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Thèse De Doctorat De L'université Pierre Et Marie Curie Laboratoire Thèse de doctorat de l’université Pierre et Marie Curie Ecole doctorale de Chimie Physique et Chimie Analytique de Paris-Centre Laboratoire Colloïdes et Matériaux Divisés Sujet de thèse : Cultures multi-parallélisées en millifluidique digitale : diversité et sélection artificielle Présentée par : Jean-Baptiste Dupin Soutenue le 15 juin 2018 Devant le Jury composé de : M. Jean-Marie François Rapporteur M. Pascal Panizza Rapporteur Mme Valérie Pichon Présidente du Jury Mme Silvia De Monte Examinatrice M. Hicham Ferhout Invité M. Jérôme Bibette Directeur de thèse M. Jean Baudry Co-encadrant 2 Remerciements Un long chemin a été parcouru pendant ces trois ans et demi de thèse au Laboratoire Colloïdes et Matériaux Divisés et je souhaite ici remercier toutes les personnes que j’ai pu rencontrer au cours de mes recherches, qui m’ont conseillé et entouré au laboratoire comme en dehors. Je remercie tout d’abord Jérôme Bibette pour m’avoir accueilli au LCMD sur un sujet, certes risqué, mais qui me motivait énormément. En tant que directeur de thèse, il a su me guider dans les directions que devaient prendre ma thèse tout en me laissant une très grande autonomie. Son accompagnement bienveillant et sa confiance m’ont laissé apprécier les avancées concluantes des travaux et m’ont ainsi fait progresser dans ma réflexion scientifique. Je tiens aussi à remercier Jean Baudry et Nicolas Bremond de qui le suivi continu et les échanges autour de la biologie, de l’instrumentation et de l’hydrodynamique m’ont été très profitables. Je remercie ensuite chacun des membres du jury de ma soutenance de thèse pour leur lecture critique et l’appréciation précieuse qu’ils ont porté sur ce travail mêlant physico-chimie, théorie de l’évolution et microbiologie : Valérie Pichon pour m’avoir fait l’honneur de présider mon jury, Jean-Marie François et Pascal Panizza pour avoir accepté la tâche d’être rapporteurs, et enfin Silvia De Monte et Hicham Ferhout pour l’intérêt qu’ils ont porté à mon travail. Je remercie Florence Condamine, technicienne au LCMD, dont le travail rythme celui du laboratoire et dont la disponibilité, la prévenance et l’organisation efficace sont des atouts certains pour l’équipe. Je remercie également Ankur Chaurasia, post-doctorant venu développer avec moi, lors de la seconde moitié de ma thèse, la technologie dont elle est l’aboutissement. Je remercie aussi Wilfried Sire, doctorant venu compléter notre duo sur le sujet pendant la rédaction de ce manuscrit. Pour leur accompagnement, leur soutien technologique et leurs conseils, je remercie Denis Cottinet, Jairo Garnica Rodrigez et Laurent Boitard, qui ont su m’accorder de leur temps avant de se dédier au lancement de la start-up Millidrop. Pour leurs discussions intéressantes et leur aide sur les questions d’évolution microbiologique, je remercie les membres du groupe de laboratoire financé par le HSFP autour de ces thématiques. Je pense notamment à Arjan de Visser, à Paul Rainey et aux membres du laboratoire Génétique de l’Evolution tels que Maxime et Guilhem. Je remercie d’ailleurs les stagiaires qui ont ponctuellement pu m’aider au développement de la technologie millifluidique : Victoria Vilchez, Théo Martel et Alexis Barthet. Je remercie les différentes personnes que j’ai pu rencontrer et côtoyer au LCMD. Je pense à Isabelle et Hélène qui facilitèrent considérablement nos démarches administratives. Je pense à Klaus et Sylvie qui partagèrent avec moi leur bureau. Je pense aux différents autres doctorants qui vécurent au laboratoire durant ma thèse : Fanny, Hugo, Perrine, Julie, Rory, Léopold, Anna, Edouard, Mathieu, Abdulwahed, Erwan, Wafa, Pablo, Aurore, Bettina, Léo et Arthur. Je pense aussi aux différentes 3 personnes, post-doctorants, startuppeurs, stagiaires, ingénieurs qui animèrent la vie du laboratoire : Lianmei, Annette, Ladislav, Koceila, Gabriel, Krzystof, Hojjat, Andrzej, Moshen, Coralie, Marie, Abdelfateh, Todor, Alicia, Asma, Karima, Ludivine, Jamie, Damien, Bernard, Gwenaëlle, Noushin, Eren, Joaquim, Mira, Magda, Millie, Guilhem, Amandine, Jérôme, et Florence A. Merci à tous ! Je remercie tous mes amis de l’ESPCI et mes amis parisiens qui ont su me soutenir pendant cette période intense. Je remercie enfin mes parents, mes grands-parents et mes deux sœurs pour leur soutien indéfectible depuis 28 ans. 4 Sommaire Remerciements ............................................................................................................................................................... 3 Sommaire ........................................................................................................................................................................ 