• International Journal of Oral Biology
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• 제32권1호
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• pp.35-43
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• 2007

Tooth loss in elderly is mainly caused by alveolar bone loss via severe periodontitis. Although the severity of periodontitis is known to be affected by age, the aging process or the genetic changes during the aging of periodontal tissue cells are not well characterized. In this study, we investigated the effect of in vitro aging on the change of gene expression pattern in periodontal fibroblasts. Gingival fibroblasts (GF) and periodontal ligament fibroblasts (PDL) were obtained from two young patients and replicative senescence was induced by sequential subcultivation. When more than 90% cells were positively stained with senescence-associated ${\beta},-galactosidase$, those cells were regarded as aged cells. In aged GF and PDL, the level of phosphorylated retinoblastoma (RB) and $p16^{INK4A}$ protein was significantly decreased and increased, respectively. However, the protein level of p53 and p21, well known senescence-inducing genes, did not increase in aged GF and PDL. Although $p27^{Kip1}$ and $p15^{INK4B}$, another cyclin-dependent kinase inhibitors, were reported to be involved in replicative senescence of human cells, they were decreased in aged GF and PDL. Because senescent cells showed flattened and enlarged cell shape and are known to have increased focal adhesion, we examined the protein level of several integrins. Aged GF and PDL showed increased protein level of integrin ${\alpha}2$, ${\alpha}v$, and ${\beta}1$. When the gene expression profiles of actively proliferating young cells and aged cells were compared by cDNA microarray of 3,063 genes and were confirmed by reverse transcription-polymerase chain reaction, 7 genes and 15 genes were significantly and commonly increased and decreased, respectively, in aged GF and PDL. Among them, included are the genes that were known to be involved in the regulation of cell cycle, gene transcription, or integrin signaling. The change of gene expression pattern in GF and PDL was minimally similar to that of oral keratinocyte. These results suggest that $p16^{INK4A}/RB$ might be involved in replicative senescence of periodontal fibroblasts and the change of gene expression profile during aging process is cell type specific.

• 식물분류학회지
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• 제52권1호
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• pp.80-83
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• 2022

Polygonatum falcatum is a perennial herb distributed in East Asia. We determined the characteristics of the complete chloroplast genome in P. falcatum for the first time, with a de novo assembly strategy. The chloroplast genome was 154,579bp in length harboring 87 protein coding genes, 38 tRNA genes and eight rRNA genes. It exhibits typical quadripartite structure comprising a large single-copy (LSC) (83,528bp), a small single-copy (SSC) (18,457bp) and a pair of inverted repeats (IRs) (26,297bp). Phylogenetic analysis of 16 chloroplast genomes from Asparagaceae reveals that the genus Polygonatum is a monophyletic group and that P. falcatum is clustered together with the congener, P. odoratum.

• Journal of Plant Biotechnology
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• 제45권1호
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• pp.45-54
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• 2018

This research was conducted to study the gene expression of coffee (Coffea arabica L.) seedlings under salt stress condition. A solution of five percent ($2.3dS\;m^{-1}$) deep sea water was used for the salt treatment, and it was thereby compared to normal irrigation water ($0.2dS\;m^{-1}$) used for the control treatment. The mRNA was extracted from the leaves of the coffee seedlings for a comprehensive analysis. In this study, a total of 19,581 genes were identified and aligned to the reference sequences available in the coffee genome database. The gene ontology analysis was performed to estimate the number of genes associated with the identified biological processes, cellular components and molecular functions. Among the 19,581 genes, 7369 (37.64%) were associated with biological processes, 5909 (30.18%) with cellular components, and 5325 (27.19%) with molecular functions. The remaining 978 (4.99%) genes were therefore grouped as unclassified. A differential gene expression analysis was performed using the DESeq2 package to identify the genes that were differentially expressed between the treatments based on fold changes and p-values. Namely, a total of 611 differentially expressed genes were identified (treatment/control) in that case. Among these, 336 genes were up-regulated while 275 of the genes were down-regulated. Of the differentially expressed genes, 60 genes showed statistically significant (p < 0.05) expression, 44 of which were up-regulated and 16 which were down-regulated. We also identified 11 differentially expressed transcription factor genes, 6 of which were up-regulated and rest 5 genes were down-regulated. The data generated from this study will help in the continued interest and understanding of the responses of coffee seedlings genes associated with salinity stress, in particular. This study will also provide important resources for further functional genomics studies.

