A Computational Framework for 3D Mechanical Modeling of Plant Morphogenesis with Cellular Resolution
Publication Date
January 08, 2015
Journal
PLOS Computational Biology
Authors
Frédéric Boudon, Jérôme Chopard, Olivier Ali, Benjamin Gilles, et al
Volume
11
Issue
1
Pages
e1003950
DOI
https://dx.plos.org/10.1371/journal.pcbi.1003950
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1003950
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/25569615
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288716
Europe PMC
http://europepmc.org/abstract/MED/25569615
Web of Science
000349309400002
Scopus
84922248938
Mendeley
http://www.mendeley.com/research/computational-framework-3d-mechanical-modeling-plant-morphogenesis-cellular-resolution
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{"title"=>"A Computational Framework for 3D Mechanical Modeling of Plant Morphogenesis with Cellular Resolution", "type"=>"journal", "authors"=>[{"first_name"=>"Frédéric", "last_name"=>"Boudon", "scopus_author_id"=>"7801411371"}, {"first_name"=>"Jérôme", "last_name"=>"Chopard", "scopus_author_id"=>"25635571300"}, {"first_name"=>"Olivier", "last_name"=>"Ali", "scopus_author_id"=>"56394097500"}, {"first_name"=>"Benjamin", "last_name"=>"Gilles", "scopus_author_id"=>"8881983600"}, {"first_name"=>"Olivier", "last_name"=>"Hamant", "scopus_author_id"=>"57131392800"}, {"first_name"=>"Arezki", "last_name"=>"Boudaoud", "scopus_author_id"=>"55933963800"}, {"first_name"=>"Jan", "last_name"=>"Traas", "scopus_author_id"=>"7004165246"}, {"first_name"=>"Christophe", "last_name"=>"Godin", "scopus_author_id"=>"7004780924"}], "year"=>2015, "source"=>"PLoS Computational Biology", "identifiers"=>{"issn"=>"15537358", "scopus"=>"2-s2.0-84922248938", "sgr"=>"84922248938", "pui"=>"602059652", "isbn"=>"1553-7358 (Electronic)\\r1553-734X (Linking)", "pmid"=>"25569615", "doi"=>"10.1371/journal.pcbi.1003950"}, "id"=>"634c627b-43f1-3602-900c-5e632091f268", "abstract"=>"The link between genetic regulation and the definition of form and size during morphogenesis remains largely an open question in both plant and animal biology. This is partially due to the complexity of the process, involving extensive molecular networks, multiple feedbacks between different scales of organization and physical forces operating at multiple levels. Here we present a conceptual and modeling framework aimed at generating an integrated understanding of morphogenesis in plants. This framework is based on the biophysical properties of plant cells, which are under high internal turgor pressure, and are prevented from bursting because of the presence of a rigid cell wall. To control cell growth, the underlying molecular networks must interfere locally with the elastic and/or plastic extensibility of this cell wall. We present a model in the form of a three dimensional (3D) virtual tissue, where growth depends on the local modulation of wall mechanical properties and turgor pressure. The model shows how forces generated by turgor-pressure can act both cell autonomously and non-cell autonomously to drive growth in different directions. We use simulations to explore lateral organ formation at the shoot apical meristem. Although different scenarios lead to similar shape changes, they are not equivalent and lead to different, testable predictions regarding the mechanical and geometrical properties of the growing lateral organs. Using flower development as an example, we further show how a limited number of gene activities can explain the complex shape changes that accompany organ outgrowth.", "link"=>"http://www.mendeley.com/research/computational-framework-3d-mechanical-modeling-plant-morphogenesis-cellular-resolution", "reader_count"=>96, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>6, "Researcher"=>36, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>4, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>8}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>6, "Researcher"=>36, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>4, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>8}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Engineering"=>4, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>8, "Mathematics"=>4, "Agricultural and Biological Sciences"=>61, "Physics and Astronomy"=>5, "Computer Science"=>6, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>4}, "Physics and Astronomy"=>{"Physics and Astronomy"=>5}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>61}, "Computer Science"=>{"Computer Science"=>6}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Mathematics"=>{"Mathematics"=>4}, "Unspecified"=>{"Unspecified"=>6}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Mexico"=>1, "United Kingdom"=>1, "Slovenia"=>1, "France"=>4, "Switzerland"=>1, "Germany"=>1, "Russia"=>1}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1863454"], "description"=>"<p><b>Upper part</b>: (<b>A-B-C</b>) Transversal sections in the young outgrowing flower bud at time points separated by 24 h. (<b>D-E-F</b>) Automatic 3D segmentation of the corresponding confocal images using the MARS-ALT pipeline <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003950#pcbi.1003950-Fernandez1\" target=\"_blank\">[19]</a>. (<b>G-H-I</b>) The analysis of growth patterns shows that growth at the abaxial side is faster than at the adaxial side, causing the floral meristem to bend towards the SAM. <b>Lower