bluuebunny/crossref_metadata_2025 huggingface dataset:
CLASSIFICATION OF INFORMATION AND COMMUNICATION TECHNOLOGY TOOLS FOR TEACHING LINEAR ALGEBRA
Authors: Dubovyk Vitalii
Published: April 2024

The article reveals the peculiarities of the classification of the means of information and communication technologies of education at various stages of the development of education. The classification of learning hardware in accordance with the current state and requirements of the educational process is highlighted. Hardware includes the following: personal computers or laptops, mobile devices, access devices to local and global networks, peripheral devices. Classifications of software tools were analyzed. It is noted that some software tools can be used in different directions when learning linear algebra. In particular, the GeoGebra environment can be used to visualize educational material on linear algebra, as a mathematical simulator, to obtain quick calculations, and this, in turn, emphasizes the need for a clear classification of software tools for learning linear algebra. Based on the analysis of scientific and methodological literature, the state of teaching linear algebra in pedagogical universities and the practice of teaching linear algebra, a separate classification of the means of information and communication technologies for teaching linear algebra is proposed: by didactic purpose; on the implementation of intellectual functions; by the nature of interaction with the user; according to the form of teaching material; according to the form of education; by object orientation; by the nature of the material used; according to the main pedagogical task; by the appearance of the user interface; by the presence of elements of artificial intelligence; by degree of interactivity; by the degree of coverage of educational material; by technology of use; by the nature of the basic information; by methods. The essence of each element of this classification is revealed and it is established that the developed classification can become an auxiliary factor in the design of methods, in particular, the method of using ICT during the teaching of linear algebra for students of pedagogical universities.
INTERDISCIPLINARY INTEGRATION IN THE PROCESS OF TEACHING HUMANITIES IN HIGHER EDUCATION INSTITUTIONS
Authors: Marchuk Iryna , Nagorna Natalia , Ivanova Nataliia
Published: April 2024

This research aims to demonstrate how interdisciplinary integration enhances the teaching of humanities to higher education applicants. We found that interdisciplinary integration is essential for preparing future specialists. It helps to achieve the strategic goal of professional training – developing a personality as a modern professional. We proved the effectiveness of this approach.We showed that certain conditions can address a key challenge of the current education sphere – developing professional competencies of a future specialist, who needs to be creative, competitive in theoretical, technical and technological issues.We used the following research methods: theoretical: analyzing and synthesizing scientific and pedagogical literature on the issues of theory and practice of professional training of future specialists; examining educational and methodological works and the best pedagogical practices to define the nature of interdisciplinary integration; assessing and comparing its effectiveness with the conventional approach to teaching humanities in the academic setting. Empirical: interviewing and testing future professionals on the levels of professional qualities; observing the process and outcomes of interdisciplinary integration in the teaching of humanities in higher education institutions. Statistical: analyzing and verifying the validity of the research results.We identified the components of the integrative training of future specialists: didactic and methodological, active and substantive.The researches established the principles of integrative learning and the methods of its implementation.The authours of the paper indicated the proportion of fundamental and applied knowledge.We outlined the criteria for selecting the optimal proportion of special and humanitarian disciplines.
The antidepressant efficacy of flurbiprofen in mice: Behavioural assessment
Authors: Alberfkani Naktal , Naser Ahmed
Published: April 2024

Flurbiprofen is a nonsteroidal anti-inflammatory medication (NSAID). The psychological effect of nonsteroidal anti-inflammatory drugs (NSAIDs) is a source of contention based on clinical and experimental evidence. As a result, the goal of our study was to assess the antidepressant effects of various flurbiprofen doses in mice. We evaluated the effect of oral administration of flurbiprofen at 10, 20, and 40 mg/kg in the tail suspension and forced swimming tests after 1 h of treatment. Fluoxetine (10 mg/kg, i.p.) was used as a positive control. Flurbiprofen at 40 mg/kg showed a significant antidepressant effect, which was revealed by a significant decrease in immobility time compared with the control group, with the group administered flurbiprofen at 10 mg/kg, and with the group given flurbiprofen at 20 mg/kg in the tail suspension test. Flurbiprofen at 40 mg/kg showed an antidepressant effect, which was revealed by a significant decrease in immobility time compared with the control group and with the group given flurbiprofen at 10 mg/kg. Flurbiprofen at 20 mg/kg had a minimal antidepressant effect in the swimming forced test, which was reflected by a non-significant decrease in immobility time compared with the control group. In conclusion, our results showed that relatively high therapeutic doses of flurbiprofen might have an antidepressant effect in a mouse model, and we recommended conducting other in vivo studies to clarify the variation in dose response.
Determination of water characteristics of trout farms for organic farming in Feke
Authors: Erçen Zeynep , Özlüer Hunt Arzu , Tabakoğlu Şefik Surhan , Yavuz Güzel Evsen , Çevik Fatma
Published: April 2024

Organic aquaculture represents a comprehensive approach to farm management and food production. It integrates the best environmental practices, promotes biodiversity conservation, preserves natural resources, and places a strong emphasis on ensuring the well-being of the fish, all in alignment with the preferences of discerning consumers.
In this study, water quality and suitability of two different trout production enterprises in Feke/Adana city in Turkey for organic fish culture was investigated. The water quality parameters evaluated include temperature, dissolved oxygen, pH, Ca, Mg, Na, K, alkalinity, nitrate nitrogen, nitrite nitrogen, ammonium nitrogen, orthophosphate phosphorus, and alkalinity.
It is seen that the head waters have a high water quality standard in terms of all their physical and chemical properties.
Postsedimentary Transformations in the Lower Triassic Deposits in the North of Varandey-Adzva Zone (Pechora Oil and Gas-Bearing Basin)
Authors: Timonina N. N. , Nechaev M. S. , Ulnyrov I. L.
Published: April 2024

