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<p>Background: The reasons why some individuals become IgE-sensitised and allergic are largely unknown, though genetic- and early life environmental factors seem to be of importance.</p><p>Objective: The overall aim of this thesis was to investigate the relationship between IgE-sensitisation and allergic disease, viral infections, genetic markers and early life cytokines.</p><p>Results: IgE-sensitised children were found to have reduced numbers of IL-12 producing cord blood mononuclear cells (CBMC), whereas children diagnosed with eczema were found to have reduced numbers of IFN-γ producing CBMC. When dividing the children into early onset of IgE-sensitisation and late onset of IgE-sensitisation we found that the children with an early onset had low numbers of PHA-induced IL-4, IL-12 and IFN-γ secreting CBMC. At the age of two there was a general exacerbation of cytokine responses in the IgE-sensitised children, and the results were similar for the children with early onset IgE-sensitisation. Children with a late onset IgE-sensitisation were more similar to the non-sensitised children, but with a specific increase in the response to cat allergen (IL-4 and IFN-γ). The mothers of IgE-sensitised children, were just as their children, found to have an exaggerated cytokine response as compared to mothers of non-sensitised children. Maternal responses correlated well to the responses seen in the child, though the samples were taken two years after delivery.</p><p>Cytomegalovirus (CMV) infection in early life was associated to reduced numbers of IL-4, and increased numbers of IFN-γ producing cells at the age of two. No association between CMV seropositivity and IgE-sensitisation was seen. Epstein-Barr virus (EBV) infection, on the other hand, was inversely correlated with IgE –sensitisation, whereas no statistically significant association to cytokine production could be seen.</p><p>We also showed that the IL12B 1188 C-allele was associated to having a positive skin prick test at the age of two. The rare alleles of the three SNPs investigated (IL12B 1188C, IL12RB1132C and IRF1 1688A) were all associated to low IL-12 production at birth.</p><p>Conclusions: Our results indicate that allergic diseases are complex traits, and that both the genetic and the cytokine background differ between the different allergic diseases. We can also conclude that the time of onset seem to play a role when investigating IgE-sensitisation, and that perhaps early and late onset IgE-sensitisation have partly different causes. CMV and EBV infection early in life are associated to a protective cytokine profile and to protection from IgE-sensitisation, respectively, again indicating the heterogeneity and the complexity of allergic diseases.</p>

La truite arc-en-ciel (Oncorhynchus mykiss), espèce d'élevage majeure en Europe et notamment en France, est l'une des espèces de poisson les mieux connues dans un grand nombre de domaines, y compris l'immunologie. Les virus qui l'infectent ont aussi été bien caractérisés, en particulier deux Novirhabdovirus, le virus de la septicémie hémorragique virale (VSHV) et le virus de la nécrose hématopoïétique infectieuse (VNHI), tous deux connus pour provoquer des pertes importantes dans les élevages aquacoles. Quelques travaux, conduits notamment à l'INRA, ont mis en évidence l'existence d'une variabilité génétique de la résistance à ces infections chez la truite (Quillet et al., 2007). Une approche combinant analyse génétique et étude des réponses cellulaires a été développée pour tenter de mieux caractériser la réponse de la truite contre le VSHV. L'objectif est de développer des outils d'amélioration de la santé dans les élevages piscicoles et de mieux comprendre les mécanismes de résistance antivirale chez les vertébrés. Tout d'abord, une démarche de cartographie de QTL (quantitative trait locus) a permis de détecter un QTL majeur de résistance au VSHV dans la région télomérique du groupe de liaison 31 de la truite arc-en-ciel. Ce QTL contrôle la survie des poissons et la croissance in vitro du virus sur explants de nageoire (VREFT), ce qui suggère fortement l'implication de mécanismes innés dans la résistance. Le QTL est retrouvé dans des croisements impliquant des reproducteurs de résistance variée, et peut expliquer jusqu'à 65% (survie) et 49% (VREFT) de la variance phénotypique observée. Enfin, l'effet du QTL est conservé quel que soit le mode d'infection employé (balnéation ou injection intrapéritonéale), suggérant que la résistance