This body of work is concerned with the genetics of craniofacial morphology and specifically with that of the cranial sutures which form fibrous articulations between the calvarial bones. The premature fusion of these sutures, known as craniosynostosis, is a common developmental abnormality and has been extensively utilised here as a tool through which to study the genetics of suture morphogenesis and craniofacial diversity. Investigations began with a search for polymorphisms associated with normal variation in human craniofacial characteristics. Denaturing High-Performance Liquid chromatography was used to identify polymorphisms in two genes causative for craniosynostosis by analysing DNA from a large cohort of individuals from four ethnogeographic populations. A single nucleotide polymorphism in fibroblast growth factor receptor 1 was identified as being associated with variation in the cephalic index, a common measure of cranial shape. To further, and specifically, investigate the molecular processes of suture morphogenesis gene expression was compared between unfused and prematurely fusing/fused suture tissues isolated from patients with craniosynostosis. Two approaches, both utilising Affymetrix gene expression microarrays, were used to identify genes differentially expressed during premature suture fusion. The first was a novel method which utilised the observation that explant cells from both fused and unfused suture tissue, cultured in minimal medium, produce a gene expression profile characteristic of minimally differentiated osteoblastic cells. Consequently, gene expression was compared between prematurely fused suture tissues and their corresponding in vitro de-differentiated cells. In addition to those genes known to be involved in suture morphogenesis, a large number of novel genes were identified which were up-regulated in the differentiated in vivo state and are thus implicated in premature suture fusion and in vivo osteoblast differentiation. The second microarray study involved an extensive analysis of 16 suture tissues and compared gene expression between unfused (n=9) and fusing/fused sutures (n=7). Again, both known genes and a substantially large number of novel genes were identified as being differentially expressed. Some of these novel genes included retinol binding protein 4 (RBP4), glypican 3 (GPC3), C1q tumour necrosis factor 3 (C1QTNF3), and WNT inhibitory factor 1 (WIF1). The known functions of these genes are suggestive of potential roles in suture morphogenesis. Realtime quantitative RT PCR (QRT-PCR) was used to verify the differential expression patterns observed for 11 genes and Western blot analysis and confocal microscopy was used to investigate the protein expression for 3 genes of interest. RBP4 was found to be localised on the ectocranial surface of unfused sutures and in cells lining the osteogenic fronts while GPC3 was localised to suture mesenchyme of unfused sutures. A comparison between each unfused suture (coronal, sagittal, metopic, and lambdoid) demonstrated that gene expression profiles are suture-specific which, based on the identification of differentially expressed genes, suggests possible molecular bases for the differential timing of normal fusion and the response of each suture to different craniosynostosis mutations. One observation of particular interest was the presence of cartilage in unfused lambdoid sutures, suggesting a role for chondrogenesis in posterior skull sutures which have generally been thought to develop by intramembranous ossification without a cartilage precursor. Finally, the effects of common media supplements used in in vitro experiments to stimulate differentiation of calvarial suture-derived cells were investigated with respect to their ability to induce in vivo-like gene expression. The response to standard differentiation medium (ascorbic acid + β-glycerophosphate) with and without dexamethasone was measured by both mineralisation and matrix formation assays and QRT-PCR of genes identified in the above described microarray studies. Both media induced collagen matrix and bone nodule formation indicative of differentiating osteoblasts. However, the genes expression profiles induced by both media differed and neither recapitulated the levels and profiles of gene expression observed in vivo for cells isolated from both fused and unfused suture tissues. This study has implications for translating results from in vitro work to the in vivo situation. Significantly, the dedifferentiation microarray study identified differentially expressed genes whose products may be considered candidates as more appropriate osteogenic supplements that may be used during in vitro experiments to better induce in vivo-like osteoblast differentiation. This study has made a substantial contribution to the identification of novel genes and pathways involved in controlling human suture morphogenesis and craniofacial diversity. The results from this research will stimulate new areas of inquiry which will one day aid in the development of better diagnostics and therapeutics for craniosynostosis, and other craniofacial and more general skeletal abnormalities.

