From angstroms to ecosystems

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“… viral latency is responsible for life-long pathogenesis and mortality risk…”

What should have been reported as the end of neo-Darwinian theory was not, so far as I know, reported at all.

On May 11, 2016, I presented RNA-mediated physics, chemistry, and molecular epigenetics as the last in a 4-part series that included What is life when it is not protected from virus driven entropy.

Nothing about the 4 presentations in 3 months was reported by anyone but me. The consequences may be severe.Who do you trust to use the latest potential weapon of mass destruction?

This DIY Lab starter kit provides all the equipment, reagents and materials you need to get started in molecular biology and genetic engineering. Also, includes the PTC Genotyping Kit and the Bioluminescent Bacterial Transformation Kit so you can run your first experiments! Comes with tutorials and instructional videos explaining the Science and how to use the equipment.

The “Science” of cell type differentiation has not been explained outside the context of the references I cited in my presentations earlier this year. Watch what happens when amateur molecular biologists or terrorists decide to start tweaking everything that is known to link energy-dependent changes from angstroms to ecosystems in all living genera. Try to track the damage to the citation linked below.

From hydrogen atom transfer in DNA base pairs to ecosystems

[1] Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
[2] Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution.
[3] Photonic Maxwell’s Demon
[4] Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
[5] Observation of Gravitational Waves from a Binary Black Hole Merger
[6] Re-criticizing RNA-mediated cell evolution: a radical perspective
[7] From Fertilization to Adult Sexual Behavior
[8] Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing
[9]   Long non-coding RNAs in innate and adaptive immunity
[10]Defective control of pre–messenger RNA splicing in human disease
[11] What is Life?
[12] Conditional iron and pH-dependent activity of a non-enzymatic glycolysis and pentose phosphate pathway
[13]Structural diversity of supercoiled DNA
[14] Metabolic Reprogramming with a Long Noncoding RNA
[15] New insights into the hormonal and behavioural correlates of polymorphism in white-throated sparrows, Zonotrichia albicollis
[16] The metabolic background is a global player in Saccharomyces gene expression epistasis
[17]Dynamics of epigenetic regulation at the single-cell level
[18] A new view of transcriptome complexity and regulation through the lens of local splicing variations
[19] Pan-neuronal imaging in roaming Caenorhabditis elegans
[20] Distinct Circuits for the Formation and Retrieval of an Imprinted Olfactory Memory
[21] System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes
[22] Nutrient-dependent/pheromone-controlled adaptive evolution: a model
[23] Role of olfaction in Octopus vulgaris reproduction
[24] Cytogenetic approaches for determining ecological stress in aquatic and terrestrial biosystems
[25] Mitochondrial functions modulate neuroendocrine, metabolic, inflammatory, and transcriptional responses to acute psychological stress
[26] Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity 
[27]Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

The Origin of Information: How to Solve It (Revised title: RNA mediated molecular epigenetics and virus driven entropy)

1] The phylogenetic utility and functional constraint of microRNA flanking sequences
[2] Structural diversity of supercoiled DNA
[3] UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair
[4] Phosphorylation-Mediated Regulation of Alternative Splicing in Cancer
[5] An Epigenetic Signature for Monoallelic Olfactory Receptor Expression
[6] Cyanobacteria use micro-optics to sense light direction
[7] Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function 
[8] Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution
[9] RNA-Mediated Regulation of HMGA1 Function
[10] An expanded sequence context model broadly explains variability in polymorphism levels across the human genome
[11] The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
[12] miR-30e controls DNA damage-induced stress responses by modulating expression of the CDK inhibitor p21WAF1/CIP1 and caspase-3
[13] Redefining part of 300 year-old classification system for grouping members of the animal kingdom
[14]  Systematic microRNAome profiling reveals the roles of microRNAs in milk protein metabolism and quality: insights on low-quality forage utilization
[15] Human milk miRNAs primarily originate from the mammary gland resulting in unique miRNA profiles of fractionated milk
[16] Neuroscience of Early-Life Learning in C. elegans
[17] Differential Odour Coding of Isotopomers in the Honeybee Brain
[18] Breast Milk Sugars Support Infant Gut Health
[19] C. elegans lifespan extension by osmotic stress requires FUdR, base excision repair, FOXO, and sirtuins

