arXiv - QuanBio - Subcellular Processes最新文献_第8页

Emergent Spatiotemporal Organization in Stochastic Intracellular Transport Dynamics 随机细胞内运输动力学中的涌现时空组织

arXiv - QuanBio - Subcellular Processes Pub Date : 2023-07-02 DOI: arxiv-2307.00639

Kunaal Joshi, Harrison York, Charles S. Wright, Rudro R. Biswas, Senthil Arumugam, Srividya Iyer-Biswas

{"title":"Emergent Spatiotemporal Organization in Stochastic Intracellular Transport Dynamics","authors":"Kunaal Joshi, Harrison York, Charles S. Wright, Rudro R. Biswas, Senthil Arumugam, Srividya Iyer-Biswas","doi":"arxiv-2307.00639","DOIUrl":"https://doi.org/arxiv-2307.00639","url":null,"abstract":"The interior of a living cell is an active, fluctuating, and crowded\u0000environment. Yet, it maintains a high level of coherent organization, which is\u0000readily apparent in the intracellular transport network. Membrane-bound\u0000compartments called endosomes play a key role in carrying cargo, in conjunction\u0000with myriad components including cargo adaptor proteins, membrane sculptors,\u0000motor proteins, and the cytoskeleton. These components coordinate to\u0000effectively navigate the crowded cell interior and transport cargo to specific\u0000intracellular locations, even though the underlying protein interactions and\u0000enzymatic reactions exhibit stochastic behavior. A major challenge is to\u0000measure, analyze, and understand how, despite the inherent stochasticity of the\u0000constituent processes, the collective outcomes show an emergent spatiotemporal\u0000order that is precise and robust. This review focuses on this intriguing\u0000dichotomy, providing insights into the known mechanisms of noise suppression\u0000and noise utilization in intracellular transport processes, and also identifies\u0000opportunities for future inquiry.","PeriodicalId":501170,"journal":{"name":"arXiv - QuanBio - Subcellular Processes","volume":"58 36","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138510945","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

Signature of (anti)cooperativity in the stochastic fluctuations of small systems: application to the bacterial flagellar motor 小系统随机波动中的(反)协同特征:在细菌鞭毛马达上的应用

arXiv - QuanBio - Subcellular Processes Pub Date : 2023-07-02 DOI: arxiv-2307.00636

María-José Franco-Oñate, Andrea Parmeggiani, Jérôme Dorignac, Frédéric Geniet, Jean-Charles Walter, Francesco Pedaci, Ashley L Nord, John Palmeri, Nils-Ole Walliser

{"title":"Signature of (anti)cooperativity in the stochastic fluctuations of small systems: application to the bacterial flagellar motor","authors":"María-José Franco-Oñate, Andrea Parmeggiani, Jérôme Dorignac, Frédéric Geniet, Jean-Charles Walter, Francesco Pedaci, Ashley L Nord, John Palmeri, Nils-Ole Walliser","doi":"arxiv-2307.00636","DOIUrl":"https://doi.org/arxiv-2307.00636","url":null,"abstract":"The cooperative binding of molecular agents onto a substrate is pervasive in\u0000living systems. To study whether a system shows cooperativity, one can rely on\u0000a fluctuation analysis of quantities such as the number of substrate-bound\u0000units and the residence time in an occupancy state. Since the relative standard\u0000deviation from the statistical mean monotonically decreases with the number of\u0000binding sites, these techniques are only suitable for small enough systems,\u0000such as those implicated in stochastic processes inside cells. Here, we present\u0000a general-purpose grand canonical Hamiltonian description of a small\u0000one-dimensional (1D) lattice gas with either nearest-neighbor or long-range\u0000interactions as prototypical examples of cooperativity-influenced adsorption\u0000processes. First, we elucidate how the strength and sign of the interaction\u0000potential between neighboring bound particles on the lattice determine the\u0000intensity of the fluctuations of the mean occupancy. We then employ this\u0000relationship to compare the theoretical predictions of our model to data from\u0000single molecule experiments on bacterial flagellar motors (BFM) of E. coli. In\u0000this way, we find evidence that cooperativity controls the mechano-sensitive\u0000dynamical assembly of the torque-generating units, the so-called stator units,\u0000onto the BFM. Finally, we estimate the stator-stator interaction potential and\u0000attempt to quantify the adaptability of the BFM.","PeriodicalId":501170,"journal":{"name":"arXiv - QuanBio - Subcellular Processes","volume":"58 47","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138510935","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

Cooperation of myosin II in muscle contraction through nonlinear elasticity 肌球蛋白II通过非线性弹性参与肌肉收缩

arXiv - QuanBio - Subcellular Processes Pub Date : 2023-06-19 DOI: arxiv-2306.10949

