protein-folding

Becoming biologically informed

RNA-mediated pathogenic mechanisms in polyglutamine diseases and amyotrophic lateral sclerosis Abstract excerpt: In this article, we describe various common RNA toxicity pathways, namely epigenetic gene silencing, nucleolar stress, nucleocytoplasmic transport, bi-directional gene transcription, repeat-associated non-ATG translation, RNA foci formation and cellular protein sequestration. Journal article conclusion: Although protein toxicity was considered to play a major role in the pathogenesis of repeat expansion diseases, we now know that mutant transcripts also induce cell dysfunction and death via multiple mechanisms, such as…

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“New” epigenetic mechanism for lifelong learning?

Critical Role of Histone Turnover in Neuronal Transcription and Plasticity Reported as: Lifelong learning is made possible by recycling of histones, study says Also reported as: New epigenetic mechanism revealed in brain cells Excerpt: In humans, researchers used a technique called 14C/12C bomb pulse dating to measure turnover. The technique is based on the fact that high levels of radioactive carbon (14C) were released into the atmosphere during the 1950s and 1960s, when open-air nuclear bomb testing occurred following the…

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microRNAs and memory: Why trust a theory?

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems Abstract excerpt: … links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding… manifested in increasing organismal complexity… My comment: The increasing organismal complexity attributed to microRNAs is manifested in the learning abilities and in the memory of…

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Protein folding and Google page rank

Pheromones.com has been on the first page of a Google search for “pheromones” for several months. See: https://www.google.com/?gws_rd=ssl#q=pheromones Today, RNA-mediated.com appeared on the first page of a Google search for “RNA mediated” See: https://www.google.com/?gws_rd=ssl#q=RNA+mediated My domains may remain in a key position for information dissemination, or they may be placed into the background by Google’s algorithms. In either case, it has become clear that RNA-mediated events link the nutrient-dependent pheromone-controlled physiology of reproduction to biodiversity in species from microbes to…

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Living the life that randomness created? (Sarcasm alert)

The Living Set Mathematical and computational approaches are making strides in understanding how life might have emerged and organized itself from the basic chemistry of early Earth. By Wim Hordijk | June 1, 2015 Excerpt: Put some E. coli in a dish with appropriate nutrients, and after a few days the dish will be teeming with new bacterial offspring. My comment: Put some genetically altered P. fluorescens in a dish and leave them “over-the-weekend” with their missing flagella over-the-weekend. Forget…

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microRNAs, glycosylation, and genomes

Summary: Given what is currently known about RNA-mediated cell type differentiation in all genera, it may be impossible for theorists to link mutations to evolution via glycosylation. miRNA proxy approach reveals hidden functions of glycosylation Abstract excerpt: Glycosylation, the most abundant posttranslational modification, holds an unprecedented capacity for altering biological function. Journal article excerpt: …glycans play a role in every major disease (1), and there are clinical examples of drugs targeting glycosylation enzymes… suggesting that glycosylation enzymes may provide fallow…

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Alternative splicings: epigenetics meets pharmacogenomics

Alternative splicing [is] …a regulated process during gene expression that results in a single gene coding for multiple proteins… [T]he proteins translated from alternatively spliced mRNAs will contain differences in their amino acid sequence and, often, in their biological functions…. See also: Alternative RNA Splicing in Evolution Excerpt: It now appears that alternative splicing is, perhaps, the most critical evolutionary factor determining the differences between human beings and other creatures. See also: From Fertilization to Adult Sexual Behavior Excerpt: Small…

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Epigenetic regulation of aging by glycine and GnRH

Summary:  “…the regulation of two genes involved with the production of glycine, the smallest and simplest amino acid, is partly responsible for some of the characteristics of aging. This indicates that the aging process in the mitochondrion is controlled by epigenetic regulation, not by mutations.” My comment: The broad-based extension of the fact that aging is epigenetically controlled, extends everything known about RNA-mediated cell type differentiation across the life history transitions of all genera. The focus here is on vertebrates,…

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Viruses and the human-like microbiome

Ocean’s microbiome has incredible diversity – and human likeness Excerpt: The microbiome of the world’s biggest ecosystem and one of the smallest appear to function in surprisingly similar ways. The New Scientist article  reports on: Structure and function of the global ocean microbiome Journal article abstract conclusion: …vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with…

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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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