metabolism

Rejecting what is known about viral microRNAs and nutrient-dependent microRNAs

Of Cells and Limits Leonard Hayflick has been unafraid to speak his mind, whether it is to upend a well-entrenched dogma or to challenge the federal government. At 86, he’s nowhere near retirement. By Anna Azvolinsky | March 1, 2015 Excerpt: The rejection letter came from Francis Peyton Rous who received the Nobel Prize a few years later for his discovery of chicken tumor viruses. My comment: My 2014 invited review of nutritional epigenetics detailed how differences in the microRNA/messenger…

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All of "like kind" in the (bigger) family

All in the (bigger) family Science 16 January 2015: Vol. 347 no. 6219 pp. 220-221 DOI: 10.1126/science.347.6219.220 by Elizabeth Pennisi Abstract: A decade of genetic data and other evidence has persuaded most researchers that insects and crustaceans, long considered widely separated branches of the arthropod family, actually belong together. The new arthropod tree puts hexapods—six-limbed creatures that include insects, springtails, and silverfish—as closer kin to crabs, lobster, shrimp, and crayfish than those “standard” crustaceans are to others such as seed…

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Dual genomes: exposing the evolution industry

Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes Excerpt: “The CDP showed a significant overrepresentation of certain gene ontology (GO) groups (global tests Po0.001–0.009), using the programme FUNC23 (Methods). These groups included GPCRs, in particular olfactory receptors (ORs), and other membrane and cell-surface proteins, as well as proteins related to the immune system, such as the MHC (Class I and II), and drug metabolism…” My comment: Biodiversity “…converges upon a ‘common diplotypic proteome (CDP)’, a distinctive subset…

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Epigenetic pharmacology and RNA-mediated transciptional landscapes

Last year, Vosshall’s group eliminated ideas about the involvement of beneficial mutations in the nutrient-dependent cell type differentiation of mosquitoes. orco mutant mosquitoes lose strong preference for humans and are not repelled by volatile DEET. This year her group showed that nutrient-dependent amino acid substitutions clearly are involved in cell type differentiation. Evolution of mosquito preference for humans linked to an odorant receptor RNA-mediated events have since been linked to sexual dimorphism in mosquitoes. Examination of the genetic basis for sexual…

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Thermodynamic constraints and ecological adaptations sans evolution

Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites Excerpt: “…a two-variable model that combines stability and stress signi ficantly improves predictions. Therefore, both the overall stability [symbol] and the stress [symbol] seem to capture distinct thermodynamic constraints on protein evolution.” My comment: Proteins do not evolve. Nutrients are required. Metabolism of nutrients to species-specific pheromones controls the physiology of reproduction in species from microbes to man. The nutrient-dependent pheromone-controlled physiology of reproduction enables epistasis via nutrient-dependent RNA-directed DNA…

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Pharmacogenomics

“The gene, cell, tissue, organ, organ-system pathway is a neuroscientifically established link between sensory input and behavior. Marts and Resnick (2007) stress the importance of this pathway in the context of a systems biology approach to pharmacogenomics.” (Kohl, 2012) “Naftolin (1981) stressed its importance to the understanding of sex differences. This pathway is sensitive to conditioning. Sensory input from an organism’s environment activates and reactivates the pathway and causes changes in hormone secretion that condition hormone-driven behavior.” (Kohl, 2012) See…

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A model of MHC 'evolution'

Sexual selection and the evolutionary dynamics of the major histocompatibility complex Excerpt: “Here, we present the results of the first model of MHC evolution incorporating both survival and reproduction, modelling the combined effects of natural selection and MHC-based disassortative mating on patterns of MHC allelic diversity.” My comment: Results from their first mathematical model can be compared to representations of biologically-based cause and effect in the context of our model. See From Fertilization to Adult Sexual Behavior. We linked RNA-mediated…

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ALPHA GENOMIX

ALPHA GENOMIX LABORATORIES INC Alpha genomics (for those unfamiliar with their spelling) Re: On this team, Dr. Hani El Shawa, is also first author of Prenatal Ethanol Exposure Disrupts Intraneocortical Circuitry, Cortical Gene Expression, and Behavior in a Mouse Model of FASD. The Journal of Neuroscience, 27 November 2013, 33(48): 18893-18905. Excerpt: “Changes in gene expression reported in this study may be caused by altered DNA methylation, an epigenetic modification that cells use to mediate gene expression (Moore et al.,…

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Nutrient-dependent gene duplication in plants (but not animals?)

Divergence of Gene Body DNA Methylation and Evolution of Plant Duplicate Genes Excerpt 1) “A recent study demonstrated that the DNA methylation in promoter may play a significant role for functional divergence of duplicated genes in human [48].” Excerpt 1 from the cited work [48]: “For 73% of gene pairs, one copy is always hypomethylated compared with the other. This refutes the idea that [RNA-directed] DNA methylation of genes is strictly determined in a tissue-by-tissue manner and indicates the presence…

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2014 and 2004 Nobel Prize in Medicine

2014 Nobel Prize in Medicine is Awarded for Discovery of Brain’s ‘Inner GPS’ Excerpt: “… gray lines show the path followed by a rat as it moves around a box looking for pieces of food.” 2014 Nobel prize in physiology or medicine for finding brain’s ‘you are here’ cells Excerpt: John Stein, professor of physiology at Oxford University, said: “This is great news and well deserved. I remember how great was the scoffing in the early 1970s when John first…

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