Reverse genetics systems that are based on either viral transcripts or cDNA genome segments cloned in plasmids have recently been reported for some of the dsRNA viruses of the Reoviridae family, namely African horsesickness virus, bluetongue virus and orthoreovirus. For rotaviruses, three reverse genetics systems which only allow the manipulation of a single genome segment have been described. These rotavirus single genome segment reverse genetics systems are not true stand-alone systems because they require a helper virus and a recombinant virus selection step. A true selection-free, plasmid- only or transcript-based reverse genetics system for rotaviruses is lacking. This study sought to identify and characterise the factors that need to be understood and overcome for the development of a rotavirus reverse genetics system using mRNA derived from the in vitro transcription of a consensus nucleotide sequence as well as from double-layered particles. The consensus whole genome sequence of the prototype rotavirus DS-1 and SA11 strains was determined using sequenceindependent whole genome amplification and 454® pyrosequencing. For the rotavirus DS-1 strain, a novel isoleucine in a minor population variant was found at position 397 in a hydrophobic region of VP4. NSP1 contained seven additional amino acids MKSLVEA at the N-terminal end due to an insertion in the consensus nucleotide sequence of genome segment 5. The first 34 nucleotides at the 5'- terminus and last 30 nucleotides at the 3'-terminal end of genome segment 10 (NSP4) of the DS-1 strain were determined in this study. The consensus genome segment 11 (NSP5/6) sequence was 821 bp in length, 148 bp longer than previously reported. The 454® pyrosequence data for a rotavirus SA11 sample with no known passage history revealed a mixed infection with two SA11 strains. One of the strains was a reassortant which contained genome segment 8 (NSP2) from the bovine rotavirus O agent. The other ten consensus genome segments of the two strains could not be differentiated. Novel minor population variants of genome segments 4 (VP4), 9 (VP7) and 10 (NSP4) were identified. Molecular clock phylogenetic analyses of the rotavirus SA11 genomes showed that the two SA11 strains were closely related to the original SA11-H96 strain isolated in 1958. Plasmids containing inserts of the consensus cDNA of the rotavirus DS-1 strain were purchased and used to generate exact capped transcripts by in vitro transcription with a T7 polymerase. Wild-type transcripts of rotavirus SA11 were obtained from in vitro transcription using purified rotavirus SA11 double-layered particles. The purified rotavirus DS-1 and SA11 transcripts were transfected into BSR, COS-7 and MA104 cells. Work on MA104 cells was discontinued due their very low transfection efficacy. In BSR and COS-7 cells, rotavirus DS-1 and SA11 transcripts induced cell death. However, no viable rotavirus was recovered following attempts to infect MA104 cells with the BSR and COS-7 transfected cell lysates. The cell death was determined to be due to apoptotic cell death mechanisms. Immunostaining showed that the DS-1 genome segment 6 (VP6) and SA11 transcripts were translated in transfected BSR and COS-7 cells. Based on visual inspection, the translation seemed to be higher in the retinoic acid-inducible gene-I (RIG-I) deficient BSR cells than in COS-7 cells. This suggested that the transfection of rotavirus transcripts induced an innate immune response which could lead to the development of an antiviral state. Therefore, the innate immune response to rotavirus transcripts was investigated in HEK 293H cells using qRT-PCR and western blot analyses. Results of this investigation showed that RIG-I, but not MDA5 sensed rotavirus transcripts in transfected HEK 293H cells. Furthermore, rotavirus transcripts induced high levels of cellular mRNA encoding the cytokines IFN-1β, IFN-λ1, CXCL10 and TNF-α. Other cytokines namely, IFN-α, IL-10, IL-12 p40 and the kinase RIP1 were not significantly induced. Inhibiting the RNA-dependent protein kinase R (PKR) reduced the induction of cytokines IFN-1β, IFN-λ1, CXCL10 and TNF-α, but the expression levels were not abrogated. The importance of a consensus sequence and the insights gained in the current study regarding the role of the innate immune response after transfection of rotavirus transcripts into cells in culture, should aid the development of a true rotavirus reverse genetics system. / Thesis (PhD (Biochemistry))--North-West University, Potchefstroom Campus, 2013

