https://phys.org/news/2025-06-growth-boost-molecule-animal-metabolism.html

"Within the animal kingdom, a naturally produced molecule known as itaconate serves a prominent role in the immune system as a defensive agent against viruses and inflammation. Itaconate is classified as a metabolite, a natural compound that arises when organisms convert food into energy.

"While itaconate is well known in animals, its presence and functions in plants are largely unexplored. Biologists at the University of California San Diego have now undertaken the first comprehensive exploration of itaconate's functions in plants. Researchers at the School of Biological Sciences, working with colleagues at Stanford University,... used chemical imaging and measurement techniques to not only prove that itaconate exists in plants, but to reveal its significant role in stimulating plant growth.

"'We found that itaconate is made in plants, particularly in growing cells," said study senior author Jazz Dickinson, an assistant professor in the Department of Cell and Developmental Biology. "Watering maize (corn) plants with itaconate made seedlings grow taller, which was exciting and encouraged us to investigate this metabolite further and understand how it interacts with plant proteins."

***

"...they described how itaconate interacts with plant-specific proteins in Arabidopsis, a member of the mustard family.

"Further investigating these dynamics, the researchers found that itaconate plays multiple key roles in plant physiology. These include involvement in several critical plant processes, such as primary metabolism and oxygen-related stress response.

"Optimizing the natural benefits of itaconate—instead of synthetically derived chemicals—could be crucial for safely maximizing crop growth to support growing global populations.

***

"...humans also make and use itaconate, the new study could offer fresh information for understanding the molecule's role in human development and growth.

Comment: this study shows how interrelated plant and animal metabolisms are.

https://phys.org/news/2025-06-protein-droplets-shield-fragile-dna.html

"Now, scientists Irene Chiolo and Chiara Merigliano at the USC Dornsife College of Letters, Arts and Sciences have discovered that a protein called Nup98, long known for helping traffic molecules in and out of the cell's nucleus, plays another surprising role: guiding the cell's most delicate repairs and reducing the risk of genetic mistakes that can lead to cancer. Their findings were published in Molecular Cell.

"With support from the National Institutes of Health, the National Science Foundation, and the American Cancer Society, the researchers revealed that Nup98 forms droplet-like structures deep inside the nucleus. These "condensates" act as protective bubbles around broken strands of DNA in areas called heterochromatin—zones where the genetic material is so tightly packed that making accurate repairs is especially challenging.

"Heterochromatin—a major focus of Chiolo's research—is filled with repeated DNA sequences, making it easy for the cell to confuse one stretch for another. Nup98's droplets help lift the damaged section out of that dense zone and create a safer space where it can be repaired accurately, reducing the chance of genetic mix-ups that could lead to cancer.

"The researchers also found that Nup98 helps mobilize the damaged site in tightly packed heterochromatin, so it can reach a different part of the nucleus where repair is safer.

"Timing is everything when it comes to DNA repair, and one of Nup98's most important roles is knowing when to say, "Not yet."

"The protein's droplet-like condensates act as a temporary shield around damaged DNA, keeping out certain repair proteins that can cause trouble if they arrive too soon. One of those proteins, called Rad51, can accidentally stitch together the wrong pieces of DNA if it gets involved too early in the process.

"'The Nup98 droplets keep Rad51 away until other mechanisms have done their work to line up the correct pieces," Chiolo said. "Only once the damaged heterochromatin moves into a different nuclear space, Rad51 can safely finish the repair."

"By coordinating this carefully staged process, Nup98 helps cells avoid dangerous genetic rearrangements—a key part of maintaining genome stability and slowing processes responsible for cancer and aging."

Comment: having start and stop controls is a logical design. Which raises the evolutionary question did DNA appear with or without a repair mechanism? Surely not without. It seems simultaneous appearance of both is required. Only can happen by design.

Biochemical controls: maintaining a memory

DAVID: maintaining a memory involves maintaining a synapse all controlled by specific proteins, no thought involved by the proteins themselves.

dhw: Once they are established, the majority of activities within cellular communities (organisms) will be automatic. It’s only when new conditions require or allow new responses that cellular intelligence comes into play – and part of these responses will clearly be intelligent use of memory. The immune system is an obvious example.

Not obvious at all. Immune responses are formulaic. Choose an enemy ligand, add a chemical killer and an antibiotic is produced.

Fungus control

QUOTES: "Zhou et al. (1) report a fungal species that resides in the human gut and produces a compound that protects against metabolic disease in mice.”

“Intestinal symbiotic fungi may be an untapped reservoir of possible therapeutic chemical compounds.”

