• Genomics & Informatics
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• 제21권2호
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• pp.22.1-22.15
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• 2023

Kidney renal clear cell carcinoma (KIRC) is one of the most aggressive cancer type of the urinary system. Metastatic KIRC patients have poor prognosis and limited therapeutic options. Ankyrin 3 (ANK3) is a scaffold protein that plays important roles in maintaining physiological function of the kidney and its alteration is implicated in many cancers. In this study, we investigated differential expression of ANK3 in KIRC using GEPIA2, UALCAN, and HPA databases. Survival analysis was performed by GEPIA2, Kaplan-Meier plotter, and OS-kirc databases. Genetic alterations of ANK3 in KIRC were assessed using cBioPortal database. Interaction network and functional enrichment analyses of ANK3-correlated genes in KIRC were performed using GeneMANIA and Shiny GO, respectively. Finally, the TIMER2.0 database was used to assess correlation between ANK3 expression and immune infiltration in KIRC. We found that ANK3 expression was significantly decreased in KIRC compared to normal tissues. The KIRC patients with low ANK3 expression had poorer survival outcomes than those with high ANK3 expression. ANK3 mutations were found in 2.4% of KIRC patients and were frequently co-mutated with several genes with a prognostic significance. ANK3-correlated genes were significantly enriched in various biological processes, mainly involved in peroxisome proliferator-activated receptor (PPAR) signaling pathway, in which positive correlations of ANK3 with PPARA and PPARG expressions were confirmed. Expression of ANK3 in KIRC was significantly correlated with infiltration level of B cell, CD8+ T cell, macrophage, and neutrophil. These findings suggested that ANK3 could serve as a prognostic biomarker and promising therapeutic target for KIRC.

• 한국정보통신학회:학술대회논문집
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• 한국정보통신학회 2022년도 추계학술대회
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• pp.450-452
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• 2022

최근 빅데이터 기반의 기계학습(Machine learning) 분석이 유전자 분석을 비롯한 다양한 축산분야에 활발하게 접목되어 주목할 만한 결과들을 도출하고 있다. 본 연구에서는 다양한 환경에서 수집된 한우고기 데이터를 기반으로 한우고기 품질에 영향을 미치는 육색, 수소이온농도, 보수력, 전단력, 가열감량에 대한 통계적 특성을 찾고, 이를 기반으로 기계학습의 선형 회귀(Linear regression) 및 회귀 트리(Regression tree) 방안을 이용하여 한우고기의 품질을 예측하는 방안을 제안하였다. 특히 통계적 분석을 통해 한우고기의 식감에 큰 영향을 주는 보수력의 경우 육색이 가장 큰 영향을 주고, 전단력, 가열감량의 경우 수소이온농도가 가장 큰 영향을 주는 요소인 것을 확인하였다. 제안 연구를 통해서 빅데이터 기반 기계학습 방안이 한우고기 품질 연구에 적용 가능함을 확인할 수 있었다. 또한 본 연구의 결과는 한우고기 품질 예측 및 품질 향상 연구에도 유용하게 활용될 수 있다.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.300-300
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• 2022

Wheat (Triticum spp.) is an important source of food worldwide and the focus of considerable efforts to identify new combinations of genetic diversity for crop improvement. In particular, wheat starch composition is a major target for changes that could benefit human health. Starches with increased levels of amylose are of interest because of the correlation between high amylose content and elevated levels of resistant starch, which has been shown to have beneficial effects on health for combating obesity and diabetes. In this study, high amylose wheat germplasms from other countries were collected and cultivated in Korea, and then the content of amylose was evaluated, we examined amylose content in 614 wheat germplasm. Furthermore, amylose content was validated using several milling processes such as roller, hammer, and grinding mill. As a result, the amylose content distribution was divided into five groups. The range of the amylose levels in whole wheat flour was 18.3% to 29.6%. In addition, the mutant lines were screened for high amylose, and two mutant lines (WX-1046 and WX-1074) exhibited a comparable amylose content to Keumkang whole wheat (19.6%). It has been established that high amylose indicated SS IIa null and necessitate GBSS. Based on these findings, it may be helpful to develop high amylose wheat germplasm and production techniques, particularly in Korea.

