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https://hdl.handle.net/1822/74501
Título: | Computational resources and strategies to construct single-molecule models of FISH |
Autor(es): | Magalhães, Beatriz T. Santos, Rita S. Azevedo, Nuno F. Lourenço, Anália |
Palavras-chave: | Fluorescence in situ hybridization Computational modeling Agent-based modeling Biological simulation Molecular diffusion |
Data: | 13-Fev-2021 |
Editora: | Springer US |
Revista: | Methods in Molecular Biology |
Citação: | Magalhães, Beatriz T.; Santos, Rita S.; Azevedo, Nuno F.; Lourenço, Anália, Computational resources and strategies to construct single-molecule models of FISH. In Nuno F. Azevedo, Carina Almeida, Fluorescence In-Situ Hybridization (FISH) for Microbial Cells: Methods and Concepts, Vol. Methods in Molecular Biology 2246, Springer US, 2021. ISBN: 978-1-0716-1115-9, 317-330. DOI: 10.1007/978-1-0716-1115-9_21 |
Resumo(s): | 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 moleculesMolecules 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. |
Tipo: | Capítulo de livro |
URI: | https://hdl.handle.net/1822/74501 |
ISBN: | 978-1-0716-1115-9 |
DOI: | 10.1007/978-1-0716-1115-9_21 |
ISSN: | 1064-3745 |
Versão da editora: | https://link.springer.com/book/10.1007/978-1-0716-1115-9 |
Arbitragem científica: | yes |
Acesso: | Acesso restrito UMinho |
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document_54195_1.pdf Acesso restrito! | 295,64 kB | Adobe PDF | Ver/Abrir |