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Sea Turtles Disease Risk Analysis and Discovery of the First Australian Green Turtle (Chelonia Mydas) Papillomavirus

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Sea Turtles Disease Risk Analysis and Discovery of the First Australian Green Turtle (Chelonia Mydas) Papillomavirus ResearchOnline@JCU This file is part of the following work: Mashkour, Narges (2019) Sea turtles disease risk analysis and discovery of the first Australian green turtle (Chelonia mydas) papillomavirus. PhD Thesis, James Cook University. Access to this file is available from: https://doi.org/10.25903/5ef1605e39520 Copyright © 2019 Narges Mashkour. The author has certified to JCU that they have made a reasonable effort to gain permission and acknowledge the owners of any third party copyright material included in this document. If you believe that this is not the case, please email [email protected] SEA TURTLES DISEASE RISK ANALYSIS AND DISCOVERY OF THE FIRST AUSTRALIAN GREEN TURTLE (Chelonia mydas) PAPILLOMAVIRUS By NARGES MASHKOUR B.Sc. in Cell and Molecular Biology M.Sc. in Biotechnology For the Degree of Doctor of Philosophy College of Public Health, Medical and Veterinary Sciences James Cook University, Australia March 29, 2019 TO WOMEN IN SCIENCE i STATEMENT OF ACCESS DECLARATION I, the undersigned, author of this work, understand that James Cook University will make this thesis available for use within the University Library and, via the Australian Digital Theses network, for use elsewhere. I understand that, as an unpublished work, a thesis has significant protection under the Copyright Act and; I do wish to place a 12-months embargo on my thesis starting at final acceptance, after which there will be no further restriction on access to this work. Signature Date STATEMENT OF SOURCES DECLARATION I declare that this thesis is my own work and has not been submitted in any form for another degree or diploma at any university or other institution of tertiary education. Information derived from the published or unpublished work of others has been acknowledged in the text and a list of references is given. Signature Date STATEMENT OF SOURCES ELECTRONIC COPY ii DECLARATION I, the undersigned, the author of this work, declare that the electronic copy of this thesis provided to the James Cook University Library is an accurate copy of the print thesis submitted, within limits of the technology available. Signature Date DECLARATION OF ETHICS The research presented and reported in this thesis was conducted with the approval of the James Cook University Research Ethics Committee and in accordance with the National Statement on Ethical Conduct in Human Research, 2007; Australian Code for the Care and Use of Animals for Scientific Purposes, 2007; and the Queensland Animal Care and Protection Act, 2001. The proposed research methodology received clearance from James Cook University Experimentation Ethics Review Commettee (A 2219). This research was conducted under permits WITK15765815 and WISP16625115 granted by Department of Environment and Heritage Protection (DEHP) and permit G382911 by Great Barrier Marine Park Authority (GBRMPA). Signature Date iii STATEMENT OF THE CONTRIBUTION OF AUTHORS This thesis was supervised by associate professor Ellen Ariel, Dr. Jennifer Elliman and associate professor Leigh Owens. As such they had significant input on the design, execution and analysis of this project as well as reviewing the individual chapters and resulted manuscripts. Dr. Graham Burgess was the expert consultant for chapter four, five and six of the thesis. He had provided valuable advice for the experiments enrichment and analysis along with reviewing the resulted chapters and manuscripts. Katrina Christy, Lauren Burchell and Kelly Johns provided editorial assistance on some chapters. Karina Jones provided the extracted DNA and the samples for the molecular survey in chapter six of the thesis. Alicia Maclaine assisted with some PCRs in chapter four and Wytamma Wirth with some PCRs in chapter six. The samples and data collection was done with the help of the JCU Turtle Health Reseach Team, Girringun and Gudjuda Aboriginal Rangers, Queensland Parks and Wildlife Service, Ecobarge, and the Turtle Hospital at Reef HQ Aquarium. Necropsies and histopathologies were done with the help of Dr. Jennifer Scott and Yissu Martinez at the veterinary pathology department. Outside the university, the necropsies were done in Queensland Parks and Wildlife Service facilities. BIV control DNA was kindly provided by Professor R. Whittington and A. Tweedie, Sydney University. This work was financially supported by the postgraduate SSA account and HDR enhancement scheme allocated from College of Public Health, Medical and Veterinary Sciences, James Cook University. I received a James Cook University Postgraduate Research Scholarship to cover my daily expenses. iv ACKNOWLEDGEMENT This thesis is a result of four years of research, learning and endeavour. I came out of my comfort zone to find myself amongst an extraordinary group of passionate people, to do fieldwork