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The immunostimulatory properties of inactivated parapoxvirus ovis (iPPVO) have been investigated in different animal species and experimental settings. This study investigated the effects of administration of iPPVO on selected events of the innate response in mice. Neutrophil activation, phagocytic activity of macrophages, serum bactericidal activity, induction and antiviral activity of interferon type I (IFN - I) and expression of several classes of cytokines were assayed following intraperitoneal inoculation of Mus musculus with iPPVO (107 TCID50). Serum from iPPVO-treated animals showed IFN-I activity against murine encephalomyocarditis virus (EMCV) between 6 and 12 hours post infection (hpi), as shown by plaque reduction. A significant activation of neutrophils at 6hpi was observed by NBT reduction test in animals treated with the iPPVO. Peritoneal macrophages from mice treated with iPPVO demonstrated a significant increase (p<0.01) in phagocytic activity against Candida albicans both in vivo (between 12 and 96 hpi) and in vitro (24 and 72 hpi). iPPVO treated mice showed increased serum bactericidal activity against Escherichia coli (p<0.05) at two periods (24 and 72 hpi). A second study evaluated the expression of cytokines in response to inoculation of iPPVO. For this, spleens and serum samples were collected from mice treated with iPPVO at different intervals after inoculation and subjected to quantification of messenger RNA (mRNA) by real time PCR (qRT-PCR) and detection/quantification of serum cytokines by ELISA. Quantification of mRNA identified a significant and transient increase in the expression of various cytokines, with variable magnitude and kinetics. mRNA expression of proinflammatory cytokines (IL-1β, TNF-α and IL-8) peaked at 24 hpi (5.4 times increase) and 48 hpi (3 and 10 times, respectively). A 15-fold increase in expression of INF-γ and 6-fold for IL-12 was observed at 48 and 24 hpi, respectively. An increase in the expression of self-regulatory cytokines (Th2) cells, especially IL-10 and IL-4 was detected at later periods (72 and 96 hpi) with peaks of 4.7 and 4.9 fold, respectively. The determination of the concentration of serum cytokines by ELISA showed an increase in IL-1β, TNF-α, IL- 12, IFN-γ and IL-10 with kinetics similar to that observed by qPCR, especially for IL-1 and INF-γ. In summary, these results demonstrate that inoculation with iPPVO stimulates transiently a number events associated with cellular and humoral innate immune responses. If taken together, these effects would likely contribute for the enhanced resistance to certain pathogens observed in animals treated with iPPVO. / As propriedades imunoestimulatórias do Parapoxvirus ovis inativado (iPPVO) têm sido verificadas em diferentes espécies animais e condições experimentais. No presente trabalho foram investigados os efeitos da administração do iPPVO sobre eventos da resposta inata de camundongos. Ativação de neutrófilos, atividade fagocítica de macrófagos, atividade bactericida do soro, indução e atividade antiviral do interferon tipo I (INF-I) e expressão de várias classes de citocinas foram investigados em diferentes intervalos após inoculação de Mus musculus pela via intraperitonial com iPPVO (dose 107 TCID50). O soro de animais tratados com iPPVO apresentou atividade de INF-I frente ao vírus da encefalomiocardite murina (EMCV) entre 6 e 12 horas pós inoculação (hpi), como demonstrado pela redução significativa de formação de placas virais. Uma significativa ativação dos neutrófilos circulantes foi observada pela técnica de redução do NBT em animais tratados com o iPPVO às 6 hpi. Macrófagos peritoneais de camundongos tratados com iPPVO demonstraram um aumento significativo (p<0,01) na atividade fagocítica frente a Candida albicans tanto in vivo (entre 12 e 96 hpi) quanto in vitro (24 e 72hpi). Camundongos tratados com iPPVO apresentaram aumento na atividade bactericida do soro frente à Escherichia coli (p<0,05) em dois períodos avaliados (24 e 72 hpi). Um segundo estudo avaliou a expressão de citocinas em resposta à inoculação do iPPVO. Para isso, amostras de baço e soro foram coletados de camundongos tratados com iPPVO em diferentes intervalos após a inoculação e submetidas a quantificação de RNA mensageiro (RNAm) por PCR em tempo real (qRT-PCR) e detecção/quantificação de citocinas no soro por ELISA. A quantificação de RNAm permitiu detectar um aumento significativo e transitório da expressão de várias citocinas, com magnitude e cinética variáveis. A expressão de RNAm das citocinas pró-inflamatórias (IL-1β, TNF-α e IL-8) atingiu o pico às 24 hpi (aumento de 5,4 vezes), 48 hpi (3 e 10 vezes, respectivamente). Um aumento de 15 vezes na expressão gênica do INF-γ, e de 6 vezes para a IL-12 foi observado às 48 e 24 hpi, respectivamente. Um incremento na expressão das citocinas auto-regulatórias (Th2), principalmente IL-10 e IL-4, foi detectado em períodos mais tardios (72 e 96 hpi) com picos de 4,7 e 4,9 vezes, respectivamente. A determinação da concentração das citocinas séricas por ELISA revelou um aumento nos níveis de IL-1β, TNF- α, IL-12, INF-γ e IL-10, com uma cinética similar à observada pela técnica de qPCR, especialmente para IL-1β e INF-γ. Em resumo, esses resultados demonstram que o tratamento com iPPVO estimula de forma significativa e transitória uma série de eventos celulares e humorais ligados à resposta imune inata. Esses efeitos, se considerados em conjunto, provavelmente contribuem para o aumento da magnitude da resposta imunológica a certos patógenos observada em animais tratados com o iPPVO.