DAVID: the same evolutionary system that dhw derides as causing 99.9$ unnecessary organisms, produced this helpful one. It is obvious others will be found as God designed helpful forms for human support.

dhw: I have never ever derided the evolutionary system! It is YOU who deride your God by insisting that he specially, messily, cumbersomely and inefficiently designed and then had to cull 99.9 out of 100 species that were irrelevant to the single purpose you impose on him (us and our food). This has nothing whatsoever to do with a fungus which helps to protect mice against metabolic disease and might possibly have untapped potential for improving human health!

On a very different note, I see that you have not replied to my new miscellany post of yesterday. I do hope this was just a technical hitch and was not due to any deterioration in your health, which is always a matter of deep concern.

I checked it. This response is the one you wanted.

DAVID: maintaining a memory involves maintaining a synapse all controlled by specific proteins, no thought involved by the proteins themselves.

Once they are established, the majority of activities within cellular communities (organisms) will be automatic. It’s only when new conditions require or allow new responses that cellular intelligence comes into play – and part of these responses will clearly be intelligent use of memory. The immune system is an obvious example.

Fungus control

QUOTES: "Zhou et al. (1) report a fungal species that resides in the human gut and produces a compound that protects against metabolic disease in mice.”

“Intestinal symbiotic fungi may be an untapped reservoir of possible therapeutic chemical compounds.”

DAVID: the same evolutionary system that dhw derides as causing 99.9$ unnecessary organisms, produced this helpful one. It is obvious others will be found as god designed helpful forms for human support.

I have never ever derided the evolutionary system! It is YOU who deride your God by insisting that he specially, messily, cumbersomely and inefficiently designed and then had to cull 99.9 out of 100 species that were irrelevant to the single purpose you impose on him (us and our food). This has nothing whatsoever to do with a fungus which helps to protect mice against metabolic disease and might possibly have untapped potential for improving human health!

On a very different note, I see that you have not replied to my new miscellany post of yesterday. I do hope this was just a technical hitch and was not due to any deterioration in your health, which is always a matter of deep concern.

https://www.quantamagazine.org/the-molecular-bond-that-helps-secure-your-memories-20250...

"The researchers discovered that a persistent bond between two proteins(opens a new tab) is associated with the strengthening of synapses, which are the connections between neurons. Synaptic strengthening is thought to be fundamental to memory formation. As these proteins degrade, new ones take their place in a connected molecular swap that maintains the bond’s integrity and, therefore, the memory.

"The researchers present “a very convincing case” that “the interaction between these two molecules is needed for memory storage,” said Karl Peter Giese(opens a new tab), a neurobiologist at King’s College London who was not involved with the work. The findings offer a compelling response to Crick’s dilemma, reconciling the discordant timescales to explain how ephemeral molecules maintain memories that last a lifetime.

***

"Every time he repeated the experiment, he saw elevated levels of a certain protein within the synapses. “By the fourth time, I was like, this is it,” he said.

"It was protein kinase M zeta, or PKMζ for short. As the rats’ hippocampal tissue was stimulated, synaptic connections strengthened and levels of PKMζ increased(opens a new tab). By the time he published his findings in 1993, he was convinced that PKMζ was crucial for memory.

***

"When Sacktor blocked the molecule’s activity an hour after a memory was formed, he saw that synaptic strengthening was reversed. This discovery suggested that PKMζ was “necessary and sufficient(opens a new tab)” to preserve a memory over time, he wrote in Nature Neuroscience in 2002. In contrast, hundreds of other localized molecules impacted synaptic strengthening only if disrupted within a few minutes of a memory’s formation. It appeared to be a singular molecular key to long-term memory.

***

"In 2016, they published a rebuttal(opens a new tab), demonstrating that in the absence of PKMζ, mice recruit a backup mechanism, involving another molecule, to strengthen synapses.

"The existence of a compensatory molecule wasn’t a surprise. “The biological system is not such that you lose one molecule and everything goes. That’s very rare,” Giese said. But identifying this compensatory molecule prompted a new question: How did it know where to go to replace PKMζ? It would take Sacktor and Fenton nearly another decade to find out.

***

"But are the KIBRA-PKMζ complexes needed to maintain memory over the long term? To find out, the researchers disrupted the complex four weeks after a memory was formed. Doing so did indeed wipe out the memory. This suggested that the interaction between KIBRA and PKMζ is crucial not only for forming memories, but also for keeping them intact over time.