n'est pas liée à des particularités des tissus superficiels (peau, mucus), premiers sites de contact entre le virus et son hôte. En parallèle, des lignées cellulaires ont été dérivées à partir d'ovaires de truites appartenant à des lignées isogéniques présentant des niveaux de résistance variable à l'infection par le VSHV. Une corrélation remarquable est observée entre la résistance à l'infection des lignées cellulaires et la survie des poissons dont elles sont issues, confirmant définitivement le rôle déterminant de mécanismes innés dans la résistance. Ce modèle cellulaire a également permis de montrer que le contrôle précoce de la prolifération virale était une étape clé de la résistance. Le parallélisme entre résistance in vitro et in vivo semble conservé lors de l'infection par un second rhabdovirus, le VNHI, bien qu'aucune corrélation dans la résistance à ces deux infections n'ait été observée dans cette étude. Par ailleurs, le QTL à effet fort identifié pour la résistance au VSHV ne joue pas un rôle majeur dans la variabilité de résistance au VNHI. Ceci suggère que, même si ils concourent à l'activation de voies de signalisation communes, les facteurs clés de la résistance aux deux virus sont différents, et leur expression contrôlée par des zones génomiques distinctes. Les résultats obtenus dans cette étude ont permis de démontrer sans équivoque le rôle clé des mécanismes innés dans la résistance de la truite à l'un de ses principaux virus, et l'existence d'une forte variabilité génétique sous-tendant l'expression des facteurs impliqués. En proposant des bases nouvelles pour aborder l'analyse des interactions hôte-virus chez la truite, ils ouvrent la voie à la découverte de mécanismes potentiellement nouveaux dans la réponse des poissons à ces infections et à une meilleure compréhension de ces mécanismes chez les vertébrés. / The rainbow trout (Oncorhynchus mykiss) is one of most significant fish model in many scientific fields, including immunology. Due to its importance in aquaculture, viruses that can infect this species have been well characterized. Two well-known Novirhabdoviruses, the viral haemorrhagic septicemia virus (VHSV) and the infectious hematopoietic necrosis virus (IHNV) cause serious damage in fish farms and represent a significant threat for aquaculture in a number of countries. Our laboratories have previously reported a wide range of susceptibility to these infections in rainbow trout depending on the host genetic background (Quillet et al., 2007). In this work, we undertook a dual approach to better characterize the antiviral response in fish. A without a priori approach led to the detection of a major QTL (quantitative trait locus) for resistance to VHSV in the telomeric region of the rainbow trout linkage group 31. This QTL controls both fish survival and viral replication in excised fin tissue (VREFT), suggesting the involvement of innate mechanisms in the resistance, and can explain up to 65% (survival) and 49% (VREFT) of the observed phenotypic variation. Additionally, this major locus was retrieved in a number of genetic backgrounds, and regardless of the infection route (waterborne infection or injection), suggesting that the virus entry in fish is not the main factor of resistance. In parallel, cell lines were derived from ovaries of several rainbow trout isogenic lines with various levels of susceptibility to infection with VHSV. Resistance of cell lines to infection by the virus was remarkably correlated with the survival of fish from which they were derived, confirming the importance of innate factors for the resistance. This model also showed that the early stage response is critical for the cellular fate after infection. The parallelism between resistance in vitro and in vivo has finally been observed after infection by a second rhabdovirus, IHNV, although no correlation in resistance to these two viruses could be detected. Moreover, no major QTL for IHNV resistance was found in the region of the VHSV QTL. This observation suggests that the key factors of resistance are different, even if they contribute to the activation of common signaling pathways. The expression of these factors is in any case controlled by distinct regions of the genome. Our work demonstrates a strong genetic determinism of resistance to a major virus in rainbow trout, based on innate mechanisms. We believe that these results pave the way for the discovery of new host response mechanisms against viruses, leading to a better understanding of antiviral immunity in vertebrates.

