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Comment by Dr. Krishna Kumari Challa on December 14, 2025 at 9:36am

Warblers borrow color-related genes from evolutionary neighbours, study finds

Wood warblers, also called New World warblers, are some of the most colorful birds in North America, with more than a hundred species in the family ranging in color from yellow, orange and red to blue, green and pink. A new study led by researchers at Penn State has uncovered several instances of the birds passing color-related genes to other species of wood warblers, including those that are not closely related.

This glimpse into the hidden evolutionary dynamics of these songbirds may help explain why some species display certain colors as well as how the group diversified into so many different species in such a relatively short evolutionary time, the researchers said.

A paper describing the research appeared Dec. 11 in the journal PLOS Biology.

It turns out that some of these birds may have borrowed colors from their neighbors, rather than evolving them independently. Scientists previously found evidence that a particular color-related gene had been shared between species within the same genus, which is one notch up on the taxonomic ladder, but now they show that there is gene movement from species in one genus to another. That means some genetic funny business was going on with these warblers millions of years ago.

In addition to the pigment melanin, which produces brown and black plumage, the colors of wood warblers are influenced by carotenoid pigments, which are responsible for bright yellow, red and orange plumage. The research team collected DNA from 400 warblers across 100 species and six subspecies, focusing on three main genes related to carotenoid pigments.

The team compared an evolutionary tree of the warblers—built using their entire genomes and representing the overall relationships among the birds—with trees they created independently for each of the three carotenoid-related genes. These gene-specific trees show similarities and differences of the individual gene across the family, and discrepancies between the trees suggest where gene exchanges may have occurred. Statistical follow-up tests confirmed the gene exchanges, which the researchers said resulted from a process called introgression.

Part 1

Comment by Dr. Krishna Kumari Challa on December 14, 2025 at 9:30am

To reach their conclusion, the researchers considered both possibilities for the lack of X-ray sources in small galaxies in their large Chandra sample. The amount of gas falling onto a black hole determines how bright or faint they are in X-rays. Because smaller black holes are expected to pull in less gas than larger black holes, they should be fainter in X-rays and often not detectable. The researchers confirmed this expectation.

However, they found that an additional deficit of X-ray sources is seen in less massive galaxies beyond the expected decline from decreases in the amount of gas falling inwards. This additional deficit can be accounted for if many of the low-mass galaxies simply don't have any black holes at their centers. The team's conclusion was that the drop in X-ray detections in lower mass galaxies reflects a true decrease in the number of black holes located in these galaxies.
This result could have important implications for understanding how supermassive black holes form. There are two main ideas: In the first, a giant gas cloud directly collapses into a black hole, which contains thousands of times the sun's mass from the start. The other idea is that supermassive black holes instead come from much smaller black holes, created when massive stars collapse.
The formation of big black holes is expected to be rarer, in the sense that it occurs preferentially in the most massive galaxies being formed, so that would explain why we don't find black holes in all the smaller galaxies, say the researchers.

Fan Zou et al, Central Massive Black Holes Are Not Ubiquitous in Local Low-mass Galaxies, The Astrophysical Journal (2025). DOI: 10.3847/1538-4357/ae06a1

Part 2

Comment by Dr. Krishna Kumari Challa on December 14, 2025 at 9:27am

Small galaxies may buck the black hole trend, Chandra finds

Most smaller galaxies may not have supermassive black holes in their centers, according to a recent study using NASA's Chandra X-ray Observatory. This contrasts with the common idea that nearly every galaxy has one of these giant black holes within their cores, as NASA leads the world in exploring the secrets of how the universe works.

A team of astronomers used data from more than 1600 galaxies collected in more than two decades of the Chandra mission. The researchers looked at galaxies ranging in heft from over ten times the mass of the Milky Way down to dwarf galaxies, which have stellar masses less than a few percent of that of our home galaxy. A paper describing these results has been published in The Astrophysical Journal.

The team has reported that only about 30% of dwarf galaxies likely contain supermassive black holes.

As material falls onto black holes, it is heated by friction and produces X-rays. Many of the massive galaxies in the study contain bright X-ray sources in their centers, a clear signature of supermassive black holes in their centers. The team concluded that more than 90% of massive galaxies—including those with the mass of the Milky Way—contain supermassive black holes.
However, smaller galaxies in the study usually did not have these unambiguous black hole signals. Galaxies with masses less than three billion suns—about the mass of the Large Magellanic Cloud, a close neighbor to the Milky Way—usually do not contain bright X-ray sources in their centers.

The researchers considered two possible explanations for this lack of X-ray sources. The first is that the fraction of galaxies containing massive black holes is much lower for these less massive galaxies. The second is the amount of X-rays produced by matter falling onto these black holes is so faint that Chandra cannot detect it.

