Journal of Biological Physics最新文献

{"title":"Interaction of chloramphenicol with titin I27 probed using single-molecule force spectroscopy","authors":"Jyoti Yadav,&nbsp;Yashwant Kumar,&nbsp;Gayathri S. Singaraju,&nbsp;Shivprasad Patil","doi":"10.1007/s10867-021-09573-w","DOIUrl":"10.1007/s10867-021-09573-w","url":null,"abstract":"<div><p>Titin is a giant elastic protein which is responsible for passive muscle stiffness when muscle sarcomeres are stretched. Chloramphenicol, besides being a broad-spectrum antibiotic, also acts as a muscle relaxant. Therefore, it is important to study the interaction between titin I27 and chloramphenicol. We investigated the interaction of chloramphenicol with octamer of titin I27 using single-molecule force spectroscopy and fluorescence spectroscopy. The fluorescence data indicated that binding of chloramphenicol with I27 results in fluorescence quenching. Furthermore, it is observed that chloramphenicol binds to I27 at a particular concentration (<span>(sim )</span> 40 μM). Single-molecule force spectroscopy shows that, in the presence of 40 μM chloramphenicol concentration, the I27 monomers become mechanically stable, resulting in an increment of the unfolding force. The stability was further confirmed by chemical denaturation experiments on monomers of I27, which corroborate the evidence for enhanced mechanical stability at 40 μM drug concentration. The free energy of stabilization for I27 (wild type) was found to be 1.95 ± 0.93 kcal/mole and I27 with 40 μM drug was 3.25 ± 0.63 kcal/mole. The results show a direct effect of the broad-spectrum antibiotic chloramphenicol on the passive elasticity of muscle protein titin. The I27 is stabilized both mechanically and chemically by chloramphenicol.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10867-021-09573-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4036626","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":"Local hemodynamic analysis after coronary stent implantation based on Euler-Lagrange method","authors":"Yuchen Wang,&nbsp;Jingmei Zhan,&nbsp;Weiguo Bian,&nbsp;Xiaoli Tang,&nbsp;Min Zeng","doi":"10.1007/s10867-021-09571-y","DOIUrl":"10.1007/s10867-021-09571-y","url":null,"abstract":"<div><p>Coronary stents are deployed to treat the coronary artery disease (CAD) by reopening stenotic regions in arteries to restore blood flow, but the risk of the in-stent restenosis (ISR) is high after stent implantation. One of the reasons is that stent implantation induces changes in local hemodynamic environment, so it is of vital importance to study the blood flow in stented arteries. Based on regarding the red blood cell (RBC) as a rigid solid particle and regarding the blood (including RBCs and plasma) as particle suspensions, a non-Newtonian particle suspensions model is proposed to simulate the realistic blood flow in this work. It considers the blood’s flow pattern and non-Newtonian characteristic, the blood cell-cell interactions, and the additional effects owing to the bi-concave shape and rotation of the RBC. Then, it is compared with other four common hemodynamic models (Newtonian single-phase flow model, Newtonian Eulerian two-phase flow model, non-Newtonian single-phase flow model, non-Newtonian Eulerian two-phase flow model), and the comparison results indicate that the models with the non-Newtonian characteristic are more suitable to describe the realistic blood flow. Afterwards, based on the non-Newtonian particle suspensions model, the local hemodynamic environment in stented arteries is investigated. The result shows that the stent strut protrusion into the flow stream would be likely to produce the flow stagnation zone. And the stent implantation can make the pressure gradient distribution uneven. Besides, the wall shear stress (WSS) of the region adjacent to every stent strut is lower than 0.5 Pa, and along the flow direction, the low-WSS zone near the strut behind is larger than that near the front strut. What’s more, in the regions near the struts in the proximal of the stent, the RBC particle stagnation zone is easy to be formed, and the erosion and deposition of RBCs are prone to occur. These hemodynamic analyses illustrate that the risk of ISR is high in the regions adjacent to the struts in the proximal and the distal ends of the stent when compared with struts in other positions of the stent. So the research can provide a suggestion on the stent design, which indicates that the strut structure in these positions of a stent should be optimized further.