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- Dietmar Schomburg
SEEK ID: https://fairdomhub.org/people/66
Location:
Germany
Expertise: Microbiology, Biochemistry, Bioinformatics, Data Management, Systems Biology, Bacterial metabolism | Metabolic engineering
Tools: Not specified
ORCID: Not specified
Related items
- Projects (3)
- Institutions (1)
- Investigations (3+1)
- Studies (3)
- Assays (5)
- Data files (3)
- Models (1)
- Publications (5)
Within the e:Bio - Innovationswettbewerb Systembiologie (Federal Ministry of Education and Research (BMBF)), the SulfoSYSBIOTECH consortium (10 partners), aim to unravel the complexity and regulation of the carbon metabolic network of the thermoacidophilic archaeon Sulfolobus solfataricus (optimal growth at 80°C and pH 3) in order to provide new catalysts ‘extremozymes’ for utilization in White Biotechnology.
Based on the available S. solfataricus genome scale metabolic model (Ulas et al., 2012)
...
Programme: e:Bio
Public web page: http://www.sulfosys.com/
Organisms: Sulfolobus solfataricus
Systems analysis of process-induced stresses: towards a quantum increase in process performance of Pseudomonas putida as the cell factory of choice for white biotechnology.
The specific goal of this project is to exploit the full biotechnological efficacy of Pseudomonas putida KT2440 by developing new optimization strategies that increase its performance through a systems biology understanding of key metabolic and regulatory parameters that control callular responses to key stresses generated
...
Programme: SysMO
Public web page: http://www.psysmo.org/
Organisms: Pseudomonas putida
Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation
Programme: SysMO
Public web page: http://sulfosys.com/
Organisms: Sulfolobus solfataricus
Present in many industrial effluents and as intermediate of lignin degradation, phenol is a widespread pollutant causing serious environmental problems, due to its toxicity to animals and humans. Removal of phenol from the environment by bacteria has been studied extensively over the past decades, but only little is known about phenol biodegradation in hostile environments. We combined metabolomics and transcriptomics together with metabolic modelling to elucidate the organism’s response to growth
...
Snapshots: No snapshots
Integrated systems biology approach including transcriptome, metabolome, proteome analyses and modelling to elucidate amino acid degradation in S. solfataricus P2.
Snapshots: No snapshots
Integrated systems biology approach including transcriptome, metabolome, biochemistry, proteome analyses and modelling to elucidate the catabolic pathway for L-fucose in S. solfataricus P2.
Snapshots: No snapshots
To investigate phenol degradation in Saccharolobus solfataricus transcriptome and metabolome analyses were performed with cells grown on phenol as sole carbon source. Cells grown on D-glucose served as reference. Metabolic modelling was used to compare efficiency of phenol utilization in terms of oxygen demand and energy yield with the reference condition.
Person responsible: Jacqueline Wolf
Snapshots: No snapshots
To investigate amino acid degradation pathways in Sulfolobus solfataricus transcriptome, proteome and metabolome analyses were performed on cells grown on caseinhydrolysate as carbon source. Cells grown with glucose served as reference condition. Metabolic modelling was used to compare the efficiency of different degradation routes.
Person responsible: Jacqueline Wolf
Snapshots: No snapshots
Submitter: Jacqueline Wolf
Assay type: Experimental Assay Type
Technology type: Gas Chromatography
Snapshots: No snapshots
Investigation: Phenol degradation in Saccharolobus solfataricu...
Study: Comparison of S. solfataricus P2 grown on pheno...
Organisms: Sulfolobus solfataricus (batch)
SOPs: No SOPs
Data files: Metabolome analysis phenol vs glucose
Intracellular and extracellular metabolome analysis
Submitter: Jacqueline Wolf
Assay type: Metabolite Profiling
Technology type: Gas Chromatography Mass Spectrometry
Snapshots: No snapshots
Investigation: Amino acid degradation in Sulfolobus solfataric...
Study: Comparison of Sulfolobus solfataricus P2 grown ...
Organisms: Sulfolobus solfataricus (batch)
SOPs: No SOPs
Data files: Amino acid depletion profile of S. solfataricus..., Calculation of amino acid uptake rates, Integrated summary of transcriptomics and prote..., Metabolomics Casaminoacids vs Glc
Growth on D-glucose served as reference scenario
Investigation: Amino acid degradation in Sulfolobus solfataric...
Study: Comparison of Sulfolobus solfataricus P2 grown ...
Organisms: Sulfolobus solfataricus
Models: Metabolic model of Sulfolobus solfataricus
SOPs: No SOPs
Data files: Biomass composition of S. solfataricus P2 grown..., Calculation of amino acid uptake rates, Description of changes made to the model compar..., Distribution of enzymes involved in oxidative S...
