@misc{RianoPachonNagelNeigenfindetal.2009,
  author    = {Riano-Pachon, Diego Mauricio and Nagel, Axel and Neigenfind, Jost and Wagner, Robert and Basekow, Rico and Weber, Elke and M{\"u}ller-R{\"o}ber, Bernd and Diehl, Svenja and Kersten, Birgit},
  title     = {GabiPD : the GABI primary database - a plant integrative "omics" database},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45075},
  year      = {2009},
  abstract  = {The GABI Primary Database, GabiPD (http:// www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different 'omics' fronts are incorporated (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for textbased retrieval of all data types in GabiPD (e.g. clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralized Gene GreenCard allows visualizing ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover, GabiPD makes available interactive genetic maps from potato and barley, and protein 2DE gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic-profiling data can be visualized through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data.},
  language  = {en}
}
@phdthesis{Krebs2009,
  author    = {Krebs, Jonas},
  title     = {Molecular and physiological characterisation of selected DOF transcription factors in the model plant Arabidopsis thaliana},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41831},
  school      = {Universit{\"a}t Potsdam},
  year      = {2009},
  abstract  = {About 2,000 of the more than 27,000 genes of the genetic model plant Arabidopsis thaliana encode for transcription factors (TFs), proteins that bind DNA in the promoter region of their target genes and thus act as transcriptional activators and repressors. Since TFs play essential roles in nearly all biological processes, they are of great scientific and biotechnological interest. This thesis concentrated on the functional characterisation of four selected members of the Arabidopsis DOF-family, namely DOF1.2, DOF3.1, DOF3.5 and DOF5.2, which were selected because of their specific expression pattern in the root tip, a region that comprises the stem cell niche and cells for the perception of environmental stimuli. DOF1.2, DOF3.1 and DOF3.5 are previously uncharacterized members of the Arabidopsis DOF-family, while DOF5.2 has been shown to be involved in the phototrophic flowering response. However, its role in root development has not been described so far. To identify biological processes regulated by the four DOF proteins in detail, molecular and physiological characterization of transgenic plants with modified levels of DOF1.2, DOF3.1, DOF3.5 and DOF5.2 expression (constitutive and inducible over-expression, artificial microRNA) was performed. Additionally expression patterns of the TFs and their target genes were analyzed using promoter-GUS lines and publicly available microarray data. Finally putative protein-protein interaction partners and upstream regulating TFs were identified using the yeast two-hybrid and one-hybrid system. This combinatorial approach revealed distinct biological functions of DOF1.2, DOF3.1, DOF3.5 and DOF5.2 in the context of root development. DOF1.2 and DOF3.5 are specifically and exclusively expressed in the root cap, including the central root cap (columella) and the lateral root cap, organs which are essential to direct oriented root growth. It could be demonstrated that both genes work in the plant hormone auxin signaling pathway and have an impact on distal cell differentiation. Altered levels of gene expression lead to changes in auxin distribution, abnormal cell division patterns and altered root growth orientation. DOF3.1 and DOF5.2 share a specific expression pattern in the organizing centre of the root stem cell niche, called the quiescent centre. Both genes redundantly control cell differentiation in the root´s proximal meristem and unravel a novel transcriptional regulation pathway for genes enriched in the QC cells. Furthermore this work revealed a novel bipartite nuclear localisation signal being present in the protein sequence of the DOF TF family from all sequenced plant species. Summing up, this work provides an important input into our knowledge about the role of DOF TFs during root development. Future work will concentrate on revealing the exact regulatory networks of DOF1.2, DOF3.1, DOF3.5 and DOF5.2 and their possible biotechnological applications.},
  language  = {en}
}
@phdthesis{Nikolovski2009,
  author    = {Nikolovski, Nino},
  title     = {Pectin: New insights from an old polymer through pectinase-based genetic screens},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-35255},
  school      = {Universit{\"a}t Potsdam},
  year      = {2009},
