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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Traditional biological and chemical methods for pathogen identification require complicated sample preparation for
reliable results. The process of identification of malignant and non-malignant growths is not easier. Two new
techniques of analysis of speckle-patterns, formed by histological sections with malignant and non-malignant growths
illuminated by laser light, were proposed in this article. One of these techniques is based on calculation of invariant
Zernike moments of speckle-field intensity spatial distribution. The second technique is based on calculation of fractal
dimension of intensity spatial distribution in speckle structure. It was shown that both of these methods give the same
results, which drastically depends on tissues features. Possibility of using Zernike moments and fractal dimensions,
formed by laser light dispersed on histological sections, in express-diagnostics of tissues with pathological changes
carrying out in vitro was investigated.
Dependence of fractal dimension n conditions of irradiation of object with laser light discussed.
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.
New field of application of fractal dimensions is proposed. A technique, based on the calculation of
fractal dimension was used for identification of malignant and non-malignant growths. It was proved
that results drastically depends on tissues properties. Nevertheless, results, which were obtained
from fractal dimension, are in good correspond to results, obtained using technique of invariant
Zernike moments. The possibility of application of both techniques to speckle-fields, formed by
laser light dispersed on histological sections, in in vitro express-diagnostics of tissues with
pathological changes is investigated.
Traditional biological and chemical methods for pathogen identification require complicated sample preparation for
reliable results. The process of identification of malignant and non-malignant growths is not easier. Optical scattering
method may be useful to detect bacterial cells in suspension and to determine malignant and non-malignant growths.
Orthogonal Zernike moments of different order were used to analyze speckle patterns, which are formed by irradiated
object of interests. Being irradiated by light every object forms a unique speckle pattern. Due to the originality of every
single speckle pattern they may be used to obtain some information about object that formed this pattern.
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