Actualités

International PhD Program 2021

 6 fully-funded PhD positions are offered in:
 Plant Genetics
 Plant Physiology & Metabolism
 Plant Molecular, Cellular & Developmental Biology
 Plant Computational Biology & Quantitative Imaging

 

Deadline for application: April 10, 2021



The Institut Jean-Pierre Bourgin is one of the largest research centers in Plant Sciences in Europe. It gathers a unique ensemble of experimental resources and pluridisciplinary expertise in biology, chemistry and computer science. IJPB teams are committed to providing PhD students with the best environment and tutoring for a successful career in science, in close association with the Paris-Saclay University, a top-ranking, internationally renowned university.

Contents

1. Who can apply?
2. How to apply?
3. Selection procedure
4. Available positions and contact


Who can apply?
We are recruiting talented and motivated early researchers who are seeking first class training in multidisciplinary Plant Sciences.

Applicants must hold (or be about to obtain) a European master degree or an equivalent degree formally entitling them to embark on doctoral studies. You will have to provide a copy of your Master’s degree or equivalent if already available, or a certificate by your university that you are pursuing a Master degree(*) that should be obtained before the starting date of the thesis.

Although basic knowledge in Plant Sciences is certainly a plus, no prior research experience in Plant Biology is required, and all applications are welcome as long as you have theoretical/practical experience in line with the subject(s) you apply for.
Applicants from all countries are eligible. A good level in English is required, as all IJPB seminars and most internal meetings are held in English. French is not required.

(*) translated into English or French if necessary

How to apply?

Beware: deadline for applications is April 10, 2021. No application will be accepted beyond this date, and incomplete files will not be considered.

Please examine closely the proposed subjects and apply for Please examine closely the proposed subjects and apply for the one(s) you wish. You are welcome to contact the PIs if you have any questions. No limit is imposed here, but be aware that you have to justify your choice in the motivation letter.

Applicants should provide (in English or French), in a single pdf file:
• CV
• Detailed motivation letter, where you can describe your academic background, professional experience (research activities, realizations…), personal centers of interest etc. You should also explicitly list the subjects you are applying for and your motivations. Please also indicate when you will be available for starting your PhD (in any case before end-2021).
• Copy of your latest degree(s), with ranks and grades whenever possible. You will have to provide a copy of your Master’s degree or equivalent later on, if not available yet.
• Contact information for 2-4 referees (name, quality, mail and telephone number). At this stage do not send any recommendation letter.

Send the complete application file to this address before the deadline:

ijpb-PhD2021@inrae.fr

Selection procedure and timeline

• April 10 2021: deadline for sending applications

• 10-20 April 2021: The selection committee will examine all the applications and directly contact the referees listed by candidates whenever necessary. Shortlisted candidates will be invited for a video-interview with the selection committee. Invitations will be sent by April 25.

• Video-Interviews will be held on May 5 & 6. The final ranking will be published on May 10. Candidates will have to send a formal acceptance before May 15, or the positions will be offered to the next ranking student on the list.

• Selected candidates are expected to start their PhD in September-December 2021, but this can be adjusted according to personal/professional constraints.

• The PhD contract is 36 months.
Gross monthly salary is ~1900 € including health and unemployment insurance. Net monthly salary is ~1500 €


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Available positions and contacts
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Position 1: "Spatio-temporal coordination of cell division in plants"
Keywords: cell division, morphogenesis, cell cycle, cytoskeleton, live imaging, microfluidics
Group "Spatial control of cell division". PI: David Bouchez



In plant cells, the spatio-temporal regulation of cell division is brought about by a constant molecular dialog between the cell cycle machinery and the microtubular cytoskeleton. The TTP complex is a protein network involved in the spatial organization of cortical microtubules. Our recent results on this complex put into question a number of ancient theories about the role of specific microtubule arrays in the determination of the division site in plant cells. This PhD project aims at identifying the molecular and cellular networks determining the position of the cell division plane, in particular early pre-mitotic signaling events, and their links with the cell cycle. Indeed, our recent results suggest that, contrary to current theories, the interphase cytoskeleton plays a major role in this process. The student will mobilize genetics, molecular biology, microscopy, microfluidics, image analysis approaches in order to characterize the microtubule cytoskeleton during late-interphase, to identify G2-specific molecular networks and to characterize their function at the cellular and multi-cellular scales

Details and inquiries: David Bouchez
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Position 2: "Study of the interplay between chromosome dynamics and meiotic recombination"
Keywords: meiosis, mutants, CrispR-Cas9, cytogenetics, live imaging, image analysis
Group "Meiosis Mechanisms". PI: Mathilde Grelon


The formation of viable gametes during meiosis relies on meiotic recombination and the formation of crossovers (COs) between homologous chromosomes. Meiotic recombination occurs during meiotic prophase, in parallel with a number of spectacular chromosomal events such as homologous chromosomes recognition and synapsis, telomere attachment and clustering to the nuclear envelope and vigorous chromosome movements. All these events are known to be connected but to which extent is an open question.
This PhD will take advantage of a number of recent progresses made in the field of chromosome imaging to tackle the long-standing question of the connection between chromosome dynamics and meiotic recombination control. The methodologies that will be used involve microscopy (immunofluorescence, classical and confocal microscopy, live imaging), image analysis, genetics and molecular biology approaches (mutant production and characterization).