• Journal of Preventive Medicine and Public Health
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• 제45권4호
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• pp.251-258
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• 2012

Objectives: The purpose of this paper was to elucidate the potential methylation levels of adjacent normal and cancer tissues by comparing them with normal colorectal tissues, and to describe the correlations between the methylation and clinical parameters in Korean colorectal cancer (CRC) patients. Methods: Hypermethylation profiles of nine genes (RASSF1, APC, $p16^{INK4a}$, Twist1, E-cadherin, TIMP3, Smad4, COX2, and ABCB1) were examined with 100 sets of cancer tissues and 14 normal colorectal tissues. We determined the hypermethylation at a given level by a percent of methylation ratio value of 10 using quantitative methylation real-time polymerase chain reaction. Results: Nine genes' hypermethylation levels in Korean CRC patient tissues were increased more higher than normal colorectal tissues. However, the amounts of $p16^{INK4a}$ and E-cadherin gene hypermethylation in normal and CRC tissues were not significantly different nor did TIMP3 gene hypermethylation in adjacent normal and cancer tissues differ significantly. The hypermethylation of TIMP3, Ecadherin, ABCB1, and COX2 genes among other genes were abundantly found in normal colorectal tissues. The hypermethylation of nine genes' methylation in cancer tissues was not significantly associated with any clinical parameters. In Cohen's kappa test, it was moderately observed that RASSF1 was related with E-cadherin, and Smad4 with ABCB1 and COX2. Conclusions: This study provides evidence for different hypermethylation patterns of cancer-associated genes in normal and CRC tissues, which may serve as useful information on CRC cancer progression.

• Asian-Australasian Journal of Animal Sciences
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• 제22권4호
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• pp.471-482
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• 2009

Nutrient availability may control muscle growth directly and indirectly through its influence on regulatory factors. We analyzed the effects of nutrient availability on the breast muscle insulin-like growth factor system. Real time RT-PCR was used to quantify the level of transcription in breast muscle from Langshan (LS) layer and Arbor Acres (AA) broiler chickens subjected to different feeding regimens during embryonic and postnatal development. The AA chickens were fed AA diet (AA, control group) while the LS chickens were either fed LS diet (LL) or AA diet (LA). According to our results, insulin-like growth factor (IGF)-II (embryonic day 16 (E16) - postnatal day 42 (P42)), IGF-I receptor (IGF-IR, E18-P42), and IGF binding protein (IGFBP)-2 (E18-P42), -5 (E16-P14), -7 (E12-P0), and -3 (E12-P0) were positively correlated with IGF-I, while IGFBP-3 (P0-P28) was negatively correlated with IGF-I. In comparison, IGF-IR (E18-P42), IGFBP-2 (E18-P42), IGFBP-5 (E14-P0), and IGFBP-3 (E16-P0) were positively correlated with IGF-II, while IGF-IR (E10-E16) and IGFBP-3 (P0-P28) were negatively correlated with IGF-II. Moreover, IGFBP-2 (E16-P42), -7 (E10-E16), and -3 (E10-E16) were positively correlated with IGF-IR, while IGFBP-3 (P0-P28) was negatively correlated with IGF-IR. Finally, IGFBP-7 (E12-P0) was positively correlated with IGFBP-3, while IGFBP-2 (P0-P28) and -7 (P0-P42) were negatively correlated with IGFBP-3. Overall, the AA chickens exhibited higher levels of IGF-I, IGF-IR, and IGFBP-2 mRNA expression than the LL chickens, while the opposite was true for IGFBP-7. No strain differences in IGF-I, IGF-IR, and IGFBP-7 mRNA expression were detected between LA and AA chickens; however, a strain difference was observed for IGFBP-2. LA chickens exhibited higher levels of IGFBP-2 than LL chickens, while the opposite was true for IGFBP-7. Our data show the first evidence that certain genes may be correlated during specific developmental periods and that strain differences in the expression of those genes in LS and AA chickens are due to differential responses to the same diet.

• Asian Pacific Journal of Cancer Prevention
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• 제16권9호
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• pp.3677-3683
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• 2015

Abnormally expressed microRNAs (miRNAs) and genes have been found to play key roles in esophageal squamous cell carcinoma (ESCC), but little is known about the underlying mechanisms. The aim of this paper was to assess inter-relationships and the regulatory mechanisms of ESCC through a network-based approach. We built three regulatory networks: an abnormally expressed network, a related network and a global network. Unlike previous examples, containing information only on genes or miRNAs, the prime focus was on relationships. It is worth noting that abnormally expressed network emerged as a fault map of ESCC. Theoretically, ESCC might be treated and prevented by correcting the included errors. In addition, the predicted transcription factors (TFs) obtained by the P-match method also warrant further study. Our results may further guide gene therapy researchers in the study of ESCC.

• Fisheries and Aquatic Sciences
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• 제16권4호
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• pp.221-227
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• 2013

In total, 131 Escherichia coli isolates from surface seawater of the Gomso Bay, of Korea, were analyzed for their susceptibility to 22 different antimicrobials and for genes associated with antimicrobial resistance and virulence. According to the disk diffusion susceptibility test, the resistance to tetracycline was most prevalent (33.6%), followed by that to ampicillin (22.1%), ticarcillin (22.1%), and trimethoprim (16.8%). More than 46.6% of the isolates were resistant to at least one antimicrobial, and 22.9% were resistant to three or more classes of antimicrobials; these were consequently defined as multidrug resistant. We further found that 29 ampicillin-resistant isolates possessed genes encoding TEM-type (93.1%) and SHV-type (6.9%) ${\beta}$-lactamases. Among the 44 tetracycline-resistant isolates, tetA and tetC were found in 35 (79.5%) and 19 (43.2%), respectively, whereas tetB was detected in only three isolates (6.8%). With regard to virulence genes, merely 0.8% (n = 1) and 2.3% (n = 3) of the isolates were positive for the enteroaggregative E. coli-associated plasmid (pCVD432) gene and the enteropathogenic E. coli-specific attaching and effacing (eae) gene, respectively. Overall, these results not only provide novel insight into the necessity for seawater sanitation in Gomso Bay, but they help reduce the risk of contamination of antimicrobial-resistant bacteria.

