bluuebunny/crossref_metadata_2025 huggingface dataset:
A formação do sentido como produto da atividade semiótica
Authors: Aparecida Ferreira da Costa Selma
Published: April 2024

Este artigo apresenta parte de uma pesquisa de Doutorado cuja finalidade é analisar as formas como a criança se apropria dos significados culturais convencionalmente elaborados pela sociedade, convertendo-os em sentidos pessoais, tendo a linguagem como mediadora deste processo. A compreensão acerca do modo como acontece a conversão do social e o cultural e a dinâmica deste processo na formação das funções psíquicas superiores torna-se relevante para a compreensão do conceito de mediação semiótica. Elucidar o modo como a criança utiliza a palavra em situações que lhes exigissem a formação de um conceito de significação e a generalização desse processo na comunicação com o outro social, nos fornece elementos para organizar situações sociais de desenvolvimento do pensamento efetivamente desenvolventes. A análise subsidia-se no método instrumental histórico genético e na Teoria Histórico-Cultural, com a finalidade de ressaltar o papel da linguagem na formação das funções psíquicas superiores. Os resultados revelaram que o processo de significação, mediado pela palavra, a partir de experiências culturais vivenciadas, possibilita à criança o desenvolvimento do pensamento verbal, e ascender da percepção imediata de objetos e fenômenos à percepção compreensiva da realidade circundante.
FORMATION OF SELF-EDUCATIONAL COMPETENCE OF FUTURE FOREIGN LANGUAGE TEACHERS IN THE PROCESS OF PROFESSIONAL TRAINING
Authors: Baidiuk Oleksandra
Published: April 2024

The article addresses a critical aspect of teacher education. It emphasizes the significance of self-educational competence in future foreign language teachers, a fundamental component in adapting to the rapidly changing educational environment and meeting international educational standards. The research highlights the necessity for teachers to continuously develop their qualifications and competence through active independent work, especially in learning modern teaching methodologies and improving language and methodological preparation.The article bases its research on ideas presented in the works of domestic and foreign scientists regarding the theoretical and methodological foundations of teacher training, professional self-development, and self-realization. Fundamental studies exploring the concept of “self-educational competence,” its nature, and essence are also of considerable scientific and practical value.The concept of “self-educational competence” is considered as an integrated quality of personality, manifested in the presence of structured and organized knowledge, skills, abilities in self-education, motivation for improvement, experience in independent activity, interest in continuous self-improvement, and value orientations that allow individuals to effectively solve tasks of self-realization, self-education, and self-development.The integration of modern information technologies in the process of learning foreign languages contributes to the formation of self-educational competence in future English teachers and enhances the effectiveness of learning.The purpose of the article is to analyze the essence of self-education competence of future foreign language teachers, to reveal competencies that demonstrate a high level of its formation.Materials and methods: theoretical – analysis, synthesis, comparison, generalization, systematization of scientific research.
Characterization of physical and chemical properties of honey from Northeastern Anatolia of Türkiye
Authors: Kılıç Altun Serap , Aydemir Mehmet Emin
Published: April 2024

The aim of this study was to investigate the physical and chemical properties of natural highland honey produced in the northeastern Anatolia region of Turkey. In 2020, 24 honey samples collected and sold during the honey harvest season were purchased from local vendors. Moisture, color, acidity, pH, conductivity, diastase and invertase activity, C13, C13 protein-honey, C4 analysis and sugar components were analyzed in honey samples. The honey samples were found to contain 17.4% moisture. The mean invertase level were found to be 156.216 U/kg. The freshness and enzymatic activity of the honey were shown by the average diastase number of 12.8 DS. The mineral content and overall purity of the honey was indicated by an electrical conductivity value of 0.17 mS/cm. The average acidity value 15.9 meq/kg, fructose/glucose ratio 1.26% and the average color value 33 mm Pfund determined. The average sugar contents in the honey samples were as follows: fructose 37.4%, glucose 29.5%, sucrose 1.4%, turanose 1.8%, maltose 0.6%, isomaltose 0.2%, erlose 0.3%, trehalose 0% hybriditose 0% maltotriose 0% fructose+glucose. 66.9%, fructose/glucose 1.26, glucose/water 2.0. The mean difference between honey protein and honey delta C13 data is -0.58 and C4 sugar ratio is 0. In conclusion, valuable findings were obtained on the physical and chemical properties of honey from the northeastern Anatolia region of Turkey. Further research can build on these findings to explore the unique properties and potential benefits of honey from this region and contribute to its value and utilization in various industries.
Local Factors of Coastal-Marine Rare-Metal-Titanium Placers Formation
Authors: Lalomov A. V.
Published: April 2024