New data on the mineral composition of Lower Triassic terrigenous deposits in the north of the Pechora oil and gas bearing basin are presented. The relevance of the study is due to the fact that terrigenous natural reservoirs confined to this part of the section have a heterogeneous structure both in area and in section. The purpose of the article was to identify the features of the formation and distribution of minerals that fill the void space of reservoirs. As a result of studying by the methods of optical microscopy, X-ray phase analysis, electron microscopy, signs of mineralogenesis processes, post-sedimentary transformations of sandy reservoirs were revealed. It is shown that the most widespread are quartz regeneration, transformation of minerals of the mica group, formation of calcite of various generations, formation of authigenic clay minerals, etc. Diagenetic changes in terrigenous rocks play a significant role in the formation of reservoir properties and lead to heterogeneity of reservoirs. It is shown that a large amount of calcite in sandstone cement leads to a significant decrease in porosity and permeability parameters. Pore cement of chlorite-smectite composition in fine-grained sandstones also leads to a decrease in the quality of reservoirs. Coarse and medium-grained sandstones with a low content of cement, predominantly of kaolinite or chlorite composition, are characterized by higher reservoir properties. Crustification cement of chlorite composition, pore-filling cement of kaolinite composition contribute to the formation of reservoirs with higher rates.
L.V. Pustovalov and the Development of His Ideas on Oil and Gas Lithology
Authors: Kuznetsov V. G. , Dmitrievsky A. N.
Published: April 2024

The article discusses the main directions of lithological research in the field of oil and gas geology, continuing and developing the ideas and research of  L.V. Pustovalov. A number of such areas are closely coordinated with other branches of geology – tectonics, stratigraphy, etc. A wide range of such studies includes the analysis of the structure and development of sedimentary basins, the elucidation of the structure of the internal structure of sedimentary complexes, the forecast and search for non-structural traps of oil and gas, the study of natural reservoirs of oil and gas at different hierarchical levels.
Early Ediacaran Positive C-Isotope Anomaly in Limestones of the Chernaya Rechka Formation of the Igarka Uplift (Northwestern Siberian Platform)
Authors: Kochnev B. B. , Pokrovsky B. G. , Kuznetsov A. B. , Marusin V. V. , Kaurova O. K. , Bykova N. V. , Ivanova N. A.
Published: April 2024

The Precambrian Chernaya Rechka Formation (Igarka Uplift) hosts a high-amplitude positive carbonate carbon isotope anomaly (up to 12.4‰) spanning through 500 m of the section and occurring simultaneously with a rise of δ13Сorg values. The similar trends of carbon isotope variations in the carbonate fraction and organic matter are not caused by local sedimentary environments since the studied anomaly-bearing carbonates accumulated in different zones of the carbonate ramp and shallow shelf. Oxygen isotope composition of these carbonates and some other geochemical criteria indicate minimal (if any) impact of post-sedimentary processes on preservation of the isotope systems. Concentrations of trace elements in the carbonate fraction indicate alternating anoxic and oxic environments that did not affected the carbon isotope composition during accumulation of the Chernaya Rechka Formation. The profound positive δ13С anomaly was putatively caused by a global deficiency of 12С in the paleo-ocean related to accumulation of methane hydrates and burial of non-oxidized organic matter. Together with geochronological and stratigraphic data, minimal 87Sr/86Sr values (0.7074) in the Chernaya Rechka Formation reveal the lower Ediacaran (lower Vendian) age of the unit (635–580 Ma). Among the closest stratigraphic analogues of the Chernaya Rechka Formation are the Dal’nyaya Taiga Group (Patom Basin) and coeval stratigraphic sequences in the southern Siberian Platform. Global nature of the positive δ13С anomaly provide its correlation with other coeval C-isotope events worldwide.
С, О, S, Sr-Isotopes in the Osveya Horizon Deposits of the Lower Eifelian on the Territory of Belarus
Authors: Makhnach А. А. , Pokrovsky B. G. , Murashko О. V.
Published: April 2024