Study of cell signalling pathways affected by pathogen entry comprises a fundamental aspect of understanding host-pathogen interactions. In this respect, the current study attempted to ascribe novel roles to Bone Morphogenesis Protein (BMP) signaling during infection. BMP pathway has been majorly studied in context of development where it plays an imperative role and its contribution to immunity has been poorly documented. Subsequent narrative talks about the perturbation of BMP signaling in context of specific signaling networks and its collaboration with other molecular players of host innate armamentarium. There is a pressing need to develop effective chemotherapy against Mycobacterium tuberculosis, the causative agent of tuberculosis, which has garnered the world’s attention as a leading cause of public health emergency. The tyrosine kinase, c-Abl was previously reported to be activated in murine bone marrow derived macrophages infected with mycobacteria. Yet, the identities of host signaling players and mechanisms exploited by mycobacteria in association with c-Abl lacked identification. Here, we deciphered an intricate signaling mechanism linking tyrosine kinase c-Abl, chromatin modifier, lysine acetyl transferase KAT5 and transcription factor, TWIST1 acting at Bmp2 and Bmp4 promoters. This molecular circuitry was observed to affect mycobacterial survival. Emerging studies suggest repurposing of c-Abl inhibitor, Imatinib, as an adjunct to existing anti-tuberculosis therapy. Through the use of Imatinib in an established model of tuberculosis, we demonstrated the ability of c-Abl inhibitors in potentiating innate immune responses. Distinctive instances report the cross regulation among Pattern Recognition Receptors (PRRs). Interestingly, TLR3 signaling cascade induced in response to its cognate ligand was dampened through c-Abl-BMP induced miR27a. TLR3 is known to activate immune surveillance upon viral infections; however, recent studies also suggest its role in tumour regression and induction of apoptosis. Our observation of mycobacteria elicited down regulation of TLR3 pathway corroborated with increased incidences of lung cancer among TB patients and mycobacterial evasion of a well characterized form of cell-death i.e. apoptosis. Further, we utilized a panel of such Mtb mutants associated with virulence and questioned their relevance in the activation of c-Abl-dependent BMP signaling. We found that nitric oxide, hypoxia and carbon monoxide-responsive mycobacterial WhiB3 and DosR, but not the sec-dependent protein secretion pathway, orchestrate mycobacteria driven c-Abl-BMP signaling. Continuing with the theme of exploring roles for BMP signaling during infection, we identified an important role for the C-type Lectin Receptor (CLR), Dectin-2, in activating Candida albicans-driven BMP signaling. Mounting evidences suggest BMP antagonists promote repair and regeneration in cells of varied lineages. We observed a role for BMP signaling in aggravating MMP2 and MMP9, factors that result in chronic non-healing wounds. Wounds are now increasingly recognized as being colonized with fungi along with bacteria. We propose a role for C. albicans orchestrated BMP signaling in contributing to enriched repressive methylation at Egf, Pdgf and Tissue Inhibitors of Matrix Metalloproteases (Timp2/3/4) promoters. Repressive H3K27me3 at these loci impedes the reparative tissue homeostasis, resulting in C. albicans endorsed impaired wound healing. Altogether, we uncovered hitherto unknown roles of BMP signaling during mycobacterial and fungal infections, enabling a better understanding of lesser studied pathways in mediating pathogenesis.

