• Korean Journal of Head & Neck Oncology
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• v.24 no.2
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• pp.155-161
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• 2008

Head and neck squamous cell carcinoma(HNSCC) still has poor outcome, and laryngeal cancer is the most frequent subtype of HNSCC. Therefore, there is a need to develop novel treatments to improve the outcome of patients with HNSCC. It is critical to gain further understanding on the molecular and chromosomal alteration of HNSCC to identify novel therapeutic targets but genetic etiology of squamous cell carcinoma of the larynx is so complex that target genes have not yet been clearly identified. Array based CGH(array-CGH) allows investigation of general changes in target oncogenes and tumor suppressor genes, which should, in turn, lead to a better understanding of the cancer process. In this study, We used genomic wide array-CGH in tissue specimens to map genomic alterations found in laryngeal squamous cell carcinomas. As results, gains of MAP2, EPHA3, EVI1, LOC389174, NAALADL2, USP47, CTDP1, MASP1, AHRR, and KCNQ5, with losses of SRRM1L, ANKRD19, FLJ39303, ZNF141, DSCAM, GPR27, PROK2, ARPP-21, and B3GAT1 were observed frequently in laryngeal squamous cell carcinoma tissue specimens. These data about the patterns of genomic alterations could be a basic step for understanding more detailed genetic events in the carcinogenesis and also provide information for diagnosis and treatment in laryngeal squamous cell carcinoma. The high resolution of array-CGH combined with human genome database would give a chance to find out possible target genes which were gained or lost clones.

• Journal of Periodontal and Implant Science
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• v.41 no.4
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• pp.192-200
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• 2011

Purpose: The aim of this study is to compare the gene expression profile in mesenchymal stem cells derived from dental tissues and bone marrow for characterization of dental stem cells. Methods: We employed GeneChip analysis to the expression levels of approximately 32,321 kinds of transcripts in 5 samples of bone-marrow-derived mesenchymal stem cells (BMSCs) (n=1), periodontal ligament stem cells (PDLSCs) (n=2), and dental pulp stem cells (DPSCs) (n=2). Each cell was sorted by a FACS Vantage Sorter using immunocytochemical staining of the early mesenchymal stem cell surface marker STRO-1 before the microarray analysis. Results: We identified 379 up-regulated and 133 down-regulated transcripts in BMSCs, 68 up-regulated and 64 down-regulated transcripts in PDLSCs, and 218 up-regulated and 231 down-regulated transcripts in DPSCs. In addition, anatomical structure development and anatomical structure morphogenesis gene ontology (GO) terms were over-represented in all three different mesenchymal stem cells and GO terms related to blood vessels, and neurons were over-represented only in DPSCs. Conclusions: This study demonstrated the genome-wide gene expression patterns of STRO-$1^+$ mesenchymal stem cells derived from dental tissues and bone marrow. The differences among the expression profiles of BMSCs, PDLSCs, and DPSCs were shown, and 999 candidate genes were found to be definitely up- or down-regulated. In addition, GOstat analyses of regulated gene products provided over-represented GO classes. These data provide a first step for discovering molecules key to the characteristics of dental stem cells.

• Korean Journal of Veterinary Service
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• v.34 no.2
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• pp.103-109
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• 2011

Asia1/Shamir that has been recommended by World Reference Laboratory for foot-and-mouth disease (FMD) is used as a vaccine strain, and is being prepared in many countries including Korea. Although it is assumed that vaccine strain Asia1/Shamir has a wide antigenicity, sufficient molecular biological analysis has not been accomplished yet. Complete genome sequence analysis showed that the region with the most severe variations was 1D region of structural protein-coding sequence; particularly amino acid 141~157 residues in 1D region RGD sites for binding to susceptible cells. In addition, five amino acids in 1D region were identified as characteristic sites that are different from other known Asia1 viruses. Asia1/Shamir strain was shown to be genetically similar to group VI that had occurred in the Middle East, but showed low level of genetic similarity to the group V viruses that had occurred in the Southeast Asia and China. It is considered that, if these viruses, group I and II including group V are introduced into Korea, care would be paid in case of inoculating the vaccine strain Shamir available in Korea.

