UV light, H2O, and epigenetic effects… (1)

By: James V. Kohl | Published on: September 25, 2020

See first: Coherently organized healthy longevity (4)
UV light, H2O, and epigenetic effects affect behavior and sympatric speciation
Submitted by James V. Kohl on 9/25/20 for presentation during the Epigenetics – From Bench to Clinic session: RNA modifications and epitranscriptomics​​ Moderator Tony Kouzarides
Title: UV light, H2O, and epigenetic effects affect behavior and sympatric speciation
James V. Kohl*
UV light-activated, H2O-dependent oxidative phosphorylation links microRNA-mediated epigenetic effects on organized genomes from bench to clinic.  For a historical perspective, see
1) Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”, 1
2) Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene, 2
3) Nutrient–dependent / pheromone–controlled adaptive evolution: a model, 3
4) Why have microRNA biomarkers not been translated from bench to clinic? 4
Energy-dependent microRNA-mediated changes in angstroms to ecosystems5 link biophysically constrained viral latency from quantum coherence to coherently organized biology6 via femtosecond blasts of ultraviolet (UV) light. Moderate amounts of UV light link differences in DNA damage to  microRNA-mediated DNA repair.6-8 For instance, “…plants alter microRNA (miRNA) biogenesis in response to light transition.”9
In species from microbes to mammals, food energy-dependent pheromone-regulated genetic processes link feedback loops from energy as information to biophysically constrained RNA-mediated protein folding chemistry via RNA abundance and RNA interference, which is required for microRNA-mediated DNA repair. 1, 10-11
The National Microbiome Initiative links what mammals eat from microbial quorum sensing in the gut to the physiology of  pheromone-regulated genetic process and reproduction via endogenous RNA interference and chromosomal rearrangements.12  Fixation of RNA-mediated  amino acid substitutions links naturally occurring light-activated carbon fixation  to energy-dependent chromosomal rearrangements.
Natural selection for energy-dependent codon optimality13 links the Precision Medicine Initiative to genome- wide details of how chromosomal rearrangements  are linked to the Creation of genotypes. For instance, the chromosomal rearrangements  link everything currently known about classical physics to chemistry via  achiral glycine in postition 6 of the gonadotropin releasing hormone decapeptide (GnRH) in jawed vertebrates.14
The biophysically constrained GnRH decapeptide hormone links molecular epigenetics from what is known about bacteria to exquisitely fine-tuned autophagy across kingdoms. For comparison, constraint-breaking mutations are linked from the viral hecatomb15 to the mutation-driven evolution of pathology.16
Detailed representations of energy-dependent natural selection for codon optimality have consistently linked biologically-based cause and effect from the energy-dependent Creation of enzymes and G protein-coupled receptors to fixation of RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. 17
Light-activated 18 energy-dependent polycombic ecological adaptations 19 are manifested in supercoiled DNA. Chromosomal inheritance links the ecological adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes and transgenerational epigenetic inheritance.8
For contrast, virus-driven energy theft links the degradation of messenger RNA to negative supercoiling, constraint breaking mutations, and the hecatombic evolution of all diseases.  Indeed, the viral hecatomb links transgenerational epigenetic inheritance in archaea to coronavirus-damaged DNA in humans, which typically is repaired by  food energy-dependent endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.20
Theorists who ignore the role of nutrition in biophysically constrained viral latency are largely to blame for all extant diseases. 21 See for instance: The Secret Language of Cells: A New Paradigm for Understanding Health and Disease. 22 See for comparison: MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. 23

