Journal of Biological Physics最新文献

{"title":"Analysis of SARS-CoV-2 interactions with the Vero cell lines by scanning electron microscopy","authors":"Zuzana Malá,&nbsp;Marek Vojta,&nbsp;Jan Loskot,&nbsp;Radek Sleha,&nbsp;Bruno Ježek,&nbsp;Josef Zelenka","doi":"10.1007/s10867-023-09638-y","DOIUrl":"10.1007/s10867-023-09638-y","url":null,"abstract":"<div><p>In this study, scanning electron microscopy (SEM) was used to study the cell structure of SARS-CoV-2 infected cells. Our measurements revealed infection remodeling caused by infection, including the emergence of new specialized areas where viral morphogenesis occurs at the cell membrane. Intercellular extensions for viral cell surfing have also been observed. Our results expand knowledge of SARS-CoV-2 interactions with cells, its spread from cell to cell, and their size distribution. Our findings suggest that SEM is a useful microscopic method for intracellular ultrastructure analysis of cells exhibiting specific surface modifications that could also be applied to studying other important biological processes.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 3","pages":"383 - 392"},"PeriodicalIF":1.8,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-023-09638-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5154716","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":"Correction to: In‑phase and anti‑phase bursting dynamics and synchronisation scenario in neural network by varying coupling phase","authors":"Thazhathethil Remi,&nbsp;Pallimanhiyil Abdulraheem Subha","doi":"10.1007/s10867-023-09637-z","DOIUrl":"10.1007/s10867-023-09637-z","url":null,"abstract":"","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 3","pages":"363 - 363"},"PeriodicalIF":1.8,"publicationDate":"2023-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-023-09637-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4578036","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-phase and anti-phase bursting dynamics and synchronisation scenario in neural network by varying coupling phase","authors":"Thazhathethil Remi,&nbsp;Pallimanhiyil Abdulraheem Subha","doi":"10.1007/s10867-023-09635-1","DOIUrl":"10.1007/s10867-023-09635-1","url":null,"abstract":"<div><p>We have analysed the synchronisation scenario and the rich spatiotemporal patterns in the network of Hindmarsh-Rose neurons under the influence of self, mixed and cross coupling of state variables which are realised by varying coupling phase. We have introduced a coupling matrix in the model to vary coupling phase. The excitatory and inhibitory couplings in the membrane potential induce in-phase and anti-phase bursting dynamics, respectively, in the two coupled system. When the off-diagonal elements of the matrix are zero, the system shows self coupling of the three variables, which helps to attain synchrony. The off-diagonal elements give cross interactions between the variables, which reduces synchrony. The stability of the synchrony attained is analysed using Lyapunov function approach. In our study, we found that self coupling in three variables is sufficient to induce chimera states in non-local coupling. The strength of incoherence and discontinuity measure validates the existence of chimera and multichimera states. The inhibitor self coupling in local interaction induces interesting patterns like Mixed Oscillatory State and clusters. The results may help in understanding the spatiotemporal communications of the brain, within the limitations of the size of the network analysed in this study.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 3","pages":"345 - 361"},"PeriodicalIF":1.8,"publicationDate":"2023-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-023-09635-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4986367","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":"Modified diffusive epidemic process on Apollonian networks","authors":"David Alencar,&nbsp;Antonio Filho,&nbsp;Tayroni Alves,&nbsp;Gladstone Alves,&nbsp;Ronan Ferreira,&nbsp;Francisco Lima","doi":"10.1007/s10867-023-09634-2","DOIUrl":"10.1007/s10867-023-09634-2","url":null,"abstract":"<div><p>We present an analysis of an epidemic spreading process on an Apollonian network that can describe an epidemic spreading in a non-sedentary population. We studied the modified diffusive epidemic process using the Monte Carlo method by computational analysis. Our model may be helpful for modeling systems closer to reality consisting of two classes of individuals: susceptible (A) and infected (B). The individuals can diffuse in a network according to constant diffusion rates <span>(D_{A})</span> and <span>(D_{B})</span>, for the classes A and B, respectively, and obeying three diffusive regimes, i.e., <span>(D_{A}&lt;D_{B})</span>, <span>(D_{A}=D_{B})</span>, and <span>(D_{A}&gt;D_{B})</span>. Into the same site <i>i</i>, the reaction occurs according to the dynamical rule based on Gillespie’s algorithm. Finite-size scaling analysis has shown that our model exhibits continuous phase transition to an absorbing state with a set of critical exponents given by <span>(beta /nu =0.66(1))</span>, <span>(1/nu =0.46(2))</span>, and <span>(gamma '/nu =-0.24(2))</span> familiar to every investigated regime. In summary, the continuous phase transition, characterized by this set of critical exponents, does not have the same exponents of the mean-field universality class in both regular lattices and complex networks.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 3","pages":"329 - 343"},"PeriodicalIF":1.8,"publicationDate":"2023-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-023-09634-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5105003","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":"Evaluation of copper-induced biomolecular changes in different porin mutants of Escherichia coli W3110 by infrared spectroscopy","authors":"Gulcin Cetin Kilicaslan,&nbsp;Rafig Gurbanov,&nbsp;Cihan Darcan","doi":"10.1007/s10867-023-09632-4","DOIUrl":"10.1007/s10867-023-09632-4","url":null,"abstract":"<div><p>Copper (Cu), one of the heavy metals, plays a vital role in many complex biochemical reactions as a trace element. However, it often becomes toxic when its concentration in the cell exceeds a certain level. Homeostasis of metals in the cell is primarily related to regulating metal transport into and out of the cell. Therefore, it is thought that porin proteins, which have a role in membrane permeability, may also play a role in developing Cu resistance. This study identified the differences between the molecular profiles of wild-type <i>Escherichia coli</i> W3110 and its seven different porin mutants exposed to Cu ions using attenuated total reflectance (ATR)–Fourier transform infrared (FTIR) spectroscopy. The results showed that the absence of porin genes elicits global changes in the structure and composition of membrane lipids and proteins, in both the absence and presence of Cu. The lack of porin genes significantly elevated the amounts of fatty acids and phospholipids. When the alterations in protein secondary structures were compared, the quantity of amide I proteins was diminished by the presence of Cu. However, the amount of amide II proteins increased in porin mutant groups independent of Cu presence or absence. The DNAs are transformed from B- and Z-form to A-form due to porin mutations and the presence of Cu ions. The lack of porin genes increased polysaccharide content independent of Cu presence. This study can help characterize Cu detoxification efficiency and guide for obtaining active living cells to be used in bioremediation.\u0000</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 3","pages":"309 - 327"},"PeriodicalIF":1.8,"publicationDate":"2023-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-023-09632-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4107679","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":"Effect of strain rates on the mechanical response of whole muscle bundle","authors":"Dat Trong Tran,&nbsp;Liren Tsai","doi":"10.1007/s10867-023-09630-6","DOIUrl":"10.1007/s10867-023-09630-6","url":null,"abstract":"<div><h2>Abstract\u0000</h2><div><p>Muscle injuries frequently happen during sports activities and exercise, which could have serious consequences if not diagnosed and treated promptly. This research aims to investigate the quasi-static and dynamic responses of over 30 fresh frog semitendinosus muscles utilizing Split Hopkinson Pressure Bars (SHPB) and a material testing system under strain rates between 0.001 ~ 200 s⁻¹. To accommodate the special shape of muscle–tendon-bone samples, PLA clampers were produced by the 3D printer to properly hold and prevent slipping during the testing process. The mechanical characteristics of the whole muscle bundle, including Young’s modulus and stress–strain curve, are illustrated at various strain rates. The findings showed that the muscle properties were sensitive to strain rate when under passive deformation. Both maximum stress and Young’s modulus increased with the rise of strain rate, and modulus at 200 s⁻¹ can be as high as 10 times compared with quasi-static conditions.