Models

Copasi file chronic inflammation Abulikemu et al 2020 (altered units TNF and MMP8); see supplemntal material: TNF and MMP7 concentration upgrade of the models All computations for the present paper were completed by using the model prepared and tested in Abulikemu et al 2018. Then, little attention was paid to the unit in which concentrations were expressed, except for the concentration of fibroblasts, which we found important for modelling the effect of confluency. This led to a predicted TNF ...

Copasi file chronic inflammation Abulikemu et al 2020 (altered units TNF and MMP8); see supplemntal material: TNF and MMP7 concentration upgrade of the models All computations for the present paper were completed by using the model prepared and tested in Abulikemu et al 2018. Then, little attention was paid to the unit in which concentrations were expressed, except for the concentration of fibroblasts, which we found important for modelling the effect of confluency. This led to a predicted TNF ...

This is a model about a ROS network that exhibits five design principles, and has been calibrated so as to predict quantitatively various steady state concentrations. 10191125.

Instructions RUN the model for steady state. For the Menadione experiment set the initial concentration of 'Menadione' species to experimental dosing i.e. 100 000 nM (0.1 mM) and make the simulation type "reaction" for both the species i.e. 'Menadione' and 'Menadione_internal'. Then run for 24 hr i.e. 1500 minutes approx. ...

Model that can be used to obtain the figures of Abudulikemu et al 2018: Abudukelimu, A., Barberis, M., Redegeld, F.A., Sahin, N., and Westerhoff, H.V. (2018). Predictable Irreversible Switching Between Acute and Chronic Inflammation. Front Immunol 9, 1596.

(Abudulikemu et al 2000 (also 2018) Standard model of acute mode Figure 32.

Particularly figure 2 of of Abudulikemu et al 2020 in press

The principles of Stealthy Engineering (Adamczyk et al.: Biotechnology Journal 2012; 7(7):877-83) are illustrated in this model by emulating a cross engineering intervention between L. lactis and S. cerevisiae.

The case study consists of replacing the native glucose uptake system of L. lactis with that native to the yeast S. cerevisiae. A modified version of Hoefnagel et al.’s model of L. lacrtis’ central metabolism was used as starting point. The total functional replacement of the PTS with the ...

The model includes glycolysis, pentosephosphate pathway, purine salvage reactions, purine de novo synthesis, redox balance and biomass growth. The network balances adenylate pool as opened moiety.