Assays
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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
The stressosome is an important sensor of environmental stresses in B. subtilis. It is formed by three protein types that form an icosahedral geometric protein complex. There are uncertanties how protein interactions take place, what the effects on the response behaviour of activation and inhibition of phosphorylation among proteins is, and what kind of proximal signal activates the stressosome in the first place. To answer these questions a computational modelling approach was developed. This ...
Submitter: Ulf Liebal
Biological problem addressed: Signal Induction
Investigation: The transition from growing to non-growing Baci...
Despite high similarity in sequence and catalytic properties, the L-lactate dehydrogenases (LDH) in lactic acid bacteria (LAB) display differences in their regulation which may arise from their adaptation to different habitats. We combined experimental and computational approaches to investigate the effects of fructose-1,6-bisphosphate (FBP), phosphate (Pi) and ionic strength (NaCl concentration) on 6 LDHs from 4 LABs studied at pH 6 and pH 7. We find: (1) The extent of activation by FBP (Kact) ...
Submitter: Anna Feldman-Salit
Biological problem addressed: Metabolism
Investigation: Investigation of glycolysis and pyruvate branch...
We here create a kinetic model for a single enzyme within the T. brucei trypanothione synthesis pathway, the enzyme trypanothione synthetase based on the insights from the laboratory experiments
Submitter: Jurgen Haanstra
Biological problem addressed: Enzymology
Investigation: Kinetic understanding of the T. brucei trypanot...
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
Kinetic characterisation en mathematical modelling of HK.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of PGI.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of PFK.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of ALD.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of TPI.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of G3PDH.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of GAPDH.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of PGK.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of PGM.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of ENO.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of PK.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation and mathematical modelling of LDH.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/penkler2aa_experiment-user/simulate
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model validation
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model validation
RobOKoD algorithm was, designed then implemented as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain. It was shown to perform better than similar methods (OptKnock, and RobustKnock).
Submitter: Natalie Stanford
Biological problem addressed: Model Analysis Type
Investigation: Designing a new way to predict engineering stra...
OptKnock algorithm was used as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain.
Submitter: Natalie Stanford
Biological problem addressed: Model Analysis Type
Investigation: Designing a new way to predict engineering stra...
RobustKnock algorithm was used as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain.
Submitter: Natalie Stanford
Biological problem addressed: Model Analysis Type
Investigation: Designing a new way to predict engineering stra...
Submitter: Jay Moore
Biological problem addressed: Metabolic Network
Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...
Time-dependent simulations of the dynamic switch between acidogenesis and solventogenesis based on the metabolic network and pH-dependent regulation of the enzymes.
Submitter: Sara Jabbari
Biological problem addressed: Metabolic Network
Investigation: The effect of pH upon the metabolic shift in Cl...
Steady state study of the effect of altering gene regulation on yields of end-products, focusing on butanol.
Submitter: Sara Jabbari
Biological problem addressed: Gene Expression
Investigation: The effect of pH upon the metabolic shift in Cl...