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https://hdl.handle.net/1822/74501
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Campo DC | Valor | Idioma |
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dc.contributor.author | Magalhães, Beatriz T. | por |
dc.contributor.author | Santos, Rita S. | por |
dc.contributor.author | Azevedo, Nuno F. | por |
dc.contributor.author | Lourenço, Anália | por |
dc.date.accessioned | 2021-10-25T10:23:58Z | - |
dc.date.issued | 2021-02-13 | - |
dc.identifier.citation | 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 | por |
dc.identifier.isbn | 978-1-0716-1115-9 | por |
dc.identifier.issn | 1064-3745 | por |
dc.identifier.uri | https://hdl.handle.net/1822/74501 | - |
dc.description.abstract | 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. | por |
dc.description.sponsorship | This work was financially supported by project POCI-01-0145-FEDER-006939 (Laboratory for Process Engineering, Environment, Biotechnology and Energy—UID/EQU/00511/2013), funded by European Regional Development Fund (ERDF) through COMPETE2020—Programa Operacional Competitividade e Internacionalização (POCI), by national funds (PIDDAC) through FCT—Fundação para a Ciência e a Tecnologia/MCTES; project “LEPABE-2-ECO-INNOVATION”—NORTE-01-0145-FEDER-000005, funded by Norte Portugal Regional Operational Programme (NORTE 2020), under PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). Also received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 810685. Additionally, it was partially supported by the Consellería de Educación, Universidades e Formación Profesional (Xunta de Galicia) under the scope of the strategic funding of ED431C2018/55-GRC Competitive Reference Group, and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit, COMPETE 2020 (POCI-01-0145-FEDER-006684), and PhD Grant SFRH/BD/143491/2019. | por |
dc.language.iso | eng | por |
dc.publisher | Springer US | por |
dc.relation | info:eu-repo/grantAgreement/FCT/5876/147284/PT | por |
dc.relation | info:eu-repo/grantAgreement/FCT/5876/147337/PT | por |
dc.relation | SFRH/BD/143491/2019 | por |
dc.relation | info:eu-repo/grantAgreement/EC/H2020/810685/EU | - |
dc.rights | restrictedAccess | por |
dc.subject | Fluorescence in situ hybridization | por |
dc.subject | Computational modeling | por |
dc.subject | Agent-based modeling | por |
dc.subject | Biological simulation | por |
dc.subject | Molecular diffusion | por |
dc.title | Computational resources and strategies to construct single-molecule models of FISH | por |
dc.type | bookPart | por |
dc.peerreviewed | yes | - |
dc.relation.publisherversion | https://link.springer.com/book/10.1007/978-1-0716-1115-9 | por |
dc.comments | CEB54195 | por |
oaire.citationStartPage | 317 | por |
oaire.citationEndPage | 330 | por |
oaire.citationConferencePlace | New York, NY | - |
oaire.citationVolume | Methods in Molecular Biology 2246 | - |
dc.date.updated | 2021-10-25T08:44:51Z | - |
dc.identifier.doi | 10.1007/978-1-0716-1115-9_21 | por |
dc.date.embargo | 10000-01-01 | - |
dc.identifier.pmid | 33576999 | por |
dc.description.publicationversion | info:eu-repo/semantics/publishedVersion | - |
sdum.journal | Methods in Molecular Biology | por |
sdum.bookTitle | Fluorescence In-Situ Hybridization (FISH) for Microbial Cells: Methods and Concepts | por |
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