• 대한한의학방제학회지
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• 제29권4호
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• pp.267-275
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• 2021

Objectives : Previously, we reported that compound K isolated from fermented ginseng by Aspillus oryzae has a wide biochemical and pharmacological effect, including anti-cancer activity in prostate cancer PC-3 cells. Despite these findings, its signaling pathway and gene expression pattern are not clearly understood. Methods : To confirm the gene expression study of treated with compound K in PC-3 cells, a cDNA microarray chip composed of 44K human cDNA probes was used. MTT assay, western blot analysis, propidium iodide staining, and annexin V/propidium iodide staining were analyzed. Results : We confirmed the differences of gene expression profiles. Then, we analyzed with the cell cycle arrest, cell death and cell proliferation related genes using DAVID database. Conclusions : Our finding should be useful for understanding genome-wide expression patterns of compound K-mediated cell cycle arrest toward induction of cell death and be helpful for finding future cancer therapeutic targets for prostate cancer cells.

• Biomolecules & Therapeutics
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• 제22권2호
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• pp.143-148
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• 2014

Marfan syndrome (MFS) is a dominantly inherited connective tissue disorder caused by mutations in the gene encoding fibrillin-1 (FBN1) and is characterized by aortic dilatation and dissection, which is the primary cause of death in untreated MFS patients. However, disease progression-associated changes in gene expression in the aortic lesions of MFS patients remained unknown. Using a mouse model of MFS, FBN1 hypomorphic mouse (mgR/mgR), we characterized the aortic gene expression profiles during the progression of the MFS. Homozygous mgR mice exhibited MFS-like phenotypic features, such as fragmentation of elastic fibers throughout the vessel wall and were graded into mgR1-4 based on the pathological severity in aortic walls. Comparative gene expression profiling of WT and four mgR mice using microarrays revealed that the changes in the transcriptome were a direct reflection of the severity of aortic pathological features. Gene ontology analysis showed that genes related to oxidation/reduction, myofibril assembly, cytoskeleton organization, and cell adhesion were differentially expressed in the mgR mice. Further analysis of differentially expressed genes identified several candidate genes whose known roles were suggestive of their involvement in the progressive destruction of aorta during MFS. This study is the first genome-wide analysis of the aortic gene expression profiles associated with the progression of MFS. Our findings provide valuable information regarding the molecular pathogenesis during MFS progression and contribute to the development of new biomarkers as well as improved therapeutic strategies.

• 한국한의학연구원논문집
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• 제8권2호통권9호
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• pp.95-107
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• 2002

Yukmijihwang-tang(YM) is a noted herbal prescription in Chinese and Korean traditional medicines, and it has been known to reinforce the vital essence and has been widely used for a variety of disease such as stroke, osteoporosis, anti-tumor, and hypothyrodism. Regarding its traditional use, YM has been known to reinforce the Yin (vital essence) of liver and kidney. Also it has been known to reinforce nutrition and biological function in brain. Recently, studies suggested that YM increase antioxidant activities and exert the protective effect against oxidant-induced liver cell injury. We investigated the high-throughput gene expression analysis on the Yukmijihwang-tang administrated in SD rats. Microarray data were validated on a limited number of genes by semiquantitative RT-PCR and Western blot analyses. The recent availability of microarrays provides an attractive strategy for elaborating an unbiased molecular profile of large number of genes in drug discovery This experimental approach offers the potential to identify molecules or cellular pathways not previously associated with herbal medicine. Total RNA from normal control brain and Yukmijihwang-tang administrated brain were hybridized to microarrays containing 10,000 rat genes. The 52 genes were found to be up-regulated(twice or more) excluding EST gene. The nine genes were found to be down-regulated(twice or more) excluding EST gene. Gene array technology was used to identify for the first time many genes expression pathway analysis that arecell cycle pathway, apoptosis pathway, electron transport chain pathway, cytoplasmic ribosomal protein pathway, fatty acid degradation pathway, and TGF-beta signaling pathway. These differentially expressed genes pathway analysis have not previously been iavestigated in the context of herbal medicine efficacy and represent novel factors for further study of the mechanism of herbal medicine efficacy.

