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

Mano, Shoji; Miwa, Takeshi; Nishikawa, Shuh-ichi; Mimura, Tetsuro; Nishimura, Mikio

doi:10.1093/nar/gkm789

Cited by 25 publications

(23 citation statements)

References 30 publications

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“…To demonstrate this utility, we performed image clustering analysis of images obtained from another database, the Plant Organelle Database (http://podb.nibb.ac.jp/Organellome/) [6], using guard cell images of nuclei labeled by GFP fusions with a nuclear localization sequence (NLS-GFP; Additional file 1: Figure S1A), mitochondria labeled by DsRed fusions with the pre-sequence of the delta-prime subunit of mitochondrial F1-ATPase (F1-ATPase-δ-DsRed; Additional file 1: Figure S1B), and chloroplasts labeled by GFP fusions with CAS, a thylakoid membrane-localized protein (CAS-GFP) [14] (Additional file 1: Figure S1C). After preprocessing (Additional file 1: Figure S1D-H), image clustering analysis was performed using the freely-available image clustering software iCluster (http://icluster.imb.uq.edu.au/) [15] (Figure 3, Additional file 2: Movie S1) and the 55 selected LIPS images (5 examples × 11 probes) that users can download as a ZIP file (860 KiB).…”

Section: Utility and Discussionmentioning

confidence: 99%

“…In the plant sciences, a few fluorescent microscopic image databases have focused on intracellular structures, such as Plant Cell Imaging (http://deepgreen.stanford.edu/) [4], the Illuminated Plant Cell (http://www.illuminatedcell.com) [5], and the Plant Organelles Database (http://podb.nibb.ac.jp/Organellome/) [6]. These databases have provided beautiful pictures of plant cell structures and cellular dynamics and have potential value as resources for model analysis [7].…”

Section: Introductionmentioning

confidence: 99%

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LIPS database with LIPService: a microscopic image database of intracellular structures in Arabidopsis guard cells

2013

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BackgroundIntracellular configuration is an important feature of cell status. Recent advances in microscopic imaging techniques allow us to easily obtain a large number of microscopic images of intracellular structures. In this circumstance, automated microscopic image recognition techniques are of extreme importance to future phenomics/visible screening approaches. However, there was no benchmark microscopic image dataset for intracellular organelles in a specified plant cell type. We previously established the Live Images of Plant Stomata (LIPS) database, a publicly available collection of optical-section images of various intracellular structures of plant guard cells, as a model system of environmental signal perception and transduction. Here we report recent updates to the LIPS database and the establishment of a database table, LIPService.DescriptionWe updated the LIPS dataset and established a new interface named LIPService to promote efficient inspection of intracellular structure configurations. Cell nuclei, microtubules, actin microfilaments, mitochondria, chloroplasts, endoplasmic reticulum, peroxisomes, endosomes, Golgi bodies, and vacuoles can be filtered using probe names or morphometric parameters such as stomatal aperture. In addition to the serial optical sectional images of the original LIPS database, new volume-rendering data for easy web browsing of three-dimensional intracellular structures have been released to allow easy inspection of their configurations or relationships with cell status/morphology. We also demonstrated the utility of the new LIPS image database for automated organelle recognition of images from another plant cell image database with image clustering analyses.ConclusionsThe updated LIPS database provides a benchmark image dataset for representative intracellular structures in Arabidopsis guard cells. The newly released LIPService allows users to inspect the relationship between organellar three-dimensional configurations and morphometrical parameters.

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Section: Utility and Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

LIPS database with LIPService: a microscopic image database of intracellular structures in Arabidopsis guard cells

2013

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“…Because of the large amounts of data generated by proteomics analyses over the past year, there have been efforts to form a database where proteomics information can be deposited and made available to the scientifi c community: the PPDB, http:// ppdb.tc.cornell.edu (Sun et al 2009 ) ; the PODB, http://proteome.dc.affrc.go.jp/Soybean/ ; the Organellome, http://podb.nibb.ac.jp/Organellome (Mano et al 2007 ) ; and the knowledge-based UniProt (Jorrín-Novo et al 2009 ) .…”

Section: Proteomic Approachmentioning

confidence: 99%

Abiotic Stress Responses in Plants: Metabolism to Productivity

Macedo

2011

Abiotic Stress Responses in Plants

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Plants are sessile beings, so the lack of mechanisms to escape from adverse conditions has fostered, through evolution, the development of unique and sophisticated responses to environmental stress. Depending on the degree of plasticity that a plant possesses to deal with a new environmental situation, in response to abiotic stress, morphological, anatomical, and physiological changes may occur. These changes can affect plant growth, productivity in agriculture, metabolic profi le, and plant nutritional potential, for example. Therefore, plant abiotic stress has been a matter of concern for the maintenance of human life on earth and especially for the world economy. To meet these challenges, genes, transcripts, proteins, and metabolites that control the architecture and/or stress resistance of crop plants in a wide range of environments will need to be identifi ed, in order to facilitate the biotechnological improvement of crop productivity. The combination of different "omics" tools, which rather than investigating a limited number of substances, enable the large-scale scanning of various substances, offers great potential for postgenomics to elucidate the genotype-phenotype relationships. This chapter is intended to be a synopsis of current knowledge on this regard. It focuses on plant proteome and metabolome affected by abiotic factors. It will include informations on recent advances in methods of omics like proteomics and metabolomics, which should be considered as a new opportunity to understand abiotic responses and identify genes responsible for important crop traits.

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“…The first version of PODB, which was launched in 2006, has been widely used as a data source for plant organelle research (Mano et al 2008). Initially, PODB consisted of three units: the organellome database, which was a compilation of static image data; the functional analysis database, which was a collection of protocols for plant organelle research; and external links to other relevant websites.…”

Section: Introductionmentioning

confidence: 99%

The Plant Organelles Database 2 (PODB2): An Updated Resource Containing Movie Data of Plant Organelle Dynamics

Mano

Miwa

Nishikawa

et al. 2010

Plant and Cell Physiology

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The Plant Organelles Database (PODB) was launched in 2006 and provides imaging data of plant organelles, protocols for plant organelle research and external links to relevant websites. To provide comprehensive information on plant organelle dynamics and accommodate movie files that contain time-lapse images and 3D structure rotations, PODB was updated to the next version, PODB2 (http://podb.nibb.ac.jp/Organellome). PODB2 contains movie data submitted directly by plant researchers and can be freely downloaded. Through this organelle movie database, users can examine the dynamics of organelles of interest, including their movement, division, subcellular positioning and behavior, in response to external stimuli. In addition, the user interface for access and submission has been enhanced. PODB2 contains all of the information included in PODB, and the volume of data and protocols deposited in the PODB2 continues to grow steadily. Moreover, a new website, Plant Organelles World (http://podb.nibb.ac.jp/Organellome/PODBworld/en/index.html), which is based on PODB2, was recently launched as an educational tool to engage members of the non-scientific community such as students and school teachers. Plant Organelles World is written in layman's terms, and technical terms were avoided where possible. We would appreciate contributions of data from all plant researchers to enhance the usefulness of PODB2 and Plant Organelles World.

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

Cited by 25 publications

References 30 publications

LIPS database with LIPService: a microscopic image database of intracellular structures in Arabidopsis guard cells

LIPS database with LIPService: a microscopic image database of intracellular structures in Arabidopsis guard cells

Abiotic Stress Responses in Plants: Metabolism to Productivity

The Plant Organelles Database 2 (PODB2): An Updated Resource Containing Movie Data of Plant Organelle Dynamics

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