A ventilação mecânica (VM) pode ser causa de lesão pulmonar sendo este fato reconhecido na literatura como Lesão Pulmonar Induzida pela Ventilação Mecânica (LPIV), onde alterações tanto fisiológicas quanto morfológicas são evidenciadas no pulmão. O objetivo desse trabalho foi avaliar a repercussão das forças envolvidas na ventilação mecânica através de diferentes mecanismos de LPIV sobre o sistema mucociliar pela análise funcional e histopatológica desse aparelho. Em um estudo controlado e randomizado vinte e sete coelhos machos da raça Nova Zelândia foram separados em quatro grupos. Nos primeiros trinta minutos foram submetidos à VM com volume corrente de 8 ml/kg peso, fluxo de 3 L/minuto, e pressão positiva expiratória final (PEEP) de 5 cm H2O e FIO2 de 0,4, sendo que o grupo Sham (n=6) foi ventilado por apenas 10 minutos. Os grupos Baixo Volume/BV (n=6; Vt 8, Ppico 17, Pmédia 9, PEEP 5, Fluxo 3), Alto Volume/AV (n=7; Vt 16, Ppico 27, Pmédia 12, PEEP 5, Fluxo 5) e Alta Pressão/AP (n=8; Vt 8, Ppico 30, Pmédia 20, PEEP 12, Fluxo 9) foram ventilados por mais 3 horas. A mecânica do sistema respiratório foi registrada pelo sistema Labview®. Foram acompanhados os valores de gasometria e sinais vitais. Amostras de tecido pulmonar foram coradas com H&E para análise de infiltrado inflamatório. Analisou-se a frequência de batimento ciliar (FBC), transporte mucociliar na traqueia (TMCT), transportabilidade em palato de rã (MCT) e ângulo de contato (AC). Amostras de pulmão e traquéia foram coradas pela técnica PAS/AB para avaliação do muco. Observamos diminuição da complacência do sistema respiratório (p<0,05) no grupo AP em comparação com os demais grupos ventilados. Os grupos BV, AV e AP apresentaram um aumento de células polimorfonucleares por área de parênquima pulmonar (p<0,001) em comparação com o grupo Sham. Não foram observadas diferenças quanto ao TMCT e AC nos grupos ventilados. A transportabilidade em palato diminuiu no grupo BV (p=0,007) ao final do protocolo de ventilação (1,42 com variações de 2,11-0,99 para 0,95 com variações de 1,15-0,92). A FBC diminuiu (p=0,047) no grupo AP quando comparamos os valores iniciais (13,51 variação de 14,49-11,62) e finais ao protocolo de VM (11,69 variação de 14,18-10,12). Respostas fisiológicas e microscopia eletrônica (ME) da traquéia corroboram a disfunção da FBC no grupo AP. Na traquéia os grupos ventilados apresentaram uma diminuição da quantidade de muco total (BV 2.018, AV 3.219 e AP 2.883) e de muco ácido (BV 672, AV 240 e AP 480) por m2 de tecido pulmonar por campo estudado (p<0.05) quando comparados com o grupo Sham (4.660 m2 de muco total e 1.873 m2 de muco ácido). Em bronquíolos distais a quantidade de muco total diminuiu nos grupos BV e AP (p<0.05) quando comparados aos grupos Sham e AV. O mesmo fenômeno foi observado com relação ao muco neutro. Concluímos que as forças geradas pela ventilação mecânica têm impacto direto sobre o aparelho mucociliar, alterando suas propriedades funcionais e sua morfologia. Aparentemente a VM acarreta desequilíbrio na produção de muco, sendo essa alteração mais visível quando utilizado um alto volume corrente e uma maior pressão média pulmonar (associada a um fluxo de ar aumentado). O aumento da pressão média com alto fluxo dos gases ventilados também ocasiona maior sofrimento celular do aparelho mucociliar, disfunção da frequência de batimento ciliar e provável perda ciliar. Tais alterações se devem provavelmente ao efeito das forças físicas geradas pela VM associadas a prováveis oscilações na resposta inflamatória e no fluxo sanguíneo local. / Mechanical ventilation (MV) can result in a medical complication named Ventilator-Induced Lung Injury (VILI), where physiologic and morphologic alterations in the lungs have been reported. In this study, we have hypothesized that MV-induced injury can have a major impact on the mucociliary system. In a randomized controlled trial twenty-seven male New Zealand rabbits were separated into four groups. During the first thirty minutes all rabbits were subjected to MV with tidal volume of 8 ml/kg of body weight, 3 L/minute of flow, positive end expiratory pressure (PEEP) of 5 cm H2O and FIO2 of 0.4. After that the study animals were divided into 4 groups: Sham (n=6) was ventilated for ten minutes, Lower Volume/LV (n=6; Vt 8, P peak 17, P mean 9, PEEP 5, Flow 3), High Volume/HV (n=7; Vt 16, P peak 27, P mean 12, PEEP 5, Flow 5) and High Pressure/HP (n=8; Vt 8, P peak 30, P mean 20, PEEP 12, Flow 9) and ventilated for 3 hours more. Respiratory system mechanics was recorded using Labview®. Blood gasometry and vital signals were monitored. Lung tissue sections were stained by H&E to analyze inflammation. We