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Comment by Dr. Krishna Kumari Challa on Friday

New study finds co-infection with 'superbug' bacteria increases SARS-CoV-2 replication

Global data shows nearly 10 percent of severe COVID-19 cases involve a secondary bacterial co-infection—with Staphylococcus aureus, also known as staph A, being the most common organism responsible for co-existing infections with SARS-CoV-2. Researchers  have found that the addition of a "superbug"—methicillin-resistant Staphylococcus aureus (MRSA)—into the mix could make the COVID-19 outcome even more deadly.

The mystery of how and why the combination of these two pathogens contributes to the severity of the disease remains unsolved. However,  researchers have made significant progress toward solving this "whodunit."

New research  has revealed that IsdA, a protein found in all strains of staph A, enhanced SARS-CoV-2 replication by 10- to 15-fold. The findings of this study are significant and could help inform the development of new therapeutic approaches for COVID-19 patients with bacterial co-infections.

Interestingly, the study, which was recently published in iScience, also showed that SARS-CoV-2 did not affect the bacteria's growth. This was contrary to what the researchers had initially expected.

https://www.cell.com/iscience/fulltext/S2589-0042(23)00052-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2589004223000524%3Fshowall%3Dtrue

Comment by Dr. Krishna Kumari Challa on Friday

SARS-CoV-2 can alter genome structure of our cells

People infected with SARS-CoV-2, the virus that causes COVID-19, may experience genome structure changes that not only may explain our immunological symptoms after infection, but also potentially link to long COVID, according to a new study by researchers.

This particular finding is quite unique and has not been seen in other coronaviruses before. It is a  unique mechanism of SARS-CoV-2 that is associated with its severe impacts on human health.

The genetic materials in our cells are stored in a structure called chromatin. Some viruses of other categories have been reported to hijack or change our chromatin so that they can successfully reproduce in our cells. Whether and how SARS-CoV-2 may affect our chromatin was not known. In this study, researchers used leading-edge methods and comprehensively characterized the chromatin architecture in human cells after a COVID-19 infection.

Researchers found that many well-formed chromatin architectures of a normal cell become de-organized after infection. For example, there is one type of chromatin architecture termed A/B compartments that can be analogous to the yin and yang portions of our chromatin. After SARS-CoV-2 infection, they found that the yin and yang portions of the chromatin lose their normal shapes and start to mix together. Such mixing may be a reason for some key genes to change in infected cells, including a crucial inflammation gene, interleukin-6,  that can cause cytokine storm in severe COVID-19 patients.

In addition, this work found that chemical modifications on chromatin were also altered by SARS-CoV-2. The changes of chemical modifications of chromatin were known to exert long-term effects on gene expression and phenotypes. Therefore, this finding may provide an unrealized new perspective to understand the viral impacts on host chromatin that can associate with long COVID.

Finding the mechanisms will offer therapeutic strategies to safeguard our chromatin and to better fight this virus.

 Ruoyu Wang et al, SARS-CoV-2 restructures host chromatin architecture, Nature Microbiology (2023). DOI: 10.1038/s41564-023-01344-8

Comment by Dr. Krishna Kumari Challa on Friday

Deceptive daisy's ability to create fake flies explained

A male fly approaches a flower, lands on top of what he thinks is a female fly, and jiggles around. He's trying to mate, but it isn't quite working. He has another go. Eventually he gives up and buzzes off, unsuccessful. The plant, meanwhile, has got what it wanted: pollen.

A South African daisy, Gorteria diffusa, is the only daisy known to make such a complicated structure resembling a female fly on its petals. The mechanism behind this convincing three-dimensional deception, complete with hairy bumps and white highlights, has intrigued people for decades.

Now researchers have identified three sets of genes involved in building the fake fly on the daisy's petals. The big surprise is that all three sets already have other functions in the plant: one moves iron around, one makes root hairs grow, and one controls when flowers are made.

The study found that the three sets of genes have been brought together in the daisy petals in a new way to build fake lady flies. The "iron moving" genes add iron to the petal's normally reddish-purple pigments, changing the color to a more fly-like blue-green. The root hair genes make hairs expand on the petal to give texture. And the third set of genes make the fake flies appear in apparently random positions on the petals.

"This daisy didn't evolve a new 'make a fly' gene. Instead it did something even cleverer—it brought together existing genes, which already do other things in different parts of the plant, to make a complicated spot on the petals that deceives male flies.

The researchers say the daisy's petals give it an evolutionary advantage, by attracting more male flies to pollinate it. The plants grow in a harsh desert environment in South Africa, with only a short rainy season in which to produce flowers, get pollinated, and set seed before they die. This creates intense competition to attract pollinators—and the petals with fake lady flies make the South African daisy stand out from the crowd.

 Beverley J. Glover, Multiple gene co-options underlie the rapid evolution of sexually deceptive flowers in Gorteria diffusa, Current Biology (2023). DOI: 10.1016/j.cub.2023.03.003. www.cell.com/current-biology/f … 0960-9822(23)00270-1

Comment by Dr. Krishna Kumari Challa on March 23, 2023 at 2:01pm

They can tell us about deep space in ways we can't learn otherwise.

