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5. Farming plant cooperation in crops

Author

Montazeaud, Germain, Rousset, François, Fort, Florian, Violle, Cyrille, Fréville, Hélène, and Gandon, Sylvain

Published
2020

6. Resampling: an improvement of Importance Sampling in varying population size models

Author

Merle, Coralie, Leblois, Raphaël, Rousset, François, and Pudlo, Pierre

Subjects
Mathematics - Statistics Theory, Mathematics - Probability, Statistics - Applications, Statistics - Computation, Statistics - Methodology
Abstract

Sequential importance sampling algorithms have been defined to estimate likelihoods in models of ancestral population processes. However, these algorithms are based on features of the models with constant population size, and become inefficient when the population size varies in time, making likelihood-based inferences difficult in many demographic situations. In this work, we modify a previous sequential importance sampling algorithm to improve the efficiency of the likelihood estimation. Our procedure is still based on features of the model with constant size, but uses a resampling technique with a new resampling probability distribution depending on the pairwise composite likelihood. We tested our algorithm, called sequential importance sampling with resampling (SISR) on simulated data sets under different demographic cases. In most cases, we divided the computational cost by two for the same accuracy of inference, in some cases even by one hundred. This study provides the first assessment of the impact of such resampling techniques on parameter inference using sequential importance sampling, and extends the range of situations where likelihood inferences can be easily performed.

Published
2016

7. Dismantling the Mantel tests

Author

Guillot, Gilles and Rousset, François

Subjects
Quantitative Biology - Populations and Evolution
Abstract

The simple and partial Mantel tests are routinely used in many areas of evolutionary biology to assess the significance of the association between two or more matrices of distances relative to the same pairs of individuals or demes. Partial Mantel tests rather than simple Mantel tests are widely used to assess the relationship between two variables displaying some form of structure. We show that contrarily to a widely shared belief, partial Mantel tests are not valid in this case, and their bias remains close to that of the simple Mantel test. We confirm that strong biases are expected under a sampling design and spatial correlation parameter drawn from an actual study. The Mantel tests should not be used in case auto-correlation is suspected in both variables compared under the null hypothesis. We outline alternative strategies. The R code used for our computer simulations is distributed as supporting material.

Published
2011

24. A widespread family of phage-inducible chromosomal islands only steals bacteriophage tails to spread in nature

Author

Rousset, François, Depardieu, Florence, Miele, Solange, Dowding, Julien, Laval, Anne-Laure, Lieberman, Erica, Garry, Daniel, Rocha, Eduardo P.C., Bernheim, Aude, Bikard, David, Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), This work was supported by grants MR/M003876/1, MR/V000772/1, and MR/S00940X/1 from the Medical Research Council (UK), BB/N002873/1, BB/V002376/1, BB/V009583/1, and BB/S003835/1 from the Biotechnology and Biological Sciences Research Council (BBSRC, UK), ERC-ADG-2014 Proposal no. 670932 Dut-signal (from EU), and Wellcome Trust 201531/Z/16/Z to J.R.P., and grants INCEPTION project (PIA/ANR-16-CONV-0005), Equipe FRM (Fondation pour la Recherche Médicale): EQU201903007835, Laboratoire d’Excellence IBEID Integrative Biology of Emerging Infectious Diseases (ANR-10-LABX-62-IBEID), and SALMOPROPHAGE ANR-16-CE16-0029 to E.P.C.R. L.M.-R. was the recipient of a Spanish postdoctoral fellowship from the Fundación Ramón Areces (2018–2020). A.F.-S. is the recipient of a fellowship from Imperial College., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CE12-0029,Salmo_prophages,Co-évolution des génomes bactériens et de leurs prophages: cooptation des prophages et conversion lysogenique chez Salmonella(2016), European Project: 670932,H2020,ERC-2014-ADG,DUT-signal(2015), University of Glasgow, King Saud Bin Abdulaziz University for Health Sciences [Riyadh] (KSAU-HS), Imperial College London, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), National University of Singapore (NUS), This work was supported by grants MR/M003876/1, MR/V000772/1 and MR/S00940X/1 from the Medical Research Council (UK), BB/N002873/1, BB/V002376/1 and BB/S003835/1 from the Biotechnology and Biological Sciences Research Council (BBSRC, UK), ERC-ADG-2014 Proposal n° 670932 Dut-signal (from EU), and Wellcome Trust 201531/Z/16/Z to JRP, and grants INCEPTION project (PIA/ANR-16-CONV-0005), Equipe FRM (Fondation pour la Recherche Médicale): EQU201903007835, Laboratoire d’Excellence IBEID Integrative Biology of Emerging Infectious Diseases [ANR-10-LABX-62-IBEID], and SALMOPROPHAGE ANR-16-CE16-0029 to EPCR., and ANR-05-GANI-0001,GenOvul,Exploitation de la variabilité génétique intra et inter-espèces pour l'étude du déterminisme génétique du taux d'ovulation(2005)

