Biophysics and Development

Personnel du RDP

Arezki BOUDAOUD

arezki.boudaoud
(33) 4 72 72 88 75
PR ENS

Françoise MONEGER

francoise.moneger
(33) 4 72 72 89 85
DR2 CNRS
Publications

Pradeep DAS

pradeep.das
(33) 4 72 72 89 37
MC ENS

Annamaria KISS

annamaria.kiss
(33) 4 72 72 89 37
IR2 INRA
Publications

Simone BOVIO

simone.bovio
(33) 4 72 72 87 62
IE ENS
Publications

Virginie BATTU

virginie.battu
(33) 4 72 72 86 07
TR UCBL

Diego HARTASANCHEZ

diego.hartasanchez_frenk
Postdoc

Antoine FRULEUX

antoine.fruleux
(33) 4 72 72 38 32
Postdoc ENS

Corentin MOLLIER

corentin.mollier
(33) 4 72 72 89 37
Thèse

Abigail DELGADO-VAQUERA

abigail.delgado_vaquera
Thèse



Publications HAL du labo/EPI 1001887;772

2021

Preprints, Working Papers, ...

titre
Dandelion pappus morphing is actuated by radially patterned material swelling
auteur
Madeleine Seale, Annamaria Kiss, Simone Bovio, Ignazio Maria Viola, Enrico Mastropaolo, Arezki Boudaoud, Naomi Nakayama
article
2021
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2020

Journal articles

titre
Gradient in cytoplasmic pressure in germline cells controls overlying epithelial cell morphogenesis
auteur
Laurie-Anne Lamiré, Pascale Milani, Gaël Runel, Annamaria Kiss, Leticia Arias, Blandine Vergier, Stève de Bossoreille, Pradeep Das, David Cluet, Arezki Boudaoud, Muriel Grammont
article
PLoS Biology, Public Library of Science, 2020, 18 (11), pp.e3000940. ⟨10.1371/journal.pbio.3000940⟩
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-03052289/file/2020_Lamir%C3%A9_Plos%20Biology.pdf BibTex
titre
Immediate targets of ETTIN suggest a key role for pectin methylesterase inhibitors in the control of Arabidopsis gynecium development
auteur
Amélie Andres Robin, Mathieu Reymond, Géraldine Brunoud, Marie-Laure Martin-Magniette, Françoise Moneger, C.P. Scutt
article
Plant Signaling and Behavior, Taylor & Francis, 2020, 15 (7), pp.1771937. ⟨10.1080/15592324.2020.1771937⟩
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-03068443/file/Paper%20HAL.pdf BibTex
titre
Robust organ size requires robust timing of initiation orchestrated by focused auxin and cytokinin signalling
auteur
Mingyuan Zhu, Weiwei Chen, Vincent Mirabet, Lilan Hong, Simone Bovio, Soeren Strauss, Erich Schwarz, Satoru Tsugawa, Zhou Wang, Richard Smith, Chun-Biu Li, Olivier Hamant, Arezki Boudaoud, Adrienne Roeder
article
Nature Plants, Nature Publishing Group, 2020, 6 (6), pp.686-698. ⟨10.1038/s41477-020-0666-7⟩
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titre
Cellular Heterogeneity in Pressure and Growth Emerges from Tissue Topology and Geometry
auteur
Yuchen Long, Ibrahim Cheddadi, Gabriella Mosca, Vincent Mirabet, Mathilde Dumond, Annamaria Kiss, Jan Traas, Christophe Godin, Arezki Boudaoud
article
Current Biology - CB, Elsevier, 2020, 30 (8), pp.1504-1516.e8. ⟨10.1016/j.cub.2020.02.027⟩
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titre
The Endosperm-Derived Embryo Sheath Is an Anti-adhesive Structure that Facilitates Cotyledon Emergence during Germination in Arabidopsis
auteur
Nicolas Doll, Simone Bovio, Angelo Gaiti, Anne-Charlotte Marsollier, Sophy Chamot, Steven Moussu, Thomas Widiez, Gwyneth Ingram
article
Current Biology - CB, Elsevier, 2020, 30 (5), pp.909-915.e4. ⟨10.1016/j.cub.2019.12.057⟩
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-03065544/file/embryo%20sheath%20current%20Biology%20ter.pdf BibTex

