• Our aim is to advance our understanding of biological systems,

    ranging from single species to multi-species systems and ecosystems,

    based on data from large-scale bioanalytical methods.

  • We develop, improve and apply

    computational methods

    for the interpretation of molecular information in biology.

  • We establish and analyse

    quantitative mathematical models.

CUBE News

  • FIRST RELEASE OF 45 PICA MODELS READY FOR DOWNLOAD

    12.06.17
    News

    The first release of 45 PICA models is available on this site in the Download area of our new website PhenDB. Brief instructions on the download page will enable you to install the PICA software and the models on a ...

  • Dr. rer. nat. Thomas Eder

    18.04.17
    Personal

    Thomas Eder has successfully defended his PhD thesis "Bioinformatic analysis of host-pathogen interactions in the light of second generation sequencing technologies". He was examined by Prof. Thomas Miethke, University of Heidelberg, Prof. Heinz Himmelbauer, BOKU University, and Prof. Arndt von Haeseler, ...

  • VarCap: a new method for genotyping of prokaryotic populations

    12.03.17
    Publication

    We created VarCap, a fully automated workflow that allows scientists to rapidly predict variants within high coverage, short read paired end sequencing data. VarCap automatically performs quality filtering, mapping, variant calling and post-filtering of the predicted variants. VarCap can be ...

  • New website for Virus Orthologous Groups (VOG)

    03.03.17
    News

    Along with the new release 80 of our Virus Orthologous Groups (VOG) we have launched a public webserver for VOGDB at http://vogdb.org. The server provides information about the VOG, interactive access to the data and a download area for ...

Latest publications

The desert plant Phoenix dactylifera closes stomata via nitrate-regulated SLAC1 anion channel.

Date palm Phoenix dactylifera is a desert crop well adapted to survive and produce fruits under extreme drought and heat. How are palms under such harsh environmental conditions able to limit transpirational water loss? Here, we analysed the cuticular waxes, stomata structure and function, and molecular biology of guard cells from P. dactylifera. To understand the stomatal response to the water stress phytohormone of the desert plant, we cloned the major elements necessary for guard cell fast abscisic acid (ABA) signalling and reconstituted this ABA signalosome in Xenopus oocytes. The PhoenixSLAC1-type anion channel is regulated by ABA kinase PdOST1. Energy-dispersive X-ray analysis (EDXA) demonstrated that date palm guard cells release chloride during stomatal closure. However, in Cl(-) medium, PdOST1 did not activate the desert plant anion channel PdSLAC1 per se. Only when nitrate was present at the extracellular face of the anion channel did the OST1-gated PdSLAC1 open, thus enabling chloride release. In the presence of nitrate, ABA enhanced and accelerated stomatal closure. Our findings indicate that, in date palm, the guard cell osmotic motor driving stomatal closure uses nitrate as the signal to open the major anion channel SLAC1. This initiates guard cell depolarization and the release of anions together with potassium.

Müller HM, Schäfer N, Bauer H, Geiger D, Lautner S, Fromm J, Riederer M, Bueno A, Nussbaumer T, Mayer K, Alquraishi SA, Alfarhan AH, Neher E, Al-Rasheid KAS, Ache P, Hedrich R
2017 - New Phytol., in press

Time-course expression QTL atlas of the global transcriptional response of wheat to Fusarium graminearum.

Fusarium head blight is a devastating disease of small grain cereals such as bread wheat (Triticum aestivum). The pathogen switches from a biotrophic to a nectrotrophic lifestyle in course of disease development forcing its host to adapt its defence strategies. Using a genetical genomics approach we illustrate genome-wide reconfigurations of genetic control over transcript abundances between two decisive time points after inoculation with the causative pathogen Fusarium graminearum. Whole transcriptome measurements have been recorded for 163 lines of a wheat doubled haploid population segregating for several resistance genes yielding 15 552 at 30 hours and 15 888 eQTL at 50 hours after inoculation. The genetic map saturated with transcript abundance-derived markers identified of a novel QTL on chromosome 6A, besides the previously reported QTL Fhb1 and Qfhs.ifa-5A. We find a highly different distribution of eQTL between time points with about 40% of eQTL being unique for the respective assessed time points. But also for more than 20% of genes governed by eQTL at either time point genetic control changes in time. These changes are reflected in the dynamic compositions of three major regulatory hotspots on chromosomes 2B, 4A and 5A. In particular control of defence-related biological mechanisms concentrated in the hotspot at 4A shift to hotspot 2B as the disease progresses. Hotspots do not colocalize with phenotypic QTL and within their intervals no higher than expected number of eQTL was detected. Thus, resistance conferred by either QTL is mediated by few or single genes. This article is protected by copyright. All rights reserved.

Samad-Zamini M, Schweiger W, Nussbaumer T, Mayer KF, Buerstmayr H
2017 - Plant Biotechnol. J., in press

Natural haplotypes of FLM non-coding sequences fine-tune flowering time in ambient spring temperatures in Arabidopsis.

Cool ambient temperatures are major cues determining flowering time in spring. The mechanisms promoting or delaying flowering in response to ambient temperature changes are only beginning to be understood. In Arabidopsis thaliana, FLOWERING LOCUS M (FLM) regulates flowering in the ambient temperature range and FLM is transcribed and alternatively spliced in a temperature-dependent manner. We identify polymorphic promoter and intronic sequences required for FLM expression and splicing. In transgenic experiments covering 69% of the available sequence variation in two distinct sites, we show that variation in the abundance of the FLM-ß splice form strictly correlate (R2 = 0.94) with flowering time over an extended vegetative period. The FLM polymorphisms lead to changes in FLM expression (PRO2+) but may also affect FLM intron 1 splicing (INT6+). This information could serve to buffer the anticipated negative effects on agricultural systems and flowering that may occur during climate change.

Lutz U, Nussbaumer T, Spannagl M, Diener J, Mayer KF, Schwechheimer C
2017 - Elife, in press

Lecture series

Advanced strategies for genome resolved metagenomics

Christian Sieber
University of Berkeley / DOE Joint Genome Institute
25.07.2017
11:00 h
Seminar room DOME 2.309; Althanstr. 14 UZA1, Level 2, Section 4)