The complex interpretation of distribution of δ13C and δ18О in carbonates, δ34S and 87Sr/86Sr in gypsum from the Osveya horizon (Lower Eifelian) on the territory of Belarus showed that significance of diagenetic isotope signals is low and variations of the values can be consistently explained within a sedimentation model. Along with intervals of sections with standard marine δ13C values, there are negative excursions of the parameter (up to –7…–11‰) marking segments of sequence with carbonate-sulphate rocks and smaller scale sulphate manifestations. The excursions correspond to evaporite episodes when the basin shallowed and, probably, dismembered into separate ponds. This led to increasing the role of continental water enriched with soil carbon in the geochemical system of sedimentation due to the land runoff activation and/or shallowing. Continental water could come from for a long time exposed land areas where the Eifelian deposits are absent until now as well as from periodically existing islands. Oxygen isotopic composition does not react to δ13C negative excursions by similar shifts due to the possible absence of significant difference between the δ18О values of atmospheric precipitation, giving rise to land water, and seawater in low latitudes where the territory of Belarus was situated in the Devonian. In 40% of the studied samples, the δ18О values range from –4 to –2‰, corresponding to the Eifelian “plateau” (~–3‰) in the generalized chemostratigraphic curve in the generalized chemostratigraphic curve constructed using calcite of brachiopod shells from several regions of the world. The δ18О values higher than –2‰ (44% of cases), probably, are the result of water evaporation, while figures –2‰ (16%) which may decrease up to –7.0…–9.5‰ at the peaks of evaporite episodes, are caused by water heating (sometimes very significant) during the basin shallowing. The activation of continental water role accompanying evaporite episodes is supported by the fact that the 87Sr/86Sr ratio in the Osveya horizon gypsum (0.708402–0.708742) is much higher than that of the Eifelian seawater according to a global estimate (0.70772), while δ34S of gypsum (15.5–21.2‰) in more than a half of the analyzed samples is lower than figures characteristic of the Middle Devonian seawater sulphate (19–20‰).
Interleukin-11 in Pathology of the Nervous System
Authors: Airapetov M. I. , Eresko S. O. , Ignatova P. D. , Lebedev A. A. , Bychkov E. R. , Shabanov P. D.
Published: April 2024

The study of the role of cytokines in various pathological conditions of the body is one of the topical areas of modern biomedicine. Interleukin 11 (IL-11) was discovered in 1990 in fibrocyte-like bone marrow stromal cells, but there has been an increased interest in the cytokine in recent years. The cytokine plays a significant role in the central nervous system; local expression of this cytokine by nerve cells has been shown. Studies show the involvement of IL-11 in the mechanisms of development of a number of pathologies of the nervous system. The review summarizes information that shows the involvement of IL-11 in the mechanisms of development of brain pathologies. Probably, in the near future, this cytokine will be able to find clinical application in the correction of mechanisms that are involved in the formation of pathological conditions of the nervous system.
Regulatory Potential of SNP Markers in the Genes of DNA Repair Systems
Authors: Babushkina N. P. , Kucher A. N.
Published: April 2024

In non-coding regions of the genome, the widest range of SNP markers associated with human diseases and petrogenetically significant features were identified. This raised the critical question of identifying the mechanisms that explain these associations. Previously, we identified a number of associations of polymorphic variants of genes encoding DNA repair proteins with multifactorial diseases. To clarify the possible mechanisms underlying established associations, we carried out a detailed annotation of the regulatory potential of the studied markers using a number of on-line resources (GTXPortal, VannoPortal, Ensemble, RegulomeDB, Polympact, UCSC, GnomAD, ENCODE, GeneHancer, EpiMap Epigenomics 2021, HaploReg, GWAS4D, JASPAR, ORegAnno, DisGeNet, OMIM). The article characterizes the regulatory potential of polymorphic variants rs560191 (in the TP53BP1 gene), rs1805800 and rs709816 (in the NBN gene), rs473297 (MRE11), rs189037 and rs1801516 (ATM), rs1799977 (MLH1), rs1805321 (PMS2), rs20579 (LIG1). Both the general characteristics of the studied markers and information on their influence on the expression of “own” and co-regulated genes, on changes in binding affinity of transcription factors are given. Known data on both adaptogenic and pathogenicity potential of these SNPs and on histone modifications co-localized with them are presented. The potential involvement in regulatory function of not only genes that contain SNPs studied but also nearby genes may explain the association of the markers with diseases and their clinical phenotypes.
Anti-Restriction Activity of ArdB Protein against EcoAI Endonuclease
Authors: Kudryavtseva A. A. , Alekhin V. A. , Lebedeva M. D. , Csefalvay E. , Weiserova M. , Manukhov I. V.
Published: April 2024

ArdB proteins are known to inhibit the activity of type I restriction–modification (RM-I) system, in particular EcoKI (family IA). The mechanism of ArdB’s activity still remains unknown; the spectrum of targets inhibited by them has been poorly studied. In this work, it was shown that the presence of the ardB gene from R64 plasmid could suppress the activity of EcoAI endonuclease (IB family) in Escherichia coli TG1 cells. The absence of specificity of ArdB to a certain RM-I system (it inhibits both the IA- and IB-family), it can be a-ssumed that the mechanism of the anti-restriction activity of this protein does not depend on both the s-equence DNA at the recognition site and the structure of the restrictase of the RM-I systems.
Phase Separation of Purified Human LSM4 Protein
Authors: Li H. , Ju Y. , Liu W. W. , Ma Y. Y. , Ye H. , Li N.
Published: April 2024