\u0000</p></div></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 2","pages":"257 - 267"},"PeriodicalIF":1.8,"publicationDate":"2023-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-023-09630-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4451561","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":"A biomechanical view of epigenetic tumor regulation","authors":"Boyuan Zhao,&nbsp;Yonggang Lv","doi":"10.1007/s10867-023-09633-3","DOIUrl":"10.1007/s10867-023-09633-3","url":null,"abstract":"<div><p>The occurrence and development of tumors depend on a complex regulation by not only biochemical cues, but also biomechanical factors in tumor microenvironment. With the development of epigenetic theory, the regulation of biomechanical stimulation on tumor progress genetically is not enough to fully illustrate the mechanism of tumorigenesis. However, biomechanical regulation on tumor progress epigenetically is still in its infancy. Therefore, it is particularly important to integrate the existing relevant researches and develop the potential exploration. This work sorted out the existing researches on the regulation of tumor by biomechanical factors through epigenetic means, which contains summarizing the tumor epigenetic regulatory mode by biomechanical factors, exhibiting the influence of epigenetic regulation under mechanical stimulation, illustrating its existing applications, and prospecting the potential. This review aims to display the relevant knowledge through integrating the existing studies on epigenetic regulation in tumorigenesis under mechanical stimulation so as to provide theoretical basis and new ideas for potential follow-up research and clinical applications.</p><h3>Graphical Abstract</h3><p>Mechanical factors under physiological conditions stimulate the tumor progress through epigenetic ways, and new strategies are expected to be found with the development of epidrugs and related delivery systems.</p>\u0000 <figure><div><div><div><picture><source><img></source></picture></div></div></div></figure>\u0000 </div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 3","pages":"283 - 307"},"PeriodicalIF":1.8,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-023-09633-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4001614","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":"Revisiting and redefining return rate for determination of the precise growth status of a species","authors":"Ayan Paul,&nbsp;Neelakshi Chatterjee,&nbsp;Sabyasachi Bhattacharya","doi":"10.1007/s10867-023-09628-0","DOIUrl":"10.1007/s10867-023-09628-0","url":null,"abstract":"<div><p>Growth curve models play an instrumental role in quantifying the growth of biological processes and have immense practical applications across all disciplines. The most popular growth metric to capture the species fitness is the “Relative Growth Rate” in this domain. The different growth laws, such as exponential, logistic, Gompertz, power, and generalized Gompertz or generalized logistic, can be characterized based on the monotonic behavior of the relative growth rate (RGR) to size or time. Thus, in this case, species fitness can be determined truly through RGR. However, in nature, RGR is often non-monotonic and specifically bell-shaped, especially in the situation when a species is adapting to a new environment [1]. In this case, species may experience with the same fitness (RGR) for two different time points. The species precise growth and maturity status cannot be determined from this RGR function. The instantaneous maturity rate (IMR), as proposed by [2], helps to determine the correct maturity status of the species. Nevertheless, the metric IMR suffers from severe drawbacks; (i) IMR is intractable for all non-integer values of a specific parameter. (ii) The measure depends on a model parameter. The mathematical expression of IMR possesses the term “carrying capacity” which is unknown to the experimenter. (iii) Note that for identifying the precise growth status of a species, it is also necessary to understand its response when the populations are deflected from their equilibrium position at carrying capacity. This is an established concept in population biology, popularly known as the return rate. However, IMR does not provide information on the species deflection rate at the steady state. Hence, we propose a new growth measure connected with the species return rate, termed the “reverse of relative of relative growth rate” (henceforth, RRRGR), which is treated as a proxy for the IMR, having similar mathematical properties. Finally, we introduce a stochastic RRRGR model for specifying precise species growth and status of maturity. We illustrate the model through numerical simulations and real fish data. We believe that this study would be helpful for fishery biologists in regulating the favorable conditions of growth so that the species can reach a steady state with optimum effort.