• Asian-Australasian Journal of Animal Sciences
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• 제18권5호
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• pp.682-685
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• 2005

Large White, an introduced European pig breed, and Meishan, a Chinese indigenous pig breed, were hybridized directly and reciprocally and a total of 260 pigs, including purebreds, Large White and Meishan, and their hybrids, White${\times}$Meishan (LM) and Meishan${\times}$Large White (ML) pigs, were bred in our laboratory. The mRNA differential display PCR (DD-PCR) was used to detect the age-dependent changes of differential gene expression in backfat tissue between hybrids and parents. Some measures were taken to reduce the false positives in our experiment. Among the total of 2,686 bands obtained, 1,952 bands (about 72.67%) were reproducible and eight patterns (fifteen kinds) of gene expression were observed. The percentage of differentially expressed genes between hybrids and parents is 56.86% at the age of four months and 57.71% at the age of six months. This indicated that the differences of gene expression between hybrids and their parents were very obvious. U-test was used to compare the patterns of gene expression between the age of four and six months, and results showed that bands occurring in only one hybrid and bands displayed in one hybrid and one parent were significantly different at p<0.05, and bands visualized in only two hybrids were significantly different at p<0.01. These indicated that differential gene expression between hybrids and parents changed at different ages.

• Genomics & Informatics
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• 제19권1호
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• pp.5.1-5.11
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• 2021

Head and neck squamous cell carcinoma (HNSCC) is the most frequent type of head and neck cancer that usually arises from the mucosal surfaces of several organs including nasal cavity, paranasal sinuses, oral cavity, tongue, pharynx, and larynx. The Wnt signaling pathway is a crucial mechanism for cellular maintenance and development. It regulates cell cycle progression, apoptosis, proliferation, migration, and differentiation. Dysregulation of this pathway correlates with oncogenesis in various tissues including breast, colon, pancreatic as well as head and neck cancers. The present study aims to assess the gene alterations in the Wnt family of genes so as to derive an association with HNSCC. Computational approaches have been utilized for the identification of gene alterations in the Wnt family of genes. Several databases such as cBioportal, STRING, and UALCAN were used for the purpose. The frequency of alteration was high in case of Wnt family member 11 (5%). Gene amplification, deep deletions, missense and truncating mutations were observed in HNSCC patients. There was a marked difference in the gene expression profile of WNT11 between grades as well as normal samples. The survival probability measured using the Kaplan-Meier curve also presented with a significant difference among male and female subjects experiencing a low/medium level expression. The female patients showed less survival probability when compared to the male subjects. This provides the prognostic significance of the WNT11 gene in HNSCC. Taken together, the present study provides clues on the possible association of WNT11 gene alterations with HNSCC, which has to be further validated using experimental approaches.

• Animal cells and systems
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• 제3권4호
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• pp.399-405
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• 1999

Characteristics of the food isolates and the clinical specimens isolates of E. coli harboring virulence factor and their correlations were analyzed. The predominant serogroup were 08 and 027 in the food isolates and 06 and 018 in the clinical isolates, respectively, showing the different patterns in serogrouping between them. In the test of antibiotic susceptibility, the food isolates were resistant to cephalothin, streptomycin, tetracycline and minocycline, and the clinical isolates were resistant to ampicillin, carbenicillin, streptomycin, cephalothin, trimethoprim/sulfamethoxazole, tetracyclino and minocycline, respectively. It shows that E.coli isolated from food sources and clinical specimens might be correlated. Plasmid profile in the food and clinical isolates showed wide diversity. Especially, large sized plasmid DNA such as 60 MDa, 90 MDa and 120 MDa were observed. The plasmid DNA (60 MDa) containing a gene encoding hemolysin was found in 43% of the food isolates and 35% of the clinical isolates. To study chromosomal homology, PFGE analysis was performed, showing different restriction patterns by Xbal. This result indicates that there were no genetic correlations between the foods and the clinical isolates.

• Genomics & Informatics
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• 제13권4호
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• pp.152-155
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• 2015

Recently, the Encyclopedia of DNA Elements (ENCODE) Analysis Working Group converted data from ChIP-seq analyses from the Broad Histone track into 15 corresponding chromatic maps that label sequences with different kinds of histone modifications in promoter regions. Here, we publish a frequency profile of the three ChromHMM promoter states, at 200-bp intervals, with particular reference to the existence of sequence patterns of promoter elements, GC-richness, and transcription starting sites. Through detailed and diligent analysis of promoter regions, researchers will be able to uncover new and significant information about transcription initiation and gene function.