Liquid–liquid phase separation of proteins occur in a number of biological processes, such as regulation of transcription, processing, and RNA maturation. Sm-like protein 4 (LSM4) is involved in multiple processes, including pre-mRNA splicing and P-bodies assembly. Before investigating the involvement of LSM4 in the separation of the two liquid phases during RNA processing or maturation, the separation of the liquid phases in an in vitro preparation of LSM4 protein should be first be detected. The mCherry-LSM4 plasmid was derived from pET30a and used to isolate mCherry-LSM4 protein from prokaryotic cells (Escherichia coli strain BL21). The mCherry-LSM4 protein was purified using Ni-NTA resin. The protein was further purified by fast protein liquid chromatography. Delta-Vision wide-field fluorescence microscopy was used to observe the dynamic liquid–liquid phase separation of the LSM4 protein in vitro. Analysis of the LSM4 protein structure using the Predictor of Natural Disordered Regions database revealed that its C-terminus contains a low complexity domain. A purified preparation of full-length human LSM4 protein was obtained from E. coli. Human LSM4 was shown to provide concentration-dependent separation of liquid–liquid phases in vitro in buffer with crowding reagents. Salts in high concentration and 1,6-hexanediol block the LSM4-induced separation of the two liquid phases. In addition, in vitro fusion of LSM4 protein droplets is observed. These results indicate that the full-length human LSM4 protein has the ability to form liquid inclusions and induce liquid–liquid phase separation in vitro.
APPswe/PS1dE9/Blg Transgenic Mouse Line for Modeling Cerebral Amyloid Angiopathy in Alzheimer’s Disease
Authors: Lysikova E. A. , Kuzubova E. V. , Radchenko A. I. , Patrakhanov E. A. , Chaprov K. D. , Korokin M. V. , Deykin A. V. , Gudyrev O. S. , Pokrovskii M. V.
Published: April 2024

Alzheimer’s disease (AD) is the most common proteinopathy, which is accompanied by a steady decrease in the patient’s cognitive functions with simultaneous accumulation of extracellular aggregates of amyloid β (Aβ) – amyloid plaques in the brain tissues and associated with neuroinflammation and neurodegeneration. Unlike humans and all other mammals, rats and mice have three amino acid substitutions in Aβ and do not reproduce the Alzheimer’s pathology. However, the appearance of amyloid plaques is observed in the brains of transgenic mice with the overexpression of human Aβ, which makes it possible to widely use these transgenic animals in biomedicine for the manifestation of AD. Transgenic mouse line APPswe/PS1dE9 is a widely used animal model for the study of the molecular mechanisms of AD. In this paper we provide a detailed description of the APPswe/PS1dE9/Blg subline of animals obtained by crossing APPswe/PS1dE9 mice on a CH3 genetic background with C57Bl6/Chg animals. We have shown no difference in parameters of offspring’s survival and fertility of this line compared to wild-type control animals. Histological analysis of the brain of APPswe/PS1dE9/Blg line confirmed the main neuromorphological feature of AD with the progression in number and size of amyloid plaques during aging. Thus, APPswe/PS1dE9/Blg line is a convenient model in the search for therapeutic strategies for AD.
Unusual Dependence between Gene Expression and Negative Selection in Euplotes
Authors: Moldovan M. A. , Gaydukova S. A.
Published: April 2024

In most of the studied organisms, gene expression is associated with a number of evolutionary features pertaining to the protein-coding sequences. In particular, gene expression positively correlates with the average intensity of negative selection and influences codon usage. Here, we study the connection between gene expression and selection patterns in two species of ciliate protists of the genus Euplotes. We find that codon usage is influenced by gene expression in these organisms, pointing at additional evolutionary constraints on mutations in heavily expressed genes relative to the genes expressed at lower rates. At the same time, at the level of synonymous vs. non-synonymous substitutions we observe a stronger constraint on the genes expressed at lower rates relative to those with higher rates of expression. Our study adds to the discussion about the general evolutionary patterns and opens new questions about the mechanisms of control of gene expression in ciliates.
The Diversity of MLE Helicase Functions in the Regulation of Gene Expression in Higher Eukaryotes
Authors: Nikolenko J. V. , Georgieva S. G. , Kopytova D. V.
Published: April 2024

MLE (Maleless) protein of D. melanogaster is a conserved helicase involved in a wide range of gene expression regulation processes. MLE ortholog, named DHX9, has been found in many higher eukaryotes, including humans. It is involved in such diverse processes as maintenance of genome stability, replication, transcription, splicing, editing and transport of cellular and viral RNAs, and translation regulation. Some of these functions have been studied in detail to date, but the most of them remain uncharacterized. The study of the functions of MLE ortholog in mammals in vivo is limited by the fact that the loss of function of this protein is lethal at the embryonic stage. Helicase MLE in D. melanogaster was originally discovered and studied for a long time as a participant in the dosage compensation process. However, in recent years, evidence has emerged that in D. melanogaster helicase MLE is involved in cellular processes similar to those in which it participates in mammals, and that many functions of this protein are conserved in evolution. In addition, in experiments on D. melanogaster new important functions of MLE were discovered, such as participation in hormone-dependent regulation of transcription, interaction with the SAGA transcription complex and other transcription cofactors and chromatin remodeling complexes. In contrast to mammals, in D. melanogaster, MLE mutations do not lead to death at the embryonic stage and allow the functions of this protein to be studied in vivo throughout ontogenesis in females and up to the pupal stage in males. The MLE ortholog in humans is a potential target for anticancer and antiviral therapy. Therefore, continued study of the functions of this helicase in the D. melanogaster model organism seems important and promising in both fundamental and practical aspects. In this review, the systematic position, domain structure, and conserved and specific functions of MLE helicase in D. melanogaster are discussed.
Insulator Protein CP190 Regulates Expression оf Spermatocyte Differentiation Genes in Drosophila melanogaster Male Germline
Authors: Romanov S. E. , Shloma V. V. , Koryakov D. E. , Belyakin S. N. , Lakitionov P. P.
Published: April 2024