• Journal of Microbiology and Biotechnology
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• v.28 no.8
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• pp.1352-1359
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• 2018

Lactobacillus plantarum is a lactic acid bacterium that promotes animal intestinal health as a probiotic and is found in a wide variety of habitats. Here, we investigated the genomic features of different clusters of L. plantarum strains via pan-genomic analysis. We compared the genomes of 108 L. plantarum strains that were available from the NCBI GenBank database. These genomes were 2.9-3.7 Mbp in size and 44-45% in G+C content. A total of 8,847 orthologs were collected, and 1,709 genes were identified to be shared as core genes by all the strains analyzed. On the basis of SNPs from the core genes, 108 strains were clustered into five major groups (G1-G5) that are different from previous reports and are not clearly associated with habitats. Analysis of group-specific enriched or depleted genes revealed that G1 and G2 were rich in genes for carbohydrate utilization (${\text\tiny{L}}-arabinose$, ${\text\tiny{L}}-rhamnose$, and fructooligosaccharides) and that G3, G4, and G5 possessed more genes for the restriction-modification system and MazEF toxin-antitoxin. These results indicate that there are critical differences in gene content and survival strategies among genetically clustered L. plantarum strains, regardless of habitats.

• Journal of Korean Biological Nursing Science
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• v.20 no.2
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• pp.55-66
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• 2018

Purpose: Peripheral neuropathy is common among colorectal cancer (CRC) patients who undergo oxaliplatin-based (OXL) chemotherapy. A pharmacogenetic approach can be used to identify patients at high-risk of developing severe neuropathy. This type of approach can also help clinicians determine the best treatment option and prevent severe neurotoxicity. The purpose of this study is to investigate the evidence of pharmacogenetic markers for OXL-induced peripheral neuropathy (OXIPN) in patients with CRC. Methods: A systematic literature search was conducted using the following databases up to December 2017: Pubmed, EMBASE, and CINAHL. We reviewed the genetic risk factors for OXIPN in observational studies and randomized controlled clinical trials (RCTs). All processes were performed independently by two reviewers. Results: Sixteen studies published in English between 2006 and 2017 were included in this review. A genome-wide association approach was used in one study and various candidate genes were tested, based on their functions (e.g., DNA damage or repair, ion channels, anti-oxidants, and nerve growth etc.). The genes associated with incidence or severity of OXIPN were ABCG2, GSTP1, XRCC1, TAC1, and ERCC1. Conclusion: This study highlighted the need and the importance of conducting pharmacogenetic studies to generate evidence of personalized OXIPN symptoms management. Additional studies are warranted to accelerate the tailored interventions used for OXIPN in patients with CRC (NRF-2014R1A1A3054386).

• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1555-1560
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• 2010

Quantum dots (QDs) are extensively employed for biomedical research as a fluorescence reporter and their use for various labeling applications will continue to increase as they are preferred over conventional labeling methods for various reasons. However, concerns have been raised over the toxicity of these particles in the biological system. Till date no thorough investigation has been carried out to identify the molecular signatures of QD mediated toxicity. In this study we evaluated the toxicity of CdSe, $Cd_{1-x}Zn_xS$/ZnS and CdSe/ZnS quantum dots having different spectral properties (red, blue, green) using human embryonic kidney fibroblast cells (HEK293). Cell viability assay for both short and long duration exposure show concentration material dependent toxicity, in the order of CdSe > $Cd_{1-x}Zn_xS$/ZnS > CdSe/ZnS. Genome wide changes in the expression of genes upon QD exposure was also analyzed by wholegenome microarray. All the three QDs show increase in the expression of genes related to apoptosis, inflammation and response towards stress and wounding. Further comparison of coated versus uncoated CdSe QD-mediated cell death and molecular changes suggests that ZnS coating could reduce QD mediated cytotoxicity to some extent only.

• Genomics & Informatics
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• v.11 no.2
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• pp.76-82
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• 2013

Over the past decade or so, dramatic developments in our ability to experimentally determine the content and function of genomes have taken place. In particular, next-generation sequencing technologies are now inspiring a new understanding of bacterial transcriptomes on a global scale. In bacterial cells, whole-transcriptome studies have not received attention, owing to the general view that bacterial genomes are simple. However, several recent RNA sequencing results are revealing unexpected levels of complexity in bacterial transcriptomes, indicating that the transcribed regions of genomes are much larger and complex than previously anticipated. In particular, these data show a wide array of small RNAs, antisense RNAs, and alternative transcripts. Here, we review how current transcriptomics are now revolutionizing our understanding of the complexity and regulation of bacterial transcriptomes.

