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Farming in the Era of Industrie 4.0

Anja-Tatjana Braun, Eduardo Colangelo, Thilo Steckel
2018 Procedia CIRP  
Braun et al. / Procedia CIRP 72 (2018) 979-984 Author name / Procedia CIRP 00 (2018) 000-000  ...  . 2 Requirements of agriculture regarding Industrie 4.0 Fig. 3 . 3 The two environments of agriculture Fig. 4 . 4 Industry 4.0 collaboration levels in high-end processes of agriculture Anja-Tatjana  ... 
doi:10.1016/j.procir.2018.03.176 fatcat:t5ou6baaazdglgsl6pychycqiy

Amino Acid Catabolism in Plants

Tatjana M. Hildebrandt, Adriano Nunes Nesi, Wagner L. Araújo, Hans-Peter Braun
2015 Molecular Plant  
doi:10.1016/j.molp.2015.09.005 pmid:26384576 fatcat:h6jiy3ns3jasbgw7o27nxrdaci

Improving Material Efficiency for Ultra-efficient Factories in Closed-loop Value Networks

Erin Sheehan, Anja-Tatjana Braun, Timm Kuhlmann, Alexander Sauer
2016 Procedia CIRP  
Infinite material circulation without losses in value or volume is a challenge for value networks, where materials are currently destroyed or lost. Today's waste prevention actions are predominantly one-dimensional and potentially create additional waste forms. To reduce waste in all dimensions, this paper first characterizes material waste forms, and then provides an analysis of their interdependencies. From these relationships a causal-loop diagram is derived, and the basis for a future
more » ... dynamics simulation model is described. The model will also examine their potential effect of waste minimization on energy consumption and productivity losses to assist manufacturers evaluate the effectiveness of waste minimization efforts. This approach is developed within the "Ultra-Efficient Factory" project funded by the Ministry of the Environment, Climate Protection and the Energy Sector Baden-Württemberg to support efficient manufacturing in small and midsized companies.
doi:10.1016/j.procir.2016.01.096 fatcat:3iqsvskwivhtlgmmp7ch6k3qmy

Adaptation of the business model canvas template to develop business models for the circular economy

Anja-Tatjana Braun, Oliver Schöllhammer, Bernd Rosenkranz
2021 Procedia CIRP  
Fig. 1 . 1 Template to develop Circular Business Models Fig. 3 . 3 Recovery modules of the developed template Anja-Tatjana Braun et al. / Procedia CIRP 99 (2021) 698-702 A.  ...  Braun et al./ Procedia CIRP 00 (2020) 000-000  ... 
doi:10.1016/j.procir.2021.03.093 fatcat:awcvdx4rjfemrhn7mu24vodfry

Real Option-based Evaluation of Eco-oriented Investment Using the Example of Closed-loop Supply Chains

Markus Weskamp, Anja-Tatjana Braun, Thomas Bauernhansl
2015 Procedia CIRP  
Natural resources should be used as effectively as possible along the entire supply chain. One approach to keep the resources on a high value-added level is the extension of classical supply chains to closed-loop supply chains, covering the whole product life cycle. This requires innovations in products and technologies as well as changes in existing value-added processes. Thus, the required redesign process comes along with extensive investment and a high level of uncertainty and flexibility
more » ... d can have a significant impact on the success of the company. This paper presents a model, based on the real options theory with a closed-loop supply chain which complements the classic investment approach with ecological aspects of the evaluation. The model allows a qualitative and quantitative assessment of investment decisions associated with uncertainty. Additionally, the possible options for action and the inherent risks are demonstrated. The expansion of the net present value method to real options with external environmental factors and entrepreneurial aspects of design enable in this case the calculation of an extended net present value for realistic evaluation of strategic investments.
doi:10.1016/j.procir.2015.06.028 fatcat:xa3aiycguvcczpgobfsjks53ka

Extended darkness induces internal turnover of glucosinolates in Arabidopsis thaliana leaves

