DNA damage, in the pituitaries of the mice that consumed IAA. Because of this finding and the earlier findings from the Flaws lab regarding ovarian cell damage, the researchers are now investigating whether and how exposing pregnant mice to IAA in drinking water affects their pups.

https://pubmed.ncbi.nlm.nih.gov/34453833/

DOI: 10.1093/toxsci/kfab106

https://researchnews.cc/news/10224/Water-disinfection-byproduct-dis...

Study suggests Sun is likely an unaccounted source of the Earth's water

Researchers have helped unravel the enduring mystery of the origins of the Earth's water, finding the Sun to be a surprising likely source. They found the solar wind, comprised of charged particles from the Sun largely made of hydrogen ions, created water on the surface of dust grains carried on asteroids that smashed into the Earth during the early days of the Solar System.

 Earth 's very water-rich compared to other rocky planets in the Solar System, with oceans covering more than 70 percent of its surface, and scientists had long puzzled over the exact source of it all.

An existing theory is that water was carried to Earth in the final stages of its formation on C-type asteroids, however previous testing of the isotopic 'fingerprint' of these asteroids found they, on average, didn't match with the water found on Earth meaning there was at least one other unaccounted for source.

New work  suggests the solar wind created water on the surface of tiny dust grains and this isotopically lighter water likely provided the remainder of the Earth's water.

This new solar wind theory is based on meticulous atom-by-atom analysis of miniscule fragments of an S-type near-Earth asteroid known as Itokawa, samples of which were collected by the Japanese space probe Hayabusa and returned to Earth in 2010. A world-class atom probe tomography system allowed the researchers to take an incredibly detailed look inside the first 50 nanometres or so of the surface of Itokawa dust grains, which they found contained enough water that, if scaled up, would amount to about 20 liters for every cubic meter of rock.

Luke Daly, Solar wind contributions to Earth's oceans, Nature Astronomy (2021). DOI: 10.1038/s41550-021-01487-w. www.nature.com/articles/s41550-021-01487-w

Researchers discover how water is regenerated on asteroids

https://phys.org/news/2021-11-sun-unaccounted-source-earth.html?utm...

Salt grain size camera!

Micro-sized cameras have great potential to spot problems in the human body and enable sensing for super-small robots, but past approaches captured fuzzy, distorted images with limited fields of view.

But now, researchers  have overcome these obstacles with an ultracompact camera the size of a coarse grain of salt. The new system can produce crisp, full colour images on par with a conventional compound camera lens 500,000 times larger in volume, the researchers reported in a paper published Nov. 29 in Nature Communications.

Enabled by a joint design of the camera's hardware and computational processing, the system could enable minimally invasive endoscopy with medical robots to diagnose and treat diseases, and improve imaging for other robots with size and weight constraints. Arrays of thousands of such cameras could be used for full-scene sensing, turning surfaces into cameras.

While a traditional camera uses a series of curved glass or plastic lenses to bend light rays into focus, the new optical system relies on a technology called a metasurface, which can be produced much like a computer chip. Just half a millimeter wide, the metasurface is studded with 1.6 million cylindrical posts, each roughly the size of the human immunodeficiency virus (HIV).

Each post has a unique geometry, and functions like an optical antenna. Varying the design of each post is necessary to correctly shape the entire optical wavefront. With the help of machine learning-based algorithms, the posts' interactions with light combine to produce the highest-quality images and widest field of view for a full-color metasurface camera developed to date.

A key innovation in the camera's creation was the integrated design of the optical surface and the signal processing algorithms that produce the image. This boosted the camera's performance in natural light conditions.

 Ethan Tseng et al, Neural nano-optics for high-quality thin lens imaging, Nature Communications (2021). DOI: 10.1038/s41467-021-26443-0

https://phys.org/news/2021-11-camera-size-salt-grain.html?utm_sourc...

Living robots that can reproduce!

To persist, life must reproduce.

Over billions of years, organisms have evolved many ways of replicating, from budding plants to sexual animals to invading viruses.

Now scientists have discovered an entirely new form of biological reproduction—and applied their discovery to create the first-ever, self-replicating living robots.

The same team that built the first living robots ("Xenobots," assembled from frog cells—reported in 2020) has discovered that these computer-designed and hand-assembled organisms can swim out into their tiny dish, find single cells, gather hundreds of them together, and assemble "baby" Xenobots inside their Pac-Man-shaped "mouth"—that, a few days later, become new Xenobots that look and move just like themselves.