L’objectif de ce travail de thèse s’inscrit dans le cadre de l’étude de la réponse immune innée contre le virus influenza porcin (SIV) et de son contrôle dans l’espèce porcine par les protéines suppressors of cytokine signaling (SOCS) et la cytokine-inducible SH2 domain containing protein (CISH). L’analyse de l’expression des ARNm de SOCS à l’homéostasie a montré une expression significative dans le thymus suggérant un rôle dans la différenciation des cellules T. La réponse immune innée contre une souche de SIV de sous-type H3N2 a été analysée in vitro et ex vivo. L’expression de transcrits impliqués dans la réponse antivirale et de SOCS a été évaluée. Une surexpression des ARNm des gènes antiviraux et de SOCS1 a été observée notamment à 24h post-infection. L’infection expérimentale des cellules NPTr par le virus H3N2 induit une activation des voies de signalisation impliquant MAPK et JAK/STAT. L’utilisation d’inhibiteurs spécifiques de la voie JAK/STAT a conduit à une diminution de l’expression des transcrits antiviraux et ceux de SOCS1 ainsi que l’expression des interférons de type I et III. Afin de développer un outil alternatif in vitro d’étude de la réponse immune innée, la culture en interface air-liquide (ALI) des cellules NPTr a été réalisée. Des cellules à mucus, des jonctions serrées et une résistance transépithéliale élevée ont été observées. Cependant, ces cellules n’ont pas développé de cils. La culture des cellules NPTr dans des conditions ALI, a permis une représentation partielle de l’épithélium respiratoire porcin et constitue ainsi une alternative d’étude in vitro. / The aim of this work was to investigate the innate immune response to swine influenza virus (SIV) and its regulation in swine by the suppressors of cytokine signaling SOCS and the cytokine-inducible SH2 domain containing protein (CISH). The assessment of SOCS constitutive mRNA expression showed significant mRNA expression of SOCS1 in thymus suggesting a key role of this protein in T cell differentiation. The innate immune response against an SIV H3N2 subtype was then assessed in vitro and ex vivo by measuring antiviral and SOCS transcripts expression. The induction of several antiviral genes along with SOCS1 gene was observed. Experimental infection of NPTr cells with H3N2 virus induced MAPK and JAK/STAT signaling pathways activation. The inhibition of JAK/STAT pathway clearly reduced antiviral transcript expression, SOCS1 and both interferon types I and III mRNA expression as well. In order to develop an alternative in vitro tool to study the innate immune response, NPTr epithelial cell line were cultured at the air-liquid interface. This system promotes the differentiation of mucus producing cells, tight junctions development and enables high trans-epithelial electronic resistance values. Nonetheless, the NPTr cells do not develop cilia. The culture of NPTr cells in ALI conditions allows a partial in vitro representation to investigate some aspects of host/respiratory pathogen interaction in pigs.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / In aquaculture, eugenol have been used and recommended as anesthetics for several fish species. Moreover, this product has attracted the attention of researchers because of its chemopreventive, anti-inflammatory and antioxidant properties, as well as, its antimicrobial potential. The aim of this study was to evaluate the activity of eugenol against the fish pathogen Aeromonas hydrophila and eugenol s effect on hematological and natural immune parameters in silver catfish (Rhamdia quelen). In vitro, eugenol showed weak activity against A. hydrophila, but in vivo, at a subinhibitory concentration (10 mg L-1), it promoted survival in infected silver catfish. Eugenol (50 μg mL-1) reduced the hemolytic activity of A. hydrophila supernatant in vitro in fish erythrocytes. Subjecting catfish to eugenol baths (5 and 10 mg L-1) for five days did not alter the hematological and immunological parameters studied in this work. Based on these results, eugenol can be used to treat or prevent bacterial diseases in fish. / Na aquicultura o eugenol tem sido utilizado e recomendado como anestésico para várias espécies de peixes. Além disso, este produto tem atraído a atenção de pesquisadores