Browsing by Author "Sawodny, Oliver"

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Open Access
Basic regulatory principles of Escherichia coli's electron transport chain for varying oxygen conditions
(2014) Henkel, Sebastian; Beek, Alexander ter; Steinsiek, Sonja; Stagge, Stefan; Bettenbrock, Katja; Teixeira de Mattos, M. Joost; Sauter, Thomas; Sawodny, Oliver; Ederer, Michael
For adaptation between anaerobic, micro-aerobic and aerobic conditions Escherichia coli's metabolism and in particular its electron transport chain (ETC) is highly regulated. Although it is known that the global transcriptional regulators FNR and ArcA are involved in oxygen response it is unclear how they interplay in the regulation of ETC enzymes under micro-aerobic chemostat conditions. Also, there are diverse results which and how quinones (oxidised/reduced, ubiquinone/other quinones) are controlling the ArcBA two-component system. In the following a mathematical model of the E. coli ETC linked to basic modules for substrate uptake, fermentation product excretion and biomass formation is introduced. The kinetic modelling focusses on regulatory principles of the ETC for varying oxygen conditions in glucose-limited continuous cultures. The model is based on the balance of electron donation (glucose) and acceptance (oxygen or other acceptors). Also, it is able to account for different chemostat conditions due to changed substrate concentrations and dilution rates. The parameter identification process is divided into an estimation and a validation step based on previously published and new experimental data. The model shows that experimentally observed, qualitatively different behaviour of the ubiquinone redox state and the ArcA activity profile in the micro-aerobic range for different experimental conditions can emerge from a single network structure. The network structure features a strong feed-forward effect from the FNR regulatory system to the ArcBA regulatory system via a common control of the dehydrogenases of the ETC. The model supports the hypothesis that ubiquinone but not ubiquinol plays a key role in determining the activity of ArcBA in a glucose-limited chemostat at micro-aerobic conditions.
Open Access
Cystoscopic depth estimation using gated adversarial domain adaptation
(2023) Somers, Peter; Holdenried-Krafft, Simon; Zahn, Johannes; Schüle, Johannes; Veil, Carina; Harland, Niklas; Walz, Simon; Stenzl, Arnulf; Sawodny, Oliver; Tarín, Cristina; Lensch, Hendrik P. A.
Monocular depth estimation from camera images is very important for surrounding scene evaluation in many technical fields from automotive to medicine. However, traditional triangulation methods using stereo cameras or multiple views with the assumption of a rigid environment are not applicable for endoscopic domains. Particularly in cystoscopies it is not possible to produce ground truth depth information to directly train machine learning algorithms for using a monocular image directly for depth prediction. This work considers first creating a synthetic cystoscopic environment for initial encoding of depth information from synthetically rendered images. Next, the task of predicting pixel-wise depth values for real images is constrained to a domain adaption between the synthetic and real image domains. This adaptation is done through added gated residual blocks in order to simplify the network task and maintain training stability during adversarial training. Training is done on an internally collected cystoscopy dataset from human patients. The results after training demonstrate the ability to predict reasonable depth estimations from actual cystoscopic videos and added stability from using gated residual blocks is shown to prevent mode collapse during adversarial training.
Open Access
D1244: Design and construction of the first adaptive high-rise experimental building
(2022) Blandini, Lucio; Haase, Walter; Weidner, Stefanie; Böhm, Michael; Burghardt, Timon; Roth, Daniel; Sawodny, Oliver; Sobek, Werner
An interdisciplinary research team of the University of Stuttgart has been working extensively since 2017 on the development and integration of adaptive systems and technologies in order to provide solutions for a more sustainable built environment. An experimental 36.5 m tall high-rise building, called D1244, was designed and completed in 2021 to show the potential of adaptive structures and facades as well as to verify on a real scale the developed systems and the related numerical predictions. The building was designed to offer a flexible experimental platform: each component is dismountable so that structural as well as facades elements can be replaced with new ones introducing new functionalities to be investigated. The structure is currently equipped with twenty-four hydraulic actuators that are installed in the columns and diagonal bracers. Strain gauge sensors and an optical tracking system are employed to monitor the state of the structural system. This paper describes the design and construction of the adaptive tower as well as the preliminary experimental testing on different scaled structural prototypes. The research work on these prototypes provided relevant information for the final set-up of the high-rise building. An outlook on future research, including the planned first structural testing phase and the implementation of adaptive facade systems, is included at the end.
