Before this I was a postdoc with Sebastian Bonhoeffer (Theoretical Biology) at ETH Zurich, working mainly on stress-response, evolvability and robustness in bacteria (read our recent publication here).
And before I was a PhD student with François Taddei and Dusan Misevic (INSERM U1001). My PhD focused on the links between second order selection and evolution of cooperation, using both microbial and in silico systems (some of our work here and here).
antoine DOT frenoy AT pasteur DOT fr
Increased evolvability under stress: stress-induced mutagenesis and death
Stress-induced mutagenesis (SIM) has been a major paradigm shift in the past decades: it postulates that as an answer to stress, bacteria increase their genome-wide mutation rate. This has been interpreted as a mechanism providing “adaptation on demand” (increased evolvability under stress, increasing the chances that a descendant is able to face the stress)
In our recent paper (Frenoy & Bonhoeffer, 2018, PLoS Biology), we challenge this view by showing that (1) current methods lead to a systematic over-estimation of mutation rate under bactericidal stress, and (2) a stress that increases mutation rate does not always increases evolvability.
Evolution of cooperation and second-order selection pressures
Because genes coding for cooperation (here public good secretion) face very different selection pressures than more classical genes coding for private traits (affecting only the individual bearing them), we wondered whether they would somehow evolve different genetic properties.
To answer this question, we adapted the Aevol platform to the study of cooperation by implementing a spatial structure and the potential to secrete a public good. Aevol is an individual-based model that has a bacterial-inspired genomic layer and is has been used to study second-order selection pressures acting on genome organization.
We found (Frénoy et al, 2013, PLoS Computational Biology) that genes related to cooperation (coding for secretion of a public good) tend to spontaneously form operons (using the same promoters and terminators) and overlap (using the same base pairs but in different reading frames) with “metabolic” (only contributing to the focal individual's private fitness in our vocabulary) genes. A large part of “cheating” (decreasing secretion) mutations are thus also impacting “private” genes, causing a drop in fitness and the mutation being wiped out by selection.
January 2018 - Now: Postdoc at Institut Pasteur (France) with Eduardo Rocha.
January 2015 - December 2017: Postdoc at ETH Zürich (Switzerland) with Sebastian Bonhoeffer: Evolvability and mutagenesis under antibiotic stress, implications for de novo evolution of resistance during antibitic treatments.
September 2011 - November 2014: PhD in National Institute of Health and Medical Research (INSERM, France) with François Taddei and Dusan Misevic: Second-order selection pressures promoting the evolution and maintenance of cooperation in microbial and in silico systems
May - July 2011: Research internship in National Museum of Natural History (MNHN, Paris) supervised by Dominique Lestel and Hollis Taylor: Evolution of music and language, the bi-constructivist approach
February 2010 - April 2011: Research internships and Master thesis in National Institute of Health and Medical Research (INSERM, Paris), supervised by François Taddei, Dusan Misevic and Julien Bénard-Capelle: Using digital and microbial tools to investigate the evolution of cooperation in biological world
May - July 2009: Research internship in Telethon Institute of Genetics and Medicine (TIGEM, Naples, Italy), supervised by Diego di Bernardo: Network enrichment analysis from gene expression data, a new tool to understand complex biological networks
June - July 2008: Research internship in National Institute for Research in Computer Science and Control (INRIA, Grenoble), supervised by Hidde de Jong (team Ibis): Analysis of gene expression measurements using reporter genes
2011 - 2014: Frontiers in life science PhD program (FDV, Université Paris Descartes)
2010 - 2011: Interdisciplinary approaches to life science M.Sc (AIV, Université Paris Diderot)
2009 - 2010: Research in computer science M.Sc (MPRI, École Normale Supérieure de Cachan)
2007 - 2009: B.Sc and Master 1 in theoretical computer science (École Normale Supérieure de Lyon)
2005 - 2007: Preparatory classes for entrance to the Grandes Écoles: Mathematics and physics (Lycée Thiers, Marseille)
September 2011 - 2014: Introduction to Matlab, in AIV master program (Université Paris Diderot)
October - December 2013: Introduction to C programming, in Mathematics and Computer Science bachelor program (Université Paris Descartes)
January - May 2012, 2013: Functional programming, in Mathematics and Computer Science bachelor program (Université Paris Descartes)
October - December 2011 - 2013: Computer architecture, in Mathematics and Computer Science bachelor program (Université Paris Descartes)
September 2011: Mathematics refresher, in AIV master program (Université Paris Diderot)
September 2010 - June 2011: Mathematics with Maple, in Preparatory classes for entrance to the Grandes Écoles (Lycée Lakanal, Sceaux)
October 2008 - February 2009: Animation of chess clubs in elementary schools and junior high schools (Lyon Olympique Échecs, Lyon)
Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria (2018). A. Frénoy, S. Bonhoeffer.PLoS Biology (html or pdf).
Modeling antibiotic treatment in hospitals: A systematic approach shows benefits of combination therapy over cycling, mixing, and mono-drug therapies (2017). B. Tepekule, H. Uecker, I. Derungs, A. Frénoy, S. Bonhoeffer.PLoS Computational Biology (html or pdf).
Second-order cooperation: Cooperative offspring as a living public good arising from second-order selection on non-cooperative individuals (2017). A. Frénoy, F. Taddei, D. Misevic.Evolution (html or pdf).
Discovery and function of a general core hormetic stress response in E. coli induced by sublethal concentrations of antibiotics (2016). A. Mathieu, S. Fleurier, A. Frénoy, J. Dairou, M.-F. Bredeche, P. Sanchez-Vizuete, X. Song, I. Matic.Cell Reports (html or pdf).
Shape matters: Lifecycle of cooperative patches promotes cooperation in bulky populations (2015). D. Misevic, A. Frénoy, A.B. Lindner, F. Taddei.Evolution (html or pdf).
Second order selection pressures promoting the evolution and maintenance of cooperation in microbial and in silico systems (2014), PhD thesis(pdf).
Genetic architecture promotes the evolution and maintenance of cooperation (2013). A. Frénoy, F. Taddei, D. Misevic.PLoS Computational Biology (html or pdf).
In silico evolution of transferable genetic elements (2013). D. Misevic, A. Frénoy, F. Taddei.In ECAL 2013: Proceedings of the twelfth European Conference on the Synthesis and Simulation of Living Systems (pdf).
Effects of public good properties on the evolution of cooperation (2012). D. Misevic, A. Frénoy, D.P. Parsons, F. Taddei.In Artificial Life XIII: Proceedings of the Thirteenth International Conference on the Simulation and Synthesis of Living Systems (pdf).
Robustness and evolvability of cooperation (2012). A. Frénoy, F. Taddei, D. Misevic.In Artificial Life XIII: Proceedings of the Thirteenth International Conference on the Simulation and Synthesis of Living Systems (pdf).