Hydrogen-atom transfer in DNA base pairs (6)

By: James V. Kohl | Published on: January 23, 2016

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Mobile small RNAs regulate genome-wide DNA methylation

Abstract excerpt:

RNA silencing at the transcriptional and posttranscriptional levels regulates endogenous gene expression, controls invading transposable elements (TEs), and protects the cell against viruses.

Conclusion:

Our conclusions underpin future research into why plants possess a system for communicating methylation status from shoot to root tissues.

The investigators found that normal p53 gene action restrains transposons, mobile genetic elements called retroelements that can make copies of themselves and move to different positions on chromosomes.

My comment: They have nearly reached the point where they must admit that all genomic instability is virus-driven and all RNA-mediated nutrient-dependent DNA repair is linked to healthy longevity. That will alert others to the fact that there is no such thing as mutation-driven evolution and put an end to the pseudoscientific nonsense touted by neo-Darwinian teleophobes.
All plants and animals possess an innate immune system that links nutrient-dependent pheromone-controlled life history transitions in microbes to mammals via the conserved molecular mechanisms exemplified in the honeybee model organism.

Animal models are often used to model human physical and mental disorders. The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, diseases of the X chromosome, learning and memory, as well as conditioned responses to sensory stimuli (Kohl, 2012).

The links from soil bacteria to ecological speciation in mammals are exemplified in The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
Conclusion:

…while fescue toxicosis appeared to have little effect upon sperm miRNA expression (with the possible exception of miRNA-146a), the miRNA profile of mature ejaculated sperm may in fact have downstream consequences upon embryonic development. The potential for sperm miRNA affecting zygote development has recently been reported in the literature [18] and has interesting implications for the use of sperm miRNA profiles as indicators of potential male fertility.

My comment: Spectrophotometric assays link energy-dependent hydrogen-atom transfer in DNA base pairs in soil bacteria or in solutions like blood via pHs to healthy longevity or to virus-driven pathology in humans via testing that integrates what is known about how UV light is linked to RNA-mediated cell type differentiation in all living genera via the physiology of reproduction. See for instance:

See also: Mettler Toledo

Excerpt:

pH Care Center

Your Source for pH Knowledge and Best Practices

pH Wellness doesn’t stem from just your meter. All components in your pH system must be working at their best to provide reliable results.

My comment: The calibration of pH in your body fluids is nutrient energy-dependent and many aspects of life history transitions can be linked to the stability of your organized genome by spectophotometric measurements. Simply put, your body is like a precision instrument with a pH system that has been calibrated by the speed of light and hydrogen-atom transfer in DNA base pairs in solutions. The biological basis of those solutions links the calibrations from the fixation of RNA-mediated amino acid substitutions to chromosomal rearrangements.

The chromosomal rearrangements link UV light from Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution to the physiology of reproduction in species from microbes to humans via pH and other assays that are performed by medical laboratory scientists. The assays are not performed by biologically uninformed neo-Darwinian theorists or anyone else that might claim mutations can be linked to anything except pathology.

See also: 2016 Pathogenetics. An introductory review

My comment: My atoms to ecosystems model of nutrient-dependent RNA-mediated amino acid substitutions and pheromone-controlled chromosomal rearrangements links ecological variation to ecological adaptations in all living genera via their supercoiled DNA. If teleophobes want to start their claims in a “warm little pond,” so be it. But that means they must start with the highly ordered hydrogen bonds of water.

If teleophobes insist on claiming the energy of the hydrogen bonds can be linked from random mutations to the evolution of increasing organismal complexity, they must start providing experimental evidence that links biophysically constrained changes in the highly ordered hydrogen bonds of water.
But teleophobes never asked about the link from physics to chemistry via the hydrogen bond energy. They never asked about the links from chemistry to the conserved molecular mechanisms of biologically-based cause and effect. Instead, teleophobes started with de Vries definition of mutation and linked their assumptions to claims about how long it might take for one species to evolve into another.
See for comparison:
Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli
Excerpt:
These structures delineate how RNR ‘reads’ the base of each effector and communicates substrate preference to the active site by forming differential hydrogen bonds, thereby maintaining the proper balance of deoxynucleotides in the cell.
Reported as:

Supply chain Chemists discover how a single enzyme maintains a cell’s pool of DNA building blocks.

Excerpt 1)
Deoxyribonucleotides are generated from ribonucleotides, which are the building blocks for RNAs — molecules that perform many important roles in gene expression. RNR, which catalyzes the conversion of ribonucleotides to deoxyribonucleotides, is an evolutionarily ancient enzyme that may have been responsible for the conversion of the earliest life forms, which were based on RNA, into DNA-based organisms, Drennan says.
My comment: The claim that this is an evolutionarily ancient enzyme cannot be placed into the context of weekend evolution of the bacterial flagellum or any model of biologically-based cause and effect that links atoms to ecosystems.
Excerpt 2)

“My lab is interested in studying both human and bacterial RNRs, because I feel like we really need to understand whether they all work the same way, or whether there are going to be differences,” she says.

My comment: She seems to not be sure that the laws of physics link hydrogen-atom transfer in DNA base pairs to biodiversity in all living genera via RNA-mediated events. It seems unlikely to me that the building blocks for RNAs would work differently in bacteria than in humans.

