Figures - E-LIB - Universität Bremen

Table of Contents
Abbreviations .......................................................................................................................................vii
Figures.................................................................................................................................................... ix
Tables ..................................................................................................................................................... ix
Summary................................................................................................................................................. x
Zusammenfassung................................................................................................................................xii
1 Introduction ..................................................................................................................................... 1
1.1 Temperature and thermal tolerance........................................................................................... 1
1.2 Fishes of the Antarctic shelf....................................................................................................... 3
1.3 Adaptation in cold stenothermal fish: from functional to molecular level ................................ 4
1.3.1 Systemic adaptations to cold environments........................................................................ 4
1.3.2 Lipids .................................................................................................................................. 5
1.3.3 Proteins ............................................................................................................................... 6
1.3.4 DNA, RNA and gene expression........................................................................................ 8
1.4 Fish model Zoarcidae............................................................................................................... 10
1.5 Key abiotic factors and climate change ................................................................................... 11
1.6 Objectives of the thesis............................................................................................................. 13
2 Materials & Methods..................................................................................................................... 15
2.1 Animals..................................................................................................................................... 15
2.1.1 General sampling protocol................................................................................................ 16
2.2 Animal incubations and experimental setups........................................................................... 17
2.2.1 Untreated animals ............................................................................................................. 17
2.2.2 Time course of warm acclimation .................................................................................... 17
2.2.3 Long-term acclimation...................................................................................................... 17
2.3 Osmolality measurements ........................................................................................................ 18
2.4 Molecular analytics.................................................................................................................. 18
2.4.1 Enzyme measurements ..................................................................................................... 18
2.4.2 RNA extraction ................................................................................................................. 20
2.4.3 Cloning of candidate genes............................................................................................... 20
2.4.4 Quantification of transcripts via qPCR............................................................................. 21
2.4.5 cDNA library construction for P. brachycephalum .......................................................... 22
2.4.6 Sequence annotation of cDNA libraries ........................................................................... 22
2.4.7 Phylogenetic analyses ....................................................................................................... 23
2.4.8 Microarray – design of a test array ................................................................................... 23
2.4.9 Microarray – compact design ........................................................................................... 24
2.4.10 Labelling, hybridization and scanning of microarrays ................................................... 25
2.5 Statistical approaches .............................................................................................................. 26
2.5.1 Univariate analyses ........................................................................................................... 26
2.5.2 Multivariate analyses ........................................................................................................ 26
2.5.3 Comparative sequence analyses........................................................................................ 26
2.5.4 Microarray analyses.......................................................................................................... 26
3 Publications .................................................................................................................................... 29
Publication I ...................................................................................................................................... 31
Publication II..................................................................................................................................... 47
Publication III.................................................................................................................................... 77
4 Discussion ..................................................................................................................................... 115
4.1 Molecular adaptations in Pachycara brachycephalum ......................................................... 115
4.1.1 Selective pressure on codon usage.................................................................................. 115
4.1.2 Proteomic cold adaptation .............................................................................................. 117
4.1.3 Functional repertoire of genes ........................................................................................ 118
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