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Branchiostoma Lanceolatum UNIVERSITA’ DEGLI STUDI DI NAPOLI FEDERICO II PhD in MODEL ORGANISMS IN BIOMEDICAL AND VETERINARY RESEARCH XXVII CICLO PhD THESIS Study of evolution, expression and function of Nitric Oxide Synthases in the cephalochordate Branchiostoma lanceolatum Coordinator: Co - Tutor: Prof. Paolo De Girolamo Dr. Salvatore D’Aniello Tutor Author: Prof Paolo De Girolamo Giovanni Annona To you and my family Index Abbreviation list .................................................................................................................. IV Abstract ............................................................................................................................ VIII Chapter 1 - Introduction ....................................................................................................... 1 1.2 The cephalochordates Amphioxus ....................................................................... 12 1.2.1 Discovery of Amphioxus ................................................................................. 12 1.2.2 Amphioxus a link between past and present ............................................... 16 1.2.2 Phylogeny .......................................................................................................... 19 1.2.3 The model system: Amphioxus ...................................................................... 21 1.2.4 Development and larval anatomy ................................................................. 25 1.2.5 Larval nervous system ..................................................................................... 32 1.3 NO/NOS Amphioxus .................................................................................................... 36 Chapter 2 - Material and Methods ...................................................................................... 40 2.1 Animal‟s culture and embryos collection ............................................................ 41 2.1.1 Adult B. lanceolatum sampling ........................................................................ 41 2.1.2 B. lanceolatum facility ........................................................................................ 44 2.1.3 B. lanceolatum spawning .................................................................................. 45 2.1.4 Embryo collection ............................................................................................. 48 2.2 Biomolecular techniques ........................................................................................ 49 2.2.1 RNA Extraction and purification ................................................................... 49 2.2.2 Reverse transcription ....................................................................................... 49 2.2.3 Polymerase Chain Reaction(PCR) .................................................................. 50 2.2.4 DNA/RNA gel electrophoresis ...................................................................... 50 2.2.5 Molecular Cloning ............................................................................................ 51 I 2.2.6 PCR colony screening ...................................................................................... 52 2.2.7 DNA sequencing .............................................................................................. 52 2.2.8 Riboprobe synthesis ......................................................................................... 53 2.2.9 Riboprobe quantification ................................................................................. 54 2.3 Primers for WISH and qPCR design .................................................................... 55 2.4 Whole mount in situ hybridization (WISH) ........................................................ 56 2.5 Quantitative PCR(qPCR) ....................................................................................... 57 2.6 NO quantization: Griess assay and DAN assay ................................................. 58 2.6.1 Bradford protein assay .................................................................................... 58 2.6.3 DAN assay ........................................................................................................ 58 2.6.4 Griess assay ...................................................................................................... 59 2.7 NO detection: DAF-FA DA assay ......................................................................... 60 2.8 Variation of NO endogenous levels during development ............................... 61 2.9 NOS phylogenetic analysis .................................................................................... 62 2.9.1 Cephalochordate evolutionary study ............................................................ 62 2.9.2 Bony fishes and chondrichthyes evolutionary study .................................. 62 2.9.3 Sequences analysis ........................................................................................... 65 Chapter 3 - Results .............................................................................................................. 66 3.1 NOS phylogeny ....................................................................................................... 67 3.1.1 Cephalochordates NOS phylogeny ............................................................... 67 3.1.2 Bony fishes and chondrichthyes NOS phylogeny ....................................... 69 3.2 Characterization of the expression levels of NOS genes in development .. 71 3.2.1 B. lanceolatum NOS-A gene expression levels .............................................. 71 3.2.2 B. lanceolatum NOS-B gene expression level ................................................. 72 3.2.3 B. lanceolatum NOS-C gene expression levels ............................................... 73 3.3 Characterization of the expression profile of NOS genes in development .... 74 II 3.3.1 B. lanceolatum NOS-A gene expression ......................................................... 74 3.3.2 B. lanceolatum NOS-B gene expression .......................................................... 74 3.3.3 B. lanceolatum NOS-C gene expression .......................................................... 75 3.3.4 B. lanceolatum SoxB1 gene expression ............................................................ 76 3.4 Endogenous NO level duringdevelopment ........................................................ 78 3.4.1 Griess assay ....................................................................................................... 78 3.4.2 DAN assay ......................................................................................................... 79 3.5 NO localization ........................................................................................................ 80 3.6 Role of NO during the development ................................................................... 81 Chapter 4 - Discussion ........................................................................................................ 83 Conclusion ........................................................................................................................... 91 Acknowledgment ................................................................................................................. 93 Collaborative project ............................................................................................................ 96 Bibliography .................................................................................................................. 99 III Abbreviation list aa Aminoacids ADH3 Alcohol dehydrogenase class III AP Alkaline Phosphatase ASSEMB Association of European Marine Biological Laboratories BH4 Tetrahydrobiopterin cofactor BR Blocking Reagent BSA Bovine Serum Albumine CaM Calmodulin Ca2+ Calcium ion Cys Cysteine cDNA complementar DNA CNS Central Nervous System diaminofluorophore 4-amino-5-methylamino-2′-7′- DAF-FM-DA difluorofluorescein diacetate DAN Diamino compound 2,3-diaminonaphthalene DC Dorsal Compartment motoneurons DDAH dimethylarginine-dimethylaminohydrolase DEPC Diethylpyrocarbonate DIG Digoxigenin DNA Deoxyribonucleic Acid dNTP deoxyribose nucleoside triphosphate ERR Estrogen-related receptor gamma Et-OH Ethanol eNOS endothelial NOS FAD Flavin Adenine Dinucleotide FMN Flavin Mononucleotide FSW Filtered Sea Water GAD Glutamic Acid Decarboxylase IV Gbx Gastrulation brain homeobox Gly Glycine GTP Guanosine triphosphate HB Hybridization Buffer Hox Homeotic gene iNOS inducible NOS LB Luria Bertani L-NA L-Nω-Nitroarginine L-NAME L-Nω-Nitroarginine Methyl Ester LPS Large Paired Neurons L-32 Ribosomal protein L32 miniprep Plasmid DNA mini preparation NED N-naphthyl-ethylenediamine NO Nitric Oxide NOS Nitric Oxide Synthase nNOS neuronal NOS ON Over Night Otx Orthodenticle (Drosophila) homolog PFA Paraformaldehyde PMC Primary Motor Center PNS Peripheral nervous system PP Phosphate MOPS 3-(N-morpholino)propanesulfonic acid NADPH nicotinamide adenine dinucleotide phosphate NaR Nitrate Reductase PCR Polymerase Chain Reaction qPCR Quantitative PCR V RNA Ribonucleic acid SA Sulfanilamide sGC Soluble Guanylate Cyclase SEM Scanning Electron Microscopy SoxB1 HMG transcription factor SoxB1 SZN Stazione Zoologica Anton Dohrn VC Ventral Compartment motoneurons VGAT Vesicular GABA/Glycine transporter VGLUT Vesicular Glutamate Transporter WB Wash buffer WS Wash Solution WISH Whole mount in situ hybridization Anatomy ap anterior process of first somite ba branchial anlage c neurenteric canal cv celebral
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