CP190 protein is one of the key components of Drosophila insulator complexes, and its study is important for understanding the mechanisms of gene regulation during cell differentiation. However, Cp190 mutants die before reaching adulthood, which significantly complicates the study of its functions in imago. To overcome this problem and to investigate the regulatory effects of CP190 in adult tissues development, we have designed a conditional rescue system for Cp190 mutants. Using Cre/loxP-mediated recombination, the rescue construct containing Cp190 coding sequence is effectively eliminated specifically in spermatocyte, allowing us to study the effect of the mutation in male germ cells. Using high-throughput transcriptome analysis we determined the function of CP190 on gene expression in germline cells. Cp190 mutation was found to have opposite effects on tissue-specific genes, which expression is repressed by CP190, and housekeeping genes, that require CP190 for activation. Mutation of Cp190 also promoted expression of a set of spermatocyte differentiation genes that are regulated by tMAC transcriptional complex. Our results indicate that the main function of CP190 in the process of spermatogenesis is the coordination of interactions between differentiation genes and their specific transcriptional activators.
Genes Associated with Increased Stress Sensitivity in Hypertensive ISIAH Rats
Authors: Fedoseeva L. A. , Smolenskaya S. E. , Markel A. L. , Redina O. E.
Published: April 2024

ISIAH rats with inherited stress-induced arterial hypertension are characterized by increased stress reactivity of the hypothalamic-pituitary-adrenal and sympathoadrenal systems. The aim of this work was to study the genetic basis of increased susceptibility to stress in hypertensive ISIAH rats. Sequencing of the adrenal transcriptomes of hypertensive ISIAH and normotensive WAG rats revealed 9 differentially expressed genes (DEGs) in the X chromosome locus, which was previously associated with an increase in blood pressure and plasma corticosterone concentrations under mild emotional stress, and also with increased adrenal weight in ISIAH rats. An analysis of the functions of the proteins encoded by these DEGs suggested that the Sms gene encoding spermine synthase is the most likely candidate gene in the X chromosome locus associated with an increased level of stress susceptibility in ISIAH rats.
Primary and Secondary microRNA Modulation of the Extrinsic Pathway Apoptosis in Hepatocellular Carcinoma
Authors: Khlebodarova T. M. , Demenkov P. S. , Ivanisenko T. V. , Antropova E. A. , Lavrik I. N. , Ivanisenko V. A.
Published: April 2024

One of the most common malignant liver diseases is hepatocellular carcinoma, which has a high recurrence rate and a low five-year survival rate. It is very heterogeneous both in structure and between patients, which complicates diagnosis, prognosis and response to treatment. In this regard, an individualized, patient-centered approach becomes important, in which the use of mimetics and hsa-miRNA inhibitors involved in the pathogenesis of the disease may be determinative. From this point of view hsa-miRNAs are of interest, their aberrant expression is associated with poor prognosis for patients and is associated with tumor progression due to dysregulation of programmed cell death (apoptosis). However, the effect of hsa-miRNA on tumor development depends not only on its direct effect on expression of genes – primary targets, but also on secondary targets mediated by regulatory pathways. And while the former are actively studied, the role of secondary targets of these hsa-miRNAs in modulating apoptosis is still unclear. The present work summarizes data on hsa-miRNAs whose primary targets are key genes of the extrinsic pathway of apoptosis. Their aberrant expression is associated with early disease relapse and poor patient outcome. For these hsa-miRNAs, using the software package ANDSystem, we reconstructed the regulation of the expression of secondary targets and analyzed their impact on the activity of the extrinsic pathway of apoptosis. The potential effect of hsa-miRNAs mediated by the action on secondary targets is shown to negatively correlate with the number of their primary targets. It is also shown that hsa-miR-373, hsa-miR-106b and hsa-miR-96 have the highest priority as the markers of hepatocellular carcinoma, whose action on the secondary targets enhances their anti-apoptotic effect.
Molecular Mechanisms to Optimize Gene Translation Elongation Differ Significantly in Bacteria with and without Non-Ribosomal Peptides
Authors: Klimenko A. I. , Lashin S. A. , Kolchanov N. A. , Afonnikov D. A. , Matushkin Yu. G.
Published: April 2024

Non-ribosomal peptides play an important role in the vital activity of bacteria and have an extremely broad field of biological activity. In particular, they act as antibiotics, toxins, surfactants, siderophores, and also perform a number of other specific functions. Biosynthesis of these molecules does not occur on ribosomes but by special enzymes that form gene clusters in bacterial genomes. We hypothesized that the presence of non-ribosomal peptide synthesis pathways is a specific feature of bacterial metabolism, which may affect other vital processes of the cell, including translational ones. This work was the first to show the relationship between the translation regulation mechanism of protein-coding genes in bacteria, which is largely determined by the efficiency of translation elongation, and the presence of gene clusters in the genomes for the biosynthesis of non-ribosomal peptides. Bioinformatic analysis of the translation elongation efficiency of protein-coding genes was performed in 11679 bacterial genomes, some of which contained gene clusters of non-ribosomal peptide biosynthesis and some of which did not. The analysis showed that bacteria whose genomes contained clusters of non-ribosomal peptide biosynthetic genes and those without such gene clusters differ significantly in the molecular mechanisms that ensure translation efficiency. Thus, among microorganisms whose genomes contain gene clusters of non-ribosomal peptide synthetases, a significantly smaller part of them is characterized by optimized regulation of the number of local inverted repeats, while most of them have genomes optimized by the averaged energy of inverted repeats studs in mRNA and additionally by codon composition. Our results suggest that the presence of non-ribosomal peptide biosynthetic pathways in bacteria may influence the structure of the overall bacterial metabolism, which is also expressed in the specific mechanisms of ribosomal protein biosynthesis.
Poly(ADP-ribose)polymerases 1 and 2: Classical Functions and Interaction with HPF1 ‒ New Histone Poly(ADP-ribosyl)ation Factor
Authors: Kurgina T. A. , Lavrik O. I.
Published: April 2024

