• 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.

• Animal Bioscience
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• 제37권3호
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• pp.461-470
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• 2024

Objective: The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits. Methods: To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, F_st, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions. Results: The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, F_st, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity. Conclusion: In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.

• Journal of Biomedical and Translational Research
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• 제19권4호
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• pp.116-124
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• 2018

Korean Native Pig (KNP) has a uniform black coat color, excellent meat quality, white colored fat, solid fat structure and good marbling. However, its growth performance is low, while the western origin Yorkshire pig has high growth performance. To take advantage of the unique performance of the two pig breeds, we raised crossbreeds (KNP ${\times}$ Yorkshire to make use of the heterotic effect. We then analyzed the liver transcriptome as it plays an important role in fat metabolism. We sampled at two stages: 10 weeks and at 26 weeks. The stages were chosen to correspond to the change in feeding system. A total of 16 pigs (8 from each stage) were sampled and RNA sequencing was performed. The reads were mapped to the reference genome and differential expression analysis was performed with edgeR package. A total of 324 genes were found to be significantly differentially expressed (${\left|log2FC\right|}$ > 1 & q < 0.01), out of which 180 genes were up-regulated and 144 genes were down-regulated. Principal Component Analysis (PCA) showed that the samples clustered according to stages. Functional annotation of significant DEGs (differentially expressed genes) showed that GO terms such as DNA replication, cell division, protein phosphorylation, regulation of signal transduction by p53 class mediator, ribosome, focal adhesion, DNA helicase activity, protein kinase activity etc. were enriched. KEGG pathway analysis showed that the DEGs functioned in cell cycle, Ras signaling pathway, p53 signaling pathway, MAPK signaling pathway etc. Twenty-nine transcripts were also part of the DEGs, these were predominantly Cys2His2-like fold group (C2H2) family of zinc fingers. A protein-protein interaction (PPI) network analysis showed that there were three highly interconnected clusters, suggesting an enrichment of genes with similar biological function. This study presents the first report of liver tissue specific gene regulation in a cross-bred Korean pig.

• 대한한의학회지
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• 제44권2호
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• pp.106-118
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• 2023

Objectives: Network pharmacology is a method of constructing and analyzing a drug-compound-target network to predict potential efficacy and mechanisms related to drug targets. In that large-scale analysis can be performed in a short time, it is considered a suitable tool to explore the function and role of herbal medicine. Thus, we investigated the potential functions and pathways of Chongmyunggongjin-dan (CMGJD) on Alzheimer's disease (AD) via network pharmacology analysis. Methods: Using public databases and PubChem database, compounds of CMGJD and their target genes were collected. The putative target genes of CMGJD and known target genes of AD were compared and found the correlation. Then, the network was constructed using Cytoscape 3.9.1. and functional enrichment analysis was conducted based on the Gene Ontology (GO) Biological process and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways to predict the mechanisms. Results: The result showed that total 104 compounds and 1157 related genes were gathered from CMGJD. The network consisted of 1157nodes and 10034 edges. 859 genes were interacted with AD gene set, suggesting that the effects of CMGJD are closely related to AD. Target genes of CMGJD are considerably associated with various pathways including 'Positive regulation of chemokine production', 'Cellular response to toxic substance', 'Arachidonic acid metabolic process', 'PI3K-Akt signaling pathway', 'Metabolic pathways', 'IL-17 signaling pathway' and 'Neuroactive ligand-receptor interaction'. Conclusion: Through a network pharmacological method, CMGJD was predicted to have high relevance with AD by regulating inflammation. This study could be used as a basis for effects of CMGJD on AD.

