Comment

Comment by Dr. Krishna Kumari Challa yesterday

The findings shed light on bacterial populations and behavior, such as the formation of biofilms.

When bacteria adhere to a surface, it does so by producing extracellular polymeric substances (EPS). This substance forms a structured community known as biofilm, such that the bacteria is embedded in a matrix of EPS, protecting the bacteria from environmental stresses like antibiotics and host immune responses.

This entire process, known as the formation of biofilms, is essential for the survival of bacterial colonies. The opposite of this phenomenon—dispersal—is equally important.

When bacteria within a biofilm detach and spread to new locations, it is known as dispersal. Dispersal can occur in response to environmental cues, nutrient availability, or as part of the life cycle of the bacteria.

This mechanism can help bacteria colonize new surfaces or host environments and can influence the spread of infectious diseases or the formation of microbial communities in various ecosystems.

Part 3

Comment by Dr. Krishna Kumari Challa yesterday

These spiral waves as observed by the researchers in bacteria are an emergent phenomenon. Emergent phenomena are a crucial aspect of complex systems, which are systems where the interaction of individual entities leads to phenomena that otherwise can't be observed.

This means we need to understand what is happening at the level of each entity, which in this case is a Pseudomonas aeruginosa bacterium. These bacteria have pilus motors, which are the key to the spiral waves.

Pilus motors are molecular motors, which are attached to pili—thin, hair-like appendages present on the bacterial cell surface. These motors play an important role in various processes for the bacterium, such as movement and surface attachment.

The propagating spiral waves resulted from the coordinated activity of the pilus motor, a grappling-hook-like motile organelle found in many bacterial species.

The mechanical movements of the pilus motors in many bacteria result in these spiral waves, which are like ripples on the bacterial surface.

The researchers found that the spiral waves resulted from the coordinated activity of pilus motors. They also observed that the waves were self-sustaining and stable, with nearly stationary spiral cores.

This stability is a characteristic shared by certain types of electrical and chemical spiral waves found in other living systems. However, the spiral waves observed in the bacteria are distinct from the other spiral waves.

Part 2

Comment by Dr. Krishna Kumari Challa on Wednesday

Scientists observe mechanical waves in bacterial communities

A new study by researchers  has reported the emergence of mechanical spiral waves in bacterial matter.

Spiral waves are commonly seen in artificial and natural systems (such as the heart). These emerge from interactions of neighboring elements, such as cardiac cells in the case of the heart. These spiral waves can have varying effects, sometimes leading to life-threatening conditions like fibrillation in the heart.

The new study, published in Nature Physics, explores spiral waves in bacteria—something that has not been observed before. In particular, the researchers' focus was on the species Pseudomonas aeruginosa. These are commonly found in soil and water and are also known to colonize hospitals.

The research is a continuation of their previous work where the authors studied long-range material transport in bacterial communities via open fluid channels.

Part 1

Comment by Dr. Krishna Kumari Challa on Tuesday

In this new study, scientists  used both single-cell and single-nucleus sequencing techniques along with advanced imaging to analyze human muscle samples from 17 individuals aged 20 to 75.

They discovered that genes controlling ribosomes, responsible for producing proteins, were less active in muscle stem cells from aged samples. This impairs the cells' ability to repair and regenerate muscle fibers as we age. Further, non-muscle cell populations within these skeletal muscle samples produced more of a pro-inflammatory molecule called CCL2, attracting immune cells to the muscle and exacerbating age-related muscle deterioration.

Age-related loss of a specific fast-twitch muscle fiber subtype, key for explosive muscle performance, was also observed. However, they discovered for the first time several compensatory mechanisms from the muscles appearing to make up for the loss. These included a shift in slow-twitch muscle fibers to express genes characteristic of the lost fast-twitch subtype, and increased regeneration of remaining fast-twitch fiber subtypes.

The researchers  also identified specialized nuclei populations within the muscle fibers that help rebuild the connections between nerves and muscles that decline with age. Knockout experiments in lab-grown human muscle cells by the team confirmed the importance of these nuclei in maintaining muscle function.

With these new insights into healthy skeletal muscle aging, researchers all over the world can now explore ways to combat inflammation, boost muscle regeneration, preserve nerve connectivity, and more. Discoveries from research like this have huge potential for developing therapeutic strategies that promote healthier aging for future generations.

 Human skeletal muscle aging atlas, Nature Aging (2024). DOI: 10.1038/s43587-024-00613-3

Part 2

Comment by Dr. Krishna Kumari Challa on Tuesday

Human muscle map reveals how we try to fight effects of aging at cellular and molecular levels

How muscle changes with aging and tries to fight its effects is now better understood at the cellular and molecular level with the first comprehensive atlas of aging muscles in humans.

