Energy-dependent RNA-mediated immunity (1)

By: James V. Kohl | Published on: March 4, 2016

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Regulatory evolution of innate immunity through co-option of endogenous retroviruses

Excerpt:

The analysis revealed a primate-specific element that orchestrates the transcriptional response to interferons. Selection can therefore act on selfish genetic elements to generate novel gene networks.

Reported as: A copy-and-paste gene regulatory network

Excerpt:

Chuong et al. provide evidence that concerted processes, involving endogenous retroviruses (ERVs), which are remarkably abundant in mammalian genomes, have contributed to the evolution of the regulatory systems that control the mammalian immune system (6).

My comment: Ecological variation is linked from nutritional epigenetics to regulation of the mammalian immune system and biophysically constrained RNA-mediated protein folding chemistry, which is linked to supercoiled DNA in all organized genomes. The complexity of how supercoiled DNA protects organized genomes from virus-driven entropy cannot be placed into the context of energy-dependent regulatory systems. Simply put, you cannot start with an innate immune system that regulates itself. You must start with the energy that regulates all metabolic networks and genetic networks.

The text and the narrative from this poster session will be available on March 16th. I am posting it here in advance because the news about regulatory evolution has been placed into the context of innate immunity by theorists who do not understand how biophysically-constrained energy-dependent cell type differentiation occurs in species from microbes to humans. Evolution does not regulate itself. The innate immune system links nutrient-dependent immune system function to supercoiled DNA, which protects all organized genomes from virus-driven entropy.

From hydrogen-atom transfer in DNA base pairs to ecosystems

Abstract:

This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on DNA base pairs in solution and RNA-mediated amino acid substitutions to chromosomal rearrangements via pheromone-controlled changes in the microRNA / messenger RNA balance. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent & pH-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Critical limits for enhanced medical care already include what is known about the RNA-mediated physics and chemistry of biologically-based ecological, social, neurogenic and socio-cognitive niche construction. The epigenetic landscape is clearly linked to the physical landscape of supercoiled DNA and top-down causation is manifested in increasing organismal complexity in species from microbes to humans. In all vertebrates and invertebrates the reciprocal relationships of species-typical nutrient-dependent & pH-dependent morphological and behavioral diversity are enabled by microRNAs, adhesion proteins, and pheromone-controlled reproduction. Ecological variation and biophysically constrained natural selection of nutrients cause the RNA-mediated behaviors that enable ecological adaptations, which include development of the brain during life history transitions. Ideas from population genetics typically exclude ecological factors, which must be linked to cell type differentiation. Theories are integrated with an experimental evidence-based approach that establishes what is currently known in the context of this mammalian model.

Summary:

The prenatal migration of GnRH neurosecretory neurons allows nutrient chemicals and human pheromones to alter GnRH pulsatility, which modulates energy-dependent hydrogen-atom transfer in DNA base pairs linked from ingestive behavior to metabolic networks and genetic networks during the concurrent maturation of the neuroendocrine, reproductive, and central nervous systems via the physiology of reproduction, sex differences in behavior, and other behavioral differences.

