Stephanie SORRES

Author's posts

PhD Defense – Ghjuvan GRIMAUD -14/06/16 @ 14h – LOV

Tuesday June 14th. 2016at 02:00 pm – in Laboratoire d’Océanographie de Villefranche-sur-Mer (LOV)

Title : Automation and optimization of a device designed to improve the performance of microalgae for energy purposes by continuing selection pressure.

Abstract : Unicellular photosynthetic organisms forming the phytoplankton are the basis of primary production. Because these organisms cannot regulate their inner temperature, the medium temperature strongly constrains their growth. Understanding the impact of this factor is topical in a global change context. In this PhD thesis we have investigated how phytoplankton adapts to temperature. By analyzing the growth rate as a function of temperature for hundreds of species we highlighted the characteristics that can be accurately described by a mathematical model. We have identied the links between the cardinal temperatures as well as their thermodynamical fundament using the mechanistic Hinshelwood model. We then challenged the Eppley hypothesis “hotter is faster” for 5 phylogenetic phytoplankton groups and determined the evolutionary limits for each of them. We have also studied the adaptation mechanisms associated to long term temperature variations by developing an evolutionary model using the adaptive dynamics theory allowing to predict
the evolutionary outcome of species adaptation to a simple temperature cycle. Our results have been compared to a selection experiment carried out in a controlled device on Tisochrysis lutea. Our method has been extended to predict the adaptation of a strain to periodic temperature profiles and study phytoplankton adaptation at the global ocean scale. In situ data of sea surface temperature have been used as a forcing variable and have permitted to show that the elevation of temperature will be critical for several species in particular for those living in areas where the annual temperature fluctuation is high such as the Mediterranean sea.

Jury members :

  • JM GUARINI, UPMC, Banyuls sur Mer
  • Jef HUISMAN, University of Amsterdam
  • JC POGGIALE, OCEANOMED – Campus de Luminy

PhD Defense – Charlotte COMBE – 09/05/2016 @14h – LOV

Title: Quantitative and qualitative effects of light on the growth of microalgae in dense crop and their production of molecules of interest”

Microalgae are a promising source of third generation biofuels. The interest on these photosynthetic microorganisms also lies within the extent of the spectrum of molecules that they can produce, such as proteins, pigments, and vitamins.

Nevertheless, further progress is still necessary to reduce the economic and environmental costs of cultivation processes and to ensure the viability of this sector. In particular, better understanding of the effect of light on the productivity of dense cultures is an essential step to optimize these processes.

The aim of this thesis is to study the quantitative and qualitative effects of light on growth and acclimation mechanisms of two species of microalgae with high biotechnological interest; Dunaliella salina and Tisochrysis lutea.

The first part of this thesis examines the response of Dunaliella salina to rapid light changes, by reproducing irradiance fluctuations typically experienced by microalgal cells in a highly turbid suspension in raceway ponds. In the second part, we analyzed the response of Dunaliella salina and Tisochrysis lutea to different light spectra. Our experimental and theoretical approach allowed us to identify the effect of colored light on productivity and pigment composition of microalgae. Furthermore, our results offer encouraging prospects for elevate understanding and use of light and improve the energy performance of these processes.

Jury members:

Dr. Claude Aflalo – Rapporteur
Pr. Yannick Huot – Rapporteur
Dr. Jean-Paul Cadoret – Examinateur
Dr. Bruno Sialve – Examinateur
Dr. Olivier Bernard – Co-directeur
Dr. Sophie Rabouille – Co-directrice
Dr. Antoine Sciandra – Directeur
Pr. Paul Nival – Président du jury


Dunaliella salina, Tisochrysis lutea, biofuel, photosynthesis, hydrodynamics, flashing light, photolimitation, LED, wavelengths,pigments, phenotypic plasticity, photoacclimation, productivity

PhD defense: Elsa ROUSSEAU – 27/05/16 @ 13h30 salle Euler Violet

Titel: Effect of genetic drift and selection on plant resistance durability to viruses.

