scholarly journals The Genetic Code, Algebraic Codes and Double Numbers

2020 ◽  
Author(s):  
Sergey V. Petoukhov
Keyword(s):  
Genetic Code ◽  
Communication Technologies ◽  
Structural Features ◽  
Rna Molecules ◽  
Doubly Stochastic ◽  
Dna And Rna ◽  
Double Numbers ◽  
Algebraic Codes ◽  
Living Organisms ◽  
Algebraic Code

The article shows materials to the question about algebraic features of the genetic code and about the dictatorial influence of the DNA and RNA molecules on the whole organism. Presented results testify in favor that the genetic code is an algebraic code related with a wide class of algebraic codes, which are a basis of noise-immune coding of information in communication technologies. Structural features of the genetic systems are associated with hypercomplex double (or hyperbolic) numbers and with bisymmetric doubly stochastic matrices. The received results confirm that represented matrix approaches are effective for modeling genetic phenomena and revealing the interconnections of structures of biological bodies at various levels of their organization. This allows one to think that living organisms are algebraically encoded entities where structures of genetic molecules have the dictatorial influence on inherited structures of the whole organism. New described algebraic approaches and results are discussed.

scholarly journals The Genetic Code, Algebraic Codes and Double Numbers

2019 ◽  
Author(s):  
Sergey V. Petoukhov
Keyword(s):  
Genetic Code ◽  
Wide Class ◽  
Communication Technologies ◽  
Hyperbolic Numbers ◽  
Double Numbers ◽  
Algebraic Codes ◽  
Structural Relations ◽  
Living Organisms ◽  
Algebraic Code

The article shows materials to the question on algebraic features of the genetic code. Presented results testify in favor that the genetic code is an algebraic code related with a wide class of algebraic codes, which are a basis of noise-immune coding of information in communication technologies. Algebraic features of the genetic code are associated with hypercomplex double (or hyperbolic) numbers. The article also presents data on structural relations of some genetically inherited macrobiological phenomena with double numbers and with their algebraic extentions. The received results confirm that multidimensional numerical systems is effective for modeling and revealing the interconnections of structures of biological bodies at various levels of their organization. This allows one to think that living organisms are algebraically encoded entities.

Multidimensional Numbers and the Genomatrices of Hydrogen Bonds

2010 ◽  
pp. 193-206
Author(s):  
Sergey Petoukhov ◽  
Matthew He
Keyword(s):  
Hydrogen Bonds ◽  
Genetic Code ◽  
Structural Features ◽  
Hyperbolic Type ◽  
Complex Numbers ◽  
Hypercomplex Numbers ◽  
Molecular Systems ◽  
Natural Systems ◽  
Double Numbers ◽  
Mathematical Properties

This chapter returns to the kind of numeric genetic matrices, which were considered in Chapter 4-6. This kind of genomatrices is not connected with the degeneracy of the genetic code directly, but it is related to some other structural features of the genetic code systems. The connection of the Kronecker families of such genomatrices with special categories of hypercomplex numbers and with their algebras is demonstrated. Hypercomplex numbers of these two categories are named “matrions of a hyperbolic type” and “matrions of a circular type.” These hypercomplex numbers are a generalization of complex numbers and double numbers. Mathematical properties of these additional categories of algebras are presented. A possible meaning and possible applications of these hypercomplex numbers are discussed. The investigation of these hyperbolic numbers in their connection with the parameters of molecular systems of the genetic code can be considered as a continuation of the Pythagorean approach to understanding natural systems.

scholarly journals Scaling and Visualization of Nucleotide Sequences

2019 ◽  
Vol 224 ◽  
pp. 03007
Author(s):  
Ivan V. Stepanyan ◽  
Abbakar M. Khussein
Keyword(s):  
Genetic Information ◽  
Visual Representations ◽  
Nucleotide Composition ◽  
Nucleotide Sequences ◽  
Coordinate Systems ◽  
Rna Molecules ◽  
Dna And Rna ◽  
Fractal Clusters ◽  
Living Organisms ◽  
Orthogonal Coordinate Systems

Algorithms for scaling and visualization of nucleotide sequences developed in this study allow identifying relationships between the biochemical parameters of DNA and RNA molecules with scale invariance, fractal clusters, nonlinear ordering and symmetry and noise immunity of visual representations in orthogonal coordinate systems. The algorithms are capable of displaying structures of the nucleotide sequences of living organisms by visualizing them in spaces of various dimensions and scales. Approximately one hundred genes (protozoa, plants, fungi, animals, viruses) were analysed and examples of visualization of the nucleotide composition of genomes of various species have been presented. The developed method contributes to an in-depth understanding of the principles of genetic coding and simplifying the perception of genetic information due to the algorithmic interpretation of the basic properties of polynucleotide fragments with visualization of the final geometric structure of the genetic code.

