Biophysics最新文献

{"title":"Refinement of Nucleosome Positions within Individual Genes Using Molecular Modeling Methods and MNase Sequencing Data","authors":"V. A. Vasilev,&nbsp;D. M. Ryabov,&nbsp;A. K. Shaytan,&nbsp;G. A. Armeev","doi":"10.1134/S0006350923050317","DOIUrl":"10.1134/S0006350923050317","url":null,"abstract":"<p>Chromatin organization plays an important role in regulating the genetic machinery of the cell. A nucleosome is a basic unit of chromatin packaging and harbors about 145 bp of DNA. The packaging of genetic material and its accessibility to transcription enzymes and other regulatory chromatin proteins depend on the positions of nucleosomes. MNase sequencing is used to examine the nucleosome positions in a genome. MNase sequencing data are sufficient for detecting the presence of nucleosomes on a sequence, but their precise locations can be problematic to establish. Additional data filtering and processing are required for accurate determination of nucleosome positions. A combined method was developed using a geometric analysis of the molecular models of nucleosome chains to select the possible nucleosome positions on the basis of MNase sequencing data. The algorithm efficiently eliminates the inaccessible nucleosome chain combinations and conformationally prohibited nucleosome positions.</p>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"68 5","pages":"747 - 754"},"PeriodicalIF":4.033,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140884624","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 Roles of Nitric Oxide and Calcium Ions in the Effects of Hydrogen Sulfide on the Contractile Activity of the Rat Jejunum","authors":"D. M. Sorokina,&nbsp;I. F. Shaidullov,&nbsp;A. R. Gizzatullin,&nbsp;F. G. Sitdikov,&nbsp;G. F. Sitdikova","doi":"10.1134/S0006350923050287","DOIUrl":"10.1134/S0006350923050287","url":null,"abstract":"<p>The roles of nitric oxide, intra- and extracellular calcium in the effects of hydrogen sulfide on spontaneous and carbachol-induced contractions of rat jejunal preparation under conditions of isometric contraction were studied. A donor of H₂S (sodium hydrosulfide) led to a decrease in the preparation tone, amplitude and frequency of spontaneous contractions, as well as parameters of the contractions caused by carbachol, a nonspecific agonist of acetylcholine receptors. The effect of the H₂S donor persisted under conditions of the inhibition of endogenous NO synthesis with L-NAME, while in the presence of the action of SNAP (an NO donor), the effects of NaHS on the amplitudes of spontaneous and carbachol-induced contractions were less pronounced. A decrease in preparation tone under the effect of NaHS was prevented by dantrolene, a blocker of ryanodine receptors. The calcium-free solution decreased the inhibitory effect of NaHS on the contractions induced by the application of carbachol. It is suggested that the inhibitory effect of H₂S is associated with the dynamics of intracellular concentration of calcium ions, and the interaction of NO and H₂S occurs at the level of common targets of the effect of the two gases.</p>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"68 5","pages":"836 - 843"},"PeriodicalIF":4.033,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140884498","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":"Minimal Model of the Dependence of Stresses in a Cerebral Vessel Wall on Smooth Muscle Cell Parameters","authors":"N. Kh. Shadrina","doi":"10.1134/S0006350923050263","DOIUrl":"10.1134/S0006350923050263","url":null,"abstract":"<p>A minimal mathematical model of the wall of a small arterial vessel was created based on the published results of experiments with rat cerebral vessels. It was assumed that the active stress has only a circumferential component and depends on the circumferential stretch, the calcium concentration in the cytoplasm, and the membrane potential of smooth muscle cells. The model of a small artery qualitatively reproduces the results of more sophisticated models of other vessels under normal physiological conditions. Unlike in a similar model with a single cell parameter taken into account, the addition of the membrane potential as one of the main parameters made it possible to detect a qualitative change that occurs in the dependence of circumferential stress on the stretch and radial coordinate with a change in vascular tone. At fixed values of the membrane potential and calcium concentration in the phase of vascular tone development, the stress decreases towards the outer wall of the vessel and increases with the increasing stretch. Once the tone has formed, the direction of changes in circumferential stress reverses.