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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
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
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
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
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
FeaSel-Net : a recursive feature selection callback in neural networks
(2022) Fischer, Felix; Birk, Alexander; Somers, Peter; Frenner, Karsten; Tarín, Cristina; Herkommer, Alois
Selecting only the relevant subsets from all gathered data has never been as challenging as it is in these times of big data and sensor fusion. Multiple complementary methods have emerged for the observation of similar phenomena; oftentimes, many of these techniques are superimposed in order to make the best possible decisions. A pathologist, for example, uses microscopic and spectroscopic techniques to discriminate between healthy and cancerous tissue. Especially in the field of spectroscopy in medicine, an immense number of frequencies are recorded and appropriately sized datasets are rarely acquired due to the time-intensive measurements and the lack of patients. In order to cope with the curse of dimensionality in machine learning, it is necessary to reduce the overhead from irrelevant or redundant features. In this article, we propose a feature selection callback algorithm (FeaSel-Net) that can be embedded in deep neural networks. It recursively prunes the input nodes after the optimizer in the neural network achieves satisfying results. We demonstrate the performance of the feature selection algorithm on different publicly available datasets and compare it to existing feature selection methods. Our algorithm combines the advantages of neural networks’ nonlinear learning ability and the embedding of the feature selection algorithm into the actual classifier optimization.
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
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
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
Adaptive method for quantitative estimation of glucose and fructose concentrations in aqueous solutions based on infrared nanoantenna optics
(2019) Schuler, Benjamin; Kühner, Lucca; Hentschel, Mario; Giessen, Harald; Tarín, Cristina
In life science and health research one observes a continuous need for new concepts and methods to detect and quantify the presence and concentration of certain biomolecules-preferably even in vivo or aqueous solutions. One prominent example, among many others, is the blood glucose level, which is highly important in the treatment of, e.g., diabetes mellitus. Detecting and, in particular, quantifying the amount of such molecular species in a complex sensing environment, such as human body fluids, constitutes a significant challenge. Surface-enhanced infrared absorption (SEIRA) spectroscopy has proven to be uniquely able to differentiate even very similar molecular species in very small concentrations. We are thus employing SEIRA to gather the vibrational response of aqueous glucose and fructose solutions in the mid-infrared spectral range with varying concentration levels down to 10 g/l. In contrast to previous work, we further demonstrate that it is possible to not only extract the presence of the analyte molecules but to determine the quantitative concentrations in a reliable and automated way. For this, a baseline correction method is applied to pre-process the measurement data in order to extract the characteristic vibrational information. Afterwards, a set of basis functions is fitted to capture the characteristic features of the two examined monosaccharides and a potential contribution of the solvent itself. The reconstruction of the actual concentration levels is then performed by superposition of the different basis functions to approximate the measured data. This software-based enhancement of the employed optical sensors leads to an accurate quantitative estimate of glucose and fructose concentrations in aqueous solutions.

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