Biophysical reports最新文献

Scanning electron microscopy of hyphal ectobiont bacteria within mycelial extracellular matrices. 菌丝胞外基质内菌丝外生菌的扫描电镜。

IF 2.7

Biophysical reports Pub Date : 2025-09-11 DOI: 10.1016/j.bpr.2025.100233

Davin Browner, Andrew Adamatzky

{"title":"Scanning electron microscopy of hyphal ectobiont bacteria within mycelial extracellular matrices.","authors":"Davin Browner, Andrew Adamatzky","doi":"10.1016/j.bpr.2025.100233","DOIUrl":"10.1016/j.bpr.2025.100233","url":null,"abstract":"Fungi and bacteria are found living in a wide variety of environments, and their interactions are important in many processes including soil health, human and animal physiology, and in biotechnological applications. Here, we investigate a single morphological feature of cocultures of planktonic bacterial growth within biofilm-forming liquid cultures of mycelium, namely, the attachment of bacterial ectobionts of species Bacillus subtilis to fungal hyphae of species Hericium erinaceus. The bacteria-in-mycelial-biofilm method was developed and utilized to allow for attachment of bacteria to hyphae via containment within exopolymeric substances (EPS) and the overall extracellular matrix of the mycelium. A graded dehydration protocol was used to selectively remove extraneous biofilm components and reveal intact bacteria and surface-interfacing features. The dehydration methods allowed for identification of specific interactions and differentiated these cultures from trivial stochastic mixing of bacteria and mycelium in liquid media. Attachment structures appear to be produced primarily by the mycelium and enveloped the bacterial ectobiont. Nanoscale surface-interfacing EPS constituents were preserved, providing a biophysical basis for a range of contact-dependent modulating properties of the bacteria on this fungal host. The mean biofilm area across triplicates was 3.90μm2±0.72μm2, and the mean percentage coverage was 18.33%±5.52%. The bacterial biofilm components could not be ruled out as co-contributing to formation of attachment structures due to the structures being present connecting individual bacteria as well as to hyphae.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100233"},"PeriodicalIF":2.7,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058734","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}

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

ATLAS: Machine learning-enhanced filament analysis for the In Vitro Motility Assay. 动态试验中习得肌动蛋白结构（ATLAS）的自动跟踪。

IF 2.7

Biophysical reports Pub Date : 2025-09-10 Epub Date: 2025-06-21 DOI: 10.1016/j.bpr.2025.100221

Sebastian Duno-Miranda, David M Warshaw, Shane R Nelson

{"title":"ATLAS: Machine learning-enhanced filament analysis for the In Vitro Motility Assay.","authors":"Sebastian Duno-Miranda, David M Warshaw, Shane R Nelson","doi":"10.1016/j.bpr.2025.100221","DOIUrl":"10.1016/j.bpr.2025.100221","url":null,"abstract":"The In Vitro Motility Assay (IVMA) is a widely used experimental system to study the chemical and mechanical activity of myosin and other cytoskeletal motor proteins. In the IVMA, myosin molecules are bound to a glass surface and propel fluorescently labeled actin filaments across the surface, which are recorded using video fluorescence microscopy. The length and velocity of the actin filaments offer a measurement of the chemomechanical activity of the myosin motor proteins. Although the assay itself is well suited for high-throughput application, current video analysis approaches are slow, labor intensive, and subject to human bias. To address this shortfall, we introduce ATLAS, an open-source, platform independent software package that utilizes state-of-the-art machine learning algorithms to identify fluorescently labeled actin filaments and then track and analyze their motion in the IVMA. Utilizing both experimental data and a large array of simulated actomyosin motility movies, we demonstrate that ATLAS accurately and efficiently measures both the velocity and length of actin filaments across a broad range of experimental conditions.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100221"},"PeriodicalIF":2.7,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12271436/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478035","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

Skeletal muscle alpha actin acetylation enhances myosin binding and increases calcium sensitivity. 骨骼肌α -肌动蛋白（ACTA1）乙酰化增强肌球蛋白结合并增加钙敏感性。

IF 2.7

Biophysical reports Pub Date : 2025-09-05 DOI: 10.1016/j.bpr.2025.100226

Samantha S Romanick, Luis Godoy, Adrian Lopez, Allison Matsumura, Kiana Boc, Travis J Stewart, Josh E Baker, Bradley S Ferguson

{"title":"Skeletal muscle alpha actin acetylation enhances myosin binding and increases calcium sensitivity.","authors":"Samantha S Romanick, Luis Godoy, Adrian Lopez, Allison Matsumura, Kiana Boc, Travis J Stewart, Josh E Baker, Bradley S Ferguson","doi":"10.1016/j.bpr.2025.100226","DOIUrl":"10.1016/j.bpr.2025.100226","url":null,"abstract":"Skeletal muscle alpha actin (ACTA1) is important for muscle contraction and relaxation, with historical studies focused on ACTA1 mutations in muscle dysfunction. Proteomics reports have consistently observed that actin, including ACTA1, is acetylated at multiple lysine sites. However, few reports have studied the effects of actin acetylation on cellular function, and fewer have examined ACTA1 acetylation on skeletal muscle function. Here, we aimed to examine how ACTA1 acetylation affected actomyosin interactions by determining actin sliding velocity, myosin binding, and calcium sensitivity. In this study, ACTA1 was chemically acetylated via acetic anhydride (AA) to increasing levels of acetylation: low-level acetylation (using 0.1 mM AA), mid-level acetylation (0.3 mM AA), and high-level acetylation (1 mM AA). We report that ACTA1 acetylation significantly decreased actin sliding velocity and actin filament length. Further analysis showed that ACTA1 acetylation significantly increased calcium sensitivity, with a loss of tropomyosin regulation noted with high-level ACTA1 acetylation. Lastly, ACTA1 acetylation enhanced skeletal myosin half maximal binding to actin. These data highlight acetylation as an additional posttranslational modification, outside of phosphorylation, in the regulation of muscle contraction and skeletal muscle alpha actin function.","PeriodicalId":72402,"journal":{"name":"Biophysical reports","volume":" ","pages":"100226"},"PeriodicalIF":2.7,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12478086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145016690","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