Local factors of formation of coastal-marine rare-metal-titanium placers were analyzed for creation of the search-oriented geological-dynamic model that allows predicting the prospects of rare-metal-titanium placer mineralization. The influence of the factors on the structure, composition, localization of placer concentrations within sedimentation basins, as well as the dynamic interaction of these factors during the formation of productive sediments was investigated. Based on the work of previous researchers who have studied in detail the issues of controlling the formation of these placers at the historical-geological and regional structural-tectonic level, a qualitative model of the formation of placer concentrations on local areas of the rank of districts, clasters, fields and specific placer bodies has been created, which can be the basis for creation of search-orientated model of the deposit and planning exploration and evaluation work. The following factors of the placer formation were studied: hydrodynamic – characterizing the types and mechanisms of placer concentrations (littoral and sublittoral) within the dynamically active coastal zone; lithodynamic – depending on the abrasion-accumulative regime of the coast and the parameters of the long-shore sediment flow; structural–dynamic – determining the possibility of the formation of economically significant productive deposits and their localization; and the factor of transgressive-regressive regime a basin that determines the structure of placer bodies and their transformation at the post-sedimentation stage. Large economically significant rare-metal-titanium placer deposits are formed only in conditions of joint realization of the positive potential of these factors. The developed qualitative model can serve as a basis for the process of digitalization of the forecasting of placer mineralization of this type.
Mineral Indicators of Hydrothermal Activity in the Surface Layer of Bottom Sediments of the Pobeda Hydrothermal Cluster (17°44.9′‒17°07.6′ N MAR)
Authors: Lyutkevich A. D. , Gablina I. F. , Narkevsky E. V. , Dobretsova I. G. , Kiselev A. A. , Gor’kova N. V.
Published: April 2024

The work is devoted to the study of ore minerals of the surface horizon of ore-bearing sediments of the Pobeda hydrothermal cluster. The following methods were used: optical microscopy, scanning electron microscopy, and X-ray spectral microanalysis. It was found that ore minerals are represented by fragments of copper and iron sulfides (isocubanite, chalcopyrite, and pyrite), newly formed iron hydroxides, and atacamite. In addition, barite and edaphogenic material in the form of silicate clasts, sometimes with sulfide inclusions, are present. Structural and morphological types of iron hydroxides are distinguished. On the basis of hydrophysical data, the location of the assumed active hydrothermal source in the area of the Pobeda-3 ore occurrence was updated. The distribution of studied minerals depending on the location relative to active hydrothermal vents is described. A decrease in the size and amount of hydrothermal mineral clasts and edaphogenic material and an increase in the degree of sulfide replacement by iron hydroxides were observed at a distance from the sources. Also, a decrease in the Cu/Fe ratio in the chemical composition of copper and iron sulfides is observed when moving away from the source. An unidentified phase of Cu3.57‒4.22Fe1.71‒2.19S4.99‒5.31 with lamellae of chalcopyrite inclusions was established in the surface horizon of the column at 37L245g.
A Method to Generate Complex Predictive Features for ML-Based Prediction of the Local Protein Structure
Authors: Milchevskiy Y. V. , Milchevskaya V. Y. , Kravatsky Y. V.
Published: April 2024

Recently, the prediction of protein structure and function from its sequence underwent a rapid increase in performance. It is primarily due to the application of machine learning methods, many of which rely on the predictive features supplied to them. It is thus crucial to retrieve the information encoded in the amino acid sequence of a protein. Here, we propose a method to generate a set of complex yet interpretable predictors, which aids in revealing factors that influence protein conformation. The proposed method allows us to generate predictive features and test them for significance in two scenarios: for a general description of the protein structures and functions, as well as for highly specific predictive tasks. Having generated an exhaustive set of predictors, we narrow it down to a smaller curated set of informative features using feature selection methods, which increases the performance of subsequent predictive modelling. We illustrate the effectiveness of the proposed methodology by applying it in the context of local protein structure prediction, where the rate of correct prediction for DSSP Q3 (three-class classification) is 81.3%. The method is implemented in C++ for command line use and can be run on any operating system. The source code is released on GitHub: https://github.com/Milchevskiy/protein-encoding-projects.
Identification of Stigma-Specific Expression Fragment in the Promoter of the Soybean Chitinase Class I Gene
Authors: Zhao C. M. , Hou H. , Xing M. G. , Xue R.-G.
Published: April 2024

The expression level of heterologous genes in transgenic plants serves as an important indicator of gene efficiency. The small number of currently known effective promoters, limits the possibilities in fine-tuning the expression of transgenes. We cloned and characterized a tissue-specific promoter fragment of the soybean chitinase class I gene (GmChi1). The GmChi1 promoter (GmChi1P) was cloned from Jungery soybean. The promoter sequence contains a number of putative cis-acting elements, including tissue-specific and stress-regulated motifs. By histochemical analysis, the GmChi1P-controlled β-glucuronidase (GUS) reporter enzyme activity was shown to be highest in the roots of transgenic Nicotiana tabacum cv. NC89 at the four-leaf sprout formation stage. Interestingly, the high GUS activity in transgenic tobacco roots was effectively suppressed by salicylic acid (SA) treatment. Deletion analysis of GmChi1P revealed that the sequences located between positions ‒719 and ‒382 contain key cis-elements responsible for the reporter uidA gene expression (encoding GUS) in leaves, roots, and wounds of Nicotiana tabacum. In addition, fluorometric analysis showed that the activity of the shortened ChiP(‒1292) to ChiP(‒719) promoters in the roots of transgenic tobacco was significantly suppressed by abscisic acid and completely suppressed by SA. The ChiP(‒382) promoter was also found to be expressed exclusively in the stigma of transgenic tobacco flowers. Using the GUS reporter enzyme, no staining was detected in other flower organs in transgenic Nicotiana tabacum, including sepals, petals, anthers, filaments, and ovaries, or in any vegetative tissues. The results indicate that the promoter fragment ChiP(‒382) can be used in tissue-specific regulation of gene expression and plant genetic engineering.
Geometric Approach to Phylogeographic Analysis Molecular Genetic Sequences: Principal Components and Dendrograms
Authors: Efimov V. M. , Efimov K. V. , Kovaleva V. Yu.
Published: April 2024