Beibei Shen, Yunxin Zhang

{"title":"Cooperation of myosin II in muscle contraction through nonlinear elasticity","authors":"Beibei Shen, Yunxin Zhang","doi":"arxiv-2306.10949","DOIUrl":"https://doi.org/arxiv-2306.10949","url":null,"abstract":"Myosin II plays a pivotal role in muscle contraction by generating force\u0000through the cooperative action of multiple motors on actin filaments. In this\u0000study, we integrate the nonlinear elasticity of the neck linker in individual\u0000myosin II and comprehensively investigate the evolution of cooperativity and\u0000dynamics at {it microstate} and {it mesostate} levels using a combined model\u0000of single and multiple motors. We find that a substantial proportion of\u0000actin-bound motors reside in the {it mid-} and {it post-power stroke} states,\u0000and our nonlinear model reveals their increased capacity for load sharing.\u0000Additionally, we systematically explore the impact of mechanical load and ATP\u0000concentration on myosin II motors. Notably, we observe that the average net\u0000distance of actin undergoes a transition from a weak load-sensitive regime at\u0000low ATP concentrations to a load-sensitive regime at higher ATP concentrations.\u0000Furthermore, increasing the load or raising the ATP concentration to saturation\u0000can enhance the efficiency and output power of myosin filament. Moreover, the\u0000efficiency of the myosin filament increases with the power stroke strength,\u0000reaching a maximum at a specific range, and subsequently declining beyond that\u0000threshold. Finally, we explore the mean run time/length and mean existence\u0000probability of myosin filament, shedding light on its overall behavior.","PeriodicalId":501170,"journal":{"name":"arXiv - QuanBio - Subcellular Processes","volume":"58 42","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138510940","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

The Core & Periphery Hypothesis: A Conceptual Basis for Generality in Cell and Developmental Biology 核心与外围假说:细胞与发育生物学共性的概念基础

arXiv - QuanBio - Subcellular Processes Pub Date : 2023-06-15 DOI: arxiv-2306.09534

Elisa Gallo, Stefano De Renzis, James Sharpe, Roberto Mayor, Jonas Hartmann

引用次数: 0

Systematic Review of Methods and Prognostic Value of Mitotic Activity. Part 2: Canine Tumors 有丝分裂活性检测方法及其预后价值的系统综述。第二部分:犬类肿瘤

arXiv - QuanBio - Subcellular Processes Pub Date : 2023-05-31 DOI: arxiv-2305.19667

Christof A. Bertram, Taryn A. Donovan, Alexander Bartel

{"title":"Systematic Review of Methods and Prognostic Value of Mitotic Activity. Part 2: Canine Tumors","authors":"Christof A. Bertram, Taryn A. Donovan, Alexander Bartel","doi":"arxiv-2305.19667","DOIUrl":"https://doi.org/arxiv-2305.19667","url":null,"abstract":"One of the most relevant prognostication tests for tumors is cellular\u0000proliferation, which is most commonly measured by the mitotic activity in\u0000routine tumor sections. The goal of this systematic review is to scholarly\u0000analyze the methods and prognostic relevance of histologically measuring\u0000mitotic activity in canine tumors. A total of 137 articles that correlated the\u0000mitotic activity in canine tumors with patient outcome were identified through\u0000a systematic (PubMed and Scopus) and manual (Google Scholar) literature search\u0000and eligibility screening process. These studies determined the mitotic count\u0000(MC, number of mitotic figures per tumor area) in 126 instances, presumably the\u0000mitotic count (method not specified) in 6 instances and the mitotic index (MI,\u0000proportion of mitotic figures per tumor cells) in 5 instances. A particularly\u0000high risk of bias was identified in the available details of the MC methods and\u0000statistical analysis, which often did not quantify the prognostic\u0000discriminative ability of the MC and only reported p-values. A significant\u0000association of the MC with survival was found in 72/109 (66%) studies. However,\u0000survival was evaluated by at least three studies in only 7 tumor types/groups,\u0000of which a prognostic relevance is apparent for mast cell tumors of the skin,\u0000cutaneous melanoma and soft tissue sarcoma of the skin. None of the studies on\u0000the MI found a prognostic relevance. Further studies on the MC and MI with\u0000standardized methods are needed to prove the prognostic benefit of this test\u0000for further tumor types.","PeriodicalId":501170,"journal":{"name":"arXiv - QuanBio - Subcellular Processes","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138532813","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

The reaction-diffusion basis of animated patterns in eukaryotic flagella 真核鞭毛动画图案的反应-扩散基础

arXiv - QuanBio - Subcellular Processes Pub Date : 2023-05-26 DOI: arxiv-2305.17032