Poly(ADP-ribose) (PAR) is a negatively charged polymer, linear and branched, consisting of ADP-ribose monomers. This polymer is synthesized by poly(ADP-ribose)polymerase (PARP) enzymes which are activated on DNA damage and use nicotinamide adenine dinucleotide (NAD+) as a substrate. The most studied members of the PARP family, PARP1 and PARP2, are the most important nuclear proteins involved in many cellular processes, including the regulation of DNA repair. PARP1 and PARP2 catalyze both the synthesis and transfer of poly(ADP-ribose) to amino acid residues of target proteins, including autoPARylation. In view of the key role in the regulation of the DNA repair process, PARP1 and PARP2 are promising targets for chemotherapy. Recently, a novel histone PARylation factor (HPF1) has been discovered to modulate PARP1/2 activity by forming a transient joint active site with PARP1/2. In the presence of HPF1, histone modification occurs at serine residues. The general mechanism of interaction between HPF1 and PARP1/2 is only beginning to be elucidated. In this review, we consider the discovery and classical mechanism of this important process in higher eukaryotes, as well as the role of a new histone PARylation factor in this HPF1 process.
Potential of Interferon Lambda as an Inhibitor of SARS-CoV-2
Authors: Oleinik L. A. , Madonov P. G. , Pykhtina M. B.
Published: April 2024

The study provides an overview of scientific results on the feasibility of using type III interferons against SARS-CoV-2. We have analyzed data obtained from the PubMed electronic database for the period 2020‒2022. The results of our own studies of pharmacological substances based on recombinant IFN-λ1 and its pegylated form are also presented. Completed and ongoing investigations allow us to position IFN-λ as an effective therapeutic agent against SARS-CoV-2.
Alterations in the Level of mRNA of Tph1, Tph2 Genes, Tryptophan Hydroxylase Activity and Serotonin Metabolism in Mouse Brain 5 Days after Lipopolysaccharide Administration
Authors: Sherbakov D. V. , Arefieva A. B. , Komleva P. D. , Iz’urov A. E. , Khotskin N. V. , Bazovkina D. V. , Kulikov A. V.
Published: April 2024

Tryptophan hydroxylases 1 and 2 (TPH1 and TPH2) play the key role in the synthesis of a neurotransmitter and hormone, serotonin (5-HT) in peripheral organs and in the brain, respectively. The main aim of the present study was to clarify the distribution of mRNA of Tph1 and Tph2 genes in brain structures in norm and after inflammation. The experiments were carried out on young (4 weeks old) males of C57BL/6 mice. The animals were divided into three groups: intact, control, injected ip with saline, and injected ip with 2 mg/kg of bacterial lipopolysaccharide (LPS). Markers of inflammation, spleen and thymus mass were assayed 5 days after the saline or LPS administration. In their frontal cortex, hippocampus, striatum, hypothalamus and midbrain the concentrations of 5-HT, its main metabolite, 5-hydroxyindole acetic acid (5-HIAA), and TPH activity were assayed in using HPLC, while Tph1 and Tph2 mRNA were quantified by quantitative real-time RT-PCR. Dramatic increase of spleen mass and decrease of thymus mass 5 days after LPS administration was shown. Significant increase of 5-HT and 5-HIAA levels in midbrain as well as decrease of 5-HIAA concentration and TPH activity in hypothalamus in mice treated with LPS and saline compared with intact animals was revealed. The highest concentration of Tph2 gene mRNA was observed in midbrain in 5-HT neuron bodies, while in this gene mRNA level was lower in 5-HT endings (cortex, hippocampus, striatum and hypothalamus). Trace amounts of Tph1 mRNA was revealed in all studied brain structures in mice of the three groups. Thus, Tph1 gene expression in the mouse brain is too low to significantly affect 5-HT synthesis in normal conditions and during inflammation.
Modern Approaches of Protein Engineering for the Creation of Enzymes with New Catalytic Properties
Authors: Tyugashev T. E. , Fedorova O. S. , Kuznetsov N. A.
Published: April 2024

Adenine-DNA-glycosylase MutY is a monofunctional enzyme and catalyzes the hydrolysis of N-glycosidic bonds with adenine residues located opposite 8-oxonuanine residues in DNA. A rational design of mutant forms of the enzyme with altered catalytic activity was carried out. An analysis of the structures of mutant forms of MutY calculated by the molecular dynamics method led to the conclusion that some mutant forms of MutY, in addition to hydrolysis of the N-glycosidic bond, may have AP-lyase activity, as in the case of bifunctional DNA glycosylases. Mutant forms of MutY containing substitutions A120K or S124K were obtained by site-directed mutagenesis, and their catalytic activity was determined. It was shown that the S120K substitution leads to the appearance of additional AP-lyase activity, while the A124K substitution completely inactivates the enzyme.
DNA Sequence-Specific Ligands. XIX. Synthesis, Spectral Properties, Virological and Biochemical Studies of Fluorescent Dimeric Trisbenzimidazoles DB3(n)
Authors: Arutyunyan A. F. , Kostyukov A. A. , Korolev S. P. , Gottikh M. B. , Susova O. Yu. , Kaluzhny D. N. , Zhuze A. L.
Published: April 2024