</p>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"68 5","pages":"844 - 850"},"PeriodicalIF":4.033,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140073042","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":"Proteostasis of Heat Shock Protein HSP90 in Skeletal Muscles of the Long-Tailed Ground Squirrel during Hibernation","authors":"Yu. V. Gritsyna,&nbsp;S. S. Popova,&nbsp;G. Z. Mikhailova,&nbsp;L. G. Bobyleva,&nbsp;S. N. Udaltsov,&nbsp;O. S. Morenkov,&nbsp;N. M. Zakharova,&nbsp;I. M. Vikhlyantsev","doi":"10.1134/S000635092305010X","DOIUrl":"10.1134/S000635092305010X","url":null,"abstract":"<p>Changes in the content of heat shock protein 90 (HSP90) in m. soleus (contains mainly fibers expressing the “slow” isoform I MyHC) and m. gastrocnemius (contains mainly fibers expressing the “fast” isoforms II MyHC) of a true hibernant, the long-tailed ground squirrel (<i>Urocitellus undulatus</i>), during different periods of the annual cycle, summer activity (seasonal control), hypothermia/winter torpor, and winter (interbout) activity, were studied. It was found that despite the development of atrophic changes that were more pronounced in the “fast” m. gastrocnemius, the content of HSP90 in both muscles did not change throughout the hibernation period. The role of HSP90 in maintaining the stability of the titin giant sarcomeric protein molecules during the periods of the animal’s entry into and exit from hypothermia, when the activity of calpain proteases increased due to the increased content of Ca²⁺ in the cytosol of muscle cells, as well as during hypothermia, when the activity of calpains most likely was not completely inhibited, was discussed. During the winter/interbout activity, when there was an increased titin turnover in the striated ground squirrel muscles, a constant content of HSP90 was apparently necessary for the correct folding of newly synthesized titin molecules and their embedding into sarcomeres, as well as for the removal of improperly folded and old titin molecules/fragments, as well as other proteins. Thus, HSP90 proteostasis in skeletal muscles of the long-tailed ground squirrel could contribute to maintaining a stable level of titin and, possibly, other sarcomeric proteins during hibernation, which, in turn, would contribute to maintaining a highly ordered sarcomeric structure and the necessary level of contractile muscle activity in different phases of the hibernation–wakefulness cycle.</p>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"68 5","pages":"851 - 856"},"PeriodicalIF":4.033,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140073047","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":"Cell Cycle Parameters and Ornithine Decarboxylase Activity in the Red Bone Marrow of Hibernating Ground Squirrels Urocitellus undulatus","authors":"G. E. Aksyonova,&nbsp;O. S. Logvinovich,&nbsp;V. N. Afanasyev,&nbsp;K. I. Lizorkina","doi":"10.1134/S0006350923050032","DOIUrl":"10.1134/S0006350923050032","url":null,"abstract":"<p>During the hibernation season, the values for the parameters of the cell cycle of red bone marrow cells in the hibernating ground squirrels <i>Urocitellus undulatus</i>, when they return to an active-like state between periods of torpor and interbout arousal, do not differ from those observed in summer-active animals. In animals that enter a state of torpor, the cumulative percentage of cells in the resting phase (G₀ phase) and pre-synthesis phase (G₁ phase) increased from 71.8 to 76.0%, the percentage of cells in the synthesis phase (S phase) decreased from 19.3 to 15.3% compared to those animals that return to an active-like state between periods of torpor and interbout arousal. The cumulative percentage of cells in the post DNA synthesis phase (G₂ phase) and mitosis (M) does not change, but (G₂ + M)/S ratio increases. When animals enter a state of torpor, changes in parameter values are observed when the animal’s body temperature drops below 25°C; this effect refers to a system whose thermal relaxation time is a nonmonotonic function of the initial temperature. The activity of the key enzyme of polyamine synthesis ornithine decarboxylase, a marker of cell activation and proliferation during interbout arousal does not significantly differ from that observed in summer-active animals; the enzymatic activity decreases sharply, when animals decrease their body temperature below 25°C and enter the state of torpor, and this activity remains at a low level during hibernation and arousal until body temperature reaches 30°C. The role of changes in the parameter values associated with proliferative activity in adaptation of hematopoietic tissue during hibernation of the Yakutian ground squirrel is discussed.