• Journal of Animal Science and Technology
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• 제65권1호
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• pp.175-182
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• 2023

Antibiotics have been used in livestock production for not only treatment but also for increasing the effectiveness of animal feed, aiding animal growth, and preventing infectious diseases at the time when immunity is lowered due to stress. South Korea and the EU are among the countries that have prohibited the use of antibiotics for growth promotion in order to prevent indiscriminate use of antibiotics, as previous studies have shown that it may lead to increase in cases of antibiotic-resistant bacteria. Therefore, this study evaluated the number of antibiotic resistance genes in piglets staging from pre-weaning to weaning. Fecal samples were collected from 8 piglets just prior to weaning (21 d of age) and again one week after weaning (28 d of age). Total DNA was extracted from the 200 mg of feces collected from the 8 piglets. Whole metagenome shotgun sequencing was carried out using the Illumina Hi-Seq 2000 platform and raw sequence data were imported to Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) pipeline for microbial functional analysis. The results of this study did not show an increase in antibiotic-resistant bacteria although confirmed an increase in antibiotic-resistant genes as the consequence of changes in diet and environment during the experiment.

• Animal Bioscience
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• 제36권9호
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• pp.1367-1375
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• 2023

Objective: Pigment production and distribution are controlled through multiple proteins, resulting in different coat color phenotypes of sheep. Methods: The expression distribution of vimentin (VIM) and transthyretin (TTR) in white and black sheep skins was detected by liquid chromatography-electrospray ionization tandem MS (LC-ESI-MS/MS), gene ontology (GO) statistics, immunohistochemistry, Western blot, and quantitative real time polymerase chain reaction (qRT-PCR) to evaluate their role in the coat color formation of sheep. Results: LC-ESI-MS/MS results showed VIM and TTR proteins in white and black skin tissues of sheep. Meanwhile, GO functional annotation analysis suggested that VIM and TTR proteins were mainly concentrated in cellular components and biological process, respectively. Further research confirmed that VIM and TTR proteins were expressed at significantly higher levels in black sheep skins than in white sheep skins by Western blot, respectively. Immunohistochemistry notably detected VIM and TTR in hair follicle, dermal papilla, and outer root sheath of white and black sheep skins. qRT-PCR results also revealed that the expression of VIM and TTR mRNAs was higher in black sheep skins than in white sheep skins. Conclusion: The expression of VIM and TTR were higher in black sheep skins than in white sheep skins and the transcription and translation were unanimous in this study. VIM and TTR proteins were expressed in hair follicles of white and black sheep skins. These results suggested that VIM and TTR were involved in the coat color formation of sheep.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.28-28
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• 2022

This paper presents the first genome assemblies of Philippine mangoes that provide valuable reference for varietal improvement and genomic studies on mango and related fruit crops. WE sequenced whole genomes of3 species, Mangifera odorata (Huani), Mangifera altissima (Paho), and Mangifera indica 'Carabao' (Sweet Elena). 'Carabao' is the major export variety of the Philippines; Paho is identified as vulnerable by the IUCN Red List of Threatened Species; Huani has fruit sap acrid which is the primary defense mechanism against insects and birds. We used Falcon, a diploid aware -de novo assembler to assemble SMRT generated long-read sequences. Falcon-unzip was employed to phase the output assembly producing larger contig sets (primary contigs) and shorter contigs corresponding to haplotypes (haplotigs). Assembly statistics were generated by comparing the assembly to a reference genome, Tommy Atkins, using Quality Assessment Tool (QUAST). Moreover, the extent of duplication and completeness of gene content was measured using Benchmarking Universal Single-Copy Orthologs (BUSCO). Draft assemblies with high duplications were processed using Purge Haplotigs and Purge Dups to lessen duplications with minimal impact on genome completeness. De novo assemblies of Huani, Paho and 'Carabao' were then generated with primary contig sizes of 463.64 Mb, 508.95 Mb and 401.51 Mb respectively. These draft assemblies of Huani, Paho and 'Carabao' showed 96.90%, 95.17% and 99.07% complete BUSCOs respectively which is comparable to 'Tommy Atkins' genome (98.6%). Using two mango transcriptome data (pooled RNA-seq from different mango varieties and tissues), 91-96% or 24-30 million reads were successfully mapped back for each generated assembly indicating high degree of completeness. The results obtained demonstrated the highly contiguous, phased, and near complete genome assembly of three Philippine mango species for structural and functional annotation of gene units, especially those with economic importance.