“'It’s the persistent association between two proteins that maintains the memory, rather than a protein that lasts by itself for the lifetime of the memory,” said Panayiotis Tsokas, a researcher working with Sacktor and lead author on the new Science Advances paper.

***

"This work also answers a question that researchers had put on the shelf. Sacktor’s earlier study showed that increasing levels of PKMζ strengthened synapses and memories. But how did the molecule know where to go within the neuron? “We figured, well, one day, maybe we’ll understand that,” Sacktor said. Now, the researchers think that KIBRA acts as a synaptic tag that guides PKMζ. If true, this would help explain how only the specific synapses involved in a particular physical memory trace are strengthened, when a neuron may have thousands of synapses that connect it to various other cells.

Comment: maintaining a memory involves maintaining a synapse all controlled by specific proteins, no thought involved by the proteins themselves.

https://www.science.org/doi/10.1126/science.adx1789?utm_source=sfmc&utm_medium=emai...

"Zhou et al. (1) report a fungal species that resides in the human gut and produces a compound that protects against metabolic disease in mice. The findings point to intestinal fungi as a potentially rich source of beneficial chemical compounds that could be harnessed for human health.

***

"One species—Fusarium foetens—was almost universally present in people from different geographic locales and readily grew under culture conditions that mimic conditions of the human gut, such as low oxygen. When inoculated into mice, F. foetens stably colonized the gastrointestinal tract without causing injury or invading deeper tissues. These characteristics suggest that F. foetens is not merely passing through from the environment but instead is well adapted to the mammalian intestine and leads a symbiotic rather than pathogenic lifestyle.

***

"To investigate the effects of F. foetens on metabolic disease, Zhou et al. used a mouse model of metabolic dysfunction–associated steatohepatitis. This disorder is characterized by fatty liver and liver inflammation and can progress to cirrhosis or liver cancer. Similar symptoms can be induced in mice by feeding them a high-fat diet for several weeks. Unexpectedly, Zhou et al. found that F. foetens reduced symptoms of steatohepatitis when inoculated into mice. By contrast, inoculation with C. albicans failed to protect against this liver condition, suggesting that the effect is species specific.

"How does F. foetens protect against metabolic dysfunction–associated steatohepatitis? Using an in vitro activity-based assay, Zhou et al. found that F. foetens selectively reduced the activity of the enzyme ceramide synthetase 6 (CerS6). CerS6 is expressed in intestinal epithelial cells, where it catalyzes the synthesis of ceramides—an important class of endogenous lipids. Notably, ceramides are exported to the bloodstream and promote the progression of fatty liver disease to metabolic dysfunction–associated steatohepatitis. Colonizing mice with F. foetens decreased intestinal CerS6 activity and reduced ceramide amounts in both the intestine and the bloodstream, whereas supplementing F. foetens–colonized mice with ceramide blunted the beneficial effects on disease progression. Thus, F. foetens reduces symptoms by inhibiting ceramide synthesis in the intestine.

"A resident intestinal fungus protects against metabolic disease
Fusarium foetens a filamentous fungus that stably colonizes the mammalian gut, secretes a metabolite called F. foetens compound 1 (FF-C1). FF-C1 binds to and inhibits ceramide synthetase 6 (CerS6) in the gut epithelium. This reduces ceramide pools in the bloodstream and protects against the development of metabolic dysfunction–associated steatohepatitis in a mouse model. Intestinal symbiotic fungi may be an untapped reservoir of possible therapeutic chemical compounds.

"Investigating the mechanistic basis for this effect, Zhou et al. found that F. foetens culture medium contains a medley of secreted metabolites and was sufficient to inhibit CerS6 in vitro. Using biochemical fractionation methods to isolate metabolites from the conditioned medium, they found that F. foetens compound 1 (FF-C1) bound tightly to CerS6 and inhibited its activity. FF-C1 is a naphthoquinone, a class of aromatic small molecules produced by many fungi (13). Administering FF-C1 was sufficient to limit the progression of steatohepatitis in mice, even in the absence of F. foetens.

***

"The findings of Zhou et al. suggest that the fungal microbiome may be a rich, untapped source of compounds with therapeutic potential. In addition to FF-C1, other compounds were isolated from F. foetens–conditioned culture medium that may selectively target different host pathways. It is also likely that other symbiotic fungi in the human gut produce compounds that interact with host pathways to promote health or limit disease. The results from this study should inspire further investigation of the human fungal microbiome to unlock the potential of these microscopic medicinal chemists.