Currently, the search for manifestations of selection under the influence of the environment in molecular sequences is usually carried out within closely related species or at the intraspecific level. It is believed that at high taxonomic levels this is unpromising due to phylogenetic relationship. Cytochrome b amino acid sequences of 67 rodent and lagomorph species with known geographic coordinates were digitized using the AAindex database. Based on more than 200 thousand features, the main components were obtained. A well-known statistical method, which has not previously been used for such problems, was used, which makes it possible to orthogonally decompose multidimensional variability into intra- and intertaxon variability and analyze them separately. Subfamily level selected. For the second principal component (17.05% of intertaxon variability), a correlation with latitude was found (r = 0.561; n = 67; p E–5). The clear division into two groups revealed by the first principal component (39.48% of intertaxon variability), which does not coincide with the taxonomic one, indicates a possible physicochemical underlying reason for the differences between them. This requires further research.
Genotype-Specific Features of Cold-Induced Sweetening Process Regulation in Potato Varieties Nikulinsky, Symphony, Nevski
Authors: Egorova A. A. , Saboiev I. A. , Kostina N. E. , Kuvaeva D. D. , Shcherban A. B. , Ibragimova S. M. , Salina E. A. , Kochetov A. V.
Published: April 2024

Increasing the shelf life of potato tubers demands their storage under low temperature. However, storage at low temperatures causes activation of cold-protective mechanism, so-called cold-induced sweetening (CIS). During this process, the starch is converted into reducing sugars such as glucose and fructose. Upon processing at high-temperature, these sugars react with free amino acids, resulting in brown, bitter-tasting products, which reduces the consumer value of potatoes. In this study, we performed expression analysis of genes associated with cold-induced sweetening in potato tubers: vacuolar invertase (Pain-1), sucrose-synthase (SUS4), invertase inhibitor (InvInh2). Potato varieties Nikulinsky, Symphony, Nevski were used. All three varieties were found to accumulate sugars at low temperatures, the maximum accumulation of reducing sugars being observed at 4°C. It was found that the expression pattern of genes associated with cold-induced sweetening differs depending on the variety and storage duration. The increased expression of vacuolar invertase and its inhibitor is more pronounced at the beginning of storage period while the increased expression of sucrose synthase is more pronounced after three months of storage. At early storage periods, high expression of invertase and low expression of inhibitor is observed in Dutch variety Symphony, and vice versa in Russian varieties Nikulinsky and Nevsky. The participation of the studied genes in the process of cold-induced sweetening is discussed.
Influence of Usnic Acid Derivative (Tyrosyl-DNA Phosphodiesterase 1 Inhibitor) on Transplanted Tumors in vivo as a Monotherapy and in Combination with Olaparib
Authors: Kornienko Т. Е. , Zakharenko А. L. , Ilina Е. S. , Chepanova А. А. , Zakharova О. D. , Dyrkheeva N. S. , Popova N. А. , Nikolin V. P. , Filimonov А. S. , Luzina О. А. , Salakhutdinov N. F. , Lavrik О. I.
Published: April 2024

Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a DNA repair enzyme that removes various adducts from the 3'‑end of DNA. Such damage is formed, for example, under the action of enzymes that introduce single-strand breaks in DNA during catalysis (for example, topoisomerase 1), as well as a number of anticancer drugs with different mechanisms of action. Poly(ADP-ribose) polymerase 1 (PARP1) is an enzyme that catalyzes the post-translational modification of various targets (PARylation), and with its help controls many processes in the cell, including DNA repair. The target of PARP1 is also Tdp1, whose PARylation attracts Tdp1 to the site of DNA damage. Olaparib is a PARP1 inhibitor used in clinical practice to treat homologous recombination deficient tumors. The main mechanism of action of olaparib is to obstruction of PARylation and thus DNA repair. In this study, we used the Tdp1 inhibitor OL7-43 in combination with olaparib to increase the antitumor effect of the latter. Despite the increase in cytotoxicity of olaparib in the presence of OL7-43 in vitro, we did not find a sensitizing effect of this compound in the Lewis and Krebs-2 carcinoma models, but it showed its own antitumor and antimetastatic effects.
Mechanism of the CRISPR/Cas9 System Specificity in Genome Editing
Authors: Kulishova L. M. , Vokhtantsev I. P. , Kim D. V. , Zharkov D. O.
Published: April 2024

The recently discovered CRISPR/Cas9 system based on the action of complementary targeted nucleases and originally intended to protect bacteria from foreign genetic elements has become a convenient tool for manipulating the genomes of living cells. The CRISPR/Cas9 genomic editing technology has moved beyond the laboratory and is already finding application in biotechnology and agriculture. However, the use of this method for editing human cells for medical purposes is limited by CRISPR/Cas9 system off-target activity, which can lead to oncogenic mutations. Therefore, many studies aim to develop variants of the CRISPR/Cas9 system with improved accuracy. The review highlights the mechanisms of precise and erroneous action of the RNA-guided nuclease Cas9, natural and artificially created variants of RNA-targeted nucleases, possibilities to modulate their specificity through guide RNA modifications, and other approaches to increase the accuracy of the CRISPR/Cas9 system in genome editing.
Recombinase Polymerase Amplification for Rapid Detection of Human Bacterial Pneumonia Pathogens
Authors: Lapa S. A. , Surzhikov S. A. , Blagodatskikh S. A. , Shershov V. E. , Chudinov A. V.
Published: April 2024

