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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.

Part 1

Comment by Dr. Krishna Kumari Challa on March 22, 2023 at 1:46pm

A quarter of the chick embryos had one or two abnormally small eyes, while others showed facial deformities, thinning heart muscles, and slow heart rates.

Neural tube defects were also noted, which occur when the neural folds that form the early brain and spinal cord fail to meet and close properly. This all links back to those neural crest cells, the researchers suspect.

https://www.sciencedirect.com/science/article/pii/S0160412023001381...

Part 2

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Comment by Dr. Krishna Kumari Challa on March 22, 2023 at 1:46pm

Nanoplastics Interfere With Developing Chicken Embryos in Terrifying Ways

A new study of chicken embryos suggests that sufficient concentrations of teensy nanoplastics speckles could interfere with the earliest stages of development, glugging up stem cells from which tissues and organs usually emerge.

These tissue defects, the study authors say, are "far more serious and extensive than has been previously reported" and include heart defects, which have not been described before in animal studies of microplastics.

Under the focused gaze of fluorescent microscopes, biologists  watched injected samples of nanometer-scale glowing plastic particles cross the embryonic gut wall and circulate into multiple organs of the chick embryos.

They used a high concentration of polystyrene particles, that would normally not be present in an organism. But it shows what nanoplastics can do in extreme cases on very young [chicken] embryos.

Nanoplastics are a fraction smaller than microplastics; both are typically produced when synthetic clothes shed plastic microfibers or larger plastics break down into ever smaller pieces under the glare of UV rays or mechanical weathering.

Past animal studies have tried to investigate the potential health risks of polystyrene microplastics, finding biochemical signs of potentially toxic effects as they accumulate in the livers, kidneys, and guts of laboratory mice. While results like those only hint at what might be happening in humans, we have good reason to be concerned. Our dependency on cheaply made plastic goods and synthetic materials is polluting our oceans and air with microscopic shards of plastic polymers making their way into our bodies and out the other side. Studies have found microplastics lodged deep in human lungs, circulating in our blood, and entering the placenta – the vital organ that shields unborn babies from pathogens and other potentially hazardous materials lurking in the mother's blood. But the possible effects of microplastics on the early development of cells and tissues that go on to form organs and bodies are largely unknown. Most studies of that kind have been in aquatic organisms, such as zebrafish.

In these latest lab experiments, the polystyrene nanoplastics (25 nanometers in size) seemed to get stuck on stem cells called neural crest cells, stopping them from migrating into place where they would normally form important tissues and organs.

In all vertebrates, neural crest cells give rise to parts of the heart, arteries, facial structures, and nervous system.

Part 1

Comment by Dr. Krishna Kumari Challa on March 22, 2023 at 1:20pm

Can synthetic polymers replace the body's natural proteins?

 Most life on Earth is based on polymers of 20 amino acids that have evolved into hundreds of thousands of different, highly specialized proteins. They catalyze reactions, form backbone and muscle and even generate movement.

But is all that variety necessary? Could biology work just as well with fewer building blocks and simpler polymers?

Some polymer scientists, think so. Thye have developed a way to mimic specific functions of natural proteins using only two, four or six different building blocks—ones currently used in plastics—and found that these alternative polymers work as well as the real protein and are a lot easier to synthesize than trying to replicate nature's design.

As a proof of concept, they used their design method, which is based on machine learning or artificial intelligence, to synthesize polymers that mimic blood plasma. The artificial biological fluid kept natural protein biomarkers intact without refrigeration and even made the natural proteins more resistant to high temperatures—an improvement over real blood plasma.

The protein substitutes, or random heteropolymers (RHP), could be a game-changer for biomedical applications, since a lot of effort today is put into tweaking natural proteins to do things they were not originally designed to do, or trying to recreate the 3D structure of natural proteins. Drug delivery of small molecules that mimic natural human proteins is one hot research field.

Instead, AI could pick the right number, type and arrangement of plastic building blocks—similar to those used in dental fillings, for example—to mimic the desired function of a protein, and simple polymer chemistry could be used to make it.

In the case of blood plasma, for example, the artificial polymers were designed to dissolve and stabilize natural protein biomarkers in the blood. Xu and her team also created a mix of synthetic polymers to replace the guts of a cell, the so-called cytosol. In a test tube filled with artificial biological fluid, the cell's nanomachines, the ribosomes, continued to pump out natural proteins as if they didn't care whether the fluid was natural or artificial.

Basically, all the data shows that we can use this design framework, this philosophy, to generate polymers to a point that the biological system would not be able to recognize if it is a polymer or if it is a protein.