These very high-energy neutrinos in the LHC are important for understanding really exciting observations in particle astrophysics.

FASERnu is an emulsion detector consisting of millimeter-thick tungsten plates alternated with layers of emulsion film. Tungsten was chosen because of its high density, which increases the likelihood of neutrino interaction; the detector consists of 730 emulsion films and a total tungsten mass of around 1 ton.

During particle experiments at the LHC, neutrinos can collide with nuclei in the tungsten plates, producing particles that leave tracks in the emulsion layers, a bit like the way ionizing radiation makes tracks in a cloud chamber.

These plates need to be developed, like photographic film, before the physicists can analyze the particle trails to find out what produced them.

Six neutrino candidates were identified and published back in 2021. Now, the researchers have confirmed their discovery, using data from the third run of the upgraded LHC that began last year, with a significance level of 16 sigma.

That means that the likelihood that the signals were produced by random chance is so low as to be almost nothing; a significance level of 5 sigma is sufficient to qualify as a discovery in particle physics.

The team's results have been presented at the 57th Rencontres de Moriond Electroweak Interaction....

Part 2

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Comment by Dr. Krishna Kumari Challa on March 23, 2023 at 1:59pm

'Ghost Particles': Scientists Finally Detect Neutrinos in Particle Collider

The ghost, at long last, is actually in the machine: For the first time, scientists have created neutrinos in a particle collider.

Those abundant yet enigmatic subatomic particles are so removed from the rest of matter that they slide through it like specters, earning them the nickname "ghost particles".

The researchers say this work represents the first direct observation of collider neutrinos and will help us to understand how these particles form, what their properties are, and their role in the evolution of the Universe.

The results, achieved using the FASERnu detector at the Large Hadron Collider, were presented at the 57th Rencontres de Moriond Electroweak Interactions and Unified Theories conference in Italy.

Neutrinos are among the most abundant subatomic particles in the Universe, second only to photons. But they have no electric charge, their mass is almost zero, and they barely interact with other particles they encounter. Hundreds of billions of neutrinos are streaming through your body right now.

Neutrinos are produced in energetic circumstances, such as the nuclear fusion that takes place inside stars, or supernova explosions. And while we may not notice them on a day-to-day basis, physicists think that their mass – however slight – probably affects the Universe's gravity (although neutrinos have pretty much been ruled out as dark matter).

Although their interaction with matter is small, it's not completely nonexistent; now and again, a cosmic neutrino collides with another particle, producing a very faint burst of light.

Underground detectors, isolated from other sources of radiation, can detect these bursts. IceCube in Antarctica, Super-Kamiokande in Japan, and MiniBooNE at Fermilab in Illinois are three such detectors.

Neutrinos produced in particle colliders, however, have long been sought by physicists because the high energies involved are not as well studied as low-energy neutrinos.

Part 1

Comment by Dr. Krishna Kumari Challa on March 23, 2023 at 1:25pm

Bats’ weird immunity could stop pandemics

The COVID-19 pandemic has propelled a niche research field to prominence: bat immunology. Bats are a possible source of catastrophic viral outbreaks in people because the animals can tolerate an exceptionally diverse array of viruses, including coronaviruses, rabies and Ebola. The biological mechanisms behind bats’ weird immune systems are slowly emerging: “There’s kind of a peace treaty,” between bats and the pathogens they host, explains virologist Joshua Hayward. Bats’ genomes seem to suck up viral information like a sponge. It is possible that this protects bats from the negative outcomes of viral infections, just as a vaccine would.

Comment by Dr. Krishna Kumari Challa on March 23, 2023 at 1:05pm

'Vampiric' water use leading to 'imminent' global crisis, UN warns

Humanity's "lifeblood"—water—is increasingly at risk around the world due to "vampiric overconsumption and overdevelopment," the UN warned in a report, published hours ahead of a major summit on the issue was set to begin 0n 22nd March, '23.

The world is "blindly traveling a dangerous path" as "unsustainable water use, pollution and unchecked global warming are draining humanity's lifeblood": United Nations.

If nothing is done, it will be a business-as-usual scenario—it will keep on being between 40 percent and 50 percent of the population of the world that does not have access to sanitation and roughly 20-25 percent of the world will not have access to safe water supply. With the global population increasing every day, in absolute numbers, there'll be more and more people that don't have access to these services.

At the UN conference, governments and actors in the public and private sectors are invited to present proposals for a so-called water action agenda to reverse that trend and help meet the development goal, set in 2015, of ensuring "access to water and sanitation for all by 2030."

Source: AFP

Comment by Dr. Krishna Kumari Challa on March 23, 2023 at 12:40pm

Vision: The first molecular processes in the eye when light hits the retina

Researchers have deciphered the molecular processes that first occur in the eye when light hits the retina. The processes—which take only a fraction of a trillionth of a second—are essential for human sight.

