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Functional Analysis of Insl5 and Insl6 Genes and Verification of Interactions Between Pelota and Its Putative Interacting Proteins

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Functional Analysis of Insl5 and Insl6 Genes and Verification of Interactions Between Pelota and Its Putative Interacting Proteins Functional Analysis of Insl5 and Insl6 Genes and Verification of Interactions between Pelota and its Putative Interacting Proteins Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultäten der Georg-August-Universität zu Göttingen vorgelegt von Ozanna Burnicka-Turek aus Bydgoszcz, Polen Göttingen, 2009 D7 Referent: Prof. Dr. W. Engel Korreferentin: Prof. Dr. S. Hoyer-Fender Tag der mündlichen Prüfung: To my husband, family and friends for their support, encouragement and love. The more you know, the harder it is to take decisive action. Once you become informed, you start seeing complexities and shades of gray. You realize that nothing is as clear and simple as it first appears. Ultimately, knowledge is paralyzing. Bill Watterson (1958 - ), Calvin & Hobbes (THERE'S TREASURE EVERYWHERE) CONTENTS TABLE OF CONTENTS page CONTENTS...............................................................................................................................I ABBREVIATIONS ............................................................................................................. VIII 1. INTRODUCTION................................................................................................................ 1 1.1. Expression and function of insulin-like genes .................................................................... 1 1.2. The pelota gene .................................................................................................................. 4 1.3. Objectives of this study....................................................................................................... 7 2. MATERIALS AND METHODS......................................................................................... 8 2.1. Materials ............................................................................................................................ 8 2.1.1. Chemicals and reagents.................................................................................................... 8 2.1.2. Buffers and solutions...................................................................................................... 11 2.1.2.1. Agarose gel electrophoresis ........................................................................................ 11 2.1.2.2. SDS-PAGE.................................................................................................................. 12 2.1.2.3. Frequently used buffers and solutions......................................................................... 13 2.1.3. Laboratory materials ...................................................................................................... 17 2.1.4. Sterilization of solutions and equipment........................................................................ 17 2.1.5. Media, antibiotics and agar-plates.................................................................................. 18 2.1.5.1. Media for bacteria ....................................................................................................... 18 2.1.5.2. Media for cell culture .................................................................................................. 18 2.1.5.3. Antibiotics ................................................................................................................... 19 2.1.5.4. IPTG/X-Gal plate ........................................................................................................ 19 2.1.6. Bacterial strains.............................................................................................................. 19 2.1.7. Cell lines......................................................................................................................... 19 2.1.8. Plasmids ......................................................................................................................... 20 2.1.9. Synthetic oligonucleotide primers.................................................................................. 20 2.1.10. Genomic and cDNA probes ......................................................................................... 23 2.1.11. Mouse strains................................................................................................................ 24 2.1.12. Antibodies .................................................................................................................... 24 2.1.13. Enzymes ....................................................................................................................... 25 2.1.14. Radioactive substances................................................................................................. 25 2.1.15. Kits ............................................................................................................................... 25 2.1.16. Instruments................................................................................................................... 26 I CONTENTS 2.2. Methods............................................................................................................................ 27 2.2.1. Isolation of nucleic acids................................................................................................ 27 2.2.1.1. Isolation of plasmid DNA ........................................................................................... 27 2.2.1.1.1. Small - scale isolation of plasmid DNA (Mini preparation) .................................... 27 2.2.1.1.2. Preparation of bacterial glycerol stocks ................................................................... 28 2.2.1.1.3. Large - scale preparation of plasmid DNA (Midi preparation)................................ 28 2.2.1.1.4. Endotoxin free preparation of plasmid DNA .......................................................... 29 2.2.1.2. Isolation of genomic DNA .......................................................................................... 30 2.2.1.2.1. Isolation of genomic DNA from mouse tails ........................................................... 30 2.2.1.2.2. Isolation of genomic DNA from tissue samples ...................................................... 30 2.2.1.2.3. Isolation of genomic DNA from ES cells ............................................................... 30 2.2.1.3. Isolation of total RNA................................................................................................. 31 2.2.1.3.1. Isolation of total RNA from tissue samples and cultured cells................................ 31 2.2.2. Determination of nucleic acid concentration ................................................................. 31 2.2.3. Gel electrophoresis......................................................................................................... 32 2.2.3.1. Agarose gel electrophoresis of DNA .......................................................................... 32 2.2.3.2. Agarose gel electrophoresis of RNA........................................................................... 32 2.2.4. Cloning techniques......................................................................................................... 33 2.2.4.1. Enzymatic modifications of DNA............................................................................... 33 2.2.4.1.1. Restriction enzyme digestion of DNA ..................................................................... 33 2.2.4.1.2. Filling-up reaction.................................................................................................... 34 2.2.4.1.3. Dephosphorylation of 5’ ends of DNA .................................................................... 34 2.2.4.2. Purification of DNA.................................................................................................... 34 2.2.4.2.1. Purification of DNA by phenol-chloroform extraction and ethanol precipitation ... 34 2.2.4.2.2. Purification of DNA fragments from agarose gel .................................................... 35 2.2.4.2.2.1. QIAquick gel extraction method........................................................................... 35 2.2.4.3. Ligation of DNA fragments ........................................................................................ 35 2.2.4.4. TA-Cloning ................................................................................................................. 36 2.2.5. Preparation of competent E.coli bacteria ....................................................................... 36 2.2.6. Transformation of competent bacteria ........................................................................... 36 2.2.7. Polymerase Chain Reaction (PCR) ................................................................................ 37 2.2.7.1. PCR amplification of DNA fragments........................................................................ 37 2.2.7.2. Genotyping of knock-out mice using PCR ................................................................. 38 2.2.7.3. Reverse transcription PCR (RT-PCR)......................................................................... 39 II CONTENTS 2.2.7.3.1. Reverse transcription or cDNA synthesis ................................................................ 39 2.2.7.3.2. One-Step RT-PCR.................................................................................................... 40 2.2.8. Non-radioactive dye terminator cycle sequencing......................................................... 41 2.2.9. Nucleic acids blotting techniques..................................................................................
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