Epigenetics Theoretical Limits of Synthetic Genomes: The Cases of Artificials &lt;em&gt;Caulobacter &lt;/em&gt;(&lt;em&gt;C. eth-2.0), Mycoplasma Mycoides (JCVI-Syn 1.0, JCVI-Syn 3.0 and JCVI_3A), E-coli and YEAST chr XII&lt;/em&gt;

Pérez, José María Hernández

doi:10.20944/preprints201907.0120.v1

Cited by 8 publications

(8 citation statements)

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“…More recently, we have shown that these same Fibonacci proportions of the genome of the mitochondria, the energy source of the human cell, are deteriorated by mutations associated with various cancers (perez, 2017). We also demonstrate how these same Fibonacci proportions of DNA make it possible to distinguish a genome of a real bacterium from its attempt at a synthetic chimera (Perez, 2019).…”

Section: Introductionmentioning

confidence: 84%

The BFP (Benford-Fibonacci-Perez) Method Validates the Consistency of COVID-19 Epidemiological Data in France and Italy

Pérez¹

2021

Preprint

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The Benford method can be used to detect manipulation of epidemiological or trial data during the validation of new drugs. We extend here the Benford method after having detected particular properties for the Fibonacci values 1, 2, 3, 5 and 8 of the first decimal of 10 runs of official epidemiological data published in France and Italy (positive cases, intensive care, and deaths) for the periods of March 1 to May 30, 2020 and 2021, each with 91 raw data. This new method – called “BFP” for Benford-Fibonacci-Perez - is positive in all 10 cases (i.e. 910 values) with an average of favorable cases close to 80%, which, in our opinion, would validate the reliability of these basic data.

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Section: Introductionmentioning

confidence: 84%

The BFP (Benford-Fibonacci-Perez) Method Validates the Consistency of COVID-19 Epidemiological Data in France and Italy

Pérez¹

2021

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“…« Thus, any codon radiates at long distance and vice versa ».The Master Code of this sequence then produces two signatures, one GENOMIC, the other for PROTEOMIC, materialized by 2 very strongly correlated curves. that is this level of coupling which will provide precious information on the COHESION or on the HETEROGENEITY [11] of this nucleotide sequence. in particular the extreme regions (mini / maxi) would be associated with biological functions such as active sites, chromosomes breakpoints, etc.…”

Section: Main Covid_19 Genes Involvedmentioning

confidence: 99%

Jean claude Perez § Luc Montagnier - COVID-19, SARS and Bats Coronaviruses Genomes Unexpected Exogenous RNA Sequences

Pérez¹

2020

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We are facing the worldwide invasion of a new coronavirus. This follows several limited outbreaks of related viruses in various locations in a recent past (SARS, MERS). Although the main objective of researchers is to bring efficient therapeutic and preventive solutions to the global population, we need also to better understand the origin of the newly coronavirus-induced epidemic in order to avoid future outbreaks. The present molecular appraisal is to study by a bio-infomatic approach the facts relating to the virus and its precursors. This article shows how 16 fragments (Env Pol and Integrase genes) from different strains, both diversified and very recent, of the HIV1, HIV2 and SIV retroviruses most likely are present into the genome of COVID-19. Among these fragments, 12 are concentrated in a very small region of the COVID-19 genome, length less than 900bases, i.e. less than 3% of the total length of this genome. In addition, these footprints are positioned in 2 functional genes of COVID-19: the orf1ab and S spike genes. To sum up, here are the two main facts which contribute to our hypothesis of a partially synthetic genome: A contiguous region representing 2.49% of the whole COVID-19 genome of which 40.99% is made up of 12 diverse fragments originating from various strains of HIV SIV retroviruses. On the other hand, these 12 fragments some of which appear concatenated. Notably, the retroviral part of these regions, which consists of 8 elements from various strains HIV1, HIV2 and SIV covers a length of 275 contiguous bases of COVID-19. The cumulative length of these 8 HIV SIV elements represents 200 bases. Consequently, the HIV SIV density rate of this region of COVID-19 is 200/275 = 72.73%, which is considerable s made of. Moreover each of these elements is made of 18 or more nucleotides and therefore may have function. They are called Exogenous Informative Elements. A major part of these 16 EIE already existed in the first SARS genomes as early as 2003. However, we demonstrate how and why a new region including 4 HIV1 HIV2 Exogenous Informative Elements radically distinguishes all COVID-19 strains from all SARS and Bat strains. We then gather facts about the possible origins of COVID_19. We have particularly analyzed this small region of 225 bases common to COVID_19 and batRaTG13 but totally absent in all SARS strains. Then, we discuss the case of bat genomes presumed to be at the origin of COVID_19. In the strain of bat RaTG13 coronavirus isolated in 2013, then sequenced in 2020, the homology profile for HIV1 Kenya 2008 fragment is identical to that of COVID_19. Finally, we have studied the most recent genetic evolution of the COVID_19 strains involved in the world epidemic. We found a significant occurrence of mutations and deletions in the 225b region.On sampling genomes, we finally show that this 225b key region of each genome, rich in EIE, evolves much faster than the corresponding whole genome.The comparative analysis of the SPIKES genes of COVID_19 and Bat RaTG13demonstrates two abnormal facts: on the one hand, the insertion of 4 contiguous amino acids in the middle of SPIKE, on the other hand, an abnormal distribution of synonymous codons in the second half of SPIKE. Finally the insertion in this region of an EIE coming from a Plasmodium Yoelii gene is demonstrated, but above all seems to explain the "strategy" pursued by having "artificially" modified the ratio of synonym codons / non-synonymous codons in this same region of 1770 COVID_19 SPIKE nucleotides.