In this work, we synthesized and characterized the properties of a series of new fluorescent narrow-groove ligands DB3(n). DB3(n) compounds based on dimeric trisbenzimidazoles have the ability to bind to the AT regions of DNA. The synthesis of DB3(n), trisbenzimidazole fragments of which are linked by oligomethylene linkers of different lengths (n = 1, 5, 9), is based on the condensation of monomeric trisbenzimidazole MB3 with α,ω-alkyldicarboxylic acids. DB3(n) proved to be effective inhibitors of the catalytic activity of HIV-1 integrase at submicromolar concentrations (0.20–0.30 µM). DB3(n) was found to inhibit the catalytic activity of DNA topoisomerase I at low micromolar concentrations.
EBF1 Promotes the Sensitivity of Cervical Cancer Cells to Cisplatin via Activating FBN1 Transcription
Authors: Shen N. N. , Lin J. H. , Liu P. P.
Published: April 2024

Cisplatin (DDP) is widely used in the chemotherapy of cervical cancer (CC), the fourth most common female malignancy worldwide. However, some patients progress to chemotherapy resistance, which leads to chemotherapy failure, tumor recurrence, and poor prognosis. Therefore, strategies to identify the regulatory mechanisms underlying CC development and increase tumor sensitivity to DDP will help improve patient survival. This research was designed to ascertain the mechanism of EBF1-dependent regulation of FBN1 which promotes chemosensitivity of CC cells. The expression of EBF1 and FBN1 was measured in CC tissues resistant or sensitive to chemotherapy and in DDP-sensitive or -resistant cells (SiHa and SiHa-DDP cells). SiHa-DDP cells were transduced with lentiviruses encoding EBF1 or FBN1 to evaluate the influence of these two proteins on cell viability, expression of MDR1 and MRP1, and cell aggressiveness. Moreover, the interaction between EBF1 and FBN1 was predicted and demonstrated. Finally, to further verify the EBF1/FB1-dependent mechanism of DDP sensitivity regulation in CC cells a xenograft mouse model of CC was established using SiHa-DDP cells transduced with lentiviruses carrying EBF1 gene and shRNA directed to FBN1.EBF1 and FBN1 showed decreased expression in CC tissues and cells, particularly in those resistant to chemotherapy. Transduction of SiHa-DDP cells with lentiviruses encoding EBF1 or FBN1 lead to decreased viability, IC50, proliferation capacity, colony formation ability, aggressiveness, and increased cell apoptosis. We have shown that EBF1 activates FBN1 transcription by binding to FBN1 promoter region. Additionally, it was revealed that FBN1 silencing reversed the promoting effect of EBF1 overexpression on chemosensitivity of CC cells in vivo. EBF1 facilitated chemosensitivity in CC cells by activating FBN1 transcription.
DNA Fragment Enrichment for High-Throughput Sequencing
Authors: Sinyakov A. N. , Kostina E. V.
Published: April 2024

Application of oligonucleotides, mainly obtained using new generation DNA synthesizers (microarray DNA synthesizers), for the enrichment of targeted genomic fragments are described. Methods of molecular hybridization, polymerase chain reaction and CRISPR-based methods for targets enrichment are considered. Examples of the practical use of the developed methods for research and diagnostic purposes are given.
Differential Expression of a Foreign Gene in Arabidopsis Mitochondria in organello
Authors: Tarasenko V. I. , Tarasenko T. A. , Gorbenko I. V. , Konstantinov Yu. M. , Koulintchenko M. V.
Published: April 2024

Genetic transformation of higher eukaryotes mitochondria in vivo is one of the unresolved and important problems. For efficient expression of foreign genetic material in mitochondria, it is necessary to select regulatory elements that ensure a high level of transcription and transcript stability. This work is aimed at studying the effectiveness of regulatory elements of mitochondrial genes flanking exogenous DNA using the phenomenon of natural competence of plant mitochondria. For this purpose, genetic constructs carrying the GFP gene under the control of the promoter regions of the RRN26 or COX1 genes and one of the two 3'-untranslated regions (3'-UTR) of mitochondrial genes were imported into isolated Arabidopsis mitochondria, followed by transcription in organello. It was shown that the level of GFP expression under the control of promoters of the RRN26 or COX1 genes in organello correlates with the level of transcription of these genes observed in vivo. At the same time, the presence of the tRNAТrp sequence in the 3'-UTR leads to a higher level of the GFP transcript than the presence in this region of the 3'-UTR of the NAD4 gene containing the binding site of the MTSF1 protein. The results obtained open up prospects for creating a system for efficient transformation of the mitochondrial genome.
Type II CRISPR-Cas System Nucleases: a Pipeline for Prediction and in vitro Characterization
Authors: Vasileva А. A. , Aliukas S. A. , Selkova P. A. , Arseniev A. N. , Chernova V. E. , Musharova O. S. , Klimuk E. I. , Khodorkovskii M. A. , Severinov K. V.
Published: April 2024

