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Proteomic Analysis of Taenia Spp. Excretion/Secretion Proteins: the Search for Taenia Solium-Specific Diagnostic Antigens

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Proteomic Analysis of Taenia Spp. Excretion/Secretion Proteins: the Search for Taenia Solium-Specific Diagnostic Antigens FACULTY OF VETERINARY MEDICINE approved by EAEVE Proteomic analysis of Taenia spp. excretion/secretion proteins: the search for Taenia solium-specific diagnostic antigens Bjorn Victor Proefschrift voorgedragen tot het behalen van de graad van Doctor in de Diergeneeskundige Wetenschappen, 2014 Promotoren: Prof. Dr. Pierre Dorny Dr. Sarah Gabri¨el Dr. Magnus Palmblad Vakgroep Virologie, Parasitologie en Immunologie Faculteit Diergeneeskunde, Universiteit Gent Salisburylaan 133, B-9820 Merelbeke \I may not have gone where I intended to go, but I think I have ended up where I needed to be." { Douglas Adams, The Long Dark Tea-Time of the Soul (1988). Acknowledgements A PhD is never a one-man show, so there are a number of people who deserve a moment in the spotlights: First and foremost, my promoters, who gave me countless opportunities, helped me find additional funding, allowed me to make mistakes, assisted me with the writing of the manuscripts and the thesis and most of all, gave me the chance to prove myself as a PhD candidate: Pierre, this is my third thesis under your supervision and I truly admire your courage! Your unit is an incredibly fun and stimulating place to work. My sincerest gratitude for your continuous support, advise, kind encouragement and constructive thinking. It is safe to say that I could never have done this without you! Thank you very much!! Sarah, you had the bad luck of sitting right next to me where you were never safe from the endless stream of questions (not even with the small forest that suddenly appeared between our desks :-). I thank you very much for the many answers, constructive comments, time and advice you gave me throughout this endeavour. Furthermore, I feel I should also give you credit for your efforts to teach me some diplomacy... Magnus, you introduced me to proteomics, mass spectrometry, scripting and whisky. I learned a great deal from you about proteomics and science in general. I really want to express my gratitude for all your help, good advice, hospitality, patience, effort, and maybe most of all, for putting up with my stubborn way of doing things... The staff at the ITM: Guy, Leen, Anke, Ellen, Gill, Caroline, Ko, Famke, Julie, Nadia and Nick: thank you for the encouragement and the fantastic times we had over a few beers... Nicolas1, thank you for the many conversations and laughs on the third floor! Katja and Kirezi1, thank you for helping me with the writing of the manuscripts. Nadia, extra thanks for your help with my thesis. Dani¨elle,thank you for sorting out the financial side of my PhD. 1No longer working at the ITM at the time of writing. Page v The staff and students at the LUMC: Andr´e,Yuri, Yassene, Rob, Alex, Linda, Kate, Katia, Simone, Tiziana, Suzanne, Dana, Anton, Hans and Hannah. Thanks you for helping me so many times, explaining everything twice, letting me sleep on your couches, sharing rooms with me during conferences and for the good times in the pub. The staff at the Veterinary Faculty (Ghent University): Peter and Jimmy, thank you for all the help and advice with the 2D-PAGE analysis. Sien, thanks for bringing the IEF strips to Antwerp. Prof. Vercruysse, thank you very much for letting me work in your lab. Dirk, thank you for the help with my thesis. Mieke, thank you for sorting out the administration in Ghent. The staff at Department of Medical Protein Research, VIB, Ghent: Lennart and S¸ule, thank you for the time and effort you put into the spectral comparison work (and I hope it's not over yet!!). Johan, thank you for your comments and advise on the EST paper. Nynke, you paved the way for me and this thesis and for that I am truly grateful! I wish to thank the School of Veterinary Medicine of the University of Zambia and the Universidad National Mayor de San Marcos in Lima (Peru) for their assistance and letting us use their facilities during the production of the ESPs. I am deeply grateful to my parents for giving me the chance to study and for supporting me in everything I've ever done (no matter how foolish!). And last but certainly not least, I want to thank Iris. What would I do without you? Without your support, this PhD would simply not exist. Thank you for always being there for me, no matter what, and for taking care of our boys during the many times I wasn't home. And to my boys, Pieter and Jeroen, thank you for always putting a smile on my face! The research leading to this thesis has received funding from: - The Research Foundation { Flanders (FWO) (project number: G.0192.10N) - The European Unions Seventh Framework Program (FP7/2007-2013) under grant agreement no. 221948 (ICONZ). - The Institute of Tropical Medicine (ITM) Secondary Research Funding (SOFI-A). Page vi Table of Contents Acknowledgementsv List of Figures xi List of Tables xv List of Abbreviations xvii 1 General Introduction1 2 Taenia solium: An Introduction5 2.1 Taenia solium taeniasis and cysticercosis...................5 2.2 Human (neuro)cysticercosis: a dead-end . ..................8 2.3 Public health and economic importance.................... 