Comment

Comment by Dr. Krishna Kumari Challa on November 4, 2025 at 8:44am

Bacteria borrow jumbo phages to spread their own defenses

A team of evolutionary biology researchers has discovered a new class of bacterial mobile genetic elements that use giant viruses—known as jumbo phages—to move between cells. The work, published in the Proceedings of the National Academy of Sciences, uncovers an unexpected twist in the long-running arms race between bacteria and their viruses.

In the study, a common bacterium was exposed to sterile filtrate from garden compost. The bacterium picked up several previously unknown DNA elements, each carrying genes that defend against phage infection. Remarkably, one of these elements, named I55, was found to hitch a ride on a jumbo phage, making it one of the first examples of a phage satellite exploiting such a large virus. The element not only spreads via the phage but also protects its bacterial host through a restriction–modification system—effectively allowing the bacterium to borrow viral machinery for its own benefit.

Yansong Zhao et al, Jumbo phage–mediated transduction of genomic islands, Proceedings of the National Academy of Sciences (2025). DOI: 10.1073/pnas.2512465122

Comment by Dr. Krishna Kumari Challa on November 4, 2025 at 7:05am

Urban settings showed larger estimated effects for PM2.5, sulfate, and ammonium compared with rural areas. Sex-stratified results indicated larger estimates for male children, with sulfate the only pollutant significantly associated among female children.

Neighborhood patterns suggested more pronounced estimated risks in lower-income and middle-income areas and in areas with higher proportions of racialized and newcomer populations.

Authors conclude that prenatal exposure to specific PM2.5 components, particularly sulfate and ammonium, was associated with autism risk, with sensitive periods in the second and third trimesters.

Postnatal ozone exposure in the first year of life was also associated with risk. Findings point to the potential importance of early-life environmental exposures.

Maxime Cloutier et al, Prenatal Exposure to Fine Particulate Matter Components and Autism Risk in Childhood, JAMA Network Open (2025). DOI: 10.1001/jamanetworkopen.2025.38882

Part 2

Comment by Dr. Krishna Kumari Challa on November 4, 2025 at 7:04am

Prenatal exposure to specific fine particles linked to autism risk

A multi-institutional team  has found that prenatal air exposure to specific particulate matter components and early-life ozone is associated with autism spectrum disorder in  children.

Fine particulate matter has been linked to adverse health outcomes, with prenatal and early postnatal exposure associated with neurodevelopmental outcomes including autism spectrum disorder.

Most previous work has focused on fine particulate matter of airborne particles with a diameter of 2.5 micrometers or less (PM2.5), leaving uncertainty about variation in toxic effects among various chemical components and timing of exposure related to sensitive points in pregnancy. A large Southern California cohort study reported associations for several components, including sulfate, and a follow-up study also noted nitrate.

In the study, "Prenatal Exposure to Fine Particulate Matter Components and Autism Risk in Childhood," published in JAMA Network Open, researchers conducted a population-based retrospective cohort study to examine associations between prenatal and first-year-of-life exposure to specific PM_2.5 components, nitrogen dioxide, and ozone with autism diagnoses, and to identify potentially sensitive gestational windows.

Looking at birth through the first five years in Ontario, covering approximately 20 years, yielded 2,183,324 children after exclusions and 19,569 children who received an autism diagnosis.

Exposure assessment assigned prenatal concentrations by maternal postal code at delivery. Weekly nitrogen dioxide and ozone and biweekly PM2.5 mass and components were estimated from conception to age 36 weeks, with first-year exposures as annual postal code–level averages weighted by time at each address. Components included black carbon, dust, ammonium, nitrate, organic matter, sulfate, and sea salt. Models integrated satellite data, chemical transport modeling, land-use regression, and ground monitoring data.

Prenatal PM_2.5 mass was associated with increased risk when adjusted for first-year averages (HR 1.15), and window-specific signals were driven by sulfate during weeks 23–36 (HR 1.11) and ammonium during weeks 21–34 (HR 1.11), after which PM_2.5 mass was no longer associated with autism.