Open Access
Holistic quality model and assessment : supporting decision-making towards sustainable construction using the design and production of graded concrete components as an example
(2022) Frost, Deniz; Gericke, Oliver; Di Bari, Roberta; Balangé, Laura; Zhang, Li; Blagojevic, Boris; Nigl, David; Haag, Phillip; Blandini, Lucio; Jünger, Hans Christian; Kropp, Cordula; Leistner, Philip; Sawodny, Oliver; Schwieger, Volker; Sobek, Werner
This paper describes a holistic quality model (HQM) and assessment to support decision-making processes in construction. A graded concrete slab serves as an example to illustrate how to consider technical, environmental, and social quality criteria and their interrelations. The evaluation of the design and production process of the graded concrete component shows that it has advantages compared to a conventional solid slab, especially in terms of environmental performance. At the same time, the holistic quality model identifies potential improvements for the technology of graded concrete. It will be shown that the holistic quality model can be used to (a) consider the whole life cycle in decision-making in the early phases and, thus, make the complexity of construction processes manageable for quality and sustainability assessments and (b) make visible interdependencies between different quality and sustainability criteria, to help designers make better-informed decisions regarding the overall quality. The results show how different quality aspects can be assessed and trade-offs are also possible through the understanding of the relationships among characteristics. For this purpose, in addition to the quality assessment of graded concrete, an overview of the interrelations of different quality characteristics is provided. While this article demonstrates how a HQM can support decision-making in design, the validity of the presented evaluation is limited by the data availability and methodological challenges, specifically regarding the quantification of interrelations.
Open Access
IL-1β and TNFα differentially influence NF-κB activity and FasL-induced apoptosis in primary murine hepatocytes during LPS-induced inflammation
(2019) Rex, Julia; Lutz, Anna; Faletti, Laura E.; Albrecht, Ute; Thomas, Maria; Bode, Johannes G.; Borner, Christoph; Sawodny, Oliver; Merfort, Irmgard
Macrophage-derived cytokines largely influence the behavior of hepatocytes during an inflammatory response. We previously reported that both TNFα and IL-1β, which are released by macrophages upon LPS stimulation, affect Fas ligand (FasL)-induced apoptotic signaling. Whereas TNFα preincubation leads to elevated levels of caspase-3 activity and cell death, pretreatment with IL-1β induces increased caspase-3 activity but keeps cells alive. We now report that IL-1β and TNFα differentially influence NF-κB activity resulting in a differential upregulation of target genes, which may contribute to the distinct effects on cell viability. A reduced NF-κB activation model was established to further investigate the molecular mechanisms which determine the distinct cell fate decisions after IL-1β and TNFα stimulation. To study this aspect in a more physiological setting, we used supernatants from LPS-stimulated bone marrow-derived macrophages (BMDMs). The treatment of hepatocytes with the BMDM supernatant, which contains both IL-1β and TNFα, sensitized to FasL-induced caspase-3 activation and cell death. However, when TNFα action was blocked by neutralizing antibodies, cell viability after stimulation with the BMDM supernatant and FasL increased as compared to single FasL stimulation. This indicates the important role of TNFα in the sensitization of apoptosis in hepatocytes. These results give first insights into the complex interplay between macrophages and hepatocytes which may influence life/death decisions of hepatocytes during an inflammatory reaction of the liver in response to a bacterial infection.
Open Access
A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen
(2014) Ederer, Michael; Steinsiek, Sonja; Stagge, Stefan; Rolfe, Matthew D.; Beek, Alexander tek; Knies, David; Teixeira de Mattos, M. Joost; Sauter, Thomas; Green, Jeffrey; Poole, Robert K.; Bettenbrock, Katja; Sawodny, Oliver
The efficient redesign of bacteria for biotechnological purposes, such as biofuel production, waste disposal or specific biocatalytic functions, requires a quantitative systems-level understanding of energy supply, carbon and redox metabolism. The measurement of transcript levels, metabolite concentrations and metabolic fluxes per se gives an incomplete picture. An appreciation of the interdependencies between the different measurement values is essential for systems-level understanding. Mathematical modeling has the potential to provide a coherent and quantitative description of the interplay between gene expression, metabolite concentrations and metabolic fluxes. Escherichia coli undergoes major adaptations in central metabolism when the availability of oxygen changes. Thus, an integrated description of the oxygen response provides a benchmark of our understanding of carbon, energy and redox metabolism. We present the first comprehensive model of the central metabolism of E. coli that describes steady-state metabolism at different levels of oxygen availability. Variables of the model are metabolite concentrations, gene expression levels, transcription factor activities, metabolic fluxes and biomass concentration. We analyze the model with respect to the production capabilities of central metabolism of E. coli. In particular, we predict how precursor and biomass concentration are affected by product formation.
