• Tuberculosis and Respiratory Diseases
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• 제83권1호
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• pp.1-13
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• 2020

For the past three decades, more than a thousand of genetic studies have been performed to find out the genetic variants responsible for the risk of asthma. Until now, all of the discovered single nucleotide polymorphisms have explained genetic effects less than initially expected. Thus, clarification of environmental factors has been brought up to overcome the 'missing' heritability. The most exciting solution is epigenesis because it intervenes at the junction between the genome and the environment. Epigenesis is an alteration of genetic expression without changes of DNA sequence caused by environmental factors such as nutrients, allergens, cigarette smoke, air pollutants, use of drugs and infectious agents during pre- and post-natal periods and even in adulthood. Three major forms of epigenesis are composed of DNA methylation, histone modifications, and specific microRNA. Recently, several studies have been published on epigenesis in asthma and allergy as a powerful tool for research of genetic heritability in asthma albeit epigenetic changes are at the starting point to obtain the data on specific phenotypes of asthma. In this presentation, we mainly review the potential role of DNA CpG methylation in the risk of asthma and its sub-phenotypes including nonsteroidal anti-inflammatory exacerbated respiratory diseases.

• Journal of Ginseng Research
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• 제32권4호
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• pp.300-304
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• 2008

14년생 인삼의 뿌리로부터 cDNA library를 제작한 후 무작위로 뽑은 EST clone 중에서 cysteine proteinase(CP) 유전자에 높은 상동성을 나타내는 clone 6개를 선발하였고 이를 바탕으로 PgCysP1을 제작하였다. 인삼의 CP 유전자는 전장의 길이가 1,398bp로 366개의 아미노산을 코딩하는 1,101bp의 ORF를 가지고 있다. PgCysP1의 아미노산 서열과 이차구조를 분석한 결과, 기존에 보고된 식물들과 높은 상동성을 나타내었으며 PgCysP1는 papain family에 속하는 것으로 확인되었다. RT-PCR 분석결과, 인삼의 PgCysP1는 NaCl, 저온, wound, salicylic acid에 대해 그 발현 양상이 상동성을 나타내는 다른식물의 CP 유전자 발현과 유사한 양성을 보였고, 이에 PgCysP1은 CP gene으로 사료되며, 앞으로 인삼 식물체의 환경 스트레스에 대한 내성 연구가 요구된다.

• Advances in Traditional Medicine
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• 제6권2호
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• pp.134-143
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• 2006

The capacities of bacterial DNA, extracted from Salmonella typhimurium, and lipopolysaccharide (LPS), extracted from Salmonella minnesota, to activate mouse peritoneal macrophages in vitro were compared. Activation was assessed by estimating e levels of 3 cytokines, IL-10, IL-12, and $IL-1{\beta}$, at time intervals of 3, 6, 9, and 24 h after addition of LPS and/or DNA to macrophage cultures. Cytokine levels in culture supernatants were determined by enzyme-linked immunosorbent assay (ELISA) and cytokine mRNA levels were estimated based on band intensity in cultured cells by reverse transcriptase-polymerase chain reaction (RT-PCR). Results obtained demonstrated the ability of DNA and LPS to elicit increased production of all 3 cytokines as compared to controls. In the amount tested, LPS appeared to be a more potent inducer of IL-12, and $IL-1{\beta}$, whereas DNA induced higher levels of IL-10. DNA and LPS, used in combination, exhibited neither an additive nor a synergistic effect. Rather, an antagonist effect appeared to occur. RT-PCR results correlated well with ELISA.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2000년도 춘계 학술대회지
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• pp.66-67
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• 2000

• Nutrition Research and Practice
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• 제11권2호
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• pp.105-113
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• 2017

BACKGROUND/OBJECTIVES: A high-fat diet (HFD) induces obesity, which is a major risk factor for cardiovascular disease and cancer, while a calorie-restricted diet can extend life span by reducing the risk of these diseases. It is known that health effects of diet are partially conveyed through epigenetic mechanism including DNA methylation. In this study, we investigated the genome-wide hepatic DNA methylation to identify the epigenetic effects of HFD-induced obesity. MATERIALS AND METHODS: Seven-week-old male C57BL/6 mice were fed control diet (CD), calorie-restricted control diet (CRCD), or HFD for 16 weeks (after one week of acclimation to the control diet). Food intake, body weight, and liver weight were measured. Hepatic triacylglycerol and cholesterol levels were determined using enzymatic colorimetric methods. Changes in genome-wide DNA methylation were determined by a DNA methylation microarray method combined with methylated DNA immunoprecipitation. The level of transcription of individual genes was measured by real-time PCR. RESULTS: The DNA methylation statuses of genes in biological networks related to lipid metabolism and hepatic steatosis were influenced by HFD-induced obesity. In HFD group, a proinflammatory Casp1 (Caspase 1) gene had hypomethylated CpG sites at the 1.5-kb upstream region of its transcription start site (TSS), and its mRNA level was higher compared with that in CD group. Additionally, an energy metabolism-associated gene Ndufb9 (NADH dehydrogenase 1 beta subcomplex 9) in HFD group had hypermethylated CpG sites at the 2.6-kb downstream region of its TSS, and its mRNA level was lower compared with that in CRCD group. CONCLUSIONS: HFD alters DNA methylation profiles in genes associated with liver lipid metabolism and hepatic steatosis. The methylation statuses of Casp1 and Ndufb9 were particularly influenced by the HFD. The expression of these genes in HFD differed significantly compared with CD and CRCD, respectively, suggesting that the expressions of Casp1 and Ndufb9 in liver were regulated by their methylation statuses.