Student Number: 9811822T - MSc Dissertation - School of Computational and Applied Mathematics - Faculty of Science / This dissertation reviews population dynamic type models of viral infection and introduces some new models to describe strain competition and the infected cell lifecycle. Laboratory data from a recent clinical trial, tracking drug resistant virus in patients given a short course of monotherapy is comprehensively analysed, paying particular attention to reproducibility. A Bayesian framework is introduced, which facilitates the inference of model parameters from the clinical data. It appears that the rapid emergence of resistance is a challenge to popular unstructured models of viral infection, and this challenge is partly addressed. In particular, it appears that minimal ordinary differential equations, with their implicit exponential lifetime (constant hazard) distributions in all compartments, lack the short transient timescales observed clinically. Directions for future work, both in terms of obtaining more informative data, and developing more systematic approaches to model building, are identified.

Introdução: As infecções virais respiratórias agudas são as doenças mais comuns em humanos e estão associadas a grande morbidade e mortalidade em crianças, principalmente menores de 2 anos de idade, sobretudo nos países em desenvolvimento e em idosos nos países desenvolvidos. As crianças que apresentam cardiopatias congênitas estão mais susceptíveis a adquirir infecção viral devido à sua mecânica pulmonar alterada, o que pode gerar diversas complicações tanto no período pré-operatório quanto no período pós-operatório, tais como aumento no tempo de internação hospitalar, maior tempo de ventilação mecânica e maiores taxas de mortalidade. Este estudo teve como objetivo identificar a epidemiologia das infecções virais respiratória em crianças com cardiopatia congênita e comparar os desfechos: tempo de internação, tempo de ventilação mecânica e mortalidade, na presença ou não de infecção viral respiratório e determinar qual o momento que essas crianças adquirem a infecção viral. Trata-se de estudo longitudinal, observacional, do tipo coorte. Foram coletadas amostras de secreção nasofaringe no período pré e pós operatório de todos os pacientes submetidos à cirurgia cardíaca e analisados os dados gerais dos pacientes durante o tempo de internação no centro de terapia intensiva pediátrica, por meio de prontuário médico, entre maio de 2013 a maio de 2014. Resultados: Foram analisados 43 pacientes. Foi encontrada elevada prevalência de vírus respiratórios (39%) em crianças com cardiopatia congênita. No presente estudo não houve diferença estatisticamente dos desfechos em relação a infecção viral respiratória no modelo estatístico bivariável, por motivo de interferência de variáveis confundidoras, idade e RACHS-1. A seguir, foram ajustados modelos de regressão multivariável, para analisar os desfechos com a variáveis idade, RACHS-1 e infecção viral. A variável infecção viral respiratória apresentou efeito estatisticamente significativo no desfecho diferença arteriovenosa de oxigênio, enquanto as covariáveis idade e RACHS-1 tiveram efeito significativamente em todos os desfechos pesquisados no estudo. Conclusão: A prevalência de infecção viral respiratória em crianças submetidas a cirurgia cardíaca é alta. A infecção viral respiratória não apresentou efeito sobre os principais desfechos, apenas na diferença arteriovenosa de oxigênio / Introduction: Acute respiratory viral infections are the most common diseases in humans and are associated with high morbidity and mortality in children, especially those under two years of age, particularly in developing countries, and in the elderly from developed countries. Children with congenital heart disease are more likely to get viral infections due to their altered lung mechanics, which can lead to several complications in both the preoperative and postoperative period, such as increased hospital stay, longer mechanical ventilation and higher mortality rates. This study aimed to identify the epidemiology of respiratory viral infections in children with congenital heart disease, to compare the outcomes: hospital stay, duration of mechanical ventilation and mortality, in the presence or absence of respiratory viral infection, and determine the time when these children acquire viral infection. This is a longitudinal, observational cohort study. Nasopharyngeal secretion samples were collected pre- and postoperatively for all patients undergoing cardiac surgery. General data of patients were obtained during hospital stay from medical records, from May 2013 to May 2014. Results: We enrolled 43 patients. We found a high prevalence of respiratory viruses (39%) in children with congenital heart disease. In this study there was no statistically significant difference in outcomes in relation to respiratory viral infection in bivariate statistical model, because of interference from confounding variables, age and RACHS-1. We then used multivariate regression models to analyze outcomes with respect to independent variables age, RACHS-1 and viral infection. Respiratory viral infection showed a statistically significant effect on the outcome arteriovenous oxygen difference, while the covariables age and RACHS-1 showed significant effects on all outcomes investigated in the study. Conclusion: The prevalence of respiratory viral infection in children undergoing cardiac surgery is high. Respiratory viral infection did not affect the outcome, just in arteriovenous oxygen difference