• 대한한의학방제학회지
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• 제31권4호
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• pp.341-360
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• 2023

Background : To investigate the effect of Hwanggeumjackyak-tang (HJT) on Dextran sulfate sodium (DSS) induced ulcerative colitis. Methods : The experimental animals were divided into three groups; group 1, normal group(Normal); group 2, DSS-induced colitis and untreated group(UT+DSS); group 3, DSS-induced colitis and HJT 200 mg-treated group(HJT200+DSS). We evaluated cytotoxicity after HJT administration and confirmed the anti-inflammatory effect by histological changes in the intestine and genetic analysis of mucosal cells after HJT administration for each group. In addition, microbiological weapons and metabolites in faeces were examined, and the correlation between gut microbiome and metabolites was also investigated. Result : HJT was not observed to be cytotoxic, even at relatively high concentrations, and was effective in protecting the barrier and preventing intestinal inflammation by suppressing the increase in mucus secretion and the expression of inflammatory factors in mucosal cells. HJT treatment affected the increase in the amount and diversity of the gut microbiome in faeces and the increase in metabolites thought to be involved in alleviating inflammation in the gut. Conclusion : This study demonstrates the therapeutic potential of HJT in ulcerative colitis. Further studies should be carried out to confirm our findings.

• Journal of Plant Biotechnology
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• 제50권
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• pp.115-126
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• 2023

A hydroponics experiment was performed to study the physiological and biochemical changes in Moroccan barley (Hordeum vulgare L.) varieties cultivated under salt stress conditions. Four barley varieties were grown under exposure to three salt concentrations, including 0, 200, and 300 mM NaCl. The ANOVA for both salt stress-sensitive and resistant varieties indicated that salt treatment represented the main source of variability in all studied traits. Salt treatment significantly reduced root and shoot dry weight (RDW and SDW), relative water content (RWC), and chlorophyll content (Chl a, Chl b, and Chl T). However, increases in electrolyte leakage (EL) along with proline and total soluble sugar (TSS) contents were recorded. In addition, large variations in all measured traits were found between varieties. The 'Massine' and 'Laanaceur' varieties displayed relatively higher RDW and SDW values. The 'Amira' and 'Adrar' varieties showed lower RWC values and Chl contents than those of the controls indicating their relative sensitivity to salt stress. Principal component analysis revealed that most of the variation was captured by PC1 (72% of the total variance) which grouped samples into three categories according to salt treatment. Correlation analyses highlighted significant associations between most parameters. Positive relationships were found between RDW, SDW, RWC, Chl content, and soluble proteins contents, while all of these parameters were negatively associated with EL intensity, proline content, and TSS content. The results from this study showed that the 'Massine' and 'Laanaceur' varieties were relatively salt-tolerant. These two salt-tolerant varieties present a good genetic background for breeding of barley varieties showing high salt tolerance.

• Oncology Letters
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• 제17권5호
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• pp.4726-4734
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• 2019

Colorectal cancer (CRC) is one of the most common types of cancers, as evidenced by the >1.2 million patient diagnoses and 600,000 mortalities globally each year. Recently, the microRNA (miR/miRNA)-34 miRNA precursor family was revealed to participate in the tumor protein (TP)-53 pathway, which is frequently involved in CRC. Furthermore, the expression of miR-34 is reportedly regulated by DNA methylation. Accordingly, the present study investigated the correlation between the methylation status of miR-34 miRNAs and miR-34 expression in paired CRC tumor and normal tissues. The methylation status of miR-34a and miR-34b/c was determined using the MethyLight assay, and the expression of miR-34a and miR-34b/c in the same paired tissues was analyzed by reverse transcription-quantitative polymerase chain reaction. The results revealed significantly elevated miR-34a (P=0.012) and miR-34b/c (P<0.0001) methylation levels in tumor tissues when compared with normal tissues, whereas only the expression of miR-34b/c differed (P=0.005) between the paired tissues. In addition, an association between TP53 haplotypes and miR-34 family expression levels was observed. The miR-34a methylation levels in the TP53 PIN A1A1 (48.56±36.49) and TP53 MSP GG (49.00±36.44) genotypes were increased in the tumor tissues when compared with normal tissues. In conclusion, it was determined that miR-34 promoter methylation and TP53 polymorphisms may be associated with CRC pathogenesis.

