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Comment by Dr. Krishna Kumari Challa on Friday

Why pumpkins accumulate pollutants

Pumpkins, squash, zucchini and their relatives accumulate soil pollutants in their edible parts. A  research team has now identified the cause, making it possible to both make the produce safer and create plants that clean contaminated soil.

The gourd family of plants comprising pumpkins, zucchini, melons, cucumbers and more are known to accumulate high levels of pollutants in their edible parts.

The pollutants don't easily break down and thus pose a health risk to people who eat the fruit. Interestingly, other plants don't do this.

In previous studies, researchers identified a class of proteins from across the gourd family that bind to the pollutants, thus enabling them to be transported through the plant. Earlier this year, they discovered that the shape of the proteins and their binding affinity to the pollutants influence the accumulation in the aboveground plant parts. Their study was published in Plant Physiology and Biochemistry.

However, these proteins exist in many other plants, and even among the gourds, there are varieties that are more prone to accumulating pollutants than others. Researchers then noticed that in the highly accumulating varieties, there are higher concentrations of the protein in the sap.

In the same journal, the  same research team has now published that they could show that the protein variants from the highly accumulating plants are indeed exported into the sap, whereas other variants are retained in the cells.

They could also pinpoint that this is likely due to a small difference in the protein's amino acid sequence that acts as a tag that tells the cell which proteins to retain within. The team proved their point by showing that unrelated tobacco plants in which they introduced the highly accumulating protein versions also exported the protein into the plant sap.

Only secreted proteins can migrate inside the plant and be transported to the aboveground parts. Therefore, this seems to be the distinguishing factor between low-pollution and high-pollution plant varieties.

Understanding the mechanism behind pollutant accumulation is crucial to creating safer produce.

Minami Yoshida et al, Extracellular secretion of major latex-like proteins related to the accumulation of the hydrophobic pollutants dieldrin and dioxins in Cucurbita pepo, Plant Physiology and Biochemistry (2025). DOI: 10.1016/j.plaphy.2025.110612

Hideyuki Inui et al, Binding affinity of major latex-like proteins toward polycyclic aromatic hydrocarbons influences their aboveground accumulation in the Cucurbitaceae family, Plant Physiology and Biochemistry (2025). DOI: 10.1016/j.plaphy.2025.110280

Comment by Dr. Krishna Kumari Challa on Friday

In studying the coupled oscillators in the gut, past researchers observed that there is indeed a staircase effect where similar frequencies lock onto those around it, allowing for the rhythmic movement of food through the digestive tract. But the height of the rises or breaks, the length of the stair runs or frequencies, and the conditions under which the staircase phenomenon occurred—essential features of biological systems—was something which had not been determined until now.
This new mathematical solution answers two longstanding biological questions at the same time: how food moves through the digestive tract and how it is churned. The team hopes this work will support further research into peristalsis-related digestive health issues known as gastrointestinal motility disorders.

The mathematics had been solved in an approximate way before now, but not in a way that gave you these breaks and what happens at the breaks. That's a critical discovery.
Now that they've solved the question of oscillations in the gut, they're back to studying the complex vasculature of the brain. If the gut is unidirectional, the vasculature in the brain has hundreds of directions. While they both feature staircases, the one in the gut goes from one level to the next, one at a time. The stairs in the brain go along different paths at different lengths all at once.

The brain is infinitely more complicated than the gut, but this is science at its best. You ask one question, it leads you somewhere else, you solve that problem, then return to your original question.

Marie Sellier-Prono et al, Defects, Parcellation, and Renormalized Negative Diffusivities in Nonhomogeneous Oscillatory Media, Physical Review Letters (2025). DOI: 10.1103/8njd-qd14. On arXiv: DOI: 10.48550/arxiv.2502.09264

Part 2

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Comment by Dr. Krishna Kumari Challa on Friday

How a chorus of synchronized frequencies helps you digest your food

Synchronization abounds in nature: from the flashing lights of fireflies to the movement of fish wriggling through the ocean, biological systems are often in rhythmic movement with each other. The mechanics of how this synchronization happens are complex.

