Postdoctoral Position : multiscale Fruit Modeling: integrating biophysical fruit growth with biochemical metabolisms in 10 fruits
Reference
1507795565
Deadline for applications
12/30/2017
Date of publication
10/12/2017

Details

Details on the type of contract
Postdoctoral contract
Duration of contract
24 months
Beginning
01/07/2018

Assignment

Name of unit of assignment
UMR1287 EGFV Ecophysiologie et Génomique Fonctionnelle de la Vigne
Address of unit of assignment
INRA Campus de la Grande Ferrade - 71 avenue Edouard Bourlaux - CS20032 33883 VILLENAVE D'ORNON CEDEX
Region of assignment
Aquitaine Limousin Poitou-Charentes

Description

Working environment

Context:

Metabolism is an obvious target for crop improvement, especially in fruits, and understanding the mechanisms linking it to crop phenotypes will help to focus breeding strategies. Modeling plays a more and more important role in dissecting complex traits, such as metabolism, into more simple and stable ones. For example, stoichiometric (Flux balance analysis) and enzyme-based kinetic models can capture a clear picture of subcellular metabolic fluxes. However, the phenotype of a given trait is often a result of complex networks working at different organization levels. For example, fruit size is a function of cell number and cell expansion, where the former is tightly related to cell division and the latter depends largely on the biophysical properties of water transport that cannot be predicted solely from metabolic reactions. Instead, process-based models can successfully simulate the biophysical processes for fruit growth, without detailed incorporation of metabolic process. Therefore, linking process based models to the genetic basis of metabolism could lead to powerful tools to manipulate fruit biomass and quality. The existence of an integrated, multi-scale model could offer a useful framework to interpret omics data, in relation to environmental factors, developmental stages and agricultural practices. The integration of cellular and molecular levels can help refine plant models, shedding light onto the complex interplay between different spatial and temporal scales in the emerging system response. In particular, the integration of an enzyme-based kinetic model into a process-based model would enable the identification of those enzymes and/or transporters having the strongest control over a trait of interest, thus opening the possibility to manipulate this trait. However, the integration of models operating at different levels of organisation and/or involving different concepts is still rather seldom.

 

The French National Research Agency (ANR) has funded an innovation project entitled "FRuit Integrative MOdelling for a Unified Selection System" (FRIMOUSS). This research project is conducted by a consortium of three research groups, including UR 1115 (INRA, Avignon), UMR 1287 (INRA, Bordeaux), and UMR 1332 (INRA, Bordeaux), with rich expertise in fruit metabolism (metabolomics and enzyme activities), fruit metabolism modeling, process-based modeling of fruit growth. In the frame of this project, UMR 1287 at INRA (French National Institute of Agronomic Research) Bordeaux is offering a position for a postdoctoral scientist, for a duration of 24 months.

 

Objectives and Missions:

Within the project, three types of models will be developed, including enzyme-based (i.e. kinetic), reaction-based (i.e. stoichiometric) and process-based (i.e. biophysical) models, based on previous model frameworks and to be applied to 9 different fruit species. The postdoctoral position aims at integrating the three types of models to provide a modelling toolbox dedicated to the manipulation of fruit quality.

The postdoctoral scientist to be recruited will

1) conduct a sensitivity analysis at steady state on preexisting models to identify kinetic parameters that exert a low control over fluxes and/or metabolite concentrations and, consequently, that can vanish in the integrated model;

2) perform an analysis of relevant time-scales involved in the process-based and kinetic models, in view of their integration. Accordingly, quasi-steady state approximations for fast reactions could be assumed, reducing the complexity of the resulting ODE system;

3) run the kinetic model in a dynamic (time dependent) mode and connect it to the process-based model via a modular approach involving minimal modifications in the original models;

4) reduce the kinetic model by lumping several less influential enzymatic reactions into one or by replacing Michaelis-Menten kinetics with simplified rate equations to reduce parameter numbers but retain reasonable model performance;

5) finally, conduct in silico analyses of the interactions between fruit biophysical properties and distribution of metabolic fluxes, and ultimately provide valuable clues for potential targets of metabolic engineering.

 

The candidate will benefit from a strong scientific expertise of the host institution in fruit metabolism and different types of modeling[1-8]. The INRA research center at Bordeaux has world-class metabolic platforms and has access to renowned institutes of higher education, excellent clusters, and a famous industry of fruit crops, especially for wine grapes, strawberries, and tomatos, which all are included in the project.

 

[1] Baldazzi et al. (2012)  Trends Plant Sci 17: 728-736

[2] Beauvoit et al. (2014)  Plant Cell 26: 3224-3242

[3] Biais et al. (2014)  Plant Physiol 164: 1204-1221

[4] Colombié et al. (2015)  Plant J 81: 24-39

[5] Colombié et al. (2017)  New Phytol 213: 1726-1739

[6] Dai et al. (2013)  J Exp Bot 64: 1345-1355

[7] Dai et al. (2016)  Front Plant Sci. 7: 649

[8] Génard et al. (2010)  Plant J 62: 344-355

Training and skills required

Required Skills

We are looking for a self-motivated individual with strong communication and organization skills, who has (recently) completed a Ph.D. thesis in Plant Sciences, Information Sciences, with an application of metabolism modeling and a high publication record. A first successful post-doc in the same research field would be highly appreciated but is not mandatory. Knowledge of programming languages (Matlab, R, Java…) and modeling platforms (Copasi or equivalent) is essential, experience in plant metabolism regulation, database, the Systems Biology Markup Language (SBML), rule-based XL language, and GroIMP platform would be an asset. Ability to communicate in English both orally and in writing is essential.

 

Your application should include a cover letter, with a brief description of your research interests, a CV, and a list of at least 2 references

Contact

Name
Dr. Zhanwu Dai / Prof. Dr. Eric Gomès
Telephone
(+33) – (0) 5 57 57 59 22 / (+33) – (0)5 57 57 59 10
Email
zhanwu.dai@inra.fr;eric.gomes@inra.fr