Epigenetics and autophagy vs mutations and evolution (8)

By: James V. Kohl | Published on: November 16, 2016

Mycobacterial RNA isolation optimized for non-coding RNA: high fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides. Epub 2014/12/30
Abstract except:  

This optimized RNA isolation procedure thus provides a means to more rigorously explore the biology of ncRNA species in mycobacteria.

Reported 2016/11/11 in the context of: Newly discovered genetic code controls bacterial survival during infections

“It is really an alternative genetic code, in which any gene family that is required to change a cell phenotype is enriched with specific codons” that correspond to specific modified tRNAs, he says.

See also: tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence
Abstract introduction: Microbial pathogens adapt to the stress of infection by regulating transcription, translation and protein modification.
My comment: The adaptations are nutrient energy-dependent and pheromone-controlled via links from the innate immune system to RNA-mediated amino acid substitutions and supercoiled DNA, which protects all organized genomes from virus-driven genomic entropy — and has done so since the beginning of life on Earth. It life was not protected by the innate immune system and RNA-mediated cell type differentiation in the context of the physiology of reproduction, there would be no life and no biodiversity. Simply put, all biodiversity is energy dependent and RNA-mediated.
The first indication of that fact is here: Effects of Carnitine on Fatty-Acid Oxidation by Muscle (1959)

Carnitine is an amino acid derivative and nutrient involved in lipid (fat) metabolism in mammals and other eukaryotes. Amino acids are biologically important organic compounds containing amine (-NH2) and carboxyl (-COOH) functional groups, along with a side-chain (R group) specific to each amino acid.[1][2][3] The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, though other elements are found in the side-chains of certain amino acids.

RNA-mediated amino acid substitutions in the cell types of all individuals of all living genera link the de novo energy-dependent creation of the first amino acid to all biodiversity on earth via the physiology of reproduction in species from microbes to humans.


Abstract introduction:

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

My comment: Simply put, the synthesis of RNA is biophysically constrained by the availability of energy.

See for comparison: Metabolic Enzymes Moonlighting in the Nucleus: Metabolic Regulation of Gene Transcription

During evolution, cells acquired the ability to sense and adapt to varying environmental conditions, particularly in terms of fuel supply. Adaptation to fuel availability is crucial for major cell decisions and requires metabolic alterations and differential gene expression that are often epigenetically driven.

My comment: They arrived at claims about evolution without putting evolution into the context of how energy-dependent molecular mechanisms link the cells acquired ability to adapt to ecological variation. Instead, the place the automagically acquired ability in to the context of evolution. Serious scientists know how to link the de novo creation of G protein-coupled receptors from chemotaxis and phototaxis to the energy-dependent physiology of receptor-mediated behavior and reproduction.
Metabolic regulation of gene transcription does not start with evolution. Metabolic networks must be linked to genetic networks via the ab initio energy, which is required for the de novo creation of G protein-coupled receptors (GPCRs). The GPCRs link the nutrient-dependent pheromone-controlled physiology of reproduction to all biodiversity. Virus-driven energy theft causes damage to GPCRs that link links the viruses to all pathology in all cell types of all living genera.
See for comparison: Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms

…differential nitrogen availability, due to differences in host environment and metabolic inputs, contributes to changes in codon bias and genome composition. Specifically, adaptation to low nitrogen availability results in reduced nitrogen content in nucleotide sequences. These results reveal a previously hidden relationship between cellular metabolism and genome evolution and provide new insight into how genome sequence evolution can be influenced by adaptation to different diets.

Reported as: Scientists uncover genetic evidence that ‘we are what we eat’ 

The results, based on novel mathematical models developed by the researchers, reveal a previously hidden relationship between cellular metabolism and evolution. They provide new insights into how DNA sequences can be influenced by adaptation to different diets.

My comment: They linked nutrient energy-dependent changes in base pairs and RNA-mediated amino acid substitutions to  the structure of supercoiled DNA, but claimed they discovered a previously hidden relationship between metabolic networks and genetic networks in all living genera that they placed back into the context of evolution.

See instead, Structural diversity of supercoiled DNA

For comparison to everything known to serious scientists about energy-dependent biophysically constrained RNA-mediated protein folding chemistry and cell type differentiation, see: The Strength of Selection against Neanderthal Introgression

Neanderthals over time accumulated many weakly deleterious alleles that in their small population were effectively neutral. However, after introgressing into larger human populations, those alleles became exposed to purifying selection. Thus, rather than being the result of hybrid incompatibilities, differences between human and Neanderthal effective population sizes appear to have played a key role in shaping our present-day shared ancestry.

Larry Kisner Sr., finally realized that energy-dependent fluorescence is the link from the anti-entropic virucidal energy of the sun to all biodiversity after he commented to “The Battlefield” FB group about “auto-fluorescence” in dinosaur bone tissue. I was banned from participation for correcting him and linking UV fluorescence to all biodiversity via nutrient energy-dependent pheromone-controlled autophagy.

He will probably now help others present my model as their own, or as some research group’s newly discovered findings. Unfortunately, his behavior and the behavior of all others like him is perfectly predictable and a horrid distraction to serious scientists who know how many more deaths will be caused by theorists and Christians who do not understand how to link energy and virus-driven energy theft to biologically-based cause and effect in all living genera.

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