Comment: the same evolutionary system that dhw derides as causing 99.9$ unnecessary organisms, produced this helpful one. It is obvious others will be found as god designed helpful forms for human support

https://www.nature.com/articles/s41586-025-09058-z

Animal and bacterial cells use nucleotidyltransferase (NTase) enzymes to respond to viral infection and control major forms of immune signaling including cGAS-STING innate immunity and CBASS anti-phage defence1-4. Here we discover a family of bacterial defence systems, which we name Hailong, that use NTase enzymes to constitutively synthesize DNA signals and guard against phage infection. Hailong protein B (HalB) is an NTase that converts deoxy-ATP into single-stranded DNA oligomers. A series of X-ray crystal structures define a stepwise mechanism of HalB DNA synthesis initiated by a C-terminal tyrosine residue that enables de novo enzymatic priming. We show that HalB DNA signals bind to and repress activation of a partnering Hailong protein A (HalA) effector complex. A 2.0 Å cryo-EM structure of the HalA–DNA complex reveals a membrane protein with a conserved ion channel domain and a unique crown domain that binds the DNA signal and gates activation. Analyzing Hailong defence in vivo, we demonstrate that viral DNA exonucleases required for phage replication trigger release of the primed HalA complex and induce protective host cell growth arrest. Our results explain how inhibitory nucleotide immune signals can serve as molecular guards against phage infection and expand the mechanisms NTase enzymes use to control antiviral immunity.

Comment: unfortunately only this abstract is available. Note these are considered molecular guards against phage infection, no thought involved.

dhw: It was Lynn Margulis (a prominent advocate of cellular intelligence) who first pointed out the massive importance of symbiosis for the progress of evolution. Looking at the current state of the world, I’m appalled by the fact that we humans, despite all our layers of conscious intelligence, continue to devote ourselves to the destructive chaos of competition rather than the constructive order of symbiosis.

DAVID: Your usual doom and gloom. Lots of research goes on in using symbiosis in agriculture.

dhw: So you don’t think that, for instance, peaceful cooperation is preferable to war? Racial harmony to racism? A helping hand to a fist in the face? I wrote the above because what is happening in Ukraine and Gaza and Sudan, and to a lesser extent with some of the social and economic policies now being pursued in the western world, sickens me to the core. I’m surprised that you don’t have similar feelings.

DAVID: You are always fussing about the darkness in some areas of the world. I have no control over happenings in Gaza, Ukraine or Sudan, so why should I fret? I do sympathize with the Ukraine people and their horrible history with Russia.

dhw: Sadly, this ties in with your attempts to brush aside the very existence of evil in your effort to ignore the problem of theodicy. I really can’t see why anyone should reject my proposal that peace is preferable to war, and my regret that humans so often opt for competition as opposed to symbiosis. I never imagined that this would lead to any sort of disagreement. I wasn’t asking you to go out on a crusade.

But that is exactly what your rhetoric calls for.

DAVID: Your usual doom and gloom. Lots of research goes on in using symbiosis in agriculture.

dhw: So you don’t think that, for instance, peaceful cooperation is preferable to war? Racial harmony to racism? A helping hand to a fist in the face? I wrote the above because what is happening in Ukraine and Gaza and Sudan, and to a lesser extent with some of the social and economic policies now being pursued in the western world, sickens me to the core. I’m surprised that you don’t have similar feelings.

DAVID: You are always fussing about the darkness in some areas of the world. I have no control over happenings in Gaza, Ukraine or Sudan, so why should I fret? I do sympathize with the Ukraine people and their horrible history with Russia.

Sadly, this ties in with your attempts to brush aside the very existence of evil in your effort to ignore the problem of theodicy. I really can’t see why anyone should reject my proposal that peace is preferable to war, and my regret that humans so often opt for competition as opposed to symbiosis. I never imagined that this would lead to any sort of disagreement. I wasn’t asking you to go out on a crusade.

dhw: It was Lynn Margulis (a prominent advocate of cellular intelligence) who first pointed out the massive importance of symbiosis for the progress of evolution. Looking at the current state of the world, I’m appalled by the fact that we humans, despite all our layers of conscious intelligence, continue to devote ourselves to the destructive chaos of competition rather than the constructive order of symbiosis.

DAVID: Your usual doom and gloom. Lots of research goes on in using symbiosis in agriculture.

dhw: So you don’t think that, for instance, peaceful cooperation is preferable to war? Racial harmony to racism? A helping hand to a fist in the face? I wrote the above because what is happening in Ukraine and Gaza and Sudan, and to a lesser extent with some of the social and economic policies now being pursued in the western world, sickens me to the core. I’m surprised that you don’t have similar feelings.