• Genomics & Informatics
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• 제21권4호
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• pp.48.1-48.8
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• 2023

Liver cancer is the fourth leading cause of death worldwide. Well-known risk factors include hepatitis B virus and hepatitis C virus, along with exposure to aflatoxins, excessive alcohol consumption, obesity, and type 2 diabetes. Genomic variants play a crucial role in mediating the associations between these risk factors and liver cancer. However, the specific variants involved in this process remain under-explored. This study utilized a bioinformatics approach to identify genetic variants associated with liver cancer from various continents. Single-nucleotide polymorphisms associated with liver cancer were retrieved from the genome-wide association studies catalog. Prioritization was then performed using functional annotation with HaploReg v4.1 and the Ensembl database. The prevalence and allele frequencies of each variant were evaluated using Pearson correlation coefficients. Two variants, rs2294915 and rs2896019, encoded by the PNPLA3 gene, were found to be highly expressed in the liver tissue, as well as in the skin, cell-cultured fibroblasts, and adipose-subcutaneous tissue, all of which contribute to the risk of liver cancer. We further found that these two SNPs (rs2294915 and rs2896019) were positively correlated with the prevalence rate. Positive associations with the prevalence rate were more frequent in East Asian and African populations. We highlight the utility of this population-specific PNPLA3 genetic variant for genetic association studies and for the early prognosis and treatment of liver cancer. This study highlights the potential of integrating genomic databases with bioinformatic analysis to identify genetic variations involved in the pathogenesis of liver cancer. The genetic variants investigated in this study are likely to predispose to liver cancer and could affect its progression and aggressiveness. We recommend future research prioritizing the validation of these variations in clinical settings.

• Animal Bioscience
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• 제37권6호
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• pp.993-1000
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• 2024

Objective: This study was conducted to investigate the differential expression of the major histocompatibility complex (MHC) gene region in Eimeria-infected broiler. Methods: We profiled gene expression of Eimeria-infected and uninfected ceca of broilers sampled at 4, 7, and 21 days post-infection (dpi) using RNA sequencing. Differentially expressed genes (DEGs) between two sample groups were identified at each time point. DEGs located on chicken chromosome 16 were used for further analysis. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis was conducted for the functional annotation of DEGs. Results: Fourteen significant (false discovery rate <0.1) DEGs were identified at 4 and 7 dpi and categorized into three groups: MHC-Y class I genes, MHC-B region genes, and non-MHC genes. In Eimeria-infected broilers, MHC-Y class I genes were upregulated at 4 dpi but downregulated at 7 dpi. This result implies that MHC-Y class I genes initially activated an immune response, which was then suppressed by Eimeria. Of the MHC-B region genes, the DMB1 gene was upregulated, and TAP-related genes significantly implemented antigen processing for MHC class I at 4 dpi, which was supported by KEGG pathway analysis. Conclusion: This study is the first to investigate MHC gene responses to coccidia infection in chickens using RNA sequencing. MHC-B and MHC-Y genes showed their immune responses in reaction to Eimeria infection. These findings are valuable for understanding chicken MHC gene function.