Saskia Brandt, Sara Fachinger, Takayuki Tohge, Alisdair R. Fernie, Hans-Peter Braun, Tatjana M. Hildebrandt, Keith R. Davis
2018 PLoS ONE  
Prolonged darkness leads to carbohydrate starvation, and as a consequence plants degrade proteins and lipids to oxidize amino acids and fatty acids as alternative substrates for mitochondrial ATP production. We investigated, whether the internal breakdown of glucosinolates, a major class of sulfur-containing secondary metabolites, might be an additional component of the carbohydrate starvation response in Arabidopsis thaliana (A. thaliana). The glucosinolate content of A. thaliana leaves was
more » ... ongly reduced after seven days of darkness. We also detected a significant increase in the activity of myrosinase, the enzyme catalyzing the initial step in glucosinolate breakdown, coinciding with a strong induction of the main leaf myrosinase isoforms TGG1 and TGG2. In addition, nitrilase activity was increased suggesting a turnover via nitriles and carboxylic acids. Internal degradation of glucosinolates might also be involved in diurnal or developmental adaptations of the glucosinolate profile. We observed a diurnal rhythm for myrosinase activity in two-week-old plants. Furthermore, leaf myrosinase activity and protein abundance of TGG2 varied during plant development, whereas leaf protein abundance of TGG1 remained stable indicating regulation at the transcriptional as well as post-translational level.
doi:10.1371/journal.pone.0202153 pmid:30092103 pmcid:PMC6084957 fatcat:hzgtvtuj2vdxjefmpvuu6zvnyq

Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction

Tatjana Braun, Julia Koehler Leman, Oliver F. Lange, Debora S Marks
2015 PLoS Computational Biology  
Recent work has shown that the accuracy of ab initio structure prediction can be significantly improved by integrating evolutionary information in form of intra-protein residue-residue contacts. Following this seminal result, much effort is put into the improvement of contact predictions. However, there is also a substantial need to develop structure prediction protocols tailored to the type of restraints gained by contact predictions. Here, we present a structure prediction protocol that
more » ... es evolutionary information with the resolution-adapted structural recombination approach of Rosetta, called RASREC. Compared to the classic Rosetta ab initio protocol, RASREC achieves improved sampling, better convergence and higher robustness against incorrect distance restraints, making it the ideal sampling strategy for the stated problem. To demonstrate the accuracy of our protocol, we tested the approach on a diverse set of 28 globular proteins. Our method is able to converge for 26 out of the 28 targets and improves the average TM-score of the entire benchmark set from 0.55 to 0.72 when compared to the top ranked models obtained by the EVFold web server using identical contact predictions. Using a smaller benchmark, we furthermore show that the prediction accuracy of our method is only slightly reduced when the contact prediction accuracy is comparatively low. This observation is of special interest for protein sequences that only have a limited number of homologs. Author Summary Recently, a breakthrough has been achieved in modeling the atomic 3D structures of proteins from their sequence alone without requiring any experimental work on the protein itself. To achieve this goal, a database of evolutionary related sequences is analyzed to find co-evolving residues, giving insight into which residues are in close proximity to each other. These residue-residue contacts can help to drive a computer simulation with an atomic-scale physical model of the protein structure from a random starting conformation PLOS Computational Biology | to a native-like 3D conformation. Although much effort is being put into the improvement of residue-residue contact predictions, their accuracy will always be limited. Therefore, structure prediction protocols with a high tolerance against incorrect distance restraints are needed. Here, we present a structure prediction protocol that combines evolutionary information with the iterative sampling approach of the molecular modeling suite Rosetta, called RASREC. RASREC has been shown to converge faster to near-native models and to be more robust against incorrect distance restraints than standard prediction protocols. It is therefore perfectly suited for restraints obtained from predicted residue-residue contacts with limited accuracy. We show that our protocol outperforms other currently published structure prediction methods and is able to achieve accurate structures, even if the accuracy of predicted contacts is low. "This is a PLOS Computational Biology Methods paper" Evolutionary Information Combined with an Iterative Sampling Strategy PLOS Computational Biology |
doi:10.1371/journal.pcbi.1004661 pmid:26713437 pmcid:PMC4694711 fatcat:orposq5e25cwtkgmgphupvcpjq

Composition and Stability of the Oxidative Phosphorylation System in the Halophile Plant Cakile maritima

Nèjia Farhat, Sarra Hichri, Tatjana Manuela Hildebrandt, Ahmed Debez, Hans-Peter Braun
2019 Frontiers in Plant Science  
., the alternative oxidase (AOX) or alternative NADH dehydrogenases Schertl and Braun, 2014) .  ...  Copyright © 2019 Farhat, Hichri, Hildebrandt, Debez and Braun. This is an openaccess article distributed under the terms of the Creative Commons Attribution License (CC BY).  ... 
doi:10.3389/fpls.2019.01010 pmid:31456813 pmcid:PMC6700300 fatcat:min2cjiwsngstitl74sqtaytbm

