• Genomics & Informatics
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• 제2권1호
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• pp.30-35
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• 2004

To investigate the XIST gene expression and its effect in a Klinefelter's patient, we used Klinefelter's syndrome (XXY) patient with azoospermia and also used a normal male (XY) and a normal female (XX) as the control, We were performed cytogenetic analysis, Y chromosomal microdeletion assay (Yq), semi-quantitative RT-PCR, and the Northern blot for Klinefelter's syndrome (KS) patient, a female and a male control, We extracted total RNA from the KS patient, and from the normal cells of the female and male control subjects using the RNA prep kit (Qiagen), cDNA microarray contained 218 human X chromosome-specific genes was fabricated. Each total RNA was reverse transcribed to the first strand cDNA and was labeled with Cy-3 and Cy-5 fluorescein, The microarray was scanned by ScanArray 4000XL system. XIST transcripts were detected from the Klinefelters patient and the female by RT-PCR and Northern blot analysis, but not from the normal male, In the cDNA microarray experiment, we found 24 genes and 14 genes are highly expressed in KS more than the normal male and females, respectively. We concluded that highly expressed genes in KS may be a resulted of the abnormal X inactivation mechanism.

• Clinical and Experimental Reproductive Medicine
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• 제50권1호
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• pp.44-52
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• 2023

Objective: The DNA integrity of spermatozoa that attach to fallopian tube (FT) cells is higher than spermatozoa that do not attach. FT epithelial cells can distinguish normal and abnormal sperm chromatin. This study investigated the effects of sperm with a high-DNA fragmentation index (DFI) from men with unexplained repeated implantation failure (RIF) on the Toll-like receptor (TLR) signaling pathway in human FT cells in vitro. Methods: Ten men with a RIF history and high-DFI and 10 healthy donors with low-DFI comprised the high-DFI (>30%) and control (<30%) groups, respectively. After fresh semen preparation, sperm were co-cultured with a human FT epithelial cell line (OE-E6/E7) for 24 hours. RNA was extracted from the cell line and the human innate and adaptive immune responses were tested using an RT2 profiler polymerase chain reaction (PCR) array. Results: The PCR array data showed significantly higher TLR-1, TLR-2, TLR-3, TLR-6, interleukin 1α (IL-1α), IL-1β, IL-6, IL-12, interferon α (IFN-α), IFN-β, tumor necrosis factor α (TNF-α), CXCL8, GM-CSF, G-CSF, CD14, ELK1, IRAK1, IRAK2, IRAK4, IRF1, IRF3, LY96, MAP2K3, MAP2K4, MAP3K7, MAP4K4, MAPK8, MAPK8IP3, MYD88, NFKB1, NFKB2, REL, TIRAP, and TRAF6 expression in the high-DFI group than in the control group. These factors are all involved in the TLR-MyD88 signaling pathway. Conclusion: The MyD88-dependent pathway through TLR-1, TLR-2, and TLR-6 activation may be one of the main inflammatory pathways activated by high-DFI sperm from men with RIF. Following activation of this pathway, epithelial cells produce inflammatory cytokines, resulting in neutrophil infiltration, activation, phagocytosis, neutrophil extracellular trap formation, and apoptosis.

• International Journal of Industrial Entomology and Biomaterials
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• 제15권1호
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• pp.75-78
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• 2007

To define the molecular mechanism of initiation and termination of diapause during the embryogenesis of silkworm, Bombyx mori, mRNA transcripts from diapausing eggs and diapause activated eggs were compared with differential expression using cDNA array. Among those clones, mRNA transcript from hsp20.8A, which was expressed at a high level in diapausing eggs that had been incubated at $25^{\circ}C$ for 30 days after oviposition, whereas, in the eggs exposed to $15^{\circ}C$ for 30 days, $5^{\circ}C$ for 60 days, the expression of mRNA decreased. On the other hand, the expression of mRNA during embryogenesis observed abundantly at 4 to 6 days after heat-HCl treatment and later at 9 to 10 days after just before hatching. This result was suggested for us that hsp20.8A was expressed in response to embryogenesis as well as physical stress.

• Asian Pacific Journal of Cancer Prevention
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• 제15권6호
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• pp.2485-2489
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• 2014

In the present study, we studied the hypermethylation of the human riboflavin transporter 2 (hRFT2) gene and regulation of protein expression in biopsies from resected tissues from Uighur cervical squamous cell carcinoma (CSCC) patients and their neighboring normal tissues. hRFT2 gene promoter region methylation sequences were mapped in cervical cancer cell line SiHa by bisulfite-sequencing PCR and quantitative detection of methylated DNA from 30 pairs of Uighur's CSCCs and adjacent normal tissues by MassARRAY (Sequenom, San Diego, CA, USA) and hRFT2 protein expression was analyzed by immunohistochemistry. In SiHa, we identified 2 CG sites methylated from all of 12CpG sites of the hRFT2 gene. Analysis of the data from quantitative analysis of single CpG site methylation by Sequenom MassARRAY platform showed that the methylation level between two CpG sites (CpG 2 and CpG 3) from CpG 1~12 showed significant differences between CSCC and neighboring normal tissues. However, the methylation level of whole target CpG fragments demonstrated no significant variation between CSCC ($0.476{\pm}0.020$) and neighboring normal tissues ($0.401{\pm}0.019$, p>0.05). There was a tendency for translocation the hRFT2 proteins from cytoplasm/membrane to nucleus in CSCC with increase in methylation of CpG 2 and CpG 3 in hRFT2gene promoter regions, which may relate to the genesis of CSCC. Our results suggested that epigenetic modifications are responsible for aberrant expression of the hRFT2 gene, and may help to understand mechanisms of cervical carcinogenesis.

• 원예과학기술지
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• 제35권1호
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• pp.108-120
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• 2017

Modern watermelon cultivars (Citrullus lanatus [Thunb.] Matsum.& Nakai var. lanatus) have fruits with diverse phenotypes, including fruit shape, rind patterns, and flesh color. Molecular markers enable efficient selection of plants harboring desirable phenotypes. In the present study, publicly available DNA markers tightly linked to fruit shape, rind stripe pattern, and flesh color were evaluated using 85 watermelon accessions with diverse fruit phenotypes. For fruit shape, the dCAPS SUN - Cla011257 marker revealed an 81% of marker - trait match for accessions with elongated or round fruits. For rind stripe pattern, the SCAR wsb6-11marker was effective for selecting Jubilee-type rind pattern from other rind patterns. For flesh color, the Clcyb.600 and Lcyb markers derived from a mutation in the Lycopene ${\beta}$ - cyclase (Lcyb) gene, were effective at selecting red or yellow flesh. Forty-eight accessions possessing diverse fruit - related traits were selected as a reference array and their genetic relationships assessed using 16 SSR markers. At a coefficient of 0.11, the 48 accessions grouped into two major clades: Clade I and Clade II. Clade I subdivided further into subclades I - 1 and I - 2 at a coefficient of 0.39. All accessions with colored flesh were classified into Clade I, whereas those with white - flesh were classified into Clade II. Differences in fruit traits between subclades I - 1 and I - 2 were observed for rind pattern and fruit color; a majority of the accessions with Crimson-type striped or non-striped rind were grouped together in subclade I - 1, while most accessions in subclade I - 2 had a Jubilee - type rind stripe pattern. These results imply that reference array watermelon accessions possess distinguishable genetic structure based on rind stripe pattern. However, no significant grouping pattern was observed based on other fruit-related traits.

• 대한두경부종양학회지
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• 제24권1호
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• pp.33-42
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• 2008

Head and neck squamous cell carcinoma(HNSCC) is notorious for its poor outcome and increasing incidence. But, the studies of cytogenetic analysis in HNSCC are relatively rare, because of difficulties in culturing solid tumor cells and complexity in chromosomal DNA abberations associated with the lesions. The purpose of this study is to evaluate the location of chromosomal aberrations in Korean HNSCC cell lines (SNU-1041, 1066, and 1076) with comparative genomic hybridization(CGH) and array based CGH(array-CGH). Chromosomal gains of 3q23-q27, 5p13-p15.3, 7p21-pter, 8q11.2-q12, 8q21.1-qter, 9q22-q34, 16q22-q24, and 20q11.2-qter, as well as chromosomal losses on 3p10-p14 were found in all 3 SNU cell lines. Losses on 3p15- p23, 4q22-q27, 4q31.3-qter, 6q14-q15, 7q31-q34, 8p12-pter, 18q21-q23, and 21q11.2-q12 were observed in 2 of 3 cell lines. In array-CGH, many genes were altered including gains of PIK3CA, MYC, EVI1, MAD1L1 genes and losses of SERPIN genes. These aberrations of gene and chromosome coincide with other results of study, generally. These data about the patterns of chromosomal aberrations could be a basic step for understanding more detailed genetic events in the carcinogenesis and also provide information for diagosis and treatment in HNSCC.

• Asian Pacific Journal of Cancer Prevention
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• 제15권11호
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• pp.4663-4670
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• 2014

Trichostatin A (TSA) is a histone deacetylase (HDAC) inhibitor. We here investigated its effects on proliferation and apoptosis of the CNE2 carcinoma cell line, and attempted to establish genome-wide DNA methylation alteration due to differentially histone acetylation status. After cells were treated by TSA, the inhibitory rate of cell proliferation was examined with a CCK8 kit, and cell apoptosis was determined by flow cytometry. Compared to control, TSA inhibited CNE2 cell growth and induced apoptosis. Furthermore, TSA was found to induce genome-wide methylation alteration as assessed by genome-wide methylation array. Overall DNA methylation level of cells treated with TSA was higher than in controls. Function and pathway analysis revealed that many genes with methylation alteration were involved in key biological roles, such as apoptosis and cell proliferation. Three genes (DAP3, HSPB1 and CLDN) were independently confirmed by quantitative real-time PCR. Finally, we conclude that TSA inhibits CNE2 cell growth and induces apoptosis in vitro involving genome-wide DNA methylation alteration, so that it has promising application prospects in treatment of NPC in vivo. Although many unreported hypermethylated/hypomethylated genes should be further analyzed and validated, the pointers to new biomarkers and therapeutic strategies in the treatment of NPC should be stressed.

