2019-01623 - PhD Position F/M Development, characterization and control of E. coli communities on an automated experimental platform

Contract type : Public service fixed-term contract

Level of qualifications required : Graduate degree or equivalent

Fonction : PhD Position

About the research centre or Inria department

Grenoble Rhône-Alpes Research Center groups together a few less than 800 people in 35 research teams and 9 research support departments.

Staff is localized on 5 campuses in Grenoble and Lyon, in close collaboration with labs, research and higher education institutions in Grenoble and Lyon, but also with the economic players in these areas.

Present in the fields of software, high-performance computing, Internet of things, image and data, but also simulation in oceanography and biology, it participates at the best level of international scientific achievements and collaborations in both Europe and the rest of the world.

Context

The position is based in project-team IBIS at Inria Grenoble - Rhône-Alpes (https://team.inria.fr/ibis/). IBIS includes experimental biology personnel at the Laboratoire Interdisciplinaire de Physique (LIPhy, 140 Av. de la physique, Grenoble; https://www-liphy.ujf-grenoble.fr/Introduction-627) of the Université Grenoble-Alpes.

Our interdisciplinary group, composed of biologists, computer scientists, mathematicians and physicists, studies bacteria, in particular E.coli, at the level of the population and at the single-cell level. Our main focus is fundamental research, but we also aim at applications in biotechnology and synthetic biology.

The project includes data analysis and modelling tasks to be carried out at Inria, as well as experimental biology tasks carried out at LIPhy. Funding is available via the Inria Project-Lab CoSy (https://project.inria.fr/iplcosy/).

 

Assignment


Different species in natural bacterial communities generally communicate in complicated ways. Our aim is to
construct precisely defined bacterial communities consisting of engineered strains of E.coli. Using this synthetic system, we will be able to analyze and control the interactions between different subpopulations. In particular, we will engineer bacteria that communicate by metabolites that are released in the medium and control the temporal expression profile of particular genes in the two populations by optogenetics. The main focus is fundamental research, with possible applications in biotechnology.

The PhD project consists in constructing some of the strains, analyzing their behavior by measuring gene expression and growth parameters, and controlling their temporal dynamics using an advanced platform of mini-bioreactors coupled to a cytometer. By this setup, our aim is to achieve feedback control not only of mean behavior, but also of variability of growth and gene expression between and within subpopulations.

Main activities

Main activities:

  • Strain construction
  • Platform programming and execution of experiments
  • Data analysis
  • Implementation of (existing) bacterial community control algorithms

Possible additional activities:

  • Model calibration, paper reading, report writing

Skills

Applicants may come from different disciplinary backgrounds – physics, biology, engineering, and computer science. Basic knowledge in microbiology is required and previous experience with some of the techniques mentioned in the project description would be appreciated. 

Good relational skills are important for the project, as it will be carried out in an interdisciplinary and international environment.

Familiarity with English is appreciated.

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 (after 6 months of employment) 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

Remuneration

Gross salary :

  • 1982€ during the 1st and 2nd year
  • 2085€ the third year