Oliver Ebenhöh

Oliver Ebenhöh
Heinrich-Heine-Universität Düsseldorf | HHU · Department of Biology

PhD

About

167
Publications
30,738
Reads
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2,443
Citations
Citations since 2017
63 Research Items
1356 Citations
2017201820192020202120222023050100150200250
2017201820192020202120222023050100150200250
2017201820192020202120222023050100150200250
2017201820192020202120222023050100150200250
Additional affiliations
December 2013 - present
Heinrich-Heine-Universität Düsseldorf
Position
  • Junior Professor
July 2013 - December 2013
Helmholtz-Zentrum Potsdam - Deutsches GeoForschungsZentrum GFZ
Position
  • Senior Researcher
August 2009 - present
University of Aberdeen
Position
  • Professor (Full)

Publications

Publications (167)
Article
Full-text available
In cyanobacteria DNA supercoiling varies over the diurnal cycle and is integrated with temporal programs of transcription and replication. We manipulated DNA supercoiling in Synechocystis sp. PCC 6803 by CRISPRi-based knockdown of gyrase subunits and overexpression of topoisomerase I (TopoI). Cell division was blocked but cell growth continued in a...
Preprint
Full-text available
Plants use light energy to produce ATP and redox equivalents for metabolism. Since during the course of a day plants are exposed to constantly fluctuating light, the supply of ATP and redox equivalents is also fluctuating. Further, if the metabolism cannot use all of the supplied energy, the excess absorbed energy can damage the plant in the form o...
Preprint
Full-text available
In humans, glycogen storage diseases result from metabolic inborn errors, and can lead to severe phenotypes and lethal conditions. Besides these rare diseases, glycogen is also associated to widely spread societal burdens such as diabetes. Glycogen is a branched glucose polymer synthesised and degraded by a complex set of enzymes. Over the past 50...
Preprint
The physiology of biological cells evolved under physical and chemical constraints such as mass conservation, nonlinear reaction kinetics, and limits on cell density. For unicellular organisms, the fitness that governs this evolution is mainly determined by the balanced cellular growth rate. We previously introduced Growth Balance Analysis (GBA) as...
Preprint
Full-text available
The synthesis and modification of fatty acids from carbohydrates are paramount for the production of lipids. Simultaneously, lipids are pivotal energy storage in human health. They are associated with various metabolic diseases and their production pathways are for instance candidate therapeutic targets for cancer treatments. The fatty acid de novo...
Article
Full-text available
Multiomics approaches need to be applied in the central Arctic Ocean to benchmark biodiversity change and to identify novel species and their genes. As part of MOSAiC, EcoOmics will therefore be essential for conservation and sustainable bioprospecting in one of the least explored ecosystems on Earth.
Preprint
Full-text available
Several commercially important secondary metabolites are produced and accumulated in high amounts by glandular trichomes (GTs), giving the prospect of exploiting trichomes as metabolic cell factories. Due to extremely high metabolic fluxes through GT particular attention was drawn to how they are achieved. The question regarding bioenergetics of th...
Article
Metabolic models are typically characterized by a large number of parameters. Traditionally, metabolic control analysis is applied to differential equation-based models to investigate the sensitivity of predictions to parameters. A corresponding theory for constraint-based models is lacking, due to their formulation as optimization problems. Here,...
Preprint
Metabolic models are typically characterized by a large number of parameters. Traditionally, metabolic control analysis is applied to differential equation-based models to investigate the sensitivity of predictions to parameters. A corresponding theory for constraint-based models is lacking, due to their formulation as optimization problems. Here,...
Preprint
Full-text available
Synthetic biology designs and constructs new biological parts, devices and systems with predetermined functionalities. With the unlimited ability to synthesise any DNA and RNA and transfer it to almost any organism, we are at the dawn of a new era in which biology is being recreated in ways never before possible. It has reached a maturity level tha...
Article
Mathematical modeling of metabolic networks is a powerful approach to investigate the underlying principles of metabolism and growth. Such approaches include, among others, differential-equation-based modeling of metabolic systems, constraint-based modeling and metabolic network expansion of metabolic networks. Most of these methods are well establ...
Article
Full-text available
COBREXA.jl is a Julia package for scalable, high-performance constraint-based reconstruction and analysis of very large-scale biological models. Its primary purpose is to facilitate the integration of modern high performance computing environments with the processing and analysis of large-scale metabolic models of challenging complexity. We report...
