Energy dependent RNA-mediated immunity (2)

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

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Neuroscience of Early-Life Learning in C. elegans

“We have long been recording behavior in worms, but we and others have concluded that, if you want to get physiologically relevant neural activity patterns, you have to look at neurons inside a behaving animal,” Samuel explained. “Only in that context are all feedback loops intact, where behavioral output modulates neural activity which, in turn, shapes behavior.”

As all serious scientists continue to link ecological variation to ecological speciation via nutrient-dependent pheromone-controlled reproduction in species from microbes to humans, my antagonists have all but disappeared.
Clearly, it is time to finally begin discussion of how virus-driven energy theft links hydrogen-atom transfer in DNA base pairs in solution from mutations to pathology instead of from nutrient-dependent RNA-mediated DNA repair via amino acid substitutions to supercoiled DNA, which protects organized genomes from virus-driven entropy.
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 early-life learning and 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. Ecological speciation in nematodes clearly links what they eat to biodiversity via the innate immune system and the physiology of reproduction, which is how ecological adaptations occur in all living genera.
See for example: Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution. My comment on this article was removed and replaced with a “response” by the authors. I forced them to admit that “The major antigenic changes of the influenza virus are primarily caused by a single amino acid near the receptor binding site.”
See also the comment by Roy Niles on Neuroscience of Early-Life Learning in C. elegans.
An editor at The Scientist warned me not to respond with any more off topic claims. It has since become perfectly clear that he knew my claims were about to expose the nonsense that has since been touted about sensory input, the immune system, learning and ecological adaptation via nutrient-dependent RNA-mediated amino acid substitutions in all living genera.

RNA-mediated molecular epigenetics and virus-driven entropy

Abstract: Energy-dependent molecular epigenetics support Einstein’s complete molecular mechanical theory via established links from microRNA flanking sequences to DNA base pair substitutions and amino acid substitutions in adhesion proteins. The adhesion proteins include heat shock proteins that link the epigenetic landscape to biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry and cell type differentiation via the structure and function of supercoiled DNA. Einstein’s theory fits into the context of Darwin’s “conditions of life” via the de novo creation of nucleic acids; the nutrient-dependent function of the ribosome; and the de novo creation of olfactory receptor genes. De novo gene creation is the “holy grail” of biophysically constrained chemistry and biologically-based cause and effect. The discoveries reviewed here link the nutrient-dependent microRNA/messenger RNA balance from metabolic networks to genetic networks and to healthy longevity or virus-driven pathology in the context of what is known about all model organisms.

Summary:

The Zika virus and other viruses steal energy that links odors and the nutrient-dependent prenatal migration of GnRH neurosecretory neurons to pheromones that also alter the HPG and HPA axes. GnRH pulsatility modulates energy-dependent hydrogen-atom transfer in DNA base pairs in blood that links 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, which are linked by RNA-mediated amino acid substitutions to morphological phenotypes and behavioral phenotypes.

Physics
Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight) — Erwin Schrödinger (1944)

Chemistry
The quantised nature of light and energy is central to all of chemistry. It explains how matter and light interact – why grass is green and the sky is blue – as well as providing the basis of all the spectroscopic methods that enable us to decode the structures of molecules. — Philip Ball (2005)

Molecular Epigenetics

The authors note that on page 17184, right column, first paragraph, line 4, “effect” should instead appear as “affect.” — Bruce McEwen (2013)

Nutritional epigenetics. Energy-dependent molecular mechanisms link Einstein’s complete molecular mechanical theory from microRNA flanking sequences to base pair substitutions in DNA and to RNA-mediated amino acid substitutions in adhesion proteins via the ribosome. The adhesion proteins include heat shock proteins that link biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry to cell type differentiation and supercoiled DNA. [1-2]

Metabolic energy-dependent alternative splicing (AS) catalyzes the removal of intronic sequences and the joining of selected exons. Biophysically constrained nutrient-dependent combinatorial differences in joined sequences link thermodynamic cycles of protein biosynthesis and degradation to the pH-dependent creation of multiple splice-variants.The splice variants link hydrogen-atom transfer in DNA base pairs in solution from the energy-dependent origin of nucleic acids, the “RNA-world,” and the genetic code to the creation of different proteins from a single gene via pH and the biophysically constrained chemistry of RNA-mediated protein folding. [3-4]For example, metabolic energy links guanine nucleotide binding proteins (G proteins) to the experience-dependent de novo creation of monoallelic G protein-coupled receptors (GPCRs). Ligand-receptor binding links the de novo creation of olfactory receptor genes, which are GPCRs, to the creation of other receptors such as photoreceptors. [5]Nutrient-dependent de novo gene creation and chemotaxis coordinate phototaxis and responses to other sensory input throughout life history transitions in all living genera. [6] Sensory input links the epigenetic landscape to the physical landscape of supercoiled DNA, which appears to protects all organized genomes from virus-driven entropy.

