Molecular genetic detection and differentiation of Xanthomonas oryzae pv. oryzicola, bacterial leaf streak agents of rice.

The genus Xanthomonas comprises phytopathogenic bacteria which infect about 400 host species, including a wide variety of economically important plants. Xanthomonas oryzae pv. oryzicola (Fang et al., 1957) Swings et al., 1990 is the causal agent of bacterial leaf streak (BLS) being one of the most destructive bacterial diseases of rice. BLS symptoms are very similar to those of bacterial blight caused by closely related Xanthomonas oryzae pv. oryzae. X. o. pv. oryzae and X. o. pv. oryzicola and often occur in rice f ields simultaneously, so separate leaves may show symptoms of both diseases. The quarantine status and high severity of the pathogen require a highly eff icient, fast and precise diagnostic method. We have developed an assay for Xanthomonas oryzae pv. oryzicola detection using real-time polymerase chain reaction (qPCR) and PCR amplicon sequencing. The DNA samples of X. o. pv. oryzae and X. o. pv. oryzicola were obtained from the collection of CIRM-CFBR (France). To evaluate the analytical sensitivity of the assay, a vector construct based on the pAL2-T plasmid was created through the insertion of X. o. pv. oryzicola target fragment (290 bp). Primers and a probe for qPCR were selected for the hpa1 gene site. They allowed identifying all the strains the sequences of which had been loaded in the GenBank NCBI Nucleotide database before November 11, 2021. The SeqX.o.all sequencing primers were selected for the hrp gene cluster sequence, namely for the nucleotide sequence encoding the Hpa1 protein, the sequencing of which allows for eff icient differentiation of X. oryzae species. The analytical specif icity of the system was tested using the DNAs of 53 closely related and accompanying microorganisms and comprised 100 % with no false-positive or false-negative results registered. The system's analytical sensitivity was not less than 25 copies per PCR reaction. Its eff icacy has been conf irmed using f ive different qPCR detection systems from different manufacturers, so it can be recommended for diagnostic and screening studies.

Mathematical model of polymerase chain reaction with temperature-dependent parameters.

The course of the real-time polymerase chain reaction (PCR) is determined by the temperature dependence of the kinetics of the component reactions, particularly the DNA strand hybridization. To investigate the effect of thermal processes on the reaction behavior, a mathematical model in which the variable rate constant of dissociation of "primer-single strand" complexes depends on temperature was proposed. The reaction medium temperature, which depends on time, was also introduced into the model. The proposed model of real-time PCR makes it possible to analyze different aspects of the reaction, which are important for the development of instruments and reagents for PCR.

Approximate analytic solution of a simple system of kinetic equations describing the enzymatic synthesis of nucleic acids.

Macroscopic kinetic models describing the process of polymerase chain reaction (PCR) are currently solved only by numerical methods, which hampers the development of effective software algorithms for processing the results of the reaction. This paper considers the application of the homotopy perturbation method for obtaining approximate analytical solution of the simplest system of enzymatic kinetic equations describing the synthesis of nucleic acid molecules during PCR. The resulting approximate analytic solution with high accuracy reproduces the results of a numerical solution of the system in a wide range of ratios of enzyme and substrate concentrations both for the case of a large excess of the substrate over the enzyme and vice versa.

Mathematics analysis of polymerase chain reaction kinetic curves.

The paper reviews different approaches to the mathematical analysis of polymerase chain reaction (PCR) kinetic curves. The basic principles of PCR mathematical analysis are presented. Approximation of PCR kinetic curves and PCR efficiency curves by various functions is described. Several PCR models based on chemical kinetics equations are suggested. Decision criteria for an optimal function to describe PCR efficiency are proposed.

Alternative solution of the simplest model of enzymatic synthesis of nucleic acids by homotopy perturbation method.

Development of methods for obtaining approximate analytical solutions of nonlinear differential equations and their systems is a rapidly developing field of mathematical physics. Earlier, an approximate solution of the simplest system of kinetic enzymatic equations for calculating dynamics of complementary strands of nucleic acids was obtained. In this study, we consider an alternative approach to selecting the basic linear approximation of the used method, which makes it possible to obtain more accurate analytical solutions of the set problem.

[A model for the formation of ring-shaped structures in colonies of mycelial fungi]. / Model' orbazovaniia kol'tsevykh struktur v koloniiakh mitselial'nykh gribov.

Mathematical model of the development of the pattern of colonies is considered. The model represents the systems of differential equations of the first order. It includes non-dimensional parameters characterizing the following features: concentration of substrate, concentration of metabolic products--growth inhibitor, mycelium and spores, radial and specific rate of mycelium growth, rate of substrate consumption and production of metabolic products, coefficients of diffusion of substrate and metabolic products, initial concentration of mycelium and substrate, time of delay of mycelium reaction on metabolic products and spore formation, threshold concentration of metabolic products. The model is adequate to the experiments with cultivation of Penicillium chrysogenum. It was shown that necessary condition for the formation of the circle periodical structures (zoning) in the colonies is an ability for the production of growth inhibitors (antibiotics, etc.). It was proved that formation of colonies of "continuous lawn" type is caused by restrictions on growth because of mycelium satiation or exhaustion of substrate. Such growth scenario is realized in experiments either on reach substrate or on hungry agar. For the appearance of regulating of "zone structure" type limitation on critical level of metabolic product concentration is very important. The number of periodical zone structures and their widths are determined by the above parameters.

[Recording the results of the indirect hemagglutination reaction in the microanalysis class by using vertical photometry]. / Registratsiia rezul'tatov reaktsii nepriamoi gemaggliutinatsii v klasse mikroanaliza s pomoshch'iu vertikal'nogo fotometrirovaniia.

A two-channel photometer is experimentally found to be suitable for vertical photometry to record the output of indirect hemagglutination, which is detected by the type of precipitates deposited on a parabolic bottom of sockets in microtitrimetric plane tables. Dynamic processes of depositing are studied as a function of sample volume and concentration of erythrocytic diagnosticum.

[General-purpose microcomputer for medical laboratory instruments]. / Universal'naia mikro-EVM dlia meditsinskikh laboratornykh priborov.

Presented in the paper is the microcomputer based on the KP580 microprocessor set. Debugging of the hardware and the software by using the unique debugging stand developed on the basis of microcomputer "Electronica-60" is discussed.

[Flow-type pulsatile cytofluorometer with increased sensitivity]. / Protochnyi impul'snyi tsitofliuroimetr povyshennoi chuvstvitel'nosti.

A new cytofluorometer is described, with sensitivity twice as high as that of the existing units.

[Possibility of using cytofluorometers to determine the ratio between normal and neoplastic cells]. / Vozmozhnost' ispol'zovaniia tsitofliurimetrov dlia opredeleniia sootnosheniia normal'nyjh i opukhelevykh kletok.

Principal possibility to use the pulsatile flowtype cytofluorometers for recording nontypical cells in biopsy material and the whole blood is considered.