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Comment by Dr. Krishna Kumari Challa on April 28, 2023 at 11:30am

How shading crops with solar panels can improve farming, lower food...

If you have lived in a home with a trampoline in the backyard, you may have observed the unreasonably tall grass growing under it. This is because many crops, including these grasses, actually grow better when protected from the sun, to an extent.

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We need to talk about gene-therapy prices

At US$3.5 million per treatment, the haemophilia gene therapy Hemgenix is the most expensive drug in the world. Other gene therapies are expected to carry similarly eye-watering p.... This puts them out of the reach of many who need them and diminishes government funders’ willingness to pay for related research. “Researchers, especially health economists, must work urgently with industry and governments to find a more affordable funding model,” argues a Nature editorial.

Comment by Dr. Krishna Kumari Challa on April 28, 2023 at 11:27am

Using microbes to get more out of mining waste

Researchers have developed a new mining technique which uses microbes to recover metals and store carbon in the waste produced by mining. Adopting this technique of reusing mining waste, called tailings, could transform the mining industry and create a greener and more sustainable future.

Tailings are a by-product of mining. They are the fine-grained waste materials left after extracting the target ore mineral, which are then stacked and stored. This method is called dry-stack tailing.

Over time, mining practices have evolved and become more efficient. But the climate crisis and rising demand for critical minerals require the development of new ore removal and processing technologies.

Old tailings contain higher amounts of critical minerals that can be extracted with the help of microbes through a process called bioleaching. The microbes help break down the ore, releasing any valuable metals that weren't fully recovered in an eco-friendly way that is much faster than natural biogeochemical weathering processes.

We can now take tailings that were produced in the past and recover more resources from those waste materials and, in doing so, also reduce the risk of residual metals entering into local waterways or groundwater.

In addition to improving resource recovery, the microbes capture carbon dioxide from the air and store it within the mine tailings as new minerals. This process aids in offsetting some of the emissions released while the mine was active and helps stabilize the tailings.

Microbial mineral carbonation could offset more than 30 per cent of a mine sites annual greenhouse gas emissions if applied to an entire mine. In addition, this microbial-driven technique gives value to historical mine tailings that are otherwise considered industrial waste.

Jenine McCutcheon et al, Microbially mediated carbon dioxide removal for sustainable mining, PLOS Biology (2023). DOI: 10.1371/journal.pbio.3002026

Comment by Dr. Krishna Kumari Challa on April 28, 2023 at 11:13am

Researchers also examined more than 10,000 genetic deletions specific to humans using both Zoonomia data and experimental analysis, and linked some of them to the function of neurons.

Other Zoonomia papers published recently revealed that mammals diversified before the mass dinosaur extinction; uncovered a genetic explanation for why a famous sled dog from the 1920s named Balto was able to survive the harsh landscape of Alaska; discovered human-specific changes to genome organization; used machine learning to identify regions of the genome associated with brain size; described the evolution of regulatory sequences in the human genome; focused on sequences of DNA that move around the genome; discovered that species with smaller populations historically are at higher risk of extinction today; and compared genes between nearly 500 species of mammals.

 Sacha Vignieri, Zoonomia, Science (2023). DOI: 10.1126/science.adi1599. www.science.org/doi/10.1126/science.adi1599

Aryn P. Wilder et al, The contribution of historical processes to contemporary extinction risk in placental mammals, Science (2023). DOI: 10.1126/science.abn5856. www.science.org/doi/10.1126/science.abn5856

 Katherine L. Moon et al, Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs, Science (2023). DOI: 10.1126/science.abn5887. www.science.org/doi/10.1126/science.abn5887

Part 3

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Comment by Dr. Krishna Kumari Challa on April 28, 2023 at 11:11am

The researchers found that at least 10% of the human genome is highly conserved across species, with many of these regions occurring outside of protein-coding genes. More than 4,500 elements are almost perfectly conserved across more than 98% of the species studied

Most of the conserved regions—which have changed more slowly than random fluctuations in the genome—are involved in embryonic development and regulation of RNA expression. Regions that changed more frequently shaped an animal's interaction with its environment, such as through immune responses or the development of its skin.

The researchers also pinpointed parts of the genome linked to a few exceptional traits in the mammalian world, such as extraordinary brain size, superior sense of smell, and the ability to hibernate during the winter.

With an eye toward preserving biodiversity, the researchers found that mammals with fewer genetic changes at conserved sites in the genome were at greater risk for extinction.

They used the mammalian genomes to study human traits and diseases. They focused on some of the most conserved single-letter genomic regions uncovered in the first paper and compared them to genetic variants that scientists have previously linked to diseases such as cancer using other methods.

