• Animal Bioscience
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• 제36권9호
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• pp.1453-1464
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• 2023

Objective: This study investigated the changes in bacterial communities within decomposing swine microcosms, comparing soil with or without intact microbial communities, and under aerobic and anaerobic conditions. Methods: The experimental microcosms consisted of four conditions: UA, unsterilized soil-aerobic condition; SA, sterilized soil-aerobic condition; UAn, unsterilized soil-anaerobic condition; and San, sterilized soil-anaerobic condition. The microcosms were prepared by mixing 112.5 g of soil and 37.5 g of ground carcass, which were then placed in sterile containers. The carcass-soil mixture was sampled at day 0, 5, 10, 30, and 60 of decomposition, and the bacterial communities that formed during carcass decomposition were assessed using Illumina MiSeq sequencing of the 16S rRNA gene. Results: A total of 1,687 amplicon sequence variants representing 22 phyla and 805 genera were identified in the microcosms. The Chao1 and Shannon diversity indices varied in between microcosms at each period (p<0.05). Metagenomic analysis showed variation in the taxa composition across the burial microcosms during decomposition, with Firmicutes being the dominant phylum, followed by Proteobacteria. At the genus level, Bacillus and Clostridium were the main genera within Firmicutes. Functional prediction revealed that the most abundant Kyoto encyclopedia of genes and genomes metabolic functions were carbohydrate and amino acid metabolisms. Conclusion: This study demonstrated a higher bacteria diversity in UA and UAn microcosms than in SA and SAn microcosms. In addition, the taxonomic composition of the microbial community also exhibited changes, highlighting the impact of soil sterilization and oxygen on carcass decomposition. Furthermore, this study provided insights into the microbial communities associated with decomposing swine carcasses in microcosm.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.107-107
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• 2022

The increase in atmospheric temperature due to climate change prolongs the period of exposure to high-temperature environments during rice cultivation. In particular, high-temperature during early seed development greatly affects on the productivity and quality of rice. The high temperature at this time not only affects the transport and distribution of assimilates from leaves to seeds and the accumulation of starch in the seeds, but also affects the leaves, which are the production organs of assimilates, and increases the consumption of assimilation products due to an increase in respiration. Therefore, in this study, rice was grown in temperature gradient chambers(TGC) to analyze the effects of high temperature on physiological responses, assimilate production, and changes in gene expression in rice leaves. Analysis of chlorophyll and sugar contents and RNA-seq experiments were performed using flag leaves collected under normal and elevated temperature conditions, respectively, during the early seed development stage, and then these results were comprehensively discussed.

• Journal of Ginseng Research
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• 제48권1호
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• pp.40-51
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• 2024

Background: Ginsenoside 20(S)-Rg3 shows promising tumor-suppressive effects in ovarian cancer via inhibiting NF-kB signaling. This study aimed to explore the downstream tumor suppressive mechanisms of ginsenoside Rg3 via this signaling pathway. Materials and methods: A systematical screening was applied to examine the expression profile of 41 kinesin family member genes in ovarian cancer. The regulatory effect of ginsenoside Rg3 on KIF20A expression was studied. In addition, we explored interacting proteins of KIF20A and their molecular regulations in ovarian cancer. RNA-seq data from The Cancer Genome Atlas (TCGA) was used for bioinformatic analysis. Epithelial ovarian cancer cell lines SKOV3 and A2780 were used as in vitro and in vivo cell models. Commercial human ovarian cancer tissue arrays were used for immunohistochemistry staining. Results: KIF20A is a biomarker of poor prognosis among the kinesin genes. It promotes ovarian cancer cell growth in vitro and in vivo. Ginsenoside Rg3 can suppress the transcription of KIF20A. GST pull-down and co-immunoprecipitation (IP) assays confirmed that KIF20A physically interacts with BTRC (β-TrCP1), a substrate recognition subunit for SCF^β-TrCP E3 ubiquitin ligase. In vitro ubiquitination and cycloheximide (CHX) chase assays showed that via interacting with BTRC, KIF20A reduces BTRC-mediated CDC25A poly-ubiquitination and enhances its stability. Ginsenoside Rg3 treatment partly abrogates KIF20A overexpression-induced CDC25A upregulation. Conclusion: This study revealed a novel anti-tumor mechanism of ginsenoside Rg3. It can inhibit KIF20A transcription and promote CDC25A proteasomal degradation in epithelial ovarian cancer.

