Open Research Online The Open University’s repository of research publications and other research outputs Re-defining the Concept of Model Species: An Experimental Approach on a Range of Marine Animals Thesis How to cite: Mutalipassi, Mirko (2019). Re-defining the Concept of Model Species: An Experimental Approach on a Range of Marine Animals. PhD thesis The Open University. For guidance on citations see FAQs. c 2018 The Author https://creativecommons.org/licenses/by-nc-nd/4.0/ Version: Version of Record Link(s) to article on publisher’s website: http://dx.doi.org/doi:10.21954/ou.ro.0000e9c1 Copyright and Moral Rights for the articles on this site are retained by the individual authors and/or other copyright owners. For more information on Open Research Online’s data policy on reuse of materials please consult the policies page. oro.open.ac.uk Re-defining the Concept of Model Species: An Experimental Approach on a Range of Marine Animals Candidate: Mirko Mutalipassi The Open University Milton Keynes (UK) Affiliated Research Centre Stazione Zoologica “Anton Dohrn” Naples (Italy) Director of studies: Dr. Valerio Zupo Internal Supervisor: Dr. Maria Costantini External supervisor: Prof. Amir Sagi Advisor: Prof. Paolo de Girolamo Thesis submitted for the degree of Doctor of Philosophy Discipline: School of Life, Health and Chemical Sciences September 2018 ABSTRACT Scientific research extensively uses model organisms to address biological, ecological and evolutionary issues. Research employs a limited variety of organisms, ranging from bacteria to complex metazoans, to answer scientific questions and investigate natural aspects. We define “Model Organisms” this small fraction of the biological biodiversity. Generally, they are a simplified tractable system used to study larger scientific questions and to answer complex problems. Researchers expect that results obtained through experiments on these MOs will be applicable to other, more complex, organisms, or to complex communities and ecosystems. Model organisms are sometimes a scarcely representative sample of the global physiological, biochemical and genetic biodiversity and the answers that they can provide could not be easily applicable and transferred to other species. This Ph.D. thesis aims at re-defining the concept of “model species” on an objective point of view. I analysed a standard range of common characteristics that can describe and rank selected model organisms on the basis of their unique features, advantages and disadvantages. I have taken into consideration various “practical” features, such as size and feeding, their reproduction and the optimization of the culture techniques; their use in some scientific fields, such as chemical ecology, stress responses and apoptosis, and the availability of molecular tools and sequenced genomes. A set of laboratory analyses was applied to test the power of selected species to answer our questions and an arbitrary score was assigned to each species for each parameter according to our results and to the data available in scientific literature. The information collected was used to objectively rank the considered model organisms, for improving future experimental approaches and indicate a possible strategy to choose adequate models for selected research. i ACKNOWLEDGEMENTS First and foremost, I would like to thank my Director of Studies Dr. Valerio Zupo for providing me all the scientific support to carry on my experiments during this Ph.D. project. I would like to thank him for encouraging my research and for allowing me to grow as scientist. His advice on both research as well as on my career have been invaluable. I really admire his ability to make complex things appear simple and I am honoured to have performed research activities under his guidance. I appreciate all his contributions of time, ideas, and funding to make my Ph.D. experience productive and stimulating. I would like to thank my internal supervisor Dr. Maria Costantini, for her expert guidance and her advices and suggestions about scientific and human issues. I would like to express my sincere thanks to my external supervisor Professor Amir Sagi of Ben- Gurion University of the Negev for his guidance, suggestions, insightful discussions and enthusiasm towards my doctoral research. I would like to express my deep gratitude to Prof. Paolo De Girolamo of University of Naples Federico II for his patient guidance, enthusiastic encouragement and for believing in me and in my skills. I can’t thank you enough for all of your support. I owe my gratitude towards Dr. Giovanna Romano, Dr. Cristina Buia, Dr. Cristina Gambi, Enzo Rando and Maurizio Lorenti, Francesco Patti, Antonio Cannavaciuolo, Anna Rando, Lucia Porzio and all the members of Benthic Ecology Lab, for