• 한국가금학회지
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• 제15권3호
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• pp.211-218
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• 1988

산난종계의 주요 경제형질인 산난양의 개량은 단기검정에 의한 조기선발이 실용화되고 있는 바 산난수에 대하여 조기선발 하였을 경우 조기선발의 최적시기 및 조기선발에서 기대되는 상관적 선발효율을 알아본 결과는 다음과 같다. 1. 2계통의 일반능력을 조사란 평균치는 초산일령에서 150.5 일과 159.1 일이었고 조기산란수는 W계통에서 후기산란수는 B계통에서 더 많이 산란하였고 총산란수는 두 계통 모두 272개로 비슷하게 산란하였다. 2. 초산일령과 산란수에 대한 유전력 및 표준오차 추정치는 두 계통에서 전자매분산성분으로 추정하였을 때 $0.37\pm0.09$~$0.49\pm0.10$과 $0.18\pm0.10$x~$0.33\pm0.08$로 추정되었다. 특히 산란수에 대한 추정치는 W계통은 모분산성분에 의한 추정치가, B계통에서는 부분산성분에 의한 추정치가 더 높았고 두 계통 모두 후기산란수에 대한 유전력보다 조기산란수에 대한 유전력이 더 높게 추정되었다. 3. 각 조사형질들 간의 유전상관 및 표준오차의 추정결과는 W와 B계통에서 전자매공분산성분에 의하여 추정하였을 때 조기산란수와의 유전상관에 있어서 후기산란수는 $0.46\pm0.15$와 $0.39\pm0.16$, 총산란수는 $0.77\pm0.07$와 $0.76\pm0.08$ 초산일령은 -$0.77\pm0.06$와 $-0.82\pm0.05$이었고 후기산란수와는 총산란수는 $0.92\pm0.03$과 $0.89\pm0.04$로 비교적 높게 추정되었으며 초산일영령 $-0.11\pm0.17$과 $-0.15\pm0.18$로 미약한 원의 상관을 보였다. 총산란수와 초산일령과의 유전상관은 W계통에서 $-0.41\pm0.13$과 B계통에서 -$0.50\pm$0.13으로 모두 원의 상관을 보여 산란수에 준한 선발은 초산일영을 단축시킨다는 것을 추측할 수 있다. 4. 선발효율의 추정결과는 초산 시부터 40주령까지의 산란수에 의하여 선발하는 것이 가장 효율적인 것으로 추정되었으나 (1.69와 1.80) 이 시기의 산란수에 의하여 선발하였을 경우 초산일령과의 견전상관을 고려할 때 초산일영을 크게 단축시킬 것으로 사료되며 또한 초산일령의 단축으로 인한 난중의 감소 및 자료수집에 필요한 경비 등을 고려할 때 31주령 이후, 특히 31주령부터 40주령까지의 산란기녹에 의하여 선발하는 것이 바람직 할 것으로 사료된다.

• 한국가금학회지
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• 제40권2호
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• pp.139-145
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• 2013

본 연구는 '우리맛닭 실용계의 외모 균일화 및 판별 마커개발을 위하여 수탉으로 이용되는 토종닭 순계 H계통 암탉 207수, 수탉 40수와 '우리맛닭' 실용계 60수의 혈액을 채취하고 DNA를 분리하였다. 모색 관련 후보 유전자 MC1R primer를 제작하여 PCR을 수행한 후, direct sequencing을 실시하였다. 개체별 모색 표현형을 조사한 결과, H계통 순계 암탉 207수 중 157수는 흑색 모색, 50수는 흑색+갈색 모색으로 조사되었다. 수탉의 경우, 40수 중 흑색 모색만 있는 개체는 없고, 흑색+갈색의 모색이 다양한 부위에 섞여 있었다. '우리맛닭' 실용계의 경우 흑색 모색 30수와 갈색 모색 30수를 암수 관계없이 샘플링하여 조사하였다. 모색 표현형과 유전형과의 연관성을 알아보기 위하여 모색 관련 후보유전자 MC1R의 sequencing 결과를 분석하여 유전자 변이를 살펴보았지만, 모색 표현형과 유전형과의 유의적인 연관성을 찾을 수 없었다. 이는 토종닭 순계 H계통의 경우, 검정색의 같은 품종 내에서 갈색 이모색을 가진 개체와의 유전적 변이를 탐색한 결과, 그 차이가 분명하게 구별되지 않은 것으로 생각되어진다. '우리맛닭' 실용계에서 haplotype 및 유전자빈도 분석을 통하여 이모색과의 연관성을 보다 명확하게 결정하기 위해서는 부계와 모계의 모색 표현형과 유전특성을 함께 고려해야 할 것으로 판단된다. '우리맛닭'의 모색 균일도 향상을 위한 모색 표현형과 관련 유전자의 연관성분석 및 유전적 특성에 대한 연구는, 향후 이를 이용하여 '우리맛닭'의 불법 유통을 막고 고품질 브랜드화를 위한 분자마커 개발의 기초 자료로 활용될 것으로 생각된다.

