PMID- 33576999
OWN - NLM
STAT- MEDLINE
DCOM- 20210330
LR  - 20210330
IS  - 1940-6029 (Electronic)
IS  - 1064-3745 (Linking)
VI  - 2246
DP  - 2021
TI  - Computational Resources and Strategies to Construct Single-Molecule Models of 
      FISH.
PG  - 317-330
LID - 10.1007/978-1-0716-1115-9_21 [doi]
AB  - 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 .
FAU - Magalhaes, Beatriz T
AU  - Magalhaes BT
AD  - Laboratory for Process Engineering, Environment, Biotechnology and Energy 
      (LEPABE), Department of Chemical Engineering, Faculty of Engineering of the 
      University of Porto, Porto, Portugal. beatriztmagalhaes95@gmail.com.
FAU - Santos, Rita S
AU  - Santos RS
AD  - Laboratory for Process Engineering, Environment, Biotechnology and Energy 
      (LEPABE), Department of Chemical Engineering, Faculty of Engineering of the 
      University of Porto, Porto, Portugal.
FAU - Azevedo, Nuno F
AU  - Azevedo NF
AD  - Laboratory for Process Engineering, Environment, Biotechnology and Energy 
      (LEPABE), Department of Chemical Engineering, Faculty of Engineering of the 
      University of Porto, Porto, Portugal.
FAU - Lourenco, Analia
AU  - Lourenco A
AD  - Escuela Superior de Ingenieria Informatica (ESEI), University of Vigo, Ourense, 
      Spain.
AD  - Centro de Investigaciones Biomedicas (CINBIO), University of Vigo, Vigo, Spain.
AD  - Sistemas Informaticos de Nueva Generacion (SING) Research Group, Galicia Sur 
      Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.
AD  - Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
RN  - 0 (Oligonucleotide Probes)
RN  - 0 (Oligonucleotides)
RN  - 0 (RNA, Ribosomal, 23S)
SB  - IM
MH  - Cell Wall/genetics
MH  - Cytosol/metabolism
MH  - Escherichia coli/genetics
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - Oligonucleotide Probes/genetics
MH  - Oligonucleotides/genetics
MH  - RNA, Ribosomal, 23S/genetics
OTO - NOTNLM
OT  - Agent-based modeling
OT  - Biological simulation
OT  - Computational modeling
OT  - Fluorescence in situ hybridization
OT  - Molecular diffusion
EDAT- 2021/02/13 06:00
MHDA- 2021/03/31 06:00
CRDT- 2021/02/12 12:13
PHST- 2021/02/12 12:13 [entrez]
PHST- 2021/02/13 06:00 [pubmed]
PHST- 2021/03/31 06:00 [medline]
AID - 10.1007/978-1-0716-1115-9_21 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2021;2246:317-330. doi: 10.1007/978-1-0716-1115-9_21.