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Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport

BACKGROUND: To study the chemical determinants of small molecule transport inside cells, it is crucial to visualize relationships between the chemical structure of small molecules and their associated subcellular distribution patterns. For this purpose, we experimented with cells incubated with a sy...

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Detalles Bibliográficos
Autores principales: Rosania, Gus R, Shedden, Kerby, Zheng, Nan, Zhang, Xinyuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852740/
https://www.ncbi.nlm.nih.gov/pubmed/24093553
http://dx.doi.org/10.1186/1758-2946-5-44
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author Rosania, Gus R
Shedden, Kerby
Zheng, Nan
Zhang, Xinyuan
author_facet Rosania, Gus R
Shedden, Kerby
Zheng, Nan
Zhang, Xinyuan
author_sort Rosania, Gus R
collection PubMed
description BACKGROUND: To study the chemical determinants of small molecule transport inside cells, it is crucial to visualize relationships between the chemical structure of small molecules and their associated subcellular distribution patterns. For this purpose, we experimented with cells incubated with a synthetic combinatorial library of fluorescent, membrane-permeant small molecule chemical agents. With an automated high content screening instrument, the intracellular distribution patterns of these chemical agents were microscopically captured in image data sets, and analyzed off-line with machine vision and cheminformatics algorithms. Nevertheless, it remained challenging to interpret correlations linking the structure and properties of chemical agents to their subcellular localization patterns in large numbers of cells, captured across large number of images. RESULTS: To address this challenge, we constructed a Multidimensional Online Virtual Image Display (MOVID) visualization platform using off-the-shelf hardware and software components. For analysis, the image data set acquired from cells incubated with a combinatorial library of fluorescent molecular probes was sorted based on quantitative relationships between the chemical structures, physicochemical properties or predicted subcellular distribution patterns. MOVID enabled visual inspection of the sorted, multidimensional image arrays: Using a multipanel desktop liquid crystal display (LCD) and an avatar as a graphical user interface, the resolution of the images was automatically adjusted to the avatar’s distance, allowing the viewer to rapidly navigate through high resolution image arrays, zooming in and out of the images to inspect and annotate individual cells exhibiting interesting staining patterns. In this manner, MOVID facilitated visualization and interpretation of quantitative structure-localization relationship studies. MOVID also facilitated direct, intuitive exploration of the relationship between the chemical structures of the probes and their microscopic, subcellular staining patterns. CONCLUSION: MOVID can provide a practical, graphical user interface and computer-assisted image data visualization platform to facilitate bioimage data mining and cheminformatics analysis of high content, phenotypic screening experiments.
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spelling pubmed-38527402013-12-13 Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport Rosania, Gus R Shedden, Kerby Zheng, Nan Zhang, Xinyuan J Cheminform Methodology BACKGROUND: To study the chemical determinants of small molecule transport inside cells, it is crucial to visualize relationships between the chemical structure of small molecules and their associated subcellular distribution patterns. For this purpose, we experimented with cells incubated with a synthetic combinatorial library of fluorescent, membrane-permeant small molecule chemical agents. With an automated high content screening instrument, the intracellular distribution patterns of these chemical agents were microscopically captured in image data sets, and analyzed off-line with machine vision and cheminformatics algorithms. Nevertheless, it remained challenging to interpret correlations linking the structure and properties of chemical agents to their subcellular localization patterns in large numbers of cells, captured across large number of images. RESULTS: To address this challenge, we constructed a Multidimensional Online Virtual Image Display (MOVID) visualization platform using off-the-shelf hardware and software components. For analysis, the image data set acquired from cells incubated with a combinatorial library of fluorescent molecular probes was sorted based on quantitative relationships between the chemical structures, physicochemical properties or predicted subcellular distribution patterns. MOVID enabled visual inspection of the sorted, multidimensional image arrays: Using a multipanel desktop liquid crystal display (LCD) and an avatar as a graphical user interface, the resolution of the images was automatically adjusted to the avatar’s distance, allowing the viewer to rapidly navigate through high resolution image arrays, zooming in and out of the images to inspect and annotate individual cells exhibiting interesting staining patterns. In this manner, MOVID facilitated visualization and interpretation of quantitative structure-localization relationship studies. MOVID also facilitated direct, intuitive exploration of the relationship between the chemical structures of the probes and their microscopic, subcellular staining patterns. CONCLUSION: MOVID can provide a practical, graphical user interface and computer-assisted image data visualization platform to facilitate bioimage data mining and cheminformatics analysis of high content, phenotypic screening experiments. BioMed Central 2013-10-05 /pmc/articles/PMC3852740/ /pubmed/24093553 http://dx.doi.org/10.1186/1758-2946-5-44 Text en Copyright © 2013 Rosania et al.; licensee Chemistry Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology
Rosania, Gus R
Shedden, Kerby
Zheng, Nan
Zhang, Xinyuan
Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport
title Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport
title_full Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport
title_fullStr Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport
title_full_unstemmed Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport
title_short Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport
title_sort visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport
topic Methodology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852740/
https://www.ncbi.nlm.nih.gov/pubmed/24093553
http://dx.doi.org/10.1186/1758-2946-5-44
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