Soybean Proteome Database 2012: update on the comprehensive data repository for soybean proteomics

The Soybean Proteome Database (SPD) was created to provide a data repository for functional analyses of soybean responses to flooding stress, thought to be a major constraint for establishment and production of this plant. Since the last publication of the SPD, we thoroughly enhanced the contents of database, particularly protein samples and their annotations from several organelles. The current release contains 23 reference maps of soybean (Glycine max cv. Enrei) proteins collected from several organs, tissues, and organelles including the maps for plasma membrane, cell wall, chloroplast, and mitochondrion, which were analyzed by two-dimensional polyacrylamide gels. Furthermore, the proteins analyzed with gel-free proteomics technique have been added and are available online. In addition to protein fluctuations under flooding, those of salt and drought stress have been included in the current release. A case analysis employing a portion of those newly released data was conducted, and the results will be shown. An ‘omics table has also been provided to reveal relationships among mRNAs, proteins, and metabolites with a unified temporal-profile tag in order to facilitate retrieval of the data based on the temporal profiles. An intuitive user interface based on dynamic HTML enables users to browse the network as well as the profiles of the multiple “omes” in an integrated fashion. The SPD is available at: http://proteome.dc.affrc.go.jp/Soybean

The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information

With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was held in Japan with the aim of annotating and manually curating all the genes in the rice genome. Here we present the Rice Annotation Project Database (RAP-DB), which has been developed to provide access to the annotation data. The RAP-DB has two different types of annotation viewers, BLAST and BLAT search, and other useful features. By connecting the annotations to other rice genomics data, such as full-length cDNAs and Tos17 mutant lines, the RAP-DB serves as a hub for rice genomics. All of the resources can be accessed through

Functional and Immunoreactive Thrombomodulin Expressed by Keratinocytes

In an immunohistopathologic study using two monoclonal antibodies that recognize independent epitopes on human thrombomodulin, we detected expression of thrombomodulin on Malpighian-layer keratinocytes, but not on the basal or upper granular-layer keratinocytes. Western blotting and thrombomodulin-specific enzyme-linked immunosorbent assay performed on both shaved skin and cultured SV4O-transformed keratinocytes showed the expression of full-length thrombomodulin, indistinguishable from endothelial thrombomodulin. Thrombomodulin was expressed by keratinocytes in 1mM calcium but not in reduced calcium. A functional assay for thrombomodulin revealed that epidermal-derived thrombomodulin possessed cofactor activity for thrombin-catalyzed protein C activation. The limited pattern of expression of thrombomodulin in epidermis implies that this molecule may be a differentiation marker of keratinocytes in addition to being a potent anticoagulant in the skin

Glyconanoparticles for colorimetric bioassays

Carbohydrate molecules are involved in many of the cellular processes that are important for life. By combining the specific analyte targeting of carbohydrates with the multivalent structure and change of solution colour as a consequence of plasmonic interactions with the aggregation of metal nanoparticles, glyconanoparticles have been used extensively for the development of bioanalytical assays. The noble metals used to create the nanocore, the methodologies used to assemble the carbohydrates on the nanoparticle surface, the carbohydrate chosen for each specific target, the length of the tether that separates the carbohydrate from the nanocore and the density of carbohydrates on the surface all impact on the structural formation of metal based glyconanoparticles. This tutorial review highlights these key components, which directly impact on the selectivity and sensitivity of the developed bioassay, for the colorimetric detection of lectins, toxins and viruses

KAIKObase: An integrated silkworm genome database and data mining tool

<p>Abstract</p> <p>Background</p> <p>The silkworm, <it>Bombyx mori</it>, is one of the most economically important insects in many developing countries owing to its large-scale cultivation for silk production. With the development of genomic and biotechnological tools, <it>B. mori </it>has also become an important bioreactor for production of various recombinant proteins of biomedical interest. In 2004, two genome sequencing projects for <it>B. mori </it>were reported independently by Chinese and Japanese teams; however, the datasets were insufficient for building long genomic scaffolds which are essential for unambiguous annotation of the genome. Now, both the datasets have been merged and assembled through a joint collaboration between the two groups.</p> <p>Description</p> <p>Integration of the two data sets of silkworm whole-genome-shotgun sequencing by the Japanese and Chinese groups together with newly obtained fosmid- and BAC-end sequences produced the best continuity (~3.7 Mb in N50 scaffold size) among the sequenced insect genomes and provided a high degree of nucleotide coverage (88%) of all 28 chromosomes. In addition, a physical map of BAC contigs constructed by fingerprinting BAC clones and a SNP linkage map constructed using BAC-end sequences were available. In parallel, proteomic data from two-dimensional polyacrylamide gel electrophoresis in various tissues and developmental stages were compiled into a silkworm proteome database. Finally, a <it>Bombyx </it>trap database was constructed for documenting insertion positions and expression data of transposon insertion lines.</p> <p>Conclusion</p> <p>For efficient usage of genome information for functional studies, genomic sequences, physical and genetic map information and EST data were compiled into KAIKObase, an integrated silkworm genome database which consists of 4 map viewers, a gene viewer, and sequence, keyword and position search systems to display results and data at the level of nucleotide sequence, gene, scaffold and chromosome. Integration of the silkworm proteome database and the <it>Bombyx </it>trap database with KAIKObase led to a high-grade, user-friendly, and comprehensive silkworm genome database which is now available from URL: <url>http://sgp.dna.affrc.go.jp/KAIKObase/</url>.</p