• Asian-Australasian Journal of Animal Sciences
• /
• 제32권3호
• /
• pp.320-333
• /
• 2019

Objective: The Shanghai Holstein cattle breed is susceptible to severe mastitis and other diseases due to the hot weather and long-term humidity in Shanghai, which is the main distribution centre for providing Holstein semen to various farms throughout China. Our objective was to determine the genetic mechanisms influencing economically important traits, especially diseases that have huge impact on the yield and quality of milk as well as reproduction. Methods: In our study, we detected the structural variations of 1,092 Shanghai Holstein cows by using next-generation sequencing. We used the DELLY software to identify deletions and insertions, cn.MOPS to identify copy-number variants (CNVs). Furthermore, we annotated these structural variations using different bioinformatics tools, such as gene ontology, cattle quantitative trait locus (QTL) database and ingenuity pathway analysis (IPA). Results: The average number of high-quality reads was 3,046,279. After filtering, a total of 16,831 deletions, 12,735 insertions and 490 CNVs were identified. The annotation results showed that these mapped genes were significantly enriched for specific biological functions, such as disease and reproduction. In addition, the enrichment results based on the cattle QTL database showed that the number of variants related to milk and reproduction was higher than the number of variants related to other traits. IPA core analysis found that the structural variations were related to reproduction, lipid metabolism, and inflammation. According to the functional analysis, structural variations were important factors affecting the variation of different traits in Shanghai Holstein cattle. Our results provide meaningful information about structural variations, which may be useful in future assessments of the associations between variations and important phenotypes in Shanghai Holstein cattle. Conclusion: Structural variations identified in this study were extremely different from those of previous studies. Many structural variations were found to be associated with mastitis and reproductive system diseases; these results are in accordance with the characteristics of the environment that Shanghai Holstein cattle experience.

• 환경생물
• /
• 제41권1호
• /
• pp.1-13
• /
• 2023

잠두위조바이러스2 (BBWV2)는 경제적으로 중요한 원예, 관상작물에 심각한 피해를 주는 바이러스 중의 하나다. BBWV2의 넓은 기주 범위, 매개충 방제의 어려움 등 효과적인 치료제가 없기 때문에, 병을 예방하거나 저항성 품종의 개발 등을 위해서는 BBWV2의 새로운 분리주들의 특성 조사와 연구가 필요하다. 본 연구에서는 2019년 금산지역의 잎들깨 재배농가에서 분리된 BBWV2 분리주(BBWV2-GS-PF)의 유전학적·생물학적 특성을 구명하고 기존에 보고된 분리주들과의 특성을 비교하였다. 순수 분리된 BBWV2-GS-PF는 기존 분리주와 달리 들깨에서 심한 모자이크 증상과 고추에서 원형 반점 증상을 보였다. BBWV2-GS-PF의 유전자 계통분석 결과, 기존에 알려진 2개의 그룹과 약 76~80%의 비교적 낮은 유전자 상동성을 보이며 계통이 분화된 것을 확인할 수 있었다.

• 농업생명과학연구
• /
• 제50권3호
• /
• pp.99-117
• /
• 2016

ssGBLUP을 이용한 전장 유전체 연관분석(ssGWAS)을 수행하기 위하여 이용한 표현형 자료는 2010년도부터 2015년까지 농협중앙회 한우개량사업소에서 후대 검정한 한우 거세우 총 1,829두의 부분육수율자료를 이용하였다. 유전체 자료는 Illumina Bovine 50K Beadchip을 활용하였으며 표현형 자료와 매칭이 되는 개체는 674두였다. 먼저 안심, 등심, 채끝 및 갈비수율의 유전체 육종가(GEBV)를 구하고 이를 통해 SNP 표지인자에 대한 효과와 SNP 표지인자의 분산을 계산하여 형질별 전체 유전분산 대비 SNP 표지인자의 효과를 추정한 후, QTL일 가능성이 있는 효과가 높은 SNP 좌위에 대한 결과를 주요하게 조사하였다. 안심수율의 경우, 상위 20개의 전체 유전분산 대비 SNP 표지인자의 효과에서 10번 염색체에서의 효과가 가장 높았는데 12,812,193 ~ 12,922,313bp 영역에서 전체 유전분산 대비 7.32 ~ 7.34%의 효과를 나타냈다. 채끝수율은 전체 유전분산에 대한 설명력이 가장 높은 SNP 표지인자를 포함하는 염색체는 24번 염색체로 38,158,543 ~ 38,347,278bp 영역이 약 8.36 ~ 8.56%의 전체 유전분산 대비 효과를 나타내었다. 등심수율은 다른 부분육 조사형질보다 낮은 SNP 표지인자의 효과를 나타내었다. 따라서 등심의 경우 보통 크기의 효과와 작은 효과를 갖는 많은 유전자들에 의해서 형질이 발현되는 것으로 사료된다.

