Biophysical reports最新文献_第5页

Menthol's disruptive effects on kanamycin-resistant Escherichia coli energy metabolism and ion fluxes. 薄荷醇对耐卡那霉素大肠杆菌能量代谢和离子通量的破坏作用。

IF 2.7

Biophysical reports Pub Date : 2025-12-10 Epub Date: 2025-11-20 DOI: 10.1016/j.bpr.2025.100240

Silvard Tadevosyan, Siranuysh Grabska, Hovakim Grabski, Ruben Abagyan, Karen Trchounian, Naira Sahakyan

引用次数: 0

Optimizing a coarse-grained model for large-scale membrane protein simulation. 大尺度膜蛋白模拟的粗粒度模型优化。

IF 2.6

Biophysical reports Pub Date : 2025-12-10 Epub Date: 2025-11-06 DOI: 10.1016/j.bpr.2025.100238

Chen Yun Wen, Yun Lyna Luo, Jesper J Madsen

引用次数: 0

Thank you to our reviewers. 感谢我们的审稿人。

IF 2.7

Biophysical reports Pub Date : 2025-12-09 DOI: 10.1016/j.bpr.2025.100239

引用次数: 0

Spatial confinement alters morphology, spreading dynamics, and mechanics of adherent platelets. 空间限制改变了血小板粘附的形态、扩散动力学和力学。

IF 2.7

Biophysical reports Pub Date : 2025-09-10 Epub Date: 2025-07-24 DOI: 10.1016/j.bpr.2025.100222

Johanna G Rodríguez, Jan Seifert, Vincent Gidlund, Carmela Rianna, Tilman E Schäffer

{"title":"Spatial confinement alters morphology, spreading dynamics, and mechanics of adherent platelets.","authors":"Johanna G Rodríguez, Jan Seifert, Vincent Gidlund, Carmela Rianna, Tilman E Schäffer","doi":"10.1016/j.bpr.2025.100222","DOIUrl":"10.1016/j.bpr.2025.100222","url":null,"abstract":"Platelets are small blood cells involved in hemostasis and wound healing. After activation, platelets interact with their surrounding environment and respond to biochemical and mechanical stimuli by mechanosensitive and haptotactic mechanisms. We used microcontact printing (μCP) to mimic the physiological conditions and limited space in small blood vessels in vitro. With μCP, we created 4-μm-wide fibrinogen lines to provide a spatially confined spreading space for platelets. We then let platelets adhere and spread on these lines while imaging them with optical microscopy and scanning ion conductance microscopy (SICM). Confined platelets showed significantly altered morphology, spreading dynamics, and mechanics compared with control platelets. Altered mechanical properties of confined platelets revealed reorganization of the actin cytoskeleton and the formation of regions of increased elastic modulus at the edges of the fibrinogen lines. Our results indicate that spatial confinement affects platelet mechanics and morphology on a subcellular level.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100222"},"PeriodicalIF":2.7,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12355061/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Reaction-diffusion model for brain spacetime dynamics. 脑时空动力学的反应-扩散模型。

IF 2.7

Biophysical reports Pub Date : 2025-09-10 Epub Date: 2025-06-16 DOI: 10.1016/j.bpr.2025.100220

Qiang Li, Vince D Calhoun

{"title":"Reaction-diffusion model for brain spacetime dynamics.","authors":"Qiang Li, Vince D Calhoun","doi":"10.1016/j.bpr.2025.100220","DOIUrl":"10.1016/j.bpr.2025.100220","url":null,"abstract":"The human brain exhibits intricate spatiotemporal dynamics, which can be described and understood through the framework of complex dynamic systems theory. In this study, we leverage functional magnetic resonance imaging (fMRI) data to investigate reaction-diffusion processes in the brain. A reaction-diffusion process refers to the interaction between two or more substances that spread through space and react with each other over time, often resulting in the formation of patterns or waves of activity. Building on this empirical foundation, we apply a reaction-diffusion framework inspired by theoretical physics to simulate the emergence of brain spacetime vortices within the brain. By exploring this framework, we investigate how reaction-diffusion processes can serve as a compelling model to govern the formation and propagation of brain spacetime vortices, which are dynamic, swirling patterns of brain activity that emerge and evolve across both time and space within the brain. Our approach integrates computational modeling with fMRI data to investigate the spatiotemporal properties of these vortices, offering new insights into the fundamental principles of brain organization. This work highlights the potential of reaction-diffusion models as an alternative framework for understanding brain spacetime dynamics.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100220"},"PeriodicalIF":2.7,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12256317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enhancing the applied force and range of axial optical tweezers. 提高轴向光镊的受力和作用范围。

