Assays
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Theoretical analysis of hypothetical sigma factor competition. Based on the model 'transcription factor competition' possible dynamics of sigma factor competition are simulated and analysed using Lineweaver-Burk representations.
Submitter: Ulf Liebal
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: The transition from growing to non-growing Baci...
Theoretical analysis of hypothetical sigma factor competition. Based on the model 'transcription factor competition' possible dynamics of sigma factor competition are simulated and analysed using Lineweaver-Burk representations.
Submitter: Ulf Liebal
Biological problem addressed: Gene Expression
Investigation: The transition from growing to non-growing Baci...
For analyzing the binding of CcpA-HPrSer46P-complexes to various cre-elements, Surface Plasmon Resonance was used. All operations were carried out on a Biacore X instrument (Biacore, Uppsala, Sweden). Biotinylated cre DNA was coupled on a Neutravidin coated chip in flowcell two, a biotinylated reference DNA in flowcell one. For visualizing only the interactions of the CcpA-HPrSer46P-complex with the cre elements, CcpA was saturated with 50µM HPrSer46P. Titrations were carried out with 5-100nM ...
Submitter: Maike Bartholomae
Assay type: Protein-protein Interaction
Technology type: Surface Plasmon Resonance
Investigation: A dynamic model of the CcpA regulation network
S. pyogenes M49 (591), E. faecalis V583, and L. lacis NZ9000 and their isogenic ldh deletion mutants were grown glucose free CDM-LAB medium in BIOLOG phenotype microarray plates PM01 and PM02. With this assay the abilitiy of the strains to grow on 190 different carbon sources was determined in 96 well format.
Submitter: Tomas Fiedler
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Investigation of glycolysis and pyruvate branch...
Biomass weight during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.
Submitter: Maksim Zakhartsev
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Kinetic analysis of metabolic system using tran...
A boolean network was created using booleannet (after experimenting with Squad and CellNetAnalyzer). This network can be simulated and visualized using additional software components that will be part of the pyMantis CMS that is developed by the Translucent project.
Submitter: Falko Krause
Biological problem addressed: Gene Regulatory Network
Investigation: ENA1 Transcription in Saccharomyces cerevisiae
The main input is the ENA review paper (Function and Regulation of the Saccharomyces cerevisiae ENA Sodium ATPase System, Ruiz&Ariño 2007) and the papers referenced. Another source are the papers linked from the ENA page of SGD http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=ENA1
Submitter: Falko Krause
Biological problem addressed: Gene Expression
Investigation: ENA1 Transcription in Saccharomyces cerevisiae
BPG degradation at 70C
Submitter: Jacky Snoep
Assay type: Metabolite Concentration
Technology type: Technology Type
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: BPG stability
BPG stability analysis
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: BPG stability