@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} } @misc{AstSchmaelzlinLoehmannsroebenetal.2012, author = {Ast, Cindy and Schm{\"a}lzlin, Elmar and L{\"o}hmannsr{\"o}ben, Hans-Gerd and van Dongen, Joost T.}, title = {Optical oxygen micro- and nanosensors for plant applications}, series = {Sensors}, volume = {12}, journal = {Sensors}, number = {6}, publisher = {MDPI}, address = {Basel}, issn = {1424-8220}, doi = {10.3390/s120607015}, pages = {7015 -- 7032}, year = {2012}, abstract = {Pioneered by Clark's microelectrode more than half a century ago, there has been substantial interest in developing new, miniaturized optical methods to detect molecular oxygen inside cells. While extensively used for animal tissue measurements, applications of intracellular optical oxygen biosensors are still scarce in plant science. A critical aspect is the strong autofluorescence of the green plant tissue that interferes with optical signals of commonly used oxygen probes. A recently developed dual-frequency phase modulation technique can overcome this limitation, offering new perspectives for plant research. This review gives an overview on the latest optical sensing techniques and methods based on phosphorescence quenching in diverse tissues and discusses the potential pitfalls for applications in plants. The most promising oxygen sensitive probes are reviewed plus different oxygen sensing structures ranging from micro-optodes to soluble nanoparticles. Moreover, the applicability of using heterologously expressed oxygen binding proteins and fluorescent proteins to determine changes in the cellular oxygen concentration are discussed as potential non-invasive cellular oxygen reporters.}, 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} } @article{ZabalzavanDongenFroehlichetal.2009, author = {Zabalza, Ana and van Dongen, Joost T. and Fr{\"o}hlich, Anja and Oliver, Sandra N. and Faix, Benjamin and Gupta, Kapuganti Jagadis and Schmalzlin, Elmar and Igal, Maria and Orcaray, Luis and Royuela, Mercedes and Geigenberger, Peter}, title = {Regulation of respiration and fermentation to control the plant internal oxygen concentration}, issn = {0032-0889}, doi = {10.1104/pp.108.129288}, year = {2009}, abstract = {Plant internal oxygen concentrations can drop well below ambient even when the plant grows under optimal conditions. Using pea (Pisum sativum) roots, we show how amenable respiration adapts to hypoxia to save oxygen when the oxygen availability decreases. The data cannot simply be explained by oxygen being limiting as substrate but indicate the existence of a regulatory mechanism, because the oxygen concentration at which the adaptive response is initiated is independent of the actual respiratory rate. Two phases can be discerned during the adaptive reaction: an initial linear decline of respiration is followed by a nonlinear inhibition in which the respiratory rate decreased progressively faster upon decreasing oxygen availability. In contrast to the cytochrome c pathway, the inhibition of the alternative oxidase pathway shows only the linear component of the adaptive response. Feeding pyruvate to the roots led to an increase of the oxygen consumption rate, which ultimately led to anoxia. The importance of balancing the in vivo pyruvate availability in the tissue was further investigated. Using various alcohol dehydrogenase knockout lines of Arabidopsis (Arabidopsis thaliana), it was shown that even under aerobic conditions, alcohol fermentation plays an important role in the control of the level of pyruvate in the tissue. Interestingly, alcohol fermentation appeared to be primarily induced by a drop in the energy status of the tissue rather than by a low oxygen concentration, indicating that sensing the energy status is an important component of optimizing plant metabolism to changes in the oxygen availability.}, language = {en} } @article{OliverLunnUrbanczykWochniaketal.2008, author = {Oliver, Sandra N. and Lunn, John Edward and Urbanczyk-Wochniak, Ewa and Lytovchenko, Anna and van Dongen, Joost T. and Faix, Benjamin and Schm{\"a}lzlin, Elmar and Fernie, Alisdair R. and Schm{\"a}elzlin, E. and Geigenberger, Peter}, title = {Decreased expression of cytosolic pyruvate kinase in potato tubers leads to a decline in pyruvate resulting in an in vivo repression of the alternative oxidase}, doi = {10.1104/pp.108.126516}, year = {2008}, abstract = {The aim of this work was to investigate the effect of decreased cytosolic pyruvate kinase (PKc) on potato (Solanum tuberosum) tuber metabolism. Transgenic potato plants with strongly reduced levels of PKc were generated by RNA interference gene silencing under the control of a tuber-specific promoter. Metabolite profiling showed that decreased PKc activity led to a decrease in the levels of pyruvate and some other organic acids involved in the tricarboxylic acid cycle. Flux analysis showed that this was accompanied by changes in carbon partitioning, with carbon flux being diverted from glycolysis toward starch synthesis. However, this metabolic shift was relatively small and hence did not result in enhanced starch levels in the tubers. Although total respiration rates and the ATP to ADP ratio were largely unchanged, transgenic tubers showed a strong decrease in the levels of alternative oxidase (AOX) protein and a corresponding decrease in the capacity of the alternative pathway of respiration. External feeding of pyruvate to tuber tissue or isolated mitochondria resulted in activation of the AOX pathway, both in the wild type and the PKc transgenic lines, providing direct evidence for the regulation of AOX by changes in pyruvate levels. Overall, these results provide evidence for a crucial role of PKc in the regulation of pyruvate levels as well as the level of the AOX in heterotrophic plant tissue, and furthermore reveal that these parameters are interlinked in vivo.}, language = {en} } @misc{LoehmannsroebenBeckHildebrandtetal.2006, author = {L{\"o}hmannsr{\"o}ben, Hans-Gerd and Beck, Michael and Hildebrandt, Niko and Schm{\"a}lzlin, Elmar and van Dongen, Joost T.}, title = {New challenges in biophotonics : laser-based fluoroimmuno analysis and in-vivo optical oxygen monitoring}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-10120}, year = {2006}, abstract = {Two examples of our biophotonic research utilizing nanoparticles are presented, namely laser-based fluoroimmuno analysis and in-vivo optical oxygen monitoring. Results of the work include significantly enhanced sensitivity of a homogeneous fluorescence immunoassay and markedly improved spatial resolution of oxygen gradients in root nodules of a legume species.}, subject = {Sauerstoff}, language = {en} }