D. G. Sochivko's research while affiliated with All-Russia Research Institute of Agricultural Biotechnology and other places

Publications (15)

Article
The purpose of the present study was to evaluate a real-time PCR system for 12 nontuberculous mycobacteria (NTM) species identification developed by Central Tuberculosis Research Institute (CTRI; Moscow, Russia) in cooperation with Syntol LLC (Moscow, Russia). NTM cultures (210 strains, 19 species), Mycobacterium tuberculosis complex (MTBC) culture...
Article
At present, many polymerase chain reaction models have been proposed for exact quantitative estimation of the reaction results. In most models, kinetics of product accumulation and kinetics of fluorescent reporter are assumed to be identical. A model of the polymerase chain reaction is proposed to study the difference of such functions in the syste...
Article
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–si...
Article
Full-text available
Real-time polymerase chain reaction (real-time PCR) is the main molecular genetic method used for qualitative and quantitative analysis of specific nucleic acid sequences in many areas of biomedical research. Theoretical study of pCr models allows to estimate the influence of various reaction components and parameters, and to determine the unknown...
Article
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...
Article
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...
Article
Full-text available
Here, we report the first draft genome sequence of the clinically relevant species Mycobacterium gordonae The clinical isolate Mycobacterium gordonae 14-8773 was obtained from the sputum of a patient with mycobacteriosis.
Article
A new noncontact method for measuring temperatures of liquids, which is based on the fluorescent probes, is proposed. The method is intended for measuring temperatures of reaction media in reactors of devices for polymerase chain reactions in real time and can be used for determining dynamic temperature parameters.
Article
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...
Article
When solving many problems in biology and med� icine, it is necessary to detect the presence of specific nucleic acid sequences in samples. For this purpose, polymerase chain reaction (PCR)—a chain enzy� matic reaction of multiplication of the analyzed DNA fragment, realized in the form of successive rounds of duplication of fragments present in th...
Article
Currently, polymerase chain reaction (PCR) is the main moleculargenetic method used for qualitative and quantitative analysis of nucleic acid specific sequences. PCR is based on the branched chain reac� tion of replication of a doublestranded DNA frag� ment (fragment replication). The reaction is carried out by cyclically repeating two stages: (1)...

Citations

... The NTM refer to mycobacteria species other than the Mycobacterium tuberculosis complex and M. leprae [2]. More than 200 NTM species were identified and some of which are known as important infectious threats, especially in industrialized countries [3,4]. These bacterial agents exist ubiquitous in the environment and are ubiquitously transmitted by inhalation, ingestion, or direct inoculation in the skin to develop infections [5]. ...
... DNA molecule melting curve analysis is based on observing the physical properties change in the test solution during the DNA double-strand denaturation. The modern method is implemented on nucleic acid analyzers after real-time PCR using fluorescent dyes, the intensity of which can vary by more than 100 times [1,2]. The method has a high sensitivity of 80-98.6 % and a specificity of 83.3-100 % [3,4]. ...
... One multiplex real-time PCR assay which allows working with DNA extracted directly from clinical material should be mentioned particularly [30]. The authors propose a design of a clinical screening assay similar to the design described in this report and in our previous publication on the detection of NTM/MTBC [31]. Samples of diagnostic material are first analyzed by real-time PCR for the presence of MTBC or NTM DNA markers, and then NTM-positive samples are sequentially analyzed using 4 multiplex PCR mixtures for species identification. ...
... The RT-PCR method is based on the dye fluorescent response observation during the polymerase chain reaction [4]. The obtained data are used to calculate the values of the threshold cycle Cq -a value that allows to compare samples with each other on quantitative analysis [5]. RT-PCR in its classical design is a temperature-controlled reaction and is accompanied by a cyclic two-or three-step temperature change, providing the processes of denaturation, annealing and elongation [6]. ...
... RT-PCR is one of the most relevant and popular methods of genetic analysis and is widely used in medical diagnostics and scientific research [3]. The market size of RT-PCR and digital PCR was estimated at US $ 4.47 billion in 2019 by Validated Market Research and is projected to reach US $ 8.26 billion by 2027, with CAGR from 2020 to 2027 will be 8.6%. ...
... A number of Actinobacteriota that encoded RuBisCO form IE and trace gas scavenging enzymes were also isolated from human-host tissue samples, including skin lesions 91 , sputum [92][93][94][95] , lymph nodes 96 , the eye 97 , gastrointestinal tract 98 and haemodialysis water 99 . This is perhaps not surprising given that opportunistic pathogens within the Mycobacterium and Rhodococcus genera are capable of oxidising CO and/or H 2 at below atmospheric levels. ...
... Calculation by these methods is hindered by the tilt and vertical displacement of real plots relative to the base line, which can be explained by factors including the tem perature dependence of background fluorescence [15]. ...
... The amplified products in the course of the reaction follow a kinetic time-discrete pattern. The amount of accumulated amplification products (S C ) is a function of the initial amount of DNA strands (S 0 ) and the amplification efficiency (E i ) after C cycles, and is described in Equation (Eq 1) [17]. The amplification kinetics gives the amount of fluorescent dye intercalated DNA template, which increases exponentially during cycling. ...
... Quantification of mtDNAcn in whole blood does not come without difficulties using qPCRbased assays. Firstly, the extraction methods greatly affects quality and reproducibility of DNA [21] and concentration of DNA affects empirical error in qPCR assays [22,23]; to adjust for this we conducted all qPCR work using the same isolated DNA sample. Secondly, given the variable nature of qPCR work, measurements were performed in triplicate. ...
... However, with appropriate execution, this method is highly technological and allows for a short time to accumulate a large array of information. For reliable testing it is necessary that in one cycle of PCR the amount of DNA is doubled and the amplification efficiency approaches the maximum [20,21]. Also, you need to carefully monitor its probable fluctuations, which can lead to incorrect results. ...