also studied the ciliary beating frequency (CBF), tracheal mucociliary transport (TMCT) in situ and in vitro, mucus contact angle (CA) and respiratory mucus viscosity. To quantify mucosubstances, tracheal samples were stained with PAS/AB. As a result we have that the respiratory system compliance decreased (p<0.05) in the HP group compared to other ventilated groups. All ventilated groups showed an increase in polymorphonuclear cells quantity per area of lung parenchyma (p<0.001) compared to the Sham group. There were no differences in TMCT and CA among ventilated groups, when initial and final measurements were compared. MCT significantly decreased in the LV group (p=0.007) after the protocol (1.42 range of 2.11-0.99 to 0.95 range of 1.15-0.92). The CBF significantly decreased (p=0.047) in the HP group when the initial (13.51 range of 14.49-11.62) and final (11.69 range of 14.18-10.12) measurements were compared. Physiological data and tracheal electronic microscopy confirm the CBF dysfunction observed in the AP group. In the trachea all ventilated groups showed a significant decrease in total mucus (LV 2,018, HV 3,219 and HP 2,883) and acid mucus (LV 672, HV 240 and HP 480) per um2 of lung tissue (p<0.05) compared to the sham group (4,660 um2 of total mucus and 1,873 um2 of acid mucus). In distal bronchioles there was a significant decrease in total mucus in the LV and HP group (p<0.05) compared to Sham and HV groups. The same phenomenon was observed regarding neutral mucus. We concluded that mechanical forces involved in MV affect mucociliary function. Mechanical ventilation probably leads to the dysfunction on the mucus production. This phenomenon is better perceived when higher volume and higher mean pressure (associated with inspired gases high flow) are used. An increase of the mean pressure combined with inspired gases high flow also leads to mucociliary cells suffering, to ciliary beat frequency dysfunction and probably cilia loss. These alterations probably occur due to the effect of the physical forces generated by the mechanical ventilation in association with the oscillation of the inflammatory response and local blood flow.

Les applications modernes sont de plus en plus dynamiques et hétérogènes. L'architecture des systèmes modernes n'est plus figée et prévisible. Il en va de même pour les besoins des utilisateurs, les capacités des ordinateurs et des réseaux, et les technologies utilisées. Il nous parait essentiel que les gestionnaires autonomiques soient dynamiquement adaptables et extensibles pour prendre en compte ces changements et faciliter la maintenance. L'objectif de notre travail est de définir et d'implanter un cadriciel, ou framework, facilitant le développement de gestionnaires autonomiques. Dans cet effort, nous visons à définir un modèle architectural permettant le développement de gestionnaires autonomiques modulaires, homogènes, souples, évolutifs, dynamiques et administrables. Un objectif important de ce travail est de clairement définir et séparer les concepts appartenant de façon générique à un gestionnaire autonomique et les aspects métier, développés au cas par cas. Le but est de permettre au experts domaine de se concentrer sur l'écriture des fonctions autonomiques et de ne pas gérer entièrement l'enchaînement et le contrôle de ces fonctions. Pour atteindre nos objectifs, nous avons tout d'abord défini la notion de tâche d'administration. Une tâche d'administration est une entité indépendante et spécialisée qui réalise une ou plusieurs fonctions d'administration. Le gestionnaire autonomique résulte de la combinaison opportuniste de ces tâches. A chaque instant, l'ensemble de tâches utilisées peut être modifié en fonction du contexte et des informations remontées par la plateforme. Des mécanismes de sélections permettent de gérer les conflits éventuels et permettent d'assurer une cohérence du comportement du gestionnaire. Nous avons ensuite défini une architecture de gestion de ces tâches permettant la combinaison opportuniste de ces tâches en fonction du contexte. Cette architecture a été implantée sous la forme d'un framework fondé sur la technologie des composants orientés services. Le framework que nous avons développé fournit un cadre pour l'intégration dynamique de fonctions autonomiques et pour leur gestion en fonction du contexte et de politiques d'administration, elles mêmes évolutives. En conclusion de ce travail, nous présentons une implémentation particulière sous la forme d'un modèle à composants de sorte que le travail des développeurs est facilité et que la réutilisation est favorisée. Enfin nous donnons un exemple d'application développée au dessus de ce framework.

