Dissertations / Theses on the topic 'IIV infections'

Le virus de l'hépatite C (VHC) est l'un des principaux facteurs étiologiques du carcinome hépatocellulaire. Le traitement des hépatites virales C a été récemment amélioré grâce à une trithérapie (interféron, ribavirine et anti-protéase virale). Néanmoins l'importance des effets secondaires et l'émergence de mutants résistants nécessitent de découvrir de nouveaux antiviraux. Dans ce contexte, notre équipe a récemment découvert que les phosphatidylinositol 4-kinases de type III (PI4KIIIα et PI4KIIIβ) étaient indispensables à la propagation du virus dans une lignée hépatique humaine, et ce, à 2 étapes de son cycle biologique : l'entrée et la réplication. L'objectif du présent travail était de poursuivre la validation de ces nouvelles cibles thérapeutiques potentielles, en approfondissant nos connaissances sur la dépendance du virus à l'égard de ces kinases au cours de son entrée. Pour cela, nous avons utilisé le modèle des hépatocytes humains primaires, système in vitro plus proche du contexte physiologique que les modèles utilisés jusqu'à présent et qui étaient basés sur l'exploitation de lignées. Deux axes ont été développés : Vérification de l'importance de l'activité kinase des PI4KIIIs au cours de l'entrée du VHC dans les hépatocytes humains primaires, à travers une approche chimique ; Validation de l'implication de ces kinases et de leur activité enzymatique au cours de l'entrée virale grâce à une approche génétique basée sur l'ARN interférence et la restauration de phénotype. En parallèle, nous avons étudié l'expression de PI4KIIIα au cours de pathologies hépatiques. Nos résultats suggèrent une implication de PI4KIIIα au cours de l'entrée du VHC dans les hépatocytes humains primaires, mais restent à confirmer quant à l'implication de PI4KIIIβ. Par ailleurs, l'analyse de l'expression de PI4KIIIα dans le carcinome hépatocellulaire (CHC) conduit à proposer cette kinase comme un nouveau marqueur moléculaire, qui pourrait améliorer les modèles de pronostic déjà établis et pourrait conduire au développement de nouvelles approches thérapeutiques pour les patients atteints d'un CHC, quelque soit l'étiologie.

Malaria remains one of the most devastating diseases worldwide, causing 450,000 deaths every year. Given the lack of an effective vaccine against Plasmodium and the increased resistance of this parasite to the current drugs and of Anopheles mosquitoes to insecticides, there is an urgent need for the development of novel control strategies to control malaria's transmission. The insulin/insulin growth factor signaling (IIS) pathway is highly conserved and has shown to regulate lifespan, metabolism, immunity and pathogen resistance. We previously showed that overexpression of Akt, a key molecule of the IIS in the fat body of Anopheles stephensi, extended lifespan and had no impact on reproduction for the first and second reproductive cycle. To further explore the role of IIS beyond lifespan and reproduction, we looked to determine IIS's role in controlling immunity by analyzing the antimicrobial transcript expression in young transgenic females compared to non-transgenic females in response to infection with E. coli and B. subtilus. We also analyzed the survival rate of both transgenic and non-transgenic mosquitoes in in response to infection with E. coli and B. subtilus. We observed that IIS influenced mosquito antimicrobial transcript gene expression and mortality rate in response to E. coli and B. subtilus. Our data suggested that overexpression of the IIS in a mosquito’s fat body altered innate immunity genes and the mosquito’s survival rate.

Infectious bronchitis virus (IBV) is the causative agent of an economically important disease of poultry. In Brazil this disease causes respiratory, renal and reproductive problems in birds of all ages, despite constant vaccination with the Massachusetts strain H120. This lack of immunological protection is known to be due the genetic variation in the spike glycoprotein of IBV, which is involved in host cell attachment, neutralization and the induction of protective immunity. Brazilian IBV variants resulting of this genetic variation are present since the 80s and this study aimed to epidemiologicaly analyze and molecularly characterize the existing variants during 2010-2015 and perform a bioinformatics analysis of the available sequences of IBV variants in a 40 year period. Of the 453 samples tested, 61.4% were positive for IBV and 75.9% of them were considered variants and were detected in birds of all ages, distributed in all five Brazilian regions. A fragment of 559-566 bp was obtained from 12 isolates, where BR-I was the predominant variant while only one isolate belonged to the BR-II genotype. Bioinformatics analysis of the sequences of 40 years of Brazilian IBV variants was performed and the ratio of non-synonymous substitutions per non-synonymous site (dn) to synonymous substitutions per synonymous site (ds) dN/dS was calculated. It revealed a predominance of codons with non-synonymous substitutions in the first third of the S1 gene and a dN/dS ratio of 0.6757, indicating that this portion of the gene was under negative selection. Additionally prediction of N-glycosilation sites showed that most of the BR-I variants (from 2003 to early 2014) present an extra site at animoacid position 20, while the newest ones lack this feature.Together these results suggest that IBV Brazilian variants had probably suffered drastic mutations in some points between the years 1983 to 2003 and after achieving an antigenic structure effective enough for invasion and replication in their hosts, the selection processes became silent.
O vírus da bronquite infecciosa das galinhas (IBV) é o agente causador de uma doença aviária economicamente importante. No Brasil, esta doença ocasiona problemas respiratórios, renais e reprodutivos em aves de todas as idades, apesar da vacinação constante com a cepa Massachusetts H120. Esta falha na proteção conferida pela vacina é ocasionada por mutações nos nucleotídeos do gene da glicoproteína da espícula, a qual está envolvida no processo de interação comas células do hospedeiro, a neutralização e a indução de imunidade protetora. As variantes brasileiras resultantes dessa mutação genética estão presentes desde os anos 80 e este estudo teve como objetivo analisar epidemiologicamente e caracterizar molecularmente os vírus variantes existentes durante 2010-2015 e realizar uma análise bioinformática das sequências disponíveis no GenBank em um período de 40 anos. Das 453 amostras analisadas, 61,4% foram positivas para IBV e 75,9% delas foram consideradas variantes e foram detectados em aves de todas as idades, distribuídos em todas as 5 regiões do Brasil. Um fragmento de 559-566 pb foi obtido a partir de 12 isolados, onde BR-I foi a variante predominante ao contrario que apenas um isolado pertencia ao genótipo BR-II. Análise bioinformática de 40 anos de variantes do IBV brasileiros revelou uma predominância de codões com as substituições não sinónimos no primeiro terço do gene S1 e uma relação dN / dS de 0,6757, indicando que esta porção do gene estava sob selecção negativa. Além disso a previsão de pontos de de N-glicosilação mostrou que a maioria das amostras variantes BR-I (entre o 2003 e início de 2014) apresentam um ponto adicional na posição 20, enquanto as variantes mais novas não apresentam esse ponto de nglicosilação. Estes resultados sugerem que as variantes brasileiras teriam sofrido mutações provavelmente drásticas em alguns pontos do genoma, entre os anos de 1983 a 2003 e depois de atingir uma estrutura antigênica eficaz o suficiente para a invasão e replicação em seus hospedeiros, o processo de seleção mudou para seleção negativa.

Influenza A virus (IAV) causes annual epidemics and sporadic pandemics of respiratory disease in humans. One of the main complications of primary IAV infection is increased susceptibility to secondary bacterial co-infection, with Staphylococcus aureus being the most common co-infecting species. Previous work identified secreted proteases from S. aureus as a pro-viral factor, leading to specific cleavage of the IAV surface hemagglutinin and increase in infectious viral titre. The aim of this study was to investigate the effect of bacterial proteases, and other secreted bacterial proteins, on IAV replication. Supernatants from the S. aureus community-associated epidemic clone USA300 were separated by size exclusion chromatography and each fraction was tested for an impact on IAV replication in primary chicken embryo fibroblast (CEF) cells. A fraction that increased viral titre by at least 10-fold was identified, but this effect was independent of known secreted proteases. Through the use of mass spectrometry fingerprinting and bacterial mutagenesis, a single protein, S. aureus lipase 1, was identified to be responsible for the pro-viral effect. Lipase 1 is expressed by an array of diverse S. aureus strains of distinct clonal origins. Both the native and recombinant form of lipase 1 were pro-viral only during the infection of primary cells, including primary human lung fibroblasts. Further validation of this interaction indicated lipase 1 was pro-viral in a concentration dependant manner and for a range of IAV strains. Investigation into the mechanism of action of lipase 1 revealed the protein acts during a single infectious cycle in a manner dependent on its active site. Time of addition studies and western blot analysis showed lipase 1 affects the later stages of virus replication, but there is no direct interaction with the virus particle; rather, the protein manipulates the cell, resulting in an increased number of infectious particles being produced. This work has identified and validated a single S. aureus protein, which affects IAV replication. Thus, it has elucidated some of the complex interactions that occur between the virus and bacteria during co-infection. It has also demonstrated a novel role for a bacterial enzyme in IAV replication, the study of which can further our understanding of both IAV and cell biology.

