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Harnvanichvech Y, Gorelova V, Sprakel J, Weijers D. The Arabidopsis embryo as a quantifiable model for studying pattern formation. QUANTITATIVE PLANT BIOLOGY 2021; 2:e3. [PMID: 37077211 PMCID: PMC10095805 DOI: 10.1017/qpb.2021.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/15/2021] [Accepted: 02/21/2021] [Indexed: 05/03/2023]
Abstract
Phenotypic diversity of flowering plants stems from common basic features of the plant body pattern with well-defined body axes, organs and tissue organisation. Cell division and cell specification are the two processes that underlie the formation of a body pattern. As plant cells are encased into their cellulosic walls, directional cell division through precise positioning of division plane is crucial for shaping plant morphology. Since many plant cells are pluripotent, their fate establishment is influenced by their cellular environment through cell-to-cell signaling. Recent studies show that apart from biochemical regulation, these two processes are also influenced by cell and tissue morphology and operate under mechanical control. Finding a proper model system that allows dissecting the relationship between these aspects is the key to our understanding of pattern establishment. In this review, we present the Arabidopsis embryo as a simple, yet comprehensive model of pattern formation compatible with high-throughput quantitative assays.
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Affiliation(s)
- Yosapol Harnvanichvech
- Physical Chemistry and Soft Matter, Wageningen University, Wageningen, The Netherlands
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Vera Gorelova
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Joris Sprakel
- Physical Chemistry and Soft Matter, Wageningen University, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Author for correspondence: Dolf Weijers, E-mail:
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2
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Majda M, Krupinski P, Jönsson H, Hamant O, Robert S. Mechanical Asymmetry of the Cell Wall Predicts Changes in Pavement Cell Geometry. Dev Cell 2020; 50:9-10. [PMID: 31265814 DOI: 10.1016/j.devcel.2019.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Mateusz Majda
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| | - Pawel Krupinski
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden
| | - Henrik Jönsson
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden; Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK; Department of Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK
| | - Olivier Hamant
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Stéphanie Robert
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden.
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Cell-Based Model of the Generation and Maintenance of the Shape and Structure of the Multilayered Shoot Apical Meristem of Arabidopsis thaliana. Bull Math Biol 2018; 81:3245-3281. [PMID: 30552627 DOI: 10.1007/s11538-018-00547-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 11/28/2018] [Indexed: 01/28/2023]
Abstract
One of the central problems in animal and plant developmental biology is deciphering how chemical and mechanical signals interact within a tissue to produce organs of defined size, shape, and function. Cell walls in plants impose a unique constraint on cell expansion since cells are under turgor pressure and do not move relative to one another. Cell wall extensibility and constantly changing distribution of stress on the wall are mechanical properties that vary between individual cells and contribute to rates of expansion and orientation of cell division. How exactly cell wall mechanical properties influence cell behavior is still largely unknown. To address this problem, a novel, subcellular element computational model of growth of stem cells within the multilayered shoot apical meristem (SAM) of Arabidopsis thaliana is developed and calibrated using experimental data. Novel features of the model include separate, detailed descriptions of cell wall extensibility and mechanical stiffness, deformation of the middle lamella, and increase in cytoplasmic pressure generating internal turgor pressure. The model is used to test novel hypothesized mechanisms of formation of the shape and structure of the growing, multilayered SAM based on WUS concentration of individual cells controlling cell growth rates and layer-dependent anisotropic mechanical properties of subcellular components of individual cells determining anisotropic cell expansion directions. Model simulations also provide a detailed prediction of distribution of stresses in the growing tissue which can be tested in future experiments.
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Hernández-Hernández V, Barrio RA, Benítez M, Nakayama N, Romero-Arias JR, Villarreal C. A physico-genetic module for the polarisation of auxin efflux carriers PIN-FORMED (PIN). Phys Biol 2018; 15:036002. [PMID: 29393068 DOI: 10.1088/1478-3975/aaac99] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Intracellular polarisation of auxin efflux carriers is crucial for understanding how auxin gradients form in plants. The polarisation dynamics of auxin efflux carriers PIN-FORMED (PIN) depends on both biomechanical forces as well as chemical, molecular and genetic factors. Biomechanical forces have shown to affect the localisation of PIN transporters to the plasma membrane. We propose a physico-genetic module of PIN polarisation that integrates biomechanical, molecular, and cellular processes as well as their non-linear interactions. The module was implemented as a discrete Boolean model and then approximated to a continuous dynamic system, in order to explore the relative contribution of the factors mediating PIN polarisation at the scale of single cell. Our models recovered qualitative behaviours that have been experimentally observed and enable us to predict that, in the context of PIN polarisation, the effects of the mechanical forces can predominate over the activity of molecular factors such as the GTPase ROP6 and the ROP-INTERACTIVE CRIB MOTIF-CONTAINING PROTEIN RIC1.
