A5011858960- Genomics and Phylogenetic Studies
- Plant Molecular Biology Research
- Plant nutrient uptake and metabolism
- Polysaccharides and Plant Cell Walls
- Plant Gene Expression Analysis
- Plant Stress Responses and Tolerance
- Photosynthetic Processes and Mechanisms
- Gene expression and cancer classification
- Genetic Mapping and Diversity in Plants and Animals
- Plant Disease Resistance and Genetics
- Plant Reproductive Biology
- Bioinformatics and Genomic Networks
- Biofuel production and bioconversion
- Microbial Metabolic Engineering and Bioproduction
- Plant biochemistry and biosynthesis
- Plant-Microbe Interactions and Immunity
- Plant Pathogens and Resistance
- Plant tissue culture and regeneration
- Biomedical Text Mining and Ontologies
- Chromosomal and Genetic Variations
- Wheat and Barley Genetics and Pathology
- Research Data Management Practices
- Scientific Computing and Data Management
- Metabolomics and Mass Spectrometry Studies
- Legume Nitrogen Fixing Symbiosis
Forschungszentrum Jülich
2016-2025
Cluster of Excellence on Plant Sciences
2020-2025
Heinrich Heine University Düsseldorf
2020-2025
Institut des Géosciences de l'Environnement
2023
RWTH Aachen University
2013-2022
Westfälische Hochschule
2020
University of York
2017
Czech Academy of Sciences, Institute of Botany
2016
Max Planck Institute of Molecular Plant Physiology
2006-2015
FH Aachen
2015
Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of that met our requirements in terms flexibility, correct handling paired-end data and high performance. We have developed Trimmomatic as a more flexible efficient tool, which correctly handle data.
Summary: Metabolomics, in particular gas chromatography–mass spectrometry (GC–MS) based metabolite profiling of biological extracts, is rapidly becoming one the cornerstones functional genomics and systems biology. Metabolite has profound applications discovering mode action drugs or herbicides, unravelling effect altered gene expression on metabolism organism performance biotechnological applications. As such technology needs to be available many laboratories. For this, an open exchange...
Recent rapid advances in next generation RNA sequencing (RNA-Seq)-based provide researchers with unprecedentedly large data sets and open new perspectives transcriptomics. Furthermore, RNA-Seq-based transcript profiling can be applied to non-model newly discovered organisms because it does not require a predefined measuring platform (like e.g. microarrays). However, these novel technologies pose challenges: the raw need rigorously quality checked filtered prior analysis, proper statistical...
Abstract The diurnal cycle strongly influences many plant metabolic and physiological processes. Arabidopsis thaliana rosettes were harvested six times during 12-h-light/12-h-dark treatments to investigate changes in gene expression using ATH1 arrays. Diagnostic sets identified from published or in-house profiles of the response light, sugar, nitrogen, water deficit seedlings 4 h darkness illumination at ambient compensation point [CO2]. Many sugar-responsive genes showed large changes,...
Affymetrix ATH1 arrays, large-scale real-time reverse transcription PCR of approximately 2200 factor genes and other gene families, analyses metabolites enzyme activities were used to investigate the response Arabidopsis phosphate (Pi) deprivation re-supply. Transcript data analysed with MapMan software identify coordinated, system-wide changes in metabolism cellular processes. Phosphorus (P) led induction or repression > 1000 involved many A subset, including P uptake, mobilization organic...
MapMan is a software tool that supports the visualization of profiling data sets in context existing knowledge. Scavenger modules generate hierarchical and essentially non-redundant gene ontologies ('mapping files'). An ImageAnnotator module visualizes on gene-by-gene basis schematic diagrams ('maps') biological processes. The PageMan uses same to statistically evaluate responses at pathway or processes level. generic structure also allows it be used for transcripts, proteins, enzymes...
Next-generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required to make these data amenable functional genomics analyses. The Mercator pipeline automatically assigns terms protein or nucleotide sequences. It uses the MapMan 'BIN' ontology, which is tailored for plant 'omics' classification procedure performs parallel searches against reference databases, compiles results and computes most likely BINs each query. In current version,...
Rising demand for food and bioenergy makes it imperative to breed increased crop yield. Vegetative plant growth could be driven by resource acquisition or developmental programs. Metabolite profiling in 94 Arabidopsis accessions revealed that biomass correlates negatively with many metabolites, especially starch. Starch accumulates the light is degraded at night provide a sustained supply of carbon growth. Multivariate analysis starch an integrator overall metabolic response. We hypothesized...
