Plant microRNAs regulate across-kingdom gene expression (2)

Multiple layers of cryptic genetic variation underlie a yeast complex trait 1/4/19

Oligos were 90 bases long with homology to either FLO8 or SFL1, with inclusion of a stop codon followed by single base frameshift deletion in the middle. Stop codons were introduced at amino acids 155 and 39 in FLO8 and SFL1, respectively. Transformed cells were plated on solid yeast nitrogen base (YNB) media lacking uracil to select for retention of the pML104 plasmid. Plasmids were then eliminated from the transformants by plating on 5-fluoroorotic acid (5-FOA). Presence of the intended genetic modifications was checked in the transformants using Sanger sequencing.

They linked natural selection for energy-dependent codon optimality to biophysically-constrained viral latency in a yeast model organism and used DNA sequencing to confirm the link from the virus-driven degradation of messenger RNA to hecatombic pathology, which could be prevented with food energy-dependent polycombic ecological adaptations (i.e., “Stop codons… at amino acids 155 and 39 in FLO8 and SFL1, respectively.”).

Without the natural selection for stop codons and fixation of amino acid substitutions, even the cell types of single-celled yeasts are not likely to be fully differentiated as is required in the context of sexual differentiation of cell types. That fact can be viewed in the context of biophysically constrained food energy-dependent pheromone controlled RNA-mediated cell type differentiation in all cells types of all individuals of all living genera.

Others can start with the Virus-mediated archaeal hecatomb in the deep seafloor and link the creation of anti-entropic virucidal light to Eukaryotic plankton diversity in the sunlit ocean in the context our 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior

…epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called “chromo domain” proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes…

Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus…

Therein lies the problem for biologically uninformed theorists and especially for human ethologists and sex researchers. The levels of complexity have been linked from energy-dependent differences in subatomic particles, called photons and electrons, to the creation of ATP, to light-activated microRNA biogenesis, to the creation of enzymes and the creation of RNA, and from alternative splicings of RNA to RNA-mediated cell type differentiation, which protects all living genera from the virus-driven degradation of their messenger RNA.

That is cryptic genetic variation must be linked to morphological and behavioral phenotypes. But how many researchers start with energy instead of genetic variation?

The implications of how many do or do not start with energy overwhelms those who try to understand how cell type differentiation occurs, especially when results are framed in attempts to profit from what they learn.

For example, see the patent on light-activated carbon fixation and naturally occurring RNA interference.

RNA-Guided Human Genome Engineering

5. Repetitive elements or endogenous viral elements can be targeted with engineered Cas+gRNA systems in microbes, plants, animals, or human cells to reduce deleterious transposition or to aid in sequencing or other analytic genomic/transcriptomic/proteomic/diagnostic tools (in which nearly identical copies can be problematic).

See also: Out of order: Beyond the bubble

Highlights

• Science and medicine are about measurement.
• What science and medicine are not is healthcare.
• But I am heartened to see a greater human connection between one end of the process and the other, because with that connection comes compassion and with compassion comes meaning. And without meaning, what is the point?

Science and medicine must link the measurement of changes in subatomic particles from differences in the energy of photons of light to everything known about how the creation of the anti-entropic virucidal energy of  sunlight links quantum physics from classical physics to the creation of all energy-dependent biodiversity on Earth via the physiology of reproduction in species from microbes to humans.

But, see my comment on quantum entanglement: Atoms can be in two places at the same time  (2/5/15)

There is no point to telling anyone who believes in the emergence of new enzymes or the evolution of pre-exisisting enyzmes that emergence and evolution are not possible. It would be like trying to tell them about the de novo creation of nutrient-dependent enzymes that link quantum physics to the ability of nutrients to enter the cell, which links ecological variation to ecological adaptation via the chemistry of protein folding and quantum biology. No matter what you tell science idiots, in their world, everything automagically evolves.

See for comparison: Nothing in Biology Makes Any Sense Except in the Light of Evolution

For example, the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.

See also: HbVar: A Database of Human Hemoglobin Variants and Thalassemias

Nearly 1800 human hemoglobin variants attest to the fact that light-activated microRNA biogenesis in the plants that we eat has been linked to all differences in all morphological and behavioral phenotypes in all individuals of all species.

But see: Desires of Microscopic Shrimp Illuminate Evolutionary Theory 12/27/14

“I’ve always been interested in speciation and how species form, but this is a whole different mechanism, that light can influence speciation,” Ellis says. “I thought it was just fabulous.”

A whole different mechanism? No. It’s the only mechanism that links Darwin’s “conditions of life” to all food energy-dependent biodiversity because the light-activated production of food is required to support the physiology of reproduction.

But see the comment from Andrew Jones (aka anonymous_9001) on Atoms can be in two places at the same time 1/29/15

Substitutions change the DNA sequence of a gene and may change the resulting amino acid sequence if it’s nonsynonymous. Expression changes alter how often a gene is transcribed. It’s not a difficult distinction to comprehend. It’s sad that you’ve yet to grasp this after many months of being repeatedly informed.

The fact that the substitutions are light energy-dependent and biophysically constrained seems to never have occurred to people like Andrew Jones, who wrote this.

Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

He concluded:

Based on his writings, both published and unpublished, James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others’ research. It was a mistake to let such a sloppy review through to be published.

But see: All in the (bigger) family (2015)

…last week at a special symposium of the annual meeting of the Society for Integrative and Comparative Biology, researchers reported… new insights about what it took for an ancient crustacean to give rise to insects.

Also reported as: ‘Junk DNA’ Used To Sort Species

miRNA sequences have been used to sort out phylogenetic relationships.

The use of miRNA sequences to sort out the phylogenetic relationships in species from yeasts to plants and from insects to mammals was placed into the context of our 1996 review at a time when microRNAs were referred to as pre-mRNAs. But what’s in a name?

See: Subatomic and Cytosis

The names of the games are linked to clarity of thoughts by ages 10+