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Comment by Dr. Krishna Kumari Challa on July 25, 2025 at 6:52am

Study links caffeine intake to decreased antibiotic potency in common bacteria

Ingredients of our daily diet—including caffeine—can influence the resistance of bacteria to antibiotics. This has been shown in a new study by a team of researchers.

They discovered that bacteria such as Escherichia coli (E. coli) orchestrate complex regulatory cascades to react to chemical stimuli from their direct environment, which can influence the effectiveness of antimicrobial drugs.

In a systematic screening, the researchers investigated how 94 different substances—including antibiotics, prescription drugs, and food ingredients—influence the expression of key gene regulators and transport proteins of the bacterium E. coli, a potential pathogen. Transport proteins function as pores and pumps in the bacterial envelope and control which substances enter or leave the cell. A finely tuned balance of these mechanisms is crucial for the survival of bacteria.

Their data shows that several substances can subtly but systematically influence gene regulation in bacteria. The findings suggest even everyday substances without a direct antimicrobial effect—e.g., caffeinated drinks—can impact certain gene regulators that control transport proteins, thereby changing what enters and leaves the bacterium.

Caffeine triggers a cascade of events starting with the gene regulator Rob and culminating in the change of several transport proteins in E. coli—which in turn leads to a reduced uptake of antibiotics such as ciprofloxacin. This results in caffeine weakening the effect of this antibiotic. The researchers describe this phenomenon as an "antagonistic interaction."

This weakening effect of certain antibiotics was not detectable in Salmonella enterica, a pathogen closely related to E. coli. This shows that even in similar bacterial species, the same environmental stimuli can lead to different reactions—possibly due to differences in transport pathways or their contribution to antibiotic uptake.

 Christoph Binsfeld et al, Systematic screen uncovers regulator contributions to chemical cues in Escherichia coli, PLOS Biology (2025). DOI: 10.1371/journal.pbio.3003260

Comment by Dr. Krishna Kumari Challa on July 24, 2025 at 10:20am

Humanity Has Dammed So Much Water It's Shifted Earth's Magnetic Poles

Recent shifts in Earth's magnetic field have human fingerprints all over them. While it is normal for our planet's magnetic poles to sporadically wander, new research shows we've now amassed enough water behind dam walls to account for at least some of the current movements. Harvard University geophysicist Natasha Valencic and colleagues calculated that the masses concentrated in just under 7,000 of Earth's biggest dams have knocked the crust's axis of rotation off kilter by around one meter (three feet) relative to the dynamo that drives the magnetic fields beneath the crust. What's more, all this water hoarding has also caused a 21-millimeter-drop in sea levels. As we trap water behind dams, not only does it remove water from the oceans, thus leading to a global sea level fall, it also distributes mass in a different way around the world This mass redistribution can impact Earth's magnetic pole positions relative to the surface. Extra weight added to a spinning sphere pulls the weighted part towards the equator, shifting the axis around which the sphere spins. So, redistributing Earth's surface weight re-orientates its spin axis, whether that be through damming water, melting glaciers, or groundwater removal. But it's only Earth's outer crust floating over its gooey inner parts – not the inner goo generating the magnetic field – that shift, leading to a different part of Earth's surface sitting over our planet's inner magnetic north. So, while north itself hasn't really moved in space, Earth's surface has shifted around, over the top of it. This phenomenon is called true polar wander.

https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2025GL115468

Comment by Dr. Krishna Kumari Challa on July 24, 2025 at 7:56am

A Fungus, Not Its Insect Host, Paints the World Red

Lac insects carry a yeast-like symbiont that produces a commercially important bright red pigment, revealing insights about insect-microbe symbiosis.

For thousands of years, artisans have been dyeing textiles, jewelry, and handicrafts with a rich, vibrant red pigment that they obtain from lac insects. The most widely-cultivated lac insect, Kerria lacca, is bright crimson because of its natural pigments called laccaic acids.

Researchers now  found that K. lacca carry a yeast-like symbiont, which produces the colorful lac pigment and provides essential nutrients that the insects’ plant diet lacks.

Their findings, published in Proceedings of the National Academy of Sciences, highlight the role of fungal symbionts in insects for providing nutrition and other metabolites.

