Acta Naturae最新文献

{"title":"BODIPY Dye Derivative for Irreversible Fluorescent Labeling of Eukaryotic Cells and Their Simultaneous Cytometric Analysis.","authors":"A Yu Frolova, S V Kutyakov, V I Martynov, S M Deyev, A A Pakhomov","doi":"10.32607/actanaturae.26879","DOIUrl":"10.32607/actanaturae.26879","url":null,"abstract":"<p><p>In this work, we synthesized a green fluorescent dye derivative, 1,3,5,7-tetramethyl-BODIPY, with a heptyl substituent at the 8-position. The obtained highly hydrophobic compound was able to rapidly and irreversibly bind to eukaryotic cells. Incubation of cells with the dye over different periods of time or at different concentrations allowed us to control the degree of cell labeling and the level of fluorescence. This made it possible to modulate the fluorescence level of different eukaryotic cell cultures and then distinguish them by their level of fluorescence signal in the green channel in cytometric experiments. The labeled cells can be combined and further analyzed in the same test tube under identical conditions using the channels in which the dye does not fluoresce. This approach has been tested on a number of tumor cell cultures containing the HER2 receptor on their surface. The representation of the receptor in these cells was analyzed in one test tube in one run using a HER2-specific ligand based on the hybrid protein DARPin9_29-mCherry, which fluoresces in the red region of the spectrum.</p>","PeriodicalId":6989,"journal":{"name":"Acta Naturae","volume":"15 4","pages":"92-99"},"PeriodicalIF":2.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10790353/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139484919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In Vitro Antiviral Activity of a New Indol-3-carboxylic Acid Derivative Against SARS-CoV-2.","authors":"A N Narovlyansky, M V Filimonova, N G Tsyshkova, A V Pronin, T V Grebennikova, E V Karamov, V F Larichev, G V Kornilayeva, I T Fedyakina, I V Dolzhikova, M V Mezentseva, E I Isaeva, V V Poloskov, L S Koval, V P Marinchenko, V I Surinova, A S Filimonov, A A Shitova, O V Soldatova, A V Sanin, I K Zubashev, A V Ponomarev, V V Veselovsky, V V Kozlov, A V Stepanov, A V Khomich, V S Kozlov, S A Ivanov, P V Shegai, A D Kaprin, F I Ershov, A L Gintsburg","doi":"10.32607/actanaturae.26623","DOIUrl":"10.32607/actanaturae.26623","url":null,"abstract":"<p><p>The coronavirus disease (COVID-19) pandemic has brought into sharp relief the threat posed by coronaviruses and laid the foundation for a fundamental analysis of this viral family, as well as a search for effective anti-COVID drugs. Work is underway to update existent vaccines against COVID-19, and screening for low-molecular-weight anti-COVID drug candidates for outpatient medicine continues. The opportunities and ways to accelerate the development of antiviral drugs against other pathogens are being discussed in the context of preparing for the next pandemic. In 2012-2015, Tsyshkova et al. synthesized a group of water-soluble low-molecular-weight compounds exhibiting an antiviral activity, whose chemical structure was similar to that of arbidol. Among those, there were a number of water-soluble compounds based on 5-methoxyindole-3-carboxylic acid aminoalkyl esters. Only one member of this rather extensive group of compounds, dihydrochloride of 6-bromo-5-methoxy-1-methyl-2-(1-piperidinomethyl)-3-(2-diethylaminoethoxy) carbonylindole, exhibited a reliable antiviral effect against SARS-CoV-2 <i>in vitro</i>. At a concentration of 52.0 μM, this compound completely inhibited the replication of the SARS-CoV-2 virus with an infectious activity of 106 TCID50/mL. The concentration curves of the analyzed compound indicate the specificity of its action. Interferon-inducing activity, as well as suppression of syncytium formation induced by the spike protein (S-glycoprotein) of SARS-CoV-2 by 89%, were also revealed. In view of its synthetic accessibility - high activity (IC₅₀ = 1.06 μg/mL) and high selectivity index (SI = 78.6) - this compound appears to meets the requirements for the development of antiviral drugs for COVID-19 prevention and treatment.</p>","PeriodicalId":6989,"journal":{"name":"Acta Naturae","volume":"15 4","pages":"83-91"},"PeriodicalIF":2.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10790354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139484940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Testing a Hypothesis of 12S rRNA Methylation by Putative METTL17 Methyltransferase.","authors":"A V Mashkovskaia, S S Mariasina, M V Serebryakova, M P Rubtsova, O A Dontsova, P V Sergiev","doi":"10.32607/actanaturae.25441","DOIUrl":"10.32607/actanaturae.25441","url":null,"abstract":"<p><p>Mitochondrial ribosome assembly is a complex multi-step process involving many additional factors. Ribosome formation differs in various groups of organisms. However, there are universal steps of assembly and conservative factors that have been retained in evolutionarily distant taxa. METTL17, the object of the current study, is one of these conservative factors involved in mitochondrial ribosome assembly. It is present in both bacteria and the mitochondria of eukaryotes, in particular mice and humans. In this study, we tested a hypothesis of putative METTL17 methyltransferase activity. MALDI-TOF mass spectrometry was used to evaluate the methylation of a putative METTL17 target - a 12S rRNA region interacting with METTL17 during mitochondrial ribosome assembly. The investigation of METTL17 and other mitochondrial ribosome assembly factors is of both fundamental and practical significance, because defects in mitochondrial ribosome assembly are often associated with human mitochondrial diseases.