You are always fussing about the darkness in some areas of the world. I have no control over happenings in Gaza, Ukraine or Sudan, so why should I fret? I do sympathize with the Ukraine people and their horrible history with Russia.

DAVID: Your usual doom and gloom. Lots of research goes on in using symbiosis in agriculture.

So you don’t think that, for instance, peaceful cooperation is preferable to war? Racial harmony to racism? A helping hand to a fist in the face? I wrote the above because what is happening in Ukraine and Gaza and Sudan, and to a lesser extent with some of the social and economic policies now being pursued in the western world, sickens me to the core. I’m surprised that you don’t have similar feelings.

DAVID: symbiosis is always an advantage to help exchanges of nutrients.

dhw: It was Lynn Margulis (a prominent advocate of cellular intelligence) who first pointed out the massive importance of symbiosis for the progress of evolution. Looking at the current state of the world, I’m appalled by the fact that we humans, despite all our layers of conscious intelligence, continue to devote ourselves to the destructive chaos of competition rather than the constructive order of symbiosis.

Your usual doom and gloom. Lots of research goes on in using symbiosis in agriculture.

It was Lynn Margulis (a prominent advocate of cellular intelligence) who first pointed out the massive importance of symbiosis for the progress of evolution. Looking at the current state of the world, I’m appalled by the fact that we humans, despite all our layers of conscious intelligence, continue to devote ourselves to the destructive chaos of competition rather than the constructive order of symbiosis.

https://www.sciencedaily.com/releases/2025/04/250414162051.htm

"Scientists use small peptides to enhance symbiosis between plants and fungi, offering a sustainable alternative to artificial fertilizers. Plant biologists discover new plant molecule, CLE16, as well as a fungal CLE16 mimic, that encourage the beneficial symbiotic relationship between plants and fungi. CLE16 supplementation in crop fields could help reduce harmful chemical fertilizer use by replacing it with sustainable, long-lasting symbiotic plant-fungus relationships for important crops like soy, corn, and wheat.

***

"In a new study, the researchers identified a key molecule produced by plant roots, a small peptide called CLE16, that encourages plants and beneficial soil fungi to interact with each other. They say boosting this symbiotic relationship, in which the fungi provide mineral nutrients to the plants through CLE16 supplementation, could be a more natural and sustainable way to encourage crop growth without the use of harmful artificial fertilizers.

***

"'By restoring the natural symbiosis between plant roots and fungi, we could help crops get the nutrients they need without the use of harmful fertilizers."

"In this mutually beneficial relationship, soil-borne arbuscular mycorrhizal fungi supply plants with water and phosphorus, which the plants accept in exchange for carbon molecules. These exchanges occur by specialized symbiotic fungal tendrils, called arbuscules, burying themselves into plant root cells. Around 80% of plants can trade resources with fungi in this way. However, the traits that support this symbiosis have been weakened over centuries of agricultural plant breeding that prioritized creating crops with the biggest yields.

***

"To begin discovering and strengthening these traits, Mueller's lab started by growing a species of arbuscular mycorrhizal fungus together with Medicago truncatula, a small Mediterranean legume. Once the two had formed a symbiotic relationship, the researchers looked to see what genes were supporting this interaction.

"The legumes had started to express large amounts of a small signaling molecule called CLE16 -- a member of the CLE family of peptides. These small signaling molecules are present in many plant species yet have been relatively understudied. Until CLE16, the only plant CLE peptides scientists had studied were working against symbiosis.

***

"To confirm that CLE16 was promoting the symbiotic relationship, Bashyal added excess CLE16 to the soil to see what would happen. The extra dose of CLE16 caused the fungal arbuscules to become more robust and live longer, ultimately increasing the abundance of these nutrient-trading structures in the roots. The result was a self-amplifying pro-symbiosis signal: The more the beneficial fungus expanded inside the roots, the more CLE16 was produced by the plant, which then promoted even more fungal colonization.

"The team then did a series of experiments to understand how CLE16 was encouraging this interaction between plants and beneficial fungi. Their findings revealed that CLE16 promotes the symbiosis via the signaling protein CORYNE (CRN), a component of the CLAVATA receptor complex known for its roles in plant responses to the environment.

***

"Mueller's team showed that many arbuscular mycorrhizal fungi also produce their own CLE16-like peptides, which also promoted symbiosis when added to the soil. The researchers think that these fungal peptides imitate the plants' own CLE16 peptides, thus enabling the beneficial fungus to amplify symbiosis by binding to the same plant CRN-CLAVATA receptor complexes."

