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Aging is amongst the strongest risk factors for neurodegenerative disease and elevated Type I interferon (IFN) signaling has been associated with both normal aging and central nervous system (CNS) diseases. Type I IFN is normally produced by nucleated cells in response to the detection of viral pathogen associated molecular patterns (PAMPs) by pathogen recognition receptors (PRRs). More recently it has been appreciated that Type I IFNs are also produced in response to endogenous stimuli, in the absence of viral pathogens. While Type I IFN signaling has been shown to be elevated in human and murine brains during normal aging, the underlying cause was unknown. Here we demonstrate by flow cytometry that aging results in increased size and numbers of mitochondria in the murine brain. Despite identifying increased mitochondrial number and mitochondrial DNA content, we found no change to mitochondrially-encoded transcripts, suggesting either deficits in mitophagy or augmented biogenesis due to insufficient oxidative phosphorylation. Interestingly, mitochondrial numbers correlated with elevated Type I IFN signaling in aging, linking mitochondria to the age-dependent innate immune response in the CNS. Using genetically engineered mice, we excluded roles for two critical innate immune pathways, STING and IRAK4, in the age-dependent increase in Type I IFN signaling in the brain. Notably, we subsequently identified a mitochondrially restricted innate immune protein, mitochondrial antiviral signaling (MAVS) as an essential molecular mediator of the age-dependent Type I IFN response; MAVS deficiency in aged mice restored Type I IFN signaling in the CNS to the levels observed in adult wildtype mice. Further, using intracerebroventricular (icv) administration of antisense oligonucleotides (ASO) as an orthogonal approach, we reduced MAVS transcript and protein expression within the CNS and thereby reduced Type I IFN signaling. Our data demonstrate a specific and selective role of MAVS expression in the CNS in Type I IFN signaling in aging. To investigate the relationship between mitochondrial aging and MAVS activation, we isolated cytoplasmic and mitochondrial RNA from young and aged animals as MAVS is most studied for its response to RNA ligands. Upon transfection into reporter cells, we found that mitochondrial RNA, but not cytoplasmic RNA, from both young and aged mice was sufficient to induce Type I IFN reporter activity in a MAVS-dependent manner. Furthermore, we attempted to mimic the increase of mitochondria observed in the aging CNS by transferring mitochondria from young and aged animals to recipient cells. Mitochondrial transfer also induced MAVS-dependent Type I IFN signaling in wildtype, but not MAVS null, mouse embryonic fibroblasts (MEFs). Collectively, our findings suggest that the accumulation of mitochondria in aging serves as a robust source of MAVS pathway ligands and implicate a novel link between mitochondrial aging and MAVS-mediated innate immune signaling in the CNS.

Artificial flight on millimeter size scales has been a major challenge due to the difficulty in making a feasible flight mechanism in terms of fabrication, thrust and power used. Many have tried to copy animal flight but there has been little success at such sizes. One proposed solution is to make small thrusters out of resonant curved cantilevers which act as wings that follow a simple 1 degree-of-freedom motion. Such wings are free of joint friction, can be planarly fabricated using well documented techniques, can be predictably scaled to different sizes, and have been shown to generate a net thrust. In this thesis, the work investigates the nature of the wings’ thrust through thorough studies of computational fluid dynamic simulations to understand how they interact with the surrounding fluid and how exactly the forces are generated. Specifically, it considers the role of unsteady lagged fluid waves generated by the wings and explains how the wing-fluid interactions relate to drag coefficients at low to high flapping amplitudes and Reynolds numbers ranging from 100 - 100 000. It then studies the effect of different wing aspect ratios on the net force and power efficiencies. The results are then extended to a general dependence on the wings’ aspect ratio which allows for this parameter to be used in optimizing the wings’ net force/power used. Test wings are then made using an updated fabrication method and Molybdenum as the curve-inducing material in an attempt to produce more environmentally-stable wings with important successes, failures and improvements discussed. Results show that such Molybdenum-based wings are practical for flight, and that resonant curved cantilevers wings can be made more feasible by simple changes to their shape. / Thesis / Master of Applied Science (MASc)

Autonomous vehicles are complex robotic and artificial intelligence systems working together to achieve safe operation in unstructured environments. The objective of this work is to provide a foundation to develop more advanced algorithms for off-road autonomy. The project explores the sensors used for off-road autonomy and the data capture process. Additionally, the point cloud data captured from lidar sensors is processed to restore some of the geometric information lost during sensor sampling. Because ground truth values are needed for quantitative comparison, the MAVS was leveraged to generate a large off-road dataset in a variety of ecosystems. The results demonstrate data capture from the sensor suite and successful reconstruction of the selected geometric information. Using this geometric information, the point cloud data is more accurately segmented using the SqueezeSeg network.

