metabolism

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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Pattern recognition: biogeochemical structure and function

Microbes Effect on the Brain Excerpt: Recent research shows dramatic effects of microbe products from the gut on mental function—depression, stress, autism, and degenerative illness. In humans, many studies show microbes affect anxiety, mood, depression and social behavior. Direct effects are through secreted products, stimulation of the enteric nervous system and travel of microbes into the brain, while indirect factors are microbes’ influence on immune function affecting behavior. Microbes produce molecules that transform into hormones and neurotransmitters or they produce…

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Ignoring systems complexity (it’s too complicated)

Host, heal thyself: Immune system self-organizes to minimize biological cost of pathogenic infections Excerpt 1) This approach allowed the scientists to create a new framework that makes it unnecessary to explicitly model intracellular communication, cell differentiation, activation of cofactors, coordination of different cell types, the interaction with the innate immune system, and the full complexity of the recognition process. My comment: Population geneticists took that approach when they invented neo-Darwinian evolution. They eliminated all aspects of nutrient-dependent cell type differentiation…

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Virus-driven cancer treatment and prevention

Blocking a metabolic pathway may shrink aggressive form of common kidney cancer Excerpt: ..the cancer cells appear to rely primarily on the metabolism of an amino acid called glutamine for their energy. My comment:  This links differences in hydrogen atom energies and the anti-entropic epigenetic effect of nutrient energy to virus-driven differences in the metabolism of glutamine and DNA repair. Those differences link viral microRNAs to entropic elasticity. The differences also link nutrient-dependent microRNAs to the stability of organized genomes…

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A special issue on nutritional epigenetics

See also: Retinoic acid + one receptor regulate the genome Two decades of scientific progress link what we detailed about RNA-mediated cell type differentiation in our 1996 review: From Fertilization to Adult Sexual Behavior.  Others have begun to learn more about the biological basis of ecological adaptations that link nutrient uptake to the pheromone-controlled physiology of reproduction in all vertebrates by the conserved molecular mechanisms of biophysically constrained RNA-mediated amino acid substitutions and the chemistry of protein folding. For example,…

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Retinoic acid + one receptor regulate the genome

See also: Epigenetics: microRNAs effect an integrative pathway for my additional comments on Master orchestrator of the genome is discovered, stem cell scientists report) Retinoic acid is a metabolite of vitamin A (retinol) that mediates the functions of vitamin A required for growth and development. The fibroblast growth factor receptor 1 “…gene provides instructions for making a protein called fibroblast growth factor receptor 1. This protein is one of four fibroblast growth factor receptors, which are related proteins that are…

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Epigenetics: microRNAs effect an integrative pathway

Global Developmental Gene Programing Involves a Nuclear Form of Fibroblast Growth Factor Receptor-1 (FGFR1) Excerpt 1) The accumulation of hypoglycosylated nuclear FGFR1 (nFGFR1) is stimulated by a variety of developmental signals, including various growth factors, hormones, and neurotransmitters as well as a reduction in cell contact. This is the reason that this pathway is referred to as integrative [1, 15]. Reported as: Master orchestrator of the genome is discovered, stem cell scientists report Summary: New research shows how a single…

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Viruses in gut microbes

Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells 5/4/15 Excerpt: Extended Data Figure 3 | Generation of H3.3-isoform-specific antibodies. Related to Fig. 1. a, Schematic of amino acid sequence differences for the canonical histones H3.1 and H3.2 versus the histone variant H3.3. H3.3 differs from H3.2 or H3.1 at only 4 or 5 amino acids, positions 31, 87, 89, 90 and 96, as indicated. My comment: The difference in amino acid substitutions can be linked…

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A genetic variant refutes neo-Darwinism

Summary: They link a single nucleotide polymorphism (SNP) to a genetic variant that decreases viability of an embryo, without linking a nutrient-dependent RNA-mediated amino acid substitution to pheromone-controlled cell type differentiation that begins in the embryo and continues throughout the life history transitions of invertebrates and vertebrates. A Benefit of Failed Pregnancy? This genome-wide association study revealed “…a striking link between mitotic aneuploidy and a single nucleotide variant (SNP rs2305957) on chromosome 4 of maternal genomes.” Excerpt: “There’s this genetic…

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The miRNA/mRNA balance: a suboptimal strategy?

Cells exercise suboptimal strategy to survive Excerpt: “Learning the secrets of alternate molecular pathways could provide clues about how to use them to patients’ advantage, she said.” My comment: The same molecular pathways control the nutrient-dependent physiology of reproduction in all genera. They link RNA-directed DNA methylation to RNA-mediated cell type differentiation via fixation of amino acid substitutions that determine cell types. See also: Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin “Mechanisms of epistasis are often best revealed through…

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