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Les arbovirus (dont le virus chikungunya, CHIKV) sont responsables de millions d'infections chaque année ; aucun vaccin n'est encore approuvé, et les traitements disponibles restent limités. De part leur circulation constante entre le moustique et l'humain, leur adaptation rapide à différents hôtes est un facteur clé pour leur pathogenèse. Le taux d'erreur particulièrement élevé de leur polymérase ARN permet une rapide diversification génique qui conduit à la génération d'un nuages de mutants, appelée quasi espèce. Les quasi espèces contiennent non seulement des génomes mutés, mais aussi des ARN recombinés à partir de deux génomes d'origine différente, ainsi que des génomes avec de grandes délétions, incapables de se répliquer sans l'aide d'un autre virion qui doit infection la même cellule, nommés génomes viraux défectifs (GVD). Une régulation étroite de la taille du nuage de mutants est clé pour une pathogenèse efficace : si trop petit, le potentiel adaptatif du virus sera impacté ; au contraire, une quasi-espèce trop grande peut mener à l'accumulation rapide de mutations délétères pour le virus. Alors que la régulation du paysage mutationnel est atteinte grâce à un taux d'erreur de la polymérase viral finement contrôlé, la recombinaison et la réplication des génomes défectifs sont influencés par le potentiel de co-infection des cellules cibles. Dans ce contexte, l'exclusion de la surinfection (ESI), un processus par lequel l'infection par un premier virus inhibe l'infection par un second virus, peut influer le dynamique de la quasi-espèce. Bien que décrite dans la plupart des familles virales, les mécanismes à l'origine de l'ESI restent mal caractérisés. Dans ce travail, je montre que CHIKV exclut une infection future par CHIKV, mais aussi par le virus Sindbis et le virus de la grippe A, mais non par le virus du Nil occidental. Je démontre que l'exclusion de CHIKV se situe au niveau de la pénétration du génome viral dans le cytoplasme, puis de sa réplication, mais n'influence ni l'attachement du virion ni la traduction de son génome. Je montre également que l'ESI est indépendant de l'action des interférons de type I, et qu'elle n'est médiée ni par la transcription cellulaire, ni par un facteur soluble. De plus, l'exclusion n'est pas due à une unique protéine virale, suggérant un potentiel rôle de la réponse cellulaire à l'infection.Déterminer l'influence des pressions immunologiques dans l'établissement de la quasi-espèce peut aider à une meilleure compréhension de l'interaction entre évolution virale et réponse immunitaire. Bien que la caractérisation non biaisée des mutations ponctuelles fût le fruit de nombreux travaux, les GVD restent peu caractérisées, en particulier chez les alphavirus. Dans la deuxième partie de ce travail, je développe des outils bio-informatiques pour isoler rapidement les GVD de données de séquençage à haut débit, et analyse les avantages et les inconvénients d'un ajout d'une étape de pré-amplification pour détecter et quantifier les GVD. À l'aide de ces outils, je fournis ensuite la première description complète des GVD produits par des passages séquentiels de CHIKV en culture cellulaire. En particulier, je montre que le type de GVD générés est très dépendants du type cellulaire, avec des motifs de séquences et des cadres de lecture ouverts différents lorsque les cellules hôtes sont des cellules de mammifère ou d'insecte. Ces résultats soulignent le role de l'environnement cellulaire dans le modelage de la quasi-espèce, et des GVD en particulier. Des travaux futurs aideront à dévoiler les mécanismes sous-jacents à cette interaction et pourraient permettre la conception de nouvelles stratégies thérapeutiques ciblant les dynamiques des quasi-espèces. / Arboviruses such as chikungunya virus (CHIKV) are responsible for millions of yearly infections, with no approved vaccines and limited treatments. Because they circulate between mosquitoes and humans, their fast adaptation potential to different hosts is key to pathogenesis. To achieve genome diversification, they rely on the error-prone nature of their self-encoded RNA-dependent RNA polymerase, which quickly generates a cloud of mutants, termed