Plants can be fully protected from their pathogens when they carry major resistance genes, but the efficiency of these genes is limited by the emergence and spread of adapted, resistance-breaking pathogen variants. This thesis studies how evolutionary forces imposed by the plants on pathogen populations may increase the durability of major resistance genes. Using plant viruses as a biological model, this thesis investigates the effect of genetic drift and selection, from the within-host to the host population level. Firstly, a stochastic epidemiological SI model at the field level showed that genetic drift could be particularly beneficial for crop yield when the fitness cost associated with virus adaptation to resistance was intermediate in susceptible plants. Then, the design and validation of a mechanistic-statistical model based on deterministic Lotka-Volterra equations and stochastic Dirichlet-multinomial processes allowed to disentangle the effects of genetic drift from those of selection on temporal data of within-host competition between virus variants. The intensities of genetic drift and selection acting on virus populations were shown to be controlled genetically by the hosts. Finally, a correlation analysis between these estimations of genetic drift and selection intensities and an experimental estimation of the durability of a major resistance gene showed that strong genetic drift during the early stages of plant infection led to an increase in resistance durability. These results open new perspectives for more durable management of plant resistance, by breeding plant varieties inducing strong genetic drift on pathogen populations

Jury members:

Fernando GARCIA ARENAL, Universidad Politécnica de Madrid


Elisabeta VERGU, INRA

Christian LANNOU, INRA


Alain VIARI, Inria

Jean Luc GOUZE, Inria

Frédéric FABRE, INRA

Keywords: genetic drift, selection, resistance durability, experimental evolution, epidemiology.

Post-doctoral fellowship : Modelling evolution of disease-associated traits under local competition with conspecifics (M/F)

Type d’offre : Post-doctorant
Lieu de travail : Sophia-Antipolis
Thème de recherche : Santé, biologie et planète numériques
Projet : BIOCORE
Responsable scientifique :
Date limite de candidature: 31/12/2015
He – She will be in charge of mathematical developments in order to understand how disease-associated traits evolve in fungal pathogens of plants. The main question will be how correlations between disease-associated traits could emerge from resource allocation models.

The post-doc will take place in collaboration with the UMR IAM of INRA Nancy in the framework of the ANR Funfit project (Funfit : A trait-based approach linking individual Fitness of Fungal plant pathogens to ecological strategies).

Funfit Modelling group: Frédéric Grognard (Biocore, Inria Sophia Antipolis), Fabien Halkett (UMR IAM, INRA Nancy), Ludovic Mailleret (UMR ISA, INRA Sophia Antipolis), Frédéric Hamelin (UMR IGEPP, Agrocampus Ouest, Rennes), Frédéric Fabre (UMR SAVE, INRA Bordeaux)

Job offer description
Fungi are among the most frequent damaging agents of plants, in natural and managed ecosystems. In recent years, they have been identified as a major cause of emerging diseases in the context of global change, especially through the establishment of alien species in new areas. Understanding this fast-moving epidemiological context is a key issue and will require greater emphasis on integrative and predictive approaches.

The study of disease-associated traits evolution is an active research field. Beyond the classical virulence-transmission trade-off, we are particularly interested in how correlations between disease-associated traits could emerge from resource allocation models.


In that context, the post-doctoral fellow will be asked to work in two complementary directions:

1) to build optimal control models on resource allocation strategies to investigate the evolutionary mechanisms responsible for the detrimental effect of fungal pathogen development on its host plant. Modelling assumptions will be based on the specific features of fungal infection (such as mycelium growth, resource extraction from host, sporulation, etc). Ultimately we aim at linking fungi fitness with disease associated traits that can be measured in experiments.

2) to study the evolution of traits in pathogen populations along an epidemic wave/colonisation gradient. This second direction, which will be the main one for the post-doctoral fellow, will consist in identifying traits involved in fungal pathogen adaptation at the population level, by comparing populations submitted to different selection pressures.

We will first develop models extending the ones developed in the first direction to account for situations where different fungi of the same species can infect the host.  Here, we aim at accounting for epidemiological situations in which host saturation is possible. In this new model, the amount of available healthy hosts will depend on local disease prevalence. Studying host co-infection, it is expected that competition will be shown to be the driving force behind the evolution through branching to the coexistence of subspecies characterized by different traits (e.g. different length of latent periods). Analytical results on small-scale models are expected.


Fungi traits and strategies will tend to be defined by the values of functions of time. The tools that will then naturally be central in the work of the post-doc will be evolutionary dynamics of function-valued traits and dynamic games theory.