• Journal of Animal Science and Technology
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• 제51권1호
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• pp.1-8
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• 2009

본 연구는 한우의 지방, 간, 등심조직에서 유전자 염기서열을 확보하여 생산된 57,598개의 유전자 발현단편 데이터의 기능규명을 실시하였다. 유전자 발현단편 서열은 Assembly 과정을 통하여 unique한 서열인 4,759 contigs와 7,587 singletons을 확보하였으며, 얻어진 전사체를 이용하여 NCBI의 non-redundant 단백질 데이터베이스에 대하여 서열유사성 검색 (BLAST)을 하여 유전자의 기능을 예측할 수 있었다. 또한 기능에 대한 모호성을 확실히 하기 위해 Gene Ontology 용어를 사용하여 한우의 세 조직에서 확보된 서열들의 생물학적 특성을 기술하였다. Gene Ontology 는 모든 기능이 계층적으로 표현되어 있기 때문에, 각 계층에 대하여 유의적인 기능 여부를 확인하기 위하여 통계 분석인 Pearson's chi-square test를 실시하여 통계적으로 유의한 기능들을 산출할 수 있었다. 그 결과, Molecular function, Biological process, Cellular component 각각의 GO category에서 13, 16, 8개의 유의적인 GO terms이 검출되었다. 또한, 한우의 세 조직에 대하여 조직특이적 유전자의 존재여부를 판단하기 위하여 Audic's test를 실시하여 세 조직에서 각각 조직특이적으로 발현되는 유전자들을 검출할 수 있었다. 이러한 생물정보학적 방법들을 사용하여 한우의 세 조직에서 발현된 대량의 서열들에 대한 기능을 예측할 수 있었으며, 통계 검증을 통하여 유의적으로 검출된 유전자들은 추후에 실험적 검증을 실시하여 충분한 정보를 확보할 수 있을 것으로 사료된다.

• 한국균학회지
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• 제47권4호
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• pp.417-425
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• 2019

다양한 생물적 스트레스로부터 경제적으로 중요한 식물을 보호하기 위한 친환경 biocontrol agents (BCAs)는 오늘날 농업 및 생태 분야에서 다양하게 사용되고 있다. 다양한 BCAs 중에서, 많은 그람 양성Bacillus 속 아종이 친환경 생물학적 살충제 및 비료로서 성공적으로 산업화되었다. 이 연구에서 우리는 식물병원성 균류의 균사생장에 길항 효과를 보여주는 BCAs 중 하나인 Bacillus thuringiensis C25가 흰날개무늬병을 일으키는Rosellinia necatrix에 대한 길항작용이 있음을 확인하였다. 주사전자현미경을 통해B. thuringiensis C25가R. necatrix의 균사 세포벽을 분해하여 균사생장을 억제하는 것을 확인하였다. B. thuringiensis C25의 전장 유전체에서 5,683 유전자 세트의 서열을 동정하였고, 잠재적으로 곰팡이 세포벽 분해 효소 (CWDE)를 암호화하는 유전자 세트를 선발하였다. R. necatrix에 대한 균사성장 억제효과는B. thuringiensis C25의 균사 세포벽 분해 유전자의 전사 활성과 높은 상관 관계가 있었다. 상세하게는, B. thuringiensis C25에서ChiA, B 및 Glycos_transf_2 유전자를 포함하는 CWDE의 전사체 수준은R. necatrix와의 공동 배양에 의해 향상되었다. 결론적으로, 본 연구에서는 B. thuringiensis C25가 R. necatrix를 제어할 수 있는 생물학적 소재가 될 수 있으며, 식물 병원체에 대한 BCA의 항진균성 메커니즘의 이해를 촉진할 수 있음을 제시하였다.

• 한국잠사곤충학회지
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• 제51권2호
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• pp.191-196
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• 2013