• Journal of Microbiology and Biotechnology
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• 제33권4호
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• pp.471-484
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• 2023

Compost is widely used as an organic additive to improve the bioremediation of diesel-contaminated soil. In this study, the effects of compost amendment on the remediation performance, functional genes, and bacterial community are evaluated during the bioremediation of diesel-contaminated soils with various ratios of compost (0-20%, w/w). The study reveals that the diesel removal efficiency, soil enzyme (dehydrogenase and urease) activity, soil CH₄ oxidation potential, and soil N₂O reduction potential have a positive correlation with the compost amendment (p < 0.05). The ratios of denitrifying genes (nosZI, cnorB and qnorB) to 16S rRNA genes each show a positive correlation with compost amendment, whereas the ratio of the CH₄-oxidizing gene (pmoA) to the 16S rRNA genes shows a negative correlation. Interestingly, the genera Acidibacter, Blastochloris, Erythrobacter, Hyphomicrobium, Marinobacter, Parvibaculum, Pseudoxanthomonas, and Terrimonas are strongly associated with diesel degradation, and have a strong positive correlation with soil CH₄ oxidation potential. Meanwhile, the genera Atopostipes, Bacillus, Halomonas, Oblitimonas, Pusillimonas, Truepera, and Wenahouziangella are found to be strongly associated with soil N₂O reduction potential. These results provide useful data for developing technologies that improve diesel removal efficiency while minimizing greenhouse gas emissions in the bioremediation process of diesel-contaminated soil.

• Tuberculosis and Respiratory Diseases
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• 제51권2호
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• pp.108-121
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• 2001

배 경 : p16 종양 억제 유전자 promoter의 aberrant methylation에 의한 불활성화가 비소세포 폐암이 발병하는 초기단계에 영향을 미치는 것으로 추측되며, DAP kinase 유전자 promoter의 hypermethylation은 유전자의 발현을 억제하여 폐암의 전이에 중요한 역할을 한다고 알려져 있다. 방 법 : 본 연구는 비소세포 폐암으로 근치적 절제술을 받은 환자 중에서 총 35 예를 대상으로 MSP률 이용하여 p16 유전자와 DAP kinase의 비정상적인 methylation의 양상을 조사하여, 폐암에서 두 유전자의 메틸화 빈도, 진단적 응용의 가능성 빛 임상적 유용성을 알고자 하였다. 결 과 : 전체 대상 35예중 p16 유전자의 aberrant methylation은 33예중 13예(39.4%)에서, DAP kinase 유전자 hypermethylation은 35예중 21예(60%)에서 확인할 수 있었다. 55 세 이상에서 p16의 aberrant methylation은 유의하게 증가되어 있었으며, DAP kinase는 병기의 진행도에 따라 발현 빈도가 증가하였으나, 통계학적 의미는 없었다. 또한 p16 유전자와 DAP kinase 유전자간의 메틸화 양상에서도 연관성은 관찰할 수 없었다. 결 론 : p16과 DAP kinase 유전자중 하나라도 비정상적인 메틸화가 발견된 경우는 전체 대상의 74.3% 로 비교적 높은 빈도로 관찰되어 폐암의 조기 진단을 위한 분자 생물학적 방법으로 이용될 수 있을 것으로 사료된다.

• Asian Pacific Journal of Cancer Prevention
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• 제16권14호
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• pp.5807-5815
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• 2015

Background: Ovarian cancer is the most common gynecological malignancy and constitutes the fifth leading cause of female cancer death. Some biological parameters have prognostic roles in patients with advanced ovarian cancer and their expression may contribute to tumor progression. The aim of this study was to investigate the potential prognostic value of SKP2, genes P27Kip1, K-ras, c-Myc, COX2 and HER2 genes expression in ovarian cancer. Materials and Methods: This study was performed on two hundred formalin fixed paraffin embedded ovarian cancer and normal adjacent tissues (NAT). Gene expression levels were assessed using real time PCR and Western blotting. Results: Elevated expression levels of SKP2, K-ras, c-Myc, HER2 and COX2 genes were observed in 61.5% (123/200), 92.5% (185/200), 74% (148/200), 96 % (192/200), 90% (180/200) and 78.5% (157/200) of cancer tissues, respectively. High expression of SKP2 and down-regulation of P27 was associated with advanced stages of cancer. Conclusions: The association between high expression of c-Myc and SKP2 with low expression of P27 suggested that the Skp2-P27 pathway may play an important role in ovarian carcinogenesis. Reduced expression of P27 is associated with advanced stage of cancer and can be used as a biological marker in clinical routine assessment and management of women with advanced ovarian cancer.