A diagnostic system based on recombinase polymerase amplification (RPA) has been developed to identify six bacterial pathogens of human pneumonia. Species-specific primers have been designed and optimized to conduct a multiplex reaction in one common volume. Labeled primers were used for reliable discrimination of amplification products close in size. Identification of the pathogen was carried out by visual analysis of the electrophoregram. The analytical sensitivity of the developed multiplex RPA was 102‒103 copies of DNA. The specificity of the system was determined by the absence of cross-amplification of the studied DNA samples of pneumonia pathogens for each pair of primers, as well as for the DNA of Mycobacterium tuberculosis H37rν, and amounted to 100%. The analysis execution time is less than an 1 h, including electrophoretic reaction control. The test system can be used in specialized clinical laboratories for rapid analysis of samples from patients with suspected pneumonia.
Improvement of Crops Using the CRISPR/Cas System: New Target Genes
Authors: Ukhatova Y. V. , Erastenkova M. V. , Korshikova E. S. , Krylova E. A. , Mikhailova A. S. , Semilet T. V. , Tikhonova N. G. , Shvachko N. A. , Khlestkina E. K.
Published: April 2024

Successful application of the CRISPR/Cas genome editing system to various crops largely depends on the correct choice of target genes that may be purposefully changed to improve yield, quality, and resistance to biotic and abiotic stressors. The objective of this work was systematizing and cataloguing the information on the confirmed target genes for crop improvement. The latest systematic review was presented on peer-reviewed scientific papers (indexed in the Scopus database) published before August 17, 2019. The present study covers the period from August 18, 2019 to March 15, 2022. The search according to the given algorithm revealed 2090 publications, and their analysis showed that only 685 original papers contained the results of gene editing for 28 crops (the search included 56 crops). A significant part of these publications described the application of genome editing to target genes previously identified in similar works or the studies were associated with reverse genetics, while only 136 publications contained data on editing new target genes whose modification was aimed at improving plant traits important for breeding. The total number of target genes in cultivated plants that were edited to improve properties of breeding value over the entire period of the CRISPR/Cas system application was 287. A detailed analysis of the editing of new target genes is presented in this review. The studies were most often aimed at increasing plant productivity and disease resistance as well as improving the properties of plant materials. Observations are made whether it was possible to obtain stable transformants at the time of publication and whether the editing technique was applied to non-model cultivars. For a number of crops, however, the range of modified cultivars was significantly expanded, specifically for wheat, rice, soybean, tomato, potato, rapeseed, grapevine, and maize. In a vast majority of cases, agrobacterium-mediated transformation was used to deliver the editing construct; less often it was bioballistics, protoplast transfection or haploinducers. The desired change in traits was most often achieved by gene knockout. In some cases, knockdown and nucleotide substitutions were applied. The base-editing and prime-editing approaches have increasingly been used to make nucleotide substitutions in crop genes. The emergence of a convenient CRISPR/Cas editing system helped to significantly intensify the development of molecular genetics specific to many crop species.
Effects of Peroxisome Proliferator-Activated Receptor γ on Modulating Angiopoietin-Like Protein 4 Synthesis in Caco-2 Cells Exposed to Clostridium butyricum
Authors: Zhao X. , Huang H. S. , Shi S. R.
Published: April 2024

Angiopoietin-like protein 4 (ANGPTL4) is considered to be one of the important circulating mediators linking intestinal microorganisms and host lipid metabolism. The objective of this study was to assess the effects of peroxisome proliferator-activated receptor γ (PPARγ) on modulating ANGPTL4 synthesis in Caco-2 cells exposed to Clostridium butyricum. The viability of Caco-2 cells and the expression of PPARγ and ANGPTL4 in Caco-2 cells were detected after the Caco-2 cells were co-cultured with C. butyricum at the concentration of 1 × 106, 1 × 107 and 1 × 108 CFU/mL. The results showed that cell viability was enhanced by C. butyricum. Besides, PPARγ and ANGPTL4 expression and secretion in Caco-2 cells was significantly increased by 1 × 107 and 1 × 108 CFU/mL of C. butyricum. Furthermore, the effects of PPARγ on modulating ANGPTL4 synthesis in Caco-2 cells regulated by 1 × 108 CFU/mL of C. butyricum was also be expounded in PPARγ activation/inhibition model based on Caco-2 cells and via ChIP technique. It was found that C. butyricum promoted the binding of PPARγ to the PPAR binding site (chr19: 8362157-8362357, located upstream of the transcriptional start site of angptl4) of the angptl4 gene in Caco-2 cells. However, the PPARγ was not the only way for C. butyricum to stimulate ANGPTL4 production. Taken together, PPARγ played a role in the regulation of ANGPTL4 synthesis by C. butyricum in Caco-2 cells.
Spatial Reconstruction of TRPC-Mechanoreceptors of the Ctenophore Mnemiopsis leidyi A. Agassiz, 1865
Authors: Kuznetsov A. V. , Vtyurina D. N.
Published: April 2024

