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The Molluscan Shell Secretome: Unlocking Calcium Pathways in a Changing World

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The Molluscan Shell Secretome: Unlocking Calcium Pathways in a Changing World The Molluscan Shell Secretome: Unlocking Calcium Pathways in a Changing World Victoria Anne Sleight Submitted for the degree of Doctor of Philosophy Heriot-Watt University School of Life Sciences September 2017 The copyright in this thesis is owned by the author. Any quotation from the thesis or use of any of the information contained in it must acknowledge this thesis as the source of the quotation or information. Abstract How do molluscs build their shells? Despite hundreds of years of human fascination, the processes underpinning mollusc shell production are still considered a black box. We know molluscs can alter their shell thickness in response to environmental factors, but we do not have a mechanistic understanding of how the shell is produced and regulated. In this thesis I used a combination of methodologies - from traditional histology, to shell damage-repair experiments and ‘omics technologies - to better understand the molecular mechanisms which control shell secretion in two species, the Antarctic clam Laternula elliptica and the temperate blunt-gaper clam Mya truncata. The integration of different methods was particularly useful for assigning putative biomineralisation functions to genes with no previous annotation. Each chapter of this thesis found reoccurring evidence for the involvement of vesicles in biomineralisation and for the duplication and subfunctionalisation of tyrosinase paralogues. Shell damage-repair experiments revealed biomineralisation in L. elliptica was variable, transcriptionally dynamic, significantly affected by age and inherently entwined with immune processes. The high amount of transcriptional variation across 78 individual animals was captured in a single mantle regulatory gene network, which was used to predict the regulation of “classic” biomineralisation genes, and identify novel biomineralisation genes. There were some general shared patterns in the molecular control of biomineralisation between the two species investigated in this thesis, but overall, the comparative work in this thesis, coupled to the growing body of literature on the evolution of molluscan biomineralisation, suggests that biomineralisation mechanisms are surprisingly divergent. Dedication To my loving family, who have always encouraged my curiosity and adventures, and instilled in me the courage and confidence to pursue a career in science. Acknowledgements The work in this thesis would not have been possible without help, support and advice from many colleagues. Firstly, animals were collected by dedicated members of the SCUBA diving teams at Rothera in Antarctica, and the UK National Facility for Scientific Diving in Oban, Scotland. Thank you to everybody involved in the great clam hunt saga that ensued during the last three years. Animal husbandry during holding, acclimation and transportation was also carried out by colleagues at Rothera, Cambridge and the Scottish Association for Marine Science. Thank you to everybody who has been involved in looking after the clams. Thank you to Deborah Power and Daniel Jackson for hosting me in their labs and for training and advice on in situ hybridisations. Thank you to Arul Marie, Sophie Berland Benjamin Marie and Jaison Arivalagan for providing the shell proteomes for both species in this thesis. Thank you to Michael Thorne for his help with various bioinformatic analyses in this thesis. Thank you to Philipp Antczak for hosting me at the University of Liverpool Computational Biology Facility and for training and guidance on differential gene expression analysis and regulatory gene networks. Thank you to Jeremy Skepper and Lyn Carter at the Cambridge Advanced Imaging Centre for sample preparation and processing for electron microscopy. Thank you to Liz Harper for advice on shell microstructure, mantle anatomy and mollusc evolution. Thank you to all the members of the CACHE network for stimulating conversations and being a fantastic network of mollusc shell colleagues. Finally, I am extremely grateful to my supervisors, Melody Clark, Lloyd Peck, Liz Dyrynda and Val Smith for their unwavering support and enthusiasm. Thank you for the scientific guidance and for making me think, and a special thank you to Melody for all the chocolate biscuits and encouragement vi Declaration Statement ACADEMIC REGISTRY Research Thesis Submission Name: Victoria Anne Sleight School/PGI: was School of Life Sciences, now School of Energy, Geoscience, Infrastructure & Society (EGIS) Version: (i.e. First, Final Degree Sought Doctor of Philosophy – Marine Resubmission, Final) (Award and Biology Subject area) Declaration In accordance with the appropriate regulations I hereby submit my thesis and I declare that: 1) the thesis embodies the results of my own work and has been composed by myself 2) where appropriate, I have made acknowledgement of the work of others and have made reference to work carried out in collaboration with other persons 3) the thesis is the correct version of the thesis for submission and is the same version as any electronic versions submitted*. 4) my thesis for the award referred to, deposited in the Heriot-Watt University Library, should be made available for loan or photocopying and be available via the Institutional Repository, subject to such conditions as the Librarian may require 5) I understand that as a student of the University I am required to abide by the Regulations of the University and to conform to its discipline. * Please note that it is the responsibility of the candidate to ensure that the correct version of the thesis is submitted. Signature of Date: Candidate: Submission Submitted By (name in capitals): Signature of Individual Submitting: Date Submitted: For Completion in the Student Service Centre (SSC) Received in the SSC by (name in capitals): Method of Submission (Handed in to SSC; posted through internal/external mail): E-thesis Submitted (mandatory for final theses) Signature: Date: viii Contents Abstract ............................................................................................................................ iii Dedication ......................................................................................................................... v Acknowledgements .......................................................................................................... vi Declaration Statement ..................................................................................................... vii Contents ........................................................................................................................... ix List of Figures ................................................................................................................ xiv List of Tables................................................................................................................ xviii INTRODUCTION – THE MOLECULAR MECHANISMS UNDERPINNING SHELL SECRETION: A METHODOLOGICAL REVIEW .......... 20 1.1 Introduction ...................................................................................................... 21 1.2 Early work on singular protein characterisations ............................................. 24 1.3 Singular Gene Expression Analysis ................................................................. 28 1.4 Empirical Investigation of Function ................................................................. 34 1.5 Global `Omics Approaches .............................................................................. 35 1.6 Conclusions and knowledge gaps ..................................................................... 40 1.7 Thesis overview ................................................................................................ 41 1.8 Thesis Species .................................................................................................. 42 1.8.1 Laternula elliptica ..................................................................................... 42 1.8.2 Mya truncata ............................................................................................. 44 1.8.3 Why compare L. elliptica and M. truncata? ............................................. 46 1.9 Thesis aims and objectives ............................................................................... 47 MATERIALS AND METHODS .............................................................. 49 2.1 Overview .......................................................................................................... 50 ix 2.2 Animal collection and husbandry ..................................................................... 50 2.2.1 L. elliptica ................................................................................................. 50 2.2.2 M. truncata ................................................................................................ 50 2.3 RNA extraction ................................................................................................. 51 2.4 Reverse Transcription ....................................................................................... 51 2.5 Candidate gene expression analyses ................................................................. 52 2.5.1 Candidate gene selection ........................................................................... 52 2.5.2 PCR and sequencing ................................................................................. 55 2.5.3 Semi-quantitative PCR (semi-qPCR) ........................................................ 55 2.5.4
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