2019

Journal articles

titre
Xyloglucans and Microtubules Synergistically Maintain Meristem Geometry and Phyllotaxis
auteur
Feng Zhao, Wenqian Chen, Julien Sechet, Marjolaine Martin, Simone Bovio, Claire Lionnet, Yuchen Long, Virginie Battu, Grégory Mouille, Françoise Monéger, Jan Traas
article
Plant Physiology, American Society of Plant Biologists, 2019, 181 (3), pp.1191-1206. ⟨10.1104/pp.19.00608⟩
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-02351790/file/Zhao%20et%20al%2C%202019_HAL%20%281%29.pdf BibTex
titre
Use of Atomic Force Microscopy to Measure Mechanical Properties and Turgor Pressure of Plant Cells and Plant Tissues
auteur
Françoise Moneger, Simone Bovio, Yuchen Long
article
Journal of visualized experiments : JoVE, JoVE, 2019, ⟨10.3791/59674⟩
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-02351801/file/Bovio%20et%20al%2C%202019.pdf BibTex

2018

Book sections

titre
Séquençage d'ADN par la technique Sanger
auteur
Denis Tagu, Françoise Monéger
article
Principes des techniques de biologie moléculaire et génomique : 3e édition revue et augmentée, Quae, 2018, Savoir Faire, 978-2-7592-2389-3
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2017

Journal articles

titre
Segmentation of 3D images of plant tissues at multiple scales using the level set method
auteur
Annamaria Kiss, Typhaine Moreau, Vincent Mirabet, Cerasela Iliana Calugaru, Arezki Boudaoud, Pradeep Das
article
Plant Methods, BioMed Central, 2017, 13 (1), ⟨10.1186/s13007-017-0264-5⟩
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02620094/file/2017_Kiss_Plant_Method_1.pdf BibTex

2016

Journal articles

titre
Multiscale quantification of morphodynamics: MorphoLeaf software for 2D shape analysis
auteur
Eric Biot, Millan Cortizo, Jasmine Burguet, Annamaria Kiss, Mohamed Oughou, Aude Maugarny Calès, Beatriz Goncalves, Bernard Adroher, Philippe Andrey, Arezki Boudaoud, Patrick Laufs
article
Development (Cambridge, England), Company of Biologists, 2016, pp.3417-3428. ⟨10.1242/dev.134619⟩
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BibTex
titre
Variable cell growth yields reproducible organ development through spatiotemporal averaging
auteur
Lilan Hong, Mathilde Dumond, Satoru Tsugawa, Aleksandra Sapala, Anne-Lise Routier-Kierzkowska, Yong Zhou, Catherine Chen, Annamaria Kiss, Mingyuan Zhu, Olivier Hamant, Richard s. Smith, Tamiki Komatsuzaki, Chun-Biu Li, Arezki Boudaoud, Adrienne h.K. Roeder
article
Developmental Cell, Elsevier, 2016, 38 (1), pp.15-32. ⟨10.1016/j.devcel.2016.06.016⟩
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2015

Journal articles

titre
MorphoGraphX: A platform for quantifying morphogenesis in 4D
auteur
Pierre Barbier de Reuille, Anne-Lise Routier-Kierzkowska, Daniel Kierzkowski, George Bassel, Thierry Schüpbach, Gerardo Tauriello, Namrata Bajpai, Sören Strauss, Alain Weber, Annamaria Kiss, Agata Burian, Hugo Hofhuis, Aleksandra Sapala, Marcin Lipowczan, Maria Heimlicher, Sarah Robinson, Emmanuelle Bayer, Konrad Basler, Petros Koumoutsakos, Adrienne Hk Roeder, Tinri Aegerter-Wilmsen, Naomi Nakayama, Miltos Tsiantis, Angela Hay, Dorota Kwiatkowska, Ioannis Xenarios, Cris Kuhlemeier, Richard Smith
article
eLife, eLife Sciences Publication, 2015, 4, ⟨10.7554/eLife.05864⟩
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titre
Mechanical stress contributes to the expression of the STM homeobox gene in Arabidopsis shoot meristems
auteur
Benoit Landrein, Annamaria Kiss, Massimiliano Sassi, Aurélie Chauvet, Pradeep Das, Millan Cortizo, Patrick Laufs, Seiji Takeda, Mitsuhiro Aida, Jan Traas, Teva Vernoux, Arezki Boudaoud, Olivier Hamant
article
eLife, eLife Sciences Publication, 2015, 4, pp.1-27. ⟨10.7554/eLife.07811⟩
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02631439/file/Landrein2015_1.pdf BibTex

