Investigations
What is an Investigation?Filters
Cyanobacterial PFKs were thought to be ATP dependent, but isolation and characterisation of 2 PFK isoenzymes from Synechocystis revealed that they belong to the PFK-A family, use ADP as phosphate donor and form a separate phylogenetic class. Their allosteric regulation via 3-PG and ATP respectively allow for flexible switching between aactive and inactive enzymes dependent on the light and carbon status.
The figures 2, 3, 4 and 6 in the main text of the manuscript: "Inhibition of the glucocorticoid-activating enzyme 11β-hydroxysteroid dehydrogenase type 1 drives concurrent 11-oxygenated androgen excess", submitted to FASEB by Lina Schiffer, Imken Oestlund, Jacky Snoep, Lorna C. Gilligan, Angela E. Taylor, Alexandra J. Sinclair, Rishi Singhal, Adrian Freeman, Ramzi Ajjan, Ana Tiganescu, Wiebke Arlt and Karl-Heinz Storbeck, are reproduced in Mathematica notebooks. The notebooks and the corresponding ...
Submitter: Jacky Snoep
Studies: CBX inhibition of HSD11B1 and effect on HSD11B1/AKR1C3 incubations, Computational analysis of combined HSD11B1/AKR1C3 ratios and HSD11B1 inh..., HSD11B1/AKR1C3 ratio experiments, Inhibition of HSD11B1 in adipose tissue
Assays: Data for HSD11B1/AKR1C3 ratio experiment in Fig. 2, Experimental data for HSD11B1/AKR1C3 incubation with CBX inhibition, Inhibition of HSD11B1 in adipose tissue, Model analysis for HSD11B1/AKR1C3 ratio experiment, Model for computational analysis of HSD11B1/AKR1C3 ratio variation and H..., Model simulations of HSD11B1/AKR1C3 incubation and cortisone and 11KA4 i..., Simulation of HSD11B1 inhibition in human adipose tissue
The investigation entails the construction and validation of a detailed mathematical model for glycolysis erythrocytes infected with the malaria parasite Plasmodium falciparum in the blood stage form.
Submitter: Dawie van Niekerk
Studies: Analysis of model for malaria-infected erythrocytes, Intra-erythrocytic malaria parasite volumes, Validation of model for malaria-infected erythrocytes
Assays: Flux vs external glucose, Flux vs parasitaemia, GLC incubation, Inhibition of glycolytic flux, Malaria parasite volume determinations, Metabolic control analysis, Stage specific fluxes, Steady-state
The oxidative Weimberg pathway for the five-step pentose degradation to α ketoglutarate from Caulobacter crescentus is a key route for sustainable bioconversion of lignocellulosic biomass to added-value products and biofuels. Here, we developed a novel iterative approach involving initial rate kinetics, progress curves, and enzyme cascades, with high resolution NMR analysis of intermediate dynamics, and multiple cycles of kinetic modelling analyses to construct and validate a quantitative model ...
Submitter: Jacky Snoep
Studies: Cell free extract, Initial rate kinetics, One pot cascade, Progress curves
Assays: Cell free extract, with Mn and NAD recycling, Cell free extract, with Mn, no NAD recycling, Cell free extract, without added Mn, with NAD recycling, KDXD, KGSADH, One pot cascade 10, One pot cascade 12, One pot cascade 13, One pot cascade 16, Progress curve KDXD, Progress curve KGSADH, Progress curve XAD, Progress curve XDH, Progress curve XLA, Progress curves combined, Steady state cell free extract, with Mn and NAD recycling, XAD, XDH, XLA
Biphasic response as a mechanism against mutant takeover in tissue homeostasis circuits
Submitter: Jacky Snoep
Studies: Figure 1C: Biphasic control can resist mutant invasion of feedback circu..., Figure 1D: Biphasic control can resist mutant invasion of feedback circu..., Figure 1G: Biphasic control can resist mutant invasion of feedback circu..., Figure 1H: Biphasic control can resist mutant invasion of feedback circu..., Figure 2: Frequency-dependent selection of mutant pancreatic beta cells., Figure 4C: Biphasic control can provide mutant resistance to stem-cell h..., Figure 4D: Biphasic control can provide mutant resistance to stem-cell h...