Probing the SELEX Process with Next-Generation Sequencing

Tatjana Schütze, Barbara Wilhelm, Nicole Greiner, Hannsjörg Braun, Franziska Peter, Mario Mörl, Volker A. Erdmann, Hans Lehrach, Zoltán Konthur, Marcus Menger, Peter F. Arndt, Jörn Glökler (+1 others)
2011 PLoS ONE  
SELEX is an iterative process in which highly diverse synthetic nucleic acid libraries are selected over many rounds to finally identify aptamers with desired properties. However, little is understood as how binders are enriched during the selection course. Next-generation sequencing offers the opportunity to open the black box and observe a large part of the population dynamics during the selection process. Methodology: We have performed a semi-automated SELEX procedure on the model target
more » ... ptavidin starting with a synthetic DNA oligonucleotide library and compared results obtained by the conventional analysis via cloning and Sanger sequencing with next-generation sequencing. In order to follow the population dynamics during the selection, pools from all selection rounds were barcoded and sequenced in parallel. Conclusions: High affinity aptamers can be readily identified simply by copy number enrichment in the first selection rounds. Based on our results, we suggest a new selection scheme that avoids a high number of iterative selection rounds while reducing time, PCR bias, and artifacts. Citation: Schü tze T,
doi:10.1371/journal.pone.0029604 pmid:22242135 pmcid:PMC3248438 fatcat:glieaok5zfhahekysqxwafqdzq

The Molecular Tweezer CLR01 Inhibits Antibody-Resistant Cell-to-Cell Spread of Human Cytomegalovirus

Sina Brenner, Berenike Braun, Clarissa Read, Tatjana Weil, Paul Walther, Thomas Schrader, Jan Münch, Jens von Einem
2021 Viruses  
Human cytomegalovirus (HCMV) uses two major ways for virus dissemination: infection by cell-free virus and direct cell-to-cell spread. Neutralizing antibodies can efficiently inhibit infection by cell-free virus but mostly fail to prevent cell-to-cell transmission. Here, we show that the 'molecular tweezer' CLR01, a broad-spectrum antiviral agent, is not only highly active against infection with cell-free virus but most remarkably inhibits antibody-resistant direct cell-to-cell spread of HCMV.
more » ... he inhibition of cell-to-cell spread by CLR01 was not limited to HCMV but was also shown for the alphaherpesviruses herpes simplex viruses 1 and 2 (HSV-1, -2). CLR01 is a rapid acting small molecule that inhibits HCMV entry at the attachment and penetration steps. Electron microscopy of extracellular virus particles indicated damage of the viral envelope by CLR01, which likely impairs the infectivity of virus particles. The rapid inactivation of viral particles by CLR01, the viral envelope as the main target, and the inhibition of virus entry at different stages are presumably the key to inhibition of cell-free virus infection and cell-to-cell spread by CLR01. Importance: While cell-free spread enables the human cytomegalovirus (HCMV) and other herpesviruses to transmit between hosts, direct cell-to-cell spread is thought to be more relevant for in vivo dissemination within infected tissues. Cell-to-cell spread is resistant to neutralizing antibodies, thus contributing to the maintenance of virus infection and virus dissemination in the presence of an intact immune system. Therefore, it would be therapeutically interesting to target this mode of spread in order to treat severe HCMV infections and to prevent dissemination of virus within the infected host. The molecular tweezer CLR01 exhibits broad-spectrum antiviral activity against a number of enveloped viruses and efficiently blocks antibody-resistant cell-to-cell spread of HCMV, thus representing a novel class of small molecules with promising antiviral activity.
doi:10.3390/v13091685 pmid:34578265 pmcid:PMC8472163 fatcat:rvptcxbczne2rlewz5kmwdieta

Estimating the number of protein molecules in a plant cell: a quantitative perspective on proteostasis and amino acid homeostasis during progressive drought stress [article]

Björn Heinemann, Patrick Künzler, Hans-Peter Braun, Tatjana M Hildebrandt
2020 bioRxiv   pre-print
., Braun, H.-P. and Hildebrandt, 615 T.M. (2019) The role of amino acid metabolism during abiotic stress release.  ...  15548627.2015.1106664. 651 Fuchs, P., Rugen, N., Carrie, C., Elsässer, M., Finkemeier, I., Giese, J., Hildebrandt, T.M., Kühn, K., 652 Maurino, V.G., Ruberti, C., Schallenberg-Rüdinger, M., Steinbeck, J., Braun  ... 
doi:10.1101/2020.03.17.995613 fatcat:tkouq653y5fmpej4azyuxcjm5u

Estimating the number of protein molecules in a plant cell: protein and amino acid homeostasis during drought

