Publications of J. Kopka

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).

Sumner, L. W., Amberg, A., Barrett, D., Beale, M. H., Beger, R., Daykin, C. A., Fan, T. W. M., Fiehn, O., Goodacre, R., Griffin, J. L., Hankemeier, T., Hardy, N., Harnly, J., Higashi, R., Kopka, J., Lane, A. N., Lindon, J. C., Marriott, P., Nicholls, A. W., Reily, M. D., Thaden, J. J. & Viant, M. R. Proposed minimum reporting standards for chemical analysis. Metabolomics 3, 211–221 (2007).

Engelsberger, W. R., Erban, A., Kopka, J. & Schulze, W. X. Metabolic labeling of plant cell cultures with K(15)NO3 as a tool for quantitative analysis of proteins and metabolites. Plant Methods 2, 14 (2006).

Kopka, J. Current challenges and developments in GC-MS based metabolite profiling technology. Journal of Biotechnology 124, 312–322 (2006).

Lisec, J., Schauer, N., Kopka, J., Willmitzer, L. & Fernie, A. R. Gas chromatography mass spectrometry-based metabolite profiling in plants. Nature Protocols 1, 387–396 (2006).

Niehl, A., Lacomme, C., Erban, A., Kopka, J., Kraemer, U. & Fisahn, J. Systemic Potato virus X infection induces defence gene expression and accumulation of beta-phenylethylamine-alkaloids in potato. Functional Plant Biology 33, 593–604 (2006).

Schauer, N., Semel, Y., Roessner, U., Gur, A., Balbo, I., Carrari, F., Pleban, T., Perez-Melis, A., Bruedigam, C., Kopka, J., Willmitzer, L., Zamir, D. & Fernie, A. R. Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nature Biotechnology 24, 447–454 (2006).

Skirycz, A., Reichelt, M., Burow, M., Birkemeyer, C., Rolcik, J., Kopka, J., Zanor, M. I., Gershenzon, J., Strnad, M., Szopa, J., Mueller-Roeber, B. & Witt, I. DOF transcription factor AtDof1.1 (OBP2) is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis. Plant Journal 47, 10–24 (2006).

Damiani, I., Morreel, K., Danoun, S., Goeminne, G., Yahiaoui, N., Marque, C., Kopka, J., Messens, E., Goffner, D., Boerjan, W., Boudet, A. M. & Rochange, S. Metabolite profiling reveals a role for atypical cinnamyl alcohol dehydrogenase CAD1 in the synthesis of coniferyl alcohol in tobacco xylem. Plant Molecular Biology 59, 753–769 (2005).

Desbrosses, G. G., Kopka, J. & Udvardi, M. K. Lotus japonicus metabolic profiling. Development of gas chromatography-mass spectrometry resources for the study of plant-microbe interactions. Plant Physiology 137, 1302–1318 (2005).