Gastrointestinal tracts from 48 helmeted guineafowl (Numida meleagris), five Swainson’s spurfowl (Pternistis swainsonii) and a single Orange River francolin (Scleroptila levaillantoides) were examined for helminth parasites. Twelve species of helminths were found in helmeted guineafowl, comprising six nematodes, five cestodes and a single acanthocephalan.Six species of nematodes were recovered fromSwainson’s spurfowl and a single nematode was recovered from the Orange River francolin. First-year guineafowl had more than twice the intensity of infection than did adult guineafowl, particularly regarding the acanthocephalan Mediorhynchus gallinarum, the caecal nematodes Subulura dentigera and S. suctoria, and the cestodes Octopetalum numida, Hymenolepis cantaniana and Numidella numida. Female guineafowl had significantly higher intensities of infection than males, especially concerning M. gallinarum, S. dentigera and N. numida and the nematode Gongylonema congolense. The recovery of the cestode Retinometra sp. from helmeted guineafowl constitutes a new host-parasite record.

La mammite bovine est l’inflammation des tissus internes de la glande mammaire des vaches laitières. Elle est la plupart du temps causée par l’intrusion d’agents pathogènes dans le canal du trayon de la glande mammaire causant ainsi une infection intramammaire (IIM). La mammite engendre des pertes économiques importantes pour l’industrie laitière en raison de la faible production du lait, des coûts de traitements élevés, la présence de résidus d’antibiotiques dans le lait suite à leur utilisation, le rejet de lait non destiné à la consommation et les faibles taux de rendement pendant la transformation du lait en divers produits laitiers. Le développement de l’inflammation est souvent associé au degré d’exposition des glandes mammaires aux pathogènes. Staphylococcus aureus est le pathogène le plus souvent responsable de la mammite bovine au Canada. Il est capable de causer des infections intramammaires persistantes sous-cliniques souvent réfractaires à l’antibiothérapie. En outre, le biofilm représente un facteur de virulence clé dans la persistance de S. aureus pendant la mammite, car il augmente la résistance des bactéries contre les antibiotiques grâce à la matrice extracellulaire qui recouvre et protège la communauté. Le biofilm représente donc, une problématique majeure de l’industrie laitière et le besoin de nouveaux outils thérapeutiques alternatifs adressant ce facteur de virulence est très urgent. Le chitosane est une molécule naturelle extraite de la carapace des crustacés. Elle est exploitée pour de multiples applications biologiques, y compris certaines activités antibiofilm. Dans cette étude, nous avons démontré que les formes de 2,6 kDa et 4 kDa empêchaient la production de biofilm des souches : S. aureus 2117 (forte productrice du biofilm) et le SARM bovin (S. aureus résistant à la méthicilline). Chez la souris, l’administration d’un chitosane de 2,6 kDa n’a démontré aucun effet inflammatoire comparativement au 4 kDa. Les tests de bactéricidie ont démontré que le 2,6 kDa était capable de tuer les bactéries incorporées dans les biofilms préformés d'une manière dose-réponse avec une réduction de > 3 log[indice inférieur 10] CFU / biofilm à la concentration de 4 mg / ml. En culture cellulaire, nous avons observé que le chitosane de 2,6 kDa pouvait empêcher la persistance du SARM bovin dans les cellules épithéliales bovines MAC-T. Les tests de combinaison sur plaque ont révélé que le 2,6 kDa produit une synergie avec les antibiotiques de la classe des macrolides (par exemple, la tilmicosine) contre S. aureus, en réduisant la CMI des deux molécules par 2-8 fois. Finalement, l'administration intramammaire de 2,6 kDa, seul (p <0,01) ou en combinaison avec la tilmicosine (p <0,0001), a réduit la colonisation de S. aureus dans les glandes mammaires de notre modèle de mammite aigu murin.

A bronquite infecciosa das galinhas (BIG) é uma doença altamente contagiosa causada por múltiplos genotipos/sorotipos do vírus da bronquite infecciosa das galinhas (IBV), um coronavirus do grupo 3. Embora classicamente associado ao trato respiratório, alguns tipos de IBV têm sido descritos com tropismo pelos rins e pelos tratos reprodutivos e entéricos, o IBV pode ser detectado em diversos tipos de tecidos, e também pode acometer aves de todas as idades. Este estudo tem como objetivo verificar a freqüência do IBV em amostras de diversos órgãos e conteúdo entérico de avós, matrizes, poedeiras comerciais e frangos de corte, genotipar as amostras detectadas e estudar a diversidade molecular entre as amostras brasileiras de IBV. Um total de 844 pools de diversos órgãos e conteúdos entéricos provenientes de 200 lotes de avós, matrizes, poedeiras comerciais e frangos de corte, das regiões Sul, Sudeste, Centro-oeste e Nordeste do Brasil, colhidas durante o período de 2007 a 2009 foram testadas para a presença de IBV com um RT-PCR dirigido à região não traduzida 3′(3′UTR). As aves amostradas apresentaram sinais clínicos compatíveis com a BIG. Todas as amostras de IBV detectadas foram tipificadas utilizando uma RT-PCR dirigida ao gene de espícula do vírus. Dezenove amostras tipificadas como variante foram submetidas ao seqüenciamento parcial da região codificadora da subunidade S1 e à análise genealógica. Considerando os pools de órgãos e de conteúdo entérico, 45,50% foram positivos para a presença de IBV, dos quais, 84,63% pertencem ao genotipo Variante e 9,89% ao sorotipo/genotipo Massachusetts. Considerando os lotes, 73,50% foram positivos para IBV, sendo 77,55% variantes e 6,12% Massachusetts. A análise genealógica revelou quatro linhagens virais, todas agrupadas em um exclusivo grupamento de genotipo brasileiro. Estes resultados demonstram que o IBV está disseminado em todas as regiões avícolas brasileiras, com um predomínio massivo de genotipos não Massachusetts e uma elevada diversidade molecular, que deve ser levada em consideração para desenvolver medidas preventivas contra o IBV.
Infectious bronchitis (IB) is a highly contagious disease of poultry caused by multiple geno/serotypes of avian infectious bronchitis virus (IBV), a group 3 coronavirus. Though classically associated to the respiratory tract, IBV strains also have been described which harbor tropism for the kidneys and the reproductive and enteric tracts, and might be detected in multiple tissues and can also affect birds of all ages. This survey aimed to assess the frequency of in multiple organs and enteric content samples from grandparents, breeders, layers and broilers, to genotype the IBV strains detected and to study the molecular diversity amongst Brazilian IBV strains. A total of 844 pools of multiple organs and enteric contents from 200 flocks of grandparents, breeders, layers and broilers from the Southern, Southeastern, Central-Western and Northeastern Brazilian regions collected between 2007 and 2009 was screened for the presence of IBV with an RT-PCR target to the 3 untranslated region (UTR). The sampled birds presented symptoms compatible with IB. All IBV strains detected were then typed using an RT-PCR target to the spike gene of the virus. Nineteen strains type as variants were submitted to partial sequencing of the S1 coding region and genealogic analysis. Regarding the organs and enteric content pools, 45.50% were positive for the presence of IBV, from which 84.63% were variant and 9.89% Massachusetts. Taking into account the flocks, 73.50% were positive for IBV, being 77.55% variants and 6.12% Massachusetts. Genealogic analysis revealed four viral lineages, all grouped in an exclusive Brazilian genotype cluster. This results shown that IBV is widespread in all Brazilian poultry regions, with a massive predominance of non-Massachusetts genotypes and a high molecular diversity, which must be taken into account in order to develop preventive measures against IB.