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“…Thirty years ago, after pioneering in A.I (Perez, 1988(Perez, , 1991, we published in a paper entitled "chaos, DNA, and neuro computers: the golden link" (Perez, 1991), presenting a numerical method to analyse dna sequences based on Fibonacci numbers . In 2017 (Perez, 1997(Perez, , 2017(Perez, , 2019, we revisited this method to démonstrate application of this method in mtDNA mutations involved on Human cancers. Fiftyeight years ago, (Montagnier L. § Kingsley Sanders F., 1963) Luc Montagnier described the isolation of an infectious double helix RNA in cells infected with a picornavirus.…”

Section: I-introductionmentioning

confidence: 99%

SARS-CoV2 Variants and Vaccines mRNA Spikes Fibonacci Numerical UA/CG Metastructures

Pérez¹

2021

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ABSTRACT. In this paper, we suggest a biomathematical numerical method for analysing mRNA nucleotides sequences based on UA/CG Fibonacci numbers proportions. This method is used to evaluate then compare the spike genes related to the main SARS-CoV2 VARIANTS currently circulating within the world population. The 10 main results proposed to be reproduced by peers are: 1/ SARS-CoV2 genome and spike evolution in one year 2020-2021. 2/ SARS-CoV2 Origins. 3/ Comparing 11 reference variants spikes. 4/ analysing 32 CAL.20C California variant patients spikes. 5/ Toward a meta mRNA Fibonacci gene end message code. 6/ Analysing S501 UK, S484 South Africa and « 2 mutations » INDIA variants. 7/ Suggesting a possible variants spike mRNA palindrome symmetry metastructure improving mRNA stability then infectiousness. 8/ Analysing Fibonacci Metastructures in the mRNA coding for the vaccines PFIZER and MODERNA. 9/ Does the CG-rich modification of the synonymous codons of the spikes of the 2 mRNA vaccines affect the expression and quantity of SARS-CoV2 antibodies? 10/ The exceptional case of the Brazilian variant P.1. Particularly, we suggest the following conjecture at mRNA folding level : CONJECTURE of SARS-CoV2 VARIANTS: The growth of long Fibonacci structures in the shape of "podiums" for almost all of the variants studied (UK, California, South Africa, India, etc.) suggests the probable folding of the Spike mRNA in the form of a "hairpin", which can strengthen the cohesion and the lifespan of this mRNA. Finally, we show that these kinds of Fibonacci matastructures disapear TOTALLY by analysing the published mRNA sequences of PFIZER and MODERNA vaccines. One fact is certain, the two mRNAs of the Moderna and Pfizer vaccines will result in a low functionality of the spike vaccine. This is because their designers by seeking greater stability, have doped to build CG rich sequences which, as soon as they are inserted into the human host, will, paradoxically, seek to mutate, like SARS-CoV2 variants, towards CG ==> UA forms in order to improve their STABILITY and LIFETIME. We conclude using new biomathematics theoretical methods (Master code and numerical standing waves), and comparing the Spikes of the two vaccines Moderna and Pfizer, that there will be very probable differences in stability and shelf life of the two respective mRNAs vaccines. However, “State of the Art” analyzes will disclose that their two protein sequences are strictly identical. By modified their synonymous codons using different strategies, no one can guarantee that the quantity of antibodies generated will be identical in the two cases. We wish to draw attention to the great ADAPTATION power - at the global scale of their genomes - of the most infectious VARIANTS, such as the BRAZIL 20J / 501Y.V3 variant (P.1). This is very worrying for the VACCINES <==> VARIANTS run: We demonstrate how the Brazilian variant P.1 which becomes uncontrollable in Brazil in April 2021 has a level of organization of long metastructures of 17,711 bases covering the genome which is 3.6 more important than that of the 2 reference genomes SARS-CoV2 and worldwide D614G. We suggest that this high level of overall structure of this variant contributes to the stability of this genome and, might explain its greater contagiousness.

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Epigenetics Theoretical Limits of Synthetic Genomes: The Cases of Artificials <em>Caulobacter </em>(<em>C. eth-2.0), Mycoplasma Mycoides (JCVI-Syn 1.0, JCVI-Syn 3.0 and JCVI_3A), E-coli and YEAST chr XII</em>

Cited by 8 publications

References 10 publications

The BFP (Benford-Fibonacci-Perez) Method Validates the Consistency of COVID-19 Epidemiological Data in France and Italy

The BFP (Benford-Fibonacci-Perez) Method Validates the Consistency of COVID-19 Epidemiological Data in France and Italy

Jean claude Perez § Luc Montagnier - COVID-19, SARS and Bats Coronaviruses Genomes Unexpected Exogenous RNA Sequences

SARS-CoV2 Variants and Vaccines mRNA Spikes Fibonacci Numerical UA/CG Metastructures

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