Systems biology takes a holistic approach to biological questions as it applies mathematical modeling to link and understand the interaction of components in complex biological systems. Multiscale modeling is the only method that can fully accomplish this aim. Mutliscale models consider processes at different levels that are coupled within the modeling framework. A first requirement in creating such models is a clear understanding of processes that operate at each level. This research focuses on modeling aspects of biological development as a complex process that occurs at many scales. Two of these scales were considered in this work: cellular differentiation, the process of in which less specialized cells acquired specialized properties of mature cell types, and morphogenesis, the process in which an organism develops its shape and tissue architecture. In development, cellular differentiation typically is required for morphogenesis. Therefore, cellular differentiation is at a lower scale than morphogenesis in the overall process of development. In this work, cellular differentiation and morphogenesis were modeled in a variety of biological contexts, with the ultimate goal of linking these different scales of developmental events into a unified model of development. Three aspects of cellular differentiation were investigated, all united by the theme of how the dynamics of gene regulatory networks (GRNs) control differentiation. Two of the projects of this dissertation studied the effect of noise and robustness in switching between cell types during differentiation, and a third deals with the evaluation of hypothetical GRNs that allow the differentiation of specific cell types. All these projects view cell types as highdimensional attractors in the GRNs and use random Boolean networks as the modeling framework for studying network dynamics. Morphogenesis was studied using the emergence of three-dimensional structures in biofilms as a relatively simple model. Many strains of bacteria form complex structures during growth as colonies on a solid medium. The morphogenesis of these structures was modeled using an agent-based framework and the outcomes were validated using structures of biofilm colonies reported in the literature.

Technology, nowadays, has given us huge computational potential, but computer sciences have major problems tapping into this pool of resources. One of the main issues is how to program and design distributed systems. Biology has solved this issue about half a billion years ago, during the Cambrian explosion: the evolution of multicellularity. The evolution of multicellularity allowed cells to differentiate and so divide different tasks to different groups of cells; this combined with evolution gives us a very good example of how massively parallel distributed computational system can function and be “programmed”. However, the evolution of multicellularity is not very well understood, and most traditional methodologies used in evolutionary theory are not apt to address and model the whole transition to multicellularity. In this thesis I develop and argue for new computational artificial life methodologies for the study of the evolution of multicellularity that are able to address the whole transition, give new insights, and complement existing methods. I argue that these methodologies should have three main characteristics: accessible across scientific disciplines, have potentiality for complex behaviour, and be easy to analyse. To design models, which possess those characteristics, I developed a model of genetic regulatory networks (GRNs) that control artificial cells, which I have used in multiple evolutionary experiments. The first experiment was designed to present some of the engineering problems of evolving multicelled systems (applied to graph-colouring), and to perfect my artificial cell model. The two subsequent experiments demonstrate the characteristics listed above: one model based on a genetic algorithm with an explicit two-level fitness function to evolve multicelled cooperative patterning, and one with freely evolving artificial cells that have evolved some multicelled cooperation as evidenced by novel measures, and has the potential to evolve multicellularity. These experiments show how artificial life models of evolution can discover and investigate new hypotheses and behaviours that traditional methods cannot.

Two major roadblocks in synthetic biology are the difficulties associated with the physical assembly of gene regulatory networks (GRNs) and the lack of characterized biological parts. In this work we aimed to address both of these issues. We developed a novel method for the assembly of GRNs called Brick- Mason assembly. We have shown that the method can assemble a 6 part network in a single day and provides significant advancements over traditional cloning methods. We used BrickMason to assemble GRNs that would allow us to compare natural yeast mechanisms of repression to the steric hindrance based mechanisms that are commonly used in synthetic GRNs in yeast. Our results show that the two mechansisms of repression are not equivalent. This finding opens possibilities for using a new class of repressor in a synthetic context in yeast.

