M. G. Baryshev’s research while affiliated with Southern Scientific Center and other places

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Publications (86)


Dynamics of angular deviations of the first chain of the selected DNA fragment over the time interval [0; 10⁻¹⁰ s] with a torque M0 = 8.00 pN·nm and a viscosity parameter of the medium λ = 1.
Dynamics of OS zones genesis and potential energy of hydrogen bonds in base pairs at M0 = 8.28 pN·nm. OS in AT pairs is shown in green, and OS in GC pairs is shown in red, and the promoter is highlighted with a darker background (a). Closed base pairs are highlighted in blue depending on the potential energy values of hydrogen bonds in accordance with the color scale shown on the right (b).
Dynamics of OS zones genesis and potential energy of hydrogen bonds in base pairs at M0 = 8.49 pN·nm. The green color in the figure indicates the OS in AT pairs, and the red color indicates the OS in GC pairs. Closed base pairs are highlighted in blue depending on the potential energy values of hydrogen bonds in accordance with the color scale shown on the right.
Dynamics of OS zones genesis and potential energy of hydrogen bonds in base pairs at M0 = 8.50 pN·nm. OS in AT pairs is shown in green, and OS in GC pairs is shown in red. Closed base pairs are highlighted in blue depending on the potential energy values of hydrogen bonds in accordance with the color scale shown on the right.
Dynamics of OS zones genesis and potential energy of hydrogen bonds in base pairs at M0 = 8.55 pN·nm. OS in AT pairs is shown in green, and OS in GC pairs is shown in red. Closed base pairs are highlighted in blue depending on the potential energy values of hydrogen bonds in accordance with the color scale shown on the right.

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Localization of Potential Energy in Hydrogen Bonds of the ATXN2 Gene
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  • Full-text available

January 2025

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19 Reads

Mikhail Drobotenko

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Oksana Lyasota

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Stepan Dzhimak

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[...]

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Anna Dorohova

It is known that a number of neurodegenerative diseases, also called diseases of waiting, are associated with the expansion of the polyQ tract in the first exon of the ATXN2 gene. In the expanded polyQ tract, the probability of occurrence of non-canonical configurations (hairpins, G-quadruplexes, etc.) is significantly higher than in the normal one. Obviously, for their formation, the occurrence of open states (OSs) is necessary. Calculations were made for these processes using the angular mechanical model of DNA. It has been established that the probability of the large OS zones genesis in a DNA segment depends not only on the “strength” of the nucleotide sequence but also on the factors determining the dynamics of DNA; localization of the energy in the DNA molecule and the potential energy of interaction between pairs of nitrogenous bases also depend on environmental parameters. The potential energy of hydrogen bonds does not remain constant, and oscillatory movements lead to its redistribution and localization. In this case, OSs effectively dissipate the energy of oscillations. Thus, mathematical modeling makes it possible to calculate the localization of mechanical energy, which is necessary for the OSs formation, and to predict the places of their origin, taking into account the mechanical oscillations of the DNA molecule.

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Ensuring Tree Protection, Growth and Sustainability by Microbial Isolates

September 2024

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74 Reads

Antimicrobial properties of the new strains of micro-organisms isolated from natural sources of various ecological niches in the Moscow region and the Republic of Tatarstan were studied. Antifungal activity of isolates was detected in a test culture of toxin-producing microscopic fungi that can cause animal and plant diseases: Aspergillus flavus, Candida albicans, Fusarium oxysporum and Penicillium spp. Of the 46 studied micro-organisms of genera Bacillus, Lactobacillus, Lactococcus and Streptomyces isolates, there are four strains (Bacillus subtilis, Lactobacillus plantarum, Propionibacterium freudenreichii and Streptomyces spp.) that showed an ability to produce biologically active metabolites with a pronounced antimicrobial potential against phytopathogenic fungi metabolites. Based on the selected four strains, a Bacterial product LRV composition has been created. Scots pine, pedunculate oak and small-leaved linden seedlings with single and double foliar treatment and Bacterial product LRV at a concentration of 10 mL/L led to an increase in the growth of the aboveground part by 31.8, 51.9 and 25.4%, respectively, and the underground part by 25.0, 37.2 and 25.7%, respectively, compared to the control. The weight of seedlings at the end of the study exceeded the control variant by an average of 26.0, 44.0 and 78.0%, respectively. Plant protection Bacterial product LRV use did not have a significant effect on the group of molds that caused the powdery mildew and Schütte disease damage to trees. The Biological product LRV provided plant protection from fungal diseases caused by Lophodermium pinastri Chev. and Microsphaera alphitoides.




