As is known, Spike surface glycoprotein (protein S) is present in all coronaviruses, including the novel SARS-CoV-2 virus causing a global pandemic in 2019. In the present day, the relevant gene S (encoding protein S) undergoes the most mutations compared with other SARS-CoV-2 genes. In the beginning of 2021, the newer variant of the SARS-CoV-2, the Delta variant B.1.617, was discovered in India. It is distinguished by the presence of a double mutation of the Spike protein. In this study, the protein S sequences have been transformed into the sequence of numbers to generate the genebased (GB-) speckles in order to identify the differences between the reference strain which was initially discovered in China, 2020 (GISAID: EPI_ISL_402124-S) and the new Delta strains which were recently found in either India (GISAID: EPI_ISL_254707; EPI_ISL_254707) or in the UK (GISAID:EPI_ISL_642476; EPI_ISL_255210). Differences in the relevant nucleotide sequences have been found and successfully characterized by means of virtual laser gene-based speckles (GB-speckles). In particularly, it has been demonstrated that implication of interference of two GB-speckles, generated on the virus nucleotide sequences, can be considered as a new direction in modern bioinformatics. It has been shown, that at the interference of two SARS–CoV-2 GB-speckle-patterns, two types of interference pictures are forming: quasi-random speckle structure without interference fringes or fringes, modulated by speckles.
The nucleotide sequences of the GPCR gene of Lumpy Skin Disease Virus (LSDV) and Sheeppox Virus (SPPV) strains have been transformed into 2D realizations of GB-speckles (Gene-Based speckles). Based on the analysis of statistical properties of corresponding GB-speckles, a possibility of differentiation between wild field LSDV and the SPPV strains which could be used as heterologous vaccines against Lumpy Skin Disease has been shown. It has been demonstrated that an application of the GB-speckles has the great perspectives from viewpoint of modern bioinformatics.
In this study, the GB-speckles were used to study the probable precursor for L. monocytogenes ST734 strains, which were detected twice in the world, namely: for the first time in Chile in 2009 and, recently, in 2019 in the Republic of Serbia. We found that these strains belong to the clonal complex I and differ fromL. monocytogenes ST1 strains by a single nucleotide change in the gene dat. This is the first report demonstrating the using GB-speckle-structures to detect evolutionary genetic changes in L. monocytogenes strains.
The gene "N" encodes the nucleocapsid structural protein of SARS–CoV-2 virus COVID-19. In the present time, nucleocapsid protein is one of the important targets for the study of both humoral and cellular immune responses to SARS–CoV-2. In this study sequence of the SARS-CoV-2 gene "N", which is encoding the relevant structural protein, has been transformed into the sequence of numbers with purpose to generate gene-based speckles. Differences in the initial nucleotide sequences have been found and characterized by means of virtual laser gene-based speckles (GBspeckles). It has been shown, that at the interference of two SARS–CoV-2 GB-speckle-patterns, two types of interference pictures are forming: quasi-random speckle structure without interference fringes or fringes, modulated by speckles. It has been demonstrated that implication of interference of two GB-speckles, generated on the virus nucleotide sequences, can be considered as a new direction in modern bioinformatics.
The nucleotide sequences of the neuraminidase gene of Highly Pathogenic Avian Influenza Virus (HPAIV) A strains have been transformed into 2D realizations of GB-speckles (Gene-Based speckles). Possibility of differentiation between different HPAIV strains using the analysis of statistical properties of corresponding GB-speckles has been shown.
GB-speckles (gene-based speckles) have been generated for two nucleotide sequences of the gene GPCR of Lumpy Skin Disease Virus and Sheeppox Virus. Statistical properties of the interfering GB-speckles have been studied. It have been demonstrated that a structure of the interference speckle patterns is very sensitive to the presence of very small differences between the comparing nucleotide sequences. Case of a formation of evident interferential fringes in resulting picture (superposition of two GB-speckle patterns) has been analyzed in details. It has been demonstrated that an application of the GB-speckles, generated on the target virus nucleotide sequences has the great perspectives from viewpoint of modern bioinformatics.