• The Plant Pathology Journal
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• 제40권1호
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• pp.30-39
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• 2024

The conservation of the endangered Korean fir, Abies koreana, is of critical ecological importance. In our previous study, a yeast-like fungus identified as Aureobasidium pullulans AK10, was isolated and shown to enhance drought tolerance in A. koreana seedlings. In this study, the effectiveness of Au. pullulans AK10 treatment in enhancing drought tolerance in A. koreana was confirmed. Furthermore, using transcriptome analysis, we compared A. koreana seedlings treated with Au. pullulans AK10 to untreated controls under drought conditions to elucidate the molecular responses involved in increased drought tolerance. Our findings revealed a predominance of downregulated genes in the treated seedlings, suggesting a strategic reallocation of resources to enhance stress defense. Further exploration of enriched Kyoto Encyclopedia of Genes and Genomes pathways and protein-protein interaction networks revealed significant alterations in functional systems known to fortify drought tolerance, including the terpenoid backbone biosynthesis, calcium signaling pathway, pyruvate metabolism, brassinosteroid biosynthesis, and, crucially, flavonoid biosynthesis, renowned for enhancing plant drought resistance. These findings deepen our comprehension of how AK10 biostimulation enhances the resilience of A. koreana to drought stress, marking a substantial advancement in the effort to conserve this endangered tree species through environmentally sustainable treatment.

• 한국패류학회지
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• 제32권4호
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• pp.263-268
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• 2016

Metallothionein (MT) family of metal-binding proteins are involved in maintaining homeostasis and heavy metal poisoning. Recently, MT has been considered as a biomarker that can identify a particular species, very similar to the use of cytochrome oxidase I (COI) gene. Satsuma myomphala species of land snails have been reported from North-East Asia, including South Korea and Japan. In particular, the land snail species have been known from only a limited area of Geoje Island, Gyeongsangnam-do province of South Korea. Genetic studies of S. myomphala has been limited with only 6 nucleotide, 2 protein registered on the NCBI server. For elucidating the genetic information of S. myomphala, we conducted RNA sequencing analysis using Illumina HiSeq 2500 next-generation platform. We screened the MT gene from the RNA-Seq database to confirm the molecular phylogenetic relationship. After sequencing, the de novo analysis and clustering generated 103,774 unigenes. After annotation against PANM database using BLAST program, we obtained MT sequence of 74 amino acid residues containing the coding region of 222 bp. Based on this sequence, we found about 53 sequences using the BLAST program in NCBI nr database. Using ClustalX alignment, Maximum-Likehood Tree of MEGA program, we confirmed the molecular phylogenetic relationships that showed similarity with mollusks such as Helix pomatia and H. aspersa, Megathura crenulata.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2022년도 추계학술대회
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• pp.36-36
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• 2022

The molecular understanding of resistance and susceptibility of host plants to scab, a most threatful disease to pome fruit production worldwide, is very limited. Comparing resistant line '93-3-98' to susceptible one 'Sweet Skin' at seven time points of 0, 0.5, 1, 2, 3, 4, 8 days post inoculation, RNA-sequencing data derived from infected and mock-inoculated young leaves were analyzed to evaluate the tolerant response and to mine candidate genes of pear to the scab pathogen Venturia nashicola. Analysis of the mapped reads showed that the infection of V. nashicola led to significant differential expression of 17,827 transcripts with more than 3-fold change in the seven pairs of libraries, of which 9,672 (54%) are up- and 8,155(46%) are down-regulated. These included mainly receptor (NB-ARC domains-containing, CC-NBS-LRR, TIR-NBS-LRR, seven transmembrane MLO family protein) and transcription factor (ethylene responsive element binding, WRKY DNA-binding protein) related gene. An arsenal of defense response of highly resistant pear accessions derived from European pear was probably supposed no sooner had V. nashicola infected its host than host genes related to disease suppression like Polyketide cyclase/dehydrase and lipid transport protein, WRKY family transcription factor, lectin protein kinase, cystein-rich RLK, calcium-dependent phospholipid-binding copine protein were greatly boosted and eradicated cascade reaction induced by pathogen within 24 hours. To identify transcripts specifically expressed in response to V. nashicola, RT-PCRs were conducted and compare to the expression patterns of seven cultivars with a range of highly resistant to highly susceptible symptom. A DEG belonging to the PR protein family genes that were higher expressed in response to V. nashicola suggesting extraordinary role in the resistance response were led to the identification. This study provides the first transcriptional profile by RNA-seq of the host plant during scab disease and insights into the response of tolerant pear plants to V. nashicola.