  1. McEwen, B. S.; Allfrey, V. G.; Mirsky, A. E., Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”. Biochim Biophys Acta 1964, 91, 23-8.
  2. Skalsky, R. L.; Cullen, B. R., Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene. PLoS One 2011, 6 (9), e24248.
  3. Kohl, J. V., Nutrient–dependent / pheromone–controlled adaptive evolution: a model. Socioaffective Neuroscience & Psychology 2013, 3.
  4. Saliminejad, K.; Khorram Khorshid, H. R.; Ghaffari, S. H., Why have microRNA biomarkers not been translated from bench to clinic? Future Oncol 2019.
  5. Samanta, T.; Kar, S., Fine-tuning Nanog expression heterogeneity in embryonic stem cells by regulating a Nanog transcript-specific microRNA. FEBS Lett 2020.
  6. Chakraborty, M.; Hu, S.; Visness, E.; Del Giudice, M.; De Martino, A.; Bosia, C.; Sharp, P. A.; Garg, S., MicroRNAs organize intrinsic variation into stem cell states Proc Natl Acad Sci U S A 2020.
  7. Bucher, D. B.; Kufner, C. L.; Schlueter, A.; Carell, T.; Zinth, W., UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair. Journal of the American Chemical Society 2016, 138 (1), 186-190.
  8. Barbu, M. G.; Condrat, C. E.; Thompson, D. C.; Bugnar, O. L.; Cretoiu, D.; Toader, O. D.; Suciu, N.; Voinea, S. C., MicroRNA Involvement in Signaling Pathways During Viral Infection. Frontiers in Cell and Developmental Biology 2020, 8 (143).
  9. Achkar, N. P.; Cho, S. K.; Poulsen, C.; Arce, A. L.; Re, D. A.; Giudicatti, A. J.; Karayekov, E.; Ryu, M. Y.; Choi, S. W.; Harholt, J.; Casal, J. J.; Yang, S. W.; Manavella, P. A., A Quick HYL1-Dependent Reactivation of MicroRNA Production Is Required for a Proper Developmental Response after Extended Periods of Light Deprivation. Dev Cell 2018, 46 (2), 236-247 e6.
  10. Daev, E. V., [Pheromonal regulation of genetic processes: research on the house mouse (Mus musculus L.)]. Genetika 1994, 30 (8), 1105-12.
  11. Boehm, U.; Zou, Z.; Buck, L. B., Feedback loops link odor and pheromone signaling with reproduction. Cell 2005, 123 (4), 683-95.
  12. Spana, E. P.; Abrams, A. B.; Ellis, K. T.; Klein, J. C.; Ruderman, B. T.; Shi, A. H.; Zhu, D.; Stewart, A.; May, S., speck, First Identified in Drosophila melanogaster in 1910, Is Encoded by the Arylalkalamine N-Acetyltransferase (AANAT1) Gene. G3 (Bethesda) 2020, 10 (9), 3387-3398.
  13. Bazzini, A. A.; Del Viso, F.; Moreno-Mateos, M. A.; Johnstone, T. G.; Vejnar, C. E.; Qin, Y.; Yao, J.; Khokha, M. K.; Giraldez, A. J., Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition. EMBO J 2016.
  14. Barran, P. E.; Roeske, R. W.; Pawson, A. J.; Sellar, R.; Bowers, M. T.; Morgan, K.; Lu, Z.-L.; Tsuda, M.; Kusakabe, T.; Millar, R. P., Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity. J Biol Chem 2005, 280 (46), 38569-38575.
  15. Danovaro, R.; Dell’Anno, A.; Corinaldesi, C.; Rastelli, E.; Cavicchioli, R.; Krupovic, M.; Noble, R. T.; Nunoura, T.; Prangishvili, D., Virus-mediated archaeal hecatomb in the deep seafloor Science Advances 2016, 2 (10).
  16. Nei, M., Mutation-Driven Evolution. Oxford Univesity Press: Oxford, UK, 2013.
  17. Irobalieva, R. N.; Fogg, J. M.; Catanese, D. J.; Sutthibutpong, T.; Chen, M.; Barker, A. K.; Ludtke, S. J.; Harris, S. A.; Schmid, M. F.; Chiu, W.; Zechiedrich, L., Structural diversity of supercoiled DNA. Nat Commun 2015, 6.
  18. de Vargas, C.; Audic, S.; Henry, N.; Decelle, J.; Mahé, F.; Logares, R.; Lara, E.; Berney, C.; Le Bescot, N.; Probert, I.; Carmichael, M.; Poulain, J.; Romac, S.; Colin, S.; Aury, J.-M.; Bittner, L.; Chaffron, S.; Dunthorn, M.; Engelen, S.; Flegontova, O.; Guidi, L.; Horák, A.; Jaillon, O.; Lima-Mendez, G.; Lukeš, J.; Malviya, S.; Morard, R.; Mulot, M.; Scalco, E.; Siano, R.; Vincent, F.; Zingone, A.; Dimier, C.; Picheral, M.; Searson, S.; Kandels-Lewis, S.; Coordinators, T. O.; Acinas, S. G.; Bork, P.; Bowler, C.; Gorsky, G.; Grimsley, N.; Hingamp, P.; Iudicone, D.; Not, F.; Ogata, H.; Pesant, S.; Raes, J.; Sieracki, M. E.; Speich, S.; Stemmann, L.; Sunagawa, S.; Weissenbach, J.; Wincker, P.; Karsenti, E., Eukaryotic plankton diversity in the sunlit ocean. Science 2015, 348 (6237).
  19. Diamond, M.; Binstock, T.; Kohl, J. V., From Fertilization to Adult Sexual Behavior. Horm Behav 1996, 30 (4), 333-53.
  20. Tumpey, T. M.; Maines, T. R.; Van Hoeven, N.; Glaser, L.; Solorzano, A.; Pappas, C.; Cox, N. J.; Swayne, D. E.; Palese, P.; Katz, J. M.; Garcia-Sastre, A., A two-amino acid change in the hemagglutinin of the 1918 influenza virus abolishes transmission. Science 2007, 315 (5812), 655-9.
  21. McNeill, E. M.; Hirschi, K. D., Roles of Regulatory RNAs in Nutritional Control. Annu Rev Nutr 2020, 40, 77-104.
  22. Lieff, J. L., The Secret Language of Cells: A New Paradigm for Understanding Health and Disease. 9/22/20 ed.; BenBella Books: 2020.
  23. Bartel, D. P., MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. Cell 2004, 116 (2), 281-297.


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