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Arkun Y. Detection of biological switches using the method of Gröebner bases. BMC Bioinformatics 2019; 20:615. [PMID: 31779580 PMCID: PMC6883700 DOI: 10.1186/s12859-019-3155-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 10/14/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bistability and ability to switch between two stable states is the hallmark of cellular responses. Cellular signaling pathways often contain bistable switches that regulate the transmission of the extracellular information to the nucleus where important biological functions are executed. RESULTS In this work we show how the method of Gröebner bases can be used to detect bistability and output switchability. The method of Gröebner bases can be seen as a multivariate, non-linear generalization of the Gaussian elimination for linear systems which conveniently seperates the variables and drastically simplifies the simultaneous solution of polynomial equations. A necessary condition for fixed-point state bistability is for the Gröbner basis to have three distinct solutions for the state. A sufficient condition is provided by the eigenvalues of the local Jacobians. We also introduce the concept of output switchability which is defined as the ability of an output of a bistable system to switch between two different stable steady-state values. It is shown that bistability does not necessarily guarantee switchability of every state variable of the system. We further show that, for a bistable system, the necessary conditions for output switchability can be derived using the Gröebner basis. The theoretical results are incorporated into an analysis procedure and applied to several systems including the AKT (Protein kinase B), RAS (Rat Sarcoma) and MAPK (Mitogen-activated protein kinase) signal transduction pathways. Results demonstrate that the Gröebner bases can be conveniently used to analyze biological switches by simultaneously detecting bistability and output switchability. CONCLUSION The Gröebner bases provides a novel methodology to analyze bistability. Results clarify the distinction between bistability and output switchability which is lacking in the literature. We have shown that theoretically, it is possible to have an output subspace of an n-dimensional bistable system where certain variables cannot switch. It is possible to construct such systems as we have done with two reaction networks.
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Affiliation(s)
- Yaman Arkun
- Department of Chemical and Biological Engineering, Koc University, Rumeli Feneri Yolu, 34450, Sariyer, Istanbul, Turkey.
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McCormick CD, Waters HN, Bezrukov L, Taginya R, Parikh V, Onyekaba GI, Levine JA, Demidowich AP, Yanovski JA, Blank PS, Zimmerberg J. Subcutaneous adipose tissue imaging of human obesity reveals two types of adipocyte membranes: Insulin-responsive and -nonresponsive. J Biol Chem 2018; 293:14249-14259. [PMID: 30006347 DOI: 10.1074/jbc.ra118.003751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/28/2018] [Indexed: 11/06/2022] Open
Abstract
In adipose tissue, resistance to insulin's ability to increase glucose uptake can be induced by multiple factors, including obesity. Impaired insulin action may take place at different spatial loci at the cellular or subcellular level. To begin to understand the spatial response to insulin in human subcutaneous adipose tissue (hSAT), we developed a quantitative imaging method for activation of a major signaling node in the glucoregulatory insulin signaling pathway. After treatment with insulin or control media, biopsied tissues were immunostained for Akt phosphorylation at Thr-308/9 (pAkt) and then imaged by confocal fluorescence microscopy automated to collect a large grid of high resolution fields. In hSAT from 40 men and women with obesity, substantial heterogeneity of pAkt densities in adipocyte membranes were quantified in each image mosaic using a spatial unit of at least twice the size of the point spread function. Statistical analysis of the distribution of pAkt spatial units was best fit as the weighted sum of two separate distributions, corresponding to either a low or high pAkt density. A "high pAkt fraction" metric was calculated from the fraction of high pAkt distributed units over the total units. Importantly, upon insulin stimulation, tissues from the same biopsy showed either a minimal or a substantial change in the high pAkt fraction. Further supporting a two-state response to insulin stimulation, subjects with similar insulin sensitivity indices are also segregated into either of two clusters identified by the amount of membrane-localized pAkt.
