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Partners

- Institute for Integrative Biology of the Cell (I2BC)
Teams: Integrated Approaches to Ion Transport, Plant Cell Signaling and Ubiquitin, Dynamics of Cell Compartmentation in plant cells
- Institut Jean-Pierre Bourgin (IJPB)
Teams: Primary Cell Wall, Spatial control of Cell Division, Cell Differentiation and Polarity, Modeling and digital imaging
- Institute of Plant Sciences Paris-Saclay (IPS2)
Teams: Regulatory non-coding RNAs in root plasticity, Stress signaling
- Laboratoire d’hydrodynamique de l’Ecole Polytechnique (LadHyX)

Abstract of the project

Systems biology approaches in cell biology require a combination of computational modelling with the measurement of cellular processes with a high spatiotemporal resolution in individual cells. This is facilitated by the recent development of genetically encoded nanosensors reporting cellular parameters. The DYNANO project addresses two bottlenecks for the adoption of these technologies: the lack of efficient experimental systems for the observation of rapid changes in cellular parameters and the need for data analysis procedures to obtain quantitative information on cellular processes. The project has brought together more than 15 scientists from the three institutes of the Labex Saclay Plant Science and the Hydrodynamics Laboratory of the Ecole Polytechnique (LadHyX). Within DYNANO, microfluidic chips for the analysis of response kinetics in parallel in multiple roots have been developed and biosensor technologies have been implemented in 4 SPS teams. DYNANO partners have implemented technologies for the analysis of cytosolic and apoplastic Ca²⁺, ROS and pH, anion fluxes and heavy metal concentrations, cytoskeleton dynamics, ubiquitination, autophagosome formation, MAP kinase activity, mechanosensing, lipid domain formation and plant microbe interactions. Moreover, DYNANO has fostered the development of methodologies for the acquisition and analysis of the data. DYNANO is expected to reinforce links with the private sector through the development of new generations of microfluidic chips and the possibility to develop platforms for the screening of cellular responses to molecules. The concerted effort around DYNANO is expected to lead to new scientific breakthroughs in the field of quantitative live cell imaging in plants.

Publications:

Demes, E., Besse, L., Satiat-Jeunemaitre, B., Thomine, S., De Angeli, A. Dynamic measurement of cytosolic pH and [NO3-] uncovers the role the vacuolar transporter AtCLCa in the control of cytosolic pH. Under revision for Proc Natl Acad Science USA

Haas, K., Wightman, R., Peaucelle, A. and Höfte, H. (2020). The role of pectin phase separation in plant cell wall assembly and growth. The Cell Surface 7, 100054

Vassanti Audemar, Yannick Guerringue, Joni Frederick, Isaty Melogno, Pauline Vinet, Avin Babataheri, Valérie Legué, Sébastien Thomine, Jean-Marie Frachisse (2023) Local compression of the root in a microfluidic device triggers a calcium signal bioRxiv 2023.05.11.540308; doi: https://doi.org/10.1101/2023.05.11.540308

Voxeur, A., Habrylo, O., Guénin, S., Miart, F., Soulié, M.-C., Rihouey, C., Pau-Roblot, C., Domon, J.M., Gutierrez, L., Pelloux, J., Mouille, G., Fagard, M., Hofte, H., and Vernhettes, S. (2019). Oligogalacturonide production upon Arabidopsis thaliana-Botrytis cinerea interaction. Proc Natl Acad Science USA, 116 (39) 19743-19752

Communications in conferences:

Miart F, Bouchez D, Legland D, Dubreucd B, Andrey P, Höfte H and Vernhettes S. The VIP-Box. International meeting on optical biosensors 15-17/11/2018, Ghent Belgium. (talk)

Miart F, Bouchez D, Legland D, Dubreucd B, Andrey P, Höfte H and Vernhettes S. Functional in vivo imaging of pH and Ca2+ dynamics in Arabidopsis thaliana growing seedlings using biosensors and VIP-Box. MiFoBIO, 5-12/10/2018, Seignosse. (poster)