For instance, in the vasculature of the brain, blood vessels oscillate, expanding and contracting as needed. When there is neural activity, the arterioles expand to increase blood flow, oxygen and nutrients. These oscillations are self-sustained, but the arterioles also work in concert with each other.

To uncover the answer, researchers looked to another part of the body: the gut. Here they found that oscillators operating at similar frequencies lock onto each other in succession, creating a staircase effect. Their work appears in Physical Review Letters.

It is known in the scientific community that if you have a self-sustained oscillation, such as an arteriole, and you add an external stimulus at a similar but not identical frequency, you can lock the two, meaning you can shift the frequency of the oscillator to that of the external stimulus. In fact, it has been shown that if you connect two clocks, they will eventually synchronize their ticking.

Researchers now found that if they applied an external stimulus to a neuron, the entire vasculature would lock at the same frequency. However, if they stimulated two sets of neurons at two different frequencies, something unexpected happened: some arterioles would lock at one frequency and others would lock at another frequency, forming a staircase effect.

The researchers found they could use a classical model of coupled oscillators with an intestinal twist to explain this.

The gut oscillates naturally due to peristalsis—the contracting and relaxing of muscles in the digestive tract—and provided a simplified model over the complex network of blood vessels in the brain. The intestine is unidirectional, meaning frequencies shift in one direction in a gradient from higher to lower. This is what enables food to move in one direction from the beginning of the small intestine to the end of the large intestine.

Coupled oscillators talk to each other and each section of the intestine is an oscillator that talks to the other sections near it. 

Normally, coupled oscillators are studied in a homogeneous setting, meaning all the oscillators are at more or less similar frequencies. In our case, the oscillators were more varied, just as in the intestine and the brain.

Part 1

Comment by Dr. Krishna Kumari Challa on Friday

Babies' gut bacteria may influence future emotional health

A child's early gut microbiome may influence their risk of developing depression, anxiety or other internalizing symptoms in middle childhood, according to a new UCLA Health study. The effect appears to be related to the way bacteria are linked to communication across emotion-related brain networks.

Published in the journal Nature Communications, the observational study found that young children whose gut microbiome had a higher representation of bacteria in the Clostridiales order and Lachnospiraceae family were at higher risk of experiencing internalizing symptoms—an umbrella term that includes symptoms of depression and anxiety—in middle childhood. The connection appeared to work indirectly: The early microbiome composition was associated with differences in connectivity across different emotion-related brain networks that were linked to anxiety and depression later in childhood.

The findings suggest that early gut bacteria could play a role in programming brain circuits tied to emotional health in later childhood. If unaddressed, symptoms of depression and anxiety can carry a higher risk of mental health challenges persisting as children develop into adolescence and adulthood.

The study provides early evidence that  git microbes could help shape mental health during the critical school-age years.

Childhood gut microbiome is linked to internalizing symptoms at school age via the functional connectome, Nature Communications (2025). DOI: 10.1038/s41467-025-64988-6

Comment by Dr. Krishna Kumari Challa on Friday

This research has profound implications. "The fundamental laws of physics cannot be contained within space and time, because they generate them. It has long been hoped, however, that a truly fundamental theory of everything could eventually describe all physical phenomena through computations grounded in these laws. Yet we have demonstrated that this is not possible. A complete and consistent description of reality requires something deeper—a form of understanding known as non-algorithmic understanding.
The team's conclusion is clear and marks an important scientific achievement.
Any simulation is inherently algorithmic—it must follow programmed rules. But since the fundamental level of reality is based on non-algorithmic understanding, the universe cannot be, and could never be, a simulation.
The simulation hypothesis was long considered untestable, relegated to philosophy and even science fiction, rather than science. This research brings it firmly into the domain of mathematics and physics, and provides a definitive answer.