</p>","PeriodicalId":6989,"journal":{"name":"Acta Naturae","volume":"15 4","pages":"75-82"},"PeriodicalIF":2.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10790355/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139484958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Membrane Partitioning of TEMPO Discriminates Human Lung Cancer from Neighboring Normal Cells.","authors":"O K Gasymov, M J Bakhishova, R B Aslanov, L A Melikova, J A Aliyev","doi":"10.32607/actanaturae.19426","DOIUrl":"10.32607/actanaturae.19426","url":null,"abstract":"<p><p>The plasma membranes of normal and cancer cells of the lung, breast, and colon tissues show considerably different lipid compositions that greatly influence their physicochemical properties. Partitioning of the spin probe 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) into the membranes of human lung normal and carcinoma cells was assessed by EPR spectroscopy to estimate the impact of the lipid compositions. The goal was to reveal potential strategies for cancer therapy attributable to the membrane properties. The study was conducted at pH values of 7.3 and 6.2, relevant to the microenvironments of normal and cancer cells, respectively. The TEMPO partitioning was examined in the temperature interval of 283-317K to reveal the efficacy of local hyperthermia used in chemotherapy. Results indicate that the TEMPO partitioning coefficient for the membranes of human lung carcinoma cells is significantly higher compared with that of neighboring normal cells. Increased partition coefficients were observed at relatively higher temperatures in both normal and cancer cells. However, compared to the normal cells, the cancer cells demonstrated higher partition coefficients in the studied temperature range. The data obtained with C12SL (spin-labeled analog of lauric acid) indicate that increased membrane dynamics of the cancer cells is a possible mechanism for enhanced partitioning of TEMPO. Free energy values for partitioning estimated for pH values of 6.2 and 7.3 show that TEMPO partitioning requires 30% less energy in the cancer cells at pH 7.3. TEMPO and its derivatives have previously been considered as theranostic agents in cancer research. Data suggest that TEMPO derivatives could be used to test if complementary alkalization therapy is effective for cancer patients receiving standard chemotherapy with local hyperthermia.</p>","PeriodicalId":6989,"journal":{"name":"Acta Naturae","volume":"15 4","pages":"111-120"},"PeriodicalIF":2.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10790361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139484943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RIPK3 Expression in Fibroblasts in an in vivo and in vitro Skin Wound Model: A Controversial Result.","authors":"I S Izumov, M S Shitova, M S Sabirov, S A Sheleg, O L Cherkashina, E P Kalabusheva, E A Vorotelyak, E I Morgun","doi":"10.32607/actanaturae.25452","DOIUrl":"10.32607/actanaturae.25452","url":null,"abstract":"<p><p>One of the major problems of regenerative medicine is the development of hypertrophic scars and keloids. The protein kinase RIPK3 is involved in necroptosis; however, recent evidence indicates that it also has non-canonical functions, including its involvement in the development of renal fibrosis. The aim of our work was to study the expression of RIPK3 in mouse and human skin models of fibrotic processes. A subpopulation of RIPK3+Vim+ cells was found in both human keloid and a mouse wound, with the cell number being significantly greater in the mouse wound bed compared to healthy skin. Real-time polymerase chain reaction (RT-PCR) detected expression of the <i>Ripk3</i> and fibroblast biomarkers <i>Acta2</i>, <i>Fap</i>, <i>Col1a1</i>, and <i>Fn1</i> in the cells isolated from the wound bed, indicating that RIPK3 can be expressed by wound bed fibroblasts. An analysis of the human fibroblasts stained with anti-RIPK3 antibodies demonstrated an increase in the fluorescence intensity in the presence of lipopolysaccharide (LPS) at concentrations of 5, 10, 25, 50, and 100 ng/ml and TGF-β at concentrations of 0.1, 1, 2, and 5 ng/ml compared to the control. At the same time, the expression levels of <i>RIPK3</i> and fibroblast activation markers in the presence of TGF-β and LPS did not differ significantly from the control. It is possible that RIPK3 expression in wound fibroblasts is not directly associated with fibrotic processes, and that kinase plays a different, yet unknown role in wound healing. KEYWORDS scarring, keloid, skin, fibroblasts, cell culture, RIPK3.