Physical biology最新文献

Why swarming insects have perplexing spatial statistics. 为什么成群的昆虫有令人困惑的空间统计。

IF 2 4区生物学

Physical biology Pub Date : 2025-06-12 DOI: 10.1088/1478-3975/addf08

Andy Reynolds

引用次数: 0

Methods in quantitative biology-from analysis of single-cell microscopy images to inference of predictive models for stochastic gene expression. 定量生物学的方法-从单细胞显微镜图像的分析到随机基因表达预测模型的推断。

IF 2 4区生物学

Physical biology Pub Date : 2025-06-10 DOI: 10.1088/1478-3975/adda85

Luis U Aguilera, Lisa M Weber, Eric Ron, Connor R King, Kaan Öcal, Alex Popinga, Joshua Cook, Michael P May, William S Raymond, Zachary R Fox, Linda S Forero-Quintero, Jack R Forman, Alexandre David, Brian Munsky

{"title":"Methods in quantitative biology-from analysis of single-cell microscopy images to inference of predictive models for stochastic gene expression.","authors":"Luis U Aguilera, Lisa M Weber, Eric Ron, Connor R King, Kaan Öcal, Alex Popinga, Joshua Cook, Michael P May, William S Raymond, Zachary R Fox, Linda S Forero-Quintero, Jack R Forman, Alexandre David, Brian Munsky","doi":"10.1088/1478-3975/adda85","DOIUrl":"10.1088/1478-3975/adda85","url":null,"abstract":"The field of quantitative biology (q-bio) seeks to provide precise and testable explanations for observed biological phenomena by applying mathematical and computational methods. The central goals of q-bio are to (1) systematically propose quantitative hypotheses in the form of mathematical models, (2) demonstrate that these models faithfully capture a specific essence of a biological process, and (3) correctly forecast the dynamics of the process in new, and previously untested circumstances. Achieving these goals depends on accurate analysis and incorporating informative experimental data to constrain the set of potential mathematical representations. In this introductory tutorial, we provide an overview of the state of the field and introduce some of the computational methods most commonly used in q-bio. In particular, we examine experimental techniques in single-cell imaging, computational tools to process images and extract quantitative data, various mechanistic modeling approaches used to reproduce these quantitative data, and techniques for data-driven model inference and model-driven experiment design. All topics are presented in the context of additional online resources, including open-source Python notebooks and open-ended practice problems that comprise the technical content of the annual Undergraduate Quantitative Biology Summer School (UQ-Bio).","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12150428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102425","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

Comparing regression-based approaches for identifying microbial functional groups. 比较基于回归的微生物功能群鉴定方法。

IF 2 4区生物学

Physical biology Pub Date : 2025-05-30 DOI: 10.1088/1478-3975/addc2a

Fang Yu, Mikhail Tikhonov

引用次数: 0

Effect of membrane tension on pore formation induced by antimicrobial peptides and other membrane-active peptides. 膜张力对抗菌肽和其他膜活性肽诱导的孔形成的影响。

IF 2 4区生物学

Physical biology Pub Date : 2025-05-06 DOI: 10.1088/1478-3975/add071

Marzuk Ahmed, Md Masum Billah, Masahito Yamazaki

{"title":"Effect of membrane tension on pore formation induced by antimicrobial peptides and other membrane-active peptides.","authors":"Marzuk Ahmed, Md Masum Billah, Masahito Yamazaki","doi":"10.1088/1478-3975/add071","DOIUrl":"https://doi.org/10.1088/1478-3975/add071","url":null,"abstract":"Membrane tension plays an important role in various aspects of the dynamics and functions of cells. Here, we review recent studies of the effect of membrane tension on pore formation in lipid bilayers and pore formation induced by membrane-active peptides (MAPs) including antimicrobial peptides (AMPs). For this purpose, the micropipette aspiration method using a patch of cell membrane/lipid bilayers and a giant unilamellar vesicle (GUV)/a total cell, and the application of osmotic pressure (Π) to suspensions of large unilamellar vesicles (LUVs) have been used. However, these conventional methods have some drawbacks for the investigation of the effect of membrane tension on the actions of MAPs such as AMPs. Recently, to overcome these drawbacks, a new Π method using GUVs has been developed. Here, we focus on this Π method as a new technique for revealing the effect of membrane tension on the MAPs-induced pore formation. Firstly, we review studies of the effect of membrane tension on pore formation in lipid bilayers as determined by conventional methods. Secondly, after a brief review of studies of the effect of Π on LUVs, we describe the estimation of membrane tension in GUVs induced by Π and the Π-induced pore formation. Thirdly, after a review of the effect of membrane tension on the MAPs-induced pore formation as obtained by the conventional methods, we describe an application of the Π method to studies of the effect of membrane tension on AMP-induced pore formation. Finally, we discuss the advantages of the Π method over conventional methods and consider future perspectives.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"22 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144040789","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

