Physical biology最新文献_第2页

Low shear-induced fibrillar fibronectin: comparative analyses of morphologies and cellular effects on bovine aortic endothelial cell adhesion and proliferation. 低剪切力诱导的纤连蛋白：对牛主动脉内皮细胞粘附和增殖的形态和细胞效应的比较分析。

IF 2 4区生物学

Physical biology Pub Date : 2024-10-18 DOI: 10.1088/1478-3975/ad838c

Hoang-Nghi Mai-Thi, Dang Phu-Hai Nguyen, Phong Le, Ngoc Quyen Tran, Cam Tu Tran, Volker R Stoldt, Khon Huynh

{"title":"Low shear-induced fibrillar fibronectin: comparative analyses of morphologies and cellular effects on bovine aortic endothelial cell adhesion and proliferation.","authors":"Hoang-Nghi Mai-Thi, Dang Phu-Hai Nguyen, Phong Le, Ngoc Quyen Tran, Cam Tu Tran, Volker R Stoldt, Khon Huynh","doi":"10.1088/1478-3975/ad838c","DOIUrl":"10.1088/1478-3975/ad838c","url":null,"abstract":"Wall shear stress (WSS) is a critical factor in vascular biology, and both high and low WSS are implicated in atherosclerosis. Fibronectin (FN) is a key extracellular matrix protein that plays an important role in cell activities. Under high shear stress, plasma FN undergoes fibrillogenesis; however, its behavior under low shear stress remains unclear. This study aimed to investigate the formation ofin vitrocell-free fibrillar FN (FFN) under low shear rate conditions and its effect on bovine aortic endothelial cell behavior. FN (500µg ml-1) was perfused through slide chambers at three flow rates (0.16 ml h-1, 0.25 ml h-1, and 0.48 ml h-1), corresponding to low shear rates of 0.35 s-1, 0.55 s-1, and 1.05 s-1, respectively, for 4 h at room temperature. The formed FN matrices were observed using fluorescence microscopy and scanning electron microscopy. Under low shear rates, distinct FN matrix structures were observed. FFN0.48 formed immense fibrils with smooth surfaces, FFN0.25 formed a matrix with a rough surface, and FFN16 exhibited nodular structures. FFN0.25 supported cell activities to a greater extent than native FN and other FFN surfaces. Our study suggests that abnormally low shear conditions impact FN structure and function and enhance the understanding of FN fibrillogenesis in vascular biology, particularly in atherosclerosis.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142375818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring sperm cell rheotaxis in microfluidic channel: the role of flow and viscosity. 探索微流控通道中精子细胞的流变性：流动和粘度的作用

IF 2 4区生物学

Physical biology Pub Date : 2024-09-24 DOI: 10.1088/1478-3975/ad7b1a

Dhiraj B Puri, Paul Jacob, Vadiraj Hemadri, Arnab Banerjee, Siddhartha Tripathi

{"title":"Exploring sperm cell rheotaxis in microfluidic channel: the role of flow and viscosity.","authors":"Dhiraj B Puri, Paul Jacob, Vadiraj Hemadri, Arnab Banerjee, Siddhartha Tripathi","doi":"10.1088/1478-3975/ad7b1a","DOIUrl":"10.1088/1478-3975/ad7b1a","url":null,"abstract":"Rheotaxis is a fundamental mechanism of sperm cells that guides them in navigating towards the oocyte. The present study investigates the phenomenon of sperm rheotaxis in Newtonian and non-Newtonian fluid media, which for the first time explores a viscosity range equivalent to that of the oviductal fluid of the female reproductive tract in rectilinear microfluidic channels. Three parameters, the progressive velocity while performing rheotaxis, the radius of rotation during rheotaxis, and the percentage of rheotactic sperm cells in the bulk and near-wall regions of the microfluidic channel were measured. Numerical simulations of the flow were conducted to estimate the shear rate, flow velocity, and the drag force acting on the sperm head at specific locations where the sperms undergo rheotaxis. Increasing the flow velocity resulted in a change in the position of rheotactic sperm from the bulk center to the near wall region, an increase and subsequent decrease in the sperm's upstream progressive velocity, and a decrease in the radius of rotation. We observed that with an increase in viscosity, rheotactic sperms migrate to the near wall regions at lower flow rates, the upstream progressive velocity of the sperm decreases for Newtonian and increases for non-Newtonian media, and the radius of rotation increases for Newtonian and decreases for non-Newtonian media. These results quantify the effects of fluid properties such as viscosity and flow rate on sperm rheotaxis and navigation, thereby paving the way for manipulating sperm behavior in microfluidic devices, potentially leading to advancements in assisted reproduction techniques.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142293605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Application of coincidence index in the discovery of co-expressed metabolic pathways. 共现指数在发现共表达代谢途径中的应用

IF 2 4区生物学

Physical biology Pub Date : 2024-08-29 DOI: 10.1088/1478-3975/ad68b6

João Paulo Cassucci Dos Santos, Odemir Martinez Bruno

{"title":"Application of coincidence index in the discovery of co-expressed metabolic pathways.","authors":"João Paulo Cassucci Dos Santos, Odemir Martinez Bruno","doi":"10.1088/1478-3975/ad68b6","DOIUrl":"10.1088/1478-3975/ad68b6","url":null,"abstract":"Analyzing transcription data requires intensive statistical analysis to obtain useful biological information and knowledge. A significant portion of this data is affected by random noise or even noise intrinsic to the modeling of the experiment. Without robust treatment, the data might not be explored thoroughly, and incorrect conclusions could be drawn. Examining the correlation between gene expression profiles is one way bioinformaticians extract information from transcriptomic experiments. However, the correlation measurements traditionally used have worrisome shortcomings that need to be addressed. This paper compares five already published and experimented-with correlation measurements to the newly developed coincidence index, a similarity measurement that combines Jaccard and interiority indexes and generalizes them to be applied to vectors containing real values. We used microarray and RNA-Seq data from the archaeonHalobacterium salinarumand the bacteriumEscherichia coli, respectively, to evaluate the capacity of each correlation/similarity measurement. The utilized method explores the co-expressed metabolic pathways by measuring the correlations between the expression levels of enzymes that share metabolites, represented in the form of a weighted graph. It then searches for local maxima in this graph using a simulated annealing algorithm. We demonstrate that the coincidence index extracts larger, more comprehensive, and more statistically significant pathways for microarray experiments. In RNA-Seq experiments, the results are more limited, but the coincidence index managed the largest percentage of significant components in the graph.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141793171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Design principles of multi-map variation in biological systems. 生物系统中多图谱变异的设计原理。

IF 2 4区生物学

Physical biology Pub Date : 2024-07-10 DOI: 10.1088/1478-3975/ad5d6c

Juan F Poyatos

引用次数: 0

Instabilities and self-organization in spatiotemporal epidemic dynamics driven by nonlinearity and noise. 非线性和噪声驱动的时空流行动力学中的不稳定性和自组织。

IF 2 4区生物学

Physical biology Pub Date : 2024-07-10 DOI: 10.1088/1478-3975/ad5d6a

Aman Kumar Singh, Subramanian Ramakrishnan, Manish Kumar

{"title":"Instabilities and self-organization in spatiotemporal epidemic dynamics driven by nonlinearity and noise.","authors":"Aman Kumar Singh, Subramanian Ramakrishnan, Manish Kumar","doi":"10.1088/1478-3975/ad5d6a","DOIUrl":"10.1088/1478-3975/ad5d6a","url":null,"abstract":"Theoretical analysis of epidemic dynamics has attracted significant attention in the aftermath of the COVID-19 pandemic. In this article, we study dynamic instabilities in a spatiotemporal compartmental epidemic model represented by a stochastic system of coupled partial differential equations (SPDE). Saturation effects in infection spread-anchored in physical considerations-lead to strong nonlinearities in the SPDE. Our goal is to study the onset of dynamic, Turing-type instabilities, and the concomitant emergence of steady-state patterns under the interplay between three critical model parameters-the saturation parameter, the noise intensity, and the transmission rate. Employing a second-order perturbation analysis to investigate stability, we uncover both diffusion-driven and noise-induced instabilities and corresponding self-organized distinct patterns of infection spread in the steady state. We also analyze the effects of the saturation parameter and the transmission rate on the instabilities and the pattern formation. In summary, our results indicate that the nuanced interplay between the three parameters considered has a profound effect on the emergence of dynamical instabilities and therefore on pattern formation in the steady state. Moreover, due to the central role played by the Turing phenomenon in pattern formation in a variety of biological dynamic systems, the results are expected to have broader significance beyond epidemic dynamics.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141470356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Tradeoffs in the design of RNA thermometers. RNA 温度计设计中的取舍。