The team found that their annotations of the genome based on evolutionary conservation revealed more connections between genetic variants and their function than the other methods. They also identified mutations that are likely causal in both rare and common diseases including cancer, and showed that using conservation in disease studies could make it easier to find genetic changes that increase risk of disease.

Part 2

Comment by Dr. Krishna Kumari Challa on April 28, 2023 at 11:08am

What makes the human genome unique?

Over the past 100 million years, mammals have adapted to nearly every environment on Earth.

Scientists with the Zoonomia Project have been cataloging the diversity in mammalian genomes by comparing DNA sequences from 240 species that exist today, from the aardvark and the African savanna elephant to the yellow-spotted rock hyrax and the zebu.

This week, in several papers in a special issue of Science, the Zoonomia team has demonstrated how comparative genomics can not only shed light on how certain species achieve extraordinary feats, but also help scientists better understand the parts of our genome that are functional and how they might influence health and disease.

In the new studies, the researchers identified regions of the genomes, sometimes just single letters of DNA, that are most conserved, or unchanged, across mammalian species and millions of years of evolution—regions that are likely biologically important. They also found part of the genetic basis for uncommon mammalian traits such as the ability to hibernate or sniff out faint scents from miles away. And they pinpointed species that may be particularly susceptible to extinction, as well as genetic variants that are more likely to play causal roles in rare and common human diseases.

The findings come from analyses of DNA samples collected by more than 50 different institutions worldwide which provided many genomes from species that are threatened or endangered.

Part 1

Comment by Dr. Krishna Kumari Challa on April 28, 2023 at 9:48am

Scientists slow aging by engineering longevity in cells

Human lifespan is related to the aging of our individual cells. Three years ago a group of  researchers deciphered essential mechanisms behind the aging process. After identifying two distinct directions that cells follow during aging, the researchers genetically manipulated these processes to extend the lifespan of cells.

As described in a new article published April 27, 2023, in Science, the team has now extended this research using synthetic biology to engineer a solution that keeps cells from reaching their normal levels of deterioration associated with aging.

Cells, including those of yeast, plants, animals and humans, all contain gene regulatory circuits that are responsible for many physiological functions, including aging. These gene circuits can operate like our home electric circuits that control devices like appliances and automobiles.

However, the researchers  uncovered that, under the control of a central gene regulatory circuit, cells don't necessarily age the same way. Imagine a car that ages either as the engine deteriorates or as the transmission wears out, but not both at the same time. They envisioned a "smart aging process" that extends cellular longevity by cycling deterioration from one aging mechanism to another.

In the new study, the researchers genetically rewired the circuit that controls cell aging. From its normal role functioning like a toggle switch, they engineered a negative feedback loop to stall the aging process. The rewired circuit operates as a clock-like device, called a gene oscillator, that drives the cell to periodically switch between two detrimental "aged" states, avoiding prolonged commitment to either, and thereby slowing the cell's degeneration.

These advances resulted in a dramatically extended cellular lifespan, setting a new record for life extension through genetic and chemical interventions.

The researchers in this study first used computer simulations of how the core aging circuit operates. This helped them design and test ideas before building or modifying the circuit in the cell. This approach has advantages in saving time and resources to identify effective pro-longevity strategies, compared to more traditional genetic strategies.

This is the first time computationally guided synthetic biology and engineering principles were used to rationally redesign gene circuits and reprogram the aging process to effectively promote longevity.

Zhen Zhou et al, Engineering longevity—Design of a synthetic gene oscillator to slow cellular aging, Science (2023). DOI: 10.1126/science.add7631. www.science.org/doi/10.1126/science.add7631

Comment by Dr. Krishna Kumari Challa on April 28, 2023 at 9:40am

Newly observed effect makes atoms transparent to certain frequencies of light

A newly discovered phenomenon dubbed "collectively induced transparency" (CIT) causes groups of atoms to abruptly stop reflecting light at specific frequencies.

CIT was discovered by confining ytterbium atoms inside an optical cavity —essentially, a tiny box for light—and blasting them with a laser. Although the laser's light will bounce off the atoms up to a point, as the frequency of the light is adjusted, a transparency window appears in which the light simply passes through the cavity unimpeded.

An analysis of the transparency window points to it being the result of interactions in the cavity between groups of atoms and light. This phenomenon is akin to destructive interference, in which waves from two or more sources can cancel one another out. The groups of atoms continually absorb and re-emit light, which generally results in the reflection of the laser's light. However, at the CIT frequency, there is a balance created by the re-emitted light from each of the atoms in a group, resulting in a drop in reflection.