The use of CRISPR-Cas bacterial adaptive immunity systems components for targeted DNA changing has opened broad prospects for programmable genome editing of higher organisms. The most widely used gene editor-s are based on the Cas9 effectors of the type II CRISPR-Cas systems. In complex with guide RNAs, Cas9 proteins are able to directionally introduce double-strand breaks into DNA regions complementary to guide RNA sequences. Despite the wide range of characterized Cas9s, the search for new Cas9 variants remains an actual task, since the available Cas9 editors have several limitations. This paper presents a workflow for the search and subsequent characterization of new Cas9 nucleases developed in our laboratory. Detailed protocols describing the bioinformatical search, cloning and isolation of recombinant Cas9 proteins, testing for nuclease activity in vitro, and determining the PAM sequence required for recognition of DNA targets, are presented. Potential difficulties that may arise, as well as ways to overcome them, are considered.
The Profile of microRNA Expression in Diffuse Large B-Cell Lymphoma
Authors: Veryaskina Yu. A. , Titov S. E. , Kovynev I. B. , Fyodorova S. S. , Shebunyaeva Ya. Yu. , Antonenko O. V. , Pospelova T. I. , Zhimulev I. F.
Published: April 2024

Non-Hodgkin’s lymphoma (NHL) is a heterogeneous group of cancers characterized by different pathogenesis and prognosis. The main methods for treating NHL are chemotherapy, immunochemotherapy, and radiation therapy; however, most of these cancers are known to be chemoresistant or return rapidly after the short chemotherapy-induced remission. Therefore, searching for alternative cytoreductive therapy options is quite relevant today. Aberrant microRNA (miRNA) expression is one of the mechanisms responsible for the emergence and progression of lymphoid malignancies. This study was aimed at identifying the miRNA expression profile in diagnostic biopsy specimens harvested from the lymph nodes affected by diffuse large B-cell lymphoma (DLBCL) and identifying miRNA markers, which can potentially be used to design a novel type of ta-rgeted anticancer drugs that would allow one to achieve maximum therapy personalization and increase its efficacy. The key study objects were histological specimens harvested from the lymph nodes by excisional d-iagnostic biopsy and treated using the conventional histomorphological formalin fixation methods. The study group consisted of patients with DLBCL (n = 52). The biopsy specimens harvested from patients with reactive lymphadenopathy (RL) (n = 40) constituted the control group. The miR-150 expression level was reduced over 12-fold (p = 3.6 × 10‒15) compared to that in the tissues of non-cancerous nodular masses. B-ioinformatic analysis revealed that miR-150 is involved in regulation of hematopoiesis and lymphopoiesis. The findings obtained in this study allow considering miR-150 a promising therapeutic target having a great potential for clinical applications.
Exploring the Prognostic Features of Hepatocellular Carcinoma via Text Mining and Data Analysis
Authors: Yang Z. H. , Wang S. X.
Published: April 2024

Transcatheter arterial chemoembolization is one of the interventional treatments for hepatocellular carcinoma (HCC). This treatment is generally used for patients with intermediate to advanced hepatocellular carcinoma, and identifying the role of HCC-related genes can help improve the efficiency of transcatheter arterial chemoembolization. To investigate the role of HCC-related genes and to provide valid evidence for transcatheter arterial chemoembolization treatment, we performed a comprehensive bioinformatics analysis. Through text mining (“hepatocellular carcinoma”) and microarray data analysis (GSE104580), we obtained a standard gene set, which was followed by gene ontology and Kyoto Gene and Genome Encyclopedia analysis. The significant 8 genes clustered in protein-protein interactions network were chosen to be used in the follow-up analysis. Through survival analysis low expression of the key genes were found to be strongly associated with survival in HCC patients in this study. The correlation between the expression of the key genes and tumor immune infiltration was assessed by Pearson correlation analysis. As a result, 15 drugs targeting seven of the eight genes have been identified, and therefore can be considered as potential components for transcatheter arterial chemoembolization treatment of HCC.
Development of a Series of Neutralizing Nanobodies against SARS-CoV-2 Spike Protein
Authors: Zhuchkov V. A. , Ivanov S. V. , Kravchenko J. E. , Chumakov S. P.
Published: April 2024

Countering the spread of new respiratory infections and reducing the damage they cause to society requires efficient strategies for rapid development of targeted therapeutics, such as monoclonal antibodies. Nanobodies, defined as variable fragments of heavy-chain camelid antibodies, have a set of characteristics that make them particularly convenient for this purpose. The speed at which the SARS-CoV-2 pandemic had spread has confirmed that a key factor in the development of therapeutics is obtaining highly effective blocking agents as soon as possible, as well as the diversity of epitopes to which these agents bind. We have optimized the process of selection of blocking nanobodies from the genetic material of camelids and obtained a panel of nanobody structures with affinity to spike protein in the lower nanomolar and picomolar ranges and high binding specificity. The subset of nanobodies that demonstrate the ability to block the interaction between the spike protein and the cellular ACE2 receptor was selected in experiments in vitro and in vivo. It has been established that the epitopes bound by the nanobodies are located in the RBD domain of the spike protein and have little overlap. The diversity of binding regions may allow the mixture of nanobodies to retain potential therapeutic efficacy towards new variants of the spike protein, and the structural features of nanobodies, in particular, their compact size and high stability, indicate the possibility of their utilization in the form of aerosols.