Our previous study has revealed that specific ornithosis antigens extracted from Сhlamydia psittaci (CP) could possess some modulatory activity on the growth of malignant solid tumors in Wistar rats. Here, in the same model we studied dose-dependent dynamics of tumor growth under the influence of CP antigen derived from CP AMK-16 strain, in doses ranged from 0.025 mg/kg to 1.25 mg/kg given as a single subcutaneous injection. Velocity of tumor growth has been estimated by t-LASCA technique.
Chlamydiaceae family is consisted of intracellular bacteria pathogenic for both humans and animals. In this paper the nucleotide sequences of the gene encoding Pgp4 protein, the well-known virulence factor in Chlamydia, have been successfully transformed into the form of the GB-speckles. Strong discrimination was found between the relevant speckle patterns derived from three Chlamydiae spp., namely Chlamydia psittaci, Chlamydia abortus and Chlamydia trachomatis.
As it has been demonstrated earlier, different types of re-coding of bacterial nucleotide sequences to gene-based specklepatterns (GB-speckles) can be used. In this paper an advanced study, devoted to optimization of this algorithm, is presented. With this purpose, investigations of statistical properties of the GB-speckles, generated on the nucleotide sequences of the gatA gene of Chlamydia trachomatis has been performed. The first- and second-order statistics of intensity fluctuations in GB-speckles have been analyzed. Perspectives of the gene identification using a statistical analysis of the homologous laser GB-speckles have been demonstrated. The analyzed nucleotide sequences of the gatA gene of C. trachomatis strains isolated in the Republic of Belarus were compared with those recently isolated in Russian Federation.
Gene-based speckles (GB-speckles) have been implied for interpretation of nucleotide sequences of the target genes of HPAIV. The 1st order statistics and correlation functions of 2D speckle structures corresponding to the several nucleotide sequences of HPAIV have been analyzed. The GB-speckles, generated for highly-pathogenic strains A/Gs/HK/739.2/02 (H5N1) and HPAIV (A/Chicken/Hong Kong/YU562/01 (H5N1)) neuraminidase (NA) have been compared with the speckles, related to three low-pathogenic strains (Influenza A virus (A/chicken/Ganzhou/GZ43/2016(H3N2)) segment 6 neuraminidase (NA) gene, Influenza A virus A/pheasant/Korea/LBM180/2008(H9N2)) segment 6 neuraminidase (NA) gene, and Influenza A virus A/chicken/Alkharj/910/2018(H5N8)) segment 6 neuraminidase (NA) gene). Perspectives of fast and precise discrimination of nucleotide sequences of the different avian influenza strains, including HPAIV variants, based on GBspeckles, are demonstrated.
Chlamydia trachomatis biodiversity has been detected in clinical urogenital samples of Chlamydia patients in the Southeastern European Region of Russia. In this paper three absolutely new nucleotide sequences of “Saratov” strains (Saratov E1/61.8-B1, Saratov E2/61.46-L38, Saratov E6/61.35-B1) have been described and transformed into the form of GB-speckles. It has been demonstrated that identification of single polymorphism in nucleotide sequences can be easily performed on the base of GB-speckles. Procedure of detection of polymorphism can be made essentially faster in the case of using of Matlab Parallel Computing Toolbox.
Gene-based speckles (GB-speckles) have been implied for interpretation of the nucleotide sequences of the seven “housekeeping genes” of Listeria monocytogenes (LM). The 1st order statistics and correlation functions of 2D speckle structures corresponding to the several concatenated nucleotide sequences of two different sequence types (STs) of LM bacteria have been analyzed. Two nucleotide sequences, namely ST7 and ST106 (the clonal complex СС7) have been compared using the related GB-speckles. Differences in the GB-speckle-structures, corresponding to two different LM STs are evidently demonstrated.
