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Ricardo Nuno Alves Molecular and Cellular Changes In Ricardo Nuno Alves Molecular and cellular changes in Atlantic halibut (Hippoglossus hippoglossus) skin during metamorphosis Universidade do Algarve Faculdade de Ciências e Tecnologias 2016 Ricardo Nuno Alves Molecular and cellular changes in Atlantic halibut (Hippoglossus hippoglossus) skin during metamorphosis Tese para a obtenção do grau de Doutor em Ciências Biológicas Especialidade em Biologia Molecular Trabalho efetuado sob a orientação de: Professora Doutora Deborah M Power Universidade do Algarve Faculdade de Ciências e Tecnologias 2016 Molecular and cellular changes in Atlantic halibut (Hippoglossus hippoglossus) skin during metamorphosis Declaração de autoria do trabalho Declaro ser a autora deste trabalho, que é original e inédito. Autores e trabalhos consultados estão devidamente citados no texto e constam da listagem de referências incluída. Copyright Ricardo Nuno Henriques Graça Alves. A Universidade do Algarve tem o direito, perpétuo e sem limites geográficos, de arquivar e publicitar este trabalho através de exemplares impressos reproduzidos em papel ou de forma digital, ou por qualquer outro meio conhecido ou que venha a ser inventado, de o divulgar através de repositórios científicos e de admitir a sua cópia e distribuição com objetivos educacionais ou de investigação, não comerciais, desde que seja dado crédito ao autor e editor. A realização deste trabalho foi possível graças ao financiamento da Fundação para a Ciência e Tecnologia (FCT) através da bolsa de doutoramento SFRH/BD/69209/2010 e ao financiamento do projeto LIFECYCLE (FP7 222719. http://www.lifecycle.gu.se/) através do Centro de Ciências do Mar (CCMAR) Aos meus pais (a minha raiz, caule e folhas) e em especial ao Santiago (my little treasure) e à minha avó Céu (o meu eterno anjo da guarda) Obrigado por toda a inspiração, luz, força e motivação ao longo destes anos, o meu Orixá (Òrișà), que me guia sempre: “Vou dar a volta no mundo eu vou ver o mundo girar mas eu só saio daqui quando o coral negro passar Essa visão do mundo, permanece ainda, não modificou, O Ilê aiyê começa onde termina o ponto de eclosão total...” In Crença e Fé “Oyá TeTê Oyá TeTê Oyá Oyá TeTê Oyá Oyá TeTê” In Oyá por Nós “Tua comida comi, Tua língua aprendi Tua música e dança bailei O teu canto entre tantos Guardei Lendas, folclores Crendices, costumes, comidas Falares, plantas e bichos lugares” In América do Amor "Mori omon kekere towa dje Olorio Mori awon arugbo tô na fé kowi Mori obinrin to dara Kpelou onan to dara Monfe ri inanan, iiyansan, ioshun, Yemandja” In Dara Eparrei oyá – Oxalá, Ogum, Xangô, Oxossi, Oxum, Nanã, Iansã e Iemanjá Agradecimentos/Acknowledgments A minha jornada ao longo dos últimos anos nesta “batalha” chamada de doutoramento culmina hoje com a entrega desta dissertação. Este foi sem dúvida o maior desafio da minha vida até hoje, e tal não seria possível se não tivesse as pessoas mais incríveis à minha volta. Foram muitos altos e baixos, e agora que estou prestes a conquistar mais uma vitória é altura de agradecer todo o apoio, motivação, carinho e atenção que sempre tiveram comigo. Sim é verdade a lista é longa, mas não posso deixar de expressar toda a minha gratidão... Espero um dia poder retribuir por tudo o que fizeram de mim e por mim… Um muito obrigado a todos... Em primeiro lugar gostaria à professora Deborah Power por me ter acolhido no seu laboratório e no projecto Lifecycle mesmo antes de ter começado a tese de doutoramento, e por ter sempre confiado no meu trabalho e ajudar-me a acreditar que seria possível. Agradeço por todo o incentivo, dedicação, partilha de conhecimentos, mas principalmente por me fazer “pensar” no que é fazer ciência. Sem a sua motivação, talento e empenho eu não teria conseguido concluir este trabalho. Obrigado pelas inúmeras horas de reuniões e foi um privilégio poder aprender consigo tudo o que sei hoje sobre o mundo da biologia molecular e das ciências biológicas em geral. Gostaria também de agradecer ao professor Adelino Canário por me receber tão bem no seu laboratório. O seu talento e motivação é algo incrível. Obrigado por ser o verdadeiro pilar do CCMAR, pois sem si o Centro não se tinha tornado no que é hoje. I would like to thank Professor Melody Clark for welcoming me to the British Antarctic Survey and giving the opportunity to do part of my bioinformatics analysis there. I am also grateful to Dr. Michael Thorne for the help during the transcriptome analysis and with all the bioinformatics tools I also would like to express my gratitude to Dr. Richard Reinhard at the Max Planck Institute for Plant Breeding Research for welcoming me in his group and for sharing his knowledge about NGS techniques. I would like to thank Dr. Mbaye Tine for teaching me everything I know about NGS libraries preparation and to Dr. Kurt Stueber for teaching me how deal with the NGS sequencing data. A