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2021-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10867-021-09571-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5051170","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":"Comparison of stenosis models for usage in the estimation of pressure gradient across aortic coarctation","authors":"Yubing Shi,&nbsp;Israel Valverde,&nbsp;Patricia V. Lawford,&nbsp;Heynric B. Grotenhuis,&nbsp;Philipp Beerbaum,&nbsp;D. Rodney Hose","doi":"10.1007/s10867-021-09572-x","DOIUrl":"10.1007/s10867-021-09572-x","url":null,"abstract":"<div><p>Non-invasive estimation of the pressure gradient in cardiovascular stenosis has much clinical importance in assisting the diagnosis and treatment of stenotic diseases. In this research, a systematic comparison is conducted to investigate the accuracy of a group of stenosis models against the MRI- and catheter-measured patient data under the aortic coarctation condition. Eight analytical stenosis models, including six from the literature and two proposed in this study, are investigated to examine their prediction accuracy against the clinical data. The two improved models proposed in this study consider comprehensively the Poiseuille loss, the Bernoulli loss in its exact form, and the entrance effect, of the blood flow. Comparison of the results shows that one of the proposed models demonstrates a cycle-averaged mean prediction error of −0.15 ± 3.03 mmHg, a peak-to-peak prediction error of −1.8 ± 6.89 mmHg, which is the best among the models studied.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2021-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10867-021-09572-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4983060","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 joint explanation of infant and old age mortality","authors":"Peter Richmond,&nbsp;Bertrand M. Roehner","doi":"10.1007/s10867-021-09569-6","DOIUrl":"10.1007/s10867-021-09569-6","url":null,"abstract":"<div><p>Infant deaths and old age deaths are very different. The former are mostly due to severe congenital malformations of one or a small number of specific organs. On the contrary, old age deaths are largely the outcome of a long process of deterioration which starts in the 20s and affects almost all organs. In terms of age-specific death rates, there is also a clear distinction: the infant death rate falls off with age, whereas the adult and old age death rate increases exponentially with age in conformity with Gompertz’s law. An additional difference is that whereas aging and old age death have been extensively studied, infant death received much less attention. To our knowledge, the two effects have never been inter-connected. Clearly, it would be satisfactory to explain the two phenomena as being two variants within the same explanatory framework. In other words, a mechanism providing a combined explanation for the two forms of mortality would be welcome. This is the purpose of the present paper. We show here that the same biological effects can account for the two cases provided there is a difference in their severity: death triggered by isolated lethal anomalies in one case and widespread wear-out anomalies in the second. We show that quite generally this mechanism leads indeed, respectively, to a declining and an upgoing death rate. Moreover, this theoretical framework leads to the conjecture that the severity of the death effects, whether in infancy or old age, is higher for organisms which comprised a larger number of organs. Finally, let us observe that the main focus of the paper is the drastic difference of the age-specific death rates (i.e., decreasing versus increasing) because this difference is found in many species, whereas the question of the best fit (e.g., Gompertz versus Weibull) is rather specific to human mortality.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2021-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10867-021-09569-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4977323","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":"Investigation of cellular morphology and proliferation on patterned electrospun PLA-gelatin mats","authors":"Alexandra Sergeevna Bogdanova,&nbsp;Anastasiia Ivanovna Sokolova,&nbsp;Elizaveta Robertovna Pavlova,&nbsp;Dmitry Vladimirovich Klinov,&nbsp;Dmitry Vladimirovich Bagrov","doi":"10.1007/s10867-021-09574-9","DOIUrl":"10.1007/s10867-021-09574-9","url":null,"abstract":"<div><p>The morphology and proliferation of eukaryotic cells depend on their microenvironment. When electrospun mats are used as tissue engineering scaffolds, the local alignment of the fibers has a pronounced influence on cells. Here we analyzed the morphology of the patterned mats produced by electrospinning of PLA-gelatin blend onto a conductive grid. We investigated the cellular morphology and proliferation of two cell lines (keratinocytes HaCaT and fibroblasts NIH 3T3) on the patterned mats. The non-patterned mats of the same chemical composition were used as control ones. The HaCaT cells predominantly grew on convex areas of the patterned mats along with increasing their nucleus area and decreasing cell area. The 3T3 cells had a lower proliferative rate when grown on the patterned mats. The results can be valuable for further development of the procedures, which allow the patterned electrospun mats development as well as for the investigation of cell-substrate interactions.