La morphogenèse des plantes repose sur deux mécanismes cellulaires : la division et l'élongation. Par ailleurs, la croissance est source de contraintes mécaniques qui affectent les cellules et guident la morphogenèse. Si les contraintes mécaniques influencent l'orientation du plan de division dans les cellules animales, rien n'est prouvé pour les cellules végétales. À l'heure actuelle, la forme de la cellule est proposée comme le facteur principal gouvernant l'orientation du plan dans les divisions symétriques : les cellules se divisent selon un des plans les plus courts. Cette règle géométrique a été validée dans des tissus à croissance ou courbure isotropes, mais les mécanismes moléculaires sous-jacents demeurent inconnus. Dans cette thèse, un pipeline a été mis au point pour analyser les divisions cellulaires dans les différents domaines du méristème apical caulinaire d'Arabidopsis thaliana et questionner l'application de la règle géométrique dans ce tissu. La zone frontière du méristème présente une proportion anormalement basse de plans de division très courts. Des simulations de tissus en croissance, dans lesquelles une règle de division mécanique a été implémentée, ont montrées le même biais sur les orientation des plans, comparé à la règle géométrique. Des ablations laser de quelques cellules de l'épiderme ont également été effectuées afin de perturber localement le patron de contraintes mécaniques. Les résultats montrent que l'orientation du plan des divisions postérieures à cette perturbation suit le nouveau patron de contraintes. Enfin, une nouvelle méthode quantitative, basée sur l'utilisation d'un micro-indenteur, a été mise au point pour quantifier la réponse du cytosquelette, et en particulier des microtubules, aux contraintes mécaniques. Le protocole de compression a été testé et validé sur les mutants katanin et spiral2, dans lesquels la réponse aux contraintes est respectivement faible ou amplifiée. / Morphogenesis during primary plant growth is driven by cell division and elongation. In turn, growth generates mechanical stress, which impacts cellular events and channels morphogenesis. Mechanical stress impacts the orientation of division plane in single animal cells; this remains to be fully demonstrated in plants. Currently, cell geometry is proposed to be the main factor determining plane orientation in symmetric divisions: cell divide along one the shortest paths. This geometrical rule was tested on tissues with rather isotropic shapes or growth and the corresponding molecular mechanism remains unknown, although it could involve tension within the cytoskeleton. To address these shortcomings, we developed a pipeline to analyze cell divisions in the different domains of the shoot apical meristem of Arabidopsis thaliana. We computed the probability of each possible planes according to cell geometry and compared the output to observed orientations. A quarter of the cells did not follow the geometrical rule. Boundary domain was enriched in long planes aligned with supracellular maximal tension lines. Computer simulations of a growing tissue following a division rule that relies on tension gave the most realistic outputs. Mechanical perturbations of local stress pattern, by laser ablations, further confirmed the importance of mechanical stress in cell division. To explore the role of microtubules in this process, we developed a microindenter-based protocol to quantify the cytoskeletal response to mechanical stress. This protocol was tested and validated in the katanin and spiral2 mutants, in which the response to stress is delayed or promoted respectively.

Esta investigação tece relações comparativas entre padrões de crescimento de redes vasculares e argumenta que no conceito de morfogênese, analogamente à biologia, há evoluções e agrupamentos gerativos em sistemas estruturais ramificados. Para a compreensão deste agrupamento gerativo, são utilizados conceitos adjacentes à geometria fractal - estudo de estruturas rugosas, porosas ou fragmentadas, que mantém sua irregularidade em grau similar para todas as escalas. Embora os fractais sejam mais conhecidos como objetos resultantes de algoritmos matemáticos em iterações sucessivas no campo das ciências computacionais, nesta pesquisa as estruturas naturais que se aproximam de modelos de geometria fractal irregular, isto é, classificadas como fractais estatísticos, e que são encontradas em vários sistemas orgânicos e minerais, têm predominância. Pesquisam-se e coletam-se in loco imagens de padrões ramificados para início de produção de trabalhos práticos. Elas são em sua maioria fotografias de seres biológicos naturais com algum grau de ramificação, mas incluem-se também estruturas estatisticamente fractais análogas a sistemas biológicos. Esses estudos de casos de ramificações são então categorizados de acordo com padrões superficiais, colorações, estruturação corporal, funcionalidade no sistema em que atuam e interação com os demais sistemas ou seres vivos presentes num dado ecossistema. A partir de seleção de alguns organismos de acordo com sua estrutura corporal e seus movimentos característicos, são produzidas arte-instalações onde estruturas biomiméticas híbridas são criadas para responder cinética e sensorialmente a estímulos humanos, ambientais e climáticos. / This survey weaves comparative relationships among growth patterns of vascular networks and argues that, in the concept of morphogenesis, in analogy to biology, there are generative clustering and evolutions in branched structural systems. To understand this generative clustering, adjacent concepts to fractal geometry are used - the study of rough, porous or fragmented structures that keep their irregularity to a similar degree at all scales. Although fractals are better known as resulting objects of mathematical algorithms in successive iterations in the field of computer science, in this research the natural structures that approximate to models of irregular fractals, i.e., classified as statistical, and that are found in various minerals and organic systems are predominant. Images of branched patterns are researched and collected in loco for a first production of practical work. They are mostly photographs of natural biological beings with some branching level, but they also include statistical fractal structures analogous to biological systems. These branching study cases are then categorized according to surface patterns, colors, body structure, functionality in the system in which they operate and interaction with other systems or living organisms present in a given ecosystem. From the selection of a few organisms according to their characteristic movements and body structure, installation artworks are experimentally designed where hybrid biomimetic structures are created to sensory and kinetically respond to human, environmental and climate stimuli.

