arXiv - QuanBio - Cell Behavior最新文献

{"title":"Dynamics of bacterial aggregates in microflows","authors":"Ana Carpio, Baldvin Einarsson, David R. Espeso","doi":"arxiv-2401.07138","DOIUrl":"https://doi.org/arxiv-2401.07138","url":null,"abstract":"Biofilms are bacterial aggregates that grow on moist surfaces. Thin\u0000homogeneous biofilms naturally formed on the walls of conducts may serve as\u0000biosensors, providing information on the status of microsystems (MEMS) without\u0000disrupting them. However, uncontrolled biofilm growth may largely disturb the\u0000environment they develop in, increasing the drag and clogging the tubes. To\u0000ensure controlled biofilm expansion we need to understand the effect of\u0000external variables on their structure. We formulate a hybrid model for the\u0000computational study of biofilms growing in laminar microflows. Biomass evolves\u0000according to stochastic rules for adhesion, erosion and motion, informed by\u0000numerical approximations of the flow fields at each stage. The model is tested\u0000studying the formation of streamers in three dimensional corner flows, gaining\u0000some insight on the effect of external variables on their structure.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139481742","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}

{"title":"Biofilms as poroelastic materials","authors":"Ana Carpio, Elena Cebrian, Perfecto Vidal","doi":"arxiv-2401.07060","DOIUrl":"https://doi.org/arxiv-2401.07060","url":null,"abstract":"Biofilms are bacterial aggregates encased in a self-produced polymeric matrix\u0000which attach to moist surfaces and are extremely resistant to chemicals and\u0000antibiotics. Recent experiments show that their structure is defined by the\u0000interplay of elastic deformations and liquid transport within the biofilm, in\u0000response to the cellular activity and the interaction with the surrounding\u0000environment. We propose a poroelastic model for elastic deformation and liquid\u0000transport in three dimensional biofilms spreading on agar surfaces. The motion\u0000of the boundaries can be described by the combined use of Von Karman type\u0000approximations for the agar/biofilm interface and thin film approximations for\u0000the biofilm/air interface. Bacterial activity informs the macroscopic\u0000continuous model through source terms and residual stresses, either\u0000phenomenological or derived from microscopic models. We present a procedure to\u0000estimate the structure of such residual stresses, based on a simple cellular\u0000automata description of bacterial activity. Inspired by image processing, we\u0000show that a filtering strategy effectively smooths out the rough tensors\u0000provided by the stochastic cellular automata rules, allowing us to insert them\u0000in the macroscopic model without numerical instability.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139481330","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}

{"title":"Biofilm mechanics and patterns","authors":"Ana Carpio, Elena Cebrian, David R. Espeso, Perfecto Vidal","doi":"arxiv-2401.05323","DOIUrl":"https://doi.org/arxiv-2401.05323","url":null,"abstract":"From multicellular tissues to bacterial colonies, three dimensional cellular\u0000structures arise through the interaction of cellular activities and mechanical\u0000forces. Simple bacterial communities provide model systems for analyzing such\u0000interaction. Biofilms are bacterial aggregates attached to wet surfaces and\u0000encased in a self-produced polymeric matrix. Biofilms in flows form filamentary\u0000structures that contrast with the wrinkled layers observed on air/solid\u0000interfaces. We are able to reproduce both types of shapes through elastic rod\u0000and plate models that incorporate information from the biomass production and\u0000differentiations process, such as growth rates, growth tensors or inner\u0000stresses, as well as constraints imposed by the interaction with environment. A\u0000more precise study of biofilm dynamics requires tackling water absorption from\u0000its surroundings and fluid transport within the biological system. This process\u0000alters the material properties of the biofilm and the overall stresses. We\u0000analyze whether poroelastic approaches can provide a suitable combined\u0000description of fluid-like and solid-like biofilm behavior.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139422389","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}

{"title":"Amplitude and Frequency encodings give cells a different lens to sense the environment","authors":"Alan Givré, Alejandro Colman-Lerner, Silvina Ponce Dawson","doi":"arxiv-2401.04089","DOIUrl":"https://doi.org/arxiv-2401.04089","url":null,"abstract":"Cells continuously sense their surroundings to detect modifications and\u0000generate responses. Very often changes in extracellular concentrations initiate\u0000signaling cascades that eventually result in changes in gene expression.\u0000Increasing stimulus strengths can be encoded in increasing concentration\u0000amplitudes or increasing activation frequencies of intermediaries of the\u0000pathway. In this Letter we show how the different way in which amplitude and\u0000frequency encoding map environmental changes impact on the cell's information\u0000transmission capabilities. While amplitude encoding is optimal for a limited\u0000range of stimuli strengths around a finite value, frequency encoding\u0000information transmission can improve or remain relatively flat as the stimulus\u0000strength increases. The apparently redundant combination of both mechanisms in\u0000some cell types may then serve the purpose of expanding the range over which\u0000stimulus strengths can be reliably discriminated. In this Letter we also\u0000discuss a possible example of this mechanism.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139408764","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}

