entropic elasticity

Preventing genomic entropy

Tethering Transposons Excerpt: Transposons—thought to be related to viruses—can copy themselves and insert randomly around the genome. A paper published today (October 15) in Science provides a greater understanding of how cells shut down these rogue jumping genes. My comment: Shouldn’t someone else be claiming that nutrient-dependent microRNAs prevent the accumulation of viral microRNAs that leads to perturbed protein folding, which links mutations to all pathology in the context of an atoms to ecosystems model? Nutrient-dependent pheromone-controlled ecological adaptations: from atoms…

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The stability of organized genomes

Beyond neo-Darwinism—an epigenetic approach to evolution Excerpt from 6/21/79 The evidence suggests… that a relative lack of natural selection may be the prerequisite for major evolutionary advance. Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Excerpt from 6/14/13 (34 years later) …the epigenetic ‘tweaking’ of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive…

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Viruses, amino acids, and somatic cell types (2)

Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain Excerpt: The RNA-seq data enabled us to detect a positive correlation between developmental changes in the magnitude of parental biases and overall gene expression for most imprinted genes. Conclusion: At the level of the organism, our data uncover how paternal and maternal alleles of Bcl-x make vastly different contributions to brain development, a result that has profound implications for the analysis of parentally-inherited polymorphisms in human health. Reported…

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Easy editing: Reinventing our RNA world

Easy DNA Editing Will Remake the World. Buckle Up. Excerpt: Most present-day animals and plants defend themselves against viruses with structures made out of RNA. My comment: RNA-mediated gene duplication and fixation of  RNA-mediated amino acid substitutions in the context of the nutrient-dependent physiology of learning, memory, and reproduction links the biophysically constrained chemistry of cell type differentiation in all genera via conserved molecular mechanisms. That fact was integrated into the science fiction novel Blood Music by Greg Bear, who…

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RNA-mediated gene duplication, fixation, and ecological adaptation

Chromosomal Arrangement of Phosphorelay Genes Couples Sporulation and DNA Replication Excerpt: The simplicity of this coordination mechanism suggests that it may be widely applicable in a variety of gene regulatory and stress-response settings. Reported as: Bacteria use DNA replication to time key decision Excerpt: “Successful sporulation requires two complete copies of the bacterial chromosome, so coordination between the sporulation decision and the completion of DNA replication is very important,” Narula said. “A good analogy might be a semester-long course in…

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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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Virus-driven death by evolutionary theory

Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic Excerpt: The data presented here indicates EBOV is able to generate and fix nucleotide and amino acid variation within co-circulating viral lineages on the time-scale of individual outbreaks, including the presence of country-specific lineages, and which may ultimately produce variants with important fitness differences. Reported as: Three Ebola virus variants identified in Guinea. Excerpt 1) The Ebola epidemic has been ongoing in West Africa for over a…

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Creating and maintaining the human virome

Comprehensive serological profiling of human populations using a synthetic human virome Excerpt from the editor’s summary: Despite differences in the rates of exposure to specific viruses, the antibody responses in most individuals targeted the same viral epitopes. My comment: Received: Fri, 05 Jun 2015 14:19:20 -0400 From an even broader perspective, this may be a step forward towards linking viruses and viral microRNAs to entropic elasticity and the anti-entropic epigenetic effects of nutrient-dependent microRNAs to cell type differentiation via the…

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Uniquely epigenomic gene regulation

A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development Excerpt: Methylation at alternative promoters or splice sites can affect transcript variants expression, whereas enhancer methylation may modulate gene expression (Jones, 2012). These are potential mechanisms for translating DNA methylation information to phenotypes. Reported as: Reprogramming of DNA observed in human germ cells for first time Excerpt: …a notable fraction of the retroelements in our genome are ‘escapees’ and retain their methylation patterns – particularly those retroelements that…

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