Ctenophore Mnemiopsis leidyi A. Agassiz, 1865 responds to gentle mechanical stimulation with intense luminescence; however, the mechanism of this phenomenon is unknown. We searched for possible mechanosensitive receptors that initiate signal transduction resulting in photoprotein luminescence. The three ortholog genes of mouse (5z96) and Drosophila (5vkq) TRPC-proteins, such as ML234550a-PA (860 aa), ML03701a-PA (828 aa) and ML038011a-PA (1395 aa), were found in the M. leidyi genome. The latter protein contains a long ankyrin helix consisting of 16 ANK domains. Study of the annotated domains and the network of interactions between the interactome proteins suggests that the ML234550a-PA and ML03701a-PA proteins carry out cytoplasmic, but ML038011a-PA provides intranuclear transduction of mechanical signals. Spatial reconstruction of the studied proteins revealed differences in their structure, which may be related to various functions of these proteins in the cell. The question of which of these proteins is involved in the initiation of luminescence after mechanical stimulation is discussed.
IL-8 Links NF-κB and Wnt/β-Catenin Pathways in Persistent Inflammatory Response Induced by Chronic Helicobacter pylori Infection
Authors: Lin L. , Xie B. , Shi J. , Zhou C. M. , Yi J. , Chen J. , He J. X. , Wei H. L.
Published: April 2024

Helicobacter pylori (H. pylori) infection can cause persistent inflammatory response in human gastric mucosal epithelial cells, which may result in the occurrence of cancer. However, the underlying mechanism of carcinogenesis has not been elucidated yet. Herein, we established the models of chronic H. pylori infection in GES-1 cells and C57BL/6J mice. Interleukin 8 (IL-8) level was detected by ELISA. The expression of NF-κB p65, IL-8, Wnt2 and β-catenin mRNA and proteins was evaluated by real-time PCR, Western blotting, immunofluorescence staining, and immunohistochemistry. The infection of H. pylori in mice was evaluated by rapid urease test, HE staining and Warthin‒Starry silver staining. The morphological changes of gastric mucosa were observed by electron microscopy. Our results showed that in H. pylori infected gastric mucosal cells along with activation of NF-κB signaling pathway and increase of IL-8 level, the expression of Wnt2 was also increased significantly, which preliminarily indicates that IL-8 can positively regulate the expression of Wnt2. Studies in chronic H. pylori infected C57BL/6J mice models showed that there was an increased incidence of premalignant lesions in the gastric mucosa tissue. Through comparing changes of gastric mucosal cell ultrastructure and analyzing the relationship between NF-κB signaling pathway and Wnt2 expression, we found that H. pylori infection activated NF-κB signal pathways, and the massive release of IL-8 was positively correlated with the high expression of Wnt2 protein. Subsequently, the activated Wnt/β-catenin signal pathways may be involved in the malignant transformation of gastric mucosal cells. Collectively, H. pylori chronic infection may continuously lead to persistent inflammatory response: activate NF-κB pathway, promote IL-8 release and thereby activate Wnt/β-catenin pathway. IL-8 probably plays an important role of a linker in coupling these two signal pathways.
Assembly and Disassembly of Nuclear Pore Complex: a View from Structural Side
Authors: Orlova А. V. , Georgieva S. G. , Kopytova D. V.
Published: April 2024

Nucleocytoplasmic exchange in the cell occurs through the nuclear pore complexes (NPCs). NPCs are large multiprotein complexes with octagonal symmetry about their axis and imperfect mirror symmetry about a plane parallel with the nuclear envelop (NE). NPC fuses the inner and outer nuclear membranes and opens up а channel between nucleus and cytoplasm. NPC is built of nucleoporins. Each nucleoporin occurs in at least eight copies per NPC. Inside the NPC forms a permeability barrier by which NPC can ensure fast and selectable transport of molecules from one side of nuclear membrane to another. NPC architecture is based on hierarchical principle of organization. Nucleoporins are integrated into complexes that oligomerizes into bigger octomeric high-order structures. These structures are the main components of NPC. In the first part of this work the main attention is paid to NPC structure and nucleoporins’ properties. The second part is dedicated to mechanisms of NPC assembly and disassembly at different stages of cell cycle.
The Effect of Adiporon on Lipid Metabolism Genes Expression in Human Macrophages
Authors: Pobozheva I. A. , Dracheva K. V. , Pchelina S. N. , Miroshnikova V. V.
Published: April 2024

Atherosclerosis is characterized by excessive uptake of cholesterol-rich low-density lipoproteins by the vascular wall macrophages. It leads to macrophage transformation into foam cells, accumulation of lipids in the intima of the arteries, atherosclerotic plaques development and following progression of cardiovascular diseases. Adiponectin, adipose tissue adipokine, has anti-atherogenic and anti-inflammatory effects that are mediated through binding to its receptors – AdipoR1 and AdipoR2. One of the mechanisms of adiponectin anti-atherogenic activity may be the participation in the regulation of reverse cholesterol transport and prevention of foam cells formation. We assumed that AdipoRon, a small-molecule adiponectin receptor agonist, could modulate the reverse cholesterol transport and inflammation genes expression in human macrophages. The aim of the present study was to investigate the effect of various concentrations of AdipoRon on the lipid metabolism ABCA1, ABCG1, APOA1, NR1H3 (LXRα), NR1H2 (LXRβ), PPARG, ACAT1 genes expression and inflammation IL6, TNFA, TLR4 genes expression in human macrophages. Primary human macrophages and THP-1 macrophages cell line were treated with various concentrations of AdipoRon. Cell viability was measured using the MTS assay. ABCA1, ABCG1, APOA1, NR1H3, NR1H2, PPARG, ACAT1, IL6, TNFA, TLR4 mRNA levels in the primary human macrophages was assessed using real-time PCR. The increase of PPARG and ABCA1 mRNA levels was shown in the primary human macrophages after 5 and 10 μM A-dipoRon treatment for 24 h. At the same time high concentration (20 μM) of AdipoRon has cytotoxic effect on macrophages, especially, on THP-1 cell line. The effect of AdipoRon on human macrophages and the investigation of potential adiponectin receptor agonists is of interest, due to the search for new approaches to the prevention and treatment of atherosclerosis.
Alternative Mechanisms of Mutagenesis at mCpG Sites during Replication and Repair
Authors: Shilkin E. S. , Petrova D. V. , Zharkov D. O. , Makarova A. V.
Published: April 2024

