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Innate Immune System Of GENETIC CHARACTERIZATION OF THE INNATE IMMUNE SYSTEM OF LAGOMORPHS (ILS, CCLS) FABIANA MARISA VIEIRA DAS NEVES TESE DE DOUTORAMENTO APRESENTADA AO INSTITUTO DE CIÊNCIAS BIOMÉDICAS ABEL SALAZAR DA UNIVERSIDADE DO PORTO EM PATOLOGIA E GENÉTICA MOLECULAR 2017 ii FABIANA MARISA VIEIRA DAS NEVES GENETIC CHARACTERIZATION OF THE INNATE IMMUNE SYSTEM OF LAGOMORPHS (ILS, CCLS) Tese de Candidatura ao grau de Doutor em Patologia e Genética Molecular submetida ao Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto. ORIENTADOR: PROFESSOR DOUTOR PEDRO JOSÉ DE CASTRO ESTEVES Professor Auxiliar Convidado Departamento de Biologia Faculdade de Ciências da Universidade do Porto Investigador principal Centro de Investigação em Biodiversidade e Recursos Genéticos CO-ORIENTADOR: PROFESSOR DOUTOR PAULO MANUEL DE CASTRO PINHO E COSTA Professor Auxiliar Convidado Departamento de Patologia e Imunologia Molecular Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto Investigador Proncipal Departamento de Genética Humana Instituto Nacional de Saúde Dr Ricardo Jorge iii iv Ao meu pimpolhito… v vi FINANCIAL SUPPORT: This study was supported by Fundação para a Ciência e Tecnologia (FCT) through a PhD grant (SFRH/BD/81916/2011) financed by Programa Operacional and União Europeia. vii viii LISTA DE PUBLICAÇÕES Ao abrigo do disposto do nº 2, alínea a) do artigo 31º do Decreto-Lei n.º115/2013 de 7 de Agosto fazem parte integrante desta tese de doutoramento os seguintes trabalhos já publicados ou submetidos para publicação: Artigo I Neves F, Abrantes J, Steinke JW, Esteves PJ. (2014) Maximum-likelihood approaches reveal signatures of positive selection in IL genes in mammals. Innate Immunity, 20(2): 184–191. doi: 10.1177/1753425913486687 Artigo II Neves F, Abrantes J, Pinheiro A, Almeida T, Costa PP, Esteves PJ. (2014) Convergent evolution of IL-6 in two leporids (Oryctolagus and Pentalagus) originated an extended protein. Immunogenetics, 66(9):589–595. doi: 10.1007/s00251-014-0787-0 Artigo III Neves F, Abrantes J, Lissovsky AA, Esteves PJ. (2015) Pseudogenization of CCL14 in the Ochotonidae (pika) family. Innate Immunity 21(6):647-654. doi: 10.1177/1753425915577455 Artigo IV Neves F, Abrantes J, Almeida T, de Matos AL, Costa PP, Esteves PJ. (2015) Genetic characterization of interleukins (IL-1α, IL-1β, IL-2, IL-4, IL-8, IL-10, IL-12A, IL-12B, IL-15 and IL-18) with relevant biological roles in lagomorphs. Innate Immunity 21(8):787-801. doi: 10.1177/1753425915606209 Artigo V Neves F, Abrantes J, Almeida T, Costa PP, Esteves PJ. (2015) Evolutionary Insights into IL17A in Lagomorphs. Mediators of Inflammation, vol. 2015, Article ID 367670, 7 pages, 2015. doi: 10.1155/2015/367670 ix Artigo VI Neves F, Abrantes J, Esteves PJ. (2016) Evolution of CCL11: genetic characterization in lagomorphs and evidence of positive and purifying selection in mammals. Innate immunity 22(5):336-343. doi: 10.1177/1753425916647471 Artigo VII Neves F, Abrantes J, Lopes AM, Magalhães MJ, Esteves PJ. Evolution of CCL16 in Glires (Rodentia and Lagomorphs) shows an unusual random pseudogenization pattern. (In preparation) x AGRADECIMENTOS Não podia finalizar este trabalho sem agradecer às pessoas que para ele contribuíram. Esta tese retrata não só o meu trabalho, mas também o contributo individual daqueles que estiveram ao meu lado, pessoal e profissionalmente. A todos os que me ajudaram a chegar ao final desta etapa, o meu mais sincero obrigado. Ao meu orientador, Professor José Pedro Esteves pela oportunidade que me deu, por ter sido crucial no desenho e construção deste projecto. Agradeço o apoio, a inspiração, a paciência. e o fato de acreditar em mim e nas minhas capacidades para levar a cabo este projeto. Obrigada por todas as ideias pertinentes que foi dando ao longo deste trabalho, pelo seu rigor e espírito crítico constante, por ser um poço de saber inesgotável e por me abrir o caminho para o crescimento pessoal e profissional. Ao meu co-orientador, Professor Paulo Pinho e Costa por me ter aceite como estudante e ajudar a percorrer este caminho. À minha chefinha, Doutora Joana Abrantes, agradeço todo o apoio ao longo destes últimos anos. Obrigada pelo apoio, disponibilidade, pelo trabalho, dedicação e por todos os bons momentos científicos e pessoais vividos. À Fundação para a Ciência e a Tecnologia (FCT), agradeço a concessão de uma Bolsa de Doutoramento (SFRH/BD/ 81916/2011). Ao Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO) e ao Centro de Testagem Molecular (CTM), agradeço a ajuda técnica proporcionada e pelas condições laboratoriais proporcionadas. Ao Bruno Maia, à Diana, à Filipina, ao Javi, à Jolyta, à Patrícia, à Sara João, à Sandrolina à Sofia Mourão, à Sofia Silva, à Susana obrigada por todos os bons momentos, tanto de descontracção, e