@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}
}
@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}
}