• Journal of Nutrition and Health
• /
• 제57권2호
• /
• pp.211-227
• /
• 2024

본 연구에서는 해조류 섭취와 염증과 관련된 유전자의 변이 및 다유전자 위험 점수 간의 상호작용이 염증에 미치는 영향을 확인하였다. 남성과 여성 모두 PRS가 높은 그룹에서 염증 발생 위험은 증가하였다. 본 연구에서는 해조류의 섭취가 염증과 직접적인 관련이 있는 것으로 밝혀지지 않았지만, 해조류 섭취와 다유전자 위험 점수 변이 사이에선 통계적으로 유의한 결과를 보였다. 특히, 낮은 해조류의 섭취는 높은 다유전자 위험 점수를 가진 여성에서 고염증 발생 위험이 높았다. 따라서 본 연구결과는 한국인에게서 작용하는 염증 및 염증질환에 대한 유전자 소인을 파악할 수 있고 면역 체계의 균형 및 건강 유지에 새로운 중재방안을 제시할 수 있음을 기대한다.

• 한국초지조사료학회지
• /
• 제27권2호
• /
• pp.109-116
• /
• 2007

환경스트레스에 강한 내성을 지닌 신품종 톨페스큐를 개발할 목적으로 산화스트레스에 의해 강하게 유도되는 SWPA2 promoter 하류에 CuZnSOD와 APX 유전자가 엽록체에 동시에 발현하도록 제작한 벡터를 Agrobacterium법을 이용하여 톨 페스큐에 도입하였다. Hygromycin이 첨가된 선발배지에서 내성을 가지며 재분화된 형질전환 식물체를 pot로 이식하여 기내 순화시킨 후, Southern 분석을 실시하여 본 결과, 발현벡터의 T-DNA 영역이 형질전환 식물체의 genome에 성공적으로 도입되었음을 확인하였다. 형질전환 식물체 잎 절편을 산화스트레스와 중금속을 포함하고 있는 용액에 처리하여 엽록체의 손상정도를 조사한 결과, 비형질 전환체에 비해 형질전환체는 강한 내성을 나타내었다. 또한 유식물체 수준에서 MV를 처리하여 내성을 비교한 결과, 비형질전환체에 비해 형질전환체는 손상을 덜 받았다. 이와 같은 연구결과는 CuZnSOD와 APX 유전자를 엽록체에 동시발현시키는 기술이 다양한 환경스트레스에 대해 복합재해내성을 가지는 다양한 작물을 개발하는데 유용하게 이용될 수 있음을 나타낸 결과이다.

• Genomics & Informatics
• /
• 제6권4호
• /
• pp.210-222
• /
• 2008

Due to the polygenic nature of cancer, it is believed that breast cancer is caused by the perturbation of multiple genes and their complex interactions, which contribute to the wide aspects of disease phenotypes. A systems biology approach for the identification of subnetworks of interconnected genes as functional modules is required to understand the complex nature of diseases such as breast cancer. In this study, we apply a 3-step strategy for the interpretation of microarray data, focusing on identifying significantly perturbed metabolic pathways rather than analyzing a large amount of overexpressed and underexpressed individual genes. The selected pathways are considered to be dysregulated functional modules that putatively contribute to the progression of disease. The subnetwork of protein-protein interactions for these dysregulated pathways are constructed for further detailed analysis. We evaluated the method by analyzing microarray datasets of breast cancer tissues; i.e., normal and invasive breast cancer tissues. Using the strategy of microarray analysis, we selected several significantly perturbed pathways that are implicated in the regulation of progression of breast cancers, including the extracellular matrix-receptor interaction pathway and the focal adhesion pathway. Moreover, these selected pathways include several known breast cancer-related genes. It is concluded from this study that the present strategy is capable of selecting interesting perturbed pathways that putatively play a role in the progression of breast cancer and provides an improved interpretability of networks of protein-protein interactions.

• Journal of Microbiology and Biotechnology
• /
• 제18권4호
• /
• pp.631-638
• /
• 2008

Tandem affinity purification (TAP) method combined with LC-MS/MS is the most accurate and reliable way to study the interaction of proteins or proteomics in a genome-wide scale. For the first time, we used a TAP-tag as a mutagenic tool to disrupt protein interactions at the specific site. Although lots of commonly used mutational tools exist to study functions of a gene, such as deletional mutations and site-directed mutagenesis, each method has its own demerit. To test the usefulness of a TAP-tag as a mutagenic tool, we applied a TAP-tag to RNA polymerase II, which is the key enzyme of gene expression and is controlled by hundreds of transcription factors even to transcribe a gene. Our experiment is based on the hypothesis that there will be interrupted interactions between Pol II and transcription factors owing to the TAP-tag attached at the C-terminus of each subunit of Pol II, and the abnormality caused by interrupted protein interactions can be observed by measuring a cell-cycle of each yeast strain. From ten different TAP-tagged strains, Rpb7- and Rpb12-TAP-tagged strains show severe defects in growth rate and morphology. Without a heterodimer of Rpb4/Rpb7, only the ten subunits Pol II can conduct transcription normally, and there is no previously known function of Rpb7. The observed defect of the Rpb7-TAP-tagged strain shows that Rpb7 forms a complex with other proteins or compounds and the interruption of the interaction can interfere with the normal cell cycle and morphology of the cell and nucleus. This is a novel attempt to use a TAP-tag as a proteomic tool to study protein interactions.

• 한국균학회소식:학술대회논문집
• /
• 한국균학회 2015년도 춘계학술대회 및 임시총회
• /
• pp.13-13
• /
• 2015

Rice blast fungus, Magnaporthe oryzae, is the most destructive pathogen of rice in the world. This fungus has a biotrophic phase early in infection and switches to a necrotrophic lifestyle after host cell death. During the biotrophic phase, the fungus competes with host for nutrients and oxygen. Continuous uptake of oxygen is essential for successful establishment of blast disease of this pathogen. Here, we report transcriptional responses of the fungus to oxygen limitation. Transcriptome analysis using RNA-Seq identified 1,047 up-regulated genes in response to hypoxia. Those genes were involved in mycelial development, sterol biosynthesis, and metal ion transport based on hierarchical GO terms and well-conserved among three different fungal species. In addition, null mutants of three hypoxia-responsive genes were generated and tested for their roles on fungal development and pathogenicity. The mutants for a sterol regulatory element-binding protein gene, MoSRE1, and C4 methyl sterol oxidase gene, ERG25, exhibited increased sensitivity to hypoxia-mimetic agent, increased conidiation, and delayed invasive growth within host cells, suggesting important roles in fungal development. However, such defects did not cause any significant decrease in disease severity. The other null mutant for alcohol dehydrogenase gene, MoADH1, showed no defect in the hypoxia-mimic condition and fungal development. Taken together, this comprehensive transcriptional profiling in response to a hypoxia condition with experimental validations would provide new insights on fungal development and pathogenicity in plant pathogenic fungi.

• 대한의생명과학회지
• /
• 제19권2호
• /
• pp.124-131
• /
• 2013

Genome-wide association studies (GWAS) have identified a number of common variants associated with serum liver enzyme homeostasis in population. In the previous study, single nucleotide polymorphisms (SNPs) in several genes have been reported to be associated with serum liver enzyme levels in European population. We aimed to confirm whether the genetic variation of SMAD2 (SMAD family member 2) gene influence the serum liver enzyme levels in Korean population. We genotyped variants in or near SMAD2 in a population-based sample including 994 unrelated Korean adult. Here, we performed association analysis to elucidate the possible relations of genetic polymorphisms in SMAD2 gene with serum liver enzyme levels. By examining genotype data of a total of 944 subjects in 5 hospital health promotion center, we discovered the SMAD2 gene polymorphisms are associated with serum liver enzyme levels. The common and highest significant polymorphism was rs17736760 (${\beta}$=3.51, P=5.31E-07) with glutamic oxaloacetic transferase (GOT), rs17736760 (${\beta}$=5.99, P=1.25E-05) with glutamic pyruvate transaminase (GPT), and rs17736760 (${\beta}$=15.68, P=9.93E-07) with gamma glutamyl transferase (GGT) in all group. Furthermore, the SNP rs17736760 was consistently associated with GOT (${\beta}$=5.25, P=1.72E-06), GPT (${\beta}$=9.97, P=1.16E-05), GGT (${\beta}$=26.13, P=3.43E-06) in men group. Consequently, we found statistically significant SNP in SMAD2 gene that are associated with serum levels of GOT, GPT, and GGT. In addition, these results suggest that the individuals with the minor alleles of the SNP in the SMAD2 gene may be more elevated serum liver enzyme levels in the Korean population.

• Molecules and Cells
• /
• 제38권9호
• /
• pp.765-772
• /
• 2015

Saussurea lappa has been reported to possess anti-atopic properties. In this study, we have confirmed the S. lappa's anti-atopic properties in Nc/Nga mice and investigated the candidate gene related with its properties using microarray. We determined the target gene using real time PCR in in vitro experiment. S. lappa showed the significant reduction in atoptic dermatitis (AD) score and immunoglobulin E compared with the AD induced Nc/Nga mice. In the results of microarray using back skin obtained from animals, we found that S. lappa's properties are closely associated with cytokine-cytokine receptor interaction and the JAK-STAT signaling pathway. Consistent with the microarray data, real-time RT-PCR confirmed these modulation at the mRNA level in skin tissues from S. lappa-treated mice. Among these genes, PI3Kca and $IL20R{\beta}$ were significantly downregulated by S. lappa treatment in Nc/Nga mouse model. In in vitro experiment using HaCaT cells, we found that the S. lappa components, including alantolactone, caryophyllene, costic acid, costunolide and dehydrocostus lactone significantly decreased the expression of PI3Kca but not $IL20R{\beta}$ in vitro. Therefore, our study suggests that PI3Kca-related signaling is closely related with the protective effects of S. lappa against the development of atopic-dermatitis.