Representation of high-dimensional cell morphology and morphodynamics in 2D latent space. 二维潜伏空间中高维细胞形态和形态动力学的表征。

IF 2 4区生物学

Physical biology Pub Date : 2025-04-24 DOI: 10.1088/1478-3975/adcd37

Christian Cunningham, Bo Sun

{"title":"Representation of high-dimensional cell morphology and morphodynamics in 2D latent space.","authors":"Christian Cunningham, Bo Sun","doi":"10.1088/1478-3975/adcd37","DOIUrl":"10.1088/1478-3975/adcd37","url":null,"abstract":"The morphology and morphodynamics of cells as important biomarkers of the cellular state are widely appreciated in both fundamental research and clinical applications. Quantification of cell morphology often requires a large number of geometric measures that form a high-dimensional feature vector. This mathematical representation creates barriers to communicating, interpreting, and visualizing data. Here, we develop a deep learning-based algorithm to project 13-dimensional (13D) morphological feature vectors into 2-dimensional (2D) morphological latent space (MLS). We show that the projection has less than 5% information loss and separates the different migration phenotypes of metastatic breast cancer cells. Using the projection, we demonstrate the phenotype-dependent motility of breast cancer cells in the 3D extracellular matrix, and the continuous cell state change upon drug treatment. We also find that dynamics in the 2D MLS quantitatively agrees with the morphodynamics of cells in the 13D feature space, preserving the diffusive power and the Lyapunov exponent of cell shape fluctuations even though the dimensional reduction projection is highly nonlinear. Our results suggest that MLS is a powerful tool to represent and understand the cell morphology and morphodynamics.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"22 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12083545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143977000","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

Fluctuation-driven synergy, redundancy, signal to noise ratio and error correction in protein allostery. 蛋白质变构中波动驱动的协同、冗余、信噪比和纠错。

IF 2 4区生物学

Physical biology Pub Date : 2025-03-05 DOI: 10.1088/1478-3975/adb9af

Burak Erman

{"title":"Fluctuation-driven synergy, redundancy, signal to noise ratio and error correction in protein allostery.","authors":"Burak Erman","doi":"10.1088/1478-3975/adb9af","DOIUrl":"10.1088/1478-3975/adb9af","url":null,"abstract":"This study explores the relationship between residue fluctuations and molecular communication in proteins, emphasizing the role of these dynamics in allosteric regulation. We employ computational tools including the Gaussian network model, mutual information, and interaction information, to analyze how stochastic interactions among residues contribute to functional interactions while also introducing noise. Our approach is based on the postulate that residues experience continuous stochastic bombardment from impulses generated by their neighbors, forming a complex network characterized by small-world scaling topology. By mapping these interactions through the Kirchhoff matrix framework, we demonstrate how conserved correlations enhance signaling pathways and provide stability against noise-like fluctuations. Notably, we highlight the importance of selecting relevant eigenvalues to optimize the signal-to-noise ratio in our analyses, a topic that has yet to be thoroughly investigated in the context of residue fluctuations. This work underscores the significance of viewing proteins as adaptive information processing systems, and emphasizes the fundamental mechanisms of biological information processing. The basic idea of this paper is the following: given two interacting residues on an allosteric path, what are the contributions of the remaining residues on this interaction. This naturally leads to the concept of synergy, redundancy and noise in proteins, which we analyze in detail for three proteins CheY, tyrosine phosphatase andβ-lactoglobulin.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143493393","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

