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

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

doi:10.1088/1612-202x/ab8b66

Cited by 7 publications

(8 citation statements)

References 16 publications

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“…Here, the size of subarea for the local contrast calculating was 2Â2 pixels. As it has been demonstrated 14 this size of subarea is close to optimal.…”

Section: Generating Gb-specklesmentioning

confidence: 62%

“…A new bioinformatics approach has been proposed very recently: 14 GB-speckles processing via an s-LASCA technique (from the spatial Laser Speckle Contrast Analysis) application. As it had been demonstrated, it is possible to extend affectability of the proposed approach comparing to current bioinformatics strategies 15 using s-LASCA imaging in the GB-speckles' processing.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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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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“…Here, the size of subarea for the local contrast calculating was 2Â2 pixels. As it has been demonstrated 14 this size of subarea is close to optimal.…”

Section: Generating Gb-specklesmentioning

confidence: 62%

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

et al. 2021

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“…The decrease of the speckle grain size when a medium scattering coefficient is enhanced has allowed for the assessment of two bacterial growth phases: One exponential highlighting bacteria increasing and one stationary indicating sporulation and cell lysis [76]. Moreover, the laser speckle contrast analysis (LASCA) is helpful in the genetic field, detecting the gene diversity by spatial LASCA processing [77,78].…”

Section: Biospeckle Analysismentioning

confidence: 99%

Biospeckle Analysis and Biofilm Electrostatic Tests, Two Useful Methods in Microbiology

Oleandro

Grilli

Rega

et al. 2021

Applied Microbiology

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The development of more sensitive methodologies, capable of quickly detecting and monitoring a microbial population present in a specific biological matrix, as well as performing to allow for the study of all its metabolic changes (e.g., during the formation of biofilm) to occur, is an essential requirement for both well-being and the food industry. Two techniques, in particular, have gained the attention of scientists: The first is “biospeckle”, an optical technique representing an innovative tool for applications in food quality, food safety, and nutraceuticals. With this technique, we can quickly evaluate and monitor the presence of bacteria (or their proliferation) in a solid or liquid biological matrix. In addition, the technique is helpful in quantifying and optimizing the correct storage time of the pro-biotics, if they are entrapped in matrices such as alginate and follow their survival rate in simulated gastro-intestinal conditions. A second technique with great chances is the “biofilm electrostatic test” (BET). BET undoubtedly represents a fast, simple, and highly reproducible tool suitable for admitting the evaluation of the in vitro bacterial capacity in order to adhere through an electrostatic interaction with a pyro-electrified carrier after only 2 h of incubation. BET could represent the way for a quick and standardized evaluation of bacterial resistance among biofilm-producing microorganisms through a fast evaluation of the potential presence of the biofilm.

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“…A principially new approach in modern bioinformatics has been suggested by Ulianova O.V. et al [ 13 ]: the application of s-LASCA technique (spatial Laser Speckle Contrast Analysis) to processing GB-speckles. As it has been demonstrated in the above-mentioned work [ 13 ], the using of s-LASCA imaging in the processing of GB-speckles allows further increasing the sensitivity of the proposed method in comparison with the classical methods of bioinformatics [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Could LASCA-imaging of GB-speckles be applied for a high discrimination and typing of pathogenic bacteria?

Ulianova

Ulyanov

Zaytsev³

et al. 2021

PLoS ONE

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In this article, the method of analysis of GB-speckles (gene-based speckles) has been adapted to the problem of detecting the differences in a group of genes (usually 5–7), used in Multi Locus Sequence Typing (MLST). This method is based on s-LASCA imaging (spatial Laser Speckle Contrast Analysis) of virtual GB-speckle and on the technique of RGB coordinates for GB-speckles, processed by the s-LASCA method. A very high sensitivity and accuracy of the new method for detecting gene polymorphism as a great alternative to classical MLST has been demonstrated. The analysis of GB-speckles, obtained for the concatenated sequences of seven genes (gatA, gidA, enoA, fumC, hemN, hflX, oppA) of three different Chlamydia trachomatis strains (E/Bour, ST94; G/9301, ST95; G/11222, ST94) has been applied as the model. The high efficiency of usage of s-LASCA-imaging of GB-speckles has been shown. The data obtained represent a significant progress in digital biology as a whole and improvements in the bio-digitalization of bacterial DNA.

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

Cited by 7 publications

References 16 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

Biospeckle Analysis and Biofilm Electrostatic Tests, Two Useful Methods in Microbiology

Could LASCA-imaging of GB-speckles be applied for a high discrimination and typing of pathogenic bacteria?

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