Virus-driven reduction of RNA polymerase II occupancy in hosts (2)

By: James V. Kohl | Published on: March 5, 2020

See: Virus-driven reduction of RNA polymerase II occupancy in hosts (1)
See: Genome-Wide Study Reveals a Novel Regulatory Pathway: Translation Affects mRNA Stability in a Codon-Dependent Manner (On Demand Webinar 6/26/19)

This webinar outlines a study that combined genome-wide and classical molecular approaches to demonstrate that translation strongly affects mRNA stability in a codon-dependent manner, ultimately influencing mRNA and protein levels in higher organisms.

See for comparison from:  2/26/20


For facts about how light-activated energy-dependent microRNA biogenesis and biophysically constrained viral latency link RNA interference to healthy longevity across kingdoms, see:
Towards Improved Molecular Identification Tools in Fine Fescue (Festuca L., Poaceae) Turfgrasses: Nuclear Genome Size, Ploidy, and Chloroplast Genome Sequencing 12/6/19

Comparative genomics suggested unique repeat signatures for each fine fescue taxon that could potentially be used for marker development for taxon identification.

The link from light-activated microRNA biogenesis in plants to prevention of virus-driven pathology manifested in fescue toxicosis is: The epidermis coordinates thermoresponsive growth through the phyB-PIF4-auxin pathway 2/26/19 because Light‐responsive ELONGATED HYPOCOTYL 5 (HY5) was shown, through a series of genetic and transgenic tag grafting experiments (b), to move from shoots to roots 3/4/19
The link from plants to insects, and to virus-driven pathology in humans is the failure of RNA interference to protect us against viral replication.
See: Mosquito RNAi is the major innate immune pathway controlling arbovirus infection and transmission 3/6/11 and Research progress in RNA interference against the infection of mosquito-borne viruses 2/20/20
The link from insects to birds is High-throughput sequencing analysis identified microRNAs associated with egg production in ducks ovaries 2/4/20 and miRNA repertoire and host immune factor regulation upon avian coronavirus infection in eggs 2/6/20 and A ‘highly pathogenic strain’ of H5N1 bird flu has been reported in China’s Hunan province 2/1/20
The link to fish is: MicroRNA-206 Regulation of Skin Pigmentation in Koi Carp (Cyprinus carpio L.) 2/12/20
The link to mice is High Levels of miR-483-3p Are Present in Serum Exosomes Upon Infection of Mice With Highly Pathogenic Avian Influenza Virus 2/11/20
The link from mice to humans is food energy-dependent pheromone-controlled fixation of EDAR V370A.
See: Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant2/14/13
The link from Feedback loops link odor and pheromone signaling with reproduction 11/18/05 to humans is Olfaction Warps Visual Time Perception 3/17/17
See also: Sexual Chemosignals: Evidence that Men Process Olfactory Signals of Women’s Sexual Arousal 2/5/20
George M. Church has linked what mice eat from the model Mouse For Actively Recording Cells!” or MARC1, to the physiology of pheromone-controlled reproduction and biophysically constrained viral latency via the mouse to human model of how EDAR V370A biophysically constrains viral latency in human populations from the Old World to the New World.

The line does not have a disease phenotype. However, when a MARC1-PB7 mouse is crossed to mice expressing cas9 universally or in a lineage-specific manner, combinatorial and cumulative barcoding starts in the progeny during their development, leading to developmentally barcoded animals that can be used for a multitude of applications, including lineage tracing.

See:  Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk 5/8/18

Environmental selection during the last ice age on the mother-to-infant transmission of vitamin D and fatty acids through breast milk The frequency of the human-specific EDAR V370A allele appears to be uniquely elevated in North and East Asian and New World populations due to a bout of positive selection likely to have occurred circa 20,000 y ago.

The claim about positive selection occurring 20,000 y ago is based on ridiculous theories.
The most recent  attack on facts known to reasearchers from all Abrahamic faiths was published as The Rocks Were There: Straight Science Answers to bent Creationist Questions, Volume 1 Paperback – 2/27/20
See my review of their pseudoscientific nonsense Serious scientists start with God’s Creation of energy as information for comparison to other reviews.

Five years after “Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system” (2/27/15) showed that the weekend resurrection of the bacterial flagellum in P. fluorescens could be observed, they use a definition of evolution and claim that “Evolution is definitely observable and (as we showed) testable.”

That’s true, but all attempts to put whatever else has been observed and tested back into the context of neo-Darwinian pseudoscientific nonsense across billions to millions of years have failed.

The triumph of common sense linked claims about God’s Creation of “Subatomic” particles from the creation of the “Periodic” table to biophysically constrained viral latency via “Cytosis” across all “Ecosystems” via Mendelian genetics and the game, “Genotype” for ages 14+.

Other readers need only start with Darwin’s “conditions of life” and link them from the food energy-dependent pheromone-controlled physiology of reproduction in bacteria to biophysically constrained coronavirus viral latency and/or to effective cancer treatment or prevention of cancer via microRNA-mediated changes in amino acids and supercoiled DNA.

For comparison, see their Appendix 3 “Amino Acid Codons”

Food energy-dependent codon optimality is controlled by the metabolism of food to species-specific pheromones, which prevent the mutations that most biologically uninformed theorists continue to link to claims about evolution over more than the past 5-10000 years.

These theorists seem to have learned nothing since the 1994 publication of “Pheromonal Regulation of Genetic Processes: Research on the House Mouse (Mus musculus L.)

Indeed, if Downard and Jackson have learned anything about the conserved food energy-dependent regulation of genetic processes, they do not take what has been learned outside the context of ridiculous theories. Instead, they expound upon the theories, which is how theorists prevent scientific progress.

The scientific progress could have been linked to the prevention of all virus-driven diseases. Instead, on 3/5/20 Wuhan party chief Chen Yixin reportedly claimed:

We will not be able to contain the spread if we do not impose unified strict measures

Use of supplements, such as vitamin D3, vitamin C, and Zinc to biophysically constrain pathology is a Creationist approach to the end of atheism and virus-driven pathology.
See: Nutrient-dependent Pheromone-Controlled Ecological Adaptations: From Angstroms to Ecosystems 4/18/18

This angstroms to ecosystems model of ecological adaptation links nutrient energy-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA/messenger RNA balance and chromosomal rearrangements via the physiology of reproduction in species from microbes to humans. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity. Species-specific pheromones link quorum-sensing in microbes from chemical ecology to the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection for codon optimality links nutritional epigenetics to the behaviors that enable ecological adaptations. All biodiversity is an ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. Simply put, olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of supercoiled DNA in the organized genomes of species from microbes to man during their development.

See also: MicroRNA targeting of the non-canonical planar cell polarity pathway in the developing neural tube 3/4/20

…microRNAs are potential coordinators of normal neural tube (NT) formation, via regulation of the crucial, planar cell polarity pathway. Any alteration in their expression during neurulation would result in abnormal NT development.

Light-activated microRNA biogenesis in plants has been linked from the assembly of the microRNA-RNA-peptide nanocomplex to the prevention and/or the effective treatment of all virus-driven pathology.
See for example: Hypoxia-induced apoptosis of Astrocytes is mediated by reduction of Dicer and activation of caspase-1 3/4/20

…astrocytic cell death during hypoxia is mediated by the ROS/caspase-1/classical caspase-dependent apoptotic pathway.

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