A bronquite infecciosa é uma doença viral, aguda e altamente contagiosa que afeta as aves da espécie Gallus gallus, de todas as idades, causando grandes perdas econômicas devido à mortalidade, queda na produção e qualidade dos ovos. Variações na sequência de aminoácidos na região hipervariável da subunidadade S1 da proteína de espícula (S) levam à emergência de novos sorotipos do vírus da bronquite infecciosa das galinhas (IBV). Este estudo teve como objetivo seqüenciar parcialmente o gene S1 para determinar a relação filogenética entre amostras vacinais e de campo com o intuito de investigar os genótipos circulantes. Cento e sessenta amostras foram coletadas, na forma de pools, de plantéis sintomáticos durante 2009/2010. Cada pool continha tecidos de 3 a 5 aves e foram compostos por diferentes órgãos (traquéia, pulmões, rins, conteúdo entérico, trato reprodutivo e swabs traqueais). As amostras foram triadas para a presença de IBV utilizando-se uma nested RT-PCR, direcionada a região 3UTR. As amostras positivas, (n=89) foram submetidas a nova nested RT-PCR dirigida para o gene S, resultando em 10 amplicons de 390pb que foram então submetidos a seqüenciamento de DNA e análise filogenética. As amostras brasileiras segregaram-se em dois grupos filogenéticos: Massachusetts (Mass) e tipos marcadamente brasileiros. Seis amostras agruparam-se no grupo Mass, com vacinas vivas atenuadas utilizadas no Brasil. Quatro amostras agruparam com cepas de campo brasileiras previamente descritas (acesso no GeneBank: FJ791257 to FJ791273). A identidade de aminoácidos no grupo Mass variou de 98% a 100%, sugerindo a detecção de vírus vacinal. Enquanto que entre as amostras brasileiras e o grupo Mass, a variabilidade de aminoácidos foi de 79% a 81%. Esses resultados mostram uma variação importante em genótipos virais circulantes nos plantéis industriais avícolas brasileiros. Portanto, o presente estudo reforça a contínua emergência e disseminação de novas linhagens de IBV no Brasil e a importância de constantes pesquisas e monitoramento, para que se compreendam aos fenômenos de emergência de novas linhagens e suas consequências, bem como para otimizar as medidas de controle do vírus.
Infectious bronchitis is a viral disease, acute and highly contagious that affects birds of the Gallus gallus species, of all ages, causing huge economic losses due to mortality, drop in production and quality eggs. Differences between serotypes of IBV are due to variations in the amino acids sequence in S1 hypervariable region subunit of spike protein (S). This study aimed to partially sequence the S1 gene to determine the phylogenetic relationship between field and vaccine viral types, and to investigate circulating genotypes in Brazil. One hundred and sixty pool samples were collected from symptomatic flocks during 2009/2010. Each pool contained tissues from 3 to 5 birds and was composed by different organs (tracheas, lungs, kidneys, enteric contents, tract reproductive and tracheal swabs). Samples were screened for the presence of IBV using a nested RT-PCR targeted to the 3UTR. Positive samples (n=56) were submitted to a nested RT-PCR target to S gene resulting in 10 amplicons of 390pb that were then submitted to DNA sequencing and analysis. Brazilian IBV genotypes segregated in two phylogenetic groups: Massachusetts (Mass) and Brazilian types. Six samples clustered in the Mass group, with live attenuated vaccines used in Brazil. Four samples grouped with field Brazilian strains previously described (GeneBank accession: FJ791257 to FJ791273). In Mass cluster aminoacids identity range from 98% to 100%, suggesting vaccine virus detection, in this last case. Moreover, the verified identity between samples from this study and Mass group ranged 79% to 81%. Therefore the present study reinforces the emergence and circulation of news lineages of IBV in commercial Brazilian flocks, as well as the importance of consistent research and monitoring to better understand this phenomen and its consequences, aiming to improved control measures against the virus.

La phospholipase A2 sécrétée de type IIA (sPLA2-IIA) est une protéine possédant une activité antibactérienne très élevée envers les bactéries à Gram positif. La mucoviscidose (MV) est une maladie génétique résultant de la mutation du gène Cftr. L'altération de la fonction du CFTR dans les poumons favorise la colonisation par des pathogènes bactériens, dont les plus retrouvés, S. aureus et P. aeruginosa, colonisent les voies aériennes de manière séquentielle: S. aureus est principalement retrouvé chez les jeunes patients et P. aeruginosa chez les adultes. Les mécanismes impliqués dans ce changement de prévalence restent cependant mal connus. Dans ce travail, nous démontrons que l'expression de la sPLA2-IIA est plus importante dans les poumons de patients MV que dans les poumons de patients non MV et augmente avec l'âge des patients. La sPLA2-IIA présente dans les expectorations de patients MV est capable de tuer spécifiquement S. aureus. L'utilisation de modèles animaux nous a permis de démontrer sa spécificité d'action contre S. aureus et l'induction de son expression par P. aeruginosa contribuant à l'élimination de S. aureus des voies respiratoires. Enfin, nous avons identifié les cellules épithéliales comme une source majeure de sPLA2-IIA chez les patients MV. Dans ces cellules, P. aeruginosa induit l'expression de la sPLA2-IIA par un mécanisme dépendant de l'injection de la toxine ExoS et du facteur de transcription KLF2. L'ensemble de ces résultats indique i) que la sPLA2-IIA induite par P. aeruginosa, participe à l'élimination de S. aureus dans les voies aériennes des patients MV et ii) qu'une bactérie élimine une autre bactérie en utilisant la défense de l'hôte
The type IIA secretory phospholipase A2 (sPLA2-IIA) is a host defense protein endowed with antibacterial activity, especially against Gram positive bacteria. Cystic fibrosis (CF) is a genetic disease due to mutations of Cftr gene. In the lungs, CFTR mutation favored bacterial colonization by bacterial pathogens, of which S. aureus and P. aeruginosa are the most isolated. These two bacterial species sequentially colonized airways of CF patients: S. aureus is predominant in young patients and P. aeruginosa in adults. But the mechanisms involved in this switch of bacterial prevalence are still unknown. In this work we showed that sPLA2-IIA levels were increased in lungs of CF patients compared to lungs of non-CF patients and that sPLA2-IIA levels increased with age of patients. sPLA2-IIA recovered from CF patients expectorations was active and killed specifically S. aureus. Using animal models of lung infection, we demonstrated the selectivity of sPLA2-IIA against S. aureus and that P. aeruginosa induced sPLA2-IIA expression, the latter contributed to S . aureus elimination from the airways. Finally, we identified epithelial cells as a major source of sPLA2-IIA in CF airways. In these cells, P. aeruginosa induced sPLA2-IIA expression through injection of ExoS toxin and activation of KLF2 transcription factor. Taken together, these results indicate that i) P. aeruginosa-induced sPLA2-IIA expression in CF airways participated to S. aureus elimination and ii) a bacteria eliminate another bacteria by manipulating host innate immunity

The Type III secretion system (T3SS) is an important virulence mechanism that allows pathogenic bacteria to translocate virulence effectors directly into the cytoplasm of eukaryotic host cells to manipulate the host cells in favor of the pathogen. Enteropathogenic Yersinia pseudotuberculosis use a T3SS to translocate effectors, Yops, that prevent phagocytosis by immune cells, and is largely dependent on it to establish and sustain an infection in the lymphoid tissues of a mammalian host. Translocation into a host cell requires specific translocator proteins, and is tightly controlled from both the bacterial and host cell cytoplasm. We aimed to investigate two of the regulatory elements, YopN and LcrV, to gain more insight into the translocation mechanism. Two separate regulatory complexes regulate expression and secretion of Yops, however, the processes are linked so that expression is induced when secretion is activated. A complex, including YopD, prevents expression of Yops, while YopN-TyeA and LcrG block secretion. LcrV is required to relieve the secretion block, by sequestering LcrG. We verified that LcrG binds to the C-terminal part of LcrV, which is consistent with what has been shown in Y. pestis. In addition to their regulatory roles, both LcrV and YopD are translocators and are assumed to interact at the bacterial surface, where LcrV promotes insertion of YopB and YopD into the host cell membrane. However, here we show that purified YopD failed to interact with LcrV, instead YopD solely interacted with a complex of LcrV-LcrG. This indicates that LcrV and YopD interact in the bacterial cytosol, which may be important for regulation of Yop expression and secretion. The established role of YopN is to block secretion prior to host cell contact. We found that deleting the central region (amino acids 76-181) had no effect on the regulatory role of YopN in expression and secretion of Yops. Interestingly, we found that, even though the YopN∆76-181 mutant secreted the translocators with similar kinetics as the wild type strain, translocation of the effector YopH, into HeLa cells, was significantly reduced. Consequently, the YopN∆76-181 mutant was unable to block phagocytosis, almost to the same level as the ∆lcrV mutant which is completely unable to translocate YopH. Our results indicate that YopN is involved in the translocation step in addition to its role in regulating secretion. Further, we show that the amino terminal of LcrV, in the context of translocation, is involved in the early intracellular targeting of YopH in order to block phagocytosis efficiently and sustain an in vivo infection. LcrV mutants that failed to efficiently target YopH intracellularly were severely attenuated also for in vivo virulence. All together, we show that LcrV and YopN are involved in more steps in the regulation of translocation, than what was known before. Our studies also highlight that early translocation is essential for Yersinia to block phagocytosis, which in the end is essential for in vivo virulence.

The clearance of viruses is largely dependent upon the activation of T cells to generate a robust immune response. However, host responses are suppressed during chronic viral infections. In this thesis, we explored the role of Top2α in DNA topology in individuals with chronic HBV, HCV, and HIV infections. We found that Top2α protein expression and activity were low in T cells derived from chronically virus-infected individuals compared to healthy subjects. Using CD4+ T cells treated with Top2α inhibitor or poisoner as a model, we demonstrated that Top2α inhibition disrupts the DNA topology, suppresses DNA repair kinase (ATM), and telomere protein (TRF2) expression, and induces T cell dysfunction. These findings reveal that Top2α inhibition is a mechanism by which viruses evade the host responses and establish persistent infection, and thus, restoring Top2α levels could be a way of boosting immune responses during chronic viral infections.

