5th-6th Sept 2018 Dublin, Ireland

The eternal significance of microRNAs (8)

Use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation and aging has been replaced by the use of model systems of biological processes.  Biological processes can be compared to so-called “evolutionary processes” to show that only biological processes need to be considered in the context of Darwin’s “conditions of life” or answers to the the question  What is Life? Schrödinger (1944).
K. L. Mettinger et al. (eds.), Exosomes, Stem Cells and MicroRNA, Advances in Experimental Medicine and Biology 1056, https://doi.org/10.1007/978-3-319-74470-4_6

This volume provides insight into the pivotal roles of stem cells, exosomes and other microvesicles in biofunction and molecular mechanisms and their therapeutic potential in translational nanomedicine. It further highlights evidence from recent studies as to how stem cell derived exosomes and microRNAs may restore and maintain tissue homeostasis, enable cells to recover critical cellular functions and begin repair regeneration.

Chapter 2 The Emerging Roles of microRNAs in Stem Cell Aging

involved in many biological processes such as developmental timing, differentiation, cell death, stem cell proliferation and differentiation, immune response, aging and cancer. Accumulating studies in recent years suggest that miRNAs play crucial roles in stem cell division and differentiation. In the present chapter, we present a brief overview of these studies and discuss their contributions toward our understanding of the importance of miRNAs in normal and aged stem cell function in various model systems.

Chapter 6  MicroRNAs, Regulatory Messengers Inside and Outside Cancer Cells

…like hormones, miRNAs can be secreted and regulate gene expression in recipient cells. Altered expression levels of miRNAs in cancer cells determine the acquisition of fundamental biological capabilities (hallmarks of cancer) responsible for the development and progression of the disease.

Model systems link the energy-dependent creation of microRNAs from microRNA biogenesis to the regulation of all cancer hallmarks. The virus-driven degradation of messenger RNA has been linked to all cancers and all other pathology in species from microbes to humans. Natural selection for energy-dependent codon optimality has been linked to healthy longevity.
See: Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition
See for comparison:  The Neutral Theory in Light of Natural Selection May 2, 2018

…50 years after its introduction by Kimura. We argue that the neutral theory was supported by unreliable theoretical and empirical evidence from the beginning, and that in light of modern, genome-scale data, we can firmly reject its universality. The ubiquity of adaptive variation both within and between species means that a more comprehensive theory of molecular evolution must be sought.

The ubiquity of adaptive variation attests to the facts about how the creation of quantized energy is linked to biophysically constrained viral latency. Adaptive variation links energy-dependent changes from angstroms to ecosystems in all living genera  via the physiology of their food energy-dependent pheromone-controlled reproduction.

For comparison to mRNA stability during the maternal-to-zygotic transition, see: Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults

The energy-dependent molecular mechanisms of recombination clearly link microRNA biogenesis to the stability of organized genomes during the life histories of all genera. Serious scientists object to the use of definitions in attempts to explain any aspect of species-specific biophysically constrained cell type differentiation.

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

…it is tiresome to raise the same objections repeatedly, wondering why researchers have not fulfilled some of the basic requirements for establishing the occurrence of an autophagic process.

 

Cases of Cytosis

Autophagy.pro vs Nature Publications Group

Autophagy is the antiphage defense strategy (James V. Kohl: December 8, 2016)

Autophagy.pro was launched on 11 December 2017

See for comparison from the Nature Publications Group.  First, they try to establish a more complicated new definition with several different pathways

Autophagy

Autophagy is a process by which cellular material is degraded by lysosomes or vacuoles and recycled. Several autophagy pathways operate within a cell, including macroautophagy, microautophagy and chaperone-mediated autophagy.

After the new definition, and the extension of vague processes and magical pathways to macroautophagy, microautophagy and chaperone-mediated autophagy, we see:

Latest Research and Reviews

An and Harper quantify ribophagy in mammalian cells and show that nutrient-deprivation-induced ribophagy is independent of the ATG8 conjugation system, whereas proteotoxic stress-induced ribophagy requires ATG5 and VPS34.

The similarities and differences between the energy-dependent changes in epigenetic effects of nutrient stress and the epigenetic effects of social stress has not been addressed in published works until recently. But see: microRNA Items: 1 to 20 of 67725.
See for comparison: ribophagy Items: 1 to 20 of 29
Food energy-dependent changes in the microRNA/messenger RNA balance biophysically constrain viral latency in species from microbes to humans. The virus-driven degradation of messenger RNA has been linked to all pathology. The “Nature Publications Group” tries to sneak up from behind with the less detailed link from ribophagy to autophagy.
Research | 11 December 2017
Systematic analysis of ribophagy in human cells reveals bystander flux during selective autophagy

Research | 11 December 2017 | open
SPLICS: a split green fluorescent protein-based contact site sensor for narrow and wide heterotypic organelle juxtaposition
Research | 11 December 2017
Autophagy induced during apoptosis degrades mitochondria and inhibits type I interferon secretion
Research | 11 December 2017 | open
RAB37 interacts directly with ATG5 and promotes autophagosome formation via regulating ATG5-12-16 complex assembly
Sour grapes?

Nobody wants to belong to the party of losers. One of the best strategies in such a case is evidently an interpretation of the change as a gradual accumulation of knowledge while their work has always been at the cutting edge. — Kalevi Kull

The losers at the “Nature Publications Group” banned me from commenting on any article (~two years ago). Predictably, the “Nature Publications Group” and all others will be forced to link the virus-driven degradation of messenger RNA to all pathology and eliminate the pseudoscientific nonsense touted by neo-Darwinian theorists and “Big Bang” cosmologists.
See also:  Journal of Genetics and DNA Research Articles in Press | Volume 1, Issue 1
The Gene Polymorphism of VMAT2 Decrease the Risk of Developing SCZ in Male Han Chinese
Biophysical and Biochemical Mechanisms of Forming and Development A Human Eukaryotic Organism from Single Pluripotent Cell into Multicellular Embryo and A Living Organism in Norm
Mouse Models for NASH: Are we there yet?
Are we All Transgenic?
Genetic Engineering 2020
On Novel Anti-viral HIV Gene Editing Platforms
2016 – 2017 Historical context:
MicroRNAs and Autophagy: Fine Players in the Control of Chondrocyte Homeostatic Activities in Osteoarthritis
Emerging connections between RNA and autophagy
I founded the domains Pheromones.com (1995), RNA-mediated.com (2015) and Autophagy.pro (2017) because the food energy-dependent species-specific production of pheromones clearly links feedback loops to all biophysically constrained RNA-mediated biodiversity via autophagy.