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Interactive 3D PDF file for the structures 10 hr juvenile of Oikopleura dioica and supplementary movie S1-20 with high resolution

Citation

Nishida, Hiroki (2021), Interactive 3D PDF file for the structures 10 hr juvenile of Oikopleura dioica and supplementary movie S1-20 with high resolution, Dryad, Dataset, https://doi.org/10.5061/dryad.hmgqnk9dw

Abstract

The larvacean, Oikopleura dioica is a planktonic chordate, which is an emerging model organism with short life cycle of 5 days and belongs to tunicates (urochordates). Organ formation in the trunk proceeds in seven hours form hatching of tailbud larvae at three hours after fertilization (hpf) to completion of organ formation in fully functional juveniles that start feeding at 10 hpf and are just miniature of adult form.

The juveniles were fixed at 10.5 hours post fertilization, 30 min after the tail shift (Nishida, H., 2008 Development of the appendicularian Oikopleura dioica: culture, genome, and cell lineages. Dev. Growth Differ. 50, S239–S256.). The data would be used as a basic morphological data of this animal to explore organ structures and cellular composition.

This PDF file allows one to view 3D juvenile of O. dioica in any desired directions. One can show or hide the organs and rotate them by mouse. Open this PDF file and activate it as described in Adobe Acrobat User Guide (https://helpx.adobe.com/acrobat/using/displaying-3d-models-pdfs.html). Click Toggle “Model Tree button” with three small rectangulars in the tool bar. Then in the left panel, one can select the organs and nuclei you want to see. Select lighting as “daylight”. Select solid or transparency mode.
The Juvenile 3D image was reconstructed with Amira software using 1967 serial section images of SBF-SEM (Serial block face scanning electron microscopy) that are available at https://doi.org/10.5061/dryad.d51c5b012.

The Zip file also contains supplementary movie S1-20 (avi file) with high resolution and the legends (PDF file).

This data is related to the paper, 3D reconstruction of structures of hatched larva and young juvenile of the larvacean Oikopleura dioica using SBF-SEM. (https://www.nature.com/articles/s41598-021-83706-y).

Methods

SBF-SEM observation was performed using a Merlin scanning electron microscope (Carl Zeiss Microscopy, Jena, Germany) equipped with a 3View in-chamber ultramicrotome system (Gatan, Pleasanton, CA). The serial slice thickness was 70 nm. Images were recorded with an accelerating voltage of 1.3 kV and a dwell time of 1.0 µs. The image size was 12,000 x 12,000 pixels, with a resolution of 8 nm, which covers an area of 96 µm x 96 µm. After 2 x 2 binning of the images to reduce noise, the image stack was automatically aligned using ‘Register Virtual Stack Slices’ in the Fiji/ImageJ software. For a 10.5 hr juvenile, 1967 images were acquired.

Usage Notes

This PDF file allows one to view 3D juvenile of O. dioica in any desired directions. One can show or hide the organs and rotate them by mouse. Open this PDF file and activate it as described in Adobe Acrobat User Guide (https://helpx.adobe.com/acrobat/using/displaying-3d-models-pdfs.html). Click Toggle “Model Tree button” with three small rectangulars in the tool bar. Then in the left panel, one can select the organs and nuclei you want to see. Select lighting as “daylight”. Select solid or transparency mode.

The Zip file also contains Supplementary movie S1-20 (avi file) with high resolution and the legends (PDF file).

Funding

The JSPS and MEXT Grants-in-Aid for Scientific Research (KAKENHI), Award: 26650079, 15H04377, 16K14735, 17KT0023, 19H03234

The MEXT Grants-in-Aid for Scientific Research (KAKENHI), Award: JP16H06280

Advanced Bioimaging Support

The JSPS and MEXT Grants-in-Aid for Scientific Research (KAKENHI), Award: 26650079, 15H04377, 16K14735, 17KT0023, 19H03234

The MEXT Grants-in-Aid for Scientific Research (KAKENHI), Award: JP16H06280

Advanced Bioimaging Support