Dataset Information

Fluorescent whole-mount method for visualizing three-dimensional relationships in intact and regenerating adult newt spinal cords.

ABSTRACT: Adult newts have the remarkable ability to regenerate their spinal cords after a complete transection injury. To understand this process, we have developed a method for visualizing the cellular and molecular events during regeneration in whole-mount preparations using fluorescent probes (streptavidins and antibodies) and confocal microscopy. This method was optimized by varying parameters associated with fixation, tissue trimming, fluorescent probe penetration, and clearing and represents a significant advance in our ability to observe the intact and regenerating newt spinal cord. These methods should also be widely applicable to the study of other newt tissues and adult tissues from other model systems.

SUBMITTER: Zukor KA

PROVIDER: S-EPMC3013515 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature

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Publications

Fluorescent whole-mount method for visualizing three-dimensional relationships in intact and regenerating adult newt spinal cords.

Zukor Katherine A KA Kent David T DT Odelberg Shannon J SJ

Developmental dynamics : an official publication of the American Association of Anatomists 20101101 11

Adult newts have the remarkable ability to regenerate their spinal cords after a complete transection injury. To understand this process, we have developed a method for visualizing the cellular and molecular events during regeneration in whole-mount preparations using fluorescent probes (streptavidins and antibodies) and confocal microscopy. This method was optimized by varying parameters associated with fixation, tissue trimming, fluorescent probe penetration, and clearing and represents a sign ...[more]

PMID: 20931649

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Project description:BackgroundTo 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.ResultsTo 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.ConclusionMOVID 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.

Dataset Information

Fluorescent whole-mount method for visualizing three-dimensional relationships in intact and regenerating adult newt spinal cords.

Publications

Fluorescent whole-mount method for visualizing three-dimensional relationships in intact and regenerating adult newt spinal cords.

Similar Datasets

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