And then these new Xenobots can go out, find cells, and build copies of themselves. Again and again.

Sam Kriegman el al., "A scalable pipeline for designing reconfigurable organisms," PNAS (2019). www.pnas.org/cgi/doi/10.1073/pnas.1910837117

https://techxplore.com/news/2020-01-team-robots.html

Flu virus shells could improve delivery of mRNA into cells

Nanoengineers  have developed a new and potentially more effective way to deliver messenger RNA (mRNA) into cells. Their approach involves packing mRNA inside nanoparticles that mimic the flu virus—a naturally efficient vehicle for delivering genetic material such as RNA inside cells.

The new mRNA delivery nanoparticles are described in a paper published recently in the journal Angewandte Chemie International Edition.

The work addresses a major challenge in the field of drug delivery: Getting large biological drug molecules safely into cells and protecting them from organelles called endosomes. These tiny acid-filled bubbles inside the cell serve as barriers that trap and digest large molecules that try to enter. In order for biological therapeutics to do their job once they are inside the cell, they need a way to escape the endosomes.

Current mRNA delivery methods do not have very effective endosomal escape mechanisms, so the amount of mRNA that actually gets released into cells and shows effect is very low. The majority of them are wasted when they get administered. Achieving efficient endosomal escape would be a game changer for mRNA vaccines and therapies. If you can get more mRNA into cells, this means you can take a much lower dose of an mRNA vaccine, and this could reduce side effects while achieving the same efficacy. It could also improve delivery of small interfering RNA (siRNA) into cells, which is used in some forms of gene therapy.

In nature, viruses do a very good job of escaping the endosome. The influenza A virus, for example, has a special protein on its surface called hemagglutinin, that when activated by acid inside the endosome, triggers the virus to fuse its membrane with the endosomal membrane. This opens up the endosome, enabling the virus to release its genetic material  into the host cell without getting destroyed.

part 1

A research team developed mRNA delivery nanoparticles that mimic the flu virus's ability to do this. To make the nanoparticles, the researchers genetically engineered cells in the lab to express the hemagglutinin protein on their cell membranes. They then separated the membranes from the cells, broke them into tiny pieces, and coated them onto nanoparticles made from a biodegradable polymer that has been pre-packed with mRNA molecules inside.

The finished product is a flu virus-like nanoparticle that can get into a cell, break out of the endosome, and free its mRNA payload to do its job: Instruct the cell to produce proteins.

The researchers tested the nanoparticles in mice. The flu-virus like nano particles effectively delivered their mRNA payloads into cells in vivo.

 Joon Ho Park et al, Virus‐Mimicking Cell Membrane‐Coated Nanoparticles for Cytosolic Delivery of mRNA, Angewandte Chemie International Edition (2021). DOI: 10.1002/anie.202113671

https://phys.org/news/2021-11-flu-virus-shells-delivery-mrna.html?u...

Part 2

Filtering microplastics trash from water with acoustic waves

Microplastics are released into the environment by cosmetics, clothing, and industrial processes or from larger plastic products as they break down naturally.

The pollutants eventually find their way into rivers and oceans, posing problems for marine life. Filtering and removing the small particles from water is a difficult task, but acoustic waves may provide a solution.

A research team used two speakers to create acoustic waves. The force produced by the waves separates the microplastics from the water by creating pressure on a tube of inflowing water. As the tube splits into three channels, the microplastic particles are pressed toward the center as the clean water flows toward the two outer channels.

The prototype device cleaned 150 liters per hour of polluted water and was tested with three different microplastics. Each plastic was filtered with a different efficiency, but all were above 56% efficient in pure water and 58% efficient in seawater. Acoustic frequency, speaker-to-pipe distance, and density of the water all affected the amount of force generated and therefore the efficiency.

The acoustic waves may impact marine life if the wave frequency is in the audible range. The group is currently studying this potential issue.

Source: News Agencies

https://www.eurekalert.org/news-releases/935152

acousticalsociety.org/asa-meetings/

https://phys.org/news/2021-11-filtering-microplastics-trash-acousti...

Engineers create perching bird-like robot

Study links high cholesterol, cardiovascular disease to plastics

Plastics, part of modern life, are useful but can pose a significant challenge to the environment and may also constitute a health concern. Indeed, exposure to plastic-associated chemicals, such as base chemical bisphenol A and phthalate plasticizers, can increase the risk of human cardiovascular disease. What underlying mechanisms cause this, however, remain elusive.

