scholarly journals Algebraic Rules for the Percentage Composition of Oligomers in Genomes

2021 ◽  
Author(s):  
Sergey Petoukhov
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Gestalt Psychology ◽  
Matrix Representations ◽  
Quantum Biology ◽  
Percentage Composition ◽  
Discrete Signals ◽  
Algebraic Properties ◽  
Prokaryotic Genomes

The article presents the author's results of studying hidden rules of structural organizations of long DNA sequences in eukaryotic and prokaryotic genomes. The results concern some rules of percentages (or probabilities) of n-plets in genomes. To reveal such rules, the author considers genomic DNA nucleotide sequences as multilayers sequences of n-plets and studies the percentage contents of n-plets in different layers. Unexpected rules of invariance of total sums of percentages in certain tetra-groupings of n-plets in different layers of genomic DNA sequences are revealed. These discovered rules are candidates for the role of universal genomic rules. A tensor family of matrix representations of interrelated DNA-alphabets of 4 nucleotides, 16 doublets, 64 triplets, and 256 tetraplets is used in the study. This matrix approach allows revealing algebraic properties of the mentioned genetic rules of probabilities, which are useful for developing algebraic and quantum biology. Some analogies of the discovered genetic phenomena with phenomena of Gestalt psychology are noted and discussed. The author connects the received results about the genomic percentages rules with a supposition of P. Jordan, who is one of the creators of quantum mechanics and quantum biology, that life's missing laws are the rules of chance and probability of the quantum world. Additional attention is paid to the algebraic features of the system of structured DNA alphabets and their relationship with the methods of algebraic holography, known in the technique of processing discrete signals. The concept of algebraic-holographic genetics is being developed for the understanding of inherited holographic properties of organisms.

scholarly journals Algebraic Rules for the Percentage Composition of Oligomers in Genomes

2021 ◽  
Author(s):  
Sergey Petoukhov
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Gestalt Psychology ◽  
Matrix Approach ◽  
Matrix Representations ◽  
Quantum Biology ◽  
Percentage Composition ◽  
Algebraic Properties ◽  
Prokaryotic Genomes

The article presents the author's results of studying hidden rules of structural organizations of long DNA sequences in eukaryotic and prokaryotic genomes. The results concern some rules of percentages (or probabilities) of n-plets in genomes. To reveal such rules, the author considers genomic DNA nucleotide sequences as multilayers sequences of n-plets and studies the percentage contents of n-plets in different layers. Unexpected rules of invariance of total sums of percentages in certain tetra-groupings of n-plets in different layers of genomic DNA sequences are revealed. These discovered rules are candidates for the role of universal genomic rules. A tensor family of matrix representations of interrelated DNA-alphabets of 4 nucleotides, 16 doublets, 64 triplets, and 256 tetraplets is used in the study. This matrix approach allows revealing algebraic properties of the mentioned genetic rules of probabilities, which are useful for developing algebraic and quantum biology. Some analogies of the discovered genetic phenomena with phenomena of Gestalt psychology are noted and discussed. The author connects the received results about the genomic percentages rules with a supposition of P. Jordan, who is one of the creators of quantum mechanics and quantum biology, that life's missing laws are the rules of chance and probability of the quantum world.

scholarly journals Algebraic Rules for the Percentage Composition of Oligomers in Genomes

2021 ◽  
Author(s):  
Sergey Petoukhov
Keyword(s):  
Quantum Mechanics ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Matrix Representations ◽  
Quantum Biology ◽  
Percentage Composition ◽  
Prokaryotic Genomes ◽  
Further Development

The article presents the author's results of studying hidden rules of structural organizations of long DNA sequences in eukaryotic and prokaryotic genomes. The results concern some rules of percentages (or probabilities) of n-plets in genomes. To reveal such rules, the author uses a tensor family of matrix representations of interrelated DNA-alphabets of 4 nucleotides, 16 doublets, 64 triplets, and 256 tetraplets. If percentages of each of these n-plets in tested genomic DNA-texts are disposed into appropriate cells of appropriate matrices, unexpected rules of invariance of total sums of their percentages in certain tetra-groupings of n-plets are revealed. The author connects the received results about these genomic percentages rules with a supposition of P. Jordan, who is one of the creators of quantum mechanics and quantum biology, that life's missing laws are the rules of chance and probability of the quantum world. Algebraic features of the genomic matrices of percentages of n-plets are analyzed and discussed. The received results can be used for further development of quantum biology.