Mir Faizal et al, Consequences of Undecidability in Physics on the Theory of Everything, Journal of Holography Applications in Physics (2025). DOI: 10.22128/jhap.2025.1024.1118. On arXiv: DOI: 10.48550/arxiv.2507.22950

Part 3

Comment by Dr. Krishna Kumari Challa on Friday

Here's a basic example using the statement, "This true statement is not provable." If it were provable, it would be false, making logic inconsistent. If it's not provable, then it's true, but that makes any system trying to prove it incomplete. Either way, pure computation fails.
So researchers have demonstrated that it is impossible to describe all aspects of physical reality using a computational theory of quantum gravity.
Therefore, no physically complete and consistent theory of everything can be derived from computation alone. Rather, it requires a non-algorithmic understanding, which is more fundamental than the computational laws of quantum gravity and therefore more fundamental than spacetime itself."
Since the computational rules in the Platonic realm could, in principle, resemble those of a computer simulation, couldn't that realm itself be simulated?

No, say the researchers. Their work reveals something deeper.

Drawing on mathematical theorems related to incompleteness and indefinability, they demonstrate that a fully consistent and complete description of reality cannot be achieved through computation alone.
It requires non-algorithmic understanding, which by definition is beyond algorithmic computation and therefore cannot be simulated. Hence, this universe cannot be a simulation, the researchers conclude.
Part 2

Comment by Dr. Krishna Kumari Challa on Friday

Mathematical proof debunks the idea that the universe is a computer simulation

It's a plot device beloved by science fiction: our entire universe might be a simulation running on some advanced civilization's supercomputer. But new research  has mathematically proven this isn't just unlikely—it's impossible.

Researchers  have shown that the fundamental nature of reality operates in a way that no computer could ever simulate.

Their findings, published in the Journal of Holography Applications in Physics, go beyond simply suggesting that we're not living in a simulated world like The Matrix. They prove something far more profound: the universe is built on a type of understanding that exists beyond the reach of any algorithm.

It has been suggested that the universe could be simulated. If such a simulation were possible, the simulated universe could itself give rise to life, which in turn might create its own simulation. This recursive possibility makes it seem highly unlikely that our universe is the original one, rather than a simulation nested within another simulation. This idea was once thought to lie beyond the reach of scientific inquiry. However, the recent research has demonstrated that it can, in fact, be scientifically addressed.

The research hinges on a fascinating property of reality itself. Modern physics has moved far beyond Newton's tangible "stuff" bouncing around in space. Einstein's theory of relativity replaced Newtonian mechanics. Quantum mechanics transformed our understanding again. Today's cutting-edge theory—quantum gravity—suggests that even space and time aren't fundamental. They emerge from something deeper: pure information.

This information exists in what physicists call a Platonic realm—a mathematical foundation more real than the physical universe we experience. It's from this realm that space and time themselves emerge.

Here's where it gets interesting. The team demonstrated that even this information-based foundation cannot fully describe reality using computation alone. They used powerful mathematical theorems—including Gödel's incompleteness theorem—to prove that a complete and consistent description of everything requires what they call "non-algorithmic understanding."

Think of it this way. A computer follows recipes, step by step, no matter how complex. But some truths can only be grasped through non-algorithmic understanding—understanding that doesn't follow from any sequence of logical steps. These "Gödelian truths" are real, yet impossible to prove through computation.

Part 1

Comment by Dr. Krishna Kumari Challa on October 30, 2025 at 9:07am

With this insight, doctors may be able to use a person's immune profile to predict how well they'll respond to a vaccine. Now that scientists can pinpoint how T cells become less effective with age, they can also start designing new vaccine formulas or immune-boosting treatments to address these issues.
Since T cells in older adults function differently, scientists could reformulate vaccines to compensate specifically for age-related cellular changes rather than using a one-size-fits-all approach. Gene-editing tools like CRISPR could also be used to reprogram a person's T cells before vaccination, essentially re-programming older immune cells to make them respond to vaccines like younger cells do—like CAR-T cell therapy that reprograms immune cells to fight cancer.
Researchers say this work goes beyond just vaccines and reveals how our immune systems change in all of us as we get older and how our bodies fight age-related disease and viruses. It also opens the door to interventions like new therapies to restore key immune cells.