<p>Ultrastructural studies of airway epithelium in airway disease are important for diagnosis and understanding the underlying pathology which helps clinicians to improve the patients' treatment.</p><p>Airway biopsies from a 5-month old boy with respiratory problems and gastro-oesophageal reflux were studied by transmission electron microscopy (TEM). The tracheal columnar cells showed accumulation of lamellar bodies, indicative of lysosomal storage disease. The patient was diagnosed with Gaucher disease type 2.</p><p>Shedding of airway epithelial cells is commonly found in asthma. The attachment of these cells to the basal lamina was investigated by TEM of biopsies from patients with asthma and healthy controls. The contact area between columnar cells and basal lamina in asthmatics was significantly less than in controls. Attachment of columnar cells to the basal lamina occurs mainly indirectly, via desmosomal attachment to basal cells. </p><p>Primary ciliary dyskinesia (PCD) is a congenital disease. It is important to differentiate PCD from acquired (secondary) ciliary dyskinesia (SCD). The number of dynein arms determined by TEM was 1.5 and 1.4 for outer and inner dynein arms, respectively in PCD, versus 7.9 and 5.2 for controls and 8.1 and 5.9 in SCD. Compared to PCD patients, SCD patients have more structurally abnormal cilia. A significant difference was found in orientation of the central microtubule pair between PCD and SCD, but also overlap. </p><p>Leukotriene receptor antagonists are a new treatment for asthma. Both corticosteroids and montelukast caused apoptosis and necrosis of airway epithelial cells, and reduced the expression of intercellular adhesion molecule-1. Treatment of cells with tumor necrosis factor-α or interferon-γ reduced the fraction of the lateral cell membrane occupied by desmosomes and this effect was counteracted by corticosteroids. </p>

Ultrastructural studies of airway epithelium in airway disease are important for diagnosis and understanding the underlying pathology which helps clinicians to improve the patients' treatment. Airway biopsies from a 5-month old boy with respiratory problems and gastro-oesophageal reflux were studied by transmission electron microscopy (TEM). The tracheal columnar cells showed accumulation of lamellar bodies, indicative of lysosomal storage disease. The patient was diagnosed with Gaucher disease type 2. Shedding of airway epithelial cells is commonly found in asthma. The attachment of these cells to the basal lamina was investigated by TEM of biopsies from patients with asthma and healthy controls. The contact area between columnar cells and basal lamina in asthmatics was significantly less than in controls. Attachment of columnar cells to the basal lamina occurs mainly indirectly, via desmosomal attachment to basal cells. Primary ciliary dyskinesia (PCD) is a congenital disease. It is important to differentiate PCD from acquired (secondary) ciliary dyskinesia (SCD). The number of dynein arms determined by TEM was 1.5 and 1.4 for outer and inner dynein arms, respectively in PCD, versus 7.9 and 5.2 for controls and 8.1 and 5.9 in SCD. Compared to PCD patients, SCD patients have more structurally abnormal cilia. A significant difference was found in orientation of the central microtubule pair between PCD and SCD, but also overlap. Leukotriene receptor antagonists are a new treatment for asthma. Both corticosteroids and montelukast caused apoptosis and necrosis of airway epithelial cells, and reduced the expression of intercellular adhesion molecule-1. Treatment of cells with tumor necrosis factor-α or interferon-γ reduced the fraction of the lateral cell membrane occupied by desmosomes and this effect was counteracted by corticosteroids.

Over the past several decades, the rate of pulmonary nontuberculous my- cobacterial (PNTM) disease has been increasing. PNTM patients gener- ally consist of lean and tall women presenting with symptoms in the sixth decade of life. They have a de nitive morphophenotype, but no consistent immunological abnormalities despite extensive investigation. I hypothesized that respiratory epithelial dysfunction might play a critical role in PNTM disease predisposition because diseases with defects of mucociliary transport have high rates of PNTM disease that increase with age, suggesting a direct connection between airway epithelial function and PNTM disease. I found that PNTM patients have a distinct respiratory epithelial phenotype ex vivo and decreased nasal nitric oxide levels in vivo. The PNTM ex vivo phenotype consists of an abnormally low resting ciliary beat frequency (CBF) and abnormal CBF response to toll-like receptor (TLR) agonists. The depressed baseline CBF response in PNTM patient cells can be normalized ex vivo by augmenting the nitric oxide-cyclic guanosine monophosphate pathway without appreciable e ect on CBF in healthy controls. In healthy controls, bacterial TLR agonists increase CBF and viral TLR agonists decrease CBF. In PNTM patients these responses are impaired and are not normalized with the normalization of the resting CBF rate. Inhibitor-induced disruption of signalling pathways associated with CBF regulation demonstrated that the majority of the CBF response to TLR agonists involves the PI-3K pathway and PKC. Inhibition of the PI-3K pathway (PI-3K , Akt1, and PDK1) closely mimicked the ex vivo phenotype seen in PNTM patient respiratory epithelia. These data identify a novel aspect of PNTM disease with in vivo and ex vivo correlates that suggest that PNTM infection is associated with abnormal function at both the CBF and TLR response levels. This phenotype is novel, reproducible, and provide a foundation with which to determine the genetic basis of PNTM infection.