Open Access
Model-based analysis of an adaptive evolution experiment with Escherichia coli in a pyruvate limited continuous culture with glycerol
(2012) Feuer, Ronny; Gottlieb, Katrin; Viertel, Gero; Klotz, Johannes; Schober, Steffen; Bossert, Martin; Sawodny, Oliver; Sprenger, Georg; Ederer, Michael
Bacterial strains that were genetically blocked in important metabolic pathways and grown under selective conditions underwent a process of adaptive evolution: certain pathways may have been deregulated and therefore allowed for the circumvention of the given block. A block of endogenous pyruvate synthesis from glycerol was realized by a knockout of pyruvate kinase and phosphoenolpyruvate carboxylase in E. coli. The resulting mutant strain was able to grow on a medium containing glycerol and lactate, which served as an exogenous pyruvate source. Heterologous expression of a pyruvate carboxylase gene from Corynebacterium glutamicum was used for anaplerosis of the TCA cycle. Selective conditions were controlled in a continuous culture with limited lactate feed and an excess of glycerol feed. After 200–300 generations pyruvate-prototrophic mutants were isolated. The genomic analysis of an evolved strain revealed that the genotypic basis for the regained pyruvate-prototrophy was not obvious. A constraint-based model of the metabolism was employed to compute all possible detours around the given metabolic block by solving a hierarchy of linear programming problems. The regulatory network was expected to be responsible for the adaptation process. Hence, a Boolean model of the transcription factor network was connected to the metabolic model. Our model analysis only showed a marginal impact of transcriptional control on the biomass yield on substrate which is a key variable in the selection process. In our experiment, microarray analysis confirmed that transcriptional control probably played a minor role in the deregulation of the alternative pathways for the circumvention of the block.
Open Access
Model-based characterization of inflammatory gene expression patterns of activated macrophages
(2016) Rex, Julia; Albrecht, Ute; Ehlting, Christian; Thomas, Maria; Zanger, Ulrich M.; Sawodny, Oliver; Häussinger, Dieter; Ederer, Michael; Feuer, Ronny; Bode, Johannes G.
Macrophages are cells with remarkable plasticity. They integrate signals from their microenvironment leading to context-dependent polarization into classically (M1) or alternatively (M2) activated macrophages, representing two extremes of a broad spectrum of divergent phenotypes. Thereby, macrophages deliver protective and pro-regenerative signals towards injured tissue but, depending on the eliciting damage, may also be responsible for the generation and aggravation of tissue injury. Although incompletely understood, there is emerging evidence that macrophage polarization is critical for these antagonistic roles. To identify activation-specific expression patterns of chemokines and cytokines that may confer these distinct effects a systems biology approach was applied. A comprehensive literature-based Boolean model was developed to describe the M1 (LPS-activated) and M2 (IL-4/13-activated) polarization types. The model was validated using high-throughput transcript expression data from murine bone marrow derived macrophages. By dynamic modeling of gene expression, the chronology of pathway activation and autocrine signaling was estimated. Our results provide a deepened understanding of the physiological balance leading to M1/M2 activation, indicating the relevance of co-regulatory signals at the level of Akt1 or Akt2 that may be important for directing macrophage polarization.
Open Access
Modeling time delay in the NFκB signaling pathway following low dose IL-1 stimulation
(2011) Witt, Johannes; Barisic, Sandra; Sawodny, Oliver; Ederer, Michael; Kulms, Dagmar; Sauter, Thomas
Stimulation of human epithelial cells with IL-1 (10 ng/ml) + UVB radiation results in sustained NFκB activation caused by continuous IKKbeta phosphorylation. We have recently published a strictly reduced ordinary differential equation model elucidating the involved mechanisms. Here, we compare model extensions for low IL-1 doses (0.5 ng/ml), where delayed IKKbeta phosphorylation is observed. The extended model including a positive regulatory element, most likely auto-ubiquitination of TRAF6, reproduces the observed experimental data most convincingly. The extension is shown to be consistent with the original model and contains very sensitive processes which may serve as potential intervention targets.
