hide
Language(s):
eng - English
Dates:
2013-10-292013
Publication Status:
Issued
Pages:
IX, 131 S.
Publishing info:
Lübeck : University of Lübeck
Table of Contents:
Table of Contents
Acknowledgements .......................................................................................................... I
Declaration of Author’s Contribution ......................................................................... II
List of Figures ................................................................................................................ V
List of Tables .............................................................................................................. VIII
Summary ....................................................................................................................... IX
1. Introduction ................................................................................................................. 1
1.1 Skin microbiota ..................................................................................................................... 2
1.1.1 Skin microbiota characterization ......................................................................................... 3
1.1.2 Factors influencing skin microbiota composition ............................................................... 6
1.1.3 Skin microbiota association with health and disease .......................................................... 7
1.2 Autoimmunity and Autoimmune diseases ......................................................................... 8
1.2.1 Why study Autoimmune diseases? ...................................................................................... 8
1.2.2 Autoimmune skin blistering diseases .................................................................................. 9
1.3 Epidermolysis Bullosa Acquisita ....................................................................................... 10
1.3.1 Mouse models to study EBA ............................................................................................. 11
1.3.2 Genetics of EBA ................................................................................................................ 13
1.4 Scope of the thesis ............................................................................................................... 15
2 Materials and Methods .............................................................................................. 19
2.1 Generation of a four way advanced intercross lines ....................................................... 19
2.2 SJL/J mice ........................................................................................................................... 19
2.3 Recombinant peptides ........................................................................................................ 20
2.4 Induction of experimental EBA and observation protocol ............................................. 20
2.5 Genomic DNA extraction for genotyping ......................................................................... 21
2.6 G4 population genotyping .................................................................................................. 21
2.7 Bacterial DNA extraction and 16S rRNA gene pyrosequencing .................................... 22
2.8 454 pyrosequencing data analysis ..................................................................................... 23
2.8.1 Pre-processing steps .......................................................................................................... 23
2.8.2 OTU determination ............................................................................................................ 24
2.8.3 Sequence alignment ........................................................................................................... 25
2.8.4 Normalization using rarefaction method ........................................................................... 26
2.8.5 Alpha diversity analysis .................................................................................................... 27
2.8.6 Beta diversity analysis ....................................................................................................... 29
2.8.7 Indicator species analysis .................................................................................................. 30
2.8.8 Taxonomy classification .................................................................................................... 31
2.9 Data preparation for QTL analysis .................................................................................. 32
2.10 Core measurement microbiota ........................................................................................ 32
2.11 QTL analysis ..................................................................................................................... 33
2.11.1 Model selection ............................................................................................................... 35
2.11.2 QTL mapping .................................................................................................................. 36
3. Results ........................................................................................................................ 40
3.1 Skin bacterial diversity ....................................................................................................... 40
3.1.1 Microbial communities in healthy and EBA afflicted individuals .................................... 45
3.1.1.1 Alpha diversity ................................................................................................................ 46
3.1.1.2 Beta diversity .................................................................................................................. 49
3.1.1.3 Indicator species analysis ................................................................................................ 51
3.2 Skin microbiota role in EBA susceptibility ...................................................................... 54
3.3 Factors influencing skin microbiota .................................................................................. 59
3.3.1 Cage .................................................................................................................................. 59
3.3.2 Family ............................................................................................................................... 60
3.4 QTL analysis of skin microbiota ....................................................................................... 60
3.4.1 Effects of immunization on QTL mapping ........................................................................ 62
3.5 Genetics association of EBA ............................................................................................... 64
3.6 Genetics and skin microbiota interaction ......................................................................... 64
4. Discussion ................................................................................................................... 71
5. Bibliography .............................................................................................................. 80
6. Appendices ................................................................................................................. 95
6.1 Appendix A – Additional figures ....................................................................................... 95
6.2 Appendix B – Additional tables ....................................................................................... 104
7. Scientific achievements during doctoral research ................................................ 122
8. Affidavit ................................................................................................................... 125
9. Copyright Statement ............................................................................................... 126
10. Index ....................................................................................................................... 131
Rev. Type:
-
Identifiers:
Other: Diss/12500
Degree:
PhD
