Comment

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?

--

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.

--

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

Comment by Dr. Krishna Kumari Challa on January 20, 2023 at 9:32am

Scientists demonstrate quantum recoil for the first time

For the first time since it was proposed more than 80 years ago, scientists have demonstrated the phenomenon of "quantum recoil," which describes how the particle nature of light has a major impact on electrons moving through materials. The research is published online recently (January 19) in the journal Nature Photonics.

Making quantum recoil a practical reality should eventually allow businesses to more accurately produce X-rays of specific energy levels, leading to superior accuracy in healthcare and manufacturing applications such as medical imaging and flaw detection in semiconductor chips.

Quantum recoil was theorized by Russian physicist and Nobel laureate Vitaly Ginzburg in 1940 to accurately account for radiation emitted when charged particles like electrons move through a medium, such as water, or materials with repeated patterns on the surface, including those on butterfly wings and graphite.

This radiation is created when the moving electrons disturb atoms in the medium or the material. As the atoms return to an undisturbed state, they emit radiation, such as X-rays.

Although the electrons are supposed to lose energy and slow down when this happens, classical theory predicts that its impact on the emitted radiation is negligible.

However, Ginzburg posited that this assumption breaks down when considering the quantum electrodynamics theory that deals with how charged particles interact with an electromagnetic field, as well as how light interacts with matter.

According to the theory, when moving electrons decelerate after disturbing nearby atoms, the energy and momentum these electrons lose should be transferred to the radiation emitted. This happens because light exists as particles that have energy and momentum, and which move in a wave as radiation.

The transfer causes the energies of the radiation released to shift from classical predictions and also affects the slowing electrons by causing them to deviate from their path of travel.

This phenomenon is known as quantum recoil. However, no one has been able to experimentally prove it—until now.

Physicists now demonstrated the phenomenon through separate experiments that bombarded electrons from a scanning electron microscope onto two very thin materials, about 1,000 times thinner than a strand of hair.

The two materials were boron nitride in a hexagonal form often used as a lubricant in paints, and graphite which is used to make rechargeable battery terminals and also found in pencil lead.

Using an energy dispersive X-ray spectrometer detector, the researchers measured the X-rays emitted from this bombardment and found that they had energies that were different from those predicted by classical theory but could instead be explained by quantum recoil.

Sunchao Huang et al, Quantum recoil in free-electron interactions with atomic lattices, Nature Photonics (2023). DOI: 10.1038/s41566-022-01132-6. www.nature.com/articles/s41566-022-01132-6

Comment by Dr. Krishna Kumari Challa on January 19, 2023 at 11:51am

New study shows 'self-cleaning' of marine atmosphere

Scientists have shed new light on the "self-cleaning" capacity of the atmosphere.

This process of self-cleaning is essential to remove gaseous pollutants and regulate green house gasses such as methane from the atmosphere.

Researchers were already aware that the atmosphere had this "self-cleaning" ability, but in a new study, experts have now shown a new process that increases the ability of the marine atmosphere to self-cleanse.

Using a combination of aircraft and ground-based observations, scientists were able to confirm the widespread presence of nitrous oxide (HONO) in the remote Atlantic troposphere formed by so-called "renoxification", whereby photolysis of aerosol nitrate returns nitrogen oxides (NOx) and HONO to the marine atmosphere. Historically, aerosol nitrate had been considered a permanent sink for NOx. This new process could increase the ability of the atmosphere to self-cleanse on a global scale. Scientists say the findings, published in Science Advances, could be highly significant for atmospheric chemistry and largely reconcile widespread uncertainty on the importance of renoxification.

Importantly, the observations showed that the efficiency of renoxification increased with relative humidity and decreased with the concentration of nitrate." "This observation reconciled the very large discrepancies in the rates of renoxification found across multiple laboratory and field studies." "It was also consistent with renoxification occurring on the surface of aerosols, rather than within their bulk, a new and exciting finding with implications for how this fundamental process is controlled and parameterized in models." Recycling of nitrogen oxides on nitrate aerosol could have important, increasing, and as yet unexplored implications for the trends and distributions of atmospheric oxidants such as tropospheric ozone, an important greenhouse gas.

Simone Andersen et al, Extensive field evidence for the release of HONO from the photolysis of nitrate aerosols, Science Advances (2023). DOI: 10.1126/sciadv.add6266. www.science.org/doi/10.1126/sciadv.add6266

Comment by Dr. Krishna Kumari Challa on January 19, 2023 at 11:48am

The fundamental principles of DNA methylation thus appear highly conserved, enabling a deep look at the evolutionary history of vertebrates. However, this does not mean that DNA methylation remained unchanged over millions of years. The genetic code of epigenetics looks clearer and more prescriptive in vertebrates than in invertebrates, even though the underlying patterns are similar. And with the emergence of reptiles, birds, and mammals, the genetic determinants of DNA methylation become even more pronounced. It seems that complex animals including humans particularly depend on epigenetic protection of the genome through DNA methylation.

Large animals with a long lifespan should in theory have a higher risk of cancer, because their bodies consist of many more cells, and these cells have more time to develop into cancer cells. Yet elephants are no more likely to develop cancer than mice or trout. Scientists refer to this as Peto's paradox. The most plausible explanation is that large animals with a long lifespan have evolved special mechanisms that substantially reduce their cancer risk.

