A5026460206- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Photosynthetic Processes and Mechanisms
- Bioinformatics and Genomic Networks
- Algal biology and biofuel production
- Microbial Community Ecology and Physiology
- Enzyme Catalysis and Immobilization
- Biofuel production and bioconversion
- thermodynamics and calorimetric analyses
- Light effects on plants
- Marine and coastal ecosystems
- Evolution and Genetic Dynamics
- Metabolomics and Mass Spectrometry Studies
- Simulation Techniques and Applications
- Protein Structure and Dynamics
- Plant nutrient uptake and metabolism
- Computational Drug Discovery Methods
- Lipid metabolism and biosynthesis
- Plant biochemistry and biosynthesis
- Advanced Thermodynamics and Statistical Mechanics
- Photoreceptor and optogenetics research
- Genomics and Phylogenetic Studies
- Protist diversity and phylogeny
- Environmental DNA in Biodiversity Studies
- Gene expression and cancer classification
Cluster of Excellence on Plant Sciences
2016-2025
Heinrich Heine University Düsseldorf
2016-2025
University of Aberdeen
2009-2016
Institute for Complex Systems
2016
GFZ Helmholtz Centre for Geosciences
2013-2014
University of Potsdam
2008-2011
Humboldt-Universität zu Berlin
2001-2010
Max Planck Institute of Molecular Plant Physiology
2007-2010
University of North Carolina at Charlotte
2009
Max Planck Society
2008-2009
Abstract A vital quest in biology is comprehensible visualization and interpretation of correlation relationships on a genome scale. Such may be represented the form networks, which usually require disassembly into smaller manageable units, or clusters, to facilitate interpretation. Several graph-clustering algorithms that used visualize biological networks are available. However, only some these support weighted edges, none provides good control cluster sizes, crucial for large networks. We...
Abstract We present an integrated analysis of the molecular repertoire Chlamydomonas reinhardtii under reference conditions. Bioinformatics annotation methods combined with GCxGC/MS-based metabolomics and LC/MS-based shotgun proteomics profiling technologies have been applied to characterize abundant proteins metabolites, resulting in detection 1069 159 metabolites. Of measured proteins, 204 currently do not EST sequence support; thus a significant portion proteomics-detected provide...
Microbes have adapted to greatly variable environments in order survive both short-term perturbations and permanent changes. A classical yet still actively studied example of adaptation dynamic is the diauxic shift Escherichia coli, which cells grow on glucose until its exhaustion then transition using previously secreted acetate. Here we tested different hypotheses concerning nature this by metabolic modeling. To reach goal, developed an open source modeling framework integrating models...
A bstract Gene structural annotation is a critical step in obtaining biological knowledge from genome sequences yet remains major challenge genomics projects. Current de novo Hidden Markov Models are limited their capacity to model complexity; while current pipelines resource-intensive and results vary quality with the available extrinsic data. Here, we build on our previous work applying Deep Learning gene calling make fully applicable, fast user friendly tool for predicting primary models...
Summary Isoprenoid molecules are essential elements of plant metabolism. Many important isoprenoids, such as chlorophylls, carotenoids, tocopherols, prenylated quinones and hormones synthesised in chloroplasts via the 2‐ C ‐methyl‐ d ‐erythritol 4‐phosphate ( MEP ) pathway. Here we develop a mathematical model diurnal regulation pathway Arabidopsis thaliana . We used both experimental theoretical approaches to integrate mechanisms potentially involved control Our data show that flux through...
The Arctic Ocean is one of the regions where anthropogenic environmental change progressing most rapidly and drastically. impact rising temperatures decreasing sea ice on marine microbial communities yet not well understood. Microbes form basis food webs in Ocean, providing energy for larger organisms. Previous studies have shown that Atlantic taxa associated with low light are robust to more polar conditions. We compared which extent melt influences light-associated phytoplankton dynamics...
