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The plant organelles database (PODB): a collection of visualized plant organelles and protocols for plant organelle research.

Mano S, Miwa T, Nishikawa S, Mimura T, Nishimura M - Nucleic Acids Res. (2007)

Bottom Line: All the data and protocols in the organellome database and the functional analysis database are populated by direct submission of experimentally determined data from plant researchers and can be freely downloaded.Our database promotes the exchange of information between plant organelle researchers for the comprehensive study of the organelle dynamics that support integrated functions in higher plants.We would also appreciate contributions of data and protocols from all plant researchers to maximize the usefulness of the database.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan.

ABSTRACT
The plant organelles database (PODB; http://podb.nibb.ac.jp/Organellome) was built to promote a comprehensive understanding of organelle dynamics, including organelle function, biogenesis, differentiation, movement and interactions with other organelles. This database consists of three individual parts, the organellome database, the functional analysis database and external links to other databases and homepages. The organellome database provides images of various plant organelles that were visualized with fluorescent and nonfluorescent probes in various tissues of several plant species at different developmental stages. The functional analysis database is a collection of protocols for plant organelle research. External links give access primarily to other databases and Web pages with information on transcriptomes and proteomes. All the data and protocols in the organellome database and the functional analysis database are populated by direct submission of experimentally determined data from plant researchers and can be freely downloaded. Our database promotes the exchange of information between plant organelle researchers for the comprehensive study of the organelle dynamics that support integrated functions in higher plants. We would also appreciate contributions of data and protocols from all plant researchers to maximize the usefulness of the database.

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The positions of chloroplasts in response to changing light conditions. Six images were drawn from the organellome database and arranged. Images near the top (A–C) and the bottom (D–F) of mesophyll cells are shown. (A and D) dark condition, (B and E) weak-light condition, (C and F) strong-light condition.
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Figure 2: The positions of chloroplasts in response to changing light conditions. Six images were drawn from the organellome database and arranged. Images near the top (A–C) and the bottom (D–F) of mesophyll cells are shown. (A and D) dark condition, (B and E) weak-light condition, (C and F) strong-light condition.

Mentions: 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).Figure 1.


The plant organelles database (PODB): a collection of visualized plant organelles and protocols for plant organelle research.

Mano S, Miwa T, Nishikawa S, Mimura T, Nishimura M - Nucleic Acids Res. (2007)

The positions of chloroplasts in response to changing light conditions. Six images were drawn from the organellome database and arranged. Images near the top (A–C) and the bottom (D–F) of mesophyll cells are shown. (A and D) dark condition, (B and E) weak-light condition, (C and F) strong-light condition.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238956&req=5

Figure 2: The positions of chloroplasts in response to changing light conditions. Six images were drawn from the organellome database and arranged. Images near the top (A–C) and the bottom (D–F) of mesophyll cells are shown. (A and D) dark condition, (B and E) weak-light condition, (C and F) strong-light condition.
Mentions: 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).Figure 1.

Bottom Line: All the data and protocols in the organellome database and the functional analysis database are populated by direct submission of experimentally determined data from plant researchers and can be freely downloaded.Our database promotes the exchange of information between plant organelle researchers for the comprehensive study of the organelle dynamics that support integrated functions in higher plants.We would also appreciate contributions of data and protocols from all plant researchers to maximize the usefulness of the database.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan.

ABSTRACT
The plant organelles database (PODB; http://podb.nibb.ac.jp/Organellome) was built to promote a comprehensive understanding of organelle dynamics, including organelle function, biogenesis, differentiation, movement and interactions with other organelles. This database consists of three individual parts, the organellome database, the functional analysis database and external links to other databases and homepages. The organellome database provides images of various plant organelles that were visualized with fluorescent and nonfluorescent probes in various tissues of several plant species at different developmental stages. The functional analysis database is a collection of protocols for plant organelle research. External links give access primarily to other databases and Web pages with information on transcriptomes and proteomes. All the data and protocols in the organellome database and the functional analysis database are populated by direct submission of experimentally determined data from plant researchers and can be freely downloaded. Our database promotes the exchange of information between plant organelle researchers for the comprehensive study of the organelle dynamics that support integrated functions in higher plants. We would also appreciate contributions of data and protocols from all plant researchers to maximize the usefulness of the database.

Show MeSH