RNA-mediated physics, chemistry, and molecular epigenetics (3)

By: James V. Kohl | Published on: May 9, 2016

Summary of the metabolic pathways altered in cancer that are described in this review

Microtargeting cancer metabolism: opening new therapeutic windows based on lipid metabolism

My comment: Metabolic networks are linked to genetic networks by the normal metabolic landscape, which is linked to healthy longevity. Virus-driven energy theft links changes in the metabolic landscape to changes in the physical landscape of supercoiled DNA, which typically maintains healthy longevity across the lifespan by preventing virus-driven entropy. When no consideration is given to facts about virus-driven entropy, you are stuck with theories about brain evolution.
See for example: Metabolic acceleration and the evolution of human brain size and life history 5/4/16 reported as: Humans have faster metabolism than closely related primates, enabling larger brains

My comment: Place that claim into this regression.

Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum 1/15/16
My comment: Copy number variation is nutrient energy dependent
Small RNAs: essential regulators of gene expression and defenses against environmental stresses in plants 2/28/16
My comment: MicroRNA flanking sequences link hydrogen atom transfer in DNA base pairs in solution to nutrient energy-dependent copy number variation.

An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers 4/1/16
reported 4/14/16 as: Scientists document rare DNA transfer between animals and plants
My comment: “Among different bacterial species existing in similar environments, DNA uptake (Palchevskiy & Finkel, 2009) appears to have epigenetically ‘fed’ interspecies methylation and speciation via conjugation (Fall et al., 2007; Finkel & Kolter, 2001; Friso & Choi, 2002). This indicates that reproduction began with an active nutrient uptake mechanism in heterospecifics and that the mechanism evolved to become symbiogenesis in the conspecifics of asexual organisms (Margulis, 1998). In yeasts, epigenetic changes driven by nutrition might then have led to the creation of novel cell types, which are required at evolutionary advent of sexual reproduction (Jin et al., 2011). These epigenetic changes probably occur across the evolutionary continuum that includes both nutrition-dependent reproduction in unicellular organisms and sexual reproduction in mammals. For example, ingested plant microRNAs influence gene expression across kingdoms (Zhang et al., 2012). In mammals, this epigenetically links what mammals eat to changes in gene expression (McNulty et al., 2011) and to new genes required for the evolutionary development of the mammalian placenta (Lynch, Leclerc, May, & Wagner, 2011) and the human brain (Zhang, Landback, Vibranovski, & Long, 2011).” — Kohl (2012)
My comment: Place all claims (above) that link nutrient-dependent ecological adaptations into the context of healthy longevity. Place all claims (below) into the context of  virus-driven energy theft and all pathology.
Wolbachia Blocks Currently Circulating Zika Virus Isolates in Brazilian Aedes aegypti Mosquitoes 5/4/16

reported 5/4/16 as: Bacteria-Infected Mosquitoes Could Slow Spread of Zika Virus

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing 5/3/16

reported 5/1/16 Australia to spend over $11mn to eradicate carps by releasing herpes virus into rivers

My comment: Place all claims about nutrient energy-dependent cell type differentiation and all claims that link virus-driven energy theft into the context of physics and chemistry linked to the conserved molecular mechanisms of cell type differentiation in twin studies. For example,  NASA’s Twins Study Explores Space Through You: Videos Highlight Omics  4/20/16

What does it take to detect entanglement with the human eye?
reported 5/3/16 as  An experiment seeks to make quantum physics visible to the naked eye

RNA splicing is a primary link between genetic variation and disease 4/29/16

3/31/16 Carl Zimmer Episode 5: Everything you thought you knew about the shape of DNA is wrong

4/24/16 Sea Slug Senses 1/15/13 The sea slug that eats the sun (video)

Saturation of recognition elements blocks evolution of new tRNA identities 4/29/16

reported 5/2/16 Discovery of a fundamental limit to the evolution of the genetic code

Two Conserved Histone Demethylases Regulate Mitochondrial Stress-Induced Longevity and Mitochondrial Stress Induces Chromatin Reorganization to Promote Longevity and UPRmt

reported 5/2/16  Genetic switch could be key to increased health and lifespan

The Role of Correlation and Solvation in Ion Interactions with B-DNA 1/19/16

delayed reporting till 5/3/16 A new model for simulating DNA’s ‘atmosphere’ of ions

5/3/16 Part I: Epigenetics: Why Your DNA Isn’t Enough C. David Allis

5/3/16 Part II: Epigenetics in Development and Disease C. David Allis

Genomic instantiation of consciousness in neurons through a biophoton field theory 6/13/14
4/18/16 Dense EM-based reconstruction of the interglomerular projectome in the zebrafish olfactory bulb and 5/1/16 Remote z-scanning with a macroscopic voice coil motor for fast 3D multiphoton laser scanning microscopy 
collectively reported 5/2/16 as Unraveling complex neuronal networks
My comment: The de novo creation of G-protein coupled receptors (GPCRs) links the epigenetic landscape to the physical landscape of supercoiled DNA via olfaction and the innate immune system.

Imaging GPCRs trafficking and signaling with total internal reflection fluorescence microscopy in cultured neurons. Delgado-Peraza F, Nogueras-Ortiz C, Acevedo Canabal AM, Roman-Vendrell C, Yudowski GA. Methods Cell Biol. 2016;132:25-33.
Chapter 1 – Localization and signaling of GPCRs in lipid rafts

Chapter 2 – Imaging GPCRs trafficking and signaling with total internal reflection fluorescence microscopy in cultured neurons
Chapter 4 – Single-molecule resolution of G protein-coupled receptor (GPCR) complexes
Chapter 13 – Resonance Energy Transfer-Based Approaches to Study GPCRs
My comment: Place everything known about nutrient energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution and cell type differentiation into the context of virus-driven energy theft and cancer.

Deletion of Amino Acid Transporter ASCT2 (SLC1A5) Reveals an Essential Role for Transporters SNAT1 (SLC38A1) and SNAT2 (SLC38A2) to Sustain Glutaminolysis in Cancer Cells (4/26/16)
reported on 5/5/16 Starving cancer the key to new treatments

The research team blocked gateways through which the cancer cell was obtaining the amino acid glutamine and found the cells almost completely stopped growing.

My comment: They prevented the viruses in the cancer cell from adapting. Otherwise, energy theft enables amino acid substitutions in the virus that would link ecological variation to healthy longevity when nutrient-stress or social stress is biophysically constrained. Links from the epigenetic landscape to the physical landscape of supercoiled DNA biophysically constrains energy-dependent RNA-mediated cell type differentiation. They have been placed into the context of mutation-driven evolution by theorists who have killed millions with their ridiculous theories.

See for comparison:

reported 5/2/16 We are pleased to announce that today marks the formal release of our latest title: Amber Palaeobiology by Dr David Penney.

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