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Suigen, South Korea

Cho S.-Y.,Chonnam National University | Kwon J.,Korea Basic Science Institute | Vaidya B.,Chonnam National University | Kim J.-O.,Chonnam National University | And 7 more authors.
Fish and Shellfish Immunology | Year: 2014

Lectins found in fish tissues play an important role in the innate immune response against viral infection. A fucose-binding type lectin, RbFTL-3, from rock bream (Oplegnathus fasciatus) was identified using expressed sequence tag (EST) analysis. The expression of RbFTL-3 mRNA was higher in intestine than other tissues of rock bream. To determine the function of RbFTL-3, VHSV-susceptible fathead minnow (FHM) cells were transfected with pcDNA3.1(+) or pcDNA3.1(+)-RbFTL-3 and further infected with VHSV. The results show that the viability of FHM cells transfected with pcDNA3.1(+)-RbFTL-3 is higher than that of cells transfected with pcDNA3.1(+) (relative cell viability: 28.9% vs 56.2%). A comparative proteomic analysis, performed to explore the proteins related to the protective effect of RbFTL-3 in the cells during VHSV infection, identified 90 proteins differentially expressed in VHSV-infected FHM cells transfected with pcDNA3.1(+) or pcDNA3.1(+)-RbFTL-3. The expression of RbFTL-3 inhibits a vascular-sorting protein (SNF8) and diminishes the loss of prothrombin, which are closely associated with controlling viral budding and hemorrhage in fish cells, respectively. Subsequent Ingenuity Pathways Analysis enabled prediction of their biofunctional groupings and interaction networks. The results suggest RbFTL-3 modulates the expression of proteins related to viral budding (SNF8, CCT5 and TUBB) and thrombin signaling (F2) to increase the viability of VHSV infected cells. © 2014 Elsevier Ltd. Source

Yun S.M.,CHA Medical University | Yoon K.,CHA Medical University | Lee S.,TheragenEtex Inc. | Kim E.,CHA Medical University | And 11 more authors.
Oncogene | Year: 2013

Fusion genes act as potent oncogenes, resulting from chromosomal rearrangements or abnormal transcription in many human cancers. Although multiple gastric cancer genomes have been sequenced, the driving recurrent gene fusions have not been well characterized. Here, we used paired-end transcriptome sequencing to identify novel gene fusions in 18 human gastric cancer cell lines and 18 pairs of primary human gastric cancer tissues and their adjacent normal tissues. Multiple samples revealed expression of PPP1R1B-STARD3 fusion transcript. The presence of PPP1R1B-STARD3 correlated with elevated levels of PPP1R1B mRNA. PPP1R1B-STARD3 fusion transcript was detected in 21.3% of primary human gastric cancers but not in adjacent matched normal gastric tissues. Based on reverse transcription PCR analysis of DNA, unlike other fusions described in gastric cancer, the PPP1R1B-STARD3 appears to be generated by RNA processing without chromosomal rearrangement. Overexpression of PPP1R1B-STARD3 in MKN-28 significantly increased cell proliferation and colony formation. This increased proliferation was mediated by activation of phosphatidylinositol-3-kinase (PI3K)/AKT signaling. Furthermore, expression of PPP1R1B-STARD3 fusion transcript enhanced the tumor growth of MKN-28 cells in athymic nude mice. These findings show that PPP1R1B-STARD3 fusion transcript has a key role in subsets of gastric cancers through the activation of PI3K/AKT signaling.Oncogene advance online publication, 25 November 2013; doi:10.1038/onc.2013.472. Source

Lim J.E.,Kyung Hee University | Shin Y.-A.,Personal Genomics Institute | Hong K.-W.,Korea National Institute of Health | Jin H.-S.,Ajou University | And 2 more authors.
Genes and Genomics | Year: 2013

Through 2011, GWASs have identified 33 genetic loci that are linked to blood pressure. Data from the 1000 Genomes Project were used to examine these loci. By searching nonsynonymous SNPs, promoter SNPs, splicing site SNPs, and gain- or loss-of-stop codon SNPs in 1000 Genomes Project data, we identified 2,113 functional variants in 66 genes in the 33 loci: 613 nonsynonymous SNPs, 1,425 promoter SNPs, 114 splice SNPs, and 15 gain- or loss-of-stop SNPs. There were no frameshift variations. Four hundred four of 613 nonsynonymous SNPs were predicted to be deleterious, based on 1000 Genomes Project data, and 1,114 of 1,425 promoter SNPs were predicted to influence the binding of transcription factors, using TFSearch. To determine whether these functional variants were causative factors of blood pressure, we analyzed KARE data, comprising 7,551 Korean individuals. The 24,962 SNPs in the 33 loci were imputed from the 1000 Genomes Project data into the KARE data. One hundred fourteen of 2,113 functional variants were successfully imputed and analyzed for their association with systolic blood pressure, diastolic blood pressure, and hypertension in the KARE cohort. As a result, 15 SNPs - 3 nonsynonymous SNPs, 11 promoter SNPs, and 1 splice site SNP - showed association signals. These results, despite the low percentage of functional variants that were analyzed, provide valuable data on the candidate variants that govern blood pressure GWAS signals. © 2013 The Genetics Society of Korea. Source

Bolser D.M.,Personal Genomics Institute | Chibon P.-Y.,Wageningen University | Palopoli N.,National University of Quilmes | Gong S.,National University of Quilmes | And 17 more authors.
Nucleic Acids Research | Year: 2012

Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase. Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project. © The Author(s) 2011. Published by Oxford University Press. Source

Ngamphiw C.,National Center for Genetic Engineering and Biotechnology | Ngamphiw C.,Chulalongkorn University | Assawamakin A.,National Center for Genetic Engineering and Biotechnology | Xu S.,CAS Shanghai Institutes for Biological Sciences | And 8 more authors.
PLoS ONE | Year: 2011

The HUGO Pan-Asian SNP consortium conducted the largest survey to date of human genetic diversity among Asians by sampling 1,719 unrelated individuals among 71 populations from China, India, Indonesia, Japan, Malaysia, the Philippines, Singapore, South Korea, Taiwan, and Thailand. We have constructed a database (PanSNPdb), which contains these data and various new analyses of them. PanSNPdb is a research resource in the analysis of the population structure of Asian peoples, including linkage disequilibrium patterns, haplotype distributions, and copy number variations. Furthermore, PanSNPdb provides an interactive comparison with other SNP and CNV databases, including HapMap3, JSNP, dbSNP and DGV and thus provides a comprehensive resource of human genetic diversity. The information is accessible via a widely accepted graphical interface used in many genetic variation databases. Unrestricted access to PanSNPdb and any associated files is available at: http://www4a.biotec.or.th/PASNP. © 2011 Ngamphiw et al. Source

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