Background: Replacement of dysfunctional β-cells in the islets of Langerhans by transdifferentiation of pancreatic acinar cells has been proposed as a regenerative therapy for diabetes. Adult acinar cells spontaneously revert to a multipotent state upon tissue dissociation in vitro and can be stimulated to redifferentiate into β-cells. Despite accumulating evidence that contact-mediated signals are involved, the mechanisms regulating acinar-to-islet cell transdifferentiation remain poorly understood. Results: In this study, we propose that the crosstalk between two contact-mediated signaling mechanisms, lateral inhibition and lateral stabilization, controls cell fate stability and transdifferentiation of pancreatic cells. Analysis of a mathematical model combining gene regulation with contact-mediated signaling reveals the multistability of acinar and islet cell fates. Inhibition of one or both modes of signaling results in transdifferentiation from the acinar to the islet cell fate, either by dedifferentiation to a multipotent state or by direct lineage switching. Conclusions: This study provides a theoretical framework to understand the role of contact-mediated signaling in pancreatic cell fate control that may help to improve acinar-to-islet cell transdifferentiation strategies for β-cell neogenesis.

Background: Replacement of dysfunctional β-cells in the islets of Langerhans by transdifferentiation of pancreatic acinar cells has been proposed as a regenerative therapy for diabetes. Adult acinar cells spontaneously revert to a multipotent state upon tissue dissociation in vitro and can be stimulated to redifferentiate into β-cells. Despite accumulating evidence that contact-mediated signals are involved, the mechanisms regulating acinar-to-islet cell transdifferentiation remain poorly understood. Results: In this study, we propose that the crosstalk between two contact-mediated signaling mechanisms, lateral inhibition and lateral stabilization, controls cell fate stability and transdifferentiation of pancreatic cells. Analysis of a mathematical model combining gene regulation with contact-mediated signaling reveals the multistability of acinar and islet cell fates. Inhibition of one or both modes of signaling results in transdifferentiation from the acinar to the islet cell fate, either by dedifferentiation to a multipotent state or by direct lineage switching. Conclusions: This study provides a theoretical framework to understand the role of contact-mediated signaling in pancreatic cell fate control that may help to improve acinar-to-islet cell transdifferentiation strategies for β-cell neogenesis.

Cette thèse s’intéresse au diagnostic et à l’observation de systèmes linéaires à commutations et à l’application au convertisseur multicellulaire série. L’objectif est de proposer des solutions pour des sous-systèmes non-observables au sens classique et dont des fautes continues ou discrètes peuvent être présentes. Après la présentation d’un état de l’art sur les techniques d’observation et de diagnostic pourles systèmes à commutations, le mémoire est scindé en deux parties. La première partie propose, d’une part, une stratégie d’estimation des états discret et continu d’un système linéaire à commutation soumis à une entrée inconnue. Un observateur hybride basé sur la théorie des modes glissants d’ordre supérieur est développé. D’autre part, deux procédures de diagnostic sont présentées. La première combine un observateur hybride et un diagnostiqueur pour détecter une faute continue. Pour la seconde, un diagnostic actif est défini sur la base de la théorie du test afin de détecter et d’isoler une faute discrète. Dans la seconde partie de ce mémoire, les étapes de la réalisation d’un convertisseur multicellulaire sont détaillées. Ensuite, un chapitre est dédié à la validation des approches théoriques d’observation et de diagnostic sur le convertisseur à trois cellules. Un observateur est synthétisé afin d’estimer les tensions des capacités. Les deux procédures de diagnostic sont appliquées pour la détection d’une variation des valeurs des capacités et le diagnostic de cellules bloquées. Enfin, une commande binaire pour le convertisseur est proposée. L’application de cette stratégie permettra, par la suite, la commande tolérante aux fautes du convertisseur. / This thesis deals with the diagnosis and the observation of a large class of switched linear systems with an application to the multicellular converter. The objective is to provide solutions for non-observable subsystems in the classical sense which can be influenced by continuous or discrete faults. After presenting a state of the art for the observation and diagnostic techniques for switched systems, the report is divided into two parts. The first part provides, in one hand, a strategy for the discrete and continuous states estimation for linear switched system with unknown input. A hybridobserver based on higher order sliding mode is developed. On the other hand, two diagnostic procedures are presented. The first one combines a hybrid observer and a discrete diagnoser to detect a continuous fault. In the second one, an active diagnosis is defined based on the testing theory to detect and isolate a discrete fault. In the second part of this thesis, the different steps to create a multicellular converter are detailed. Then, a chapter is dedicated to the validation of the theoretical approaches for the observation and diagnosis of the three cells converter. An observer is designed to estimate the capacitor voltages. The two proposed diagnosis procedures are applied to detect a change in the capacitance values and to diagnose locked cells. Finally, a binary control for the converter is proposed. The implementation of this strategy will allow, in the future, the fault tolerant control of the converter.

