intracellular signaling

Energy-dependent physical and biophysical constraints (5)

Summary: Emmy Noethe’s theorems were developed in the early 1900’s. Richard Feynman inadvertently or purposefully alluded to them as examples of human idiocy. Discover Magazine resurrected the examples of human idiocy in a 2017 article. For comparison, Choi et al., (2017) support the claims that intercellular and interkingdom communication is energy-dependent and controlled by the metabolism of food energy to pheromones. It is obvious that pheromones biophysically constrain the virus-driven degradation of messenger RNA. That fact links everything currently known…

Read More

Energy-dependent microRNA biogenesis

Published May 3, 2017 Genetic variation and RNA structure regulate microRNA biogenesis …primary sequence determinants and RNA structure are key regulators of miRNA biogenesis. Genetic variation aka primary sequence determinants are energy-dependent and RNA-mediated. Energy-dependent RNA methylation is an experience-dependent link from natural selection for energy-dependent codon optimality. Natural selection for energy-dependent codon optimality links ATP-dependent microRNA biogenesis to RNA biosynthesis. Ridiculous attempts to portray energy-dependent top-down causation as if genetic variation came first may continue for another 52 years.…

Read More

Open Science: Closed to facts about microRNAs

See my 5-part series on: The tipping point? 50, 000 publications Imagine how we could accelerate innovation, stimulate economic growth and all the solutions we need to live on a healthy and sustainable planet, if we were to open up our science fully and allow a free flow of scientific knowledge.” says Kamila Markram, a neuroscientist and the CEO of Frontiers, one of the largest Open Access science publishers in the world and a leader in the Open Science movement.…

Read More

Chromatin: The structure of DNA (2)

A Genetically Encoded Probe for Live-Cell Imaging of H4K20 Monomethylation Excerpt (with my emphasis): Highlights •    A histone H4K20me1-specific live-cell probe, H4K20me1-mintbody, was developed. •    Dynamics and replication timing of Xi were visualized. •    Critical amino acids for the stability and/or folding of the mintbody were revealed. Reported as: Catching histones by the tail: A new probe to track histone modifications in living cells Excerpt: H4K20me1 is most likely associated with the tight packing of a redundant (inactivated) female X…

Read More

Chromatin: The structure of DNA (3)

See:  Chromatin: The structure of DNA (2) Inherited parental methylation shifts over time, may have functional effects in the brain and other tissues Excerpt: …researchers have theorized that inherited methylation, also referred to as parental imprinting, largely remains stable throughout development, except during two important developmental milestones: after fertilization and during the creation of sperm and egg cells. Altered gene imprinting at other times has been associated with developmental disorders and cancer. My comment: Theorists have historically failed to learn…

Read More

Light energy-dependent active motifs

Active Motif claims that Active Motif is the industry leader in developing and delivering innovative tools to enable epigenetics and gene regulation research. See how the role of light is portrayed in LightSwitch™ Luciferase Assay System (with my emphasis) Excerpt 1) Combined with our large collection of miRNA Mimics and Inhibitors, you have everything needed to study miRNA-3´UTR interactions, validate miRNA targets, measure RNA stability, translation efficiency and the functional impact of miRNAs on a gene-by-gene basis. Excerpt 2) The…

Read More

The miRNA/mRNA balance: a suboptimal strategy?

Cells exercise suboptimal strategy to survive Excerpt: “Learning the secrets of alternate molecular pathways could provide clues about how to use them to patients’ advantage, she said.” My comment: The same molecular pathways control the nutrient-dependent physiology of reproduction in all genera. They link RNA-directed DNA methylation to RNA-mediated cell type differentiation via fixation of amino acid substitutions that determine cell types. See also: Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin “Mechanisms of epistasis are often best revealed through…

Read More

Single-cell level assay of protein biosynthesis and degradation

High-throughput detection of miRNAs and gene-specific mRNA at the single-cell level by flow cytometry Excerpt: “We use this technique to show modulation of a microRNA critical for T-cell function, miR-155. We adapt this assay for simultaneous detection of mRNA and proteins by ImageStream technology.” Reported as: Technology breakthrough reveals cellular transcription process My comment: Their assay simultaneously detects epigenetically-effected changes in the miRNA/mRNA balance and proteins, which link nutrient-uptake to the physical landscape of DNA in the organized genomes of…

Read More