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Molecular Signal Processing
Bioorganic Chemistry
Biochemistry of Plant Interactions
Cell and Metabolic Biology
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Publications
Publications - Cell and Metabolic Biology
Publications
Precise annotation of time and spatial distribution of enzymes involved in plant secondary metabolism by gel electrophoresis are usually difficult due to their low abundance. Therefore, effective methods to enrich these enzymes are required to correlate available transcript and metabolite data with the actual presence of active enzymes in wild-type and mutant plants or to monitor variations of these enzymes under various types of biotic and abiotic stress conditions. S-Adenosyl-L-methionine-dependent O-methyltransferases play important roles in the modification of natural products such as phenylpropanoids or alkaloids. In plants they occur as small superfamilies with defined roles for each of its members in different organs and tissues. We explored the use of S-adenosyl-L-homocysteine as a selectivity function in affinity-based protein profiling supported by capture compound mass spectrometry. Due to their high affinity to this ligand it was possible to identify developmental changes of flower-specific patterns of plant natural product O-methyltransferases and corroborate the absence of individual O-methyltransferases in the corresponding Arabidopsis knockout lines. Developmental changes in the OMT pattern were correlated with transcript data obtained by qPCR.
Books and chapters
Searching and mining nuclear magnetic resonance (NMR)-spectra of naturally occurring substances is an important task to investigate new potentially useful chemical compounds. Multi-dimensional NMR-spectra are relational objects like documents, but consists of continuous multi-dimensional points called peaks instead of words. We develop several mappings from continuous NMR-spectra to discrete text-like data. With the help of those mappings any text retrieval method can be applied. We evaluate the performance of two retrieval methods, namely the standard vector space model and probabilistic latent semantic indexing (PLSI). PLSI learns hidden topics in the data, which is in case of 2D-NMR data interesting in its owns rights. Additionally, we develop and evaluate a simple direct similarity function, which can detect duplicates of NMR-spectra. Our experiments show that the vector space model as well as PLSI, which are both designed for text data created by humans, can effectively handle the mapped NMR-data originating from natural products. Additionally, PLSI is able to find meaningful ”topics” in the NMR-data.
Books and chapters
Searching and mining nuclear magnetic resonance (NMR)-spectra of naturally occurring products is an important task to investigate new potentially useful chemical compounds. We develop a set-based similarity function, which, however, does not sufficiently capture more abstract aspects of similarity. NMR-spectra are like documents, but consists of continuous multi-dimensional points instead of words. Probabilistic semantic indexing (PLSI) is an retrieval method, which learns hidden topics. We develop several mappings from continuous NMR-spectra to discrete text-like data. The new mappings include redundancies into the discrete data, which proofs helpful for the PLSI-model used afterwards. Our experiments show that PLSI, which is designed for text data created by humans, can effectively handle the mapped NMR-data originating from natural products. Additionally, PLSI combined with the new mappings is able to find meaningful ”topics” in the NMR-data.
Publications
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Publications
In our studies on tyrosinase-catalyzed tyrosine hydroxylation, possibly involved in betalain biosynthesis, we have evaluated different assays for the detection and quantification of the enzymatic product Dopa with respect to sensitivity, simplicity, and suitability for automatization. A tyrosinase assay including reversed-phase high-performance liquid chromatography with isocratic elution and fluorescence detection has been developed (native fluorescence of Dopa; excitation at 281 nm, emission at 314 nm). This improved assay was sensitive (detection limit: 2 pmol Dopa) and showed a wide linear range of Dopa detection (10 pmol–20 nmol Dopa). The method proved to be suitable for high-performance liquid chromatography with an autosampler and has been applied for measuring tyrosinase activity of cell cultures and different tissues ofPortulaca grandiflora.
This page was last modified on 27 Jan 2025 .