</p>","PeriodicalId":6989,"journal":{"name":"Acta Naturae","volume":"15 4","pages":"65-74"},"PeriodicalIF":2.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10790357/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139484855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Potential and Application of iPSCs in Gene and Cell Therapy for Retinopathies and Optic Neuropathies.","authors":"E V Lapshin, Y G Gershovich, A V Karabelsky","doi":"10.32607/actanaturae.25454","DOIUrl":"10.32607/actanaturae.25454","url":null,"abstract":"<p><p>This review focuses on <i>in vitro</i> modeling of diseases and the development of therapeutic strategies using iPSCs for the two most common types of optical pathologies: hereditary neuropathies and retinopathies. Degeneration of retinal ganglion cells and the subsequent optic nerve atrophy leads to various types of neuropathies. Damage to photoreceptor cells or retinal pigment epithelium cells causes various retinopathies. Human iPSCs can be used as a model for studying the pathological foundations of diseases and for developing therapies to restore visual function. In recent years, significant progress has also been made in creating ganglionic and retinal organoids from iPSCs. Different research groups have published data pertaining to the potential of using iPSCs for the modeling of optic neuropathies such as glaucoma, Leber hereditary optic neuropathy, etc., including in the development of therapeutic approaches using gene editing tools.</p>","PeriodicalId":6989,"journal":{"name":"Acta Naturae","volume":"15 4","pages":"56-64"},"PeriodicalIF":2.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10790360/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139484960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cooperation and Competition of RNA Secondary Structure and RNA-Protein Interactions in the Regulation of Alternative Splicing.","authors":"M A Vorobeva, D A Skvortsov, D D Pervouchine","doi":"10.32607/actanaturae.26826","DOIUrl":"10.32607/actanaturae.26826","url":null,"abstract":"<p><p>The regulation of alternative splicing in eukaryotic cells is carried out through the coordinated action of a large number of factors, including RNA-binding proteins and RNA structure. The RNA structure influences alternative splicing by blocking <i>cis</i>-regulatory elements, or bringing them closer or farther apart. In combination with RNA-binding proteins, it generates transcript conformations that help to achieve the necessary splicing outcome. However, the binding of regulatory proteins depends on RNA structure and, vice versa, the formation of RNA structure depends on the interaction with regulators. Therefore, RNA structure and RNA-binding proteins are inseparable components of common regulatory mechanisms. This review highlights examples of alternative splicing regulation by RNA-binding proteins, the regulation through local and long-range RNA structures, as well as how these elements work together, cooperate, and compete.</p>","PeriodicalId":6989,"journal":{"name":"Acta Naturae","volume":"15 4","pages":"23-31"},"PeriodicalIF":2.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10790352/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139484921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Muscarinic Cholinoreceptors in Skeletal Muscle: Localization and Functional Role.","authors":"I V Kovyazina, A A Khamidullina","doi":"10.32607/actanaturae.25259","DOIUrl":"10.32607/actanaturae.25259","url":null,"abstract":"<p><p>The review focuses on the modern concepts of the functions of muscarinic cholinoreceptors in skeletal muscles, particularly, in neuromuscular contacts, and that of the signaling pathways associated with the activation of various subtypes of muscarinic receptors in the skeletal muscles of cold-blooded and warm-blooded animals. Despite the long history of research into the involvement of muscarinic receptors in the modulation of neuromuscular transmission, many aspects of such regulation and the associated intracellular mechanisms remain unclear. Now it is obvious that the functions of muscarinic receptors in skeletal muscle are not limited to the autoregulation of neurosecretion from motor nerve endings but also extend to the development and morphological rearrangements of the synaptic apparatus, coordinating them with the degree of activity. The review discusses various approaches to the study of the functions of muscarinic receptors in motor synapses, as well as the problems arising when interpreting experimental data. The final part of the review is devoted to an analysis of some of the intracellular mechanisms and signaling pathways that mediate the effects of muscarinic agents on neuromuscular transmission.</p>","PeriodicalId":6989,"journal":{"name":"Acta Naturae","volume":"15 4","pages":"44-55"},"PeriodicalIF":2.