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2021-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10867-021-09574-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4979853","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":"Unwrapping the phase portrait features of adventitious crackle for auscultation and classification: a machine learning approach","authors":"Sankararaman Sreejyothi,&nbsp;Ammini Renjini,&nbsp;Vimal Raj,&nbsp;Mohanachandran Nair Sindhu Swapna,&nbsp;Sankaranarayana Iyer Sankararaman","doi":"10.1007/s10867-021-09567-8","DOIUrl":"10.1007/s10867-021-09567-8","url":null,"abstract":"<div><p>The paper delves into the plausibility of applying fractal, spectral, and nonlinear time series analyses for lung auscultation. The thirty-five sound signals of bronchial (BB) and pulmonary crackle (PC) analysed by fast Fourier transform and wavelet not only give the details of number, nature, and time of occurrence of the frequency components but also throw light onto the embedded air flow during breathing. Fractal dimension, phase portrait, and sample entropy help in divulging the greater randomness, antipersistent nature, and complexity of airflow dynamics in BB than PC. The potential of principal component analysis through the spectral feature extraction categorises BB, fine crackles, and coarse crackles. The phase portrait feature-based supervised classification proves to be better compared to the unsupervised machine learning technique. The present work elucidates phase portrait features as a better choice of classification, as it takes into consideration the temporal correlation between the data points of the time series signal, and thereby suggesting a novel surrogate method for the diagnosis in pulmonology. The study suggests the possible application of the techniques in the auscultation of coronavirus disease 2019 seriously affecting the respiratory system.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2021-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10867-021-09567-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5449400","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":"Comparison of cultured cell attachment on a temperature-responsive polymer, poly-l-lysine, and collagen using modeling curves and a thermal-controlled quartz crystal microbalance","authors":"Abdullah Hussain A. Alsaleem,&nbsp;Sae Ito,&nbsp;Kiyoshi Naemura,&nbsp;Hiroshi Muramatsu","doi":"10.1007/s10867-021-09568-7","DOIUrl":"10.1007/s10867-021-09568-7","url":null,"abstract":"<div><p>The characteristics of cultured cell attachment onto poly-<span>l</span>-lysine (PLL), collagen, and the thermoresponsive polymer poly(<i>N</i>-isopropylacrylamide) (PNIPAM) were studied using a quartz crystal microbalance (QCM). A QCM with microscope cameras enclosed in a Peltier chamber was developed to enable QCM measurements and microphotographic imaging to be conducted in a temperature-controlled CO₂ incubator. Human hepatoma cell line HepG2 cells were cultured on the quartz crystals coated with PLL, collagen, and PNIPAM. Response curves of the resonant frequency of the quartz crystals during the cell attachment process were analyzed on the basis of the parameters of modeling curves fit to the experimentally obtained curves. Analysis of the fitting curves showed that the time constants of the first-lag response were 11?h for PLL, 16?h for collagen, and 38?h for PNIPAM and that the frequency change for the PNIPAM films was six times smaller than those for the PLL and collagen films. These findings were supported by photographic images showing wider cell spread on PLL and collagen than on PNIPAM. The response of cells on PNIPAM was measured during a thermal cycle from 37 to 20?°C to 37?°C. In the resonance frequency–resonance resistance (<i>F</i>–<i>R</i>) diagram, the slopes of Δ<i>R</i>/Δ<i>F</i> corresponding to the cell attachment process and those corresponding to the thermal cycling process differed; the positions in the <i>F</i>–<i>R</i> diagram also shifted to higher resonant frequencies after the thermal cycle. These results suggested that the mass effect decreased as a result of the weakening of the cell attachment strength by the thermal cycle because the molecular brushes of PNIPAM were disarranged.</p></div>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2021-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10867-021-09568-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4924721","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":"Logical modeling of thymus and natural killer lymphocyte differentiation","authors":"Jianting Ye,&nbsp;Qingxi Chen,&nbsp;Ruiqi Wang","doi":"10.1007/s10867-021-09563-y","DOIUrl":"https://doi.org/10.1007/s10867-021-09563-y","url":null,"abstract":"<p>Thymus (T) and natural killer (NK) lymphocytes are important barriers against diseases. Therefore, it is necessary to understand regulatory mechanisms related to the cell fate decisions involved in the production of these cells. Although some individual information related to T and NK lymphocyte cell fate decisions have been revealed, the related network and its dynamical characteristics still have not been well understood. By integrating individual information and comparing with experimental data, we construct a comprehensive regulatory network and a logical model related to T and NK lymphocyte differentiation. We aim to explore possible mechanisms of how each lineage differentiation is realized by systematically screening individual perturbations. When determining the perturbation strategies, the state transition can be used to identify the roles of specific genes in cell type selection and reprogramming. In agreement with experimental observations, the dynamics of the model correctly restates the cell differentiation processes from common lymphoid progenitors to CD4+ T cells, CD8+ T cells, and NK cells. Our analysis reveals that some specific perturbations can give rise to directional cell differentiation or reprogramming. We test our in silico results by using known experimental observations. The integrated network and the logical model presented here might be a good candidate for providing qualitative mechanisms of cell fate specification involved in T and NK lymphocyte cell fate decisions.