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The most exciting phrase to hear in science, the one that heralds the most discoveries, is not Eureka! but ‘That’s funny…’ (Isaac Asimov) Promoter: Prof. dr. ir. Guy Smagghe Laboratory of Agrozoology Department of Crop protection Faculty of Bioscience Engineering Ghent University Chair of the examination committee: Prof. Dr. Els J.M. Van Damme Department of Molecular Biotechnology Faculty of Bioscience Engineering Ghent University Members of the examination committee: Prof. Dr. ir. Peter Bossier Department of Animal Production Faculty of Bioscience Engineering Ghent University Prof. Dr. Dirk de Graaf Department of Physiology Faculty of Sciences Ghent University Prof. Dr. Jozef Vanden Broeck Department of Biology Faculty of Science Catholic University of Leuven Prof. Dr. Luc Swevers Institute of Biology National Centre for Scientific Research “Demokritos”, Athens, Greece Dean: Prof. dr. ir. Guido Van Huylenbroeck Rector: Prof. dr. Paul Van Cauwenberge Key role and diversity of EcR/USP and other nuclear receptors in selected Arthropoda species ir. Olivier Christiaens Thesis submitted in fulfillment of the requirements for the degree of Doctor (PhD) in Applied Biological Sciences Dutch translation of the title: Sleutelrol en diversiteit van EcR/USP en andere nucleaire receptoren in geselecteerde geleedpotigen Front cover: (Above) Compilation of: a schematic picture of chromosomes in a cell unwinding into a DNA double helix strand (right-under), the canonical 1-dimensional structure of nuclear receptors (right-above), the holo- and apo-structure of a steroid receptor ligand binding domain (left-under) and the structure of 20-hydroxy-ecdysone (left-above). (Below) A banner of pictures (from left to right) from Acyrthosiphon pisum (picture by Alex Wild), Tetranychus urticae (picture by Eric Erbe, USDA) and Bombus terrestris (www.wikipedia.com). Please refer to this work as follows: Christiaens, O. (2013). Key role and diversity of EcR/USP and other nuclear receptors in selected Arthropoda species. Ghent University, Ghent, Belgium. ISBN: 978-90-5989-618-5 This study was financially supported by a PhD grant from the Bijzonder Onderzoeksfonds (BOF) The author and the promoters give the permission to use this thesis for consulation and to copy parts of it for personal use. Every other use is subject to the copyright laws, more specifically the source must be extensively specified when using results from this thesis. Table of contents List of abbreviations Objectives and outline of this study Chapter I: Introduction and general background ......................................- 1 - 1. General introduction on arthropod phylogeny ................................................ - 2 - 1.1. Hexapoda ............................................................................................... - 5 - 1.2. Chelicerata ............................................................................................. - 7 - 2. Nuclear receptors ............................................................................................ - 7 - 2.1. Definition .............................................................................................. - 7 - 2.2. Structure and working mechanism of nuclear receptors ....................... - 8 - 2.3. Diversity and evolution of nuclear receptors ...................................... - 14 - 2.4. Overview and function of the different NRs in arthropods ................. - 22 - 3. Ecdysone signaling pathway ........................................................................ - 32 - 3.1. Insect growth, moulting and metamorphosis ...................................... - 32 - 3.2. Ecdysone biosynthesis ......................................................................... - 34 - 3.3. Ecdysone signaling cascade ................................................................ - 34 - 3.4. The ecdysone receptor as a pest control target .................................... - 37 - 4. Arthropods used in this thesis ....................................................................... - 38 - 4.1. Acyrthosiphon pisum ........................................................................... - 38 - 4.2. Bombus terrestris ................................................................................ - 41 - 4.3. Tetranychus urticae ............................................................................. - 44 - 5. RNAi ............................................................................................................. - 48 - 5.1. Molecular mechanism ......................................................................... - 48 - 5.2. RNAi efficiency and efficacy .............................................................. - 49 - 5.3. RNAi as a possible pest control tool ................................................... - 50 - 5.4. DsRNA delivery .................................................................................. - 52 - 5.5. RNAi in Hemiptera and aphids ........................................................... - 55 - Chapter II: Diversity of nuclear receptors in the animal kingdom . - 57 - 1. Introduction................................................................................................... - 59 - 2. Material and methods ................................................................................... - 60 - 2.1. Acyrthosiphon pisum ........................................................................... - 60 - I 2.2. Bombus terrestris and Bombus impatiens ........................................... - 62 - 2.3. Tetranychus urticae ............................................................................. - 