Labroots Neuroscience virtual event: YouTube video < 10 minutes. From hydrogen atom transfer in DNA base pairs to ecosystems Published on 2 Mar 2016

Presented March 16 and 17, 2016  Login for free and go to the Poster Hall section on Neuron Biology for a full screen display of the poster or see the poster displayed on Figshare

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.

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.

Citations: From hydrogen-atom transfer in DNA base pairs to ecosystems

[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

 

 

 

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