scholarly journals Tensor Rules in the Stochastic Organization of Genomes and Genetic Stochastic Resonance in Algebraic Biology

2021 ◽  
Author(s):  
Sergey V. Petoukhov
Keyword(s):  
Quantum Mechanics ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Analytical Tool ◽  
Prokaryotic Genomes ◽  
Algebraic Biology ◽  
Dna Nucleotide Sequence ◽  
A Chain ◽  
Product Of Matrices

The article is devoted to the new results of the author, which add his previously published ones, of studying hidden rules and symmetries in structures of long single-stranded DNA sequences in eukaryotic and prokaryotic genomes. The author uses the existence of different alphabets of n-plets in DNA: the alphabet of 4 nucleotides, the alphabet of 16 douplets, the alphabet of 64 triplets, etc. Each of such DNA alphabets of n-plets can serve for constructing a text as a chain of these n-plets. Using this possibility, the author represents any long DNA nucleotide sequence as a bunch of many so-called n-texts, each of which is written on the basis of one of these alphabets of n-plets. Each of such n-texts has its individual percents of different n-plets in its genomic DNA. But it turns out that in such multi-alphabetical or multilayer presentation of each of many genomic DNA, analyzed by the author, universal rules of probabilities and symmetry exist in interrelations of its different n-texts regarding their percents of n-plets. In this study, the tensor product of matrices and vectors is used as an effective analytical tool borrowed from the arsenal of quantum mechanics. Some additions to the topic of algebra-holographic principles in genetics are also presented. Taking into account the described genomic rules of probability, the author puts also forward a concept of the important role of stochastic resonances in genetic informatics.

scholarly journals Hyperbolic Rules of the Oligomer Cooperative Organization of Eukaryotic and Prokaryotic Genomes

2020 ◽  
Author(s):  
Sergey Petoukhov
Keyword(s):  
Quantum Information ◽  
Dna Sequences ◽  
Coding System ◽  
Harmonic Progression ◽  
General Rules ◽  
Prokaryotic Genomes ◽  
Algebraic Invariants ◽  
Cooperative Organization ◽  
Long Genes

The author's method of oligomer sums for analysis of oligomer compositions of eukaryotic and prokaryotic genomes is described. The use of this method revealed the existence of general rules for cooperative oligomeric organization of a wide list of genomes. These rules are called hyperbolic because they are associated with hyperbolic sequences including the harmonic progression 1, 1/2, 1/3, .., 1/n. These rules are demonstrated by examples of quantitative analysis of many genomes from the human genome to the genomes of archaea and bacteria. The hyperbolic (harmonic) rules, speaking about the existence of algebraic invariants in full genomic sequences, are considered as candidates for the role of universal rules for cooperative organization of genomes. The described phenomenological results were obtained as consequences of the previously published author's quantum-information model of long DNA sequences. The oligomer sums method was also applied to the analysis of long genes and viruses including the COVID-19 virus; this revealed, in characteristics of many of them, the phenomenon of rhythmically repeating deviations from model hyperbolic sequences; these deviations are associated with DNA triplets and should be systematically analyzed for a deeper understanding the genetic coding system. The topics of the algebraic harmony in living bodies and of the quantum-information approach in biology are discussed.

scholarly journals Nucleotide Epi-Chains and New Nucleotide Probability Rules in Long DNA Sequences

2019 ◽  
Author(s):  
Sergey V. Petoukhov
Keyword(s):  
Quantum Mechanics ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Nucleotide Sequences ◽  
Quantum Biology ◽  
Biological Meaning ◽  
Prokaryotic Genomes

One of creators of quantum mechanics P. Jordan in his work on quantum biology claimed that life's missing laws were the rules of chance and probability of the quantum world. The article presents author’s results of studying probabilities of nucleotides on so-called epi-chains of long DNA sequences of various eukaryotic and prokaryotic genomes. DNA epi-chains are algorithmically constructed subsequencies of DNA nucleotide sequences. According to the algorithm of construction of any epi-chain of the order n, the epi-chain is such nucleotide subsequence, in which the numerations of adjacent nucleotides differ by n    (n = 2, 3, 4,…). Correspondingly each epi-chain of order n contains n times less nucleotides than the original DNA sequence. The presented results unexpectedly show that nucleotide probabilities on such DNA epi-chains of different orders are practically identical to nucleotide probabilities in the original long DNA sequence. These data allow considering DNA as a regular rich set of epi-chains, which can play a certain role in genetic and epigenetic phenomena as the author belives. Appropriate rules of nucleotide probabilities on epi-chains of long DNA sequences are formulated for further their tests on a wider set of biological genomes. These phenomenological data and their possible biological meaning are discussed.