New approach to soil fertility management: Biogeosystem Technique methodology (critical review)

February 2024

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150 Reads

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2 Citations

A standard management soil priming effect is short term. A current soil plowing, irrigation and waste utilization soil priming action shortcomings elimination is needed. The Biogeosystem Technique (BGT*) priming action system was developed for soil management to provide a higher-level priming effect. The BGT* is focused on a soil biogeochemical cycle activation similar to the biodegradation in a colon of a live organism as an efficient benchmark bioreactor. Fluorescence in situ hybridization showed a cooperation of bacteria within polymicrobial biofilms and a probability of the polymicrobial biofilms biodegradation process acceleration and soil organic matter (SOM) regime improvement. The soil priming actions the BGT* technological management is capable of providing are based on the BGT* constituents, whose essence, applications and corresponding detailed data are presented in available studies. The main BGT* components are as follows. The illuvial horizon intra-soil milling artificial soil aggregation (a form of crumbling and mixing) priming action provides the soil structuring, a SOM content increase and an annual yield increment direct priming effects. A long-term secondary priming effect is a technology life cycle with higher profitability compared to the standard moldboard, chiseling and three-tier plowing. Land Degrad Dev. 2024;1-15. wileyonlinelibrary.com/journal/ldr


Structure and Neuroprotector Properties of a Complex Compound of Lithium with Comenic Acid

December 2023

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96 Reads

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1 Citation

The structure, antioxidant and neuroprotective properties of lithium comenate (lithium 5-hydroxy-4-oxo-4H-pyran-2-carboxylate) were studied. Lithium comenate was obtained by reacting comenic acid (H2Com) with lithium hydroxide in an aqueous solution. The structure of lithium comenate was confirmed via thermal analysis, mass spectrometry, IR, NMR and UV spectroscopy. The crystal structure was studied in detail via X-ray diffraction. The compound crystallized in a non-centrosymmetric space group of symmetry of the orthorhombic system Pna21 in the form of a hydrate, with three water molecules entering the first coordination sphere of the cation Li⁺ and one molecule forming a second environment through non-valent contacts. The gross formula of the complex compound was established [Li(HCom)(H2O)3]·H2O. It has been established that lithium comenate has a pronounced neuroprotective activity under the excitotoxic effect of glutamate, increasing the survival rate of cultured rat cerebellar neurons more than two-fold. It has also been found that the pre-stress use of lithium comenate at doses of 1 and 2 mg/kg has an antioxidant effect, which is manifested in a decrease in oxidative damage to the brain tissues of mice subjected to immobilization stress. Based on the data available in the literature, we believe that the high neuroprotective and antioxidant efficacy of lithium comenate is a consequence of the mutual potentiation of the pharmacological effects of lithium and comenic acid.



8-Oxoguanine-DNA-Glycosylase Gene Polymorphism and the Effects of an Alternating Magnetic Field on the Sensitivity of Peripheral Blood

October 2023

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29 Reads

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3 Citations

Background The production of reactive oxygen species (ROS) in animals and cells often results from exposure to low-intensity factors, including magnetic fields. Much of the discussion about the initiation of oxidative stress and the role of ROS and radicals in the effects of magnetic fields has centered on radical-induced DNA damage. Methods The DNA concentration in the final solution was determined spectrophotometrically. Typing of the polymorphic variant rs1052133 of the 8-oxoguanin DNA glycosylase (hOGG1) gene was performed by polymerase chain reaction. An enzyme immunoassay was performed to determine the level of 8-oxyguanine in DNA. To process samples exposed to an alternating magnetic field, the authors developed a device for the automated study of biological fluids in an alternating magnetic field. The content of hydrogen peroxide in aqueous solutions of DNA was determined using the spectrophotometric method. Results It was experimentally determined that an increase in the concentration of hydrogen peroxide in an aqueous medium by 3–5 times under the action of a low-frequency magnetic field reduces the resistance of the genomic material to oxidative modification and the accumulation of 8-oxyguanine in DNA. A model is proposed for the mechanism of action of a low-frequency magnetic field on aqueous solutions of nucleic acids and proteins, which satisfies the model of a chemical oscillator for the transformations of reactive oxygen species in an aqueous medium. The model illustrates the oscillating nature of the processes occurring in an aqueous solution of DNA and makes it possible to predict changes in the concentration of hydrogen peroxide in an aqueous solution of biopolymers, depending on the frequency of the acting low-intensity magnetic field. Conclusions The key element in the mechanisms involved in the effects of low-intensity magnetic field on living systems is the occurrence of ROS generation in the aquatic environment of chemical oscillators, in which the competition of physical and chemical processes (electron transfers, reactions of decay and addition of radicals, spin magnetically induced conversion, synthesis, and decay of the longest-lived form—hydrogen peroxide) is controlled by a magnetic field.