Comment: symbiosis is always an advantage to help exchanges of nutrients.

https://www.sciencedaily.com/releases/2025/03/250320144617.htm

"Mitochondria are the powerhouses in our cells, producing the energy for all vital processes. Using cryo-electron tomography, researchers at the University of Basel, Switzerland, have now gained insight into the architecture of mitochondria at unprecedented resolution. They discovered that the proteins responsible for energy generation assemble into large "supercomplexes," which play a crucial role in providing the cell's energy.

"Most living organisms on our planet-whether plants, animals, or humans -contain mitochondria in their cells. Their main function is to supply energy for nearly all cellular processes. To achieve this, mitochondria use the oxygen we breathe and carbohydrates from food to regenerate ATP, the universal energy currency of cells. This function is performed by proteins known as the respiratory complexes, which work together in the energy-generating process.

***

"Using state-of-the-art cryo-electron tomography, researchers led by Dr. Florent Waltz and Prof. Ben Engel at the Biozentrum of the University of Basel were able to create high-resolution images of the respiratory chain directly inside cells at a resolution never achieved before.

"'Our data show that the respiratory proteins organize in specific membrane regions of mitochondria, stick together and form one main type of supercomplex," explains Florent Waltz, SNSF Ambizione Fellow and first author of the study. "Using the electron microscope, individual supercomplexes were clearly visible -- we could directly see their structures and how they work. The respiratory supercomplexes pump protons across the mitochondrial membrane. The ATP production complexes, which act similarly to a watermill, use this flow of protons to drive ATP generation."

"The researchers examined mitochondria in living cells of the alga Chlamydomonas reinhardtii. "We were very surprised that all the proteins were actually organized in such supercomplexes," says Waltz. "This architecture might make ATP production more efficient, optimize electron flow, and minimize energy loss."

"In addition to the supercomplexes, the researchers were also able to examine the membrane architecture of the mitochondria more closely. "It's somewhat reminiscent of lung tissue: the inner mitochondrial membranes have many folds that increase the surface area to fit as many respiratory complexes as possible," says Engel."

Comment: as usual it is hard to imagine that chance mutations created this dynamic mechanism.

https://www.quantamagazine.org/how-metabolism-can-shape-cells-destinies-20250321/

“'Instead of thinking about the gene expression networks just happening to interact with metabolism, it’s really metabolism driving [developmental decision-making],” he said, “and gene expression networks are the tools by which that occurs.”

"This idea — that cell metabolism is an integral but unheralded part of the developmental process — isn’t fantastical. In another field of biology, epigenetics, researchers have already detailed the process by which metabolites turn genes on and off. But they needed the work of developmental biologists to connect more of the dots.

***

"Epigeneticists who study this process have, over the past few decades, elucidated a complex system by which proteins and enzymes activate or repress certain genes. The meters-long strand of DNA in every cell is wound around proteins called histones. With the help of specific enzymes, molecules that scientists call “chemical modifications” or “epigenetic marks” attach to the histones and cause the DNA to unspool, exposing different genes for activation. These modifications can thereby activate some genes and deactivate others, influencing the biochemical processes in a cell and therefore the functions that cell performs.

“'Those chemical modifications that decorate [histones] and modify gene expression — they’re metabolites, full stop,” said Finley, the cancer biologist. “Chemical modifications themselves are metabolites, and their removal is dependent on metabolites.”

***

"The nucleus’s metabolic activity was specific to the functions in that compartment, including epigenetic activity. “There are a lot of metabolic enzymes that are actually in the nucleus and are dynamically regulated in the nucleus,” said Wellen, who now heads a lab at the University of Pennsylvania. “We were really excited to find that.”

***

“'What is intriguing is that all of this is associated with a massive accumulation of metabolic enzymes in the nucleus,” said Żylicz, the developmental biologist. These enzymes make molecules, which then activate other enzymes that remove epigenetic marks and lay down new ones as cells grow, divide and take on different fates.

"During this period, the cell moves many enzymes(opens a new tab) from the cytoplasm and mitochondria to the nucleus. That way, the metabolites necessary for gene activity can be produced locally, in the nucleus, where they are needed, Żylicz said. “The moment where you reprogram the epigenome — that happens to be the same time when you’re also really using this nucleus as a metabolic compartment.”

***

“'This is particularly exciting because if changing metabolism can change cell fate in a meaningful way, there is the possibility that you might be able to manipulate that therapeutically, where aberrant decisions of differentiation are causal for the disease — like in many forms of cancer,” said Rutter, who was not involved in the study.