Shigella flexneri attacks cells of the intestinal tract, causing over 1 million deaths annually from bacterial dysentery. A type III secretion system (T3SS) initiates the host-pathogen interaction and transports virulence factors directly into host cells via a needle complex (NC) comprising an extracellular needle and membrane-spanning basal body. Rings formed by the single-pass membrane proteins MxiG and MxiJ are arranged concentrically within the inner membrane ring (IMR) of the NC. The Neterminal domain of MxiG (MxiG-N) is the predominant IMR cytoplasmic structure, however it was structurally and functionally uncharacterised. Determination of the solution structure of MxiG-N in this study revealed it to be a forkhead associated (FHA) domain, although subsequent analyses of conserved residues suggested it does not have the canonical role in cell-signalling via phospho-threonine recognition. Subsequent positioning of the structure in the electron microscopy (EM) density for the S. flexneri NC supported models with 24-fold symmetry in the IMR. Both MxiG and MxiJ also have significant periplasmic domains, which were purified to homogeneity in this study, facilitating preliminary characterisation of their structures and intermolecular interactions. In addition, the entire IMR within the context of intact basal bodies was isolated and visualised in vitro by EM. The essential function of MxiG-N could be to localise the putative cytoplasmic ring (Cering) at the base of the T3SS. Although absolutely required for secretion, the Csring component, Spa33, was structurally uncharacterised. The crystal structure of the Cvterminal domain of Spa33 (Spa33-C) was determined in this study, showing an intertwined dimer that aligned with homologous structures and exhibited a novel interaction with the N-terminus of the ATPase regulator, MxiN. Subsequently, Spa33-C was identified as an altemative translation product of spa33 that formed a 2: 1 complex with Spa33 in vitro. This complex oligomerised further, demonstrating for the first time that Spa33 has the propensity to form the ordered, high molecular weight assemblies that would be required for C-ring formation in S. flexneri.

The first aim of this research was to determine the prevalence of IBV in broilers within the Canterbury province, New Zealand, in late winter and to search for associations with management or environmental factors. The second aim was to study how ambient stressors affect the immune system in birds, their adaptive capacity to respond, and the price that they have to pay in order to return to homeostasis. In a case control study, binary logistic regression analyses were used to seek associations between the presence of IBV in broilers and various risk factors that had been linked in other studies to the presence of different avian pathogens: ambient ammonia, oxygen, carbon dioxide, humidity and litter humidity. Pairs of sheds were selected from ten large broiler farms in Canterbury. One shed (case) from each pair contained poultry that had a production or health alteration that suggested the presence of IBV and the other was a control shed. Overall, IBV was detected by RT-PCR in 50% of the farms. In 2 of the 5 positive farms (but none of the control sheds) where IBV was detected there were accompanying clinical signs that suggested infectious bronchitis (IB). Ambient humidity was the only risk factor that showed an association (inverse) with the prevalence of IBV (p = 0.05; OR = 0.92). It was concluded within the constraints of the totally enclosed management systems described, that humidity had an influence on the presence of IBV, but temperature, ammonia, carbon dioxide, oxygen or litter humidity had no effect. In another study environmental temperatures were changed in order to affect the biological function and adaptive capacity of chickens following infection with IBV. The 'affective states' of the animal were assessed by measuring levels of corticosterone (CORT) in plasma and tonic immobility (TI). It was found that low (10 +/- 2°C) and high (30 +/- 2°C) temperatures exacerbated the respiratory signs and lesions in birds infected with IBV as compared to those housed at moderate (20 +/- 2°C) temperatures. The chickens housed at high temperatures showed significantly decreased growth, a higher proportion of hepatic lesions (principally haemorrhages) and a longer tonic immobility period, but there was no significant alteration in the plasma levels of CORT. The birds housed at low temperatures developed a higher proportion of heart lesions (hydropericardium, ventricular hypertrophy) and had significantly higher levels of plasma CORT than birds housed under moderate and/or high temperatures. The specific antibody response to IBV decreased in birds housed under high temperatures. Interestingly the birds housed at high temperatures developed significantly higher levels of haemagglutinin antibodies to sheep red blood cells (SRBC) than those birds housed under low or moderated temperatures. Cell mediated immunity was not significantly affected by heat or cold stress in the first 13 days of treatment but at 20 days the levels of interferon gamma in the birds subjected to low temperatures were lower than in the high temperature group. In other trials, the exogenous administration of low physiological doses of oral CORT (as compared to high pharmacological doses typically used in such experiments) to birds resulted in suppression or enhancement of the immune response depending on duration of treatment and/or dose and nature of the antigen. To our knowledge, this is the first study to show that exogenous CORT can produce an enhancement in the immune response in chickens. iv In conclusion, environmental stressors such as high or low temperatures do affect the physiology of the fast-growing broiler. The adjustments the birds have to make to maintain homeostasis impacts on the course of common infectious diseases, such as IB, that normally is mild in the New Zealand poultry industry. The administration of exogenous CORT showed that this hormone may be part of the physiological stress response and acts as a messenger to prepare the immune system for potential challenges (e.g., infection).

La production d'oxyde nitrique (NO) par l'enzyme iNOS (inducible NO synthase) est impliquée dans le contrôle de nombreuses infections causées par des pathogènes intracellulaires. Cependant, la nature des signaux nécessaires à l'induction d'iNOS in vivo et les mécanismes responsables de son activité antimicrobienne restent à définir. En particulier, plusieurs études suggèrent que le NO exerce son activité de manière intrinsèque : l'induction d'iNOS par les cellules infectées leur permettrait donc de contrôler individuellement leur charge microbienne. Alternativement, la capacité du NO à diffuser à travers les membranes cellulaires pourrait bien jouer un rôle déterminant dans le contrôle de ces infections à pathogènes intracellulaires. Les contributions respectives de ces deux modes d'action dans le contrôle de l'infection restent inconnues. Dans cette thèse, nous démontrons dans le cadre de l'infection par Leishmania major que iNOS est rapidement induite en réponse à l'IFNy et le TNF par les phagocytes mononucléés recrutés au site d'infection mais ne confère aucune capacité intrinsèque à contrôler les parasites. Au contraire, nous démontrons que la diffusion du NO permet de tuer les parasites aussi bien dans les cellules exprimant iNOS que dans les cellules à proximité et que la production collective de NO par de nombreux phagocytes et nécessaire pour atteindre une activité antimicrobienne efficace. Finalement, en s'appuyant sur une méthode innovante impliquant une protéine photoconvertible, nous démontrons que ce milieu riche en NO limite le métabolisme et ainsi la prolifération du parasite in vivo, permettant ainsi de contrôler efficacement l'infection par Leishmania
The production of nitric oxide (NO) by the inducible NO synthase (iNOS) plays a critical role in the control of many infections with intracellular pathogens. However, the signais mediating iNOS induction in vivo and the precise mechanisms underlying its antimicrobial activity at the site of infection remain unclear. In particular, several studies have promoted the idea that NO production in infected cells may enable them to individually control their pathogen burden. Alternatively, the ability of NO to diffuse efficiently across cell membranes may be critical for the control of infection with intracellular pathogens. Whether pathogen control primarily depends on cell-intrinsic or cell-extrinsic activity of NO is unknown. In this thesis, we demonstrate that during Leishmania major infection, iNOS is rapidly induced in recruited mononuclear phagocytes in response to IFNy and TNF. We show that this rapid iNOS induction does not confer any cell-intrinsic ability to lower parasite content. Ln fact, we demonstrate that the diffusion of NO promotes equally effective parasite killing in producing and bystander cells and that the collective production of NO by numerous phagocytes is necessary to exert an effective antimicrobial activity. Altogether, we prOpose that in contrast to a cell-autonomous control of intracellular pathogens, this cooperative mechanism generates an antimicrobial milieu that provides the basis for pathogen containment at the tissue level. Finally, using a new method based on a photoconvertible protein, we demonstrate that this NO-rich microenvironment controls Leishmania infection in part by dampening parasite metabolism and subsequent proliferation in vivo

Pseudomonas aeruginosa (P. A) est, à cause de sa virulence, un des agents pathogènes les plus connus notamment dans les cas d'infections nosocomiales et dans la mucoviscidose où la morbidité et la mortalité des patients sont engagées. Si la capacité d'antibiorésistance de P. A explique cette réalité, il ne faut cependant pas ignorer la diversité des toxines qu'elle produit. Parmi celles qui font sa force, la pertinence des facteurs de virulence sécrétés et injectés par le système de sécrétion du type III (SSTIII) est plus qu'avérée, a contrario de ceux sécrétés par le SSTII. Il existe bien une vaste littérature sur le rôle de LasB in vitro, mais rare sont les études mentionnant son action directe sur les cellules myéloïdes. Pour les enrichir, nous avons justement inscrit ce manuscrit dans cette rareté et finalement, en plus de démontrer que LasB est bien la toxine majeure sécrétée par le SSTII, nous montrons pour la première fois qu'elle est capable d'agir de manière directe sur les macrophages alvéolaires (MA). En effet, au travers de nos travaux, LasB s'est révélée être une toxine ciblant et inhibant l'activité bactériolytique des MA in vivo, ex vivo et in vitro et ce, dans des conditions non-opsoniques comme peuvent l'être celles des alvéoles naïves et saines. Toutefois, même si les technologies utilisées ont été nombreuses, le mécanisme sous-jacent à cette action directe de LasB sur les MA reste une énigme. Malgré cela, notre étude apporte de nouveaux éléments permettant de comprendre pourquoi chez des individus immunologiquement sensibles P. A, en échappant à la réponse de l'hôte, s'implante précocement puis irrémédiablement dans leur poumon
Because of its virulence Pseudomonas aeruginosa (P. A) is one of the main pathogens causing numerous cases of nosocomial infections. It is also present in the airways of cystic fibrosis patients in which it is associated with an increased morbidity and mortality. Although this can partly be explained by its antibiotic resistance, the diversity of toxins it produces should not be ignored. Among those, the relevance of virulence factors secreted and injected through the type III secretion system (TIIISS) is undeniable, however those secreted by the TIISS are underestimated. There is indeed a vast literature on the role of the elastase LasB in vitro, but studies indicating its direct action on myeloid cells are rare. To enrich them, we have registered our manuscript in this rarity and finally, in addition to demonstrating that LasB is the major toxin secreted by the TIISS, we show for die first time that LasB is able to act directly on alveolar macrophages (AM). Indeed, throughout our work, LasB bas proved to be a toxin targeting and inhibiting the bacteriolytic activity of AM in vivo, ex vivo and in vitro and in non-opsonic conditions as can those of naive and healthy alveoli. Although different pathways using numerous techniques have been investigated, the underlying mechanism for this direct action of LasB on AM remains unclear. Nevertheless, our study provides new evidence that contributes to understand why in immunologically susceptible individuals, P. A is setting up early and irrevocably in their lung at least partly by escaping the host's immune response

