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DNA-Based Assays and Biosensors for the Detection of Toxic Microalgae and Viruses in the Marine Environment

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DNA-Based Assays and Biosensors for the Detection of Toxic Microalgae and Viruses in the Marine Environment DNA-based assays and biosensors for the detection of toxic microalgae and viruses in the marine environment ANNA TOLDRÀ FILELLA Doctoral Thesis 2019 Doctoral Thesis DNA-based assays and biosensors for the detection of toxic microalgae and viruses in the marine environment ANNA TOLDRÀ FILELLA Supervised by: Dr. Mònica Campàs Co-supervised by: Dr. Ciara K. O’Sullivan IRTA - Departament d’Enginyeria Química (URV) Tarragona 2019 I II I STATE that the present study, entitled “DNA-based assays and biosensors for the detection of toxic microalgae and viruses in the marine environment”, presented by Anna Toldrà Filella for the award of the degree of Doctor, has been carried out under my supervision at the Department Chemical Engineering of this university, and that it fulfils all the requirements to be eligible for the International Doctorate Award. Tarragona, 5th July 2019 Dr. Mònica Campàs Dr. Ciara K. O’Sullivan III IV Even stars collide, and out of their crashing new worlds are born Charles Chaplin In: As I began to love myself poem V VI AGRAÏMENTS La gent sol pensar que sóc una persona de poques paraules. Els que em coneixeu bé sabeu que no és sempre així, i encara menys quan es tracta d’agrair. Aquesta tesi no l’he feta sola. Hi ha intervingut molta gent, alguns m’heu guiat, altres ajudat i d’altres acompanyat, en un punt o en tot el procés. Anem a pams. En primer lloc, vull agrair a l’IRTA i a la Universitat Rovira i Virgili per haver-me acollit durant aquest període i per, juntament amb el Banco Santander, haver-me concedit la beca predoctoral Martí Franquès. També agrair als projectes nacionals (SEASENSING: BIO2014-56024-C2-2-R; CIGUASENSING: BIO2017-87946-C2-2-R) i europeus (VIVALDI H2O2: 678589) pels quals he treballat. Aquesta tesi no hagués estat possible sense la Mònica, la meva tutora. Hi ha situacions que et fan un gir a la vida. Conèixe’t en va ser una. Aquella tarda de juliol de 2015 vaig saber que series una tutora excel·lent. La intuïció no em va enganyar. Gràcies per endinsar-me al món dels biosensors, un món que m’ha apassionat i he gaudit, dia rere dia. Gràcies per la teva dedicació constant, però també per la teva exigència. Gràcies per ser una molt bona professional, però més enllà d’això, una gran persona. Gràcies per haver cregut en mi des del principi. I a la meva tutora de la URV, la Ciara, per haver estat al meu costat sempre que ho he necessitat, i malgrat la distància. Gràcies, també, per haver confiat en mi. Tan important és el que faig com amb qui ho faig. Mònica, Laia, Sandra i Greta, heu estat un grup immillorable. Un grup humil i sa. Gràcies Laia i Sandra per haver-me rebut amb els braços oberts. Per haver-me ajudat i aconsellat en tot moment, i per ser dos clars exemples a seguir. I a tu, Greta, per aquesta frescor i alegria que desprens, i per treure’m sempre un somriure. I, encara que no formis part del grup de les “Biosensors Girls”, a tu Àngels, per ser com ets, per haver-me acompanyat durant casi tota la tesi i per tots els moments compartits. Durant aquests quasi quatre anys he tingut l’oportunitat de treballar amb diversos grups d’investigació, amb maneres de pensar i fer diferents. Ha estat un repte, però tota una experiència que m’emporto i que m’ha enriquit personal i professionalment. Persones del grup AMiC (Aigües Marines i Continentals), del grup d’aqüicultura, del grup de biosensors de la URV i del grup de qualitat alimentària i mediambiental de l’INL. De totes elles, en primer lloc, m’agradaria agrair al Karl. Gràcies per haver-te implicat tant en la meva tesi i obrir-me les portes al camp de la biologia molecular. Gràcies per aportar una visió biològica a una ment tan matemàtica com la meva. I sobretot no pateixis, que quan marxi de l’IRTA la meva llibreta de laboratori continuarà allí. Al Jorge, per aportar-me un enfoc més global i aplicat de les tècniques de detecció de microalges. Al Carles, per ajudar-me amb l’anàlisi de dades, i al Yanis, per mostrar- VII me els àmbits “no purament tècnics” de la investigació. Al grup d’aqüicultura, a la Dolors, l’Ana Roque, la Noèlia, l’Isasi i l’Edgar, per ser partíceps de tot el treball de l’herpesvirus. A la Marta i la Raphaela, per haver-me acollit a l’INL durant tres mesos. Al grup de la URV (Míriam, Ivan i