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / This thesis presents an analysis of geodynamic and morphogenesis of the dune field in the Canoa Quebrada region located in the municipality of Aracati inserted in the state of CearÃ. It covers the area formed by fluvial-marine plain, the strip of beach and dune field located on the right bank of the mouth of the river Jaguaribe. The estimated time frame corresponds to the dynamic analysis of the dune field based on migration rates from 1988 to 2013. The objectives of this study are to analyze the environmental dynamics of the mobile dune field towards the mangrove ecosystem located at the mouth of the river Jaguaribe. Associated with the methodological approach, we used a set of techniques necessary for the completion of this research. From then analyzed through GIS aerial photographs of the 80 on the scale of 1: 25,000 and 2004 Quickbird the years of satellite images, 2010 and 2013 associated with the study of wind dynamics based on the variation of records their migration rates. In the study area, we find the moving dunes of the longitudinal type, small occurrence barcanoids, expressive occurrence and prevalence of sand sheets. The vegetation point of view, semi-fixed dunes were identified in contact with the mangrove ecosystem. These dunes can be classified as semi-fixed shapeless. There is no occurrence of fixed dunes or cemented dunes in the region. As for dune generations in Canoa Quebrada, dominates the generation D1, characterized by the occurrence of current dunes, furniture. In contact with the mangrove ecosystem, the semi-fixed dunes combine with the previous generation of dunes to the current, the current sub-type, defining the existence of D2 generation dunes. The average migration of the dune field during that period of 40 years was 7m / year. In the years 2010-2013 virtually no migration occurred, but the dunes continue to migrate towards the mangrove ecosystem. / Esta Tese apresenta uma anÃlise da geodinÃmica e morfogÃnese do campo de dunas na regiÃo de Canoa Quebrada localizada no municÃpio do Aracati inserido no estado do CearÃ. Abrange a Ãrea formada pela planÃcie fluvio-marinha, a faixa de praia e o campo de dunas localizados na margem direita da foz do rio Jaguaribe. O recorte temporal avaliado corresponde à anÃlise da dinÃmica do campo de dunas com base nas taxas de migraÃÃo no perÃodo de 1988 a 2013. Os objetivos dessa pesquisa foram analisar a dinÃmica ambiental do campo de dunas mÃveis em direÃÃo ao ecossistema manguezal localizado na foz do rio Jaguaribe. Associado à abordagem metodolÃgica, utilizou-se um conjunto de tÃcnicas necessÃrias à realizaÃÃo da presente pesquisa. A partir de entÃo, analisou-se atravÃs do geoprocessamento de fotografias aÃreas da dÃcada de 80 na escala de 1:25.000 e imagens de satÃlites Quickbird dos anos de 2004, 2010 e 2013 associados ao estudo da dinÃmica eÃlica com base nos registros da variaÃÃo de suas taxas de migraÃÃo. Na Ãrea de estudo, encontramos dunas mÃveis do tipo longitudinais, de pequena ocorrÃncia, barcanÃides, de expressiva ocorrÃncia e a predominÃncia dos lenÃÃis de areias. Do ponto de vista de cobertura vegetal, foram identificadas dunas semi-fixas no contato com o ecossistema manguezal. Essas dunas podem ser classificadas como semi- fixas sem forma definida. NÃo hà ocorrÃncia de dunas fixas ou de dunas cimentadas na regiÃo. Quanto Ãs geraÃÃes dunares, em Canoa Quebrada, domina a geraÃÃo D1, caracterizada pela ocorrÃncia de dunas atuais, mÃveis. No contato com o ecossistema manguezal, as dunas semi-fixas se combinam com a geraÃÃo de dunas anteriores Ãs atuais, do tipo sub-atuais, definindo a existÃncia de dunas de geraÃÃo D2. A taxa mÃdia de migraÃÃo no campo de dunas durante todo esse perÃodo de 40 anos foi de 7m/ano. Nos anos de 2010 a 2013 praticamente nÃo ocorreu migraÃÃo, mas as dunas continuam migrando em direÃÃo ao ecossistema manguezal.

