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Phenotypic and Molecular Characterization of Clinical Isolates of Bipolaris, Curvularia, Exserohilum and Pithomyces

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Phenotypic and Molecular Characterization of Clinical Isolates of Bipolaris, Curvularia, Exserohilum and Pithomyces PHENOTYPIC AND MOLECULAR CHARACTERIZATION OF CLINICAL ISOLATES OF BIPOLARIS, CURVULARIA, EXSEROHILUM AND PITHOMYCES Keith Cassia Da Cunha Dipòsit Legal: T 1479-2014 ADVERTIMENT. L'accés als continguts d'aquesta tesi doctoral i la seva utilització ha de respectar els drets de la persona autora. Pot ser utilitzada per a consulta o estudi personal, així com en activitats o materials d'investigació i docència en els termes establerts a l'art. 32 del Text Refós de la Llei de Propietat Intel·lectual (RDL 1/1996). Per altres utilitzacions es requereix l'autorització prèvia i expressa de la persona autora. En qualsevol cas, en la utilització dels seus continguts caldrà indicar de forma clara el nom i cognoms de la persona autora i el títol de la tesi doctoral. 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No se autoriza su reproducción u otras formas de explotación efectuadas con fines lucrativos ni su comunicación pública desde un sitio ajeno al servicio TDR. Tampoco se autoriza la presentación de su contenido en una ventana o marco ajeno a TDR (framing). Esta reserva de derechos afecta tanto al contenido de la tesis como a sus resúmenes e índices. WARNING. Access to the contents of this doctoral thesis and its use must respect the rights of the author. It can be used for reference or private study, as well as research and learning activities or materials in the terms established by the 32nd article of the Spanish Consolidated Copyright Act (RDL 1/1996). Express and previous authorization of the author is required for any other uses. In any case, when using its content, full name of the author and title of the thesis must be clearly indicated. Reproduction or other forms of for profit use or public communication from outside TDX service is not allowed. Presentation of its content in a window or frame external to TDX (framing) is not authorized either. These rights affect both the content of the thesis and its abstracts and indexes. UNIVERSITAT ROVIRA I VIRGILI PHENOTYPIC AND MOLECULAR CHARACTERIZATION OF CLINICAL ISOLATES OF BIPOLARIS, CURVULARIA, EXSEROHILUM AND PITHOMYCES Keith Cassia Da Cunha DL:T 1479-2014 UNIVERSITAT ROVIRA I VIRGILI Phenotypic and Molecular Characterization of Clinical Isolates of Bipolaris, Curvularia, Exserohilum and Pithomyces Keith Cássia da Cunha Doctoral Thesis Directed by Drs. Josepa Gené Díaz, José Francisco Cano Lira and Josep Guarro Artigas Facultat de Medicina i Ciències de la Salut Departament de Ciències Mèdiques Bàsiques Reus 2014 UNIVERSITAT ROVIRA I VIRGILI PHENOTYPIC AND MOLECULAR CHARACTERIZATION OF CLINICAL ISOLATES OF BIPOLARIS, CURVULARIA, EXSEROHILUM AND PITHOMYCES Keith Cassia Da Cunha DL:T 1479-2014 UNIVERSITAT ROVIRA I VIRGILI PHENOTYPIC AND MOLECULAR CHARACTERIZATION OF CLINICAL ISOLATES OF BIPOLARIS, CURVULARIA, EXSEROHILUM AND PITHOMYCES Keith Cassia Da Cunha DL:T 1479-2014 Departament de Ciències Mèdiques Bàsiques Carrer Sant Llorenç 21 43201. Reus Tel: 977759341 Drs. Josepa Gené Díaz, José Francisco Cano Lira and Josep Guarro Artigas, professors of the Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili CERTIFY THAT: The present work entitled “Phenotypic and Molecular Characterization of Clinical Isolates of Bipolaris, Curvularia, Exserohilum and Pithomyces” presented by Keith Cássia da Cunha to obtain the degree of doctor by Universitat Rovira i Virgili, has been carried out under their supervision at the Unitat de Micologia i Microbiologia Ambiental, Departament de Ciències Mèdiques Bàsiques, and that it fulfills the requirements to obtain the International Doctorate Mention. Reus, 14 March 2014 Josepa Gené Dìaz José F. Cano Lira Josep Guarro Artigas UNIVERSITAT ROVIRA I VIRGILI PHENOTYPIC AND MOLECULAR CHARACTERIZATION OF CLINICAL ISOLATES OF BIPOLARIS, CURVULARIA, EXSEROHILUM AND PITHOMYCES Keith Cassia Da Cunha DL:T 1479-2014 UNIVERSITAT ROVIRA I VIRGILI PHENOTYPIC AND MOLECULAR CHARACTERIZATION OF CLINICAL ISOLATES OF BIPOLARIS, CURVULARIA, EXSEROHILUM AND PITHOMYCES Keith Cassia Da Cunha DL:T 1479-2014 ACKNOWLEDGMENT A greater challenge than writing this thesis was using only two pages to thank the people who were part of this process, particularly