Thermodynamic cycles of protein biosynthesis and degradation link the biophysically-constrained chemistry of nutrient energy-dependent RNA-mediated alternative splicings and protein folding from receptor-mediated amino acid substitutions to supercoiled DNA. The physiology of reproduction links chromosomal rearrangements to species-specific ecological adaptations. Weekend evolution of the resurrected flagellum [1] appears to be an energy-dependent pheromone-controlled ecological adaptation. Feedback loops facilitate the resurrection. It was placed into the context of nutrient energy-dependent immune system function. Two energy-dependent amino acid substitutions were linked to the rapid development of a complex functional structure. The energy-dependent RNA-mediated adaptation was biophysically constrained.
Chemists have since used femtosecond blasts of UV light to stimulate DNA repair via hydrogen-atom transfer in the base pairs guanine (G) and cytosine (C), which were in a solution.[2] The reactions appear to link the speed of light [3] on contact with water from an anti-entropic energy source to the de novo creation of nucleic acids [4] and to RNA-mediated DNA repair .[5] An astrobiological representation of top-down causation [6] links what has been reported in the context of molecular epigenetics and RNA-mediated cell type differentiation [7-10]
The speed of the chemical reactions appears to link Schrodinger’s claims about the anti-entropic energy of sunlight [11] to the nutrient energy-dependent stability of organized genomes via hydrogen-atom transfer in DNA base pairs in solution [12] and to pheromone-controlled RNA-mediated DNA repair in the context of the physiology of reproduction and supercoiled DNA.[13] Chromosomal rearrangements link supercoiled DNA from chemical ecology to organized genomes and biodiversity.[14] Supercoiled DNA appears to protect all living genera from virus-driven pathology in the context of ecological speciation.[15]
That likelihood was reported in the context of an article that links transgenerational epigenetic inheritance in all living genera to what we eat in the context of a yeast model organism.[16] The yeast model organism has repeatedly been linked to human cell type differentiation via nutrient-dependent pheromone-controlled epigenetic effects.[17] The yeast model organism also was linked to ecological speciation in nematodes in the context of splicing variations;[18] neuronal imaging in roaming C. elegans; [19] and “Distinct Circuits for the Formation and Retrieval of an Imprinted Olfactory Memory.”[20] Feedback loops and circuits link ecological adaptations in behavior to predatory nematodes with teeth.[21]
Chemical ecology appears to drive invertebrate and vertebrate species-specific adaptations via ecological, social, neurogenic, and socio-cognitive niche construction. Nutrients are metabolized to pheromones that epigenetically effect hormones. The hormones affect behavior in the same way food odors classically condition behavior associated with food preferences. In mammals, feedback loops link the epigenetic effects of olfactory/pheromonal input on gonadotropin releasing hormone (GnRH) neurosecretory neurons to changes in brain tissue. For example: glucose and pheromones alter the secretion of GnRH and luteinizing hormone (LH). Secretion of LH is the measurable proxy for genetically predisposed differences in hypothalamic GnRH pulse frequency and amplitude and the downstream effects of GnRH, which is the central regulator of genetically predisposed nutrient-dependent individual survival and pheromone-controlled species survival.
This model of systems biology [22] represents the conservation of top-down causation and bottom-up organization paired with hormone activation of behaviors via the 1) thermodynamics of nutrient stress-induced and social stress-induced intracellular changes in the microRNA / messenger RNA (miRNA/mRNA) balance; 2) alternative splicings linked to intermolecular changes in DNA (e.g., in genes); 3) non-random experience-dependent stochastic variations in de novo gene expression; 4) biosynthesis of odor receptors; 5) the required gene-cell-tissue-organ-organ system pathway that links sensory input directly to gene activation in neurosecretory cells and to miRNA-facilitated learning and memory in the adaptively evolved mammalian brain; and 6) the reciprocity that links the thermodynamics of gene expression to behavior and altered organism-level thermoregulation in species from microbes to man.
The complexity of linking energy-dependent RNA-mediated amino acid substitutions from DNA base pairs in solution to the physiology of reproduction and to biodiversity will probably help others understand why models that link atoms to ecosystems have been virtually ignored for two decades. Now, the models link angstroms to ecosystems. Many behavioral development specialists tend to examine only one or two levels of lineage-specific links. Typically, their levels of examination do not include links from quantum physics to energy-dependent RNA-mediated events or links from chemical ecology to the de novo creation of olfactory receptor genes and links from amino acid substitutions to differences in behavior.
Examples of nutrient-dependent RNA-mediated amino acid substitutions linked to behavior clarify the involvement of seemingly futile thermodynamic control of intracellular and intermolecular interactions, which result in de novo creation of olfactory receptor genes. Thermodynamically controlled cycles of RNA transcription and protein degradation are responsible for organism-level changes in pheromone production, which enable accelerated changes in the miRNA/mRNA balance and thermoregulation of controlled nutrient-dependent ecological adaptation.
In this mammalian model, food odors associated with nutrient uptake and species-specific pheromones associated with conspecifics control changes in the miRNA/mRNA balance. Those changes enable differential gene expression in GnRH neurons during developmental transitions required for successful nutrient-dependent pheromone-controlled reproduction, which occurs in species from microbes to man. Recent data extend this mammalian model of conserved molecular mechanisms across the continuum of ecological adaptations to selection for phenotypic expression associated with pheromones in a human population.
Across species comparisons of epigenetic effects on pangenomic microbial nutrient-dependent reproduction and on hormone-controlled invertebrate and vertebrate social and sexual behavior[22] indicate that pheromones alter cytogenetic parameters [23] and the development of the brain and behavior via molecular mechanisms that are conserved in species from microbes to humans.
Mitochondria link nutrient-stress and social stress from epigenetic effects on hormones to affects of hormones on behavior.[24] RNA-mediated amino acid substitutions link stress to behavioral development during life history transitions. Mutations are biophysically constrained by the availability of food and absence of social stress. Biophysically constrained physiological controls are required in the context of ecological adaptation. Others have linked nutrient-dependent changes in the miRNA/mRNA balance, adhesion proteins, and biophysically constrained alternative splicings of RNA to healthy longevity and to virus-driven pathology. [25-26]Conclusion: An environmental drive links nutrient uptake in unicellular organisms to pheromone-controlled socialization in insects. This model makes it clearer that, in mammals, nutrients associated with food odors and pheromones cause biophysically constrained changes in hormones, which have developmental affects on the control of behavior [27] in nutrient-dependent reproductively fit individuals that signal their fitness via pheromones.