devido a suas propriedades quimiopreventivas, antiinflamatórias e antioxidantes, bem como, o seu potencial antimicrobiano. O objetivo deste estudo foi avaliar a atividade do eugenol contra o patógeno de peixes Aeromonas hydrophila e seu efeito sobre parâmetros hematológicos e de imunidade natural em jundiás (Rhamdia quelen). O eugenol mostrou fraca atividade contra A. hydrophila in vitro, mas in vivo, a uma concentração subinibitória (10 mg/L) promoveu a sobrevivência de jundiás infectados. In vitro o eugenol (50 μg/mL) reduziu a atividade hemolítica do sobrenadante de A. hydrophila em eritrócitos de peixe. A exposição de jundiás ao eugenol (5 e 10 mg/L) através de banhos durante cinco dias não alterou os parâmetros hematológicos e imunológicos estudados neste trabalho. Com base nestes resultados, o eugenol pode ser usado para tratar ou prevenir infecções bacterianas em peixes.

Fundação de Amparo a Pesquisa do Estado de Minas Gerais / Neospora caninum is an intracellular parasite that has the dog as its definitive host and other mammals, especially cattle, as intermediate hosts. Economically, neosporosis is an important disease in Veterinary medicine due to the induction of relevant clinical signs, as abortions in cattle and neuromuscular paralysis in dogs. The aim of this study was to evaluate the role of the TLR adaptor protein TRIF in the resistance against N. caninum infection. For this, in vitro experiments with bone marrow derived macrophages (BMDMs) from C57BL/6 wild-type (WT) and TRIF knockout (TRIF-/-) mice, stimulated by tachyzoites and in vivo infections, were performed in order to investigate the production of cytokines and antibodies, cellular and tissue parasitism, histological changes during different phases of infection and survival analysis. We observed that TRIF-/- BMDMs presented notable defects in inflammatory cytokine production in relation to WT macrophages. Additionally, we found that the concentration of NO, IL-12p40, IFN-y and TNF were decreased in peritoneal fluids and lungs of TRIF-/- mice, while IL-2, IFN-γ, TNF and IL-17 were reduced in sera of these animals compared to WT mice. Higher parasite burden was observed in peritoneal cells, lungs and brain during the acute and chronic phases of infection, which were associated with inflammatory changes in the analyzed tissues, while TRIF-/- mice survival rate decreased 2-fold compared to WT. In conclusion, our results show that TRIF is required for resistance against the infection induced by N. caninum, regulating the production of key Th1 cytokines and participating in the control of the tissue parasitism and inflammatory lesions induced against the parasite. / Neospora caninum é um parasito intracelular que tem como hospedeiro definitivo o cão e outros mamíferos, especialmente bovinos, como hospedeiros intermediários. Economicamente, a neosporose é uma doença de grande importância na medicina veterinária por induzir relevantes sinais clínicos, como abortos em bovinos e paralisia neuromuscular em cães. O objetivo deste estudo foi avaliar o papel da molécula adaptadora TRIF da via de sinalização dos TLRs na resistência contra a infecção por N. caninum. Para isso, experimentos in vitro com macrófagos derivados de medula óssea (BMDMs) obtidos de camundongos do tipo selvagem (WT) e TRIF knockout (TRIF-/-) estimulados com taquizoítos e infecções in vivo foram realizadas a fim de se investigar a produção de citocinas e anticorpos, parasitismo celular e tecidual, alterações histológicas durante diferentes fases da infecção e análise de sobrevida. Nós observamos que BMDMs TRIF-/- apresentaram reduções significativas na produção de citocinas inflamatórias em relação a macrófagos WT. Adicionalmente, foi visto que as concentrações de NO, IL-12p40, IFN- e TNF foram diminuídas no lavado peritoneal e nos pulmões de camundongos TRIF-/-, enquanto que IL-2, IFN-γ, TNF e IL-17 foram reduzidas no soro desses animais em comparação aos WT. Alta carga parasitária foi encontrada nas células peritoneais, pulmões e cérebro durante as fases aguda e crônica da infecção, associada com alterações teciduais inflamatórias significativas nos pulmões. Além disso, camundongos TRIF-/- tiveram uma taxa de sobrevida 2 vezes menor quando comparada aos animais WT. Concluindo, nossos resultados mostram que TRIF é requerido para a resistência contra a infecção induzida por N. caninum, regulando a produção de citocinas chave do perfil Th1 de resposta imune e participando no controle do parasitismo tecidual e das lesões inflamatórias oriundas desta infecção. / Mestre em Imunologia e Parasitologia Aplicadas

Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-03-03T12:21:26Z No. of bitstreams: 1 alexandrebittencourtpigozzo.pdf: 866787 bytes, checksum: c6792b0cf7e2393b912ea7c1c8fdae2c (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-03-06T20:06:30Z (GMT) No. of bitstreams: 1 alexandrebittencourtpigozzo.pdf: 866787 bytes, checksum: c6792b0cf7e2393b912ea7c1c8fdae2c (MD5) / Made available in DSpace on 2017-03-06T20:06:30Z (GMT). No. of bitstreams: 1 alexandrebittencourtpigozzo.pdf: 866787 bytes, checksum: c6792b0cf7e2393b912ea7c1c8fdae2c (MD5) Previous issue date: 2011-02-28 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O sistema imunológico humano (SIH) é composto por uma rede complexa de células, tecidos e órgãos especializados em defender o organismo contra doenças. Para atingir tal objetivo, o SIH identifica e extermina uma ampla gama de agentes patogênicos externos, como vírus e bactérias, além de células do próprio organismo que podem estar se comportando de forma anormal, e que poderiam dar origem a tumores, caso não fossem eliminadas. O SIH é ainda responsável pelo processo de eliminação de células mortas e renovação de algumas estruturas do organismo. A compreensão do SIH é, portanto, essencial. Entretanto a sua complexidade e a interação entre seus muitos componentes, nos mais diversos níveis, torna a tarefa extremamente complexa. Alguns de seus aspectos, no entanto, podem ser melhor compreendidos se modelados computacionalmente, permitindo a pesquisadores da área realizar um grande volume de experimentos e testar um grande número de hipóteses em um curto período de tempo. A longo prazo, pode-se vislumbrar um quadro onde todo o SIH poderá ser simulado, permitindo aos cientistas desenvolverem e testarem vacinas e medicamentos contra várias doenças, bem como contra a rejeição de órgãos e tecidos transplantados, diminuindo o uso de animais experimentais. Neste contexto, o presente trabalho visa implementar e simular computacionalmente um modelo matemático do SIH, sendo o objetivo principal reproduzir a dinâmica de uma resposta imune ao lipopolissacarídeo (LPS) em um pequena seção de um tecido. O modelo matemático é composto de um sistema de equações diferenciais parciais (EDPs) que incorpora a dinâmica de alguns tipos de células e moléculas do SIH durante uma resposta imune ao LPS no tecido. / The Human Immune System (HIS) consists of a complex network of cells, tissues and organs. The HIS plays an crucial role in defending the body against diseases. To achieve this goal, the immune system identifies and kills a wide range of external pathogens such as viruses and bacteria, and the body's own cells which are behaving abnormally. If these cells were not eliminated, they could give rise to tumors. The HIS is also responsible for removing dead cells and replacing some of the structures of the body. The understanding of the HIS is therefore essential. However, its complexity and the intense interaction among several components, in various levels, make this task extremely complex. Some of its aspects, however, may be better understood if a computational model is used, which allows researchers to test a large number of hypotheses in a short period of time. In the future we can envision a computer program that can simulate the entire HIS. This computer program will allow scientists to develop and test new drugs against various diseases, as well as to treat organ or tissue transplant rejection, without requiring animals experiments. In this scenario, our work aims to implement and simulate a mathematical model of the HIS. Its main objective is to reproduce the dynamics of a immune response to lipopoly-saccharides (LPS) in a microscopic section of a tissue. The mathematical model is composed of a system of partial differential equations (PDEs) that defines the dynamics of some tissues and molecules of the HIS during the immune response to the LPS.

