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Comment by Dr. Krishna Kumari Challa on August 17, 2024 at 9:23am

The banana apocalypse is near, but biologists  have found a key to their survival

The bananas in your supermarket and that you eat for breakfast are facing functional extinction due to the disease Fusarium wilt of banana (FWB), caused by a fungal pathogen called Fusarium oxysporum f.sp. cubense (Foc) tropical race 4 (TR4).

However, thanks to recent research by an international team of scientists  we now know that Foc TR4 did not evolve from the strain that wiped out commercial banana crops in the 1950s, and that the virulence of this new strain seems to be caused by some accessory genes that are associated the production of nitric oxide.

The research, published in Nature Microbiology, opens the door to treatments and strategies that can slow—if not control—the as-of-yet unchecked spread of Foc TR4.

The kind of banana we eat today is not the same as the one your grandparents ate. Those old ones, the Gros Michel bananas, are functionally extinct, victims of the first Fusarium outbreak in the 1950s.

Today, the most popular type of commercially available banana is the Cavendish variety, which was bred as a disease-resistant response to the Gros Michel extinction. For about 40 years, the Cavendish banana thrived across the globe in the vast monocultured plantations that supply the majority of the world's commercial banana crop.

But by the 1990s, the good times for the Cavendish banana had begun to come to a close. There was another outbreak of banana wilt. It spread like wildfire from southeast Asia to Africa and Central America.

Scientists have spent the last 10 years studying this new outbreak of banana wilt.

As a result of their hard work, we now know that the Cavendish banana-destroying pathogen TR4 did not evolve from the race that decimated the Gros Michel bananas. TR4's genome contains some accessory genes that are linked to the production of nitric oxide, which seems to be the key factor in TR4's virulence.

While the research team working on the problem  doesn't yet know exactly how these activities contribute to disease infestation in Cavendish banana, they were able to determine that the virulence of Foc TR4 was greatly reduced when two genes that control nitric oxide production were eliminated.

Identifying these accessory genetic sequences opens up many strategic avenues to mitigate—or even control—the spread of Foc TR4.

The researchers are quick to point out that the ultimate problem facing one of our favorite fruits is the practice of monocropping.

When there's no diversity in a huge commercial crop, it becomes an easy target for pathogens.

Virulence of the banana wilt-causing fungal pathogen Fusarium oxysporum tropical race 4 is mediated by nitric oxide biosynthesis and accessory genes, Nature Microbiology (2024). DOI: 10.1038/s41564-024-01779-7

Comment by Dr. Krishna Kumari Challa on August 17, 2024 at 7:57am

Entanglement means the two-photon state is not a classical combination of two photon states. Instead, measuring or interacting with one of the photons instantly affects the same property of the second photon, no matter how far away it is.
Entanglement has been demonstrated for a system whose members are over 1,000 km apart. Nothing like it exists in classical physics; it is purely a quantum phenomenon. Here entanglement would raise the possibility of much faster signaling along the sections of myelin that encase segments of the axon's length.

One possibility, the authors write, is that the entanglement of photons could transform into entanglement along potassium ion channels in the neuron. If so, the opening and closing of one channel may affect the performance of another somewhere else.
These results are a combination of two phenomena that exist but are still largely mysterious: consciousness (let alone quantum consciousness) and quantum entanglement.
the researchers didn't say there is a direct connection. At this early stage, their primary goal is to identify possible mechanisms of neural synchronization, which affects numerous neurobiological processes. Through this work, they hope to gain a better understanding.

Zefei Liu et al, Entangled biphoton generation in the myelin sheath, Physical Review E (2024). DOI: 10.1103/PhysRevE.110.024402. On arXiv: DOI: 10.48550/arxiv.2401.11682

Part 3

Comment by Dr. Krishna Kumari Challa on August 17, 2024 at 7:54am

To remedy this problem, researchers investigated if there could be entangled photons within this axon-myelin system that could, though the magic of quantum entanglement, communicate instantly across the involved distances.
A tricarboxylic acid cycle releases energy stored in nutrients, with a cascade of infrared photons released during the cycling process. These photons couple to vibrations from carbon-hydrogen (C-H) bonds in lipid molecules and excite them to a higher vibrational energy state. As the bond then transitions to a lower vibrational energy state, it releases a cascade of photons.

The researchers applied cavity quantum electrohydrodynamics to a perfect cylinder surrounded by the myelin, making the reasonable assumption that the outer wall of the myelin sheath is a perfectly cylindrical conducting wall.
Using quantum mechanical techniques, they quantized the electromagnetic fields and the electric field inside the cavity, as well as the photons—that is, treated them all as quantum objects—and then, with some simplifying assumptions, solved the resulting equations.

Doing so gave the wavefunction for the system of the two photons interacting with the matter inside the cavity. They then calculated the photons' degree of entanglement by determining its quantum entropy, a measure of disorder, using an extension of classical entropy developed by the science polymath John von Neumann.
The researchers showed that the two photons can indeed have higher rate of being entangled under occasions.
The conducting wall limits the electromagnetic wave modes that can exist inside the cylinder, making the cylinder an electromagnetic cavity that keeps most of its energy within it. These modes are different from the continuous electromagnetic waves ("light") that exist in free space.