Viruses-driven pathology. Retroviral integrase catalyses the integration of viral DNA into host target DNA. [7] Viruses enter cells and they steal metabolic energy to replicate. [8] The stolen energy is required to link AS to the de novo creation of receptors that allow different nutrients to enter different cell types. Theoretically, this is how the an accumulation of viruses prevents nutrient-dependent cell type differentiation. The viruses link perturbed protein folding to pathology via metabolic networks and genetic networks in the context of the Precision Medicine Initiative.[9]

Neo-Darwinian theorists ignore biophysically constrained RNA-mediated protein folding chemistry. They use statistical inferences and assumptions to link definitions of mutation to definitions of evolution. They link evolution to biodiversity in different species. [10]

Neo-Darwinists typically do not include the role of virus-driven pathology for comparison to the role of nutritional epigenetics in the context of healthy longevity. They typically fail to link transgenerational epigenetic inheritance from the physiology of nutrient-dependent pheromone-controlled reproduction in soil bacteria to the bull sperm microRNAome via nutrient-dependent microRNAs and biophysically constrained protein folding chemistry in all living genera.[11]

More than 47,000 published works link nutrient energy-dependent microRNAs to biophysically constrained RNA-mediated DNA repair and cell type differentiation. The most recent addition linked a specific microRNA DNA repair.[12]

Many recent news reports continue to claim the conserved molecular mechanisms and pathways of cell type differentiation via DNA repair may not link unicellular life to multicellular life.[13] Theorists and science news journalists who fail to link unicellular life to multicellular life via changes in the nutrient-dependent microRNA/messenger RNA balance and/or virus-driven pathology exemplify a failure that is addressed in the context of the integrated facts about microRNAs, which are displayed here

For example, the quality of foraging in crustaceans and insects links microRNA flanking sequences from sunlight to energy metabolism and genetic networks via amino acids and transgenerational epigenetic inheritance of sex differences in morphological and behavioral phenotypes in bulls and cows.[14] Conserved molecular mechanisms link nutrient energy-dependent changes in microRNAs to cell type differentiation and morphological and behavioral phenotypes of humans. [15]

In the context of what is currently known about the links from atoms to ecosystems in all invertebrates and all vertebrates, it has become obvious that viruses steal the nutrient dependent-energy that links hydrogen-atom transfer in DNA base pairs in solution to cell type differentiation in all living genera.Biophysically constrained RNA-mediated protein folding chemistry links UV light to chemotaxis, phototaxis, learning, memory and supercoiled DNA in the honeybee model organism. Nutrient-dependent metabolic networks and genetic networks link RNA-mediated DNA repair and supercoiled DNA to protection against virus-driven entropy in all organized genomes. [16-18]A drug that is commonly used to prevent the model organism C. elegans from laying eggs appears to alter nutrient energy-dependent RNA-mediated DNA repair via microRNAS that link pH, temperature, and oxygen levels from the absence of stress to healthy longevity. [19] The nematode may be the first model organism used to link virus-driven energy theft to pathology in the context of what is known about the nutrient-dependent innate immune system of all cell types in all living genera; the physiology of reproduction; and how ecological variation is linked to ecological adaptation in the context of speciation. (P. pacificus is an adapted C. elegans.)

1] The phylogenetic utility and functional constraint of microRNA flanking sequences

[2] Structural diversity of supercoiled DNA

[3] UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair

[4] Phosphorylation -Mediated Regulation of Alternative Splicing in Cancer

[5] An Epigenetic Signature for Monoallelic Olfactory Receptor Expression

[6] Cyanobacteria use micro-optics to sense light direction

[7] Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function

[8] Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

[9] RNA-Mediated Regulation of HMGA1 Function

[10] An expanded sequence context model broadly explains variability in polymorphism levels across the human genome

[11] The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

[12] miR-30e controls DNA damage-induced stress responses by modulating expression of the CDK inhibitor p21WAF1/CIP1 and caspase-3

[13] Redefining part of 300 year-old classification system for grouping members of the animal kingdom

[14] Systematic microRNAome profiling reveals the roles of microRNAs in milk protein metabolism and quality: insights on low-quality forage utilization

[15] Human milk miRNAs primarily originate from the mammary gland resulting in unique miRNA profiles of fractionated milk

[16] Neuroscience of Early-Life Learning in C. elegans

[17] Differential Odour Coding of Isotopomers in the Honeybee Brain

[18] Breast Milk Sugars Support Infant Gut Health

[19] C. elegans lifespan extension by osmotic stress requires FUdR , base excision repair, FOXO, and sirtuins

Narrative:

My name is James Kohl. I’m a medical laboratory scientist. I don’t know anyone who has ever performed patient testing and reported their results in the context of a series of mutations and the biodiversity of human tissue types. Other medical laboratory scientists us experimental evidence of biologically-based cause and effect to link what is known about the difference between nutrient-dependent healthy longevity and pathology.