Subjects
small capsid formation, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV]Life Sciences [q-bio], packaging, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Microbiology, tail, bacteriophage, Virology, Parasitology, convergent evolution, pathogenicity islands, gene transfer, PICI
Abstract

Phage satellites interfere with helper phage packaging through the production of small-capsids, where only satellites can be packaged. So far, in all the analysed systems, the satellite-sized capsids are composed of phage proteins. Here we report the first demonstration that a family of phage-inducible chromosomal island (PICIs), a type of satellites, encodes all the proteins required for both the production of the small-sized capsids and the exclusive packaging of the PICIs into these capsids. Therefore, this new family, that we have named cf-PICIs (capsid forming PICIs), only requires phage tails to generate infective PICI particles. Remarkably, the representative cf-PICI reproduces without cost for their helper phages, suggesting that the relationship between these elements is not parasitic but commensalistic. Finally, our phylogenomic studies indicate that cf-PICIs are present both in Gram-positive and Gram-negative bacteria and have evolved at least three times independently to spread widely into the satellite universe.

Published
2022

25. Phages and their satellites encode hotspots of antiviral systems

Author

Rousset, François, primary, Depardieu, Florence, additional, Miele, Solange, additional, Dowding, Julien, additional, Laval, Anne-Laure, additional, Lieberman, Erica, additional, Garry, Daniel, additional, Rocha, Eduardo P.C., additional, Bernheim, Aude, additional, and Bikard, David, additional

Published
2022
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36. Are Host Genetics the Predominant Determinant of Persistent Nasal Staphylococcus aureus Carriage in Humans?

Author

Ruimy, Raymond, Angebault, Cécile, Djossou, Félix, Dupont, Claire, Epelboin, Loïc, Jarraud, Sophie, Lefevre, Laurence Armand, Bes, Michèle, Lixandru, Brandusa Elena, Bertine, Mélanie, Miniai, Assiya El, Renard, Magaly, Bettinger, Régis Marc, Lescat, Mathilde, Clemont, Olivier, Peroz, Gilles, Lina, Gerard, Tavakol, Mehri, Vandenesch, François, van Belkum, Alex, Rousset, François, and Andremont, Antoine

Published
2010

38. Emergence and Dissemination of Extended-Spectrum β-Lactamase—Producing Escherichia coli in the Community: Lessons from the Study of a Remote and Controlled Population

Author

Woerther, Paul-Louis, Angebault, Cécile, Lescat, Mathilde, Ruppé, Etienne, Skurnik, David, Mniai, Assiya El, Clermont, Olivier, Jacquier, Hervé, Costa, Anaelle Da, Renard, Magaly, Bettinger, Régis Marc, Epelboin, Loïc, Dupont, Claire, Guillemot, Didier, Rousset, François, Arlet, Guillaume, Denamur, Erick, Djossou, Félix, and Andremont, Antoine

Published
2010

43. Correction

Author

Lehmann, Laurent, Rousset, François, Roze, Denis, and Keller, Laurent

Published
2007
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47. The impact of genetic diversity on gene essentiality within the E. coli species