special thanks to my Max Planck lab colleagues Christoph Bast, Eva Reucker and Anni Stollberg for all the great moments we shared at the Max Planck facilities. Um agradecimento muito especial e o mais sincero possível à minha colega e companheira da saga “transcriptome analysis”, Ana Gomes. Foste sem dúvida uma peça chave na construção da minha tese, desde as infinitas horas de linhas de comando no Linux, até à preparação do capítulo 2. Obrigado por teres tido tanta paciência para mim ao longo destes últimos anos, pelas inúmeras correcções e críticas sempre construtivas. A tua ajuda nesta fase final foi muito importante. Nunca te vou conseguir agradecer. Nesta longa jornada quero agradecer a todos os meus colegas do grupo CME (Comparative Molecular Endocrinology). Espero não me esquecer de ninguém pois a lista é grande. Um agradecimento aos que ficaram e aos que já foram embora: João Cardoso, Patrícia Pinto, Rute Martins, Rute Félix, Patrícia Mateus, Rita Costa, Ângela, Elsinha, Xana (matrafas), Lili, Maria, Marlene, Pedro Palma, Vera, Bela, Flávia, Sandrinha, Xaninha, Nadège, Peter, Mar, Pedro Guerreiro, André, Soraia, xiii Eduarda, Alex, Juan, Sílvia, Zélia, Nádia, Bruno, João Saraiva, Alex e todos os que me possa ter esquecido . A todos, um muito obrigado. Cada um de vocês me ajudou à sua maneira. Agradecer à minha estrelinha, à minha Dondocs, Patrícia Mateus é pouco para expressar a gratidão que sinto por ti, por essa pessoa que tu és. De colegas passámos a ser grandes amigos e acho que tu foste uma das coisas mais importantes que o PhD me deu. Obrigado pelas inúmeras horas de apoio incondicional. Estarei sempre aqui para ti. Rita Costa, a tua simplicidade, educação, inteligência e especialmente respeito por todos os colegas fez-me aprender muito contigo. Nos últimos anos sempre me ajudaste nos melhores e piores momentos em todas as técnicas e mais algumas. Foste o meu primeiro pilar no grupo e só te tenho agradecer por isso. És sem dúvida uma investigadora guerreira. Tenho muito orgulho em ter tido o privilégio de trabalhar contigo. João Cardoso, o “velhote”, Rute Martins, a “santinha” e Patrícia Pinto, a “rainha do carnaval molecular” foram três companheiros ao longo desta jornada, os meus “papás”. Aprendi imenso com vocês e agradeço as inúmeras horas de trabalho que partilhámos juntos. Obrigado por todos os conselhos que sempre me deram. Aprendi mesmo muito com vocês. À Joana (ruculinha) e Carina (nina) pela ajuda preciosa durante a realização dos milhares de cortes histológicos da tiróide dos meus “halibuts” e das centenas de colorações. Espero de certa maneira também ter contribuído para a vossa aprendizagem. Agradecer aos meus camaradas do mítico grupo “Gang do E4”, Odete, Tomé, Sofia, Mahaut, Nadège e ao Professor Pedro Rodrigues e ao Doutor Luís Conceição. Nadège, és hoje uma amiga em que posso afirmar que estiveste disponível durante todo o meu doutoramento, sempre disposta a ajudar. Isto sim é amizade e na realidade qualquer doutorando necessita de alguém assim por perto. O primeiro grupo de investigação onde trabalhei, ajudaram-me a criar forças e defesas para levar este doutoramento a bom porto. Muito obrigado. I would like to thank my new endocrinologists friends, Kenneth Shang-Chien Lee, Florencia, Marylin and Mariano. Thank you for always be very positive and for sent all the inspiring messages and for give me the hope to finish the thesis. Rafael Nóbrega conhecer-te no CECE em Rennes foi um privilégio para mim. Tens sido também um bom apoio para mim sempre com as tuas mensagens carregadas de positividade. Recentemente, voltei a perceber o que é trabalhar em grupo, o verdadeiro sentido de uma equipa. Obrigado ao Doutor António Marques, chefe e amigo por me teres aceitado no teu grupo de investigação no IPMA. Agradeço a paciência “imensa” que tens tido ao longo deste último ano e meio, OBRIGADO. Agradeço claro às man@s que tiveram de me aturar e não foi pouco: Ana Luísa (a das bichas), Vera Liane (mana queimada), Carolina (crossfit), Patrícia (mana mãe) e recentemente a Fabíola (Zuca). Mais do que colegas de trabalho, têm sido amigas incansáveis e nunca vou esquecer isso. Realmente sabe muito bem trabalhar com vocês. Muito mais do que o ambiente da investigação fez com que conseguisse acabar a tese e foram inúmeros os amigos e família que sempre estiveram presentes. Não posso deixar de os citar, pois sinto que este doutoramento também é vosso. Eu tenho a sorte de poder dizer que tenho muitos e sinceros amigos. Sem falar que tenho a melhor família do mundo. Obrigado FARO por teres sido a minha casa durante quase 12 anos. Realmente o Algarve é o melhor sítio para se viver. Aos meus grandes e bons amigos do grande curso de BMP adquiridos ao longo dos últimos treze anos… O curso acabou mas a amizade ficou...o poder saber que vocês estiveram lá para me xiv apoiar sempre, mesmo nos maus momentos...Nós somos especiais e sabemos disso.
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