A System for Modelling Cell–Cell Interactions during Plant Morphogenesis

Dupuy, Lionel; Mackenzie, Jonathan Peter; Rudge, Tim; Haseloff, Jim

doi:10.1093/aob/mcm235

Cited by 84 publications

(82 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Beam theory (37) and 2D finite element analysis were able to reproduce a variety of morphogenetic behavior. Plate or shell theory could be used with similar techniques to simulate 3D growth (38) and could be coupled to detailed models of cell function (39).…”

Section: A Simple Experimental System For Quantitative Analysis Of Plantmentioning

confidence: 99%

Coordination of plant cell division and expansion in a simple morphogenetic system

Dupuy

Mackenzie

Haseloff

2010

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

126

107

View full text Add to dashboard Cite

Morphogenesis in plants arises from the interplay of genetic and physical interactions within a growing network of cells. The physical aspects of cell proliferation and differentiation are genetically regulated, but constrained by mechanical interactions between the cells. Higher plant tissues consist of an elaborate three-dimensional matrix of active cytoplasm and extracellular matrix, where it is difficult to obtain direct measurements of geometry or cell interactions. To properly understand the workings of plant morphogenesis, it is necessary to have biological systems that allow simple and direct observation of these processes. We have adopted a highly simplified plant system to investigate how cell proliferation and expansion is coordinated during morphogenesis. Coleocheate scutata is a microscopic fresh-water green alga with simple anatomical features that allow for accurate quantification of morphogenetic processes. Image analysis techniques were used to extract precise models for cell geometry and physical parameters for growth. This allowed construction of a deformable finite element model for growth of the whole organism, which incorporated cell biophysical properties, viscous expansion of cell walls, and rules for regulation of cell behavior. The study showed that a simple set of autonomous, cell-based rules are sufficient to account for the morphological and dynamic properties of Coleochaete growth. A variety of morphogenetic behavior emerged from the application of these local rules. Cell shape sensing is sufficient to explain the patterns of cell division during growth. This simplifying principle is likely to have application in modeling and design for engineering of higher plant tissues.biophysics | Coleochaete | dynamics | morphogenesis microscopy

show abstract

Section: A Simple Experimental System For Quantitative Analysis Of Plantmentioning

confidence: 99%

Coordination of plant cell division and expansion in a simple morphogenetic system

Dupuy

Mackenzie

Haseloff

2010

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

126

107

View full text Add to dashboard Cite

show abstract

“…Complications that occur in the application of such models to animal tissues, such as the topological transitions when cells change their neighbors, occur only in a limited set of situations, such as cell separation during lateral root emergence . Such models have been developed for plant tissues by a number of authors (Rudge and Haseloff, 2005;Jönsson et al, 2006;Dupuy et al, 2008;Hamant et al, 2008;Stoma et al, 2008;Merks et al, 2011).…”

Section: Multiscale Modeling Techniques: a Brief Overviewmentioning

confidence: 99%

“…Since mechanical properties of plant cells are dominated by their walls, vertex-based models provide a natural framework for computational simulation of tissue-scale mechanics (Rudge and Haseloff, 2005;Jönsson et al, 2006;Dupuy et al, 2008;Hamant et al, 2008). The Lockhart equation (or one of its variants) is a common building block in such models, as it describes microstructural processes in a simple form.…”

Section: Mechanicsmentioning

confidence: 99%

“…Many of these models have incorporated anisotropy in the mechanical properties of cells (e.g., by allowing the elastic properties of cell walls to depend upon their direction relative to the microtubule direction in each cell) (Hamant et al, 2008). Another feature common to many models is to treat the cell walls as bending beams (Dupuy et al, 2008), for instance, in the investigation of the effect of depolymerizing microtubules in a growing plant root (Corson et al, 2009).…”

Section: Mechanicsmentioning

confidence: 99%

See 1 more Smart Citation

Multiscale Systems Analysis of Root Growth and Development: Modeling Beyond the Network and Cellular Scales

et al. 2012

View full text Add to dashboard Cite

Over recent decades, we have gained detailed knowledge of many processes involved in root growth and development. However, with this knowledge come increasing complexity and an increasing need for mechanistic modeling to understand how those individual processes interact. One major challenge is in relating genotypes to phenotypes, requiring us to move beyond the network and cellular scales, to use multiscale modeling to predict emergent dynamics at the tissue and organ levels. In this review, we highlight recent developments in multiscale modeling, illustrating how these are generating new mechanistic insights into the regulation of root growth and development. We consider how these models are motivating new biological data analysis and explore directions for future research. This modeling progress will be crucial as we move from a qualitative to an increasingly quantitative understanding of root biology, generating predictive tools that accelerate the development of improved crop varieties.

show abstract

“…Blain et al 2004;Rudge & Haseloff 2005;Dupuy et al 2007). It is thus perhaps surprising that very little consideration is given to the process of modelling and simulation itself (Webb 2001).…”

Section: Understanding Modelling and Simulationmentioning

confidence: 99%

Methods for improving simulations of biological systems: systemic computation and fractal proteins

Bentley

2009

J. R. Soc. Interface.

View full text Add to dashboard Cite

Modelling and simulation are becoming essential for new fields such as synthetic biology. Perhaps the most important aspect of modelling is to follow a clear design methodology that will help to highlight unwanted deficiencies. The use of tools designed to aid the modelling process can be of benefit in many situations. In this paper, the modelling approach called systemic computation (SC) is introduced. SC is an interaction-based language, which enables individual-based expression and modelling of biological systems, and the interactions between them. SC permits a precise description of a hypothetical mechanism to be written using an intuitive graph-based or a calculus-based notation. The same description can then be directly run as a simulation, merging the hypothetical mechanism and the simulation into the same entity. However, even when using well-designed modelling tools to produce good models, the best model is not always the most accurate one. Frequently, computational constraints or lack of data make it infeasible to model an aspect of biology. Simplification may provide one way forward, but with inevitable consequences of decreased accuracy. Instead of attempting to replace an element with a simpler approximation, it is sometimes possible to substitute the element with a different but functionally similar component. In the second part of this paper, this modelling approach is described and its advantages are summarized using an exemplar: the fractal protein model. Finally, the paper ends with a discussion of good biological modelling practice by presenting lessons learned from the use of SC and the fractal protein model.

show abstract

A System for Modelling Cell–Cell Interactions during Plant Morphogenesis

Abstract: Plant morphogenesis is fundamentally a cellular process and the CellModeller software, through its underlying generic model, provides an advanced research tool to analyse coupled physical and biological morphogenetic mechanisms.

Cited by 84 publications

References 42 publications

Coordination of plant cell division and expansion in a simple morphogenetic system

Coordination of plant cell division and expansion in a simple morphogenetic system

Multiscale Systems Analysis of Root Growth and Development: Modeling Beyond the Network and Cellular Scales

Methods for improving simulations of biological systems: systemic computation and fractal proteins

Contact Info

Product

Resources

About