Genome-scale metabolic networks which have been automatically derived through sequence comparison techniques are necessarily incomplete. We propose a strategy that incorporates genomic data and metabolite profiles into modeling approaches to arrive at improved gene annotations more complete genome-scale networks. The core of our is an algorithm computes minimal sets reactions by draft network has be extended in order consistent with experimental observations. A particular strength approach...
In the light, photosynthesis provides carbon for metabolism and growth. dark, plant growth depends on reserves that were accumulated during previous light periods. Many plants accumulate part of their newly-fixed as starch in leaves day remobilise it to support at night. The daily rhythms accumulation degradation are dynamically adjusted changing conditions such is almost but not totally exhausted dawn. This requires allocation a larger proportion newly fixed under low conditions, use...
Photosynthetic eukaryotes house two photosystems with distinct light absorption spectra. Natural fluctuations in quality and quantity can lead to unbalanced or excess excitation, compromising photosynthetic efficiency causing photodamage. Consequently, these organisms have acquired several adaptive mechanisms, collectively referred as non-photochemical quenching (NPQ) of chlorophyll fluorescence, which modulates the organization function apparatus. The ability monitor NPQ processes...
Strigolactones are key regulators of plant development and interaction with symbiotic fungi; however, quantitative tools for strigolactone signaling analysis lacking. We introduce a genetically encoded hormone biosensor used to analyze strigolactone-mediated processes, including the study components involved in perception/signaling complex structural specificity sensitivity natural synthetic strigolactones Arabidopsis, providing insights into stereoselectivity perception. Given high...
Genome-scale metabolic network models can be used for various analyses including the prediction of responses to changes in environment. Legumes are well known their rhizobial symbiosis that introduces nitrogen into global nutrient cycle. Here, we describe a fully compartmentalised, mass and charge-balanced, genome-scale model clover Medicago truncatula, which has been adopted as organism legumes. We employed flux balance analysis demonstrate is capable producing biomass components...
Constraint-based metabolic models offer a scalable framework to investigate biological systems using optimality principles. Construction and simulation of detailed that utilize multiple kinds constraint poses significant coding overhead, complicating implementation new types analyses. We present an improved version the constraint-based modeling package COBREXA, which utilizes hierarchical model construction decouples implemented analysis algorithms into independent, yet re-combinable,...
Photorespiration causes a substantial decrease in crop yield because of mitochondrial decarboxylation. Alternative pathways (APs) have been designed to relocate the decarboxylation step or even fix additional carbon. To improve success transferring those engineered APs from model species crops, we must understand how they will interact with metabolism and plant physiology affects their performance. Here, used multiple mathematical modeling techniques analyze compare existing AP designs. We...
Plant diseases caused by pathogenic bacteria or fungi cause major economic damage every year and destroy crop yields that could feed millions of people. Only a thorough understanding the interaction between plants phytopathogens can we hope to develop strategies avoid treat outbreak large-scale pests. Here, studied plant-pathogen pairs at metabolic level. We selected five pairs, for which both genomes were fully sequenced, constructed corresponding genome-scale networks. present theoretical...
Plants are permanently exposed to rapidly changing environments, therefore it is evident that they had evolve mechanisms enabling them dynamically adapt such fluctuations. Here we study how plants can be trained enhance their photoprotection and elaborate on the concept of short-term illumination memory in Arabidopsis thaliana. By monitoring fluorescence emission dynamics systematically observe extent non-photochemical quenching (NPQ) after previous light exposure recognise quantify effect....
The photosynthetic electron transport chain (PETC) provides energy and redox equivalents for carbon fixation by the Calvin-Benson-Bassham (CBB) cycle. Both of these processes have been thoroughly investigated underlying molecular mechanisms are well known. However, it is far from understood which ensured that supply photosynthesis matches demand downstream processes. Here, we deliver a theoretical analysis to quantitatively study supply-demand regulation in photosynthesis. For this, connect...