Now in a mouse study,  researchers found a phthalate—a chemical used to make plastics more durable—led to increased plasma cholesterol levels. Dicyclohexyl phthalate, or DCHP, strongly binds to a receptor called pregnane X receptor, or PXR.

DCHP 'turns on' PXR in the gut, inducing the expression of key proteins required for cholesterol absorption and transport. Experiments show that DCHP elicits high cholesterol by targeting intestinal PXR signaling.

Mice exposed to DCHP had in their intestines higher circulating "ceramides"—a class of waxy lipid molecules associated with increased cardiovascular disease risk  in humans—in a way that was PXR-dependent.

This, too, points to the potentially important role of PXR in contributing to the harmful effects of plastic-associated chemicals on cardiovascular health in humans.

"Effects of dicyclohexyl phthalate exposure on PXR activation and lipid homeostasis in miceEnvironmental Health Perspectives (2021). " doi.org/10.1289/EHP9262

https://medicalxpress.com/news/2021-12-links-high-cholesterol-cardi...

Safely delivering radiation to cancer patients in a 'FLASH'

Researchers at Lawrence Livermore National Laboratory (LLNL) have shown for the first time the potential for linear induction accelerators (LIAs) to deliver effective, targeted doses of "FLASH" radiation to cancer patients. The new technique selectively kills cancer cells with minimal damage to healthy cells. The approach is outlined in a Scientific Reports paper.

Efforts to deliver a rapid, high, targeted dose of therapy radiation, or FLASH radiotherapy (FLASH-RT) at the required depth, have required large, complex machines the size of gymnasiums and have so far proven impractical for clinical use. In the Scientific Reports paper, the authors note that LIAs powerful enough to deliver the necessary dose rate to cancer cells can be built only 3 meters long.

Researchers have combined technologies that were developed for weapons—either diagnostics or weapon design itself—and spinning off something that could potentially be a major breakthrough in cancer radiotherapy.

 Stephen E. Sampayan et al, Megavolt bremsstrahlung measurements from linear induction accelerators demonstrate possible use as a FLASH radiotherapy source to reduce acute toxicity, Scientific Reports (2021). DOI: 10.1038/s41598-021-95807-9

https://phys.org/news/2021-12-safely-cancer-patients.html?utm_sourc...

When variations in Earth's orbit drive biological evolution

Coccolithophores are microscopic algae that form tiny limestone plates, called coccoliths, around their single cells. The shape and size of coccoliths varies according to the species. After their death, coccolithophores sink to the bottom of the ocean and their coccoliths accumulate in sediments, which faithfully record the detailed evolution of these organisms over geological time.

A team of scientists led by CNRS researchers show, in an article published in Nature on December 1, 2021, that certain variations in Earth's orbit have influenced the evolution of coccolithophores. To achieve this, no less that 9 million coccoliths, spanning an interval of 2.8 million years and several locations in the tropical ocean, were measured and classified using automated microscope techniques and artificial intelligence.

The researchers observed that coccoliths underwent cycles of higher and lower diversity in size and shape, with rhythms of 100 and 400 thousand years. They also propose a cause: the more or less circular shape of Earth's orbit around the Sun, which varies at the same rhythms. Thus, when Earth's orbit is more circular, as is the case today (this is known as low eccentricity), the equatorial regions show little seasonal variation and species that are not very specialized dominate all the oceans. Conversely, as eccentricity increases and more pronounced seasons appear near the equator, coccolithophores diversify into many specialized species, but collectively produce less limestone.

Crucially, due to their abundance and global distribution, these organisms are responsible for half of the limestone (calcium carbonate, partly composed of carbon) produced in the oceans and therefore play a major role in the carbon cycle and in determining ocean chemistry. It is therefore likely that the cyclic abundance patterns of these limestone producers played a key role in ancient climates, and may explain hitherto mysterious climate variations in past warm periods.

In other words, in the absence of ice, the biological evolution of micro-algae could have set the tempo of climates. This hypothesis remains to be confirmed.

Luc Beaufort, Cyclic evolution of phytoplankton forced by changes in tropical seasonality, Nature (2021). DOI: 10.1038/s41586-021-04195-7. www.nature.com/articles/s41586-021-04195-7

https://phys.org/news/2021-12-variations-earth-orbit-biological-evo...

Pharmaceutical waste contaminates India's main rivers

India's major rivers are thick with heavy metals, dyes, toxic chemicals and pharmaceutical products, a study shows.