Comment by Dr. Krishna Kumari Challa on December 14, 2025 at 9:20am

Teams developed and shared sophisticated debugging tools, such as "Pooled PCRtag Mapping" (which allows researchers to screen hundreds of yeast colonies simultaneously to pinpoint which genetic changes caused problems) and "CRISPR D-BUGS' (combines gene editing with selection strategies).

The lessons from yeast are already informing bold new projects.

Plants grow slowly and are far more difficult to engineer than yeast, so this project uses an ingenious approach: building the synthetic plant chromosomes inside yeast cells first, then transferring the newly constructed chromosome into plant cells.

 Building synthetic chromosomes one yeast at a time: insights from Sc2.0, Nature Biotechnology (2025). DOI: 10.1038/s41587-025-02913-4

Part 2

Comment by Dr. Krishna Kumari Challa on December 14, 2025 at 9:18am

How to build a genome: Scientists release troubleshooting manual for synthetic life

Leading synthetic biologists have shared hard-won lessons from their decade-long quest to build the world's first synthetic eukaryotic genome in a Nature Biotechnology paper. Their insights could accelerate development of the next generation of engineered organisms, from climate-resilient crops to custom-built cell factories.

The Synthetic Yeast Genome Project (Sc2.0) involved a large, evolving global consortium of 200-plus researchers from more than ten institutions, who jointly set out to redesign and chemically synthesize all 16 chromosomes of baker's yeast from scratch. Macquarie University contributed to the synthesis of two of these chromosomes, comprising around 12% of the project overall.

The process for each chromosome followed the same design principles: removing unstable genetic elements; introducing molecular 'watermarks' to distinguish synthetic DNA from natural sequences; and adding the gene-shuffling system "SCRaMbLE" so researchers could rearrange genes and test their functions.

Unlike traditional genetic engineering, which tweaks existing genomes, Sc2.0 was the first to rewrite an entire genome from the ground up—all 12 million base pairs of it.

Completing all 16 synthetic chromosomes lets us understand genome function at a scale that was simply impossible before.

The chromosomes were assembled in large chunks containing thousands of base pairs, then integrated into living yeast cells step by step, relying on yeast's own cellular machinery to stitch the synthetic pieces into place.

Despite the standardized design principles, every research team encountered similar problems. The paper catalogs these 'bugs' systematically, offering future synthetic biologists a roadmap of what to avoid.

Tiny DNA watermarks, designed to be silent, occasionally disrupted gene function in unexpected ways. Some genes flagged as non-essential turned out to cause significant growth problems when removed.

Yeast cannot regenerate mitochondrial genomes from scratch, so any damage required researchers to perform a genetic rescue operation, where they identified and fixed the problem, then had to reintroduce healthy mitochondria through careful breeding.

Part 1

Comment by Dr. Krishna Kumari Challa on December 14, 2025 at 9:12am

The team also assessed whether the ZOE MB health-ranked SGBs were more abundant in participants with a defined disease. Indeed, they found that people in the control group had higher favorably ranked gut microbes than people with disease, and that those with diseases had more unfavorably ranked gut microbes than those without disease.

Dietary interventions were also found to increase favorable microbes and reduce unfavorable ones. The team analyzed data from two studies, referred to as ZOE METHOD and BIOME, in which participants either followed a personalized dietary intervention program (PDP) designed to improve the microbiome or took a prebiotic supplement. The microbiomes of these participants changed significantly by the end of the studies.

"The dietary intervention groups of both clinical trials that aimed at improving diet using different approaches (prebiotic blend for BIOME and PDP for METHOD) showed the highest number of significantly changing SGBs. Focusing on the most significant gut microbial SGBs with the largest change in relative abundance after dietary interventions, they found increasing Bifidobacterium animalis—a bacterium present in dairy-based foods and in the microbiome of people consuming larger amounts of them, an unknown Lachnospiraceae bacterium and R. hominis both previously associated with a vegan diet, and another unknown Lachnospiraceae bacterium linked to a vegetarian diet," the authors explain.

In addition to linking known bacterial species to measures of health and diet, the team also discovered many key health-associated microbes that were previously uncharacterized species.

Francesco Asnicar et al, Gut micro-organisms associated with health, nutrition and dietary interventions, Nature (2025). DOI: 10.1038/s41586-025-09854-7

Part2

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Comment by Dr. Krishna Kumari Challa on December 14, 2025 at 9:10am

Which gut microbes matter most? Large study ranks bacteria by health and diet links

The gut microbiome has been a rising star in the world of health science over the last several years, garnering interest from both researchers and the general public. This is mostly due to its connection to general health and diseases, like type 2 diabetes and heart disease, as well as the fact that it is a modifiable element of human health. However, the science surrounding the fascinating world of gut microbes is still developing and there is much to learn.

