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- Pawel Sierocinski
FAIRDOMHub ID: https://seek.sysmo-db.org/people/264
Location:
NL
Disciplines: Experimentalist
Expertise: Genetics, Microbiology
Tools: Microarray analysis, Fermentation, Transcriptomics
ORCID: Not specified
Related items
- Projects (1)
- Institutions (1)
- Investigations (1)
- Studies (1)
- Assays (5)
- Data files (0+6)
- SOPs (4+1)
- Publications (2)
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
The Sulfolobus systems biology (‘‘SulfoSYS’’)-project represented the first (hyper-)thermophilic Systems Biology project, funded within the European trans-national research initiative ‘‘Systems Biology of Microorganisms’’. Within the SulfoSYS-project, focus lies on studying the effect of temperature variation on the central carbohydrate metabolism (CCM) of S. solfataricus that is characterized by the branched Entner–Doudoroff (ED)-like pathway for sugar (glucose, galactose) degradation and the
...
Snapshots: No snapshots
Studies: Pilot experiment - S. solfataricus grown at 70 and 80 C.
Assays: Comparison of proteome of S. solfataricus at 70 and 80C, Comparison of transcriptome of S. solfataricus at 70 and 80C, Enzyme activity tests for S. solfataricus, Fermentation of S. solfataricus at 70 and 80C in a batch fermenter, Intracellular metabolomics of S. solfataricus at 70 and 80C
The pilot experiment has been set up in order to develop uniform SOPs for the Sulfosys consortium. It comprises proteomics, transcriptomics, metabolomics as well as enzymatic essays. Cells for all the members of the consortium have been obtained from the same batch fermentations according to fermentation SOP of Sulfosys. The pilot resulted in creating a procedures for all the techniques used in consortium.
Person responsible: Pawel Sierocinski
Snapshots: No snapshots
Investigation: Analysis of Central Carbon Metabolism of Sulfol...
Assays: Comparison of proteome of S. solfataricus at 70 and 80C, Comparison of transcriptome of S. solfataricus at 70 and 80C, Enzyme activity tests for S. solfataricus, Fermentation of S. solfataricus at 70 and 80C in a batch fermenter, Intracellular metabolomics of S. solfataricus at 70 and 80C
The pilot experiment was conducted in order to create SOPs and to gain insight in transcriptome of cells grown at 70 and 80C
Contributor: Pawel Sierocinski
Assay type: Transcriptional Profiling
Technology type: Microarray
Snapshots: No snapshots
Investigation: Analysis of Central Carbon Metabolism of Sulfol...
Study: Pilot experiment - S. solfataricus grown at 70 ...
Organisms: Sulfolobus solfataricus (batch)
SOPs: Sulfosys - SOP microarray
Data files: No Data files
Samples obtained form the central fermentation facility of Sulfosys have been compared using iTRAQ (isobaric tag for relative and absolute quantification). A pilot experiment resulted in creation of SOP and initial data on cells grown at 70 and 80C
Contributor: Pawel Sierocinski
Assay type: Protein Expression Profiling
Technology type: Isotope Ratio Mass Spectrometry
Snapshots: No snapshots
Investigation: Analysis of Central Carbon Metabolism of Sulfol...
Study: Pilot experiment - S. solfataricus grown at 70 ...
Organisms: Sulfolobus solfataricus (batch)
SOPs: Sulfosys - SOP proteomics
Data files: 1 hidden item
In order to get uniform data from all geographically separated partners in a consortium, central fermentation facility has been set-up. Based on empirical data, standard procedures for growing S. solfataricus cells have been developed.
Contributor: Pawel Sierocinski
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Analysis of Central Carbon Metabolism of Sulfol...
Study: Pilot experiment - S. solfataricus grown at 70 ...
Organisms: Sulfolobus solfataricus (batch)
SOPs: Sulfosys - SOP fermentation
Data files: 6 hidden items
Based on initial cell material, series of SOPs connected with assays of enzymes involved in Central Carbon Metabolism of S. solfataricus have been developed.
Contributor: Pawel Sierocinski
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Analysis of Central Carbon Metabolism of Sulfol...
Study: Pilot experiment - S. solfataricus grown at 70 ...
Organisms: Sulfolobus solfataricus (chemostat)
SOPs: 1 hidden item
Data files: 2 hidden items
Pilot experiment concerning metabolome of S. solfataricus was conducted in order to acquire SOPs regarding the technique and gain insight on differences in metabolite concentrations at 70 and 80C
Contributor: Pawel Sierocinski
Assay type: Metabolomics
Technology type: Gas Chromatography Mass Spectrometry
Snapshots: No snapshots
Investigation: Analysis of Central Carbon Metabolism of Sulfol...
Study: Pilot experiment - S. solfataricus grown at 70 ...
Organisms: Sulfolobus solfataricus (batch)
SOPs: Sulfosys - SOP metabolomics
Data files: No Data files
SOPs related with medium composition, fermentation and stocking of S. solfataricus.
Creator: Pawel Sierocinski
Contributor: Pawel Sierocinski
Investigations: Analysis of Central Carbon Metabolism of Sulfol... and 1 hidden item
Studies: Pilot experiment - S. solfataricus grown at 70 ... and 1 hidden item
Assays: Fermentation of S. solfataricus at 70 and 80C i... and 1 hidden item
Standard procedure regarding intracellular metabolome analysis using GC-MS.
Creator: Pawel Sierocinski
Contributor: Pawel Sierocinski
Protocol for RNA isolation, cDNA synthesis and labeling and hybridization and cleanup of Sulfolobus solfataricus microarray
Creator: Pawel Sierocinski
Contributor: Pawel Sierocinski
Standard operating procedures regarding iTraq based proteomics.
Creator: Pawel Sierocinski
Contributor: Pawel Sierocinski
All contributors
Abstract (Expand)
Authors: Melanie Zaparty, Susanne Gertig, Patrick Haferkamp, Theresa Kouril, Andrea Manica, Trong Khoa Pham, Kerstin Schreiber, Pawel Sierocinski, Mathias Von Jan, Patricia Wieloch, Sonja-Verena Albers, Arnold Driessen, Hans-Peter Klenk, Christa Schleper, Dietmar Schomburg, John Van Der Oost, Phil Wright, Bettina Siebers, Esser Dominik,Reimann Julia,Teichmann Daniela,van Wolferen Marleen
Date Published: 31st Aug 2009
Journal: Extremophiles
PubMed ID: 19802714
Citation:
Abstract (Expand)
Authors: None
Date Published: 4th Dec 2009
Journal: J. Proteome Res.
PubMed ID: 19954172
Citation: