Computational modeling of development by epithelia, mesenchyme and their interactions: a unified model

Marín-Riera, Miquel; Brun‐Usan, Miguel; Zimm, Roland; Välikangas, Tommi; Salazar‐Ciudad, Isaac

doi:10.1093/bioinformatics/btv527

Cited by 54 publications

(67 citation statements)

References 30 publications

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“…At present Chaste (81) (83,84), further work is required to make progress in this area. In particular, the development of methodologies to interface models that include descriptions of cell shape, mechanics and biochemical signalling in different ways and on different scales, will be crucial.…”

Section: Model Choice and Implementationmentioning

confidence: 99%

Mechanocellular models of epithelial morphogenesis

Fletcher

Cooper

Baker

2017

Phil. Trans. R. Soc. B

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Embryonic epithelia achieve complex morphogenetic movements, including in-plane reshaping, bending and folding, through the coordinated action and rearrangement of individual cells. Technical advances in molecular and live-imaging studies of epithelial dynamics provide a very real opportunity to understand how cell-level processes facilitate these large-scale tissue rearrangements. However, the large datasets that we are now able to generate require careful interpretation. In combination with experimental approaches, computational modelling allows us to challenge and refine our current understanding of epithelial morphogenesis and to explore experimentally intractable questions. To this end a variety of cell-based modelling approaches have been developed to describe cell-cell mechanical interactions, ranging from vertex and 'finite element' models that approximate each cell geometrically by a polygon representing the cell's membrane, to immersed boundary and subcellular element models that allow for more arbitrary cell shapes. Here we review how these models have been used to provide insight into epithelial morphogenesis and describe how such models could help future efforts to decipher the forces and mechanical and biochemical feedbacks that guide cell and tissue-level behaviour. In addition, we discuss current challenges associated with using computational models of morphogenetic processes in a quantitative and predictive way.

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Section: Model Choice and Implementationmentioning

confidence: 99%

Mechanocellular models of epithelial morphogenesis

Fletcher

Cooper

Baker

2017

Phil. Trans. R. Soc. B

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“…The mathematical model used in this study, the SpiralMaker, is a modification of a general model of animal embryonic development, the EmbryoMaker (Marin-Riera et al, 2016), that allows us to implement each of the developmental rules studied in this article. [The EmbryoMaker software implementing the model is available for download (http://www.…”

Section: Methodsmentioning

confidence: 99%

“…Therein each cell is represented as a set of subcellular elements (spheric elastic volumes) in three-dimensional space. The physical interactions between the subcellular elements (hereafter nodes) allows each whole cell to display visco-elastic properties like those observed in real cells (Newman, 2005;Sandersius and Newman, 2008;Marin-Riera et al, 2016). Thus, nodes can adhere to one another ( preferentially to nodes from the same cell but also to nodes from other cells) but repel each other if they are too close (reiterating the physical fact that two cells can not occupy exactly the same position in space).…”

Section: Introductionmentioning

confidence: 98%

A set of simple cell processes are sufficient to model spiral cleavage

et al. 2016

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During cleavage, different cellular processes cause the zygote to become partitioned into a set of cells with a specific spatial arrangement. These processes include the orientation of cell division according to: an animal-vegetal gradient; the main axis (Hertwig's rule) of the cell; and the contact areas between cells or the perpendicularity between consecutive cell divisions (Sachs' rule). Cell adhesion and cortical rotation have also been proposed to be involved in spiral cleavage. We use a computational model of cell and tissue biomechanics to account for the different existing hypotheses about how the specific spatial arrangement of cells in spiral cleavage arises during development. Cell polarization by an animal-vegetal gradient, a bias to perpendicularity between consecutive cell divisions (Sachs' rule), cortical rotation and cell adhesion, when combined, reproduce the spiral cleavage, whereas other combinations of processes cannot. Specifically, cortical rotation is necessary at the 8-cell stage to direct all micromeres in the same direction. By varying the relative strength of these processes, we reproduce the spatial arrangement of cells in the blastulae of seven different invertebrate species.

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“…Isaac Salazar‐Ciudad (University of Helsinki) presented a theoretical approach to evodevo, beginning with the question: if you were to design a gene network from scratch, what would it look like? To build a general model of animal development, Salazar‐Ciudad computationally generated a variety of random developmental gene networks and produced the corresponding phenotypes in silico (Marin‐Riera, Brun‐Usan, Zimm, Välikangas, & Salazar‐Ciudad, ). He found that mutations tend to decrease the complexity of phenotypes, and that most gene networks produce morphologies that are highly sensitive to noise.…”

Section: Theory and Modeling Approaches To Evodevomentioning

confidence: 99%

The second biennial meeting of the Pan‐American Society for Evolutionary Developmental Biology

Callier

2018

J Exp Zool Pt B

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Evodevo is concerned with understanding how phenotypes develop and evolve, how organismal diversity is generated and maintained, and how evolutionary innovations originate. The second Pan-American Society for Evolutionary Developmental Biology (PASEDB) meeting in Calgary, Canada, showcased a great variety of species and study systems, and a variety of approaches to address these questions. Although there were, like at the first PASEDB meeting, many developmental genetic and genomic studies, much of the work moved beyond comparative developmental genetics toward more integrative studies that seek explanations at different levels of the organismal hierarchy.

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Computational modeling of development by epithelia, mesenchyme and their interactions: a unified model

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 54 publications

References 30 publications

Mechanocellular models of epithelial morphogenesis

Mechanocellular models of epithelial morphogenesis

A set of simple cell processes are sufficient to model spiral cleavage

The second biennial meeting of the Pan‐American Society for Evolutionary Developmental Biology

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