L’immunité innée représente la première ligne de défense d’un organisme face à une infection virale, en engendrant une réponse rapide capable de restreindre la menace microbienne. Dans la cellule, les récepteurs Toll-likes (TLRs) et les hélicases cytosoliques RIG-I like (RLRs) représentent les deux systèmes majeurs de reconnaissance des virus. Les acides nucléiques viraux sont notamment reconnus les hélicases cytosoliques RIG-I et MDA5. Ces deux protéines possèdent deux domaines CARD impliqués dans le recrutement de la protéine adaptatrice MAVS, capable d’induire l’activation des promoteurs interférons (IFNs) de type I et de NF-B pour la mise en place d’une réponse antivirale. De façon surprenante, MAVS est localisée au niveau de la mitochondrie et a besoin de cette association au compartiment mitochondrial pour exercer sa fonction. Bien que de nombreuses études aient montré le rôle crucial de la protéine mitochondriale MAVS dans la signalisation antivirale des RLRs, sa régulation est encore mal connue à ce jour. Ce travail de doctorat a permis de mettre en évidence que la dégradation de MAVS suite à une infection virale est nécessaire à la transduction du signal antiviral. Nous avons ainsi déterminé que l’E3 ubiquitine ligase TRIM25 induit l’ubiquitination puis la dégradation de MAVS quelques heures après une infection virale. De plus, nous avons montré que l’activation du signalosome aboutissant à la production des IFNs de type I et dépendant de MAVS n’a lieu que suite à sa translocation de la mitochondrie vers le cytosol permise par la dégradation de MAVS. Enfin, nous avons mis en évidence le rôle essentiel de l’élongation du réseau mitochondrial suite à une infection virale pour la transduction du signal dépendant de MAVS. / Innate Immunity acts as the first line of the host defense against viral infection, providing a rapid response to restrict the microbial threats. Toll-like receptors (TLRs) and cytosolic RIG-I-like helicases (RLRs) are the two major receptor systems for detecting virus. Viral nucleic acids are recognised by the helicases RIG-I and MDA5. These receptors contain two CARD domains involve in the recruitment of the mitochondrial antiviral signaling adaptor MAVS whose activation triggers a rapid production of type 1 interferons (IFNs) and of pro-inflammatory cytokines. Interestingly, it has been reported that MAVS must be localized to mitochondria to exert its function. While MAVS is essential for this signaling, its function and regulation remain unclear. In this work, we report that RLR activation triggers MAVS ubiquitination by the E3 ubiquitin ligase TRIM25 and marks it for proteasomal degradation concomitantly with downstream signaling. MAVS appears to function as a recruitment platform to first assemble a signaling complex, then the proteasome-mediated MAVS degradation is required to unleash into the cytosol this signaling complex allowing the signalosome activation and ensuing type I IFNs production. Futhermore, we reported that mitochondrial dynamics regulate MAVS-mediated signaling after viral infection.

Wirtszellen verfügen über bisher unzureichend verstandene zellautonome Immunmechanismen zur Abwehr von intrazellulären Bakterien. In dieser Arbeit wurden zwei Abwehrmechanismen charakterisiert, die in Endothelzellen und Makrophagen Infektionen durch C. pneumoniae bekämpfen. Es konnte gezeigt werden, dass C. pneumoniae über einen MAVS-abhängigen Signalweg in humanen Endothelzellen erkannt wird. Diese Erkennung aktiviert die Transkriptionsfaktoren IRF3 und IRF7 und nachfolgend eine IRF3/7-abhängige Typ I-IFN-Produktion. Typ I-IFN bewirken auto- und parakrin eine Kontrolle der intrazellulären Infektion mit C. pneumoniae. Zum anderen wurde gezeigt, dass das mitochondriale Molekül NLRX1 eine zellautonome Abwehr gegen C. pneumoniae in Endothelzellen und in Makrophagen vermittelt. Diese NLRX1-abhängige intrazelluläre Abwehr ist unabhängig von verschiedenen, bisher mit NLRX1 in Verbindung gebrachten Signalwegen. Die Ergebnisse zeigen somit zum ersten Mal, dass NLRX1 eine zellautonome Abwehr gegen intrazelluläre Bakterien vermittelt. Daraus gewonnene Erkenntnisse sowie die Ergebnisse zukünftiger Arbeiten zur Klärung der NLRX1- und MAVS-aktivierenden chlamydialen Moleküle und den durch Typ-I-IFN-abhängigen intrazellulären Abwehrmechanismen könnten bei der Erforschung neuartiger antibakterieller Therapien hilfreich sein. Diese ist angesichts der weltweiten signifikanten Zunahme von mehrfach-resistenten Infektionserregern, unbedingt notwendig. / The cell autonomous defense mechanisms against intracellular bacteria in host cells are so far insufficiently understood. In the present work two defense mechanisms involved in the elimination of C. pneumoniae in endothelial cells and in macrophages were characterized. It could be shown that C. pneumoniae is recognized by a MAVS-dependent signaling pathway in human endothelial cells. This recognition activates the transcription factors IRF3 and IRF7 and subsequently an IRF3/7-dependent type I-IFN production. Type-I-IFNs induce an auto- and paracrine control mechanism against the intracellular infection with C. pneumoniae. Additionally it could be shown for the first time that the mitochondrial NLR molecule NLRX1 mediates a cell autonomous defense mechanism against C. pneumoniae and most likely other intracellular bacteria in human endothelial cells and murine macrophages. This NLRX1-dependent intracellular defense mechanism is independent of the different mechanisms which were so far linked to NLRX1. The outcome of this work and future studies to identify chlamydial molecules responsible for the activation of the MAVS- and NLRX1-dependent signaling pathways as well as the effector mechanisms responsible for Type-I-IFN-dependent control of intracellular chlamydial replication could be very helpful in the development of novel antibacterial therapies.