10 2.4 Eradication, elimination, control and prevention............... 11 2.5 Diagnosis of Taenia solium ........................... 15 2.5.1 Cysticercosis............................... 16 2.5.2 Taeniasis................................. 26 3 The Hitchhiker's Guide to Proteomics 31 3.1 Proteomics: what's in a name?........................ 31 3.2 Tandem mass spectrometry-based proteomics................ 33 3.2.1 Sample preparation and separation.................. 33 3.2.2 Liquid chromatography and tandem mass spectrometry....... 36 3.2.3 Data analysis.............................. 40 3.3 Helminth proteomics.............................. 48 4 Rationale and Objectives 53 Page vii 5 Partially Sequenced Organisms, Decoy Searches and False Discovery Rates 55 5.1 Introduction................................... 56 5.2 Materials and methods............................. 57 5.2.1 Databases................................ 57 5.2.2 Sample preparation........................... 57 5.2.3 Liquid chromatography { tandem mass spectrometry........ 58 5.2.4 Analysis pipeline............................ 58 5.3 Results and discussion............................. 59 5.3.1 Dataset................................. 59 5.3.2 PeptideProphet false discovery rate estimations for composite databases................................ 59 5.3.3 PeptideProphet false discovery rate estimations without decoy databases................................ 61 5.4 Conclusions................................... 61 6 Proteomic Analysis of Taenia solium Metacestode Excretion/Secretion Proteins 63 6.1 Introduction................................... 64 6.2 Materials and methods............................. 65 6.2.1 Parasite material and excretion/secretion proteins.......... 65 6.2.2 One-dimensional polyacrylamide gel electrophoresis......... 65 6.2.3 In-gel trypsin digest.......................... 65 6.2.4 Liquid chromatography { tandem mass spectrometry........ 66 6.2.5 Data analysis.............................. 66 6.2.6 Databases................................ 67 6.3 Results and discussion............................. 68 6.3.1 Taenia solium metacestodes and in vitro excretion/secretion protein production................................ 68 6.3.2 One-dimensional polyacrylamide gel electrophoresis......... 68 6.3.3 Data analysis.............................. 68 6.3.4 Proteins identified in Taenia solium excretion/secretion proteins.. 70 6.3.5 Relative protein abundance...................... 73 6.3.6 Taenia solium proteins......................... 73 6.3.7 Proteins matching sequences from other species........... 74 6.4 Conclusions................................... 75 7 Use of Expressed Sequence Tags for the Identification of Taenia solium Metacestode Excretion/Secretion Proteins 77 7.1 Introduction................................... 78 Page viii 7.2 Materials and methods............................. 78 7.2.1 Generation of the dataset....................... 78 7.2.2 Database design and data analysis.................. 79 7.3 Results and discussion............................. 79 7.3.1 Identified proteins and Gene Ontology annotation.......... 79 7.3.2 Comparison between the two studies................. 84 7.4 Conclusions................................... 84 8 The Search for Differential Proteins 87 8.1 Introduction................................... 88 8.2 Materials and methods............................. 89 8.2.1 Parasite material and excretion/secretion proteins.......... 89 8.2.2 Two-dimensional polyacrylamide gel electrophoresis......... 90 8.2.3 One-dimensional polyacrylamide gel electrophoresis and in-gel trypsin digest.................................. 90 8.2.4 Liquid chromatography { tandem mass spectrometry........ 91 8.2.5 Data analysis { spectral comparison.................. 91 8.3 Results and discussion............................. 94 8.3.1 Parasite material and excretion/secretion proteins.......... 94 8.3.2 Two-dimensional polyacrylamide gel electrophoresis......... 94 8.3.3 One-dimensional polyacrylamide gel electrophoresis......... 95 8.3.4 Data analysis { spectral comparison.................. 95 8.4 Conclusions................................... 100 9 General Discussion 101 9.1 Introduction................................... 101 9.2 Proteomics bioinformatics........................... 102 9.3 Taenia solium protein analysis......................... 103 9.4 Towards a Taenia solium-specific antigen detection assay.......... 106 9.5 Conclusions and recommendations......................
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