To characterize the lac insect, the research  team sequenced its genome, as well as that of its known symbionts: bacteria belonging to the genus Wolbachia, and an unidentified yeast-like fungus. They discovered that neither the lac insect nor Wolbachia carried the genes required to produce the molecules that make up laccaic acids. However, genes in the yeast-like symbiont encoded various enzymes that did, indicating the fungus as the only plausible source of the pigment. 

The researchers validated that the pigment originated in the yeast-like symbiont by spraying lac insects with fungicides. Depleting the fungal symbiont reduced the expression of genes required for pigment synthesis. Mass spectrometry revealed lower concentrations of laccaic acids in fungicide-treated insects, which also appeared paler in comparison to untreated insects. However, the fungicide treatment did not eliminate the yeast completely. “Therefore, the insects weren't completely colorless”.

Vaishally, et al. An endosymbiotic origin of the crimson pigment from the lac insect. Proc Natl Acad Sci USA. 2025;122(25):e2501623122.

Vashishtha A, et al. Co-existence, phylogeny and putative role of Wolbachia and yeast-like symbiont (YLS) in Kerria lacca (Kerr). Curr Microbiol. 2011;63(2):206-212.

https://www.the-scientist.com/a-fungus-not-its-insect-host-paints-t...

Comment by Dr. Krishna Kumari Challa on July 24, 2025 at 6:29am

Scientists use dental floss to deliver vaccines without needles

Flossing your teeth at least once a day is an essential part of any oral health routine. But it might also one day protect other parts of the body as scientists have created a novel, needle-free vaccine approach using a specialized type of floss.

In a study published in Nature Biomedical Engineering, researchers demonstrated that when floss laced with vaccine  components, such as proteins and inactive viruses, was applied along the gum lines of mice, it triggered an immune response.

This method of vaccine delivery is effective because the areas of gum between the teeth are highly permeable, allowing them to absorb vaccine molecules easily.

In the experiment, researchers flossed 50 mice every two weeks for 28 days, which wasn't an easy task. To floss each mouse, one person had to gently pull their jaw down with the metal ring from a keychain while another did the flossing.

Four weeks after the final vaccine dose, the mice were exposed to a lethal strain of flu.

All rodents that received the floss-based vaccine survived while the unvaccinated animals died. Additionally, the mice that had been flossed had a more widespread immune response throughout their bodies. Flu antibodies were detected in their feces, saliva and even in their bone marrow.

Finding antibodies in the bone marrow suggests the mice's bodies had established a long-term immune response. The researchers also saw an increase in T Cells (a type of immune cell that fights off infections) in the mice's lungs and spleen.

Next, the researchers wanted to see whether flossing would be a viable approach for humans. So they asked 27 healthy volunteers to floss with dental picks coated with food dye. On average, the dye reached the gums about 60% of the time.

The mouth and nose are the primary entry points for many viruses, making the oral cavity an ideal site for vaccine delivery. However, scientists have faced significant hurdles in developing needle-free vaccine alternatives for these areas due to the body's tough defenses against foreign invaders. A floss-based approach could bypass these challenges, offering a promising new method.

 Rohan S. J. Ingrole et al, Floss-based vaccination targets the gingival sulcus for mucosal and systemic immunization, Nature Biomedical Engineering (2025). DOI: 10.1038/s41551-025-01451-3

Comment by Dr. Krishna Kumari Challa on July 23, 2025 at 2:15pm

Engineered bacteria pave the way for vegan cheese and yogurt

Bacteria are set to transform the future of dairy-free milk products. Scientists have successfully engineered E. coli to produce key milk proteins essential for cheese and yogurt production, without using any animal-derived ingredients. This paves the way for plant-based dairy alternatives that mimic traditional dairy at a molecular level but are sustainable and cruelty-free.

A recent study published in Trends in Biotechnology reported two methods for producing casein (a milk protein) that are nutritionally and functionally similar to bovine casein.

Casein is a highly sought-after component in both infant and adult diets, as it is digestible, of high quality, and provides several essential amino acids our body needs.

The food and pharmaceutical industries have utilized microorganisms as cell factories for the large-scale production of biomolecules, dietary supplements, and enzymes for quite some time. Scientists were curious to see if the same approach could be used for recombinant casein proteins, produced through genetic engineering in microbial cell factories. However, these techniques often fail to replicate a key factor that imparts casein its unique properties—phosphorylation, a biological process where a phosphate group is added to a protein.

