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Comment by Deepak Menon on January 22, 2023 at 7:10am

Very very interesting research on the DNA trap. Will these trap specific viruses and how will they recognise them?

Comment by Dr. Krishna Kumari Challa on January 21, 2023 at 11:10am

How antioxidants produced by mitochondria reach the cell surface to protect against death

Antioxidants are often advertised as a cure-all in nutrition and offered as dietary supplements. However, our body also produces such radical scavengers itself, one of which is coenzyme Q. Now researchers have discovered how the substance, which is produced in our mitochondria, reaches the cell surface and protects our cells from dying.

Coenzyme Q is an antioxidant that is essential for our body. A deficiency of coenzyme Q leads to serious diseases such as Leigh syndrome—a hereditary disease in which certain brain regions become affected and, among other things, muscle weakness  can occur. A deficiency of coenzyme Q is also one of the first signs of aging and can occur as early as the early 20s. But why can't we simply take this substance in with our food?

Because Coenzyme Q is a highly hydrophobic molecule that our bodies absorb very little from food.  But it is also a problem in our cells that coenzyme Q is not water soluble. The antioxidant is formed in mitochondria and must pass through the watery cell interior called cytoplasm to the surface of the cells in order to neutralize oxidized lipid species.

With this new research work, scientists have now been able to identify the proteins involved in coenzyme Q transport from the mitochondria to the cell surface.

The researchers found that an enzyme called STARD7 helps transport the coenzyme. This protein is not only localized in the mitochondria, but also inside the cytoplasm. The mitochondria actively transport coenzyme Q to the cell surface to protect cells from cell death. It is as if the mitochondria deliver band-aids to the surface to protect the cell. This again shows that mitochondria are not only important as an energy supplier for our cells, but also play crucial regulatory roles.

A precise understanding of this transport process will enable Coenzyme Q to be delivered into the cells of affected patients and thus provide a new therapeutic approach for diseases such as Leigh syndrome.

Soni Deshwal et al, Mitochondria regulate intracellular coenzyme Q transport and ferroptotic resistance via STARD7, Nature Cell Biology (2023). DOI: 10.1038/s41556-022-01071-y

Comment by Dr. Krishna Kumari Challa on January 21, 2023 at 10:58am

Using origami DNA to trap large viruses and prevent infections

A team of researchers has found that it is possible to build origami DNA structures that can be used to trap large viruses. In their paper published in the journal Cell Reports Physical Science, the group describes how they built their structures and how well they worked when tested.

As the global pandemic continues, albeit in a less deadly phase, the medical science community continues to look for ways to prevent people from becoming infected with not just the SARS-CoV-2 virus, but all viruses. One such approach involves the use of structures designed to attract viruses and when they come close enough, to trap them. In this new effort, the researchers have tested the idea of using origami DNA. DNA origami involves strands of DNA manipulated to create two or three-dimensional shapes, all at the nanoscale. In this new work, the researchers expanded on prior work done by some of the team members who together had developed a process for using DNA origami to trap very small viral particles. To create larger traps for larger viruses, the team used both long and short strands of DNA that had been designed to stick together in useful ways. They then used them to create triangular 2D building blocks that when placed near each other would snap together like puzzle pieces. They then set to work creating structures that they believed could serve as virus traps. After confirming that the structures they had in mind had the desired shapes, they coated the insides of them with chemicals or antibodies that are known to bind with viruses. They then tested the traps by placing them in the vicinity of live viruses. They found that the traps worked as hoped, capturing viruses as large as 100nm in diameter. When trapped, viruses were unable to bond with other cells, thus preventing infections. The researchers tested their traps with several types of viruses—from Zika, to influenza to SARS-CoV-2—and found that they worked equally well on all of them. They also found that they could make them more durable by shining a UV light on them and by covering them with an oligosine polymer. They next plan to test their traps in live lab animals.

