Boolean model of the gene regulatory network of Pseudomonas aeruginosa CCBH4851
IntroductionPseudomonas aeruginosa infections are one of the leading causes of death in immunocompromised patients with cystic fibrosis, diabetes, and lung diseases such as pneumonia and bronchiectasis. Furthermore, P. aeruginosa is one of the main multidrug-resistant bacteria responsible for nosoco...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-11-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1274740/full |
| _version_ | 1797392431910486016 |
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| author | Márcia da Silva Chagas Marcelo Trindade dos Santos Marcio Argollo de Menezes Fabricio Alves Barbosa da Silva |
| author_facet | Márcia da Silva Chagas Marcelo Trindade dos Santos Marcio Argollo de Menezes Fabricio Alves Barbosa da Silva |
| author_sort | Márcia da Silva Chagas |
| collection | DOAJ |
| description | IntroductionPseudomonas aeruginosa infections are one of the leading causes of death in immunocompromised patients with cystic fibrosis, diabetes, and lung diseases such as pneumonia and bronchiectasis. Furthermore, P. aeruginosa is one of the main multidrug-resistant bacteria responsible for nosocomial infections worldwide, including the multidrug-resistant CCBH4851 strain isolated in Brazil.MethodsOne way to analyze their dynamic cellular behavior is through computational modeling of the gene regulatory network, which represents interactions between regulatory genes and their targets. For this purpose, Boolean models are important predictive tools to analyze these interactions. They are one of the most commonly used methods for studying complex dynamic behavior in biological systems.Results and discussionTherefore, this research consists of building a Boolean model of the gene regulatory network of P. aeruginosa CCBH4851 using data from RNA-seq experiments. Next, the basins of attraction are estimated, as these regions and the transitions between them can help identify the attractors, representing long-term behavior in the Boolean model. The essential genes of the basins were associated with the phenotypes of the bacteria for two conditions: biofilm formation and polymyxin B treatment. Overall, the Boolean model and the analysis method proposed in this work can identify promising control actions and indicate potential therapeutic targets, which can help pinpoint new drugs and intervention strategies. |
| first_indexed | 2024-03-08T23:48:17Z |
| format | Article |
| id | doaj.art-ea18bf1bfb014b5c8a44e114346f0d9b |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-08T23:48:17Z |
| publishDate | 2023-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-ea18bf1bfb014b5c8a44e114346f0d9b2023-12-13T16:04:42ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-11-011410.3389/fmicb.2023.12747401274740Boolean model of the gene regulatory network of Pseudomonas aeruginosa CCBH4851Márcia da Silva Chagas0Marcelo Trindade dos Santos1Marcio Argollo de Menezes2Fabricio Alves Barbosa da Silva3Scientific Computing Program (PROCC), FIOCRUZ, Rio de Janeiro, BrazilNational Laboratory of Scientific Computing, Rio de Janeiro, BrazilInstitute of Physics, Fluminense Federal University, Niterói, BrazilScientific Computing Program (PROCC), FIOCRUZ, Rio de Janeiro, BrazilIntroductionPseudomonas aeruginosa infections are one of the leading causes of death in immunocompromised patients with cystic fibrosis, diabetes, and lung diseases such as pneumonia and bronchiectasis. Furthermore, P. aeruginosa is one of the main multidrug-resistant bacteria responsible for nosocomial infections worldwide, including the multidrug-resistant CCBH4851 strain isolated in Brazil.MethodsOne way to analyze their dynamic cellular behavior is through computational modeling of the gene regulatory network, which represents interactions between regulatory genes and their targets. For this purpose, Boolean models are important predictive tools to analyze these interactions. They are one of the most commonly used methods for studying complex dynamic behavior in biological systems.Results and discussionTherefore, this research consists of building a Boolean model of the gene regulatory network of P. aeruginosa CCBH4851 using data from RNA-seq experiments. Next, the basins of attraction are estimated, as these regions and the transitions between them can help identify the attractors, representing long-term behavior in the Boolean model. The essential genes of the basins were associated with the phenotypes of the bacteria for two conditions: biofilm formation and polymyxin B treatment. Overall, the Boolean model and the analysis method proposed in this work can identify promising control actions and indicate potential therapeutic targets, which can help pinpoint new drugs and intervention strategies.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1274740/fullBoolean modelgene regulatory network (GRN)pseudomonas aeruginosasystem biology and systems modelingmultidrug resistance (MDR) |
| spellingShingle | Márcia da Silva Chagas Marcelo Trindade dos Santos Marcio Argollo de Menezes Fabricio Alves Barbosa da Silva Boolean model of the gene regulatory network of Pseudomonas aeruginosa CCBH4851 Frontiers in Microbiology Boolean model gene regulatory network (GRN) pseudomonas aeruginosa system biology and systems modeling multidrug resistance (MDR) |
| title | Boolean model of the gene regulatory network of Pseudomonas aeruginosa CCBH4851 |
| title_full | Boolean model of the gene regulatory network of Pseudomonas aeruginosa CCBH4851 |
| title_fullStr | Boolean model of the gene regulatory network of Pseudomonas aeruginosa CCBH4851 |
| title_full_unstemmed | Boolean model of the gene regulatory network of Pseudomonas aeruginosa CCBH4851 |
| title_short | Boolean model of the gene regulatory network of Pseudomonas aeruginosa CCBH4851 |
| title_sort | boolean model of the gene regulatory network of pseudomonas aeruginosa ccbh4851 |
| topic | Boolean model gene regulatory network (GRN) pseudomonas aeruginosa system biology and systems modeling multidrug resistance (MDR) |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1274740/full |
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