Unser 10. Leibniz Plant Biochemistry Symposium am 7. und 8. Mai war ein großer Erfolg. Thematisch ging es in diesem Jahr um neue Methoden und Forschungsansätze der Naturstoffchemie. Die exzellenten Vorträge über Wirkstoffe…
Omanische Heilpflanze im Fokus der Phytochemie IPB-Wissenschaftler und Partner aus Dhofar haben jüngst die omanische Heilpflanze Terminalia dhofarica unter die phytochemische Lupe genommen. Die Pflanze ist reich an…
Geschmack ist vorhersagbar: Mit FlavorMiner. FlavorMiner heißt das Tool, das IPB-Chemiker und Partner aus Kolumbien jüngst entwickelt haben. Das Programm kann, basierend auf maschinellem Lernen (KI), anhand der…
Results of scientific work in chemistry can usually be obtained in the form of materials and data. A big step towards transparency and reproducibility of the scientific work can be gained if scientists publish their data in research data repositories in a FAIR manner. Nevertheless, in order to make chemistry a sustainable discipline, obtaining FAIR data is insufficient and a comprehensive concept that includes preservation of materials is needed. In order to offer a comprehensive infrastructure to find and access data and materials that were generated in chemistry projects, we combined the infrastructure Chemotion repository with an archive for chemical compounds. Samples play a key role in this concept: we describe how FAIR metadata of a virtual sample representation can be used to refer to a physically available sample in a materials’ archive and to link it with the FAIR research data gained using the said sample. We further describe the measures to make the physically available samples not only FAIR through their metadata but also findable, accessible and reusable.
Publikation
Birschwilks, M.; Sauer, N.; Scheel, D.; Neumann, S.;Arabidopsis thaliana is a susceptible host plant for the holoparasite Cuscuta specPlanta2261231-1241(2007)DOI: 10.1007/s00425-007-0571-6
Arabidopsis thaliana and Cuscuta spec. represent a compatible host–parasite combination. Cuscuta produces a haustorium that penetrates the host tissue. In early stages of development the searching hyphae on the tip of the haustorial cone are connected to the host tissue by interspecific plasmodesmata. Ten days after infection, translocation of the fluorescent dyes, Texas Red (TR) and 5,6-carboxyfluorescein (CF), demonstrates the existence of a continuous connection between xylem and phloem of the host and parasite. Cuscuta becomes the dominant sink in this host–parasite system. Transgenic Arabidopsis plants expressing genes encoding the green fluorescent protein (GFP; 27 kDa) or a GFP–ubiquitin fusion (36 kDa), respectively, under the companion cell (CC)-specific AtSUC2 promoter were used to monitor the transfer of these proteins from the host sieve elements to those of Cuscuta. Although GFP is transferred unimpedly to the parasite, the GFP–ubiquitin fusion could not be detected in Cuscuta. A translocation of the GFP–ubiquitin fusion protein was found to be restricted to the phloem of the host, although a functional symplastic pathway exists between the host and parasite, as demonstrated by the transport of CF. These results indicate a peripheral size exclusion limit (SEL) between 27 and 36 kDa for the symplastic connections between host and Cuscuta sieve elements. Forty-six accessions of A.thaliana covering the entire range of its genetic diversity, as well as Arabidopsishalleri, were found to be susceptible towards Cuscutareflexa.
Publikation
Gaida, A.; Neumann, S.;MetHouse: Raw and Preprocessed Mass Spectrometry DataJ. Integr. Bioinformatics4107-114(2007)DOI: 10.1515/jib-2007-56
We are developing a vendor-independent archive and on top of that a data warehouse for mass spectrometry metabolomics data. The archive schema resembles the communitydeveloped object model, the Java implementation of the model classes, and an editor (for both mzData XML files and the database) have been generated using the Eclipse Modeling Framework. Persistence is handled by the JDO2 -compliant framework JPOX. The main content of the Data Warehouse are the results of the signal processing and peak-picking tasks, carried out using the XCMS package from Bioconductor, putative identification and mass decomposition are added to the warehouse afterwards.We present the system architecture, current content, performance observations and describe the analysis tools on top of the warehouse.Availability: http://msbi.ipb-halle.de/
Bücher und Buchkapitel
Tautenhahn, R.; Böttcher, C.; Neumann, S.;Annotation of LC/ESI-MS Mass SignalsLecture Notes in Computer Science4414371-380(2007)ISBN:978-3-540-71233-6DOI: 10.1007/978-3-540-71233-6_29
Mass spectrometry is the work-horse technology of the emerging field of metabolomics. The identification of mass signals remains the largest bottleneck for a non-targeted approach: due to the analytical method, each metabolite in a complex mixture will give rise to a number of mass signals. In contrast to GC/MS measurements, for soft ionisation methods such as ESI-MS there are no extensive libraries of reference spectra or established deconvolution methods. We present a set of annotation methods which aim to group together mass signals measured from a single metabolite, based on rules for mass differences and peak shape comparison.Availability: The software and documentation is available as an R package on http://msbi.ipb-halle.de/