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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 organellome database graphical user interface. (A) A search window provides five parameters for queries. Users can select an organelle name from the pull-down menu and/or enter text in the text boxes for other parameters. (B) A result window shows a table containing thumbnail images of visualized organelles as well as annotations. Clicking on the image in the left column gives access to the detailed information page. (C) Detailed information on At3g33650 is shown as a representative data page.
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Figure 4: The organellome database graphical user interface. (A) A search window provides five parameters for queries. Users can select an organelle name from the pull-down menu and/or enter text in the text boxes for other parameters. (B) A result window shows a table containing thumbnail images of visualized organelles as well as annotations. Clicking on the image in the left column gives access to the detailed information page. (C) Detailed information on At3g33650 is shown as a representative data page.

Mentions: The organellome database is a fully searchable database. Users can access the ‘Search’ page by clicking on the term ‘Organellome database’ located on the homepage (http://podb.nibb.ac.jp/Organellome/) and at the top of each page in the database. From the ‘Search’ page in the organellome database (Figure 4A), users may search for specific data using five parameters for queries: organelle name, protein name, gene accession number, fluorescent probes and keywords. By combining these different search parameters, more complex searches can be performed. Leaving the input boxes empty retrieves all entries. To choose an organelle name, users must specify one organelle from the pull-down menu. Currently, the organellome database encompasses the following 18 organelles: apoplast, cell wall, endoplasmic reticulum, endosome, Golgi apparatus, microfilament, microtubule, mitochondrion, mitochondrion and plastid (for cases of dual localization), nucleus, peroxisome, plasma membrane, plastid, prevacuolar compartment, tonoplast, trans-Golgi network, vacuole and ‘other’. The term ‘other’ describes labeling of unidentified organelles. Upon requests from submitters and users, we will include additional organelle names in this pull-down menu. In addition to the specific labeling, we accept bright field and differential interference contrast images to provide important information on the positions of organelles in cells (Figure 3A, D and G). When a submitter provides double- or triple-staining data (Figure 3A–G), the information on each stain is stored individually, providing up to three channels for each image. Users can select which channel(s) to search in the ‘Search field’ on the bottom in the ‘Search’ page.Figure 4.


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 organellome database graphical user interface. (A) A search window provides five parameters for queries. Users can select an organelle name from the pull-down menu and/or enter text in the text boxes for other parameters. (B) A result window shows a table containing thumbnail images of visualized organelles as well as annotations. Clicking on the image in the left column gives access to the detailed information page. (C) Detailed information on At3g33650 is shown as a representative data page.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: The organellome database graphical user interface. (A) A search window provides five parameters for queries. Users can select an organelle name from the pull-down menu and/or enter text in the text boxes for other parameters. (B) A result window shows a table containing thumbnail images of visualized organelles as well as annotations. Clicking on the image in the left column gives access to the detailed information page. (C) Detailed information on At3g33650 is shown as a representative data page.
Mentions: The organellome database is a fully searchable database. Users can access the ‘Search’ page by clicking on the term ‘Organellome database’ located on the homepage (http://podb.nibb.ac.jp/Organellome/) and at the top of each page in the database. From the ‘Search’ page in the organellome database (Figure 4A), users may search for specific data using five parameters for queries: organelle name, protein name, gene accession number, fluorescent probes and keywords. By combining these different search parameters, more complex searches can be performed. Leaving the input boxes empty retrieves all entries. To choose an organelle name, users must specify one organelle from the pull-down menu. Currently, the organellome database encompasses the following 18 organelles: apoplast, cell wall, endoplasmic reticulum, endosome, Golgi apparatus, microfilament, microtubule, mitochondrion, mitochondrion and plastid (for cases of dual localization), nucleus, peroxisome, plasma membrane, plastid, prevacuolar compartment, tonoplast, trans-Golgi network, vacuole and ‘other’. The term ‘other’ describes labeling of unidentified organelles. Upon requests from submitters and users, we will include additional organelle names in this pull-down menu. In addition to the specific labeling, we accept bright field and differential interference contrast images to provide important information on the positions of organelles in cells (Figure 3A, D and G). When a submitter provides double- or triple-staining data (Figure 3A–G), the information on each stain is stored individually, providing up to three channels for each image. Users can select which channel(s) to search in the ‘Search field’ on the bottom in the ‘Search’ page.Figure 4.

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
Related in: MedlinePlus