As it has been demonstrated earlier, different types of re-coding of nucleotide sequences to gene-based speckle-patterns (GB-speckles) can be used. In this paper an advanced study, devoted to optimization of this algorithm, is presented. With this purpose, investigations of statistical properties of the GB-speckles, generated on the nucleotide sequences of the fumC gene of Chlamydia trachomatis, have been performed. The first- and the second-order statistics of intensity fluctuations in GB-speckles have been analyzed. Perspectives of the gene identification using a statistical analysis of laser GB-speckles have been demonstrated. The analyzed nucleotide sequences of the fumC gene of C. trachomatis strains have been isolated in the Republic of Belarus.
In this report, the influence of C. psittaci (CP) antigens on the process of a development of a malignant solid tumor in the inbred Wistar white rats in experimental conditions has been successfully studied. Velocity of growing of a tumor has been estimated by s-LASCA technique. Measurement of statement of a tumor has been performed daily after each of three serial injections of the CP specific ornithosis antigen derived from two different CP strains, the Rostinovo-70 and the АМК. Single injection solutions were administered in a volume of 1 ml. We found, that both antigens could initiate the marked decrease of the growth of malignant tumors in the animal model used.
Gene-based speckles (GB-speckles) have been implied for interpretation of nucleotide sequences of the target genes of Avian Influenza Virus (AIV). The 1st and 2nd order statistics of 2D speckle structures corresponding to the nucleotide sequences of AIV have been analyzed. It has been shown that these GB-speckles are forming in the case of small number of scatterers and they obey to non-Gaussian statistics. These GB-speckles are characterizing by essential spatial inhomogeneity. Potentials of proposed laser speckle technique for the AIV target genes identification are demonstrated.
Formation of output signal of device, realizing Doppler technique, has been studied. Naïve embryo (non-infected fertilized chicken eggs) has been used as a test object. Dependence of first frequency-weighted spectral moment of output signal on the day of observation of chicken embryo has been investigated. The possibility of adaption of the Doppler diagnostics for monitoring of viability and detection of pathology of development of chicken embryo, infected with Chlamydia trachomatis cells, is discussed.
As it has been demonstrated earlier, different types of re-coding of nucleotide sequences to gene-based speckle-patterns (GB-speckles) can be used. In this paper the advanced study, devoted to optimization of the basic algorithm, is presented. Investigations of statistical properties of GB-speckles, generated on nucleotide sequences of omp1 gene of Chlamydia trachomatis, has been performed. Part II of the present paper is dedicated to analysis of first- and second-order statistics of phase fluctuations in GB-speckles with purpose of optimization of algorithm of re-coding.
Methods of t-LASCA and s-LASCA imaging have been adapted to the problem of monitoring of blood microcirculation in naïve chicken embryo. Set-up for LASCA imaging of the model chicken embryo is mounted. The novel original technique of preparing of optical windows for observation of a naïve chicken embryo is suggested. This technique is based on a removal of part of the natural egg shell using a citric acid solution with further optical clearing using glycerol and glucose.
As it has been demonstrated earlier, different types of re-coding of nucleotide sequences to gene-based speckle-patterns (GB-speckles) can be used. In this paper the advanced study, devoted to optimization of the basic algorithm, is presented. With this purpose, investigations of statistical properties of GB-speckles, generated on nucleotide sequences of omp1 gene of Chlamydia trachomatis, has been performed. First- and second-order statistics of intensity fluctuations in GB speckles has been analyzed. Part I of the paper is devoted to investigations of statistical properties of phase fluctuations in GB-speckles.
Prototype of laser scanning speckle-microscope has been designed. It has been demonstrated experimentally, that signal of speckle microscope is increased drastically in the presence of gold nanoparticles. It has been demonstrated the unique possibility of detection of a single C. trachomatis cell in a tested sample using speckle-microscopy.
