Biophysics最新文献

{"title":"Rotenone, Rhodamine 123, and Janus Green Induce Damage to Nuclear DNA in Ascites Tumor Cells from Mice. Rotenone and Rhodamine in X-Ray Irradiated Cells Contribute to the Maintenance of Genome Integrity","authors":"E. A. Kuznetsova,&nbsp;N. P. Sirota","doi":"10.1134/S000635092470074X","DOIUrl":"10.1134/S000635092470074X","url":null,"abstract":"<div><p>The mitochondrial inhibitors rotenone and rhodamine 123 and the Janus Green B dye are being studied in order to develop pharmacological agents that cause mitochondrial dysfunction and apoptosis. Since mitochondrial dysfunction is associated with the production of reactive oxygen species, it seems relevant to compare the DNA damage induced by these substances to cells of ascitic Ehrlich carcinoma and murine lymphocytic leukemia P388 with exposure to a known inducer of reactive oxygen species, that is, ionizing (X-ray) radiation. The level of DNA damage was assessed using an alkaline version of the Comet assay. The level of DNA damage induced by rotenone was comparable to irradiation at a dose of 4 Gy in both cell types. Post-radiation incubation reduced the level of DNA damage, which indicates DNA repair. Treatment of Ehrlich’s ascitic carcinoma cells with rhodamine 123 followed by washing did not cause this increase; however, irradiation at a dose of 4 Gy in the presence of rhodamine 123 induced an increase in the level of DNA damage, which significantly decreased after 1 h incubation. It can be assumed that pretreatment of cells with rotenone and rhodamine 123, which impair the work of mitochondria, contributed to the preservation of the integrity of nuclear DNA in irradiated cells. Exposure to Janus Green B caused increased DNA damage and cell death. Based on the alkaline version of the Comet assay, damage induced by these compounds can be considered as single- and double-strand breaks and alkali-labile (apurine/apirimidine) sites in DNA.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 4","pages":"656 - 666"},"PeriodicalIF":4.033,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143496957","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":"Noncontact Atomic Force Microscopy for Studies of Biomolecules in Liquids","authors":"T. Mamedov,&nbsp;A. Shvirst,&nbsp;M. V. Fedotova,&nbsp;G. N. Chuev","doi":"10.1134/S0006350924700702","DOIUrl":"10.1134/S0006350924700702","url":null,"abstract":"<p><b>Abstract</b>—Noncontact atomic force microscopy, a type of scanning probe microscopy, has been actively used in the last 2 decades to study hydrated biomolecules. In particular, as the analysis of modern literature shows, it is very promising in the study of adsorbed biomacromolecules and biomacromolecular complexes at the interface or on the surface of membranes. This mini-review describes the basics of this method and its application to biomolecules; the requirements for the method and the possibilities of its extension due to additional processing of the experimental data obtained using theoretical analysis, molecular modeling and machine learning are discussed.</p>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 4","pages":"617 - 629"},"PeriodicalIF":4.033,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143496822","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 Kinetics of Oxidation of 3-Aminopyridin-2(1H)-ones by Hydrogen Peroxide in the Presence of Horseradish Peroxidase","authors":"V. S. Shubina,&nbsp;Yu. V. Shatalin,&nbsp;A. L. Shatsauskas,&nbsp;A. S. Fisyuk","doi":"10.1134/S0006350924700660","DOIUrl":"10.1134/S0006350924700660","url":null,"abstract":"<div><p>The aim of this study was to evaluate the kinetic parameters of the oxidation of some 3-aminopyridine-2(1H)-ones by hydrogen peroxide catalyzed by horseradish peroxidase and the affinity of horseradish peroxidase to these compounds. It has been shown that the oxidation of 3-aminopyridine-2(1H)-ones follows kinetics of the pseudo-first order. A hyperbolic decrease in the observed reaction rate constant (<i>k</i>_obs) was also found with an increase in the initial concentration of 3-aminopyridine-2(1H)-ones. The dependence of <i>k</i>_obs on the concentration of the enzyme was linear, suggesting competitive inhibition of oxidation by the reaction product. It was found that an increase in the polarity of the substituent in the fourth position leads to an increase in the rate of oxidation of pyridinones. <i>V</i>_max/<i>K</i>_m values were also higher for compounds carrying polar substituents in the fourth position. This kinetic parameter (<i>V</i>_max/<i>K</i>_m) reflects the substrate specificity of the enzyme. The data we obtained clarify the mechanisms of interaction between horseradish peroxidase and 3-aminopyridinones and suggest that 3-aminopyridinones can be used to develop sensitive methods for the detection of hydrogen peroxide and modification of immune enzyme analysis techniques.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 4","pages":"591 - 596"},"PeriodicalIF":4.033,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143496832","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":"Innovative Biophysical Approaches for Quercetin Extraction from Plant Cells","authors":"A. G. Pogorelov,&nbsp;L. G. Ipatova,&nbsp;A. I. Panait,&nbsp;A. A. Stankevich,&nbsp;A. K. Yunusova,&nbsp;V. N. Pogorelova","doi":"10.1134/S0006350924700696","DOIUrl":"10.1134/S0006350924700696","url":null,"abstract":"<div><p>A method of extraction of quercetin from a plant cell based on the combined action of ultrasound and a metastable fraction of an aqueous solution is proposed. This treatment leads to more efficient release of the cytoplasmic component due to etching and/or mechanical destruction of the plant cell envelope. The oxidized fraction of the solution has the most pronounced extractive properties; however, it acts on quercetin by oxidizing the chromophore part of the molecule. According to the criterion of pigment preservation, the best extraction medium is the reduced fraction of water. Analytical methods were used to analyze the extract samples: UV-Vis spectroscopy, gel electrophoresis of proteins, ¹H NMR spectroscopy, and QCM weighing, as well as scanning electron microscopy.