Olena) i, finalment, a tots als membres del grup AMiC i de l’IRTA de la Ràpita, en especial a la María Rey, Vane Castan, Jose Luís i Marga, per la vostra ajuda en els mostrejos i els cultius de microalgues. Durant aquesta etapa he vist arribar i marxar molta gent. Estudiants que han acabat la tesi i altres que l’han començada com la Wendy, la Sandra Ramos, la Maria Belenguer, la Joana, el Riki, el Faiz i el Javi. Gràcies per haver-me “suportat” en aquests mesos finals i molts ànims, perquè amb esforç i ganes tot s’aconsegueix. El resultat final és molt gratificant. Però no tot ha estat feina, gràcies pels dijous a l’Eixam compartint converses amb la Marta, la Giada, la Núria Vila, la Míriam, el Nil, l’Òscar, l’Anna Sanjuan, l’Ana Genua, la Cindy, el David Mateu, la Vane del Río i molts dels qui ja he anomenat. Com ho trobaré a faltar! Gràcies a la Ràpita i al Delta, per haver-me acollit, per aquests racons únics i per haver- me ensenyat paraules i expressions tan fantàstiques com “m’he n’he ris”, “salvar” “meló de moro” i “hasta demà”. La Ràpita, aquest poble on he treballat, però on també he “xalat”, plorat, crescut, conegut, descobert...i que és i serà la meva segona casa. I per últim, però especialment importants, a la meva família i amics. Als meus pares, la meva germana i avis. Per, simplement, ser-hi sempre. Per sempre creure en mi i en les meves possibilitats, encara que us hagi fet patir molt. A tu Albert, per escoltar-me quan t’explico els experiments, per saber què és un biosensor i quan una ostra està viva o morta. Per aguantar el meu estrès, per acompanyar-me durant aquesta etapa i per estimar-me quan més ho he necessitat. A tots els amics i amigues de Reus i d’arreu (Glòria, Marina, Carlota, Iris, Anna, Soraya, Leire, La colla “pessigolla”... i molts més!), per recolzar-me i sempre anant-me preguntant com portava la tesi. I a l’Eva, per ensenyar-me a creure en mi mateixa i a estimar-me. Res d’això hagués estat possible sense ella. Gràcies de tot cor. VIII AKNOWLEDGMENTS People tend to believe that I am a woman of few words. Those who know me well know that this is not always true, especially when it comes to thank people. Obviously, I did not do this thesis alone. Many people have intervened, some have guided me, others helped and others accompanied, at some point or in the whole process. Let's go step by step. Firstly, I would like to thank IRTA and Univeritat Rovira i Virgili for the opportunity to conduct my research and, together with the Banco Santander, for awarding me with the pre-doctoral scholarship Martí Franquès. Additionally, I want to thank the Spanish (SEASENSING: BIO2014-56024-C2-2-R; CIGUASENSING: BIO2017-87946-C2-2-R) and European (VIVALDI H2O2: 678589) projects that I worked for. This thesis would not have been possible without Mònica, my supervisor. There are situations that change your life. Meeting you was one of them. That afternoon of July 2015 I knew that you would be an excellent supervisor. The time did not prove me wrong. Thanks for allowing me to discover the biosensors field, a world that has fascinated me and I have enjoyed, day by day. Thank you for your constant dedication, but also for your high level of demand. Thank you for being a very good professional, but beyond that, a great person. Thank you for believing in me from the very beginning. Additionally, I would like to thank my supervisor from URV, Ciara, for being always there whenever I needed you, and despite the distance. Thank you, too, for having believed in me. What I do is equally important to with whom I do it. Mònica, Laia, Sandra and Greta, you were an excellent group. A humble and healthy group. Thank you Laia and Sandra for receiving me with open arms. For your valuable help and advice, and for being two clear examples to follow. And to you, Greta, for this freshness you transmit, and for always making me smile. And, even if you are not part of the "Biosensors Girls" group, to you Àngels, for being as you are, for having accompanied me for almost all the thesis and for all shared moments. During these almost four years I have had the opportunity to work with various research groups, with different ways of thinking and doing. It has been a challenge, but also an experience that I take with me and has been extremely enriching both personally and professionally. People from the AMiC group (Marine and Continental Waters), the aquaculture group, the URV biosensors group and the food and environmental quality group of INL. From all of them, first, I would like to thank Karl.
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