5-Methyl-2'-deoxycytidine (mC) at CpG sites plays a key role in the epigenetic gene function regulation, cell differentiation and carcinogenesis. Despite the importance of mC for normal cell function, CpG dinucleotides are known as mutagenesis hotspots. mC is deaminated with the formation of T, causing C→T transitions. However, several recent studies demonstrated the effect of epigenetic modifications of C on the fidelity and efficiency of DNA polymerases and excision repair enzymes. This review summarizes the known data indicating the existence of mutagenesis mechanisms independent of deamination at CpG sites.
Identification of Clinical Isolates of Bacillus cereus Group and Their Characterization by Mass Spectrometry and Electron Microscopy
Authors: Smirnova T. A. , Polyakov N. B. , Karpov D. S. , Solovyev A. I. , Shevlyagina N. V. , Andreevskaya S. G. , Shcherbinin D. N. , Plieva Z. S. , Kozlova V. A. , Pereborova A. A. , Bogdanov I. A. , Grumov D. A. , Zubasheva M. V. , Poddubko S. V. , Grechnikov A. A. , Sukhina M. A. , Zhukhovitsky V. G.
Published: April 2024

Bacillus cereus is a spore-forming bacterium found in the environment mainly in soil. Bacillus spores are known to be extremely resistant not only to environmental factors, but also to various sanitation regimes. This leads to spore contamination of toxin-producing strains in hospital and food equipment and, therefore, poses a great threat to human health. Two clinical isolates identified as B. cereus and B. cytotoxicus were investigated in the present work. It was shown that their calcium ion content was significantly lower than that of the reference strains. According to electron microscopy, one of the isolates SRCC 19/16 has an enlarged exosporium, and isolate SRCC 1208 shows large electron-dense inclusions of unclear nature during sporulation. We can assume that it contains a biologically active component with a cytotoxic effect and possibly plays a role in pathogenesis. Comparative chemical, biochemical, physiological, and ultrastructural analysis of spores of clinical isolates and reference strains of B. cereus was performed. The results obtained deepen our understanding of the properties of spores that contribute to the increased pathogenicity of B. cereus group species.
microRNA Biogenesis during Cellular Senesence Induced by Chronic Stress of the Endoplasmic Reticulum
Authors: Kubatiev A. A. , Moskovtsev A. A. , Zaichenko D. M. , Mikryukova A. A. , Astafeva I. R. , Malakho S. G.
Published: April 2024

MicroRNAs are small non-coding regulatory RNAs about 22 nt long, post-transcriptional and transcriptional regulators of gene expression that stabilize the cellular phenotype and play an important role in differentiation, development, and apoptosis. MicroRNA biogenesis includes several precisely controlled post-transcriptional stages of processing and transport, including cytoplasmic cleavage of pre-miRNA by type III ribonuclease DICER with the formation of a mature duplex included in the RISC complex. The role of miRNA and its biogenesis are not well understood in such an important process as cellular stress. Cellular stress is a non-specific cellular response to non-physiological stimuli that can switch a cell to death or cellular senescence. The global decrease in microRNA levels is a key feature of cancer cells and an important reason for the formation of a malignant phenotype. In this work, using flow cytometry and high-throughput analysis of gene expression, we showed that chronic endoplasmic reticulum (ER) stress, one of the types of cellular stress associated with impaired protein folding in the ER, leads to the formation of a cellular aging phenotype in fibroblast-like FRSN cells. Despite the fact that acute ER stress can reduce miRNA biogenesis, chronic stress does not lead to a significant drop in global miRNA expression and is accompanied by only a slight decrease in DICER1 mRNA expression. Under chronic ER stress, we found an increase in cell population heterogeneity in terms of lysosomal beta-galactosidase activity, which does not exclude induced or initial cell heterogeneity and in terms of expression of microRNA biogenesis pathway components.
DNA Methylation Profile of CD14+ Monocytes Changes in Primary Progressive Multiple Sclerosis
Authors: Kiselev I. S. , Kulakova O. G. , Baturina O. A. , Kabilov M. R. , Boyko A. N. , Favorova O. O.
Published: April 2024

Multiple sclerosis (MS) is a chronic autoimmune inflammatory and neurodegenerative disease of the central nervous system, characterized by significant clinical heterogeneity. In 10–15% of patients, primary progressive MS (PPMS) develops, in which, unlike the most common relapsing-remitting form of MS, neurodegeneration steadily progresses and, as a consequence, neurological symptoms continuously increase. Peculiarities of epigenetic regulation of gene expression may be one of the reasons for the differences in the pathogenesis of two MS forms. DNA methylation is one of the key epigenetic mechanisms that remains almost unexplored in different cell populations of PPMS patients. The aim of this work was to identify differential methylation profiles of CpG sites in the CD14+ monocyte DNA that characterize PPMS. Genome-wide analysis of DNA methylation in PRMS patients and healthy individuals identified 169 differentially methylated positions (DMPs), 90.5% of which were hypermethylated in PRMS patients. More than half of all DMPs are located in/near known genes and within CpG islands and their neighboring regions, which indicates their high functional significance. We found six differentially methylated regions (DMRs) in genes OR2L13, CAT, LCLAT1, HOXA5, RNF39, and CRTAC1 involved in inflammation and neurodegeneration, which indicates active epigenetic regulation of their expression.
Nitric Oxide(II) in Biology of Chlorophyta
Authors: Ermilova E. V.
Published: April 2024