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Affiliation(s)
| | | | | | | | - Viraj Parikh
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Ginikanwa I Onyekaba
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Jordan A Levine
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Andrew P Demidowich
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Jack A Yanovski
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
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Cheng G, Tang X, Zhang J. Hepatocyte growth factor exerts beneficial effects on mice with type II diabetes‑induced chronic renal failure via the NF‑κB pathway. Mol Med Rep 2018; 18:3389-3396. [PMID: 30066918 DOI: 10.3892/mmr.2018.9297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/13/2017] [Indexed: 11/06/2022] Open
Abstract
Type II diabetes is associated with a low quality of life and inflammation, and is often accompanied by varying degrees of chronic renal failure. Chronic renal failure is considered one of the most important factors that aggravates diabetes and contributes to renal insufficiency in patients with diabetes though cellular fibrosis. It has previously been reported that hepatocyte growth factor (HGF) serves extensive biological roles, and is a multifunctional antifibrotic factor that is involved in kidney development, acute injury and regeneration. The present study aimed to investigate whether HGF exerts beneficial effects on type II diabetes‑induced chronic renal failure in a mouse model. Plasma concentration levels of HGF, tumor necrosis factor (TNF)‑α, monocyte chemoattractant protein (MCP)‑1, interleukin (IL)‑1 and IL‑6 were analyzed prior to and following treatment with HGF. Blood urea nitrogen, plasma creatinine concentrations, and electrolyte, total serum protein, parathyroid hormone and C‑reactive protein levels were analyzed by ELISA. The mechanism underlying the effects of the HGF‑mediated signaling pathway was also investigated in mice with type II diabetes‑induced chronic renal failure. Histological analysis was used to determine the therapeutic effects of HGF on mice with type II diabetes‑induced chronic renal failure. The results indicated that HGF exhibited lower plasma concentrations in mice with type II diabetes‑induced chronic renal failure compared with in healthy mice. In addition, treatment with HGF relieved chronic renal failure via inhibition of inflammation. The results indicated that TNF‑α, MCP‑1 and IL‑1 serum concentration levels were downregulated following treatment with HGF. Conversely, IL‑6 and vascular endothelial growth factor concentration was increased in the HGF‑treated mice compared with in the control mice. The results also demonstrated that HGF treatment downregulated the expression of nuclear factor (NF)‑κB molecules, and target molecules C‑C motif chemokine ligand (Ccl)2, Ccl5, intercellular adhesion molecule 1 and TNF‑α. The present study demonstrated that HGF markedly improved renal failure induced by type II diabetes in a mouse model; histological analyses revealed that renal cell injury was improved following treatment with HGF. In conclusion, these results suggested that HGF may exert beneficial effects on type II diabetes‑induced chronic renal failure via regulation of the NF‑κB signaling pathway.
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Affiliation(s)
- Guiming Cheng
- Department of Nephrology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510282, P.R. China
| | - Xun Tang
- Department of Nephrology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510282, P.R. China
| | - Jun Zhang
- Department of Nephrology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510282, P.R. China
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Dynamic Modeling and Analysis of the Cross-Talk between Insulin/AKT and MAPK/ERK Signaling Pathways. PLoS One 2016; 11:e0149684. [PMID: 26930065 PMCID: PMC4773096 DOI: 10.1371/journal.pone.0149684] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/02/2016] [Indexed: 12/26/2022] Open
Abstract
Feedback loops play a key role in the regulation of the complex interactions in signal transduction networks. By studying the network of interactions among the biomolecules present in signaling pathways at the systems level, it is possible to understand how the biological functions are regulated and how the diseases emerge from their deregulations. This paper identifies the key feedback loops involved in the cross-talk among the insulin-AKT and MAPK/ERK signaling pathways. We developed a mathematical model that can be used to study the steady-state and dynamic behavior of the interactions among these two important signaling pathways. Modeling analysis and simulation case studies identify the key interaction parameters and the feedback loops that determine the normal and disease phenotypes.
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Cruz JC, Flôr AFL, França-Silva MS, Balarini CM, Braga VA. Reactive Oxygen Species in the Paraventricular Nucleus of the Hypothalamus Alter Sympathetic Activity During Metabolic Syndrome. Front Physiol 2015; 6:384. [PMID: 26779026 PMCID: PMC4688401 DOI: 10.3389/fphys.2015.00384] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 11/27/2015] [Indexed: 12/31/2022] Open
Abstract
The paraventricular nucleus of the hypothalamus (PVN) contains heterogeneous populations of neurons involved in autonomic and neuroendocrine regulation. The PVN plays an important role in the sympathoexcitatory response to increasing circulating levels of angiotensin II (Ang-II), which activates AT1 receptors in the circumventricular organs (OCVs), mainly in the subfornical organ (SFO). Circulating Ang-II induces a de novo synthesis of Ang-II in SFO neurons projecting to pre-autonomic PVN neurons. Activation of AT1 receptors induces intracellular increases in reactive oxygen species (ROS), leading to increases in sympathetic nerve activity (SNA). Chronic sympathetic nerve activation promotes a series of metabolic disorders that characterizes the metabolic syndrome (MetS): dyslipidemia, hyperinsulinemia, glucose intolerance, hyperleptinemia and elevated plasma hormone levels, such as noradrenaline, glucocorticoids, leptin, insulin, and Ang-II. This review will discuss the contribution of our laboratory and others regarding the sympathoexcitation caused by peripheral Ang-II-induced reactive oxygen species along the subfornical organ and paraventricular nucleus of the hypothalamus. We hypothesize that this mechanism could be involved in metabolic disorders underlying MetS.