Une grande part des muqueuses à l’intérieur du corps humain sont recouvertes de cils qui, par leurs mouvements coordonnés, conduisent à une circulation de la couche de fluide nappant la muqueuse. Dans le cas de la paroi interne des bronches, ce processus permet l’évacuation des impuretés inspirées à l’extérieur de l’appareil respiratoire.Dans cette thèse, nous nous intéressons aux effets du ou des cils sur le fluide, en nous plaçant à l’échelle du cil, et on considère pour cela les équations de Stokes incompressible. Due à la finesse du cil, une simulation directe demanderait un raffinement important du maillage au voisinage du cil, pour un maillage qui évoluerait à chaque pas de temps. Cette approche étant trop onéreuse en terme de coûts de calculs, nous avons considéré l’asymptotique d’un diamètre du cil tendant vers 0 et d’une vitesse qui tend vers l’infini : le cil est modélisé par un Dirac linéique de forces en terme source. Nous avons montré qu’il était possible de remplacer ce Dirac linéique par une somme de Dirac ponctuels distribués le long du cil. Ainsi, nous nous sommes ramenés, par linéarité, à étudier le problème de Stokes avec en terme source une force ponctuelle. Si les calculs sont ainsi simplifiés (et leurs coûts réduits), le problème final est lui plus singulier, ce qui motive une analyse numérique fine et l’élaboration d’une nouvelle méthode de résolution.Nous avons d’abord étudié une version scalaire de ce problème : le problème de Poisson avec une masse de Dirac en second membre. La solution exacte étant singulière, la solution éléments finis est à définir avec précaution. La convergence de la méthode étant dégradée dans ce cas-là, par rapport à celle dans le cas régulier, nous nous sommes intéressés à des estimations locales. Nous avons démontré une convergence quasi-optimale en norme Hs (s ě 1) sur un sous-domaine qui exclut la singularité. Des résultats analogues ont été obtenus dans le cas du problème de Stokes.Pour palier les problèmes liés à une mauvais convergence sur l’ensemble du domaine, nous avons élaboré une méthode pour résoudre des problème elliptiques avec une masse de Dirac ou une force ponctuelle en terme source. Basée sur celle des éléments finis standard, elle s’appuie sur la connaissance explicite de la singularité de la solution exacte. Une fois données la position de chacun des cils et leur paramétrisation, notre méthode rend possible la simulation directe en 3d d’un très grand nombre de cils. Nous l’avons donc appliquée au cas du transport mucociliaire dans les poumons. Cet outil numérique nous donne accès à des informations que l’on ne peut avoir par l’expérience, et permet de simuler des cas pathologiques comme par exemple une distribution éparse des cils. / Numerous mucous membranes inside the human body are covered with cilia which, by their coordinated movements, lead to a circulation of the layer of fluid coating the mucous membrane, which allows, for example, in the case of the internal wall of the bronchi, the evacuation of the impurities inspired outside the respiratory system.In this thesis, we integrate the effects of the cilia on the fluid, at the scale of the cilium. For this, we consider the incompressible Stokes equations. Due to the very small thickness of the cilia, the direct computation would request a time-varying mesh grading around the cilia. To avoid too prohibitive computational costs, we consider the asymptotic of a zero diameter cilium with an infinite velocity: the cilium is modelled by a lineic Dirac of force in source term. In order to ease the computations, the lineic Dirac of forces can be approached by a sum of punctual Dirac masses distributed along the cilium. Thus, by linearity, we have switched our initial problem with the Stokes problem with a punctual force in source term. Thus, we simplify the computations, but the final problem is more singular than the initial problem. The loss of regularity involves a deeper numerical analysis and the development of a new method to solve the problem.We have first studied a scalar version of this problem: Poisson problem with a Dirac right-hand side. The exact solution is singular, therefore the finite element solution has to be defined with caution. In this case, the convergence is not as good as in the regular case, and thus we focused on local error estimates. We have proved a quasi-optimal convergence in H1-norm (s ď 1) on a sub-domain which does not contain the singularity. Similar results have been shown for the Stokes problem too.In order to recover an optimal convergence on the whole domain, we have developped a numerical method to solve elliptic problems with a Dirac mass or a punctual force in source term. It is based on the standard finite element method and the explicit knowl- edge of the singularity of the exact solution. Given the positions of the cilia and their parametrisations, this method permits to compute in 3d a very high number of cilia. We have applied this to the study of the mucociliary transport in the lung. This numerical tool gives us information we do not have with the experimentations and pathologies can be computed and studied by this way, like for example a small number of cilia.