quasispecies. Quasispecies contain not only mutated genomes, but also shuffled genomes of different parental origin (through a process known as recombination), as well as genomes with large deletions, unable to replicate without the co-infection with a full-length helper genome, and thus termed defective viral genomes (DVGs). A tight regulation of the mutant cloud size is key to pathogenesis: if too small, it will limit the adaptation potential of the virus, whilst too big a quasispecies may lead to the fast accumulation of deleterious mutations. While regulation of the mutational landscape is achieved through the finely tuned error rate of the viral polymerase, recombination and DVG replication are influenced by the co-infection potential of the target cells.In this context, superinfection exclusion (SIE), a process by which infection by a first virus prevents infection by a second, closely related virus, can regulate quasispecies dynamics. While described in most viral families, mechanisms underlying SIE remain poorly characterised. Here, I show that CHIKV infection excludes subsequent infection by CHIKV, Sindbis virus and influenza A virus, but not West Nile virus. I demonstrate that CHIKV exclusion occurs at two steps, impacting independently viral penetration and replication, but does not directly influence binding, nor viral protein translation. I further show that SIE is interferon independent, and does not rely on host cell transcription nor on soluble cellular factors. Moreover, exclusion is not mediated by the action of a single CHIKV protein, suggesting that a cellular response may be at play. Assessing how different immunological pressures can shape quasispecies landscape may prove useful to a more thorough understanding of the interplay between viral evolution and the immune response. Although the unbiased study of point mutations has received much attention, less is known about the characteristics of DVGs, especially in alphaviruses. In the second part of this work, I develop bioinformatics tools to quickly isolate DVGs from next-generation sequencing data, and assess the advantages and drawbacks of pre-amplification steps to detect and quantify DVGs. Using these tools, I provide the first unbiased description of the DVG landscape generated through serial passaging of CHIKV in cell culture. In particular, I show that the DVG landscape is highly dependent on the cell type, with sequence patterns and open reading frames differing between DVGs generated in mammalian and insect cells. These results highlight the role of the cellular environment in shaping quasispecies, and DVGs in particular. Future work will help uncover the mechanisms underlying this crosstalk and may prove useful for the design of treatments targeting quasispecies dynamics.

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No description available.

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Completion of work and rights and duties resulting from defective work This thesis focuses on the analysis and description of selected aspects of a contract for work which are completion of work and rights and duties resulting from defective work. The selected aspects are dealt with in this thesis according to their regulation after the recodification of civil law in Act no. 89/2012 Coll., the Civil Code. This new legislation is analyzed and at the same time compared with the legislation from which it partly arose and that was abolished by the Civil Code, i.e. Act no. 40/1964 Coll., the Civil Code, as amended, and Act no. 513/1991 Coll., the Commercial Code, as amended. The goal of this thesis is to analyze the current legal regulation of the selected aspects of a contract for work and compare it with the previous legislation, then to briefly summarize some conclusions drawn from existing case law in this area, consider comprehensibility and applicability of the new legislation in question, make some recommendations to parties concluding a contract for work and submit several proposals for a modification of the legislation de lege ferenda. The thesis is composed of five chapters, each of them dealing with different aspects of the new legislation of a contract for work as it is regulated by the Civil...