The study, published in December in the journal Science of the Total Environment, found high concentrations of pharmaceutical waste as well as toxic metals such as arsenic, zinc, chromium, lead and nickel in the Cauvery, a major river in southern India.

These  observations are alarming. The researchers' environmental risk assessment has shown that pharmaceutical contaminants pose medium to high risk to selected aquatic lifeforms of the riverine system.

Pharmaceutical products found in the river included anti-inflammatories like ibuprofen and diclofenac, anti-hypertensives such as atenolol and isoprenaline, enzyme inhibitors like perindopril, stimulants like caffeine, antidepressants such as carbamazepine, and antibiotics such as ciprofloxacin.

India is among the world's biggest producers of pharmaceutical drugs. Although there are regulations governing effluents from manufacturing units, there is very little real monitoring by regulators such as the state pollution control boards. For instance, the Karnataka State Pollution Control Board takes samples only once in every three months and only during the day whereas illegal dumping of effluents is often done at night.

"Clearly there is a need to ensure that wastewater treatment systems are working optimally to reduce the level of contaminants reaching the rivers," the researchers said.

Jayakumar Renganathan et al, Spatio-temporal distribution of pharmaceutically active compounds in the River Cauvery and its tributaries, South India, Science of The Total Environment (2021). DOI: 10.1016/j.scitotenv.2021.149340

https://phys.org/news/2021-12-pharmaceutical-contaminates-india-mai...

Provided by SciDev.Net

Device instantly detects sepsis via sweat

 Every year, millions of  adults develop sepsis, a life-threatening complication that arises when the body has an overwhelming immune response to an infection. According sepsis causes more than 20 percent of all deaths worldwide.

A crucial aspect of treating sepsis is to catch it at an early stage when a patient’s infection is still curable. Current methods to diagnose sepsis, however, rely on tests that can take days to yield results, while early sepsis can turn into full-blown septic shock within only one hour after the first symptoms emerge.

This means that doctors often need to wait for the results of a test, and the results may not even be accurate if the patient developed a condition after the sample was taken.

The students consulted with sepsis survivors, scientists, and clinicians at the University of Rochester Medical Center to design a sepsis-sensing device, which they named “Bio-Spire,” a combination of “biology” and “perspire.” Bio-Spire is a biosensor that continuously monitors the levels of biomarkers in sweat. Unlike blood, sweat is a noninvasive medium to collect, and unlike saliva or urine, biomarkers in sweat can be continuously analyzed. The levels of biomarkers in blood and in sweat are correlated, so changes in the amount of biomarkers in sweat are indicative of changes in the blood.

That is, a change in biomarker levels in a patient’s sweat can signify a deterioration of the patient’s condition—and may signify sepsis.

Doctors use many different tools to diagnose patients, one of which is the presence and concentration of certain biomarkers—molecules such as proteins or sugar that are associated with a particular disease, condition, or biological process. There are several ways to measure biomarker concentrations, including test strips and lab-on-a-chip devices, but many of these approaches only show biomarker concentrations at one specific point in time. These methods can also be expensive, and many take hours to perform.

In order to address this problem, a team of 12 undergraduate students  developed a novel device that instantaneously diagnoses sepsis based on biomarkers in a person’s sweat. The device offers a noninvasive way to monitor sepsis in real-time and uses materials that are environmentally friendly and affordable, making the device easily deployable in low-income countries.

Bio-Spire is designed to collect a tiny amount of sweat from a patient’s skin and wick the sweat past an integrated set of electrodes covered in biomarker detectors. The biomarker detectors consist of short pieces of DNA receptors attached to a small sheet of graphene—an ultra-thin layer of material that is highly conductive. The students synthetically created their own graphene and DNA in an environmentally-friendly manner by using engineered biological components.

When the sleeve-like device is placed on a patient’s arm, biomarkers associated with sepsis bind to the DNA receptors, changing the conductivity of the graphene sheet and triggering an electrical resistance in the electrodes, which is then recorded on a computer. The students created software that displays the concentrations of sepsis biomarkers in real time, permitting health care workers to receive up-to-the-minute updates on a patient’s condition.

https://www.rochester.edu/newscenter/what-is-sepsis-diagnosis-devic...

https://researchnews.cc/news/10312/Rochester-students--award-winnin...