As lesões térmicas corporais (LTC) são um sério problema de saúde, atingindo principalmente crianças. A extensão e a profundidade da lesão são fatores que alteram várias estruturas. Alterações gastrintestinais também são relatadas, sendo a principal delas, a atrofia das mucosas, provocando ulcerações e a perda da barreira seletiva. Na presente pesquisa avaliou-se através de técnicas histoquímicas, imunohitoquimicas e de microscopia de luz, as alterações ocorridas nos componentes do plexo mioentérico e na espessura da mucosa do jejuno em três porções: oral (O), média (M) e aboral (A), de ratos adultos com 30% da superfície corpórea exposta ao escaldamento, 4 dias (q4) e 10 dias (q10) após a LTC. Verificou-se em q10 o não restabelecimento da massa corpórea, a diminuição da área do jejuno, bem como espessura de sua mucosa. No plexo mioentérico, a área média do perfil celular dos neurônios NADPH não variou, tendo estes uma menor densidade em q10, sendo estes corpos altamente reativos em q4 e q10. Varicosidades grandes destacaram-se em q4 e q10, quando pela SP e VIP. / Burn is a determinant factor to alter body structures as the striated muscle. It also determines gastrintestinal mucosal atrophy what produce loss of selective barrier. With histochemical, immunohistochemical and light microscopy methods the myenteric plexus (MP) of the jejunum was evaluated in rats submitted to burn injury. The scalding was performed in 30% of the body surface. The MP and the mucosa of the oral (O), middle (M) and aboral (A) parts of the jejunum were analyzed four (q4) and ten (q10) days post-lesion. The loss of weight due the burn is not recovered in q10 where the jejunal surface area and the thickness of the mucosa decreased. The neuronal profile of nitregic neurons was similar in q4, q10. The density of nitregic neurons was lower in q10 showing that the time post injury is an important factor able to alter this parameter. The q4 and q10 groups exhibited neuronal bodies highly reactive to NADPH. The immunoreactivity to SP and VIP in q4 and q10 was expressed mainly in large varicosities.

O Eucalyptus cloeziana se destaca pelas propriedades tecnológicas da sua madeira, principalmente em razão da sua durabilidade, densidade e resistência. Entretanto, essa espécie apresenta limitações quanto ao enraizamento adventício de estacas, dificultando a obtenção de mudas clonais e o avanço nos programa de melhoramento da espécie. Nesta perspectiva, o presente trabalho teve por objetivo avaliar a micropropagação de E. cloeziana a partir de materiais juvenis e adultos como uma técnica para a propagação da espécie. Para tanto, o trabalho foi dividido em quatro partes. No primeiro estudo, estabeleceu-se um protocolo de organogênese indireta de E. cloeziana a partir de hipocótilos e cotilédones. No segundo estudo avaliou-se o resgate de matrizes adultas de E. cloeziana através da indução de brotações epicórmicas em megaestacas. No terceiro estudo definiu-se um protocolo de micropropagação via proliferação de gemas axilares de matrizes adultas de E. cloeziana. Por último, no quarto estudo avaliou-se o rejuvenescimento in vitro de matrizes adultas de E. cloeziana por meio da micropropagação via proliferação de gemas axilares e a microestaquia, a partir das matrizes rejuvenescidas in vitro,para comprovar a viabilidade do cultivo in vitro como alternativa de propagação da espécie. A organogênese indireta de E. cloeziana mostrou-se possível e dependente do tipo de explante, dos reguladores de crescimento, suas concentrações e combinações utilizadas nas diferentes fases de morfogênese. As brotações adventícias foram micropropagadas e aclimatizadas com sucesso, obtendo-se mudas clonais de E. cloeziana. No resgate das matrizes adultas de E. cloeziana ocorreu maior indução de brotações epicórmicas para as megaestacas coletadas na época do ano com maior pluviosidade e temperatura. O diâmetro médio das megaestacas, compreendido entre 2,0 e 5,0 cm, correspondeu ao mais adequado para a obtenção de maior número de brotações epicórmicas no resgate das matrizes adultas de E. cloeziana. O protocolo de micropropagação das matrizes adultas de E. cloeziana foi estabelecido com sucesso, utilizando como explantes, brotações epicórmicas induzidas nas megaestacas. A multiplicação in vitro das microcepas foi realizada