J.A.J. Metz, M. Gyllenberg (2001) How should we define fitness in structured metapopulation models? Including an application to the calculation of evolutionary stable dispersal strategies. Proceedings of the Royal Society B: Biological Sciences, 268:499-508

U.Dieckmann, M. Heino, K. Parvinen (2006). The adaptive dynamics of function-valued traits. Journal of Theoretical Biology, 241 :370-389

A.R. Akhmetzhanov, F. Grognard, L. Mailleret (2011) Optimal life-history strategies in seasonal consumer-resource dynamics. Evolution, Wiley-Blackwell, 65:3113—3125.

Skills and profile
The post-doctoral fellow should either have a PhD thesis in Applied Mathematics with a strong knowledge in dynamic game theory, or a PhD thesis in evolutionary biology with a strong theoretical component.
Gross Salary per month : 2621 euros
Starting date: Between October 1st, 2015 and February 1st, 2016 Contract Duration: 20 monthsBusiness Restaurant on site
Additional information
Place of work: Inria Sophia Antipolis Méditerranée

Required documents and sending of the application

Please send your detailed Resume and Covering letter showing your interest and letters of recommendation.

  1. directly on the web site Inria
  2. by email to :M. Frédéric Grognard, Researher in the BIOCORE team:

 Applications will be admitted until the position is filled


Inria’s disabilities policy: All positions at the institute are open to disabled people.

Post-Doctoral fellowship: Control and optimal control of bacterial growth

Subject: Control and optimal control of bacterial growth.

Duration: 12 months

Location: INRIA Sophia-Antipolis (South of France, near Nice)
Contact: Gouze Jean-Luc


Santé, biologie et planète numérique

Tags: Gene networks, biological models, control, dynamical systems, computational biology, numerical simulation


The study of genetic regulatory networks has taken a qualitative leap through the use of modern genomic techniques that allow simultaneous measurement of the expression levels of all genes of an organism. In addition to high-throughput experimental methods, approaches in mathematics and computer science will be indispensable for analyzing the dynamics of genetic regulatory networks. BIOCORE team applies mathematical and computational methods from Control Theory and Dynamical Systems to the study of models of genetic networks and more general biological networks (metabolic networks, signaling networks…).


The general goal of this work is to design control strategies for improving product yield and productivity in E coli bacteria.

The Gene Expression Machinery of this bacterium has been modified (by techniques of genetic engineering) to obtain a strain where a chemical inducer controls the expression of RNA polymerase (an enzyme needed for the expression of the genes).

A simplified dynamical model of this controlled GEM will be developed (with our partners) and studied.

We will notably characterize the transients towards steady states and their duration, as well as the

dependence of these properties on the concentrations of nutrients and inducer in the medium. Moreover, the possibility to externally adjust transients by choosing appropriate nutrients and inducer concentrations provides control parameters for, in the first place, the satisfaction of some biological constraints on the

variables and dynamical behavior , and secondly, the optimization of product yield. Using

optimal control, computer simulation and optimization, we will design control laws, possibly including

feedback. The above analysis will also be carried out for fed-batch cultures in a fermenter,

the condition most relevant for industrial biotechnological processes.


The work is done in collaboration with IBIS Inria Team (Grenoble) within the BIO-INFORMATIQUE ANR RESET project (see
We are looking for an applied mathematician with a  background in the analysis of dynamical systems, and familiar with control theory (and optimal control). In addition, we expect a strong motivation to work on biological applications in genomics.


Web page of JL Gouze
Web page of M. Chaves


Soutenance de Thèse de Doctorat de HUBERT BONNEFOND au LOV le 9 Décembre 2015

HUBERT BONNEFOND soutiendra sa thèse de doctorat intitulée “Amélioration de microalgues à vocation énergétique par pression de sélection continue

le 09 décembre 2015 au Laboratoire d’Océanographie de Villefranche-sur-mer

devant le jury composé de:

  • Jean-Paul CADORET (Rapporteur)
  • Tomas MORRISONOTTO (Rapporteur)
  • Gael BOUGARAN (Examinateur)
  • Louis CHEVIN (Examinateur)
  • Patrick MAYZAUD (Examinateur)
  • Alice GUEUDET (Examinateur)
  • Olivier BERNARD (Directeur)
  • Antoine SCIANDRA (Directeur)