La glycogénose de type Ia (GSDIa) est une maladie métabolique rare causée par une déficience en glucose-6-phosphatase (G6Pase), due à des mutations de la sous-unité catalytique (G6PC). Cette enzyme confère au foie, aux reins et à l’intestin la capacité de produire du glucose. Les patients atteints de GSDIa sont donc incapables de produire du glucose et souffrent d’hypoglycémies sévères lors de jeûnes courts. De plus, la déficience en G6Pase provoque une accumulation de glucose-6 phosphate dans le foie et les reins, conduisant à l’accumulation de glycogène et de lipides. A long terme, la plupart des patients souffre d’une maladie chronique rénale (MCR), qui peut évoluer en insuffisance rénale, nécessitant une mise sous dialyse ou une transplantation rénale. Cette MCR se caractérise par une fibrose, ainsi que par le développement de kystes dans les stades tardifs. Au niveau du foie, les patients développent une hépatomégalie et une stéatose hépatique qui peut évoluer vers le développement d’adénomes ou carcinomes hépatocellulaires. Le but de mes travaux de thèse a été d’identifier les mécanismes moléculaires impliqués dans l’établissement de la pathologie rénale et la formation des kystes, à l’aide de modèles murins invalidés pour le gène G6pc spécifiquement dans les reins (souris K.G6pc-/-). Alors que la GSDIa est une maladie caractérisée par l’accumulation hépatique et rénale de glycogène, nous avons d’abord montré que le développement de la fibrose, à l’origine de la perte de la fonction rénale, était induit par l’accumulation de lipides, indépendamment du contenu en glycogène. De plus, l’utilisation d’un agoniste de PPARα, le fénofibrate, en diminuant le contenu lipidique rénal, a ralenti l’installation de la fibrose et l’évolution de la MCR. Le mécanisme moléculaire impliqué est l’activation du système rénine angiotensine par les dérivés lipidiques, qui induit l’expression du facteur profibrotique TGFβ1. De même, le fénofibrate en limitant l’accumulation de lipides hépatiques a prévenu le développement d’atteintes hépatiques caractéristiques de la GSDI. Ainsi, l’activation du catabolisme des lipides par des agonistes de PPARα semble une stratégie thérapeutique intéressante pour réduire la progression des maladies rénales et hépatique de la GSDI. La deuxième partie de mes résultats suggèrent que le développement de kystes rénaux chez les patients atteints de la GSDI pourrait être causé par une altération du cil primaire, organelle jouant un rôle clé dans le maintien d’une structure et fonction normale des reins. En effet, une augmentation de la longueur du cil primaire a pu être observée dans les reins des souris K.G6pc-/- associée à une dérégulation de différentes protéines impliquées dans sa structure et sa fonction, par rapport aux souris contrôles. Nous avons également mis en évidence une reprogrammation métabolique de type Warburg, caractérisée par une activation accrue de la glycolyse aérobie, une inhibition de l’oxydation mitochondriale du pyruvate et une production de lipides. Ainsi, l’ensemble de ces perturbations va favoriser la prolifération cellulaire et le développement de kystes, et pourrait mener au développement de tumeur rénale comme observée chez une souris K.G6pc-/-. En conclusion nous avons démontré que, dans le cadre de la GSDI, l’accumulation de lipides dans les reins et le foie, secondaire à la déficience en G6Pase, joue un rôle clé dans le développement des complications hépatiques et rénales à long terme. Également, la reprogrammation métabolique rénale de type Warburg, prenant place dans le cadre de la GSDI, associée à un défaut du cil primaire pourrait être à l’origine de la formation des kystes et de tumeurs rénales. Ces études, en permettant une meilleure compréhension de la physiopathologie des complications à long terme de la GSDIa, offrent de nouvelles perspectives concernant les stratégies thérapeutiques à développer pour une meilleure prise en charge des patients atteints de GSDIa / Glycogen storage disease type Ia (GSDIa) is a rare metabolic disease caused by glucose-6-phosphatase (G6Pase) deficiency, due to mutations on the gene encoding G6Pase catalytic subunit (G6PC). This enzyme confers to the liver, kidneys and intestine the ability to produce glucose. Thus, patients with GSDIa are unable to ensure endogenous glucose production and suffer from severe hypoglycemia during fasting in the absence of nutritional control. In addition, G6Pase deficiency causes intracellular accumulation of glucose-6 phosphate in the liver and kidneys, leading to metabolic defects and the accumulation of glycogen and lipids. Over time, most adult patients suffer from chronic kidney disease (CKD), which can progress to kidney failure, requiring dialysis or kidney transplantation. This nephropathy is characterized in particular by tubulo-interstitial fibrosis and glomerulosclerosis, as well as by the development of cysts in the late stages. Moreover, patients develop hepatomegaly and hepatic steatosis that may progress to the development of hepatocellular adenomas or carcinomas. The aim of my thesis was to identify the molecular mechanisms involved in the establishment of renal pathology and cyst formation in GSDIa, by using mouse models where G6pc gene is specifically deleted in the kidneys (K.G6pc-/- mice). While GSDIa is a disease characterized by glycogen accumulation in the