scholarly journals WUHAN COVID-19 SYNTHETIC ORIGINS AND EVOLUTION

2020 ◽  
Vol 8 (2) ◽  
pp. 285-324 ◽  
Author(s):  
Jean-Claude PEREZ
Keyword(s):  
Fibonacci Numbers ◽  
Small Region ◽  
Adaptation Strategy ◽  
Formal Proof ◽  
Global Strategy ◽  
Whole Numbers ◽  
Synthetic Genome ◽  
Entire Sequence ◽  
Different Strains ◽  
Artificial Origin

The main result of this updated release is the formal proof that 2019-nCoV coronavirus is partially a SYNTHETIC genome. We proof the CONCENTRATION in a small région of wuhan New genome (300bp) of 3 different régions from HIV1 ENVELOPPE gene and 3 others from HIV2 and SIV (ENV and POL RT). All this is remarkable and bears the mark of a desire for organization of a human nature: LOGIC, SYMETRIES. In this article, we demonstrate also that there is a kind of global human hosts adaptation strategy of SARS viruses as well as a strategy of global evolution of the genomes of the different strains of SARS which have emerged, mainly in China, between years 2003 first SARS genomes and the last 2019 COVID-19 Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome. This global strategy, this temporal link, is materialized in our demonstration by highlighting stationary numerical waves controlling the entire sequence of their genomes. Curiously, these digital waves characterizing the 9 SARS genomes studied here are characteristic whole numbers: the "Fibonacci numbers", omnipresent in the forms of Nature, and which our research for several decades has shown strong links with the proportions of nucleotides in DNA. Here we demonstrate that the complexity and fractal multiplicity of these Fibonacci numerical waves increases over the years of the emergence of new SARS strains. We suggest that this increase in the overall organization of the SARS genomes over the years reflects a better adaptation of SARS genomes to the human host. The question of a link with pathogenicity remains open. However, we believe that this overall strategy for the evolution of the SARS genomes ensures greater unity, consistency and integrity of the genome. Finally, we ask ourselves the question of a possible artificial origin of this genome, in particular because of the presence of fragments of HIV1, HIV2 and SIV retroviruses.

Wuhan nCoV-2019 SARS Coronaviruses Genomics Fractal Metastructures Evolution and Origins

2020 ◽  
Author(s):  
Jean-Claude Perez
Keyword(s):  
Fibonacci Numbers ◽  
Adaptation Strategy ◽  
Formal Proof ◽  
Global Strategy ◽  
Whole Numbers ◽  
Johannes Kepler ◽  
Synthetic Genome ◽  
Entire Sequence ◽  
Different Strains ◽  
Artificial Origin

Wuhan nCoV-2019 SARS Coronaviruses Genomics Fractal Metastructures Evolution and Origins “Where there is matter, there is geometry.” Johannes Kepler Jean-claude PEREZ, PhD Maths § Computer Science Bordeaux University, RETIRED interdisciplinary researcher (IBM Emeritus, IBM European Research Center on Artificial Intelligence), 7 avenue de terre-rouge F33127 Martignas Bordeaux metropole France, phone 33 0781181112 [email protected] ABSTRACT : The main result of this updated release is the formal proof that 2019-nCoV coronavirus is partially a SYNTHETIC genome. We proof the CONCENTRATION in a small région of wuhan New genome of 3 different régions from HIV1 ENVELOPPE GENE. In this article, we demonstrate that there is a kind of global human hosts adaptation strategy of SARS viruses as well as a strategy of global evolution of the genomes of the different strains of SARS which have emerged, mainly in China, between years 2003 first SARS genomes and the last 2020 nCoV-2019 Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome. This global strategy, this temporal link, is materialized in our demonstration by highlighting stationary numerical waves controlling the entire sequence of their genomes. Curiously, these digital waves characterizing the 9 SARS genomes studied here are characteristic whole numbers: the "Fibonacci numbers", omnipresent in the forms of Nature, and which our research for several decades has shown strong links with the proportions of nucleotides in DNA. Here we demonstrate that the complexity and fractal multiplicity of these Fibonacci numerical waves increases over the years of the emergence of new sArs strains. We suggest that this increase in the overall organization of the SARS genomes over the years reflects a better adaptation of SARS genomes to the human host. The question of a link with pathogenicity remains open. However, we believe that this overall strategy for the evolution of the SARS genomes ensures greater unity, consistency and integrity of the genome. Finally, we ask ourselves the question of a possible artificial origin of this genome, in particular because of the presence of fragments of HIV1 retrovirus. KEYWORDS : SARS, Wuhan nCoV-2019, Fibonacci numbers, Fractal genome, Numerical stationary periodic waves, HIV1, synthetic genomes.