This in a way  fooling the biology. The whole idea is that if you really design it and inject your plastics as a part of an ecosystem, they should behave like a protein. If the other proteins are like, 'Okay, you are part of us,' then that's OK.

The design framework also opens the door to designing hybrid biological systems, where plastic polymers interact smoothly with natural proteins to improve a system, such as photosynthesis. And the polymers could be made to naturally degrade, making the system recyclable and sustainable.

Zhiyuan Ruan, Shuni Li, Alexandra Grigoropoulos, Hossein Amiri, Shayna L. Hilburg, Haotian Chen, Ivan Jayapurna, Tao Jiang, Zhaoyi Gu, Alfredo Alexander-Katz, Carlos Bustamante, Haiyan Huang, Ting Xu. Population-based heteropolymer design to mimic protein mixtures. Nature, 2023; 615 (7951): 251 DOI: 10.1038/s41586-022-05675-0

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Comment by Dr. Krishna Kumari Challa on March 22, 2023 at 12:58pm

Mechanical engineers explore kitchen uses for 3D printing

Cooking devices that incorporate three-dimensional (3D) printers, lasers, or other software-driven processes may soon replace conventional cooking appliances such as ovens, stovetops, and microwaves. But will people want to use a 3D printer—even one as beautifully designed as a high-end coffee maker—on their kitchen counters to calibrate the exact micro- and macro-nutrients they need to stay healthy? Will 3D food printing improve the ways we nourish ourselves? What sorts of hurdles will need to be overcome to commercialize such a technology?

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COVID origin linked to raccoon dogs

There’s more evidence supporting the hypothesis that SARS-CoV-2 first spilled over from animals to humans at a market in Wuhan, China. An analysis looked at publicly posted genetic data from COVID-positive swabs taken from drains, stalls and the ground at the market in early 2020. Six samples contained DNA from racoon dogs (Nyctereutes procyonoides), which can catch SARS-CoV-2 and spread it to others of their species, even if they don’t have symptoms. “The most logical hypothesis is that raccoon dogs were infected by SARS-CoV-2 and shed the virus,” says virologist Leo Poon. It’s not the final word on the pandemic’s origin, because the study doesn’t confirm whether the animals were actually infected or whether viral RNA in the swabs came from other sources.

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How to defuse the climate time bomb

Global temperatures will reach 1.5 °C above pre-industrial levels in the early 2030s, according to estimates in a new report by the Intergovernmental Panel on Climate Change (IPCC) that United Nations secretary-general António Guterres called a “how-to guide to defuse the climate time bomb”. To stop warming from crossing a dangerous threshold, industrialized nations will need to cut greenhouse-gas emissions in half by 2030 and achieve net zero b.... Cost-effective ways of doing this, such as solar and wind energy, already exist. The report also suggests that large-scale carbon dioxide removal will be needed, which has raised doubt among some scientists because the technology still barely exists.

Comment by Dr. Krishna Kumari Challa on March 21, 2023 at 12:57pm

How our native language shapes our brain wiring

Scientists have found evidence that the language we speak shapes the connectivity in our brains that may underlie the way we think. With the help of magnetic resonance tomography, they looked deep into the brains of native German and Arabic speakers and discovered differences in the wiring of the language regions in the brain.

Researchers  compared the brain scans of 94 native speakers of two very different languages and showed that the language we grow up with modulates the wiring in the brain. Two groups of native speakers of German and Arabic respectively were scanned in a magnetic resonance imaging (MRI) machine.

The high-resolution images not only show the anatomy of the brain, but also allow to derive the connectivity between the brain areas using a technique called diffusion-weighted imaging. The data showed that the axonal white matter connections of the language network adapt to the processing demands and difficulties of the mother tongue.
Arabic native speakers showed a stronger connectivity between the left and right hemispheres than German native speakers. This strengthening was also found between semantic language regions and may be related to the relatively complex semantic and phonological processing in Arabic.

Native German speakers showed stronger connectivity in the left hemisphere language network. They argue that their findings may be related to the complex syntactic processing of German, which is due to the free word order and greater dependency distance of sentence elements.

Brain connectivity is modulated by learning and the environment during childhood, which influences processing and cognitive reasoning in the adult brain. This study provides new insights how the brain adapts to cognitive demands, that is, the structural language connectome is shaped by the mother tongue.