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Affiliation(s)
- Josiane C Cruz
- Centro de Biotecnologia, Universidade Federal da Paraíba João Pessoa, Brazil
| | - Atalia F L Flôr
- Centro de Biotecnologia, Universidade Federal da Paraíba João Pessoa, Brazil
| | | | - Camille M Balarini
- Centro de Biotecnologia, Universidade Federal da ParaíbaJoão Pessoa, Brazil; Centro de Ciências da Saúde, Universidade Federal da ParaíbaJoão Pessoa, Brazil
| | - Valdir A Braga
- Centro de Biotecnologia, Universidade Federal da Paraíba João Pessoa, Brazil
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Lizunov VA, Stenkula KG, Blank PS, Troy A, Lee JP, Skarulis MC, Cushman SW, Zimmerberg J. Human adipose cells in vitro are either refractory or responsive to insulin, reflecting host metabolic state. PLoS One 2015; 10:e0119291. [PMID: 25768970 PMCID: PMC4359092 DOI: 10.1371/journal.pone.0119291] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 01/12/2015] [Indexed: 01/14/2023] Open
Abstract
While intercellular communication processes are frequently characterized by switch-like transitions, the endocrine system, including the adipose tissue response to insulin, has been characterized by graded responses. Yet here individual cells from adipose tissue biopsies are best described by a switch-like transition between the basal and insulin-stimulated states for the trafficking of the glucose transporter GLUT4. Two statistically-defined populations best describe the observed cellular heterogeneity, representing the fractions of refractive and responsive adipose cells. Furthermore, subjects exhibiting high systemic insulin sensitivity indices (SI) have high fractions of responsive adipose cells in vitro, while subjects exhibiting decreasing SI have increasing fractions of refractory cells in vitro. Thus, a two-component model best describes the relationship between cellular refractory fraction and subject SI. Since isolated cells exhibit these different response characteristics in the presence of constant culture conditions and milieu, we suggest that a physiological switching mechanism at the adipose cellular level ultimately drives systemic SI.
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Affiliation(s)
- Vladimir A. Lizunov
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States of America
| | - Karin G. Stenkula
- Experimental Diabetes, Metabolism, and Nutrition Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States of America
- Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Paul S. Blank
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States of America
| | - Aaron Troy
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States of America
| | - Jo-Ping Lee
- Experimental Diabetes, Metabolism, and Nutrition Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Monica C. Skarulis
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Samuel W. Cushman
- Experimental Diabetes, Metabolism, and Nutrition Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Joshua Zimmerberg
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States of America
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Cizmeci D, Arkun Y. Regulatory networks and complex interactions between the insulin and angiotensin II signalling systems: models and implications for hypertension and diabetes. PLoS One 2013; 8:e83640. [PMID: 24400038 PMCID: PMC3882141 DOI: 10.1371/journal.pone.0083640] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/05/2013] [Indexed: 12/30/2022] Open
Abstract
The cross-talk between insulin and angiotensin II signalling pathways plays a significant role in the co-occurrence of diabetes and hypertension. We developed a mathematical model of the system of interactions among the biomolecules that are involved in the cross-talk between the insulin and angiotensin II signalling pathways. We have identified several feedback structures that regulate the dynamic behavior of the individual signalling pathways and their interactions. Different scenarios are simulated and dominant steady-state, dynamic and stability characteristics are revealed. The proposed mechanistic model describes how angiotensin II inhibits the actions of insulin and impairs the insulin-mediated vasodilation. The model also predicts that poor glycaemic control induced by diabetes contributes to hypertension by activating the renin angiotensin aystem.
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Affiliation(s)
- Deniz Cizmeci
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Yaman Arkun
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
- * E-mail:
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