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.

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 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 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 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 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.

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.

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.

Role of Transcriptional Read-Through in PRE Activity in Drosophila melanogaster

Acta Naturae ◽  
2016 ◽  
Vol 8 (2) ◽  
pp. 79-86 ◽  
Author(s):  
P. V. Elizar’ev ◽  
D. V. Lomaev ◽  
D. A. Chetverina ◽  
P. G. Georgiev ◽  
M. M. Erokhin
Keyword(s):  
Dna Sequences ◽  
Cell Types ◽  
Transcription Terminator ◽  
Response Elements ◽  
Polycomb Response Elements ◽  
The Individual ◽  
Multicellular Organisms ◽  
Different Cell Types ◽  
Main Factor

Maintenance of the individual patterns of gene expression in different cell types is required for the differentiation and development of multicellular organisms. Expression of many genes is controlled by Polycomb (PcG) and Trithorax (TrxG) group proteins that act through association with chromatin. PcG/TrxG are assembled on the DNA sequences termed PREs (Polycomb Response Elements), the activity of which can be modulated and switched from repression to activation. In this study, we analyzed the influence of transcriptional read-through on PRE activity switch mediated by the yeast activator GAL4. We show that a transcription terminator inserted between the promoter and PRE doesnt prevent switching of PRE activity from repression to activation. We demonstrate that, independently of PRE orientation, high levels of transcription fail to dislodge PcG/TrxG proteins from PRE in the absence of a terminator. Thus, transcription is not the main factor required for PRE activity switch.

Gender, Technology and the New Woman

2017 ◽  
Author(s):  
Lena Wånggren
Keyword(s):  
Nineteenth Century ◽  
New Woman ◽  
New Technologies ◽  
Gender And Sexuality ◽  
Literary Texts ◽  
Late Nineteenth Century ◽  
Gender And Technology ◽  
The New Woman ◽  
Grant Allen

This book examines late nineteenth-century feminism in relation to technologies of the time, marking the crucial role of technology in social and literary struggles for equality. The New Woman, the fin de siècle cultural archetype of early feminism, became the focal figure for key nineteenth-century debates concerning issues such as gender and sexuality, evolution and degeneration, science, empire and modernity. While the New Woman is located in the debates concerning the ‘crisis in gender’ or ‘sexual anarchy’ of the time, the period also saw an upsurge of new technologies of communication, transport and medicine. This book explores the interlinking of gender and technology in writings by overlooked authors such as Grant Allen, Tom Gallon, H. G. Wells, Margaret Todd and Mathias McDonnell Bodkin. As the book demonstrates, literature of the time is inevitably caught up in a technological modernity: technologies such as the typewriter, the bicycle, and medical technologies, through literary texts come to work as freedom machines, as harbingers of female emancipation.

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