De par sa capacité à détecter les microorganismes et à mettre en place une défense anti-infectieuse rapide, l’immunité innée représente la première ligne de défense de l’hôte. La réponse immunitaire innée est déclenchée par des motifs microbiens moléculaires universels et conservés reconnus par des récepteurs innés parmi lesquels les "Toll-like Receptors" (TLR). L’activation de ces récepteurs induit une inflammation locale et une réponse antimicrobienne adaptée au pathogène. Ces propriétés biologiques ont permis de d’envisager l’utilisation des TLR comme cible thérapeutique antiinfectieuse. Dans ce contexte il a été montré que la flagelline, le composant majeur des flagelles bactériens et le seul agoniste de TLR5 décrit à ce jour, possédait des propriétés anti-infectieuses. Des études chez la souris ont montré que la flagelline induisait une forte production, par des cellules lymphoïdes innées, d’IL-22, une cytokine impliquées dans la protection des muqueuses. Par ailleurs, la forte expression de TLR5 par les cellules épithéliales laisse présager un rôle de ces cellules dans les propriétés anti-infectieuses de la flagelline. Toutefois, les mécanismes moléculaires et cellulaires effecteurs responsables des effets antimicrobiens de l’agoniste de TLR5 restent à définir.Au cours de ce travail de thèse, nous avons étudié les capacités anti-infectieuses de la flagelline dans deux modèles infectieux chez la souris. Nous avons tout d’abord montré que l’administration systémique de flagelline, en prophylaxie c’est-à-dire préalablement au challenge infectieux, permettait de protéger d’une infection intestinale par Yersinia pseudotuberculosis. La protection induite par la flagelline est observable lors d’une infection par la voie muqueuse mais est absente lors d’un challenge infectieux par la voie systémique, démontrant ainsi le caractère muqueux de la protection. L’effet protecteur de la flagelline dans notre modèle est dépendant de l’expression de TLR5 et indépendant de l’IL-22. Cette étude suggère donc un mécanisme original de protection médié par la flagelline, indépendant de l’IL-22.Nous avons également analysé la capacité anti-infectieuse de la flagelline dans un modèle murin d’infection respiratoire à Streptococcus pneumoniae. Nous avons notamment montré que la flagelline pouvait être utilisée en thérapeutique lorsqu’elle était associée à un antibiotique. En effet, l’association d’amoxicilline ou de co-trimoxazole avec la flagelline (voie intranasale) a permis de protéger des souris infectées par une dose létale de S. pneumoniae comparativement à l’antibiotique seul. L’efficacité de cette thérapie est dépendante de l’activation de TLR5 et est associée à une infiltration pulmonaire importante de polynucléaires neutrophiles. Ce traitement combinatoire améliore également la protection dans un modèle de surinfection pneumococcique post-grippale. Ces résultats montrent que la combinaison agoniste de TLR5/antibiotique améliore la réponse anti-infectieuse pulmonaire et permettent d’envisager de nouvelles stratégies antibactériennes dans le cas d’infections où les antibiotiques montrent leurs limites (infections nosocomiales, bactéries multirésistantes…). / With its ability to sense micro-organisms and to induce a rapid defense against infections, innate immunity represents the first line of host’s defense. The innate immune response is triggered by universal and conserved microbial molecular patterns recognized by innate receptors including the Toll-like receptors (TLRs). Activation of these receptors induces local inflammation and antimicrobial response against pathogens. These biological properties have allowed considering the use of TLR as anti-infective therapeutic target. In this context it has been shown that flagellin, the major component of bacterial flagella and the agonist of TLR5, had anti-infectious properties. It was shown that flagellin induces a strong production by innate lymphoid cells of IL-22, a cytokine involved in the protection of mucosa. Furthermore, the strong expression of TLR5 by epithelial cells suggests a role for these cells in the anti-infectious properties of flagellin. However, the molecular and cellular mechanisms responsible for the antimicrobial effects of the TLR5 agonist remained to be defined.In this thesis, we studied the anti-infectious