Making the most of phylogeny - OPUS - Universität Würzburg

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Contents Contents 5. Transcriptome analyzed at different levels in Hypsibius dujardini and Milnesium tardigradum: Specific adaptations, motifs and clusters as well as general protective pathways 47 6. Proteomic analysis of tardigrades: towards a better understanding of molecular mechanisms by anhydrobiotic organisms 99 7. Stress response in tardigrades: differential gene expression of molecular chaperones 137 8. Tardigrade bioinformatics: Molecular adapations, DNA j family and dynamical modelling 147 9. The ITS2 Database III—sequences and structures for phylogeny 161 10. Including RNA Secondary Structures improves Accuracy and Robustness in Reconstruction of Phylogenetic Trees 167 11. ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales) 181 12. Distinguishing species in Paramacrobiotus (Tardigrada) via compensatory base change analysis of internal transcribed spacer 2 secondary structures, with the description of three new species 195 IV. General Discussion and Conclusion 223 Summary 233 Zusammenfassung 235 Bibliography 237 Contributions 251 Curriculum Vitae 255 List of Publications 257 Erklärung 261 viii
List of Figures Contents List of Figures 1. First drawing of a ‘waterbear’ . . . . . . . . . . . . . . . . . . . . . . . 4 2. Ranges for often used phylogenetic markers . . . . . . . . . . . . . . 8 3. Organisation of a typical eukaryotic rRNA cistron . . . . . . . . . . . 8 4. Secondary structure of the ITS2 of the Dahlia brevis . . . . . . . . . . 9 5. Annotation pipeline . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 ix
Page 1: Making the most of phylogeny: Uniqu
Page 4 and 5: Eingereicht am: . . . . . . . . . .
Page 7: Contents Acronyms xi I. Introductio
Page 12 and 13: Acronyms Acronyms xii ITS2 internal
Page 15 and 16: Part I. Introduction Thesis outline
Page 17 and 18: Part I. Introduction The phylum Tar
Page 19 and 20: Part I. Introduction Internal trans
Page 21 and 22: Part I. Introduction Internal trans
Page 23: Part II. Material and Methods 11
Page 27 and 28: Chapter 2. Methods 2.1. Bioinformat
Page 29 and 30: Part II. Material and Methods Bioin
Page 31 and 32: Part II. Material and Methods Bioin
Page 33: Part III. Results 21
Page 36 and 37: BMC Genomics BioMed Central Researc
Page 38 and 39: BMC Genomics 2009, 10:469 http://ww
Page 47 and 48: Chapter 4. Transcriptome survey of
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Chapter 5. Transcriptome analyzed a
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Abstract Tardigrades are unique met
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adiation and cold 17; 18; 19 and H.
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non-directional cDNA library. For t
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available ESTs from both species co
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Individual COG/KOGs: Among the COGs
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anches, but have only Lea 4 protein
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emains a question mark in Fig. 5. H
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(posttranslational modification) an
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other aspects of the adaptation pro
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tolerance in man. It is a recombina
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We used primer3 90 for the design o
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cathode buffer (25 mM Tris-HCl pH 9
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24. Ostareck-Lederer, A., Ostareck,
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59. Gaudermann, P., Vogl, I., Zient
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91. Bork, P. & Gibson, T. J. (1996)
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Fig. 2. PCR validation of heat shoc
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Fig. 7. Comparison of COGs/KOGs spe
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Table IIa. Subset of important COGs
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KOG0660:[T]Mitogen-activated protei
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Table III. Enzymes in metabolic pat
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ec:5.3.3.2 isopentenyl-diphosphate
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Table IVa. Specific stress pathway
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Chapter 6. Proteomic analysis of ta
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Figure 1. SEM images of M. tardigra
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listed in Table 2. The individual i
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Table 1. Overview of identified pro
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Table 2. Cont. Sequence coverage No
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Table 3. Identified proteins withou
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Table 3. Cont. Spot no. Accession n
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Table 3. Cont. Spot no. Accession n
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Figure 8. Detection of hsp60 and hs
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Unique proteins, when analyzed on t
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(version 56.1, September 2008, The
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Chapter 7. Stress response in tardi
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Due to the remarkable ability of ta
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Fig. 1 Alignment of two α-crystall
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active state. This leads to the ass
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Pfaffl MW, Horgan GW, Dempfle L (20
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Tardigrade bioinformatics: Molecula
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searched against the next more exte
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Concerted changes in tardigrade ada
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mit dynamischen Modellierungstechni
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Tables and Figures Table 1: Bioinfo
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Figure 1: Maximum likelihood tree f
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Chapter 9. The ITS2 Database III—
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D276 Nucleic Acids Research, 2010,
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D278 Nucleic Acids Research, 2010,
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Chapter 10. Including RNA Secondary
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Keller et al. Biology Direct 2010,
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BMC Evolutionary Biology Research a
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BMC Evolutionary Biology 2008, 8:21
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Chapter 12. Distinguishing species
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Abstract Distinguishing species in
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Distinguishing species in Paramacro
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ITS 2 gene amplification and sequen
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References Distinguishing species i
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Figure legends Distinguishing speci
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221
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Part IV. General Discussion and Con
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Summary succeeded to show the benef
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Zusammenfassung der internal transc
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Bibliography Bibliography Bavan, S.
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Bibliography Bibliography 146.4 (Ap
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Bibliography Bibliography Horikawa,
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Bibliography Bibliography Letunic,
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Bibliography Bibliography Pertea, G
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Bibliography Bibliography Schultz,
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Bibliography Bibliography Westh, P.
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Contributions Markus Grohme wrote t
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Contributions model and the ITS2 se
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List of Publications Publications a
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List of Publications Förster, F.,
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Making the most of phylogeny - OPUS - Universität Würzburg

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