liver and kidneys, we first showed that the development of fibrosis, which causes progressive loss of kidney function, was induced by intracellular accumulation of lipids, regardless of glycogen content. The molecular mechanism probably involved is the activation of the renin angiotensin system by lipid derivatives such as diacylglycerol, which induced the expression of the profibrotic factor TGFβ1 and an epithelial-mesenchymal transition. In addition, the use of a PPARα agonist, i.e. fenofibrate, by decreasing renal lipid content, reduced the development of fibrosis and CKD evolution. Similarly, fenofibrate treatment prevented the accumulation of lipids in the liver and the development of liver damages that cause tumor development. Thus, the activation of lipid catabolism by PPARα agonists such as fenofibrate seems to be an interesting therapeutic strategy to reduce the progression of renal and hepatic diseases of GSDIa. The second part of my results suggest that the development of renal cysts in GSDI patients may be caused by an alteration of the primary cilia, a non-motile organelle that plays a key role in maintaining normal kidney structure and function. Indeed, defects in the primary cilia are involved in many polycystic kidney diseases. In summary, an increase in the length of the primary cilia was observed in the kidneys of K.G6pc-/- mice, which could be explained by a deregulation of the expression of different proteins involved in cilia structure and function, compared to control mice. We also demonstrated a metabolic reprogramming leading to a Warburg metabolism, characterized by the increased activation of aerobic glycolysis and the inhibition of mitochondrial pyruvate oxidation and lipid production in K.G6pc-/- mice. Thus, all these disorders would promote cell proliferation and cyst development, and could lead to the development of renal tumor, as recently observed in one K.G6pc-/- mouse (out of 36 studied mice). In conclusion, we have shown that, in GSDI, the accumulation of lipids in the kidneys and liver that occurs secondary to G6Pase deficiency plays a key role in the development of hepatic and renal long-term complications. In addition, the Warburg like metabolic reprogramming taking place in the GSDIa kidneys, associated with a defect in the primary cilia, could be at the origin of cysts formation and renal tumors. These new studies, by providing a better understanding of the pathophysiology of long-term complications of GSDIa, offer new perspectives on therapeutic strategies to be developed for better management of patients

[ES] Los cilios son estructuras eucariotas complejas conservadas evolutivamente que, proyectando desde la superficie de las células, desempeñan un gran número de funciones biológicas. Los cilios se clasifican tradicionalmente en móviles o sensoriales y en su composición intervienen cientos de proteínas. Este conjunto de genes que codifican para los componentes ciliares se conoce como cilioma. Las mutaciones en el cilioma subyacen a un grupo cada vez mayor de enfermedades multisistémicas altamente pleiotrópicas denominadas globalmente como ciliopatías. Estas enfermedades se caracterizan, entre otros síntomas, por retraso mental, defectos sensoriales y/o trastornos metabólicos. A pesar de que se estima que 1 de cada 1.000 personas está afectada por estas enfermedades, las bases moleculares de las ciliopatías son todavía poco conocidas. El adecuado ensamblaje y funcionalidad del cilio requieren de la expresión estrechamente coordinada de los componentes del cilio; sin embargo, se sabe poco sobre la lógica reguladora que controla la transcripción del cilioma. La mayoría de los genes del cilioma son compartidos tanto por cilios móviles como sensoriales. Los factores de transcripción (FTs) de la familia RFX tienen un papel evolutivamente conservado en la regulación transcripcional del cilioma tanto móvil como sensorial. En los vertebrados, la transcripción del cilioma móvil también está regulada directamente por FoxJ1, un FT de la familia forkhead (FKH). Sin embargo, hasta la fecha, se desconocen los FTs que actúan junto a RFX en la transcripción del cilioma sensorial en cualquier organismo. En este trabajo, hemos identificado a FKH-8, un FT de la familia FKH, como selector terminal del cilioma sensorial de C. elegans. fkh-8 se expresa de forma consistente en las sesenta neuronas sensoriales ciliadas de C. elegans, se une a las regiones reguladoras de los genes del cilioma sensorial, también es necesario para la correcta expresión de los genes del cilioma y actúa de forma sinérgica con el conocido regulador maestro de la ciliogénesis DAF19/RFX. En consecuencia, los mutantes para fkh-8 muestran una amplia gama de defectos de comportamiento en una plétora de paradigmas sensoriales, incluyendo la olfacción, la gustación y la mecano-sensación. Así, hemos identificado, por primera vez, un FT que actúa junto con los FTs de la familia RFX en la regulación directa del cilioma sensorial. Además, nuestros resultados, junto con trabajos anteriores, muestran que los FTs FKH y RFX actúan conjuntamente en la regulación de los cilios tanto móviles como sensoriales, lo que sugiere que esta lógica reguladora podría ser un rasgo evolutivo antiguo anterior a la subespecialización funcional de los cilios. Finalmente, esperamos que los resultados de nuestro trabajo ayuden a entender