properties of flagellin in two infectious murine models. We first showed that systemic administration of flagellin, prior to infectious challenge, protect against an intestinal infection with Yersinia pseudotuberculosis. The protection induced by flagellin is observable upon infection by mucosal route but is absent during a challenge by the systemic route, thus demonstrating the role of the mucosa for the protection. The anti-bacterial effect in this model is dependent on the expression of TLR5 and independent of the innate lymphoid cells’ IL-22 production. This study suggests a novel mechanism of flagellin-mediated protection, independent of the IL-22.We also analyzed the anti-infectious abilities of flagellin in a murine model of respiratory infection by Streptococcus pneumoniae. In particular, we showed that flagellin could be used in therapy when combined to an antibiotic. Indeed, the combination of amoxicillin or co-trimoxazole with flagellin protected mice infected with a lethal dose of S. pneumoniae compared to antibiotic standalone. The effectiveness of this therapy was dependent on the activation of TLR5 and was associated with pulmonary infiltration of neutrophils. This combinatory treatment also improved the protection in a model of post-influenza pneumococcal superinfection. These results show that the combination of TLR5 agonist / antibiotic ameliorates pulmonary anti-infectious response and allow to consider new antibacterial strategies against infections when antibiotics reach their limits (nosocomial infections, multiresistant bacteria ...).

Durant ma thèse, nous avons identifier PlpA comme une cytotoxine conservée dans des isolats cliniques d'origines diverses, contrairement à son homologue, le facteur de virulence ExoU de Pseudomonas aeruginosa. Un rôle dans la cytotoxicité envers des cellules phagocytaires de l'immunité innée a été attribué à PlpA, et celui-ci dépend de l'intégrité de la dyade catalytique Ser/Asp, caractéristique des protéines de la famille des patatines. Un interactome réalisé in vivo dans des cellules hôtes nous a permis d'identifier des transporteurs de la mitochondrie comme partenaires de PlpA. L'interaction de PlpA avec ses partenaires mitochondriaux, aurait de manière inattendue un effet anti-apoptotique sur les macrophages, mais conduit cependant, à la mort de ceux-ci vraisemblablement par un phénomène de nécrose induite.PlpD a précédemment été caractérisée par Salacha et ses collaborateurs comme étant l'archétype du Système de Sécrétion de Type Vd (2010). Bien que le mécanisme précis de sécrétion de cette protéine reste à ce jour mal connu, nos travaux ont permis de lui attribuer un rôle dans la compétition bactérienne, conférant ainsi un avantage compétitif aux souches qui la possède. D'ailleurs, l'analyse phylogénétique de PlpD (Salacha et al., 2010 ; Heinz & Lithgow 2014) révèle la conservation de cette protéine au sein de nombreuses espèces vivants dans un environnement hostile, suggérant ainsi la nécessité de cette protéine dans l'implantation et la conservation de niches écologiques, que se soit dans l'environnement ou au cours d'infections polymicrobiennes chez un organisme hôte. / During my PhD, in the PAO1 strain of Pseudomonas aeruginosa, we identified PlpA as a cytotoxin conserved in clinical isolates of various origins, contrary to its virulence factor ExoU homologues. A cytotoxic role of PlpA has been highlighted against phagocytic cells, and showed to depend on the integrity of its Ser/Asp catalytic dyad. An in vivo interactome allowed us to identify mitochondrial transporters as partners of PlpA. Interestingly, PlpA interaction with these partners has an anti-apoptotic effect on macrophages but ultimely allows macrophages death probably by a necroptosis phenomenon. PlpD was previously described by Salacha and collaborators as the SST5d archetype (Salacha et al., 2010). While its exact secretion mechanism remains poorly understood, our work allowed showing that it played a role in bacterial competition. PlpD phylogenetic analysis (Salacha et al., 2010 ; Heinz & Lithgow 2014) revealed its conservation in many species living in hostile environments, suggesting its necessity in the implantation and conservation of ecological niches in the environment or during polymicrobial infections into host organism.

