Biophysics最新文献

{"title":"Analysis of RNA Editing in Conserved Sequence Blocks of the Trypanosomatid RPS12 Gene","authors":"E. S. Gerasimov,&nbsp;Y. A. Rudenskaya,&nbsp;E. A. Bryushkova,&nbsp;O. A. Korzhavina,&nbsp;A. A. Kolesnikov","doi":"10.1134/S0006350924701082","DOIUrl":"10.1134/S0006350924701082","url":null,"abstract":"<div><p>The RPS12 gene in the mitochondrial genome encodes an important protein from the small ribosomal subunit. The transcript of this gene can undergo RNA editing in a number of organisms, for instance it is edited actively in all tripanosomatida. In this study, a comparison between the sequences of edited mRNA and tertiary structures of the proteins when mRNA were translated from some of the members of Tripanosomatidae family showed that tertiary structures of the RPS12 gene remained unchanged in all species while only two short conserved regions were found in the primary structure of the gene. Using computer modeling it was demonstrated that these regions encode amino acids that are turned in the decoding center of the ribosome. The nature of editing patterns demonstrates that evolutionary conservation of these regions is independent of the editing process; moreover, an evolutionary tendency to reduction of editing process in a number of sites was seen within the conserved sites of the RPS12 gene.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 6","pages":"1003 - 1009"},"PeriodicalIF":4.033,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143638536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanisms of Cancer Cell Radioresistance: Modern Trends and Research Prospects","authors":"M. G. Sharapov,&nbsp;E. E. Karmanova,&nbsp;S. V. Gudkov","doi":"10.1134/S0006350924701161","DOIUrl":"10.1134/S0006350924701161","url":null,"abstract":"<div><p>Radiation therapy occupies one of the key places in the arsenal of cancer treatment methods. This non-invasive method has been actively used for many decades and has demonstrated high effectiveness in combating various types of malignant neoplasms. Despite significant progress in ionizing radiation delivery technologies and the introduction of targeted radiosensitizers and immunotherapy, classical radiation therapy faces limitations related to radioresistance of tumor cells. This is due to a variety of factors, such as genetic mutations, metabolic features of cancer cells, their ability to repair DNA, the presence of a tumor microenvironment, and many others. Radioresistance of tumors reduces the success of treatment, which makes it necessary to search for new approaches to improve the effectiveness of radiation therapy. This review discusses the basic principles of radiation therapy and the properties of cancer cells that affect their radiosensitivity. Both the existing methods of overcoming cancer cell radioresistance and the prospects for their further development are being considered, which can significantly improve the effectiveness of cancer treatment.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 6","pages":"1064 - 1088"},"PeriodicalIF":4.033,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143638538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Formation of Complex Spatial Structures of DNA in the Process of Ab Initio Synthesis","authors":"N. V. Zyrina,&nbsp;O. M. Selivanova,&nbsp;E. V. Shevchenko,&nbsp;V. N. Antipova","doi":"10.1134/S0006350924701069","DOIUrl":"10.1134/S0006350924701069","url":null,"abstract":"<div><p>Products with a complex spatial organization were formed during <i>ab initio</i> synthesis using the large fragment of the Bst DNA polymerase. Using the analysis of AFM images of products obtained with the addition of a minimal amount of the nicking endonuclease Nt. BspD6I during this synthesis it was possible to describe the structures that formed as a result of this synthesis and suggest that their formation occurs by the mechanism of recombination-dependent replication.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 6","pages":"985 - 989"},"PeriodicalIF":4.033,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143638614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Morphological and Functional Characteristics of the Trematode Fasciola hepatica Musculature","authors":"N. D. Kreshchenko","doi":"10.1134/S0006350924701185","DOIUrl":"10.1134/S0006350924701185","url":null,"abstract":"<div><p>The morphological structure and functional properties of musculature in a flatworm <i>Fasciola hepatica</i> (Trematoda, Fasciolidae), a dangerous parasite of farm animals and humans, have been studied. The flatworm body musculature was stained histochemically with fluorescently labeled phalloidin and analyzed using fluorescence microscopy. The presence of staining was found in the longitudinal, circular, and diagonal muscle fibers of the worm’s body wall, as well as in the circular and diagonal muscle fibers surrounding the lumens of the branched intestine, as well as in the tubular muscle structures of the reproductive tract. Densely packed and intensely stained layers of muscle fibers were found in the ventral and oral suckers of the flatworm. Physiological studies conducted on muscle preparations isolated from <i>F. hepatica</i>, demonstrated the presence of spontaneous contractile activity of the muscles. The neuropeptide GYIRF, from the family of FMRFamide-like peptides, at concentrations of 1–10 µM, additionally stimulated the contraction of muscle preparations of <i>F. hepatica</i>, increasing the frequency and amplitude of muscle contractions compared with their basic activity. The information obtained will be used in further study of the mechanisms of muscle contraction in parasitic worms, whose musculature is the target of existing antiparasitic drugs.