arXiv - QuanBio - Cell Behavior最新文献_第2页

Physical limits on galvanotaxis depends on cell morphology and orientation 电泳的物理限制取决于细胞形态和方向

arXiv - QuanBio - Cell Behavior Pub Date : 2024-07-24 DOI: arxiv-2407.17420

Ifunanya Nwogbaga, Brian A. Camley

{"title":"Physical limits on galvanotaxis depends on cell morphology and orientation","authors":"Ifunanya Nwogbaga, Brian A. Camley","doi":"arxiv-2407.17420","DOIUrl":"https://doi.org/arxiv-2407.17420","url":null,"abstract":"Galvanotaxis is believed to be driven by the redistribution of transmembrane\u0000proteins and other molecules, referred to as \"sensors\", through electrophoresis\u0000and electroosmosis. Here, we update our previous model of the limits of\u0000galvanotaxis due to stochasticity of sensor movements to account for cell shape\u0000and orientation. Computing the Fisher information, we find that cells in\u0000principle possess more information about the electric field direction when\u0000their long axis is parallel to the field, but that for weak fields\u0000maximum-likelihood estimators of the field direction may actually have lower\u0000variability when the cell's long axis is perpendicular to the field. In an\u0000alternate possibility, we find that if cells instead estimate the field\u0000direction by taking the average of all the sensor locations as its directional\u0000cue (\"vector sum\"), this introduces a bias towards the short axis, an effect\u0000not present for isotropic cells. We also explore the possibility that cell\u0000elongation arises downstream of sensor redistribution. We argue that if sensors\u0000migrate to the cell's rear, the cell will expand perpendicular the field - as\u0000is more commonly observed - but if sensors migrate to the front, the cell will\u0000elongate parallel to the field.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141770805","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

Understanding cell populations sharing information through the environment, as reinforcement learning 将细胞群通过环境共享信息理解为强化学习

arXiv - QuanBio - Cell Behavior Pub Date : 2024-07-21 DOI: arxiv-2407.15298

Masaki Kato, Tetsuya J. Kobayashi

{"title":"Understanding cell populations sharing information through the environment, as reinforcement learning","authors":"Masaki Kato, Tetsuya J. Kobayashi","doi":"arxiv-2407.15298","DOIUrl":"https://doi.org/arxiv-2407.15298","url":null,"abstract":"Collective migration is a phenomenon observed in various biological systems,\u0000where the cooperation of multiple cells leads to complex functions beyond\u0000individual capabilities, such as in immunity and development. A distinctive\u0000example is cell populations that not only ascend attractant gradient\u0000originating from targets, such as damaged tissue, but also actively modify the\u0000gradient, through their own production and degradation. While the optimality of\u0000single-cell information processing has been extensively studied, the optimality\u0000of the collective information processing that includes gradient sensing and\u0000gradient generation, remains underexplored. In this study, we formulated a cell\u0000population that produces and degrades an attractant while exploring the\u0000environment as an agent population performing distributed reinforcement\u0000learning. We demonstrated the existence of optimal couplings between gradient\u0000sensing and gradient generation, showing that the optimal gradient generation\u0000qualitatively differs depending on whether the gradient sensing is logarithmic\u0000or linear. The derived dynamics have a structure homogeneous to the\u0000Keller-Segel model, suggesting that cell populations might be learning.\u0000Additionally, we showed that the distributed information processing structure\u0000of the agent population enables a proportion of the population to robustly\u0000accumulate at the target. Our results provide a quantitative foundation for\u0000understanding the collective information processing mediated by attractants in\u0000extracellular environments.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141770809","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

Visitation Dynamics of $d$-Dimensional Fractional Brownian Motion d$维分数布朗运动的访问动力学

arXiv - QuanBio - Cell Behavior Pub Date : 2024-07-16 DOI: arxiv-2407.11655

L. Régnier, M. Dolgushev, O. Bénichou

引用次数: 0

A Primitive Model for Predicting Membrane Currents in Excitable Cells Based Only on Ion Diffusion Coefficients 仅根据离子扩散系数预测可兴奋细胞膜电流的原始模型

arXiv - QuanBio - Cell Behavior Pub Date : 2024-07-12 DOI: arxiv-2407.09474

Vivaan Patel, Joshua D. Priosoetanto, Aashutosh Mistry, John Newman, Nitash P. Balsara

