Ccoffinn: Automated Wave Tracking in Cultured Cardiac Monolayers.
Ontology highlight
ABSTRACT:
SUBMITTER: Tomek J
PROVIDER: S-EPMC5072981 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The complex structure of cardiac tissue is considered to be one of the main determinants of an arrhythmogenic substrate. This study is aimed at developing the first mathematical model to describe the formation of cardiac tissue, using a joint in silico-in vitro approach. First, we performed experiments under various conditions to carefully characterise the morphology of cardiac tissue in a culture of neonatal rat ventricular cells. We considered two cell types, namely, cardiomyocytes and fibroblasts. Next, we proposed a mathematical model, based on the Glazier-Graner-Hogeweg model, which is widely used in tissue growth studies. The resultant tissue morphology was coupled to the detailed electrophysiological Korhonen-Majumder model for neonatal rat ventricular cardiomyocytes, in order to study wave propagation. The simulated waves had the same anisotropy ratio and wavefront complexity as those in the experiment. Thus, we conclude that our approach allows us to reproduce the morphological and physiological properties of cardiac tissue.
| S-EPMC5554264 | biostudies-literature
Project description:Rotating spiral waves of electrical activity in the heart can anchor to unexcitable tissue (an obstacle) and become stable pinned waves. A pinned rotating wave can be unpinned either by a local electrical stimulus applied close to the spiral core, or by an electric field pulse that excites the core of a pinned wave independently of its localization. The wave will be unpinned only when the pulse is delivered inside a narrow time interval called the unpinning window (UW) of the spiral. In experiments with cardiac monolayers, we found that other obstacles situated near the pinning centre of the spiral can facilitate unpinning. In numerical simulations, we found increasing or decreasing of the UW depending on the location, orientation and distance between the pinning centre and an obstacle. Our study indicates that multiple obstacles could contribute to unpinning in experiments with intact hearts.
| S-EPMC6834031 | biostudies-literature
Project description:One-cell-thick monolayers are the simplest tissues in multicellular organisms, yet they fulfill critical roles in development and normal physiology. In early development, embryonic morphogenesis results largely from monolayer rearrangement and deformation due to internally generated forces. Later, monolayers act as physical barriers separating the internal environment from the exterior and must withstand externally applied forces. Though resisting and generating mechanical forces is an essential part of monolayer function, simple experimental methods to characterize monolayer mechanical properties are lacking. Here, we describe a system for tensile testing of freely suspended cultured monolayers that enables the examination of their mechanical behavior at multi-, uni-, and subcellular scales. Using this system, we provide measurements of monolayer elasticity and show that this is two orders of magnitude larger than the elasticity of their isolated cellular components. Monolayers could withstand more than a doubling in length before failing through rupture of intercellular junctions. Measurement of stress at fracture enabled a first estimation of the average force needed to separate cells within truly mature monolayers, approximately ninefold larger than measured in pairs of isolated cells. As in single cells, monolayer mechanical properties were strongly dependent on the integrity of the actin cytoskeleton, myosin, and intercellular adhesions interfacing adjacent cells. High magnification imaging revealed that keratin filaments became progressively stretched during extension, suggesting they participate in monolayer mechanics. This multiscale study of monolayer response to deformation enabled by our device provides the first quantitative investigation of the link between monolayer biology and mechanics.