Blastodinium, a genus of the phytoplanktonic dinoflagellates, was found to be inhabiting the gut region of the copepod species Labidocera. Copepods are ubiquitous in aquatic environments, being the most numerous multicellular organisms on planet earth. Being primary consumers, they play important ecological roles, passing energy from one trophic level to the next. As zooplankton, estuarine copepods contribute substantially to carbon cycling as they undergo diurnal migration to avoid daylight UV-B damage and surface water predation. Blastodinium are presumed to infect copepods via ingestion of zoospores by juvenile hosts, who function as microhabitats for acquiring nutrients in non-photosynthetic species or in nutrient-limited environments. Blastodinium may hinder reproduction of copepod hosts, thereby influencing local copepod populations and, by extension, food webs up to humanity. Copepod populations may also help contain disease spread, such as malaria and Dengue fever, through their consumption of mosquito larvae in standing water. Further evaluation of copepods for Blastodinium may help shed light on the limited knowledge of this species and the nature of its relationship with copepods, as well as its effects on copepod populations and the higher order consequences of its parasitism.

The development of shape in multicellular organisms has intrigued human minds for millenia. Empowered by modern genetic techniques, molecular biologists are now striving to not only dissect developmental processes, but to exploit their modularity for the design of custom living systems used in bioproduction, remediation, and regenerative medicine. Currently, our capacity to harness this potential is fundamentally limited by a lack of spatiotemporal control over gene expression in multicellular systems. While several synthetic genetic circuits for control of multicellular patterning have been reported, hierarchical induction of gene expression domains has received little attention from synthetic biologists, despite its fundamental role in biological self-organization. In this thesis, I introduce the first synthetic genetic system implementing population-based AND logic for programmed hierarchical patterning of bacterial populations of Escherichia coli, and address fundamental prerequisites for implementation of an analogous genetic circuit into the emergent multicellular plant model Marchantia polymorpha. In both model systems, I explore the use of bacteriophage T7 RNA polymerase as a gene expression engine to control synthetic patterning across populations of cells. In E. coli, I developed a ratiometric assay of bacteriophage T7 RNA polymerase activity, which I used to systematically characterize different intact and split enzyme variants. I utilized the best-performing variant to build a three-color patterning system responsive to two different homoserine lactones. I validated the AND gate-like behavior of this system both in cell suspension and in surface culture. Then, I used the synthetic circuit in a membrane-based spatial assay to demonstrate programmed hierarchical patterning of gene expression across bacterial populations. To prepare the adaption of bacteriophage T7 RNA polymerase-driven synthetic patterning from the prokaryote E. coli to the eukaryote M. polymorpha, I developed a toolbox of genetic elements for spatial gene expression control in the liverwort: I analyzed codon usage across the transcriptome of M. polymorpha, and used insights gained to design codon-optimized fluorescent reporters successfully expressed from its nuclear and chloroplast genomes. For targeting of bacteriophage T7 RNA polymerase to these cellular compartments, I functionally validated nuclear localization signals and chloroplast transit peptides. For spatiotemporal control of bacteriophage T7 RNA polymerase in M. polymorpha, I characterized spatially restricted and inducible promoters. For facilitated posttranscriptional processing of target transcripts, I functionally validated viral enhancer sequences in M. polymorpha. Taking advantage of this genetic toolbox, I introduced inducible nuclear-targeted bacteriophage T7 RNA polymerase into M. polymorpha. I showed implementation of the bacteriophage T7 RNA polymerase/PT7 expression system accompanied by hypermethylation of its target nuclear transgene. My observations suggest operation of efficient epigenetic gene silencing in M. polymorpha, and guide future efforts in chassis engineering of this multicellular plant model. Furthermore, my results encourage utilization of spatiotemporally controlled bacteriophage T7 RNA polymerase as a targeted silencing system for functional genomic studies and morphogenetic engineering in the liverwort. Taken together, the work presented enhances our capacity for spatiotemporal gene expression control in bacterial populations and plants, facilitating future efforts in synthetic morphogenesis for applications in synthetic biology and metabolic engineering.