scholarly journals Epigenetic Modulation of Chromatin States and Gene Expression by G-Quadruplex Structures

2020 ◽  
Vol 21 (11) ◽  
pp. 4172 ◽  
Author(s):  
Chiara Reina ◽  
Vincenzo Cavalieri
Keyword(s):  
Gene Expression ◽  
Noncoding Rna ◽  
Biological Activities ◽  
Regulation Of Gene Expression ◽  
Three Dimensional ◽  
Structural Features ◽  
Rna Molecules ◽  
Dna And Rna ◽  
G Quadruplex ◽  
Epigenetic Modulation

G-quadruplexes are four-stranded helical nucleic acid structures formed by guanine-rich sequences. A considerable number of studies have revealed that these noncanonical structural motifs are widespread throughout the genome and transcriptome of numerous organisms, including humans. In particular, G-quadruplexes occupy strategic locations in genomic DNA and both coding and noncoding RNA molecules, being involved in many essential cellular and organismal functions. In this review, we first outline the fundamental structural features of G-quadruplexes and then focus on the concept that these DNA and RNA structures convey a distinctive layer of epigenetic information that is critical for the complex regulation, either positive or negative, of biological activities in different contexts. In this framework, we summarize and discuss the proposed mechanisms underlying the functions of G-quadruplexes and their interacting factors. Furthermore, we give special emphasis to the interplay between G-quadruplex formation/disruption and other epigenetic marks, including biochemical modifications of DNA bases and histones, nucleosome positioning, and three-dimensional organization of chromatin. Finally, epigenetic roles of RNA G-quadruplexes in post-transcriptional regulation of gene expression are also discussed. Undoubtedly, the issues addressed in this review take on particular importance in the field of comparative epigenetics, as well as in translational research.

Regulatory aspects of RNAi in plant production.

2021 ◽  
pp. 154-158
Author(s):  
Werner Schenkel ◽  
Achim Gathmann
Keyword(s):  
Small Rna ◽  
Plant Protection ◽  
Plant Protection Products ◽  
Plant Production ◽  
The European Union ◽  
Relevant Aspect ◽  
Rna Molecules ◽  
Rnai Technology ◽  
Living Organisms ◽  
Intended Use

Abstract Technologies based on RNA interference (RNAi) may be used in plant production in different contexts. With respect to applicable regulations, a major distinction is to be made between plants producing small RNA molecules due to modifications of the genome and topically applied plant protection products (PPPs) based on double-stranded RNA (dsRNA). The first group may be further divided into those using RNAi technology to achieve changes in the plant's metabolism and those where plant-produced RNA molecules are intended to impact other organisms that interact with the plant. For PPPs, relevant aspects are whether the product contains living organisms or only purified molecules. The intended use of the product is another relevant aspect with respect to regulation. It is expected that PPPs will be among the first products utilizing the RNAi mechanism in the European Union. This chapter discusses the regulation of modified RNAi plants and the regulation of PPPs utilizing RNAi mechanisms.

scholarly journals Lead-seq: transcriptome-wide structure probing in vivo using lead(II) ions

2020 ◽  
Vol 48 (12) ◽  
pp. e71-e71 ◽  
Author(s):  
Christian Twittenhoff ◽  
Vivian B Brandenburg ◽  
Francesco Righetti ◽  
Aaron M Nuss ◽  
Axel Mosig ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Yersinia Pseudotuberculosis ◽  
Structural Information ◽  
Dimethyl Sulfate ◽  
Bacterial Pathogen ◽  
Structural Features ◽  
Global Scale ◽  
Rna Molecules ◽  
Different Temperatures

Abstract The dynamic conformation of RNA molecules within living cells is key to their function. Recent advances in probing the RNA structurome in vivo, including the use of SHAPE (Selective 2′-Hydroxyl Acylation analyzed by Primer Extension) or kethoxal reagents or DMS (dimethyl sulfate), provided unprecedented insights into the architecture of RNA molecules in the living cell. Here, we report the establishment of lead probing in a global RNA structuromics approach. In order to elucidate the transcriptome-wide RNA landscape in the enteric pathogen Yersinia pseudotuberculosis, we combined lead(II) acetate-mediated cleavage of single-stranded RNA regions with high-throughput sequencing. This new approach, termed ‘Lead-seq’, provides structural information independent of base identity. We show that the method recapitulates secondary structures of tRNAs, RNase P RNA, tmRNA, 16S rRNA and the rpsT 5′-untranslated region, and that it reveals global structural features of mRNAs. The application of Lead-seq to Y. pseudotuberculosis cells grown at two different temperatures unveiled the first temperature-responsive in vivo RNA structurome of a bacterial pathogen. The translation of candidate genes derived from this approach was confirmed to be temperature regulated. Overall, this study establishes Lead-seq as complementary approach to interrogate intracellular RNA structures on a global scale.

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