• Biomedical Science Letters
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• v.26 no.1
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• pp.28-36
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• 2020

High blood pressure (HTN) is a condition in which blood pressure is kept higher than normal. Blood pressure trait measures systolic blood pressure (SBP) which is the highest pressure and diastolic blood pressure (DBP) which is the lowest blood pressure. Pulse pressure (PP) is the difference between systolic and diastolic blood pressure. Hypertension is known as a disease caused by the interaction of the environment and genetic factors. To date, studies have been conducted to find genes associated with hypertension. Genome-Wide Association Study (GWAS) analysis using European data from the UK Biobank reported new 535 loci were associated with blood pressure trait. Among them, 12 genes have been reported to have a significant correlation with SBP, DBP and PP. In the study, 12 genes polymorphisms were extracted based on KARE (Korean association resource) and then we performed linear regression of blood pressure trait. As a result, 6 SNPs of the 3 genes (rs12355413 and rs11006736 of ARMC4, rs2290883, rs2290884 and rs11039014 of LRP4, rs7234941 of BCL2) showed statistically significant correlation (P<0.05) with blood pressure trait. Of the 3 genes, 6 SNPs in 2 genes (rs9651357, rs12355413, rs11006736, rs1889522 of ARMC4 and rs4987774, rs7234941 of BCL2) showed significant correlation with hypertension. These results suggest that genetic polymorphisms of ARMC4, LRP4 and BCL2 genes are associated with blood pressure traits and hypertension in Korean population. Moreover, we expected to help understand the pathogenesis of hypertension.

• Journal of Ginseng Research
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• v.36 no.4
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• pp.449-460
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• 2012

Plants have versatile detoxification systems to encounter the phytotoxicity of the wide range of natural and synthetic compounds present in the environment. Glutathione S-transferase (GST) is an enzyme that detoxifies natural and exogenous toxic compounds by conjugation with glutathione (GSH). Recently, several roles of GST giving stress tolerance in plants have demonstrated, but little is known about the role of ginseng GSTs. Therefore, this work aimed to provide further information on the GST gene present in Panax ginseng genome as well as its expression and function. A GST cDNA (PgGST) was isolated from P. ginseng cDNA library, and it showed the amino acid sequence similarity with theta type of GSTs. PgGST in ginseng plant was induced by exposure to metals, plant hormone, heavy metals, and high light irradiance. To improve the resistance against environmental stresses, full-length cDNA of PgGST was introduced into Nicotiana tabacum. Overexpression of PgGST led to twofold increase in GST-specific activity compared to the non-transgenic plants, and the GST overexpressed plant showed resistance against herbicide phosphinothricin. The results suggested that the PgGST isolated from ginseng might have a role in the protection mechanism against toxic materials such as heavy metals and herbicides.

• Korean Journal of Plant Resources
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• v.30 no.3
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• pp.323-330
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• 2017

Eleutherococcus senticosus (Siberian ginseng) is an important medicinal tree found in northeast Asia. In this study, we analyzed the genome-wide distribution of microsatellites in E. senticosus. By sequencing 711 clones from an SSR-enriched genomic DNA library, we obtained 12 polymorphic SSR markers, which also revealed successful amplicons in E. senticosus accessions. Using the developed SSR markers, we estimated genetic diversity and population structure among 131 E. senticosus accessions in Korea and China. The number of alleles ranged from 2 to 11, with an average of 7.4 alleles. The mean values of observed heterozygosity ($H_O$) and expected heterozygosity ($H_E$) were 0.59 and 0.56, respectively. The average polymorphism information content (PIC) was 0.51 in all 131 E. senticosus accessions. E. senticosus accessions in Korea and China showed a close genetic similarity. Significantly low pairwise genetic divergence was observed between the two regions, suggesting a relatively narrow level of genetic basis among E. senticosus accessions. Our results not only provide molecular tools for genetic studies in E. senticosus but are also helpful for conservation and E. senticosus breeding programs.