part</b>: Different attempts were made to regulate the mechanical parameters in time so as to reproduce this differential growth behavior. On the left:representation of the zones used in the simulation (CZ  =  Central Zone, Fr  =  Frontier, Pr  =  Primordium, Ad  =  Adaxial zone, Ab  =  Abaxial zone, Pe  =  Periphery). For all the simulations, the rigidity was decreased (light gray) in Pr (relative to CZ and Pe, and in the anisotropic zone Fr, the direction of maximum rigidity was set ortho-radially to Pr. With such an initial configuration, a globular and symmetric dome emerges normal to the surface (<b>J-K</b>). Then by tuning the mechanical properties of the Ad/Ab regions we could obtain different asymmetric developments: increasing the rigidity of Ad cells (medium gray) resulted in a restricted development of the upper part of the primordium (<b>L-M</b>) while, by contrast, an increased rigidity of the Ab cells (medium gray) shifted the primordium development upwards (<b>N-O</b>) as expected. Finally a growing dome with correct development of the Ad/Ab regions could be obtained when the abaxial cells where also imposed a high degree of anisotropy (orientation shown by the thick black bars oriented circumferentially in the Ab, (<b>P-Q</b>)). The table under the snapshots illustrates the relative variations of Elastic modulus used for each case. The x and y coordinates respectively refer to the axial and circumferential directions, as exposed on sub-figures (J) and (K). Numerical values used in the simulations and corresponding movies are available as Supporting Information.</p>", "links"=>[], "tags"=>["shape changes", "framework", "3 D Mechanical Modeling", "control cell growth", "morphogenesi", "cell wall", "turgor pressure", "model"], "article_id"=>1286688, "categories"=>["Uncategorised"], "users"=>["Frédéric Boudon", "Jérôme Chopard", "Olivier Ali", "Benjamin Gilles", "Olivier Hamant", "Arezki Boudaoud", "Jan Traas", "Christophe Godin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003950.g005", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_First_stages_of_development_of_a_flower_bud_/1286688", "title"=>"First stages of development of a flower bud.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-08 03:33:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1863468"], "description"=>"<p>Schematic representation of the different configurations at different time and the deformations between them.</p>", "links"=>[], "tags"=>["shape changes", "framework", "3 D Mechanical Modeling", "control cell growth", "morphogenesi", "cell wall", "turgor pressure", "model"], "article_id"=>1286701, "categories"=>["Uncategorised"], "users"=>["Frédéric Boudon", "Jérôme Chopard", "Olivier Ali", "Benjamin Gilles", "Olivier Hamant", "Arezki Boudaoud", "Jan Traas", "Christophe Godin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003950.g007", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_the_different_configurations_at_different_time_and_the_deformations_between_them_/1286701", "title"=>"Schematic representation of the different configurations at different time and the deformations between them.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-08 03:33:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1863401"], "description"=>"<p>A tissue region is in general observed as a deformed object in a real tissue (A) due to local stresses internal to the tissue (light blue arrows). Taken outside its tissue context, without any stress on its borders, the region has a rest shape (B). Note that this rest shape is not actually observed. The transformation matrix to pass from the rest shape to the observed deformed shape is denoted . Due to changes in stress distribution in time, at a subsequent date the stress configuration acting on the region changes (dark blue arrows) and induces a new deformation of the region (C). If the intensity of the elastic deformation between the former rest shape (B) and the new deformed object (C) is above a certain threshold, then plastic growth is triggered: the rest shape is remodeled by the cell by adding material to the wall (D) which reduces the elastic strain. This change is made according to a constitutive rule that describes the material plasticity (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003950#s4\" target=\"_blank\">Model</a> section below). As a result, the transformation from the old rest state (B) to the new deformed state has been decomposed as a product of a reversible term and an irreversible term representing growth.</p>", "links"=>[], "tags"=>["shape changes", "framework", "3 D Mechanical Modeling", "control cell growth", "morphogenesi", "cell wall", "turgor pressure", "model"], "article_id"=>1286651, "categories"=>["Uncategorised"], "users"=>["Frédéric Boudon", "Jérôme Chopard", "Olivier Ali", "Benjamin Gilles", "Olivier Hamant", "Arezki Boudaoud", "Jan Traas", "Christophe Godin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003950.g003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Formalization_of_plastic_growth_of_a_small_region_of_wall_/1286651", "title"=>"Formalization of plastic growth of a small region of wall.