• Tuberculosis and Respiratory Diseases
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• 제50권1호
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• pp.12-28
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• 2001

배경 : 면역 증강성 CpG 올리고 뉴클레오티드(immunostimulatory CpG-oligodeoxynucleotides, ISS CpG-ODN)는 $T_{H1}$ 형 면역 반응은 항진시키고, $T_{H2}$ 형의 반응은 감소시키는 것으로 보고되고 있다. 본 연구에서는 백서 천식 모델에서 ISS CpG-ODN으로 인한 면역 반응의 변화가 천식의 주요한 병태 생리 현상인, 기도 과민성, 호산구성 염증 및 점액 과다 분비에 미치는 효과에 대하여 고찰하고자 하였다. 대상 및 방법 : 천식 모델을 형성하지 않은 10마리의 정상 대조군과 ovalbumin(OVA)의 감작 및 유발로 천식 모델이 형성된 26마리의 백서를, 천식 대조군 11마리, 천식-CpG 치료군 15마리로 나누어 실험하였다. 천식-CpG 치료군은 연구 16일과 20일에 ISS CpG-ODN을, 천식 대조군은 생리 식염수를 투여하였다. CpG-ODN 혹은 생리 식염수 투여 후, 특이 기도 저항, 기관지 폐포 세척액(bronchoalveolar lavage fluid, BALF) 내의 $T_{H1}$ 형 사이토카인 (cytokine)인 IFN-${\gamma}$와 $T_{H2}$ 형 사이토카인인 IL-4의 농도 및 호산구의 분획, 폐조직 내 호산구의 침윤 및 배상 세포의 이형성과 MUC5AC 유전자의 발현을 고찰하였다. 결과 : ISS CpG-ODN 투여 후 천식 대조군과 비교하여, 천식-CpG 치료군에서 기관지 폐포 세척액 내에서 IFN-${\gamma}$의 농도는 유의하게 높았고, IL-4의 농도는 유의하게 낮았다. 특이 기도 저항, 기관지 폐포 세척액 내의 호산구의 분획 및 폐조직에서의 호산구의 침윤은 천식-CpG 치료군에서 천식 대조군에 비하여 유의하게 감소하였다. 그러나 점액 과다 분비의 지표인 배상 세포의 이형성 및 MUC5AC 유전자의 발현 정도는 천식 대조군과 천식-CpG 치료군간에 유의한 차이가 없었다. 결론 : 백서 천식 모델에서 면역 증강성 CpG 올리고 뉴클레오티드는 $T_{H1}$ 형 면역 반응은 항진시키고, $T_{H2}$ 형의 반응은 감소시킴으로써, 천신의 주요한 병태 생리 현상인 기도 과민성 및 호산구서 염증은 억제하나, 점액과다 분비에는 유의한 영향이 없었다.

• BMB Reports
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• 제38권6호
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• pp.739-747
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• 2005

Full-length cDNA sequences of four novel SPATA4 genes in chimpanzee, cow, chicken and ascidian were identified by bioinformatic analysis using mouse or human SPATA4 cDNA fragment as electronic probe. All these genes have 6 exons and have similar protein molecular weight and do not localize in sex chromosome. The mouse SPATA4 sequence is identified as significantly changed in cryptorchidism, which shares no significant homology with any known protein in swissprot databases except for the homologous genes in various vertebrates. Our searching results showed that all SPATA4 proteins have a putative conserved domain DUF1042. The percentages of putative SPATA4 protein sequence identity ranging from 30% to 99%. The high similarity was also found in 1 kb promoter regions of human, mouse and rat SPATA4 gene. The similarities of the sequences upstream of SPATA4 promoter also have a high proportion. The results of searching SymAtlas (http://symatlas.gnf.org/SymAtlas/) showed that human SPATA4 has a high expression in testis, especially in testis interstitial, leydig cell, seminiferous tubule and germ cell. Mouse SPATA4 was observed exclusively in adult mouse testis and almost no signal was detected in other tissues. The pI values of the protein are negative, ranging from 9.44 to 10.15. The subcellular location of the protein is usually in the nucleus. And the signal peptide possibilities for SPATA4 are always zero. Using the SNPs data in NCBI, we found 33 SNPs in human SPATA4 gene genomic DNA region, with the distribution of 29 SNPs in the introns. CpG island searching gives the data about CpG island, which shows that the regions of the CpG island have a high similarity with each other, though the length of the CpG island is different from each other.This research is a fundamental work in the fields of the bioinformational analysis, and also put forward a new way for the bioinformatic analysis of other genes.

