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Comment by Dr. Krishna Kumari Challa on August 9, 2024 at 8:15am

Study observes that similarities between physical and biological systems might be greater than we think

A crowd or a flock of birds have different characteristics from those of atoms in a material, but when it comes to collective movement, the differences matter less than we might think. We can try to predict the behavior of humans, birds, or cells based on the same principles we use for particles.

This is the finding of a study published in the Journal of Statistical Mechanics: Theory and Experiment, JSTAT, conducted by an international team of researchers.  The study, based on the physics of materials, simulated the conditions that cause a sudden shift from a disordered state to a coordinated one in "self-propelled agents" (like biological ones).

"In a way, birds are flying atoms", say the researchers, " It may sound strange, but indeed, one of our main findings was that the way a walking crowd moves, or a flock of birds in flight, shares many similarities with the physical systems of particles". 

In the field of collective movement studies, it has been assumed that there is a qualitative difference between particles (atoms and molecules) and biological elements (cells, but also entire organisms in groups). It was especially believed that the transition from one type of movement to another (for example, from chaos to an orderly flow, known as a phase transition) was completely different.

The crucial difference for physicists in this case has to do with the concept of distance. Particles moving in a space with many other particles influence each other primarily based on their mutual distance. For biological elements, however, the absolute distance is less important.

Take a pigeon flying in a flock: what matters to it are not so much all the closest pigeons, but those it can see." In fact, according to the literature, among those it can see, it can only keep track of a finite number, due to its cognitive limits.

The pigeon, in the physicists' jargon, is in a "topological relationship" with other pigeons: two birds could be at quite a large physical distance, but if they are in the same visible space, they are in mutual contact and influence each other.

It was long thought that this type of difference led to a completely different scenario for the emergence of collective motion This new study, however, suggests that this is not a crucial difference.

These statistical models, based on the physics of particles, can  also help us understand biological collective movement.

Fluctuation-Induced First Order Transition to Collective Motion, Journal of Statistical Mechanics Theory and Experiment (2024). DOI: 10.1088/1742-5468/ad6428

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Comment by Dr. Krishna Kumari Challa on August 9, 2024 at 7:49am

Based on their findings, the researchers designed a lensless fluorescence system using large (1–2 mm2) LEDs and detectors, which have recently become available in UV wavelengths. It works by using UV light to excite proteins from harmful microbes and then detecting the resulting fluorescence.

In addition to demonstrating the lensless system's sensitivity, they also showed that it produced a fluorescence signal that is about double the strength of a lensed system. They found that the performance of the lensed system was limited by its numerical aperture, the use of larger sources and detectors and the finite imaging distance required between the components and the sample.

The researchers are now developing a pocket-sized version of the lensless fluorometers for field testing.

 Asim Maharjan et al, Lensless fluorometer outperforms lensed system, Optica (2024). DOI: 10.1364/OPTICA.527289

Part 2

Comment by Dr. Krishna Kumari Challa on August 9, 2024 at 7:48am

Lens-free fluorescence instrument detects deadly microorganisms in drinking water

Researchers have shown that a fluorescence detection system that doesn't contain any lenses can provide highly sensitive detection of deadly microorganisms in drinking water. With further development, the new approach could provide a low-cost and easy-to-use way to monitor water quality in resource-limited settings such as developing countries or areas affected by disasters.

It could also be useful when water safety results are needed quickly, such as for swimming events, a concern highlighted during the Paris Olympics.

Current methods used to assess microbial contamination in water require culturing the water samples and then quantifying harmful bacteria. This can take over 18 hours, making it impractical when immediate confirmation of water safety is needed. This is also a key reason why water surveillance is ineffective in developing countries, where the required skilled human resources, infrastructure and reagents are not readily available.

The  new water monitoring fluorometer can detect fluorescent proteins from bacteria in water down to levels of less than one part per billion, without using any lenses.

This sensitivity meets the World Health Organization's criteria for detecting fecal contamination in drinking water.

During development, the researchers closely examined the fundamentals of optical signal generation in applications like water quality monitoring.

They discovered that while optical lenses are commonly used in devices such as cameras, microscopes and telescopes, these optical components often reduce performance for practical situations that don't require images.

This was an important finding because lenses account for a significant share of the costs of optical systems and their bulk and weight make it difficult to create practical portable devices.

The new analysis revealed that using a light source, detectors and sample sizes that are all as large and as close to each other as possible produces a stronger signal, leading to better performance for water quality monitoring.

Part 1

Comment by Dr. Krishna Kumari Challa on August 9, 2024 at 7:37am

However, it was also similar to the microbiome in an industrial habitat: namely, on solar panels. The authors proposed that the constant thermal shock, electromagnetic radiation, and desiccation in such highly irradiated environments has repeatedly selected for highly resistant microbes, in the same manner as in microwaves.