First-year ozone exposure was associated with autism risk with HR 1.09. Weekly models indicated significant windows for PM_2.5 during gestational weeks 14 to 32, sulfate during weeks 23 to 36, ammonium during weeks 21 to 34, and ozone during weeks 26 to 30, with reported window-specific HRs of 1.12 for PM_2.5, 1.11 for sulfate, 1.11 for ammonium, and 1.03 for ozone.

Black carbon, organic matter, dust, sea salt were not significant after adjustments, suggesting that specific chemical and not general PM_2.5 exposure associations.

Part 1

Comment by Dr. Krishna Kumari Challa on November 2, 2025 at 12:11pm

Chimpanzees rationally revise their beliefs

New evidence? No problem. Chimps can weigh conflicting clues, just like humans

Study is first to suggest our closest relatives think about their own thoughts

 Chimpanzees rationally revise their beliefs on the basis of evidence. 

In a series of play-based experiments at a Ugandan chimp sanctuary, researchers watched as the apes assessed the quality of the evidence before them, altered their behavior based on what they saw, and even revised their beliefs in light of new information. The results, published recently in Science, suggest chimpanzees can use the evidence in front of them to make smart decisions—and strengthen the case that these great apes think about their own thoughts, with awareness of what they do and don’t know.

https://www.science.org/doi/10.1126/science.adq5229

Comment by Dr. Krishna Kumari Challa on November 2, 2025 at 12:06pm

AI gets ‘brain rot’ from social media
Artificial intelligence (AI) chatbots trained on ‘brain rot’ content — vapid social media posts that are the equivalent of mental junk food — are worse at generating accurate information. Researchers found that chatbots given a diet of popular and sensationalist Twitter/X posts skipped steps in their reasoning process (or didn’t use reasoning at all), spat out wrong answers and demonstrated ‘dark traits’ such as psychopathy and increased levels of narcissism.

Nature 
 arXiv preprint (not peer reviewed)

Comment by Dr. Krishna Kumari Challa on November 1, 2025 at 8:45am

The question was: How can a cuckoo reliably pass on the right egg color? After all, a female might not know what her own egg looks like.
Presumably, a female cuckoo will return to a nest of the type in which she was raised. For the egg color to really match, however, it needs to be encoded in the bird's genes. As far back as the 1930s, the hypothesis was formulated that the responsible genes reside somewhere on the maternal lineage.

The current analyses now confirm that the base color of the eggs of the European cuckoo is inherited almost exclusively via the female sex chromosome—the W chromosome—and mitochondria. The patterning, by contrast, depends to a greater extent on autosomal genes, which come from both parents. In the Oriental cuckoos studied, whose eggs were all whitish-green and differed only in their patterning, the researchers found no inheritance via the maternal lineage.
Inheritance via the W chromosome ensures that daughters always lay eggs with the same base color as their mothers. For new adaptations, however, this type of inheritance is suboptimal, as the possibilities of genetic variation are limited and more strongly dependent on random mutations than in the case of DNA inherited from both parents.
The researchers observed that a gene which 's possibly involved in egg coloration evidently 'migrated' from the autosomes [the non-sex chromosomes inherited from both parents] to the W chromosome.
Matrilineal inheritance shapes how genetic variation is spread across a species. When traits matter for both males and females, adapting to different hosts can quickly drive populations apart—and eventually create new species. In the cuckoo, by contrast, females can freely mate with any male without losing their adaptation to their host. The flow of genetic information across the rest of the genome is preserved.
And that is precisely what the researchers observed: The huge cuckoo population throughout Eurasia is almost genetically identical within DNA regions inherited from both parents.
But this evolutionary advantage does not protect the cuckoo from the dangers of the present. In many regions of Europe, populations are significantly declining, because their habitats are disappearing. "Without intact habitats, this fascinating system risks vanishing on our doorstep," caution the researchers.