</p>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2021-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10867-021-09563-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4728740","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":"Non-extensitivity and criticality of atomic hydropathicity around a voltage-gated sodium channel’s pore: a modeling study","authors":"Markos N. Xenakis,&nbsp;Dimos Kapetis,&nbsp;Yang Yang,&nbsp;Jordi Heijman,&nbsp;Stephen G. Waxman,&nbsp;Giuseppe Lauria,&nbsp;Catharina G. Faber,&nbsp;Hubert J. Smeets,&nbsp;Patrick J. Lindsey,&nbsp;Ronald L. Westra","doi":"10.1007/s10867-021-09565-w","DOIUrl":"https://doi.org/10.1007/s10867-021-09565-w","url":null,"abstract":"<p>Voltage-gated sodium channels (NavChs) are pore-forming membrane proteins that regulate the transport of sodium ions through the cell membrane. Understanding the structure and function of NavChs is of major biophysical, as well as clinical, importance given their key role in cellular pathophysiology. In this work, we provide a computational framework for modeling system-size-dependent, i.e., cumulative, atomic properties around a NavCh’s pore. We illustrate our methodologies on the bacterial NavAb channel captured in a closed-pore state where we demonstrate that the atomic environment around its pore exhibits a bi-phasic spatial organization dictated by the structural separation of the pore domains (PDs) from the voltage-sensing domains (VSDs). Accordingly, a mathematical model describing packing of atoms around NavAb’s pore is constructed that allows—under certain conservation conditions—for a power-law approximation of the cumulative hydropathic dipole field effect acting along NavAb’s pore. This verified the non-extensitivity hypothesis for the closed-pore NavAb channel and revealed a long-range hydropathic interactions law regulating atom-packing around the NavAb’s selectivity filter. Our model predicts a PDs-VSDs coupling energy of <span>(sim !282.1)</span> kcal/mol corresponding to a global maximum of the atom-packing energy profile. Crucially, we demonstrate for the first time how critical phenomena can emerge in a single-channel structure as a consequence of the non-extensive character of its atomic porous environment.</p>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2021-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10867-021-09565-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5021911","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":"Inclusion of Laponite nanoparticles in a lyotropic lamellar phase","authors":"Girlane Castro Costa Leite,&nbsp;Gilson Carlos Castro Costa Leite","doi":"10.1007/s10867-021-09564-x","DOIUrl":"https://doi.org/10.1007/s10867-021-09564-x","url":null,"abstract":"<p>In this work, we consider a ternary system formed by a surfactant with a lamellar phase (lecithin) that was doped with a solution of Laponite at 1% by volume. The inclusion of nanoparticles in the lamellar phase was investigated by the small-angle X-ray scattering (SAXS) technique, which revealed three types of structures according to the observed scattering pattern. The lamellar period increased linearly with hydration up to a certain limit; this type of behavior is not the same as that found for a similar system using AOT as a surfactant. In the region that corresponds to an isotropic phase, it was observed that the period corresponds to 60??, and in the lamellar system of pure lecithin, with the same volumetric fraction (1/<i>φ</i>?=?0.66), the corresponding periodicity is 62??, indicating that the presence of Laponite nanoparticles increases the attractive interaction, reducing the lamellar period, causing the bilayer to become more rigid, that is, with less fluctuations. In the more diluted region, the periodicity reached a limit value of 64??, which is slightly higher than the lamellar system in the absence of Laponite particles, so there was an expansion of the lamellar phase due to the lack of consistency of Laponite nanoparticles. In the more concentrated lamellar phase (under strong confinement), it was observed that the distance between the bilayers decreased, establishing a long-range order.</p>","PeriodicalId":612,"journal":{"name":"Journal of Biological Physics","volume":null,"pages":null},"PeriodicalIF":1.8,"publicationDate":"2021-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10867-021-09564-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4549256","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}