</p>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"68 5","pages":"792 - 799"},"PeriodicalIF":4.033,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140884690","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":"Searching for Sequencing Signal Anomalies Associated with Genomic Structural Variations","authors":"I. V. Bezdvornykh,&nbsp;N. A. Cherkasov,&nbsp;A. A. Kanapin,&nbsp;A. A. Samsonova","doi":"10.1134/S0006350923050056","DOIUrl":"10.1134/S0006350923050056","url":null,"abstract":"<p>Genomic structural variations (SVs) are among the main sources of genetic diversity. Structural variants as mutagens may significantly affect human health, causing hereditary diseases and cancers. Existing methods analyze high-throughput sequencing data to find structural variants. Despite substantial progress in their development, the methods still fail to detect structural variations with an accuracy sufficient for their use in diagnosis. Analysis of the sequencing coverage signal (i.e., the number of aligned sequencing reads for every point of a genome) holds the new potential for designing approaches to structural variation detection and can be used as time-series analysis. A method to detect repetitive patterns in the coverage signal was developed based on the time series-assessing algorithms KNN (K-nearest neighbor) and SAX (Symbolic Aggregation Approximation). Using the rich dataset encompassing the full genomes of 911 individuals with different ethnic backgrounds from the Human Genome Diversity Project, generalized patterns of the coverage signal were constructed for regions in the vicinity of breakpoints corresponding to various structural variant types. The patterns were used to develop a software package for fast detection of anomalies in the coverage signal.</p>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"68 5","pages":"755 - 759"},"PeriodicalIF":4.033,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140076531","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":"Analysis of the Development of Trends in the Current Epidemic Situation during Spread of the New SARS-CoV-2 Strains and Factors of their Regional Differentiation","authors":"A. Yu. Perevaryukha","doi":"10.1134/S0006350923050202","DOIUrl":"10.1134/S0006350923050202","url":null,"abstract":"&lt;p&gt;Specific processes of the local epidemic dynamics of COVID-19 are analyzed with a comparison of the qualitative differences between fluctuations in 2020 and 2023. A study using the methods of nonlinear dynamics on the development of epidemic processes in the context of a rapidly changing situation required classification of typical trends and unique situations that sometimes change at an extraordinary rate. A rather sharp change in the local trends is a distinctive feature of the modern pandemic: the effect at attenuation of the primary outbreak of morbidity and a sudden sharp beginning of a new epidemic wave after a long trend of decreasing daily infections. Minimizing the infections did not become a victory over the virus, but created a false illusion of success. The existing experience in constructing predictions based on the models of past epidemic processes did not help when encountering a new evolving virus. The previously obtained understanding of the development and completion of epidemic processes for influenza strains interfered when predicting the scenario for the completion of the distribution of the new infection, which is also associated with the event-based nature of the process and the variety of dynamic situations. The victory over COVID that was declared by many countries in the minimum phase after a peak was premature. New Zealand and Japan, which selected the strategy of strict lockdown measures in 2020 experienced an increase in the cases of infections at the beginning of 2023 due to new strains breaking through vaccine immunity. The pandemics of the “Spanish” flu and “swine” flu respiratory viruses (many individuals made predictions based on this analogy) died out naturally after the passage of two or three waves. At the beginning of 2023 (against the background of a global positive trend), a record increase in the indices of both mortality and daily morbidity due to the emergence of locally circulating “alarming” strains was observed in some countries. The current stage with the isolation of stable regional strains substantiates the classification of a number of differentiated properties of the dynamics of regional epidemic situations. Among the observed effects of the epidemic, extreme phenomena of instantaneous destruction of established regimes (a sharp transition from long-damping oscillations to a new exponential outbreak in the number of infections) upon bifurcation are separately highlighted. The selected variants for the development of epidemic transient oscillatory processes are individually described by equations with a delay for local epidemic trends. Equations for the description of three variants of development of the observed stages of local epidemics are proposed. At this stage, the task of constructing a generalizing predictive model of the pandemic for the description of interconnected regional processes is insoluble. The January 2024 Covid wave of recombinant strains JN, XDD from the descendants of the ","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"68 