Author

Rousset, François, Caballero, José, Piastra-Facon, Florence, Fernández-Rodríguez, Jesús, Clermont, Olivier, Denamur, Erick, Rocha, Eduardo, Bikard, David, Biologie de Synthèse - Synthetic biology, Institut Pasteur [Paris] (IP), Collège Doctoral, Sorbonne Université (SU), Eligo Bioscience, Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 677823), by the French Government’s Investissement d’Avenir programme and by Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (ANR-10-LABX-62-IBEID). F.R. is supported by a doctoral scholarship from Ecole Normale Supérieure. E.D. was partially supported by the ‘Fondation pour la Recherche Médicale’ (Equipe FRM 2016, grant no. DEQ20161136698). E.P.C.R. was partially supported by the ‘Fondation pour la Recherche Médicale’ (Equipe FRM EQU201903007835)., We thank B. Dupuy for sharing the use of the anaerobic chamber, as well as O. Tenaillon, P.-A. Kaminsky, G. Sezonov, A. Danchin and A. Calvo-Villamañan for useful discussions. We thank the P2M platform (Institut Pasteur, Paris, France) for genome sequencing and V. Briolat from the Biomics platform, C2RT, Institut Pasteur, Paris, France, supported by France Génomique (ANR-10-INBS-09-09) and IBISA. We also thank J. Rodríguez-Beltrán and S. Brisse for providing a strain of Citrobacter freundii and Klebsiella pneumoniae, respectively, ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 677823,H2020,ERC-2015-STG,CRISPAIR(2016), Bikard, David, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Study of the interplay between CRISPR interference and DNA repair pathways towards the development of novel CRISPR tools - CRISPAIR - - H20202016-03-01 - 2021-02-28 - 677823 - VALID, Institut Pasteur [Paris], Collège doctoral [Sorbonne universités], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Université Sorbonne Paris Nord, and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)

Subjects
MESH: Gene Expression, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: DNA Transposable Elements, MESH: Genetic Fitness, MESH: Escherichia coli, MESH: Species Specificity, MESH: Genetic Variation, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Genome, Bacterial, MESH: Phylogeny, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Genes, Essential
Abstract

International audience; Bacteria from the same species can differ widely in their gene content. In E. coli, the set of genes shared by all strains, known as the core genome, represents about half the number of genes present in any strain. While recent advances in bacterial genomics have unraveled genes required for fitness in various experimental conditions at the genome scale, most studies have focused on single model strains. As a result, the impact of this genetic diversity on core processes of the bacterial cell remains largely under-investigated. Here, we developed a new CRISPR interference platform for highthroughput gene repression that is compatible with most E. coli isolates and closely-related species. We applied it to assess the importance of ~3,400 nearly ubiquitous genes in 3 growth conditions in 18 representative E. coli strains spanning most common phylogroups and lifestyles of the species. Our screens revealed extensive variations in gene essentiality between strains and conditions. Investigation of the genetic determinants for these variations highlighted the importance of epistatic interactions with mobile genetic elements. In particular, we showed how prophage-encoded defense systems against phage infection can trigger the essentiality of persistent genes that are usually nonessential. This study provides new insights into the evolvability of gene essentiality and argues for the importance of studying various isolates from the same species under diverse conditions.

Published
2021

49. Laminar-turbulent transition regimes in the conical Taylor-Couette flow system

Author

Yahi Fatma, Bouabdallah Ahcene, Hamnoune Yasmina, Botton Valéry, Henry Daniel, Millet Séverine, Rousset François, and Adachi Takahiro

Subjects
Physics, QC1-999
Abstract

The present work is intended to experimentally study the Taylor-Couette flow between coaxial cones. The inner cone is rotated and the outer cone is maintained fixed. Both cones have the same apex angle Φ =12°, giving a constant annular gap δ =0.12. The height of the fluid column is H=155 mm. The working fluid is assumed as Newtonian and has constant properties (as density and viscosity) within the range of the required experimental conditions. By means of visualization techniques, the critical thresholds related to the onset of various instabilities have been obtained and the corresponding flow modes have been identified. Using images processing, spatio-temporal diagrams have also been calculated, showing the characteristics (wavelength, drift velocity) of the downward helical motion. The results obtained for these transition regimes are compared to those of Wimmer et al. [1-3].

Published
2017
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