Making the most of phylogeny - OPUS - Universität Würzburg

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Eingereicht am: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Thomas Dandekar 1. Gutachter: Prof. Dr. Thomas Dandekar 2. Gutachter: Prof. Dr. Markus Engstler Tag des Promotionskolloquiums: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Doktorurkunde ausgehändigt am: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Acknowledgements I would like to express my gratitude to my academic advisor Prof. Dr. Thomas Dandekar for his guidance and constant support in helping me to conduct and complete this work. In addition, I want to thank Prof. Dr. Markus Engstler for serving on my advisory committee. I am thankful to the BMBF project FUNCRYPTA (FKZ 0313838B) for funding. Thanks to my collaborators at the University of Stuttgart, the German Cancer Research Center in Heidelberg, the University of Applied Sciences in Wildau and the company Oncoscience in Wedel who have contributed experimental work, advice, fruitful discussions, nice meetings and a wonderful 11 th International Symposium on Tardigrada 2009 in Tübingen. I am also grateful to the journal ‘Cell Stress and Chaperones’ for the permission to print my publication ‘Stress response in tardigrades: differential gene expression of molecular chaperones’ in this thesis. Many thanks to all the people I have met in the Department of Bioinformatics at the University of Würzburg. Special thanks to all of my roommates Dr. Roland Schwarz, Dr. Dr. Marcus Diettrich, Dr. Armin Robubi, Nicole Philippi, Michael Seidl, Gaby Wangorsch and Felix Bemm for their help and their exercised patience. I must not forget to thank our coffee machine, which always provided me with the fuel I needed ;). Thanks to Sabine and Alexander Keller for proof-reading this thesis. A big thank you goes to Prof. Dr. Jörg Schultz, Dr. Matthias Wolf, Dr. Tobias Müller, Gaby Wangorsch, and Christian Koetschan for the helpful comments during the creation of this thesis. I owe everything to my family who has always supported and encouraged me over the years. I especially want to thank Sabine for her inspiration, continuous encouragement and patience (“I will leave the office in 5 minutes”) during my studies. Finally, I want to express my deepest appreciation to my beloved parents for their love, affection, and unlimited support during my life and studies. v
Page 1: Making the most of phylogeny: Uniqu
Page 7 and 8: Contents Acronyms xi I. Introductio
Page 9: List of Figures Contents List of Fi
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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Mali et al. BMC Genomics 2010, 11:1
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Mali et al. BMC Genomics 2010, 11:1
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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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