Agilent technology and energy-dependent autophagy

By: James V. Kohl | Published on: December 21, 2017

The first step towards understanding the link from the creation of energy to metabolism-related cellular function is called energy phenotyping. It requires the  technology to measure energy-dependent changes in RNA-mediated metabolic switches via the RNA interference (RNAi) screening strategy. Endogenous RNAi must then be linked  to the prevention of the virus-driven degradation of messenger RNA that causes all pathology.
Scientists discover possible master switch for programming cancer immunotherapy

…they employed an RNA interference screening strategy which can test the actual function of thousands of factors simultaneously.

See also: Energy as information and constrained endogenous RNA interference (video 6:46 minutes)

Feedback loops link quantized energy as information to biophysically constrained RNA-mediated protein folding chemistry. Light induced energy-dependent changes link angstroms to ecosystems from classical physics to chemistry/chirality and to molecular epigenetics/autophagy. The National Microbiome Initiative links microbial quorum sensing to the physiology of reproduction via endogenous RNA interference and chromosomal rearrangements. The rearrangements link energy-dependent fixed amino acid substitutions to the Precision Medicine Initiative via genome wide inferences of natural selection. This detailed representation of energy-dependent natural selection for codon optimality links biologically- based cause and effect from G protein-coupled receptors to RNA-mediated amino acid substitutions and the functional structure of supercoiled DNA. Energy-dependent polycombic ecological adaptations are manifested in supercoiled DNA. Chromosomal inheritance links the adaptations from morphological phenotypes to healthy longevity via behavioral phenotypes. For contrast, virus-driven energy theft is the link from messenger RNA degradation to negative supercoiling, constraint breaking mutations, and hecatombic evolution. The viral hecatomb links transgenerational epigenetic inheritance from archaea to Zika virus-damaged DNA, which typically is repaired by endogenous RNA interference and fixation of RNA-mediated amino acid substitutions in organized genomes.

See also: Measuring the Metabolic Switch in Cancer Cells – Agilent (pdf)

Yoshida used TRAP1-null cells and transient TRAP1 mutants on an Agilent Seahorse XF96 Analyzer to show that TRAP1 regulates a metabolic switch between oxidative phosphorylation and aerobic glycolysis in immortalized mouse fibroblasts and in human tumor cells. TRAP1 deficiency promotes increased mitochondrial respiration, fatty acid oxidation, accumulation of TCA intermediates, ATP, and ROS, while suppressing glucose metabolism.

The virus-driven degradation of messenger RNA is the only perfectly obvious reason for changes in oxidative phosphorylation and aerobic glycolysis that prevent the metabolism of glucose. Natural selection for energy-dependent codon optimality links the creation of energy to the metabolism of glucose via the creation of enzymes that metabolize food energy. Energy-dependent RNA-mediated error-free DNA repair and fixation of amino acid substitutions is required to link the creation of enzymes and the species-specific production of pheromones from the physiology of reproduction to biophysically constrained viral latency and all morphological and behavioral phenotypes in all living genera.
In that context, energy-dependent natural selection for codon optimality links biologically-based cause and effect from hydrogen-atom transfer in DNA base pairs in solution to the transgenerational epigenetic inheritance of healthy longevity. For contrast, the virus-driven theft of quantized energy links changes in non-coding RNAs to all pathology.
For example, see: Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene
See also: A Concise Review of MicroRNA Exploring the Insights of MicroRNA Regulations in Bacterial, Viral and Metabolic Diseases
The link from the virus-driven theft of quantized energy to glioblastoma may be the best example of how viruses are readily linked to the cell death gene in all cell types of all individuals of all living genera. That fact is more obvious with further examination of details provided for free in book chapters from Codon Publishing.
See: Noncoding RNAs in Glioblastoma  Free book chapter from Codon Publishing

The vast majority of the human genome is transcribed into noncoding RNAs. Among these, microRNAs (miRNA) and long noncoding RNAs (lncRNA) are frequently deregulated in cancer, where they regulate a wide variety of functions.

