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Oct 2021 DOI 10.14302/issn.2641-5526.jmid-21-3900
In this theoretical discovery of a law of Life, there is MATHEMATICS (Geometry, Bits and Numbers) that UNIFY 3 universes as complementary as ATOMIC MASS, WAVES, and INFORMATION (DNA, RNA and Amino Acids). The discovery of a simple numerical formula for the projection of all the atomic mass of life-sustaining CONHSP bioatoms leads to the emergence of a set of Nested CODES unifying all the biological, genetic and genomic components by unifying them from bioatoms up to 'to whole genomes. In particular, we demonstrate the existence of a digital meta-code common to the three languages of biology that are RNA, DNA and amino acid sequences. Through this meta-code, genomic and proteomic images appear almost analogous and correlated. The analysis of the textures of these images then reveals a binary code as well as an undulatory code whose analysis on the human genome makes it possible to predict the alternating bands constituting the cariotypes of the chromosomes. The application of these codes to perspectives in astrobiology, cancer, and specifically in INFORMATION THEORY with the emergence of binary codes and regions of local stability (voting process), whose fractal nature we demonstrate, is illustrated. PREFACE by Professor Luc Montagnier Addendum by Robert Friedman M.D After the discovery of the DNA double helix structure allowing both the stable storage of genetic information and its transfer through messenger RNA to protein synthesis organelles themselves structured by RNA most abundant in cells, the ribosomal. This wonder of nature exists in ALL living beings from the virus to humans and is based on two codes, the linear sequence of nucleotides and that derived from codons where three nucleotides allow with a certain flexibility - synonymous codons - the choice in the twenty amino acids. But we are missing a third CODE the one governing at multicellular beings from the rotifer to human, the stabilized modulation of gene expression in a nutshell the differentiation of cells from the single cell of the fertilized egg. It is logical to think that this program which begins as soon as fertilization is written in the DNA. We are also prone to associate it with non-coding DNA sequences although they control gene expression. I introduce here the notion developed by Jean-Claude Pérez of mathematical harmony, a higher order present in all living beings and whose existence it finds in genomes, including those of viruses. Thus the natural evolution of variants of the genome of coronavirus Covid 19 tends towards increasingly long Fibonacci series. It remains to determine the Who, the How and the Why of such developments. I will bet with my mathematician colleague that waves and fractals play a role. Luc Montagnier ADDENDUM Jean-claude has given scientists a strong new direction for research. He has identified a unified field of science guided by the Golden Ratio and Fibonacci Sequence. By identifying an overall guiding principle that makes possible fractal-like nesting at all levels of biological manifestation, future researchers can begin with the "whole" instead of the "parts". If we know that complex systems are organized at varying levels by the Golden Ratio and Fibonacci Sequence, we can look for those universal patterns first and then fill in the gaps with small details to complete the picture. It's like having an overall view of a crossword puzzle before beginning to assemble the individual pieces. Without an overarching vision and guiding principle, completing the puzzle is infinitely more difficult. Once scientists and researchers realize and begin using this "SECRET IN HIDDEN IN PLAIN SIGHT," their discoveries will be orders of magnitude more fruitful. Robert Friedman M.D
Apr 2018
The global analysis of 3 human genomes of increasing levels of evolution (neanderthal / sapiens build34 of 2003 / sapiens hg38 of 2013) reveals 2 levels of numerical constraints controlling, structuring and optimizing the DNA sequences of these genomes. A global constraint - which we will call "HGO" for "Human Genome Optimum" - optimizes the genome at its global scale of 3.5 billion base pairs. This same operator when applied to each of the 24 individual chromosomes reveals a hierarchical structure of these 24 chromosomes according to a numerical spectrum of amplitude ½ Phi extending from chromosome 4 to chromosome 19. This first level of comparison reveals a very Great analogy between these 3 genomes. Then we introduce a global analysis method of roughness or fractal texture of the DNA sequences at the level of each chromosome. After having demonstrated that the chromosome4 seems to play a privileged role in the human genome, radically differentiating it from the 23 other chromosomes, we limit the study to