Category: Publications

[Press Release] Development of life sciences by sharing image data

Drs Koji Kyoda, Hitoya Itoga, Yuki Yamagata (RIKEN R-IH), et al. developed and published a public repository and high-value database that facilitates the sharing and re-using of image data in the life sciences. In this paper, we describe the international positioning and functions of the SSBD.

The SSBD is positioned as one of the core ecosystems of the international consortium ‘foundingGIDE’, which aims to promote the standardisation and sharing of FAIR image data, and is expected to enhance the transparency and reliability of science and contribute to the development of science throughout society through the advancement of open science. The project is expected to contribute to the development of science in society as a whole through the advancement of open science.

Learn more about the study on Press Release by RIKEN. (In Japanese only)

Reference

Kyoda, K., Itoga, H., Yamagata, Y., Fujisawa, E., Wang, F., Miranda-Miranda, M., Yamamoto, H., Nakano, Y., Tohsato, Y., Onami, S.(2024) SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data. Nucleic Acids Res. gkae860. https://doi.org/10.1093/nar/gkae860

Behind the Paper “Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective”

Dr. Yuki Yamagata (R-IH Life Science Data Sharing Unit) et al. published a paper in BMC Medical Informatics and Decision Making on the development of an otology related to COVID-19 infectious processes. We published a video to introduce our study on YouTube.

We developed the HoIP ontology to organize cellular senescence knowledge from a homeostasis disturbance perspective. HoIP was assessed, and relationships between cellular senescence, COVID-19, and diabetes were inferred. This framework elucidates mechanisms linking cellular and organismal aging. Lean more about the study at https://go.nature.com/3yLP0QO.

Reference

Yamagata, Y., Fukuyama, T., Onami, S. et al. Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective. Sci Data 11, 485 (2024). https://doi.org/10.1038/s41597-024-03331-y

[Press Release] Development and publication of the zebrafish brain gene expression database

Dr Towako Hiraki-Kajiyama(Assistant professor at Graduate School of Life Science, Tohoku University, former researcher at RIKEN CBS) and Yoshihiro Yoshihara (TL at Riken CBS) et al. with Drs Hiroya Itoga and Shuichi Onami established the database for scanned data of brain sections of zebrafish.

The database uses SSBD (https://ssbd.riken.jp/) and OMERO (https://openmicroscopy.org) as infrastructures.The database and anatomical findings will contribute to future neuroscience research using zebrafish.

Learn more about the study on Press Release from RIKEN. (In Japanese only)

Reference

Hiraki-Kajiyama, T., Miyasaka, N., Ando, R., Wakisaka, N., Itoga, H., Onami, H. I. S., & Yoshihara, Y. (2024). An atlas and database of neuropeptide gene expression in the adult zebrafish forebrain. Journal of Comparative Neurology, 532, e25619. https://doi.org/10.1002/cne.25619

[Press Release] Steady-state chromatin motion throughout interphase

Drs. Soya Shinkai and Shuichi Onami together with Shiori Iida (SOKENDAl) and Prof. Kazuhiro Maeshima (NIG) et. al. have investigated the local movements of chromatin in living human cells using super-resolution fluorescence microscopy.

Learn more about the study on Press Release from the National Institute of Genetics.

Reference

Iida S., Shinkai, S., Itoh, Y., Tamura, S., Kanemaki, M. T., Onami, S., Maeshima, K. (2022). Single-nucleosome imaging reveals steady-state motion of interphase chromatin in living human cells. Sci. Adv. 8, eabn5626.

https://doi.org/10.1126/sciadv.abn5626

Improvement in image quality via the pseudo confocal effect in multidirectional digital scanned laser light-sheet microscopy

Our TL Onami and DR Kaneshiro (Laboratory for Comprehensive Bioimaging, RIKEN BDR) et al. proposed a new pseudo confocal system that combines multiline scanning for light-sheet illumination combined and simple image construction.  By further combining our method with multidirectional digital scanned laser light-sheet microscopy (mDSLM), we demonstrated improvement of image quality in biological samples.

https://doi.org/10.1364/OE.423783

Texture-Based Screening to Identify Genes Involved in Reproductive Aging in C. elegans

Dr Momoko Imakubo et al.’s study on analysis of genes involved in reproductive aging in C. elegans oocytes by using an image database of RNAi embryos and image processing has been published online at https://doi.org/10.17706/ijbbb.2021.11.3.40-49.

Congratulations to our former student trainee Momoko Imakubo who earned her PhD from Kobe University in March 2021 on her achievement. We wish you all the best in your future endeavour!

[Press Release] Launch of “NeuroGT Database”, a brain atlas of neurogenic tagging CreER mouse drivers

Drs. Yukako Tohsato and Hiroya Itoga in our SSBD team, together with Prof. Tatsumi Hirata (NIG) and colleagues, developed the “NeuroGT database,” which contains whole-brain image data of tagged neurons based on time of neurogenesis. Through NeuroGT, researchers can find suitable neurogenic tagging driver lines for their research.

Learn more about Neuro GT on the National Institute of Genetics Press Release.

Reference

Hirata, T., Tohsato, Y., Itoga, H. et al. NeuroGT: A brain atlas of neurogenic tagging CreER drivers for birthdate-based classification and manipulation of mouse neurons. Cell Rep. Methods 1, 100012 (2021). https://doi.org/10.1016/j.crmeth.2021.100012