Open Access
Path planning for graded concrete element fabrication
(2023) Blagojevic, Boris; Sawodny, Oliver
The technology of functionally graded concrete (FGC) is a new methodology in the field of concrete construction, striving for mass savings by adjusting the elements interior design. A promising approach herein is meso-gradation, where concrete hollow spheres are placed inside the formwork before casting the element; this allows up to 50% mass savings without a loss in load-bearing capacity, whilst also ensuring recyclability compared to e.g. bubble decks. In order to prevent damage/displacement of the spheres during automated fabrication, the extruded concrete flow must avoid the spheres, whilst neatly covering the elements area in order to prevent cavities. Both requirements formulate a complex path planning problem that must be solved in order to achieve automated fabrication. In this paper, we propose a method for solving this problem, which is based on theoretical findings on Hamiltonian triangulations. Our approach is based on the idea that the elements area is triangulated, such that all sphere centers are corners of triangles. For each triangle, a smooth path can be planned straightforwardly on a consideration of the geometry, such that the global path is made of a sequence of local ones. This necessitates finding a triangulation that is hamiltonian, i.e. a sequence where all triangles are visited exactly once. To this end, we first present a new class of triangulations and proof their hamiltonicity, followed by an algorithm that generates such triangulations on certain FGC element geometries. This is followed by the local path planning problem, whose special structure with start/end tangential and curvature constraints facilitates the use of a polar coordinate approach.
Open Access
Process evaluation for smart concrete road construction : road surface and thickness evaluation using high-speed LiDAR technology
(2021) Skalecki, Patric; Sesselmann, Maximilian; Rechkemmer, Sabrina; Britz, Thorsten; Großmann, Andreas; Garrecht, Harald; Sawodny, Oliver
The enhancement of new quality criteria in highway construction is a key aspect to improving the construction process and lifetime of road. In particular, mobile laser scanning systems are nowadays able to provide realistic 3D elevation profiles of a road to detect anomalies. In this context, this study utilizes a high-accuracy high-speed mobile mapping vehicle and evaluates a weighted longitudinal profile as an improved measure for evenness analysis. For comparison a classical method with a rolling straight edge was evaluated on the same road section and observed effects are discussed. The second focus is the areal reconstruction of the road thickness. For this purpose, a modern method was developed to spatially synchronize two high-speed laser scans using reference boxes next to the road, to transfer the point clouds into a surface model and to calculate the layer thickness. This procedure was conceptually validated by some pointwise measurements of the layer thickness. With this information, imperfections in the base layer could be detected automatically over a wide area at an early stage and countermeasures might be initiated before constructing the highway.
Open Access
A rapid method for the extraction and analysis of carotenoids and other hydrophobic substances suitable for systems biology studies with photosynthetic bacteria
(2013) Bóna-Lovász, Judit; Bóna, Aron; Ederer, Michael; Sawodny, Oliver; Ghosh, Robin
A simple, rapid, and inexpensive extraction method for carotenoids and other non-polar compounds present in phototrophic bacteria has been developed. The method, which has been extensively tested on the phototrophic purple non-sulphur bacterium Rhodospirillum rubrum, is suitable for extracting large numbers of samples, which is common in systems biology studies, and yields material suitable for subsequent analysis using HPLC and mass spectroscopy. The procedure is particularly suitable for carotenoids and other terpenoids, including quinones, bacteriochlorophyll a and bacteriopheophytin a, and is also useful for the analysis of polar phospholipids. The extraction procedure requires only a single step extraction with a hexane/methanol/water mixture, followed by HPLC using a Spherisorb C18 column, with a mobile phase consisting of acetone-water and a non-linear gradient of 50%-100% acetone. The method was employed for examining the carotenoid composition observed during microaerophilic growth of R. rubrum strains, and was able to determine 18 carotenoids, 4 isoprenoid-quinones, bacteriochlorophyll a and bacteriopheophytin a as well as four different phosphatidylglycerol species of different acyl chain compositions. The analytical procedure was used to examine the dynamics of carotenoid biosynthesis in the major and minor pathways operating simultaneously in a carotenoid biosynthesis mutant of R. rubrum.