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 2","pages":"195 - 234"},"PeriodicalIF":1.8,"publicationDate":"2023-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-023-09628-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4872010","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":"Electrostatic effects on water-soluble fullerene derivatives interaction with cytochrome c and cytochrome c oxidase","authors":"Darya A. Poletaeva,&nbsp;Raisa A. Kotelnikova,&nbsp;Irina I. Faingold,&nbsp;Olga A. Kraevaya,&nbsp;Pavel A. Troshin,&nbsp;Alexander I. Kotelnikov","doi":"10.1007/s10867-023-09631-5","DOIUrl":"10.1007/s10867-023-09631-5","url":null,"abstract":"<div><h2>Abstract\u0000</h2><div><p>Water-soluble fullerene derivatives are good candidates for various biological applications such as anticancer or antimicrobial therapy, cytoprotection, enzyme inhibition, and many others. Their toxicity, both in tissue culture and in vivo, is a critical characteristic for the development and restriction of these applications. The effects of six water-soluble cationic and anionic polysubstituted fullerene derivatives on cytochrome c oxidase activity in rat brain mitochondria and the possibility of cytochrome c binding were studied. We found that the ability of these fullerene derivatives to bind with cytochrome c oxidase and charged molecules like eosin Y strongly depends on their electrostatic charge. As was shown, the cationic fullerene derivative inhibits cytochrome c oxidase that has the overall negative electrostatic potential completely, unlike anionic derivatives. Thus, it confirms the essential role of electrostatic interactions in the interaction of fullerene derivatives with the active site of enzymes. The results explore how cationic fullerene derivatives play a role in mitochondrial dysfunction, oxidative stress, and cytotoxicity.\u0000</p></div></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 2","pages":"269 - 282"},"PeriodicalIF":1.8,"publicationDate":"2023-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-023-09631-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4728797","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":"Probing the binding of morin with alpha-2-macroglobulin using multi-spectroscopic and molecular docking approach","authors":"Sana Ansari,&nbsp;Mohammad Khalid Zia,&nbsp;Shamila Fatima,&nbsp;Haseeb Ahsan,&nbsp;Fahim H. Khan","doi":"10.1007/s10867-023-09629-z","DOIUrl":"10.1007/s10867-023-09629-z","url":null,"abstract":"<div><p>Alpha-2-macroglobulin (α₂M) is an essential antiproteinase that is widely distributed in human plasma. The present study was aimed at investigating the binding of a potential therapeutic dietary flavonol, morin, with human α₂M using a multi-spectroscopic and molecular docking approach. Recently, flavonoid-protein interaction has gained significant attention, because a majority of dietary bioactive components interact with proteins, thereby altering their structure and function. The results of the activity assay exhibited a 48% reduction in the antiproteolytic potential of α₂M upon interaction with morin. Fluorescence quenching tests unequivocally confirmed quenching in the fluorescence of α₂M in the presence of morin, conforming complex formation and demonstrating that the binding mechanism involves a dynamic mode of interaction. Synchronous fluorescence spectra of α₂M with morin showed perturbation in the microenvironment around tryptophan residues. Furthermore, structural changes were observed through CD and FT-IR, showing alterations in the secondary structure of α₂M induced by morin. FRET further supports the results of the dynamic mode of quenching. Moderate interaction is shown by binding constant values using Stern–Volmer’s fluorescence spectroscopy. Morin binds to α₂M at 298 K with a binding constant of 2.7 × 10⁴ M⁻¹, indicating the strength of the association. The α₂M-morin system was found to have negative ΔG values, which suggests that the binding process was spontaneous. Molecular docking also reveals the different amino acid residues involved in this binding process, revealing that the binding energy is -8.1 kcal/mol.\u0000</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":"49 2","pages":"235 - 255"},"PeriodicalIF":1.8,"publicationDate":"2023-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10867-023-09629-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4545438","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}