Izvestiya of Saratov University.

Physics

ISSN 1817-3020 (Print)
ISSN 2542-193X (Online)

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Ulyanov S. S., Ulianova O. V., Zaitsev S. S., Saltykov I. V., Ulyanov A. S., Feodorova V. A. The interference of GB-speckles in molecular discrimination of bacterial pathogens: The use of the s-LASCA method on the Chlamydia psittaci model. Izvestiya of Saratov University. Physics , 2021, vol. 21, iss. 4, pp. 315-328. DOI: 10.18500/1817-3020-2021-21-4-315-328, EDN: QTABPN

This is an open access article distributed under the terms of Creative Commons Attribution 4.0 International License (CC-BY 4.0).
Published online: 
30.11.2021
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Language: 
Russian
Heading: 
Biophysics and medical physics
Article type: 
Article
UDC: 
577.32
DOI: 
10.18500/1817-3020-2021-21-4-315-328
EDN: 
QTABPN

The interference of GB-speckles in molecular discrimination of bacterial pathogens: The use of the s-LASCA method on the Chlamydia psittaci model

Autors: 
Ulyanov Sergei Sergeevich, Saratov State University
Ulianova Onega Vladimirovna, Saratov Branch of Federal Research Center for Virology and Microbiology
Zaitsev Sergei Sergeevich, Saratov Branch of Federal Research Center for Virology and Microbiology
Saltykov Iurii Vladimirovich, Saratov State Agrarian University named after N.I. Vavilov
Ulyanov Aleksandr Sergeevich, Saratov State University
Feodorova Valentina Anatol'evna, Saratov State University
Abstract: 

Background and Objectives: In the article it has been demonstrated how virtual optical speckles may be generated from the nucleotide sequences of 7 housekeeping genes of Chlamydia psittaci. Such speckles are called as GB- speckles (gene-based speckles). In the article specific features of the formation of interference patterns have been studied with the superposition, as raw GB-speckle and GB-speckle, processed by the s-LASCA method (Laser Speckle Contrast Analysis). It has been shown, that the contrast of interfering GB-speckles may be used to identify the presence of polymorphism in nucleotide sequences of bacterial pathogens which are used for Multi Locus Sequence Typing (MLST). Materials and Methods: In this work, using the interference of generated GB-speckle implementations, a comparison of concatenated nucleotide sequences, 7 household genes (namely, gatA, gidA, enoA, fumC, hemN, hflX, oppA) was performed for three bacterial strains of the C. psittaci, belonging to different sequence types (ST): ST 28, ST24, ST43. The generated GB-speckles were processed using the s-LASCA method. The polymorphism of these genes allows for intraspecific typing of bacteria by MLST. This method is widely used in molecular evolutionary analysis to establish the phylogenetic relationship and population structure of microorganisms, as well as to investigate the origin of epidemiologically significant strains of pathogens in molecular epidemiology. Results: When multiple SNP appear in the compared bacterial nucleotide sequences, the system of interference fringes may be destroyed due to the appearance of random amplitude modulation. If there is interference of GB-speckles that have been processed by the s-LASCA method, then the interference pattern does not have any interference fringes at all, but contains only non-Gaussian speckles with a contrast of more than 4. However, such high contrast values of interfering speckles are an indicator of the presence of an evident polymorphism in the targeted DNA fragments of bacterial pathogens. It has been shown that the new class of speckles, namely, GB-speckles that have been processed by the s-LASCA method, have unique statistical properties and have no analogues in nature. Special attention has been paid to the study of GB-speckle interference issues. It has been established that when the initial speckle fields interfere, regular fringes can appear in the interference pattern (with minimal differences in the initial nucleotide sequences belonging to different sequence types). Conclusion: The structure of the resulting interference patterns is unique. Interference fringes are completely absent in such pictures. The speckle structure is described by non-Gaussian statistics, and the speckles themselves look like bright flashes on a dark background. The contrast of interfering GB-speckles processed by the s-LASCA method is significantly higher than unity and lies in the range [4.4; 10.6]. Such high contrast values can serve as a reliable and unmistakable sign of the presence of polymorphisms in bacterial target genes.

Key words: 
GB-speckle
s-LASCA method
bioinformatics
Chlamydia psittaci
MLST
Acknowledgments: 
This study was funded by the Russian Science Foundation (project No. 17-16-01099) (continued).
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Received: 
09.08.2021
Accepted: 
15.09.2021
Published: 
30.11.2021
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