An ensemble of atoms strongly coupled to the same optical field can lead to unexpected results.

Through conventional quantum optics measurement techniques, researchers found that their system had reached an unexplored regime, revealing new physics.

Besides the transparency phenomenon, the researchers also observed that the collection of atoms can absorb and emit light from the laser either much faster or much slower compared to a single atom depending on the intensity of the laser. These processes, called superradiance and subradiance, and their underlying physics are still not understood properly because of the large number of interacting quantum particles.

 Mi Lei et al, Many-body cavity quantum electrodynamics with driven inhomogeneous emitters, Nature (2023). DOI: 10.1038/s41586-023-05884-1

Comment by Dr. Krishna Kumari Challa on April 27, 2023 at 9:19am

Over the course of two field seasons, in 2019 and 2020, the study authors scoured the Changbaishan region for rivers and streams. They collected water samples from around two dozen sites and used radiocarbon dating to estimate the amount of "deep carbon," meaning carbon from the depths of Earth, that had seeped into the water. They compared deep carbon estimates to estimates of carbon incorporated into minerals through silicate weathering.

The researchers found that the Changbaishan region is a small net carbon source. Every year, the region releases at least 600 more tons of carbon than it incorporates—about the amount that 41 average Americans put into the atmosphere on an annual basis. That seems small, but over geological timescales, the impact could be significant.

The Changbaishan volcanic region is just one of many around the world, the researchers point out. Future work should examine wider areas to gain a full understanding of how volcanoes contribute to Earth's carbon cycle.

More information: Jun Zhong et al, Assessing the Deep Carbon Release in an Active Volcanic Field Using Hydrochemistry, δ 13 C DIC and Δ 14 C DIC, Journal of Geophysical Research: Biogeosciences (2023). DOI: 10.1029/2023JG007435

Part 2

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Comment by Dr. Krishna Kumari Challa on April 27, 2023 at 9:18am

Do volcanoes add more carbon than they take away?

In a new study published in the Journal of Geophysical Research: Biogeosciences, researchers discovered that a volcano in northeast China emits a small net amount of carbon each year. Over geological timescales, that could have a significant impact on our planet's carbon cycle.

Volcanic areas continue to emit carbon dioxide long after eruptions are over. Conversely, atmospheric carbon dioxide (CO₂) is constantly locked away into minerals on Earth's surface through a process called silicate weathering. Whether volcanoes release more CO₂ through degassing or capture more CO₂ through silicate weathering is an open question.

The authors of the new study investigated whether the Changbaishan volcanic area in northeast China is a net source or sink of atmospheric carbon. The region has been active for at least 2.7 million years, but it has not erupted since 1903, making the area a prime spot for analyzing long-term carbon leakage.

Part 1

Comment by Dr. Krishna Kumari Challa on April 27, 2023 at 8:32am

Astronomers solve the 60-year mystery of quasars, the most powerful objects in the universe

Scientists have unlocked one of the biggest mysteries of quasars—the brightest, most powerful objects in the universe—by discovering that they are ignited by galaxies colliding.

First discovered 60 years ago, quasars can shine as brightly as a trillion stars packed into a volume the size of our solar system. In the decades since they were first observed, what could trigger such powerful activity has remained a mystery. New work by scientists has now revealed that it is a consequence of galaxies crashing together.

The collisions were discovered when researchers, using deep imaging observations from the Isaac Newton Telescope in La Palma, observed the presence of distorted structures in the outer regions of the galaxies that are home to quasars.

Most galaxies have supermassive black holes at their centers. They also contain substantial amounts of gas—but most of the time this gas is orbiting at large distances from the galaxy centers, out of reach of the black holes. Collisions between galaxies drive the gas towards the black hole at the galaxy center; just before the gas is consumed by the black hole, it releases extraordinary amounts of energy in the form of radiation, resulting in the characteristic quasar brilliance.

The ignition of a quasar can have dramatic consequences for entire galaxies—it can drive the rest of the gas out of the galaxy, which prevents it from forming new stars for billions of years into the future.

This is the first time that a sample of quasars of this size has been imaged with this level of sensitivity. By comparing observations of 48 quasars and their host galaxies with images of over 100 non-quasar galaxies, researchers concluded that galaxies hosting quasars are approximately three times as likely to be interacting or colliding with other galaxies.

J C S Pierce et al, Galaxy interactions are the dominant trigger for local type 2 quasars, Monthly Notices of the Royal Astronomical Society (2023). DOI: 10.1093/mnras/stad455

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