Application of virtual phase-shifting speckle-interferometry for detection of polymorphism in the Chlamydia trachomatis omp1 gene

Feodorova, Valentina A.; Saltykov, Yury V.; Zaytsev, Sergey; Ulyanov, Sergey S.; Ulianova, Onega V.

doi:10.1117/12.2314700

“…10 Essential advancement in the area of GB-speckles has been reported in previous years. According to previously published reports, [4][5][6][7][8][9]11 implementation of speckle-optics methods, like speckle-interferometry and subtraction of speckle-images as well as speckle-correlometry for processing of GB-speckles, provides considerable progress in the current bioinformatics toolbox. This can become crucial to significantly improve existing routine methods of laboratory diagnostics of infectious diseases.…”

Section: Introductionmentioning

confidence: 99%

“…4 This is ensured by the development of the exclusive system of interferential fringes which are generated by the model interference pattern led by the existence of any type of mutations. Additionally, the method of virtual phase-shifting speckle-interferometry was reported to be efficacious 11 to investigate of polymorphism of the C. trachomatis omp1 gene. This approach allowed the detection of the C. trachomatis omp1 gene with SNPs, including both a single SNP and a combination of several SNPs in the bacterial strains with genetic mutations (11 known subtypes in total) had been developed.…”

Section: Introductionmentioning

confidence: 99%

Discrimination of the SARS–CoV-2 strains using of coloured s-LASCA-imaging of GB-speckles, developed for the gene “S” nucleotide sequences

Ulianova

¹

,

Saltykov

²

,

Ulyanov

³

et al. 2021

F1000Res

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0

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Background: A recent bioinformatics technique involves changing nucleotide sequences into 2D speckles. This technique produces speckles called GB-speckles (Gene Based speckles). All classical strategies of speckle-optics, namely speckle-interferometry, subtraction of speckle-images as well as speckle-correlometry have been inferred for processing of GB-speckles. This indicates the considerable improvement in the present tools of bioinformatics. Methods: Colour s-LASCA imaging of virtual laser GB-speckles, a new method of high discrimination and typing of pathogenic viruses, has been developed. This method has been adapted to the detecting of natural mutations in nucleotide sequences, related to the spike glycoprotein (coding the gene «S») of SARS–CoV-2 gene as the molecular target. Results: The rate of the colouring images of virtual laser GB-speckles generated by s-LASCA can be described by the specific value of R. If the nucleotide sequences compared utilizing this approach the relevant images are completely identical, then the three components of the resulting colour image will be identical, and therefore the value of R will be equal to zero. However, if there are at least minimal differences in the matched nucleotide sequences, then the value of R will be positive. Conclusion: The high effectiveness of an application of the colour images of GB-speckles that were generated by s-LASCA- has been demonstrated for discrimination between different variants of the SARS–CoV-2 spike glycoprotein gene.

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“…10 Essential advancement in the area of GB-speckles has been reported in previous years. According to previously published reports, [4][5][6][7][8][9]11 implementation of speckle-optics methods, like speckle-interferometry and subtraction of speckle-images as well as speckle-correlometry for processing of GB-speckles, provides considerable progress in the current bioinformatics toolbox. This can become crucial to significantly improve existing routine methods of laboratory diagnostics of infectious diseases.…”

Section: Introductionmentioning

confidence: 99%

Discrimination of the SARS–CoV-2 strains using of coloured s-LASCA-imaging of GB-speckles, developed for the gene “S” nucleotide sequences

Ulianova

¹

,

Saltykov

²

,

Ulyanov

³

et al. 2021

F1000Res

Self Cite

0

View full text Add to dashboard Cite

Background: A recent bioinformatics technique involves changing nucleotide sequences into 2D speckles. This technique produces speckles called GB-speckles (Gene Based speckles). All classical strategies of speckle-optics, namely speckle-interferometry, subtraction of speckle-images as well as speckle-correlometry have been inferred for processing of GB-speckles. This indicates the considerable improvement in the present tools of bioinformatics. Methods: Colour s-LASCA imaging of virtual laser GB-speckles, a new method of high discrimination and typing of pathogenic viruses, has been developed. This method has been adapted to the detecting of natural mutations in nucleotide sequences, related to the spike glycoprotein (coding the gene «S») of SARS–CoV-2 gene as the molecular target. Results: The rate of the colouring images of virtual laser GB-speckles generated by s-LASCA can be described by the specific value of R. If the nucleotide sequences compared utilizing this approach the relevant images are completely identical, then the three components of the resulting colour image will be identical, and therefore the value of R will be equal to zero. However, if there are at least minimal differences in the matched nucleotide sequences, then the value of R will be positive. Conclusion: The high effectiveness of an application of the colour images of GB-speckles that were generated by s-LASCA- has been demonstrated for discrimination between different variants of the SARS–CoV-2 spike glycoprotein gene.

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“…Such speckles are called gene-based (GB) speckles [4,6,7]. As has been shown in [4][5][6][7][8], application of speckle interferometry and speckle correlometry for processing GB-speckles will lead to both a significant improvement in existing bioinformatics tools and the creation of new ones. This is critical for improving laboratory diagnostic s of infectious and non-infectious diseases of humans and animals.…”

Section: Introductionmentioning

confidence: 99%

“…The method of virtual phase-shifting speckle interferometry (four-bucket technique) has been applied [8] to the investigation of polymorphism of two variants of the omp1 gene of C. trachomatis (namely, strains E/Bour (E1 subtype) and E/IU-4 2 0755u4 (E2 subtype)).…”

Section: Introductionmentioning

confidence: 99%

LASCA-imaging of gene-based speckles: application to detection of the gene polymorphism in a bacterial model

Ulianova

¹

,

Ulyanov²,

Zaytsev³

et al. 2020

View full text Add to dashboard Cite

A current trend in modern bioinformatics is representation of nucleotide sequences in the form of gene-based (GB) speckles. In this letter GB-speckles have been processed using the s-LASCA (laser speckle contrast analysis) technique. Statistical properties of s-LASCA images of GB-speckles have been analyzed. It is shown that application of the s-LASCA technique allows us to essentially increase the the sensitivity of detection of a single nucleotide polymorphism using GB-speckles.

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Application of virtual phase-shifting speckle-interferometry for detection of polymorphism in the Chlamydia trachomatis omp1 gene

Cited by 6 publications

References 5 publications

Discrimination of the SARS–CoV-2 strains using of coloured s-LASCA-imaging of GB-speckles, developed for the gene “S” nucleotide sequences

Discrimination of the SARS–CoV-2 strains using of coloured s-LASCA-imaging of GB-speckles, developed for the gene “S” nucleotide sequences

Discrimination of the SARS–CoV-2 strains using of coloured s-LASCA-imaging of GB-speckles, developed for the gene “S” nucleotide sequences

LASCA-imaging of gene-based speckles: application to detection of the gene polymorphism in a bacterial model

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