Alba Monferrer et al, DNA origami traps for large viruses, Cell Reports Physical Science (2023). DOI: 10.1016/j.xcrp.2022.101237

Comment by Dr. Krishna Kumari Challa on January 21, 2023 at 10:39am

74,963 Kinds of Ice

There are somewhere between 20 and 74,963 kinds of ice. Water can do all kinds of weird stuff when it freezes. So far scientists have experimentally shown crystal structures for 19 kinds of ice. Or maybe 20, depending on who you ask. We’re going to charge through as many as we can in ten minutes or so.

Comment by Dr. Krishna Kumari Challa on January 21, 2023 at 10:20am

Ripples in fabric of universe may reveal start of time

Scientists have advanced in discovering how to use ripples in space-time known as gravitational waves to peer back to the beginning of everything we know. The researchers say they can better understand the state of the cosmos shortly after the Big Bang by learning how these ripples in the fabric of the universe flow through planets and the gas between the galaxies.

We can't see the early universe directly, but maybe we can see it indirectly if we look at how gravitational waves from that time have affected matter and radiation that we can observe today.

adapted this technique from their research into fusion energy, the process powering the sun and stars that scientists are developing to create electricity on Earth without emitting greenhouse gases or producing long-lived radioactive waste. Fusion scientists calculate how electromagnetic waves move through plasma, the soup of electrons and atomic nuclei that fuels fusion facilities known as tokamaks and stellarators.

It turns out that this process resembles the movement of gravitational waves through matter. Researchers basically put plasma wave machinery to work on a gravitational wave problem.

Gravitational waves, first predicted by Albert Einstein in 1916 as a consequence of his theory of relativity, are disturbances in space-time caused by the movement of very dense objects. They travel at the speed of light and were first detected in 2015 by the Laser Interferometer Gravitational Wave Observatory (LIGO) through detectors in Washington State and Louisiana.

Researchers 

created formulas that could theoretically lead gravitational waves to reveal hidden properties about celestial bodies, like stars that are many light years away. As the waves flow through matter, they create light whose characteristics depend on the matter's density.

A physicist could analyze that light and discover properties about a star millions of light years away. This technique could also lead to discoveries about the smashing together of neutron stars and black holes, ultra-dense remnants of star deaths. They could even potentially reveal information about what was happening during the Big Bang and the early moments of our universe.

Deepen Garg et al, Gravitational wave modes in matter, Journal of Cosmology and Astroparticle Physics (2022). DOI: 10.1088/1475-7516/2022/08/017

Comment by Dr. Krishna Kumari Challa on January 20, 2023 at 11:19am

(1) Researchers submerge cells in a hydrogel solution containing sodium acrylate. (2) Water-absorbing polymers of sodium polyacrylate build up to form a gel. (3) Water added to the gel occupies space in between the polymers, causing the gel and cells to swell. (4) Cells are viewed with the naked eye using a stain for protein-rich components.

ONS M’SAAD; CC-BY-NC-NC 4.0

Comment by Dr. Krishna Kumari Challa on January 20, 2023 at 11:19am

New Swelling Technique Makes Cells Visible to the Naked Eye

A new technique, called Unclearing Microscopy, physically inflates and then stains cells to circumvent the need for expensive microscopes.

ABOVE:A sample of cells enlarged via Unclearing MicroscopyONS M’SAAD; CC-BY-NC-NC 4.0

Microscopes have been fine-tuned to image cells in granular detail, with the most sophisticated instruments capable of resolving individual atoms within a protein. The expense of microscopes creates an economic divide, however, hindering research at organizations with less funding.

In 2015, scientists developed a technique called expansion microscopy that physically enlarges cells, making some small features large enough to view with simple microscopes. In a preprint uploaded to bioRxiv on December 2, Bewersdorf and his colleague Ons M’Saad further developed the technique, enabling cells to be seen with the naked eye and increasing detail with a simple microscope.

The team developed a two-step strategy that involves both expanding and staining cells, and tested their technique on human cells and mouse brain tissue. First, they submerged the samples in a hydrogel solution containing small compounds that behave as liquid until they link up into polymer chains that absorb water and congeal into a gel. These included sodium polyacrylate, a super-absorbent powder found in diapers. After the cells take in the solution, water absorption swells the gel, physically expanding cells to about the same size as sesame seeds.