s retrovírus humanos incluem o vírus da imunodeficiência humana (HIV), agente causal da síndrome da imunodeficiência adquirida (AIDS), e os vírus linfotrópicos de células T humanas do tipo I (HTLV-I) e do tipo II (HTLV-II), estes associados etiologicamente a doenças de natureza linfoproliferativa e/ou neurodegenerativa. Apresentam as mesmas formas de transmissão, resultando em fatores comuns de risco e em sobreposição de populações expostas. Embora os três vírus sejam linfotrópicos, o HIV se apresenta com altas taxas de replicação e proporciona a morte celular em todos os estágios da infecção, enquanto o HTLV-I e o HTLV-II podem causar proliferação e eventualmente transformação celular. O efeito do HTLV-I e do HTLV-II sobre o sistema imunológico como um dos fatores que interferem na evolução da AIDS envolve um grande interesse e ainda é motivo de controvérsia. Pesquisas in vitro sugerem que o HTLV-I e o HTLV-II podem aumentar a replicação e a expressão do HIV. Alguns estudos clínico-epidemiológicos apontam na direção de que exista efeito da concomitância das infecções pelo HIV e pelo HTLV-I ou pelo HTLV-II sobre a evolução da progressão da AIDS. Em um estudo anterior, desenvolvido entre portadores do HIV atendidos no Centro de Referência em AIDS de Santos-SP, observou-se uma soroprevalência de 6,0% da infecção pelo HTLV-I e de 7,4% pelo HTLV-II, o que poderia justificar a investigação de possível modificação na evolução da história natural da infecção pelo HIV nesses pacientes co-infectados. O presente trabalho foi desenvolvido, como um estudo de coorte retrospectiva, visando a avaliar o tempo de sobrevida dos portadores do HIV na população estudada e sua associação com as infecções pelo HTLV-I e pelo HTLV-II, bem como com outros fatores prognósticos e marcadores de progressão. Dos 495 portadores do HIV acompanhados entre 1997 e 2002, em um número total de 23.031,5 pacientes-mês, foi observado que 145 pacientes evoluíram para o óbito em decorrência da AIDS. A análise multivariada pelo modelo dos riscos proporcionais de Cox indicou que o tempo de evolução para o óbito por AIDS na população estudada foi associado de forma independente à raça negra (HR ajustado 1,50 - IC 95% 1,03-2,17), com menos de três anos de escolaridade formal (HR ajustado 1,90 - IC 95% 1,12-3,25), com os linfócitos CD4+ em número inferior a 200 células/mm³ no início do estudo (HR ajustado 4,44 - IC 95% 2,70-7,31), com a classificação CDC em categoria B ou C no início do estudo (HR ajustado 3,63 - IC 95% 1,54-8,56), com a soropositividade anti-HTLV-I (HR ajustado 1,95 - IC 95% 1,08-3,52), com a soropositividade anti-HCV (HR ajustado 1,76 - IC 95% 1,20-2,60) e com o uso de esquemas terapêuticos altamente ativos (HAART) em menos de 50% do tempo de seguimento (HR ajustado 2,36 - IC 95% 1,61-3,45). Não houve associação significativa com a soropositividade anti-HTLV-II. O estudo reforça as evidências de que a infecção pelo HTLV-I constitui um fator prognóstico de menor sobrevida em portadores do HIV
Human retroviruses include the human immunodeficiency virus (HIV), etiologic agent of the acquired immunodeficiency syndrome (AIDS), and also the human T-cell lymphotropic virus types I (HTLV-I) and II (HTLV-II), which can cause lymphoproliferative and/or neurodegenerative diseases. The three retroviruses present similar transmission patterns and share common risk factors resulting in overlap of exposed populations. Although these retroviruses are all lymphotropic, HIV has a high replication rate and induces cell death throughout the course of infection, whereas HTLV-I and HTLV-II can cause cell proliferation and occasionally cell transformation. HTLV-I and HTLV-II effects on the immune system and their interference in the progression of AIDS is a matter of great interest and still controversial. In vitro studies suggest that HTLV-I and HTLV-II may increase the replication and expression of HIV. Clinical epidemiologic studies indicate possible effects of simultaneous infections by HIV and HTLV-I or HTLV-II on the progression of AIDS. In a previous study, carried out among HIV-positive patients treated at an AIDS center in Santos - SP (Centro de Referência em AIDS de Santos), a seroprevalence of 6.0% for HTLV-I and of 7.4% for HTLV-II infections was observed, what enables further investigation on a possible modification in the progression of HIV disease in co-infected patients. This study was carried out with a retrospective cohort design, aimed at evaluating the survival time of HIV-positive patients in the studied group and its association with HTLV-I and HTLV-II infections, as well as with other prognostic factors and progression markers. Four hundred and ninety-five patients were monitored between 1997 and 2002. In this period, in a total of 23,031.5 patients/month, 145 AIDS related deaths were reported. Multivariate analysis using Cox proportional hazards model showed AIDS to be associated in the studied group with the following variables: black race (adjusted HR 1.50 - 95% CI 1.03-2.17), less than three-year education (adjusted HR 1.90 - 95% CI 1.12-3.25), less than 200 CD4+ baseline cells/mm3 (adjusted HR 4.44 - 95% CI 2.70-7.31), CDC classification B or C at study onset (adjusted HR 3.63 - 95% CI 1.54-8.56), anti-HTLV-I seropositivity (adjusted HR 1.95 - 95% CI 1.08-3.52), anti-HCV seropositivity (adjusted HR 1.76 - 95% CI 1.20-2.60), use of Highly Active Antiretroviral Therapy (HAART) in less than 50% of follow-up (adjusted HR 2.36 - 95% CI 1.61-3.45). There was no significant association with anti-HTLV-II seropositivity. This study provides further evidence that HTLV-I infection is a prognostic factor leading to reduced survival time of HIV-infected individuals

The vector-borne protozoan Leishmania spp. cause the spectrum of disease known as leishmaniasis in human and animal hosts. The most common manifestations of leishmaniasis are the chronic, ulcerative skin disease cutaneous leishmaniasis (CL), and the more serious visceral leishmaniasis (VL) in which parasites take up residence in internal organs, causing death if not treated. The role of neutrophils (PMNs) in the immune response to CL and VL is unclear. It is s generally thought that PMNs are only a short-lived effector cell, and have been disregarded as playing a role in chronic Leishmania spp. infection. As both CL and VL are diseases characterized by increased inflammatory immune mediators, we hypothesized that PMNs from human or animal models of chronic leishmaniasis would display different properties from PMNs from healthy controls. We found in a subset of CL and VL patients circulating PMNs expressing HLA-DR, the human form of MHC class II, a molecule thought to be restricted primarily to professional antigen cells. When we examined PMNs recruited to CL skin lesions in human patients, or similar lesions in experimental murine model of CL, we found significantly increased MHC class II+ PMNs. Circulating HLA-DR+ PMNs also expressed the co-stimulatory molecules CD80, CD86 and CD40. While this suggested an antigen-presenting cell-like phenotype by these HLA-DR+ PMNs, compared to conventional HLA-DR- PMNs, HLA-DR+ PMNs showed not only a neutrophil-like appearance and function, but in fact increased activation, degranulation, intracellular MPO and phagocytosis of parasites and zymosan particles. Incubation of healthy control whole blood with inflammatory cytokines resulted in increased HLA-DR+ PMNs and the presence of hladrb1 mRNA, suggesting a connection between neutrophil “priming” and upregulation of HLA-DR. In addition to HLA-DR+ PMNs in CL patients, we also identified the presence of so-called “low-density” neutrophils (LD-PMNs). These neutrophils, which are enriched in low-density fractions following centrifugation of blood over a density gradient, are reported in numerous disease states, including cancer, HIV, and systemic lupus erythematosus. In some disease states, LD-PMN are reported to be immunosuppressive toward T cell activation and proliferation. However, LD-PMNs from leishmaniasis patients showed no evidence of immunosuppression. Additionally, we found that LD-PMNs show significantly increased surface expression of MHC class II, suggesting a heretofore unappreciated connection between these atypical neutrophil phenotypes. We also investigated the in vitro interactions with different Leishmania infantum life-stages, both those that cause acute infection (promastigotes) and amastigotes, which are found during chronic stages of the disease. We found that PMNs are readily infected by all L. infantum life-stages, but that amastigotes may have different methods of interacting with PMN surface receptors and are better equipped to avoid PMN anti-microbial responses. These data suggest that circulating PMNs in chronic leishmaniasis may have unique phenotypes and interact differently with the Leishmania spp. life-cycle present during chronic infection. Further investigation of the role of PMNs and atypical PMN phenotypes in chronic disease may help identify new immunomodulatory roles for this cell type.

