The eternal significance of microRNAs (4)

By: James V. Kohl | Published on: April 20, 2018

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Conclusion: Conserved energy biophysically constrains viral latency.
Metatranscriptomics

High-throughput sequencing and analysis of microbial community cDNA are providing valuable insight into in situ microbial activity and metabolism in the oceans.

When faced with the eternal significance of quantized energy-dependent natural selection for codon optimality, theorists must attack the basics of what is known to serious scientists about biophysically constrained life on Earth.
See for example: Virus-mediated archaeal hecatomb in the deep seafloor
By starting with “raw assemblies” instead of the energy from sunlight that must be linked to the “Assemblies Trinity,” pseudoscientists link “data” to codon optimality. They fail to link the creation of virucidal light from differential gene expression before they link the data to results that are meaningless outside the context of an energy source.
All results can be predicted only in the context of the energy-dependent biophysical constraints that prevent the virus-driven degradation of messenger RNA from destroying the supercoiled DNA that is required to maintain viral latency and healthy longevity.
Nutrition, microRNAs, and Human Health (2017)

MicroRNAs (miRs) hybridize with complementary sequences in mRNA and silence genes by destabilizing mRNA or preventing translation of mRNA.

The authors recapitulate the claims from my 2014 invited review of nutritional epigenetics but fail to address the most important aspect of biophysically constrained viral latency, which requires the energy-dependent creation of microRNAs that prevent the translation of mRNA. The destabilizing effects of viruses are eliminated when enough food energy is available to support RNA-directed DNA methylation and fixation of amino acid substitutions in organized genomes.
See: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

This atoms to ecosystems model of ecological adaptations 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; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.

See for comparison: Prediction of 5-Fluorouracil Toxicity Associated With Dihydropyrimidine Dehydrogenase Gene (DPYD) Polymorphism Using the Secondary Structure Prediction Programs
The predicted toxicity must be linked from the energy-dependent creation of dehydrogenase gene polymorphisms. The failure to do that has led to class action litigation.
See also: DPYD dihydropyrimidine dehydrogenase [ Homo sapiens (human) ]

The protein encoded by this gene is a pyrimidine catabolic enzyme and the initial and rate-limiting factor in the pathway of uracil and thymidine catabolism. Mutations in this gene result in dihydropyrimidine dehydrogenase deficiency, an error in pyrimidine metabolism associated with thymine-uraciluria and an increased risk of toxicity in cancer patients receiving 5-fluorouracil chemotherapy. Two transcript variants encoding different isoforms have been found for this gene.

Finding isoforms is of little use if researchers do not know how the isoforms are created.
medical Definition of isoform.:

any of two or more functionally similar proteins that have a similar but not identical amino acid sequence and are either encoded by different genes or by RNA transcripts from the same gene which have had different exons removed.

Most researchers know nothing about energy-dependent biophysical constraints on the creation of amino acid substitutions in the isoforms.
See for example: NSF’s Big Ideas: Understanding the Rules of Life and The Quantum Leap
The rules of life that include fixation of amino acid substitutions in organized genomes could have been linked from the quantum leap to biophysically constrained viral latency and healthy longevity in all living genera. Instead the presenters failed to answer any of my questions.

1) Has anyone place the rules of Life and the Quantum Leap into the context of food energy-dependent biophysically constrained viral latency and sympatric speciation?
2) Do you think that this parody accurately represents what was known in 2014 about the importance of energy-dependent base pair changes to biophysically constrained protein folding chemistry? All About that Base (Meghan Trainor Parody) 12/10/14
3) Do you agree that questions about genome adaptations compared to the evolution of organized genome are ambiguous in the context of what is known about natural selection for quantized energy-dependent codon optimality?
4) Has the difference in the energy of two photons been linked from altered proton gradients to the protential of hydrogen (pH) and RNA-mediated DNA repair via the creation of microRNAs and enzymes?
NSF funding is largely used to support theories about the emergence of energy and evolution of all biodiversity.
This work would be funded by NSF: The evolutionary history of vertebrate RNA viruses
They claim that the evolutionary history of vertebrates matches the history of the RNA viruses, which they claim is because the viruses evolved. Viruses must steal the quantized energy of sunlight from cell types or they cannot replicate. Does that sound like vertebrate viruses are capable of evolution?
That nonsense was reported as: New study transforms understanding of virus origins and evolution
See also: Estimating evolutionary rates in giant viruses using ancient genomes