Epithelial-mesenchymal transitions (EMTs) are fundamental and indispensable to embryonic morphogenesis throughout the animal kingdom. At the onset of gastrulation in the sea urchin embryo, micromere-derived primary mesenchyme cells (PMCs) undergo an EMT process to ingress into the blastocoel, and these cells later become the larval skeleton. Much has been learned about PMC specification in sea urchin embryos. However, much less is known about how states of the sequentially progressing PMC gene regulatory network (GRN) controls the EMT process during PMC ingression. Transcriptional regulators such as Snail and Twist have emerged as important molecules for controlling EMTs in many model systems. Sea urchin snail and twist genes were cloned from Lytechinus variegates, and each has been experimentally connected to the PMC regulatory network; these experiments demonstrate several requirements for PMC ingression, and in doing so, begin to illustrate how a gene regulatory network state controls morphogenesis. Functional knockdown analyses of Snail with morpholino-substituted antisense oligonucleotides (MASO) in whole embryos and chimeras demonstrated that Snail is required in micromeres for PMC ingression. Investigations also show that Snail downregulates cadherin expression as an evolutionarily conserved mechanism, and Snail positively regulates a required endocytic clearance of epithelial membrane molecules during EMT. Perturbation experiments indicate that Twist has accessory roles in regulating PMC ingression, and possibly plays a maintenance role in PMC specification network state. In addition, Twist also functions in the post-EMT network state, particularly in directing PMC differentiation and skeletogenesis. The recently annotated sea urchin genome accelerates the discovery of new genes and holds strong promise of mapping out a complete canvas of the micromere-PMC gene regulatory network. Using the genome resources we successfully cloned several newly identified PMC genes, and found most of them to be expressed in micromeres just prior to ingression of the nascent PMCs. Current experiments focus on the roles of these genes in preparing for, executing, and/or controlling the mesenchymal behavior following PMC ingression. The functions and inter-relationships of these genes will greatly augment our understanding of how a gene regulatory network state controls a crucial morphogenetic event. / Dissertation

Two major roadblocks in synthetic biology are the difficulties associated with the physical assembly of gene regulatory networks (GRNs) and the lack of characterized biological parts. In this work we aimed to address both of these issues. We developed a novel method for the assembly of GRNs called Brick- Mason assembly. We have shown that the method can assemble a 6 part network in a single day and provides significant advancements over traditional cloning methods. We used BrickMason to assemble GRNs that would allow us to compare natural yeast mechanisms of repression to the steric hindrance based mechanisms that are commonly used in synthetic GRNs in yeast. Our results show that the two mechansisms of repression are not equivalent. This finding opens possibilities for using a new class of repressor in a synthetic context in yeast.

Two major roadblocks in synthetic biology are the difficulties associated with the physical assembly of gene regulatory networks (GRNs) and the lack of characterized biological parts. In this work we aimed to address both of these issues. We developed a novel method for the assembly of GRNs called Brick- Mason assembly. We have shown that the method can assemble a 6 part network in a single day and provides significant advancements over traditional cloning methods. We used BrickMason to assemble GRNs that would allow us to compare natural yeast mechanisms of repression to the steric hindrance based mechanisms that are commonly used in synthetic GRNs in yeast. Our results show that the two mechansisms of repression are not equivalent. This finding opens possibilities for using a new class of repressor in a synthetic context in yeast.

La régénération est un mode de développement, qui suite à un stresse physique permet de reformer à l’identique des structures biologiques initialement développer au cours de l’embryogénèse. De plus ce phénomène, plus ou moins important en fonction des organismes, est néanmoins répandu chez les métazoaires, suggérant ainsi une origine monophylogénique. D’où l’hypothèse d’un lien étroit entre la régénération et l’embryogénèse. En me basant sur cette hypothèse j’ai employé comme modèle pendant ma thèse, l’anémone de mer Nematostella vectensis. Ce modèle cnidaire offre effectivement l’opportunité unique de comparer la régénération d’un corps entier, dite extrême, à l’embryogénèse et ainsi étudier leurs liens au niveau moléculaire. Initialement établie entant que modèle d’embryologie permettant d’étudier l’évolution des réseaux de régulation génétique (RRG) orchestrant les moments clé de l’embryogénèse et s’imposer en tant que modèle d’étude de la régénération extrême. Tout d’abord, au cours de ma thèse j’ai participé à caractérisation tissulaire et cellulaire de la régénération de ce model afin d’en établir un répertoire de référence des étapes clés. En employant ce répertoire et le criblage de 80 d’inhibiteur de kinase, j’ai pu identifier plusieurs voies de signalisation régissant différente étape de la régénération, impliquant les MAPKs, JNK et ERK ainsi que plusieurs récepteurs de facteurs de croissances. Notamment ERK a également été décrit dans le processus de gastrulation chez Nematostella, dont j’ai contribué à l’établissement du RRG associé. C’est donc en me basant sur ce RRG et une base de donnée transcriptomic complète de la régénération de ce modèle, que j’ai pu établir le RRG en aval de ERK associé à la régénération. Par cette approche j’ai pu démontrer la relation au niveau moléculaire entre ces processus développementaux et surtout identifier des aspects spécifiques à la régénération. / Regeneration is a developmental process, which allow to regrow missing structures initially develop during embryogenesis, in response to an injury. Although, this ability to regenerate can be more or less dramatic depending on the organism, it is widely spread among metazoan. As such, suggesting a monophyletic origin and a tight link with embryogenesis has also been hypothesized. Based on this hypothesis, I used during my thesis the sea anemone Nematostella vectensis, a cnidarian model offers the unique opportunity to compare, whole body regeneration and embryogenesis to investigate their molecular links. In fact, Nematostella was established as an embryonic model to investigate evolution of gene regulatory network (GRN) underlying key stages e.g. gastrulation, but recently it has been a rising model to study whole body regeneration. I started to my thesis by carefully characterizing hallmarks of Nematostella regeneration starting from tissular to molecular level, establishing a comprehensive regeneration time line. By taking advantage of this tool, in association to the screening of 80 kinases inhibitors, I have identify several signaling pathways regulating various steps of regeneration in Nematostella, including the MAPK ERK, JNK and growth factor receptors. In parallel I participated to the study of ERK role during Nematostella gastrulation and the underpinning (GRN). Which offered a solid groundwork for the comparison with regeneration at the GRN level. Combining a candidate approach based on the embryonic GRN and a global transcriptomic analysis of regeneration, I have been able to bring evidence on the relationship between embryogenesis and regeneration and additionally to identify regeneration specific aspects.