Details and inquiries: Mathilde Grelon
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Position 3: “Wall integrity signaling and growth control in plants”
Keywords: Root hair, microfluidics, Rapid Alkalinisation Factor signaling, growth oscillations, quantitative imaging, apoplastic pH, pectin, Arabidopsis
Group “Primary Cell Wall”, PI: Herman Höfte


A central and poorly understood question in plant biology is how the polymer network of the cell wall can expand without losing its integrity. Understanding this process is essential for the modeling of plant morphogenesis in response to changing environments. The polyanionic pectic polymer homogalacturonan (HG) shows a variety of charge patterns, through the action of distinct pectin methylesterase (PME) activities. HG charge is critical in vivo since PME activity, depending on the context, can either promote or inhibit cell growth. Interestingly, HG binds, in a charge-dependent manner, polycationic peptides of the Rapid ALkalinization Factor (RALF) family. Some RALFs are essential for cell expansion and, when not sequestered in the cell wall, are thought to signal through a membrane receptor complex feeding back on the cell wall pH and pH-dependent PME activity. This PhD student will use Arabidopsis roothairs as a simple growth model to investigate and model how oscillations in growth and surface pH can be controlled by the pH-dependent interaction of RALF peptides with their receptors and pectins respectively. He will use quantitative live cell imaging on roothairs grown in microfluidic rootchips, genetics, CRISPR-Cas9 mutagenesis, protein biochemistry and immunolocalisation techniques combined with super-resolution microscopy..
Refs: Gonneau et al. Curr. Biol. 2018; Voxeur and Höfte Glycobiology, 2016

Details and inquiries: Herman Höfte
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Position 4: “Statistical atlasing for the reconstruction and analysis of spatio-temporal dynamics during the cell cycle”
Keywords : image processing, data analysis, spatial normalization, machine learning, fluorescence microscopy
Group “Modeling and Digital Imaging”, PI : Philippe Andrey

Investigating fundamental dynamic processes such as cell division largely relies on the exploitation of microscopy images. However, a major obstacle in biological imaging is the impossibility to acquire live images of cells over long periods of time, at high resolution, and using an arbitrary number of fluorescence channels. As a result, images of different cells observed at different time-points are typically acquired when studying complex spatio-temporal cellular processes. This raises the need of integrating data from large image samples to infer and reconstruct the complete spatio-temporal dynamics of studied processes. The main objective of the PhD is to design an algorithmic strategy to address this problem, combining 3D quantitative image analysis, spatial normalization, and statistical data analysis. The developed algorithms will be validated based on simulated microscopy images and on time-lapse data. They will be applied to build a statistical spatio-temporal atlas of cellular dynamics in plant root cells and to investigate the links between cell division and cell dynamics during interphase.

Details and inquiries : Philippe Andrey
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Position 5: “Computational modeling of plant multi-cellular growth and morphogenesis”

Keywords : cell division and growth, computer model, quantitative image analysis, plant embryogenesis
Group “Modeling and Digital Imaging”, PI : Philippe Andrey. In collaboration with Jean-Christophe Palauqui, group “Cell differentiation and polarity


Cell division and differential cell growth are the two major cellular mechanisms that underlie the elaboration of specific shapes in plant development. A fundamental question that remains largely unsolved is to understand the respective contributions and the coordination of these two mechanisms in the morphogenesis of plant organs, and how they are orchestrated with molecular processes. Embryogenesis in the model plant Arabidopsis thaliana is a unique system to address these questions, showing stereotyped shape transitions and symmetry breaking within a few generations downstream the first embryonic cell. The objective of this PhD project is to develop a 3D multicellular and multiscale model of growing plant tissues to investigate the coupling between cell division and cell growth. The project will benefit from a large collection of 3D embryo images available in the lab to build and validate the model. The project will combine quantitative 3D image analysis and computer modeling and will provide a better understanding of the role of self-organization in the emergence of plant embryonic shapes.

Details and inquiries : Philippe Andrey
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Position 6: “Discovering the stress-inducible specialized metabolome in seeds”
Keywords : Untargeted metabolomics, Metabolite Plasticity, Arabidopsis thaliana, transcriptomics, Abiotic stress, Biotic stress
Group “Seed Development and Quality”, PI : Massimiliano Corso. In collaboration with Loïc Lepiniec, group “Seed Development and Quality” and Grégory Mouille, group “Cell to Cell adhesion and communication


Plants produce thousands of Specialized Metabolites (SMs) in different plant tissues and organs, particularly in seeds that accumulate large amounts of various SMs classes with an essential impact on physiological functions. Many seed SMs are essential nutritional compounds and are part of the arsenal of compounds that protect these organs to a wide range of abiotic and biotic stresses. While most studies have focused on the regulation of SMs pathways by stresses in plant vegetative tissues, little is known about these processes in seeds, which are particularly important in many Brassicaceae species where they constitute the final product for industrial or nutritional purposes. We aim at filling this gap by (1) discovering the seed SMs landscapes of Arabidopsis thaliana species from plants subjected to biotic or abiotic stresses, and (2) elucidate the common and specific pathways that control the accumulation of seed SMs in control and stress conditions. The seed specialized metabolome of these species will be induced by biotic stress, and by drought or heat abiotic stresses. The PhD will use untargeted metabolomic and transcriptomic analyses to identify the metabolic pathways induced by the stresses in seeds. The analyses will generate a list of candidate genes with a role in SMs accumulation that are common or specific among the stresses considered. Metabolomic, imaging and molecular biology techniques will be used to confirm the role of the genes in the regulation of SMs pathways. The project will identify genetic factors that regulate SMs accumulation in control and stress condition in seeds.

Details and inquiries :  Massimiliano Corso
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International PhD Program 2021