Phosphorylation of serine residues (amino acid components) is critical for casein's ability to bind calcium, which makes milk stable and provides it with nutritional properties. Calcium binding also ensures the formation of nanoscale protein structures called casein micelles, which act as delivery agents for bioavailable calcium and phosphate.

To overcome this issue, the researchers adopted two main strategies. First, they engineered bacteria to co-express three Bacillus subtilis protein kinases, which are enzymes that catalyze the addition of phosphate groups to proteins. Second, they designed a phosphomimetic version of αs1-casein, in which serine residues normally phosphorylated in the naturally occurring protein were replaced with aspartic acid to mimic the negative charge and functional effects of phosphorylation.

The team carried out structural analysis, calcium-binding tests, and simulated gastrointestinal digestion of the derived αs1-casein. The results indicated that both the phosphorylated and phosphomimetic caseins of bacterial origin had a high calcium-binding capacity, and their digestibility and structure were comparable to that of cattle-derived casein.

The researchers highlighted that while kinase-mediated phosphorylation provides a route for closely mimicking native casein, phosphomimetic casein provides a simpler path for producing functionally similar proteins. 

 Suvasini Balasubramanian et al, Production of phosphorylated and functional αs1-casein in Escherichia coli, Trends in Biotechnology (2025). DOI: 10.1016/j.tibtech.2025.05.015

Comment by Dr. Krishna Kumari Challa on July 23, 2025 at 2:10pm

Quantum internet moves closer as researchers teleport light-based information

Quantum teleportation is a fascinating process that involves transferring a particle's quantum state to another distant location, without moving or detecting the particle itself. This process could be central to the realization of a so-called "quantum internet," a version of the internet that enables the safe and instant transmission of quantum information between devices within the same network.

Quantum teleportation is far from a recent idea, as it was experimentally realized several times in the past. Nonetheless, most previous demonstrations utilized frequency conversion rather than natively operating in the telecom band.

Researchers recently demonstrated the teleportation of a telecom-wavelength photonic qubit (i.e., a quantum bit encoded in light at the same wavelengths supporting current communications) to a telecom quantum memory. Their paper, published in Physical Review Letters, could open new possibilities for the realization of scalable quantum networks and thus potentially a quantum internet.

 Yu-Yang An et al, Quantum Teleportation from Telecom Photons to Erbium-Ion Ensembles, Physical Review Letters (2025). DOI: 10.1103/3wh8-2gh1.

Comment by Dr. Krishna Kumari Challa on July 19, 2025 at 9:41am

The researchers also investigated how sleepy a participant felt when they woke up. While participants felt the sleepiest when awoken from REM sleep, the impact of the slow waves in non-REM sleep stages is quite intriguing.

They found a new aspect in which slow waves can present very distinct and opposite behaviors. Some slow waves are actually acting like arousal elements—they are part of the 'wake up!' signal. The more these waves occur just before awakening, the more alert you tend to feel upon awakening. While the other slow waves—whether they are present before waking up or persisting after—are the reason we sometimes feel so sleepy in the first moments of the day.
These findings can be used for future research into sleep disorders, such as insomnia or conditions involving incomplete awakenings.

Aurélie M. Stephan et al, Cortical activity upon awakening from sleep reveals consistent spatio-temporal gradients across sleep stages in human EEG, Current Biology (2025). DOI: 10.1016/j.cub.2025.06.064

Part 2

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Comment by Dr. Krishna Kumari Challa on July 19, 2025 at 9:37am

Scientists discover a signature 'wave' of activity as the brain awakens from sleep

Each morning, your brain embarks on a remarkable series of events: it transitions from being asleep, potentially in an alternate reality, to waking up. Within a short time, you regain waking consciousness, reorient yourself and reconnect with your surroundings, becoming ready to interact with the world again. But how does your brain accomplish this transition so safely and efficiently?

To better understand the awakening brain, researchers  analyzed over 1,000 awakenings using high-density EEG recordings on a second-by-second basis.

The study, published in Current Biology, reveals that the brain doesn't wake up all at once. Instead, it orchestrates a precise sequence of activation.

The researchers worked with high-density EEG data, which offers information about the time and location of brain activity. When looking at the activity progression throughout the awakening brain, they observed a clear sequence: it starts in central and frontal brain regions and gradually spreads toward the back of the brain.