• International Journal of Oral Biology
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• 제32권1호
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• pp.13-22
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• 2007

The stem cell research is emerging as a cutting edge topic for a new treatment for many chronic diseases. Recently, dental stem cell would be possible for regeneration of tooth itself as well as periodontal tissue. However, the study of the cell characterization is scarce. Therefore, we performed the genetic profiling and the characterization of mouse fetus/neonate derived dental tissue and cell to find the identification during dental development. We separated dental arch from mandibles of 14.5 d fetal mice and neonate 0 d under the stereoscope, and isolated dental cells primarily from the tissues. Then, we examined morphology and the gene expression profiles of the primary cells and dental tissues from fetus/neonate and adult with RT-PCR. Primary dental cells showed heterogeneous but the majority was shown as fibroblast-like morphology. The change of population doubling time levels (PDLs) showed that the primary dental cells have growth potential and could be expanded under our culture conditions without reduction of growth rate. Immunocytochemical and flow cytometric analyses were performed to characterize the primary dental cell populations from both of fetus (E14.5) and neonate. Alpha smooth muscle actin (${\alpha}-SMA$), vimentin, and von Willebrand factor showed strong expression, but desmin positive cells were not detected in the primary dental cells. Most of the markers were not uniformly expressed, but found in subsets of cells, indicating that the primary dental cell population is heterogeneous, and characteristics of the populations were changed during culture period. And mesenchymal stem cell markers were highly expressed. Gene expression profile showed Wnt family and its related signaling molecules, growth factors, transcription factors and tooth specific molecules were expressed both fetal and neonatal tissue. The tooth specific genes (enamelin, amelogenin, and DSPP) only expressed in neonate and adult stage. These expression patterns appeared same as primary fetal and neonatal cells. In this study we isolated primary cells from whole mandible of fetal and neonatal mice. And we investigated the characteristics of the primary cells and the profile of gene expressions, which are involved in epithelial-mesenchymal interactions during tooth development. Taken together, the primary dental cells in early passages or fetal and neonatal mandibles could be useful stem cell resources.

• 한국식품위생안전성학회지
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• 제35권3호
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• pp.219-224
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• 2020

본 연구는 2018년 10월에서 2019년 9월까지 부산지역 유통 판매되고 있는 872건의 다양한 식품을 대상으로 B. cereus 오염도를 분석하였다. 총 872건 중 78건(8.9%)에서 B. cereus 검출되었으며 식품별 B. cereus 검출률은 김치·절임·조림·젓갈류에서 23.9%, 조미식품 19.4%, 바로 섭취가능한 농산물 10.5%, 조리식품 7.3%, 즉석섭취식품 5.6%, 신선편의식품 5.0%, 즉석조리식품 0.0% 순으로 분포하였으며 통계적으로 유의한 차이가 있었다. B. cereus 오염 수준은 불검출에서 최대 20,000 CFU/g로 평균 48 CFU/g였으며, 식품별 B.cereus 오염도에는 차이가 없었다. 78건의 검체에서 분리된 113주의 B. cereus의 독소 유전자 확인 시험을 수행하였다. 식품에서 분리된 113주를 대상으로 B. cereus 독소유전자 확인 결과 최소 1종류에서 최대 5종류의 독소 유전자가 검출되었으며 총 18개 profile로 분류되었다. 장독소 5종(Cytk-nheA-entFM-bceT-hblC)을 모두 보유한 경우가 34주(30.1%)로 가장 많았다.

• 대한한방내과학회지
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• 제29권3호
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• pp.543-553
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• 2008

Objective: The goal of this study was to determine the anti-asthma mechanism of SF on TNF-${\alpha}$ induced activation on A549 (human type II-like epithelial) cells. Using oligonucleotide microarray, we sought to establish the molecular mechanism of the protective effects of SF on A549 cells. Material & Methods : Cells were cultured in three different conditions: 1) negative control group was cultured in normal condition of DMEM, 2) positive control group was activated with TNF-${\alpha}$, IL-4. and IL-1${\beta}$, and 3) SF treated group was previously treated with 0.1${\mu}g/ml$ SF after TNF-${\alpha}$, IL-4. and IL-1 activation. Cells of positive control and SF treated groups were cultured for 30 min, 1hr, 3hr and 6hr. Results : The comparative analysis of the gene expression profile revealed that proinflammatory cytokines such as IL1F8, IL1F9, IL1R1. IL1RN, IL1RAPL1, IL8, TNFRSF4, TNFSF10c, TNFSF13, TRAF5, and TRAF7 and inflammation-related genes including MMP2, MMP11, MMP14, MMP15, MMP16, MMP19, MMP25, and MMP27 were down regulated with SF treatment. Cell adhesion molecule genes such as ITGB1, ITGBL1, selectin P ligand, selectin E, ICAM2, ICAM3, VCAM1, PECAM, FCER1G and MMP28 genes were also down-regulated in SF treated A549 cells. Conclusion : These results suggest that the anti-asthmatic effects of SF could be mediated by regulating specific genes related with cell adhesion, proinflammatory cytokine and inflammation-related genes in A549 cells.