• Nuclear Engineering and Technology
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• 제26권1호
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• pp.119-125
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• 1994

핵연료봉의 과도상태 출력준위는 핵연료봉의 과도상태 거동에서 가장 중요한 변수중의 하나이다. 핵연료 성능 데이타베이스의 분석과 핵연료의 과도상태 거동에 영향을 줄 수 있는 핵연료봉 출력이력, 속중성자속, 농축도 및 주기길이 등의 인자들의 민감도 분석을 통해서, ANS 과도조건 I 및 II에서 핵연료봉의 기계적 건전성이 유지되는 허용가능 과도상태 출력을 구하기 위해 일반적으로 적용이 가능한 방법론이 유도되었으며, 이를 통해 17$\times$17 KOFA 핵연료봉의 허용가능 과도상태 출력이 연소도의 함수로써 결정되었다. 이 방법론을 도입함으로써, 현재와 같이 매 주기마다 핵연료봉 과도상태 설계분석을 수행할 필요가 없이 단지 해당주기에서의 과도상태 최대 출력준위 평가로써 핵연료봉의 과도상태 설계를 대체할 수 있으며, 17$\times$17 KOFA 핵연료에 대하 낮은 연소도영역에서 기존의 최대 허용 과도상태 출력 준위인 591 w/cm보다 큰 최대 689.5 w/cm까지 허용함으로써 원자로 운전에 유연성을 줄 수 있다.

• Asian-Australasian Journal of Animal Sciences
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• 제32권9호
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• pp.1458-1468
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• 2019

Objective: As one of the most important metabolic organs, the liver plays vital roles in modulating the lipid metabolism. This study was to compare miRNA expression profiles of the Large White liver between two different developmental periods and to identify candidate miRNAs for lipid metabolism. Methods: Eight liver samples were collected from White Large of 70-day fetus (P70) and of 70-day piglets (D70) (with 4 biological repeats at each development period) to construct sRNA libraries. Then the eight prepared sRNA libraries were sequenced using Illumina next-generation sequencing technology on HiSeq 2500 platform. Results: As a result, we obtained 346 known and 187 novel miRNAs. Compared with the D70, 55 down- and 61 up-regulated miRNAs were shown to be significantly differentially expressed (DE). Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analysis indicated that these DE miRNAs were mainly involved in growth, development and diverse metabolic processes. They were predicted to regulate lipid metabolism through adipocytokine signaling pathway, mitogen-activated protein kinase, AMP-activated protein kinase, cyclic adenosine monophosphate, phosphatidylinositol 3 kinase/protein kinase B, and Notch signaling pathway. The four most abundantly expressed miRNAs were miR-122, miR-26a and miR-30a-5p (miR-122 only in P70), which play important roles in lipid metabolism. Integration analysis (details of mRNAs sequencing data were shown in another unpublished paper) revealed that many target genes of the DE miRNAs (miR-181b, miR-145-5p, miR-199a-5p, and miR-98) might be critical regulators in lipid metabolic process, including acyl-CoA synthetase long chain family member 4, ATP-binding casette A4, and stearyl-CoA desaturase. Thus, these miRNAs were the promising candidates for lipid metabolism. Conclusion: Our study provides the main differences in the Large White at miRNA level between two different developmental stages. It supplies a valuable database for the further function and mechanism elucidation of miRNAs in porcine liver development and lipid metabolism.

• 정보관리학회지
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• 제40권3호
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• pp.1-23
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• 2023

이 연구는 우리나라 지자체가 운영하는 통합도서관들을 대상으로 통합검색 서비스의 기능적 특성을 분석하는 것을 목적으로 한다. 분석대상은 서울시의 25개 지자체에서 운영하는 통합도서관들이며, 분석항목은 통합검색과 관련된 12가지 영역의 서비스 기능들로 선택하였다. 연구의 결과는 다음과 같다. 첫째, 통합도서관은 자치구 내 공공도서관과 작은도서관의 연합체이며, 통합검색 서비스를 제공하고 있다. 제공되는 통합검색 서비스의 기능, 서지정보의 항목과 패싯의 유형이 다양하지 못하다. 둘째, 검색결과의 레코드는 타이틀 형식이 아니라, 대부분 아이템 형식이었다. 셋째, 도서정보를 보완하는 보강정보는 책에 대한 소개와 연관정보, 책과 관련된 키워드, 대출관련 정보 등으로 구성된다. 넷째, 통합검색이 디스커버리형 검색보다, 통합목록DB를 기반으로 하는 통합OPAC의 형태를 나타내고 있다. 자치구 내 공공도서관이나 작은도서관들에 분산되어 있는 소장목록DB들에 대한 통합검색을 제공하는데 집중하고 있다. 다섯째, 대부분의 통합도서관은 유사한 서비스 형태를 제공한다. 이 결과를 바탕으로 국내 공공도서관들이 디스커버리형 통합검색 서비스를 기대할 수 있는 개선방안을 제안하였다.