5 Introduction ................................................................................................................................................................... 9 I Compréhension et gestion de la diversité .......................................................................................................13 I.1 Théorie de l'évolution, sélection naturelle des populations ................................................................13 I.1.A Histoire de l'idée d'évolution : la question de la diversité du vivant ........................................13 I.1.A.1 Des origines à l’acceptation de la question de l’évolution ....................................................13 I.1.A.2 La théorie de Lamarck et les conditions de l'évolution .........................................................15 I.1.A.3 Darwin et la Sélection naturelle .................................................................................................16 I.1.A.4 Vers une théorie synthétique de l'évolution ............................................................................17 I.1.A.5 Dernières découvertes et relativité de la théorie synthétique de l’évolution ......................18 I.1.B Les Clefs de l’évolution ...................................................................................................................19 I.1.B.1 La dérive génétique .....................................................................................................................19 I.1.B.1.1 L’effet fondateur ....................................................................................................................20 I.1.B.1.2 L’effet d’étranglement ...........................................................................................................20 I.1.B.1.3 La diversité spécifique ..........................................................................................................21 I.1.B.1.4 Diminution systématique de la diversité : Théorie neutre de l’évolution et de la coalescence .................................................................................................................................................22 I.1.B.2 Fécondation non aléatoire .........................................................................................................23 I.1.B.3 Le flux génique ............................................................................................................................23 I.1.B.4 Les sources de diversité : notion de mutation ........................................................................25 I.1.B.5 La sélection ...................................................................................................................................27 I.1.B.5.1 Un facteur de l’évolution ......................................................................................................27 I.1.B.5.2 Impact sur la diversité ...........................................................................................................28 I.1.B.5.3 Formes de sélection ..............................................................................................................29 I.1.B.5.4 Compétition entre sélection naturelle et sélection aléatoire ...........................................29 I.1.B.5.5 La sélection artificielle ..........................................................................................................30 I.1.B.6 La diversité en question ..............................................................................................................31 I.2 Microbiologie et évolution .......................................................................................................................32 I.2.A Présentation de Escherichia coli ........................................................................................................32 I.2.A.1 Les bactéries .................................................................................................................................32 I.2.A.2 Cycle cellulaire bactérien ............................................................................................................34 I.2.A.3 E. coli, modèle de laboratoire .....................................................................................................34 I.2.B L’adaptabilité de E. coli ....................................................................................................................35 I.2.B.1 Valeur sélective (fitness) .............................................................................................................35 I.2.B.2 Variabilité et diversifications : du bruit non héritable aux mutations génétiques .............37 I.2.B.3 Evolution microbiologique en laboratoire ..............................................................................38 I.2.C Stress antibiotique
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