62 - 2.4. Phylogenetic analysis .......................................................................... - 64 - 3. Results and Discussion ................................................................................. - 64 - 3.1. Nuclear receptors in Acyrthosiphon pisum .......................................... - 64 - 3.2. Nuclear receptors in Bombus ............................................................... - 72 - 3.3. Nuclear receptors in Tetranychus urticae ........................................... - 78 - 4. Conclusion .................................................................................................... - 86 - Chapter III: The ecdysone receptor heterodimer ............................... - 91 - 1. Introduction................................................................................................... - 93 - 2. Material and Methods ................................................................................... - 93 - 2.1. Sequence analysis ................................................................................ - 93 - 2.2. Phylogenetic analysis .......................................................................... - 93 - 2.3. 3D-modeling and ligand docking of the ligand binding pockets of ApEcR and TuEcR .............................................................................. - 94 - 3. Results and Discussion ................................................................................. - 95 - 3.1. EcR ...................................................................................................... - 95 - 3.2. RXR/Ultraspiracle ............................................................................. - 104 - 4. Conclusions ................................................................................................ - 112 - Chapter IV: Ecdysone biosynthesis in Acyrthosiphon pisum and Tetranychus urticae ........................................................ - 113 - 1. Introduction................................................................................................. - 115 - 2. Material and methods ................................................................................. - 116 - 2.1. Annotation of Halloween genes ........................................................ - 116 - 2.2. Confirmation of expression ............................................................... - 117 - 2.3. Identification of PonA as a major ecdysteroid in T. urticae ............. - 117 - 3. Results and Discussion ............................................................................... - 118 - 3.1. Halloween genes in Acyrthosiphon pisum......................................... - 118 - 3.2. Ecdysteroid biosynthesis in T. urticae .............................................. - 121 - 4. Conclusion .................................................................................................. - 124 - Chapter V: RNAi ................................................................................ - 125 - 1. Introduction................................................................................................. - 126 - 2. Development of a microinjection protocol ................................................. - 126 - II 2.1. Microinjection setup .......................................................................... - 126 - 2.2. Sedation and immobilization ............................................................. - 127 - 2.3. Microcapillaries ................................................................................. - 128 - 2.4. Needle insertion ................................................................................. - 129 - 2.5. Volume .............................................................................................. - 129 - 2.6. Toxicity of injected water, buffer and dye ........................................ - 129 - 3. RNAi experiments
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    Cladistics Cladistics 33 (2017) 574–616 10.1111/cla.12182 The spider tree of life: phylogeny of Araneae based on target-gene analyses from an extensive taxon sampling Ward C. Wheelera,*, Jonathan A. Coddingtonb, Louise M. Crowleya, Dimitar Dimitrovc,d, Pablo A. Goloboffe, Charles E. Griswoldf, Gustavo Hormigad, Lorenzo Prendinia, Martın J. Ramırezg, Petra Sierwaldh, Lina Almeida-Silvaf,i, Fernando Alvarez-Padillaf,d,j, Miquel A. Arnedok, Ligia R. Benavides Silvad, Suresh P. Benjamind,l, Jason E. Bondm, Cristian J. Grismadog, Emile Hasand, Marshal Hedinn, Matıas A. Izquierdog, Facundo M. Labarquef,g,i, Joel Ledfordf,o, Lara Lopardod, Wayne P. Maddisonp, Jeremy A. Millerf,q, Luis N. Piacentinig, Norman I. Platnicka, Daniele Polotowf,i, Diana Silva-Davila f,r, Nikolaj Scharffs, Tamas Szuts} f,t, Darrell Ubickf, Cor J. Vinkn,u, Hannah M. Woodf,b and Junxia Zhangp aDivision of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th St., New York, NY 10024, USA; bSmithsonian Institution, National Museum of Natural History, 10th and Constitution, NW Washington, DC 20560-0105, USA; cNatural History Museum, University of Oslo, Oslo, Norway; dDepartment of Biological Sciences, The George Washington University, 2029 G St., NW Washington, DC 20052, USA; eUnidad Ejecutora Lillo, FML—CONICET, Miguel Lillo 251, 4000, SM. de Tucuman, Argentina; fDepartment of Entomology, California Academy of Sciences, 55 Music Concourse Drive, Golden State Park, San Francisco, CA 94118, USA; gMuseo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’—CONICET, Av. Angel Gallardo 470, C1405DJR, Buenos Aires, Argentina; hThe Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA; iLaboratorio Especial de Colecßoes~ Zoologicas, Instituto Butantan, Av.