Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein 5/6/16

Summary excerpt:

Visualizing a response to light

Many biological processes depend on detecting and responding to light. The response is often mediated by a structural change in a protein that begins when absorption of a photon causes isomerization of a chromophore bound to the protein

Article excerpt:

Ultrafast fluorescence and transient absorption spectroscopy of PYP have shown that excited state decay is multi-phasic (3, 5, 39). The fast (sub-picosecond) time constants are significantly more productive in creating the cis-like photoproduct than the slow (picosecond) time constants; the long-lived excited state population primarily decays back to the ground state (5, 36)

reported on 5/5/16 as

Scientists watch bacterial sensor respond to light in real time


The researchers had already studied light-induced structural changes in PYP at LCLS, revealing atomic motions as fast as 10 billionths of a second. By tweaking their experiment, they were now able to improve their speed limit 100,000 times and capture reactions in the protein that are 1,000 times faster than any seen in an X-ray experiment before.

My comment: Their results link femtosecond blasts of ultraviolet (UV) light from hydrogen-atom transfer in DNA base pairs in solution and microRNA flanking sequences to energy-dependent changes in the microRNA (miRNA)/messenger RNA (mRNA) balance. Changes in pH and changes in the miRNA/mRNA link the energy-dependent physiology of reproduction to healthy longevity via what is known about supercoiled DNA, which protects the organized genomes of all living genera from virus-driven entropy.

See also: Edward Snowden nominated for Nobel peace prize

Withholding information is usually a tactical measure. Promoting ignorance that fails to link the de novo creation of G protein-coupled receptors (GPCRs) to morphological and behavioral diversity contributes to belief in ridiculous theories and beliefs about other people that are based on those ridiculous theories.

If you can’t link energy-dependent changes to hydrogen-atom transfer in DNA base pairs in solution via the speed of light on contact with water, you may have missed everything known about how angstroms are linked to ecosystems via the creation of the sun and energy-dependent creation of GPCRs. The GPCRs link the epigenetic landscape to receptor-mediated behaviors via nutrient-dependent hormone organization and hormone activation in all vertebrates and invertebrates.

Information dissemination

4/6/16 Race/Ethnicity-Specific Association of Vitamin D and Global DNA Methylation: Cross-Sectional and Interventional Findings

reported on 5/2/16 in Engaging Epigenetics Experts:


This PLoS ONE study is the first to show that vitamin D regulates global DNA methylation in humans. This is important because decreased global DNA methylation is associated with higher disease risks, (cancer, cardiovascular, immune function). Our bodies need sunshine to be healthy!

See for comparison:

“…calcitriol is the active form of vitamin D. Its effects on the microRNA(miRNA)/messenger RNA (mRNA) balance appear to protect against perturbed protein folding, which is associated with colorectal cancer. MiRNA-627 targets the mRNA that encodes an enzyme linked to histone demethylation and amino acid substitutions that increase stability of hydrogen bonds in DNA, which are important to protein folding (Padi, Zhang, Rustum, Morrison, & Guo, 2013). Rarely does a week go by without yet another report that details cause and effect in the context of miRNAs (Follert, Cremer, & Beclin, 2014). For example, the potential for therapeutic use of miRNA-126-5p to treat atherosclerosis was reported in time for me to note the importance of miRNAs to cell type differentiation via the circulatory system (Schober et al., 2014).” — Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

My comment: My invited review of nutritional epigenetics was returned without review. It linked the conserved molecular mechanisms of Vitamin D regulation of global DNA methylation to energy-dependent healthy longevity and to energy-loss, which I have since linked from virus-driven energy theft to all pathology.