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 4","pages":"609 - 616"},"PeriodicalIF":4.033,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143496689","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":"Theta Oscillations and the Comparator Function of the Hippocampus","authors":"V. F. Kitchigina","doi":"10.1134/S0006350924700799","DOIUrl":"10.1134/S0006350924700799","url":null,"abstract":"<div><p>Detecting environmental changes/novelty is of basic importance for adaptive behavior. By comparing the current context with the previous one, living organisms can make predictions and adjust their actions. The mechanisms and structures of the brain involved in the function of comparison have not yet been sufficiently elucidated. The available studies emphasize the special contribution of the hippocampus to the process of comparison; it is indicated that the identification of novelty is carried out by hippocampal neurons through the mechanisms of match/mismatch, or misalignment. Here, we provide information about existing hypotheses of how these mechanisms occur, which other brain structures are involved in detecting inconsistencies, how they are related to the hippocampus, and what processes contribute to this. In particular, it is assumed that it is not novelty in itself, but only novelty that contrasts with previously acquired experience that initiates the process of misalignment. The arguments that the theta rhythm plays a crucial role in the functioning of the hippocampus as a comparator are analyzed. Theta oscillations caused by the appearance of a new signal or a change in a situation mediate the mechanism of temporal coordination of structures involved in the comparison function. In comparison, the theta rhythm functions as an active filter: it participates in the selection and transmission of a new signal to the registration system in the hippocampus. An increase in theta oscillations and their coherence in the brain structures processing new information serves as a signal of misalignment, facilitating a change in behavior strategy. In addition to theta rhythm, gamma oscillations are also involved in comparison: during the generation of theta rhythm in the prefrontal cortex, the temporary coincidence of gamma oscillations in other areas of the brain with a certain phase of the theta cycle can perform the function of comparison during the memorization process. A deep understanding of the mechanisms of comparator function and its disorders can help in the treatment of pathologies such as schizophrenia, Alzheimer’s disease, and temporal lobe epilepsy.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 4","pages":"706 - 719"},"PeriodicalIF":4.033,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143496687","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":"Penetration of Polyphenols through Acetic Acid Damaged Skin","authors":"V. S. Shubina,&nbsp;Yu. V. Shatalin","doi":"10.1134/S0006350924700866","DOIUrl":"10.1134/S0006350924700866","url":null,"abstract":"<div><p>Previously, we showed that taxifolin derivatives, taxifolin pentaglutarate and a conjugate of taxifolin with glyoxylic acid, improve the mechanical properties of collagen-based materials. In the process of degradation of such materials, biologically active polyphenols are released into the surrounding medium. Two approaches were used to assess the penetration of polyphenols through damaged skin. In the case of taxifolin pentaglutarate and taxifolin (used for comparison), a fluorescent label was introduced into the structure of the polyphenol. In the case of the conjugate, a fluorescent analogue was obtained. It has been shown that the application of polyphenolic compounds on the damaged skin leads to the formation of a fluorescent layer on its surface. Fluorescent derivatives of taxifolin and taxifolin pentaglutarate have been found to accumulate in hair follicles. In the case of taxifolin, fluorescence was observed in deeper layers of the dermis than in the case of taxifolin pentaglutarate, indicating better penetration of taxifolin. The fluorescent analog accumulated in the appendages of the skin to a lesser extent than other compounds. Thus, the data we obtained indicate the accumulation of polyphenols in the hair follicles, from which they can gradually be released into the surrounding tissue. In general, the results we obtained indicate that biologically active polyphenols are able to exert a prolonged effect when applied topically. This may be important in the treatment of burns, in particular in the treatment of second-degree burns, in which many skin derivatives remain intact.