IF 2 4区生物学

Physical biology Pub Date : 2024-07-10 DOI: 10.1088/1478-3975/ad5d6b

Krishan Kumar Gola, Abhilash Patel, Shaunak Sen

引用次数: 0

Mechanical compression regulates tumor spheroid invasion into a 3D collagen matrix 机械压缩调节肿瘤小球向三维胶原基质的侵袭

IF 2 4区生物学

Physical biology Pub Date : 2024-04-15 DOI: 10.1088/1478-3975/ad3ac5

Mrinal Pandey, Young Joon Suh, Minha Kim, Hannah Jane Davis, Jeffrey E Segall, Mingming Wu

{"title":"Mechanical compression regulates tumor spheroid invasion into a 3D collagen matrix","authors":"Mrinal Pandey, Young Joon Suh, Minha Kim, Hannah Jane Davis, Jeffrey E Segall, Mingming Wu","doi":"10.1088/1478-3975/ad3ac5","DOIUrl":"https://doi.org/10.1088/1478-3975/ad3ac5","url":null,"abstract":"Uncontrolled growth of tumor cells in confined spaces leads to the accumulation of compressive stress within the tumor. Although the effects of tension within 3D extracellular matrices (ECMs) on tumor growth and invasion are well established, the role of compression in tumor mechanics and invasion is largely unexplored. In this study, we modified a Transwell assay such that it provides constant compressive loads to spheroids embedded within a collagen matrix. We used microscopic imaging to follow the single cell dynamics of the cells within the spheroids, as well as invasion into the 3D ECMs. Our experimental results showed that malignant breast tumor (MDA-MB-231) and non-tumorigenic epithelial (MCF10A) spheroids responded differently to a constant compression. Cells within the malignant spheroids became more motile within the spheroids and invaded more into the ECM under compression; whereas cells within non-tumorigenic MCF10A spheroids became less motile within the spheroids and did not display apparent detachment from the spheroids under compression. These findings suggest that compression may play differential roles in healthy and pathogenic epithelial tissues and highlight the importance of tumor mechanics and invasion.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"58 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140616327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dynamical model of antibiotic responses linking expression of resistance genes to metabolism explains emergence of heterogeneity during drug exposures. 抗生素反应动态模型将抗药性基因的表达与新陈代谢联系起来，解释了药物接触过程中出现的异质性。

IF 2 4区生物学

Physical biology Pub Date : 2024-04-02 DOI: 10.1088/1478-3975/ad2d64

Mirjana Stevanovic, João Pedro Teuber Carvalho, Philip Bittihn, Daniel Schultz

{"title":"Dynamical model of antibiotic responses linking expression of resistance genes to metabolism explains emergence of heterogeneity during drug exposures.","authors":"Mirjana Stevanovic, João Pedro Teuber Carvalho, Philip Bittihn, Daniel Schultz","doi":"10.1088/1478-3975/ad2d64","DOIUrl":"10.1088/1478-3975/ad2d64","url":null,"abstract":"Antibiotic responses in bacteria are highly dynamic and heterogeneous, with sudden exposure of bacterial colonies to high drug doses resulting in the coexistence of recovered and arrested cells. The dynamics of the response is determined by regulatory circuits controlling the expression of resistance genes, which are in turn modulated by the drug's action on cell growth and metabolism. Despite advances in understanding gene regulation at the molecular level, we still lack a framework to describe how feedback mechanisms resulting from the interdependence between expression of resistance and cell metabolism can amplify naturally occurring noise and create heterogeneity at the population level. To understand how this interplay affects cell survival upon exposure, we constructed a mathematical model of the dynamics of antibiotic responses that links metabolism and regulation of gene expression, based on the tetracycline resistancetetoperon inE. coli. We use this model to interpret measurements of growth and expression of resistance in microfluidic experiments, both in single cells and in biofilms. We also implemented a stochastic model of the drug response, to show that exposure to high drug levels results in large variations of recovery times and heterogeneity at the population level. We show that stochasticity is important to determine how nutrient quality affects cell survival during exposure to high drug concentrations. A quantitative description of how microbes respond to antibiotics in dynamical environments is crucial to understand population-level behaviors such as biofilms and pathogenesis.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10988634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139983583","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}