"In some ways, this interplay between metabolism and genes is obvious: We know that life is influenced by both its genes and its environment. This new, exciting field of research shows at a molecular level how the materials available to our cells influence their fates, and ours."

Comment: so, it is not just genes ordering everything around. There is an active interplay and feedback from metabolic enzymes directing the cells toward goals. This cannot happen by chance.

https://www.quantamagazine.org/a-new-chemical-view-of-ecosystems-20250305/

"The biological world is awash in chemical signals. Ants lead their nest mates to food with winding trails of pheromones, plants exude aerosols to warn their neighbors of herbivores, and everything you experience as “smell” is a molecule latching onto your nose. Some molecular messages find their targets; most linger unread in the environment. But sometimes, other species — chemical eavesdroppers, bystanders or visitors — can pick up and interpret the signals in their own way. If the message is powerful enough, the impact can ripple out across an ecosystem.

"In 2007, biologists named these potent molecules after a popular concept in ecology. “Keystone species,” such as starfish in Pacific Northwest tidepools, aren’t abundant, but they have outsize effects on the food web — making those species as crucial to their ecosystems as a load-bearing keystone in an archway. If they’re removed, the idea goes, the entire ecosystem could collapse into a different form. “Keystone molecules,” then, are rare chemicals that can structure, shape and alter connections between species across entire ecosystems.

***

"Now, a comprehensive study published in Science Advances has combined field work, chemical analysis and community ecology to lend fresh support to the keystone molecule theory(opens a new tab). Researchers studying pungent Alderia sea slugs in a California mudflat isolated molecules new to science from their unappetizing slime. As the scientists studied this cocktail and later introduced it to the mudflat, they recorded profound effects on other species and on the overall nature of the habitat.

“'One small, simple molecule can be tying together these seemingly unrelated species and whole ecosystem processes,” said study author Patrick Krug(opens a new tab), a marine biologist at California State University, Los Angeles. “It is now being recognized as this general phenomenon that we’ve just been kind of oblivious to.”

***

"In a 2013 paper, they identified four outstanding examples(opens a new tab): tetrodotoxin, a neurotoxin produced by many animals including the newts, pufferfish and octopuses; saxitoxin, which is made by algae and makes shellfish toxic to predators; pyrrolizidine alkaloids, a widespread plant-produced poison that deters herbivores and attracts insects; and dimethylsulfoniopropionate (DMSP), a sulfur-rich compound produced by marine algae.

"Across many ecosystems, these chemicals have widespread effects. DMSP, for example, is the ocean’s dinner bell: When the algae are eaten by krill and fish, the chemical leaches into the water and can form gas plumes over the ocean. Seabirds smell the plume from miles away. They follow it to feast on fish and then fly back to their nests, where they deposit excrement laden with nutrients that fuel plant growth on land.

***

"We are intuitively familiar with the power of chemical signals. The smell of baking bread or stinking garbage can completely alter our behavior. In the case of Alderia sea slugs, their chemistry overwhelms the local food web. (my bold)
***

"Krug’s experiment confirmed that when alderenes seep into the mud, they restructure the entire community. They drive species out. They affect the quality and content of the soil. They’re used as a reproductive defense by an unrelated species; they’ve even compelled an organism from a different animal phylum to evolve into a slug mimic. The rare chemical has become the main structural element within the mudflat ecosystem — like a keystone in an archway.

“'You have a single slug species making some pretty straightforward little chemical defenses, and it’s changing who’s there and who’s not there,” said Kubanek, who was not involved in the research. “The slug goo is having a really big effect on the whole ecosystem.'”

Comment: animals and plants speak to each other in chemical signals, which create automatic responses as my bold insists. That some key molecules shape ecosystems is an amazing but a logical discovery.

https://www.sciencedaily.com/releases/2025/01/250122145817.htm

"The cells that line your small intestine have to balance two seemingly contradictory jobs: absorbing nutrients from food, while keeping a wary eye out for pathogens trying to invade your body.

"'This is a surface where pathogens can sneak in," says La Jolla Institute for Immunology (LJI) Assistant Professor Miguel Reina-Campos, Ph.D. "That's a massive challenge for the immune system."

"So how do immune cells keep the gut safe? New research led by scientists at LJI, UC San Diego, and the Allen Institute for Immunology shows that pathogen-fighting immune cells called tissue-resident memory CD8 T cells (TRM cells) go through a surprising transformation -- and relocation -- as they fight infections in the small intestine.

"In fact, these cells literally rise up higher in the tissue to fight infections before pathogens can spread to deeper, more vulnerable areas.