See also: Epigenetic Mechanisms of Glioblastoma Free book chapter from Codon Publishing

Aberrant DNA methylation is a common event in the genesis and progression of tumors. The application of next-generation sequencing enables the identification and mapping of DNA methylation and its derivatives, 5fC and 5hmC, to base-pair resolution. This chapter describes nine novel hypermethylation genes and six hypomethylation genes, identified by constructing a DNA methylation profile, in glioblastoma. Abnormal promoter methylation and histone modifications were associated with differential expression of miRNAs in glioblastoma: miR-185 reversed global DNA methylation and the methylation level of the hypermethylation genes by targeting DNMT; and miR-101 regulated histone methylation of hypomethylation genes by targeting EED, EZH2, and DNMT3A. The long noncoding RNA CASC2c directly bound to miR-101 via microRNA response elements, and there was a reciprocal repression between CASC2c and miR-101. Despite being competitors they both led to the overexpression of their target hypomethylation genes CPEB1, PRDM16, and LMO3. Taken together, glioblastoma is a complicated pathological process with deregulated methylation and histone modifications. Focal differentially methylated region and differentially methylated site studies will be helpful for the identification of regulatory elements of transcription. Studies of intragenic and distant intergenic alterations in DNA methylation will help elucidate the nature of epigenetic deregulation in glioblastoma.

The Seahorse XF Cell Energy Phenotype Test kit is a simple assay kit that simultaneously measures the two major energy producing pathways in live cells – mitochondrial respiration and glycolysis, allowing rapid determination of energy phenotypes of cells and investigation of metabolic switching.
The simultaneous measurement of two major energy-producing pathways in live cells allows serious scientists to report their findings in the context of what is known about mitochondrial respiration and glycolysis. Glycolysis is epigenetically effected and RNA-mediated. No magic of evolution or nonsense about natural selection for anything except food and reproduction is required to explain how rapid metabolic switching determines whether or not viral latency is biophysically constrained across the time-space continuum.
See: From Fertilization to Adult Sexual Behavior (1996)

Yet another kind of 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 (Saunders, Chue, Goebl, Craig, Clark, Powers, Eissenberg, Elgin, Rothfield, and Earnshaw, 1993; Singh, Miller, Pearce, Kothary, Burton, Paro, James, and Gaunt, 1991; Trofatter, Long, Murrell, Stotler, Gusella, and Buckler, 1995). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.

See: Epigenetic modifications poster (Abcam)
Also from Abcam: Mechanisms of Recombination conference
The bottom line is The secret to safe DNA repair  (2015)

…if you don’t have this enzyme, then this error-free repair is stopped. You can’t do it. If you can’t do the error-free repair, among other things that happen is that you expect these cells to be cancer prone.

Clearly, the creation of the enzyme is energy-dependent and biophysically constrained by the pheromone-controlled physiology of reproduction. Pseudoscientists seem to know nothing about that, and most serious scientists are not telling you the facts that link the virus-driven degradation of messenger RNA to the “death gene” via the mechanisms that fail during recombination.
But see: microRNA autophagy  and also see: See:  Agilent Seahorse XF Publications Alert for December 2017
Selected publications
Autophagy maintains the metabolism and function of young and old stem cells
Ho, T. T., Warr, M. R., Adelman, E. R., Lansinger, O. M., Flach, J., Verovskaya, E. V., Figueroa, M. E. and Passegue, E.
Nature. 2017 Mar 9, 543 (7644):205-210.
Involvement of autophagy in the outcome of mitotic catastrophe
Sorokina, I. V., Denisenko, T. V., Imreh, G., Tyurin-Kuzmin, P. A., Kaminskyy, V. O., Gogvadze, V. and Zhivotovsky, B.
Sci Rep. 2017 Nov 6, 7 (1):14571.
Sugar or Fat?-Metabolic Requirements for Immunity to Viral Infections
Shehata, H. M., Murphy, A. J., Lee, M. K. S., Gardiner, C. M., Crowe, S. M., Sanjabi, S., Finlay, D. K. and Palmer, C. S.
Front Immunol. 2017 Oct 16, 8:1311.
System-wide Benefits of Intermeal Fasting by Autophagy
Martinez-Lopez, N., Tarabra, E., Toledo, M., Garcia-Macia, M., Sahu, S., Coletto, L., Batista-Gonzalez, A., Barzilai, N., Pessin, J. E., Schwartz, G. J., Kersten, S. and Singh, R.
Cell Metab. 2017 Dec 5, 26 (6):856-871 e5.
Late-onset Alzheimer’s disease is associated with inherent changes in bioenergetics profiles
Sonntag, K. C., Ryu, W. I., Amirault, K. M., Healy, R. A., Siegel, A. J., McPhie, D. L., Forester, B. and Cohen, B. M.
Sci Rep. 2017 Oct 25, 7 (1):14038.