Open Access
Rapid sampling of Escherichia coli after changing oxygen conditions reveals transcriptional dynamics
(2017) Wulffen, Joachim von; Ulmer, Andreas; Jäger, Günter; Sawodny, Oliver; Feuer, Ronny
Escherichia coli is able to shift between anaerobic and aerobic metabolism by adapting its gene expression, e.g., of metabolic genes, to the new environment. The dynamics of gene expression that result from environmental shifts are limited, amongst others, by the time needed for regulation and transcription elongation. In this study, we examined gene expression dynamics after an anaerobic-to-aerobic shift on a short time scale (0.5, 1, 2, 5, and 10 min) by RNA sequencing with emphasis on delay times and transcriptional elongation rates (TER). Transient expression patterns and timing of differential expression, characterized by delay and elongation, were identified as key features of the dataset. Gene ontology enrichment analysis revealed early upregulation of respiratory and iron-related gene sets. We inferred specific TERs of 89 operons with a mean TER of 42.0 nt/s and mean delay time of 22.4 s. TERs correlate with sequence features, such as codon bias, whereas delay times correlate with the involvement of regulators. The presented data illustrate that at very short times after a shift in oxygenation, extensional changes of the transcriptome, such as temporary responses, can be observed. Besides regulation, TERs contribute to the dynamics of gene expression.
Open Access
A systems biology approach to analyse leaf carbohydrate metabolism in Arabidopsis thaliana
(2011) Henkel, Sebastian; Nägele, Thomas; Hörmiller, Imke; Sauter, Thomas; Sawodny, Oliver; Ederer, Michael; Heyer, Arnd G.
Plant carbohydrate metabolism comprises numerous metabolite interconversions, some of which form cycles of metabolite degradation and re-synthesis and are thus referred to as futile cycles. In this study, we present a systems biology approach to analyse any possible regulatory principle that operates such futile cycles based on experimental data for sucrose (Scr) cycling in photosynthetically active leaves of the model plant Arabidopsis thaliana. Kinetic parameters of enzymatic steps in Scr cycling were identified by fitting model simulations to experimental data. A statistical analysis of the kinetic parameters and calculated flux rates allowed for estimation of the variability and supported the predictability of the model. A principal component analysis of the parameter results revealed the identifiability of the model parameters. We investigated the stability properties of Scr cycling and found that feedback inhibition of enzymes catalysing metabolite interconversions at different steps of the cycle have differential influence on stability. Applying this observation to futile cycling of Scr in leaf cells points to the enzyme hexokinase as an important regulator, while the step of Scr degradation by invertases appears subordinate.
Open Access
Transition of an anaerobic Escherichia coli culture to aerobiosis: balancing mRNA and protein levels in a demand-directed dynamic flux balance analysis
(2016) Wulffen, Joachim von; Sawodny, Oliver; Feuer, Ronny
The facultative anaerobic bacterium Escherichia coli is frequently forced to adapt to changing environmental conditions. One important determinant for metabolism is the availability of oxygen allowing a more efficient metabolism. Especially in large scale bioreactors, the distribution of oxygen is inhomogeneous and individual cells encounter frequent changes. This might contribute to observed yield losses during process upscaling. Short-term gene expression data exist of an anaerobic E. coli batch culture shifting to aerobic conditions. The data reveal temporary upregulation of genes that are less efficient in terms of energy conservation than the genes predicted by conventional flux balance analyses. In this study, we provide evidence for a positive correlation between metabolic fluxes and gene expression. We then hypothesize that the more efficient enzymes are limited by their low expression, restricting flux through their reactions. We define a demand that triggers expression of the demanded enzymes that we explicitly include in our model. With these features we propose a method, demand-directed dynamic flux balance analysis, dddFBA, bringing together elements of several previously published methods. The introduction of additional flux constraints proportional to gene expression provoke a temporary demand for less efficient enzymes, which is in agreement with the transient upregulation of these genes observed in the data. In the proposed approach, the applied objective function of growth rate maximization together with the introduced constraints triggers expression of metabolically less efficient genes. This finding is one possible explanation for the yield losses observed in large scale bacterial cultivations where steady oxygen supply cannot be warranted.