Björn Heinemann, Patrick Künzler, Holger Eubel, Hans-Peter Braun, Tatjana M Hildebrandt
2020 Plant Physiology  
During drought stress, cellular proteostasis on the one hand and amino acid homeostasis on the other hand are severely challenged, because the decrease in photosynthesis induces massive proteolysis, leading to drastic changes in both the proteome and the free amino acid pool. Thus, we selected progressive drought stress in Arabidopsis (Arabidopsis thaliana) as a model to investigate on a quantitative level the balance between protein and free amino acid homeostasis. We analyzed the mass
more » ... ion of the leaf proteome based on proteomics datasets, and estimated how many protein molecules are present in a plant cell and its subcellular compartments. In addition, we calculated stress-induced changes in the distribution of individual amino acids between the free and protein-bound pools. Under control conditions, an average Arabidopsis mesophyll cell contains about 25 billion protein molecules, of which 80% are localized in chloroplasts. Severe water deficiency leads to degradation of more than 40% of the leaf protein mass, and thus causes a drastic shift in distribution toward the free amino acid pool. Stress-induced proteolysis of just half of the 340 million RubisCO hexadecamers present in the chloroplasts of a single mesophyll cell doubles the cellular content of free amino acids. A major fraction of the amino acids released from proteins is channeled into synthesis of proline, which is a compatible osmolyte. Complete oxidation of the remaining fraction as an alternative respiratory substrate can fully compensate for the lack of photosynthesis-derived carbohydrates for several hours.
doi:10.1093/plphys/kiaa050 pmid:33721903 pmcid:PMC8133651 fatcat:adchzwmouvfvrldgcz5zjhu5di

Proteome adaptations in Ethe1-deficient mice indicate a role in lipid catabolism and cytoskeleton organization via post-translational protein modifications

Tatjana M. Hildebrandt, Ivano Di Meo, Massimo Zeviani, Carlo Viscomi, Hans‑Peter Braun
2013 Bioscience Reports  
., Viscomi, C. and Braun, H-P . (2013) Proteome adaptations in Ethe1 deficient mice indicate a role in lipid catabolism and cytoskeleton organization via post-translational protein modifications.  ...  Massimo Zeviani and Hans-Peter Braun supervised the work and revised the paper.  ...  AUTHOR CONTRIBUTION Tatjana Hildebrandt designed the study, performed the proteomics experiments and co-expression analysis, analysed and interpreted the data, and wrote the paper.  ... 
doi:10.1042/bsr20130051 pmid:23800285 pmcid:PMC3827611 fatcat:wjcdikhzufan5oa45bg4f7um5y

PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies

Jouhyun Jeon, Roland Arnold, Fateh Singh, Joan Teyra, Tatjana Braun, Philip M. Kim
2016 BMC Bioinformatics  
The identification of structured units in a protein sequence is an important first step for most biochemical studies. Importantly for this study, the identification of stable structured region is a crucial first step to generate novel synthetic antibodies. While many approaches to find domains or predict structured regions exist, important limitations remain, such as the optimization of domain boundaries and the lack of identification of non-domain structured units. Moreover, no integrated tool
more » ... exists to find and optimize structural domains within protein sequences. Results: Here, we describe a new tool, PAT (http://www.kimlab.org/software/pat) that can efficiently identify both domains (with optimized boundaries) and non-domain putative structured units. PAT automatically analyzes various structural properties, evaluates the folding stability, and reports possible structural domains in a given protein sequence. For reliability evaluation of PAT, we applied PAT to identify antibody target molecules based on the notion that soluble and well-defined protein secondary and tertiary structures are appropriate target molecules for synthetic antibodies. Conclusion: PAT is an efficient and sensitive tool to identify structured units. A performance analysis shows that PAT can characterize structurally well-defined regions in a given sequence and outperforms other efforts to define reliable boundaries of domains. Specially, PAT successfully identifies experimentally confirmed target molecules for antibody generation. PAT also offers the pre-calculated results of 20,210 human proteins to accelerate common queries. PAT can therefore help to investigate large-scale structured domains and improve the success rate for synthetic antibody generation.
doi:10.1186/s12859-016-1001-1 pmid:27039071 pmcid:PMC4818438 fatcat:e3fdmfsa6vcubigdufqcxdwzhm

157-nm pellicles for photolithography: mechanistic investigation of the deep-UV photolysis of fluorocarbons

Kwangjoo Lee, Steffen Jockusch, Nicholas J. Turro, Roger H. French, Robert C. Wheland, Michael F. Lemon, Andre M. Braun, Tatjana Widerschpan, Paul Zimmerman, Bruce W. Smith
2004 Optical Microlithography XVII  
Chemical actinometry to determine the light intensity at 172 nm and l85nm was performed as described by Braun et al. utilizing the photocleavege of water and scavenging of the generated OH-radicals with  ... 
doi:10.1117/12.534381 fatcat:heuaobqa5bbj3gxgrqkp52zgsm
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