• 생명과학회지
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• 제26권10호
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• pp.1137-1152
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• 2016

세포는 다양한 인체 질환에 관련되어 있는 저산소 환경을 인지하고 반응하며 적응한다. 저산소 상태에 적응하기 위해서는 hypoxic 유전자의 발현을 증가시키고 aerobic 유전자의 발현을 감소시키는 유전자 발현 조절이 필요하다. 최근 연구에서 미토콘드리아 호흡계가 이러한 유전자 발현 조절에 관여됨이 밝혀지고 있다. 본 연구에서는 호흡이 가능한 곰팡이(Saccharomyces cerevisiae)와 호흡이 불가능한 돌연변이 곰팡이를 실험대상으로 하여 미토콘드리아 호흡계가 저산소 환경에서 유전자 발현 조절에 관여됨을 DNA microarray 기법을 이용하여 전체 유전자를 대상으로 조사하였다. 산소 농도가 감소함에 반응하여 많은 유전자의 발현에 변화가 있었으며, 이러한 차별적인 발현 양상을 보이는 유전자는 여러 그룹으로 분류할 수 있었다. 대부분의 hypoxic 그리고 aerobic 유전자는 저산소 상태에 적응하는 발현 양상을 위해서는 미토콘드리아 호흡계가 필요하였다. 그러나 일부 hypoxic 그리고 aerobic 유전자는 미토콘드리아 호흡계와 무관하게 저산소 상태에 적응하는 발현 양상을 보였다. 이러한 결과는 미토콘드리아 호흡계가 저산소 환경에 적응하는 유전자 발현 조절에 필요하며, 또한 여러 기전을 통하여 이러한 유전자 발현 조절에 관여함을 제시한다. 또한 microarray 실험 결과에서 도출된 산소 농도에 대해 차별적인 발현을 보이는 유전자에 대하여 gene ontology 및 promoter 분석을 수행하였고 이러한 추가 분석 결과는 산소에 의해 조절되는 유전자와 함께 세포가 저산소 환경에 적응하는 기작을 이해하는 데 유용한 자료가 될 것으로 기대된다.

• Asian-Australasian Journal of Animal Sciences
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• 제22권6호
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• pp.871-884
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• 2009

Gene expression profiling is a useful tool for identifying critical genes and pathways in metabolism. The objective of this study was to determine the major differences in the expression of genes associated with metabolism and metabolic regulation in liver and mammary tissues of lactating cows. We used the Michigan State University bovine metabolism (BMET) microarray; previously, we have designed a bovine metabolism-focused microarray containing known genes of metabolic interest using publicly available genomic internet database resources. This is a high-density array of 70mer oligonucleotides representing 2,349 bovine genes. The expression of 922 genes was different at p<0.05, and 398 genes (17%) were differentially expressed by two-fold or more with 222 higher in liver and 176 higher in mammary tissue. Gene ontology categories with a high percentage of genes more highly expressed in liver than mammary tissues included carbohydrate metabolism (glycolysis, glucoenogenesis, propanoate metabolism, butanoate metabolism, electron carrier and donor activity), lipid metabolism (fatty acid oxidation, chylomicron/lipid transport, bile acid metabolism, cholesterol metabolism, steroid metabolism, ketone body formation), and amino acid/nitrogen metabolism (amino acid biosynthetic process, amino acid catabolic process, urea cycle, and glutathione metabolic process). Categories with more genes highly expressed in mammary than liver tissue included amino acid and sugar transporters and MAPK, Wnt, and JAK-STAT signaling pathways. Real-time PCR analysis showed consistent results with those of microarray analysis for all 12 genes tested. In conclusion, microarray analyses clearly identified differential gene expression profiles between hepatic and mammary tissues that are consistent with the differences in metabolism of these two tissues. This study enables understanding of the molecular basis of metabolic adaptation of the liver and mammary gland during lactation in bovine species.

• 한국어류학회지
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• 제32권3호
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• pp.117-129
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• 2020

생물의 종 구분에 이용하는 지표 중 체색은 특징이 뚜렷한 형태 지표로서, 어류의 종 동정에 유용한 형태형질이다. 개볼락은 한국 중부와 남부, 일본 홋카이도 남쪽 등지에 분포하는 상업적으로 중요한 어종으로, 피부에 반점의 유무 및 마킹이 있는 위치에 따라 4개의 아종으로 구분하는 복잡한 체색 특성을 갖는다. 그러나 개볼락의 다양한 체색 패턴과 관련된 유전자 탐색 및 유전자 변이 발굴 등 체색 형성에 관여하는 유전자 규명에 관한 연구는 없다. 이에 따라 본 연구에서는 개볼락의 체색 패턴 관련 유전자 발굴 및 유전자 발현 특성을 규명하기 위한 기초 연구로 체색 타입별 피부 전사체를 프로파일링하였다. 개볼락을 Wild type (반점과 marking 없음)과 Color type (반점과 마킹 모두 있음)으로 구분하였고, 피부 전사체를 RNA-seq 방법을 이용하여 분석하였다. 개볼락 피부 전사체의 발현량을 비교하여 체색 타입별 차등발현유전자 164개를 확보하였다. 이들 차등발현유전자의 기능을 Gene ontology(GO) 분석으로 확인한 결과, 2개는 molecular function, 46개는 biological process, 6개는 cellular component 기능그룹에 속하였다. 차등발현유전자 중 CTL (Galactose-specific lectin nattectin), CUL1 (Cullin-1), CMAS (N-acylneuraminate cytidylyltransferase), NMRK2 (Nicotinamide riboside kinase 2), ALOXE3 (Hydroperoxide isomerase ALOXE3), SLC4A7 (Sodium bicarbonate cotransporter 3) 등은 특정 체색 타입 특이적인 발현양상을 나타냈다. 이번 연구는 개볼락의 체색 패턴 형성에 관여하는 전사체를 탐색한 첫 번째 연구로, 체색 형성 관련 기능유전자 발굴을 위한 후보유전자로 개볼락의 체색 타입별 차등발현유전자를 확보한 것에 의의가 있다. 향후에는 이들 후보유전자의 발현양상 및 기능을 분석하여 개볼락의 복잡한 체색 패턴과 관련된 기능유전자의 특성을 밝히고자 한다.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2018년도 춘계학술발표회
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• pp.5-5
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• 2018

Ginseng (Panax ginseng C.A. Meyer), one of the most widely used medicinal plants in traditional oriental medicine, is used for the treatment of various diseases. It has been classified according to its cultivation environment, such as field cultivated ginseng (FCG) and mountain cultivated ginseng (MCG). However, little is known about differences in gene expression in ginseng roots between field cultivated and mountain cultivated ginseng. In order to investigate the whole transcriptome landscape of ginseng, we employed High-Throughput sequencing technologies using the Illumina HiSeqTM2500 system, and generated a large amount of sequenced transcriptome from ginseng roots. Approximately 77 million and 87 million high-quality reads were produced in the FCG and MCG roots transcriptome analyses, respectively, and we obtained 256,032 assembled unigenes with an average length of 1,171 bp by de novo assembly methods. Functional annotations of the unigenes were performed using sequence similarity comparisons against the following databases: the non-redundant nucleotide database, the InterPro domains database, the Gene Ontology Consortium database, and the Kyoto Encyclopedia of Genes and Genomes pathway database. A total of 4,207 unigenes were assigned to specific metabolic pathways, and all of the known enzymes involved in starch and sucrose metabolism pathways were also identified in the KEGG library. This study indicated that alpha-glucan phosphorylase 1, putative pectinesterase/pectinesterase inhibitor 17, beta-amylase, and alpha-glucan phosphorylase isozyme H might be important factors involved in starch and sucrose metabolism between FCG and MCG in different environments.

• Nutrition Research and Practice
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• 제14권4호
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• pp.412-422
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• 2020

BACKGROUND/OBJECTIVES: This study investigates correlations between circulating microRNAs (miRNAs) and obesity-related parameters among young women (aged 20-30 years old) in Korea. SUBJECTS/METHODS: We analyzed TaqMan low density arrays (TLDAs) of circulating miRNAs in 9 lean (body mass index [BMI] < 25 kg/㎡) and 15 obese (BMI > 25 kg/㎡) women. We also performed gene ontology (GO) analyses of the biological functions of predicted miRNA target genes, and clustered the results using the database for annotation, visualization and integrated discovery. RESULTS: The TLDA cards contain 754 human miRNAs; of these, the levels of 8 circulating miRNAs significantly declined (> 2-fold) in obese subjects compared with those in lean subjects, including miR-1227, miR-144-5p, miR-192, miR-320, miR-320b, miR-484, miR-324-3p, and miR-378. Among them, miR-484 and miR-378 displayed the most significant inverse correlations with BMI (miR-484, r = -0.5484, P = 0.0056; miR-378, r = -0.5538, P = 0.0050) and visceral fat content (miR-484, r = -0.6141, P = 0.0014; miR-378, r = -0.6090, P = 0.0017). GO analysis indicated that genes targeted by miR-484 and miR-378 had major roles in carbohydrate and lipid metabolism. CONCLUSION: Our result showed the differentially expressed circulating miRNAs in obese subjects compared to lean subjects. Although the mechanistic study to reveal the causal role of miRNAs remains, these miRNAs may be novel biomarkers for obesity.

• 한국정보과학회논문지:컴퓨팅의 실제 및 레터
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• 제15권5호
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• pp.375-379
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• 2009

도메인은 단백질의 진화와 삼차구조 및 분자 기능의 기본 단위체이다. 단백질은 한 개 이상의 도메인들로 구정 되며, 단백질의 기능 또한 각 도메인이 가진 기능의 집합으로 구현된다. 단백질은 특정 기능을 담당하기 위해 진화되어 왔으므로, 도메인 또한 단백질 내에서 기능을 위한 특정 조합 패턴, 즉 보존도메인 조합을 가진다. 본 논문은 각 도메인 조합의 진화상 보존 정도를 측정할 수 있는 연관성 규칙 기반 계산 기법을 제안한다. 제안된 기법은 기존 기법에서 주로 고려되었던 도메인 조합의 빈도뿐 아니라, 조합 내 소속 도메인간의 상호 의존도를 측정하여 주어진 조합의 보존 정도를 산출한다. 이를 기반으로 S.cerevisiae의 단백질을 대상으로 보존 도메인 조합을 추출하였으며, Gene Ontology를 이용하여 그 생물학적 의미를 분석하였다. 그 결과 제안된 기법으로 추출된 보존 도메인 조합은 기존의 것에 비해 조합 내 기능의 유사도가 높았으며, 따라서 제안된 기법이 생물학적 기능의 협업 위해 보존된 도메인 조합의 추출에 우수하다 할 것이다. 또한 S.cerevisiae 단백질체에는 서로 의존도가 높고 자주 나타나는 보존 도메인 조합이 존재하며, 그러한 조합들은 molecular function의 협업과 관련 있음을 밝혀냈다.

• Genes and Genomics
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• 제40권12호
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• pp.1279-1285
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• 2018

Interdigitating dendritic cell sarcoma (IDCS) is an aggressive neoplasm and is an extremely rare disease, with a challenging diagnosis. Etiology of IDCS is also unknown and most studies with only case reports. In our case, immunohistochemistry showed that the tumor cells were positive for S100, CD45, and CD68, but negative for CD1a and CD21. This study aimed to investigate the causative factors of IDCS by sequencing the protein-coding regions of IDCS. We performed whole-exome sequencing with genomic DNA from blood and sarcoma tissue of the IDCS patient using the Illumina Hiseq 2500 platform. After that, we conducted Sanger sequencing for validation of sarcoma-specific variants and gene ontology analysis using DAVID bioinformatics resources. Through comparing sequencing data of sarcoma with normal blood, we obtained 15 nonsynonymous single nucleotide polymorphisms (SNPs) as sarcoma-specific variants. Although the 15 SNPs were not validated by Sanger sequencing due to tumor heterogeneity and low sensitivity of Sanger sequencing, we examined the function of the genes in which each SNP is located. Based on previous studies and gene ontology database, we found that POLQ encoding DNA polymerase theta enzyme and FNIP1 encoding tumor suppressor folliculin-interacting protein might have contributed to the IDCS. Our study provides potential causative genetic factors of IDCS and plays a role in advancing the understanding of IDCS pathogenesis.

• Journal of Acupuncture Research
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• 제37권2호
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• pp.128-135
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• 2020

Background: Classical acupuncture is being used in the treatment of rheumatoid arthritis (RA). To explore the biological response to acupuncture, a network-based analysis was performed on gene expression data collected from an animal model of RA treated with acupuncture. Methods: Gene expression data were obtained from published microarray studies on blood samples from rats with collagen induced arthritis (CIA) and non-CIA rats, both treated with manual acupuncture. The weighted gene co-expression network analysis was performed to identify gene clusters expressed in association with acupuncture treatment time and RA status. Gene ontology and pathway analyses were applied for functional annotation and network visualization. Results: A cluster of 347 genes were identified that differentially downregulated expression in association with acupuncture treatment over time; specifically in rats with CIA with module-RA correlation at 1 hour after acupuncture (-0.27; p < 0.001) and at 34 days after acupuncture (-0.33; p < 0.001). Functional annotation showed highly significant enrichment of porphyrin-containing compound biosynthetic processes (p < 0.001). The network-based analysis also identified a module of 140 genes differentially expressed between CIA and non-CIA in rats (p < 0.001). This cluster of genes was enriched for antigen processing and presentation of exogenous peptide antigen (p < 0.001). Other functional gene clusters previously reported in earlier studies were also observed. Conclusion: The identified gene expression networks and their hub-genes could help with the understanding of mechanisms involved in the pathogenesis of RA, as well understanding the effects of acupuncture treatment of RA.

• 대한의생명과학회지
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• 제18권3호
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• pp.313-318
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• 2012

Acanthamoeba is an opportunistic pathogen known to cause granulomatous amoebic encephalitis and amebic keratitis. Acanthamoeba exhibits life cycle consisting of trophozoite and cyst, and the cyst is highly resistant to variable antibiotics and therapeutic agents. To understand the encystation mechanism of Acanthamoeba, the expression profiles of trophozoite and cyst were compared by gene ontology (GO) analysis. Ribosomal proteins and cytoskeletal proteins were highly expressed in trophozoite. In cyst, various protease, and signal transduction - and protein turnover - related proteins were highly expressed. These results correlated with eukaryotic orthologous groups (KOG) assignment and microarray analysis of Acanthamoeba trophozoite and cyst ESTs. The information of differential expression profiles of trophozoite and cyst would provide important clues for research on encystation mechanism of cyst forming protozoa including Acanthamoeba.

• Journal of Microbiology and Biotechnology
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• 제19권10호
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• pp.1103-1108
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• 2009

The human immunodeficiency virus (HIV)-l protein Tat acts as a transcription transactivator that stimulates expression of the infected viral genome. It is released from infected cells and can similarly affect neighboring cells. The nucleocapsid is an important protein that has a related significant role in early mRNA expression, and which contributes to the rapid viral replication that occurs during HIV-1 infection. To investigate the interaction between the Tat and nucleocapsid proteins, we utilized cDNA micro arrays using pTat and flag NC cotransfection in HEK 293T cells and reverse transcription-polymerase chain reaction to validate the micro array data. Four upregulated genes and nine downregulated genes were selected as candidate genes. Gene ontology analysis was conducted to define the biological process of the input genes. A proteomic approach using PathwayStudio determined the relationship between Tat and nucleocapsid; two automatically built pathways represented the interactions between the upregulated and downregulated genes. The results indicate that the up- and downregulated genes regulate HIV-1 replication and proliferation, and viral entry.