Mechanism of action of the low-frequency electromagnetic field on aqueous solutions of biopolymers

October 2023

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6 Reads

Биофизика

This paper presents the mechanism of signal transformation by which a signal from the magnetic component of the low-frequency electromagnetic field with extremely low energy is changed into chemical and biochemical signals which elicit a biological response in aqueous solutions of biopolymers based on nucleic acids and proteins. A theoretical model developed shows that the basis of oxidative DNA damage and conformational transitions of proteins is a universal mechanism associated with a change in the amount of the most long-lived form - hydrogen peroxide in a chemical oscillator of mutual transformations of reactive oxygen species under the influence of low-intensity electromagnetic field exposure. It has been experimentally established that the quantitative content of hydrogen peroxide in solutions of biopolymers resonantly depends on the frequency of applied field. Conformational changes in proteins are accompanied by an increase in the availability and activity of the nucleophilic centers that are potential targets for reactive oxygen species. Complete unfolding and denaturation of the amino acid chain of the protein under the influence of low-frequency electromagnetic field exposure do not occur. It has been shown that enhanced hydrogen peroxide formation at 3 Hz and 50 Hz leads to oxidative modification of nitrogenous bases in DNA.


Study of the Magnesium Comenate Structure, Its Neuroprotective and Stress-Protective Activity

April 2023

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134 Reads

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6 Citations

The crystal structure and the biological activity of a new coordination compound of magnesium ions with comenic acid, magnesium comenate, was characterized and studied. Quantitative and qualitative analysis of the compound was investigated in detail using elemental X-ray fluorescent analysis, thermal analysis, IR-Fourier spectrometry, UV spectroscopy, NMR spectroscopy, and X-ray diffraction analysis. Based on experimental analytical data, the empirical formula of magnesium comenate [Mg(HCom)2(H2O)6]·2H2O was established. This complex compound crystallizes with eight water molecules, six of which are the hydration shell of the Mg²⁺ cation, and two more molecules bind the [Mg(H2O)6]²⁺ aquacation with ionized ligand molecules by intermolecular hydrogen bonds. The packing of molecules in the crystal lattice is stabilized by a branched system of hydrogen bonds with the participation of solvate water molecules and oxygen atoms of various functional groups of ionized ligand molecules. With regard to the biological activity of magnesium comenate, a neuroprotective, stress-protective, and antioxidant effect was established in in vitro and in vivo models. In in vitro experiments, magnesium comenate protected cerebellar neurons from the toxic effects of glutamate and contributed to the preservation of neurite growth parameters under oxidative stress caused by hydrogen peroxide. In animal studies, magnesium comenate had a stress-protective and antioxidant effect in models of immobilization–cold stress. Oral administration of magnesium comenate at a dose of 2 mg/kg of animal body weight for 3 days before stress exposure and for 3 days during the stress period led to a decrease in oxidative damage and normalization of the antioxidant system of brain tissues against the background of induced stress. The obtained results indicate the advisability of further studies of magnesium comenate as a compound potentially applicable in medicine for the pharmacological correction of conditions associated with oxidative and excitotoxic damage to nerve cells.


Citations (65)


... Using mathematical modeling methods, it was shown that with an increase in the length of the CAG tract, the probability of the appearance of additional large open state (OS) zones in it increases. A correlation was established between this probability and statistical data on the age of onset of the disease [54]. It is obvious that for the emergence of secondary structures (hairpins, G-quadruplexes, etc.), a necessary condition is the appearance of large OS zones in the CAG tract. ...

Reference:

Localization of Potential Energy in Hydrogen Bonds of the ATXN2 Gene
Abnormal open states patterns in the ATXN2 DNA sequence depends on the CAG repeats length
  • Citing Article
  • July 2024

International Journal of Biological Macromolecules

... Soil vulnerability combined natural and anthropogenic effects hinder a circular economy principals' implementation (Duanyang Xu et al. 2024) and a natural capital expanded technological reproduction (Brander et al. 2024;Kalinitchenko et al. 2024;Mao and Jiao 2024;Seidl et al. 2024). The soil is an important ecosphere ingredient providing a humans and planet health (Kopittke et al. 2024), and the soil restoration and soil solution correct management are needed (Smith et al. 2021;Yadav et al. 2023). ...