their intellectual support and for extending their lab facilities that facilitated successful completion of my work. My time at Villa Dohrn was made enjoyable in large part due to the many friends that became a part of my life. These years of long and irregular working hours would not have been possible without the presence of friends, lab-mates and colleagues that helped me out as much as they could. I always felt surrounded by a great affection. Great thanks to Valerio Mazzella, Anna Cecilia Buono, Giulia Valvassori, Antonia Chiarore, Claudia Gargiulo, Alice Mirasole, Sara Fioretti for the shared coffees, lunches and dinners, the laughs, the days spent studying and working and for the evenings spent together. We have shared moments of deep anxiety but also of big excitement. Special thanks to my great friends Marco Munari and Francesca Glaviano. We have shared so much life during these years that you have become fundamental in my growth as a man even before as a researcher. You always managed to make me feel special. A special thanks to my family for their patience and endurance. Without their help I certainly would never have reached this goal. Words cannot express how grateful I am for all of the sacrifices that you’ve made on my behalf. Last but not least, I would thank my beloved Nadia Ruocco for each day she makes me smiling to life, for all her love and encouragement. “You're the best thing about me, the best thing that ever happened a boy, I'm the kind of trouble that you enjoy!” ii TABLE OF CONTENTS ABSTRACT ........................................................................................................................ I ACKNOWLEDGEMENTS ........................................................................................................ II TABLE OF CONTENTS .......................................................................................................... III LIST OF FIGURES ............................................................................................................... VI LIST OF TABLES ................................................................................................................ XII CHAPTER 1: INTRODUCTION ................................................................................................. 1 1.1 MODEL ORGANISMS .......................................................................................... 6 1.2 AQUATIC MODEL ORGANISMS ............................................................................. 11 1.3 HOW TO SELECT A MODEL ORGANISMS: CHALLENGES AND CONTROVERSIES ..................... 18 1.4 AIMS ........................................................................................................... 20 1.4.1 ECOTOXICOLOGY AND STRESS RESPONSES ................................................ 23 1.4.2 APOPTOSIS...................................................................................... 30 1.4.2.1 HIPPOLYTE INERMIS – COCCONEIS SPP. COEVOLUTION ................... 31 1.4.3 CHEMICAL ECOLOGY ........................................................................... 35 1.4.4 SUPPORTING SPECIES: A SOURCE OF COMPOUNDS ...................................... 39 CHAPTER 2: CULTURE OF AQUATIC MODEL ORGANISMS ............................................................. 45 2.1 AUTOMATED CULTURE OF AQUATIC MODEL ORGANISMS ........................................... 45 2.1.1 ABSTRACT ....................................................................................... 45 2.1.2 INTRODUCTION ................................................................................. 47 2.1.3 MATERIALS AND METHODS .................................................................. 50 2.1.3.1 GENERAL LAYOUT ................................................................ 50 2.1.3.2 LARVAL REARING UNITS ........................................................ 51 2.1.3.3 AUTOMATION .................................................................... 52 2.1.3.4 COLLECTION OF OVIGEROUS FEMALES ....................................... 53 2.1.3.5 WATER ANALYSES AND LARVAL DENSITY MEASURES ...................... 54 2.1.3.6 DATA TREATMENT ............................................................... 54 2.1.4 RESULTS ......................................................................................... 57 2.1.4.1 AUTOMATIC LARVAL CULTURE ................................................ 57 2.1.3.2 CONTROL LARVAL CULTURE .................................................... 64 iii 2.1.5 DISCUSSION .................................................................................... 66 CHAPTER 3: ECO-TOXICOLOGICAL TESTS ................................................................................. 70 3.1 SPECIFIC TOXICITY OF HALOMICRONEMA METAZOICUM