Publications of J. Kopka

van Dongen, J. T., Frohlich, A., Ramirez-Aguilar, S. J., Schauer, N., Fernie, A. R., Erban, A., Kopka, J., Clark, J., Langer, A. & Geigenberger, P. Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of arabidopsis plants. Annals of Botany 103, 269–280 (2009).

Boettcher, C., Centeno, D., Freitag, J., Hoefgen, R., Koehl, K. I., Kopka, J., Kroymann, J., Matros, A., Mock, H.-P., Neumann, S., Pfalz, M., von Roepenack-Lahaye, E., Schauer, N., Trenkamp, S., Zurbriggen, M. & Fernie, A. R. Teaching (and learning from) metabolomics: The 2006 PlantMetaNet ETNA Metabolomics Research School. Physiologia Plantarum 132, 136–149 (2008).

Cartieaux, F., Contesto, C., Gallou, A., Desbrosses, G., Kopka, J., Taconnat, L., Renou, J. P. & Touraine, B. Simultaneous interaction of Arabidopsis thaliana with Bradyrhizobium sp strain ORS278 and Pseudomonas syriugae pv. tomato DC3000 leads to complex transcriptome changes. Molecular Plant-Microbe Interactions 21, 244–259 (2008).

Eisenhut, M., Huege, J., Schwarz, D., Bauwe, H., Kopka, J. & Hagemann, M. Metabolome Phenotyping of Inorganic Carbon Limitation in Cells of the Wild Type and Photorespiratory Mutants of the Cyanobacterium Synechocystis sp Strain PCC 6803. Plant Physiology 148, 2109–2120 (2008).

Hoehenwarter, W., van Dongen, J. T., Wienkoop, S., Steinfath, M., Hummel, J., Erban, A., Sulpice, R., Regierer, B., Kopka, J., Geigenberger, P. & Weckwerth, W. A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment. Proteomics 8, 4214–4225 (2008).

Kempa, S., Krasensky, J., Dal Santo, S., Kopka, J. & Jonak, C. A Central Role of Abscisic Acid in Stress-Regulated Carbohydrate Metabolism. PLoS One 3, e3935 (2008).

Levine, L. H., Kasahara, H., Kopka, J., Erban, A., Fehrle, I., Kaplan, F., Zhao, W., Littell, R. C., Guy, C., Wheeler, R., Sager, J., Mills, A. & Levine, H. G. Physiologic and metabolic responses of wheat seedlings to elevated and super-elevated carbon dioxide. Advances in Space Research 42, 1917–1928 (2008).

Lüdemann, A., Strassburg, K., Erban, A. & Kopka, J. TagFinder for the quantitative analysis of gas chromatography - mass spectrometry (GC-MS)-based metabolite profiling experiments. Bioinformatics 24, 732–737 (2008).

Sanchez, D. H., Lippold, F., Redestig, H., Hannah, M. A., Erban, A., Kraemer, U., Kopka, J. & Udvardi, M. K. Integrative functional genomics of salt acclimatization in the model legume Lotus japonicus. Plant Journal 53, 973–987 (2008).

Sanchez, D. H., Redestig, H., Kraemer, U., Udvardi, M. K. & Kopka, J. Metabolome-ionome-biomass interactions: What can we learn about salt stress by multiparallel phenotyping? Plant Signaling & Behavior 3, 598–600 (2008).

Strehmel, N., Hummel, J., Erban, A., Strassburg, K. & Kopka, J. Retention index thresholds for compound matching in GC-MS metabolite profiling. Journal of Chromatography B-Analytical Technologies in the Biomedical and Life Sciences 871, 182–190 (2008).

Dauwe, R., Morreel, K., Goeminne, G., Gielen, B., Rohde, A., van Beeumen, J., Ralph, J., Boudet, A. M., Kopka, J., Rochange, S. F., Halpin, C., Messens, E. & Boerjan, W. Molecular phenotyping of lignin-modified tobacco reveals associated changes in cell-wall metabolism, primary metabolism, stress metabolism and photorespiration. Plant Journal 52, 263–285 (2007).

Hannah, M. A., Kraemer, K. M., Geffroy, V., Kopka, J., Blair, M. W., Erban, A., Vallejos, C. E., Heyer, A. G., Sanders, F. E., Millner, P. A. & Pilbeam, D. J. Hybrid weakness controlled by the dosage-dependent lethal (DL) gene system in common bean (Phaseolus vulgaris) is caused by a shoot-derived inhibitory signal leading to salicylic acid-associated root death. New Phytologist 176, 537–549 (2007).

Hernandez, G., Ramirez, M., Valdes-Lopez, O., Tesfaye, M., Graham, M. A., Czechowski, T., Schlereth, A., Wandrey, M., Erban, A., Cheung, F., Wu, H. C., Lara, M., Town, C. D., Kopka, J., Udvardi, M. K. & Vance, C. P. Phosphorus stress in common bean: Root transcript and metabolic responses. Plant Physiology 144, 752–767 (2007).

Huege, J., Sulpice, R., Gibon, Y., Lisec, J., Koehl, K. I. & Kopka, J. GC-EI-TOF-MS analysis of in vivo carbon-partitioning into soluble metabolite pools of higher plants by monitoring isotope dilution after 13CO2 labelling. Phytochemistry 68, 2258–2272 (2007).

Kaplan, F., Kopka, J., Sung, D. Y., Zhao, W., Popp, M., Porat, R. & Guy, C. L. Transcript and metabolite profiling during cold acclimation of Arabidopsis reveals an intricate relationship of cold-regulated gene expression with modifications in metabolite content. Plant Journal 50, 967–981 (2007).

Kempa, S., Rozhon, W., Samaj, J., Erban, A., Baluska, F., Becker, T., Haselmayer, J., Schleiff, E., Kopka, J., Hirt, H. & Jonak, C. A plastid-localized glycogen synthase kinase 3 modulates stress tolerance and carbohydrate metabolism. Plant Journal 49, 1076–1090 (2007).

Leple, J. C., Dauwe, R., Morreel, K., Storme, V., Lapierre, C., Pollet, B., Naumann, A., Kang, K. Y., Kim, H., Ruel, K., Lefebvre, A., Joseleau, J. P., Grima-Pettenati, J., De Rycke, R., Andersson-Gunneras, S., Erban, A., Fehrle, I., Petit-Conil, M., Kopka, J., Polle, A., Messens, E., Sundberg, B., Mansfield, S. D., Ralph, J., Pilate, G. & Boerjan, W. Downregulation of cinnamoyl-coenzyme a reductase in poplar: multiple-level phenotyping reveals effects on cell wall polymer metabolism and structure. Plant Cell 19, 3669–3691 (2007).

Parveen, I., Moorby, J. M., Fraser, M. D., Allison, G. G. & Kopka, J. Application of gas chromatography-mass spectrometry metabolite profiling techniques to the analysis of heathland plant diets of sheep. Journal of Agricultural and Food Chemistry 55, 1129–1138 (2007).

Schaarschmidt, S., Kopka, J., Ludwig-Mueller, J. & Hause, B. Regulation of arbuscular mycorrhization by apoplastic invertases: enhanced invertase activity in the leaf apoplast affects the symbiotic interaction. Plant Journal 51, 390–405 (2007).