BAG3 directly stabilizes Hexokinase 2 mRNA and promotes aerobic glycolysis in pancreatic cancer cells
An, M. X., Li, S., Yao, H. B., Li, C., Wang, J. M., Sun, J., Li, X. Y., Meng, X. N. and Wang, H. Q.
J Cell Biol. 2017 Dec 4, 216 (12):4091-4105.
Drug resistance induces the upregulation of H2S-producing enzymes in HCT116 colon cancer cells
Untereiner, A. A., Pavlidou, A., Druzhyna, N., Papapetropoulos, A., Hellmich, M. R. and Szabo, C.
Biochem Pharmacol. 2017 Oct 20, [epub ahead of print]
ISG15 governs mitochondrial function in macrophages following vaccinia virus infection
Baldanta, S., Fernandez-Escobar, M., Acin-Perez, R., Albert, M., Camafeita, E., Jorge, I., Vazquez, J., Enriquez, J. A. and Guerra, S.
PLoS Pathog. 2017 Oct 27, 13 (10):e1006651.
High throughput measurement of metabolism in planarians reveals activation of glycolysis during regeneration
Osuma, E. A., Riggs, D. W., Gibb, A. A. and Hill, B. G.
Regeneration. 2017 Nov 02, [epub ahead of print]
Current technical approaches to brain energy metabolism
Barros, L. F., Bolanos, J. P., Bonvento, G., Bouzier-Sore, A. K., Brown, A., Hirrlinger, J., Kasparov, S., Kirchhoff, F., Murphy, A. N., Pellerin, L., Robinson, M. B. and Weber, B.
Glia. 2017 Nov 7, [epub ahead of print]
Glucose-regulated protein 75 determines ER–mitochondrial coupling and sensitivity to oxidative stress in neuronal cells
Honrath, B., Metz, I., Bendridi, N., Rieusset, J., Culmsee, C. and Dolga, A. M.
Cell Death Discovery. 2017 Nov 06, [epub ahead of print]

Associations Between Microbiota, Mitochondrial Function, and Cognition in Chronic Marijuana Users
Panee, J., Gerschenson, M. and Chang, L.
J Neuroimmune Pharmacol. 2017 Nov 4, [epub ahead of print]
RNA cytosine methyltransferase Nsun3 regulates embryonic stem cell differentiation by promoting mitochondrial activity
Trixl, L., Amort, T., Wille, A., Zinni, M., Ebner, S., Hechenberger, C., Eichin, F., Gabriel, H., Schoberleitner, I., Huang, A., Piatti, P., Nat, R., Troppmair, J. and Lusser, A.
Cell Mol Life Sci. 2017 Nov 4, [epub ahead of print]
Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins
Samandi, S., Roy, A. V., Delcourt, V., Lucier, J. F., Gagnon, J., Beaudoin, M. C., Vanderperre, B., Breton, M. A., Motard, J., Jacques, J. F., Brunelle, M., Gagnon-Arsenault, I., Fournier, I., Ouangraoua, A., Hunting, D. J., Cohen, A. A., Landry, C. R., Scott, M. S. and Roucou, X.
Elife. 2017 Oct 30, 6.
The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12
Shen, H., Campanello, G. C., Flicker, D., Grabarek, Z., Hu, J., Luo, C., Banerjee, R. and Mootha, V. K.
Cell. 2017 Nov 2, 171 (4):771-782 e11.

See also: Research areas for this month include:

See for comparison: 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.

Latest Research and Reviews

For example:

Dual role of autophagy in hallmarks of cancer

Quantitative assessment of cell fate decision between autophagy and apoptosis

The Nature Publications Group has fallen far behind the data and technical expertise of all the serious scientists in the world. It seems likely that they will attempt to portray autophagy as something besides the innate phage defense system and fail miserably.

Autophagy is the antiphage defense strategy December 8, 2016

What would you do if your publisher arrived at the “Autophagy Party” more than a year late and you had to introduce them as a supporter of neo-Darwinian nonsense and “Big Bang” cosmology?
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

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