For both the general public and laboratory personnel, the researchers recommend regularly disinfecting microwaves with a diluted bleach solution or a commercially available disinfectant spray. In addition, it is important to wipe down the interior surfaces with a damp cloth after each use to remove any residue and to clean up spills immediately to prevent the growth of bacteria.

The microwave bacteriome: biodiversity of domestic and laboratory microwave ovens, Frontiers in Microbiology (2024). DOI: 10.3389/fmicb.2024.1395751

Part 2

Comment by Dr. Krishna Kumari Challa on August 9, 2024 at 7:36am

Microbes conquer the next extreme environment: Your microwave

Since the industrial revolution, microbes have successfully colonized one novel type of habitat after another: for example, marine oil spills, plastic floating in the oceans, industrial brownfields, and even the interior of the International Space Station.

However, it turns out that one extreme environment harboring a specialized community of highly adapted microbes is much closer to home: inside microwaves. This finding has now been reported for the first time by researchers  in a study in Frontiers in Microbiology. It's not only important from the perspective of hygiene, but could also inspire biotechnological applications—if the strains found inside microwaves can be put to good use in industrial processes that require especially hardy bacteria.

The research results reveal that domestic microwaves have a more 'anthropized' microbiome, similar to kitchen surfaces, while laboratory microwaves harbour bacteria that are more resistant to radiation.

Researchers sampled microbes from inside 30 microwaves: 10 each from single-household kitchens, another 10 from shared domestic spaces--for example, corporate centers, scientific institutes, and cafeterias--and 10 from molecular biology and microbiology laboratories. The aim behind this sampling scheme was to see if these microbial communities are influenced by food interactions and user habits.

The team used two complementary methods to inventorize the microbial diversity: next-generation sequencing and cultivation of 101 strains in five different media.

In total, the researchers found 747 different genera within 25 bacterial phyla. The most frequently encountered phyla were Firmicutes, Actinobacteria, and especially Proteobacteria.

They found that the composition of the typical microbial community partly overlapped between shared domestic and single-household domestic microwaves, while laboratory microwaves were quite different. The diversity was lowest in single-household microwaves, and highest in laboratory ones.

Part 1

Comment by Dr. Krishna Kumari Challa on August 8, 2024 at 12:24pm

Building on this, the team modeled how landscapes respond to this mantle-driven uplift. They found that migrating mantle instabilities give rise to a wave of surface erosion that lasts tens of millions of years and moves across the continent at a similar speed. This intense erosion removes a huge weight of rock that causes the land surface to rise further, forming elevated plateaus.
Their landscape evolution models show how a sequence of events linked to rifting can result in an escarpment as well as a stable, flat plateau, even though a layer of several thousands of meters of rocks has been eroded away.
The team's study provides a new explanation for the puzzling vertical movements of cratons far from the edges of continents, where uplift is more common.
The team has concluded that the same chain of mantle disturbances that trigger diamonds to quickly rise from Earth's deep interior also fundamentally shape continental landscapes, influencing a host of factors from regional climates and biodiversity to human settlement patterns.

Thomas Gernon, Co-evolution of craton margins and interiors during continental break-up, Nature (2024). DOI: 10.1038/s41586-024-07717-1. www.nature.com/articles/s41586-024-07717-1

Part 2

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Comment by Dr. Krishna Kumari Challa on August 8, 2024 at 12:17pm

Scientists uncover hidden forces causing continents to rise

Scientists have answered one of the most puzzling questions in plate tectonics: how and why "stable" parts of continents gradually rise to form some of the planet's greatest topographic features?

They have found that when tectonic plates break apart, powerful waves are triggered deep within the Earth that can cause continental surfaces to rise by over a kilometer.
Their findings help resolve a long-standing mystery about the dynamic forces that shape and connect some of the Earth's most dramatic landforms—expansive topographic features called 'escarpments' and 'plateaus' that profoundly influence climate and biology.

The new research examined the effects of global tectonic forces on landscape evolution over hundreds of millions of years. The findings are published Aug 8 in the journal Nature.

The research  results help explain why parts of the continents previously thought of as "stable" experience substantial uplift and erosion, and how such processes can migrate hundreds or even thousands of kilometers inland, forming sweeping elevated regions known as plateaus, like the Central Plateau of South Africa.

The researchers  discovered that when continents split apart, the stretching of the continental crust causes stirring movements in Earth's mantle (the voluminous layer between the crust and the core).

This process can be compared to a sweeping motion that moves towards the continents and disturbs their deep foundations.

The team noticed an interesting pattern: the speed of the mantle "waves" moving under the continents in their simulations closely matched the speed of major erosion events that swept across the landscape in Southern Africa following the breakup of the ancient supercontinent Gondwana.

The scientists pieced together evidence to propose that the Great Escarpments originate at the edges of ancient rift valleys, much like the steep walls seen at the margins of the East African Rift today. Meanwhile, the rifting event also sets about a "deep mantle wave" that travels along the continent's base at about 15–20 kilometers per million years.