scholarly journals COVID-19, SARS and Bats Coronaviruses Genomes Unexpected Exogeneous RNA Sequences

2020 ◽  
Author(s):  
jean-claude perez ◽  
Luc Montagnier
Keyword(s):  
Small Region ◽  
Recent Past ◽  
Rna Sequences ◽  
Synthetic Genome ◽  
The World ◽  
Cumulative Length ◽  
Different Strains ◽  
Bat Coronavirus ◽  
Global Population ◽  
Density Rate

We human 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 new outbreaks. The present molecular appraisal is to study by a bio-infomatic approach the facts relating to the virus and its precursors. This article demonstrates how 16 « Exogeneous Informative Elements » 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 fingerprints, 12 of them would be concentrated in a very small region of the genome COVID-19 of 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 is 40.99% made up of 12 diverse Exogeneous  Informative Elements (EIE) fragments originating from various strains of HIV SIV retroviruses. On the other hand, these 12  Exogeneous Informative Elements, some of them appear concatenated, that is to say placed side by side in the genome of COVID-19, and this despite natures, strains, and years of emergence all different. Notably, the retroviral part of these regions, which consists of 8 motifs 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 motifs represents 200 bases. Consequently, the HIV SIV density rate of this region of COVID-19 is 200/275 = 72.73%, which is considerable.A major part of these 16 EIE Elements already existed in the first SARS genomes as early as 2003. However, we demonstrate how and why a new region including 4 HIV1 HIV2 Exogeneous Informative Elements radically distinguishes all COVID-19 strains from all SARS and Bat strains. Particularly, we will be interested in the Bat RaTG13 strain whose genomic proximity to COVID-19 will be thoroughly analyzed. Then, we gather facts about the possible origins of COVID_19, we have particularly analyze 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 bat coronavirus isolated in 2013, then sequenced in 2020, the homology profile for HIV1 Kenya 2008 fingerprint is identical to that of COVID_19. (collected end december 2019, then sequenced in 2020). Finally, we have studied the most recent genetic evolution of the COVID_19 strains involved in the world epidemic. We found an astoneshing 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.

scholarly journals COVID-19, SARS AND BATS CORONAVIRUSES GENOMES PECULIAR HOMOLOGOUS RNA SEQUENCES

2020 ◽  
Vol 8 (7) ◽  
pp. 217-263
Author(s):  
Jean Claude Perez ◽  
Luc Montagnier
Keyword(s):  
Small Region ◽  
Functional Genes ◽  
Genome Length ◽  
Recent Past ◽  
Rna Sequences ◽  
Synthetic Genome ◽  
Cumulative Length ◽  
Different Strains ◽  
Global Population ◽  
Density Rate

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 current 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 itsprecursors. 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 have high percentage of homology into parts of the genome of COVID_19. Moreover each of these elements is made of 18 or more nucleotides and therefore may have a function. They are called Exogenous Informative Elements (EIE).. Among these EIE, 12 are concentrated in a very small region of the COVID-19 genome, length less than 900 bases, i.e. less than 3% of the total length of this genome. In addition, these EIE are positioned in two functional genes of COVID-19: the orf1ab and S spike genes. 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. Some of these 12 EIE appear concatenated. Notably, the retroviral part of these regions, which consists of 8 elements from various strainsof 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%.

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

2020 ◽  
Author(s):  
jean-claude perez
Keyword(s):  
Small Region ◽  
Plasmodium Yoelii ◽  
The Other ◽  
Rna Sequences ◽  
Synonymous Codons ◽  
Synthetic Genome ◽  
Other Hand ◽  
Cumulative Length ◽  
The One ◽  
Different Strains

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.

scholarly journals The INDIA Mutations and B.1.617 Variant: Is There a Global "Strategy" for Mutations and Evolution of Variants of The SARS-CoV2 Genome?