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-08 03:33:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1863467"], "description"=>"<p>Abaxial sepals start to grow out first (middle and right image). (B) Growth patterns and gene expression profiles. The respective development of the different zone is indicated by small bars at the meristem surface. This growth pattern is accompanied by a change in gene expression patterns. At stage one, the floral bud is characterized by adaxially (light blue) and abaxially (dark blue) expressed genes. Other genes such as LFY and ANT are first expressed throughout the young flower. When the sepals start to grow out abaxial and adaxial domains are again established in these young organs (resp. dark and light pink), characterized by specific expression patterns (e.g. REV or FIL). Other genes, such as ANT or AHP6 will finally remain active throughout the pink zones that will generate the sepals (dark and light pink). Boundary zones, characterized by genes like CUC (red) separate the primordia from the meristem proper, where genes like STM (green) are active. For review of expression patterns see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003950#pcbi.1003950-LaRota1\" target=\"_blank\">[27]</a>. (C) Creation of a 3D geometric model of a flower bud. From left to right: confocal image; automatic cell segmentation using Mars-Alt pipeline <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003950#pcbi.1003950-Fernandez1\" target=\"_blank\">[19]</a>; construction of a mesh based on cell vertices; transverse section of the mesh showing the geometric representation of the inner layers. (D) Mechanical simulation of a flower bud development and its regulation by genes. Progression in the flower bud development is shown at three different stages, from primordia initiation to early stage 3 (see Supporting <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003950#pcbi.1003950.s008\" target=\"_blank\">Movie S5</a>).</p>", "links"=>[], "tags"=>["shape changes", "framework", "3 D Mechanical Modeling", "control cell growth", "morphogenesi", "cell wall", "turgor pressure", "model"], "article_id"=>1286700, "categories"=>["Uncategorised"], "users"=>["Frédéric Boudon", "Jérôme Chopard", "Olivier Ali", "Benjamin Gilles", "Olivier Hamant", "Arezki Boudaoud", "Jan Traas", "Christophe Godin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003950.g006", "stats"=>{"downloads"=>2, "page_views"=>65, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Transverse_sections_of_confocal_images_showing_floral_bud_development_between_stage_1_and_early_stage_3_/1286700", "title"=>"(A) Transverse sections of confocal images showing floral bud development between stage 1 and early stage 3.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-08 03:33:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1863469"], "description"=>"<p>a) the system in its resting configuration (). b) the system deformed by a the loading forces, at mechanical equilibrium (). Orange, blue and gray arrows represent respectively the loading (turgor-related) force, the elastic forces and the sum of viscous drag and friction force.</p>", "links"=>[], "tags"=>["shape changes", "framework", "3 D Mechanical Modeling", "control cell growth", "morphogenesi", "cell wall", "turgor pressure", "model"], "article_id"=>1286702, "categories"=>["Uncategorised"], "users"=>["Frédéric Boudon", "Jérôme Chopard", "Olivier Ali", "Benjamin Gilles", "Olivier Hamant", "Arezki Boudaoud", "Jan Traas", "Christophe Godin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003950.g008", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_1D_version_of_a_unit_element_of_the_biomechanical_model_/1286702", "title"=>"1D version of a unit element of the biomechanical model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-08 03:33:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1863382"], "description"=>"<p>The different horizontal layers represent different levels of biological organization. The plain black arrows symbolize the downward stream of regulation between growth hormones and actual growth through transcription factors activation and physical quantities modulation. The red plain arrows depict the indirect, integrated relationships between transcription factor activation, physical quantities modulation and cell wall irreversible extension our computational framework attempts to grasp. Finally the black dashed upward arrows stand for possible feedback mechanisms from shape changes on the biochemical regulation of growth.</p>", "links"=>[], "tags"=>["shape changes", "framework", "3 D Mechanical Modeling", "control cell growth", "morphogenesi", "cell wall", "turgor pressure", "model"], "article_id"=>1286638, "categories"=>["Uncategorised"], "users"=>["Frédéric Boudon", "Jérôme Chopard", "Olivier Ali", "Benjamin Gilles", "Olivier Hamant", "Arezki Boudaoud", "Jan Traas", "Christophe Godin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003950.g001", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_view_of_the_regulation_of_growth_in_multicellular_tissues_/1286638", "title"=>"Schematic view of the regulation of growth in multicellular tissues.