IF 2.7

Biophysical reports Pub Date : 2025-09-10 Epub Date: 2025-06-16 DOI: 10.1016/j.bpr.2025.100219

Zheng Zhang, Joshua N Milstein

引用次数: 0

Escherichia coli FocA/B-dependent H⁺ and K⁺ fluxes: Influence of exogenous versus endogenous formate. 大肠杆菌FocA/ b依赖性H+和K+通量：外源与内源甲酸的影响

IF 2.7

Biophysical reports Pub Date : 2025-09-10 Epub Date: 2025-08-08 DOI: 10.1016/j.bpr.2025.100225

L Grigoryan, A Babayan, A Vassilian, A Poladyan, G Sawers, K Trchounian

{"title":"Escherichia coli FocA/B-dependent H+ and K+ fluxes: Influence of exogenous versus endogenous formate.","authors":"L Grigoryan, A Babayan, A Vassilian, A Poladyan, G Sawers, K Trchounian","doi":"10.1016/j.bpr.2025.100225","DOIUrl":"10.1016/j.bpr.2025.100225","url":null,"abstract":"Escherichia coli translocates formate/formic acid bidirectionally across the cytoplasmic membrane by the FocA/FocB formate channels during fermentation. Depending on the pH and whether formate is supplied exogenously or generated internally, the mechanisms of translocation differ. This study elucidates the role of these channels in dependence on FOF1 ATPase activity in stationary phase cells after cultivation by mixed-carbon fermentation at pH 7.5. In cells cultivated with glucose plus glycerol, exogenously added formate increased the N,N'-dicyclohexylcarbodiimide (DCCD)-sensitive (FOF1 ATPase-dependent) proton flux in single or double foc mutants. Moreover, exogenously supplied formate also increased the DCCD-sensitive potassium flux, but only in mutants where focB was absent. In the cells grown on glucose, glycerol, and formate, addition of formate in the whole-cell assays increased FOF1 ATPase activity by ∼60% compared with cells grown on a mixture of only glucose and glycerol. In a focA mutant cultivated to the stationary phase on glucose, glycerol, and formate, FOF1 ATPase activity was double that compared with cells grown on only glucose and glycerol, while in a focA-focB double-null mutant FOF1 ATPase activity decreased by ∼50% in formate assays. These data suggest that the cell regulates the mechanism of formate translocation depending on whether formate is generated internally or added exogenously. Thus, FOF1-ATPase activity and the FocA/FocB channels together with formate hydrogenlyase activity combine to balance pH and ion gradients during fermentation in stationary phase cells in response to whether formate is generated metabolically or supplied in high concentration from the environment.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100225"},"PeriodicalIF":2.7,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12396580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144818418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantification of mechanical-cytoskeletal coupling in human corneal cells across myopia severity. 人角膜细胞机械-细胞骨架偶联在近视严重程度上的定量分析。

IF 2.7

Biophysical reports Pub Date : 2025-09-10 Epub Date: 2025-05-20 DOI: 10.1016/j.bpr.2025.100213

Geng Junyuan, Lu Yue, Li Shuangcheng, Wang Yan, Zhao Xin

{"title":"Quantification of mechanical-cytoskeletal coupling in human corneal cells across myopia severity.","authors":"Geng Junyuan, Lu Yue, Li Shuangcheng, Wang Yan, Zhao Xin","doi":"10.1016/j.bpr.2025.100213","DOIUrl":"10.1016/j.bpr.2025.100213","url":null,"abstract":"Myopia is a prevalent refractive eye disorder closely associated with alterations in corneal biomechanical properties. As fundamental units of corneal tissue, corneal cells significantly influence myopia progression through their nanomechanical characteristics. However, the biophysical mechanisms underlying this process, particularly in human corneal cells, remain unclear. This study investigates the coupling between mechanical properties and cytoskeletal morphology in human corneal cells across varying myopia severity levels. Utilizing atomic force microscopy (AFM), the Young's modulus and adhesion properties of corneal cells obtained from patients with low, moderate, and high myopia were assessed. Additionally, the cytoskeletal morphological variations were quantified by calculating the fractal dimension from AFM topography images. Experimental results reveal that with increasing myopia severity, corneal cells exhibit decreased stiffness, increased adhesion, and reduced regularity and stability of the cytoskeletal network. This evidence highlights a coupling relationship between biomechanical properties and cytoskeletal morphology in human corneal cells during myopia development at the cellular scale, offering significant insights into the pathogenesis of myopia and potential avenues for innovative preventive strategies. VIDEO ABSTRACT.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100213"},"PeriodicalIF":2.7,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12171550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Single-molecule localization microscopy error is sensor dependent and larger than theory predicts. 单分子定位显微镜的误差与传感器有关，并且比理论预测的要大。