2021 ◽  
Author(s):  
Jean-claude Perez
Keyword(s):  
Numerical Method ◽  
Fibonacci Numbers ◽  
Global Strategy ◽  
Messenger Rnas ◽  
Whole Genomes ◽  
Frequent Mutations

In this paper, we run for all INDIA mutations and variants a biomathematical numerical method for analysing mRNA nucleotides sequences based on UA/CG Fibonacci numbers proportions (Perez, 2021). In this study, we limit ourselves to the analysis of whole genomes, all coming from the mutations and variants of SARS-CoV2 sequenced in India in 2020 and 2021. We then demonstrate - both on actual genomes of patients and on variants combining the most frequent mutations to the SARS-CoV2 Wuhan genomes and then to the B.1.617 variant - that the numerical Fibonacci AU / CG metastructures increase considerably in all cases analyzed in ratios of up to 8 times. We can affirm that this property contributes to a greater stability and lifespan of messenger RNAs, therefore, possibly also to a greater INFECTUOSITY of these variant genomes.

scholarly journals THE INDIA MUTATIONS AND B.1.617 DELTA VARIANTS: IS THERE A GLOBAL "STRATEGY" FOR MUTATIONS AND EVOLUTION OF VARIANTS OF THE SARS-COV2 GENOME?

2021 ◽  
Vol 9 (6) ◽  
pp. 418-459
Author(s):  
Jean Claude Perez
Keyword(s):  
None None ◽  
Exponential Growth ◽  
Reference Genome ◽  
Fibonacci Numbers ◽  
Global Strategy ◽  
Messenger Rnas ◽  
Average Increase ◽  
Whole Genomes ◽  
Frequent Mutations ◽  
Reference Strains

In this paper, we run for all INDIA mutations and variants a biomathematical numerical method for analysing mRNA nucleotides sequences based on UA/CG Fibonacci numbers proportions (Perez, 2021). In this study, we limit ourselves to the analysis of whole genomes, all coming from the mutations and variants of SARS-CoV2 sequenced in India in 2020 and 2021. We then demonstrate - both on actual genomes of patients and on variants combining the most frequent mutations to the SARS-CoV2 Wuhan genomes and then to the B.1.617 variant - that the numerical Fibonacci AU / CG metastructures increase considerably in all cases analyzed in ratios of up to 8 times. We can affirm that this property contributes to a greater stability and lifespan of messenger RNAs, therefore, possibly also to a greater INFECTUOSITY of these variant genomes. Out of a total of 108 genomes analyzed: None ("NONE") of them contained a number of metastructures LOWER than those of the reference SARS-CoV2 Wuhan genome. Eleven (11) among them contained the same number of metastructures as the reference genome. 97 of them contained a GREATER number of metastructures than the reference genome, ie 89.81% of cases. The average increase in the number of metastructures for the 97 cases studied is 4.35 times the number of SARS-CoV2 UA/CG 17711 Fibonacci metastructures. Finally, we put a focus on B.1.617.2 crucial exponential growth Indian variant. Then, we demonstrate, by analyzing the main worldwide 19 variants, both at the level of spikes and of whole genomes, how and why these UA / CG metastuctures increase overall in the variants compared to the 2 reference strains SARS-CoV2 Wuhan and D614G. Then, we discuss the possible risk of ADE for vaccinated people. To complete this article, an ADDENDUM by Nobelprizewinner Luc Montagnier vas added at the end of this paper.

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

2019 ◽  
Author(s):  
Jean-claude Perez
Keyword(s):  
Caulobacter Crescentus ◽  
Fibonacci Numbers ◽  
Three Dimensional ◽  
Craig Venter ◽  
Discussion Section ◽  
Craig Venter Institute ◽  
E Coli ◽  
Synthetic Genome ◽  
Mycoplasma Mycoides ◽  
Dna Strands

In (Venetz et al., 2019), authors rebuilt the essential genome of Caulobacter crescentus through the process of chemical synthesis rewriting and studied the genetic information content at the level of its essential genes. Then, they reduced the native Caulobacter crescentus native Caulobacter NA1000 genome sequence real genome ( 4042929 bp ) to the 785,701-bp reduced synthetic genome. Here we demonstrate the existence of a palindromic-like mirror structure that exists in real genomes and disappears totally in the synthetic genome. This biomathematic meta-organization is based on characteristic proportions of Fibonacci numbers between DNA single strand nucleotides proportions TC / AG on the one hand and TG / AC on the other hand. In both cases, we suggest that this meta-structure enhances the three-dimensional cohesion of the two DNA strands of the genome. We then generalize this study to the different synthetic genomes and synthetic cells published by the Craig Venter Institute on Mycoplasma Mycoides JCVI-syn1.0 (in 2010), JCVI-syn3.0 (in 2016) and JCVI-syn3A (in 2019). Finally, in the discussion section, we extend this study to synthetic genomes of E-Coli and Yeast chromosome XII.

scholarly journals The INDIA Mutations and B.1.617 Variant: Is There a Global "Strategy" for Mutations and Evolution of Variants of The SARS-CoV2 Genome?