Article
Full-text available
During photosynthesis, organisms respond to their energy demand and ensure the supply of energy and redox equivalents that sustain metabolism. Hence, the photosynthetic apparatus can, and in fact should, be treated as an integrated supply-demand system. Any imbalance in the energy produced and consumed can lead to adverse reactions, such as the pro...
Preprint
Full-text available
In cyanobacteria DNA supercoiling varies over the diurnal light/dark cycle and is integrated with temporal programs of transcription and replication. We manipulated DNA supercoiling in Synechocystis sp. PCC 6803 by CRISPRi-based knock-down of gyrase subunits and overexpression of topoisomerase I, and characterized the phenotypes. Cell division was...
Article
Full-text available
The application of thermodynamics to microbial growth has a long tradition that originated in the middle of the 20th century. This approach reflects the view that self-replication is a thermodynamic process that is not fundamentally different from mechanical thermodynamics. The key distinction is that a free energy gradient is not converted into me...
Preprint
Full-text available
COBREXA.jl is a Julia package for scalable, high-performance constraint-based reconstruction and analysis of very large-scale biological models. Its primary purpose is to facilitate the integration of modern high performance computing environments with the processing and analysis of large-scale metabolic models of challenging complexity. We report...
Preprint
Full-text available
Chlorophyll a fluorescence is a powerful indicator of photosynthetic energy conversion in plants and photosynthetic microorganisms. One of the most widely used measurement techniques is Pulse Amplitude Modulation (PAM) fluorometry. Unfortunately, parameter settings of PAM instruments are often not completely described in scientific articles althoug...
Article
Full-text available
Background Computational mathematical models of biological and biomedical systems have been successfully applied to advance our understanding of various regulatory processes, metabolic fluxes, effects of drug therapies, and disease evolution and transmission. Unfortunately, despite community efforts leading to the development of SBML and the BioMod...
Preprint
Full-text available
The application of thermodynamics to microbial growth has a long tradition that originated in the middle of the 20 th century. This approach reflects the view that self-replication is a thermodynamic process that is not fundamentally different from mechanical thermodynamics. The key distinction is that a free energy gradient is not converted into m...
Article
Full-text available
Today massive amounts of sequenced metagenomic and metatranscriptomic data from different ecological niches and environmental locations are available. Scientific progress depends critically on methods that allow extracting useful information from the various types of sequence data. Here, we will first discuss types of information contained in the v...
Preprint
Full-text available
Background Mathematical modeling of metabolic networks is a powerful approach to investigate the underlying principles of metabolism and growth. Such approaches include, amongst others, differential equations based modeling of metabolic systems, constraint based modeling and topological analysis of metabolic networks. Most of these methods are well...
Article
Full-text available
One contribution of 17 to a theme issue 'Integrative research perspectives on marine conservation'. Today massive amounts of sequenced metagenomic and metatranscriptomic data from different ecological niches and environmental locations are available. Scientific progress depends critically on methods that allow extracting useful information from th...
Preprint
Full-text available
Background Computational mathematical models of biological and biomedical systems have been successfully applied to advance our understanding of various regulatory processes, metabolic fluxes, effects of drug therapies and disease evolution or transmission. Unfortunately, despite community efforts leading to the development of SBML or the BioModels...
Article
Full-text available
Starch, a plant-derived insoluble carbohydrate composed of glucose polymers, is the principal carbohydrate in our diet and a valuable raw material for industry. The properties of starch depend on the arrangement of glucose units within the constituent polymers. However, key aspects of starch structure and the underlying biosynthetic processes are n...
Article
Full-text available
Understanding microbial growth with the use of mathematical models has a long history that dates back to the pioneering work of Jacques Monod in the 1940s. Monod’s famous growth law expressed microbial growth rate as a simple function of the limiting nutrient concentration. However, to explain growth laws from underlying principles is extremely cha...
Preprint
Full-text available
To understand microbial growth with mathematical models has a long tradition that dates back to the pioneering work of Jacques Monod in the 1940s. Growth laws are simple mathematical expressions that aim at describing growth rates of microbes as functions of external parameters, in particular nutrient concentrations. These laws are now widely appli...