This is one of the first studies to document differences between the brains of people who grew up with different native languages and could give researchers a way to understand cross-cultural processing differences in the brain. In a next study, the research team will analyze longitudinal structural changes in the brains of Arabic-speaking adults as they learn German over six months. Xuehu Wei et al, Native language differences in the structural connectome of the human brain, NeuroImage (2023). DOI: 10.1016/j.neuroimage.2023.119955

Comment by Dr. Krishna Kumari Challa on March 21, 2023 at 12:49pm

Bacteria-killing viruses deploy genetic code-switching to deceive hosts

Scientists have confirmed that bacteria-killing viruses called bacteriophages deploy a sneaky tactic when targeting their hosts: They use a standard genetic code when invading bacteria, then switch to an alternate code at later stages of infection.

Their study provides crucial information on the life cycle of phages. It could be a key step toward the development of new technologies such as therapeutics targeting human pathogens or of methods to control phage-bacterial interactions in applications ranging from plant production to carbon sequestration.

Scientists have predicted since the mid-1990s that some organisms may use an alternate genetic code, but the process had never been observed experimentally in phages.

Researchers now obtained the first experimental validation of this theory using uncultivated phages in human fecal samples and the lab's high-performance mass spectrometry to reveal the intricacies of how phage proteins are expressed in the host organism. The work is detailed in Nature Communications.

The scientists confirmed that the phages convert a genome-coding signal that usually halts protein production to instead express a different amino acid entirely, one that supports replication of the phage. That code switch allows the phage to take over the bacteria's biological processes.

These phages use a standard genetic code early on as they infect bacteria, one that's compatible with the bacterial host. Once the phages are integrated into the host, they hijack the machinery and begin pumping out phage proteins. By the late stage of infection, the host bacterium is unable to stop producing phages and dies.

Recognizing this change to an alternate genetic code helps ensure that scientists' assumptions about phage protein structure and function are correct.

Samantha L. Peters et al, Experimental validation that human microbiome phages use alternative genetic coding, Nature Communications (2022). DOI: 10.1038/s41467-022-32979-6

Comment by Dr. Krishna Kumari Challa on March 21, 2023 at 12:36pm

Researchers discover molecular basis for alkaline taste

Whether or not animals can taste basic or alkaline food and how they do it has remained a mystery until now. A research group recently addressed this question, as they similarly did for sour taste in 2021 on the lower end of the pH scale. Their work, published recently in Nature Metabolism, identified a previously unknown chloride ion channel, which they named alkaliphile (Alka), as a taste receptor for alkaline pH.

The level of pH, which is a scale of how acidic or basic a substance is, must be just right to instigate many biological processes, such as breaking down food and creating enzymatic reactions. While researchers are familiar with sour taste, which is associated with acids and allows people to sense the acidic end of the pH scale, little is known about how animals perceive bases on the opposite end of the pH spectrum. Detecting both acids and bases, which are commonly present in food sources, is important because they can significantly impact the nutritional properties of what animals consume.

Researchers now found that Alka is expressed in the fly's gustatory receptor neurons (GRNs), the counterpart of taste receptor cells of mammals. When facing neutral food versus alkaline food, wild-type flies normally choose neutral foods because of the toxicity of high pH. In contrast, flies lacking Alka lose the ability to discriminate against alkaline food when presented with it. If the pH of a food is too high, it can be harmful and cause health concerns in humans such as muscle spasms, nausea, and numbness. Likewise, after fruit flies eat food with high pH, their lifespan can be shortened.

This work demonstrates that Alka is critical for flies to stay away from harmful alkaline environments. Detecting the alkaline pH of food is an advantageous adaptation that helps animals avoid consuming toxic substances. 

To understand how Alka senses high pH, the researchers performed electrophysiological analyses and found that Alka forms a chloride ion (Cl-) channel that is directly activated by hydroxide ions (OH-). Like olfactory sensory neurons in mammals, the concentration of Cl- inside the fly's GRN is typically higher than outside this nerve cell. The researchers propose that when exposed to high-pH stimuli, the Alka channel opens, leading to negatively charged Cl- flowing from inside to outside the fly's GRN. This efflux of Cl- activates the GRN, ultimately signaling to the fly brain that the food is alkaline and should be avoided.

In addition, the scientists studied how flies detect the taste of alkaline substances using light-based optogenetic tools. They found that when they turned off alkaline GRNs, the flies were no longer bothered by the taste of alkaline food. Conversely, they activated these alkaline GRNs by shining red light on them. Interestingly, when these flies were given sweet food and exposed to red light at the same time, the flies did not want to eat the sweet food anymore. Alkaline taste can make a big impact on what flies choose to eat.

Overall, they have established that Alka is a new taste receptor dedicated to sensing the alkaline pH of food.

Yali Zhang, Alkaline taste sensation through the alkaliphile chloride channel in Drosophila, Nature Metabolism (2023). DOI: 10.1038/s42255-023-00765-3. www.nature.com/articles/s42255-023-00765-3

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