[1] Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

[2] Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution.

[3] Photonic Maxwell’s Demon

[4] Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism

[5] Observation of Gravitational Waves from a Binary Black Hole Merger

[6] Re-criticizing RNA-mediated cell evolution: a radical perspective

[7] From Fertilization to Adult Sexual Behavior

[8] Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

[9] Long non-coding RNAs in innate and adaptive immunity

[10]Defective control of pre–messenger RNA splicing in human disease

[11] What is Life?

[12] Conditional iron and pH-dependent activity of a non-enzymatic glycolysis and pentose phosphate pathway

[13] Structural diversity of supercoiled DNA

[14] Metabolic Reprogramming with a Long Noncoding RNA

[15] New insights into the hormonal and behavioural correlates of polymorphism in white-throated sparrows, Zonotrichia albicollis

[16] The metabolic background is a global player in Saccharomyces gene expression epistasis

[17] Dynamics of epigenetic regulation at the single-cell level

[18] A new view of transcriptome complexity and regulation through the lens of local splicing variations

[19] Pan-neuronal imaging in roaming Caenorhabditis elegans

[20] Distinct Circuits for the Formation and Retrieval of an Imprinted Olfactory Memory

[21] System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes

[22] Nutrient-dependent/pheromone-controlled adaptive evolution: a model

[23] Role of olfaction in Octopus vulgaris reproduction

[24] Cytogenetic approaches for determining ecological stress in aquatic and terrestrial biosystems

[25] Mitochondrial functions modulate neuroendocrine , metabolic, inflammatory, and transcriptional responses to acute psychological stress

[26] Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

[27]Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

Narrative:

