Sunlight, hydrophobicity and biodiversity (1)

A five-coordinate Mn(iv) intermediate in biological water oxidation: spectroscopic signature and a pivot mechanism for water binding 11/17/15

…a multi-step process that involves the redox-active tyrosine residue and includes oxidation and deprotonation of the catalytic cluster, as well as the binding of a water molecule.

See for comparison: Molecular Diagnostics April 6-7, 2016 What is life when it is not protected from virus-driven entropy?

The anti-entropic force of virucidal ultraviolet light (UV) links guanine–cytosine (G⋅C) Watson–Crick base pairing from hydrogen-atom transfer in DNA base pairs in solution to supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy. For example, protection of DNA from permanent UV damage occurs in the context of photosynthesis and nutrient-dependent RNA-directed DNA methylation, which links RNA-mediated amino acid substitutions to DNA repair. In the context of thermodynamic cycles of protein biosynthesis and degradation, DNA repair enables the de novo creation of G protein coupled receptors (GPCRs). Olfactory receptor genes are GPCRs. The de novo creation of olfactory receptor genes links chemotaxis and phototaxis from foraging behavior to social behavior in species from microbes to humans. Foraging behavior links ecological variation to ecological adaptation in the context of this atoms to ecosystems model of biophysically constrained energy-dependent RNA-mediated protein folding chemistry. Protein folding chemistry links nutrient-dependent microRNAs from microRNA flanking sequences to energy transfer and cell type differentiation in the context of adhesion proteins, and supercoiled DNA that protects all organized genomes from virus-driven entropy.

The link to the hydrophobicity of supercoiled DNA appears at the beginning of time with the Creation of photosynthesis in Five-coordinate MnIV intermediate in the activation of nature’s water splitting cofactor 8/7/19

Recent results have shown that nature’s water splitting catalyst inserts an additional water molecule into what appears to be a solvent inaccessible site late in its reaction cycle. The emerging consensus of the field is that this water molecule is one of the substrates of the reaction. Here, we show that this water molecule does not come directly from solvent. It instead represents an earlier bound water, which is inserted into this site via facile structural tautomerism. The trigger for this process is cofactor oxidation. This then allows an additional water to bind from solvent to a more open site of the cofactor. In this way the cofactor carefully regulates water uptake, preventing water insertion earlier in the reaction cycle.

For extension of the facts about the energy-dependent properly-timed prevention of water insertion (i.e., hydrophobicity) in supercoiled DNA, see Inflamm-aging micrornas may integrate signals from food and gut microbiota by modulating common signalling pathways 8/8/19

Supported by a” Pubmed” search and our previous research, a trio of experimentally validated inflamma-miRs were considered: miR-155, miR-146a and miR-21. Our in silico study supports the hypothesis that these inflamma-miRs could modulate some pathways, such as lysine degradation and lengthening of fatty acids which are involved in the modulation of microbiota composition, i.e. prevotella, ruminococcus and oscillibacter and vice versa. Food homologues to human miR-21, miR-155 and miR-146a were found in cow fat, cow milk, and eggs suggesting that they may be able of targeting, and probably exacerbating, inflammation related pathways. If these data will be experimentally validated, they will further support the relevance of a nutraceutical approach for a healthy aging.

How Nature splits water and powers the planet 8/8/19

The splitting of two water molecules into oxygen using sunlight is the first step of photosynthesis, a process performed by plants and cyanobacteria.

Their PubMed search does not support any claims about how “Nature” created sunlight. Like my Pubmed searches for “microRNA” their search suggests that the Creation of sunlight was required to link “nature’s” splitting of water from the first step of photosynthesis to the all biophysically constrained power on the planet, Earth.

See for comparison how these three reports from “The Tipping Point” series linked a “Pubmed” search for “microRNA” to nutrient-dependent pheromone-controlled biophysically constrained viral latency via everything known to serious scientists about the light-activated assembly of the microRNA-RNA-peptide nanocomplex, hydrophobicity, and the physiology of reproduction in all living genera.

See also:

The tipping point (revisited): 90K (1) 8/7/19

The tipping point (revisited): 90K (2) 8/8/19

The tipping point (revisited): 90K (3) 8/8/19

and: Role of AKT and mTOR Signaling Pathways in the Induction of Epithelial-Mesenchymal Transition (EMT) Process 8/8/19 from researchers in Iran who are helping others to eliminate virus-driven cancers.

Epithelial-mesenchymal transition (EMT) is a critical process in the development of many tissues and organs in multicellular organisms that its important role in the pathogenesis of metastasis and tumor cell migration has been firmly established. Decreased adhesive capacity, cytoskeletal reorganization, and increased mobility are hallmarks of the EMT. Several molecular mechanisms promote EMT, Including regulation of the levels of specific cell-surface proteins, ECM-degrading enzymes, and altering the expression of certain transcription factors and microRNAs. EMT process is modulated through multiple signaling pathways including the AKT/mTOR pathway. AKT is a key component in numerous processes which was recently shown to regulate the EMT through suppression of the expression of E-cadherin via EMT transcription factors. On the other hand, mTOR complexes can also regulate the EMT through the regulation of cell’s actin cytoskeleton by altering the PKC phosphorylation state and direct phosphorylation and activation of Akt. Here we review the effect of AKT and mTOR on EMT and consequently metastasis and cell motility.

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Author: James Kohl

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