Claire Gustafson, Multi-omic profiling reveals age-related immune dynamics in healthy adults, Nature (2025). DOI: 10.1038/s41586-025-09686-5. www.nature.com/articles/s41586-025-09686-5

Prat2

Comment by Dr. Krishna Kumari Challa on October 30, 2025 at 9:04am

How age affects vaccine responses and how to make them better

 Scientists are learning why vaccines can trigger a weaker response in older adults, around age 65, and what can be done to improve them. These insights open the door to designing more effective vaccines.

In the largest study of its kind, published in Nature, scientists discover that our T cells—key players in coordinating immune responses—undergo profound and specific changes as we age. These changes, far from being random or a byproduct of chronic disease and inflammation, are a fundamental feature of healthy aging and will happen to all of us as we get older.

Inflammation is not driving healthy aging. Scientists think inflammation is driven by something independent from just the age of a person.

This is important because there's been research showing similar findings that inflammation and aging don't go hand in hand, and your immune system is just changing with age.

The changes also point to why vaccines, including the annual flu shot and COVID-19 boosters, tend to be less effective in older adults.

T cells are a critical part of our immune system that help "train" white blood cells, called B cells, to produce antibodies in response to viruses and vaccines. But this study found that memory T cells in older adults undergo a dramatic shift toward what is known as a "Th2-like" state, which is a change in gene expression that fundamentally alters how these cells respond to threats.
Researchers found this shift directly affects B cells' ability to generate strong antibody responses. In other words, the flu shot might still deliver the right viral components, but if the memory T cells aren't functioning properly, the body struggles to respond effectively.
Part 1

Comment by Dr. Krishna Kumari Challa on October 30, 2025 at 8:55am

An industrial microbe converts carbon monoxide into biofuel

How do you turn toxic waste into fuel? Ask the microbe. A team of scientists  experimentally demonstrates the molecular tricks used by the gas-converting microbe Clostridium autoethanogenum to transform industrial waste gases into ethanol—a finding with enormous implications for sustainable fuel and chemical production.

First isolated from rabbit droppings, Clostridium autoethanogenum can thrive on pure carbon monoxide, a deadly gas for most organisms, including human beings. This extraordinary microbe consumes the poison to build cellular materials from the carbon and derives its energy through successive chemical reactions. These reactions can help to produce valuable chemicals and fuels, perfect for driving sustainable biotechnology.

While the organism is currently widely used in industrial plants to produce ethanol, the exact mechanism behind its ethanol production remains unclear. A key step suspected in the reaction was the reduction of acetate to acetaldehyde. However, some scientists did not believe this was possible to carry out for organisms. This study, published in Nature Chemical Biology, now settles this dispute and solves the mystery.

The enzyme putatively responsible for the challenging chemical reaction is known as the aldehyde: ferredoxin oxidoreductase (AFOR). It contains tungsten, the heaviest atom found in biology. In addition, there is a cluster of iron and sulfur, giving it a pretty dark brown colour.
Using advanced techniques, the scientists purified the enzyme from C. autoethanogenum and determined its atomic structure through X-ray crystallography. With the three-dimensional structure, the scientists depicted the tungsten-containing element and described its surroundings with outstanding precision. However, there was a problem: the enzyme was inactive.

However, with long and hard work researchers found a way to reactivate it.

Scientists knew that the enzyme would not reduce acetate easily because of the laws of thermodynamics, so they looked for inspiration in the tricks used by the microbe when growing on carbon monoxide. 

The solution was to mix different enzymes on top of the AFOR. The scientists built an "artificial pathway" in a tube and successfully produced ethanol from acetate, confirming that the full reaction sequence is biologically feasible inside the cell.

The process can also be transferred to other organisms. This will drastically enlarge the potential sources of microbial biofuel production.

This is another step forward in green energy production through gas bioconversion.

Carbon-monoxide-driven bioethanol production operates through a tungsten-dependent catalyst, Nature Chemical Biology (2025). DOI: 10.1038/s41589-025-02055-3.

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