My name is James Kohl and I am a medical laboratory scientist. I have performed testing in different departments of medical laboratories. My experiences led me to update this model to include what is known about the role that nutrient-dependent microRNAs play in linking energy transfer to biologically-based cause and effect.
For comparison, behavioral ecologists tend to focus on evolutionary causes. Some of them may not know that behavior must link nutrient-dependent chemotaxis and phototaxis from ecological variation to the physiology of reproduction and ecological adaptations. The behaviors that link chemotaxis and phototaxis are energy-dependent.
That explains why physicists, chemists, and molecular biologists link the epigenetic landscape to the physical landscape of biophysically constrained supercoiled DNA. They don’t start from a gene-centric theory. Instead, they extend links from atoms to ecosystems across disciplines. That fact is addressed in this model of biologically-based top-down causation.
I start with
Thermodynamic cycles of protein biosynthesis and degradation. The cycles link energy-dependent protein folding to supercoiled DNA.
The physiology of reproduction links chromosomal rearrangements to species-specific ecological adaptations.
For example, the bacterial flagellum is an energy-dependent pheromone-controlled ecological adaptation. Researchers linked two nutrient-dependent amino acid substitutions to the weekend development of the flagellum, which allowed Pseudomonas fluorescens to respond to chemical cues associated with light.
Feedback loops link the chemical cues and the light from chemotaxis and phototaxis to the nutrient-dependent resurrection of the genetically edited-out missing flagellum. Amino acid substitutions link the feedback loops to nutrient energy-dependent immune system function and the physiology of reproduction. Two energy-dependent amino acid substitutions were linked to the rapid development of a complex functional structure that some behavior ecologists may claim evolved.
For contrast, chemists have since used femtosecond blasts of UV light to stimulate nutrient-dependent DNA repair via hydrogen-atom transfer in base pairs in solution. The chemical reactions link the speed of light on contact with water from the anti-entropic energy of the sun to the creation of nucleic acids, which link base pair changes to energy-dependent RNA-mediated DNA repair. The femtosecond blasts of UV light can be placed into the context of an astrobiological representation of top-down causation. That’s how astrophysicists can help link what has been reported in the context of molecular epigenetics to RNA-mediated cell type differentiation.
My focus is on chemical ecology because two of the most commonly studied energy-dependent epigenetic modifications link changes in base pairs to RNA-mediated amino acid substitutions and protein folding via nutrient-dependent DNA methylation.
The energy-dependent creation of microRNAs is the largest contributor to epigenetic changes associated with the structure of supercoiled DNA and healthy longevity via methylation.
Ecologists cannot link epigenetic effects to behavior via evolution if they skip Schrodinger’s answer to his question “What is Life.” Most of them also skip from Darwin’s nutrient-dependent “conditions of life” and simply claim that species evolve. Schrodinger placed what is now known about ecological variation; nutrient-dependent microRNAs; and RNA-mediated DNA repair into the context of weekend evolution of the bacterial flagellum. He started with the sun’s anti-entropic energy. That’s what this model does.
The citations to articles link the speed of light on contact with water from quantum physics to the creation of nucleic acids and microRNA flanking sequences. The microRNA flanking sequences link nutrient-dependent hydrogen-atom transfer in DNA base pairs in solution to RNA-mediated amino acid substitutions and cell type differentiation in all living genera.
Examples that link nutrient-dependent microRNAS to RNA-mediated events have been placed into the context of this mammalian model. More than 47,000 published works link nutrient-dependent microRNAs to cell type differentiation in species from microbes to humans.
In this model, the experimental evidence converges. The decapeptide hormone, gonadotropin releasing hormone (GnRH) links the nutrient-dependent creation of microRNAs to the innate immune system. The nutrient-dependent immune system is linked to the physiology of reproduction via pheromone-controlled systems biology and behavior.
Food odors associated with nutrient uptake and species-specific pheromones control GnRH-linked changes in the nutrient energy-dependent microRNA/messenger RNA balance. Changes in base pairs enable differential gene expression in GnRH neurons during developmental transitions. The energy-dependent transitions are required for successful nutrient-dependent pheromone-controlled reproduction. Recent data extends this mammalian model of conserved molecular mechanisms across the continuum of ecological adaptations via selection for phenotypic expression associated with pheromones in human populations.
The term epigenetics is used to describe heritable genetic modifications that are not attributable to changes in the primary DNA sequence. In this model, epigenetic modifications link hydrogen-atom transfer in DNA base pairs in solution from RNA-mediated amino acid substitutions to gene expression. The creation of genes and epigenetic effects on gene expression underpin the development, regulation, and maintenance of all normal cells.
Nutritional epigenetics links all other environmental factors from base pair changes to microRNAs, adhesion proteins and supercoiled DNA via RNA-mediated events.
For example, nutrients link the prenatal migration of GnRH-secreting neurons, which allows food odors and human pheromones to alter the GnRH pulse. The GnRH pulse modulates energy-dependent hydrogen-atom transfer in DNA base pairs in all body fluids. The hydrogen-atom transfer in DNA base pairs links what mammals eat to metabolic networks and genetic networks during the concurrent maturation of the neuroendocrine, reproductive, and central nervous systems via the physiology of reproduction, sex differences in behavior, and other behavioral differences.
So far as I know there is no other model of biophysically constrained protein folding chemistry that links energy from epigenesis to epistasis in species from microbes to humans.
See also:
https://rna-mediated.com/energy-dependent-rna-mediated-immunity-2/