Certains motifs moléculaires associés à la mort cellulaire semblent identifier les cancers prompts à répondre à une thérapie cytotoxique. Ceci en élaborant une réponse anti-tumorale basées sur une réponse T protectrice. Mon travail de thèse montre que le traitement par chimiothérapie immunogène active des voies moléculaires mimant une infection virale. Ceci conduit au niveau des cellules tumorales à une signalisation autocrine via l’IFNαβ / IFNAR1/2, initiée par la reconnaissance d’ARN double brin (dsRNA) endogène par les Récepteurs endosomaux de Reconnaissance des Motifs (PRRs). De façon plus détaillée, nous montrons que les axes TLR3/TRIF (senseurs endosomaux de dsRNA) et IFNAR1/2 (Récepteurs de l’IFN de Type I) doivent signaliser au niveau de la cellule tumorale pour que la chimiothérapie puisse aboutir à l’induction de l’axe CXCL10/CXCR3 et éliciter une réponse efficace in vivo. L’analyse du profil ARN de cellules tumorales Tlr3+/+ (mais pas Tlr3-/-) exposées aux anthracyclines a révélé une forte empreinte virale/IFN, indispensable à l’efficacité/activité anti-tumorale. Le fait d’affecter les axes TLR3 ou IFNAR1/2 au niveau tumorale soit à l’aide d’anticorps neutralisants, soit à l’aide de modèles KO abroge le relarguage de CXCL10 induit par la chimiothérapie, et ainsi la capacité à contrôler la pousse tumorale à moins que de l’IFNαβ ou du CXCL10 exogène soit co-administré aux anthracyclines. De plus la chimiorésistance des tumeurs traitées par des molécules n’induisant pas de signature virale peux être réversée par de l’IFN de Type I exogène. Enfin, la détection d’une signature IFN au niveau de biospies de cancers du sein humains permet de prédire la bonne réponse au traitement adjuvant par anthracyclines. D’un point de vue de l’évolution, alors que les tumeurs (comme les virus) ont élaboré des mécanismes pour échapper aux réponses IFN, la signature virale induite par la chimiothérapie devrait contribuer à contrecarrer cette immunoédition. / Distinct cell death-associated molecular patterns might define cancers proned to respond to a cytotoxic therapy by mounting a protective T cell-based anticancer immunity. My PhD Thesis work shows that immunogenic chemotherapy phenocopies viral infection leading to autocrine IFNαβ/IFNAR1/2 signalling in tumor cells initiated by recognition of self dsRNA by endosomal pattern recognition receptors (PRRs). In detail, TLR3/TRIF (endosomal dsRNA sensors) and IFNAR1/2 (Type I IFN receptors) must signal within the tumor cells so that chemotherapy can induce downstream CXCL10/CXCR3 axis and elicit therapeutic responsiveness in vivo. RNA profiling of Tlr3+/+ (but not Tlr3-/-) tumor cells exposed to anthracyclines revealed a strong IFN/viral fingerprint, indispensable for the tumoricidal activity. Neutralization by antibodies or genetic defects affecting tumor –associated TLR3 or IFNAR1/2 compromised chemotherapy-induced CXCL10 release and tumor control unless exogenous IFNαβ or CXCL10 are concomitantly supplied to anthracyclines. Moreover, chemoresistance of tumors treated by drugs failing to induce a viral signature can be reversed by exogenous Type I IFN. Finally, the IFN fingerprint of human breast cancers allowed to predict tumors proned to benefit from adjuvant anthracyclines. From an evolutionary viewpoint, while tumors (like viruses) have evolved mechanisms to evade an IFN response, chemotherapy-induced viral mimicry might contribute to bypass such as immunoediting.