the exhaustive analysis of different whole chromosomes4 relative to the 6 primates Homosapiens, Neanderthal, Chimpanzee, Orang-outan, Gorilla and Macaque. There are then remarkable resonances and periods - based on the sequences of Fibonacci and Lucas - totally differentiating the chromosomes 4 of these different primate species: 21 base pairs period for the chimpanzee and the urang-outan, 34 bases pairs period for Man, and 55 base pairs period for the gorilla. Finally, the major result is that the comparative analysis of the respective chromosomes4 of sapiens and neanderthal shows for the first time major differences in long-range fractal structures between the DNA sequences of these two genomes. Thus, while the chromosome4 of sapiens has an obvious resonance of 34 nucleotides, that of Neanderthal seems "torn" between two attractors of fractal textures, one on this same resonance 34, but with a roughness radically different from that of sapiens, While the other resonance is tuned to the number of Lucas 123. Finally, on a more theoretical level, this method reveals properties of "discrete digital standing waves" such as periods, resonances, phase shifts or phase positions. To conclude, we suggest that this chromosome4 could possibly play a role as a "referential" with respect to each of the 23 other chromosomes of the nuclear genome and possibly also with respect to the mitochondrial mtDNA genome.
Apr 2018 DOI 10.14302/issn.2326-0793.jpgr-18-2004
Human proteome project was revolutionized about 40 years ago with purpose of summarizing whole proteomic data at one place. It was launched after human genome project to map and observe all proteins. The goal related proteomic study is to draft the entire human proteome in disease diagnosis by using bioinformatics tools. Pillars of human proteome project provide different databases related to proteins at transcriptional and translational level. Human proteome organization(HUPO) published biology disease HUPO whose aim is to measure protein and proteome by life and processes related to human diseases. Different human organ like plasma, liver, brain and diabetic base project are used to characterize human disease and health. Major data resources accumulated in databases like peptides Atlas, GPMDB and neXtProt for proteins. Matrices of human proteome project identify and characterize the protein products as Post translational modification (PTM), splice various isoforms from 20,300 proteins. Matrices related to different years make proteomes counterpart by magnify the research biomedical community with high output of instruments and specimen pre-analytical protocols. CALIPHO multidisciplinary group provides information about protein complexities, interactions, function and structure complexities after Uniport and Swissprot. Different bioinformatics tools are used for structural and functional annotations of protein, disease diagnosis and mutations due to protein. Extensive study of human proteome project has been proved helpful in disease treatment at translational and post- translational levels. In future, human proteome project along with bioinformatics will include protein profiling, biomarkers, Mass spectrophotometer technique and cross analysis of different proteome projects.
Oct 2017 DOI 10.14302/issn.2572-5424.jgm-17-1609
DUF1220 proteins regions show the largest Homo-Sapiens lineage-specific increase in copy number of any protein-coding region in the human genome and map principally to 1q21.1. DUF1220 deletions have been associated with microcephaly and macrocephaly, respectively. DUF1220 copy number has been linked to both brain size in humans and brain evolution among primates. Remarkably, dosage variations involving DUF1220 sequences have now been linked to human brain expansion, autism severity, total IQ, and cognitive and mathematical aptitude scores. We analyzed in chromosome 1q a total of 245 DUF1220 proteins. Finally the method is extended analysing the long 1q21 region from 7 other close primates like Neanderthal, great apes : chimp, gorilla, orangutan and monkeys : macaque, marmoset, vervet. This remarkable property is confirmed by comparing these primates to other mammals such as mice, rabbit, cow, dolphin and Elephant. We then show four classes of multi-periodic fractal structures for all 19 DUF1220 regions and 19 NBPF genes studied cases. The analysis of these spectra of fractal periods1 reveals a simple linear interdependence, hierarchization and unification between the numerical sequences of each of these 4 spectra and the sequences of Fibonacci and Lucas. Given the evidence of this numerical relationship, we suggest that this discovery may be one of the major causes of a cognitive development of man superior to that of the great primates. Finally the mathematical roots of this whole numbers resonance patterns is discussed.