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 6","pages":"1102 - 1112"},"PeriodicalIF":4.033,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143638355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Effect of Immobilization Method on DNA Stretching Characteristics","authors":"M. A. Didin","doi":"10.1134/S0006350924701070","DOIUrl":"10.1134/S0006350924701070","url":null,"abstract":"<div><p>The problem of stretching a flexible polymer molecule with specified conditions at the ends under the action of a fixed force is considered. A mathematical model has been constructed for various energy functions describing the elasticity of the polymer and various immobilization methods. It is shown that the dependence of stretching on the length of the polymer is linear. The results of numerical calculations are presented. The results obtained make it possible to improve the analysis of experimental data on polymer stretching. The theory provides several verifiable predictions, including experimental methods that improve the accuracy of measurements.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 6","pages":"990 - 1002"},"PeriodicalIF":4.033,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143638613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic Analysis of Arctic Polar Bear Populations Using Historical Samples","authors":"A. A. Kanapin,&nbsp;A. A. Samsonova,&nbsp;A. V. Abramov,&nbsp;M. V. Sablin,&nbsp;V. V. Platonov,&nbsp;H. H. Mustafin,&nbsp;S. A. Chekrygin,&nbsp;D. Hirata","doi":"10.1134/S0006350924701306","DOIUrl":"10.1134/S0006350924701306","url":null,"abstract":"<div><p>This study analyzed genetic data using DNA isolated from museum specimens of polar bears in the collection of the Zoological Institute of the Russian Academy of Sciences. The unique data obtained in this study made it possible to characterize the population structure of polar bears in the past and to lay the foundation for further research. Methods of DNA isolation used in archaeogenetics and paleogenetics were applied to historical materials. These methods provided a sufficient quantity and quality of DNA suitable for high-throughput sequencing. The analysis of genetic variants made it possible to reveal the population structure of spatial and temporal polar bear populations in the Russian Arctic regions and its changes associated with the economic activities that unfolded in the first third of the 20th century.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 6","pages":"1213 - 1216"},"PeriodicalIF":4.033,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143638338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Effects of Ethidium Bromide on Purinergic Modulation of Myoneural Transmission and Skeletal Muscle Contraction","authors":"A. N. Gorshunova,&nbsp;A. Yu. Teplov,&nbsp;S. N. Grishin,&nbsp;R. D. Mukhamedzyanov,&nbsp;A. E. Khairullin","doi":"10.1134/S0006350924701203","DOIUrl":"10.1134/S0006350924701203","url":null,"abstract":"<div><p>The problem of changes in myoneural transmission in the presence of an intercalating agent, ethidium bromide, which has a known inhibitory effect on neuromuscular transmission, has been investigated, but the nature of such an effect remains unclear. To solve the question of the possible participation in this process of known modulators of synaptic transmission, that is, purines (ATP and adenosine), we evaluated their effects in the presence of this agent. After holding a frog neuromuscular preparation in a perfusing solution containing ethidium bromide, the amplitude of postsynaptic responses and muscle contraction forces decreased. Under these conditions, both purines additionally exerted their usual suppressive effect on both the amplitude of postsynaptic responses and the strength of skeletal muscle contraction. Thus, the inhibitory effect of ethidium bromide on neuromuscular transmission is not associated with an increase in the inhibitory effect of endogenous purines caused by the quantum release of the neurotransmitter.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 6","pages":"1121 - 1125"},"PeriodicalIF":4.033,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143638341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Effect of Dinitrosyl Iron Complexes with a Ligand Based on N-acethyl-L-cysteine upon Inhalation Delivery of These Complexes into the Body of Rats","authors":"A. A. Timoshin,&nbsp;K. B. Shumaev,&nbsp;V. L. Lakomkin,&nbsp;A. A. Abramov,&nbsp;E. K. Ruuge","doi":"10.1134/S0006350924701239","DOIUrl":"10.1134/S0006350924701239","url":null,"abstract":"<div><p>The aim of the work was to study the effect of dinitrosyl iron complexes (DNIC) with a ligand based on <i>N</i>-acetyl-L-cysteine upon its prolonged administration into the rat body by inhalation. It was found that as a result of this, an effective transfer of stabilized forms of NO occurred through the alveolar wall into the lung tissue. Accumulation of dinitrosyl iron complexes with protein ligands in the lungs and other organs, an increase in their total NO level, as well as a significant and prolonged hypotensive effect were observed.