***

"Their work showed that the small intestine holds two types of TRM cells. These cells are split between the tiny, finger-like "villi" structures that line the small intestine or the "crypts" between the protruding villi.

"The researchers found that progenitor-like TRM cells live closer to the crypts between the villi. On the other hand, differentiated TRM occupy more exposed regions at the top of the villi. "Differentiated immune cells are more exposed at the top of the villi, and that's where they have a better ability to protect you from infections," says Reina-Campos.

Meanwhile, a reserve population of progenitor-like TRM cells continues to lie low in the "crypts. "These cells can replenish the pool of effector T cells, so the immune system keeps them as back-ups in the deeper parts of the tissue," adds Reina-Campos.

***

"Looking at small intestines after a viral infection, the scientists found that the gut releases chemical signals to instruct immune cells where to go and what to do. "This study offers a new resource for finding signals that position immune residents to strengthen our gut immunity," says Reina-Campos.

***

"The new study gives researchers a detailed look at how immune cells interact with each other and their cellular gameboard."

Comment: these specialized T cells are under tight chemical controls to place them exactly where needed. The control proteins are yet to be delineated. Another pure example of design.

https://www.sciencedaily.com/releases/2025/01/250110143657.htm

"Plant scientists from the University of Nottingham, in collaboration with Shanghai Jiao Tong University, have identified how abscisic acid (ABA), a plant hormone known for its role in drought response, influences root growth angles in cereal crops such as rice and maize.

***

"The study highlights how ABA and auxin, another key hormone, work together to shape root growth angle, providing a potential strategy to develop drought-resistant crops with improved root system architecture.

***

"Plants rely on their root systems, the primary organs for interacting with soil, to actively seek water. In drought conditions, water often depletes in the topsoil and remains accessible only in the deeper subsoil layers. Abscisic acid (ABA) plays an important role in helping plants adapt to these challenging conditions. This new study gives new insights into how ABA changes root growth angles to enable plants to reach out deeper subsoils in search of water.

"The researchers discovered a new mechanism where ABA promotes the production of auxin, which enhances root gravitropism to grow them at steeper angles in response to drought. Experiments showed that plants with genetic mutations that block ABA production had shallower root angles and weaker root bending response to gravity compared to normal plants. These defects were linked to lower auxin levels in their roots. By adding auxin externally, the researchers restored normal root growth in these mutants, showing that auxin is key to this process."

Comment: Clearly a designed system to direct root growth. Plants could not have adapted to land without this mechanism available in the beginning.

https://www.the-scientist.com/ts-digest/issue/what-s-the-difference-between-a-voltage-c...

"During gestation, the placenta takes on the roles of many of the fetus’ developing organs and serves as a barrier between parent and child. Critical to this is the outermost layer of the organ, the syncytiotrophoblast (STB), a single, multinucleated cell that forms from repeated fusion events between mononucleated cytotrophoblasts (CTB). In addition to producing pregnancy hormones, the STB plays important roles in nutrient and waste exchange and metabolism. Unlike many organs, which achieve multifunctionality through specialized cell types, the STB is a single giant cell with billions of individual nuclei.

“'Despite it being one cell, there might be specialized regions that are doing different functions,” said Madeline Keenen, a biochemist at Duke University. Researchers believe that one way this massive cell possibly achieves this is through specialized gene expression. “These nuclei could actually act as independent agents,” she added. Keenen, who has studied genome compaction and regulation in mononucleated cells, wanted to explore how the STB regulates its billions of genomes. Given the cell’s syncytial structure, single-cell approaches were limited, so she turned to single-nucleus RNA sequencing (snRNA-seq).

"In a bioRxiv preprint, Keenen and her colleagues reported their findings from snRNA-seq experiments on trophoblast organoids derived from human placental tissue.1 They identified three subpopulations of nuclei present in both models: STB-1, STB-2, and STB-3. The first population exhibited an intermediate gene expression profile, indicative of a population likely transitioning from CTB to STB. STB-2 nuclei expressed genes involved in oxygen sensing while STB-3 nuclei exhibited a more differentiated gene profile characterized by more STB markers and transport molecules.

"The nuclei subtypes identified by Keenen and her team are similar to the subpopulations that were recently identified in first trimester and full-term placental tissues, demonstrating the strength of these newer organoid models."

Comment: the placenta is a nine-month organ, supplying all of the fetus's needs, oxygen and nutrients and clearing CO2. It is impossible to imagine how this could be evolved stepwise as proposed by Darwin evolutionary mechanics. Only design fits.