Die Plant Science Student Conference (PSSC) wird seit 20 Jahren im jährlichen Wechsel von Studierenden der beiden Leibniz-Institute IPK und IPB organisiert. Im Interview erläutern Christina Wäsch (IPK) und Carolin Apel (IPB),…
Über 600 Gäste kamen am 4. Juli ans IPB zur Langen Nacht, die Wissen schafft, um bei unserem Wissenschafts-Quiz-Parcours viel Neues zu erfahren und ihre Kenntnisse unter Beweis zu stellen. Unser Programm in diesem Jahr…
Ried, M. K.; Banhara, A.; Hwu, F.-Y.; Binder, A.; Gust, A. A.; Höfle, C.; Hückelhoven, R.; Nürnberger, T.; Parniske, M.;A set of Arabidopsis genes involved in the accommodation of the downy mildew pathogen Hyaloperonospora arabidopsidisPLOS Pathog.15e1007747(2019)DOI: 10.1371/journal.ppat.1007747
The intracellular accommodation structures formed by plant cells to host arbuscular mycorrhiza fungi and biotrophic hyphal pathogens are cytologically similar. Therefore we investigated whether these interactions build on an overlapping genetic framework. In legumes, the malectin-like domain leucine-rich repeat receptor kinase SYMRK, the cation channel POLLUX and members of the nuclear pore NUP107-160 subcomplex are essential for symbiotic signal transduction and arbuscular mycorrhiza development. We identified members of these three groups in Arabidopsis thaliana and explored their impact on the interaction with the oomycete downy mildew pathogen Hyaloperonospora arabidopsidis (Hpa). We report that mutations in the corresponding genes reduced the reproductive success of Hpa as determined by sporangiophore and spore counts. We discovered that a developmental transition of haustorial shape occurred significantly earlier and at higher frequency in the mutants. Analysis of the multiplication of extracellular bacterial pathogens, Hpa-induced cell death or callose accumulation, as well as Hpa- or flg22-induced defence marker gene expression, did not reveal any traces of constitutive or exacerbated defence responses. These findings point towards an overlap between the plant genetic toolboxes involved in the interaction with biotrophic intracellular hyphal symbionts and pathogens in terms of the gene families involved.
Publikation
Emami Khoonsari, P.; Moreno, P.; Bergmann, S.; Burman, J.; Capuccini, M.; Carone, M.; Cascante, M.; de Atauri, P.; Foguet, C.; Gonzalez-Beltran, A. N.; Hankemeier, T.; Haug, K.; He, S.; Herman, S.; Johnson, D.; Kale, N.; Larsson, A.; Neumann, S.; Peters, K.; Pireddu, L.; Rocca-Serra, P.; Roger, P.; Rueedi, R.; Ruttkies, C.; Sadawi, N.; Salek, R. M.; Sansone, S.-A.; Schober, D.; Selivanov, V.; Thévenot, E. A.; van Vliet, M.; Zanetti, G.; Steinbeck, C.; Kultima, K.; Spjuth, O.;Interoperable and scalable data analysis with microservices: applications in metabolomicsBioinformatics353752-3760(2019)DOI: 10.1093/bioinformatics/btz160
MotivationDeveloping a robust and performant data analysis workflow that integrates all necessary components whilst still being able to scale over multiple compute nodes is a challenging task. We introduce a generic method based on the microservice architecture, where software tools are encapsulated as Docker containers that can be connected into scientific workflows and executed using the Kubernetes container orchestrator.ResultsWe developed a Virtual Research Environment (VRE) which facilitates rapid integration of new tools and developing scalable and interoperable workflows for performing metabolomics data analysis. The environment can be launched on-demand on cloud resources and desktop computers. IT-expertise requirements on the user side are kept to a minimum, and workflows can be re-used effortlessly by any novice user. We validate our method in the field of metabolomics on two mass spectrometry, one nuclear magnetic resonance spectroscopy and one fluxomics study. We showed that the method scales dynamically with increasing availability of computational resources. We demonstrated that the method facilitates interoperability using integration of the major software suites resulting in a turn-key workflow encompassing all steps for mass-spectrometry-based metabolomics including preprocessing, statistics and identification. Microservices is a generic methodology that can serve any scientific discipline and opens up for new types of large-scale integrative science.Availability and implementationThe PhenoMeNal consortium maintains a web portal (https://portal.phenomenal-h2020.eu) providing a GUI for launching the Virtual Research Environment. The GitHub repository https://github.com/phnmnl/ hosts the source code of all projects.