Results from the current study indicate that DNA methylation constitutes such a cancer-protective mechanism. Higher theoretical risk of cancer was generally associated with higher DNA methylation levels. This correlation was particularly evident in birds. Most birds have a low risk of cancer, even big birds with long lifespans such as eagles and penguins. The higher DNA methylation levels in large and long-lived birds may thus help protect them against cancer.

Overall, this study provides the most comprehensive analysis of epigenetics in its evolutionary context to date. It also establishes new methods for studying DNA methylation in diverse animal species. For many species, no high-quality genomes are yet available, which is why the team developed and optimized a method the analyze DNA methylation independently of any reference genomes.

This new method allows us to explore the interplay of genetics and epigenetics in all those animal species that were hardly accessible for epigenetic analyses. Hopefully, such evolutionary and comparative analyses will lead to a better understanding of epigenetics in humans, in diseases such as cancer, and in healthy aging.

Johanna Klughammer et al, Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species, Nature Communications (2023). DOI: 10.1038/s41467-022-34828-y

Part 2

**

Comment by Dr. Krishna Kumari Challa on January 19, 2023 at 11:45am

A molecular zoo of epigenetics

Our genes are encoded in the DNA sequence of the genome, which is highly similar across the diverse cell types of our body. Yet, each cell can only access those genes that are in an epigenetically permissive state. The epigenome thus provides a form of molecular access control to the genes—epigenetic "software" that protects our genetic "hardware" from activation in the wrong cells.

This layer of regulatory control has been essential for the development of complex organisms comprising of many hundred different cell types. Moreover, epigenetic regulation helps reduce our risk of cancer by protecting critical areas of the genome from accidental activation.

DNA methylation is the best known and arguably the most important epigenetic mechanism. Methyl groups (CH₃) mark those parts of the DNA that are to be tightly packaged and protected from faulty activation. DNA methylation has many roles throughout our lives—ranging from the fertilized egg to the adult organism, in diseases such as cancer and in the biological aging of our bodies.

DNA methylation provides the cells with epigenetic memory, ensuring that a liver cell always remains a liver cell and a heart cell always remains a heart cell—even though all cells in our body are equipped with the same genes.

DNA methylation is well-studied only in mammals, most notably in mice and humans. In a decade-long effort to fill critical gaps in our understanding of epigenetics, scientists from Bock's research group at CeMM have now mapped and analyzed DNA methylation profiles across 580 different animal species.

The data of the study data show that DNA methylation in animals followed very similar principles 500 million years ago as it does today.

Researchers looked at the relationship between DNA methylation and the underlying genetic DNA sequence in mammals, birds, reptiles, amphibians, fish and invertebrates. The patterns are very similar. For example, they were able to predict the distribution of DNA methylation in elephants genome using a model they  had created for the octopus. These epigenetic patterns therefore very likely existed in the last common ancestor of these animals, a very long time ago.

Part 1

Comment by Dr. Krishna Kumari Challa on January 19, 2023 at 10:37am

 How iron dysregulation might contribute to neurodegenerative diseases

Past neuroscience research consistently found a link between deviations from the "normal" iron metabolism, also known as iron dysregulation, and different neurodegenerative diseases, including Parkinson's disease (PD) and Multiple Sclerosis (MS). Specifically, brain regions associated with these diseases have been found to be often populated by microglia (i.e., resident immune cells) packed with Iron.

While the association between iron dysregulation and neurodegenerative diseases is well documented, the ways in which iron accumulation affects the physiology of microglia and neurodegeneration are yet to be fully grasped. Researchers  have recently carried out a study aimed at filling this gap in the literature, by better understanding how microglia respond to iron.

For years it has been known that iron accumulates in affected brain regions in PD, MS and other neurodegenerative diseases.

The key objective of the recent work  was to better understand how iron accumulation in microglia affects these cells' functioning and health. Their work builds on their previous studies, and on the 2012 discovery of an iron-dependent form of cell death, known as ferroptosis.

Ferroptosis is a form of cell death that is mediated by iron-dependent lipid peroxidation, a process that damages lipids by oxidizing them. In their paper, the researchers' hypothesized that iron-laden microglia are susceptible to ferroptosis and that this might play a role in neurodegenerative diseases.

To conduct their experiments, the researchers grew microglia in a tri-culture system. Using a series of genetic and experimental techniques, they then showed that these microglia are highly responsive to iron and also susceptible to ferroptosis.

In addition, the team showed that an overload of iron causes a shift in the microglial transcriptional state, which overlaps with a transcriptomic signature observed in microglia in brain tissue from deceased patients with PD. When they removed microglia from their tri-culture system, the researchers observed that iron-induced neurotoxicity in the system significantly slowed down. This suggests that microglia responses to iron overload play a crucial role in neurodegeneration.

Sean K. Ryan et al, Microglia ferroptosis is regulated by SEC24B and contributes to neurodegeneration, Nature Neuroscience (2022). DOI: 10.1038/s41593-022-01221-3

Jonathan D. Proto et al, Disrupted microglial iron homeostasis in progressive multiple sclerosis, bioRxiv (2021). DOI: 10.1101/2021.05.09.443127

• ‹ Previous
• 1
• …
• 432
• 433
• 434
• 435
• 436
• …
• 1082
• Next ›
• Page