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PDF (Archana Iyer Thesis 28Th Cycle ) International PhD Program in Biomolecular Sciences Centre for Integrative Biology XXVIII Cycle Mechanisms of brain wiring by axonal miRNAs: miR-181 and miR-182 Tutor and Advisor Dr. Marie-Laure Baudet CIBIO - University of Trento Ph.D. Thesis of Archana Iyer CIBIO - University of Trento Academic Year 2015-2016 This thesis is dedicated to my beloved mother Acknowledgements I would like to express my sincere gratitude to my supervisor Dr. Marie-Laure Baudet for her relentless support and guidance that helped me grow as a scientist. Marie- Laure has been an incredible mentor and I am thankful for her insightful comments and encouragement to answer very cool biological questions and teaching me challenging techniques. She has helped immensely in channeling my ideas, supported me when I faltered and provided many opportunities that have enabled me to reach this stage and for which I am eternally grateful. Big hugs and thanks to all my lab members– Stephanie, Michela, Simone, Eloina, Antoneta, Lorenzo and Emma for their love and family like support. Stephanie thanks for the wonderful cakes, positive encouragement during laser capture sessions, for proof-reading my thesis and for all the bioinformatic analysis. Michi thanks for your love that will be ‘engrained’ in my head, your adorable company during cultures, laser capture sessions and our lovely vinbrule evenings. Elo, many thanks to you for your cheerful presence, lots of support in addition to all the fantastic help with the qPCR. Simo, thanks for your crazy ideas, brotherly love (and annoyance) and tons of help for my work. Anto, thanks for your enthusiasm and lovely spirit. I would also like to thank past lab members – Fabio (thanks for your company and teaching/struggling with me on the LCM), Sara (thanks to your smile and hugs that encouraged me a lot), Sindhu (thanks for being there for me and for all the upliftment in times of need), Silvia and Marco thanks for your help and all the fun we had. Many thanks to Emma, Katia and Lorenzo, for being so helpful, kind and wonderful and who made my lab work and the ordering processes extremely easy. I would like to express my sincere thanks to all our collaborators- especially Prof Christine Holt, Dr. Anäis Bellon, Dr. Cei Abreu Goodger and his lab. I am thankful to Dr. Vladimir Benes and the Genecore Facility for the library preparation and sequencing. I would like to thank the then Tutor of mine, Prof Paolo Macchi for his scientific enthusiasm. I also would like to thank my PhD co-ordinator, Prof Anna Cereseto for 3 running a very excellent PhD program. I am thankful to my PhD committee and external referees for their time and valuable feedback. I am very grateful to the Animal house facility guys especially Sergio, Ilaria and Marta for managing the facility in a fantastic manner and providing animals. Ilaria, many thanks for extending your assistance always. I thank the Advanced Imaging Facility incharge- Giorgina and Sara for their time and support with the microscopes. Many thanks to the HTS facility people – Valentina, Michael and Pamela for assisting me with the bioanalyzer runs. Also am thankful to Dr. Gabriela Viero and her post doc Marta for the bioanalyzer runs at the FBK. Immense thanks to Betty for organizing all the PhD events and helping making the bureaucratic processes very easy. Extended thanks to Giorgia Moser and Patrizia Paoli for help with the administrative procedures. I thank all my dear batchmates–Annachiara, Dario, Steve, Natthakan, Toan, Cristiana and Vasundhara for making my PhD a very memorable time and for all the merriment. Also specially thankful to Debasmita (thanks for your love and fantastic company, for late nights in CIBIO, our never-ending blabbering, enjoyable experience with food and more food), Annachiara(thanks for your love, strong support, our endless talks and our CIBIO dinners), Dario(for being such an amazing companion at all times), Ruben and Kavitha (for your loving presence that included crazy and lovely moments that giving me tons of memories and support), Jacopino (for the immense fun and laughter) Steve (for your wonderful company, your car rides and for sharing joyful and troublesome times), Francesca and Tiziana for their wonderful uplifting spirit and love. Without any of you I would not have been able to get past difficult times. My sincere thanks also goes to Prof Simona Casarosa and Dr. Andrea Messina for their initiative to establish the frog facility. I am thankful to Dr. Albrecht Haase for introducing me to the two-photon microscope and the fun imaging session. Tons of thanks to CIBIO management guys- Anna Helander, Paolo Struffi, Marco Adami and 4 Luca Andreetti for their invaluable help and immense support in managing lab life in CIBIO. My thanks to the Povo2 reception office team who aided in many aspects. I would like to thank all the people in CIBIO for assisting me in many ways and for the enjoyable company. And finally I would like to enormously thank my beloved family who are miles away and yet have always made me feel supported by their excellent virtual presence. I thank my dearest parents for their endless love and constant reassurance that made me believe in myself. Thanks to my dear brother who in countless ways has always cheered me up. My sincere thanks go to my parents-in-law for their love and encouragement. And last but not least, am very thankful to my loving husband for his strong support, trust, patience and confidence in me that enabled me to reach this stage. 5 Table of Contents LIST OF FIGURES .....................................................................................................................................10 LIST OF TABLES .......................................................................................................................................13 LIST OF ABBREVIATIONS .....................................................................................................................14 ABSTRACT .................................................................................................................................................17 CHAPTER 1: INTRODUCTION ..........................................................................................................18 1.1 AXON GUIDANCE .............................................................................................................................18 1.1.1 Structure of a Growth Cone ......................................................................................................................... 19 1.2 MECHANISMS OF AXON GUIDANCE ..................................................................................................20 1.1.2 Extra cellular matrix adhesion .............................................................................................................. 21 1.1.3 Cell surface adhesion molecules ................................................................................................................ 22 1.1.4 Canonical guidance cues .............................................................................................................................. 23 1.1.4.1 Netrins ........................................................................................................................................................................... 23 1.1.4.2 Semaphorins ............................................................................................................................................................... 27 1.1.4.3 Slits .................................................................................................................................................................................. 29 1.1.4.4 Ephrins .......................................................................................................................................................................... 31 1.1.4.5 Morphogens and growth factors ...................................................................................................................... 33 1.3 XENOPUS RETINO-TECTAL SYSTEM ..................................................................................................34 1.3.1 Formation of optic vesicle ............................................................................................................................ 34 1.3.2 Birth of retinal cells ........................................................................................................................................ 35 1.3.3 Axonogenesis ..................................................................................................................................................... 36 1.3.4 Extension towards Optic Nerve Head ...................................................................................................... 38 1.3.5 Optic chiasm ...................................................................................................................................................... 39 1.3.6 Optic Tract ......................................................................................................................................................... 40 1.3.7 Target termination and branching .......................................................................................................... 43 1.4 AXONS: SPECIALIZED SUB COMPARTMENTS OF NEURONS ................................................................50 1.4.1 Need for local protein synthesis ...............................................................................................................
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