• Asian-Australasian Journal of Animal Sciences
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• 제33권10호
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• pp.1544-1557
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• 2020

Objective: Genomic selection (GS) is becoming popular in animals' genetic development. We, therefore, investigated the single-step genomic best linear unbiased prediction (ssGBLUP) as tool for GS, and compared its efficacy with the traditional pedigree BLUP (pedBLUP) method. Methods: A total of 9,952 males born between 1997 and 2018 under Hanwoo proven-bull selection program was studied. We analyzed body weight at 12 months and carcass weight (kg), backfat thickness, eye muscle area, and marbling score traits. About 7,387 bulls were genotyped using Illumina 50K BeadChip Arrays. Multiple-trait animal model analyses were performed using BLUPF90 software programs. Breeding value accuracy was calculated using two methods: i) Pearson's correlation of genomic estimated breeding value (GEBV) with EBV of all animals (r_M1) and ii) correlation using inverse of coefficient matrix from the mixed-model equations (r_M2). Then, we compared these accuracies by overall population, info-type (PHEN, phenotyped-only; GEN, genotyped-only; and PH+GEN, phenotyped and genotyped), and bull-types (YBULL, young male calves; CBULL, young candidate bulls; and PBULL, proven bulls). Results: The r_M1 estimates in the study were between 0.90 and 0.96 among five traits. The r_M1 estimates varied slightly by population and info-type, but noticeably by bull-type for traits. Generally average r_M2 estimates were much smaller than r_M1 (pedBLUP, 0.40 to0.44; ssGBLUP, 0.41 to 0.45) at population level. However, r_M2 from both BLUP models varied noticeably across info-types and bull-types. The ssGBLUP estimates of r_M2 in PHEN, GEN, and PH+ GEN ranged between 0.51 and 0.63, 0.66 and 0.70, and 0.68 and 0.73, respectively. In YBULL, CBULL, and PBULL, the r_M2 estimates ranged between 0.54 and 0.57, 0.55 and 0.62, and 0.70 and 0.74, respectively. The pedBLUP based r_M2 estimates were also relatively lower than ssGBLUP estimates. At the population level, we found an increase in accuracy by 2.0% to 4.5% among traits. Traits in PHEN were least influenced by ssGBLUP (0% to 2.0%), whereas the highest positive changes were in GEN (8.1% to 10.7%). PH+GEN also showed 6.5% to 8.5% increase in accuracy by ssGBLUP. However, the highest improvements were found in bull-types (YBULL, 21% to 35.7%; CBULL, 3.3% to 9.3%; PBULL, 2.8% to 6.1%). Conclusion: A noticeable improvement by ssGBLUP was observed in this study. Findings of differential responses to ssGBLUP by various bulls could assist in better selection decision making as well. We, therefore, suggest that ssGBLUP could be used for GS in Hanwoo proven-bull evaluation program.

• 식물병연구
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• 제14권3호
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• pp.143-152
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• 2008

도열병에 대한 감수성 정토가 다른 두 품종의 혼합재배에 의한 무농약 도열병 방제효과를 조사하였다. 재배 생력화를 위해 도열병 저항성을 제외한 품질을 비롯한 벼의 유전적 형질이 유사한 품종조합을 선발한 결과 '호평벼'와 '남평벼'의 조합을 1:1로 종자 혼합을 통한 혼합재배를 실시하였을 때 50.4%의 이삭도열병 방제효과가 있었다(2007). 단일재배시 최대 67.4%까지 우점을 보이던 KJ-101레이스가 혼합재배구에서 최소 29.4%로 감소하였고 그 외의 기타 레이스들이 차지하는 비율은 5.4%에서 9.0%로 증가하였으며 11개의 새로운 레이스가 분리되었다. 단독 혹은 혼합재배에 관계없이 분리된 레이스의 수는 유사하였으나 혼합재배 시 새로운 레이스가 차지하는 비율이 12.5%에서 62.5%로 증가하였고 레이스 간 밀도의 차이는 23.6%에서 8.8%로 감소하였다. 이러한 병원균 레이스 다양성의 변화와 레이스 밀도의 균형이 혼합재배에 의한 도열병 발생의 감소와 깊은 관련이 있을 것으로 추정되며 이와 더불어 혼합재배 효과에 대한 좀 더 명확한 설명을 위해 병원력을 비롯한 레이스의 유전적 형질에 관한 연구가 추후 보완되어져야 할 것이다.