Justin Merondun et al, Genomic architecture of egg mimicry and its consequences for speciation in parasitic cuckoos, Science (2025). DOI: 10.1126/science.adt9355

Part 2

Comment by Dr. Krishna Kumari Challa on November 1, 2025 at 8:40am

How parasitic cuckoos lay host-matching eggs while remaining a single species

European cuckoos lay very different eggs depending on the host species. Genetic analyses have revealed how this adaptation is inherited without leading to speciation.

Bright blue, white, greenish, speckled, or striped—cuckoo eggs exhibit an extraordinary variety. This range of colors is the result of an evolutionary race with over 100 avian host species. Cuckoos famously do not incubate their eggs, but secretly lay them in the nests of other bird species.

To ensure that the host does not recognize the cuckoo egg and throw it out of its nest, the egg must closely resemble the eggs of its host parent. However, every female cuckoo is tied to lay eggs of a specific color and pattern. This suggests that various evolutionary lineages of the European cuckoo (Cuculus canorus) exist, with each of them adapted to a specific avian host species.

An international team has now deciphered the genetic basis of these adaptations and shown how the cuckoo remains a single species. This calls for explanation, because as cuckoos evolve specialized adaptations to exploit new hosts, these populations could begin to genetically diverge to the point of forming new species.

For their study, the researchers analyzed some 300 genomes of the European and 50 of the Oriental cuckoo (Cuculus optatus), its eastern sister species. Subsequently, they checked which gene variants corresponded to the egg coloration.

The paper is published in the journal Science.

Part 1

Comment by Dr. Krishna Kumari Challa on October 31, 2025 at 9:57am

Synthetic biology to supercharge photosynthesis in crops

 Researchers have created tiny compartments to help supercharge photosynthesis, potentially boosting wheat and rice yields while slashing water and nitrogen use.

How can we make plants fix carbon more efficiently? Scientists ask this question most of the time. 

So they engineered nanoscale "offices" that can house an enzyme called Rubisco in a confined space, enabling scientists to fine-tune compatibility for future use in crops, which should allow them to produce food with fewer resources. Their research is published in Nature Communications.

Rubisco is a common enzyme in plants that is essential for "fixing" carbon dioxide for photosynthesis, the chemical process that uses sunlight to make food and energy for plants.

Rubisco is very slow and can mistakenly react with oxygen instead of CO₂ which triggers a whole other process that wastes energy and resources. This mistake is so common that important food crops such as wheat, rice, canola and potatoes have evolved a brute-force solution: mass-produce Rubisco.

In some leaves, up to 50% of the soluble protein is just copies of this one enzyme, representing a huge energy and nitrogen expense for the plant. It's a major bottleneck in how efficiently plants can grow.

Some organisms solved this problem millions of years ago. Algae and cyanobacteria house Rubisco in specialized compartments and supply them with concentrated CO₂. They're like tiny home offices that allow the enzyme to work faster and more efficiently, with everything it needs close at hand.

Scientists have been trying for years to install these natural CO₂-concentrating systems into crops. But even the simplest of these Rubisco-containing compartments from cyanobacteria, called carboxysomes, are structurally complicated. They need multiple genes working in precise balance and can only house their native Rubisco.

Researchers in the current study 

took a different approach, using encapsulins. These are simple bacterial protein cages that require just one gene to build. Think of it like Lego blocks that automatically snap into place, rather than assembling complicated flat-pack furniture.

To load Rubisco inside, the researchers added a short "address tag" of 14 amino acids to the enzyme that, like a zip code, directs the enzyme to its destination inside the assembling compartment.

This worked well. 

Crops with this elevated CO2-fixing technology could produce higher yields while using less water and nitrogen fertilizer. These are critical advantages as climate change and population growth put pressure on global food systems.

Taylor N. Szyszka et al, Reprogramming encapsulins into modular carbon-fixing nanocompartments, Nature Communications (2025). DOI: 10.1038/s41467-025-65307-9

Comment by Dr. Krishna Kumari Challa on October 31, 2025 at 9:49am

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 October 31, 2025 at 8:38am

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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