NO is a gaseous signaling redox-active molecule that functions in various eukaryotes. However, its synthesis, turnover, and effects in cells are specific in plants in several aspects. Compared with higher plants, the role of NO in Chlorophyta has not been investigated enough. Yet, some of the mechanisms for controlling levels of this signaling molecule have been characterized in model green algae. In Chlamydomonas reinhardtii, NO synthesis is carried out by a dual system comprising nitrate reductase and NO-forming nitrite reductase. Other mechanisms that might produce NO from nitrite are associated with components of mitochondrial electron-transport chain. In addition, NO formation in some green algae proceeds by oxidative mechanism similar to that in mammals. Recent discovery of L-arginine-dependent NO synthesis in colorless alga Polytomella parva suggests the existence of a protein complex with enzyme activity that are similar to animal nitric oxide synthase. This latter finding paves the way for further research into potential members of the NO synthases family in Chlorophyta. Beyond synthesis, the regulatory processes to maintain intracellular NO levels are also an integral part for its function in cells. Members of the truncated hemoglobins family with dioxygenase activity can convert NO to nitrate, as was shown for C. reinhardtii. In addition, the implication of NO reductases in NO scavenging has also been described. Even more intriguing, unlike in animals, the typical NO/cGMP signaling module appears not to be used by green algae. S-nitrosylated glutathione, which is considered the main reservoir for NO, provides NO signals to proteins. In Chlorophyta, protein S-nitrosation is one of the key mechanisms of action of the redox molecule. In this review, we discuss the current state-of-the-art and possible future directions related to the biology of NO in green algae.
Antioxidant and Geroprotective Properties of the Extract of Mountain Ash (Sorbus aucuparia L.) Fruits
Authors: Platonova E. Yu. , Golubev D. A. , Zemskaya N. V. , Shevchenko O. G. , Patov S. A. , Shaposhnikov M. V. , Moskalev A. A.
Published: April 2024

Plant polyphenols are characterized by a wide range of biological activities, including antioxidant properties, and have a high geroprotective potential. The purpose of this work was to investigate the effect of the extract of rowan berries (Sorbus aucuparia L.) on the lifespan and stress resistance of Drosophila melanogaster with the identification of possible mechanisms of its biological activity. It has been established that the ethanol extract of S. aucuparia berries, the main components of which are rutin and cyanidin-3-rutinoside, has a pronounced antioxidant activity in vitro. At the same time, treatment with rowan berry extract increased the r-esistance of D. melanogaster males to starvation, but reduced resistance to hyperthermia. In females, the e-xtract reduced resistance to oxidative stress but increased resistance to hyperthermia. The effects of rowan berry extract on longevity depended both on its concentration and on the sex of fruit flies. In response to treatment with rowan berry extract, D. melanogaster males and females showed slight differences in the background level of expression of cellular stress response genes, including heat shock genes (hsp27, hsp68, hsp83), oxidative stress resistance genes (hif1, nrf2, sod1), circadian rhythm genes (clk, per), and the longevity gene sirt1, which may explain the differences in the observed effects.
Tumor Metabolic Heterogeneity
Authors: Shirmanova M. V. , Sinyushkina S. D. , Komarova A. D.
Published: April 2024

Currently, much attention in oncology is devoted to the issues of tumor heterogeneity, which creates serious problems in the diagnosis and therapy of malignant neoplasms. Intertumoral and intratumoral differences relate to various characteristics and aspects of the vital activity of tumor cells, including cellular metabolism. This review provides general information about the tumor metabolic heterogeneity with a focus on energy metabolism, its causes, mechanisms and research methods. Among the methods, fluorescence lifetime imaging is described in more detail as a new promising method for observing metabolic heterogeneity at the cellular level. The review demonstrates the importance of studying the features of tumor metabolism and identifying intra- and intertumoral metabolic differences.
Effects of Grain Size on the Activity of H-MFI Zeolites in Liquid-Phase Condensation of Propene with Formaldehyde
Authors: Bedenko S. P , Mukusheva A. A , Malyavin V. V. , Dement'ev K. I.
Published: April 2024

This study investigated the activity of H-MFI catalysts modified by the top-down method in the liquid-phase Prins reaction between propene and formaldehyde. The physicochemical characterization of the catalyst demonstrated that grinding the catalyst reduces the specific surface area and affects the micropore to mesopore ratio in the samples. Reducing the grain size was found to increase the initial substrate consumption rate and reduce the diffusion limitations in the system. At the same time, grinding shifts the product composition towards a higher proportion of byproducts. An assessment of the kinetic curves enabled the researchers to propose a number of equations that accurately reflect catalyst deactivation. Both the reaction rate and deactivation rate vary directly with the zeolite dispersion, while the deactivation of the sample is more sensitive to the grain size.
Kinetic Model and Mechanism of Heterogeneous Hydrogenation of Strained Polycyclic Compounds Derived from 5-Vinyl-2-norbornene
Authors: Zamalyutin V. V , Katsman E. A. , Flid V. R.
Published: April 2024

