The Circadian Clock of the Mexican Blind Cavefish, Astyanax Mexicanus
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THE CIRCADIAN CLOCK OF THE MEXICAN BLIND CAVEFISH, ASTYANAX MEXICANUS Andrew David Beale University College London Thesis submitted For the FulFilment oF the requirements For the degree of Doctor of Philosophy. 2013 I, Andrew David Beale, conFirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. 2 ABSTRACT The prevalence oF circadian clocks in most, iF not all, organisms on the planet implies they are an adaptive trait. However, only a Few studies provide evidence to support this. To address this issue directly, we examined circadian clock Function in the Mexican caveFish, Astyanax mexicanus. This species has spent a signiFicant period oF its evolutionary history in constant darkness, away from the daily cycles of the surface environment. Many caveFish populations have adapted For liFe in the dark by reducing eyes and pigmentation and enhancing sensory processes relevant in darkness, such as mechanosensation. Have caveFish retained the circadian clock architecture in the absence oF the primary entraining cue, light? This thesis presents evidence For: i. The presence oF a light-entrainable molecular circadian clock in Astyanax caveFish. Robust circadian rhythms oF per1 expression are exhibited in cavefish, but with reduced amplitude and altered phase relative to their surFace Fish ancestors. ii. Alterations in the light input pathway, especially the raised expression oF a putative clock repressor, per2b. We propose that this dampens the amplitude oF core clock gene expression rhythms observed in cavefish. iii. Absence oF circadian rhythmicity in wild caveFish. iv. A developmental delay in the appearance oF light-detection in caveFish embryos v. Upregulation oF two DNA repair genes, CPD phr and ddb2, in caveFish. This eFFect is accentuated in the wild, leading us to propose that dampening of the circadian clock in caveFish may be a by-product oF selection For raised expression oF DNA repair Family genes and light-induced genes. 3 By examining multiple aspects oF the circadian biology oF A. mexicanus surface and caveFish, the data presented in this thesis supports the hypothesis that the clock gives a fitness advantage through the provision of internal temporal order but suggests the clock may be partially reduced in aperiodic environments. 4 TABLE OF CONTENTS List of Figures ......................................................................................................................................................... 12 List of tables ........................................................................................................................................................... 15 Acknowledgements ............................................................................................................................................ 16 1 General introduction .................................................................................................................................. 18 1.1 General introduction to the circadian clock ............................................................................ 20 1.2 Circadian clock organisation .......................................................................................................... 22 1.3 The molecular circadian clock ....................................................................................................... 22 1.4 Zebrafish and the circadian clock ................................................................................................ 25 1.4.1 The molecular clock oF zebraFish ......................................................................................... 27 1.5 Light input to the zebrafish circadian clock ............................................................................ 30 1.5.1 Detection oF light by the zebraFish clock .......................................................................... 30 1.5.2 Transduction oF light ................................................................................................................ 32 1.5.3 Development oF the light input pathway and circadian clock ................................ 35 1.6 Cave animals ......................................................................................................................................... 37 1.6.1 Clocks in cave animals and the adaptive value of clocks .......................................... 39 1.6.2 Astyanax caveFish as a model system ................................................................................. 42 1.7 Thesis aims ............................................................................................................................................ 46 2 Materials and Methods .............................................................................................................................. 47 5 2.1 Biological materials ........................................................................................................................... 48 2.1.1 Animal husbandry ...................................................................................................................... 48 2.1.2 Embryo collection ...................................................................................................................... 48 2.1.3 Astyanax cell lines ...................................................................................................................... 49 2.1.4 TransFection oF cells .................................................................................................................. 49 2.2 Field studies .......................................................................................................................................... 50 2.3 Laboratory experiments .................................................................................................................. 51 2.3.1 Adult Fish ........................................................................................................................................ 51 2.3.2 Embryo experiments ................................................................................................................ 52 2.3.3 Cell lines ......................................................................................................................................... 53 2.4 RNA extraction and cDNA synthesis ........................................................................................... 53 2.5 Cloning Astyanax genes .................................................................................................................... 54 2.6 Quantitative PCR ................................................................................................................................. 57 2.6.1 Assay ................................................................................................................................................ 57 2.6.2 Primer design and veriFication ............................................................................................. 57 2.6.3 Assay setup ................................................................................................................................... 58 2.6.4 Data analysis ................................................................................................................................. 60 2.7 Behavioural studies ........................................................................................................................... 60 2.8 Whole mount in situ hybridisation ............................................................................................. 60 2.9 DNA repair assays ............................................................................................................................... 62 6 2.9.1 Quantitation of repair of UV-induced DNA damage by ELISA ................................ 62 2.10 Overexpression oF CPD phr in zebrafish cells ...................................................................... 63 2.10.1 Tol2 system recombination (Kwan et al., 2007) ........................................................ 63 2.10.2 TransFection oF zebraFish cells ........................................................................................... 64 3 Examination oF the circadian system oF Astyanax mexicanus in the laboratory .............. 65 3.1 Introduction .......................................................................................................................................... 66 3.2 Methods ................................................................................................................................................... 68 3.2.1 Biological materials ................................................................................................................... 68 3.2.2 Cloning of Astyanax mexicanus clock genes .................................................................... 68 3.2.3 Quantitative PCR ......................................................................................................................... 69 3.2.4 Behavioural studies ................................................................................................................... 69 3.3 Results ..................................................................................................................................................... 70 3.3.1 Analysis oF Astyanax surface and caveFish clock