Introdução: As infecções virais respiratórias agudas são as doenças mais comuns em humanos e estão associadas a grande morbidade e mortalidade em crianças, principalmente menores de 2 anos de idade, sobretudo nos países em desenvolvimento e em idosos nos países desenvolvidos. As crianças que apresentam cardiopatias congênitas estão mais susceptíveis a adquirir infecção viral devido à sua mecânica pulmonar alterada, o que pode gerar diversas complicações tanto no período pré-operatório quanto no período pós-operatório, tais como aumento no tempo de internação hospitalar, maior tempo de ventilação mecânica e maiores taxas de mortalidade. Este estudo teve como objetivo identificar a epidemiologia das infecções virais respiratória em crianças com cardiopatia congênita e comparar os desfechos: tempo de internação, tempo de ventilação mecânica e mortalidade, na presença ou não de infecção viral respiratório e determinar qual o momento que essas crianças adquirem a infecção viral. Trata-se de estudo longitudinal, observacional, do tipo coorte. Foram coletadas amostras de secreção nasofaringe no período pré e pós operatório de todos os pacientes submetidos à cirurgia cardíaca e analisados os dados gerais dos pacientes durante o tempo de internação no centro de terapia intensiva pediátrica, por meio de prontuário médico, entre maio de 2013 a maio de 2014. Resultados: Foram analisados 43 pacientes. Foi encontrada elevada prevalência de vírus respiratórios (39%) em crianças com cardiopatia congênita. No presente estudo não houve diferença estatisticamente dos desfechos em relação a infecção viral respiratória no modelo estatístico bivariável, por motivo de interferência de variáveis confundidoras, idade e RACHS-1. A seguir, foram ajustados modelos de regressão multivariável, para analisar os desfechos com a variáveis idade, RACHS-1 e infecção viral. A variável infecção viral respiratória apresentou efeito estatisticamente significativo no desfecho diferença arteriovenosa de oxigênio, enquanto as covariáveis idade e RACHS-1 tiveram efeito significativamente em todos os desfechos pesquisados no estudo. Conclusão: A prevalência de infecção viral respiratória em crianças submetidas a cirurgia cardíaca é alta. A infecção viral respiratória não apresentou efeito sobre os principais desfechos, apenas na diferença arteriovenosa de oxigênio / Introduction: Acute respiratory viral infections are the most common diseases in humans and are associated with high morbidity and mortality in children, especially those under two years of age, particularly in developing countries, and in the elderly from developed countries. Children with congenital heart disease are more likely to get viral infections due to their altered lung mechanics, which can lead to several complications in both the preoperative and postoperative period, such as increased hospital stay, longer mechanical ventilation and higher mortality rates. This study aimed to identify the epidemiology of respiratory viral infections in children with congenital heart disease, to compare the outcomes: hospital stay, duration of mechanical ventilation and mortality, in the presence or absence of respiratory viral infection, and determine the time when these children acquire viral infection. This is a longitudinal, observational cohort study. Nasopharyngeal secretion samples were collected pre- and postoperatively for all patients undergoing cardiac surgery. General data of patients were obtained during hospital stay from medical records, from May 2013 to May 2014. Results: We enrolled 43 patients. We found a high prevalence of respiratory viruses (39%) in children with congenital heart disease. In this study there was no statistically significant difference in outcomes in relation to respiratory viral infection in bivariate statistical model, because of interference from confounding variables, age and RACHS-1. We then used multivariate regression models to analyze outcomes with respect to independent variables age, RACHS-1 and viral infection. Respiratory viral infection showed a statistically significant effect on the outcome arteriovenous oxygen difference, while the covariables age and RACHS-1 showed significant effects on all outcomes investigated in the study. Conclusion: The prevalence of respiratory viral infection in children undergoing cardiac surgery is high. Respiratory viral infection did not affect the outcome, just in arteriovenous oxygen difference