Voxeur A, Fabien M, Soulié MC, Rihouey C, Mouille G, Fagard M, Hofte H and Vernhettes S Signaling pathways to control cell wall integrity during development and plant attack. INUPRAG meeting 4-6/06/2018 in Barcelona, Spain. (talk)

Frederick J., Guerringue Y., Frachisse J-M., Thomine S. (2018) Root Mechanosensing in Microfluidic Devices

4th International Conference on Physics and Biological Systems (Gif-sur-Yvette, France) (poster)

Höfte, H (2018) The role of cell wall integrity signalling in growth regulation. Peptides and Receptors, 6th European workshop on peptide signaling in plants. Antequerra, Spain, (talk Keynote Speaker)

Hofte, H. (2018). Cell wall integrity signaling in growth control. International Conference « Plant Physiology and Biochemistry » Vienna, 9-10/7/2018. (talk invited speaker)

Hofte, H. (2018). Cell wall integrity signaling in growth control. « Norwegian Plant Biology » ,30-31 May (Bergen, Norway) (talk invited speaker)

Frederick J., Guerringue Y., Frachisse J-M., Thomine S. (2018) Root Mechanosensing in Microfluidic Devices

4th International Conference on Physics and Biological Systems (Gif-sur-Yvette, France) (poster)

Höfte, H. (2019) The role of cell wall integrity signalling in growth regulation. International Symposium on Plant Receptor Kinases and Cell Signaling, Beijing (talk invited speaker).

Höfte, H. (2019) The role of cell wall integrity signalling in growth regulation. 12e Journées du Réseau Français de la Paroi, Roscoff, (talk invited speaker)..

Frederick J., Y. Guerringue Y., Frachisse J.-M., Audemar V., Babataheri A., Thomine S. (2019) Plantuidics: a microfabrication unit to boost microfluidic applications in plants. DIM ELICIT day (Institut Pasteur, Paris, France)

Frederick J., Frachisse J-M., Guerringue Y., Babataheri A., Thomine S. (2019) A Microfluidics Study of Calcium Signaling in Root Mechanosensing. 18th International Workshop on Plant Membrane Biology, (Glasgow, UK) (poster)

Uyttewaal M, Pastuglia M, Goncalvez C, De Tauzia-Moreau ML, Belcram K, Dalmais B, Frederick J, Bouchez D (2019) Time-lapse analysis of cell division in Arabidopsis using a RootChip microfluidic device. Fourth French Microtubule Network Meeting (Rennes, France) (poster)

Vassanti Audemar, Yannick Guerringue, Joni Frederik, Isaty Melogno, Pauline Vinet, Avin Babataheri, Sébastien Thomine, Jean-Marie Frachisse (2022) Dynamics of the calcium signal elicited by mechanical stimulation of the root in the model plant Arabidopsis. Bioprobe-PhysChemCell2022, (ENS Paris-Saclay, France) (oral presentation)

Vassanti Audemar, Yannick Guerringue, Joni Frederik, Isaty Melogno, Pauline Vinet, Avin Babataheri, Sébastien Thomine, Jean-Marie Frachisse (2023) Dynamics of the calcium signal elicited by mechanical stimulation of Arabidopsis root. Plant Biology Europe (Marseille, France) (oral presentation)

Jessica Marion, Vassanti Audemar, Sébastien Thomine (2023) Regulation of intracellular free zinc concentration in Arabidopsis thaliana roots. Plant Biology Europe (Marseille, France) (poster)

Patent

A VIP-BOX : un nouvel outil pour l’imagerie fonctionnelle automatisée et à haut débit de plantules entières poussant à la verticale DI-RV_18
UMR1318 IJPB VERSAILLES BAP INRA
VERNHETTES Samantha
PLANTINNOV

We developed the VIP-box [Vertical Imaging of the Plant], a 3D-printable open-source imaging platform to simultaneously record within-organ growth patterns and gene expression or chemical signalling through long-time period and at high-throughput. We validate the VIP-box by monitoring cytosolic and apoplastic pH, calcium and hormones signalling using genetically encoded biosensors and provide an image analysis pipeline to integrate both fluorescence signals and growth patterns. This system can be used for the simultaneous analysis of various genetic backgrounds and environmental conditions. The VIP-box can be installed on different microscope stands.