This wave convectively removes layers of rock from the continental roots.

Much like how a hot-air balloon sheds weight to rise higher, this loss of continental material causes the continents to rise—a process called isostasy.

Part 1

Comment by Dr. Krishna Kumari Challa on August 8, 2024 at 11:09am

Nanomaterials may enhance plant tolerance to high soil salt levels

Soil salt concentrations above the optimal threshold for plant growth can threaten global food security by compromising agricultural productivity and crop quality. An analysis published in Physiologia Plantarum has examined the potential of nanomaterials—which have emerged over the past decade as a promising tool to mitigate such "salinity stress"—to address this challenge.

Nanomaterials, which are tiny natural or synthetic materials, can modulate a plant's response to salinity stress through various mechanisms, for example by affecting the expression of genes related to salt tolerance or by enhancing physiological processes such as antioxidant activities.
When investigators assessed 495 experiments from 70 publications related to how different nanomaterials interact with plants under salinity stress, they found that nanomaterials enhance plant performance and mitigate salinity stress when applied at lower dosages. At higher doses, however, nanomaterials are toxic to plants and may even worsen salinity stress.

Also, plant responses to nanomaterials vary across plant species, plant families, and nanomaterial types.

Meta-analysis of nanomaterials and plants interaction under salinity stress, Physiologia Plantarum (2024). DOI: 10.1111/ppl.14445

Comment by Dr. Krishna Kumari Challa on August 8, 2024 at 11:05am

Processing traumatic memories during sleep leads to changes in the brain associated with improvement in PTSD symptoms

Currently, the first-choice treatment for PTSD is exposure-based psychotherapy, where therapists help rewire the emotions associated with the traumatic memory in the patient's brain, shifting from fear and arousal to a more neutral response.

PTSD is a mental health disorder that can occur after experiencing or witnessing a traumatic event. People with PTSD may experience flashbacks, nightmares, heightened vigilance, hyper-arousal, and mood and sleep problems. Currently available treatments for PTSD include eye movement desensitization and reprocessing (EMDR), where therapists guide patients through their traumatic memories while using a moving light or clicking sounds to distract them.

However, up to 50% of patients fail to respond well to this treatment.

EMDR has shown positive results, but  that success is low and dropping out from the treatment program is common among patients because revisiting traumatic memories is emotionally demanding.

In a study published on August 7 in Current Biology, scientists show for the first time that reactivating therapeutically-altered memories during sleep leads to more brain activity related to memory processing, which is associated with a reduction in PTSD symptoms.

Sleep provides a unique opportunity to enhance the memory of newly formed emotional reactions to traumatic events. During sleep, the brain focuses on consolidating memories and storing information for the long term.

Previous research has shown that if someone forms a new memory in the presence of an experimentally administered sound or scent, exposing them to the sound or scent while they sleep can improve their ability to recall that memory after waking up. This memory-enhancement technique is called targeted memory reactivation (TMR).

TMR has no negative effects on these patients. None of the patients reported more nightmares or worsened sleep after TMR.

Many psychiatric disorders, such as phobias, anxiety disorders, and addiction, are also related to maladaptive memories. This new work can inspire future research to explore the beneficial effects of TMR in treating other conditions.

Targeted memory reactivation to augment treatment in post-traumatic stress disorder, Current Biology (2024). DOI: 10.1016/j.cub.2024.07.019. www.cell.com/current-biology/f … 0960-9822(24)00922-9

Comment by Dr. Krishna Kumari Challa on August 8, 2024 at 10:55am

DNA fragments help detect kidney organ rejection

Findings from a study published in Nature Medicine show that donor-derived cell-free DNA (dd-cfDNA), also called liquid biopsy, has the potential for early detection of kidney transplant rejection.

The international study enrolled a diverse population of nearly 3,000 kidney transplant recipients—both adult and pediatric—from 14 transplantation centers in Europe and the U.S. The Department of Pediatrics at Washington University School of Medicine in St. Louis contributed one of the two pediatric datasets involved in the study.
When cells undergo apoptosis or necrosis, they release small fragments of DNA, known as cell-free DNA (cf-DNA), into the bloodstream. In inflammation associated with transplant rejection, dying cells release donor-derived cell-free DNA (dd-cfDNA). Researchers found those dd-cfDNA levels were strongly correlated with different types of transplant rejection, including antibody-mediated rejection, T cell-mediated rejection and mixed rejection. The study found similar accuracy in children and adults.

Often unnecessary and invasive graft biopsies are currently considered the "gold standard" in diagnosing transplant rejection, but dd-cfDNA could provide a non-invasive, accurate biomarker to reduce the need for biopsy.

While biopsies will continue as the method of rejection diagnosis, dd-cfDNA may improve early rejection diagnosis and enhance the care of kidney transplant recipients.

Olivier Aubert et al, Cell-free DNA for the detection of kidney allograft rejection, Nature Medicine (2024). DOI: 10.1038/s41591-024-03087-3

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