GB-speckles, simulated for nucleotide sequences of the omp1 gene of Chlamydia trachomatis, have been processed by s-LASCA technique. Properties of LASCA-images of the GB-speckles have been analyzed. Perspectives of application of suggested technique in modern bioinformatics have been demonstrated. Interference of the GB-speckle, generated for nucleotide sequences of the omp1 gene of different Chlamydia trachomatis strains has been also studied. It has been demonstrated that s-LASCA technique is very helpful tool for detection of natural mutations in bacteria.
For the first time gene-based speckles (GB-speckles) have been applied for analysis of nucleotide sequences of the gene GPCR of the Lumpy Skin Disease Virus (LSDV). The 1st and 2nd order statistics of the 2D speckle structures corresponding to nucleotide sequences of LSDV have been analyzed. It has been shown that these GB-speckles are forming in the case of small number of scatterers and they obey to non-gaussian statistics. It has been demonstrated that application of the GB-speckles, generated on the target virus nucleotide sequences has the great perspectives from viewpoint of modern bioinformatics.
Analysis of structural properties of the interfering GB-speckles, generated for nucleotide sequences of Lumpy Skin Disease Virus (LSDV), has been carried out. It has been shown, that at the interference of two LSDV GB-specklepatterns, three types of interference pictures are forming: quasi-random speckle structure without interference fringes, fringes, modulated by speckles, or having bends and pure regular fringes without visible speckle-modulation. It has been found, that width of fringes and their orientation depend on position of SNP in comparing nucleotide sequences. It has been demonstrated that implication of interference of two GB-speckles, generated on the target virus nucleotide sequences, can be considered as a new direction in modern bioinformatics.
Pulse wave from naïve fertilized chicken eggs has been clearly detected using laser photoplethysmography. Highfrequency modulation of intensity of illuminating laser light has been used to enhance output signal of experimental setup and to increase the S/N ratio. The form of pulse wave has been analyzed for naïve embryo on different stages of their development.
Method of speckle-microscopy has been adapted to the problem of detection of Chlamydia trachomatis microbial cells in aqueous suspension and fixed on the glass. Combined system “C. trachomatis bacterial cell”-“monoclonal antibody”- “gold nanoparticle” has been used as a complicated scattering element in the case of formation of biospeckles with a small number of scatterers. Optical model of diffraction of strongly focused Gaussian beam on combined scattering system, containing gold nanoparticles, has been suggested. Simulation of speckles, forming with a small number of scattering nanoparticles, has been carried out. It has been demonstrated that the usage of nanoparticles allows to enhance essentially the output signal of speckle-microscope.
Method of speckle-microscopy has been adapted to the problem of detection of Chlamydia trachomatis microbial cells in clinical samples. Prototype of laser scanning speckle-microscope has been designed. Spatial resolution and output characteristics of this microscope have been analyzed for the case of scanning of C. trachomatis bacteria inclusions – Elementary Bodies (EBs) inside the human cells, fixed on the glass. It has been demonstrated, that presence of C. trachomatis microbial cells in the sample can be easily detected using speckle microscopy.
Theory of diffusing wave spectroscopy has been firstly adapted to the problem of rapid detection of Chlamydia trachomatis bacteria in blood samples of Chlamydia patients. Formula for correlation function of temporal fluctuations of speckle intensity is derived for the case of small number of scattering events. Dependence of bandwidth of spectrum on average number of scatterers is analyzed. Set-up for detection of the presence of C. trachomatis cells in aqueous suspension is designed. Good agreement between theoretical results and experimental data is shown. Possibility of detection of the presence of C. trachomatis cells in probing volume using diffusing wave spectroscopy with a small number of scatterers is successfully demonstrated for the first time.
Principles of two-cascaded laser speckle-microscopy prospect for application to express diagnostics of chlamydial infection are developed. Prototype of two-cascaded speckle-microscope is designed and tested. Specific case of illumination of bacterial cells by dynamic speckles is considered. Express method of detection of epithelial cells, containing defects, which are caused by Chlamydia trachomatis bacteria, is suggested. Results of improved recognition of C. trachomatis bacteria are discussed.