The generation of memory T cells following primary exposure to a pathogen is a critical feature of the vertebrate immune system which has evolved as a protective mechanism in order to defend the host against repeated assaults by the patnogen. Memory T cells are long-lived, undergo rapid proliferation upon re-activation, mediate a robust secondary response and clear the pathogen much more efficiently. These aspects have made the generation of memory T cells an attractive goal for the production of both prophylactic and therapeutic vaccines. However, the degeneracy of the T cell receptor, whereby a given T cell recognizes more than one epitope, allows the T cell to be modulated by epitope variants which could be self-ligands, ligands related to the original epitope but altered in sequence, or completely unrelated epitopes. Experiments in both mice and humans show that such cross-reactive stimulation of memory T cells results in complete, partial, or no activation of T cells, and in some cases, even alters the functional identity of the T cell (for example, T helper 1 cells start secreting IL-4, IL-5 and become part of a T helper 2 response). In the context of secondary infection of immune organisms with pathogens containing mutated or related T cell epitopes, such alterations at the cellular level translate into drastic changes in the overall clinical outcome of the infection. Thus, the presence of cross-reactive T cells in the memory population implies that the protective or pathologic nature of the secondary immune response is a consequence of the host's infection history. Although several murine models of heterologous infection resulting in altered pathological outcome have been studied, the exact immune correlates of protection versus immunopathology are still unclear. This thesis addresses this issue in dengue virus infections in humans. Dengue fever (DF) and Dengue Hemorrhagic Fever (DHF) are two disease manifestations caused by infections of humans by the dengue viruses. These are a group of 4 serologically distinct flaviviruses (D1-4) which often co-circulate among endemic populations. While primary infection with any of the four serotypes can result in the more severe clinical disease characterized by DHF, epidemiological data from several outbreaks show that 80% - 90% of DHF cases occur among individuals with secondary infection. This implies that prior immunity to dengue is actually a risk factor for developing severe disease. In these DHF cases, there are increased numbers of CD69+ CD8+ T cells in circulation, with increases observed in the frequency of epitope-specific T cells, and the serum levels of several T cell produced cytokines, chemokines, and immune receptors are highly elevated. Since the four serotypes share 65% - 75% amino acid sequence homology, the possibility that unconserved T cell epitope sequences stimulated cross-reactive responses was borne out in in vitroexaminations. In these studies, peripheral blood mononuclear cells (PBMC) and cloned T cells from both vaccinated and infected donors contained large populations of memory T cells that were cross-reactive for heterologous viral serotypes in proliferation and CTL assays. These data suggest that the severity of disease seen in DHF patients can be attributed to an immunopathologic secondary response during heterologous infection, and highlight a role for serotype cross-reactive T cells in this process. This thesis addresses the hypothesis that the recognition of the natural variants of dengue virus T cell epitopes by serotype cross-reactive CD8+ T cells of a dengue-immune donor results in an altered secondary response profile, with the changes reflected in both the quantitative and qualitative nature of the response. In order to compare the functional profile of the secondary response of dengue-immune PBMC re-activated with heterologous serotypes, we focused on a panel of 4 donors who were vaccinated with live attenuated monovalent vaccines corresponding to D1, D2, or D4 serotypes. We screened a panel of peptides predicted to bind to HLA-A*0201 for cytokine responses and identified 4 novel epitopes that were highly immunogenic in all four donors. Direct ex vivo stimulation of donor PBMC with the heterologous sequences of these epitopes also showed sizeable serotype cross-reactive T cell populations. CFSE- and intracellular staining for cytokines and chemokines showed that these cross-reactive T cells not only expanded but also produced IFNγ, TNFα, and MIP-1β. Multi-parameter staining revealed functionally diverse populations comprised of single cytokine (IFNγ+, TNFα+, MIP-1β+, double cytokine (IFNγ+TNFα+, IFNγ+MIP-1β+, TNFα+MIP-1β+, and triple cytokine (IFNγ+TNFα+MIP-1β+ secreting sub-sets. Stimulation with the epitope variants altered the magnitude of the overall response as well as the relative sizes of these sub-sets. The patterns of responses revealed the effects of epitope immunogenicity, infection history and donor-specific variability. All 4 donors showed the highest cytokine response to a -single epitope (NS4b 2353). The same two peptide variants (D2 NS4a 2148 and D3 NS4b 2343) induced the highest response in all 4 donors regardless of the serotype of primary dengue infection. Interestingly, the epitope variants which showed the highest immunogenecity in our donors corresponded to the D2 and D3 serotypes which have been documented as being more virulent as well as a viral risk factor for DHF. In one donor, the response to all peptide variants was dominated by the same cytokine sub-sets. These data suggested that the dengue-immune memory T cell repertoire was functionally diverse and underwent alterations in size after secondary stimulation. Therefore, we also investigated the effect of epitope variants on dengue-specific CD8+T cell clones isolated from vaccinated and infected donors in order to determine if epitope variants induced altered functional outcomes at the clonal level. The epitope variants functioned either as strong agonists (particularly the D2 and D3 sequences), partial agonists, or null ligands. Some variants were able to induce cytolysis but not other effector functions at low concentrations. The variant ligands also influenced the hierarchy of cytokine responses within each clone. The third part of this thesis focused on the characterization of the frequency and phenotypic profile of epitope-specific CD8+ T cells in patients with DHF and DF at different times in the disease course in order to better understand the kinetics of the response and delineate any differences between the immune profile of severe vs. moderate disease. Tetramer staining for a previously identified HLA-B*07 restricted epitope was combined with staining for activation markers (CD69, CD38, HLA-DR), homing receptors (CCR7, CD62L), and programmed death receptor 1 (PD-1). The DHF subjects had early T cell activation with higher frequencies of tetramer+CD69+ cells as compared to DF subjects, in whom T cell frequencies peaked around the time of defervescence. While each subject had a unique phenotypic profile of tetramer+ cells, there was a difference between DF and DHF subjects in terms of CCR 7 expression; all subjects expressed low levels of CCR7 during acute illness but only the DHF subjects did not show upregulation of CCR7 on tetramer+ cells during convalescence. These data suggest that there is a sustained alteration in memory phenotype in those who recovered from severe dengue disease. A majority of the tetramer+cells also expressed PD-1 during acute illness but not during convalescence. Double-staining with variant tetramers allowed us to directly visualize serotype cross-reactivity of the epitope-specific population, and showed that secondary stimulation did induce the expansion of cells with low avidity for that secondary serotype and higher avidity to the variant. Furthermore, the ratios of these sub-sets changed during the course of the response. Taken together, these studies suggest that the immune response to heterologous secondary dengue infection is mediated by a heterogeneous population of serotype-cross reactive T cells that have different functional avidities to epitope variants and is influenced by the serotype of the secondary infection as well as the prior infection history of the individual. The preferential expansion of clones which secrete IFNγ but not inflammatory MIP-1β or TNFα or a repertoire characterized by a higher ratio of cytolytic to cytokine producing clones could limit immune mediated damage while efficiently clearing the virus. This information will be useful in the design of vaccine strategies aimed at inducing protective cross-reactive responses against all 4 dengue serotypes while preventing immunopathological outcomes following secondary infection.

The innate immune system is a multicomponent response governed by intricate mechanisms of induction, regulation and resolution to elicit antimicrobial defenses. In recent years, the complexity of eukaryotic transcriptomes has become the subject of intense scrutiny and curiosity. It has been established, that RNA polymerase II (RNAPII) transcribes hundreds to thousands of long noncoding RNAs (lncRNAs), often in a stimulus and cell-type specific manner. However, the functional significance of these transcripts has been particularly controversial. While the number of identified lncRNAs is growing, our understanding of how lncRNAs themselves regulate other genes is quite limited. In chapter 2, a novel lncRNA is identified, more specifically, a natural antisense transcript, that mediates the transcription of the pro-inflammatory cytokine IL-1α. Through loss-of-function studies, I report the necessity of this transcript in mediating IL-1α mRNA expression by affecting RNAPII binding to the IL-1α promoter after toll-like receptor signaling. For the first time, I show that IL-1α is regulated at the transcriptional level. As a second independent component of this thesis, we explore the role of the innate immune response after infection by the malaria-causing parasite, Plasmodium berghei ANKA (PbA), and how innate immune components are both beneficial and detrimental to the host depending on when and where inflammation is triggered during infection. We attempt to identify the “malarial toxin” responsible for aberrations in the immune response that is detrimental for disease outcomes and the innate signaling pathways that are involved. Many pathogens induce pathological inflammatory conditions that lead to irreparable homeostatic imbalances and become fatal to the host. Here, type I Interferon signaling is required to dampen parasite load during liver-stage infections, but leads to host mobidity if these pathways are activated in the erythrocytic phase of infection. Together, this thesis provides new insights on how components of the innate immune system are regulated, and how dysregulation of immunity can potentially lead to adverse effects during active infections.