A new study, published in Nature, has added significantly to our understanding of the human microbiome. The study team analyzed the gut microbiome, diet and health markers from over 34,500 people in the US and UK, and linked hundreds of specific gut microbe species to key indicators of health and diet. The data come from the Zoe PREDICT program in the UK and US, which is run by the microbiome testing company Zoe.

The researchers used machine learning to link certain gut microbe species in 34,694 study participants to diet and common health risk factors such as BMI, triglycerides, blood glucose and HbA1c, as well as clinical markers that are intermediary measures of cardiometabolic health. Out of 661 non-rare microbial species, the researchers focused in on the 50 that were most favorably associated with good health and the 50 that were the most unfavorably associated with good health.

This process resulted in the development of the "ZOE Microbiome Health Ranking 2025" and "Diet Ranking 2025," used to score microbes as either favorable or unfavorable for health on a scale of 0 to 1. Those closer to zero are considered positively correlated to the health markers and those closer to one are negatively correlated. This was done for all 661 microbes studied.

The ranking system identified hundreds of gut microbe species—described as species-level genome bins (SGBs) in the paper—significantly associated with health markers and diet quality. They found that favorable microbes were more common in people with lower BMI and fewer diseases, while unfavorable microbes were more common in those with obesity and disease. A part of the study focusing on BMI, used data from 5,348 healthy individuals, and divided them into three BMI categories; healthy weight, overweight and obese.

"Meta-analysis based on linear regression on single cohorts showed that individuals with healthy weight carried, on average, 5.2 more of the 50 favorably ZOE MB health-ranked SGBs than people with obesity," the study team writes.

part1

Comment by Dr. Krishna Kumari Challa on December 14, 2025 at 9:04am

City raccoons showing signs of domestication

Urban raccoons exhibit shorter snouts compared to rural populations, a trait associated with early domestication syndrome. This morphological change is likely driven by the advantages of tameness and reduced aggression in accessing human food waste. The findings suggest that proximity to humans can induce domestication-related traits in wild species.

Artem Apostolov et al, Tracking domestication signals across populations of North American raccoons (Procyon lotor) via citizen science-driven image repositories, Frontiers in Zoology (2025). DOI: 10.1186/s12983-025-00583-1

Comment by Dr. Krishna Kumari Challa on December 14, 2025 at 9:03am

Scientists decode blood's hidden messengers

Every second, trillions of tiny parcels travel through your bloodstream—carrying vital information between your body's cells. Now, scientists have opened this molecular mail for the first time, revealing its contents in astonishing detail. 

In research published in Nature Cell Biology, Professor  they have mapped the complete molecular blueprint of extracellular vesicles (EVs)—nanosized particles in blood that act as the body's secret messengers. 

For decades, researchers have known that EVs exist, ferrying proteins, fats, and genetic material that mirror the health of their cells of origin. But because blood is a complex mixture—packed with cholesterol, antibodies, and millions of other particles—isolating EVs has long been one of science's toughest challenges.

These vesicles are like tiny envelopes sent between cells, delivering molecular updates about what's happening inside the body, Until now, researchers just couldn't open them properly to read the messages inside.

But now using ultra-pure isolation techniques and cutting-edge multi-omics profiling, the team identified 182 proteins and 52 lipids that make up the core structure of human plasma EVs. They also pinpointed another set of molecules that distinguish EVs from other particles in the bloodstream—effectively decoding the body's molecular communication system. 

To make this discovery accessible, the researchers developed EVMap, a free, interactive online resource that lets scientists worldwide explore the molecular makeup of blood EVs. 

By decoding this molecular language, we can begin to read the body's own health reports, say the researchers. They have already identified EV signatures linked to early heart disease, which could pave the way for simple blood tests that predict risk long before symptoms appear.

  Alin Rai et al, Multi-omics identify hallmark protein and lipid features of small extracellular vesicles circulating in human plasma, Nature Cell Biology (2025). DOI: 10.1038/s41556-025-01795-7

Comment by Dr. Krishna Kumari Challa on December 14, 2025 at 9:03am

Monkeys have rhythm and can tap along to the beat

Macaque monkeys can keep time to music and move to the beat. Well, at least two adult macaques can, who were trained by researchers to tap along to different kinds of music. Their work challenges the so-called vocal-learning hypothesis, which holds that only species with complex vocal learning, like humans and songbirds, can spontaneously move to the groove. Macaques are not vocal learners. 

To explain this ability, the study authors proposed their "four components (4Cs) hypothesis." According to this idea, musical beat perception is not unique to vocal learners but rather arises from the combination of four general abilities.

That is being able to hear the beat in music (auditory detection), anticipating the next beat (prediction), acting on the feedback (auditory-motor feedback) and the ability to coordinate these processes through reward (reward-based reinforcement).

Vani G. Rajendran et al, Monkeys have rhythm, Science (2025). DOI: 10.1126/science.adp5220

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