CD8 T cells play a critical role in the clearance of pathogenic bacteria, viruses, and protozoan parasites. Upon encountering their cognate antigen through either infection or vaccination, naïve CD8 T cells undergo robust proliferative expansion, which is followed by contraction and the formation of a memory population. Memory CD8 T cells are long-lived, and because they persist in increased numbers and possess enhanced functional abilities compared to naïve CD8 T cells, they are able to provide the host with increased protection following re-infection. Because of these properties, vaccines designed to elicit memory CD8 T cells have the potential to reduce health care burdens related to infection with pathogens including human immuno deficiency virus (HIV), malaria, influenza, and hepatitis virus. However, stimulating protective CD8 T cell responses against these pathogens through vaccination has proven challenging. Therefore, a better understanding of the properties of memory CD8 T cells generated following vaccination, and the characteristics of memory CD8 T cells best suited for providing protection against diverse pathogens is needed. While memory CD8 T cells can be maintained for as long as the life of the host, evidence suggests that their properties change with time after infection. Because CD8 T cell-mediated protection is based upon both the numbers and quality or functional abilities of memory cells present at the time of re-infection, changes in memory CD8 T cell function over time could impact their ability to provide protection upon re-infection. Therefore, a better understanding of how memory CD8 T cells change with time after infection is needed. As part of the studies presented in this thesis, I found that the phenotype and function of memory CD8 T cells including localization, interleukin (IL)-2 cytokine production, responsiveness to homeostatic cytokines, metabolic capabilities, and proliferation and secondary memory generation potential change with time after infection. Interestingly functional changes could not be completely explained by changes in subset composition that occur with time, as changes over time were also seen in defined CD62Lhi subsets. Importantly, functional changes of memory CD8 T cells that occurred with time led to an increased ability to provide protection against a chronic viral infection. These data improve our knowledge of the capabilities of memory CD8 T cells generated following infection, and suggests that the outcome of vaccination strategies designed to elicit protective memory CD8 T cells using single or prime-boost immunizations will depend upon the timing between antigen encounters. Following re-infection, memory CD8 T cells become activated and produce effector cytokines and cytolytic molecules that aid the host in clearing invading microbes. Activation can be triggered not only through cognate antigen recognition, but also by antigen-independent cytokine driven signals. However, our knowledge of how antigen-dependent and –independent signals contribute to CD8 T cell activation and protection following infection is incomplete. In the second part of my thesis, I show that the ability of memory CD8 T cells to become activated in response to inflammation decreases with time after infection, that antigen and inflammation act synergistically to induce activation of memory CD8 T cells, that the presence of cognate antigen enhances activation of memory CD8 T cells that contribute to clearance of infection, and that bystander memory CD8 T cell responses following unrelated bacterial infection do not provide the host with a protective benefit. Together, the data in this thesis further our understanding of memory CD8 T cells generated following infection and/or vaccination, and the properties of memory CD8 T cells important for providing protection upon re-infection with invading pathogens.

This work was aimed to investigate the basic viral infection protocols mainly focusing on Nicotiana benthamiana hairy root cultures and wild-type tobacco mosaic virus (TMV). The application of transgenic virus containing the gene for green fluorescent protein (GFP) for foreign protein production in plant tissue cultures and whole plants was also studied. The effect on viral accumulation of the form of plant tissue culture used, such as hairy roots, shooty teratomas and suspended cells, was investigated. Viral infection was shown to have no effect on culture growth and morphology. Hairy root cultures are a superior host for viral propagation and production in vitro. The maximum specific rate of viral accumulation occurred mainly during the root growth phase. The average maximum virus concentration in the hairy roots was 0.82 ?? 0.14 mg g-1 dry weight and virus protein represented a maximum of approximately 6% of total soluble protein in the root biomass. Proportional scale-up of TMVinfected hairy roots in shake flasks and bioreactors can be achieved without changing the average virus concentration accumulated in the hairy roots. The level of viral accumulation was much lower in N. benthamiana hairy roots infected with transgenic virus containing GFP (TMVGFPC3) compared with TMV and low levels or no GFP was detected. Viral accumulation and GFP production in whole plants was studied using different generations of transgenic TMV-GFPC3 virus. Hybrid viruses with the foreign gene GFPC3 deleted may have been formed in successive TMV-GFPC3 generations, resulting in the loss of GFP production and enhanced viral infectivity. In vitro generated RNA transcript and first generation TMV-GFPC3 were found to be more suitable for infection than the second generation TMV-GFPC3. However, the accumulation of GFP and virus concentration did not occur at the same ratio. Provided a more genetically stable transgenic viral vector is used for infection, transient viral infection of hairy roots can be a potential alternative system for foreign protein production than plants grown in the field as the containment or safety issues can be addressed.