New approach to soil fertility management: Biogeosystem Technique methodology (critical review)

... The largest number of reports at the congress were on the topic of medical biophysics. These reports covered a wide range of topics, from the development of methods for studying oxidative stress in neurodegenerative diseases [17], and neuroprotective drugs [18], to research in the field of protecting the body from the development of diabetes by blocking the formation of excess amounts of the protein VDAC1 using specific blocking molecules and genetic engineering methods [19]. In addition, in her report, Brazhe N.A. presented the finding that astrocytes, rather than neurons, may be a suitable "target" both for the prevention of age-related changes in the body and for the treatment of various types of neurodegeneration [20]. ...

Structure and Neuroprotector Properties of a Complex Compound of Lithium with Comenic Acid

... This explains the non-monotonicity of the formation of OS zones with an increase in the magnitude of the torque M0, which can be seen when comparing Figure 4 (M0 = 8.50 pN·nm) and Figure 5 (M0 = 8.55 pN·nm). This non-monotonicity has been systematically identified in the works [57,58]. From Figure 2b, it is clear that the distribution of the potential energy of hydrogen bonds depends on time: at first, the potential energy is evenly distributed between base pairs, and then it is redistributed and localized on individual DNA sections. ...

Medium viscosity influence on the open states genesis in a DNA molecule
  • Citing Article
  • December 2023

... Bifunctional glycosylases are capable of completely removing both the damaged base and the phosphate backbone from the DNA. Among them, OGG1 is noteworthy as it removes 8-oxoG, the most common type of mtDNA damage arising from oxidative stress or exposure to drugs and xenobiotics [38,39]. OGG1 contains an N-terminal mitochondrial targeting signal (MTS) that facilitates its transport into mitochondria [40]. ...

8-Oxoguanine-DNA-Glycosylase Gene Polymorphism and the Effects of an Alternating Magnetic Field on the Sensitivity of Peripheral Blood

... Despite an improved understanding of the pathophysiology of RVO, identifying its modifiable risk factors is imperative to discover potential pathways for preventive and therapeutic interventions. Magnesium (Mg), an essential dietary mineral, is fundamental to several physiological processes, including blood pressure regulation [7], blood glucose control [8], and nerve function [9]. Its established role in vascular tone and blood pressure regulation and its vasodilatory properties collectively suggest its potential to reduce the risk of cardiovascular disease [10,11]. ...

Study of the Magnesium Comenate Structure, Its Neuroprotective and Stress-Protective Activity

... A new approach is membrane surface modification, which allows for a significant improvement in the properties and characteristics of the material for many areas of its application [51][52][53]. In particular, the use of metal nanoparticles as modifiers shows significant promise [54][55][56][57][58]. Thus, the application of a developed nanostructured coating to the surface of a Pd-containing hydrogen-permeable membrane can significantly increase its stability and permeability at low temperatures [59,60]. ...

Investigation of the Dependence of Electrocatalytic Activity of Copper and Palladium Nanoparticles on Morphology and Shape Formation

... Previous investigations into the Peyrard-Bishop model have employed diverse methodologies. Numerical simulations have shed light on its behavior under various conditions [8], while perturbation methods and analytical approaches have yielded approximate solutions [9]. However, the quest for exact analytical solutions and their stability analysis remains an active area of research. ...

Review of Mathematical Models Describing the Mechanical Motion in a DNA Molecule
  • Citing Article
  • March 2023

Biophysics

... These data point out not only the significance of the AT/GC ratio for the initiation of the DNA denaturation process but also the importance of this ratio for bubble lifetimes and the stability of their particular groups. Furthermore, using such a mathematical approach, it is possible to reduce the proportion of both false positive and false negative results in the analysis of the intensity of hydrogen bond dissociation when studying DNA molecular dynamics [85,86]. ...

Influence of Single Deuterium Replacement on Frequency of Hydrogen Bond Dissociation in IFNA17 under the Highest Critical Energy Range

... Palladium is a silvery lustrous white metal widely used as catalyst and jewellery. Palladium nanoparticles (PdNPs) are made from a noble metal and are being used in many new technologies like pro drug activation, photo-thermal agent, and anti-bacterial treatment and they offer great potential for many applications (Maciej Serda et al., 2013).Previous studies shows that Pd-Ag bimetallic has better catalytic performance (Gulbagça et al., 2022), better stability and high hydrogen flux (Pushankina et al., 2022) and enhanced biological activity (Sivamaruthi et al., 2019). Both silver and palladium nanoparticles are synthesised with different approaches but plant extracts are an ideal choice for biological synthesisdue to their eco-friendly nature, and affordability (Vinodhini et al., 2022).According to Sahayaraj and Ravi (2008), the little, fragrant Vitex negundo plant has five characteristic foliolate leaves (Sahayaraj & Ravi, 2008). ...

Synthesis and Study of Palladium Mono- and Bimetallic (with Ag and Pt) Nanoparticles in Catalytic and Membrane Hydrogen Processes