Making the most of phylogeny - OPUS - Universität Würzburg

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BMC Genomics 2009, 10:469 http://www.biomedcentral.com/1471-2164/10/469 6. Baumann H: Die Anabiose der Tardigraden. Zool Jahrb 1922, 45:501-556. 7. Baumann H: Bemerkungen zur Anabiose von Tardigraden. Zool Anz 1927, 72:175-179. 8. Horikawa DD, Sakashita T, Katagiri C, Watanabe M, Kikawada T, Nakahara Y, Hamada N, Wada S, Funayama T, Higashi S, Kobayashi Y, Okuda T, Kuwabara M: Radiation tolerance in the tardigrade Milnesium tardigradum. Int J Radiat Biol 2006, 82:843-848. 9. Hengherr S, Worland MR, Reuner A, Brümmer F, Schill RO: Freeze tolerance, supercooling points and ice formation: comparative studies on the subzero temperature survival of limnoterrestrial tardigrades. J Exp Biol 2009, 212:802-807. 10. Hengherr S, Worland MR, Reuner A, Brümmer F, Schill RO: High- Temperature Tolerance in Anhydrobiotic Tardigrades Is Limited by Glass Transition. Physiol Biochem Zool 2009, 82(6):749-755. 11. 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BMC Genomics 2009, 10:469 http://www.biomedcentral.com/1471-2164/10/469 53. Schill RO, Mali B, Dandekar T, Schnölzer M, Reuter D, Frohme M: Molecular mechanisms of tolerance in tardigrades: new perspectives for preservation and stabilization of biological material. Biotechnol Adv 2009, 27:348-352. 54. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JGR, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E: The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002, 12:1611-1618. Publish with BioMed Central and every scientist can read your work free of charge "BioMed Central will be the most significant development for disseminating the results of biomedical research in our lifetime." Sir Paul Nurse, Cancer Research UK Your research papers will be: available free of charge to the entire biomedical community peer reviewed and published immediately upon acceptance cited in PubMed and archived on PubMed Central yours — you keep the copyright Submit your manuscript here: BioMedcentral http://www.biomedcentral.com/info/publishing_adv.asp Page 10 of 10 (page number not for citation purposes)
Page 1: Making the most of phylogeny: Uniqu
Page 4 and 5: Eingereicht am: . . . . . . . . . .
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
Page 49 and 50: Mali et al. BMC Genomics 2010, 11:1
Page 59 and 60: Chapter 5. Transcriptome analyzed a
Page 61 and 62: Abstract Tardigrades are unique met
Page 63 and 64: adiation and cold 17; 18; 19 and H.
Page 65 and 66: non-directional cDNA library. For t
Page 67 and 68: available ESTs from both species co
Page 69 and 70: Individual COG/KOGs: Among the COGs
Page 71 and 72: anches, but have only Lea 4 protein
Page 73 and 74: emains a question mark in Fig. 5. H
Page 75 and 76: (posttranslational modification) an
Page 77 and 78: other aspects of the adaptation pro
Page 79 and 80: tolerance in man. It is a recombina
Page 81 and 82: We used primer3 90 for the design o
Page 83 and 84: cathode buffer (25 mM Tris-HCl pH 9
Page 85 and 86: 24. Ostareck-Lederer, A., Ostareck,
Page 87 and 88: 59. Gaudermann, P., Vogl, I., Zient
Page 89 and 90: 91. Bork, P. & Gibson, T. J. (1996)
Page 91 and 92: Fig. 2. PCR validation of heat shoc
Page 93 and 94: Fig. 7. Comparison of COGs/KOGs spe
Page 95 and 96:
Table IIa. Subset of important COGs
Page 97 and 98:
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
Page 103 and 104:
Table IVa. Specific stress pathway
Page 111 and 112:
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
Page 143 and 144:
Figure 8. Detection of hsp60 and hs
Page 145 and 146:
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
Page 151 and 152:
Due to the remarkable ability of ta
Page 153 and 154:
Fig. 1 Alignment of two α-crystall
Page 155 and 156:
active state. This leads to the ass
Page 157:
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
Page 173 and 174:
Chapter 9. The ITS2 Database III—
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D276 Nucleic Acids Research, 2010,
Page 177 and 178:
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.
Page 252 and 253:
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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