Cells remain invisible by this point because their contents have been diluted 8,000 times with water,” M’Saad tells The Scientist. “We needed to come up with an augmented stain to ‘unclear’ the cells so that they appear vivid.”

The new technique, which the team patented and named “Unclearing Microscopy,” involves two staining methods. The first uses large stainable polymers to augment the signal, making the cell more visible. The research team achieved this by targeting all the proteins in the cell with small molecules that subsequently link up with other compounds under light to produce large polymers that can be stained blue. The other technique involved depositing silver on the sample in increasing concentrations until the researchers determined the optimal dose that, in concert with the other technique, amplified the signal more than 100,000 times. This enhanced the contrast enough to view cells with the naked eye.

https://www.biorxiv.org/content/10.1101/2022.11.29.518361v1

Comment by Dr. Krishna Kumari Challa on January 20, 2023 at 10:50am

Why gas stoves matter to the climate, and the gas industry: Keeping...

Gas stoves are a leading source of hazardous indoor air pollution, but they emit only a tiny share of the greenhouse gases that warm the climate. Why, then, have they assumed such a heated role in climate politics?

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Quantum computer solves protein puzzle

Physicist and code specialist Dr. Sandipan Mohanty has been working on molecular biology simulations for the world's fastest supercomputers for 20 years. Such simulations help to unravel the building blocks of life and provide new insights into cellular machinery.

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Harvesting energy from moving trains

The Virginia Tech Center for Vehicle Systems and Safety (CVeSS) and the Railway Technologies Laboratory want to harness the energy created by moving trains and transform that energy into usable electricity.

Comment by Dr. Krishna Kumari Challa on January 20, 2023 at 10:00am

Stopping a childhood cancer in its tracks

Ewing sarcoma causes tumors to grow in bones or the soft tissues surrounding them. Once a tumor begins to spread to other parts of the body, it can be very difficult to halt the disease's progression. Even for patients with positive outcomes, treating Ewing sarcoma often causes toxic side effects.

Scientists  have discovered a new drug target for Ewing sarcoma, a rare kind of cancer usually diagnosed in children and young adults. Their experiments show that the cells causing this cancer can essentially be reprogrammed with the flick of a genetic switch.

Shutting down a single protein forces the cancer cells to take on a new identity and behave like normal connective tissue cells, a dramatic change that reins in their growth. This discovery suggests researchers may be able to stop Ewing sarcoma by developing a drug that blocks the protein known as ETV6.

Christopher Vakoc, ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation, Nature Cell Biology (2023). DOI: 10.1038/s41556-022-01060-1. www.nature.com/articles/s41556-022-01060-1

Comment by Dr. Krishna Kumari Challa on January 20, 2023 at 9:54am

'Living medicine' created to tackle drug-resistant lung infections

Researchers have designed the first "living medicine" to treat lung infections. The treatment targets Pseudomonas aeruginosa, a type of bacteria that is naturally resistant to many types of antibiotics and is a common source of infections in hospitals.

The treatment involves using a modified version of the bacterium Mycoplasma pneumoniae, removing its ability to cause disease and repurposing it to attack P. aeruginosa instead. The modified bacterium is used in combination with low doses of antibiotics that would otherwise not work on their own.

Researchers tested the efficacy of the treatment in mice, finding that it significantly reduced lung infections. The "living medicine" doubled mouse survival rate compared to not using any treatment. Administering a single, high dose of the treatment showed no signs of toxicity in the lungs. Once the treatment had finished its course, the innate immune system cleared the modified bacteria in a period of four days.

Luis Serrano, Engineered live bacteria suppress Pseudomonas aeruginosa infection in mouse lung and dissolve endotracheal-tube biofilms, Nature Biotechnology (2023). DOI: 10.1038/s41587-022-01584-9. www.nature.com/articles/s41587-022-01584-9

Ariadna Montero‐Blay et al, Bacterial expression of a designed single‐chain IL ‐10 prevents severe lung inflammation, Molecular Systems Biology (2023). DOI: 10.15252/msb.202211037

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