See also: AMP-activated protein kinase mediates mitochondrial fission in response to energy stress

Reported as: How the cell’s power station survives attacks

The Salk team found that when cells are exposed to mitochondria damage, a central cellular fuel gauge, the enzyme AMPK, sends an emergency alert to mitochondria instructing them to break apart into many tiny mitochondrial fragments. Interestingly, AMPK is activated by the widely used diabetes therapeutic metformin, as well as exercise and a restricted diet. The new findings suggest that some of the benefits from these therapies may result from their effects in promoting mitochondrial health.

Excerpt:

On one hand, AMPK is known to be important for type 2 diabetes, immune disease and cancer. On the other hand, mitochondrial dysfunction is becoming increasing connected to metabolic diseases and neurodegenerative diseases. We’re making some of the first steps in connecting these two things that have major disease implications.

My comment: Did I already mention that these researchers claim to be making some of the first steps connecting metabolic networks and genetic networks, which we detailed in our 1996 Hormones and Behavior review of RNA-mediated cell type differentiation? This echo from Science Mission attests to the fact that the Salk researchers are approximately two decades behind the learning curve of information that links atoms to ecosystems in all living genera.
See also: DNA and RNA structure: nucleic acids as genetic material
Excerpt:

Last month (Clinical Issues), we covered the definition of molecular diagnostics (MDx) as the detection of nucleic acids to provide clinical information. The methods used to do so, as well as the intrinsic biological roles of DNA and RNA in the storage and transmission of an organism’s genetic information, turn out to be intimately related to their physical structures. As a precursor to understanding MDx methods we must therefore turn our attention this month to DNA and RNA structure.

My comment: The structure of DNA and RNA is nutrient-dependent. Nutrients are fuel for the thermoregulation of cellular metabolism manifested in microbes and in every cell of every tissue in every organism. For example, glucose uptake is essential.
See: A Sugary Path to the Nucleus and Sweet Enough to Flower
Excerpt:

In making the developmental switch from vegetative growth to flowering, plants integrate diverse information, including photoperiod, hormone signals, and carbohydrate status.

My comment: Ecological variation links the sun’s biological energy from soil bacteria to the root and shoots that link flowering plants to the conserved molecular mechanisms of RNA-mediated cell type differentiation in all living genera.
Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin
Excerpt: Mechanisms of epistasis are often best revealed through detailed examinations of interactions between amino acid mutations in the same protein that contribute to variation in a measurable biochemical phenotype
See also: Repeated elevational transitions in hemoglobin function during the evolution of Andean hummingbirds
My comment: Some researchers still claim that the amino acid substitutions that differentiate the cell types that carry hemoglobin in deer mice and in hummingbirds are example of mutations that can somehow be linked to the evolution of biodiversity exemplified in HbVar: A Database of Human Hemoglobin Variants and Thalassemias.
They tout pseudoscientific nonsense because they never learned to link atoms to ecosystems via hydrogen-atom transfer in DNA base pairs.
See for comparison: Detection of hemoglobinopathies and thalassemias using automated separation systems
Excerpt:

The hemoblobinopathies, or HB variants, are attributable to amino acid substitution(s) in either globin chain. Currently, 1,181 total hemoglobin variants have been characterized.

My comment: Even some of my trade publications continue to report these amino acid substitutions as if they were mutations. If those who reported such claims had ever learned how RNA-mediated cell type differentiation occurs, they would report the amino acid substitutions in the context of Dobzahsky’s claim:
Excerpt:

…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla. ( p. 127)

Excerpt:

During cell death, the DNA gets chopped into small pieces by enzymes that like to cut in the easily accessible, unprotected sections of DNA in between the nucleosomes.

My comment: The test links ecological variation to nutrient-dependent RNA-mediated DNA repair via microRNAs and adhesion proteins. The adhesion proteins link supercoiled DNA to protection from virus-driven entropy in the organized genomes of all living genera.

The organized genomes are linked from chromosomal rearrangements and the physiology of reproduction to ecological adaptations and all biodiversity. The headline: “New blood test may explain…” attests to an attempt to explain away the ignorance of teleophobic neo-Darwinian theorists.

The teleophobes tried to explain healthy longevity in the context of the absence of mutations. For comparison, all serious scientists know that healthy longevity arises via the fixation of nutrient energy-dependent amino acid substitutions in the presence of the pheromone-controlled cell type differentiation of species from microbes to humans. The conserved molecular mechanisms of cell type differentiation have been revealed in the context of models that link atoms to ecosystems.After approximately 60,000 hours in the lab, I claim that every test I have ever performed attests to that fact.
See also: Blood gases is a measurement of how much oxygen and carbon dioxide is in your blood. It also determines the acidity (pH) of your blood.

This is an example a blood test that links atoms to ecosystems via the oxygen carrying capacity of your red blood cells, which may be altered by any one of more than 1180 human hemoglobin variants. The fixation of one nutrient-dependent RNA-mediated amino acid substitution differentiates the cell type of chimpanzees and modern humans from the cell types of gorillas.
No medical laboratory scientist or testing assistants I worked with from 2001 until 2013 was happy to learn that the blood gas instruments had not been calibrated for the elevation above sea level at which the tests were being performed. Only one laboratory supervisor was happy to have test results be accurately reported after I discovered the problem that was about to cause the discontinuation of testing.