It is these discrete modes that result in the frequent production of highly entangled photons within the myelin cavity, whose rate of production can be significantly enhanced compared to two untangled photons.
Part 2

Comment by Dr. Krishna Kumari Challa on August 17, 2024 at 7:51am

Photon entanglement could explain the rapid brain signals behind consciousness

Understanding the nature of consciousness is one of the hardest problems in science. Some scientists have suggested that quantum mechanics, and in particular quantum entanglement, is the key to unraveling the phenomenon.

Now, a research group in China has shown that many entangled photons can be generated inside the myelin sheath that covers nerve fibers. It could explain the rapid communication between neurons, which so far has been thought to be below the speed of sound, too slow to explain how the neural synchronization occurs.

The paper is published in the journal Physical Review E.

The brain communicates within itself by firing electrical signals called synapses between neurons, which are the main components of nervous tissue. It is the synchronized activity of millions of neurons that consciousness (among other brain business) relies on. But the way this precise synchronization takes place is unknown.

Connections between neurons are called axons—long structures akin to electrical wires—and covering them is a coating ("sheath") made of myelin, a white tissue made of lipids.

Comprised of up to hundreds of layers, myelin insulates the axons, as well as shaping them and delivering energy to the axons. (In actuality, a series of such sheaths stretches across the length of the axon. The myelin sheath is typically about 100 microns long, with 1 to 2 micron gaps between them.) Recent evidence suggests myelin also plays an important role in promoting synchronization between neurons.

But the speed at which signals propagate along the axons is below the speed of sound, sometimes much below—too slow to create the millions of neuron synchronizations that are the basis for all the amazing things the brain can do.

Part 1

Comment by Dr. Krishna Kumari Challa on August 16, 2024 at 10:04am

Turns out that DdrC scans for breaks along the DNA and when it detects one it snaps shut—like a mousetrap. This trapping action has two key functions.

It neutralizes it (the DNA damage), and prevents the break from getting damaged further. And it acts like a little molecular beacon. It tells the cell 'Hey, over here. There's damage. Come fix it.

Typically proteins form complicated networks that enable them to carry out a function. DdrC appears to be something of an outlier, in that it performs its function all on its own, without the need for other proteins. The team was curious whether the protein might function as a "plug-in" for other DNA repair systems.

They tested this by adding it to a different bacterium: E. coli. It actually made the bacterium over 40 times more resistant to UV radiation damage. This seems to be a rare example where you have one protein and it really is like a standalone machine.

In theory, this gene could be introduced into any organism—plants, animals, humans—and it should increase the DNA repair efficiency of that organism's cells.

DdrC is just one out of hundreds of potentially useful proteins in this bacterium. The next step is to prod further, look at what else this cell uses to fix its own genome—because  scientists are sure to find many more tools where they have no idea how they work or how they're going to be useful until they look. And they are looking for them now.

Robert Szabla et al, DdrC, a unique DNA repair factor from D. radiodurans, senses and stabilizes DNA breaks through a novel lesion-recognition mechanism, Nucleic Acids Research (2024). DOI: 10.1093/nar/gkae635

Part 2

Comment by Dr. Krishna Kumari Challa on August 16, 2024 at 10:00am

Newly discovered protein stops DNA damage

Researchers have discovered a protein that has the never-before-seen ability to stop DNA damage in its tracks. The finding could provide the foundation for developing everything from vaccines against cancer, to crops that can withstand the increasingly harsh growing conditions brought on by climate change.

The researchers found the protein—called DdrC (for DNA Damage Repair Protein C)—in a fairly common bacterium called Deinococcus radiodurans (D. radiodurans), which has the decidedly uncommon ability to survive conditions that damage DNA—for example, 5,000 to 10,000 times the radiation that would kill a regular human cell.  Deinococcus also excels in repairing DNA that has already been damaged.

Newly discovered protein stops DNA damage: Could lead to cancer vaccines and drought-resistant crops

Part 1

Comment by Dr. Krishna Kumari Challa on August 16, 2024 at 9:32am

Why do plants wiggle?

Sunflower plants wiggling ( known as  "circumnutations")

Plants don't usually shift around like animals but, instead, move by growing in different directions over time.

Plants naturally and consistently arranged themselves into a zig-zag pattern, almost like the teeth of a zipper. The arrangement likely helps the plants maximize their access to sunlight as a group.

In greenhouse experiments and computer simulations, researchers showed that sunflowers take advantage of circumnutations to search the environment around them for patches of sunlight.

For climbing plants, it's obvious that it's about searching for supports to twine on.

 If they moved with just the right amount of randomness, however, the sunflowers formed that tell-tale zig-zag, which, in real life plants, provides a lot of access to sunlight.

 Chantal Nguyen et al, Noisy Circumnutations Facilitate Self-Organized Shade Avoidance in Sunflowers, Physical Review X (2024). DOI: 10.1103/PhysRevX.14.031027

Comment by Dr. Krishna Kumari Challa on August 16, 2024 at 9:08am

Sleep resets neurons for new memories the next day, study finds

While everyone knows that a good night's sleep restores energy, a new  study finds it resets another vital function: memory.

