Assays
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L. lactis, E. faecalis and S. pyogenes are referred to as LAB because of the fact that in the presence of glucose lactate is produced as the main fermentation product . This metabolic pathway is relatively inefficient, since only 2 ATP are generated from one glucose molecule. All three LAB possess the genetic make up for mixed acid fermentation, a more effective way of fermentation generating 3 ATP per molecule of glucose. All three genomes reveal (at least) two genes encoding a lactate dehydrogenase ...
Submitter: Martijn Bekker
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Investigation of glycolysis and pyruvate branch...
This .csv file shows the numbers of different cytochrome molecules per cell from steady-state continuously-grown cultures at various aerobiosis levels (0%, 31%, 56%, 85% and 115% AAU).
Submitter: Alison Graham
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Steady state studies for different oxygen avail...
To estimate the relative level of plasma-membrane potential in the wild type, single trk1 and trk2 or double trk1 trk2 mutants, the diSC3(3) fluorescent probe was added to cells grown under various conditions and the levels of cell fluorescence were monitored.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: K+ Starvation in Saccharomyces cerevisiae
To estimate the relative level of plasma-membrane potential in the wild type, single trk1 and trk2 or double trk1 trk2 mutants, the diSC3(3) fluorescent probe was added to cells grown under various conditions and the levels of cell fluorescence were monitored.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Submitter: Jay Moore
Biological problem addressed: Metabolic Network
Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...
Concentration of glycolytic intermediates over time
Submitter: Katy Wolstencroft
Assay type: Discontinuous Enzymatic
Technology type: Enzymatic Activity Measurements
Investigation: Yeast Glycolytic Oscillations
Metabolite profiling on T. brucei exposed to methylene blue has been carried out using LC-MS to investigate metabolic changes caused by oxidative stress
Submitter: Dong-Hyun Kim
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography Mass Spectrometry
Investigation: Metabolite profiling, quantification and flux q...
Submitter: Sebastian Curth
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Investigation: Investigation on the effect of pulsed metabolit...
Submitter: Sebastian Curth
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Investigation: Investigation on the effect of pulsed metabolit...
Measurement of intra- and extra-cellular metabolome.
Submitter: Ulf Liebal
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Investigation: The transition from growing to non-growing Baci...
Submitter: Jay Moore
Assay type: Metabolite Profiling
Technology type: Gas Chromatography Mass Spectrometry
Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...
Study: Timeseries 1
This Excel template is the general (master) template for any type of metabolomics data. It can be used as it is, or extended and modified to create a more specific templates for particular technologies and assay types.
Submitter: Katy Wolstencroft
Assay type: Metabolomics
Technology type: Technology Type
Investigation: Creating data sheet template for 'omics data
Lumped kinetic model of L. lactis glycolysis, formulated with ordinary differential equations. Simulations are in line with experimental data
Submitter: Mark Musters
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Investigation of glycolysis and pyruvate branch...
Model prediction of the conversion of 3PG to fructose-6-phosphate and the gluconeogenic pathway intermediates. https://jjj.bio.vu.nl/models/experiments/kouril3_experiment-user/simulate
Submitter: Jacky Snoep
Biological problem addressed: Metabolic Network
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Modelling the degradation of BPG, GAP and DHAP at high temperature
Submitter: Jacky Snoep
Biological problem addressed: Metabolism
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Based on a kinetic model a description of the potassium current is achieved. Its properties with respect to changes in membrane potential and potassium concentrations are derived.
Submitter: Falko Krause
Biological problem addressed: Model Analysis Type
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Study: Kinetic properties of Trk
Submitter: Katy Wolstencroft
Biological problem addressed: Model Analysis Type
Investigation: Yeast Glycolytic Oscillations
The RNAseq data on mRNA processing and mRNA decay were used to update a previously published model and to interrogate which process should be dependent on mRNA length
Submitter: Jurgen Haanstra
Biological problem addressed: Model Analysis Type
Investigation: Gene expression in Trypanosoma brucei
The dynamic model describes response of yeast metabolic network on metabolic perturbation (i.e. glucose-pulse). One compartmental ODE-based model of yeast anaerobic metabolism includes: glycolysis, pentose phosphate reactions, purine de novo synthesis pathway, purine salvage reactions, redox reactions and biomass growth. The model describes metabolic perturbation of steady state growing cells in chemostat.
Submitter: Maksim Zakhartsev
Biological problem addressed: Metabolic Network
Investigation: Kinetic analysis of metabolic system using tran...
This assay is designed to measure the decay kinetics of mRNA in T. brucei blood forms. T. brucei lacks the canonical transcriptional regulation employed by other eukaryotes through transcription factors, and relies almost entirely on regulation of mRNA decay and further downstream steps in order to control gene expression. 3 replicates of 8 time points were taken to measure mRNA abundance in the cell using RNA-seq. The first time point was fot WT, untreated cells; the second was 5 min after the ...
Submitter: Abeer Fadda
Assay type: Transcriptomics
Technology type: Technology Type
Investigation: Gene expression in Trypanosoma brucei