scholarly journals Pan-embryo cell dynamics of germlayer formation in zebrafish

2017 ◽  
Author(s):  
Gopi Shah ◽  
Konstantin Thierbach ◽  
Benjamin Schmid ◽  
Anna Reade ◽  
Ingo Roeder ◽  
...  
Keyword(s):  
Cell Movement ◽  
Initial Distribution ◽  
Embryo Cell ◽  
Local Region ◽  
Cell Dynamics ◽  
Fate Specification ◽  
Movement Characteristics ◽  
Global Movement ◽  
Spatio Temporal ◽  
Distinct Distribution

AbstractCell movements are coordinated across spatio-temporal scales to achieve precise positioning of organs during vertebrate gastrulation. In zebrafish, mechanisms governing such morphogenetic movements have so far only been studied within a local region or a single germlayer. Here, we present pan-embryo analyses of fate specification and dynamics of all three germlayers simultaneously within a gastrulating embryo, showing that cell movement characteristics are predominantly determined by its position within the embryo, independent of its germlayer identity. The spatially confined fate specification establishes a distinct distribution of cells in each germlayer during early gastrulation. The differences in the initial distribution are subsequently amplified by a unique global movement, which organizes the organ precursors along the embryonic body axis, giving rise to the blueprint of organ formation.

scholarly journals Multi-scale imaging and analysis identify pan-embryo cell dynamics of germlayer formation in zebrafish

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Gopi Shah ◽  
Konstantin Thierbach ◽  
Benjamin Schmid ◽  
Johannes Waschke ◽  
Anna Reade ◽  
...  
Keyword(s):  
Cell Movement ◽  
Automated Analysis ◽  
Embryo Cell ◽  
Tissue Formation ◽  
Cell Dynamics ◽  
Multi Scale ◽  
Movement Characteristics ◽  
Global Movement ◽  
Spatio Temporal ◽  
Distinct Distribution

AbstractThe coordination of cell movements across spatio-temporal scales ensures precise positioning of organs during vertebrate gastrulation. Mechanisms governing such morphogenetic movements have been studied only within a local region, a single germlayer or in whole embryos without cell identity. Scale-bridging imaging and automated analysis of cell dynamics are needed for a deeper understanding of tissue formation during gastrulation. Here, we report pan-embryo analyses of formation and dynamics of all three germlayers simultaneously within a developing zebrafish embryo. We show that a distinct distribution of cells in each germlayer is established during early gastrulation via cell movement characteristics that are predominantly determined by their position in the embryo. The differences in initial germlayer distributions are subsequently amplified by a global movement, which organizes the organ precursors along the embryonic body axis, giving rise to the blueprint of organ formation. The tools and data are available as a resource for the community.

scholarly journals Spatio-temporal Inversion using the Selection Kalman Model

2020 ◽  
Author(s):  
Maxime Conjard ◽  
Henning Omre
Keyword(s):  
Gaussian Distribution ◽  
Extreme Event ◽  
Recursive Algorithm ◽  
Initial Distribution ◽  
Pollution Source ◽  
Pollution Monitoring ◽  
Initial State ◽  
Linear Dynamic ◽  
Spatio Temporal ◽  
Spatial Histogram

<p>The challenge in data assimilation for models representing spatio-temporal phenomena is made harder when the spatial histogram of the variable of interest appears with multiple modes. Pollution source identification constitutes one example where the pollution release represents an extreme event in a fairly homogeneous background. Consequently, our prior belief is that the spatial histogram is bimodal. The traditional Kalman model is based on a Gaussian initial distribution and Gauss-linear dynamic and observation models. This model is contained in the class of Gaussian distribution and is therefore analytically tractable. These properties that make its strenght also render it unsuitable for representing multimodality. To address the issue, we define the selection Kalman model. It is based on a selection-Gaussian initial distribution and Gauss-linear dynamic and observation models. The selection-Gaussian distribution may represent multimodality, skewness and peakedness. It can be seen as a generalization of the Gaussian distribution. The proposed selection Kalman model is contained in the class of selection-Gaussian distributions and therefore analytically tractable. The recursive algorithm used for assessing the selection Kalman model is specified. We present a synthetic case study of spatio-temporal inversion of an initial state containing an extreme event. The study is inspired by pollution monitoring. The results suggest that the use of the selection Kalman model offers significant improvements compared to the traditional Kalman model when reconstructing discontinuous initial states. </p>

ON THE REPRESENTATION, LEARNING AND TRANSFER OF SPATIO-TEMPORAL MOVEMENT CHARACTERISTICS

2004 ◽  
Vol 01 (04) ◽  
pp. 613-636 ◽  
Author(s):  
WINFRIED ILG ◽  
GÖKHAN H. BAKIR ◽  
JOHANNES MEZGER ◽  
MARTIN A. GIESE
Keyword(s):  
Representation Learning ◽  
Movement Sequences ◽  
Movement Trajectories ◽  
Movement Characteristics ◽  
Human Movements ◽  
Complex Sequences ◽  
Movement Representation ◽  
Spatio Temporal ◽  
Morphable Models ◽  
Complex Movement

In this paper we present a learning-based approach for the modeling of complex movement sequences. Based on the method of Spatio-Temporal Morphable Models (STMMs) we derive a hierarchical algorithm that, in a first step, identifies automatically movement elements in movement sequences based on a coarse spatio-temporal description, and in a second step models these movement primitives by approximation through linear combinations of learned example movement trajectories. We describe the different steps of the algorithm and show how it can be applied for modeling and synthesis of complex sequences of human movements that contain movement elements with a variable style. The proposed method is demonstrated on different applications of movement representation relevant for imitation learning of movement styles in humanoid robotics.

Time-lapse imaging: the state of the art†

2019 ◽  
Vol 101 (6) ◽  
pp. 1146-1154 ◽  
Author(s):  
Raquel Del Gallego ◽  
José Remohí ◽  
Marcos Meseguer
Keyword(s):  
Embryo Development ◽  
Clinical Success ◽  
Time Lapse ◽  
Embryo Cell ◽  
Cell Dynamics ◽  
Vitro Fertilization ◽  
Cycle Lengths ◽  
Novel Concept ◽  
Time Lapse Imaging

Abstract The introduction of time-lapse imaging to clinical in vitro fertilization practice enabled the undisturbed monitoring of embryos throughout the entire culture period. Initially, the main objective was to achieve a better embryo development. However, this technology also provided an insight into the novel concept of morphokinetics, parameters regarding embryo cell dynamics. The vast amount of data obtained defined the optimal ranges in the cell-cycle lengths at different stages of embryo development. This added valuable information to embryo assessment prior to transfer. Kinetic markers became part of embryo evaluation strategies with the potential to increase the chances of clinical success. However, none of them has been established as an international standard. The present work aims at describing new approaches into time-lapse: progress to date, challenges, and possible future directions.

scholarly journals Pax6 modulates intra-retinal axon guidance and fasciculation of retinal ganglion cells during retinogenesis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Soundararajan Lalitha ◽  
Budhaditya Basu ◽  
Suresh Surya ◽  
Vadakkath Meera ◽  
Paul Ann Riya ◽  
...  
Keyword(s):  
Axon Guidance ◽  
Ganglion Cells ◽  
Transcriptome Profiling ◽  
Retinal Ganglion ◽  
Temporal Expression ◽  
Fate Specification ◽  
Extracellular Matrix Molecules ◽  
Coordinated Expression ◽  
Spatio Temporal ◽  
Retinal Axon

Abstract Intra-retinal axon guidance involves a coordinated expression of transcription factors, axon guidance genes, and secretory molecules within the retina. Pax6, the master regulator gene, has a spatio-temporal expression typically restricted till neurogenesis and fate-specification. However, our observation of persistent expression of Pax6 in mature RGCs led us to hypothesize that Pax6 could play a major role in axon guidance after fate specification. Here, we found significant alteration in intra-retinal axon guidance and fasciculation upon knocking out of Pax6 in E15.5 retina. Through unbiased transcriptome profiling between Pax6fl/fl and Pax6−/− retinas, we revealed the mechanistic insight of its role in axon guidance. Our results showed a significant increase in the expression of extracellular matrix molecules and decreased expression of retinal fate specification and neuron projection guidance molecules. Additionally, we found that EphB1 and Sema5B are directly regulated by Pax6 owing to the guidance defects and improper fasciculation of axons. We conclude that Pax6 expression post fate specification of RGCs is necessary for regulating the expression of axon guidance genes and most importantly for maintaining a conducive ECM through which the nascent axons get guided and fasciculate to reach the optic disc.

scholarly journals An Easy-to-Fabricate Cell Stretcher Reveals Density-Dependent Mechanical Regulation of Collective Cell Movements in Epithelia

2021 ◽  
Author(s):  
Kevin C. Hart ◽  
Joo Yong Sim ◽  
Matthew A. Hopcroft ◽  
Daniel J. Cohen ◽  
Jiongyi Tan ◽  
...  
Keyword(s):  
Low Cost ◽  
Cell Movement ◽  
Time Lapse ◽  
Adherent Cell ◽  
Dependent Manner ◽  
Cell Dynamics ◽  
Density Dependent ◽  
Cell Movements ◽  
Tissue Biology ◽  
Mechanical Regulation

Abstract Introduction Mechanical forces regulate many facets of cell and tissue biology. Studying the effects of forces on cells requires real-time observations of single- and multi-cell dynamics in tissue models during controlled external mechanical input. Many of the existing devices used to conduct these studies are costly and complicated to fabricate, which reduces the availability of these devices to many laboratories. Methods We show how to fabricate a simple, low-cost, uniaxial stretching device, with readily available materials and instruments that is compatible with high-resolution time-lapse microscopy of adherent cell monolayers. In addition, we show how to construct a pressure controller that induces a repeatable degree of stretch in monolayers, as well as a custom MATLAB code to quantify individual cell strains. Results As an application note using this device, we show that uniaxial stretch slows down cellular movements in a mammalian epithelial monolayer in a cell density-dependent manner. We demonstrate that the effect on cell movement involves the relocalization of myosin downstream of Rho-associated protein kinase (ROCK). Conclusions This mechanical device provides a platform for broader involvement of engineers and biologists in this important area of cell and tissue biology. We used this device to demonstrate the mechanical regulation of collective cell movements in epithelia.

scholarly journals Accumulation of Tetrahymena pyriformis on Interfaces

Micromachines ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1339
Author(s):  
Kohei Okuyama ◽  
Yukinori Nishigami ◽  
Takuya Ohmura ◽  
Masatoshi Ichikawa
Keyword(s):  
Single Cell ◽  
Solid Wall ◽  
Tetrahymena Pyriformis ◽  
Behavioral Model ◽  
Bottom Surface ◽  
Environmental Biology ◽  
Cell Dynamics ◽  
Pattern Dynamics ◽  
Spatio Temporal ◽  
Accumulation Coefficients

The behavior of ciliates has been studied for many years through environmental biology and the ethology of microorganisms, and recent hydrodynamic studies of microswimmers have greatly advanced our understanding of the behavioral dynamics at the single-cell level. However, the association between single-cell dynamics captured by microscopic observation and pattern dynamics obtained by macroscopic observation is not always obvious. Hence, to bridge the gap between the two, there is a need for experimental results on swarming dynamics at the mesoscopic scale. In this study, we investigated the spatial population dynamics of the ciliate, Tetrahymena pyriformis, based on quantitative data analysis. We combined the image processing of 3D micrographs and machine learning to obtain the positional data of individual cells of T. pyriformis and examined their statistical properties based on spatio-temporal data. According to the 3D spatial distribution of cells and their temporal evolution, cells accumulated both on the solid wall at the bottom surface and underneath the air–liquid interface at the top. Furthermore, we quantitatively clarified the difference in accumulation levels between the bulk and the interface by creating a simple behavioral model that incorporated quantitative accumulation coefficients in its solution. The accumulation coefficients can be compared under different conditions and between different species.

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