The main pathways of liquid-phase hydrogenation of 5-ethenylbicyclo[2.2.1]hept-2-ene (5-vinyl-2-norbornene, VNE) in the presence of PK-25 palladium catalyst (Pd/γ-Al2O3, 0.25% Pd) were studied. All the reaction products were identified, and the material balance was examined. The effect of the prevalent adsorption of the norbornene double bond on the Pd active site (AS) was confirmed. The parallel-consecutive scheme of the process mechanism, based on the set of experimental and theoretical data, was suggested. It involves the successive substrate hydrogenation and significant role of the isomerization of the vinyl group into the ethylidene group in intermediates on AS in a hydrogen atmosphere. The reaction is zero-order in a wide interval of initial VNE concentrations. An adequate kinetic model of the process, based on the Langmuir–Hinshelwood approach and the concept of multiple adsorption of substrates on one AS, was developed. Five steps, including two parallel steps, significantly contribute to the reaction rate. Their rate constants and the adsorption constants of AS complexes with unsaturated compounds were estimated.
Experimental and Kinetic Modeling of n-Heptane Hydroconversion over Mesoporous Pt/MSU Catalyst. Effect of Site Activity and Residence Time
Authors: Mohammad Javad Asadinasab , Touba Hamoule
Published: April 2024

A zeolite-based mesostructured (MSU) molecular sieve material was synthesized, characterized, and used in the preparation of Pt (0.6 and 1 wt %) supported catalysts for hydroconversion of n-heptane under the experimental conditions of 300–450°C and 760 mmHg. Samples were characterized by X-ray diffraction (XRD), N2 adsorption-desorption isotherm, and NH3-TPD (temperature-programmed deposition) techniques. The activity test shows that catalysts have good activity and selectivity for isomerization reaction. Also, increasing metal sites, selectivity tends to the production of aromatization reaction in the heterogeneous catalytic process. Based on experimental results, a kinetic model of this reaction was carried out. Based on other publications and combining the examined features, a network of the reaction was proposed. It can be claimed that the results of converging the feed from the kinetic model are in good agreement with the experimental results. Some of the superiorities of this model compared to other models are the determination of kinetics parameters, source of isomers, aromatic, and cracked products distinctly with emphasis on the effect of site activity and residence time over metal-acid sites.
Neutralization of Acidic Exhaust Gas Components by Overbased Additives in Marine Oils: Effects of the Acid Composition on the Neutralization Mechanism
Authors: Bakunin V. N. , Volkov V. V. , Bakunina Yu. N.
Published: April 2024

Using a combination of IR spectroscopy and small-angle X-ray scattering methods, the study investigates the initial steps of the neutralization of commercial additives, such as overbased calcium alkylbenzene sulfonate and calcium alkyl salicylate, by a number of model acids. The model acids included sulfuric acid, nitric acid (both simulating acidic products of marine fuel combustion), and acetic acid. For the sulfonate additive, it was shown that the amorphous CaCO3 core crystallizes, predominantly into vaterite, with a simultaneous slight increase in the size of the additive’s solid core. In the case of the salicylate additive, no CaCO3 crystallization was observed, and the solid core was slightly reduced in size. The paper proposes an explanation for these transformations, which rests on the difference in the strength of the acids that constitute the shell of the additive’s nanoparticles, and in the water solubility of the calcium salts produced.
Bitumen Resistance to Plastic Deformation at High Temperatures
Authors: Gordeeva I. V. , Dudareva T. V. , Krasotkina I. A. , Gorbatova V. N. , Nikol'skiy V. G. , Zvereva U. G. , Obukhov A. G.
Published: April 2024

A number of Russian bitumen samples with the penetration range of 60 to 120×0.1 mm were rheologically investigated in the temperature range of 46–70°C to evaluate their resistance to plastic rutting using relevant oscillatory and rotational rutting parameters. Based on an assessment of correlations between structural and rheological parameters, the best correlations were observed between the Gaestel Colloidal Index (CI) and the rheological parameters R3.2 and tgδ. The study demonstrated that modified bitumen must be used for pavements with extreme (“E”) traffic loading in Russian regions where PG 52 or higher grade binders are required.
Combined Adsorptive and Ultrasonic Treatment to Remove Metals from Fuel Oil
Authors: Kobotaeva N. S. , Skorokhodova T. S.
Published: April 2024

The study investigated removal of metals (Ni, V, Cr, Fe, Ti, and Mo) from fuel oil using ultrasonic treatment (UST) and adsorbents such as carbon black, carbon nanotubes, aluminum oxyhydroxide (AlO(OH)), iron oxyhydroxide (FeO(OH)), and titanium dioxide (TiO2). Combined adsorption/UST provided a somewhat higher demetallization degree than the use of adsorbents alone. Compounds of iron, chromium, and molybdenum, which presumably complex with petroleum feedstock components due to intermolecular bonding, were removed almost completely (95%). The removal of titanium compounds reached 60%. For these metals, no correlation between the removal degree and the physicochemical properties of the adsorbents was found. For vanadium and nickel, the highest removal degrees (37 and 23%, respectively) were achieved when an iron oxyhydroxide adsorbent was used in combination with UST. This can likely be associated with the superiority of the FeO(OH) adsorbent in negative surface charge and specific surface area compared to the other samples.