Der MHC I Pathway ist ein Teil des Immunsystems und stellt mittels Antigenen an der Zelloberfläche den Proteinstatus der Körperzellen dar. Ziel dieser Arbeit ist durch die Entwicklung von Modellen zu Proteinsynthese und Abbau sowie den Teilschritten des MHC I Pathways und der Untersuchung von Simulationsergebnissen das Verständnis der zugrunde liegenden Prozesse zu verbessern und gegebenenfalls die Qualität der Antigenprädiktion zu verbessern. Es wurden statistische Modelle für den Transport der Peptide in das ER mittels TAP, das Schneiden von Peptidbindungen durch das Proteasom und das cytosolische sowie endoplasmatische Trimmen von Peptiden entwickelt. Weiterhin wurden kinetische Modelle zur Synthese und Abbau von viralen Proteinkonstrukten, zur proteasomalen Erstellung von Proteinfragmenten und zum Simulieren des Gesamtprozesses von Infektion bis zur Antigenpräsentation entwickelt. Es wurde gezeigt, dass eine DRiP Rate von 10 Prozent die Antigenpräsentation unabhängig von der Lebenszeit der Proteine gewährleistet und für langlebige Proteine der Anteil der Antigene aus DRiPs die Gesamtmenge der Antigene dominiert. So wird gewährleistet, dass an der Zelloberfläche der Status der momentanen Proteinsynthese dargestellt wird. Die erstellten Teilmodelle der Schritte des MHC I Pathways sind jeweils auf in vitro Daten des jeweiligen Prozesses trainiert und ermöglichen zusammen mindestens die gleiche Vorhersagequalität, wie Pathway Modelle, die auf in vivo Daten trainiert worden sind. Dies zeigt, dass alle wesentlichen Prozesse zur Antigenpräsentation von den erstellten Modulen erfasst werden. Die Module können je nach Bedarf und Fragestellung zu Modellen kombiniert werden. Ein Vorhersagetool wurde auf http://mhc-pathway.net zur Verfügung gestellt. Durch Modellanalysen können der relative Beitrag der einzelnen Schritte des Pathways und die Vorraussetzungen für ein potentielles Antigen bestimmt werden. Das kinetische Modell der Prozesse von Infektion bis Antigenpräsentation erlaubt das Verfolgen aller Peptide und das Analysieren der Prozesse die zur Erstellung von Epitopen führen. Die quantitativen Vorhersagen können experimentell validiert werden. Die proteasomale Fragmenterstellung ist der Teilprozess, der noch am wenigsten gut verstanden ist und bedarf noch weiterer experimenteller Untersuchungen. / The MHC I antigen presentation pathway is part of the immune system and enables cells to show their proteome state at the cell surface. This works aims at improving the understanding of the MHC I pathway and the prediction of antigens from the source proteins where appropriate. The means are the development of models for protein synthesis, degradation and the individual steps of the pathway as well as the analysis of simulation results. Statistical models for the transport of peptides into the ER by TAP, the cleavage of peptide bonds by the proteasome, and the cytosolic and endoplasmic trimming of peptides have been developed. Furthermore, kinetic models for synthesis and degradation of viral protein constructs, for proteasomal generation of protein fragments, and for the simulation of the entire process from viral infection of a cell to the resulting antigen presentation were created. It has been shown that a DRiP rate of 10% is sufficient to have antigen presentation independent of the source protein’s live time and that the antigens derived from the DRiP pool dominate the antigen presentation for long lived proteins. This mechanism enables the presentation of the current protein synthesis state of the cell. Each developed model of a part of the MHC I pathway is trained on in vitro data and together they provide at least the same prediction quality as pathway models that are based on in vivo data. This shows that all processes that contribute significantly to antigen presentation are covered in the developed models. The models for the individual parts can be combined according to the demand and question. A prediction tool has been provided at http://mhc-pathway.net. The contribution of each part of the pathway can be assessed by model supported analysis of the individual steps. It is possible to determine the traits of a potential antigen. The kinetic model of the pathway from infection to antigen presentation enables the generation of time curves for each possible peptide and the analysis of the processes that lead to the development of antigens. The quantitative predictions allow for experimental validation. The proteasomal fragment generation is the least good understood part of the MHC I pathway and requires further experimental study.