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-08 03:33:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1863397"], "description"=>"<p>(A) In the single-cell case, the mechanical (elastic) stresses (, dark blue double arrows) undergone by the cell wall are due to the inner pressure (, light blue single arrows) of the cell. The mechanical equilibrium within this wall is regulated by the cell itself. (B) In a tissular case, (here a shoot apical meristem), mechanical stresses within the outer cell walls of the L1 layer (light red cells), can be modulated by remote cells (here in light green). In this case the stem (light blue cells) plays the role of a base on which the inner cells rely in order to push the L1 layer upward. (C) Three main modalities of growth can be considered in a multicellular context (details on the stresses equilibrium within the outer cell wall are represented in the zooming views). From an initial state (C1) of the growing tissue three scenarios are considered: (C2) & (C3) present cell-autonomous ways where growth of a given cell is triggered by an increase of its inner pressure or a modulation of its wall mechanical properties respectively. (C4) represents a non-cell-autonomous case in which growth of the studied cell is initiated by physical alteration of its neighbors. (C5) All three modifications result in the local outgrowth of the considered region.</p>", "links"=>[], "tags"=>["shape changes", "framework", "3 D Mechanical Modeling", "control cell growth", "morphogenesi", "cell wall", "turgor pressure", "model"], "article_id"=>1286647, "categories"=>["Uncategorised"], "users"=>["Frédéric Boudon", "Jérôme Chopard", "Olivier Ali", "Benjamin Gilles", "Olivier Hamant", "Arezki Boudaoud", "Jan Traas", "Christophe Godin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003950.g002", "stats"=>{"downloads"=>2, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Origin_of_forces_driving_growth_in_a_multicellular_tissue_/1286647", "title"=>"Origin of forces driving growth in a multicellular tissue.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-08 03:33:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1863436"], "description"=>"<p>(<b>A</b>) Face, top and inside view of an artificial dome made of cells with mechanical properties. The transversal cut shows the inner cells. The basal faces of cells shown in blue here are constrained to keep in a horizontal plane. (<b>B-E</b>) Growth of a multi-cellular dome. In all the simulations, the gray scale code on the initial dome represents regions with different rigidities. A different color code is then used on the other steps to figure mechanical stress intensity, <i>c.f.</i> color scale on the top right corner. (<b>B</b>) Homogeneous dome: all cells are isotropic with identical elasticity, plasticity threshold and growth speed. (<b>C</b>) Mechanical anisotropy is imposed on the lower half of epidermis to model the effect of microtubules circumferential orientation. Axial growth emerges. (<b>D</b>) Analysis of the extent of the anisotropic zone on growth. From left to right: Initial state of the simulation with circumferential anisotropy imposed up to 80% of the dome height: The resulting growth is axial. Initial state with a dome anisotropy limited to 40% of the dome height: The corresponding growth is globular. (<b>E</b>) Growth with a gradient of circumferential anisotropy from the bottom to the top of the dome: The resulting growth is inbetween purely axial and isotropic. (<b>F-J</b>) Creation of a lateral dome. (<b>F</b>) The rigidity of the cells in a small region at the flank of the meristem is decreased (cell autonomous regulation). During growth a lateral bump starts to form. The simulated dome is shown at two time points (middle and right). (<b>G</b>) Transversal cuts of a dome showing tentative generations of a bump with non-cell autonomous stresses: (G-1) Decreasing wall rigidity (10-fold) in a group of inner cells (blue cells with <i>i.e.</i> low mechanical stress): No visible bump emerges; (G-3) Increasing the turgor pressure (3-fold) in the same group of cells (red cells <i>i.e.</i> high mechanical stress): A shallow bump emerges and inner tissues are compressed inside. Compare with the reference situation (G-2) corresponding to a transversal cut of F middle. (<b>H</b>) Similar to F, but cells surrounding the primordium region are made stiffer. A well marked dome appears (middle and right). (<b>I</b>) Similar to F, but cells surrounding the primordium region are made stiffer in the bump ortho-radial direction only (anisotropy in boundary region). (<b>J</b>) Simulation similar to H, combining a smaller decrease of rigidity with an increase of the walls synthesis rate (namely extensibility) in the primordium. Movies corresponding to each simulation are available as Supporting Information.</p>", "links"=>[], "tags"=>["shape changes", "framework", "3 D Mechanical Modeling", "control cell growth", "morphogenesi", "cell wall", "turgor pressure", "model"], "article_id"=>1286680, "categories"=>["Uncategorised"], "users"=>["Frédéric Boudon", "Jérôme Chopard", "Olivier Ali", "Benjamin Gilles", "Olivier Hamant", "Arezki Boudaoud", "Jan Traas", "Christophe Godin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003950.g004", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Growth_regulation_mechanisms_and_their_impact_on_shape_development_/1286680", "title"=>"Growth regulation mechanisms and their impact on shape development.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-08 03:33:13"}

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  • {"unique-ip"=>"7", "full-text"=>"5", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"11", "full-text"=>"10", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}

Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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