• Animal Bioscience
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• 제37권1호
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• pp.28-38
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• 2024

Objective: Tibetan chickens, which have unique adaptations to extreme high-altitude environments, exhibit phenotypic and physiological characteristics that are distinct from those of lowland chickens. However, the mechanisms underlying hypoxic adaptation in the liver of chickens remain unknown. Methods: RNA-sequencing (RNA-Seq) technology was used to assess the differentially expressed genes (DEGs) involved in hypoxia adaptation in highland chickens (native Tibetan chicken [HT]) and lowland chickens (Langshan chicken [LS], Beijing You chicken [BJ], Qingyuan Partridge chicken [QY], and Chahua chicken [CH]). Results: A total of 352 co-DEGs were specifically screened between HT and four native lowland chicken breeds. Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analyses indicated that these co-DEGs were widely involved in lipid metabolism processes, such as the peroxisome proliferator-activated receptors (PPAR) signaling pathway, fatty acid degradation, fatty acid metabolism and fatty acid biosynthesis. To further determine the relationship from the 352 co-DEGs, protein-protein interaction network was carried out and identified eight genes (ACSL1, CPT1A, ACOX1, PPARC1A, SCD, ACSBG2, ACACA, and FASN) as the potential regulating genes that are responsible for the altitude difference between the HT and other four lowland chicken breeds. Conclusion: This study provides novel insights into the molecular mechanisms regulating hypoxia adaptation via lipid metabolism in Tibetan chickens and other highland animals.

• 한국정보통신학회:학술대회논문집
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• 한국정보통신학회 2015년도 춘계학술대회
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• pp.768-770
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• 2015

유전체 염기서열 분석비용이 크게 감소하면서 유전체 정보 생산이 본격화됨에 따라 시스템 생물학 기반의 통합 및 표준화된 오믹스 데이터베이스 구축이 필요하다. 이에 따라 현재 진행중인 연구 수행의 결과로 얻어진 차세대유전체서열(NGS) 및 전사체(transcriptome) 등의 대용량 정보를 수집하였고 이를 표준화 형식에 맞춰 농업생명공학정보센터(NABIC)에 등록하였다. 또한 농업생명자원 생물정보를 품목별, 개체별로 통합 저장소를 구축하였으며 농업생명자원 생물정보를 품목별, 개체별로 통합 저장소를 구축하였다. 농업생명공학정보센터 오믹스 정보등록시스템 서비스와의 연계 및 확충작업을 하기위해 시스템 기능 개선 및 유지보수 작업을 수행하였다.

• 한국패류학회지
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• 제32권3호
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• pp.185-188
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• 2016

본 연구를 통하여 업데이트된 PANM 데이터베이스 버전 II는 버전 I 에 비해 많은 양의 정보가 추가되었다. 하지만 여전히 NCBI nr 데이터베이스에 비해 적은 양으로서, NGS 분석에 있어 많은 시간을 절약하게 해줄 수 있다. 또한 웹 인터페이스의 개선으로 인하여 직관성 및 신뢰성을 더욱 더 확보할 수 있었다. 개별적인 서버를 운용하여 NGS 데이터를 분석하는 연구자들을 위해 PANM 데이터베이스의 다운로드가 가능하도록 하였고 이로 인해 NGS 데이터 분석 시간이 줄어들 수 있을 것이다. 앞으로 꾸준한 PANM 데이터베이스 업데이트를 통하여 연체동물을 연구하는 연구자들은 물론 절지동물, 선형동물을 연구하는 연구자들에게도 많은 도움이 될 것으로 생각되며, 추가적으로 구축된 두족류 전용 데이터베이스 역시 두족류를 연구하는 연구자들에게 매우 유용하리라 사료되어진다.

• Journal of Microbiology and Biotechnology
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• 제30권8호
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• pp.1169-1179
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• 2020

In this study, two soybean genotypes, i.e., aluminum-tolerant Baxi 10 (BX10) and aluminumsensitive Bendi 2 (BD2), were used as plant materials and acidic red soil was used as growth medium. The soil layers from the inside to the outside of the root are: rhizospheric soil after washing (WRH), rhizospheric soil after brushing (BRH) and rhizospheric soil at two sides (SRH), respectively. The rhizosphere bacterial communities were analyzed by high-throughput sequencing of V4 hypervariable regions of 16S rRNA gene amplicons via Illumina MiSeq. The results of alpha diversity analysis showed that the BRH and SRH of BX10 were significantly lower in community richness than that of BD2, while the WRH exhibited no significant difference between BX10 and BD2. Among the three sampling compartments of the same soybean genotype, WRH had the lowest community richness and diversity while showing the highest coverage. Beta diversity analysis results displayed no significant difference for any compartment between the two genotypes, or among the three different sampling compartments for any same soybean genotype. However, the relative abundance of major bacterial taxa, specifically nitrogen-fixing and/or aluminum-tolerant bacteria, was significantly different in the compartments of the BRH and/or SRH at phylum and genus levels, indicating genotype-dependent variations in rhizosphere bacterial communities. Strikingly, as compared with BRH and SRH, the WRH within the same genotype (BX10 or BD2) always had an enrichment effect on rhizosphere bacteria associated with nitrogen fixation.