본 연구는 누에 수정란 초기에 발현하는 유전자를 대량 선발하고, 유용 유전자의 프로모터를 개발하기 위한 연구의 일환으로 추진하였다. 산란 후 2 ~ 16시간이 경과한 누에알로부터 cDNA 유전자은행을 제작하였다. 제작된 cDNA 유전자은행으로 전체 960개 클론을 무작위 추출하여 부분 염기서열 분석을 통해 EST를 제작하였다. 분석된 652개 ESTs 중 염기서열 상동성 분석을 통해 156개의 기존 알려진 유전자와 178개의 미지의 유전자로 구성된 334개 독립유전자를 최종 선발하여 'eegEST'로 명명하였다. eegEST 분석 결과, 기존 염기서열 정보가 알려진 156개 독립유전자 중 2회 이상 출현한 유전자 수는 143개로 전체의 34%를 차지하였으며, Hsp20.8 유전자(12회)와 ubiqutin-like 유전자(11회)가 가장 높은 출현 빈도를 나타내었다. 또한 eegEST 독립유전자의 추정 기능에 따른 분류에서 곤충 수정란 발생초기에 확인할 수 있는 기관 형성과 관련한 유전자가 전체 24%를 차지하고 있었다. 본 연구에서 작성된 누에 수정란 초기 발현유전자 데이터베이스(eegEST)는 곤충 발생학 연구를 위한 정보제공 뿐 아니라 형질전환누에 제작을 위한 프로모터 개발 연구에 활용될 수 있을 것으로 기대한다.

• Molecules and Cells
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• 제28권6호
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• pp.529-536
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• 2009

Genome sequencing of the pig is being accelerated because of its importance as an evolutionary and biomedical model animal as well as a major livestock animal. However, information on expressed porcine genes is insufficient to allow annotation and use of the genomic information. A series of expressed sequence tags of 5' ends of five full-length enriched cDNA libraries (SUSFLECKs) were functionally characterized. SUSFLECKs were constructed from porcine abdominal fat, induced fat cells, loin muscle, liver, and pituitary gland, and were composed of non-normalized and normalized libraries. A total of 55,658 ESTs that were sequenced once from the 5′ ends of clones were produced and assembled into 17,684 unique sequences with 7,736 contigs and 9,948 singletons. In Gene Ontology analysis, two significant biological process leaf nodes were found: gluconeogenesis and translation elongation. In functional domain analysis based on the Pfam database, the beta transducin repeat domain of WD40 protein was the most frequently occurring domain. Twelve genes, including SLC25A6, EEF1G, EEF1A1, COX1, ACTA1, SLA, and ANXA2, were significantly more abundant in fat tissues than in loin muscle, liver, and pituitary gland in the SUSFLECKs. These characteristics of SUSFLECKs determined by EST analysis can provide important insight to discover the functional pathways in gene networks and to expand our understanding of energy metabolism in the pig.

• Asian-Australasian Journal of Animal Sciences
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• 제25권8호
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• pp.1102-1116
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• 2012

During embryo implantation in pigs, the uterine endometrium undergoes dramatic morphological and functional changes accompanied with dynamic gene expression. Since the greatest amount of embryonic losses occur during this period, it is essential to understand the expression and function of genes in the uterine endometrium. Although many reports have studied gene expression in the uterine endometrium during the estrous cycle and pregnancy, the pattern of global gene expression in the uterine endometrium in response to the presence of a conceptus (embryo/fetus and associated extraembryonic membranes) has not been completely determined. To better understand the expression of pregnancy-specific genes in the endometrium during the implantation period, we analyzed global gene expression in the endometrium on day (D) 12 and D15 of pregnancy and the estrous cycle using a microarray technique in order to identify differentially expressed endometrial genes between D12 of pregnancy and D12 of the estrous cycle and between D15 of pregnancy and D15 of the estrous cycle. Results showed that the global pattern of gene expression varied with pregnancy status. Among 23,937 genes analyzed, 99 and 213 up-regulated genes and 92 and 231 down-regulated genes were identified as differentially expressed genes (DEGs) in the uterine endometrium on D12 and D15 of pregnancy compared to D12 and D15 of the estrous cycle, respectively. Functional annotation clustering analysis showed that those DEGs included genes involved in immunity, steroidogenesis, cell-to-cell interaction, and tissue remodeling. These findings suggest that the implantation process regulates differential endometrial gene expression to support the establishment of pregnancy in pigs. Further analysis of the genes identified in this study will provide insight into the cellular and molecular bases of the implantation process in pigs.