mejor las bases biológicas de las ciliopatías huérfanas / [CA] Els cilis són estructures eucariotes complexes conservades evolutivament que, projectant des de la superfície de les cèl·lules, exerceixen un gran nombre de funcions biològiques. Els cilis es classifiquen tradicionalment en mòbils o sensorials i en la seua composició intervenen centenars de proteïnes. Aquest conjunt de gens que codifiquen per als components ciliars es coneix com el cilioma. Les mutacions en el cilioma subjauen a un grup cada vegada major de malalties multisistèmiques altament pleiotròpiques denominades globalment com ciliopaties. Aquestes malalties es caracteritzen, entre altres símptomes, per retard mental, defectes sensorials i/o trastorns metabòlics. A pesar que s'estima que 1 de cada 1.000 persones està afectada per aquestes malalties, les bases moleculars de les ciliopaties són encara poc conegudes. L'adequat assemblatge i funcionalitat del cili requereixen de l'expressió estretament coordinada dels components del cili; no obstant això, se sap poc sobre la lògica reguladora que controla la transcripció del cilioma. La majoria dels gens del cilioma són compartits tant per cilis mòbils com sensorials. Els factors de transcripció (FTs) de la família RFX tenen un paper evolutivament conservat en la regulació transcripcional del cilioma tant mòbil com sensorial. En els vertebrats, la transcripció del cilioma mòbil també està regulada directament per FoxJ1, un FT de la família forkhead (FKH). No obstant això, fins hui, es desconeixen els FTs que actuen al costat de RFX en la transcripció del cilioma sensorial en qualsevol organisme. En aquest treball, hem identificat a FKH-8, un FT de la família FKH, com a selector terminal del cilioma sensorial de C. elegans. fkh-8 s'expressa de manera consistent en les seixanta neurones sensorials ciliades de C. elegans, s'uneix a les regions reguladores dels gens del cilioma sensorial, també és necessari per a la correcta expressió dels gens del cilioma i actua de manera sinèrgica amb el conegut regulador mestre de la ciliogènesi DAF-19/RFX. En conseqüència, els mutants per a fkh-8 mostren una àmplia gamma de defectes de comportament en una plètora de paradigmes sensorials, incloent la olfacció, la gustació i la mecano-sensació. Així, hem identificat, per primera vegada, un FT que actua juntament amb els FTs de la família RFX en la regulació directa del cilioma sensorial. A més, els nostres resultats, juntament amb treballs anteriors, mostren que els FTs FKH i RFX actuen conjuntament en la regulació dels cilis tant mòbils com sensorials, la qual cosa suggereix que aquesta lògica reguladora podria ser un tret evolutiu antic anterior a la subespecialització funcional dels cilis. Finalment, esperem que els resultats del nostre treball ajuden a entendre millor les bases biològiques de les ciliopaties òrfenes. / [EN] Cilia are complex evolutionary conserved eukaryotic structures that, projecting from cell surfaces, perform a variety of biological roles. Cilia are traditionally classified into motile or sensory and hundreds of proteins take part in their composition. This set of genes coding for ciliary components is known as the ciliome. Mutations in the ciliome underlie an ever-growing group of highly pleiotropic multisystemic diseases globally termed as ciliopathies. These diseases are characterized, among other symptoms, by mental retardation, sensory defects and/or metabolic disorders. Despite an estimated 1 in 1,000 people affected by these diseases, the molecular bases of the ciliopathies are still poorly understood. Proper cilium assembly and functionality requires the tightly co-regulated expression of ciliary components; however, little is known about the regulatory logic controlling ciliome transcription. Most ciliome genes are shared between motile and sensory cilia. RFX transcription factors (TFs) have an evolutionarily conserved role in the transcriptional regulation of both motile and sensory ciliome. In vertebrates, transcription of motile ciliome is also directly regulated by FoxJ1, a Forkhead (FKH) TF. However, to date, TFs working together with RFX in the transcription of the sensory ciliome are unknown in any organism. In this work, we have identified FKH-8, a FKH TF, as a terminal selector of the sensory ciliome in C. elegans. fkh-8 is consistently expressed within the sixty ciliated sensory neurons of C. elegans, it binds the regulatory regions of the sensory ciliome genes, it is also required for correct ciliome gene expression and acts synergistically with the known master regulator of the ciliogenesis DAF-19/RFX. Accordingly, fkh-8 mutants display a wide range of behavioural defects in a plethora of sensory mediated paradigms, including olfaction, gustation, and mechano-sensation. Thus, we have identified, for the first time, a TF that acts together with RFX TFs in the direct regulation of the sensory ciliome. Moreover, our results, together with previous work, show that FKH and RFX TFs act together in the regulation of both motile and sensory cilia, suggesting this regulatory logic could be an ancient trait pre-dating functional sub-specialization of cilia. Finally, we hope our results could help better understand the biological basis of orphan ciliopathies. / This thesis project has been made possible thanks to a pre-doctoral fellowship from the FPI Programme (BES-2015-072799) conferred by the (now extinct) Spanish Ministry of Economy & Competitivity. The following grants also provided a funding frame throughout the whole research process: “Estudio de los mecanismos transcripcionales que regulan la diferenciación de las neuronas monoaminérgicas y su conservación evolutiva.” SAF2014-56877-R “Dissecting the gene regulatory mechanisms that generate serotonergic neurons and their link to mental disorders.” ERC-St 281920 “Programas de regulación transcripcional asociados a enfermedades genéticas.” SAF2017-84790-R “Regulatory rules and evolution of neuronal gene expression.” ERC-Co 101002203 / Brocal Ruiz, R. (2022). Transcriptional Regulatory Logic of Cilium Formation in C. Elegans [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/181667 / TESIS

