Thomas Julou
Senior Scientist at the Biozentrum (Basel)
In my research, I combine quantitative experiments and theoretical models to elucidate how robust properties observed in bacterial populations arise from the seemingly stochastic dynamics observed in individual cells. Because bacteria are small and the chemical reactions involved in gene expression are inherently stochastic, different individual bacteria display different properties – so called phenotypes – even when they are genetically identical and exposed to the same environment. My projects investigate the molecular mechanisms underlying this phenotypic variability, as well as its functional and evolutionary implications.
In practice, I develop new tools to study bacteria with single-cell resolution, in particular using microfluidics and image analysis. In parallel, 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 more about these approaches? Please contact me to discuss current opportunities to work together. In particular, I always welcome applications from talented and enthusiastic students and postdocs.
Projects
Gene expression and survival during starvation
with Théo Gervais, Bor Kavčič, Erik van Nimwegen.
We study how bacteria react to starvation at the single-cell level. Stay tuned!
Together with Nathalie Balaban (Hebrew Univ Jerusalem) and Roberto Kolter (Harvard Medical School), we organized a 3-weeks workshop on the quantiative biology of non-growing microbes at KITP (UCSB) in October 2022.
Single-cell gene regulation in bacteria
with Théo Gervais, Diana Blank, Gwendoline Bellement, Luca Galbusera, Erik van Nimwegen.
We aim at understanding how seamingly coordinated gene regulation behaviours emerge at the population level while the underlying dynamics are instrinsically noisy at the individual level. In particular, we study the induction dynamics of the lac operon and of the LexA regulon in E. coli at the single-cell level.
New preprint out on the global effect of dilution due to growth on the sensitivity on gene circuits: we discovered fast growing bacteria require stronger signal to switch on circuits controlled by positive feedback loops, and that growth-arrested bacteria become extremely sensitive to environmental cues.
Noise propagation in gene networks
with Arantxa Urchueguia, Dany Chauvin, Erik van Nimwegen.
Stemming from the observation that regulatory interactions promote gene expression noise (Wolf, et al. 2015), these experimental projects focused 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.
Article in PLoS Biology on the global features of gene expression noise in E. coli and how tightly coupled it is with gene regulation.
Stochasticity of gene expression
with Dany Chauvin, Björn Kscheschinski, Théo Gervais, Erik van Nimwegen.
We acquire high accuracy datasets of bacteria lineages to characterize the variability of activity of constitutive promoters, and ask questions such as how fluctuations of gene expression couple to fluctuations of cell growth, or how gene expression noise compares between growth and starvation.
In order to address these questions, we develop dedicated inference procedures allowing to compare several models of bacteria physiology and to take measurement noise into account.
Advanced methods for single-cell analysis of bacteria populations
with Michael Mell, 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.
Kaiser M, Jug F, Julou T, et al. (2018) Nat. Commun. 9, 212.
Past projects
Read more here on my past research projects…
Contact
If you are a human or friendly sentient AI: my email is thomas.julou, followed immediately by @normalesup.org
Thomas Julou
Biozentrum – University of Basel
Spitalstrasse 41
4056 Basel
Switzerland
To visit us, the Biozentrum is easily accessible from Basel main station by bus 30 (stop on the left when exiting the station; direction Bad Bf, stop UKBB) and from the airport by bus 50 (stop Kanenfeldplatz). Our lab is located on the 8th floor, first “quadrant” of the Biozentrum (room 08.018).