  abstract  = {Pectic polysaccharides, a class of plant cell wall polymers, form one of the most complex networks known in nature. Despite their complex structure and their importance in plant biology, little is known about the molecular mechanism of their biosynthesis, modification, and turnover, particularly their structure-function relationship. One way to gain insight into pectin metabolism is the identification of mutants with an altered pectin structure. Those were obtained by a recently developed pectinase-based genetic screen. Arabidopsis thaliana seedlings grown in liquid medium containing pectinase solutions exhibited particular phenotypes: they were dwarfed and slightly chlorotic. However, when genetically different A. thaliana seed populations (random T-DNA insertional populations as well as EMS-mutagenized populations and natural variations) were subjected to this treatment, individuals were identified that exhibit a different visible phenotype compared to wild type or other ecotypes and may thus contain a different pectin structure (pec-mutants). After confirming that the altered phenotype occurs only when the pectinase is present, the EMS mutants were subjected to a detailed cell wall analysis with particular emphasis on pectins. This suite of mutants identified in this study is a valuable resource for further analysis on how the pectin network is regulated, synthesized and modified. Flanking sequences of some of the T-DNA lines have pointed toward several interesting genes, one of which is PEC100. This gene encodes a putative sugar transporter gene, which, based on our data, is implicated in rhamnogalacturonan-I synthesis. The subcellular localization of PEC100 was studied by GFP fusion and this protein was found to be localized to the Golgi apparatus, the organelle where pectin biosynthesis occurs. Arabidopsis ecotype C24 was identified as a susceptible one when grown with pectinases in liquid culture and had a different oligogalacturonide mass profile when compared to ecotype Col-0. Pectic oligosaccharides have been postulated to be signal molecules involved in plant pathogen defense mechanisms. Indeed, C24 showed elevated accumulation of reactive oxygen species upon pectinase elicitation and had altered response to the pathogen Alternaria brassicicola in comparison to Col-0. Using a recombinant inbred line population three major QTLs were identified to be responsible for the susceptibility of C24 to pectinases. In a reverse genetic approach members of the qua2 (putative pectin methyltransferase) family were tested for potential target genes that affect pectin methyl-esterification. The list of these genes was determined by in silico study of the pattern of expression and co-expression of all 34 members of this family resulting in 6 candidate genes. For only for one of the 6 analyzed genes a difference in the oligogalacturonide mass profile was observed in the corresponding knock-out lines, confirming the hypothesis that the methyl-esterification pattern of pectin is fine tuned by members of this gene family. This study of pectic polysaccharides through forward and reverse genetic screens gave new insight into how pectin structure is regulated and modified, and how these modifications could influence pectin mediated signalling and pathogenicity.},
  language  = {en}
}
@misc{Voigt2009,
  type      = {Master Thesis},
  author    = {Voigt, Matthias},
  title     = {Entwicklung von bioinformatischen Visualisierungswerkzeugen f{\"u}r Metabolitdaten von N{\"a}hrstoffmangelsituationen bei Arabidopsis thaliana},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-33047},
  school      = {Universit{\"a}t Potsdam},
  year      = {2009},
  abstract  = {Diese Arbeit umfasst die Archivierung, Visualisierung anhand bioinformatischer Methoden und Interpretation eines vorhandenen Messdatensatz (Element [ICP-MS]-, Ionen [IC]- und Metabolitdaten [RP-HPLC und GC/TOF-MS]) der Pflanze Arabidopsis thaliana getrennt in Bl{\"a}tter und Wurzeln. Die Pflanzen wurden den sechs Mangelsituationen der N{\"a}hrstoffe Eisen, Kalium, Magnesium, Stickstoff, Phosphor und Schwefel ausgesetzt und zu neun Messzeitpunkten [0.5-, 1-, 2-, 3-, 4-, 5-, 6-, 7-in Tagen und „resupply" (vier Stunden nach dem vierten Tag)] analysiert. Es erfolgte die Integration der Messdaten in eine SQlite-Datenbank. Die Veranschaulichung erfolgte mit Hilfe der Programmiersprache R. Anhand einiger Pakete zur Erweiterung des Funktionsumfangs von R wurde erstens eine Schnittstelle zur SQLite- Datenbank hergestellt, was ein Abfragen an diese erm{\"o}glichte und zweitens verhalfen sie zu der Erstellung einer Reihe zus{\"a}tzlicher Darstellungsformen (Heatmap, Wireframe, PCA). Selbstgeschriebene Skripte erlaubten den Datenzugriff und die grafische Ausgabe als z. B. Heatmaps. In der Entstehung dieser Arbeit sind weiterhin zwei weitere Visualisierungsformen von PCA-Daten entwickelt worden: Das Abstandsdiagramm und die animierte PCA. Beides sind hilfreiche Werkzeuge zur Interpretation von PCA-Plots eines zeitlichen Verlaufes. Anhand der Darstellungen der Element- und Ionendaten ließen sich die N{\"a}hrstoffmangelsituationen durch Abnahme der entsprechenden Totalelemente und Ionen nachweisen. Weiterhin sind starke {\"A}hnlichkeiten der durch RP-HPLC bestimmten Metaboliten unter Eisen-, Kalium und Magnesiummangel erkannt worden. Allerdings gibt es nur eine geringe Anzahl an Interkationen der Metabolitgehalte, da der Großteil der Metabolitlevel im Vergleich zur Kontrolle unver{\"a}ndert blieb. Der Literaturvergleich mit zwei Publikationen, die den Phosphat- und Schwefelmangel in Arabidopsis thaliana untersuchten, zeigte ein durchwachsenes Ergebnis. Einerseits gab es eine gleiche Tendenz der verglichenen Aminos{\"a}uren zu verzeichen, aber andererseits wiesen die Visualisierungen auch Gegens{\"a}tzlichkeiten auf. Der Vergleich der mit RP-HPLC und GC/TOF-MS gemessenen Metaboliten erbrachte ein sehr kontroverses Ergebnis. Zum einen wurden {\"U}bereinstimmungen der gleichen Metaboliten durch gemeinsame Cluster in den Heatmaps beobachtet, zum anderen auch Widerspr{\"u}che, exemplarisch in den Abstandsdiagrammen der Bl{\"a}tterdaten jedes Verfahrens, in welchen unterschiedliche Abstandsh{\"o}hepunkte erkennbar sind.},
  language  = {de}
}