com êxito no meio de cultura WPM suplementado com BAP e ANA, cujas concentrações variaram entre os genótipos. Os tratamentos de \"pulse\" com GA3 não foi adequado para promover o alongamento in vitro das brotações, o qual foi obtido coma redução da concentração do BAP (0,1 mg L-1). A aclimatização e o enraizamento ex vitro das microestacas foi realizada com sucesso nos miniestufas, garantindo a obtenção de mudas clonais das matrizes adultas de E. cloeziana para a composição de um microjardim clonal. As microcepas das árvores matrizes de E. cloeziana apresentaram diferentes taxas de multiplicação in vitro, apresentando especificidades dos materiais genéticos à micropropagação. Os resultados da microestaquia das matrizes rejuvenescidas in vitro de E. cloeziana corroboraram as evidências de rejuvenescimento desses genótipos durante a micropropagação. Além disso, constatou-se que outros fatores, além da maturidade, podem estar atuando diretamente na recalcitrância do E. cloeziana ao enraizamento adventício. Dessa forma, comprovou-se a importância da micropropagação como uma ferramenta para a clonagem de E. cloeziana, abrindo perspectivas para investigações futuras para otimizar os métodos de propagação da espécie. / Eucalyptus cloeziana has importance for its wood technologic characteristics, mainly the durability, density and resistance. Moreover, this species has limitations on adventitious rooting of cuttings, having difficulties to obtain clonal seedlings and to advance in the improvement programs. In this perspective, the present work aimed to evaluate the E. cloeziana micropropagation by juvenile and mature explants as a technique for propagation this specie. Therefore, the work was divided into four basic studies. The first study was the establishment of the protocol to indirect organogenesis to E. cloeziana hypocotyls and cotyledons. In the second study evaluated the rescue of E. cloeziana adult matrices for epicormic shoots induction in crow branches. In the third study was definite a micropropagation protocol by axillary branching of E. cloeziana adult matrices. Finally, in the fourth study was evaluated the in vitro rejuvenation of E. cloeziana adult matrices to micropropagation by axillary branching and the micro-cutting technique of in vitro rejuvenated matrices to prove the in vitro culture viability to the propagation of this specie. The indirect organogenesis E. cloeziana was dependent of explant type and growth regulator and its concentration used in the different morphogenesis phases. The adventitious shoots were multiplicities and acclimatized with success to obtain E. cloeziana clonal seedlings. The vegetative rescue results of E. cloeziana adult matrices showed a higher induction epicormic shoots from branches collected in warmer and rain season. The medium diameter between 2.0 and 5.0 cm was considered the better to obtain higher epicormic shoots number in vegetative rescue. The micropropagation protocol of E. cloeziana adult matrices was realized with success using epicormic shoots, induced in the branches, like explants. The shoots in vitro multiplication was realized on WPM medium culture, supplemented with BA and NAA. The better growth regulators concentrations were different for each genotype. Treatments pulse with GA3 was not suitable to promote the elongation of shoots in vitro, which was obtained by the BA concentration reduction at 0.1 mg L-1. The in vitro shoots acclimatization and ex vitro rooting was performed in mini-incubators with success and it permit to obtain clonal seedlings from E. cloeziana adult matrices to form a clonal micro-garden. The shoots of E. cloeziana adult matrices showed different in vitro multiplication rates with specific-genotype responses to micropropagation. The micro-cutting technique results of E. cloeziana adult matrices provide evidence that occurred in vitro rejuvenation of these genotypes, during the micropropagation. Therefore, the nursery results showed that other factors, not only maturation, can be involved in the adventitious recalcitrance of E. cloeziana. In conclusion, the importance micropropagation like a biotechnological tool to propagation of E. cloeziana was proved and opened important perspectives for future investigations to optimize the propagation methods for this specie.

