Viruses in gut microbes

Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells


Extended Data Figure 3 | Generation of H3.3-isoform-specific antibodies. Related to Fig. 1. a, Schematic of amino acid sequence differences for the canonical histones H3.1 and H3.2 versus the histone variant H3.3. H3.3 differs from H3.2 or H3.1 at only 4 or 5 amino acids, positions 31, 87, 89, 90 and 96, as indicated.

My comment: The difference in amino acid substitutions can be linked from nutrient-dependent RNA-directed DNA methylation to the RNA-mediated de novo creation of olfactory receptor genes and experience-dependent classically conditioned behaviors that link nutrient-dependent pheromone-controlled feedback loops and chromatin loops in species from microbes to man via the conserved molecular mechanisms of the biophysically constrained chemistry of protein folding during life history transitions that are exemplified in the honeybee model organism.
Kohl (2012) conclusion: Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000).
Kohl (2013) conclusion:  Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.
Kohl (2013) excerpt: The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, diseases of the X chromosome, learning and memory, as well as conditioned responses to sensory stimuli (Kohl, 2012).
The facts that 1) biodiversity is nutrient-dependent and that 2) metabolic networks are linked to genetic networks via RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all genera may not become clearer. The links from 1) viruses and viral microRNAs to entropic elasticity and 2) from the anti-entropic effects of nutrient-dependent microRNAs that enable fixation of the RNA-mediated amino acid substitutions in the organized genomes of different populations will continue to become clearer, each time endogenous retroviral element silencing is considered.  Endogenous retroviruses (ERVs) include human endogenous retroviruses (HERVs) that link the metabolism of nutrients by our gut microbes to the nutrient-dependent pheromone-controlled biological basis of cell type differentiation in all genera. See for example:
How Modern Life Depletes Our Gut Microbes

The tribe had about 50 percent more ecological diversity than the average American has, Dominguez-Bello and her colleagues reported Friday in the journal Science Advances.

My comment: The link from ecological variation to ecological diversity is RNA-mediated. The balance of viral microRNAs and nutrient-dependent microRNAs links ecological variation from the microRNA/messenger RNA balance to the nutrient-dependent physiology of reproduction. Successful reproduction links the fixation of RNA-mediated amino acid substitutions to cell type differentiation and ecological adaptations in all genera.
Chowing Down On Meat, Dairy Alters Gut Bacteria A Lot, And Quickly

“These bacteria are members of a community that have lived in harmony with us for thousands of years,” says Kashyap, who wasn’t involved in the study. “You can’t just pick out one member of this whole team and say it’s bad. Most bacteria in the gut are here for our benefit, but given the right environment, they can turn on us and cause disease.”

My comment: The bacteria contain the viruses that link entropic elasticity and the anti-entropic epigenetic effects of nutrients via RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate all cell types in all organisms of all species.
How Bacteria In The Gut Help Fight Off Viruses

“We were very, very surprised that a bacteria component offered powerful protection against a viral infection,” Gewirtz says. “The basic thinking before was that bacteria have certain components on their surface that activate the immune system to fight bacteria, not viruses.”

My comment: The role of viruses in cell type differentiation was placed into the context of human ecological adaptation in 1999 and in 2003 in books by Greg Bear.
Gut Bacteria Might Guide The Workings Of Our Minds

Gut microbes may also communicate with the brain in other ways, scientists say, by modulating the immune system or by producing their own versions of neurotransmitters.

My comment: The link from viral microRNAs and nutrient-dependent microRNAs to immune system function is RNA-mediated. Until the role of viruses and viral microRNAs is acknowledged, researchers will continue to be confused about aspects of biologically based cell type differentiation that must be known before “Combating Evolution to Fight Disease” can be successful.
See also: What happens when populations hit the borders of expansion?

Why does a species not adapt to an ever-wider range of conditions, gradually expanding its geographical range? In their paper published on May 5 in PNAS (Proceedings of the National Academy of Sciences), Jitka Polechova and Nick Barton at the Institute of Science and Technology Austria (IST Austria) seek to answer this question, which lies at the interface between ecology and evolution.

My comment: Nutrient uptake lies at the interface between ecological variation and RNA-mediated ecological adaptation. See: Evolutionary Rewiring. Without re-evolution of the bacterial flagellum, which occurred ‘over-the-weekend’ the organisms would have starved to death. There is no experimental evidence that links ecological variation to ecological adaptations via evolution, which suggests that the interface in the claims of Jitka Polechova and Nick Barton is merely another aspect of neo-Darwinian theory that should be promptly dismissed. Alternatively, an explanation of why evolution did not occur during ~2 billion years should be offered in the same context as the century old theories about mutations that population geneticists incorporated into their ridiculous theories. See: Scientists discover organism that hasn’t evolved in more than 2 billion years.
Extreme evolutionary stasis does not fit the picture that evolutionary theorists have presented. But, clearly, they must claim that extreme stasis and evolution over the weekend fit, or else their other claims become increasingly suspect — as if they were never based on experimental evidence of biologically-based cause and effect.

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