…this suggests that these viruses could have diverged at least hundreds of thousands of years ago, and hence have evolved over longer time-scales than previously suggested. We propose that the evolutionary rate and time-scale of pithovirus evolution should be reconsidered in the light of these observations and that future estimates of the rate of giant virus evolution should be carefully examined in the context of their biological plausibility.

All their suggestions have become more ridiculous as more facts about the creation of microRNAs have been placed into the context of biophysically constrained viral latency.
See: MicroRNAs in neural development: from master regulators to fine-tuners

The proper formation and function of neuronal networks is required for cognition and behavior. Indeed, pathophysiological states that disrupt neuronal networks can lead to neurodevelopmental disorders such as autism, schizophrenia or intellectual disability. It is well-established that transcriptional programs play major roles in neural circuit development. However, in recent years, post-transcriptional control of gene expression has emerged as an additional, and probably equally important, regulatory layer. In particular, it has been shown that microRNAs (miRNAs), an abundant class of small regulatory RNAs, can regulate neuronal circuit development, maturation and function by controlling, for example, local mRNA translation. It is also becoming clear that miRNAs are frequently dysregulated in neurodevelopmental disorders, suggesting a role for miRNAs in the etiology and/or maintenance of neurological disease states. Here, we provide an overview of the most prominent regulatory miRNAs that control neural development, highlighting how they act as ‘master regulators’ or ‘fine-tuners’ of gene expression, depending on context, to influence processes such as cell fate determination, cell migration, neuronal polarization and synapse formation.

See also: Learning-dependent chromatin remodeling highlights noncoding regulatory regions linked to autism
They identified a single nucleotide polymorphism known as rs6010065. It is associated with differences in microRNAs linked to autism spectrum disorder.
See also: A Common Allele in FGF21 Associated with Sugar Intake Is Associated with Body Shape, Lower Total Body-Fat Percentage, and Higher Blood Pressure
A single nucleotide polymorphism known as rs838133 was linked from food energy-dependent changes in microRNAs to biophysically constrained viral latency and healthy longevity in the mouse-primate-human model of pheromone-controlled reproduction.
I reiterate: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

In the context of quantized energy as information-driven changes in the microRNA/messenger RNA balance, a single nucleotide polymorphism known as rs3827760, 1540T/C, 370A, V370A, and/or Val370Ala was linked to conserved morphological and behavioral phenotypes in mice and humans.

See: Epigenetics and Autism Spectrum Disorder: Is There a Correlation?

At a time when all serious scientists have linked energy-dependent changes in electrons to ecosystems, questions about correlations are irrelevant.

See: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

Functional connectivity is energy dependent and biophysically constrained by by the energy-dependent physiology of reproduction.

It is time for all biologically uniformed science idiots to admit that the source of all energy-dependent changes in every organism on Earth is sunlight.

See: Resolving sub-cellular miRNA trafficking and turnover at single-molecule resolution

Regulation of microRNA (miRNA) localization and stability is critical for their extensive cytoplasmic RNA silencing activity and emerging nuclear functions. Here, we have developed single-molecule fluorescence-based tools to assess the subcellular trafficking, integrity, and activity of miRNAs.

The regulation of microRNA (miRNA) localization and stability is quantized energy-dependent and pheromone controlled in the context of everything known to serious scientists about biophysically constrained protein folding chemistry and supercoiled DNA, which protects all organized genomes from virus-driven energy theft and genomic entropy.
Why symmetry gets really interesting when it is broken

Energy is conserved…because the laws of physics are the same now as they were a millennium ago…

Long-range coherence and energy storage in biological systems (1968)

The supplied energy is thus not completely thermalized but stored in a highly ordered fashion.

Conserved energy biophysically constrains viral latency.