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Comment by Dr. Krishna Kumari Challa on January 17, 2023 at 12:08pm

How the last 12,000 years have shaped what humans are today

How the last 12,000 years have shaped what humans are today

While humans have been evolving for millions of years, the past 12,000 years have been among the most dynamic and impactful for the way we live today, according to an anthropologist who organized a special journal feature on the topic in the Proceedings of the National Academy of Sciences.

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Our toilets can yield excellent alternatives for widespread polluti...

To tackle the climate crisis, biodiversity loss, and pollution, humanity will need to move to a circular economy, where all resources are recycled. Why not recycle our own body waste too as fertilizer, provided there is no risk that harmful microbes or traces from pharmaceuticals end up in the consumed crops? Most nutrients needed for plant growth occur in human urine and feces. Urine is especially rich in nitrogen and potassium, and also contains trace amounts of metals such as boron, zinc, and iron. Feces could in theory supply other nutrients such as phosphorus, calcium, and magnesium or valuable organic carbon to soils.

Comment by Dr. Krishna Kumari Challa on January 17, 2023 at 11:47am

Blood vessel protein found to reduce mortality in infectious disease

The vascular system plays an essential role in carrying oxygen and nutrients throughout the body, but too much vascular permeability, or space between the cells lining the blood vessels, can have devastating results. Recently, researchers  have shed new light on a key protein involved in vascular permeability and its impact on mortality in infectious disease.

In a new study published in PNAS, researchers  have demonstrated the potential of endothelial cell-specific protein Roundabout4 (Robo4) as a therapeutic target to reduce mortality resulting from severe infection. Robo4 is expressed by endothelial cells that line the blood vessels. These cells regulate vascular permeability and allow for the exchange of substances from the blood vessels into the surrounding tissue and vice versa.

During the body's immune response, vascular permeability facilitates the movement of important immune cells and the elimination of dangerous pathogens. However, in severe immune responses, such as may occur in infectious diseases like COVID-19, an excessive increase in vascular permeability, known as vascular hyperpermeability, may lead to organ damage and death.

Currently, no drugs directly suppress vascular hyperpermeability. Because Robo4 has been previously shown to play a role in vascular permeability, the researchers  set out to explore Robo4 as a potential target to reduce vascular permeability in severe infection.

To investigate the effects of Robo4 on vascular hyperpermeability, researchers generated an endothelial cell-specific mouse model of conditional Robo4 overexpression. Upon exposing these mice to lipopolysaccharide (LPS), which induces a severe immune response, the mice exhibited decreased vascular permeability and increased rates of survival.

 Researchers found  that treatment with ALK1 inhibitor increases Robo4 expression and reduces mortality in mice under sepsis and SARS-CoV-2 conditions. Increasing Robo4 expression may represent a strategy to reduce vascular permeability and alleviate severe infections.

The researchers screened a library of drugs using a mouse endothelial cell line to identify pathways that are involved in the regulation of Robo4 and found that two competitive SMAD signaling pathways appear to regulate Robo4 expression. When the researchers treated LPS-injected mice with a drug that inhibits ALK1-SMAD signaling, they observed increased Robo4 expression, decreased vascular permeability, and reduced mortality. A reduction in mortality was also observed in mice exposed to SARS-CoV-2, the virus that causes COVID-19.

Maaya Morita et al, Upregulation of Robo4 expression by SMAD signaling suppresses vascular permeability and mortality in endotoxemia and COVID-19 models, Proceedings of the National Academy of Sciences (2023). DOI: 10.1073/pnas.2213317120

Comment by Dr. Krishna Kumari Challa on January 17, 2023 at 11:34am

Highly accurate test for common respiratory viruses uses DNA as 'bait'

Researchers have developed a new test that "fishes" for multiple respiratory viruses at once using single strands of DNA as bait and gives highly accurate results in under an hour.

The test uses DNA "nanobait" to detect the most common respiratory viruses—including influenza, rhinovirus, RSV and COVID-19—at the same time. In comparison, PCR (polymerase chain reaction) tests, while highly specific and highly accurate, can only test for a single virus at a time and take several hours to return a result.

While many common respiratory viruses have similar symptoms, they require different treatments. By testing for multiple viruses at once, the researchers say their test will ensure patients get the right treatment quickly and could also reduce the unwarranted use of antibiotics.

In addition, the tests can be used in any setting, and can be easily modified to detect different bacteria and viruses, including potential new variants of SARS-CoV-2, the virus which causes COVID-19. 

The researchers based their test on structures built from double strands of DNA with overhanging single strands. These single strands are the "bait": they are programmed to "fish" for specific regions in the RNA of target viruses. The nanobaits are then passed through very tiny holes called nanopores. Nanopore sensing is like a ticker tape reader that transforms molecular structures into digital information in milliseconds. The structure of each nanobait reveals the target virus or its variant.

The researchers showed that the test can easily be reprogrammed to discriminate between viral variants, including variants of the virus that causes COVID-19. The approach enables near 100% specificity due to the precision of the programmable nanobait structures.

