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Molecular Characterization of Biological Rhythms in the Beach Amphipod Talitrus Saltator (Montagu)

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Molecular Characterization of Biological Rhythms in the Beach Amphipod Talitrus Saltator (Montagu) Molecular Characterization of Biological Rhythms in the beach amphipod Talitrus saltator (Montagu) Laura Sophie Hoelters 2018 As thesis submitted at the Institute of Biological, Environmental and Rural Sciences (Aberystwyth University), for the degree of Doctor of Philosophy. Declaration Word count of thesis: 39.837 This work has not previously been accepted in substance for any degree and is not being concurrently submitted in candidature for any degree. Signed………………………………………………...(candidate) Date: 07.10.2018 STATEMENT 1 This thesis is the result of my own investigations, except where otherwise stated. Where correction services have been used, the extent and nature of the correction is clearly marked in a footnote(s). Other sources are acknowledged by footnotes giving explicit references. A bibliography is appended. Signed………………………………………………...(candidate) Date: 07.10.2018 STATEMENT 2 I hereby give consent for my thesis, if accepted, to be available for photocopying and for inter-library loan, and for the title and summary to be made available to outside organisations. Signed………………………………………………... (candidate) Date: 07.10.2018 ii Acknowledgements My first and foremost thanks goes to Dr David Wilcockson for supervision, project development and experimental ideas. The supervision was characterized by constant fair support, freedom of work and ideas, teaching in rational thinking and science practice as well as a deeply rooted knowledge in the field. I highly appreciate the guidance on treading the path of a researcher. I also thank Prof. Dr Karl Hoffman for secondary supervision and inspiring science conversations. During my collaboration with Università degli Studi di Firenze (Florence University, Italy), Prof. Dr Alberto Ugolini provided friendly guidance and support, which I am thankful for. I was impressed with his inventive genius and his lifelong dedication to his research and deep knowledge in his field. Here, special thanks also goes to Alice, Anna-Maria and Linda for help with collecting sandhoppers. Thank you Eli, Alun, Rory, Joseph, Martin, Martin, Andrew, Nathan and Joanna for being such excellent colleagues, teachers and co-workers. Naturally, I am also grateful to my peer IBERS PhD students, the great people in my office(s) who made my everyday work even more fun and easy. I also thank the ISTM (Karlsruhe Institute of Technology) for being my friends and office mates while writing the thesis. Obviously, I also want to thank DCDS and Aberystwyth University for funding my thesis and for giving me the possibility to work in their laboratories. I thank my extended family for substantial interest in my work, continuous encouragement and support. Especially I thank my mother for taking care of my daughter Sophia during the time while I completed writing. My very personal gratitude is also due to my husband Tobias, who was my ‘rock in the waves’. Thank you for never stopping to believe in me. iii To my daughter. iv Summary The supralittoral sandhopper, Talitrus saltator (Montagu, 1808) exhibits prominent circadian behavioural phenotypes such as locomotor activity rhythm and time- compensated celestial navigation. To investigate the molecular underpinnings of these behaviours, a circadian transcriptome was assembled from time-series RNA- seq data with template from brain tissue samples. Rhythmically expressed clock and clock- associated genes were identified and compared to homologous sequences in the literature. Investigating the time-compensation aspect of Talitrus navigation, evidence for an anatomically discrete antennal moon compass clock was discovered while solar orientation was found to be antennae independent. Further, the time- compensation mechanism of solar navigation and rhythmic locomotor activity is likely linked to clock gene expression as molecular and behavioural phenotypes agree. Immunohistochemical staining indicated at least four neurons as potential central pacemaker cells in the cerebral ganglia. The circadian clock output was also researched through analysing ‘crustacean hyperglycaemic hormone’ (CHH) which was- contrary to other crustaceans- not expressed rhythmically in the brain. Immunolocalisation of CHH protein and mRNA confirm distinct staining patterns in agreement with findings in the literature. The present thesis connects molecular data with behavioural phenotypes and provides clear progress in the research of biological rhythms in arthropods. v Table of contents Declaration.............................................................................................................................. ii Acknowledgements ............................................................................................................... iii Summary ................................................................................................................................ v List of Abbreviations ............................................................................................................. 9 List of Figures ...................................................................................................................... 12 List of Tables ........................................................................................................................ 14 CHAPTER 1: GENERAL INTRODUCTION .................................................................... 1 1.1 BIOLOGICAL CLOCKS .................................................................................................. 1 1.2 BIOLOGICAL RHYTHMS IN MARINE ENVIRONMENTS ........................................ 2 1.3 MOLECULAR BASIS OF CIRCADIAN CLOCKS ........................................................ 7 1.4 TALITRUS SALTATOR BIOLOGY ................................................................................... 9 1.5 OBJECTIVES .................................................................................................................. 11 CHAPTER 2: GENERAL METHODS ............................................................................. 13 2.1 ANIMAL HUSBANDRY ............................................................................................... 13 2.2 LOCOMOTOR ACTIVITY MEASUREMENT ............................................................. 13 2.3 RNA EXTRACTION ...................................................................................................... 14 2.4 REVERSE TRANSCRIPTION (RT) .............................................................................. 14 2.5 POLYMERISE CHAIN REACTION (PCR) .................................................................. 15 2.6 AGAROSE GEL ELECTROPHORESIS ........................................................................ 15 2.7 5’ AND 3’ RAPID AMPLIFICATION OF CDNA ENDS (RACE) PCR ...................... 15 2.8 CLONING ....................................................................................................................... 17 2.9 SEQUENCING ................................................................................................................ 17 2.10 SEQUENCE ANALYSIS .............................................................................................. 18 2.11 QUANTITATIVE REAL-TIME PCR (qRT-PCR) ....................................................... 18 2.12 IMMUNOLOCALISATION OF PEPTIDES ................................................................ 20 CHAPTER 3: CIRCADIAN TRANSCRIPTOME AND CLOCK GENE SEQUENCING .......................................................................................................... 22 3.1 ABSTRACT .................................................................................................................... 22 3.2 INTRODUCTION ........................................................................................................... 22 3.2.1 Circadian transcriptome sequencing ......................................................................... 22 3.2.2 The invertebrate circadian clock ............................................................................... 23 3.2.3 Objective ................................................................................................................... 31 3.3 MATERIALS AND METHODS .................................................................................... 31 3.3.1 Locomotor activity measurement ............................................................................. 31 3.3.2 Tissue harvest and RNA extraction .......................................................................... 31 3.3.3 Sequencing ............................................................................................................... 33 3.3.4 Sequence confirmation ............................................................................................. 33 3.3.5 De novo transcriptome assembly .............................................................................. 34 3.3.6 Full length sequence confirmation of core clock genes ............................................ 35 3.3.7 Functional annotation with Blast2GO ...................................................................... 36 3.3.8 Quantification of mRNA transcripts ......................................................................... 36 3.3.9 Identification of rhythmically expressed transcripts ................................................. 37 3.3.10 Sequence analysis software .................................................................................... 37 3.4 RESULTS .......................................................................................................................
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