1
|
Kloska SM, Pałczyński K, Marciniak T, Talaśka T, Miller M, Wysocki BJ, Davis P, Wysocki TA. Queueing theory model of pentose phosphate pathway. Sci Rep 2022; 12:4601. [PMID: 35301361 PMCID: PMC8930976 DOI: 10.1038/s41598-022-08463-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/08/2022] [Indexed: 11/25/2022] Open
Abstract
Due to its role in maintaining the proper functioning of the cell, the pentose phosphate pathway (PPP) is one of the most important metabolic pathways. It is responsible for regulating the concentration of simple sugars and provides precursors for the synthesis of amino acids and nucleotides. In addition, it plays a critical role in maintaining an adequate level of NADPH, which is necessary for the cell to fight oxidative stress. These reasons prompted the authors to develop a computational model, based on queueing theory, capable of simulating changes in PPP metabolites’ concentrations. The model has been validated with empirical data from tumor cells. The obtained results prove the stability and accuracy of the model. By applying queueing theory, this model can be further expanded to include successive metabolic pathways. The use of the model may accelerate research on new drugs, reduce drug costs, and reduce the reliance on laboratory animals necessary for this type of research on which new methods are tested.
Collapse
Affiliation(s)
- Sylwester M Kloska
- Faculty of Medicine, Nicolaus Copernicus University Ludwik Rydygier Collegium Medicum, 85-094, Bydgoszcz, Poland.
| | - Krzysztof Pałczyński
- Faculty of Telecommunications, Computer Science and Electrical Engineering, Bydgoszcz University of Science and Technology, 85-796, Bydgoszcz, Poland
| | - Tomasz Marciniak
- Faculty of Telecommunications, Computer Science and Electrical Engineering, Bydgoszcz University of Science and Technology, 85-796, Bydgoszcz, Poland
| | - Tomasz Talaśka
- Faculty of Telecommunications, Computer Science and Electrical Engineering, Bydgoszcz University of Science and Technology, 85-796, Bydgoszcz, Poland
| | - Marissa Miller
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Omaha, NE, 68182, USA
| | - Beata J Wysocki
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, 68182, USA
| | - Paul Davis
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, 68182, USA
| | - Tadeusz A Wysocki
- Faculty of Telecommunications, Computer Science and Electrical Engineering, Bydgoszcz University of Science and Technology, 85-796, Bydgoszcz, Poland. .,Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Omaha, NE, 68182, USA.
| |
Collapse
|
2
|
Kloska S, Pałczyński K, Marciniak T, Talaśka T, Nitz M, Wysocki BJ, Davis P, Wysocki TA. Queueing theory model of Krebs cycle. Bioinformatics 2021; 37:2912-2919. [PMID: 33724355 DOI: 10.1093/bioinformatics/btab177] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/08/2021] [Accepted: 03/11/2021] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION Queueing theory can be effective in simulating biochemical reactions taking place in living cells, and the article paves a step toward development of a comprehensive model of cell metabolism. Such a model could help to accelerate and reduce costs for developing and testing investigational drugs reducing number of laboratory animals needed to evaluate drugs. RESULTS The article presents a Krebs cycle model based on queueing theory. The model allows for tracking of metabolites concentration changes in real time. To validate the model, a drug-induced inhibition affecting activity of enzymes involved in Krebs cycle was simulated and compared with available experimental data. AVAILABILITYAND IMPLEMENTATION The source code is freely available for download at https://github.com/UTP-WTIiE/KrebsCycleUsingQueueingTheory, implemented in C# supported in Linux or MS Windows. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Sylwester Kloska
- Faculty of Medicine, Nicolaus Copernicus University Ludwik Rydygier Collegium Medicum, 85-067 Bydgoszcz, Poland
| | - Krzysztof Pałczyński
- Faculty of Telecommunications, Computer Science and Electrical Engineering, UTP University of Science and Technology, 85-796 Bydgoszcz, Poland
| | - Tomasz Marciniak
- Faculty of Telecommunications, Computer Science and Electrical Engineering, UTP University of Science and Technology, 85-796 Bydgoszcz, Poland
| | - Tomasz Talaśka
- Faculty of Telecommunications, Computer Science and Electrical Engineering, UTP University of Science and Technology, 85-796 Bydgoszcz, Poland
| | - Marissa Nitz
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Omaha, NE 68182, USA
| | - Beata J Wysocki
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Paul Davis
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Tadeusz A Wysocki
- Faculty of Telecommunications, Computer Science and Electrical Engineering, UTP University of Science and Technology, 85-796 Bydgoszcz, Poland.,Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Omaha, NE 68182, USA
| |
Collapse
|
3
|
Panchal AR, Comte B, Huang H, Kerwin T, Darvish A, des Rosiers C, Brunengraber H, Stanley WC. Partitioning of pyruvate between oxidation and anaplerosis in swine hearts. Am J Physiol Heart Circ Physiol 2000; 279:H2390-8. [PMID: 11045976 DOI: 10.1152/ajpheart.2000.279.5.h2390] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The goal of this study was to measure flux through pyruvate carboxylation and decarboxylation in the heart in vivo. These rates were measured in the anterior wall of normal anesthetized swine hearts by infusing [U-(13)C(3)]lactate and/or [U-(13)C(3)] pyruvate into the left anterior descending (LAD) coronary artery. After 1 h, the tissue was freeze-clamped and analyzed by gas chromatography-mass spectrometry for the mass isotopomer distribution of citrate and its oxaloacetate moiety. LAD blood pyruvate and lactate enrichments and concentrations were constant after 15 min of infusion. Under near-normal physiological concentrations of lactate and pyruvate, pyruvate carboxylation and decarboxylation accounted for 4.7 +/- 0.3 and 41.5 +/- 2.0% of citrate formation, respectively. Similar relative fluxes were found when arterial pyruvate was raised from 0.2 to 1.1 mM. Addition of 1 mM octanoate to 1 mM pyruvate inhibited pyruvate decarboxylation by 93% without affecting carboxylation. The absence of M1 and M2 pyruvate demonstrated net irreversible pyruvate carboxylation. Under our experimental conditions we found that pyruvate carboxylation in the in vivo heart accounts for at least 3-6% of the citric acid cycle flux despite considerable variation in the flux through pyruvate decarboxylation.
Collapse
Affiliation(s)
- A R Panchal
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106-4970, USA
| | | | | | | | | | | | | | | |
Collapse
|