James F. Cass, Hermes Bloomfield-Gadelha

{"title":"The reaction-diffusion basis of animated patterns in eukaryotic flagella","authors":"James F. Cass, Hermes Bloomfield-Gadelha","doi":"arxiv-2305.17032","DOIUrl":"https://doi.org/arxiv-2305.17032","url":null,"abstract":"We show that the flagellar beat of bull spermatozoa and Chlamydomonas\u0000Reinhardtii can be modelled by a minimal, geometrically nonlinear\u0000reaction-diffusion system. Model solutions are spatio-temporally animated\u0000patterns describing flagellar bending waves, connecting beating patterns of\u0000cilia and flagella with chemical patterns from classical reaction-diffusion\u0000systems. Instead of chemical species freely reacting and diffusing in space,\u0000our system describes the tug-of-war reaction-kinetics of molecular motors that\u0000are anchored in the flagellar structure, but the shear deformation that they\u0000generate can diffuse away via the bending elasticity of the flagellum.\u0000Synchronization of the reaction-kinetics in neighbouring elements occurs via a\u0000sliding-control mechanism. We derive from first principles the\u0000reaction-diffusion basis of animated patterns as a direct consequence of the\u0000high internal energy dissipation by the flagellum relative to the external\u0000dissipation by the surrounding fluid. By fitting nonlinear, large-amplitude\u0000solutions of a specific motor cross-bridge reaction-kinetics, we show that\u0000reaction-diffusion successfully accounts for beating patterns of both bull\u0000sperm and Chlamydomonas (wild-type and mbo2-mutant). Our results suggest that\u0000the flagellar beat occurs far from equilibrium, in the strongly nonlinear\u0000regime, and that a unified mechanism may exist for dynein molecular motor\u0000control that is regulated by axonemal sliding, without requiring\u0000curvature-sensing or the fine-tuning of basal compliance, and only weakly\u0000influenced by hydrodynamic dissipation and the cell body boundary condition.\u0000High internal dissipation allows the emergence of base-to-tip autonomous\u0000travelling waves, independently of the external fluid viscosity. This enables\u0000progressive swimming in low viscosity environments, and may be critical for\u0000external fertilizers and aquatic microorganisms.","PeriodicalId":501170,"journal":{"name":"arXiv - QuanBio - Subcellular Processes","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138532856","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

AI-based analysis of super-resolution microscopy: Biological discovery in the absence of ground truth 基于人工智能的超分辨率显微镜分析:在缺乏基本事实的情况下的生物学发现

arXiv - QuanBio - Subcellular Processes Pub Date : 2023-05-26 DOI: arxiv-2305.17193

Ivan R. Nabi, Ben Cardoen, Ismail M. Khater, Guang Gao, Timothy H. Wong, Ghassan Hamarneh

引用次数: 0

Enhanced fluctuation in heterogeneous chromatic medium emerging by transient-linking activity 瞬态连接活性增强了异质色介质的波动

arXiv - QuanBio - Subcellular Processes Pub Date : 2023-05-09 DOI: arxiv-2305.05521

Rakesh Das, Takahiro Sakaue, G. V. Shivashankar, Jacques Prost, Tetsuya Hiraiwa

引用次数: 0

Active thermodynamic force driven mitochondrial alignment 主动热力学力驱动线粒体排列

arXiv - QuanBio - Subcellular Processes Pub Date : 2023-05-09 DOI: arxiv-2305.05553

Masashi K. Kajita, Yoshiyuki Konishi, Tetsuhiro S. Hatakeyama

引用次数: 0

Systematic Review of Methods and Prognostic Value of Mitotic Activity. Part 1: Feline Tumors 有丝分裂活性检测方法及其预后价值的系统综述。第一部分:猫科动物肿瘤

arXiv - QuanBio - Subcellular Processes Pub Date : 2023-05-02 DOI: arxiv-2305.01403

Christof A. Bertram, Taryn A. Donovan, Alexander Bartel

{"title":"Systematic Review of Methods and Prognostic Value of Mitotic Activity. Part 1: Feline Tumors","authors":"Christof A. Bertram, Taryn A. Donovan, Alexander Bartel","doi":"arxiv-2305.01403","DOIUrl":"https://doi.org/arxiv-2305.01403","url":null,"abstract":"Increased proliferation is a key driver of tumorigenesis, and quantification\u0000of mitotic activity is a standard task for prognostication. The goal of this\u0000systematic review is scholarly analysis of all available references on mitotic\u0000activity in feline tumors, and to provide an overview of the measuring methods\u0000and prognostic value. A systematic literature search in PubMed and Scopus and a\u0000manual search in Google Scholar was conducted. All articles on feline tumors\u0000that correlated mitotic activity with patient outcome were identified. Data\u0000analysis revealed that of the eligible 42 articles, the mitotic count (MC,\u0000mitotic figures per tumor area) was evaluated in 39 instances and the mitotic\u0000index (MI, mitotic figures per tumor cells) in three instances. The risk of\u0000bias was considered high for most studies (26/42, 62%) based on small study\u0000populations, insufficient details of the MC/MI methods, and lack of statistical\u0000measures for diagnostic accuracy or effect on outcome. The MC/MI methods varied\u0000markedly between studies. A significant association of the MC with survival was\u0000determined in 21/29 (72%) studies, while one study found an inverse effect.\u0000There were three tumor types with at least four studies and a prognostic\u0000association was found in 5/6 studies on mast cell tumors, 5/5 on mammary tumors\u0000and 3/4 on soft tissue sarcomas. The MI was shown to correlate with survival by\u0000two research groups, however a comparison to the MC was not conducted. An\u0000updated systematic review will be needed with of new literature for different\u0000tumor types.","PeriodicalId":501170,"journal":{"name":"arXiv - QuanBio - Subcellular Processes","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138532806","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