The innate immune system is a multicomponent response governed by intricate mechanisms of induction, regulation and resolution to elicit antimicrobial defenses. In recent years, the complexity of eukaryotic transcriptomes has become the subject of intense scrutiny and curiosity. It has been established, that RNA polymerase II (RNAPII) transcribes hundreds to thousands of long noncoding RNAs (lncRNAs), often in a stimulus and cell-type specific manner. However, the functional significance of these transcripts has been particularly controversial. While the number of identified lncRNAs is growing, our understanding of how lncRNAs themselves regulate other genes is quite limited. In chapter 2, a novel lncRNA is identified, more specifically, a natural antisense transcript, that mediates the transcription of the pro-inflammatory cytokine IL-1α. Through loss-of-function studies, I report the necessity of this transcript in mediating IL-1α mRNA expression by affecting RNAPII binding to the IL-1α promoter after toll-like receptor signaling. For the first time, I show that IL-1α is regulated at the transcriptional level. As a second independent component of this thesis, we explore the role of the innate immune response after infection by the malaria-causing parasite, Plasmodium berghei ANKA (PbA), and how innate immune components are both beneficial and detrimental to the host depending on when and where inflammation is triggered during infection. We attempt to identify the “malarial toxin” responsible for aberrations in the immune response that is detrimental for disease outcomes and the innate signaling pathways that are involved. Many pathogens induce pathological inflammatory conditions that lead to irreparable homeostatic imbalances and become fatal to the host. Here, type I Interferon signaling is required to dampen parasite load during liver-stage infections, but leads to host mobidity if these pathways are activated in the erythrocytic phase of infection. Together, this thesis provides new insights on how components of the innate immune system are regulated, and how dysregulation of immunity can potentially lead to adverse effects during active infections.

The innate immune system is a critical first line of defense against invading pathogens. Innate immunity directly detects pathogens, sets up an appropriate adaptive response, and can directly kill pathogens. Drosophila may lack an adaptive immune response, but have a robust innate immune system with a variety of defense effector mechanisms. While the responses to bacteria, fungi, and RNA viruses have been well characterized, not much is known about the response to DNA viruses. My studies have set out to characterize the Drosophila immune response to a DNA virus, utilizing the large dsDNA virus, Invertebrate Iridescent Virus 6 (IIV-6). IIV-6 infection causes shortened lifespan, and in later stages of infection, flies present with abdominal swelling and iridescent blue color. Our objectives were to identify pathways flies use to protect themselves from IIV-6 infection, determine how this protection is mediated, and to identify any immune inhibitors that IIV-6 uses to suppress innate immune signaling. I have found that IIV-6 strongly up-regulates a class of stress proteins with unknown function, termed Turandots, after infection in vivo or in vitro. This induction is dependent upon viral replication, requires JAK-STAT activation, and activation of p38b MAPK. In addition, the unpaireds, which function as JAK-STAT ligands, are upregulated after IIV-6 infection in a p38b-dependent manner. Together, this data suggests that p38b activation leads to production of unpaired cytokines and activation of JAK-STAT signaling to induce Turandots. I have also found that IIV-6 infected cells secrete protective factors. This response is induced within 12 hours of IIV-6 infection, exosome-mediated, and provides robust protection to naive cells challenged with an mCherry-expressing strain of IIV-6. Additionally, IIV-6 inhibits two major immune responses in Drosophila, the IMD and Toll pathways. Stimulation of IIV-6 infected Drosophila S2* cells with either IMD or Toll stimulators results in very poor antimicrobial peptide responses. Yet, IMD and Relish are still cleaved upon stimulation in IIV-6 infected cells, indicating that the block is downstream. In support of this finding, IIV-6 infected flies respond very poorly to infection with the enterobacteria Erwinia carotovora carotovora compared to mock-injected flies.

Estudos recentes têm apresentado resultados in vitro satisfatórios em pacientes com Imunodeficiência Comum Variável (ICV) que receberam vacinas contra tétano, influenza e meningococo. No entanto, existem poucos ensaios clínicos que avaliem a resposta clínica e laboratorial após a exposição a antígenos específicos. O presente estudo tem como objetivo avaliar a resposta clínica à imunização contra antígenos protéicos e polissacarídicos (influenza, H1N1 e pneumococo) em pacientes com diagnóstico de ICV seguidos no ambulatório de Imunodeficiências Primárias do Serviço de Imunologia Clínica e Alergia do HC-FMUSP. O diagnóstico dos pacientes foi estabelecido de acordo com os critérios da OMS / PAGID / ESID. Um grupo de 37 pacientes foi vacinado contra a influenza A (H2N3), gripe H1N1 e pneumococo e outro grupo com 16 pacientes, não foi vacinado. A avaliação clínica foi realizada através da aplicação de um score com avaliação dos seguintes parâmetros clínicos: pneumonia, sinusite, otite média, infecções de vias aéreas superiores (IVAS), amigdalites, diarréia, bronquiectasias, hospitalizações, uso de antibióticos, uso de antibióticos profiláticos, sepse e meningite. O score foi aplicado durante os 12 meses que precederam a vacinação e 12 meses posteriores à administração das vacinas. O mesmo score foi aplicado ao grupo controle, com os pacientes que não foram vacinados. A determinação da IgG contra os sorotipos do pneumococo foi feita por ELISA. A determinação da IgG específica H1N1 foi feita por hemaglutinação indireta, enquanto que a dosagem da IgG específica para influenza, por ELISA, utilizando o kit comercial RIDASCREEN ® Influenza. O grupo de pacientes vacinados incluiu 37 pacientes (51% mulheres), com idade entre 20 e 78 anos (mediana= 33 anos). Observou-se uma mediana de 7 anos de atraso no diagnóstico de ICV. A mediana de idade do grupo de pacientes (n=16, 37,5% mulheres) que não receberam a vacina foi de 41 anos e a mediana de atraso no diagnóstico foi de 8 anos. Observamos que as infecções de vias aéreas superiores (IVAS), sinusites e pneumonias foram as manifestações mais freqüentes no grupo controle. IVAS seguida por pneumonia e sinusite foram as manifestações infecciosas mais freqüentes em mulheres (80%, 78% e 55%, respectivamente). Entretanto, em homens observamos IVAS seguido por sinusite e pneumonia (78%, 65% e 35%, respectivamente). Observou-se redução significativa no score relativo ao número de infecções respiratórias superiores, sinusites e pneumonias um ano após a administração das vacinas (p <0,001). Os dados foram comparados com pacientes ICV não vacinados e neste grupo não houve diferença entre os scores dos dois períodos de 12 meses . Após a vacinação, observou-se uma tendência a aumento no título de anticorpos específicos para a H2N3, mas sem resultado significativo. Em relação aos resultados obtidos com as sorologias para o H1N1 e o pneumococo, não se observou resposta após a vacinação. Concluindo, houve redução do número de infecções, principalmente das IVAS, sinusites e pneumonias em pacientes com ICV após a vacinação contra a influenza, H1N1 e pneumococo. Embora não tenhamos encontrado correlação entre a redução do número de infecções e os títulos de anticorpos específicos para as vacinas testadas, a melhora clínica observada nos pacientes com ICV reforça o benefício da vacinação
Recent studies have shown satisfactory in vitro results in patients with CVID who received immunization against tetanus, influenza and meningococcus. However, there are only a few studies that evaluate the clinical and laboratory response after exposure to specific antigens in these patients. This study aims to evaluate the clinical response to immunization with protein and polysaccharide antigens (influenza, H1N1 and pneumococcus) in CVID patients followed at the Primary Immunodeficiency outpatient clinic of the Division of Clinical Immunology and Allergy, Hospital das Clínicas, FMUSP. CVID patients were diagnosed according the WHO/PAGID/ ESID criteria. Thirty-seven patients were immunized against influenza (H2N3), H1N1 and pneumococcal polysaccharide vaccine while another group with 16 CVID patients were not vaccinated. Clinical evaluation was performed through a score with assessment of the following parameters: pneumonia, sinusitis, otitis media, upper respiratory infections (URI), tonsillitis, diarrhea, bronchiectasis, hospitalizations, use of antibiotic therapy, and use of prophylactic antibiotics, sepsis and meningitis. The score was applied during the 12 months prior to immunization and one year after the administration of vaccines. The same score was applied to the group of CVID patients who weren´t immunized. Determination of IgG antibodies to pneumococcal serotypes was made by ELISA. H1N1-specific IgG was detected by indirect hemagglutination while the determination of influenzaspecific IgG was performed by ELISA, using the RIDASCREEN ® Influenza kit. The group of patients who were vaccinated included 37 patients (51% women), aged 20 to 78 years (mean 33 years). This group presented a median delay in the diagnosis of 7 years. The control group consisted of 16 patients (37.5% females) who were not immunized. Their median age was 41 years and the median delay in the diagnosis was 8 years. URI followed by pneumonia and sinusitis were the most frequent infections in women (80%, 78% and 55% respectively). However in men, URI followed by sinusitis and pneumonia were the most frequent (78%, 65% and 35% respectively). We observed a significant reduction in the score of URI, sinusitis and pneumonias in the year post administration of the vaccines (p <0.001). Conversely, there was no difference in the infections pre and post supposed vaccination scores in the group of CVID patients who were not immunized. There was no significant change in specific antibody titers to influenza and pneumococcus after vaccination. Regarding H1N1, there was no statistically significant production of antibodies to H1N1, although we observed a slight non-durable increase in antibody titers. In conclusion, there was a reduction in the number of infections, mainly sinusitis, URIs and pneumonias in patients with CVID vaccinated against influenza, H1N1 and pneumococcus. While we found no correlation between the reduction in the number of infections and specific antibody titers for the vaccines administered, the clinical improvement observed in CVID patients reinforces the benefit of vaccination