Assays: Biphasic control can provide mutant resistance to stem-cell homeostatic ..., Biphasic control can provide mutant resistance to stem-cell homeostatic ..., Biphasic control can resist mutant invasion of feedback circuits., Biphasic control can resist mutant invasion of feedback circuits., Biphasic control can resist mutant invasion of feedback circuits., Biphasic control can resist mutant invasion of feedback circuits., Frequency-dependent selection of mutant pancreatic beta cells.
Frequency doubling in the cyanobacterial circadian clock
Submitter: Jacky Snoep
Studies: Figure 4B: A minimal mathematical model, containing an incoherent feedfo..., Figure 6C and D: The clock-sigC circuit represents a general mechanism t...
Assays: Frequency doubling in the cyanobacterial circadian clock, Frequency doubling in the cyanobacterial circadian clock
Submitter: Dawie van Niekerk
Studies: Allosteric regulation of phosphofructokinase controls the emergence of g..., Heterogeneity of glycolytic oscillatory behaviour in individual yeast cells, Sustained glycolytic oscillations in individual isolated yeast cells
Assays: gustavsson1-4 models, gustavsson5 model
Submitter: Jacky Snoep
Studies: Entrainment of heterogeneous glycolytic oscillations in single cells
Assays: No Assays
Submitter: Jacky Snoep
Studies: Substrate preferences for AKR1C3, and implications of varying AKR1C3:17B...
Assays: No Assays
The gluconeogenic conversion of 3-phosphoglycerate via 1,3-bisphosphoglycerate to glyceraldehyde-3-phosphate was compared at 30 C and at 70 C. At 30 C it was possible to produce 1,3-bisphosphoglycerate from 3-phosphoglycerate with phosphoglycerate kinase, but at 70 C, 1,3- bisphosphoglycerate was dephosphorylated rapidly to 3-phosphoglycerate, effectively turning the phosphoglycerate kinase into a futile cycle. At both temperatures it was possible to convert 3-phosphoglycerate to glyceraldehyde ...
Submitter: Jacky Snoep
Studies: BPG stability, PGK-30C, PGK-70C, PGK-GAPDH 30C & 70C
Assays: BPG degradation, BPG stability analysis, PGK - GAPDH models, PGK 30C data, PGK 30C model, PGK 70 data, PGK 70C model, PGK-GAPDH 30, PGK-GAPDH 70
Drug detoxification dynamics explain the postantibiotic effect
Protein abundance of AKT and ERK pathway components governs cell-type- specific regulation of proliferation
The investigation entails the construction and validation of a detailed mathematical model for glycolysis of the malaria parasite Plasmodium falciparum in the blood stage trophozoite form.
Submitter: Dawie van Niekerk
Studies: Model analysis, Model construction, Model validation
Assays: ALD, ATPASE, Culturing and synchronisation of P. falciparum, ENO, G3PDH, GAPDH, GLC incubation, GLCtr, GLYtr, HK, Inhibition of glucose transport, Inhibition of lactate flux, LACtr, LDH, PFK, PGI, PGK, PGM, PK, PYRtr, Steady state, Supply-demand analysis, TPI, Trophozoite Isolation and Lysate Preparation
Design principles of nuclear receptor signaling: how complex networking improves signal transduction
Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range
An investigation in the central carbon metabolism of S. solfataricus with a focus on the unique temperature adaptations and regulation; using a combined modelling and experimental approach.
Submitter: Jacky Snoep
Studies: Carbon Loss at High Temperature, Model Gluconeogenesis
Assays: Experimental Validation Gluconeogenesis in S. solfataricus, FBPAase, FBPAase Modelling, GAPDH, GAPDH Modelling, Model Validation Gluconeogenesis in S. solfataricus, Modelling Metabolite Degradation at High Temperature, PGK, PGK Modelling, Reconstituted Gluconeogenesis System, TPI, TPI Modelling, Temperature Degradation of Gluconeogenic Intermediates