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Affiliation(s)
- Valeria Hernández-Hernández
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico. Current Address: Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon, France. Author to whom any correspondence should be addressed
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5
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Cerutti G, Ali O, Godin C. DRACO-STEM: An Automatic Tool to Generate High-Quality 3D Meshes of Shoot Apical Meristem Tissue at Cell Resolution. FRONTIERS IN PLANT SCIENCE 2017; 8:353. [PMID: 28424704 PMCID: PMC5372818 DOI: 10.3389/fpls.2017.00353] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 02/28/2017] [Indexed: 06/01/2023]
Abstract
Context: The shoot apical meristem (SAM), origin of all aerial organs of the plant, is a restricted niche of stem cells whose growth is regulated by a complex network of genetic, hormonal and mechanical interactions. Studying the development of this area at cell level using 3D microscopy time-lapse imaging is a newly emerging key to understand the processes controlling plant morphogenesis. Computational models have been proposed to simulate those mechanisms, however their validation on real-life data is an essential step that requires an adequate representation of the growing tissue to be carried out. Achievements: The tool we introduce is a two-stage computational pipeline that generates a complete 3D triangular mesh of the tissue volume based on a segmented tissue image stack. DRACO (Dual Reconstruction by Adjacency Complex Optimization) is designed to retrieve the underlying 3D topological structure of the tissue and compute its dual geometry, while STEM (SAM Tissue Enhanced Mesh) returns a faithful triangular mesh optimized along several quality criteria (intrinsic quality, tissue reconstruction, visual adequacy). Quantitative evaluation tools measuring the performance of the method along those different dimensions are also provided. The resulting meshes can be used as input and validation for biomechanical simulations. Availability: DRACO-STEM is supplied as a package of the open-source multi-platform plant modeling library OpenAlea (http://openalea.github.io/) implemented in Python, and is freely distributed on GitHub (https://github.com/VirtualPlants/draco-stem) along with guidelines for installation and use.
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Affiliation(s)
- Guillaume Cerutti
- Virtual Plants INRIA Team, UMR AGAP, CIRAD, INRIA, INRAMontpellier, France
| | - Olivier Ali
- Virtual Plants INRIA Team, UMR AGAP, CIRAD, INRIA, INRAMontpellier, France
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS-Lyon, INRA, Centre National de la Recherche ScientifiqueLyon, France
| | - Christophe Godin
- Virtual Plants INRIA Team, UMR AGAP, CIRAD, INRIA, INRAMontpellier, France
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6
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Draelants D, Avitabile D, Vanroose W. Localized auxin peaks in concentration-based transport models of the shoot apical meristem. J R Soc Interface 2016; 12:rsif.2014.1407. [PMID: 25878130 DOI: 10.1098/rsif.2014.1407] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We study the formation of auxin peaks in a generic class of concentration-based auxin transport models, posed on static plant tissues. Using standard asymptotic analysis, we prove that, on bounded domains, auxin peaks are not formed via a Turing instability in the active transport parameter, but via simple corrections to the homogeneous steady state. When the active transport is small, the geometry of the tissue encodes the peaks' amplitude and location: peaks arise where cells have fewer neighbours, that is, at the boundary of the domain. We test our theory and perform numerical bifurcation analysis on two models that are known to generate auxin patterns for biologically plausible parameter values. In the same parameter regimes, we find that realistic tissues are capable of generating a multitude of stationary patterns, with a variable number of auxin peaks, that can be selected by different initial conditions or by quasi-static changes in the active transport parameter. The competition between active transport and production rate determines whether peaks remain localized or cover the entire domain. In particular, changes in the auxin production that are fast with respect to the cellular life cycle affect the auxin peak distribution, switching from localized spots to fully patterned states. We relate the occurrence of localized patterns to a snaking bifurcation structure, which is known to arise in a wide variety of nonlinear media, but has not yet been reported in plant models.