Some tissues can 'breathe' without oxygen

Humans need oxygen molecules for a process called cellular respiration, which takes place in our cells' mitochondria. Through a series of reactions called the electron transport chain, electrons are passed along in a sort of cellular relay race, allowing the cell to create ATP, the molecule that gives our cells energy to complete their vital functions.

At the end of this chain, two electrons remain, which are typically passed off to oxygen, the "terminal electron acceptor." This completes the reaction and allows the process to continue with more electrons entering the electron transport chain.

In the past, however, scientists have noticed that cells are able to maintain some functions of the electron transport chain, even in the absence of oxygen. "This indicated that mitochondria could actually have partial function, even when oxygen is not the electron acceptor. How does this work? How are mitochondria capable of maintaining these electron inputs when oxygen is not the terminal electron acceptor?"

Scientists  have found the answer to these questions recently. Their research shows that when cells are deprived of oxygen, another molecule called fumarate can step in and serve as a terminal electron acceptor to enable mitochondrial function in this environment. 

The research answers a long-standing mystery in the field of cellular metabolism, and could potentially inform research into diseases that cause low oxygen levels in tissues, including ischemia, diabetes and cancer.

Jessica B. Spinelli et al, Fumarate is a terminal electron acceptor in the mammalian electron transport chain, Science (2021). DOI: 10.1126/science.abi7495

Part 1

The researchers began their investigation into how cells can maintain mitochondrial function without oxygen by using mass spectrometry to measure the quantities of molecules called metabolites that are produced through cellular respiration in both normal and low-oxygen conditions. When cells were deprived of oxygen, researchers noticed a high level of a molecule called succinate.

When you add electrons to oxygen at the end of the electron transport chain, it picks up two protons and becomes water. When you add electrons to fumarate, it becomes succinate. This led the researchers to think that maybe this accumulation of succinate that's occurring could actually be caused by fumarate being used as an electron acceptor, and that this reaction could explain the maintenance of mitochondrial functions in hypoxia.

Usually, the fumarate-succinate reaction runs the other direction in cells—a protein complex called the SDH complex takes away electrons from succinate, leaving fumarate. For the opposite to happen, the SDH complex would need to be running in reverse.

Through a series of assays, however, the researchers were able to ascertain that this complex was indeed running in reverse in cultured cells, largely due to accumulation of a molecule called ubiquinol, which the researchers observed to build up under low-oxygen conditions.

https://phys.org/news/2021-12-tissues-oxygen.html?utm_source=nwlett...

Part 2

A Fusion Reaction Has Generated More Energy Than Absorbed by The Fuel

For the first time, a fusion reaction has achieved a record 1.3 megajoule energy output – and for the first time, exceeding energy absorbed by the fuel used to trigger it.

Inertial confinement fusion involves creating something like a tiny star. It starts with a capsule of fuel, consisting of deuterium and tritium – heavier isotopes of hydrogen. This fuel capsule is placed in a hollow gold chamber about the size of a pencil eraser called a hohlraum.

Then, 192 high-powered laser beams are blasted at the hohlraum, where they are converted into X-rays. These X-rays implode the fuel capsule, heating and compressing it to conditions comparable to those in the center of a star – temperatures in excess of 100 million degrees Celsius (180 million Fahrenheit) and pressures greater than 100 billion Earth atmospheres – turning the fuel capsule into a tiny blob of plasma.

And, just as hydrogen fuses into heavier elements in the heart of a main-sequence star, so too does the deuterium and tritium in the fuel capsule. The whole process takes place in just a few billionths of a second. The goal is to achieve ignition – a point at which the energy generated by the fusion process exceeds the total energy input.

The experiment, conducted on 8 August, fell just short of that mark; the input from the lasers was 1.9 megajoules. But it's still tremendously exciting, because according to the team's measurements, the fuel capsule absorbed over five times less energy than it generated in the fusion process. The result also opens up new avenues for experimental research.

https://meetings.aps.org/Meeting/DPP21/Session/AR01.1

https://www.sciencealert.com/for-the-first-time-a-fusion-reaction-h...

Humans Are Doomed to Go Extinct

Habitat degradation, low genetic variation and declining fertility are setting Homo sapiens up for collapse 

The first international framework on open science was adopted by 193 countries attending UNESCO’s General Conference. By making science more transparent and more accessible, the UNESCO Recommendation on Open Science will make science more equitable and inclusive. 

Through open science, scientists and engineers use open licenses to share their publications and data, software and even hardware more widely. Open science should, thus, enhance international scientific cooperation. 