Background: The reasons why some individuals become IgE-sensitised and allergic are largely unknown, though genetic- and early life environmental factors seem to be of importance. Objective: The overall aim of this thesis was to investigate the relationship between IgE-sensitisation and allergic disease, viral infections, genetic markers and early life cytokines. Results: IgE-sensitised children were found to have reduced numbers of IL-12 producing cord blood mononuclear cells (CBMC), whereas children diagnosed with eczema were found to have reduced numbers of IFN-γ producing CBMC. When dividing the children into early onset of IgE-sensitisation and late onset of IgE-sensitisation we found that the children with an early onset had low numbers of PHA-induced IL-4, IL-12 and IFN-γ secreting CBMC. At the age of two there was a general exacerbation of cytokine responses in the IgE-sensitised children, and the results were similar for the children with early onset IgE-sensitisation. Children with a late onset IgE-sensitisation were more similar to the non-sensitised children, but with a specific increase in the response to cat allergen (IL-4 and IFN-γ). The mothers of IgE-sensitised children, were just as their children, found to have an exaggerated cytokine response as compared to mothers of non-sensitised children. Maternal responses correlated well to the responses seen in the child, though the samples were taken two years after delivery. Cytomegalovirus (CMV) infection in early life was associated to reduced numbers of IL-4, and increased numbers of IFN-γ producing cells at the age of two. No association between CMV seropositivity and IgE-sensitisation was seen. Epstein-Barr virus (EBV) infection, on the other hand, was inversely correlated with IgE –sensitisation, whereas no statistically significant association to cytokine production could be seen. We also showed that the IL12B 1188 C-allele was associated to having a positive skin prick test at the age of two. The rare alleles of the three SNPs investigated (IL12B 1188C, IL12RB1132C and IRF1 1688A) were all associated to low IL-12 production at birth. Conclusions: Our results indicate that allergic diseases are complex traits, and that both the genetic and the cytokine background differ between the different allergic diseases. We can also conclude that the time of onset seem to play a role when investigating IgE-sensitisation, and that perhaps early and late onset IgE-sensitisation have partly different causes. CMV and EBV infection early in life are associated to a protective cytokine profile and to protection from IgE-sensitisation, respectively, again indicating the heterogeneity and the complexity of allergic diseases.

The usual approach to the study of signaling pathways in biological systems is to assume that high numbers of cells and of perfectly mixed molecules within cells are involved. To study the temporal evolution of the system averaged over the cell population, ordinary differential equations are usually used. However, this approach has been shown to be inadequate if few copies of molecules and/or cells are present. In such situation, a stochastic or a hybrid stochastic/deterministic approach needs to be used. Moreover, considering a perfectly mixed system in cases where spatial effects are present can be an over-simplifying assumption. This can be corrected by adding diffusion terms to the ordinary differential equations describing chemical reactions and proliferation kinetics. However, there exist cases in which both stochastic and spatial effects have to be considered. We study the relevance of differential equations, stochastic Gillespie algorithm, and deterministic and stochastic reaction-diffusion models for the study of important biological processes, such as viral infection and early carcinogenesis. To that end we have developed two optimized libraries of C functions for R (r-project.org) to simulate biological systems using Petri Nets, in a pure deterministic, pure stochastic, or hybrid deterministic/stochastic fashion, with and without spatial effects. We discuss our findings in the terms of specific biological systems including signaling in innate immune response, early carcinogenesis and spatial spread of viral infection.