[Frontiers in Bioscience, Landmark, 24, 700-711, March 1, 2019]

Speckle-interferometry and speckle-correlometry of GB-speckles

Onega V. Ulianova 1 , Sergey S. Zaytsev 1 , Yury V. Saltykov 1 , Anna Lyapina 1 , Irina Subbotina 1 , Nadezhda Filonova 1 , Sergey S. Ulyanov 1 , Valentina A. Feodorova 1

1Federal Research Center for Virology and Microbiology, Branch in Saratov, Saratov, 410028, Russia

TABLE OF CONTENTS

1. Abstract
2. Introduction
3. Transformation of sequence of nucleotides in gene-based speckle pattern
    3.1. Algorithm of re-coding of a nucleotide sequence
    3.2. Algorithm of generating of 2D speckle pattern, based on a nucleotide sequence
    3.3. Generating of gene-based speckles
4. Comparison of GB-speckles, based on similar genovars: cross-correlation technique
5. Comparison of GB-speckles, based on similar С. trachomatis genovars of different subtypes: speckle-interferometry
6. Optical processing of GB-speckles: detection of genetic mutations in a gene of micro-organisms
7. Conclusions
8. Acknowledgements
9. References

1. ABSTRACT

A new method of coding of genetic information using laser speckles has been developed. Specific technique of transforming the nucleotide of gene into a speckle pattern (gene-based speckles or GB-speckles) is suggested. Reference speckle patterns of omp1 gene of typical wild strains of Chlamydia trachomatis of genovars D, E, F, G, and J are generated. This is the first report in which perspectives of the proposed technique in the bacterial gene identification and detection of natural genetic mutations in bacteria as a single nucleotide polymorphism (SNP) are demonstrated. The usage of GB-speckles can be viewed as the next step on the way to the era of digital biology.

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Abbreviations: bp, base pairs; C. trachomatis, Chlamydia trachomatis; DNA, deoxyribonucleic acid; DOE, diffraction optical element; Gb, gigabyte; GB-speckles, gene-based speckles; HOE, holographic optical element; Kb, kilobyte; omp1, gene encoded the outer membrane protein 1 in C. trachomatis; ompP, gene encoded the outer membrane protease OmpP in Escherichia coli; ompT, gene encoded the outer membrane protease OmpT in Escherichia coli; pgtE, gene encoded the PgtE protease in Salmonella enterica; Pla, Plasmin activator; RNA, ribonucleic acid; SNP, single nucleotide polymorphism; sopA, gene encoded the SopA protease in Shigella flexneri; Zb, zettabyte.

Key Words: Chlamydia trachomatis, genovar, subtype/typing, nucleotide sequence, speckle pattern, speckle-correlometry, speckle-interferometry

Send correspondence to: Valentina A. Feodorova, Federal Research Center for Virology and Microbiology, Branch in Saratov, Saratov, 410028, Russia, Tel: 7-8452-200-825, Fax: 7-8452-200-830, E-mail: feodorovav@mail.ru