| S-EPMC3478631 | biostudies-literature
Project description:Advancing human induced pluripotent stem cell derived cardiomyocyte (hiPSC-CM) technology will lead to significant progress ranging from disease modeling, to drug discovery, to regenerative tissue engineering. Yet, alongside these potential opportunities comes a critical challenge: attaining mature hiPSC-CM tissues. At present, there are multiple techniques to promote maturity of hiPSC-CMs including physical platforms and cell culture protocols. However, when it comes to making quantitative comparisons of functional behavior, there are limited options for reliably and reproducibly computing functional metrics that are suitable for direct cross-system comparison. In addition, the current standard functional metrics obtained from time-lapse images of cardiac microbundle contraction reported in the field (i.e., post forces, average tissue stress) do not take full advantage of the available information present in these data (i.e., full-field tissue displacements and strains). Thus, we present "MicroBundleCompute," a computational framework for automatic quantification of morphology-based mechanical metrics from movies of cardiac microbundles. Briefly, this computational framework offers tools for automatic tissue segmentation, tracking, and analysis of brightfield and phase contrast movies of beating cardiac microbundles. It is straightforward to implement, runs without user intervention, requires minimal input parameter setting selection, and is computationally inexpensive. In this paper, we describe the methods underlying this computational framework, show the results of our extensive validation studies, and demonstrate the utility of exploring heterogeneous tissue deformations and strains as functional metrics. With this manuscript, we disseminate "MicroBundleCompute" as an open-source computational tool with the aim of making automated quantitative analysis of beating cardiac microbundles more accessible to the community.
| S-EPMC10965069 | biostudies-literature
Project description:The automated quantification of the behaviour of freely moving animals is increasingly needed in applied ethology. State-of-the-art approaches often require tags to identify animals, high computational power for data collection and processing, and are sensitive to environmental conditions, which limits their large-scale utilization, for instance in genetic selection programs of animal breeding. Here we introduce a new automated tracking system based on millimetre-wave radars for real time robust and high precision monitoring of untagged animals. In contrast to conventional video tracking systems, radar tracking requires low processing power, is independent on light variations and has more accurate estimations of animal positions due to a lower misdetection rate. To validate our approach, we monitored the movements of 58 sheep in a standard indoor behavioural test used for assessing social motivation. We derived new estimators from the radar data that can be used to improve the behavioural phenotyping of the sheep. We then showed how radars can be used for movement tracking at larger spatial scales, in the field, by adjusting operating frequency and radiated electromagnetic power. Millimetre-wave radars thus hold considerable promises precision farming through high-throughput recording of the behaviour of untagged animals in different types of environments.
| S-EPMC8662461 | biostudies-literature
Project description:Engineered monolayers created using microabrasion and micropatterning methods have provided a simplified in vitro system to study the effects of anisotropy and fiber direction on electrical propagation. Interpreting the behavior in these culture systems has often been performed using classical computer models with continuous properties. However, such models do not account for the effects of random cell shapes, cell orientations, and cleft spaces inherent in these monolayers on the resulting wavefront conduction. This work presents a novel methodology for modeling a monolayer of cardiac tissue in which the factors governing cell shape, cell-to-cell coupling, and degree of cleft space are not constant but rather are treated as spatially random with assigned distributions. This modeling approach makes it possible to simulate wavefront propagation in a manner analogous to performing experiments on engineered monolayer tissues. Simulated results are compared to previously published measured data from monolayers used to investigate the role of cellular architecture on conduction velocities and anisotropy ratios. We also present an estimate for obtaining the electrical properties from these networks and demonstrate how variations in the discrete cellular architecture affect the macroscopic conductivities. The simulations support the common assumption that under normal ranges of coupling strength, tissues with relatively uniform distributions of cell shapes and connectivity can be represented using continuous models with conductivities derived from random discrete cellular architecture using either global or local estimates. The results also reveal that in the presence of abrupt changes in cell orientation, local estimates of tissue properties predict smoother changes in conductivity that may not adequately predict the discrete nature of propagation at the transition sites.
| S-EPMC2862160 | biostudies-literature
Project description:Force generation within cells, mediated by motor proteins along cytoskeletal networks, maintains the function of multicellular structures during homeostasis and when generating collective forces. Here, we describe the use of chromatin dynamics to detect cellular force propagation [a technique termed SINK (sensors from intranuclear kinetics)] and investigate the force response of cells to disruption of the monolayer and changes in substrate stiffness. We find that chromatin dynamics change in a substrate stiffness-dependent manner within epithelial monolayers. We also investigate point defects within monolayers to map the impact on the strain field of a heterogeneous monolayer. We find that cell monolayers behave as a colloidal assembly rather than as a continuum since the data fit an exponential decay; the lateral characteristic length of recovery from the mechanical defect is ∼50 µm for cells with a 10 µm spacing. At distances greater than this characteristic length, cells behave similarly to those in a fully intact monolayer. This work demonstrates the power of SINK to investigate diseases including cancer and atherosclerosis that result from single cells or heterogeneities in monolayers.This article has an associated First Person interview with the first author of the paper.