Researchers applied single-cell technologies and advanced imaging to analyze human skeletal muscle samples from 17 individuals across the adult lifespan. By comparing the results, they shed new light on the many complex processes underlying age-related muscle changes.

The atlas, published April 15 in Nature Aging, uncovers new cell populations that may explain why some muscle fibres age faster than others. It also identifies compensatory mechanisms the muscles employ to combat aging.

The findings offer avenues for future therapies and interventions to improve muscle health and quality of life as we age.

This study is part of the international Human Cell Atlas initiative to map every cell type in the human body, to transform understanding of health and disease.

As we age, our muscles progressively weaken. This can affect our ability to perform everyday activities like standing up and walking. For some people, muscle loss worsens, leading to falls, immobility, a loss of autonomy and a condition called sarcopenia. The reasons why our muscles weaken over time have remained poorly understood till now.

Part 1

Comment by Dr. Krishna Kumari Challa on Tuesday

Evolution's recipe book: How 'copy paste' errors led to insect flight, octopus camouflage and human cognition

Seven hundred million years ago, a remarkable creature emerged for the first time. Though it may not have been much to look at by today's standards, the animal had a front and a back, a top and a bottom. This was a groundbreaking adaptation at the time, and one which laid down the basic body plan which most complex animals, including humans, would eventually inherit.

The inconspicuous animal resided in the ancient seas of Earth, likely crawling along the seafloor. This was the last common ancestor of bilaterians, a vast supergroup of animals including vertebrates (fish, amphibians, reptiles, birds, and mammals), and invertebrates (insects, arthropods, mollusks, worms, echinoderms and many more).

To this day, more than 7,000 groups of genes can be traced back to the last common ancestor of bilaterians, according to a study of 20 different bilaterian species including humans, sharks, mayflies, centipedes and octopuses. The findings were made by researchers at the Centre for Genomic Regulation (CRG) in Barcelona and are published today in the journal Nature Ecology & Evolution.

Remarkably, the study found that around half of these ancestral genes have since been repurposed by animals for use in specific parts of the body, particularly in the brain and reproductive tissues. The findings are surprising because ancient, conserved genes usually have fundamental, important jobs that are needed in many parts of the body.

When the researchers took a closer look, they found a series of serendipitous "copy paste" errors during bilaterian evolution were to blame. For example, there was a significant moment early in the history of vertebrates. A bunch of tissue-specific genes first appeared coinciding with two whole genome duplication events.

Animals could keep one copy for fundamental functions, while the second copy could be used as raw material for evolutionary innovation. Events like these, at varying degrees of scale, occurred constantly throughout the bilaterian evolutionary tree.

The authors of the study found many examples of new, tissue-specific functions made possible by the specialization of these ancestral genes.

The specialization of ancestral genes also laid some foundations for the development of complex nervous systems

Evolution of tissue-specific expression of ancestral genes across vertebrates and insects, Nature Ecology & Evolution (2024). DOI: 10.1038/s41559-024-02398-5

Comment by Dr. Krishna Kumari Challa on Tuesday

The study also found that different bird species have different impacts in terms of seed dispersal. Smaller birds disperse more seeds, but they can only spread small seeds from trees with lower carbon storage potential. In contrast, larger birds such as the Toco toucan or the Curl-crested jay disperse the seeds of trees with a higher carbon storage potential. The problem is that the larger birds are less likely to move across highly fragmented landscapes.
This crucial information enables us to pinpoint active restoration efforts—like tree planting—in landscapes falling below this forest cover threshold, where assisted restoration is most urgent and effective.
Allowing larger frugivores to move freely across forest landscapes is critical for healthy tropical forest recovery.
This study demonstrates that especially in tropical ecosystems seed dispersal mediated by birds, plays a fundamental role in determining the species that can regenerate.

Frugivores enhance potential carbon recovery in fragmented landscapes, Nature Climate Change (2024). DOI: 10.1038/s41558-024-01989-1

Comment by Dr. Krishna Kumari Challa on Tuesday

Tropical forests can't recover naturally without fruit eating birds, carbon recovery study shows

New research illustrates a critical barrier to natural regeneration of tropical forests. Their models—from ground-based data gathered in the Atlantic Forest of Brazil—show that when wild tropical birds move freely across forest landscapes, they can increase the carbon storage of regenerating tropical forests by up to 38%.

Fruit eating birds such as the Red-Legged Honeycreeper, Palm Tanager, or the Rufous-Bellied Thrush play a vital role in forest ecosystems by consuming, excreting, and spreading seeds as they move throughout a forested landscape.