scholarly journals Toxin-Antitoxin Gene Pairs Found in Tn3 Family Transposons Appear To Be an Integral Part of the Transposition Module

mBio ◽  
2020 ◽  
Vol 11 (2) ◽  
Author(s):  
Gipsi Lima-Mendez ◽  
Danillo Oliveira Alvarenga ◽  
Karen Ross ◽  
Bernard Hallet ◽  
Laurence Van Melderen ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Bacterial Population ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Plasmid Maintenance ◽  
Gene Pairs ◽  
Prokaryotic Genomes ◽  
Replicative Transposition ◽  
Genetic Context

ABSTRACT Much of the diversity of prokaryotic genomes is contributed by the tightly controlled recombination activity of transposons (Tns). The Tn3 family is arguably one of the most widespread transposon families. Members carry a large range of passenger genes incorporated into their structures. Family members undergo replicative transposition using a DDE transposase to generate a cointegrate structure which is then resolved by site-specific recombination between specific DNA sequences (res) on each of the two Tn copies in the cointegrate. These sites also carry promoters controlling expression of the recombinase and transposase. We report here that a number of Tn3 members encode a type II toxin-antitoxin (TA) system, typically composed of a stable toxin and a labile antitoxin that binds the toxin and inhibits its lethal activity. This system serves to improve plasmid maintenance in a bacterial population and, until recently, was believed to be associated with bacterial persistence. At least six different TA gene pairs are associated with various Tn3 members. Our data suggest that several independent acquisition events have occurred. In contrast to most Tn3 family passenger genes, which are generally located away from the transposition module, the TA gene pairs abut the res site upstream of the resolvase genes. Although their role when part of Tn3 family transposons is unclear, this finding suggests a potential role for the embedded TA in stabilizing the associated transposon with the possibility that TA expression is coupled to expression of transposase and resolvase during the transposition process itself. IMPORTANCE Transposable elements (TEs) are important in genetic diversification due to their recombination properties and their ability to promote horizontal gene transfer. Over the last decades, much effort has been made to understand TE transposition mechanisms and their impact on prokaryotic genomes. For example, the Tn3 family is ubiquitous in bacteria, molding their host genomes by the paste-and-copy mechanism. In addition to the transposition module, Tn3 members often carry additional passenger genes (e.g., conferring antibiotic or heavy metal resistance and virulence), and three were previously known to carry a toxin-antitoxin (TA) system often associated with plasmid maintenance; however, the role of TA systems within the Tn3 family is unknown. The genetic context of TA systems in Tn3 members suggests that they may play a regulatory role in ensuring stable invasion of these Tns during transposition.

scholarly journals Toxin-antitoxin gene pairs found in Tn3 family transposons appear to be an integral part of the transposition module

2019 ◽  
Author(s):  
Gipsi Lima-Mendez ◽  
Danillo Oliveira Alvarenga ◽  
Karen Ross ◽  
Bernard Hallet ◽  
Laurence Van Melderen ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Bacterial Population ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Plasmid Maintenance ◽  
Gene Pairs ◽  
Prokaryotic Genomes ◽  
Replicative Transposition ◽  
Genetic Context