2013

Journal articles

titre
Network function shapes network structure: the case of the Arabidopsis flower organ specification genetic network
auteur
Adrien Henry, Françoise Monéger, Areejit Samal, Olivier C. Martin
article
Molecular BioSystems, Royal Society of Chemistry, 2013, 9 (7), pp.1726 - 1735. ⟨10.1039/c3mb25562j⟩
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2012

Journal articles

titre
A Light-Regulated Genetic Module Was Recruited to Carpel Development in Arabidopsis following a Structural Change to SPATULA
auteur
Matthieu Reymond, Geraldine Brunoud, Aurélie Chauvet, Jaime F. Martinez-Garcia, Marie-Laure Magniette, Françoise Monéger, C.P. Scutt
article
The Plant cell, American Society of Plant Biologists (ASPB), 2012, 24 (7), pp.2812 - 2825. ⟨10.1105/tpc.112.097915⟩
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We study morphogenesis in plants, notably at the shoot apex of Arabidopsis. We focus on robustness of morphogenesis, by analyzing cellular variability and exploring mechanisms that enhance or buffer such variability. To do so, we combine approaches from molecular biology, live imaging, biophysics, data analysis, and modeling. We address these questions and use these approaches in four main topics:
 Mechanics of morphogenesis
 Floral Growth Patterns
 Gene Regulatory Networks
 Modelling Plant Morphogenesis

Useful tools


Mechanics of Morphogenesis

Leader : Arezki Boudaoud

Morphogenesis is the remarkable process by which a developing organism acquires its shape. While molecular and genetic studies have been highly successful in explaining the cellular basis of development and the role of biochemical gradients in coordinating cell fate, understanding morphogenesis remains a central challenge for both developmental biology and biophysics. Indeed, shape is imposed by structural elements, so that an investigation of morphogenesis must address how these elements are controlled at the cell level, and how the mechanical properties of these elements lead to specific growth patterns. Using plants as model systems, we tackle the following questions. (i) Does the genetic and molecular identity of a cell correspond to a mechanical identity. (ii) Do the mechanical properties of the different cell domains predict shape changes. (iii) How does the intrinsic stochasticity of cell mechanics and cell growth lead to reproducible shapes?

Floral Growth Patterns

Leader : Pradeep Das

The emergence of stereotypical shapes and sizes of tissues and organs requires the coordinated regulation of very specific growth patterns across space and time during development. We seek to gain a clear understanding of how the underlying molecular, genetic and physical events govern growth. The most obvious way to measure and describe growth is at the cellular level. Over the last several years, we have developed a software pipeline to computationally track the growth of Arabidopsis flowers at cell resolution and in 4 dimensions (space and time; Fernandez et al., Nature Methods, 2010). We are now in the process of using segmented time course data to statistically analyse floral growth leading up to the first morphogenetic events. Naturally, these patterns are a result of the genetic and mechanical events occurring during development. To this end, we are also examining the link between growth and patterning, and between patterning and mechanics.

Gene Regulatory Networks

Leader : Françoise Monéger

We also perform modeling on gene regulatory networks and develop approaches aiming at integrating different types of data (expression patterns, direct interactions, genetic interactions) in an integrative coherent model. More recently, we focused on the cell wall and on the enzymes involved in cell wall remodeling in order to understand how molecular networks and transcription factors in particular control flower morphogenesis. Our project aims at identifying among 30 transcription factors expressed in the flower, the target genes encoding protein involved in cell wall and try to understand how the regulation of the expression of these genes leads to the control of the flower shapes.

Modelling Plant Morphogenesis

Leader : Annamaria Kiss

In order to be able to model the emergence of an organ’s shape, it is essential to begin with the analysis of data in connection with morphogenesis. Therefore we develop tools for image segmentation (level set, MARS on Openalea) and for data analysis (plugin on MorphoGraphX) and specifically, we carry out the quantitative and statistical analyses of serial images of developing organs, such as leaves, flowers or meristems. In parallel, we are also studying mechanical models of plant tissue. The goal is first to infer mechanical properties from images, and then, using these properties we are seeking to reproduce by modelling the emergence of forms at the tissular level.

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  • Tools

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    Images Fiji - http://fiji.sc/Fiji Inkscape - rudiments, basics, advanced, other tutorials... Gimp - http://www.gimp.org, http://openclassrooms.com, https://www.youtube.com Plant Illustrations- a collection of illustrations and pictures of plants, roots, shoots, inflorescences,
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  • Useful links

    , by yfesseli

    – Tools developed in the team on the Forge of the CBP
    – A collection of general software
    – Le Wiki du RIB (service informatique du RDP/LBMC/CIRI)
    – How to make figures and presentations that are friendly to Colorblind people