photo by G. Hofman
Senior Scientist at the Biozentrum (Basel)
In my research, I use microbes to address questions related to phenotypic variability, i.e. to study the range of phenotypes realised by microbial cells with the same genetic information in the same environment. My interests and projects range from the molecular mechanisms underlying phenotypic variability to its evolutionary implications for microbial populations. Beyond their fundamental interests, understanding these questions is also critical to prevent the emergence of antibiotics “persistence” and to optimise synthesis processes in biotechnological industries.
In practice, I use and develop single-cell methodologies – primarily based on microfluidics, quantitative light microscopy and quantitative flow cytometry. Moreover, I cherish a very tight integration of the experimental and modelling components for every project. I implement and promote reproducible practices for experimental research and data analysis, and rely as much as possible on open source tools.
Have overlapping interests? Want to learn about these approaches? Please contact me to discuss current opportunities to work together. In particular, I always welcome applications of talented and enthusiastic students and postdocs.
Noise propagation in gene networks
with Arantxa Urchueguia, Gwendoline Bellement, Luca Galbusera, Erik van Nimwegen.
Stemming from the observation that regulatory interactions promote gene expression noise (Wolf, et al. 2015), these experimental projects focus on how the induction of regulated promoters affects their noise properties, and on the propagation of gene expression noise at the scale of the whole genome in several environments.
Stochasticity of gene expression
with Athos Fiori, Diana Blank, Erik van Nimwegen.
We acquire high accuracy datasets of bacteria lineages to address questions such as the variability of activity of constitutive promoters, how fluctuations of gene expression couple to fluctuations of cell growth, or the impact of gene expression noise on gene regulation in fluctuating environments. We also study the impact of gene expression noise on growth lags, as well as its impact on the selection of growth lags.
Advanced methods for single cell analysis of bacteria populations
with Guillaume Witz, Matthias Kaiser, Florian Jug, Erik van Nimwegen.
Harnessing recent developments in microfluidics, image analysis, click chemistry, etc, to achieve higher throughput and better resolution in the study of bacteria population with single-cell resolution.
Age-associated phenotypes of budding yeast
with Gregory Paul, Peter Horvath, Yves Barral.
Even in unicellular species such as bacteria and yeasts, systematic effects can be observed as time passes or as cells undergo consecutive divisions. This has been proposed to be a relevant model to study senescence and indeed constitutes a fascinating case of phenotypic variability. I focused on bringing together the knowledge of molecular mechanisms involved in increased longevity and the implications of senescence on population dynamics and life history strategies. However, a comprehensive framework is still missing to understand the evolutionary origins and implications of senescence in microbes.
Public goods dynamics in clonal populations of bacteria
with Nicolas Desprat, Thierry Mora, David Bensimon, Vincent Croquette.
While interested in the dynamics of siderophore producers and non-producers in spatially structured environments, we discovered that there is a large variability of siderophore abundance between producer cells in a clonal population. We characterised the temporal dynamics of siderophore abundance in details and showed that rapid exchanges between neighbouring cells support the astonishingly large variability.
Monitoring microbial population size at low density
with Vincent Croquette, Nicolas Desprat, David Bensimon.
Using the fluctuations of scattered light to measure the abundance of bacteria and yeasts at low concentration; this was initially meant to be a detection device for the project of experimental evolution in a spatially structured environment, and has been completed and published independently.
Experimental evolution in a spatially structured environment
with Nicolas Desprat, Vincent Croquette, David Bensimon.
A sustained attempt to evolve motile bacteria in a double gradient of temperature and nutrients. By maintaining a temperature gradient from 30 to 60ºC and delivering nutrients at the top, we aimed at studying adaptation in a structured environment; since the sensitivity to temperature is a complex trait that depends on the history, this is also a promising setup to study the interplay between physiological acclimation and genetic adaptation. This project was hindered by practical constraints as explained in details in my PhD thesis.
If you are a human or friendly sentient AI: my email is thomas.julou, followed immediately by @normalesup.org
Computational and Systems Biology
Biozentrum – University of Basel
If you visit us, Biozentrum can easily be reached from Basel main station with bus 30 (stop on the left when exiting the station; direction Bad Bf, stop Bernouillanum) and from the airport with bus 50 (stop Kanenfeldplatz). Our lab is on the 6th floor of Pharmazentrum (room PZ6020).