Le monde fait face à une crise environnementale sans précédent, due à l’action toujours plus marquée de l’homme sur son milieu. Depuis le début de l’ère industrielle, l’utilisation massive des énergies fossiles a provoqué un dérèglement climatique planétaire. Les microalgues offrent la possibilité de produire des biocarburants avec une empreinte carbone réduite, mais nécessitent encore de nombreuses améliorations pour être économiquement viables. Une de ces améliorations, à l’instar de l’agriculture moderne, réside dans la sélection de souches plus productives. Dans ce travail de thèse, nous avons développé la sélection par pression continue qui consiste à utiliser les processus de l’évolution pour faire émerger des populations d’intérêt.
Une première voie explorée a cherché à utiliser la température, paramètre crucial de la croissance des microalgues, comme moteur de sélection. En soumettant une culture à des variations diurnes de température durant une année, nous sommes parvenus à adapter une souche de Tisochrysis lutea à une gamme de températures plus large, la rendant donc plus tolérante aux variations ce paramètre.
La seconde voie a cherché à accroitre la capacité de Cylindrotheca closterium à emmagasiner ou au contraire mobiliser son azote intracellulaire, propriété physiologiquement liée à sa capacité à produire des lipides. En forçant une population de microalgues à s’adapter à des apports discontinus d’azote (succession d’états de satiété et de carence), il a été possible de sélectionner les individus les plus riches en lipides.
Enfin, nous avons modifié l’appareil pigmentaire de Tisochrisis lutea pour la rendre plus transparente à la lumière. En soumettant cette espèce à une succession de chocs lumineux, il a été possible de sélectionner les individus possédant les antennes photosynthétiques les plus petites, permettant une productivité accrue.

Research Engineer in Design of metabolic models for microalgae under non balanced growth (M/F)

The work will then consist in:

  • Review of the existing metabolic microalgal models and understand the DRUM approach (Baroukh et al. 2014).
  • Add an heterotrophic pathway
  • Use bioinformatics tool to build metabolic networks or complete/add pathways, of interest
  • Reduce and calibrate the model using the DRUM framework.
  • Test the model accuracy in a wide variety of situations


References :

  • Baroukh, C., Muñoz-Tamayo, R., Steyer, J. P., & Bernard, O. (2014). DRUM: a new framework for metabolic modeling under non-balanced growth. Application to the carbon metabolism of unicellular microalgae.
  • Baroukh, C., Muñoz-Tamayo, R., Bernard, O., & Steyer, J. P. (2015). Mathematical modeling of unicellular microalgae and cyanobacteria metabolism for biofuel production. Current opinion in biotechnology, 33, 198-205.
  • Baroukh, C., Muñoz-Tamayo, R., Steyer, J. P., & Bernard, O. (2015). A state of the art of metabolic networks of unicellular microalgae and cyanobacteria for biofuel production. Metabolic engineering, 30, 49-60.
Skills and profile
The candidate must have a PhD with a recognized experience in metabolic modelling (FBA, FVA, FCA, EFMs, DFBA), with knowledge of associated tools (to solve linear optimization problems, to compute EFMs, to find relevant enzyme in KEGG or Metacyc, …) . Knowledge of kinetic modelling, parameters’ estimation and microalgal metabolism would be appreciated.


Additional information
Contract duration : 16 months

Expected starting date : 1st January 2016

Gross salary per month : from 2600 to 3300 euros depending on diploma and experience

Place of work : The candidate will be based at Inria Sophia-Antipolis, and interact frequently with Fermentalg.

Business restaurant on site


Required documents and sending of the application

Please send your detailed Resume and Covering letter showing your interest and letters of recommendation.

  1. directly on the web site Inria
  2. by email to the scientist manager :

Applications must be sent before : 31/12/2015

Philipp Hartmann’s PhD defense- 14/04/14

PhD defense “Effect of hydrodynamics on light utilization in large scale cultures of microalgae” by Philipp HARTMANN, Wednesday May 14th @ 14H00 in Salle Trégouboff, OBSERVATOIRE OCEANOGRAPHIQUE, STATION ZOOLOGIQUE, Villefranche sur mer

Continue reading

SOFTWARE ENGINEER Upgrade of a bioreactor monitoring software and support of a start-up for its implementation on an experimental plant

See job offer:  BiocorePosteIE

Please contact