Les cils motiles et statiques jouent d’importants rôles dans la détermination de l’axe gauche-droite (GD) qui, en général, est mis en place par l’intermédiaire de flux directionnels générés dans des structures spécialisées appelées organisateurs gauche-droite (OGD). C’est ce point clé du développement qui dictera une organogenèse asymétrique. Dans mon projet de thèse, nous avons développé une méthode, appelée 3D-Cilia Map, et analysé l’organisation tridimensionnelle de l’implantation des cils afin d’extraire les paramètres clés responsables de la mise en place du flux directionnel et par conséquent de l’asymétrie GD. En résumé, nos résultats suggèrent qu’un mécanisme de signalisation chimique serait le plus plausible pour induire la rupture de la symétrie GD. Plus tard, les cellules réguleront intrinsèquement l’orientation asymétrique des cils à leur surface. Le travail présenté ici contribue de façon importante à nos connaissances actuelles concernant le comportement des cils et les mécanismes de sensation des flux dans l’établissement de l’axe gauche droite au sein de l’organisateur gauche-droite du poisson zèbre. / Both motile and immotile cilia play important roles in left-right (LR) axis determination, which generally involves cilia-mediated directional flows in organized structures (LR organizers, LRO) in which the LR symmetry is broken, thus driving asymmetric organogenesis in the developing embryos. In my PhD project we aimed to developed a method (3D-Cilia Map) and analyze the three-dimensional organization of ciliary implantation in order to extract the key parameters modulating the directional flow involved in breaking the axis of symmetry in the zebra fish LRO. Altogether, our results suggest the initial mechanism to break the LR symmetry is most likely to be based on the transport of achemical signal, while later, cells intrinsically provide their cilia the cues to orient asymmetrically. The work presented here represents an important contribution to our current understanding of cilia behaviors and flow-sensing mechanisms in the establishment of the left-right axis in the zebra fish LRO.

Motile cilia are hair-like cell appendages that actively bend themselves, thus driving the surrounding fluid in motion. For many microorganisms, such as unicellular Paramecium, cilia are essential for their motility. Higher animals, including mammals, utilize cilia for transporting fluids. For example, in humans, large collections of cilia, called cilia carpets, remove mucus and pathogens from the airways. Cilia constitute an example of biological oscillators that can spontaneously synchronize their beat in the form of metachronal waves, i.e., traveling waves of cilia phase. These waves may arise purely by hydrodynamic interactions between the cilia and supposedly enhance fluid transport. Our goal is to theoretically understand how the properties of individual cilia, e.g., cilia beat pattern, determine the emergent behavior, e.g., the direction of the metachronal wave. Additionally, we address the robustness of hydrodynamically-induced synchronization with respect to intrinsic active fluctuations of the cilia beat and disorder of intrinsic cilia frequencies. Both of these effects are not yet well understood. In this thesis, we studied metachronal synchronization in cilia carpets using a theoretical physicist’s toolbox. First, we proposed a novel multi-scale modeling framework Lagrangian Mechanics of Active Systems (LAMAS) to describe fluid-structure interactions for active elastic structures, such as cilia. We quantified hydrodynamic interactions between cilia using detailed hydrodynamic simulations with a realistic cilia beat pattern. In the dynamical simulations for N = 2 cilia, we found that cilia would synchronize either in-phase or anti-phase, depending on their relative positions. For a lattice of N ≫ 1 cilia, we found the emergence of metachronal waves, many of which are locally stable. Nevertheless, just a single wave has a predominantly large basin of attraction, i.e., it is likely to be selected from a random initial condition. In the presence of noise, synchronization abruptly breaks up beyond a characteristic noise strength. Likewise, for cilia with non-identical intrinsic frequencies, synchronization is lost beyond a characteristic level of frequency disorder. In large cilia carpets, noise excites long-wavelength perturbations, whose relaxation times are proportional to the square of the system length. Thus, in large systems, we predict locally synchronized domains, instead of the global synchronization.