Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography
- Penn State College of Medicine, United States
- Duke University, United States
- The University of Chicago, United States
- Motorola Mobility, United States
- Argonne National Laboratory, United States
Abstract
Organismal phenotypes frequently involve multiple organ systems. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective. To determine how synchrotron-based X-ray micro-tomography (micro-CT) can yield 3-dimensional whole-organism images suitable for quantitative histological phenotyping, we scanned whole zebrafish, a small vertebrate model with diverse tissues, at ~1-micron voxel resolutions. Using micro-CT optimized for cellular characterization (histotomography), brain nuclei were computationally segmented and assigned to brain regions. Shape and volume were computed for populations of nuclei such as those of motor neurons and red blood cells. Striking individual phenotypic variation was apparent from color maps of computed cell density. Unlike histology, histotomography allows the detection of phenotypes that require millimeter scale context in multiple planes. We expect the computational and visual insights into 3D tissue architecture provided by histotomography to be useful for reference atlases, hypothesis generation, comprehensive organismal screens, and diagnostics.
Data availability
ViewTool is publically available (http://3D.fish). Digital histology is publicly available from our Zebrafish Lifespan Atlas (http://bio-atlas.psu.edu) (Cheng, 2004). Registered and unregistered 8-bit reconstructions of the heads of five zebrafish larvae involved in analysis are available on Dryad (https://datadryad.org/) along with scripts written for cell nuclei detection, analysis, and sample registration. Full resolution scans, including raw projection data, are available from researchers upon request as a download or by transfer to physical media.
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Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomographyDryad Digital Repository, doi:10.5061/dryad.4nb12g2.
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ViBE-Z: A Framework for 3D Virtual Colocalization Analysis in Zebrafish Larval Brainshttp://vibez.informatik.uni-freiburg.de.
Article and author information
Author details
Patrick La Riviere
Funding
NIH Office of the Director (R24-OD018559)
- Patrick La Riviere
- Keith Cheng
National Institutes of Health (R24-RR017441)
- Patrick La Riviere
- Keith Cheng
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: All procedures on live animals were approved by the Institutional Animal Care and Use Committee (IACUC) at the Pennsylvania State University, ID: PRAMS201445659, Groundwork for a Synchrotron MicroCT Imaging Resource for Biology (SMIRB).
Copyright
© 2019, Ding et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography
eLife 8:e44898.
https://doi.org/10.7554/eLife.44898
Further reading
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- Developmental Biology
By enabling researchers to image whole zebrafish with cellular resolution, X-ray histotomography will improve our understanding of the biological differences between individuals of the same species.
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- Developmental Biology
Wing dimorphism is a common phenomenon that plays key roles in the environmental adaptation of aphid; however, the signal transduction in response to environmental cues and the regulation mechanism related to this event remain unknown. Adenosine (A) to inosine (I) RNA editing is a post-transcriptional modification that extends transcriptome variety without altering the genome, playing essential roles in numerous biological and physiological processes. Here, we present a chromosome-level genome assembly of the rose-grain aphid Metopolophium dirhodum by using PacBio long HiFi reads and Hi-C technology. The final genome assembly for M. dirhodum is 447.8 Mb, with 98.50% of the assembled sequences anchored to nine chromosomes. The contig and scaffold N50 values are 7.82 and 37.54 Mb, respectively. A total of 18,003 protein-coding genes were predicted, of which 92.05% were functionally annotated. In addition, 11,678 A-to-I RNA-editing sites were systematically identified based on this assembled M. dirhodum genome, and two synonymous A-to-I RNA-editing sites on CYP18A1 were closely associated with transgenerational wing dimorphism induced by crowding. One of these A-to-I RNA-editing sites may prevent the binding of miR-3036-5p to CYP18A1, thus elevating CYP18A1 expression, decreasing 20E titer, and finally regulating the wing dimorphism of offspring. Meanwhile, crowding can also inhibit miR-3036-5p expression and further increase CYP18A1 abundance, resulting in winged offspring. These findings support that A-to-I RNA editing is a dynamic mechanism in the regulation of transgenerational wing dimorphism in aphids and would advance our understanding of the roles of RNA editing in environmental adaptability and phenotypic plasticity.