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Affiliation(s)
- Delphine Draelants
- Department of Mathematics and Computer Science, Universiteit Antwerpen, Middelheimlaan 1, 2020 Antwerpen, Belgium
| | - Daniele Avitabile
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Wim Vanroose
- Department of Mathematics and Computer Science, Universiteit Antwerpen, Middelheimlaan 1, 2020 Antwerpen, Belgium
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7
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Bassel GW, Smith RS. Quantifying morphogenesis in plants in 4D. CURRENT OPINION IN PLANT BIOLOGY 2016; 29:87-94. [PMID: 26748353 DOI: 10.1016/j.pbi.2015.11.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/04/2015] [Accepted: 11/10/2015] [Indexed: 06/05/2023]
Abstract
Plant development occurs in 3D space over time (4D). Recent advances in image acquisition and computational analysis are now enabling development to be visualized and quantified in its entirety at the cellular level. The simultaneous quantification of reporter abundance and 3D cell shape change enables links between signaling processes and organ morphogenesis to be accomplished organ-wide and at single cell resolution. Current work to integrate this quantitative 3D image data with computational models is enabling causal relationships between gene expression and organ morphogenesis to be uncovered. Further technical advances in imaging and image analysis will enable this approach to be applied to a greater diversity of plant organs and will become a key tool to address many questions in plant development.
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Affiliation(s)
- George W Bassel
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Richard S Smith
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany.
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8
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Barbier de Reuille P, Routier-Kierzkowska AL, Kierzkowski D, Bassel GW, Schüpbach T, Tauriello G, Bajpai N, Strauss S, Weber A, Kiss A, Burian A, Hofhuis H, Sapala A, Lipowczan M, Heimlicher MB, Robinson S, Bayer EM, Basler K, Koumoutsakos P, Roeder AHK, Aegerter-Wilmsen T, Nakayama N, Tsiantis M, Hay A, Kwiatkowska D, Xenarios I, Kuhlemeier C, Smith RS. MorphoGraphX: A platform for quantifying morphogenesis in 4D. eLife 2015; 4:05864. [PMID: 25946108 PMCID: PMC4421794 DOI: 10.7554/elife.05864] [Citation(s) in RCA: 303] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 04/03/2015] [Indexed: 12/25/2022] Open
Abstract
Morphogenesis emerges from complex multiscale interactions between genetic and mechanical processes. To understand these processes, the evolution of cell shape, proliferation and gene expression must be quantified. This quantification is usually performed either in full 3D, which is computationally expensive and technically challenging, or on 2D planar projections, which introduces geometrical artifacts on highly curved organs. Here we present MorphoGraphX ( www.MorphoGraphX.org), a software that bridges this gap by working directly with curved surface images extracted from 3D data. In addition to traditional 3D image analysis, we have developed algorithms to operate on curved surfaces, such as cell segmentation, lineage tracking and fluorescence signal quantification. The software's modular design makes it easy to include existing libraries, or to implement new algorithms. Cell geometries extracted with MorphoGraphX can be exported and used as templates for simulation models, providing a powerful platform to investigate the interactions between shape, genes and growth.