引用次数: 0

E. coli do not count single molecules 大肠杆菌不计算单个分子

arXiv - QuanBio - Cell Behavior Pub Date : 2024-07-09 DOI: arxiv-2407.07264

Henry H. Mattingly, Keita Kamino, Jude Ong, Rafaela Kottou, Thierry Emonet, Benjamin B. Machta

{"title":"E. coli do not count single molecules","authors":"Henry H. Mattingly, Keita Kamino, Jude Ong, Rafaela Kottou, Thierry Emonet, Benjamin B. Machta","doi":"arxiv-2407.07264","DOIUrl":"https://doi.org/arxiv-2407.07264","url":null,"abstract":"Organisms must perform sensory-motor behaviors to survive. What bounds or\u0000constraints limit behavioral performance? Previously, we found that the\u0000gradient-climbing speed of a chemotaxing Escherichia coli is near a bound set\u0000by the limited information they acquire from their chemical environments. Here\u0000we ask what limits their sensory accuracy. Past theoretical analyses have shown\u0000that the stochasticity of single molecule arrivals sets a fundamental limit on\u0000the precision of chemical sensing. Although it has been argued that bacteria\u0000approach this limit, direct evidence is lacking. Here, using information theory\u0000and quantitative experiments, we find that E. coli's chemosensing is not\u0000limited by the physics of particle counting. First, we derive the physical\u0000limit on the behaviorally-relevant information that any sensor can get about a\u0000changing chemical concentration, assuming that every molecule arriving at the\u0000sensor is recorded. Then, we derive and measure how much information E. coli's\u0000signaling pathway encodes during chemotaxis. We find that E. coli encode two\u0000orders of magnitude less information than an ideal sensor limited only by shot\u0000noise in particle arrivals. These results strongly suggest that constraints\u0000other than particle arrival noise limit E. coli's sensory fidelity.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141587944","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

Engineering morphogenesis of cell clusters with differentiable programming 利用可分化程序设计细胞簇的形态发生

arXiv - QuanBio - Cell Behavior Pub Date : 2024-07-08 DOI: arxiv-2407.06295

Ramya Deshpande, Francesco Mottes, Ariana-Dalia Vlad, Michael P. Brenner, Alma dal Co

{"title":"Engineering morphogenesis of cell clusters with differentiable programming","authors":"Ramya Deshpande, Francesco Mottes, Ariana-Dalia Vlad, Michael P. Brenner, Alma dal Co","doi":"arxiv-2407.06295","DOIUrl":"https://doi.org/arxiv-2407.06295","url":null,"abstract":"Understanding the rules underlying organismal development is a major unsolved\u0000problem in biology. Each cell in a developing organism responds to signals in\u0000its local environment by dividing, excreting, consuming, or reorganizing, yet\u0000how these individual actions coordinate over a macroscopic number of cells to\u0000grow complex structures with exquisite functionality is unknown. Here we use\u0000recent advances in automatic differentiation to discover local interaction\u0000rules and genetic networks that yield emergent, systems-level characteristics\u0000in a model of development. We consider a growing tissue with cellular\u0000interactions are mediated by morphogen diffusion, differential cell adhesion\u0000and mechanical stress. Each cell has an internal genetic network that it uses\u0000to make decisions based on its local environment. We show that one can\u0000simultaneously learn parameters governing the cell interactions and the genetic\u0000network for complex developmental scenarios, including the symmetry breaking of\u0000an embryo from an initial cell, the creation of emergent chemical\u0000gradients,homogenization of growth via mechanical stress, programmed growth\u0000into a prespecified shape, and the ability to repair from damage. When combined\u0000with recent experimental advances measuring spatio-temporal dynamics and gene\u0000expression of cells in a growing tissue, the methodology outlined here offers a\u0000promising path to unravelling the cellular basis of development.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141568113","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

