Modeling the mechanism pathways of first line drug in Tuberculosis using Petri nets

Singh, Gajendra Pratap; Jha, Madhuri; Singh, Mamtesh; Naina,

doi:10.1007/s13198-019-00940-4

Cited by 10 publications

(2 citation statements)

References 35 publications

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“…It has been used to model various biological pathways/processes, e.g., metabolism, signal transduction, gene regulation, protein complex assembly, metabolic disorders for biomedical data prediction, and enzyme kinetic modeling (Koch et al, 2017). Recently, PN are used for modeling of biological pathways (PHA; C3 pathway), networks for processes involved in diagnostics, treatment, and multi drug resistance in tuberculosis (Gupta et al, 2019;Singh and Jha, 2019;Singh et al, 2020).…”

Section: Metabolic Network Modelingmentioning

confidence: 99%

Challenges and Perspectives of Polyhydroxyalkanoate Production From Microalgae/Cyanobacteria and Bacteria as Microbial Factories: An Assessment of Hybrid Biological System

Afreen

Tyagi

Singh

et al. 2021

Front. Bioeng. Biotechnol.

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Polyhydroxyalkanoates (PHAs) are the biopolymer of choice if we look for a substitute of petroleum-based non-biodegradable plastics. Microbial production of PHAs as carbon reserves has been studied for decades and PHAs are gaining attention for a wide range of applications in various fields. Still, their uneconomical production is the major concern largely attributed to high cost of organic substrates for PHA producing heterotrophic bacteria. Therefore, microalgae/cyanobacteria, being photoautotrophic, prove to have an edge over heterotrophic bacteria. They have minimal metabolic requirements, such as inorganic nutrients (CO2, N, P, etc.) and light, and they can survive under adverse environmental conditions. PHA production under photoautotrophic conditions has been reported from cyanobacteria, the only candidate among prokaryotes, and few of the eukaryotic microalgae. However, an efficient cultivation system is still required for photoautotrophic PHA production to overcome the limitations associated with (1) stringent management of closed photobioreactors and (2) optimization of monoculture in open pond culture. Thus, a hybrid system is a necessity, involving the participation of microalgae/cyanobacteria and bacteria, i.e., both photoautotrophic and heterotrophic components having mutual interactive benefits for each other under different cultivation regime, e.g., mixotrophic, successive two modules, consortium based, etc. Along with this, further strategies like optimization of culture conditions (N, P, light exposure, CO2 dynamics, etc.), bioengineering, efficient downstream processes, and the application of mathematical/network modeling of metabolic pathways to improve PHA production are the key areas discussed here. Conclusively, this review aims to critically analyze cyanobacteria as PHA producers and proposes economically sustainable production of PHA from microbial autotrophs and heterotrophs in “hybrid biological system.”

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Section: Metabolic Network Modelingmentioning

confidence: 99%

Challenges and Perspectives of Polyhydroxyalkanoate Production From Microalgae/Cyanobacteria and Bacteria as Microbial Factories: An Assessment of Hybrid Biological System

Afreen

Tyagi

Singh

et al. 2021

Front. Bioeng. Biotechnol.

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“…Different approaches used for modeling GRNs are described in the literature ( Miyagi et al., 2002 ; Hardy and Robillard, 2004 ; Anitha et al., 2016 ; Livigni et al., 2016 ; Pennisi et al., 2016 ; Singh et al., 2020 ). These approaches include differential equations, stochastic simulations, flux balance analysis, graphical models, and Petri nets (PNs).…”

Section: Introductionmentioning

confidence: 99%

Expression Profile of Genes Related to the Th17 Pathway in Macrophages Infected by Leishmania major and Leishmania amazonensis: The Use of Gene Regulatory Networks in Modeling This Pathway

Gonçalves

Pulido

Mathias³

et al. 2022

Front. Cell. Infect. Microbiol.

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Leishmania amazonensis and Leishmania major are the causative agents of cutaneous and mucocutaneous diseases. The infections‘ outcome depends on host–parasite interactions and Th1/Th2 response, and in cutaneous form, regulation of Th17 cytokines has been reported to maintain inflammation in lesions. Despite that, the Th17 regulatory scenario remains unclear. With the aim to gain a better understanding of the transcription factors (TFs) and genes involved in Th17 induction, in this study, the role of inducing factors of the Th17 pathway in Leishmania–macrophage infection was addressed through computational modeling of gene regulatory networks (GRNs). The Th17 GRN modeling integrated experimentally validated data available in the literature and gene expression data from a time-series RNA-seq experiment (4, 24, 48, and 72 h post-infection). The generated model comprises a total of 10 TFs, 22 coding genes, and 16 cytokines related to the Th17 immune modulation. Addressing the Th17 induction in infected and uninfected macrophages, an increase of 2- to 3-fold in 4–24 h was observed in the former. However, there was a decrease in basal levels at 48–72 h for both groups. In order to evaluate the possible outcomes triggered by GRN component modulation in the Th17 pathway. The generated GRN models promoted an integrative and dynamic view of Leishmania–macrophage interaction over time that extends beyond the analysis of single-gene expression.

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Applications of Petri Net Modeling in Diverse Areas

Singh

Jha

Singh

2021

Advances in Intelligent Systems and Computing

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Modeling the mechanism pathways of first line drug in Tuberculosis using Petri nets

Cited by 10 publications

References 35 publications

Challenges and Perspectives of Polyhydroxyalkanoate Production From Microalgae/Cyanobacteria and Bacteria as Microbial Factories: An Assessment of Hybrid Biological System

Challenges and Perspectives of Polyhydroxyalkanoate Production From Microalgae/Cyanobacteria and Bacteria as Microbial Factories: An Assessment of Hybrid Biological System

Expression Profile of Genes Related to the Th17 Pathway in Macrophages Infected by Leishmania major and Leishmania amazonensis: The Use of Gene Regulatory Networks in Modeling This Pathway

Applications of Petri Net Modeling in Diverse Areas

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