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Affiliation(s)
| | - Anne-Lise Routier-Kierzkowska
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Daniel Kierzkowski
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - George W Bassel
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | | | | | - Namrata Bajpai
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Sören Strauss
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Alain Weber
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Annamaria Kiss
- Reproduction et Développement des Plantes, Ecole Normale Supérieure de Lyon, Lyon, France
- Laboratoire Joliot Curie, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Agata Burian
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Department of Biophysics and Morphogenesis of Plants, University of Silesia, Katowice, Poland
| | - Hugo Hofhuis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Aleksandra Sapala
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Marcin Lipowczan
- Department of Biophysics and Morphogenesis of Plants, University of Silesia, Katowice, Poland
| | | | - Sarah Robinson
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Emmanuelle M Bayer
- Laboratory of Membrane Biogenesis, University of Bordeaux, Bordeaux, France
| | - Konrad Basler
- Institute of Molecular Life Sciences, Zurich, Switzerland
| | | | - Adrienne HK Roeder
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, United States
| | | | - Naomi Nakayama
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Angela Hay
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dorota Kwiatkowska
- Department of Biophysics and Morphogenesis of Plants, University of Silesia, Katowice, Poland
| | | | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Richard S Smith
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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9
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Cartenì F, Giannino F, Schweingruber FH, Mazzoleni S. Modelling the development and arrangement of the primary vascular structure in plants. ANNALS OF BOTANY 2014; 114:619-27. [PMID: 24799440 PMCID: PMC4156123 DOI: 10.1093/aob/mcu074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS The process of vascular development in plants results in the formation of a specific array of bundles that run throughout the plant in a characteristic spatial arrangement. Although much is known about the genes involved in the specification of procambium, phloem and xylem, the dynamic processes and interactions that define the development of the radial arrangement of such tissues remain elusive. METHODS This study presents a spatially explicit reaction-diffusion model defining a set of logical and functional rules to simulate the differentiation of procambium, phloem and xylem and their spatial patterns, starting from a homogeneous group of undifferentiated cells. KEY RESULTS Simulation results showed that the model is capable of reproducing most vascular patterns observed in plants, from primitive and simple structures made up of a single strand of vascular bundles (protostele), to more complex and evolved structures, with separated vascular bundles arranged in an ordered pattern within the plant section (e.g. eustele). CONCLUSIONS The results presented demonstrate, as a proof of concept, that a common genetic-molecular machinery can be the basis of different spatial patterns of plant vascular development. Moreover, the model has the potential to become a useful tool to test different hypotheses of genetic and molecular interactions involved in the specification of vascular tissues.
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Affiliation(s)
- Fabrizio Cartenì
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, 80055 Portici (Na), Italy
- For correspondence. E-mail
| | - Francesco Giannino
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, 80055 Portici (Na), Italy
| | - Fritz Hans Schweingruber
- Swiss Federal Institut of Forest, Snow and Landscape Research WSL, CH- 8903 Birmensdorf, Switzerland
| | - Stefano Mazzoleni
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, 80055 Portici (Na), Italy
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Wabnik K, Robert HS, Smith RS, Friml J. Modeling framework for the establishment of the apical-basal embryonic axis in plants. Curr Biol 2013; 23:2513-8. [PMID: 24291090 DOI: 10.1016/j.cub.2013.10.038] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 09/17/2013] [Accepted: 10/15/2013] [Indexed: 11/17/2022]
Abstract
The apical-basal axis of the early plant embryo determines the body plan of the adult organism. To establish a polarized embryonic axis, plants evolved a unique mechanism that involves directional, cell-to-cell transport of the growth regulator auxin. Auxin transport relies on PIN auxin transporters, whose polar subcellular localization determines the flow directionality. PIN-mediated auxin transport mediates the spatial and temporal activity of the auxin response machinery that contributes to embryo patterning processes, including establishment of the apical (shoot) and basal (root) embryo poles. However, little is known of upstream mechanisms guiding the (re)polarization of auxin fluxes during embryogenesis. Here, we developed a model of plant embryogenesis that correctly generates emergent cell polarities and auxin-mediated sequential initiation of apical-basal axis of plant embryo. The model relies on two precisely localized auxin sources and a feedback between auxin and the polar, subcellular PIN transporter localization. Simulations reproduced PIN polarity and auxin distribution, as well as previously unknown polarization events during early embryogenesis. The spectrum of validated model predictions suggests that our model corresponds to a minimal mechanistic framework for initiation and orientation of the apical-basal axis to guide both embryonic and postembryonic plant development.
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Affiliation(s)
- Krzysztof Wabnik
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Hélène S Robert
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium; Mendel Centre for Genomics and Proteomics of Plants Systems, Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic
| | - Richard S Smith
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland; Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Jiří Friml
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, 9052 Gent, Belgium; Mendel Centre for Genomics and Proteomics of Plants Systems, Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic; Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria.