and live in one of the most beautiful places in the world. In this humble acknowledgement I would like to show my gratitude to the people whom without, this project would not have been possible. First I should thank Associate Professor Ellen Ariel for accepting me into her research group, her home and her heart. I will miss our interesting and long-lasting chats. I am profoundly grateful for the opportunity to research what I was, and still am, so enthusiastic about. You spent your valuable time helping me through the ups and downs of this journey. Through it all, you would always allow me to choose and plan the path, as you have always believed this is “my” PhD. My research would have been impossible without the aid and support of my two other advisors Dr. Jennifer Elliman and Associate Professor Leigh Owens. Thank you for enriching my research proposal and for all of the valuable feedback during the progress meetings. Sorry for the many lunch breaks that I interrupted with questions and requests. My sincere thanks to Dr. Graham Burgess; you helped me think outside the box and encouraged me to always examine and investigate. I could not have carried on with some of my experiments without your expertise and consultation. A very special gratitude goes out to James Cook University for giving me the prestigious James Cook University Postgraduate Research Scholarship (JCUPRS) to live in Australia without financial concerns; and for Higher Degree by Research Enhancement Scheme (HDRES) grants to enrich my core research and to travel, presenting my findings in notable conferences. Dear staff and postgraduate students of JCU Veterinary and Biomedical Sciences, it was great sharing laboratories, the tearoom and undercroft with all of you during the last four years. The Friday BBQs and TGI monthly meetings were the highlights of my JCU life. Sherie, Sandra, Tina and Candi, our kind and supportive admin ladies, I will never forget your help with package deliveries, travel bookings and meeting preparations. Jenni and Yissu, thanks for helping with the necropsies and the histopathological analysis. Katy, Bethany, Grace, Helma, Helen and Christine you have given me invaluable help with all the technical support in the laboratories. You are doing an amazing job to keep this old school of us up and running. Katy, thanks for being a great friend and also for giving me your time to read and edit some of my chapters and providing valuable feedback. v I humbly thank my thesis reviewers, thank you for accepting to review my research in the midst of all your activities. It was fantastic to have the opportunity to be a part of the Turtle Health Research Team. Your ever lasting love for the ocean, turtles and conservation is incredible. I learnt so much from all of you and hope to one day see the ultimate goal of having a pure nature without the adverse impact of humans has been achieved. I should thank all the volunteers and collaborators who helped with sample collections and also provided samples for the project. My noisy but lovely office-mates, Shaun, Edith, Karina, Asmor, Kitikarn, Napadol, Alicia, Suchandan, Sara and Femke, I wish you all the best in your future careers. We lived a happy non-conflict life in oppose to our international mixture from various backgrounds, cultures and research interests. I travelled through your life stories and learned to accept and respect. Coming to a new place, especially a new country where you do not know anybody can be intimidating. From day one, I had the support of two angels for whom I am so grateful. Legana and Noushin, your friendship will never fade and I won’t forget your care taking and hospitality to help me settle down in Townsville. My heartfelt thanks go to my family for all your encouragement. I also should say how grateful I am for unending inspirations from my in-laws. I wish I could enjoy this achievement by your side, however, I know that physical distance is of no concern as we live in each other’s mind and heart. Thank you mom, you always believed in me and have provided constant moral support in my life. I will never forget how you say: “It doesn’t matter. It’ll be alright.” Dad, thanks for allowing me to swim against the current, even though it is sometimes in contrary to traditions. And finally, last but by no means least, my fabulous Ramin, my husband and true friend through all these years of experiencing, learning, enduring, enjoying and loving. I know many years down the road this piece of writing is a remembrance for being tough and determined and we would enjoy the outcomes. May God richly bless all of you… vi ABSTRACT Sea turtle populations are in decline, which has been attributed to threats such as predation, bycatch, unsustainable harvesting, habitat degradation, and pollution. The impact of these threats has resulted in the listing of six out of seven sea turtles in the IUCN red list of endangered animals. Infectious diseases are listed among the top five reasons for global species extinctions, but these have not been thoroughly evaluated in sea turtles.
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