- Electron Micrograph Database
- Perceptive Organelles Database
- Organelles Movie Database
- Organellome Database
- Functional Analysis Database
- External Links
This database contains electron micrographs in various tissues during different developmental stages in wild-type and mutant plants.
This database contains images and movies of organelles in various tissues during different developmental stages in response to environmental stimuli.
IMPORTANT: QuickTime must be installed on your computer to view these movies. Please download a free version of QuickTime player from the Apple Web site at http://www.apple.com/downloads>.
This database contains time-lapse images, Z slices and projection images of organelles in various tissues during different developmental stages, visualized using fluorescent and non-fluorescent probes.
IMPORTANT: QuickTime must be installed on your computer to view these movies. Please download a free version of QuickTime player from the Apple Web site at http://www.apple.com/downloads>.
This database contains images for cellular structures that are composed of organelle images in various tissues during different developmental stages, visualized with fluorescent and non-fluorescent probes.
This database is a collection of protocols for plant organelle research.
Access to biological databases.
Welcome to the Plant Organelles Database Version 3 (PODB3)
The Plant Organelles Database Version 3 (PODB3) is a specialized database project to promote a comprehensive understanding of organelle dynamics, including organelle function, biogenesis, differentiation, movement, and interactions with other organelles.
This database consists of 6 individual parts, 'The Electron Micrograph Database', 'The Perceptive Organelles Database', 'The Organelles Movie Database', 'The Organellome Database', 'The Functional Analysis Database', and 'External Links to other databases and Web pages'. All the data and protocols in these databases are populated by direct submission of experimentally determined data from plant researchers. We would also appreciate your active contributions by submission of data and protocols to our database. Please see 'Submit Data to the PODB3' below for submitting data and protocols. If you have any questions, comments or suggestions, please contact us at "podb@nibb.ac.jp".
About the database
Our database serves only to provide biological information, and does NOT collect, generate, or distribute genetic resources such as the DNA, seeds, and transgenic plants that were used in our database. To request such genetic resources, you should contact the submitter directly. However, when genetic resources used in the PODB3 have been donated to international stock centers, and when the stock numbers are provided, users can obtain such genetic resources via links to the stock center which carries them.
The data in the PODB3 are free only to non-profit institutions, universities, and colleges. Please be aware that any disclaimer, copying or use of the contents of our database by a commercial entity is prohibited.
Submit data to the PODB3
The PODB3 welcomes data submissions from plant researchers. There are differences in the way data should be submitted to 'The Electron Micrograph Database', 'The Perceptive Organelles Database', 'The Organelles Movie Database', 'The Organellome Database' and 'The Functional Analysis Database'. Please take a look at the specific guidelines below for submitting data and protocols. Corrections, revisions, or updates of submitted data and protocols to the PODB3 can be made at any time, but users are NOT able to correct, revise, or update the data by themselves. In such cases, please contact podb@nibb.ac.jp.
Submit data to the Electron Micrograph Database
Submit data to the Perceptive Organelles Database
Submit data to the Organelles Movie Database
Submit data to the Organellome Database
Submit data to the Functional Analysis Database
To cite this database
We request that you cite the following papers when you refer the PODB3.
[Original papers]
Mano, S., Nakamura, T., Kondo, M., Miwa, T., Nishikawa, S., Mimura, T., Nagatani, A., and Nishimura, M. (2014) The Plant Organelles Database 3 (PODB3) update 2014: integrating electron micrographs and new options for plant organelle research. Plant Cell Physiol. 55: e1.
Mano, S., Miwa, T., Nishikawa, S. Mimura, T. and Nishimura, M. (2011) The Plant Organelles Database 2 (PODB2): An updated resource containing movie data of plant organelle dynamics. Plant Cell Physiol. 52: 244-253.
Mano, S., Miwa, T., Nishikawa, S. Mimura, T. and Nishimura, M. (2008) The Plant Organelles Database (PODB): a collection of visualized plant organelles and protocols for plant organelle research. Nucleic Acids Res. 36: D929-D937.
[Review articles]
Mano, S., Kimori, Y., Takeda, T., Miwa, T., Nishikawa, S., Mimura, T., Nagatani, A., and Nishimura, M. (2013) Using image-based resources: databases for plant organelle dynamics and applications based on image information. In Introduction to Sequence and Genome Analysis. Edited by Mishra, A., Nawaz, Z. and Shahid, Z. pp.83-109. iConcept Press.
Mano, S., Miwa, T., Nishikawa, S. Mimura, T. and Nishimura, M. (2009) Seeing is believing: On the use of image databases for visually exploring plant organelle dynamics. Plant Cell Physiol. 5: 2000-2014.
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