Shoko Kawamoto

Non-overlapping expression of Olig3 and Olig2 in the embryonic neural tube

Olig family is a novel sub-family of basic helix-loop-helix transcription factors recently identified. Olig1 and Olig2 were first reported to promote oligodendrocyte differentiation, and later Olig2 was reported to be involved in motoneuron specification as well. Olig3 was isolated as a third member of Olig family, but its precise expression pattern is poorly understood. Here, we describe detailed Olig3 expression analyses in the neural tube of embryonic mice. Olig3 was first detected in the dorsal neural tube from the midbrain/hindbrain boundary to the spinal cord. In E11.5 spinal cord, Olig3 was transiently expressed in the lateral margin of the subventricular zone as three ventral clusters at the level of the p3, p2 and p0 domains, as well as in the dorsal neural tube. Olig3 was co-expressed with Nkx2.2 in the lateral margin of the p3 domain. In forebrain, Olig3 was expressed in the dorsal thalamus while Olig2 was complementarily expressed in the ventral thalamus with an adjacent boundary at E12.5. Olig3 is specifically and transiently expressed in different types of progenitors of embryonic central nervous system and then disappears in the course of development.

BodyParts3D: 3D structure database for anatomical concepts

BodyParts3D is a dictionary-type database for anatomy in which anatomical concepts are represented by 3D structure data that specify corresponding segments of a 3D whole-body model for an adult human male. It encompasses morphological and geometrical knowledge in anatomy and complements ontological representation. Moreover, BodyParts3D introduces a universal coordinate system in human anatomy, which may facilitate management of samples and data in biomedical research and clinical practice. As of today, 382 anatomical concepts, sufficient for mapping materials in most molecular medicine experiments, have been specified. Expansion of the dictionary by adding further segments and details to the whole-body model will continue in collaboration with clinical researchers until sufficient resolution and accuracy for most clinical application are achieved. BodyParts3D is accessible at: http://lifesciencedb.jp/ag/bp3d/.

Gene expression profiling of mucosal addressin cell adhesion molecule-1+ high endothelial venule cells (HEV) and identification of a leucine-rich HEV glycoprotein as a HEV marker.

High endothelial venule (HEV) cells support lymphocyte migration from the peripheral blood into secondary lymphoid tissues. Using gene expression profiling of mucosal addressin cell adhesion molecule-1+ mesenteric lymph node HEV cells by quantitative 3′-cDNA collection, we have identified a leucine-rich protein, named leucine-rich HEV glycoprotein (LRHG) that is selectively expressed in these cells. Northern blot analysis revealed that LRHG mRNA is ∼1.3 kb and is expressed in lymph nodes, liver, and heart. In situ hybridization analysis demonstrated that the mRNA expression in lymph nodes is strictly restricted to the HEV cells, and immunofluorescence analysis with polyclonal Abs against LRHG indicated that the LRHG protein is localized mainly to HEV cells and possibly to some lymphoid cells surrounding the HEVs. LRHG cDNA encodes a 342-aa protein containing 8 tandem leucine-rich repeats of 24 aa each and has high homology to human leucine-rich α2-glycoprotein. Similar to some other leucine-rich repeat protein family members, LRHG can bind extracellular matrix proteins that are expressed on the basal lamina of HEVs, such as fibronectin, collagen IV, and laminin. In addition, LRHG binds TGF-β. These results suggest that LRHG is likely to be multifunctional in that it may capture TGF-β and/or other related humoral factors to modulate cell adhesion locally and may also be involved in the adhesion of HEV cells to the surrounding basal lamina.

Isolation and characterization of a Ca 2+ -activated chloride channel from human corneal epithelium

Purpose. Transparency of the cornea is maintained through the activity of secretory mechanisms in the epithelium and endothelium, which offset the tendency of the stroma to imbibe fluid and swell. These secretory mechanisms establish osmotic gradients thereby providing the osmotic driving forces for coupled fluid transport from the stroma into both the tears and the anterior chamber. To further characterize the mechanism of epithelial Cl secretion, we cloned a cDNA encoding a Ca 2+ -dependent chloride channel, an abundant mRNA in human corneal epithelium. We investigated the abundance of all known human chloride channels in corneal epithelium to identify those responsible for regulating chloride conductance in this tissue. Methods. For the isolation of a full-length cDNA clone, a probe was selected from a set of expressed sequenced tag (EST) clones classified as unique to corneal epithelium (http://bodymap. ims.u-tokyo.ac.jp). The expression patterns of the corresponding gene encoding novel chloride channel gene in human cornea and other tissues were examined by reverse transcription-polymerase chain reaction (RT-PCR). Quantitative PCR was performed to clarify the expression level of the novel chloride channel gene in cornea relative to that in other human tissues. Results. We cloned a new Ca 2+ -activated chloride channel, CLCA2, from corneal epithelium. The full length cDNA clone encoded 943 amino acids with 62% identity to bovine Ca 2+ -activated chloride channel. The CLCA2 gene mapped to human chromosome 1p32. Quantitative expression analysis by RT-PCR showed that it is the most abundant chloride channel in corneal epithelium. Conclusion. High and tissue specific expression of the CLCA2 gene in human corneal epithelium implies an important role in corneal transparency maintenance.

BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression

BodyMap-Xs () is a database for cross-species gene expression comparison. It was created by the anatomical breakdown of 17 million animal expressed sequence tag (EST) records in DDBJ using a sorting program tailored for this purpose. In BodyMap-Xs, users are allowed to compare the expression patterns of orthologous and paralogous genes in a coherent manner. This will provide valuable insights for the evolutionary study of gene expression and identification of a responsive motif for a particular expression pattern. In addition, starting from a concise overview of the taxonomical and anatomical breakdown of all animal ESTs, users can navigate to obtain gene expression ranking of a particular tissue in a particular animal. This method may lead to the understanding of the similarities and differences between the homologous tissues across animal species. BodyMap-Xs will be automatically updated in synchronization with the major update in DDBJ, which occurs periodically.

The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms

The Human Anatomic Gene Expression Library (H-ANGEL) is a resource for information concerning the anatomical distribution and expression of human gene transcripts. The tool contains protein expression data from multiple platforms that has been associated with both manually annotated full-length cDNAs from H-InvDB and RefSeq sequences. Of the H-Inv predicted genes, 18 897 have associated expression data generated by at least one platform. H-ANGEL utilizes categorized mRNA expression data from both publicly available and proprietary sources. It incorporates data generated by three types of methods from seven different platforms. The data are provided to the user in the form of a web-based viewer with numerous query options. H-ANGEL is updated with each new release of cDNA and genome sequence build. In future editions, we will incorporate the capability for expression data updates from existing and new platforms. H-ANGEL is accessible at http://www.jbirc.aist.go.jp/hinv/h-angel/.

Semantic wiki as a lightweight knowledge management system

Since its birth in 1995, Wiki has become more and more popular This paper presents a Semantic Wiki, a Wiki extended to include the ideas of Semantic Web The proposed Semantic Wiki uses a simple Wiki syntax to write labeled links which represent RDF triples By enabling the writing of labeled links, Semantic Wiki may provide an easy-to-use and flexible environment for an integrated management of content and metadata, so that Semantic Wiki may be used as a lightweight knowledge management system.

Transformation‐specific Decrease of Phosphorylation of 80K Protein, a Substrate of Protein Kinase C, in NIH3T3 Cells

Phosphorylation in normal and transformed NIH3T3 cells of the 80K protein, a specific substrate for protein kinase C, was compared by means of two‐dimensional gel analysis. We obtained evidence that NIH3T3 cells transformed by the c‐raf or H‐ras oncogene maintained a decreased level of phosphorylation of the 80K protein, with or without phorbol ester (TPA)‐stimulation, at all concentrations of serum tested while normal NIH3T3 cells maintained an elevated level of phosphorylation of the 80K protein. Furthermore, NIH3T3 cells transformed by N‐ras, K‐ras, src, mos or polyoma middle T antigen exhibited a decreased level of phosphorylation of the 80K protein. These events were confirmed by an analysis of a hormone‐inducible H‐ras transformant. Thus, phosphorylation of the 80K protein is inversely correlated with cellular transformation.

Towards a Data Hub for Biodiversity with LOD

Because of a huge variety of biological studies focused on different targets, i.e., from molecules to ecosystem, data produced and used in each field is also managed independently so that it is difficult to know the relationship among them. We aim to build a data hub with LOD to connect data in different biological fields to enhance search and use of data across the fields. We build a prototype data hub on taxonomic information on species, which is a key to retrieve data and link to databases in different fields. We also demonstrate how the data hub can be used with an application to assist search on other database.

Translation of hepatitis B virus DNA polymerase from the internal AUG codon, not from the upstream AUG codon for the core protein

Hepatitis B virus DNA replicates via its own polymerase that also acts as reverse transcriptase (Summers and Mason, 1982). This enzyme is encoded by a 3.5 Kb mRNA transcript covering the whole genome. Since the same transcript also codes for the core protein, and since the core open reading frame (ORF) is located upstream of the pol ORF, it has been suggested that the polymerase is first produced as a core-pol fusion protein that subsequently undergoes cleavage. This is already known to be the case with retrovirus reverse transcriptase, for which a gag-pol fusion protein is made first and the latter protein is liberated by proteolytic cleavage. We investigated this problem using mutants that were modified at the translation initiation codon for the core and precore ORF. Our findings suggested that polymerase translation occurred from the internal AUG codon independently of core protein synthesis, and that obligatory production of the core-pol fusion protein is accordingly unlikely.