RNA methylation, RNA-directed DNA methylation, learning and memory

sink testing

Lab medicine The illegal practice of providing false test results on clinical specimens–eg, vials of blood, urine specimens, that were deliberately discarded–ie, down the sink, without actually testing them

Pylori Story #1: Acid Attack

Pylori Story #2: Journey to the Center of the Stomach

The “Modern Synthesis” is analogous to sink testing in the medical laboratory.

See for example: Replace the Modern Synthesis (Neo-Darwinism): An Interview With Denis Noble


[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent…. The anglophone tradition was taught. I was taught, and so were my contemporaries, and so were the younger scientists. Evolution was defined as “changes in gene frequencies in natural populations.” The accumulation of genetic mutations was touted to be enough to change one species to another…. No, it wasn’t dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact.

The assumptions that were taught as fact led to this revelation: “It was really surprising,” Dr. Bernstein said. “Why would a metabolism gene cause cancer?”

The facts about biologically-based nutrient-dependent RNA-mediated cell type differentiation, which is perturbed by viruses, led to this revelation:

See for example: Breath Test for Stomach Cancer
My comment: The test for H. pylori is one of the simplest tests to perform in the lab. The breath test for stomach cancer will link gut bacteria from metabolic networks to genetic networks in all invertebrates and vertebrates via what is currently known about RNA-mediated cell type differentiation and the stability of all organized genomes in all living genera.
DNA methylation changes in plasticity genes accompany the formation and maintenance of memory

The ability to form memories is a prerequisite for an organism’s behavioral adaptation to environmental changes. At the molecular level, the acquisition and maintenance of memory requires changes in chromatin modifications. In an effort to unravel the epigenetic network underlying both short- and long-term memory, we examined chromatin modification changes in two distinct mouse brain regions, two cell types and three time points before and after contextual learning. We found that histone modifications predominantly changed during memory acquisition and correlated surprisingly little with changes in gene expression. Although long-lasting changes were almost exclusive to neurons, learning-related histone modification and DNA methylation changes also occurred in non-neuronal cell types, suggesting a functional role for non-neuronal cells in epigenetic learning. Finally, our data provide evidence for a molecular framework of memory acquisition and maintenance, wherein DNA methylation could alter the expression and splicing of genes involved in functional plasticity and synaptic wiring.

See also: Search Results for ‘RNA-directed DNA methylation’

I don’t think this will become clearer.

  1. Base pair changes are nutrient energy-dependent
  2. RNA-directed DNA methylation is nutrient-dependent
  3. RNA-mediated amino acid substitutions are nutrient-dependent
  4. Alternative splicings of microRNAs are nutrient-dependent
  5. Chromatin modification is nutrient-dependent
  6. Histone modifications are nutrient-dependent
  7. Plasticity is nutrient-dependent
  8. DNA repair is nutrient-dependent
  9. Ecological adaptation is nutrient-dependent


  1. Nutrient-dependent epigenetically-effected learning and memory links RNA-directed DNA methylation from microRNAs to cell adhesion proteins and supercoiled DNA in the organized genomes of all living genera.
  2. Alternative splicings of microRNAs are linked from the microRNA/messenger RNA balance to learning and memory via amino acid substitutions in the histones of supercoiled DNA .
  3. Viruses steal the nutrient energy that links the perturbed microRNA/messenger RNA balance to mutation-driven pathology.

See also: Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements

This study demonstrates that decoupling transcriptional changes from post-transcriptional changes and integrating them with epigenetic alterations in a computational framework can elucidate the transcriptional network that tunes and amplifies the effect of miRNA loss. The computational framework introduced here may benefit studies of miRNAs by shifting emphasis to the rewired transcriptional networks that cause the majority of the transcript-level changes.

Re: “…the rewired transcriptional networks that cause the majority of the transcript-level changes.” They link the nutrient-dependent pheromone-controlled physiology of reproduction to weekend evolution of the bactrerial flagellum.
See: Evolutionary Rewiring

The results highlight the importance of gene duplication in evolution, said Hughes, and the ability of the resulting diverged proteins to “moonlight” in roles aside from their main function. Indeed, said Jeff Barrick of the University of Texas in Austin who was not involved in the work, such cross-talk gives organisms “greater robustness,” allowing them “to restore a function even though they are missing a genetic part.”

My comment: Indeed, Barrick makes no mention of his own work with Richard Lenski, like this one:
Large Chromosomal Rearrangements during a Long-Term Evolution Experiment with Escherichia coli

IMPORTANCE Bacterial chromosomes are dynamic structures shaped by long histories of evolution.

My comment: The long histories were just reduced to the history of weekend evolution of the bacterial flagellum via nutrient-dependent pheromone controlled chromosomal rearrangements.

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