It only involves a microscopic change of a protein in our retina, and this change occurs within an incredibly small time frame: it is the very first step in our light perception and ability to see. It is also the only light-dependent step. Researchers have established exactly what happens after the first trillionth of a second in the process of visual perception, with the help of the SwissFEL X-ray free-electron laser of the PSI.

At the heart of the action is our light receptor, the protein rhodopsin. In the human eye it is produced by sensory cells, the rod cells, which specialize in the perception of light. Fixed in the middle of the rhodopsin is a small kinked molecule: retinal, a derivative of vitamin A. When light hits the protein, retinal absorbs part of the energy. With lightning speed, it then changes its three-dimensional form so the switch in the eye is changed from "off" to "on." This triggers a cascade of reactions whose overall effect is the perception of a flash of light.

But what happens in detail when retinal transforms from what is known as the 11-cis form into the all-trans form? This is what the scientists observed now:

The protein absorbs part of the light energy to briefly inflate a tiny amount—"like our chest expanding when we breathe in, only to contract again shortly afterwards."

During this "breathing in" stage, the protein temporarily loses most of its contact with the retinal that sits in its middle. "Although the retinal is still connected to the protein at its ends through chemical bonds, it now has room to rotate." At that moment, the molecule resembles a dog on a loose leash that is free to give a jerk.

Shortly afterwards the protein contracts again and has the retinal firmly back in its grasp, except now in a different more elongated form. "In this way the retinal manages to turn itself, unimpaired by the protein in which it is held."

The transformation of the retinal from 11-cis kinked form into the all-trans elongated form only takes a picosecond, or one trillionth (10-12) of a second, making it one of the fastest processes in all of nature.

The only way of recording and analyzing such rapid biological processes is with an X-ray free-electron laser like the SwissFEL. The SwissFEL allows us to study in detail the fundamental processes of the human body, such as vision.

Valerie Panneels, Ultrafast structural changes direct the first molecular events of vision, Nature (2023). DOI: 10.1038/s41586-023-05863-6. www.nature.com/articles/s41586-023-05863-6

Comment by Dr. Krishna Kumari Challa on March 23, 2023 at 12:31pm

The physics of photosynthesis is seriously impressive. Observing charge transport through cells opens up remarkable opportunities for new discoveries on how nature operates.

Since the electrons from photosynthesis are dispersed through the whole system, that means we can access them. The fact that we didn't know this pathway existed is exciting, because we could be able to harness it to extract more energy for renewables.

The researchers say that being able to extract charges at an earlier point in the process of photosynthesis, could make the process more efficient when manipulating photosynthetic pathways to generate clean fuels from the Sun. In addition, the ability to regulate photosynthesis could mean that crops could be made more able to tolerate intense sunlight.

Jenny Zhang, Photosynthesis re-wired on the pico-second timescale, Nature (2023). DOI: 10.1038/s41586-023-05763-9. www.nature.com/articles/s41586-023-05763-9

Part 2

Comment by Dr. Krishna Kumari Challa on March 23, 2023 at 12:29pm

Photosynthesis 'hack' could lead to new ways of generating renewable energy

Researchers have 'hacked' the earliest stages of photosynthesis, the natural machine that powers the vast majority of life on Earth, and discovered new ways to extract energy from the process, a finding that could lead to new ways of generating clean fuel and renewable energy.

An international team of physicists, chemists and biologists was able to study photosynthesis—the process by which plants, algae and some bacteria convert sunlight into energy—in live cells at an ultrafast timescale: a millionth of a millionth of a second.

Despite the fact that it is one of the most well-known and well-studied processes on Earth, the researchers found that photosynthesis still has secrets to tell. Using ultrafast spectroscopic techniques to study the movement of energy, the researchers found the chemicals that can extract electrons from the molecular structures responsible for photosynthesis do so at the initial stages, rather than much later, as was previously thought.

This 'rewiring' of photosynthesis could improve ways in which it deals with excess energy, and create new and more efficient ways of using its power. The results are reported in the journal Nature.

While photosynthesis is a natural process, scientists have also been studying how it could be used as to help address the climate crisis, by mimicking photosynthetic processes to generate clean fuels from sunlight and water, for example.

Researchers were originally trying to understand why a ring-shaped molecule called a quinone is able to 'steal' electrons from photosynthesis. Quinones are common in nature, and they can accept and give away electrons easily. The researchers used a technique called ultrafast transient absorption spectroscopy to study how the quinones behave in photosynthetic cyanobacteria.

No one had properly studied how this molecule interplays with photosynthetic machineries at such an early point of photosynthesis: so now some scientists thought they were just using a new technique to confirm what they already knew. Instead, they found a whole new pathway, and opened the black box of photosynthesis a bit further.

Using ultrafast spectroscopy to watch the electrons, the researchers found that the protein scaffold where the initial chemical reactions of photosynthesis take place is 'leaky', allowing electrons to escape. This leakiness could help plants protect themselves from damage from bright or rapidly changing light.

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