@misc{NikoloskivanDongen2011,
  author    = {Nikoloski, Zoran and van Dongen, Joost T.},
  title     = {Modeling alternatives for interpreting the change in oxygen-consumption rates during hypoxic conditions},
  series = {New phytologist : international journal of plant science},
  volume    = {190},
  journal   = {New phytologist : international journal of plant science},
  number    = {2},
  publisher = {Wiley-Blackwell},
  address   = {Malden},
  issn      = {0028-646X},
  doi       = {10.1111/j.1469-8137.2011.03674.x},
  pages     = {273 -- 276},
  year      = {2011},
  language  = {en}
}
@article{GajdanowiczMichardSandmannetal.2011,
  author    = {Gajdanowicz, Pawel and Michard, Erwan and Sandmann, Michael and Rocha, Marcio and Correa, Luiz Gustavo Guedes and Ramirez-Aguilar, Santiago J. and Gomez-Porras, Judith L. and Gonzalez, Wendy and Thibaud, Jean-Baptiste and van Dongen, Joost T. and Dreyer, Ingo},
  title     = {Potassium (K plus ) gradients serve as a mobile energy source in plant vascular tissues},
  series = {Proceedings of the National Academy of Sciences of the United States of America},
  volume    = {108},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  number    = {2},
  publisher = {National Acad. of Sciences},
  address   = {Washington},
  issn      = {0027-8424},
  doi       = {10.1073/pnas.1009777108},
  pages     = {864 -- 869},
  year      = {2011},
  abstract  = {The essential mineral nutrient potassium (K(+)) is the most important inorganic cation for plants and is recognized as a limiting factor for crop yield and quality. Nonetheless, it is only partially understood how K(+) contributes to plant productivity. K(+) is used as a major active solute to maintain turgor and to drive irreversible and reversible changes in cell volume. K(+) also plays an important role in numerous metabolic processes, for example, by serving as an essential cofactor of enzymes. Here, we provide evidence for an additional, previously unrecognized role of K(+) in plant growth. By combining diverse experimental approaches with computational cell simulation, we show that K(+) circulating in the phloem serves as a decentralized energy storage that can be used to overcome local energy limitations. Posttranslational modification of the phloem-expressed Arabidopsis K(+) channel AKT2 taps this "potassium battery," which then efficiently assists the plasma membrane H(+)-ATPase in energizing the transmembrane phloem (re) loading processes.},
  language  = {en}
}
@article{HoehenwarterLarhlimiHummeletal.2011,
  author    = {H{\"o}henwarter, Wolfgang and Larhlimi, Abdelhalim and Hummel, Jan and Egelhofer, Volker and Selbig, Joachim and van Dongen, Joost T. and Wienkoop, Stefanie and Weckwerth, Wolfram},
  title     = {MAPA Distinguishes genotype-specific variability of highly similar regulatory protein isoforms in potato tuber},
  series = {Journal of proteome research},
  volume    = {10},
  journal   = {Journal of proteome research},
  number    = {7},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1535-3893},
  doi       = {10.1021/pr101109a},
  pages     = {2979 -- 2991},
  year      = {2011},
  abstract  = {Mass Accuracy Precursor Alignment is a fast and flexible method for comparative proteome analysis that allows the comparison of unprecedented numbers of shotgun proteomics analyses on a personal computer in a matter of hours. We compared 183 LC-MS analyses and more than 2 million MS/MS spectra and could define and separate the proteomic phenotypes of field grown tubers of 12 tetraploid cultivars of the crop plant Solanum tuberosum. Protein isoforms of patatin as well as other major gene families such as lipoxygenase and cysteine protease inhibitor that regulate tuber development were found to be the primary source of variability between the cultivars. This suggests that differentially expressed protein isoforms modulate genotype specific tuber development and the plant phenotype. We properly assigned the measured abundance of tryptic peptides to different protein isoforms that share extensive stretches of primary structure and thus inferred their abundance. Peptides unique to different protein isoforms were used to classify the remaining peptides assigned to the entire subset of isoforms based on a common abundance profile using multivariate statistical procedures. We identified nearly 4000,proteins which we used for quantitative functional annotation making this the most extensive study of the tuber proteome to date.},
  language  = {en}
}
@article{PaparelliGonzaliParlantietal.2012,
  author    = {Paparelli, Eleonora and Gonzali, Silvia and Parlanti, Sandro and Novi, Giacomo and Giorgi, Federico M. and Licausi, Francesco and Kosmacz, Monika and Feil, Regina and Lunn, John Edward and Brust, Henrike and van Dongen, Joost T. and Steup, Martin and Perata, Pierdomenico},
  title     = {Misexpression of a chloroplast aspartyl protease leads to severe growth defects and alters carbohydrate metabolism in arabidopsis},
  series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  volume    = {160},
  journal   = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants},
  number    = {3},
  publisher = {American Society of Plant Physiologists},
  address   = {Rockville},
  issn      = {0032-0889},
  doi       = {10.1104/pp.112.204016},
  pages     = {1237 -- 1250},
  year      = {2012},
  abstract  = {The crucial role of carbohydrate in plant growth and morphogenesis is widely recognized. In this study, we describe the characterization of nana, a dwarf Arabidopsis (Arabidopsis thaliana) mutant impaired in carbohydrate metabolism. We show that the nana dwarf phenotype was accompanied by altered leaf morphology and a delayed flowering time. Our genetic and molecular data indicate that the mutation in nana is due to a transfer DNA insertion in the promoter region of a gene encoding a chloroplast-located aspartyl protease that alters its pattern of expression. Overexpression of the gene (oxNANA) phenocopies the mutation. Both nana and oxNANA display alterations in carbohydrate content, and the extent of these changes varies depending on growth light intensity. In particular, in low light, soluble sugar levels are lower and do not show the daily fluctuations observed in wild-type plants. Moreover, nana and oxNANA are defective in the expression of some genes implicated in sugar metabolism and photosynthetic light harvesting. Interestingly, some chloroplast-encoded genes as well as genes whose products seem to be involved in retrograde signaling appear to be down-regulated. These findings suggest that the NANA aspartic protease has an important regulatory function in chloroplasts that not only influences photosynthetic carbon metabolism but also plastid and nuclear gene expression.},
  language  = {en}
}