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Rao2014 - Yeast glycolysis (reduced model)

ABSTRACT: This is the reduced model corresponding to "glucose upshift" condition described in the paper "Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics" by van Eunen et al published in Plos Comput Biol, 2012.

SUBMITTER: Shodhan Rao

PROVIDER: MODEL1403250002 | BioModels | 2014-09-15

REPOSITORIES: BioModels

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Publications

A model reduction method for biochemical reaction networks.

Rao Shodhan S van der Schaft Arjan A van Eunen Karen K Bakker Barbara M BM Jayawardhana Bayu B

BMC systems biology 20140503

<h4>Background</h4>In this paper we propose a model reduction method for biochemical reaction networks governed by a variety of reversible and irreversible enzyme kinetic rate laws, including reversible Michaelis-Menten and Hill kinetics. The method proceeds by a stepwise reduction in the number of complexes, defined as the left and right-hand sides of the reactions in the network. It is based on the Kron reduction of the weighted Laplacian matrix, which describes the graph structure of the comp ...[more]

PMID: 24885656

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vanEunen2012 - Yeast Glycolysis (glucose upshift)

Project description:This is corresponding to the model of yeast glycolysis "glucose upshift" condition described in the paper "Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics" by van Eunen et al published in Plos Comput Biol, 2012.

2014-09-15 | MODEL1403250001 | BioModels

Rao2014 - Fatty acid beta-oxidation (reduced model)

Project description:This represents the reduced version of the "time course model" of Van Eunen et al (2013): Biochemical competition makes fatty-acid beta-oxidation vulnerable to substrate overload. The SBML was created from that of the original model and produces identical results when a time-course of 25 mins is run in COPASI

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Bexkens2024 - Schistosoma mansoni glycolysis

Project description:A kinetic model of S. mansoni glycolysis in which we can vary the allosteric regulation on lactate dehydrogenase (LDH). Because not enough kinetic data are available for all the schistosome enzymes to construct a complete schistosome glycolysis model de novo, we here adjusted the well-established glycolysis model of the eukaryotic microbe Saccharomyces cerevisiae (Teusink et al., 2000; van Eunen et al., 2012; van Heerden et al., 2014). We removed reactions from the yeast model that are not used in schistosomes and added glycogen metabolism, a Krebs cycle, respiration and an allosterically regulated LDH that was parameterized on multiple in vitro kinetic data sets for schistosome LDH. Additional files are published on Zenodo: https://zenodo.org/records/10401097

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Restricted glycolysis is a primary cause of the reduced growth rate of zinc-deficient yeast cells.

Project description:Zinc is required for many critical processes, including intermediary metabolism. In Saccharomyces cerevisiae, the Zap1 activator regulates the transcription of ∼80 genes in response to Zn supply. Some Zap1-regulated genes are Zn transporters that maintain Zn homeostasis, while others mediate adaptive responses that enhance fitness. One adaptive response gene encodes the 2-cysteine peroxiredoxin Tsa1, which is critical to Zn-deficient (ZnD) growth. Depending on its redox state, Tsa1 can function as a peroxidase, a protein chaperone, or a regulatory redox sensor. In a screen for possible Tsa1 regulatory targets, we identified a mutation (cdc19S492A) that partially suppressed the tsa1Δ growth defect. The cdc19S492A mutation reduced activity of its protein product, pyruvate kinase isozyme 1 (Pyk1), implicating Tsa1 in adapting glycolysis to ZnD conditions. Glycolysis requires activity of the Zn-dependent enzyme fructose-bisphosphate aldolase 1, which was substantially decreased in ZnD cells. We hypothesized that in ZnD tsa1Δ cells, the loss of a compensatory Tsa1 regulatory function causes depletion of glycolytic intermediates and restricts dependent amino acid synthesis pathways, and that the decreased activity of Pyk1S492A counteracted this depletion by slowing the irreversible conversion of phosphoenolpyruvate to pyruvate. In support of this model, supplementing ZnD tsa1Δ cells with aromatic amino acids improved their growth. Phosphoenolpyruvate supplementation, in contrast, had a much greater effect on growth rate of WT and tsa1Δ ZnD cells, indicating that inefficient glycolysis is a major factor limiting yeast growth. Surprisingly however, this restriction was not primarily due to low fructose-bisphosphate aldolase 1 activity, but instead occurs earlier in glycolysis.

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Reduced Nicotinamide Mononucleotide (NMNH) Potently Enhances NAD+, Suppresses Glycolysis and Cell Growth

Project description:In the present study, we developed a chemical method to produce dihydro nicotinamide mononucleotide (NMNH), which is the reduced-form of nicotinamide mononucleotide (NMN). We demonstrated that NMNH was a better nicotinamide adenine dinucleotide (NAD+) enhancer compared to NMN both in vitro and in vivo mediated by mononucleotide adenylyltransferase (NMNAT). Additionally, NMNH increased the reduced NAD (NADH) levels in cells and in mouse liver. Metabolomic analysis revealed that NMNH inhibited glycolysis and TCA cycle. In vitro experiments demonstrated that NMNH induced cell cycle arrest and suppressed cell growth. Nevertheless, NMNH treatment did not cause observable difference in mice. Taken together, our work demonstrates that NMNH is a potent NAD+ enhancer, and suppresses glycometabolism and cell growth.

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Hansen2019 - Seven species reduced model of blood coagulation

Project description:its a seven species reduced model of Hockin 2002. Model uses different level of reduction (5,7,9,11) and testing the best alignment with Hockin model results).

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Hansen2019 - Nine species reduced model of blood coagulation

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Reduced Intensity Conditioning for Non-Malignant Disorders Undergoing UCBT, BMT or PBSCT

Project description:The objective of this study is to evaluate the efficacy of using a reduced-intensity condition (RIC) regimen with umbilical cord blood transplant (UCBT), double cord UCBT, matched unrelated donor (MUD) bone marrow transplant (BMT) or peripheral blood stem cell transplant (PBSCT) in patients with non-malignant disorders that are amenable to treatment with hematopoietic stem cell transplant (HSCT). After transplant, subjects will be followed for late effects and for ongoing graft success.

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