Self-organizing patterns arise in a variety of ways in nature, the complex patterning observed on animal coats is such an example. It is already known that the mechanisms responsible for pattern formation starts at the developmental stage of an embryo. However, the actual process determining cell fate has been, and still is, unknown. The mathematical interest for pattern formation emerged from the theories formulated by the mathematician and computer scientist Alan Turing in 1952. He attempted to explain the mechanisms behind morphogenesis and how the process of spatial cell differentiation from homogeneous cells lead to organisms with different complexities and shapes. Turing formulated a mathematical theory and proposed a reaction-diffusion system where morphogens, a postulated chemically active substance, moderated the whole mechanism. He concluded that this process was stable as long as diffusion was neglected; otherwise this would lead to a diffusion-driven instability, which is the fundamental part of pattern formation. The mathematical theory describing this process consists of solving partial differential equations and Turing considered deterministic reaction-diffusion systems.   This thesis will start with introducing the reader to the problem and then gradually build up the mathematical theory needed to get an understanding of the stochastic reaction-diffusion systems that is the focus of the thesis. This study will to a large extent simulate stochastic systems using numerical computations and in order to be computationally feasible a compartment-based model will be used. Noise is an inherent part of such systems, so the study will also discuss the effects of noise and morphogen kinetics on different geometries with boundaries of different complexities from one-dimensional cases up to three-dimensions.

Streptococcus pneumoniae (ou pneumocoque) est un agent pathogène humain responsable de maladies invasives et potentiellement mortelles. Les mécanismes impliqués dans le processus d'invasion restent largement inconnus, mais plusieurs observations suggèrent que les processus de signalisation impliquant la phosphorylation des protéines participeraient au caractère invasif du pneumocoque. Le génome de S. pneumoniae code pour une seule tyrosine-kinase (CpsD) et une seule sérine/thréonine-kinase (StkP). Cette dernière serait notamment impliquée dans la virulence, la compétence et la division cellulaire. Elle représente donc une cible thérapeutique potentielle intéressante pour lutter contre les infections liées au pneumocoque. L'objectif de cette thèse a donc été de caractériser le rôle de cette sérine/thréonine-kinase StkP dans la division cellulaire du pneumocoque. StkP est une protéine transmembranaire qui se caractérise par la présence de motifs structuraux conservés dans son domaine catalytique appelés motifs de Hanks. De plus, StkP possède un domaine extracellulaire composé de la répétition de quatre domaines PASTA (Penicillin-binding protein And Serine/Threonine kinase Associated). Le modèle actuel suggère que ces domaines PASTA seraient capables de fixer des fragments de la paroi cellulaire afin de permettre l'activation de StkP qui se comporterait donc comme un récepteur membranaire permettant de réguler la division cellulaire du pneumocoque. Mes travaux de thèse ont permis de revisiter ce modèle en démontrant que les domaines PASTA ne servent pas uniquement à contrôler l'activité protéine-kinase de StkP mais également à contrôler l'épaisseur de la paroi cellulaire et ainsi permettre la constriction de la cellule. Plus précisément, j'ai démontré que le domaine PASTA distal est spécialisé dans l'interaction avec une hydrolase de la paroi cellulaire alors que les trois autres domaines PASTA sont nécessaires à l'activité kinase de StkP mais également au positionnement du domaine PASTA distal. Ainsi, le domaine extracellulaire de StkP se comporterait comme une règle permettant de définir l'épaisseur de la paroi cellulaire de la bactérie. Ces travaux permettent donc de proposer un nouveau modèle d'activation et de régulation de la division cellulaire par la sérine/thréonine-kinase StkP / Streptococcus pneumoniae (the pneumococcus) is one of the most important human pathogens that causes potentially fatal invasive diseases. Mechanisms required for the pneumococcal invasion process remain largely unknown, but several observations suggest that phosphorylation-based signaling processes will be at play in the invasiveness of the pneumococcus. S. pneumoniae encodes only one tyrosine-kinase (CpsD) and one serine/threonine-kinase (StkP). The latter would be involved in virulence, competence, and cell division. StkP represent therefore a promising target to combat pneumococcal infections. My aims were to better understand the role of StkP in pneumococcal cell division. StkP is a transmembrane protein characterized by the presence of a series of conserved structural motifs called Hanks motifs in its catalytic domain. In addition, StkP possesses an extracellular domain composed of the repetition of four PASTA domains (Penicillin-binding protein And Serine/Threonine kinase Associated). The current model proposes that PASTA domains are able to bind cell wall fragments resulting in StkP kinase activation. StkP would thus behave as an authentic kinase receptor regulating cell division. My thesis works has allowed to revisit this model by showing that PASTA domains do not only serve StkP kinase activation. Rather, they contribute to determine the cell wall thickness and govern cell constriction. More precisely, I demonstrated that the distal PASTA domain possesses unique features for the binding of a cell wall hydrolase whereas the other three contributes to StkP kinase activation and the positioning of the distal PASTA domain. Thus, the extracellular domain of StkP acts as a ruler determining the cell wall thickness. This work allows to propose an alternative model of activation and regulation of cell division by the serine/threonine-kinase StkP

