RNA methylation

Secular humanism and ecoterrorism

June 2, 2016
James Kohl
Adaptations, Alternative Splicings, Ecology, Model Organisms, Physics, RNA Directed, RNA methylation, RNA-directed DNA methylation, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, RNA-mediated toxicity, RNA–Mediated Epigenetic Heredity, Variations
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Noncoding RNAs Not So Noncoding Excerpt: “Were there going to be dozens of [micropeptides]? Were there going to be hundreds, like there are hundreds of microRNAs?” says Ingolia. “We just didn’t know.” See also: Number of microRNAs in Human Genome Skyrockets Excerpt: “…researchers from Thomas Jefferson University in Philadelphia have released data that adds another 3,707 novel miRNA sequences to the human genome, in addition to the 1,900 sequences previously described. The results from this study were published recently in…

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MicroRNA-mediated RNA epigenetics

January 4, 2016
James Kohl
Adaptations, Alternative Splicings, Ecology, Model Organisms, Nutrigenomics, Pharmacogenomics, RNA Directed, RNA methylation, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, RNA-mediated toxicity, RNA–Mediated Epigenetic Heredity, Variations
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RNA Epigenetics DNA isn’t the only decorated nucleic acid in the cell. Modifications to RNA molecules are much more common and are critical for regulating diverse biological processes. Excerpt: …specific alternative splicing types, such as intron retention, exon skipping, and alternative first or last exon usage, were highly correlated with m6A decoration. And silencing the m6A methylating protein METTL3 affected global gene expression and alternative splicing patterns in both human and mouse cells.2 My comment: “Silencing” a protein effects global…

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

January 4, 2016
James Kohl
Adaptations, Alternative Splicings, Ecology, Model Organisms, RNA Directed, RNA methylation, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, RNA-mediated toxicity, RNA–Mediated Epigenetic Heredity, Variations
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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

January 1, 2016
James Kohl
Adaptations, Ecology, Model Organisms, RNA Directed, RNA methylation, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, RNA-mediated toxicity, RNA–Mediated Epigenetic Heredity, Variations
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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?

December 27, 2015
James Kohl
Adaptations, Alternative Splicings, biophotonics, Diseases & Disorders, Ecology, Light Energy, Model Organisms, Neuronal Plasticity, Nutrigenomics, Pharmacogenomics, Physics, RNA Directed, RNA methylation, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, RNA-mediated toxicity, RNA–Mediated Epigenetic Heredity, Variations
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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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Are mutations beneficial?

November 17, 2014
James Kohl
Adaptations, Alternative Splicings, Diseases & Disorders, Ecology, Model Organisms, Nutrigenomics, RNA Directed, RNA methylation, RNA-directed DNA methylation, RNA-mediated epigenetic regulation of gene expression, RNA-mediated gene silencing, RNA-mediated toxicity, RNA–Mediated Epigenetic Heredity, Variations
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Researchers develop non-invasive method to detect tumor-causing mutations in saliva Excerpt: “…a multiplexible electrochemical sensor uses electrode chips to enable vesicular entities in saliva called exosomes to rapidly release molecular constituents (DNA, RNA and proteins) while simultaneously detecting any mutations in tumor-causing DNA sequences. The total detection time is less than 10 minutes and required a small saliva sample.” My comment: This news about multiplexing attests to the complexity of systems biology, which links amino acid substitutions to mutated DNA…

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Biophysically constrained beginnings of RNA and DNA

September 8, 2014
James Kohl
Adaptations, Alternative Splicings, Autophagy, biophotonics, Diseases & Disorders, Ecology, Light Energy, Model Organisms, Physics, RNA Directed, RNA methylation, Variations
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Any anonymous participant in the discussion of: DNA may have had humble beginnings as nutrient carrier (Sep 01, 2014 by Adam Hadhazy) asks: “when are you going to keep quiet?” In a series of responses, I have explained the problem I have with honoring his request. The following excerpts from Wikipedia and other sources are loosely strung together because there is no point to providing more extensive details of biologically-based cause and effect until others accept the fact that mutations…

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