Feeders and Expellers, Two Types of Animalcules With Outboard Cilia, Have Distinct Surface Interactions 进食者和排泄者这两种具有外向纤毛的动物分子具有不同的表面相互作用

arXiv - QuanBio - Cell Behavior Pub Date : 2024-06-29 DOI: arxiv-2407.00439

Praneet Prakash, Marco Vona, Raymond E. Goldstein

{"title":"Feeders and Expellers, Two Types of Animalcules With Outboard Cilia, Have Distinct Surface Interactions","authors":"Praneet Prakash, Marco Vona, Raymond E. Goldstein","doi":"arxiv-2407.00439","DOIUrl":"https://doi.org/arxiv-2407.00439","url":null,"abstract":"Within biological fluid dynamics, it is conventional to distinguish between\u0000\"puller\" and \"pusher\" microswimmers on the basis of the forward or aft location\u0000of the flagella relative to the cell body: typically, bacteria are pushers and\u0000algae are pullers. Here we note that since many pullers have \"outboard\" cilia\u0000or flagella displaced laterally from the cell centerline on both sides of the\u0000organism, there are two important subclasses whose far-field is that of a\u0000stresslet, but whose near field is qualitatively more complex. The ciliary beat\u0000creates not only a propulsive force but also swirling flows that can be\u0000represented by paired rotlets with two possible senses of rotation, either\u0000\"feeders\" that sweep fluid toward the cell apex, or \"expellers\" that push fluid\u0000away. Experimental studies of the rotifer $Brachionus~plicatilis$ in\u0000combination with earlier work on the green algae $Chlamydomonas~reinhardtii$\u0000show that the two classes have markedly different interactions with surfaces.\u0000When swimming near a surface, expellers such as $C.~reinhardtii$ scatter from\u0000the wall, whereas a feeder like $B.~plicatilis$ stably attaches. This results\u0000in a stochastic \"run-and-stick\" locomotion, with periods of ballistic motion\u0000parallel to the surface interrupted by trapping at the surface.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":"81 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141503322","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

High Throughput Parameter Estimation and Uncertainty Analysis Applied to the Production of Mycoprotein from Synthetic Lignocellulosic Hydrolysates 高通量参数估计和不确定性分析在利用合成木质纤维素水解物生产菌体蛋白中的应用

arXiv - QuanBio - Cell Behavior Pub Date : 2024-06-28 DOI: arxiv-2407.00209

Mason Banks, Mark Taylor, Miao Guo

{"title":"High Throughput Parameter Estimation and Uncertainty Analysis Applied to the Production of Mycoprotein from Synthetic Lignocellulosic Hydrolysates","authors":"Mason Banks, Mark Taylor, Miao Guo","doi":"arxiv-2407.00209","DOIUrl":"https://doi.org/arxiv-2407.00209","url":null,"abstract":"The current global food system produces substantial waste and carbon\u0000emissions while exacerbating the effects of global hunger and protein\u0000deficiency. This study aims to address these challenges by exploring the use of\u0000lignocellulosic agricultural residues as feedstocks for microbial protein\u0000fermentation, focusing on Fusarium venenatum A3/5, a mycelial strain known for\u0000its high protein yield and quality. We propose a high throughput microlitre\u0000batch fermentation system paired with analytical chemistry to generate\u0000time-series data of microbial growth and substrate utilisation. An unstructured\u0000biokinetic model was developed using a bootstrap sampling approach to quantify\u0000uncertainty in the parameter estimates. The model was validated against an\u0000independent dataset of a different glucose-xylose composition to assess the\u0000predictive performance. Our results indicate a robust model fit with high\u0000coefficients of determination and low root mean squared errors for biomass,\u0000glucose, and xylose concentrations. Estimated parameter values provided\u0000insights into the resource utilisation strategies of Fusarium venenatum A3/5 in\u0000mixed substrate cultures, aligning well with previous research findings.\u0000Significant correlations between estimated parameters were observed,\u0000highlighting challenges in parameter identifiability. This work provides a\u0000foundational model for optimising the production of microbial protein from\u0000lignocellulosic waste, contributing to a more sustainable global food system.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141524256","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