AbstractMuch of the diversity of prokaryotic genomes is contributed by the tightly controlled recombination activity of transposons (Tn). The Tn3 family is arguably one of the most widespread transposon families. Members carry a large range of passenger genes incorporated into their structures. Family members undergo replicative transposition using a DDE transposase to generate a cointegrate structure which is then resolved by site-specific recombination between specific DNA sequences (res) on each of the two Tn copies in the cointegrate. These sites also carry promoters controlling expression of the recombinase and transposase. We report here that a number of Tn3 members encode a type II toxin-antitoxin (TA) system, typically composed of a stable toxin and a labile antitoxin that binds the toxin and inhibits its lethal activity. This system serves to improve plasmid maintenance in a bacterial population and, until recently, was believed to be associated with bacterial persistence. At least six different TA gene pairs are associated with various Tn3 members. Our data suggest that several independent acquisition events have occurred. In contrast to most Tn3 family passenger genes which are generally located away from the transposition module, the TA gene pairs abut the res site upstream of the resolvase genes. Although their role when part of Tn3 family transposons is unclear, this finding suggests a potential role for the embedded TA in stabilizing the associated transposon with the possibility that TA expression is coupled to expression of transposase and resolvase during the transposition process itself.ImportanceTransposable Elements (TEs) are important in genetic diversification due to their recombination properties and their ability to promote horizontal gene transfer. Over the last decades, much effort has been made to understand TE transposition mechanisms and their impact on prokaryotic genomes. For example, the Tn3 family is ubiquitous in bacteria, moulding their host genomes by the paste-and-copy mechanism. In addition to the transposition module, Tn3 members often carry additional passenger genes (e.g., conferring antibiotic or heavy metal resistance and virulence) and three were previously known to carry a toxin-antitoxin (TA) system often associated with plasmid maintenance; however, the role of TA systems within the Tn3 family is unknown. The genetic context of TA systems in Tn3 members suggests that they may play a regulatory role in ensuring stable invasion of these Tn during transposition.

PCR detection of Neospora caninum in water buffalo foetal tissues

2014 ◽  
Vol 59 (1) ◽  
pp. 1-4 ◽  
Author(s):  
Clementina Auriemma ◽  
Maria Lucibelli ◽  
Giorgia Borriello ◽  
Esterina Carlo ◽  
Alessandra Martucciello ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Water Buffalo ◽  
Southern Italy ◽  
Neospora Caninum ◽  
Tissue Samples ◽  
Elisa Kit ◽  
Pcr Assays ◽  
High Level

AbstractThe seroprevalence of Neospora caninum was surveyed by an ELISA kit on two water buffalo herds of Southern Italy. Seropositive samples were detected in 47% and 59% of individuals, respectively, thus indicating high level of exposure to the parasite even if the possibility of vertical transmission cannot be excluded. Tissue samples collected from three aborted fetuses from the same herds were investigated for N. caninum presence by PCR assays targeting the 18S and the Nc5 DNA sequences, respectively. Both methods have shown the presence of N. caninum DNA in heart and brain. Sequencing of the Nc5 genomic DNA confirmed the presence of N. caninum in the samples; phylogenetic analysis of the obtained sequences showed high homology among the Neospora recovered from different samples. The present study suggests an important role of N. caninum as a possible abortive agent for water buffaloes.

scholarly journals Hyperbolic Rules of the Oligomer Cooperative Organization of Eukaryotic and Prokaryotic Genomes

2020 ◽  
Author(s):  
Sergey Petoukhov
Keyword(s):  
Quantum Information ◽  
Dna Sequences ◽  
Amino Acid Sequences ◽  
Literary Texts ◽  
Harmonic Progression ◽  
General Rules ◽  
Prokaryotic Genomes ◽  
Cooperative Organization ◽  
Long Genes

The author's method of oligomer sums for analysis of oligomer compositions of eukaryotic and prokaryotic genomes is described. The use of this method revealed the existence of general rules for cooperative oligomeric organization of a wide list of genomes. These rules are called hyperbolic because they are associated with hyperbolic sequences including the harmonic progression 1, 1/2, 1/3, .., 1/n. These rules are demonstrated by examples of quantitative analysis of many genomes from the human genome to the genomes of archaea and bacteria. The hyperbolic (harmonic) rules, speaking about the existence of algebraic invariants in full genomic sequences, are considered as candidates for the role of universal rules for the cooperative organization of genomes. The described phenomenological results were obtained as consequences of the previously published author's quantum-information model of long DNA sequences. The oligomer sums method was also applied to the analysis of long genes and viruses including the COVID-19 virus; this revealed, in characteristics of many of them, the phenomenon of such rhythmically repeating deviations from model hyperbolic sequences, which are associated with DNA triplets. In addition, an application of the oligomer sums method are shown to the analysis of the following long sequences: 1) amino acid sequences in long proteins like the protein Titin; 2) phonetic sequences of long Russan literary texts (for checking of thoughts of many authors that phonetic organization of human languages is deeply connected with the genetic language). The topics of the algebraic harmony in living bodies and of the quantum-information approach in biology are discussed.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

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