Preprint
Today massive amounts of sequenced metagenomic and -transcriptomic data from different ecological niches and environmental locations are available. Scientific progress depends critically on methods that allow extracting useful information from the various types of sequence data. Here, we will first discuss types of information contained in the vari...
Article
Full-text available
The Q-cycle mechanism entering the electron and proton transport chain in oxygenic photosynthesis is an example of how biological processes can be efficiently investigated with elementary microscopic models. Here we address the problem of energy transport across the cellular membrane from an open quantum system theoretical perspective. We model the...
Preprint
Full-text available
Glucosinolates are a fascinating class of specialised metabolites found in the plants of Brassicacea family. The variation in glucosinolate composition across different Arabidopsis ecotypes could be a result of allelic compositions at different biosynthetic loci. The contribution of methylthioalkylmalate synthase (MAM) genes to diversity of glucosi...
Article
Full-text available
A device that counts and records the number of events experienced by an individual cell could have many uses in experimental biology and biotechnology. Here, we report a DNA-based 'latch' that switches between two states upon each exposure to a repeated stimulus. The key component of the latch is a DNA segment whose orientation is inverted by the a...
Article
Full-text available
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 and the underlying molecular mechanisms are well known. However, it is far from understood by which mechanisms it is ensured that energy and...
Article
Full-text available
Escherichia coli diauxie is a fundamental example of metabolic adaptation, a phenomenon that is not yet completely understood. Further insight into this process can be achieved by integrating experimental and computational modeling methods. We present a dynamic metabolic modeling approach that captures diauxie as an emergent property of subpopulati...
Preprint
Full-text available
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 and the underlying molecular mechanisms are well known. However, it is far from understood by which mechanisms it is ensured that energy and...
Article
Full-text available
The modelbase package is a free expandable Python package for building and analysing dynamic mathematical models of biological systems. Originally it was designed for the simulation of metabolic systems, but it can be used for virtually any deterministic chemical processes. modelbase provides easy construction methods to define reactions and their...
Preprint
Full-text available
Microbes have adapted to greatly variable environments in order to survive both short-term perturbations and permanent changes. A classical, yet still actively studied example of adaptation to dynamic environments is the diauxic shift of Escherichia coli , in which cells grow on glucose until its exhaustion, and then transition to using previously...
Article
Full-text available
Algae are capable of accumulating nutrients from aqueous waste, which makes them a potential fertilizer. The ability of the fast growing Chlorella vulgaris strain IPPAS C1 to accumulate phosphorus (P) was probed in V-shaped plastic foil photobioreactors. The P uptake was 0.13–0.53 g(P)·m⁻²·day⁻¹ when the algal culture densities were kept between 0....
Article
Full-text available
Genome-scale metabolic network models can be used for various analyses including the prediction of metabolic responses to changes in the environment. Legumes are well known for their rhizobial symbiosis that introduces nitrogen into the global nutrient cycle. Here, we describe a fully compartmentalised, mass and charge-balanced, genome-scale model...
Preprint
The Q-cycle mechanism entering the electron and proton transport chain in oxygenic photosynthesis is a paradigmatic example of how biological processes can be efficiently investigated with elementary microscopic models. Here we address the problem of energy transport across the cellular membrane from an open quantum system theoretical perspective....
Preprint
Full-text available
The modelbase package is a free expandable Python package for building and analysing dynamic mathematical models of biological systems. Originally it was designed for the simulation of metabolic systems, but it can be used for virtually any deterministic chemical processes. modelbase provides easy construction methods to define reactions and their...
Article
Full-text available
Dual-state genetic switches that can change their state in response to input signals can be used in synthetic biology to encode memory and control gene expression. A transcriptional toggle switch (TTS), with two mutually repressing transcription regulators, was previously used for switching between two expression states. In other studies, serine in...
Article
Full-text available
Global warming exposes plants to severe heat stress, with consequent crop yield reduction. Organisms exposed to high temperature stresses typically protect themselves with a heat shock response (HSR), where accumulation of unfolded proteins initiates the synthesis of heat shock proteins through the heat shock transcription factor HSF1. While the mo...
Article
Phosphorus (P) is an essential non-renewable nutrient that frequently limits plant growth. It is the foundation of modern agriculture and, to a large extent, demand for P is met from phosphate rock deposits which are limited and becoming increasingly scarce. Adding an extra stroke to this already desolate picture is the fact that a high percentage...