• 한국생명과학회:학술대회논문집
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• 한국생명과학회 2000년도 제28회 학술심포지엄
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• pp.3-8
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• 2000

The complete genome sequence of a Gram-positive bacterium .Bacillus subtilis has recently been reported and it is now clear that more than 50% of its ORFs have no known function (1). To study the global gene expression in B. subtilis at single gene resolution, we have tested the glass DNA microarrays in a step-wise fashion. As a preliminary experiment, we have created arrays of PCR products for 14 ORF whose transcription patterns have been well established through transcriptional mapping analysis. We measured changes in mRNA transcript levels between early exponential and stationary phase by hybridizing fluorescently labeled cDNA (with Cy3-UTP and Cy5-UTP) onto the array. We then compared the microarray data to confirm that the transcription patterns of these genes are well consistent with the known Northern analysis data. Since the preliminary test has been successful, we scaled up the experiments to ${\sim}$94% of the 4,100 annotated ORFs for the complete genome sequence of B. subtilis. Using this whole genomic microarray, we searched genes that are catabolite-repressive and those that are under the control of ${\sigma}^{Y}$, one of the functionally unknown ECF sigma factors. From these results, we here report that we have established DNA microarray techniques that are applicable for the whole genome of B. subtilis.

• International Journal of Advanced Culture Technology
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• 제5권2호
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• pp.9-18
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• 2017

The purpose of this study is to find out how to use emotional activity rate in sentence. The aim is to estimate the Emotion-Codon status of emotion-DNA wiggling as well as the sequence of codons in which amino acids of human body are spread. It is as if the amino acids are translated from the DNA of the human body, and the emotions that cooperate with each other are diversified and refined. Through these attempts, we anticipate the change of emotions by literary works and present the direction of the synapse working and the direction of the encoding. Therefore, this study analyzed the emotional activity of Rated Emotion-Codon, which works as Rated Sijo. At this time, the emotional change in the human body, in which the sentence is more clearly pronounced, is predicted and detected. This result shows how emotions can activate the human body. This state of activation is an indicator of how much the sentence pushes the physiological action of the human body. It is judged that Codon is constructed precisely for the activation of the rated Sijo additive definition by this index. Our result is evidenced by the fact that three sentences of Rated Sijo show an array with the same rating as the Rated Codon's, The first sentence fuses with the sentiment between the second sentence and the third sentence of Rated Sijo. The emotional symbols between the sentence symbols "A, U, J, L" in the first base of the Codon table and the sentences fusing between the sentences of the first sentence and the third sentence are "A, U, J, L". The emotional symbols between the sentences flowing in the second base of the Codon table and between the sentences of the first sentence and the second sentence are structured in the third base of the Codon table as "A, U, J, L". The Rated Sijo, which is resiliently and precisely assigned to the human body's Rated Emotion-Codon, will require a rich experience in our Rated Life.

• 한국지능정보시스템학회:학술대회논문집
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• 한국지능정보시스템학회 2005년도 춘계학술대회
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• pp.198-201
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• 2005

DNA microarray 칩은 신약 개발, 유전적 질환 진단, Bio-molecular 상호작용 연구, 유전자의 기능연구 등 폭넓게 사용되고 있다. 이 논문은 cDNA mimcroarray 데이터를 분석하기 위한 웹형태의 시스템 개발에 대한 내용을 다룬다. 하나의 cDNA microarray에는 수 백에서 수 만개의 유전자가 심어져 있으며, 데이터를 분석할 때 대량의 데이터와 다양한 형태의 오류로 인해서 데이터간의 차이를 보정하는 분석 도구와 통계적 기법들이 사용되어야 한다. 본 논문에서는 가상 칩 뷰어를 이용하여 실제 microarray 데이터의 foreground intensity에서 백그라운드의 intensity를 제거하여 일반화된 칩 이미지를 생성한다. 이 가상 칩 뷰어는 여러 가지 필터효과와 서로 다른 두 형광의 차이를 조정하는 global normalization 기법을 사용하여 발현 유전자 분석을 시각적으로 할 수 있고, 중복된 마이크로어레이 칩 데이터를 통하여 시간이 많이 걸리는 분석전 칩의 유효성을 검토할 수 있다. 칩 데이터의 normalization을 위한 통계 방법으로 R 통계 도구와 linear 모델을 사용하여 microarray 칩의 유전자 발현 양상을 분석한다. 통계적 방법을 사용하지 않은 데이터를 추출, 이 데이터의 패턴 그래프 그리고 발현 레벨을 분류하여 마이크로어레이의 각 스팟의 유효성 검토의 정확성을 높였다. 이 시스템은 칩의 유효성 검토, 스팟의 유효성 검토, 유전자 선정에 대해 분석의 용이성과 정확성을 높일 수 있었다.