{"title":"Quantifying T cell morphodynamics and migration in 3D collagen matrices","authors":"Yeeren I. Low","doi":"arxiv-2401.03595","DOIUrl":"https://doi.org/arxiv-2401.03595","url":null,"abstract":"T cells undergo large shape changes (morphodynamics) when migrating. While\u0000progress has been made elucidating the molecular basis of cell migration,\u0000statistical characterization of morphodynamics and migration has been limited,\u0000particularly in physiologically realistic 3D environments. A previous study (H.\u0000Cavanagh et al., J. R. Soc. Interface 19: 20220081) found discrete states of\u0000dynamics as well as periodic oscillations of shape. However, we show that these\u0000results are due to artifacts of the analysis methods. Here, we present a\u0000revised analysis of the data, applying a method based on an underdamped\u0000Langevin equation. We find that different shape modes have different\u0000correlation times. We also find novel non-Gaussian effects. This study provides\u0000a framework in which quantitative comparisons of cell morphodynamics and\u0000migration can be made, e.g. between different biological conditions or\u0000mechanistic models.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139412445","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}

{"title":"Cell information processing via frequency encoding and excitability","authors":"Alan Givré, Silvina Ponce Dawson","doi":"arxiv-2312.17629","DOIUrl":"https://doi.org/arxiv-2312.17629","url":null,"abstract":"Cells continuously interact with their environment and respond to changes\u0000accordingly. Very often changes in the concentration of extracellular\u0000substances occur which, through receptor binding, give rise to a sequence of\u0000intracellular changes in what is called a signaling cascade. Increasing\u0000intensities of the external stimulus can result in increasing concentrations or\u0000increasing activation of the internal messengers or can induce a pulsatile\u0000behavior of increasing frequency with stimulus strength. This last behavior has\u0000been observed in intracellular Ca$^{2+}$ signals in which Ca$^{2+}$ is released\u0000from the endoplasmic reticulum through Inositol Trisphosphate Receptors\u0000(IP$_3$Rs), an ubiquitous signaling mechanism involved in many processes of\u0000physiological relevance. A statistical analysis of the time intervals between\u0000subsequent IP$_3$R-mediated Ca$^{2+}$ pulses observed experimentally has\u0000revealed an exponential dependence with the external stimulus strength in\u0000several cell types. This type of dependence, which is reminiscent of Kramers'\u0000law for thermally activated barrier crossing, has also been derived for certain\u0000excitable systems. Excitable systems have a stable stationary solution and,\u0000upon perturbations that surpass a threshold, perform a long excursion in phase\u0000space before returning to equilibrium. In this paper we use a very simple\u0000mathematical model of IP$_3$R-mediated Ca$^{2+}$ signals and published\u0000experimental results to derive the scaling law between the interpulse time and\u0000the external stimulus strength.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139066950","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}

{"title":"Minimal vertex model explains how the amnioserosa avoids fluidization during Drosophila dorsal closure","authors":"Indrajit Tah, Daniel Haertter, Janice M. Crawford, Daniel P. Kiehart, Christoph F. Schmidt, Andrea J. Liu","doi":"arxiv-2312.12926","DOIUrl":"https://doi.org/arxiv-2312.12926","url":null,"abstract":"Dorsal closure is a process that occurs during embryogenesis of Drosophila\u0000melanogaster. During dorsal closure, the amnioserosa (AS), a one-cell thick\u0000epithelial tissue that fills the dorsal opening, shrinks as the lateral\u0000epidermis sheets converge and eventually merge. During this process, the aspect\u0000ratio of amnioserosa cells increases markedly. The standard 2-dimensional\u0000vertex model, which successfully describes tissue sheet mechanics in multiple\u0000contexts, would in this case predict that the tissue should fluidize via cell\u0000neighbor changes. Surprisingly, however, the amnioserosa remains an elastic\u0000solid with no such events. We here present a minimal extension to the vertex\u0000model that explains how the amnioserosa can achieve this unexpected behavior.\u0000We show that continuous shrinkage of the preferred cell perimeter and cell\u0000perimeter polydispersity lead to the retention of the solid state of the\u0000amnioserosa. Our model accurately captures measured cell shape and orientation\u0000changes and predicts non-monotonic junction tension that we confirm with laser\u0000ablation experiments.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138823412","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}

