Codon-dependent mRNA stability (1)

By: James V. Kohl | Published on: June 25, 2019

Laser Destroys Cancer Cells Circulating in the Blood (6/12/19)

Imagine shooting bad guys in video games, or shining ultraviolet light on bacteria. If that kind of thing (i.e., killing viruses in cancer cells) feels good to you, imagine how satisfying it would be to point this laser at your loved one’s cancer cells.

In vivo liquid biopsy using Cytophone platform for photoacoustic detection of circulating tumor cells in patients with melanoma

These data suggest the potential of in vivo blood testing with the Cytophone for early melanoma screening, assessment of disease recurrence, and monitoring of the physical destruction of CTCs through real-time CTC counting.

The ability to detect and kill cancer cells with a noninvasive procedure links technological advances in laser-assisted cell type counting and cell type differentiaion from the mid-1970s to Identifying brain tumors by differential mobility spectrometry analysis of diathermy smoke via a relatable “smoking gun” in the context of how Olfaction Warps Visual Time Perception.
The links from the creation of the sense of smell in bacteria to our visual perception of mass and energy are relatable, not debatable.
See: Artificial Nose identifies Malignant Tissue in Brain Tumours during Surgery (6/16/19)

The technology is based on differential mobility spectrometry (DMS), wherein flue gas ions are fed into an electric field. The distribution of ions in the electric field is tissue-specific, and the tissue can be identified on the basis of the resulting “odour fingerprint.”

Our visual perception of energy and mass has been linked to “warped” subjective time by the neural energy that collectively represents multisensory inputs at subsecond scales. The creation of the energy links the creation of subatomic particles to the creation of ATP and RNA via the light-activated assembly of the microRNA-RNA-peptide nanocomplex, which is exemplified via the neural energy in peptides and neuropeptide release in the model organism Caenorhabditis elegans.
See: mir-234 controls neuropeptide release at the Caenorhabditis elegans neuromuscular junction (6/12/19)

Previous studies have revealed that miR-137 is required for the development of dendrites and for controlling the release of fast-acting neurotransmitters. Here, we analyzed the function a miR-137 family member (called mir-234) in the nematode animal model using anatomical, behavioral, electrophysiological and neuropeptide analysis. We reveal for the first time that mir-234/miR-137 is required for the release of slow-acting neuropeptides, which may also be of relevance for controlling human brain function.

Differences in the primitive nervous system of C. elegans and differences in human brain function have been placed into the context of how what organisms eat must be linked from their metabolism to their pheromone-controlled physiology of reproduction and the development of behavior linked to physical performance via the nutrient-dependent pheromone-controlled physiology of reproduction in a performance-enhancing microbe.
See: Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism (6/24/19)

Taken together, these studies reveal that V. atypica improves run time via its metabolic conversion of exercise-induced lactate into propionate, thereby identifying a natural, microbiome-encoded enzymatic process that enhances athletic performance.

Eric Topol (physician-scientist, author, editor) wrote:

Whoa. The gut #microbiome of elite athletes (marathon runners) has a bacterium that enhances performance, makes mice run longer, and this is mediated via lactate metabolism @NatureMedicine (file under more #microbiome amazing stuff)

His new book is Deep Medicine: How Artificial Intelligence Can Make Healthcare Human Again

Anyone who still focuses on the role of artificial intelligence in health care probably missed ignored the facts in Nutrient-dependent/pheromone-controlled adaptive evolution: a model (6/14/13)
For example, liberals who thought they were highly evolved mutants failed to link the viruses carried by their ancestors to the nutrient stress and social stress-linked degradation of messenger RNA, which links mutations to to reduced athletic performance and reduced cognition in people who claim that Darwin’s works linked “conditions of life” to mutation-driven evolution.
We are all mutants (2014)

See also:

Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement. (7/26/13)
See for review of the facts about ecological speciation:
Tracking niche variation over millennial timescales in sympatric killer whale lineages (10/7/13)

Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].

The differences in amino acid composition among different tissues can lead to large differences in trophic discrimination [38].

See also: Predicting Gene Ontology Function of Human MicroRNAs by Integrating Multiple Networks (1/29/19)

MicroRNAs (miRNAs) are small endogenous non-coding RNAs and take critical part in many human biological processes. Inferring the functions of miRNAs perhaps is an important strategy for understanding the pathogenesis of disease at the molecular level.

There is no need to infer the functions of miRNAs. Light-activated miRNA biogenesis links the assembly of the miRNA-RNA-peptide nanocomplex to biophysically constrained viral latency and healthy longevity in all living genera.
See for example: Viral delivery of a microRNA to Gba to the mouse central nervous system models neuronopathic Gaucher disease (6/21/19)

Importantly, these impairments can be prevented by simultaneous administration of a miR-resistant GCase, demonstrating that the pathological effects are specifically due to Gba mRNA reduction.

The link from microRNAs in milk exosomes to prevention of pathology may not have been clear until this example of how delivery of any enzyme restored the miRNA/mRNA balance. The light-activated assembly of the miRNA-RNA-peptide nanocomplex is obviously required to create enzymes. In this case, the link from the creation of sunlight to microRNA-mediated DNA repair in the context of the physiology of reproduction and transgenerational epigenetic inheritance should be perfectly clear.
See also:
Virus-mediated archaeal hecatomb in the deep seafloor
Eukaryotic plankton diversity in the sunlit ocean
Subatomic: An Atom-Building Board Game
Cytosis: A Cell Biology Board Game
The extent of codon usage bias in human RNA viruses and its evolutionary origin (2003)

…the strong correlation between base and dinucleotide composition and codon usage bias suggested that mutation pressure rather than natural (translational) selection is the most important determinant of the codon bias observed.

See for comparison: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition (2016)
There is no such thing as an evolutionary origin of codon identity. It is light-activated and microRNAs are the endogenous substrates that must be linked from the maternal-to-zygotic transition in mammals to all biodiversity via the physiology of pheromone-controlled reproduction in bacteria.

See also: Biological Information: New Perspectives

It is obvious to all serious scientists that the virus-driven degradation of mRNA must be biophysically constrained by food energy and the physiology of reproduction. It is impossible to teach that fact to biologically uninformed science idiots.
But see: Role of Exosomes in Crosstalk Between Cancer-Associated Fibroblasts and Cancer Cells

And watch: Genome-Wide Study Reveals a Novel Regulatory Pathway: Translation Affects mRNA Stability in a Codon-Dependent Manner (2019)

This webinar will outline a study that combined genome-wide and classical molecular approaches to demonstrate that translation strongly affects mRNA stability in a codon-dependent manner, ultimately influencing mRNA and protein levels in higher organisms.

Ribosomes are the most abundant RNA-binding structures in the cell, and while their main function is to decode nucleotides into amino acid sequences, translation can also affect mRNA stability depending on codon composition. This regulatory pathway is different from codon usage or bias and is known as “codon optimality,” defined as the property of given codons to regulate mRNA stability in a translation-dependent manner.

Natural selection for energy-dependent codon optimality links microRNA biogenesis to the genesis of all biodiversity via food energy-dependent pheromone-controlled biophysically constrained viral latency in species from microbes to humans.

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