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Comment by Dr. Krishna Kumari Challa on November 25, 2021 at 8:44am

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

Comment by Dr. Krishna Kumari Challa on November 25, 2021 at 8:26am

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

Comment by Dr. Krishna Kumari Challa on November 25, 2021 at 8:24am

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

Comment by Dr. Krishna Kumari Challa on November 25, 2021 at 8:23am

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

Comment by Dr. Krishna Kumari Challa on November 24, 2021 at 1:42pm

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

Comment by Dr. Krishna Kumari Challa on November 24, 2021 at 1:42pm

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

Comment by Dr. Krishna Kumari Challa on November 24, 2021 at 1:41pm

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

Comment by Dr. Krishna Kumari Challa on November 24, 2021 at 11:31am

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...

Comment by Dr. Krishna Kumari Challa on November 24, 2021 at 9:54am

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...

Comment by Dr. Krishna Kumari Challa on November 23, 2021 at 12:12pm

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

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