Ewa Urbanczyk-Wochniak
Postdoctoral Fellow
Joined the Noble Foundation in April 2005

The recently developed methods allow the nonbiased, simultaneous, and rapid determination of metabolites in plants, using different species as an experimental system. My primary interest is focused on the development and application of high spatial and anatomically resolved metabolomics data. This includes spatially resolved tissues, which are analyzed using multiple metabolite profiling techniques recently developed and under construction by our team. The goal of these efforts is a better comprehension of spatially resolved biochemical processes.

 The technical advance of high-throughput techniques provides the opportunity to generate complementary transcriptomic, metabolic, and proteomic datasets, which allow a detailed insight into plant systems, but generate a huge amount of profiling data. I am also involved in developing bioinformatics tools specifically designed for Medicago truncatula, which is a combination of biological pre-knowledge, data visualization, and bioinformatics solutions, which help the interpretation process by an individual researcher. Specific Medicago biochemical pathways (MediCyc) were computationally predicted for available sequences using MetaCyc reference database. MediCyc is  crated using the Pathway Tools software developed by Peter Karp's group at  SRI. The manual curation of the database, including correcting pathways and adding missing pathways, is on-going.

So far I have been concentrating mainly on primary metabolism (mostly carbohydrate and amino acids pathways), so now I would like to broaden my understanding on how the changes in primary metabolism regulate the secondary processes - especially at the level of different metabolites - with consequences for important natural products. Focusing on that topic could give more comprehensive insight into the functional aspects of plant metabolism regulation in general.  For my MSc and PhD theses at the Warsaw Agricultural University in Poland I investigated mainly the flower development process using cucumber as a model plant, concentrating in particular on sex differentiation, while mastering the RT-PCR technique. Then I joined the Max Planck Institute of Molecular Plant Physiology in Germany, where during my post-doctoral fellowship under Prof. Lothar Willmitzer & Dr. Alisdair Fernie supervision I studied the response of plant metabolism to different genetic or environmental alterations at the transcript and metabolite levels.

 Publications
1. Urbanczyk-Wochniak E., Usadel B., Thimm O., Nunes-Nesi A., Carrari F., Davey M., Blaesing O., Kowalczyk M., Weicht D., Polinceusz A., Meyer S., Stitt M., and Fernie A.R. (2006) Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: effects of genetic and environmental alterations in energy metabolism in the leaf. Plant Molecular Biology (in press).
2. Clément B., Pollmann S., Weiler E., Urbanczyk-Wochniak E., Otten L. (2006) The Agrobacterium vitis T-6b oncoprotein induces auxin-independent cell expansion in tobacco. Plant J. (in press).
3. Geigenberger P., Regierer B., Nunes-Nesi A., Leisse A., Urbanczyk-Wochniak E., Springer F., van Dongen J.T., Kossmann J., Fernie A.R. (2005) Inhibition of de novo pyrimidine synthesis in growing potato tubers leads to a compensatory stimulation of the pyrimidine salvage pathway and a subsequent increase in biosynthetic performance. Plant Cell 17: 2077-2088.
4. Davies H.V., Shepherd L.V.T., Burrell M.M., Carrari F., Urbanczyk-Wochniak E., Leisse A., Hancock R.D., Taylor M., Viola R., Ross H., McRae D., Willmitzer L., Fernie A.R. (2005) Modulation of fructokinase activity of potato (Solanum tuberosum) results in substantial shifts in tuber metabolism. Plant Cell Physiol. 46: 1103-1115.
5. Urbanczyk-Wochniak E., Baxter C., Kolbe A., Kopka J., Sweetlove L. J., Fernie A. R. (2005) Profiling of diurnal patterns of metabolite and transcript abundance in potato leaves reveals specific set of metabolic pathways are transcriptionally regulated, but suggests that the majority of the metabolic network is under post-transcriptional control. Planta 221: 891 - 903
6. Urbanczyk-Wochniak E., Fernie A. R. (2005) Metabolic profiling reveals altered nitrogen nutrient regimes have diverse effects on the metabolism of hydroponically-grown tomato (Lycopersicon esculentum) plants. J Exp Bot. 56: 309-321.
7. Urbanczyk-Wochniak E., Luedemann A., Kopka J., Selbig J., Roessner-Tunali U., Willmitzer L., Fernie A.R. (2003) Parallel analysis of transcript and metabolic profiles: a new approach in systems biology.  EMBO Rep. 4: 989-993.
8. Urbanczyk-Wochniak E., Leisse A., Roessner-Tunali U., Lytovchenko A., Reismeier J., Willmitzer L., Fernie A.R. (2003) Expression of a bacterial xylose isomerase in potato tubers results in an altered hexose composition and a consequent induction of metabolism. Plant Cell Physio. 44: 1359-1367.
9. Roessner-Tunali U., Urbanczyk-Wochniak E., Czechowski T., Kolbe A,. Willmitzer L., Fernie A.R. (2003) De novo amino acid biosynthesis in potato tubers is regulated by sucrose levels. Plant Physiol. 133: 683-692.
10. Przybecki Z., Kowalczyk M.E., Siedlecka E., Urbanczyk-Wochniak E., Malepszy S. (2003) The isolation of cDNA clones from cucumber (Cucumis sativus L.) floral buds coming from plants differing in sex.  Cell Mol Biol Lett. 8: 421-438.
11. Witkowicz J., Urbanczyk-Wochniak E., Przybecki Z. (2003) AFLP marker polymorphism in cucumber (Cucumis sativus L.) near isogenic lines differing in sex expression. Cell Mol Biol Lett. 8: 857-857.
12. Carrari F., Urbanczyk-Wochniak E., Willmitzer L., Fernie A.R. (2003) Engineering central metabolism in crop species: learning the system. Metab Eng.  5: 191-200
13. Urbanczyk-Wochniak E., Filipecki M., Przybecki Z .(2002) A useful protocol for in situ RT-PCR on plant tissues. Cell Mol Biol Lett.7: 7-18.
14. Urbanczyk-Wochniak E., Przybecki Z. (2001) The role of MADS-box genes in flower morphogenesis. Acta Physiologiae Plantarum 23: 241-253.