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 4","pages":"784 - 791"},"PeriodicalIF":4.033,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143496748","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 Degree of Specificity of Synaptic Contacts during Neurotransplantation","authors":"Z. N. Zhuravleva","doi":"10.1134/S0006350924700738","DOIUrl":"10.1134/S0006350924700738","url":null,"abstract":"<div><p>Transplantation of immature nerve tissue is a promising biotechnological approach to repair damaged brain tissue. The success of transplantation therapy depends on a genetic program for the differentiation of donor neuronal precursors and the accuracy of neural connections both in the neurotransplants themselves and in the recipient’s brain. The degree of specificity of synaptic contacts during transplantation of the hippocampal formation into the rat neocortex was studied. Using the method of electron microscopy, it was shown that in the transplants themselves mainly specific forms of synapses were differentiated, which were topographically correctly located on the soma-dendritic surface of neurons. The axons of the transplanted neurons growing into the recipient’s brain formed synaptic contacts with normally unusual neurons. During the formation of nonspecific axonal connections, they modified the composition and distribution of neurotransmitter vesicles in presynaptic terminals, as well as inducing structural and chemical reorganization in postsynaptic dendrites.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 4","pages":"649 - 655"},"PeriodicalIF":4.033,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143496954","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":"1H-NMR Spectroscopy of Blood Plasma for Detection of Changes in Metabolism during the Development of M-1 Sarcoma in Rats","authors":"A. Y. Egorov,&nbsp;A. S. Bykov,&nbsp;T. I. Ponomareva,&nbsp;M. V. Molchanov,&nbsp;N. M. Pankratova,&nbsp;A. N. Pankratov,&nbsp;A. G. Arakelyan,&nbsp;S. N. Koryakin,&nbsp;M. A. Timchenko","doi":"10.1134/S0006350924700829","DOIUrl":"10.1134/S0006350924700829","url":null,"abstract":"<div><p>The effectiveness of ¹H-NMR-based metabolomic analysis for the detection of metabolic changes during carcinogenesis was assessed based on a comparison of the quantitative composition of metabolites in the blood plasma of healthy rats and rats that receiving M-1 sarcoma grafts. Plasma was collected from the rats under study on day 12 and day 36 after sarcoma transplantation to identify metabolites associated with tumor development. Analysis of the NMR spectra using multivariate statistical methods showed differences in the composition of metabolites for the groups of animals under study as soon as on day 12 after sarcoma transplantation; on day 36 the differences were significant. Twenty three metabolites were quantified. On day 12, only the lactate and allantoin levels were significantly different between the groups, while on day 36, the levels of nine metabolites were different between the two groups. All of the identified metabolites are involved in cancer metabolism, which makes ¹H-NMR spectroscopy a promising method for cancer diagnosis.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 4","pages":"738 - 748"},"PeriodicalIF":4.033,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143496956","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":"Increased Drug Resistance in Acute lymphoblastic Leukemia Cells in Three-Dimensional High-Density Cell Cultures","authors":"D. Y. Shtatnova,&nbsp;M. I. Kobyakova,&nbsp;Ya. V. Lomovskaya,&nbsp;E. I. Fetisova,&nbsp;K. S. Krasnov,&nbsp;R. S. Fadeev","doi":"10.1134/S0006350924700775","DOIUrl":"10.1134/S0006350924700775","url":null,"abstract":"<p>In this study, the development process of drug resistance in acute lymphoblastic leukemia cells (Jurkat, MOLT 3, and MOLT 4 cell lines) was examined in high-density cell cultures. It has been shown that in high- density cultures of acute lymphoblastic leukemia cells resistance to the action of chemotherapeutic drugs in- creases comparing to the cells cultured under low-density conditions. The results obtained after investigation of the mechanism underlying increased drug resistance in acute lymphoblastic leukemia cells in high-density cell cultures showed that an increase in drug resistance in high-density cultures of cells can be mediated by a change in their proliferative activity. These findings can be applied in developing a strategy to overcome drug resistance in acute lymphoblastic leukemia cells, which depends on the density of the cell culture.</p>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 4","pages":"692 - 696"},"PeriodicalIF":4.033,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143496960","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":"Proteins of the Hepatopancreas of the Snow Crab and Red King Crab with Antibacterial Activity","authors":"V. G. Molchanov,&nbsp;A. Y. Yegorov,&nbsp;D. A. Osetrina,&nbsp;V. Yu. Novikov,&nbsp;N. M. Novojilov,&nbsp;A. A. Timchenko,&nbsp;E. A. Sogorin,&nbsp;M. A. Timchenko","doi":"10.1134/S0006350924700787","DOIUrl":"10.1134/S0006350924700787","url":null,"abstract":"<div><p>During their long existence, crustaceans, despite the absence of a highly specific adaptive immune system, like vertebrates, have successfully adapted to survive in their natural habitat that is rich in microorganisms, in particular, due to antimicrobial peptides. One valuable source of antimicrobial peptides is the hepatopancreas (HPC), which is a waste product of crab fishing and processing. Using the method of zymography and ¹H-NMR spectroscopy we found that an extract from the hepatopancreas of the snow crab contains a small peptide (about 3 kDa) that hydrolyzes the cell wall and polysaccharide of the cell wall of <i>M. lysodeikticus</i>. This peptide may be of interest for practical use. A protein (about 14 kDa) was isolated from the hepatopancreas of the Red king crab using heparin–sepharose chromatography, which also exhibits activity against the cell wall of the gram-positive bacterium <i>M. lysodeikticus</i>, as was shown by zymography and turbidimetry.</p></div>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"69 4","pages":"697 - 705"},"PeriodicalIF":4.033,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143496961","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}