The PODB is publicly available through the Website. This database consists of three individual parts, the organellome database, the functional analysis database and a compilation of external links to other databases and homepages.
The organellome database is a searchable database of plant organelle images visualized with fluorescent and nonfluorescent probes in various tissues at different developmental stages. The term ‘organellome’ is a coined word that means the comprehensive understanding of organelle dynamics. We do not limit the term ‘organellome’ to membrane-enclosed organelles (the endoplasmic reticulum, mitochondria, chloroplasts and so on), and we accept images of all kinds of cellular compartments, including cytoskeleton components, such as microtubules and microfilaments, the plasma membrane and the cell wall. We also accept organelle images of any plant species. In contrast to several of the protein localization databases, our database has been populated by experimental data submitted directly by plant researchers, rather than by sequence-based prediction data based on primary amino acid sequences. Through the organellome database, users can easily examine the dynamics of organelles, such as movements and morphological changes, as well as protein localization at the various developmental stages. For example, our database provides a series of pictures of changes in actin filaments through the progression of the cell cycle in suspension-cultured tobacco cells (Figure 1), showing that actin filaments drastically change in shape, length, thickness, number and position (25). Another example (Figure 2) shows the positions of chloroplasts in Arabidopsis mesophyll cells in response to changes in light conditions (26,27). By comparing these images, users can grasp the sequence of photorelocation of chloroplasts: dark-adapted chloroplasts are localized on the bottom of cells (compare Figure 2A with D), chloroplasts group together near the cell surface and cell bottom in the weak-light condition (Figure 2B and E) and chloroplasts move away from the cell surface to avoid photodamage from strong light (Figure 2C and F).
It is additionally expected that the organellome database will have great utility when researchers come across unidentified organelles, or when the localization of a protein of interest is unclear, because the organellome database will assist users by comparing their results with the deposited data. The ER-derived organelles ER bodies (Figure 3H) are a good representative of organelles that were identified by comparison of unknown structures with known images, in this case visualization of the ER using ER-targeted GFP (28). ER bodies were originally described as mystery organelles (29), but the morphology of the unidentified GFP-labeled organelles triggered their identification as ER bodies (28). Although it would be very difficult and time-consuming to search for references relevant to unidentified organelles, users can easily examine several organelles through the organellome database. For this purpose, we are now updating the organellome database for the use of image-based data mining (see the Future Plans for Database Development Section).
The functional analysis database is a collection of protocols for plant organelle research. Most laboratories have their own protocols, including tips for running the experiments effectively, which are suitable for their own research projects. Unfortunately, these protocols are scattered across the literature in research papers, books and the homepages of individual scientists. Our functional analysis database provides such protocols in one place, where users can easily find several protocols that were developed and established in different laboratories in addition to information on person(s) who are familiar with such approaches and techniques. When users want to introduce novel approaches and techniques, they can access the reference for a protocol, download protocols as PDF files (if provided), and contact submitters to obtain more detailed information. If several protocols are provided for one technique, users can compare such protocols and adopt them for their own experiments. For example, four protocols for the isolation of intact vacuoles have been deposited. One is suitable for cultured Arabidopsis cells, another two for Arabidopsis leaves and the other for suspension-cultured Catharanthus cells. Users can draw on these protocols and test the protocols in their own laboratories.
Our database also contains an external links page with links to other biological databases and homepages. The links are limited to transcriptomics and proteomics, because the microarray and mass spectrometry techniques are also endorsed as part of our joint research project. To provide our users with more comprehensive resources, links to several other databases are included in this page as well.
The PODB provides more features than other existing databases. Many plant researchers are interested in specific organelle(s) and use various plants as materials for their research. However, integrated functions in higher plants require biological and metabolic processes involving several organelles. Investigators often have to address organelles and plants that have not previously been part of their research programs. To meet this need to compare plant species, we do not restrict the species for which we accept data. Thus, the PODB contains all kinds of organelles from several plant species and can provide a good starting resource for this information.
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 to produce the data (see Data Submission section about donation). To request such genetic resources, users should contact the submitter directly; a contact person is listed in each entry.
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