Ce travail présente un modèle théorique de morphogenèse animale, sous la forme d’un système complexe émergeant de nombreux comportements, processus internes, expressions et interactions cellulaires. Son implémentation repose sur un automate cellulaire orienté système multi-agents avec un couplage énergico-génétique entre les dynamiques cellulaires et les ressources.Notre objectif est de proposer des outils permettant l’étude numérique du développement de tissus cellulaires à travers une approche hybride (discrète/continue et qualitative/quantitative) pour modéliser les aspects génétiques, énergétiques et comportementaux des cellules. La modélisation de ces aspects s’inspire des principes de la théorie de la viabilité et des données expérimentales sur les premiers stades de division de l’embryon du poisson-zèbre.La théorie de la viabilité appliquée à la morphogenèse pose cependant de nouveaux défis en informatique pour pouvoir implémenter des algorithmes dédiés aux dynamiques morphologiques. Le choix de données biologiques pertinentes à considérer dans le modèle à proposer, la conception d’un modèle basé sur une théorie nouvelle, l’implémentation d’algorithmes adaptés reposant sur des processeurs puissants et le choix d’expérimentations pour éprouver nos propositions sont les enjeux fondamentaux de ces travaux. Les hypothèses que nous proposons sont discutées au moyen d’expérimentations in silico qui ont porté principalement sur l’atteignabilité et la capturabilité de formes de tissus ; sur la viabilité de l’évolution d’un tissu pour un horizon de temps ; sur la mise en évidence de nouvelles propriétés de tissus et la simulation de mécanismes tissulaires essentiels pour leur contrôlabilité face à des perturbations ; sur de nouvelles méthodes de caractérisation de tissus pathologiques, etc. De telles propositions doivent venir en appoint aux expérimentations in vitro et in vivo et permettre à terme de mieux comprendre les mécanismes régissant le développement de tissus. Plus particulièrement, nous avons mis en évidence lors du calcul de noyaux de viabilité les relations de causalité ascendante reliant la maintenance des cellules en fonction des ressources énergétiques disponibles et la viabilité du tissu en croissance. La dynamique de chaque cellule est associée à sa constitution énergétique et génétique. Le modèle est paramétré à travers une interface permettant de prendre en compte le nombre de coeurs à solliciter pour la simulation afin d’exploiter la puissance de calcul offerte par les matériels multi-coeurs. / This work presents a theoretical model of animal morphogenesis, as a complex system from which emerge cellular behaviors, internal processes, interactions and expressions. Its implementation is based on a cellular automaton oriented multi-agent system with an energico-genetic coupling between the cellular dynamics and resources. Our main purpose is to provide tools for the numerical study of tissue development through a hybrid approach (discrete/continuous and qualitative/quantitative) that models genetic, behavioral and energetic aspects of cells. The modeling of these aspects is based on the principles of viability theory and on experimental data on the early stages of the zebrafish embryo division. The viability theory applied to the morphogenesis, however, raises new challenges in computer science to implement algorithms dedicated to morphological dynamics. The choice of relevant biological data to be considered in the model to propose, the design of a model based on a new theory, the implementation of suitable algorithms based on powerful processors and the choice of experiments to test our proposals are fundamental issues of this work. The assumptions we offer are discussed using in silico experiments that focused on the reachability and catchability of tissue forms ; on the viability of the evolution of a tissue for a time horizon ; on the discovery of new tissue properties and simulation of tissue mechanisms that are fondamental for their controllability face to disruptions ; on new pathological tissue characterization methods, etc. Such proposals must come extra to support experiments in vitro and in vivo and eventually allow a better understanding of the mechanisms governing the development of tissues.In particular, we have highlighted through the computing of viability kernels the bottom causal relationship between the maintenance of cells according to available energy resources and the viability of the tissue in growth. The model is set through an interface that takes into account the number of cores to solicit for simulation in order to exploit the computing power offered by multicore hardware.