Jacky Snoep

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
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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.

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.

PGK-GAPDH reactions were studied in vitro at 30 and 70 using yeast or Sso enzymes

SED-ML:
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig4b/simulate
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig4c/simulate

PGK reaction at 30 C. Yeast PGK was incubated at 30 C, in the presence or absence of the ATP recycling system, and the conversion of 3 PG to BPG was followed.
SED-ML simulations
Fig. 1A: https://jjj.bio.vu.nl/models/experiments/kouril2017_fig1a/simulate

PGK reaction at 70C. Sulfolobus solfataricus PGK was incubated at 70C in presence and absence of an ATP recycling system.
Changes in metabolite concentrations was followed via 31P NMR or enzymatic analyses.

SED-ML:
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig3b/simulate
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig3c/simulate
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig3d/simulate

BPG produced with yeast PGK was incubated at 70 C,upon which BPG rapidly dephosphorylates to 3PG.
SED-ML:
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig2b/simulate

After the removal of the extracellular antibiotic, efflux and inhibition dynamics combine to delay the synthesis of ribosomes in a concentration-dependent manner (panel ii). Colors indicate increasing antibiotic concentration, as shown in panel ii.

SED-ML simulation
https://jjj.bio.vu.nl/models/experiments/srimani2017_fig2cii/simulate

Growth-factor deprived mCFU-E cells (5x106 cells per condition) and BaF3-EpoR cells (1x107 cells per condition) were stimulated with different Epo doses and absolute concentrations were determined for pEpoR (B), pAKT (C), ppERK (D). The scale for pS6 (E) was estimated in arbitrary units. GTP-Ras (F) and ppERK were determined upon stimulation with indicated, color-coded Epo doses. pEpoR was analyzed by immunoprecipitation followed by immunoblotting, GTP-Ras was analyzed after pulldown using a
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Transcriptional response to a sudden increase in extracellular ligand (hormone), for the six network designs of (A). The transcriptional response is taken to equal the ratio ReNrL/Retotal, i.e., the fraction of REs attaching ligand-bound NR. The ligand concentration was increased from 0 to 0.005 nM and maintained constant at the latter level. The observation that design 6 is higher than all other designs at long times is robust for parameter changes up to a factor of 3.

Experimental data for the yeast PGK incubations at 30C, with and without recycling of ATP.

Changes in metabolite concentrations were either quantified via 31P NMR or enzymatically

BPG degradation at 70C

Simulation results of TPI experimental data for GAP and DHAP saturation.

Simulation results of temperature degradation of gluconeogenic intermediates

Simulation results of experimental data of the reconstituted gluconeogenic system

Simulation results of PGK experimental data for ADP, ATP, 3PG and BPG saturation.

Simulation results of FBPAase of experimental data for DHAP and GAP saturation

Simulation results of GAPDH experimental data for BPG, NADPH, NADP, GAP, and Pi

PGK-GAPDH model Sulfolobus kouril8

PGK-GAPDH model yeast kouril7

PGK-GAPDH models yeast and Sulfolobus Fig. 4 in manuscript

PGK 70C model, Fig 3 in manuscript

PGK 70C SBML

BPG stability notebook

PGK yeast Fig1a

SOP for the determination of external metabolites (Glc, Pyr, Gly, Lac) in intact trophozoite incubations, and for the determination of intracellular metabolite concentrations.

SOP for the cultivation conditions of Plasmodium falciparum, including the protocol for synchronisation.

SOP for measurement of G3PDH activity in extracts.

SOP for measurement of ALD activity in extracts.

SOP for measurement of glucose transport activity in intact trophozoites.

SOP for measurement of GAPDH activity in extracts.

SOP for measurement of ENO activity in extracts.

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Talk by Jacky Snoep, Stellenbosch University, SA

Presentation of data management concepts for ERASysAPP projects at IMOMESIC kick off meeting on 8 th of May 2015 in Heidelberg. Part I presented by Olga Krebs

Carole Goble's talk at ERASysAPP - EXCHANGE Networking and Info Day for research projects of the first ERASysAPP call (a day before PALs meeting)

Poster presented at SWAT4LS - Semantic web applications and tools for life science- in Berlin at 10 of december 2014 by Olga Krebs

Presentation by Carole Goble at the International Semantic Web Conference 2013 in Sydney Australia about the use of semantic web technology in SEEK and RightField.