Ulrich Keyser, Simultaneous identification of viruses and viral variants with programmable DNA nanobait, Nature Nanotechnology (2023). DOI: 10.1038/s41565-022-01287-x. www.nature.com/articles/s41565-022-01287-x

Comment by Dr. Krishna Kumari Challa on January 17, 2023 at 11:09am

Mathematics at the speed of light

Researchers created a nanostructured surface capable of solving equations using light. This discovery opens exciting new opportunities in the field of analog processing based on optical metasurfaces.

The world's ever-growing needs for efficient computing have been driving researchers from diverse research fields to explore alternatives to the current digital computing paradigm. The processing speed and energy efficiency of standard electronics have become limiting factors for novel disruptive applications entering our everyday life, such as artificial intelligence, machine learning, computer vision, and many more. In this context, analog computing has resurfaced and regained significant attention as a complementary route to traditional architectures.

Optical analog processing refers to the use of light to perform analog computations, as opposed to traditional electronic methods which use electricity. One major benefit of using light to perform specific computing tasks is that it can operate at much higher speeds than electronic methods, as the computation is performed at the speed of light traveling through very thin nanostructured surfaces called metasurfaces. In addition, optical analog processing can be more energy efficient than electronic methods, since it does not generate heat in the same way that electronic circuits do. This makes it well-suited for use in high-performance computing applications where speed and energy efficiency are important.

The  researchers developed a thin dielectric nanostructure, called a metagrating, and incorporated a semi-transparent mirror into the sample to continuously send back the signal to the nanostructures, each time multiplied by the metagrating scattering matrix.

They used  a special optimization technique to design the unit cell of the nanostructured array, or metagrating, that can perform the desired matrix multiplication. Each mathematical problem requires a specific design for the metagrating, but in theory one could engineer a surface with multiple parallel gratings to solve several integral equations in parallel.

These results demonstrate the possibility of solving complex mathematical problems and a generic matrix inversion at speeds that are far beyond those of the typical digital computing methods. Indeed, the solution converges in about 349 fs (i.e., less than one thousand-millionth of a second), orders of magnitude faster than the clock speed of a conventional processor.

Andrea Cordaro et al, Solving integral equations in free space with inverse-designed ultrathin optical metagratings, Nature Nanotechnology (2023). DOI: 10.1038/s41565-022-01297-9

Comment by Dr. Krishna Kumari Challa on January 16, 2023 at 12:08pm

Does Light Experience Time?

Comment by Dr. Krishna Kumari Challa on January 16, 2023 at 10:06am

Building blocks of life found in meteorite that crash landed on Earth

New research has been published on the organic analysis of the Winchcombe meteorite that crash landed onto a driveway in Winchcombe, Gloucestershire in 2021. The research found organic compounds from space that hold the secrets to the origin of life.

In the study, the analysis found a range of organic matter, which reveals that the meteorite was once from part of an asteroid where liquid water occurred, and if it that asteroid had been given access to the water, a chemical reaction could have occurred leading to more molecules turning into amino acids and protein—the building blocks of life. The Winchcombe meteorite is a rare carbon rich chondritic meteorite (approximately 4% of all recovered meteorites, containing up to 3.5 weight percent of carbon) and is the first ever meteorite of this type to be found in the U.K. with an observed meteorite fall event, with more than 1,000 eyewitnesses and numerous footages of the fireball. The amino acid abundance of Winchcombe is ten times lower than other types of carbonaceous chondritic meteorites and was a challenge to study due to the limited detection of amino acids, but with the meteorite so promptly recovered and curated, the team were able to study the organic content of the meteorite prior to its interaction with the Earth's environment. The organic matter suggests the meteorite could represent a class of unique, weak meteorite not previously studied.

Winchcombe belongs to a rare type of carbonaceous meteorite which typically contains a rich inventory of organic compounds and water. The first Winchcombe meteorite stone was recovered within 12 hours of the fireball observation event and properly curated to restrict any terrestrial contamination. This allowed the researchers to study the organic signature truly essential to the meteorite itself.

Studying the organic inventory of the Winchcombe meteorite provided scientists with a window into the past, how simple chemistry kick started the origin of life at the birth of our solar system. Discovering these life's precursor organic molecules allowed them to comprehend the fall of similar material to the surface of the Earth, prior to the emergence of life on our own planet.

Queenie H. S. Chan et al, The amino acid and polycyclic aromatic hydrocarbon compositions of the promptly recovered CM2 Winchcombe carbonaceous chondrite, Meteoritics & Planetary Science (2023). DOI: 10.1111/maps.13936

Comment by Dr. Krishna Kumari Challa on January 15, 2023 at 2:48pm

Mucus-Eating Gut Bacteria May Promote Fever After Cancer Treatment

The expansion of mucus-degraders in the mouse gut—possibly due to poor nutrition—thins the colon’s mucus layer and may weaken defenses against blood-infecting microbes.

One of the most common consequences of cytotoxic cancer treatments, such as chemotherapy and radiation, is the loss of a type of white blood cell called neutrophils—a phenomenon known as neutropenia. In some severe cases of neutropenia, patients develop a fever. Research published November 16 in Science Translational Medicine links this fever to mucus-degrading bacteria in the gut, specifically the commensal Akkermansia muciniphila. The study authors show that these microbes thin the mucus layer in mice, potentially exposing hosts to further bacterial infections—a finding that hints at possible ways to stave off treatment-related fevers in humans.

https://www.science.org/doi/10.1126/scitranslmed.abo3445

Comment by Dr. Krishna Kumari Challa on January 15, 2023 at 2:38pm

Humans Are Still Evolving Thanks to Microgenes

A study sheds light on the tiny genes that have evolved in human genomes since we split from our mammalian ancestors.

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Humans are still evolving new genes, according to a study published in Cell Reports on December 20. As our lineage evolved, at least 155 human genes sprung up from DNA regions previously thought of as “junk,” including two human-specific genes that emerged since humans branched off from chimpanzees around 4 to 6 million years ago, the researchers report.

The genes described in the new study went undiscovered for so long because they’re teeny: They top out at about 300 nucleotides in length, while a typical human gene is 10 to 15,000 base pairs on average. Even though they possess start and stop codons that allow them to be read by cells’ transcriptional machinery just like traditional genes, these so-called microgenes—sometimes called short open reading frames (sORFs)—have long been assumed to be nonfunctional.

But recent studies found that knocking out sORFs stunts cell growth, indicating they’re important after all. One 2020 study, for example, found hundreds of functional sORFs in human cells, both in the coding and noncoding regions of the genome. The number was intriguing to evolutionary biologists and they were compelled to investigate these genetic oddities further, launching what became the newly published research. “We find species-specific genes everywhere,” the researchers say. “So there has to be an evolutionary route for them to originate.”

Using data from the 2020 study, the team scanned human and vertebrate genomes for functional sORFs that produced proteins. Then, using known human and vertebrate phylogenetic information, they predicted the evolutionary relationships among the sORFs estimated when in evolutionary history new microgenes had come about.

Through this process, the team identified 155 microgenes that all vertebrates share. Forty-four of these are critical for cell growth, according to data from the previous study. Three have disease markers associated with ailments such as muscular dystrophy, retinitis pigmentosa, and Alazami syndrome. The team also found one microgene—associated with human heart tissue—that cropped up after chimps and humans split off from gorillas about 7 to 9 million years ago.

The researchers found that these new genes had emerged from the noncoding regions of DNA, rather than by mutation or duplication of existing genes. While gene duplication is thought to be the main source of new genes in all species, the appearance of microgenes might explain how humans developed some uniquely human characteristics, as well as how other animals gained uniquely species-specific phenotypes.

https://www.cell.com/cell-reports/fulltext/S2211-1247(22)01696-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124722016965%3Fshowall%3Dtrue

Comment by Dr. Krishna Kumari Challa on January 15, 2023 at 2:21pm

How Rocky Planets Form

Comment by Dr. Krishna Kumari Challa on January 15, 2023 at 1:26pm

Blue light might be bad for humans - but good for mangoes

 We’re often told to limit our “screen time,” thanks in part to the harsh blue light that screens can emit. Plants can detect blue light too, but instead of causing sleepless nights for our green friends, it could help make their fruits taste better. Researchers now report in ACS’ Journal of Agricultural and Food Chemistry that mangoes can become redder, sweeter and more ripe when exposed to blue light over several days.

Plants rely on sunlight to carry out photosynthesis and ripen their fruits. Studies have shown that exposure to light can affect the appearance of some fruits’ peels and can increase the amount of sugar and pigments in fruits such as tomatoes, which contain chlorophyll throughout their flesh. However, other fruits such as mangoes only contain this pigment in their thick peels, which could change how light affects the flesh. Plus, sunlight contains many colors, so different wavelengths could have different effects. So, researchers wanted to investigate how blue light impacts the quality and ripeness of mangoes.

To understand this phenomenon, the researchers placed a group of mangoes in blue light and another group in darkness for nine days. They found that mangoes in blue light contained far more anthocyanins in their peels, making them redder than those left in the dark. The flesh of these mangoes was also softer, sweeter and more yellow, and had more sucrose and carotenoids than the other group. In further tests, the team found that light-responsive genes involved in the photosynthesis pathway, as well as key genes involved in producing sucrose, anthocyanin and carotenoids, were upregulated under blue light. This meant that the mangoes could directly perceive this light and trigger an internal genetic signaling pathway, say the researchers. The effect was more pronounced in the peel than in the flesh, indicating that the blue light did not penetrate much past the skin. The researchers say that this work could help shed light on the complex relationship behind colored light and the internal quality of fruit.

https://www.acs.org/pressroom/presspacs/2022/acs-presspac-december-....

https://pubs.acs.org/doi/abs/10.1021/acs.jafc.2c07137

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