anti-entropic

Becoming biologically informed (3)

July 23, 2015
James Kohl
Adaptations, Alternative Splicings, Diseases & Disorders, Ecology, Human Pheromones, Model Organisms, Neuronal Plasticity, Nutrigenomics, Pharmacogenomics, Physics, RNA Directed, Variations
No Comments

See also: Becoming biologically informed and Becoming biologically informed (2) Now available for free: New Perspectives on microRNA in Disease and Therapy (July 22, 2015) My comments: Perhaps someone will correct me if I am wrong. The microRNAs do not appear to participate in a direct response to viruses. But, over long periods of time they may fine-tune the microRNA/messenger RNA balance in the organized genomes of all living genera.  If so, the changes are manifested in morphology and in…

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Easy editing: Reinventing our RNA world

July 23, 2015
James Kohl
Adaptations, base editing, Diseases & Disorders, Ecology, Model Organisms, Nutrigenomics, Pharmacogenomics, RNA Directed, RNA editing, Variations
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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

July 11, 2015
James Kohl
Adaptations, Alternative Splicings, Diseases & Disorders, Ecology, Model Organisms, Nutrigenomics, Pharmacogenomics, RNA Directed
One Comment

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?

July 2, 2015
James Kohl
Adaptations, Alternative Splicings, Diseases & Disorders, Ecology, Human Brain, Human Pheromones, Model Organisms, Neuronal Plasticity, Nutrigenomics, Pharmacogenomics, Physics, RNA Directed, Variations
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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?

July 1, 2015
James Kohl
Adaptations, Diseases & Disorders, Ecology, Model Organisms, Neuronal Plasticity, Nutrigenomics, Pharmacogenomics, RNA Directed, Variations
No Comments

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

June 25, 2015
James Kohl
Adaptations, Ecology, Model Organisms, RNA Directed, Variations
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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

June 5, 2015
James Kohl
Adaptations, Diseases & Disorders, Ecology, Model Organisms, Nutrigenomics, Pharmacogenomics, RNA Directed
One Comment

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

June 5, 2015
James Kohl
Adaptations, Alternative Splicings, Diseases & Disorders, Ecology, Model Organisms
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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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MicroRNAs and inappropriate functions

June 4, 2015
James Kohl
Diseases & Disorders, RNA Directed
No Comments

Oxidative Modification of miR-184 Enables It to Target Bcl-xL and Bcl-w Highlights •miRNAs are oxidized by ROS •Oxidized miR-184 mismatches with the 3′ UTRs of Bcl-xL and Bcl-w •Oxidized miR-184 promotes apoptosis via suppressing Bcl-xL and Bcl-w •Oxidized miR-184 increases the susceptibility of the heart to I/R injury Summary MicroRNAs (miRNAs) are small non-coding RNAs, and they bind to complementary sequences in the three prime untranslated regions (3′ UTRs) of target mRNA transcripts, thereby inhibiting mRNA translation or promoting mRNA…

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30 years of theoretical nonsense

June 2, 2015
James Kohl
Adaptations, Ecology
No Comments

Brain Drain The brain contains lymphatic vessels similar to those found elsewhere in the body, a mouse study shows. By Ashley P. Taylor | June 1, 2015 Excerpt: “If you go into the literature, 20 years ago, the idea was that if you see immune cells in the brain, something must be going wrong…” In our 1996 Hormones and Behavior review article, we wrote (with my emphasis): Immunological Factors The immune system has long been known to perceive certain sexual…

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