@misc{ĆwiekKupczyńskaAltmannArendetal.2016,
  author    = {Ćwiek-Kupczyńska, Hanna and Altmann, Thomas and Arend, Daniel and Arnaud, Elizabeth and Chen, Dijun and Cornut, Guillaume and Fiorani, Fabio and Frohmberg, Wojciech and Junker, Astrid and Klukas, Christian and Lange, Matthias and Mazurek, Cezary and Nafissi, Anahita and Neveu, Pascal and van Oeveren, Jan and Pommier, Cyril and Poorter, Hendrik and Rocca-Serra, Philippe and Sansone, Susanna-Assunta and Scholz, Uwe and van Schriek, Marco and Seren, {\"U}mit and Usadel, Bj{\"o}rn and Weise, Stephan and Kersey, Paul and Krajewski, Paweł},
  title     = {Measures for interoperability of phenotypic data},
  series = {Plant methods},
  journal   = {Plant methods},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-407299},
  pages     = {18},
  year      = {2016},
  abstract  = {Background: Plant phenotypic data shrouds a wealth of information which, when accurately analysed and linked to other data types, brings to light the knowledge about the mechanisms of life. As phenotyping is a field of research comprising manifold, diverse and time ‑consuming experiments, the findings can be fostered by reusing and combin‑ ing existing datasets. Their correct interpretation, and thus replicability, comparability and interoperability, is possible provided that the collected observations are equipped with an adequate set of metadata. So far there have been no common standards governing phenotypic data description, which hampered data exchange and reuse. Results: In this paper we propose the guidelines for proper handling of the information about plant phenotyping experiments, in terms of both the recommended content of the description and its formatting. We provide a docu‑ ment called "Minimum Information About a Plant Phenotyping Experiment", which specifies what information about each experiment should be given, and a Phenotyping Configuration for the ISA ‑Tab format, which allows to practically organise this information within a dataset. We provide examples of ISA ‑Tab ‑formatted phenotypic data, and a general description of a few systems where the recommendations have been implemented. Conclusions: Acceptance of the rules described in this paper by the plant phenotyping community will help to achieve findable, accessible, interoperable and reusable data.},
  language  = {en}
}
@article{UsadelKuschinskyRossoetal.2004,
  author    = {Usadel, Bj{\"o}rn and Kuschinsky, Anja M. and Rosso, Mario G. and Eckermann, Nora and Pauly, Markus},
  title     = {RHM2 is involved in mucilage pectin synthesis and is required for the development of the seed coat in Arabidopsis},
  year      = {2004},
  abstract  = {Pectins are major components of primary plant cell walls and the seed mucilage of Arabidopsis. Despite progress in the structural elucidation of pectins, only very few enzymes participating in or regulating their synthesis have been identified. A first candidate gene involved-in the synthesis of pectinaceous rhamnogalacturonan I is RHM2, a putative plant ortholog to NDP-rhamnose biosynthetic enzymes in bacteria. Expression studies with a promoter beta-glucuronidase construct and reverse transcription PCR data show that RHM2 is expressed ubiquitously. Rhm2 T-DNA insertion mutant lines were identified using a reverse genetics approach. Analysis of the rhm2 seeds by various staining methods and chemical analysis of the mucilage revealed a strong reduction of rhamnogalacturonan I in the mucilage and a decrease of its molecular weight. In addition, scanning electron microscopy of the seed surface indicated a distorted testa morphology, illustrating not only a structural but also a developmental role for RGI or rhamnose metabolism in proper testa formation},
  language  = {en}
}
@phdthesis{Usadel2004,
  author    = {Usadel, Bj{\"o}rn},
  title     = {Untersuchungen zur Biosynthese der pflanzlichen Zellwand = [Identification and characterization of genes involved in plant cell wall synthesis]},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-2947},
  school      = {Universit{\"a}t Potsdam},
  year      = {2004},