STIPS algorithm enables tracking labyrinthine patterns and reveals distinct rhythmic dynamics of actin microridges. STIPS算法可以跟踪迷宫模式，揭示肌动蛋白微脊的独特节奏动态。

IF 2 4区生物学

Physical biology Pub Date : 2025-02-03 DOI: 10.1088/1478-3975/ada862

Rajasekaran Bhavna, Mahendra Sonawane

{"title":"STIPS algorithm enables tracking labyrinthine patterns and reveals distinct rhythmic dynamics of actin microridges.","authors":"Rajasekaran Bhavna, Mahendra Sonawane","doi":"10.1088/1478-3975/ada862","DOIUrl":"10.1088/1478-3975/ada862","url":null,"abstract":"Tracking and motion analyses of semi-flexible biopolymer networks from time-lapse microscopy images are important tools that enable quantitative measurements to unravel the dynamic and mechanical properties of biopolymers in living tissues, crucial for understanding their organization and function. Biopolymer networks are challenging to track due to continuous stochastic transitions, such as merges and splits, which cause local neighborhood rearrangements over short time and length scales. To address this, we propose the Spatio Temporal Information on Pixel Subsets algorithm to track these events by creating pixel subsets that link trajectories across frames. Using this method, we analyzed actin-enriched protrusions, or 'microridges,' which form dynamic labyrinthine patterns on squamous cell epithelial surfaces, mimicking 'active Turing-patterns.' Our results reveal two distinct actomyosin-based rhythmic dynamics in neighboring cells: a common pulsatile mechanism between 2 and 6.25 min period governing both fusion and fission events contributing to pattern maintenance, and cell area pulses predominantly exhibiting 10 min period.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142953504","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

Electrical homeostasis of the inner mitochondrial membrane potential. 线粒体内膜电位的电稳态。

IF 2 4区生物学

Physical biology Pub Date : 2025-01-31 DOI: 10.1088/1478-3975/adaa47

Peyman Fahimi, Lázaro A M Castanedo, P Thomas Vernier, Chérif F Matta

引用次数: 0

Quantum features of the transport through ion channels in the soft knock-on model. 软撞击模型中离子通道输运的量子特征。

IF 2 4区生物学

Physical biology Pub Date : 2024-12-27 DOI: 10.1088/1478-3975/ad9cde

Mateusz Polakowski, Miłosz Panfil

引用次数: 0

Emergence of temporal noise hierarchy in co-regulated genes of multi-output feed-forward loop. 多输出前馈回路共调基因中出现的时间噪声层次结构

IF 2 4区生物学

Physical biology Pub Date : 2024-12-05 DOI: 10.1088/1478-3975/ad9792

Mintu Nandi

{"title":"Emergence of temporal noise hierarchy in co-regulated genes of multi-output feed-forward loop.","authors":"Mintu Nandi","doi":"10.1088/1478-3975/ad9792","DOIUrl":"10.1088/1478-3975/ad9792","url":null,"abstract":"Natural variations in gene expression, called noise, are fundamental to biological systems. The expression noise can be beneficial or detrimental to cellular functions. While the impact of noise on individual genes is well-established, our understanding of how noise behaves when multiple genes are co-expressed by shared regulatory elements within transcription networks remains elusive. This lack of understanding extends to how the architecture and regulatory features of these networks influence noise. To address this gap, we study the multi-output feed-forward loop motif. The motif is prevalent in bacteria and yeast and influences co-expression of multiple genes by shared transcription factors (TFs). Focusing on a two-output variant of the motif, the present study explores the interplay between its architecture, co-expression (symmetric and asymmetric) patterns of the two genes, and the associated noise dynamics. We employ a stochastic modeling approach to investigate how the binding affinities of the TFs influence symmetric and asymmetric expression patterns and the resulting noise dynamics in the co-expressed genes. This knowledge could guide the development of strategies for manipulating gene expression patterns through targeted modulation of TF binding affinities.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142732078","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