Post-Doctoral Research Visit F/M Post-doc: computational and biophysical modeling of guard cells in leaves

Inria

France

October 9, 2022

Description

2022-05346 - Post-Doctoral Research Visit F/M Post-doc: computational and biophysical modeling of guard cells in leaves

Contract type : Fixed-term contract

Level of qualifications required : PhD or equivalent

Fonction : Post-Doctoral Research Visit

About the research centre or Inria department

The Inria research centre in Lyon (previously the Lyon branch of the Inria centre in Grenoble) is the 9th Inria research centre, formally created in December 2021. It brings together approximately 270 people (including 110 Inria employees) in 15 research teams and research support services.

Its staff are distributed at this stage on 2 campuses: in Villeurbanne La Doua (Centre / INSA Lyon / UCBL) on the one hand, and Lyon Gerland (ENS de Lyon) on the other. A third site should be opened in the course of 2022. The teams are mainly hosted with our partners. The centre's teams work closely with research and higher education institutions (ENS de Lyon, UCBL, INSA Lyon, etc.), their laboratories, and other research organisations in Lyon (CNRS, INRAE, competitiveness clusters, etc.), but also with Lyon and regional economic players. Many international collaborations are also underway.

The Lyon centre is active in the fields of software, distributed and high- performance computing, embedded systems, quantum computing and privacy in the digital world, but also in digital health and computational biology.

Context

To regulate gas exchange between environment and photosynthetic tissues, plants are able to inflate and deflate specific cells, called guard cells. Two guard cells delimit stomata pores at the surface of leaves and are able to control the aperture of the stomata pore to regulate gas exchange (CO2, H20) with atmosphere..

The principal biochemical and biophysical actors participating to the guard cells volume changes mechanisms have been identified in the last two decades. These are signaling pathways and ion transport systems (active transporters and ion channels) residing in the two major membranes of the guard cells, the plasma and the vacuolar membrane.

However, an integrated view of how the key molecular actors functionally interact and are coordinated between the different cell compartments involved in opening/closing the stomata is still incomplete. Further, the coupling between the ion fluxes and the biomechanical stresses occurring in the cell are still to be understood.

To understand this mechanisms and their functional interactions, we aim to develop a combination of experimental and computational modeling approaches in the context of the ANR project NetFlux.

Assignment

The goal for of this postdoc position will be to develop models and computational tools to understand how ion regulation is regulated in a multicompartment system (the cell exterior, the cell cytoplasm and the vacuolar compartment).

In a first step an electrophysiological model will be constructed to account for the ion-based processes driving the water potential inside the cell and the vacuole. Then this model will be coupled with an hydraulic/mechanical model with the aim to account for the main fluxes of water within the system. The modeling approach will be developed in close collaboration with the biologists partners in Montpellier and Cadarache and that develop a multidisciplinary experimental approach based on fluorescent microscopy, molecular biology, genetics and biophysics.

References

  • Ibrahim Cheddadi, Michel Génard, Nadia Bertin, Christophe Godin (2019). Coupling water fluxes with cell wall mechanics in a multicellular model of plant development. PLoS computational biology. https: // dx.doi.org/1371/journal.pcbi.1007121
  • Elsa Demes, Laetitia Besse, Paloma Cubero-Font, Béatrice Satiat- Jeunemaitre, Sébastien Thomine, Alexis De Angeli. Measurement of cytosolic pH and NO 3- uncovers the role the vacuolar transporter AtCLCa in the control of cytosolic pH. N.A.S. Jun. 117(26) : 15343-15353
  • Paloma Cubero-Font and Alexis De Angeli Connecting vacuolar and plasma membrane transport networks New Phytologist 02 October 2020 https: // doi.org/10.1111/nph.16983

    Skills

    Scientific skills: a PhD in applied mathematics with applications in computational physics/biophysics or in physics/biophysics with experience in numerical modelling would be ideal. Interest in biological systems and morphogenesis is highly recommended.

    Technical skills: numerical methods (ODE/PDE), parallel computing, GPU, scientific programming (python), interdisciplinary environment.

    Benefits package
  • Subsidized meals
  • Partial reimbursement of public transport costs
  • Leave: 7 weeks of annual leave + 10 extra days off due to RTT (statutory reduction in working hours) + possibility of exceptional leave (sick children, moving home, etc.)
  • Possibility of teleworking (90 days / year) and flexible organization of working hours
  • Professional equipment available (videoconferencing, loan of computer equipment, etc.)
  • Social, cultural and sports events and activities
  • Access to vocational training
  • Social security coverage under conditions
  • Remuneration

    2746€ gross salary / month

    General Information
  • Theme/Domain : Computational Biology Biologie et santé, Sciences de la vie et de la terre (BAP A)

  • Town/city : ENS de Lyon - Laboratoire RDP

  • Inria Center : Centre Inria de Lyon
  • Starting date : 2023-01-01
  • Duration of contract : 12 months
  • Deadline to apply : 2022-10-09
  • Contacts
  • Inria Team : MOSAIC
  • Recruiter : Godin Christophe / Christophe.Godin@inria.fr
  • About Inria

    Inria is the French national research institute dedicated to digital science and technology. It employs 2,600 people. Its 200 agile project teams, generally run jointly with academic partners, include more than 3,500 scientists and engineers working to meet the challenges of digital technology, often at the interface with other disciplines. The Institute also employs numerous talents in over forty different professions. 900 research support staff contribute to the preparation and development of scientific and entrepreneurial projects that have a worldwide impact.

    Instruction to apply

    Applications must be submitted online on the Inria website.

    Processing of applications sent by other channels is not guaranteed.

    Defence Security : This position is likely to be situated in a restricted area (ZRR), as defined in Decree No. 2011-1425 relating to the protection of national scientific and technical potential (PPST).Authorisation to enter an area is granted by the director of the unit, following a favourable Ministerial decision, as defined in the decree of 3 July 2012 relating to the PPST. An unfavourable Ministerial decision in respect of a position situated in a ZRR would result in the cancellation of the appointment.

    Recruitment Policy : As part of its diversity policy, all Inria positions are accessible to people with disabilities.

    Warning : you must enter your e-mail address in order to save your application to Inria. Applications must be submitted online on the Inria website. Processing of applications sent from other channels is not guaranteed.

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