For example, after I submitted the abstract for this poster presentation, an article linked everything known about quantum physics to induction of gonadotropin releasing hormone messenger RNA expression. Gonadotropin releasing hormone (or GnRH) links all cell type differentiation in vertebrates to all the microRNAs in the bull sperm that is linked to fertility.
I don’t think that the authors realized they had linked docosahexaenoic acid and another fatty acid from microRNA-9 and microRNA-200 to nutrient-dependent transcription factors and human fertility. The transcription factors link the development of the olfactory systems and the immune systems of all vertebrates to GnRH synthesis in hormone-secreting neurons. Neurons that secrete GnRH are linked to every aspect of nutrient-dependent vertebrate morphological and behavioral diversity.
If you only look at the works cited in this poster session, you could link everything known about nutrient-dependent cell type differentiation to healthy longevity. You could also link everything known about viruses to all pathology. For example, the nematode model of learning and memory links amino acid sensing to RNA-mediated amino acid substitutions that protect our organized genomes from virus-driven changes in nerve cells that alter olfactory acuity and specificity in Alzheimer’s disease.
In two weeks, Cori Bargmann will receive an award that links a single neuron to all works on the lifespan and behavior of the nematode, C. elegans. That neuron integrates information from multiple chemical cues including food, oxygen and pheromones. The integration of the cues controls the expression of social behavior in the context of changes in pH. She is scheduled to present: “Genes, neurons, circuits and behavior: an integrated approach in a compact brain.
Her work links cell type differentiation in a compact neuronal system to everything known to scientists inside and outside the hospital laboratory. Many scientists know how ecological variation and ecological adaptation link atoms to ecosystems in all living genera. For example, food, oxygen, pH, and temperature link the nutrient-dependent pheromone-controlled physiology of reproduction from C. elegans to the GnRH neuronal system of all vertebrates. All behavior is linked to supercoiled DNA in species from microbes to humans.Supercoiled DNA is the link from RNA-mediated DNA repair to examples of ecological adaptation. In this model, nutrient-dependent microRNAs link energy-dependent changes from hydrogen-atom transfer in DNA base pairs in solution to the molecular mechanisms that link morphological and behavioral phenotypes to survival of the species via their physiology of reproduction.
In the first part of this poster session, six citations link everything known about nutritional epigenetics from microRNAs to RNA-mediated amino acid substitutions. The substitutions differentiate all cell types in all living genera. Fixation of beneficial amino acid substitutions in organized genomes is the key to ecological adaptation. Fixation occurs in the context of the energy-dependent physiology of reproduction.
In the second part of this poster, 4 more citations link virus-driven energy theft to all pathology.
Part 3 links 9 more citations and examples of biologically-based cause and effect from the Zika virus to differences in human craniofacial and behavioral phenotypes.
The key to the model of nutrient-dependent transgenerational epigenetic inheritance of healthy longevity compared to virus-driven pathology is the energy that is required for RNA-mediated cell type differentiation.The Zika virus and other viruses steal energy that links odors and the immune system to the GnRH neuronal system in all vertebrates from a single neuron in C. elegans. Nutrient energy-dependent prenatal migration of GnRH-secreting neurons links the epigenetic effects of food odors and pheromones to changes in the HPG and HPA axes that link hormones to behavior.The energy-dependent GnRH pulse modulates energy-dependent hydrogen-atom transfer in DNA base pairs in blood. Our blood links what nematodes eat from their metabolic networks and genetic networks to the stability of all organized genomes when the networks lead to supercoiled DNA.In all vertebrates, the neurons that secrete GnRH link metabolic networks to genetic networks during the concurrent maturation of the neuroendocrine, reproductive, and central nervous systems. The GnRH neuronal system can be compared to a single neuron in C. elegans because GnRH links the physiology of reproduction, sex differences in behavior, and other behavioral differences that link RNA-mediated amino acid substitutions to morphological phenotypes and behavioral phenotypes. For example, what nematodes eat links the behavior of C. elegans to the behavior of P. pacificus, a predatory nematode with teeth.I’ve added quotations from Schrödinger, Philip Ball, and Bruce McEwen. I hope their works will encourage others to learn more about the anti-entropic energy of the sun and how it links light and energy to the biophysically constrained chemistry of protein folding. Protein folding starts with epigenetic Effects on genes that are linked to Affects on behavior in the context of the systems biology represented in this model.In the early 1990s I learned to differentiate between the effects on hormones and the affects of hormones on behavior. That led me to link the sun’s virucidal energy from UV light to supercoiled DNA, which protects organized genomes from virus-driven entropy.
From the perspective of physics, higher animals metabolize food and they return the degraded forms of food which are the power supply that link soil bacteria to the growth of plants. But, sunlight is the source of anti-entropic energy in plants.
The quantised nature of light and energy links all of Einstein’s theories to chemistry. Quantum physics explains how matter and light interact, which most people can link to the reasons why grass is green and the sky is blue. Medical laboratory scientists know that the nature of light and energy is measured in the spectroscopic methods that enable us to decode the structures of molecules, which link hydrogen-atom transfer in DNA base pairs to the visible spectrum of light, but also to UV light and infrared light.
In the context of light, chemistry and molecular epigenetics, medical laboratory scientists learn the difference between an “effect” on their test results and an affect on their behavior.
The epigenetic effects of the sun’s biological energy are linked to affects on behavior in all living genera by supercoiled DNA that protects organized genomes from virus-driven entropy.