Os problemas da poluição atmosférica atingem todos os grandes centros urbanos, em particular as megacidades com população maior do que 10 milhões de habitantes. Emissões veiculares e industriais destacam-se entre as principais responsáveis pelas altas concentrações de poluentes do ar nesses centros urbanos. Os diferentes componentes da poluição atmosférica, a dose e o tempo de exposição, podem levar a diversos impactos na saúde humana. Esse estudo teve por objetivo avaliar a genotoxicidade da poluição atmosférica (PM2,5 e NO2) e sua correlação com modificações no perfil de metilação das citocinas IL-10 e TNF-alfa, em trabalhadores da cidade de São Paulo/SP ocupacionalmente expostos. Participaram deste estudo 57 indivíduos do gênero masculino, com idades variando entre 28 e 66 anos de idade, trabalhadores em turnos diários de atividades externas na cidade de São Paulo e, portanto, ocupacionalmente expostos à poluição atmosférica. Foram recrutadas 3 categorias de profissionais: 1) controladores de tráfego (n=18); 2) taxistas (n=21) e profissionais do Instituto Florestal (n=18). Esses trabalhadores foram divididos em dois grupos em função dos locais de trabalho e exposição: 1) grupo área urbana (AU), composto pelos controladores de tráfego e taxistas e 2) grupo área periurbana (APU), composto pelos profissionais do Instituto Florestal. Amostradores individuais de poluição atmosférica foram utilizados para a coleta dos poluentes PM2,5 e NO2. A análise da genotoxicidade foi realizada pelo teste de micronúcleos nas células epiteliais da mucosa oral e em linfócitos do sangue periférico. O perfil de metilação das citocinas IL-10 e TNFalfa foi realizado por sequenciamento de nova geração. Nossos resultados mostraram uma diferença na concentração do PM2,5 entre os grupos (AU=32,92?g.m-3, APU=25,77ug.m-3; p=0,0311). Não foi encontrada diferença na concentração de NO2 entre os grupos. Foram encontradas diferenças nas frequências de micronúcleos, tanto em mucosa oral (AU=2,78%, APU=1,16%; p < 0,0001) quanto em linfócitos periféricos (AU=1,51%, APU=0,73%; p < 0,0001). Também foi encontrada diferença na metilação média do gene IL-10 entre os grupos (AU=25%, APU=30%; p=0,0120). Não foi encontrada diferença na metilação média do gene TNF-alfa entre os grupos. Concluímos que os trabalhadores da área urbana da cidade estão expostos a maiores concentrações de PM2,5, possuem maiores frequências de micronúcleos tanto em células da mucosa oral quanto em linfócitos periféricos e apresentam um perfil de hipometilação do gene IL-10 em comparação com os trabalhadores da área periurbana da cidade / The problems of air pollution affect all major urban centers, particularly megacities with populations greater than 10 million. Vehicular and industrial emissions stand out among the main responsible for the high concentrations of air pollutants in these urban centers. The different components of air pollution, the dose and time of exposure, can lead to different impacts on human health. This study aimed to evaluate the genotoxicity of air pollution (PM2,5 and NO2) and its correlation with changes in the methylation profile of the cytokines IL-10 and TNF-alpha in workers of São Paulo/SP occupationally exposed. The study included 57 male individuals, with age range between 28 and 66 years old, workers in daily shifts of outdoor activities in the São Paulo city and therefore occupationally exposed to air pollution. Were recruited professional of three categories: 1) traffic controllers (n=18); 2) taxi drivers (n=21) and professionals from the Forestry Institute (n=18). These workers were divided into two groups according to workplaces and exposure: 1) urban area group (UA), composed of traffic controllers and taxi drivers and 2) peri-urban area group (PUA), composed of professionals from the Forestry Institute. Individual samplers of air pollution were used for the collection of PM2,5 and NO2 pollutants. The analysis was performed by genotoxicity micronucleus test in the buccal mucosa epithelial cells and in peripheral blood lymphocytes. The methylation profile of the cytokines IL-10 and TNF-alpha was