• BMB Reports
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• 제56권10호
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• pp.569-574
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• 2023

Aberrant DNA methylation plays a pivotal role in the onset and progression of colorectal cancer (CRC), a disease with high incidence and mortality rates in Korea. Several CRC-associated diagnostic and prognostic methylation markers have been identified; however, due to a lack of comprehensive clinical and methylome data, these markers have not been validated in the Korean population. Therefore, in this study, we aimed to obtain the CRC methylation profile using 172 tumors and 128 adjacent normal colon tissues of Korean patients with CRC. Based on the comparative methylome analysis, we found that hypermethylated positions in the tumor were predominantly concentrated in CpG islands and promoter regions, whereas hypomethylated positions were largely found in the open-sea region, notably distant from the CpG islands. In addition, we stratified patients by applying the CpG island methylator phenotype (CIMP) to the tumor methylome data. This stratification validated previous clinicopathological implications, as tumors with high CIMP signatures were significantly correlated with the proximal colon, higher prevalence of microsatellite instability status, and MLH1 promoter methylation. In conclusion, our extensive methylome analysis and the accompanying dataset offers valuable insights into the utilization of CRC-associated methylation markers in Korean patients, potentially improving CRC diagnosis and prognosis. Furthermore, this study serves as a solid foundation for further investigations into personalized and ethnicity-specific CRC treatments.

• BMB Reports
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• 제57권3호
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• pp.161-166
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• 2024

Aberrant DNA methylation plays a critical role in the development and progression of colorectal cancer (CRC), which has high incidence and mortality rates in Korea. Various CRC-associated methylation markers for cancer diagnosis and prognosis have been developed; however, they have not been validated for Korean patients owing to the lack of comprehensive clinical and methylome data. Here, we obtained reliable methylation profiles for 228 tumor, 103 adjacent normal, and two unmatched normal colon tissues from Korean patients with CRC using an Illumina Infinium EPIC array; the data were corrected for biological and experiment biases. A comparative methylome analysis confirmed the previous findings that hypermethylated positions in the tumor were highly enriched in CpG island and promoter, 5' untranslated, and first exon regions. However, hypomethylated positions were enriched in the open-sea regions considerably distant from CpG islands. After applying a CpG island methylator phenotype (CIMP) to the methylome data of tumor samples to stratify the CRC patients, we consolidated the previously established clinicopathological findings that the tumors with high CIMP signatures were significantly enriched in the right colon. The results showed a higher prevalence of microsatellite instability status and MLH1 methylation in tumors with high CMP signatures than in those with low or non-CIMP signatures. Therefore, our methylome analysis and dataset provide insights into applying CRC-associated methylation markers for Korean patients regarding cancer diagnosis and prognosis.

• Environmental Engineering Research
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• 제25권1호
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• pp.62-70
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• 2020

Here in this work, a 4-chlorophenol (4-CP)-degrading bacterial strain Bacillus subtilis (B. subtilis) MF447840.1 was isolated from the drain outside the Hyundai car service center, Agartala, Tripura, India. 16S rDNA technique used carried out for genomic recognition of the bacterial species. Isolated bacterial strain was phylogenetically related with B. subtilis. This strain was capable of breaking down both phenol and 4-CP at the concentration of 1,000 mg/L. Also, the isolated strain can able to metabolize five diverse aromatic molecules such as 2-chlorophenol, 2,4-dichlorophenol, 2,4,6-trichlorophenol, 4-nitrophenol, and pentachlorophenol for their growth. An extensive investigation was performed to portray the kinetics of cell growth along with 4-CP degradation in the batch study utilizing 4-CP as substrate. Various unstructured models were applied to evaluate the intrinsic kinetic factors. Levenspiel's model demonstrates a comparatively enhanced R² value (0.997) amongst every analyzed model. The data of specific growth rate (μ), saturation constant (K_S), and Y_X/S were 0.11 h^-1, 39.88 mg/L, along with 0.53 g/g, correspondingly. The isolated strain degrades 1,000 mg/L of 4-CP within 40 h. Therefore, B. subtilis MF447840.1 was considered a potential candidate for 4-CP degradation.