Method of phase-shifting speckle-interferometry has been used as a new tool with high potency for modern bioinformatics. Virtual phase-shifting speckle-interferometry has been applied for detection of polymorphism in the of Chlamydia trachomatis omp1 gene. It has been shown, that suggested method is very sensitive to natural genetic mutations as single nucleotide polymorphism (SNP). Effectiveness of proposed method has been compared with effectiveness of the newest bioinformatic tools, based on nucleotide sequence alignment.
Theory of formation of speckled speckles at diffraction of focused Gaussian beam in the suspension, containing of Chlamydia trachomatis (CT) is presented. Optical model of scattering of light in suspension of Chlamydia is suggested. Formula for bandwidth of spectrum of intensity fluctuations in speckled speckles is derived. It has been demonstrated, that speckle-microscopy can be used for detection of CT bacteria for any concentration of the relevant cells in suspension.
Methods of t-LASCA and s-LASCA imaging have been firstly adapted to the problem of monitoring of blood microcirculation in chicken embryo model. Set-up for LASCA imaging of chicken embryo is mounted. Disorders of blood microcirculation in embryonated chicken egg, infected by Chlamydia trachomatis, are detected. Speckle-imaging technique is compared with white-light ovoscopy and new method of laser ovoscopy, based on the scattering of coherent light, advantages of LASCA imaging for the early detection of developmental process of chlamydial agent is demonstrated.
New method of coding of genetic information using coherent optical fields is developed. Universal technique of transformation of nucleotide sequences of bacterial gene into laser speckle pattern is suggested. Reference speckle patterns of the nucleotide sequences of omp1 gene of typical wild strains of Chlamydia trachomatis of genovars D, E, F, G, J and K and Chlamydia psittaci serovar I as well are generated. Algorithm of coding of gene information into speckle pattern is optimized. Fully developed speckles with Gaussian statistics for gene-based speckles have been used as criterion of optimization.
Specific method of transformation of nucleotide of gene into speckle pattern is suggested. Reference speckle pattern of omp1 gene of typical wild strains of Chlamydia trachomatis of genovars D, E, F, G, J and K and Chlamydia psittaci as well is generated. Perspectives of proposed technique in the gene identification and detection of natural genetic mutations as single nucleotide polymorphism (SNP) are demonstrated.
New method of photoinactivation of plague microbes (bacteria Yersiniapestis) has been suggested. Rate of growth of colonies of Y.pestis EV NIIEG at specific regimes of photo processing have been analyzed. Dependence of growth on exposure time and concentrations of photosensitizer (methylene blue) has been studied. Number of colony forming units of Y.pestis EV NIIEG bacteria as a function of intensity of light and concentration of methylene blue has been scrutinized.
Methods t-LASCA and s-LASCA has been adopted for diagnostics of malignant tissue on animal models. Investigations
of tumors on inbred mice (line BALB/c) after the inoculation of syngeneic myeloma cells (line Sp.2/0–Ag.8) and on
inbred mice (line SHK) with spontaneous tumors have been carried out. The efficiency of application of t-LASCA with
illumination by wide laser beam for tumor investigations has been proven. It also has been found that method of LASCA
with illumination of tissue by strongly focused laser beam is absolutely non-productive.
Method t-LASCA has been adopted for diagnostics of malignant tissue on animal models. Investigations of tumors on
inbred mice (line BALB/c) after the inoculation of syngeneic myeloma cells (line Sp.2/0-Ag.8) have been carried out.
The efficiency of application of t-LASCA for tumor investigations has been proven. It has been also found that map of
time-averaged speckles is more informative rather than LASCA-image.
New field of application of fractal dimensions is proposed. A technique, based on the calculation of fractal
dimension, was used for express-diagnostics and identification of bacteria of the vaccine strain Yersinia pestis EV
line NIIEG. Purpose of this study was the experimental investigation of properties of speckle patterns, formed
under laser illumination of a single colony of the strain that was grown on different agars.
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