those at the Universitat Rovira i Virgili in Reus, Spain. First, I want to thank all my family, who encouraged me to accept this challenge, and who, even at a distance, gave me the support and affection that I needed. I would like to sincerely thank Dr. Luis Zaror for having opened the door to my coming to Spain, where as he hoped, I learned many things about fungi and especially about life. Thank you so much to my "scientific mother" Dr. Margarete T. G. de Almeida, for having gotten me started in mycology, for having invested in me, for supporting me before I made the decision, and for having been the person who was always there cheering for me for these last four years. Thank you for being my sponsor for the CAPES scholarship. I would like to show my gratitude to Dr. Josep Guarro for having me in his lab, where I had the opportunity to work with very qualified personnel, and to improve my knowledge. Thank you for making me do things the hard way, for scolding me by saying “hay que estudiar ingles”, and many other pieces of advice. I would like to thank my adviser, Dr. Josepa Gené for helping to direct this thesis, for her patience, for her corrections, and for her example of professionalism. Thanks to Dr. José Cano for his guidance in molecular biology, for his friendship, and for being the person that I knew would always be there when I needed someone. Thanks to all the other professors of the Microbiology Unit of URV: J. Pastor, A.Stchigel, D. Garcia, J. Capilla, E. Mayayo, M. J. Figueras, R. Beaz, and I. Pujol, for their teachings and advice. Thanks to Dr. D. Sutton for giving all of his clinical samples, thus making the development of this thesis possible. Thank you so much to Dr. C. Decock for accepting me in his laboratory for 5 months. He shared his passion for mycology with me, and it was inspiring and encouraging. The experience in his lab was wonderful and incomparable. I also want to UNIVERSITAT ROVIRA I VIRGILI PHENOTYPIC AND MOLECULAR CHARACTERIZATION OF CLINICAL ISOLATES OF BIPOLARIS, CURVULARIA, EXSEROHILUM AND PITHOMYCES Keith Cassia Da Cunha DL:T 1479-2014 express my gratitude to the other people who helped me during my stay in Belgium: Monica, Irene, Stefania, Anita, Yurelkys, Cinthya, Paul, Diogo, Ugo, Diana, Vivian, and the staff at MUCL. Thank you to Michele Corbisier for welcoming me into her home and sharing many good times with me, and for helping to improve my French. Thank you also to my French teacher Bernard Delwiche for the pleasant classes. I would like to show my gratitude to Danielle Deremo for the numerous English classes, for being so understanding, for helping me always, even outside the classroom with endless corrections. And I also want to thank her for listening to all my dramas, for being much more than my English teacher − for being a friend. Thanks to the lab technicians Núria Pilas, Carme Sanmartí, Cati Nuñez, and Mónica Azor for your help during these years. Thanks to Montse and Inma, for your help and good will. Thank you to all of my lab partners with whom I have worked over these four years in particular to Hugo for teaching me many things when I arrived, and for the collaboration on the work on Curvularia. I also want to thank Margara, Adela, Katy, Marta and Yasmina for making the work environment more pleasant. And to my Brazilian friends Natalia Seron, Juliana Cintra and Vanessa Beneton who supported me for these four years even at a distance, thank you. Thanks to all my colleagues who I have shared many moments with in Spain: Nuria, Xavi, Daisy, Margara, Adela, Jordi, Merche, Laura, Monica, Tere, Gemma, Coia, Ainhoa, Vero, and Nadege: you have definitely made this process easier. Thanks to the URV and CAPES (Brazil) for the scholarship. UNIVERSITAT ROVIRA I VIRGILI PHENOTYPIC AND MOLECULAR CHARACTERIZATION OF CLINICAL ISOLATES OF BIPOLARIS, CURVULARIA, EXSEROHILUM AND PITHOMYCES Keith Cassia Da Cunha DL:T 1479-2014 INDEX LIST OF FREQUENTLY USED ABBREVIATIONS ................................................. i-iv 1. INTRODUCTION ........................................................................................................... 1 1.1. Overview of filamentous fungi ................................................................................ 3 1.2. Molecular biology applied to the taxonomy and the identification of filamentous fungi ..................................................................................................
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