5","pages":"874 - 888"},"PeriodicalIF":4.033,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140073045","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 Specificity of Interactions between Endoinulinase from Aspergillus ficuum and Mono-, Di-, and Polysaccharides","authors":"S. M. Makin,&nbsp;A. N. Dubovitskaya,&nbsp;D. Yu. Bogomolov,&nbsp;M. S. Kondratyev,&nbsp;M. G. Holyavka,&nbsp;V. G. Artyukhov","doi":"10.1134/S0006350923050159","DOIUrl":"10.1134/S0006350923050159","url":null,"abstract":"<p>The aim of this study was to analyze the features of the spatial organization of the endoinulinase molecule from <i>Aspergillus ficuum</i> after its binding to mono-, di-, and polysaccharides. This study examined changes in volume and number of internal cavities upon binding of inulinase to mono- (glucose, fructose), di- (sucrose, mannose), and polysaccharides (inulin). Transformations in the quantity and length of tunnels and pores were described, and the reorganization of the composition and localization of charged and hydrophobic amino acid residues clusters on the surface of the enzyme molecule was analyzed. It was shown that the models of inulinase in the complex with sucrose (an alternative substrate) and mannose (an activator) exhibit the same types of internal structures. A similar pattern was found in the formation of complexes with fructose (a reaction product) and glucose (an inhibitor). In addition, it was established that both charged and hydrophobic clusters do not undergo significant changes in chemical composition after the binding of inulinase to mono-, di-, and polysaccharides, i.e., the interaction between inulinase and carbohydrates mentioned above primarily affects the internal structures of the enzyme. The specificity of the binding of inulinases to various ligands should be taken into account while developing modern industrial biocatalysts based on inulinase.</p>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"68 5","pages":"731 - 737"},"PeriodicalIF":4.033,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140076368","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 Combined Effects of Melatonin and Diethyldithiocarbamate on Mouse N1E-115 Neuroblastoma Cells (Clone C-1300)","authors":"S. N. Myakisheva,&nbsp;Y. L. Baburina,&nbsp;M. I. Kobyakova,&nbsp;R. R. Krestinin,&nbsp;L. D. Sotnikova,&nbsp;O. V. Krestinina","doi":"10.1134/S0006350923050184","DOIUrl":"10.1134/S0006350923050184","url":null,"abstract":"<p>The effects of sodium diethyldithiocarbamate, melatonin, and their combined use on proliferative activity, changes in cytosolic Ca²⁺, membrane potential, and production of reactive oxygen species in the culture of mouse N1E-115 neuroblastoma cells (clone C-1300) were studied. Sodium diethyldithiocarbamate and melatonin have been shown to inhibit proliferation and enhance cell differentiation. At the same time, the content of the anti-apoptotic protein Bcl-2 decreased, while the content of the pro-apoptotic protein Bax increased, which might suggest the launch of an apoptotic cascade. However, the use of these two drugs together did not enhance the observed effects. Apparently, the mechanisms by which diethyldithiocarbamates and melatonin acted on cells were different.</p>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"68 5","pages":"800 - 807"},"PeriodicalIF":4.033,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140076369","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 Taxifolin, a Conjugate of Taxifolin with Glyoxylic Acid, and Naringenin on the Functional Activity of Neutrophils","authors":"V. S. Shubina,&nbsp;M. I. Kobyakova,&nbsp;Yu. V. Shatalin","doi":"10.1134/S0006350923050275","DOIUrl":"10.1134/S0006350923050275","url":null,"abstract":"<p>The aim of this work was to study the effect of taxifolin, a conjugate of taxifolin with glyoxalic acid, and naringenin on the phagocytosis of latex beads by neutrophils and the adhesive properties of these cells. It has been shown that taxifolin did not affect the phagocytic activity and adhesive properties of neutrophils. The conjugate of taxifolin with glyoxylic acid significantly inhibited the phagocytic activity of neutrophils. The conjugate also significantly enhanced the adhesion of these cells. Naringenin reduced the phagocytic activity of neutrophils, however, to a lesser extent than the conjugate. Naringenin also inhibited the adhesion of neutrophils. The data obtained indicate that polyphenols can affect the functional activity of neutrophils; this effect can play an important role in modulating the inflammatory process, in particular when prolonged activation of neutrophils leads to damage of the body’s own cells and tissues.</p>","PeriodicalId":493,"journal":{"name":"Biophysics","volume":"68 5","pages":"772 - 778"},"PeriodicalIF":4.033,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140884803","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}