Polarization- and Chaos-Game-Based Fingerprinting of Molecular Targets of Listeria Monocytogenes Vaccine and Fully Virulent Strains.

Autor:	Zimnyakov DA; Physics Department, Yury Gagarin State Technical University of Saratov, 77 Polytechnicheskaya Str., 410054 Saratov, Russia.; Laboratory for Fundamental and Applied Research, Saratov State University of Genetics, Biotechnology and Engineering Named after N.I. Vavilov, 335 Sokolovaya Str., 410005 Saratov, Russia., Alonova MV; Physics Department, Yury Gagarin State Technical University of Saratov, 77 Polytechnicheskaya Str., 410054 Saratov, Russia., Lavrukhin MS; Laboratory for Fundamental and Applied Research, Saratov State University of Genetics, Biotechnology and Engineering Named after N.I. Vavilov, 335 Sokolovaya Str., 410005 Saratov, Russia., Lyapina AM; Laboratory for Fundamental and Applied Research, Saratov State University of Genetics, Biotechnology and Engineering Named after N.I. Vavilov, 335 Sokolovaya Str., 410005 Saratov, Russia., Feodorova VA; Laboratory for Fundamental and Applied Research, Saratov State University of Genetics, Biotechnology and Engineering Named after N.I. Vavilov, 335 Sokolovaya Str., 410005 Saratov, Russia.; Department for Microbiology and Biotechnology, Saratov State University of Genetics, Biotechnology and Engineering Named after N.I. Vavilov, 335 Sokolovaya Str., 410005 Saratov, Russia.
Jazyk:	angličtina
Zdroj:	Current issues in molecular biology [Curr Issues Mol Biol] 2023 Dec 13; Vol. 45 (12), pp. 10056-10078. Date of Electronic Publication: 2023 Dec 13.
DOI:	10.3390/cimb45120628
Abstrakt:	Two approaches to the synthesis of 2D binary identifiers ("fingerprints") of DNA-associated symbol sequences are considered in this paper. One of these approaches is based on the simulation of polarization-dependent diffraction patterns formed by reading the modeled DNA-associated 2D phase-modulating structures with a coherent light beam. In this case, 2D binarized distributions of close-to-circular extreme polarization states are applied as fingerprints of analyzed nucleotide sequences. The second approach is based on the transformation of the DNA-associated chaos game representation (CGR) maps into finite-dimensional binary matrices. In both cases, the differences between the structures of the analyzed and reference symbol sequences are quantified by calculating the correlation coefficient of the synthesized binary matrices. A comparison of the approaches under consideration is carried out using symbol sequences corresponding to nucleotide sequences of the hly gene from the vaccine and wild-type strains of Listeria monocytogenes as the analyzed objects. These strains differ in terms of the number of substituted nucleotides in relation to the vaccine strain selected as a reference. The results of the performed analysis allow us to conclude that the identification of structural differences in the DNA-associated symbolic sequences is significantly more efficient when using the binary distributions of close-to-circular extreme polarization states. The approach given can be applicable for genetic differentiation immunized from vaccinated animals (DIVA).
Databáze:	MEDLINE
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