| S-EPMC6031382 | biostudies-literature
Project description:Collective cell migration is an umbrella term for a rich variety of cell behaviors, whose distinct character is important for biological function, notably for cancer metastasis. One essential feature of collective behavior is the motion of cells relative to their immediate neighbors. We introduce an AI-based pipeline to segment and track cell nuclei from phase-contrast images. Nuclei segmentation is based on a U-Net convolutional neural network trained on images with nucleus staining. Tracking, based on the Crocker-Grier algorithm, quantifies nuclei movement and allows for robust downstream analysis of collective motion. Because the AI algorithm required no new training data, our approach promises to be applicable to and yield new insights for vast libraries of existing collective motion images. In a systematic analysis of a cell line panel with oncogenic mutations, we find that the collective rearrangement metric, D2 min, which reflects non-affine motion, shows promise as an indicator of metastatic potential.
| S-EPMC9287486 | biostudies-literature
Project description:BackgroundSlow wave sleep (SWS) plays an important role in neurophysiologic restoration. Experimentally testing the effect of SWS disruption previously required highly time-intensive and subjective methods. Our goal was to develop an automated and objective protocol to reduce SWS without affecting sleep architecture.New methodWe developed a custom Matlab™ protocol to calculate electroencephalogram spectral power every 10s live during a polysomnogram, exclude artifact, and, if measurements met criteria for SWS, deliver increasingly louder tones through earphones. Middle-aged healthy volunteers (n=10) each underwent 2 polysomnograms, one with the SWS disruption protocol and one with sham condition.ResultsThe SWS disruption protocol reduced SWS compared to sham condition, as measured by spectral power in the delta (0.5-4Hz) band, particularly in the 0.5-2Hz range (mean 20% decrease). A compensatory increase in the proportion of total spectral power in the theta (4-8Hz) and alpha (8-12Hz) bands was seen, but otherwise normal sleep features were preserved. N3 sleep decreased from 20±34 to 3±6min, otherwise there were no significant changes in total sleep time, sleep efficiency, or other macrostructural sleep characteristics.Comparison with existing methodThis novel SWS disruption protocol produces specific reductions in delta band power similar to existing methods, but has the advantage of being automated, such that SWS disruption can be performed easily in a highly standardized and operator-independent manner.ConclusionThis automated SWS disruption protocol effectively reduces SWS without impacting overall sleep architecture.
| S-EPMC5399676 | biostudies-literature
Project description:BackgroundThe preparation consisting of a head-fixed mouse on a spherical or cylindrical treadmill offers unique advantages in a variety of experimental contexts. Head fixation provides the mechanical stability necessary for optical and electrophysiological recordings and stimulation. Additionally, it can be combined with virtual environments such as T-mazes, enabling these types of recording during diverse behaviors.New methodIn this paper we present a low-cost, easy-to-build acquisition system, along with scalable computational methods to quantitatively measure behavior (locomotion and paws, whiskers, and tail motion patterns) in head-fixed mice locomoting on cylindrical or spherical treadmills.Existing methodsSeveral custom supervised and unsupervised methods have been developed for measuring behavior in mice. However, to date there is no low-cost, turn-key, general-purpose, and scalable system for acquiring and quantifying behavior in mice.ResultsWe benchmark our algorithms against ground truth data generated either by manual labeling or by simpler methods of feature extraction. We demonstrate that our algorithms achieve good performance, both in supervised and unsupervised settings.ConclusionsWe present a low-cost suite of tools for behavioral quantification, which serve as valuable complements to recording and stimulation technologies being developed for the head-fixed mouse preparation.
| S-EPMC7957302 | biostudies-literature