Article
Full-text available
Question: An ecosystem is a complex network of dynamic spatio-temporal interactions among organisms as well as between organisms and the environment. Mathematical models with their abstraction capability are essential to capture the underlying phenomena and connect the different scales at which these systems act. Differential equation models and c...
Article
Full-text available
The photosynthetic carbon reduction cycle, or Calvin-Benson-Bassham (CBB) cycle, is now contained in every standard biochemistry textbook. Although the cycle was already proposed in 1954, it is still the subject of intense research, and even the structure of the cycle, i.e. the exact series of reactions, is still under debate. The controversy about...
Article
Full-text available
Abstract:The pennate diatomPhaeodactylum tricornutumis a model organism able to synthesizeindustrially-relevant molecules. Commercial-scale cultivation currently requires large monocultures,prone to bio-contamination. However, little is known about the identity of the invading organisms.To reduce the complexity of natural systems, we systematically...
Preprint
The pennate diatom Phaeodactylum tricornutum is a model organism able to synthesize industrially-relevant molecules. Commercial-scale cultivation currently requires large monocultures, prone to bio-contamination. However, little is known about the identity of the invading organisms. To reduce the complexity of natural systems, we systematically inv...
Conference Paper
Full-text available
The photosynthetic carbon reduction cycle, or Calvin-Benson-Bassham Cycle, is now contained in every standard biochemistry textbook. Although the cycle was already proposed in 1954, it is still subject of intense research, and even the structure of the cycle, i.e. the exact series of reactions, is still under debate. The controversy about the cycle...
Article
Full-text available
Starch is the most widespread and abundant storage carbohydrate in plants and the main source of carbohydrate in the human diet. Owing to its remarkable properties and commercial applications, starch is still of growing interest. Its unique granular structure made of intercalated layers of amylopectin and amylose has been unraveled thanks to recent...
Article
Full-text available
The last few years have seen the advancement of high-throughput experimental techniques produce an extraordinary amount of data. Bioinformatics and statistical analyses have become instrumental to interpreting the information coming from e.g. sequencing data, and often motivate further targeted experiments. The broad discipline of "computational bi...
Article
Full-text available
The ability of phototrophs to colonise different environments relies on robust protection against oxidative stress, a critical requirement for the successful evolutionary transition from water to land. Photosynthetic organisms have developed numerous strategies to adapt their photosynthetic apparatus to changing light conditions in order to optimis...
Article
Full-text available
Serine integrases catalyse site-specific recombination to integrate and excise bacteriophage genomes into and out of their host's genome. These enzymes exhibit remarkable directionality; in the presence of the integrase alone, recombination between attP and attB DNA sites is efficient and irreversible, giving attL and attR products which do not rec...
Preprint
Full-text available
Global warming is exposing plants to more frequent heat stress, with consequent crop yield reduction. Organisms exposed to large temperature increases protect themselves typically with a heat shock response (HSR). To study the HSR in photosynthetic organisms we present here a data driven mathematical model describing the dynamics of the HSR in the...
Article
Full-text available
Histone proteins are key elements in the packing of eukaryotic DNA into chromosomes. A little understood control system ensures that histone gene expression is balanced with DNA replication so that histone proteins are produced in appropriate amounts. Disturbing or disrupting this system affects genome stability and gene expression, and has detrime...
Data
H2B-GFP expression does not affect the cell cycle of U2OS cells. U2OS cells transfected with plasmids pEGFP- H2B (H2B-GFP) or pEGFP (GFP) were subjected to antibiotic selection to produce stable lines. Asynchronous growing cells were pulse labelled with BrdU for 30 min, fixed, and then stained with 7-AAD to measure DNA replication and content. Stai...
Data
The post processing of the flow cytometry data from synchronised cell cultures to derive the V5 time course for the mathematical model. (PDF)
Data
The data analysis of the Northern Blots and the derivation of the degradation constants for the mathematical model. (PDF)
Preprint
Full-text available
The pennate diatom Phaeodactylum tricornutum is a model organism able to synthesise industrially-relevant molecules. Large-scale monocultures are prone to bio-contamination, however, little is known about the identity of the invading organisms. To gain insight into the bacterial community associated with diatoms, we translated the complexity of a n...