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10790362/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139486934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modern Approaches to the Genome Editing of Antibiotic Biosynthetic Clusters in Actinomycetes.","authors":"J A Buyuklyan, Yu V Zakalyukina, I A Osterman, M V Biryukov","doi":"10.32607/actanaturae.23426","DOIUrl":"10.32607/actanaturae.23426","url":null,"abstract":"<p><p>Representatives of the phylum <i>Actinomycetota</i> are one of the main sources of secondary metabolites, including antibiotics of various classes. Modern studies using high-throughput sequencing techniques enable the detection of dozens of potential antibiotic biosynthetic genome clusters in many actinomycetes; however, under laboratory conditions, production of secondary metabolites amounts to less than 5% of the total coding potential of producer strains. However, many of these antibiotics have already been described. There is a continuous \"rediscovery\" of known antibiotics, and new molecules become almost invisible against the general background. The established approaches aimed at increasing the production of novel antibiotics include: selection of optimal cultivation conditions by modifying the composition of nutrient media; co-cultivation methods; microfluidics, and the use of various transcription factors to activate silent genes. Unfortunately, these tools are non-universal for various actinomycete strains, stochastic in nature, and therefore do not always lead to success. The use of genetic engineering technologies is much more efficient, because they allow for a directed and controlled change in the production of target metabolites. One example of such technologies is mutagenesis-based genome editing of antibiotic biosynthetic clusters. This targeted approach allows one to alter gene expression, suppressing the production of previously characterized molecules, and thereby promoting the synthesis of other unknown antibiotic variants. In addition, mutagenesis techniques can be successfully applied both to new producer strains and to the genes of known isolates to identify new compounds.</p>","PeriodicalId":6989,"journal":{"name":"Acta Naturae","volume":"15 3","pages":"4-16"},"PeriodicalIF":2.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10615194/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71419622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of the Association between the Tgfb1 Gene Haplotype and Liver Diseases in Children.","authors":"R M Kurabekova,&nbsp;O E Gichkun,&nbsp;O M Tsirulnikova,&nbsp;I E Pashkova,&nbsp;V A Fomina,&nbsp;O P Shevchenko,&nbsp;S V Gautier","doi":"10.32607/actanaturae.19425","DOIUrl":"https://doi.org/10.32607/actanaturae.19425","url":null,"abstract":"Transforming growth factor-β1 (TGF-β1), a cytokine with immunosuppressive and pro-fibrogenic activity, is a potential marker of infection, liver transplant rejection, and fibrosis. Its levels in the blood and tissues depend on many factors; however, the role of gene polymorphism is still unclear. In this work, the distribution frequency of three single nucleotide polymorphism (SNP) variants of the Tgfb1 gene, namely rs1800469, rs1800470, and rs1800471, was studied in children with end-stage liver disease (ESLD). The study included 225 pediatric liver recipients aged 1 month to 16 years (median, 8 months), including 100 boys and 125 girls, and 198 healthy individuals aged 32.7 ± 9.6 years, including 78 men and 120 women. The indication for liver transplantation in children was ESLD, which was mostly caused by congenital and inherited liver diseases. SNPs were detected by real-time polymerase chain reaction using TaqMan probes and DNA isolated from peripheral blood. SNP frequency distribution was in Hardy–Weinberg equilibrium and did not differ between children with liver diseases and the healthy ones. Analysis of the SNPs frequency based on allelic interaction models did not reveal any differences between patients and the healthy individuals. Evaluation of linkage disequilibrium for Tgfb1 polymorphic variant pairs revealed a statistically significant linkage between all studied variants. Seven haplotypes, which are variants of SNP combinations, were observed in the studied groups of patients and healthy individuals. A total of 80% of the group had three haplotypes, whose frequencies did not differ between patients and the healthy individuals. Significant differences were found in the frequency of the haplotypes A-A-C, G-G-C, and G-A-G (at rs1800469, rs1800470, and rs1800471, respectively), which were observed up to 11 times more often in recipients compared to the healthy individuals. It is possible that these haplotypes are ESLD-predisposing variants, which may also contribute to the development of complications after liver transplantation in children.","PeriodicalId":6989,"journal":{"name":"Acta Naturae","volume":"15 3","pages":"75-81"},"PeriodicalIF":2.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10615185/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71419617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}