No description available.

No description available.

Les dégénérescences lobaires fronto-temporale (DLFT) sont des démences neurodégénératives rares. 30-50% des DLFT a une cause génétique, la plupart sont des mutations des gènes C9orf72 et progranuline (GRN). L'objectif de la thèse a été d'élargir le spectre mutationnel et phénotypique des mutations GRN. Nous avons identifié les premières délétions partielles du gène GRN chez des patients avec progranulinémie baisse (la progranulinémie est abaissée en cas de mutation), mais sans mutation détectée par séquençage. Nous avons contribué à élargir le spectre clinique de la maladie en décrivant un phénotype d'atrophie corticale postérieure et des lésions de la substance blanche cérébrale chez des patients GRN, caractéristique évocatrice de cette forme génétique. Enfin, nous avons étudié la phase présymptomatique de la maladie, alors que se développent les premiers essais thérapeutiques, par une approche longitudinale avec IRM et TEP-FDG. Le métabolisme cérébral est réduit dans le lobe temporal latéral gauche 20 ans avant l'apparition des symptômes et, après 20 mois, dans les régions frontales et l'épaisseur corticale dans les régions temporales gauche. Le lobe temporal latéral pourrait être donc l'"épicentre " de la maladie, et le processus lésionnel pourrait, secondairement, progresser vers les régions frontales. J'ai également contribué à définir les phénotypes associés aux mutations de gènes plus rares de DLFT/DLFT-SLA. TARDBP est associé à un large spectre phénotypique; TBK1 est caractérisé par une démence sémantique ou aphasie non fluent associés à l'atteinte de la corne antérieure. Cette étude importante souligne le rôle de ces mutations dans le spectre clinique des DLFT. / Frontotemporal lobar degeneration (FTLD) are rare neurodegenerative dementias. 30-50% of FTLD has a genetic cause, most are mutations in C9orf72 and in progranulin gene (GRN). The aim of the thesis was to expand the mutational and phenotypic spectrum of GRN mutations. We identified the first partial deletions of GRN gene in patients with low plasmatic progranulin (the plasmatic progranulin is low in case of mutation), but without mutation detected by sequencing. We contributed to expand the clinical spectrum of the disease by describing a posterior cortical atrophy phenotype and lesions of the cerebral white matter in GRN patients, evocative feature of this genetic form. Finally, we studied the presymptomatic stage of the disease, while the first clinical trials develop, for a longitudinal approach with MRI and FDG-PET. The cerebral metabolism is reduced in the left temporal lobe 20 years before clinical onset and, after 20 months, the metabolism is reduced in the frontal regions and the cortical thickness in the left temporal regions. The lateral temporal lobe could thus be the "epicenter" of the disease, and the lesional process could secondarily progress towards the frontal regions. I also contributed to define the phenotypes associated with rare gene mutations in FTLD/FTLD-ALS. TARDBP is associated with a wide phenotypic spectrum; TBK1 is characterized by semantic dementia or not fluent aphasia associated with involvement of the anterior horn. This important study highlights the role of these mutations in the clinical spectrum of FTLD.