Learning or experiencing new things activates neurons in the hippocampus, a region of the brain vital for memory. Later, while we sleep, those same neurons repeat the same pattern of activity, which is how the brain consolidates those memories that are then stored in a large area called the cortex. But how is it that we can keep learning new things for a lifetime without using up all of our neurons?

A study, "A Hippocampal Circuit Mechanism to Balance Memory Reactivation During Sleep,"  published in Science, finds at certain times during deep sleep, certain parts of the hippocampus go silent, allowing those neurons to reset.

This mechanism could allow the brain to reuse the same resources, the same neurons, for new learning the next day.

The hippocampus is divided into three regions: CA1, CA2 and CA3. CA1 and CA3 are involved in encoding memories related to time and space and are well-studied; less is known about CA2, which the current study found generates this silencing and resetting of the hippocampus during sleep.

The researchers now realized that there are other hippocampal states that happen during sleep where everything is silenced. The CA1 and CA3 regions that had been very active were suddenly quiet. It's a reset of memory, and this state is generated by the middle region, CA2.

Cells called pyramidal neurons are thought to be the active neurons that matter for functional purposes, such as learning. Another type of cell, called interneurons, has different subtypes. The researchers discovered that the brain has parallel circuits regulated by these two types of interneurons—one that regulates memory, the other that allows for resetting of memories.

The researchers think they now have the tools to boost memory, by tinkering with the mechanisms of memory consolidation, which could be applied when memory function falters, such as in Alzheimer's disease. Importantly, they also have evidence for exploring ways to erase negative or traumatic memories, which may then help treat conditions such as post-traumatic stress disorder.

The result helps explain why all animals require sleep, not only to fix memories, but also to reset the brain and keep it working during waking hours. 

 Lindsay A. Karaba et al, A hippocampal circuit mechanism to balance memory reactivation during sleep, Science (2024). DOI: 10.1126/science.ado5708. www.science.org/doi/10.1126/science.ado5708

Comment by Dr. Krishna Kumari Challa on August 16, 2024 at 8:59am

The new study focuses on the MEC, but not on the stored information needed for spatial navigation or an animal's current location. Instead, the experiments performed now concentrate on how this brain region creates maps of future positions, which are continuously updated as animals move.

While rats traversed an open square field in search of freely available water that was moved around to different locations, the researchers recorded all movements, which included hundreds of trajectories. At the same time, they recorded the activity of individual brain cells in the MEC.

Afterward, they checked how well the  brain activity over time matched the rats' changing positions.

They found that the activity of some brain cells in the MEC created an internal grid that mapped future positions within the field. For example, an MEC cell might encode a certain location in the field, but only when a rat reached a spot 30 cm to 40 cm earlier in a route that eventually crossed that location—regardless of which direction the rat was coming from.

This is very different from the grid cells that helped win the Nobel Prize, which become active only when an animal is currently in a particular location. The authors call the newly discovered neurons "predictive grid cells," and conducted several follow-up experiments to get a better idea of what exactly they encode.

First, they tested whether the newly discovered grid cells predicted the future location in terms of distance or time from the present. They found that both were encoded, although the "gridness" of the cells was higher when considering distance.

They also found that future positions were faithfully encoded in different situations, whether the rats were trying to go to specific targets or if they were randomly foraging for food. This means that the function of the predictive grid cells is not limited to goal-directed behavior.

This study provides important insights into the mechanisms of spatial navigation and episodic memory formation in hippocampal and entorhinal cortical circuits.

Ayako Ouchi et al, Predictive grid coding in the medial entorhinal cortex, Science (2024). DOI: 10.1126/science.ado4166. www.science.org/doi/10.1126/science.ado4166

Comment by Dr. Krishna Kumari Challa on August 16, 2024 at 8:54am

Navigating the future: Brain cells that plan where to go

Researchers  have discovered a region of the brain that encodes where an animal is planning to be in the near future. Linked to internal maps of spatial locations and past movements, activity in the newly discovered grid cells accurately predicts future locations as an animal travels around its environment.

Published in Science on August 15, the study helps explain how planned spatial navigation is possible.

It might seem effortless, but navigating the world requires quite a bit of under-the-hood brain activity. For example, simply walking around a supermarket picking up groceries requires internalized maps of the outside world, information about one's own changing position and speed, and memories about where one has been and what one is trying to buy.

Much of this kind of information is contained in cells within two connected parts of the brain—the hippocampus and the medial entorhinal cortex, or MEC for short—which are extremely similar in all mammals, from rats to humans. In particular, the MEC contains maps of an animal's current location in space, a discovery that won the Nobel Prize for Physiology or Medicine in 2014.

Prediction grid cells in the medial entorhinal cortex became active before rats entered the region of space that they encode. In this video, activity of two neurons is represented by the flashing of red and blue squares. for convenience, the squares are placed in the location of the grid that the neurons encode. Credit: RIKEN

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