Tomato (Solanum lycopersicum) is a well-studied model of fleshy fruit development and ripening. well understood from hormonal-regulatory perspective, developmental changes in pigment cell wall metabolism are also characterized. However, more general aspects metabolic change during have not been studied despite the importance context final composition ripe fruit. In this study, we quantified abundance broad range metabolites by gas chromatography-mass spectrometry, analyzed number principal...
Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved thrive arid habitats. Because of its extreme stress tolerance and unusual morphology, an important donor germplasm for the cultivated lycopersicum. Introgression lines (ILs) which large genomic S. lycopersicum are replaced with corresponding segments from can show remarkably superior agronomic performance. Here we describe high-quality genome assembly parents IL population. By...
Significance One of the most important technological advances by humans is domestication plant species for production food. We have used high-throughput sequencing to identify changes in DNA sequence and gene expression that differentiate cultivated tomato its wild relatives. also hundreds candidate genes evolved new protein sequences or changed levels response natural selection Taken together, our analyses provide a snapshot genome evolution under artificial conditions.
Abstract The balance between the supply and utilization of carbon (C) changes continually. It has been proposed that plants respond in an acclimatory manner, modifying C to minimize harmful periods depletion. This hypothesis predicts signaling events are initiated by small status. We analyzed global transcriptional response a gradual depletion during night extension night, where becomes severely limiting from 4 h onward. was interpreted using published datasets for sugar, light, circadian...
Microarray technology has become a widely accepted and standardized tool in biology. The first microarray data analysis programs were developed to support pair-wise comparison. However, as experiments have more routine, large scale common, which investigate multiple time points or sets of mutants transgenics. To extract biological information from such high-throughput expression data, it is necessary develop efficient analytical platforms, combine manually curated gene ontologies with...
Abstract Background Genome-wide transcript profiling and analyses of enzyme activities from central carbon nitrogen metabolism show that levels undergo marked rapid changes during diurnal cycles after transfer to darkness, whereas in are smaller delayed. In the starchless pgm mutant, where sugars depleted every night, there accentuated levels. Enzyme this mutant do not larger changes; instead, they shift towards found wild type several days darkness. This indicates change slowly, integrating...
Abstract Tomato (Solanum lycopersicum) is an established model to study fleshy fruit development and ripening. ripening regulated independently cooperatively by ethylene transcription factors, including nonripening (NOR) ripening-inhibitor (RIN). Mutations of NOR, RIN, the receptor Never-ripe (Nr), which block perception inhibit ripening, have proven be great tools for advancing our understanding developmental programs regulating In this study, we present systems analysis nor, rin, Nr at...
The fungal pathogen Ustilago maydis establishes a biotrophic relationship with its host plant maize (Zea mays). Hallmarks of the disease are large tumours in which proliferation occurs. Previous studies suggested that classical defence pathways not activated. Confocal microscopy, global expression profiling and metabolic now shows U. is recognized early triggers responses. Many these response genes downregulated at later time points, whereas several associated suppression cell death induced....
Summary Arabidopsis seedlings were subjected to 2 days of carbon starvation, and then resupplied with 15 m sucrose. The transcriptional metabolic response was analyzed using ATH1 arrays, real‐time quantitative (q)RT‐PCR analysis >2000 transcription regulators, robotized assays enzymes from central metabolism metabolite profiling. Sucrose led within 30 min greater than threefold changes the transcript levels for >100 genes, including 20 ubiquitin‐targeting proteins, four trehalose...
Abstract The model organism Arabidopsis thaliana is readily used in basic research due to resource availability and relative speed of data acquisition. A major goal transfer acquired knowledge from crop species. However, the identification functional equivalents well-characterized genes other plants a nontrivial task. It well documented that transcriptionally coordinated tend be functionally related such relationships may conserved across different species even kingdoms. To exploit...
The extreme sensitivity of the microsporogenesis process to moderately high or low temperatures is a major hindrance for tomato (Solanum lycopersicum) sexual reproduction and hence year-round cropping. Consequently, breeding parthenocarpy, namely, fertilization-independent fruit set, considered valuable goal especially maintaining sustainable agriculture in face global warming. A mutant capable setting high-quality seedless (parthenocarpic) was found following screen EMS-mutagenized...
Article13 October 2009Open Access Ribosome and transcript copy numbers, polysome occupancy enzyme dynamics in Arabidopsis Maria Piques Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam-Golm, Germany Search for more papers by this author Waltraud X Schulze Melanie Höhne Björn Usadel Yves Gibon GermanyPresent address: INRA Bordeaux, University Bordeaux 1&2, UMR619 Fruit Biology, F-33883 Villenave d'Ornon, France Johann Rohwer Permanent Triple-J Group Cell Department...