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 6","pages":"1147 - 1152"},"PeriodicalIF":4.033,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143638354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hybrid Models of Evolutionary Transformations of SAR-CoV-2 Epidemic Waves","authors":"A. Yu. Perevaryukha","doi":"10.1134/S0006350924701264","DOIUrl":"10.1134/S0006350924701264","url":null,"abstract":"&lt;div&gt;&lt;p&gt;The specific variants of the development of the current epidemic situation due to regularly updated SAR-CoV-2 strains are analyzed and methods for modeling special scenarios of the spread of this infection are compared. The relevance of the development of the modeling methodology is due to the renewed growth of waves of COVID cases in a number of regions in 2024 as an unusual variant of the pulsating epidemic process. The latest outbreaks of infections are determined by the activity of the BA.2.86 Pirola strain evolutionary branch, which has managed to split and is more effective in terms of affinity and antibody avoidance than the previously dominant Omicron EG.5 and XBB.1.5 lines. In 2024, the strains maintained sufficient transmissibility with reduced affinity for the ACE2 receptor and a lower replication rate compared to Delta, and at the same time, the virus persistence time increased. In the situation of population immunization, the trend of virus evolution has changed with an emphasis on complicating the phylogenetic tree and selecting Spike protein variants that provide balanced characteristics for replication and antibody avoidance. The potential of variability in coronavirus proteins is clearly not exhausted, and methods for predicting their promising mutations are under development. Methods of computational study of epidemic scenarios based on modified by expanding the set of statuses of individuals in office “SIR models” are discussed. Variants of SIR-based systems of equations do not describe the resumption of COVID waves, which was observed as early as 2020. Status transition schemes are in principle poorly suited for describing nonlinear oscillatory modes of an epidemic, even when second-order oscillatory equations are included in a linear SIR scheme. The models developed by the author for attenuating COVID waves based on equations with delay and threshold effects have been modified to take into account that the new Omicron lines change the modes of oscillations. The changes in oscillation modes that we have identified with an increase in repeated cases are not described only by rearranging the parameters of the equations with damping functions. According to the observed epidemic schedules of COVID waves, a restructuring of regulatory functions is required in the models. It is proposed to model aspects of the transitional phases of the modern epidemic by special computational means, based on the nature of nonlinear oscillations. An original method of forming a structure for a hybrid model based on a set of right-hand sides of differential equations with heterogeneous parameters of delayed regulation generating relaxation oscillations and redefined predicates in violation of the criterion of truth is substantiated. It has been shown that the change in the binding affinity of S protein variants with ACE2 is a key indicator for modeling the periods of attenuation and activation of waves associated with the evolution of the vir","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 6","pages":"1169 - 1189"},"PeriodicalIF":4.033,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143638617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Control of the Activity of Mobile Elements in Cancer Cells as a Strategy for Anticancer Therapy","authors":"S. R. Pavlov,&nbsp;V. V. Gursky,&nbsp;M. G. Samsonova,&nbsp;A. A. Kanapin,&nbsp;A. A. Samsonova","doi":"10.1134/S000635092470115X","DOIUrl":"10.1134/S000635092470115X","url":null,"abstract":"<div><p>One important direction in cancer prevention is the development of novel strategies that can be used in treatment by affecting the mechanisms of the regulatory pathways and genomic elements involved in malignant transformation. The strategy proposed in this study is to initiate cell death mechanisms in response to the depletion of the energy resources within a cancer cell due to the uncontrolled spread of mobile genetic elements throughout its genome. The calculation results obtained using a preliminary mathematical model that simulates the cellular bioenergetic balance, taking the energy consumption for retrotransposition of the mobile elements such as LINE-1 and SINE into account, show that this scenario is plausible. Intracellular resources undergo a critical redistribution when affecting the genomic defense mechanisms and the LINE-1 transcription rate. This leads to a sharp increase in energy consumption for retrotransposon transcription that causes a significant decrease in the pool of free ATP in the cell.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 6","pages":"1060 - 1063"},"PeriodicalIF":4.033,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143638339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}