If you’re not interested in at least scanning the works I have already presented, published, or those that editors returned without review, you’re not likely to grasp the magnitude of the problem with reviewers. Most of what is being published as mainstream science attempts to continue to support the ridiculous theories invented by neo-Darwinists. If you believe in the ridiculous theories, you won’t look for accurate representations of biophysically constrained energy-dependent cause and effect. You will miss the link from nutrition to DNA methylation and the link from virus-driven energy theft to hypomethylation and cancer. Virus-driven energy theft will continue to be ignored and biologically uninformed theorists will help the viruses to kill us all.

For more examples of ignorance about cell type differentiation, see:

An inter‐species protein–protein interaction network across vast evolutionary distance 4/22/16

Altered primary chromatin structures and their implications in cancer development 3/23/16

Identification of a Novel RNA Virus Lethal to Tilapia 9/17/14

Structure and mechanism of the ATPase that powers viral genome packaging 7/8/15

Ancient Virus DNA Gives Stem Cells the Power to Transform  3/30/14

Virus-based piezoelectric energy generation 5/13/12 reported as: A virus that creates electricity 5/16/12

See also: Is Biodiversity Research Biased? 4/11/16

The report of a virus that “creates” electricity shows how reports that link viruses to pathology are placed into the context of a battle between neo-Darwinian theorists and serious scientists. Biodiversity research is biased by the neo-Darwinian theorists. Anyone who attests facts forces biologically uninformed theorists to add to their theories. None of their theories link energy-dependent biologically-based cause and effect, which means that none of their existing theories have any explanatory power.

For example, On day two of the Molecular Diagnostics event, Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity was reported as Virus fighter may have played a key role in human evolution.

Genetic and environmental influences interact with age and sex in shaping the human methylome was reported with no mention of how energy-dependent RNA-dircted DNA methylation must be linked to supercoiled DNA via the immune system so that all organized genomes are protected against virus-driven energy theft and entropy.

Thus, even after others admit that no experimental evidence links mutations to the biophysically constrained chemistry of energy-dependent RNA-mediated protein folding, they do not admit that Schrodinger’s claim about the anti-entropic energy of sunlight in “What is life?” (1944) was correct. Instead, one day after the Molecular Diagnostics event Ribose and related sugars from ultraviolet irradiation of interstellar ice analogs was reported as Scientists say the ‘R’ in RNA may be abundant in space.

The ultraviolet irradiation was not linked to ultraviolet absorption on contact with water on Earth, which left serious scientists to ask for an explanation of what ultraviolet irradiation in deep space has to do with energy-dependent hydrogen-atom transfer in DNA base pairs in solution and the link from the RNA-mediated innate immune system to supercoiled DNA. Instead, on April 8, 2016, Electrolytes induce long-range orientational order and free energy changes in the H-bond network of bulk water was reported as A single ion impacts a million water molecules and  Viruses work together to attack their hosts was reported based on a published work from October 14, 2015.

See also: Comprehensive Transcriptome Profiles of Streptococcus mutans UA159 Map Core Streptococcal Competence Genes 4/26/16

Reported on 4/20/16 as Scientists sharpen view of gene transfer between pathogenic bacteria

Excerpt 1)

Bacteria possess the ability to take up DNA from their environment, a skill that enables them to acquire new genes for antibiotic resistance or to escape the immune response.

Excerpt 2)

Our findings — that two-thirds of the core activated genes in streptococcus have transformation functions — suggest that this is an ancient response, maintained because of its value in promoting ready access to external DNA.

My comment: Femtosecond changes in time constants link fast or slow changes in energy-dependent hydrogen-atom transfer in DNA base pairs in solution from the speed of light on contact with water to thermodynamic cycles of protein biosynthesis and degradation.  Virus-driven energy theft perturbs those cycles. That is how viruses are linked from the accumulation of mutations to all pathology. Watch closely as each day goes by and more news reports try to misrepresent what is known about biophysically constrained energy-dependent RNA-mediated protein folding chemistry.  Theorists are scared, and they will do anything they can to help science journalists continue to misrepresent the facts known to serious scientists who are Combating Evolution to Fight Disease.


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