  abstract  = {Even though the structure of the plant cell wall is by and large quite well characterized, its synthesis and regulation remains largely obscure. However, it is accepted that the building blocks of the polysaccharidic part of the plant cell wall are nucleotide sugars. Thus to gain more insight into the cell wall biosynthesis, in the first part of this thesis, plant genes possibly involved in the nucleotide sugar interconversion pathway were identified using a bioinformatics approach and characterized in plants, mainly in Arabidopsis. For the computational identification profile hidden markov models were extracted from the Pfam and TIGR databases. Mainly with these, plant genes were identified facilitating the "hmmer" program. Several gene families were identified and three were further characterized, the UDP-rhamnose synthase (RHM), UDP-glucuronic acid epimerase (GAE) and the myo-inositol oxygenase (MIOX) families. For the three-membered RHM family relative ubiquitous expression was shown using variuos methods. For one of these genes, RHM2, T-DNA lines could be obtained. Moreover, the transcription of the whole family was downregulated facilitating an RNAi approach. In both cases a alteration of cell wall typic polysaccharides and developmental changes could be shown. In the case of the rhm2 mutant these were restricted to the seed or the seed mucilage, whereas the RNAi plants showed profound changes in the whole plant. In the case of the six-membered GAE family, the gene expressed to the highest level (GAE6) was cloned, expressed heterologously and its function was characterized. Thus, it could be shown that GAE6 encodes for an enzyme responsible for the conversion of UDP-glucuronic acid to UDP-galacturonic acid. However, a change in transcript level of variuos GAE family members achieved by T-DNA insertions (gae2, gae5, gae6), overexpression (GAE6) or an RNAi approach, targeting the whole family, did not reveal any robust changes in the cell wall. Contrary to the other two families the MIOX gene family had to be identified using a BLAST based approach due to the lack of enough suitable candidate genes for building a hidden markov model. An initial bioinformatic characterization was performed which will lead to further insights into this pathway. In total it was possible to identify the two gene families which are involved in the synthesis of the two pectin backbone sugars galacturonic acid and rhamnose. Moreover with the identification of the MIOX genes a genefamily, important for the supply of nucleotide sugar precursors was identified. In a second part of this thesis publicly available microarray datasets were analyzed with respect to co-responsive behavior of transcripts on a global basis using nearly 10,000 genes. The data has been made available to the community in form of a database providing additional statistical and visualization tools (http://csbdb.mpimp-golm.mpg.de). Using the framework of the database to identify nucleotide sugar converting genes indicated that co-response might be used for identification of novel genes involved in cell wall synthesis based on already known genes.},
  subject      = {Zellwand},
  language  = {en}
}
@article{SulpicePylIshiharaetal.2009,
  author    = {Sulpice, Ronan and Pyl, Eva-Theresa and Ishihara, Hirofumi and Trenkamp, Sandra and Steinfath, Matthias and Witucka-Wall, Hanna and Gibon, Yves and Usadel, Bj{\"o}rn and Poree, Fabien and Piques, Maria Conceicao and von Korff, Maria and Steinhauser, Marie Caroline and Keurentjes, Joost J. B. and Guenther, Manuela and Hoehne, Melanie and Selbig, Joachim and Fernie, Alisdair R. and Altmann, Thomas and Stitt, Mark},
  title     = {Starch as a major integrator in the regulation of plant growth},
  issn      = {0027-8424},
  doi       = {10.1073/pnas.0903478106},
  year      = {2009},
  abstract  = {Rising demand for food and bioenergy makes it imperative to breed for increased crop yield. Vegetative plant growth could be driven by resource acquisition or developmental programs. Metabolite profiling in 94 Arabidopsis accessions revealed that biomass correlates negatively with many metabolites, especially starch. Starch accumulates in the light and is degraded at night to provide a sustained supply of carbon for growth. Multivariate analysis revealed that starch is an integrator of the overall metabolic response. We hypothesized that this reflects variation in a regulatory network that balances growth with the carbon supply. Transcript profiling in 21 accessions revealed coordinated changes of transcripts of more than 70 carbon-regulated genes and identified 2 genes (myo-inositol-1- phosphate synthase, a Kelch-domain protein) whose transcripts correlate with biomass. The impact of allelic variation at these 2 loci was shown by association mapping, identifying them as candidate lead genes with the potential to increase biomass production.},
  language  = {en}
}
@article{RyngajlloChildsLohseetal.2011,
  author    = {Ryngajllo, Malgorzata and Childs, Liam H. and Lohse, Marc and Giorgi, Federico M. and Lude, Anja and Selbig, Joachim and Usadel, Bj{\"o}rn},