done by next generation sequencing. Our results showed a difference in PM2,5 concentration between the groups (UA=32,92ug.m-3, PUA=25,77ug.m-3; p=0,0311). No difference was found in NO2 concentrations between groups. Differences were found in the frequency of micronuclei in both buccal mucosa (UA=2,78%, PUA=1,16%; p < 0,0001) and in peripheral lymphocytes (UA=1,51%, PUA=0,73%; p < 0.0001). Difference was also found in average methylation of the IL-10 gene between the groups (UA=25%, PUA=30%; p=0,0120). There was no difference in the average methylation of TNF-alpha gene between the groups. We conclude that the workers of the urban area of the city are exposed to higher concentrations of PM2,5, have higher frequencies of micronuclei in both the buccal mucosa cells and in peripheral lymphocytes and have a hypomethylation profile of IL-10 gene in comparison with workers the peri-urban area of the city

Os problemas da poluição atmosférica atingem todos os grandes centros urbanos, em particular as megacidades com população maior do que 10 milhões de habitantes. Emissões veiculares e industriais destacam-se entre as principais responsáveis pelas altas concentrações de poluentes do ar nesses centros urbanos. Os diferentes componentes da poluição atmosférica, a dose e o tempo de exposição, podem levar a diversos impactos na saúde humana. Esse estudo teve por objetivo avaliar a genotoxicidade da poluição atmosférica (PM2,5 e NO2) e sua correlação com modificações no perfil de metilação das citocinas IL-10 e TNF-alfa, em trabalhadores da cidade de São Paulo/SP ocupacionalmente expostos. Participaram deste estudo 57 indivíduos do gênero masculino, com idades variando entre 28 e 66 anos de idade, trabalhadores em turnos diários de atividades externas na cidade de São Paulo e, portanto, ocupacionalmente expostos à poluição atmosférica. Foram recrutadas 3 categorias de profissionais: 1) controladores de tráfego (n=18); 2) taxistas (n=21) e profissionais do Instituto Florestal (n=18). Esses trabalhadores foram divididos em dois grupos em função dos locais de trabalho e exposição: 1) grupo área urbana (AU), composto pelos controladores de tráfego e taxistas e 2) grupo área periurbana (APU), composto pelos profissionais do Instituto Florestal. Amostradores individuais de poluição atmosférica foram utilizados para a coleta dos poluentes PM2,5 e NO2. A análise da genotoxicidade foi realizada pelo teste de micronúcleos nas células epiteliais da mucosa oral e em linfócitos do sangue periférico. O perfil de metilação das citocinas IL-10 e TNFalfa foi realizado por sequenciamento de nova geração. Nossos resultados mostraram uma diferença na concentração do PM2,5 entre os grupos (AU=32,92?g.m-3, APU=25,77ug.m-3; p=0,0311). Não foi encontrada diferença na concentração de NO2 entre os grupos. Foram encontradas diferenças nas frequências de micronúcleos, tanto em mucosa oral (AU=2,78%, APU=1,16%; p < 0,0001) quanto em linfócitos periféricos (AU=1,51%, APU=0,73%; p < 0,0001). Também foi encontrada diferença na metilação média do gene IL-10 entre os grupos (AU=25%, APU=30%; p=0,0120). Não foi encontrada diferença na metilação média do gene TNF-alfa entre os grupos. Concluímos que os trabalhadores da área urbana da cidade estão expostos a maiores concentrações de PM2,5, possuem maiores frequências de micronúcleos tanto em células da mucosa oral quanto em linfócitos periféricos e apresentam um perfil de hipometilação do gene IL-10 em comparação com os trabalhadores da área periurbana da cidade / The problems of air pollution affect all major urban centers, particularly megacities with populations greater than 10 million. Vehicular and industrial emissions stand out among the main responsible for the high concentrations of air pollutants in these urban centers. The different components of air pollution, the dose and time of exposure, can lead to different impacts on human health. This study aimed to evaluate the genotoxicity of air pollution (PM2,5 and NO2) and its correlation with changes in the methylation profile of the cytokines IL-10 and TNF-alpha in workers of São Paulo/SP occupationally