What is life when it is not protected from virus driven entropy

[1] Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins
[2] Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
[3] The phylogenetic utility and functional constraint of microRNA flanking sequences
[4] Structural diversity of supercoiled DNA
[5] Single-molecule fluorescence measurements reveal the reaction mechanisms of the core-RISC, composed of human Argonaute 2 and a guide RNA
[6] Regulatory evolution of innate immunity through co-option of endogenous retroviruses
[7] UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair
[8] An Epigenetic Signature for Monoallelic Olfactory Receptor Expression
[9] Experience Affects Critical Period Plasticity in the Visual Cortex through an Epigenetic Regulation of Histone Post-Translational Modifications
[10] Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function
[11] Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution
[12] RNA-Mediated Regulation of HMGA1 Function
[13] An expanded sequence context model broadly explains variability in polymorphism levels across the human genome
[14] Ligand-Controlled C(sp3)–H Arylation and Olefination in Synthesis of Unnatural Chiral α–Amino Acids
[15] Dissipation Bounds All Steady-State Current Fluctuations
[16] Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity
[17] The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
[18]  Systematic microRNAome profiling reveals the roles of microRNAs in milk protein metabolism and quality: insights on low-quality forage utilization
[19] Human milk miRNAs primarily originate from the mammary gland resulting in unique miRNA profiles of fractionated milk
20] Design and synthesis of a minimal bacterial genome
[21] A Small RNA-Catalytic Argonaute Pathway Tunes Germline Transcript Levels to Ensure Embryonic Divisions
[22] Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos
[23] Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity
[24] Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
See also:
Neuroscience of Early-Life Learning in C. elegans
Differential Odour Coding of Isotopomers in the Honeybee Brain
Breast Milk Sugars Support Infant Gut Health
C. elegans lifespan extension by osmotic stress requires FUdR, base excision repair, FOXO, and sirtuins
Ancient virus found hibernating in the human genome—and it might wake up

RNA-mediated physics, chemistry, and molecular epigenetics

[1] A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution
[2] Climate warming is predicted to reduce omega-3, long-chain, polyunsaturated fatty acid production in phytoplankton
[3] Maternal choline intake alters the epigenetic state of fetal cortisol-regulating genes in humans
[4] Electrolytes induce long-range orientational order and free energy changes in the H-bond network of bulk water
[5] Serial interactome capture of the human cell nucleus
[6] Pado, a fluorescent protein with proton channel activity can optically monitor membrane potential, intracellular pH, and map gap junctions
[7] Dissipation Bounds All Steady-State Current Fluctuations
[8] Physicists prove energy input predicts molecular behavior
[9] Metabolic Regulation of Histone Post-Translational Modifications
[10] Architecture of the symmetric core of the nuclear pore
[11] Structural diversity of supercoiled DNA
[12] The 3.8 Å resolution cryo-EM structure of Zika virus
[13] Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia.
[14] Force distribution in a semiflexible loop
[15] Mammalian elongation factor 4 regulates mitochondrial translation essential for spermatogenesis
[16] The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression
[17] Human milk miRNAs primarily originate from the mammary gland resulting in unique miRNA profiles of fractionated milk
[18] From Mosquitos to Humans: Genetic Evolution of Zika Virus
[19] Comprehensive Transcriptome Profiles of Streptococcus mutans UA159 Map Core Streptococcal Competence Genes
[20]  A Tunable Mechanism Determines the Duration of the Transgenerational Small RNA Inheritance in C. elegans
[21] Resveratrol Attenuates Trimethylamine-N-Oxide (TMAO)-Induced Atherosclerosis by Regulating TMAO Synthesis and Bile Acid Metabolism via Remodeling of the Gut Microbiota
[22] Wolbachia Blocks Viral Genome Replication Early in Infection without a Transcriptional Response by the Endosymbiont or Host Small RNA Pathways
[23] Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes
[24] Identification of Amino Acid Substitutions Supporting Antigenic Change of Influenza A(H1N1)pdm09 Viruses;
[25] Nutrient-dependent/pheromone-controlled adaptive evolution: a model
[26] The phylogenetic utility and functional constraint of microRNA flanking sequences;
[27] Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity
[28] Olfactory organ of Octopus vulgaris: morphology, plasticity, turnover and sensory characterization
[29] From Fertilization to Adult Sexual Behavior
[30] Endolysosomal trafficking of viral G protein-coupled receptor functions in innate immunity and control of viral oncogenesis
[31] An Epigenetic Signature for Monoallelic Olfactory Receptor Expression
[32] Mitochondrial functions modulate neuroendocrine, metabolic, inflammatory, and transcriptional responses to acute psychological stress
[33] Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity
[34] Evolution of Constrained Gonadotropin-releasing Hormone Ligand Conformation and Receptor Selectivity
[35] Induction of FOS immunoreactivity in central accessory olfactory structures of the female rat following exposure to conspecific males,
[36] Stimulus-specific combinatorial functionality of neurona c-fos enhancers
[37]  Allosteric switch regulates protein–protein binding through collective motion
[38] Stress-induced gene expression and behavior are controlled by DNA methylation and methyl donor availability in the dentate gyrus,
[39] Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation
[40] Rapid Down-Regulation of Glucocorticoid Gene Expression in the Dentate Gyrus after Acute Stress in vivo: Role of DNA Methylation and microRNA Activity
[41] Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders
[42] Molecular requirements for a pandemic influenza virus: An acid-stable hemagglutinin protein
[43] Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant
[44] The SNP rs1625579 in miR-137 gene and risk of schizophrenia in Chinese population: A meta-analysis
[45] COMT val158met polymorphism and molecular alterations in the human dorsolateral prefrontal cortex: Differences in controls and in schizophrenia
[46] Reduced protein synthesis in schizophrenia patient-derived olfactory cells
[47] Stress dynamically regulates behavior and glutamatergic gene expression in hippocampus by opening a window of epigenetic plasticity
[48] Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults
[49] Essential role for a novel population of binucleated mammary epithelial cells in lactation

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