{"title":"Inferring geometrical dynamics of cell nucleus translocation","authors":"Sirine Amiri, Yirui Zhang, Andonis Gerardos, Cécile Sykes, Pierre Ronceray","doi":"arxiv-2312.12402","DOIUrl":"https://doi.org/arxiv-2312.12402","url":null,"abstract":"The ability of eukaryotic cells to squeeze through constrictions is limited\u0000by the stiffness of their large and rigid nucleus. However, migrating cells are\u0000often able to overcome this limitation and pass through constrictions much\u0000smaller than their nucleus, a mechanism that is not yet understood. This is\u0000what we address here through a data-driven approach using microfluidic devices\u0000where cells migrate through controlled narrow spaces of sizes comparable to the\u0000ones encountered in physiological situations. Stochastic Force Inference is\u0000applied to experimental nuclear trajectories and nuclear shape descriptors,\u0000resulting in equations that effectively describe this phenomenon of nuclear\u0000translocation. By employing a model where the channel geometry is an explicit\u0000parameter and by training it over experimental data with different sizes of\u0000constrictions, we ensure that the resulting equations are predictive to other\u0000geometries. Altogether, the approach developed here paves the way for a\u0000mechanistic and quantitative description of dynamical cell complexity during\u0000its motility.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138819896","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}

{"title":"Memoryless Chemotaxis with Discrete Cues","authors":"Jacob Knight, Paula García-Galindo, Johannes Pausch, Gunnar Pruessner","doi":"arxiv-2312.11346","DOIUrl":"https://doi.org/arxiv-2312.11346","url":null,"abstract":"A wide array of biological systems can navigate in shallow gradients of\u0000chemoattractant with remarkable precision. Whilst previous approaches model\u0000such systems using coarse-grained chemical density profiles, we construct a\u0000dynamical model consisting of a chemotactic cell responding to discrete cue\u0000particles. For a cell without internal memory, we derive an effective velocity\u0000with which the cell approaches a point source of cue particles. We find that\u0000the effective velocity becomes negative beyond some homing radius, which\u0000represents an upper bound on the distance within which chemotaxis can be\u0000reliably performed. This work lays the foundation for the analytical\u0000characterisation of more detailed models of chemotaxis.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138745585","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}

{"title":"Spheroidal Molecular Communication via Diffusion: Signaling Between Homogeneous Cell Aggregates","authors":"Mitra Rezaei, Hamidreza Arjmandi, Mohammad Zoofaghari, Kajsa Kanebratt, Liisa Vilen, David Janzen, Peter Gennemark, Adam Noel","doi":"arxiv-2312.04427","DOIUrl":"https://doi.org/arxiv-2312.04427","url":null,"abstract":"Recent molecular communication (MC) research has integrated more detailed\u0000computational models to capture the dynamics of practical biophysical systems.\u0000This research focuses on developing realistic models for MC transceivers\u0000inspired by spheroids - three-dimensional cell aggregates commonly used in\u0000organ-on-chip experimental systems. Potential applications that can be used or\u0000modeled with spheroids include nutrient transport in an organ-on-chip system,\u0000the release of biomarkers or reception of drug molecules by a cancerous tumor\u0000site, or transceiver nanomachines participating in information exchange. In\u0000this paper, a simple diffusive MC system is considered where a spheroidal\u0000transmitter and receiver are in an unbounded fluid environment. These\u0000spheroidal antennas are modeled as porous media for diffusive signaling\u0000molecules, then their boundary conditions and effective diffusion coefficients\u0000are characterized. Further, for either a point source or spheroidal\u0000transmitter, Green's function for concentration (GFC) outside and inside the\u0000receiving spheroid is analytically derived and formulated in terms of an\u0000infinite series and confirmed by a particle-based simulator (PBS). The provided\u0000GFCs enable computation of the transmitted and received signals in the\u0000spheroidal communication system. This study shows that the porous structure of\u0000the receiving spheroid amplifies diffusion signals but also disperses them,\u0000thus there is a trade-off between porosity and information transmission rate.\u0000Also, the results reveal that the porous arrangement of the transmitting\u0000spheroid not only disperses the received signal but also attenuates it. System\u0000performance is also evaluated in terms of bit error rate (BER). Decreasing the\u0000porosity of the receiving spheroid is shown to enhance system performance.\u0000Conversely, reducing the porosity of the transmitting spheroid can adversely\u0000affect system performance.","PeriodicalId":501321,"journal":{"name":"arXiv - QuanBio - Cell Behavior","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138554108","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}