@phdthesis{Foerster2010,
  author    = {F{\"o}rster, Frank},
  title     = {Making the most of phylogeny: Unique adaptations in tardigrades and 216374 internal transcribed spacer 2 structures},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-51466},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {The phylum Tardigrada consists of about 1000 described species to date. The animals live in habitats within marine, freshwater and terrestrial ecosystems allover the world. Tardigrades are polyextremophiles. They are capable to resist extreme temperature, pressure or radiation. In the event of desiccation, tardigrades enter a so-called tun stage. The reason for their great tolerance capabilities against extreme environmental conditions is not discovered yet. Our Funcrypta project aims at finding answers to the question what mechanisms underlie these adaption capabilities particularly with regard to the species Milnesium tardigradum. The first part of this thesis describes the establishment of expressed sequence tags (ESTs) libraries for different stages of M. tardigradum. From proteomics data we bioinformatically identified 144 proteins with a known function and additionally 36 proteins which seemed to be specific for M. tardigradum. The generation of a comprehensive web-based database allows us to merge the proteome and transcriptome data. Therefore we created an annotation pipeline for the functional annotation of the protein and nucleotide sequences. Additionally, we clustered the obtained proteome dataset and identified some tardigrade-specific proteins (TSPs) which did not show homology to known proteins. Moreover, we examined the heat shock proteins of M. tardigradum and their different expression levels depending on the actual state of the animals. In further bioinformatical analyses of the whole data set, we discovered promising proteins and pathways which are described to be correlated with the stress tolerance, e.g. late embryogenesis abundant (LEA) proteins. Besides, we compared the tardigrades with nematodes, rotifers, yeast and man to identify shared and tardigrade specific stress pathways. An analysis of the 50 and 30 untranslated regions (UTRs) demonstrates a strong usage of stabilising motifs like the 15-lipoxygenase differentiation control element (15-LOX-DICE) but also reveals a lack of other common UTR motifs normally used, e.g. AU rich elements. The second part of this thesis focuses on the relatedness between several cryptic species within the tardigrade genus Paramacrobiotus. Therefore for the first time, we used the sequence-structure information of the internal transcribed spacer 2 (ITS2) as a phylogenetic marker in tardigrades. This allowed the description of three new species which were indistinguishable using morphological characters or common molecular markers like the 18S ribosomal ribonucleic acid (rRNA) or the Cytochrome c oxidase subunit I (COI). In a large in silico simulation study we also succeeded to show the benefit for the phylogenetic tree reconstruction by adding structure information to the ITS2 sequence. Next to the genus Paramacrobiotus we used the ITS2 to corroborate a monophyletic DO-group (Sphaeropleales) within the Chlorophyceae. Additionally we redesigned another comprehensive database—the ITS2 database resulting in a doubled number of sequence-structure pairs of the ITS2. In conclusion, this thesis shows the first insights (6 first author publications and 4 coauthor publications) into the reasons for the enormous adaption capabilities of tardigrades and offers a solution to the debate on the phylogenetic relatedness within the tardigrade genus Paramacrobiotus.},
  subject      = {Phylogenie},
  language  = {en}
}
@misc{Selig2007,
  type      = {Master Thesis},
  author    = {Selig, Christian},
  title     = {The ITS2 Database - Application and Extension},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-23895},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2007},
  abstract  = {Der internal transcribed spacer 2 (ITS2) des ribosomalen Genrepeats ist ein zunehmend wichtiger phylogenetischer Marker, dessen RNA-Sekund{\"a}rstruktur innerhalb vieler eukaryontischer Organismen konserviert ist. Die ITS2-Datenbank hat zum Ziel, eine umfangreiche Ressource f{\"u}r ITS2-Sequenzen und -Sekund{\"a}rstrukturen auf Basis direkter thermodynamischer als auch homologiemodellierter RNA-Faltung zu sein. Ergebnisse: (a) Eine komplette Neufassung der urspr{\"u}nglichen die ITS2-Datenbank generierenden Skripte, angewandt auf einen aktuellen NCBI-Datensatz, deckte mehr als 65.000 ITS2-Strukturen auf. Dies verdoppelt den Inhalt der urspr{\"u}nglichen Datenbank und verdreifacht ihn, wenn partielle Strukturen mit einbezogen werden. (b) Die Endbenutzer-Schnittstelle wurde neu geschrieben, erweitert und ist jetzt in der Lage, benutzerdefinierte Homologiemodellierungen durchzuf{\"u}hren. (c) Andere m{\"o}glichen RNA-Strukturaufkl{\"a}rungsmethoden (suboptimales und formenbasiertes Falten) sind hilfreich, k{\"o}nnen aber Homologiemodellierung nicht ersetzen. (d) Ein Anwendungsfall der ITS2-Datenbank in Zusammenhang mit anderen am Lehrstuhl entwickelten Werkzeugen gab Einblick in die Verwendung von ITS2 f{\"u}r molekulare Phylogenie.},
  subject      = {Phylogenie},
  language  = {en}
}