Submitter: Theresa Kouril
Assay type: Metabolite Profiling
Technology type: Gas Chromatography Mass Spectrometry
Snapshots: No snapshots
Investigation: L-fucose degradation in Sulfolobus solfataricus P2
Study: Comparison of S. solfataricus grown on l-fucose...
Organisms: Sulfolobus solfataricus (batch)
SOPs: No SOPs
Data files: Metabolomics L-fuc vs D-glc
Genome scale metabolic model of Sulfolobus solfataricus
specific scenario: modelling of L-fucose degradation pathways
Investigation: L-fucose degradation in Sulfolobus solfataricus P2
Study: Comparison of S. solfataricus grown on l-fucose...
Organisms: Sulfolobus solfataricus
Models: Metabolic model of Sulfolobus solfataricus
SOPs: No SOPs
Data files: No Data files
Sulfolobus solfataricus P2 was cultivated on 1 % Caseinhydrolysate. Samples of the culture supernatants were taken at regular intervalls and analyzed by GC-MS. To evaluate the stability of amino acids under cultivation conditions an additional non-inoculated control culture was also analyzed.
Creators: Jacqueline Wolf, Dietmar Schomburg, Meina Neumann-Schaal, Julia Hofmann
Submitter: Jacqueline Wolf
Intracellular metabolome analysis of S. solfataricus P2 grown on caseinhydrolysate or D-glucose as sole carbon source.
Samples were analyzed with GC-MS. CoA derivatives were analyzed with LC-MS.
Creators: Jacqueline Wolf, Dietmar Schomburg
Submitter: Jacqueline Wolf
Comparative GC-MS based metabolomics of S. solfataricus growing on either L-fucose or D-glucose. CoA derivatives were analysed via HPLC-MS
Creators: Jacqueline Wolf, Dietmar Schomburg
Submitter: Jacqueline Wolf
Metabolic model of Sulfolobus solfataricus P2 in the SBML (xml) and metano (txt, sce, fba) format. Scenarios are specific for growth on D-glucose or L-fucose as sole carbon source. Different theoretical routes of L-fucose degradation were modeled (E. coli-like, Xanthomonas-like and lactaldehyde-forming). Highest overall agreement between the model and experimental data was observed for the lactaldehyde-forming route.
Creators: Jacqueline Wolf, Helge Stark, Dietmar Schomburg
Submitter: Jacqueline Wolf
Model type: Metabolic network
Model format: SBML
Environment: Not specified
Organism: Sulfolobus solfataricus
Investigations: L-fucose degradation in Sulfolobus solfataricus P2
Studies: Comparison of S. solfataricus grown on l-fucose...
Modelling analyses: Metabolic model of Sulfolobus solfataricus
Abstract (Expand)
Authors: A. S. Figueiredo, T. Kouril, D. Esser, P. Haferkamp, P. Wieloch, D. Schomburg, P. Ruoff, B. Siebers, J. Schaber
Date Published: 12th Jul 2017
Publication Type: Not specified
PubMed ID: 28692669
Citation: PLoS One. 2017 Jul 10;12(7):e0180331. doi: 10.1371/journal.pone.0180331. eCollection 2017.
Abstract (Expand)
Authors: Helge Stark, Jacqueline Wolf, Andreas Albersmeier, Trong K. Pham, Julia D. Hofmann, Bettina Siebers, Jörn Kalinowski, Phillip C. Wright, Meina Neumann-Schaal, Dietmar Schomburg
Date Published: 29th May 2017
Publication Type: Not specified
DOI: 10.1111/febs.14105
Citation: FEBS J 86 : 156
Abstract (Expand)
Authors: J. Wolf, H. Stark, K. Fafenrot, A. Albersmeier, T. K. Pham, K. B. Muller, B. Meyer, L. Hoffmann, L. Shen, S. P. Albaum, T. Kouril, K. Schmidt-Hohagen, M. Neumann-Schaal, C. Brasen, J. Kalinowski, P. C. Wright, S. V. Albers, D. Schomburg, B. Siebers
Date Published: 10th Sep 2016
Publication Type: Not specified
PubMed ID: 27611014
Citation: Mol Microbiol. 2016 Sep 9. doi: 10.1111/mmi.13498.
Abstract (Expand)
Authors: , I. F. Escapa, C. Jager, J. Puchalka, , , ,
Date Published: 20th Mar 2012
Publication Type: Not specified
PubMed ID: 22433058
Citation:
All contributors
Abstract (Expand)
Authors: , Dominik Esser, , , , , , Julia Reimann, , , Daniela Teichmann, Marleen van Wolferen, , , , , , , , , ,
Date Published: 31st Aug 2009
Publication Type: Not specified
PubMed ID: 19802714
Citation: