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Kent Academic Repository Full Text Document (Pdf) Kent Academic Repository Full text document (pdf) Citation for published version Ward, Jacob (2019) From Birds to Drug-Resistant Cancer, a novel In situ Methodology to Explore Divergent Genome Evolution. Doctor of Philosophy (PhD) thesis, University of Kent,. DOI Link to record in KAR https://kar.kent.ac.uk/81916/ Document Version UNSPECIFIED Copyright & reuse Content in the Kent Academic Repository is made available for research purposes. Unless otherwise stated all content is protected by copyright and in the absence of an open licence (eg Creative Commons), permissions for further reuse of content should be sought from the publisher, author or other copyright holder. Versions of research The version in the Kent Academic Repository may differ from the final published version. Users are advised to check http://kar.kent.ac.uk for the status of the paper. Users should always cite the published version of record. Enquiries For any further enquiries regarding the licence status of this document, please contact: [email protected] If you believe this document infringes copyright then please contact the KAR admin team with the take-down information provided at http://kar.kent.ac.uk/contact.html From Birds to Drug-Resistant Cancer cells, a Novel in situ Methodology to Explore Divergent Genome Evolution A thesis submitted to the University of Kent for the degree of DOCTOR OF PHILOSOPHY In the Faculty of Sciences 2019 Jacob Ward School of Biosciences Declaration No part of this thesis has been submitted in support of an application for any degree or qualification of the University of Kent or any other University or institute of learning Jacob Ward I Acknowledgements Firstly it was with great honour to work under supervision of Prof. Darren Griffin these past few years, whose friendship, guidance and generosity has made this entire work possible and his teachings will stay with me throughout my future career. My thanks also extends to Dr Ellis, whose support and infectious enthusiasm has been invaluable during time spent throughout the PhD, alongside Dr Skinner, where both were foolish enough to listen to my preposterous ramblings and hypothesises regarding the interphase plotting presented in this thesis and aid in its creation. I am also grateful for the friendship shown by Dr Mansfield who I admire and aspire to be as good of a teacher as she is one day. My thanks extent to current and past members of the Griffin and Ellis Lab, who have been of great support and teaching throughout my time as a member of the laboratory. Whether it is through friendship, compassion or the acknowledgment of my previously undiscovered in-humane strength to break multiple pieces of equipment; I shall take memories made with them forward and cherish them fondly. I am grateful for the support Michael Ellis (Digital Scientific UK) has provided, from his aid in using his image capturing software to enabling the creation of the new method and for his perspective into possible avenues of improving current technologies. I wish to extend my thanks for the cell lines kindly provided by Prof. Michaelis and Dr Lowndes, on which many sections of this thesis use extensively and I hope my work is of somewhat a benefit to their future research. I also extend a very special thanks to members of the UMC and associated friends, to Dr Munn for exceptional phlebotomy skills, to Mr Jackson for his excellent down to earth chats, to the work of Prof. Hale, Dr Babiker and Mr Tomlinson and lastly a very special thanks to Mrs Shrimpton whose widely admired ability to write a stern letter has been of great help and I am eternally grateful for her dedication to aid in my time spent here. The friends I have made and friends who have stayed with me, for keeping me in line and sane I am thankful for and I wish many more years of friendship towards. Last but not least, my better-half and partner Jessie Norbury for being by my side throughout my journey these last few years supporting me through what life challenges us with. Nothing would be possible without you. II Dedicated to My Parents, Julie and Simon Along with My Grandparents, Doreen and Brian III Table of Contents Declaration ........................................................................................................... I Acknowledgements ............................................................................................. II Table of Contents ............................................................................................... IV List of figures ...................................................................................................... IX List of tables ...................................................................................................... XII List of abbreviations ......................................................................................... XIII Abstract ............................................................................................................. XV 1. Introduction - An overview of cytogenetics ...................................................... 1 1.1 The Chromosome .................................................................................................... 1 1.1.1 A brief history of the chromosome ................................................................. 1 1.1.2 Eukaryote chromosome structure ................................................................... 1 1.1.3 The cell cycle and cell division ......................................................................... 3 1.1.3.1 Interphase .................................................................................................. 3 1.1.3.2 Mitosis ....................................................................................................... 4 1.1.4 Chromosomal abnormities and aberrations ................................................... 6 1.1.4.1 Aneuploidy ................................................................................................. 6 1.1.4.2 Deletions .................................................................................................... 6 1.1.4.3 Duplications ............................................................................................... 7 1.1.4.4 Translocations............................................................................................ 8 1.1.4.5 Inversions................................................................................................. 10 1.1.4.6 Rings ........................................................................................................ 11 1.1.4.7 Isochromosomes ..................................................................................... 11 1.1.5 Cytogenetic methods of past and present .................................................... 13 1.1.5.1 Karyotyping .............................................................................................. 13 1.1.5.2 Whole chromosome banding .................................................................. 15 1.1.5.3 In situ hybridisation ................................................................................. 16 1.1.5.4 Digital/Virtual Karyotyping ......................................................................... 21 1.1.5.5 Fluorescence microscopy ........................................................................ 24 1.2 Comparative Genomics.......................................................................................... 25 1.2.1 Evolutionary genomics .................................................................................. 27 1.2.1.1 Chromosomal mechanisms of evolution and speciation ........................ 28 1.2.2 Animal genomics ........................................................................................... 29 1.2.3 Avian Genomics ............................................................................................. 31 1.2.3.1The Galliformes ........................................................................................ 32 IV 1.2.3.1.1 The Chicken ...................................................................................... 32 1.2.3.1.1.1 Nuclear organisation in chicken ................................................ 32 1.3 The Biology of Cancer ............................................................................................ 34 1.3.1 A brief overview of cancer ............................................................................. 34 1.3.2 Causes of Tumorigenesis ............................................................................... 38 1.3.2.1 Environmental Carcinogens ..................................................................... 38 1.3.2.2 Infectious agents ..................................................................................... 41 1.3.2.3 Genetic contributions .............................................................................. 43 1.3.2.3.1 Oncogenes ........................................................................................ 45 1.3.2.3.2 Tumour suppressor genes ................................................................ 47 1.3.2.3.3 Epigenetics and microRNAs .............................................................. 49 1.3.3 The treatment of cancer ................................................................................ 50 1.3.4 Cancer Genomics ........................................................................................... 54 1.3.4.1 Heterogeneity of cancer .........................................................................
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