IF 2.7

Biophysical reports Pub Date : 2025-09-10 Epub Date: 2025-07-24 DOI: 10.1016/j.bpr.2025.100223

Alfonso Brenlla, Laila Deen, Paolo Annibale

{"title":"Single-molecule localization microscopy error is sensor dependent and larger than theory predicts.","authors":"Alfonso Brenlla, Laila Deen, Paolo Annibale","doi":"10.1016/j.bpr.2025.100223","DOIUrl":"10.1016/j.bpr.2025.100223","url":null,"abstract":"Since the advent of stochastic localization microscopy approaches in 2006, the number of studies employing this strategy to investigate the subdiffraction limit features of fluorescently labeled structures in biology, biophysics and solid state samples has increased exponentially. Underpinning all these approaches is the notion that the position of single molecules can be determined to high precision, provided enough photons are collected. The determination of exactly how precisely, has been demanded to formulas that try to approximate the so-called Cramer-Rao lower bound based on input parameters such as the number of photons collected from the molecules, or the size of the camera pixel. These estimates should, however, be matched to the experimental localization precision, which can be easily determined if, instead of looking at single beads, we study the distance between a pair. We revisit here a few key works, observing how these theoretical determinations tend to routinely underestimate the experimental localization precision of the order of a factor 2. A software-independent metric to determine, based on each individual setup, the appropriate value to set on the localization error of individual emitters is provided.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100223"},"PeriodicalIF":2.7,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12347845/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Assessing protein-lipid interactions with a low-cost, accessible centrifugation assay. 评估蛋白质-脂质相互作用与低成本，易于获得的离心试验。

IF 2.7

Biophysical reports Pub Date : 2025-09-10 Epub Date: 2025-07-25 DOI: 10.1016/j.bpr.2025.100224

Citlayi G Villaseñor, Alexandra Karagiaridi, Valentina S Dimitrova, Delfin G Buyco, Isabella Candal, Anastasia Smirnova, Heather W Pinkett, Neha P Kamat

{"title":"Assessing protein-lipid interactions with a low-cost, accessible centrifugation assay.","authors":"Citlayi G Villaseñor, Alexandra Karagiaridi, Valentina S Dimitrova, Delfin G Buyco, Isabella Candal, Anastasia Smirnova, Heather W Pinkett, Neha P Kamat","doi":"10.1016/j.bpr.2025.100224","DOIUrl":"10.1016/j.bpr.2025.100224","url":null,"abstract":"Assessing protein insertion and association with membranes is often a critical step that follows protein synthesis for both fundamental studies on protein folding and structure as well as translational applications that harness proteins for their activity. Traditionally, membrane protein association with membranes involves ultracentrifugation, which can be time-consuming and inaccessible in low-resource scientific environments. In this study, we develop an accessible method to purify vesicle-integrated cell-free expressed proteins from unincorporated protein or lysed membranes. We use a table-top microcentrifuge, capable of reaching speeds up to 21,130 × g, and a sucrose gradient to effectively separate the bulk of the cell-free expression components from proteoliposomes. We validate our approach can be used to measure membrane association of a variety of proteins, such as peripheral and transmembrane proteins as well as lipid-specific proteins, and that our method can be extended to membrane proteins derived from cellular membranes. Our approach provides a more accessible, cost-effective, and low-volume alternative for isolating proteoliposomes from misfolded and unassociated membrane proteins that should be applicable for fundamental biophysical studies and applications involving cell-free expressed membrane proteins.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100224"},"PeriodicalIF":2.7,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12406267/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144735799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0