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Some Pages of This Thesis May Have Been Removed for Copyright Restrictions Some pages of this thesis may have been removed for copyright restrictions. If you have discovered material in Aston Research Explorer which is unlawful e.g. breaches copyright, (either yours or that of a third party) or any other law, including but not limited to those relating to patent, trademark, confidentiality, data protection, obscenity, defamation, libel, then please read our Takedown policy and contact the service immediately ([email protected]) Mathematical modelling of hypoxia and temperature signalling pathways in lifespan. Suhayl Mulla Doctor of Philosophy Aston University March 2019 © Suhayl Mulla 2019 Suhayl Mulla asserts his moral right to be identified as the author of this thesis This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with its author and that no quotation from the thesis and no information derived from it may be published without appropriate permission or acknowledgement Aston University Mathematical modelling of hypoxia and temperature signalling pathways in lifespan. Suhayl Mulla Doctor of Philosophy 2019 Thesis Summary A crucial step towards our understanding of ageing is the identification and characterisation of lifespan modifiers. Currently, investigations into lifespan modifiers use the non-parametric Kaplan-Meier estimator and the log-rank statistical test. Few studies employ parametric modelling to investigate lifespan modifiers and those that do use models which demonstrate monophasic lifespan. Recent studies have identified two phases of lifespan in C. elegans which cannot currently be modelled by monophasic parametric models. The aim of this research was to develop a biphasic parametric model (Bilogistic model) capable of modelling biphasic lifespan in C. elegans. The Bilogistic model has 5 parameters: the f parameter defines the proportion of lifespan in the early phase and late phase, and two death rates (k1 & k2) and two time phases (t1 & t2) for the early and late phases. The Bilogistic model was applied to lifespan data from flies, bees and mice to identify and quantify parameters. Two predictive models (chronological and biological) which used the Bilogistic model were developed and applied to temperature interventions in both wild type and trpa-1(ok999) mutants. Critical time points of interventions were identified, and indicated times at which the effects of intervention were lost. Also observed was that early lifespan conditions are important in determining the overall lifespan. The relationship between the HIF-1 (hypoxia) and TRPA-1 (temperature) signalling pathways were investigated in C. elegans mutants at different temperatures and oxygen concentrations. A relationship whereby TRPA-1 signals to HIF-1 was identified in mammalian cells but was not found to be applicable to C. elegans. In conclusion, a novel Bilogistic model has been developed and used to investigate the role of the TRPA-1 and HIF- 1 pathways in C. elegans lifespan. However further work is required to fully understand the interaction between these pathways and how they act to regulate lifespan. Key words: C. elegans, Lifespan, Parametric modelling, Temperature, Hypoxia 2 Acknowledgments Firstly I would like thank my supervisors at Aston University, Dr Alex Cheong, Dr Michael Stich and Dr Zita Balklava for providing me with the opportunity to do this PhD. I would like to thank Alex for his continuous guidance, encouragement and support throughout my PhD. I would also like to express my gratitude to Michael for all his advice particularly for his expertise in mathematics. I am also grateful to Zita for the valuable assistance in the lab and for helping me with all of my worm work. Thank you to my placement students Adele Ludlam and Tajlima Miah for all of their assistance in the lab during their placement year. I would like to thank the past and present friends and colleagues at Aston for the support, help and laughs throughout my PhD. Finally a huge thank you to my friends and family, in particular thank you to my parents for all of their support over the years and for the encouragement to keep going until the end. Thank you everyone. 3 Table of Contents List of Abbreviations ...............................................................................................................9 List of Figures.......................................................................................................................14 List of Tables ........................................................................................................................18 List of Equations ...................................................................................................................19 Chapter 1.0: General introduction .....................................................................................20 1.1 Ageing and its implications .....................................................................................21 1.2 C. elegans as a model organism ............................................................................22 1.2.1 C. elegans physiology ..........................................................................................22 1.2.2 C. elegans life cycle .............................................................................................23 1.2.3 C. elegans lifespan ...............................................................................................24 1.3 Factors of ageing and their role in C. elegans .............................................................25 1.3.1 Calorie restriction .................................................................................................26 1.3.2 DNA damage theory of ageing .............................................................................27 1.3.3 The free radical theory of ageing ..........................................................................28 1.3.4 Energy Maintenance Theory of Ageing .................................................................29 1.3.5 Genetic control of ageing ......................................................................................29 1.3.6 Hormesis ..............................................................................................................30 1.3.7 Other nutrient sensors ..........................................................................................30 1.3.8 Telomere length and loss .....................................................................................31 1.4 Temperature and Lifespan ..........................................................................................31 1.4.1 Rate of living theory ..............................................................................................31 1.4.2 Genetic thermoregulation, AFD neuron and Heatshock proteins ..........................32 1.4.3 TRPA-1 and thermoregulation of lifespan .............................................................33 1.4.4 DAF-16 and longevity ...........................................................................................36 1.5 Oxygen and ageing .....................................................................................................38 1.5.1 Oxygen and organisms.........................................................................................38 1.5.2 Hypoxia in C. elegans...........................................................................................38 1.5.3 Neuronal response to oxygen ...............................................................................39 1.5.4 HIF-1 signalling in hypoxia ...................................................................................39 1.5.5 HIF in C. elegans..................................................................................................41 1.5.6 Lifespan and HIF-1 ...............................................................................................42 1.6 Measures of ageing ....................................................................................................43 1.6.1 Lifespan and chronological age as a measure of ageing ......................................43 1.6.2 Biological age as an alternative measure of ageing ..............................................43 1.6.3 Healthspan ...........................................................................................................44 1.6.4 Frailty Index ..........................................................................................................45 1.6.5 Applying frailty index to mortality ..........................................................................45 4 1.7 Measurement of lifespan .............................................................................................46 1.7.1 Traditional lifespan assay methods.......................................................................46 1.7.2 Digital lifespan assays ..........................................................................................46 1.8 Lifespan analysis ........................................................................................................48 1.8.1 Kaplan-Meier estimator and other non-parametric models ...................................48 1.8.2 Parametric modelling ............................................................................................49 1.9 Two phases of C. elegans lifespan .............................................................................50 1.10 Thesis justification, hypothesis and aims ..................................................................51
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