引用次数: 0

Structural maturation of myofilaments in engineered 3D cardiac microtissues characterized using small angle x-ray scattering. 利用小角 X 射线散射表征工程三维心脏微组织中肌丝的结构成熟。

IF 2 4区生物学

Physical biology Pub Date : 2024-03-20 DOI: 10.1088/1478-3975/ad310e

Geoffrey van Dover, Josh Javor, Jourdan K Ewoldt, Mikhail Zhernenkov, Patryk Wąsik, Guillaume Freychet, Josh Lee, Dana Brown, Christopher S Chen, David J Bishop

{"title":"Structural maturation of myofilaments in engineered 3D cardiac microtissues characterized using small angle x-ray scattering.","authors":"Geoffrey van Dover, Josh Javor, Jourdan K Ewoldt, Mikhail Zhernenkov, Patryk Wąsik, Guillaume Freychet, Josh Lee, Dana Brown, Christopher S Chen, David J Bishop","doi":"10.1088/1478-3975/ad310e","DOIUrl":"10.1088/1478-3975/ad310e","url":null,"abstract":"Understanding the structural and functional development of human-induced pluripotent stem-cell-derived cardiomyocytes (hiPSC-CMs) is essential to engineering cardiac tissue that enables pharmaceutical testing, modeling diseases, and designing therapies. Here we use a method not commonly applied to biological materials, small angle x-ray scattering, to characterize the structural development of hiPSC-CMs within three-dimensional engineered tissues during their preliminary stages of maturation. An x-ray scattering experimental method enables the reliable characterization of the cardiomyocyte myofilament spacing with maturation time. The myofilament lattice spacing monotonically decreases as the tissue matures from its initial post-seeding state over the span of 10 days. Visualization of the spacing at a grid of positions in the tissue provides an approach to characterizing the maturation and organization of cardiomyocyte myofilaments and has the potential to help elucidate mechanisms of pathophysiology, and disease progression, thereby stimulating new biological hypotheses in stem cell engineering.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140060350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Coupled action potential and calcium dynamics underlie robust spontaneous firing in dopaminergic neurons. 动作电位和钙动力学耦合是多巴胺能神经元强劲自发点火的基础。

IF 2 4区生物学

Physical biology Pub Date : 2024-03-01 DOI: 10.1088/1478-3975/ad2bd4

Hadeel Khamis, Ohad Cohen

{"title":"Coupled action potential and calcium dynamics underlie robust spontaneous firing in dopaminergic neurons.","authors":"Hadeel Khamis, Ohad Cohen","doi":"10.1088/1478-3975/ad2bd4","DOIUrl":"10.1088/1478-3975/ad2bd4","url":null,"abstract":"Dopaminergic neurons are specialized cells in the substantia nigra, tasked with dopamine secretion. This secretion relies on intracellular calcium signaling coupled to neuronal electrical activity. These neurons are known to display spontaneous calcium oscillationsin-vitroandin-vivo, even in synaptic isolation, controlling the basal dopamine levels. Here we outline a kinetic model for the ion exchange across the neuronal plasma membrane. Crucially, we relax the assumption of constant, cytoplasmic sodium and potassium concentration. We show that sodium-potassium dynamics are strongly coupled to calcium dynamics and are essential for the robustness of spontaneous firing frequency. The model predicts several regimes of electrical activity, including tonic and 'burst' oscillations, and predicts the switch between those in response to perturbations. 'Bursting' correlates with increased calcium amplitudes, while maintaining constant average, allowing for a vast change in the calcium signal responsible for dopamine secretion. All the above traits provide the flexibility to create rich action potential dynamics that are crucial for cellular function.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139932493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0