2021 ◽  
Author(s):  
Jean-claude Perez
Keyword(s):  
Numerical Method ◽  
None None ◽  
Reference Genome ◽  
Fibonacci Numbers ◽  
Global Strategy ◽  
Messenger Rnas ◽  
Average Increase ◽  
Whole Genomes ◽  
Frequent Mutations

ABSTRACT. In this paper, we run for all INDIA mutations and variants a biomathematical numerical method for analysing mRNA nucleotides sequences based on UA/CG Fibonacci numbers proportions (Perez, 2021). In this study, we limit ourselves to the analysis of whole genomes, all coming from the mutations and variants of SARS-CoV2 sequenced in India in 2020 and 2021. We then demonstrate - both on actual genomes of patients and on variants combining the most frequent mutations to the SARS-CoV2 Wuhan genomes and then to the B.1.617 variant - that the numerical Fibonacci AU / CG metastructures increase considerably in all cases analyzed in ratios of up to 8 times. We can affirm that this property contributes to a greater stability and lifespan of messenger RNAs, therefore, possibly also to a greater INFECTUOSITY of these variant genomes. Out of a total of 108 genomes analyzed: - None ("NONE") of them contained a number of metastructures LOWER than those of the reference SARS-CoV2 Wuhan genome. - Eleven (11) among them contained the same number of metastructures as the reference genome. - 97 of them contained a GREATER number of metastructures than the reference genome, ie 89.81% of cases. The average increase in the number of metastructures for the 97 cases studied is 4.35 times the number of SARS-CoV2 UA/CG 17711 Fibonacci metastructures.

Pythagorean Triples from Harmonic Sequences

2001 ◽  
Vol 94 (3) ◽  
pp. 218-222
Author(s):  
Angelo S. DiDomenico ◽  
Randy J. Tanner
Keyword(s):  
Mathematics Teacher ◽  
Fibonacci Numbers ◽  
Whole Numbers ◽  
Multiplication Tables ◽  
Pythagorean Triples ◽  
Mathematical Experience ◽  
Ancient Times

Pythagorean triples have intrigued generations of mathematics explorers, including students, since ancient times. One of their most charming features is their connection with various other areas of mathematics. In the Mathematics Teacher, for example, authors have shown that Pythagorean triples can be generated from the Fibonacci numbers (Bertucci 1991), from geometric sequences (Carbeau 1993), and from both the addition and multiplication tables of whole numbers (DiDomenico 1993, 1995). These findings are indeed fascinating; when shared with students, they spark interest and curiosity and lead to a truly enriching mathematical experience. Students, in fact, independently found that Pythagorean triples could be generated from Fibonacci numbers and geometric sequences. This article reveals another surprising connection that shows how all primitive Pythagorean triples can be generated from harmonic sequences.

Ultrastructural Changes of the Symbiotic Chlorella-Like Alga Isolated from Hydra Viridis

1982 ◽  
Vol 40 ◽  
pp. 320-321
Author(s):  
K.W. Lee ◽  
R.H. Meints ◽  
D. Kuczmarski ◽  
J.L. Van Etten
Keyword(s):  
Time Course ◽  
Reciprocal Cross ◽  
Ultrastructural Level ◽  
Ultrastructural Changes ◽  
Symbiotic Relationship ◽  
Cell Recognition ◽  
Green Hydra ◽  
Different Strains ◽  
Hydra Viridis

The physiological, biochemical, and ultrastructural aspects of the symbiotic relationship between the Chlorella-like algae and the hydra have been intensively investigated. Reciprocal cross-transfer of the Chlorellalike algae between different strains of green hydra provide a system for the study of cell recognition. However, our attempts to culture the algae free of the host hydra of the Florida strain, Hydra viridis, have been consistently unsuccessful. We were, therefore, prompted to examine the isolated algae at the ultrastructural level on a time course.

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