DNA methylation

Informing the biologically uninformed

Please help those who are not biologically uninformed link the latest information from Science Magazine to RNA-mediated cell type differentiation in all genera. For example, see:  Eukaryotic plankton diversity in the sunlit ocean Introduction: The sunlit surface layer of the world’s oceans functions as a giant biogeochemical membrane between the atmosphere and the ocean interior (1). My comment: That fact links the anti-entropic epigenetic effects of the sun’s biological energy from the de novo creation of amino acids to RNA-mediated…

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One amino acid substitution, genes, and brain activity

After a sip of milkshake, genes and brain activity predict weight gain Excerpt: …one-third of the population possesses a second genetic variant associated with fewer dopamine receptors. In these individuals it is response in the dorsal striatum, a region critical for forming habits, that predicts weight gain. People with this genotype are also more prone to addiction and impulsive behavior… My comment: The link from nutritional epigenetics to the metabolic networks and genetic networks that control behavior is clear. Behavior…

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Batch effect vs epigenetic effects

A reanalysis of mouse ENCODE comparative gene expression data [awaiting peer review] was reported as: Batch Effect Behind Species-Specific Results? Excerpt: genes in the mouse heart were expressed in a pattern more similar to that of other mouse tissues, such as the brain or liver, than the human heart. My comment: If that was an accurate representation of biologically-based cause and effect, it could not be supported by what is currently known about the biophysically constrained chemistry of nutrient-depenent pheromone-controlled…

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Bee-birthed epigenetics and primate cell types

Summary: This is a fantastic video representation of how nutrient-dependent pheromone-controlled RNA-directed DNA methylation links ecological variation to RNA-mediated ecological adaptations via amino acid substitutions in all genera. The Birth of a Bee Excerpt: After the queen bee lays a single egg in a cell of the comb, the worker bees feed the egg for a few days until it hatches into a larva. The larva continues to eat and grow until Day 10. Then, the worker bees cap the…

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Scientists lose. A sci-fi author gains credibility

Phage spread antibiotic resistance Excerpt 1) nearly half of the 50 chicken meat samples purchased from supermarkets, street markets, and butchers in Austria contained viruses that are capable of transferring antibiotic resistance genes from one bacterium to another—or from one species to another. Excerpt 2) Until recently, transduction of antibiotic resistance via phage was assumed to be a very minor source of the spread of resistance, said Hilbert. My comment: Bacteriophages were linked to cell type differentiation in species from…

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Vitamin B3 and DNA repair

Role of Nicotinamide in DNA Damage, Mutagenesis, and DNA Repair Conclusion: Nicotinamide, which is the dietary precursor for NAD+, provides a substrate for PARP-1 activity…. In various murine models, PARP-1 inhibition was shown to favor apoptotic cell death, reduce inflammatory response, and reduce genomic sensitivity to various carcinogens. However, extrapolation of these data to human, particularly when physiological regimes involved in human carcinogenesis, should be done cautiously. Further studies are needed to determine the effect of high-dose nicotinamide on in…

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Ignoring systems complexity (it’s too complicated)

Host, heal thyself: Immune system self-organizes to minimize biological cost of pathogenic infections Excerpt 1) This approach allowed the scientists to create a new framework that makes it unnecessary to explicitly model intracellular communication, cell differentiation, activation of cofactors, coordination of different cell types, the interaction with the innate immune system, and the full complexity of the recognition process. My comment: Population geneticists took that approach when they invented neo-Darwinian evolution. They eliminated all aspects of nutrient-dependent cell type differentiation…

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Virus-driven cancer treatment and prevention

Blocking a metabolic pathway may shrink aggressive form of common kidney cancer Excerpt: ..the cancer cells appear to rely primarily on the metabolism of an amino acid called glutamine for their energy. My comment:  This links differences in hydrogen atom energies and the anti-entropic epigenetic effect of nutrient energy to virus-driven differences in the metabolism of glutamine and DNA repair. Those differences link viral microRNAs to entropic elasticity. The differences also link nutrient-dependent microRNAs to the stability of organized genomes…

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The microbiome, pharmacogenetics, and privacy

Microbiomes raise privacy concerns DNA from microbes living on the human body can be used to identify individuals. Ewen Callaway 11 May 2015 Excerpt: The odds of identifying someone on the basis of their microbiome is low… My comment: The microbiome links top-down causation from nutrient-dependent RNA-directed DNA methylation to RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all genera via the biophysically constrained chemistry of protein folding during life history transitions. The link to…

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A special issue on nutritional epigenetics

See also: Retinoic acid + one receptor regulate the genome Two decades of scientific progress link what we detailed about RNA-mediated cell type differentiation in our 1996 review: From Fertilization to Adult Sexual Behavior.  Others have begun to learn more about the biological basis of ecological adaptations that link nutrient uptake to the pheromone-controlled physiology of reproduction in all vertebrates by the conserved molecular mechanisms of biophysically constrained RNA-mediated amino acid substitutions and the chemistry of protein folding. For example,…

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