Le VIH-1 manipule les cellules présentatrices d’antigènes (APC) qui orchestrent les réponses immunes innées et adaptatrices, pour se propager dans l’hôte et établir le réservoir viral. Au laboratoire, nous étudions le rôle de l’autophagie dans les interactions entre les cellules dendritiques (DC) et le VIH-1 et la présentation des antigènes viraux. Dans divers modèles, la macroautophagie et l’autophagie médiée par les chaperonnes (CMA) semblent en effet être impliquées dans l’apprêtement d’antigènes sur les molécules du CMH. Ainsi, nous avons montré, dans une étude précédente, que la macroautophagie participait à la dégradation du VIH entrant dans les DC, conduisant à l’activation de lymphocytes T (LT) CD4+ spécifiques du VIH-1.Bien que sa réplication y soit limitée, le VIH-1 peut également infecter productivement les DC. J’ai donc voulu vérifier si les protéines virales néosynthétisées du virus peuvent constituer une source additionnelle d’antigènes. J’ai montré que, de façon remarquable, dans les DC infectées, des antigènes endogènes du VIH-1 peuvent être présentés par les molécules du CMH-II aux LT CD4 spécifiques. En utilisant différents outils, comme des inhibiteurs de l’autophagie ou des shRNA, j’ai montré que ni la macroautophagie ni la CMA ne contribuent significativement à l’apprêtement d’épitopes de la protéine virale Gag néosynthétisée sur les molécules du CMH-II. En parallèle, j’ai utilisé une protéine de fusion, Gag-LC3, pour acheminer spécifiquement Gag dans les autophagosomes (LC3+) des DC. Dans ce contexte, les drogues qui inhibent la macroautophagie réduisent drastiquement la présentation d’épitopes de Gag aux LT CD4. De façon remarquable, la présence de Gag dans les autophagosomes conduit à la génération d’épitopes antigéniques qui, dans le contexte infectieux, ne sont pas apprêtés sur les molécules de CMH-II par la voie endogène. Ainsi, diriger des protéines du VIH dans les autophagosomes conduirait à des variations dans le répertoire des antigènes endogènes présentés sur les molécules de CMH-II. Pour évaluer l’impact de l’autophagie sur la réplication du VIH dans les DC, j’ai ensuite analysé si la protéine Gag néosynthétisée pouvait être dégradée dans les autophagosomes. Dans les DC infectées, contrairement aux observations déjà décrites dans les macrophages, Gag ne colocalise ni avec les vésicules autophagiques LC3+, ni avec p62, une protéines adaptatrice impliquée dans le ciblage des protéines dans les autophagosomes. Ces résultats suggèrent que, dans ce contexte, les virions nouvellement produits ne sont pas acheminés et dégradés dans les autophagosomes. La protéine de fusion Gag-LC3 est utilisée dans ces expériences comme contrôle positif de colocalisation. Pour déterminer si mes observations pouvaient révéler un mécanisme d’échappement développé par VIH-1, j’ai utilisé différentes souches virales mutantes, modulé le flux autophagique avec des drogues et des ligands TLR, et exprimé Gag dans les DC en l’absence d’autres protéines virales. Dans l'ensemble, mon travail suggère que le VIH-1 ne manipule pas la macroautophagie dans les DC productivement infectées. En outre, la modulation de l’autophagie dans les DC (à l'aide de shRNA) n'a aucune incidence sur la réplication du VIH-1 et sur sa propagation.Mes travaux mettent en lumière la complexité des interactions entre l’autophagie et le VIH-1 dans les DC. Contrairement à ce qui a été observé lors des étapes d’entrée du virus, le virus ne semble pas être acheminé dans les autophagosomes une fois les DC infectées, et l’autophagie ne participe pas à l’apprêtement des antigènes néosynthétisés sur les molécules de CMH II. Cependant, les DC infectées activent de façon efficace les LT CD4 spécifiques du virus. Forcer l’acheminement d’antigènes du VIH dans les autophagosomes augmente fortement cette activation, et semble conduire à une diversification du répertoire des épitopes présentés sur les molécules de CMH-II par la voie endogène
HIV-1 manipulates antigen-presenting cells (APC) such as dendritic cells (DC), witch orchestrate innate and adaptive immune responses, in order to propagate in the host and to establish viral reservoirs. We are studying the role of autophagic processes in DC/HIV-1 interactions with a focus on antigen presentation. We have previously shown that macroautophagy in DC participates in the degradation of incoming HIV-1 particles leading to activation of HIV-1-specific (HS) CD4 T cells. HIV-1 can also productively infect DC. I thus first asked whether neo-synthetized viral proteins might represent an additional source of HIV-1 antigens. Remarkably, I have shown using infected monocyte derived DC that de novo expression of Gag leads to the activation of HS CD4 T cells, highlighting that this antigen is endogenously processed in order to be presented into MHC-II molecules. Since macroautophagy and chaperon-mediated autophagy (CMA) are known to be involved in this process for other viral antigens and model antigens, I then dissected the role of these two pathways. Using several tools including inhibitors and shRNA, I demonstrated that in HIV-1-infected DC neither macroautophagy nor CMA contribute significantly to the processing of HIV-1-Gag epitopes into MHC-II molecules. I also used a Gag-LC3 fusion protein to specifically channel Gag into LC3+ autophagic vesicles in DC. In this context, inhibiting autophagy dramatically reduced the presentation of HIV-1-Gag epitopes to CD4+ T cells. Strikingly, channelling Gag into autophagosomes generated epitopes that were not processed endogenously in the context of HIV-1 infection. Thus specifically directing HIV-1 proteins toward autophagosomes might influence the repertoire of MHC II-restricted HIV-1 antigens. I further analyzed whether autophagy could affect HIV-1 replication in infected DC. In these cells, in contrast to what has been described in macrophages, Gag did not colocalize with LC3 or with the autophagic adaptor p62, suggesting that newly-produced HIV-1 particles are not sequestrated into autophagosomes. The Gag-LC3 fusion protein was used here as a positive control of colocalization. To determine whether my findings might reveal a DC-specific escape mechanism developed by HIV-1, I used various HIV-1 mutants, enhanced autophagic flux using drugs or TLR ligands, and expressed Gag in the absence of other HIV-1 proteins. Overall, my work suggests that HIV-1 does not manipulate autophagy in productively-infected DC. Moreover, modulating autophagy in DC (using shRNA) does not impact HIV-1 replication and propagation. Finally, my work highlights the complexity of the interactions between the autophagic process and HIV-1 replication in DC. Unlike during viral entry, HIV-1 does not seem to be targeted into autophagosomes after viral replication in infected DC, and autophagy does not contribute significantly to the processing of endogenous viral antigens. Nonetheless HIV-1-infected DC efficiently activates HS CD4 T cells, and targeting HIV antigens into autophagosomes greatly enhances this activation and might broaden the repertoire of MHC-II-restricted antigen. Further dissection of the various routes of endogenous HIV antigen processing would aid in the development of innovative vaccines

To improve understanding of factors associated with intimate partner violence (IPV) and explore its role in sexually transmitted infection (STI) acquisition, we analyzed partnership-level correlates of IPV among men who have sex with men (MSM) and transgender women (TW) in Peru. In a 2017 cross-sectional study of rectal STI screening and HIV prevention, MSM/TW completed a sociobehavioral survey addressing demographic characteristics, sexual risk behaviors, and substance use, and were tested for rectal gonorrhea and chlamydia, syphilis, and HIV. Generalized estimating equations estimated individual- and partner-level correlates of IPV. Of 576 participants (median age, 27 years), 7.9% (36/456) of MSM and 15.0% (18/120) of TW reported IPV with ≥ 1 of their last three partners. MSM/TW reporting IPV were more likely to meet criteria for an alcohol use disorder (74.1%) than participants reporting no IPV (56.7%; p <.01). Physical violence (4.5% MSM; 9.2% TW) was associated with stable partnerships (aPR 3.79, 95% CI 1.79–8.04), partner concurrency (4.42, 1.19–16.40), and participant alcohol (4.71, 1.82–12.17) or drug use (5.38, 2.22–13.02) prior to sex. Psychological violence (4.5% MSM; 5.0% TW) was associated with stable partnerships (2.84, 1.01–7.99). Sexual IPV was reported by 1.1% of MSM and 5.0% of TW. Physical, psychological, and sexual IPV were reported in sexual partnerships of Peruvian MSM and TW, particularly with stable partners and in conjunction with substance use.
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