exposed. The study included 57 male individuals, with age range between 28 and 66 years old, workers in daily shifts of outdoor activities in the São Paulo city and therefore occupationally exposed to air pollution. Were recruited professional of three categories: 1) traffic controllers (n=18); 2) taxi drivers (n=21) and professionals from the Forestry Institute (n=18). These workers were divided into two groups according to workplaces and exposure: 1) urban area group (UA), composed of traffic controllers and taxi drivers and 2) peri-urban area group (PUA), composed of professionals from the Forestry Institute. Individual samplers of air pollution were used for the collection of PM2,5 and NO2 pollutants. The analysis was performed by genotoxicity micronucleus test in the buccal mucosa epithelial cells and in peripheral blood lymphocytes. The methylation profile of the cytokines IL-10 and TNF-alpha was done by next generation sequencing. Our results showed a difference in PM2,5 concentration between the groups (UA=32,92ug.m-3, PUA=25,77ug.m-3; p=0,0311). No difference was found in NO2 concentrations between groups. Differences were found in the frequency of micronuclei in both buccal mucosa (UA=2,78%, PUA=1,16%; p < 0,0001) and in peripheral lymphocytes (UA=1,51%, PUA=0,73%; p < 0.0001). Difference was also found in average methylation of the IL-10 gene between the groups (UA=25%, PUA=30%; p=0,0120). There was no difference in the average methylation of TNF-alpha gene between the groups. We conclude that the workers of the urban area of the city are exposed to higher concentrations of PM2,5, have higher frequencies of micronuclei in both the buccal mucosa cells and in peripheral lymphocytes and have a hypomethylation profile of IL-10 gene in comparison with workers the peri-urban area of the city

<p>Abstract</p><p>The signification of the eyesight for children’s development and learning- how do pedagogues support and stimulate children with defective vision in their development and learning in pre-school?</p><p>These issues are based on my purpose of the field survey investigations, where I have interviewed three pedagogues and also performed an observation.</p><p>My main conclusion and results describe that the vision is the high-powered engine in children’s development and learning. It also tells us that those around the children are very important for optimum development and learning, especially when it comes to supporting and stimulating children with defective vision in their necessities. Our other senses are a compensation to make it easier for children with defective visions in their lives. But all our senses are equally important for children with defective vision as they are for seeing children in their development and learning with their whole body in pre-school.</p><p>Keywords:</p><p>Eyesight, children with defective vision, development and learning in pre-school, pedagogues, pedagogical support and stimulation</p> / <p>Sammanfattning</p><p>Vilken betydelse har synsinnet för barns utveckling och lärande? Hur kan pedagoger med hjälp av olika pedagogiska insatser eller hjälpmedel, stödja och stimulera barn som är synskadade i deras utveckling samt i sitt lärande i förskolan?</p><p>Dessa frågeställningar speglar mitt syfte med denna uppsats. Frågeställningarna i sin tur har under processens gång också vidarebearbetats till tre frågeområden, vilka också har varit centrala i undersökningens genomförande av en observation och intervjuer med tre pedagoger.</p><p>Huvudresultatet och min slutsats visar att synsinnet är motorn i ett barns utveckling och lärande. Om ett barn har en synskada är omgivningens förhållningssätt, bemötande och agerande livsviktigt för att stödja samt stimulera barnet optimalt utifrån de behov barnet har.</p><p>För att underlätta tillvaron för synskadade barn är våra övriga sinnen ett exempel på kompensatoriska hjälpinsatser, dessutom är de viktiga för alla barn i deras utveckling och lärande med hela kroppen i förskolan.</p><p>Nyckelord:</p><p>Synsinnet, synskadade barn, utveckling och lärande i förskolan, pedagoger, pedagogiska hjälpinsatser</p>