RNA-directed DNA methylation

Virus-driven disorder prevention and health promotion

The dynamic epigenome and its implications for behavioral interventions: a role for epigenetics to inform disorder prevention and health promotion Excerpt: Evidence has also been growing about the role of epigenetic modification in response to the social environment. My comment: Unexpectedly, Szyf et al., (2016) fail to mention all the evidence of epigenetically-effected RNA-mediated cause and effect that has accumulated since we published our 1996 Hormones and Behavior review. That may explain why they also failed to link energy-dependent hydrogen-atom…

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Hydrogen-atom transfer in DNA base pairs (6)

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. See also: Tumor-suppressing gene restrains mobile elements that can lead to genomic instability Excerpt: The investigators found that normal p53 gene action restrains transposons, mobile genetic elements…

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Ecological genomics: teleophobes respond (too late)

Forecasting Ecological Genomics: High-Tech Animal Instrumentation Meets High-Throughput Sequencing Conclusion: Twenty years ago, an essay about sequencing genomes and remotely tracking animals across the globe in real time would have been the subject of science fiction. In 2015, there are over 50,000 animals being tracked [12], and single research groups now sequence dozens, up to hundreds, of individual genomes [17,82]. By embracing new technology and integrating these data streams into an ecological genomic framework (Fig 1), we are now poised…

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Ecological law, cooperation, and DNA repair

Ecological laws: what would they be and why would they matter? Abstract excerpt: … I argue, the existence of ecological laws would make ecological explanations irreducible to even the most complete possible physical explanations of the same phenomena. Ecological laws would make ecology genuinely autonomous from physics. My comment: This is a fool’s argument.  Serious scientists know physics and chemistry must be linked to biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry. The links must be placed into the context of…

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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 Excerpt: [W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et…

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Epigenetic (re)programming of behavior

Epigenetic (re)programming of caste-specific behavior in the ant Camponotus floridanus Excerpt: Our results suggest that behavioral plasticity in animals may be regulated in an epigenetic manner via histone modification. My comment: Experimental manipulation of a single gene changed behavior. The evidence suggests all invertebrate and all vertebrate morphological and behavioral phenotypes can be linked via nutrient-dependent changes in microRNAs, adhesion proteins, and supercoiled DNA. See: The phylogenetic utility and functional constraint of microRNA flanking sequences My comment: Nutrient-dependent RNA methylation, RNA-directed…

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Does metabolism link beneficial mutations to cancer?

Viruses steal nutrients needed by the cell. The theft deregulates protein folding, which is how viruses perturb biophysically constrained nutrient energy-dependent protein folding chemistry. The theft of nutrients by viruses links mutations to all pathology. Nutrients are required for RNA methylation and RNA-directed DNA methylation. Cell types do not hypermethylate unless nutrient-dependent hypermethylation is required to protect organized genomes from virus-driven entropy. Simply put, viruses cause nutrient-dependent hypermethylation when hypermethylation is required to protect organized genomes from virus-driven entropy. Evolutionary…

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RNA-mediated theory killers (4)

DNA methylation and microRNA biomarkers for noninvasive detection of gastric and colorectal cancer Excerpt: At this moment, DNA methylation and non-coding RNA including with microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) represent the largest body of available literature on epigenetic biomarkers with the highest potential for cancer diagnosis. My comment: The SLC19A3 microRNA was mentioned in the context of cancer and brain development in The impact of new technologies on clinical decision-making in health care. The location of the base…

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RNA-mediated regulatory mechanisms link microbes to humans (3)

See also: RNA-mediated regulatory mechanisms link microbes to humans and RNA-mediated regulatory mechanisms link microbes to humans (2) Regulation of gene expression The effects of miRNA dysregulation of gene expression seem to be important in cancer.[10] For instance, in gastrointestinal cancers, a 2015 paper identified nine miRNAs as epigenetically altered and effective in down-regulating DNA repair enzymes.[11] The effects of miRNA dysregulation of gene expression also seem to be important in neuropsychiatric disorders, such as schizophrenia, bipolar disorder, major depressive…

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