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New insights on the role of lipid metabolism in the metabolic reprogramming of macrophages
(Frontiers Media, 2020)
Macrophage activation is intimately linked to metabolic reprogramming. Inflammatory (M1) macrophages are able to sustain inflammatory responses and to kill pathogens, mostly by relying on aerobic glycolysis and fatty acid ...
Metabolic networks from (M, R) systems and autopoiesis perspective
(2002)
This paper is the first one of a series devoted to the analysis of metabolic networks. Its aim is to establish the theoretical framework for this analysis. Two different lines of research are considered: the one about ...
Continuous Modeling of Metabolic Networks With Gene Regulation in Yeast and In Vivo Determination of Rate Parameters
(2012-09)
A continuous model of a metabolic network
including gene regulation to simulate metabolic fluxes during
batch cultivation of yeast Saccharomyces cerevisiae was
developed. The metabolic network includes reactions ...
Traceability, reproducibility and wiki-exploration for "a-la-carte" reconstructions of genome-scale metabolic models
(Public Library Science, 2018-05)
Genome-scale metabolic models have become the tool of choice for the global analysis of microorganism metabolism, and their reconstruction has attained high standards of quality and reliability. Improvements in this area ...
Genome-scale reconstruction of Salinispora tropica CNB-440 metabolism to study strain-specific adaptation
(Springer, 2015)
The first manually curated genome-scale metabolic model for Salinispora tropica strain CNB-440 was constructed. The reconstruction enables characterization of the metabolic capabilities for understanding and modeling the ...
Integration of biological networks for Acidithiobacillus thiooxidans Describes a modular gene regulatory organization of bioleaching pathways
(Frontiers Media, 2020)
Acidithiobacillus thiooxidansis one of the most studied biomining species, highlighting its ability to oxidize reduced inorganic sulfur compounds, coupled with its elevated capacity to live under an elevated concentration ...
From reconstruction to C-4 metabolic engineering: a case study for overproduction of polyhydroxybutyrate in bioenergy grasses
(Elsevier, 2018-08)
The compartmentalization of C-4 plants increases photosynthetic efficiency, while constraining how material and energy must flow in leaf tissues. To capture this metabolic phenomenon, a generic plant metabolic reconstruction ...
Organizational invariance and metabolic closure: Analysis in terms of M;R systems
(Elsevier Ltd., 2005-08-24)
This article analyses the work of Robert Rosen on an interpretation of metabolic networks that he called ðM;RÞ systems. His
main contribution was an attempt to prove that metabolic closure (or metabolic circularity) could ...
Analysis of metabolic networks of Streptomyces leeuwenhoekii C34 by means of a genome scale model: Prediction of modifications that enhance the production of specialized metabolites
(Wiley, 2018)
The first genome scale model (GSM) for Streptomyces leeuwenhoekii C34 was developed to study the biosynthesis pathways of specialized metabolites and to find metabolic engineering targets for enhancing their production. ...
Inflammation-associated suppression of metabolic gene networks in acute and chronic liver disease
(Springer, 2020)
Inflammation has been recognized as essential for restorative regeneration. Here, we analyzed the sequential processes during onset of liver injury and subsequent regeneration based on time-resolved transcriptional regulatory ...