Computational Resources and Strategies to Construct Single-Molecule Models of FISH
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , |
Tipo de documento: | Livro |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | https://hdl.handle.net/10216/140769 |
Resumo: | Currently, the interactions occurring between oligonucleotides and the cellular envelope of bacteria are not fully resolved at the molecular level. Understanding these interactions is essential to gain insights on how to improve the internalization of the tagged oligonucleotides during fluorescence in situ hybridization (FISH). Agent-based modeling (ABM) is a promising in silico tool to dynamically simulate FISH and bring forward new knowledge on this process. Notably, it is important to simulate the whole bacterial cell, including the different layers of the cell envelope, given that the oligonucleotide must cross the envelope to reach its target in the cytosol. In addition, it is also important to characterize other molecules in the cell to best emulate the cell and represent molecular crowding. Here, we review the main information that should be compiled to construct an ABM on FISH and provide a practical example of an oligonucleotide targeting the 23S rRNA of Escherichia coli. (c) 2020, Springer Science+Business Media, LLC, part of Springer Nature. |
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Computational Resources and Strategies to Construct Single-Molecule Models of FISHCurrently, the interactions occurring between oligonucleotides and the cellular envelope of bacteria are not fully resolved at the molecular level. Understanding these interactions is essential to gain insights on how to improve the internalization of the tagged oligonucleotides during fluorescence in situ hybridization (FISH). Agent-based modeling (ABM) is a promising in silico tool to dynamically simulate FISH and bring forward new knowledge on this process. Notably, it is important to simulate the whole bacterial cell, including the different layers of the cell envelope, given that the oligonucleotide must cross the envelope to reach its target in the cytosol. In addition, it is also important to characterize other molecules in the cell to best emulate the cell and represent molecular crowding. Here, we review the main information that should be compiled to construct an ABM on FISH and provide a practical example of an oligonucleotide targeting the 23S rRNA of Escherichia coli. (c) 2020, Springer Science+Business Media, LLC, part of Springer Nature.2021-02-132021-02-13T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/bookapplication/pdfhttps://hdl.handle.net/10216/140769eng10.1007/978-1-0716-1115-9_21Beatriz T. MagalhãesRita S. SantosNuno F. AzevedoAnália Lourençoinfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-29T14:13:00Zoai:repositorio-aberto.up.pt:10216/140769Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T23:57:11.295072Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Computational Resources and Strategies to Construct Single-Molecule Models of FISH |
title |
Computational Resources and Strategies to Construct Single-Molecule Models of FISH |
spellingShingle |
Computational Resources and Strategies to Construct Single-Molecule Models of FISH Beatriz T. Magalhães |
title_short |
Computational Resources and Strategies to Construct Single-Molecule Models of FISH |
title_full |
Computational Resources and Strategies to Construct Single-Molecule Models of FISH |
title_fullStr |
Computational Resources and Strategies to Construct Single-Molecule Models of FISH |
title_full_unstemmed |
Computational Resources and Strategies to Construct Single-Molecule Models of FISH |
title_sort |
Computational Resources and Strategies to Construct Single-Molecule Models of FISH |
author |
Beatriz T. Magalhães |
author_facet |
Beatriz T. Magalhães Rita S. Santos Nuno F. Azevedo Anália Lourenço |
author_role |
author |
author2 |
Rita S. Santos Nuno F. Azevedo Anália Lourenço |
author2_role |
author author author |
dc.contributor.author.fl_str_mv |
Beatriz T. Magalhães Rita S. Santos Nuno F. Azevedo Anália Lourenço |
description |
Currently, the interactions occurring between oligonucleotides and the cellular envelope of bacteria are not fully resolved at the molecular level. Understanding these interactions is essential to gain insights on how to improve the internalization of the tagged oligonucleotides during fluorescence in situ hybridization (FISH). Agent-based modeling (ABM) is a promising in silico tool to dynamically simulate FISH and bring forward new knowledge on this process. Notably, it is important to simulate the whole bacterial cell, including the different layers of the cell envelope, given that the oligonucleotide must cross the envelope to reach its target in the cytosol. In addition, it is also important to characterize other molecules in the cell to best emulate the cell and represent molecular crowding. Here, we review the main information that should be compiled to construct an ABM on FISH and provide a practical example of an oligonucleotide targeting the 23S rRNA of Escherichia coli. (c) 2020, Springer Science+Business Media, LLC, part of Springer Nature. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-02-13 2021-02-13T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/book |
format |
book |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://hdl.handle.net/10216/140769 |
url |
https://hdl.handle.net/10216/140769 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
10.1007/978-1-0716-1115-9_21 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799135892837761024 |