Statistical description of mobile oscillators in embryonic pattern formation 胚胎模式形成过程中移动振荡器的统计描述

arXiv - QuanBio - Cell Behavior Pub Date : 2024-06-16 DOI: arxiv-2406.10936

Koichiro Uriu, Luis G. Morelli

{"title":"Statistical description of mobile oscillators in embryonic pattern formation","authors":"Koichiro Uriu, Luis G. Morelli","doi":"arxiv-2406.10936","DOIUrl":"https://doi.org/arxiv-2406.10936","url":null,"abstract":"Synchronization of mobile oscillators occurs in numerous contexts, including\u0000physical, chemical, biological and engineered systems. In vertebrate embryonic\u0000development, a segmental body structure is generated by a population of mobile\u0000oscillators. Cells in this population produce autonomous gene expression\u0000rhythms, and interact with their neighbors through local signaling. These cells\u0000form an extended tissue where frequency and cell mobility gradients coexist.\u0000Gene expression kinematic waves travel through this tissue and pattern the\u0000segment boundaries. It has been shown that oscillator mobility promotes global\u0000synchronization. However, in vertebrate segment formation, mobility may also\u0000introduce local fluctuations in kinematic waves and impair segment boundaries.\u0000Here we derive a general framework for mobile oscillators that relates local\u0000mobility fluctuations to synchronization dynamics and pattern robustness. We\u0000formulate a statistical description of mobile phase oscillators in terms of a\u0000probability density. We obtain and solve diffusion equations for the average\u0000phase and variance, revealing the relationship between local fluctuations and\u0000global synchronization in a homogeneous population of oscillators. Analysis of\u0000the probability density for large mobility identifies a mean-field transition,\u0000where locally coupled oscillators start behaving as if each oscillator was\u0000coupled with all the others. We extend the statistical description to\u0000inhomogeneous systems to address the gradients present in the vertebrate\u0000segmenting tissue. The theory relates pattern stability to mobility, coupling\u0000and pattern wavelength. The general approach of the statistical description may\u0000be applied to mobile oscillators in other contexts, as well as to other\u0000patterning systems where mobility is present.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141529057","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

Collective Invasion: When does domain curvature matter? 集体入侵：域曲率何时重要？

arXiv - QuanBio - Cell Behavior Pub Date : 2024-06-12 DOI: arxiv-2406.08291

Joseph J. Pollacco, Ruth E. Baker, Philip K. Maini

{"title":"Collective Invasion: When does domain curvature matter?","authors":"Joseph J. Pollacco, Ruth E. Baker, Philip K. Maini","doi":"arxiv-2406.08291","DOIUrl":"https://doi.org/arxiv-2406.08291","url":null,"abstract":"Real-world cellular invasion processes often take place in curved geometries.\u0000Such problems are frequently simplified in models to neglect the curved\u0000geometry in favour of computational simplicity, yet doing so risks inaccuracy\u0000in any model-based predictions. To quantify the conditions under which\u0000neglecting a curved geometry are justifiable, we examined solutions to the\u0000Fisher-Kolmogorov-Petrovsky-Piskunov (Fisher-KPP) model, a paradigm nonlinear\u0000reaction-diffusion equation typically used to model spatial invasion, on an\u0000annular geometry. Defining $epsilon$ as the ratio of the annulus thickness\u0000$delta$ and radius $r_0$ we derive, through an asymptotic expansion, the\u0000conditions under which it is appropriate to ignore the domain curvature, a\u0000result that generalises to other reaction-diffusion equations with constant\u0000diffusion coefficient. We further characterise the nature of the solutions\u0000through numerical simulation for different $r_0$ and $delta$. Thus, we\u0000quantify the size of the deviation from an analogous simulation on the\u0000rectangle, and how this deviation changes across the width of the annulus. Our\u0000results grant insight into when it is appropriate to neglect the domain\u0000curvature in studying travelling wave behaviour in reaction-diffusion\u0000equations.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141529059","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