  title     = {SLocX predicting subcellular localization of Arabidopsis proteins leveraging gene expression data},
  series = {Frontiers in plant science},
  volume    = {2},
  journal   = {Frontiers in plant science},
  publisher = {Frontiers Research Foundation},
  address   = {Lausanne},
  issn      = {1664-462X},
  doi       = {10.3389/fpls.2011.00043},
  pages     = {19},
  year      = {2011},
  abstract  = {Despite the growing volume of experimentally validated knowledge about the subcellular localization of plant proteins, a well performing in silico prediction tool is still a necessity. Existing tools, which employ information derived from protein sequence alone, offer limited accuracy and/or rely on full sequence availability. We explored whether gene expression profiling data can be harnessed to enhance prediction performance. To achieve this, we trained several support vector machines to predict the subcellular localization of Arabidopsis thaliana proteins using sequence derived information, expression behavior, or a combination of these data and compared their predictive performance through a cross-validation test. We show that gene expression carries information about the subcellular localization not available in sequence information, yielding dramatic benefits for plastid localization prediction, and some notable improvements for other compartments such as the mito-chondrion, the Golgi, and the plasma membrane. Based on these results, we constructed a novel subcellular localization prediction engine, SLocX, combining gene expression profiling data with protein sequence-based information. We then validated the results of this engine using an independent test set of annotated proteins and a transient expression of GFP fusion proteins. Here, we present the prediction framework and a website of predicted localizations for Arabidopsis. The relatively good accuracy of our prediction engine, even in cases where only partial protein sequence is available (e.g., in sequences lacking the N-terminal region), offers a promising opportunity for similar application to non-sequenced or poorly annotated plant species. Although the prediction scope of our method is currently limited by the availability of expression information on the ATH1 array, we believe that the advances in measuring gene expression technology will make our method applicable for all Arabidopsis proteins.},
  language  = {en}
}
@article{ObelUsadelChooetal.2004,
  author    = {Obel, Nicolai and Usadel, Bj{\"o}rn and Choo, Tze Siang and Pauly, Markus},
  title     = {Analysing cell wall biosynthesis to study its role in biotic and abiotic stress reactions},
  isbn      = {3-00-011587-0},
  year      = {2004},
  language  = {en}
}
@article{LicausiGiorgiSchmaelzlinetal.2011,
  author    = {Licausi, Francesco and Giorgi, Federico Manuel and Schmaelzlin, Elmar and Usadel, Bj{\"o}rn and Perata, Pierdomenico and van Dongen, Joost Thomas and Geigenberger, Peter},
  title     = {HRE-Type Genes are regulated by Growth-Related Changes in internal Oxygen Concentrations During the normal development of Potato (Solanum tuberosum) Tubers},
  series = {Plant \& cell physiology},
  volume    = {52},
  journal   = {Plant \& cell physiology},
  number    = {11},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0032-0781},
  doi       = {10.1093/pcp/pcr128},
  pages     = {1957 -- 1972},
  year      = {2011},
  abstract  = {The occurrence of hypoxic conditions in plants not only represents a stress condition but is also associated with the normal development and growth of many organs, leading to adaptive changes in metabolism and growth to prevent internal anoxia. Internal oxygen concentrations decrease inside growing potato tubers, due to their active metabolism and increased resistance to gas diffusion as tubers grow. In the present work, we identified three hypoxia-responsive ERF (StHRE) genes whose expression is regulated by the gradual decrease in oxygen tensions that occur when potato tubers grow larger. Increasing the external oxygen concentration counteracted the modification of StHRE expression during tuber growth, supporting the idea that the actual oxygen levels inside the organs, rather than development itself, are responsible for the regulation of StHRE genes. We identified several sugar metabolism-related genes co-regulated with StHRE genes during tuber development and possibly involved in starch accumulation. All together, our data suggest a possible role for low oxygen in the regulation of sugar metabolism in the potato tuber, similar to what happens in storage tissues during seed development.},
  language  = {en}
}