boa disposição como em todo o apoio técnico e laboratorial que precisei. À Sara Ferreira à Sandra Rodrigues e à Márcia, agradeço a prontidão com que sempre me ajudaram na resolução de diversas situações. Agradeço de um modo muito especial ao pessoal do CIBIO, e que cada um à sua maneira me fez sentir parte de um grupo e ajudou com que estes 4 anos fossem muito descontraídos e cheios de alegria, calor humano e bons momentos. Ao pessoal do Aquário: ao Gui, ao João Maia, à Licas, à Rita, à Té, ao Ubuntu e à Vânia pelos momentos descontraídos e excelentes miminhos culinários. Às xi minhas companheiras de viagens e de pequeno-almoço, Soraia e Guida, um muitíssimo obrigada. Obrigada Guidinha pela valiosa ajuda nas figuras. Aos meus “imídios” (Joana, Guida, Ana M, AnaP, PP; Tereza, Maria e Diogo) pela imprescindível ajuda e acompanhamento mas também companheirismo e a boa disposição. À Teresinha “do bar” que tão bem me alimentou tanto física como psicologicamente um grande obrigada. A todos os meus amigos que sempre foram estando presente ao longo destes 4 anos e que, de diferentes maneiras demonstraram a sua amizade, preocupação e apoio (Brunito, Sapinhos, Helena, Marlene, Stéphanie, Anabela, Tixa). E, por fim, às pessoa mais importantes da minha vida: À minha Mãe. A minha força. Aquela que acredita em mim incondicionalmente e a quem devo a pessoa em que me tornei. Sem ti nada na minha vida teria sido possível. O teu amor, o teu sacrifício, a tua dedicação e a tua motivação são e serão sempre o meu pilar. És sem dúvida o meu Modelo a seguir e espero conseguir continuar a deixar-te orgulhosa das minhas decisões. À minha irmã, que me mostrou que nada é impossível, que vale a pena lutar pelos sonhos e seguir aquilo que acreditamos. Por toda o caminho que desbravou para mim desde sempre e por toda a amizade, amor e apoio. Ao Filipe pela amizade e amor, pelo carinho e companheirismo, por não me deixares ir a baixo nos maus momentos e me fazeres crer que tudo iria sempre correr bem. Pela paciência para me aturares (e bem sei que não é nada fácil) e, principalmente, por tornares esta vida muito melhor. Ao meu pimpolhito que todos os dias me ensina a ser e a tornar-me melhor pessoa. Sem dúvida o meu maior desafio e a minha maior e melhor prenda de sempre. xii Index of contents Lista de Publicações.............................................................................................................. ix Agradecimentos .................................................................................................................... xi Index of contents ..................................................................................................................... xiii Index of figures ....................................................................................................................... xvi Index of tables ........................................................................................................................ xviii Abbreviations ...................................................................................................................... xix Resumo ............................................................................................................................. xxiii Summary........................................................................................................................... xxix Chapter 1 .....................................................................................................................................33 General Introduction .................................................................................................................33 1. The Lagomorpha order ................................................................................................. 34 1.1. Phylogeny .............................................................................................................34 1.1.1. The Ochotonidae family ..................................................................................... 34 1.1.2. The Leporidae family .........................................................................................35 2. Immune system ............................................................................................................37 2.1. Innate Immunity ....................................................................................................37 2.1.1. Cytokines ..........................................................................................................38 The European rabbit interleukins ............................................................................... 44 2.1.2. Chemokines ......................................................................................................45
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