Les thérapies anticancéreuses basées sur des principes physiques (radiofréquences, ultrasons, laser, électroporation...) ont considérablement augmenté lors de la dernière décennie. Leurs objectifs sont de détruire directement les cellules cancéreuses, de favoriser l'entrée ciblée de molécules thérapeutiques ou encore de stimuler le système immunitaire du patient afin d'éliminer la tumeur. Le plasma froid suscite l'intérêt dans le domaine de l'oncologie grâce à sa capacité à générer des espèces réactives oxygénées (ROS) et azotées (RNS) qui peuvent être génotoxiques et cytotoxiques pour les cellules cancéreuses. Deux approches d'utilisation du plasma sont étudiées : soit l'exposition directe de cellules au jet plasma, soit l'exposition indirecte via l'utilisation d'un Milieu Activé par Plasma (PAM). Le PAM étant plus facile à délivrer par injection dans la tumeur, c'est cette approche qui est choisie lors de ces travaux. Le travail de thèse présenté consiste à étudier l'effet génotoxique et cytotoxique du PAM, obtenu après exposition du milieu au jet de plasma d'hélium, sur des tumeurs in vitro et in vivo. Pour les études in vitro, nous avons choisi d'utiliser un modèle 3D : le sphéroïde (MCTS - MultiCellular Tumor Spheroid). Ce modèle présente des caractéristiques proches du modèle in vivo grâce à son organisation en sphéroïde. Les MCTS présentent en effet des gradients de pénétration d'oxygène, de nutriments et de prolifération cellulaire. La première partie de la thèse concerne l'identification et la quantification des espèces générées dans le PAM. Les méthodes d'analyses utilisées sont la résonance paramagnétique électronique, la fluorimétrie, la colorimétrie, la chromatographie en phase liquide et la spectrométrie de masse. Ces analyses ont mis en évidence que la toxicité du PAM était due à plusieurs facteurs : d'un côté la génération de ROS et RNS mais aussi à la dégradation des nutriments pour les cellules contenues dans le milieu via par exemple l'oxydation et la nitrosylation des acides aminés. La deuxième partie est dédiée à l'étude des effets du PAM sur les MCTS HCT-116 (cancer du côlon).[...] / Cancer therapies based on physical principles (radiofrequency, ultrasound, laser, electroporation...) have considerably increased in the last decade. Their objectives are to directly destroy cancer cells, to favor the targeted entry of therapeutic molecules or to stimulate the patient's immune system in order to eliminate the tumor. Cold plasma still arouses interest in the field of oncology through its ability to generate reactive oxygen species (ROS) and nitrogen species (RNS) which can be genotoxic and cytotoxic for cancer cells. Two approaches to the use of plasma are studied: either direct exposure of cells to the plasma jet, or indirect exposure via the use of a Plasma Activated Medium (PAM). The PAM being easier to deliver by injection into the tumor, this approach was chosen in this work. The work presented consists in studying the genotoxic and cytotoxic effects of PAM resulting from exposure of the medium to the helium plasma jet on in vitro and in vivo tumors. For in vitro studies, we chose to use a 3D model: the spheroid (MCTS - MultiCellular Tumor Spheroid). This model has similar characteristics to the in vivo model thanks to its spheroidal organization. The spheroids have indeed gradients of oxygen penetration, nutrients and cell proliferation. The first part of the thesis concerns the identification and quantification of the species generated in PAM. The analytical methods used are paramagnetic electronic resonance, fluorimetry, colorimetry, liquid chromatography and mass spectrometry. These analyses revealed that the toxicity of PAM was due to several factors: on the one hand to the generation of ROS and RNS and on the other hand to the degradation of cell nutrients contained in the medium via, for example, the oxidation and nitrosylation of the amino acids. The second part is dedicated to the study of the effects of PAM on HCT-116 (colon cancer) spheroids[...]