Researchers develop ice cube that doesn't melt or grow mold

Researchers have developed a new type of cooling cube that could revolutionize how food is kept cold and shipped fresh without relying on ice or traditional cooling packs.

These plastic-free, "jelly ice cubes" do not melt, are compostable and anti-microbial, and prevent cross-contamination.

The cooling cubes contain more than 90 percent water and other components to retain and stabilize the structure. They are soft to the touch like a gelatin dessert and change color depending on temperature. These reusable cubes can be designed or cut to any shape and size needed. You can use it for 13 hours for cooling, collect it, rinse it with water and put it in the freezer to freeze again for the next use.

The jelly ice cubes offer an alternative to traditional ice and could potentially reduce water consumption and environmental impact. They also offer stable temperatures to reduce food spoilage and could be ideal for meal prep companies, shipping businesses and food producers who need to keep items cold.

The application could potentially reduce water consumption in the food supply chain and food waste by controlling microbial contaminations. The research was published in the American Chemical Society's journal, Sustainable Chemistry & Engineering.

Jiahan Zou et al, Sustainable and Reusable Gelatin-Based Hydrogel "Jelly Ice Cubes" as Food Coolant. II: Ideal Freeze–Thaw Conditions, ACS Sustainable Chemistry & Engineering (2021). DOI: 10.1021/acssuschemeng.1c06309

https://phys.org/news/2021-11-ice-cube-doesnt-mold.html?utm_source=...

Scientists discover potential cause of Alzheimer's disease

Prevailing theories posit plaques in the brain cause Alzheimer's disease. New research instead points to cells' slowing ability to clean themselves as the likely cause of unhealthy brain buildup.

Along with signs of dementia, doctors make a definitive Alzheimer's diagnosis if they find a combination of two things in the brain: amyloid plaques and neurofibrillary tangles. The plaques are a buildup of amyloid peptides, and the tangles are mostly made of a protein called tau.

Roughly 20% of people have the plaques, but no signs of dementia. This makes it seem as though the plaques themselves are not the cause.

For this reason, researchers investigated understudied aspects of tau protein. They wanted to understand whether a close examination of tau could reveal more about the mechanism behind the plaques and tangles.

A key but difficult-to-detect difference in the form of tau allowed the scientists to distinguish between people who expressed no outward signs of dementia from those who did. These results have now been published in the Journal of Proteome Research.

Researchers scanned all the proteins in donated brain samples. Those with brain buildup but no dementia had normal tau while a different-handed form of tau was found in those who developed plaques or tangles as well as dementia.

Most proteins in the body have a half-life of less than 48 hours. However, if the protein hangs out too long, certain amino acids can convert into the other-handed isomer.

In general, the process of clearing spent or defective proteins from cells, known as autophagy, slows down in people over the age of 65. 

 Evan E. Hubbard et al, Does Data-Independent Acquisition Data Contain Hidden Gems? A Case Study Related to Alzheimer's Disease, Journal of Proteome Research (2021). DOI: 10.1021/acs.jproteome.1c00558

https://medicalxpress.com/news/2021-11-scientists-potential-alzheim...

Evidence emerges for dark-matter free galaxies

An international team of astronomers led by researchers from the Netherlands has found no trace of dark matter in the galaxy AGC 114905, despite taking detailed measurements over a course of forty hours with state-of-the-art telescopes. They will present their findings in Monthly Notices of the Royal Astronomical Society.

discovered six galaxies with little to no dark matter, they were told "measure again, you'll see that there will be dark matter around your galaxy". However, after forty hours of detailed observations using the Very Large Array (VLA) in New Mexico (United States), the evidence for a dark matter-free galaxy only became stronger.

The galaxy in question, AGC 114905, is about 250 million light-years away. It is classified as an ultra-diffuse dwarf galaxy, with the name 'dwarf galaxy' referring to its luminosity and not to its size. The galaxy is about the size of our own Milky Way but contains a thousand times fewer stars. The prevailing idea is that all galaxies, and certainly ultra-diffuse dwarf galaxies, can only exist if they are held together by dark matter.

The researchers collected data on the rotation of gas in AGC 114905 for 40 hours between July and October 2020 using the VLA telescope. Subsequently, they made a graph showing the distance of the gas from the center of the galaxy on the x-axis and the rotation speed of the gas on the y-axis. This is a standard way to reveal the presence of dark matter. The graph shows that the motions of the gas in AGC 114905 can be completely explained by just normal matter.

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