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11
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Megraw M, Mukherjee S, Ohler U. Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. Genome Biol 2013; 14:R85. [PMID: 23972209 PMCID: PMC4054853 DOI: 10.1186/gb-2013-14-8-r85] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 08/23/2013] [Indexed: 12/02/2022] Open
Abstract
WaRSwap is a randomization algorithm that for the first time provides a practical network motif discovery method for large multi-layer networks, for example those that include transcription factors, microRNAs, and non-regulatory protein coding genes. The algorithm is applicable to systems with tens of thousands of genes, while accounting for critical aspects of biological networks, including self-loops, large hubs, and target rearrangements. We validate WaRSwap on a newly inferred regulatory network from Arabidopsis thaliana, and compare outcomes on published Drosophila and human networks. Specifically, sustained input switches are among the few over-represented circuits across this diverse set of eukaryotes.
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12
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Abstract
The precise arrangement of plant organs, also called phyllotaxis, has fascinated scientists from multiple disciplines. Whereas early work focused on morphological observations of phyllotaxis, recent findings have started to reveal the mechanisms behind this process, showing how molecular regulation and biochemical gradients interact with physical components to generate such precise patterns of growth. Here, I review new insights into the regulation of phyllotactic patterning and provide an overview of the various factors that can drive these robust growth patterns.
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Affiliation(s)
- Jan Traas
- Laboratoire de Reproduction et Développement des Plantes, 46 allée d'Italie, 69364 Lyon, Cedex 07, France.
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13
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Beleyur T, Abdul Kareem VK, Shaji A, Prasad K. A mathematical basis for plant patterning derived from physico-chemical phenomena. Bioessays 2013; 35:366-76. [PMID: 23386477 DOI: 10.1002/bies.201200126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The position of leaves and flowers along the stem axis generates a specific pattern, known as phyllotaxis. A growing body of evidence emerging from recent computational modeling and experimental studies suggests that regulators controlling phyllotaxis are chemical, e.g. the plant growth hormone auxin and its dynamic accumulation pattern by polar auxin transport, and physical, e.g. mechanical properties of the cell. Here we present comprehensive views on how chemical and physical properties of cells regulate the pattern of leaf initiation. We further compare different computational modeling studies to understand their scope in reproducing the observed patterns. Despite a plethora of experimental studies on phyllotaxis, understanding of molecular mechanisms of pattern initiation in plants remains fragmentary. Live imaging of growth dynamics and physicochemical properties at the shoot apex of mutants displaying stable changes from one pattern to another should provide mechanistic insights into organ initiation patterns.
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Affiliation(s)
- Thejasvi Beleyur
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
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14
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Roeder AHK. When and where plant cells divide: a perspective from computational modeling. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:638-644. [PMID: 22939706 DOI: 10.1016/j.pbi.2012.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/02/2012] [Accepted: 08/12/2012] [Indexed: 06/01/2023]
Abstract
Computational modeling of growing plant tissues raises two basic questions about plant cell division: when does a cell decide to divide and where is the new wall placed? Although biologists and modelers commonly assume that a cell divides after it reaches a threshold size, two recent experiments show that models with variable division sizes better replicate the tissue. Similarly, comparing model predictions with living plant cells reveals that the choice of division plane is variable, although the shortest path dividing a cell in half (i.e. the minimal surface area) is the most probable division plane.
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Affiliation(s)
- Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology and Plant Biology Department, Cornell University, 239 Weill Hall, Ithaca, NY 14853 USA.
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15
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Abstract
The use of computational techniques increasingly permeates developmental biology, from the acquisition, processing and analysis of experimental data to the construction of models of organisms. Specifically, models help to untangle the non-intuitive relations between local morphogenetic processes and global patterns and forms. We survey the modeling techniques and selected models that are designed to elucidate plant development in mechanistic terms, with an emphasis on: the history of mathematical and computational approaches to developmental plant biology; the key objectives and methodological aspects of model construction; the diverse mathematical and computational methods related to plant modeling; and the essence of two classes of models, which approach plant morphogenesis from the geometric and molecular perspectives. In the geometric domain, we review models of cell division patterns, phyllotaxis, the form and vascular patterns of leaves, and branching patterns. In the molecular-level domain, we focus on the currently most extensively developed theme: the role of auxin in plant morphogenesis. The review is addressed to both biologists and computational modelers.
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Affiliation(s)
| | - Adam Runions
- Department of Computer Science, University of Calgary, Calgary, AB T2N 1N4, Canada
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