Early innate response of intestinal epithelial cells is the first line defense against enteric pathogens. Toxoplasma gondii infections acquired naturally via the peroral route, encounter intestinal epithelial cells early post-infection. Although the population structure of T. gondii is known to be highly clonal, clinical strains of T. gondii have been classified into three genotypes based on their virulence. In this study we investigated whether human intestinal epithelial cell immune response to T. gondii is virulence dependent. We demonstrated distinct virulence of the three T. gondii genotype strains evaluated in human intestinal epithelial cells by their capacity to replicate and induce host cell cytotoxicity. The early host innate mechanisms such as activation of signaling pathways and induction of innate effectors were likewise differentially elicited by the three T. gondii strains. Low levels of TLR dependent NF-kB activation and a failure to rapidly up-regulate innate cytokine and chemokine genes was observed after virulent Type I strain infection. In contrast, early innate response to the less virulent Type II strain was rapid, efficient and led to high levels of IL-8 and IL-6 secretion, whereas response to Type III parasites was intermediate. Early expression of b-defensin 2 gene was suppressed specifically by virulent Type I strain and its activation prior to infection in intestinal epithelial cells led to decreased parasite viability. These findings provide evidence for T. gondii strain virulence dependent down-modulation of early human intestinal epithelial cell innate responses and highlight the importance of these cells in host defense against this infection. / Doctorat en Sciences biomédicales et pharmaceutiques / info:eu-repo/semantics/nonPublished

Mon projet a porté sur la caractérisation du mécanisme moléculaire des enzymes d'arenavirus (une 3'-5' exoribonucléase et une endonuclease) impliquées dans l'inhibition de la réponse innée IFN de type I et dans le vole de coiffe respectivement, et le développement d'une stratégie thérapeutique basée sur leur structures. Premièrement, j'ai résolu deux structures cristallographiques à haute résolution du domaine exoribonucléases du virus Mopeia (NP-exo MOPV) -un homologue du virus Lassa pathogène- en complexe avec deux ions différents. Ensuite, j'ai effectué une caractérisation fonctionnelle de l’activité exoribonucléase 3'-5' codée par ce domaine. Une corrélation entre la structure et la fonction de NP-exo MOPV démontre que; L’activité exoribonucléase 3'-5' est conservée chez les arenavirus pathogènes ainsi que chez les non-pathogènes. J'ai démontré pour la première fois que l'exoribonucléase est capable d'exciser un ARN misapparié, suggérant ainsi une potentielle activité de correction d'erreur par cette enzyme. Avec la structure de NP-exo MOPV, j'ai développé une stratégie in silico pour identifier des inhibiteurs potentiels spécifiques contre son activité et un inhibiteur a était identifié.En parallèle, nous avons résolu deux structures cristallographiques du domaine de l'endonuclease du virus de la LCMV en complexe avec deux ions catalytiques et deux composés appartenant a la famille des diketo. En résumé, ce travail éclaircit le rôle des exoribonucléases de la famille d'Arenaviridae allant de l’évasion de l'immunité innée à son implication directe dans la réplication. Il ouvre également la voie au développement des inhibiteurs contre ces nucléases. / My PhD work focused on the characterization of the molecular mechanism of two arenavirus enzymes - a 3'-5' exoribonuclease and an endonuclease - implicated in type I IFN suppression and mRNA cap-snatching respectively and the design of a structure based-drug strategy against them. First I solved two high resolution crystal structures of the exoribonuclease domain of Mopeia virus (NP-exo MOPV) -a non pathogenic homologue of the highly pathogenic Lassa virus- in complex with different metal ions. Next I performed an in depth functional characterization of the 3'-5' exoribonuclease activity encoded by this domain. By correlating the structure and function of NP-exo MOPV, I showed that; the 3'-5' exoribonuclease activity is conserved in pathogenic as well as in non-pathogenic arenaviruses. Also, I showed for the first time that this enzyme is able to excise a mismatched RNA suggesting that, arenaviruses might posses a mechanism to limit error incorporation by the RdR polymerase during replication. Using the crystal structure of NP-exo MOPV I designed a structure-based strategy to identify potential inhibitors specific for the 3'-5' exoribonuclease activity and have identified a potential inhibitor.Alongside, we solved two crystal structures of the endonuclease domain of LCMV in complex with two catalytic ions and two compounds belonging to the diketo family.In conclusion, this work has a deep implication extending the role of the Arenaviridae exoribonuclease from innate immunity evasion to direct implication in replication. It also paves the way for the development of inhibitors against these arenavirus nucleases.