This study describes a method for conducting the structural dynamic analysis of a crane fly (family Tipulidae) forewing under different airflow conditions. Wing geometry is captured via micro-computed tomography scanning. A finite element model of the forewing is developed from the reconstructed model of the scan. The finite element model is validated by comparing the natural frequencies of an elliptical membrane with similar dimensions of the crane fly forewing to its analytical solution. Furthermore, a simulation of the fluid-structure interaction of the forewing under different airflows is performed by coupling the finite element model of the wing with a computation fluid dynamics model. From the finite element model, the mode shapes and natural frequencies are investigated; similarly, from the fluid-structure interaction, the time-varying out-of-plane deformation, and the coefficients of drag and lift are determined.

The goal of this project is to use inspiration acquired from bird flight to optimize the wing planform of micro-air vehicle wings. Micro-air vehicles are used by the military for surveillance and for search and rescue missions by civilian first-responders. These vehicles fly in the same low Reynolds number regime as birds, and have low aspect ratios similar to the pheasants and grouse of the order Galliformes. Conventional analysis is difficult for low Reynolds numbers, prompting use of biologically inspired methods of optimization. Genetic algorithms, which mimic the process of evolution in nature, were used to define wing shapes that were tested in wind tunnel experiments. In these experiments, lift-drag ratios at various angles of attack were measured on scale model micro-air vehicle wings (with variable length feathers) similar in shape to a bird wing. The planform shape of the scale model wing evolved in the wind tunnel flow over successive generations to ultimately produce superior wings with higher lift-drag ratios. The low angle of attack wings were easily optimized into a wing shape different from and potentially more efficient than the oft-used Zimmerman planform. The process was repeated for a higher angle of attack, near stall conditions, which yielded a different wing planform shape. Chord distributions of the optimized low angle of attack wings were found to closely match the same distributions of birds from the order Galliformes. Results from flow visualization studies meant to illuminate possible physics responsible for the higher lift-drag ratios were also investigated.

The adenosine deaminase acting on RNA (ADAR) enzymes catalyse the hydrolytic deamination of adenosine (A) to inosine (I) in double stranded (ds) RNA. Mutations in ADAR1 underlie the autoimmune disorder Aicardi Goutiѐres syndrome (AGS). Patients with AGS display heightened levels of type I interferon (IFN) and IFN stimulated genes (ISGs). The first aim of my thesis was to determine whether the mutations found in the human ADAR1 gene affected RNA editing. I found that the ADAR1 mutants identified in the AGS patients have reduced editing activity. Interestingly, the mutations have a greater effect on the IFN-inducible cytoplasmic isoform, ADAR1p150 than on the constitutive ADAR1p110 isoform. These results imply that A-to-I editing plays a role in regulating the type I IFN response. The Adar1 null mouse dies by E12.5 with a type I IFN signature similar to that observed in the AGS patients. The second aim of my thesis was to characterize the immune signalling pathway aberrantly activated in the absence of Adar1. A colleague in our research group rescued the Adar1 null mouse to birth by blocking the cellular response to cytoplasmic dsRNA by generating a double mutant with the mitochondrial antiviral signalling adaptor, Mavs. In the Adar1-/-; Mavs-/- mutant I found that the aberrant immune response is rescued at E11.5. This indicates that MAVS is the downstream adaptor in the aberrant immune response that underlies the embryonic lethality in the Adar1-/- mouse. The third aim of my thesis was to determine if the lack of inosine modification within cellular RNA was triggering the aberrant immune response in the Adar1-/- mouse. To study this, Adar1-/-; p53 -/- mouse embryonic fibroblasts (MEFs) were generated. By reintroducing various ADAR isoforms into the Adar1-/-; p53 -/- MEFs I found that to rescue the aberrant immune response requires both catalytic activity and the location of an ADAR protein within the cytoplasm. Moreover, I demonstrated that transfecting inosine-containing dsRNA oligonucleotides into Adar1-/-; p53 -/- MEFs suppresses the aberrant immune response. Overall my results suggest that A-to-I editing by ADAR1 is an essential RNA modification that is required by the cell to distinguish between ‘self’ and ‘non-self’ RNA. Editing of cellular RNAs prevents an autoimmune response whereas editing of viral RNA may act to suppress a heightened antiviral immune response and prevent long-term damage to the cell.