Between 70% to 90% of the tree species in tropical forests are dependent on animal seed dispersal. This initial process is essential for allowing forests to grow and function. While earlier studies have established that birds are important for forest biodiversity, researchers now have a quantitative understanding of how they contribute to forest restoration. The new study, published in the journal Nature Climate Change provides evidence of the important contribution of wild birds (frugivores) in forest regeneration. Researchers compared the carbon storage potential that could be recovered in landscapes with limited fragmentation, with that of highly fragmented landscapes. Their data shows that highly fragmented landscapes restrict the movement of birds, thereby reducing the potential of carbon recovery by up to 38%.
Across the Atlantic Forest region in Brazil, the researchers found that it is critical to maintain a minimum of 40% forest cover. They also find that a distance of 133 meters (approximately 435 feet) or less between forested areas ensures that birds can continue to move throughout the landscape and facilitate ecological recovery.

Part 1

Comment by Dr. Krishna Kumari Challa on Monday

How did this unusual exception emerge? What distinguishes the enzyme from all others, causing it to form a fractal shape? Teaming up with structural biologist at the university of Marburg, the team eventually managed to determine the molecular structure of this assembly using electron microscopy, which illuminated how it achieves its fractal geometry.
It now became clear how exactly this protein manages to assemble into a fractal: Normally, when proteins self-assemble, the pattern is highly symmetrical: each individual protein chain adopts the same arrangement relative to its neighbors. Such symmetrical interactions always lead to patterns that become smooth on large scales.

The key to the fractal protein was that its assembly violated this rule of symmetry. Different protein chains made slightly different interactions at different positions in the fractal. This was the basis for forming the Sierpiński triangle, with its large internal voids, rather than a regular lattice of molecules.

Self-assembly is often used by evolution to regulate enzymes, but in this case the cyanobacterium that this enzyme is found in does not seem to care much whether or not its citrate synthase can assemble into a fractal.
When the team genetically manipulated the bacterium to prevent its citrate synthase from assembling into the fractal triangles, the cells grew just as well under a variety of conditions. This prompted them to wonder whether this might just be a harmless accident of evolution. Such accidents can happen when the structure in question isn't too difficult to construct.
To test their theory, the team recreated the evolutionary development of the fractal arrangement in the laboratory. To do this, they used a statistical method to back-calculate the protein sequence of the fractal protein as it was millions of years ago.

By then producing these ancient proteins biochemically they were able to show that the arrangement arose quite suddenly through a very small number of mutations and was then immediately lost again in several cyanobacterial lineages, so that it only remained intact in this single bacterial species.
The fact that something so complex-looking as a molecular fractal could emerge so easily in evolution suggests that more surprises and much beauty may still lie hidden in so far undiscovered molecular assemblies of many biomolecules.

Franziska L. Sendker et al, Emergence of fractal geometries in the evolution of a metabolic enzyme, Nature (2024). DOI: 10.1038/s41586-024-07287-2

Part 2

Comment by Dr. Krishna Kumari Challa on Monday

Discovery of the first fractal molecule in nature

An international team of researchers has stumbled upon the first regular molecular fractal in nature. They discovered a microbial enzyme—citrate synthase from a cyanobacterium—that spontaneously assembles into a pattern known as the Sierpinski triangle. Electron microscopy and evolutionary biochemistry studies indicate that this fractal may represent an evolutionary accident.

The study is published in Nature.

Snowflakes, fern leaves, romanesco cauliflower heads: many structures in nature have a certain regularity. Their individual parts resemble the shape of the whole structure. Such shapes, which repeat from the largest to the smallest, are called fractals. But regular fractals that match almost exactly across scales, as in the examples above, are very rare in nature.

Molecules also have a certain regularity. But if you look at them from a great distance, you can no longer see any signs of this. Then you see smooth matter whose features no longer match those of the individual molecules. The degree of fine structure we see depends on our magnification—in contrast to fractals, where self-similarity persists at all scales. In fact, regular fractals at the molecular level are completely unknown in nature till now.

This is somewhat surprising. After all, molecules can assemble themselves into all sorts of wonderful shapes. Scientists have extensive catalogues of self-assembled complex molecular structures. However, there has never been a regular fractal among them. It turns out that almost all regular-looking self-assemblies lead to the kind of regularity that becomes smooth on large scales.

Researchers now discovered a microbial enzyme—citrate synthase from a cyanobacterium—that spontaneously assembles into a regular fractal pattern known as the Sierpiński triangle. This is an infinitely repeating series of triangles made up of smaller triangles.

The protein makes these beautiful triangles and as the fractal grows, we see these larger and larger triangular voids in the middle of them, which is totally unlike any protein assembly we've ever seen before.

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