This progression likely reflects how signals from subcortical arousal centers (deeper in the brain) reach the cortex, with shorter paths to frontal areas and longer ones toward regions further back.

To better understand how the brain navigates waking up at any moment, the researchers specifically studied awakening patterns in two stages: REM sleep, commonly associated with vivid dreams, and non-REM sleep, also known as deep sleep.

When participants awoke from non-REM sleep, their brain activity first showed a brief surge in slower sleep-like waves immediately followed by faster activity related to wakefulness. When participants awoke from REM sleep, the slower waves were skipped, leading to a more direct boost in faster brain activity.

"The brain responds differently to arousing signals depending on the stage it's in", the researchers say. "In non-REM sleep, neurons that connect arousal centers to the cortex alternate between states of activity and silence—a dynamic known as 'bistability.'

"As a result of this bistability, any arousing stimulus first triggers a slow wave, before transitioning to faster activity. In contrast, REM sleep does not have this bistable pattern, so the cortex immediately responds with the fast, wake-like, activity."

Part 1

Comment by Dr. Krishna Kumari Challa on July 19, 2025 at 9:28am

To directly test whether MER11 sequences can control gene expression, the team used a technique called lentiMPRA (lentiviral massively parallel reporter assay). This method allows thousands of DNA sequences to be tested at once by inserting them into cells and measuring how much each one boosts gene activity.

The researchers applied this method to nearly 7,000 MER11 sequences from humans and other primates, and measured their effects in human stem cells and early-stage neural cells.

The results showed that MER11_G4 (the youngest subfamily) exhibited a strong ability to activate gene expression. It also had a distinct set of regulatory "motifs," which are short stretches of DNA that serve as docking sites for transcription factors, the proteins that control when genes are turned on. These motifs can dramatically influence how genes respond to developmental signals or environmental cues.

Further analysis revealed that the MER11_G4 sequences in humans, chimpanzees, and macaques had each accumulated slightly different changes over time. In humans and chimpanzees, some sequences gained mutations that could increase their regulatory potential in human stem cells.

Young MER11_G4 binds to a distinct set of transcription factors, indicating that this group gained different regulatory functions through sequence changes and contributes to speciation
The study offers a model for understanding how "junk" DNA can evolve into regulatory elements with important biological roles. By tracing the evolution of these sequences and directly testing their function, the researchers have demonstrated how ancient viral DNA has been co-opted into shaping gene activity in primates.

Xun Chen et al, A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage, Science Advances (2025). DOI: 10.1126/sciadv.ads9164. www.science.org/doi/10.1126/sciadv.ads9164

Part 2

Comment by Dr. Krishna Kumari Challa on July 19, 2025 at 9:27am

Study reveals hidden regulatory roles of 'junk' DNA

A new international study suggests that ancient viral DNA embedded in our genome, which were long dismissed as genetic "junk," may actually play powerful roles in regulating gene expression. Focusing on a family of sequences called MER11, researchers have shown that these elements have evolved to influence how genes turn on and off, particularly in early human development.

The findings are published in the journal Science Advances.

Transposable elements (TEs) are repetitive DNA sequences in the genome that originated from ancient viruses. Over millions of years, they spread throughout the genome via copy-and-paste mechanisms.

Today, TEs make up nearly half of the human genome. While they were once thought to serve no useful function, recent research has found that some of them act like "genetic switches," controlling the activity of nearby genes in specific cell types.

However, because TEs are highly repetitive and often nearly identical in sequence, they can be difficult to study. In particular, younger TE families like MER11 have been poorly categorized in existing genomic databases, limiting our ability to understand their role.

To overcome this, the researchers developed a new method for classifying TEs. Instead of using standard annotation tools, they grouped MER11 sequences based on their evolutionary relationships and how well they were conserved in the primate genomes.

This new approach allowed them to divide MER11A/B/C into four distinct subfamilies, namely, MER11_G1 through G4, ranging from oldest to youngest.

This new classification revealed previously hidden patterns of gene regulatory potential. The researchers compared the new MER11 subfamilies to various epigenetic markers, which are chemical tags on DNA and associated proteins that influence gene activity. This showed that this new classification aligned more closely with actual regulatory function compared with previous methods.

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