• Journal of Plant Biotechnology
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• 제43권3호
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• pp.347-358
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• 2016

브라시노스테로이드는 식물의 생장과 발육 과정에 있어서 중요한 역할을 담당 할 뿐 아니라 생물학적/ 비 생물학적 스트레스에 대한 복합 저항성을 보인다고 알려져 있다. 따라서 본 연구에서는 브라시노스테로이드와 광범위스트레스 내성을 연결하는 중요한 생물학적 네트워크를 이해하기 위해, Agilent Arabidopsis $4{\times}44K$ oligo chip을 이용하여 브라시노스테로이드 신호가 강화된 bes1-D 계통의 전 전사체 비교분석을 수행하였다. 그 결과 bes1-D 계통에서 DEGs (Differentially Expressed Genes)를 1,091 (562 up-regulated, 529 down-regulated) 개 선발하였다. 또한 선발된 유전자들의 GO 와 단백질 상호작용 네트워크 분석을 통해 대사, 발달, 스트레스, 면역, 방어 반응에 관련된 주요 브라시노스테로이드 신호전달과 연결된 스트레스 관련 유전자군을 분리하였다. 선발된 유전자중 NB-ARC와 FLS2는 bes1-D 계통이 야생형 En-2 계통에 비해 약 6배 정도의 발현량이 증가되었으며, TIR1, TSA1, OCP3 유전자등은 bes1-D 계통이 야생형 En-2 계통에 비해 발현이 감소되었다. 또한 브라시노스테로이드 활성형 계통이 야생형 식물체 계통에 비해 가뭄 스트레스 및 병원균에 대해 저항력이 향상되었다. 따라서 microarray 분석을 통한 유전자 간 발현 네트워크와 유전체 정보를 결합하여 대단위 주요 기능 유전자들을 동정할 수 있는 방법을 고안하여 실험에 사용하였다. 이를 통해 기능 획득 돌연변이 bes1-D가 식물들이 다양한 스트레스 환경에 적응할 수 있는 반응을 조절한다는 사실을 보여주고 있다.

• 한국산림과학회지
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• 제100권2호
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• pp.292-304
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• 2011

본 연구는 우리나라의 벌채제도와 외국의 벌채제도를 비교하여 입목벌채 허가제도 개선에 관한 시사점을 도출하는 한편, 벌채업무 담당 그룹(공무원)과 목재벌채 실행그룹(산림소유자, 벌채업자, 산림조합, 산림법인)을 대상으로 입목벌채 제도에 대한 인식 및 활성화 요인 등에 관한 설문조사를 실시하여 제도 개선에 필요한 기초 자료를 제공하고자 수행되었다. 독일과 일본의 벌채제도를 분석한 결과, 산림의 다양한 기능발휘를 저해 할 수 있는 개벌 면적은 축소하고 있는 추세이며, 벌채기준으로 획일적인 벌기령을 적용하지 않고 지역 산림여건을 감안하는 유연한 산림시업의 표준으로서 벌기령을 활용하는 한편, 벌채 후 갱신확보를 위해 지역에 맞는 적절한 갱신방법을 제시하는 벌채제도를 운용한다는 시사점을 도출하였다. 입목벌채 허가제도에 대한 인식 및 활성화 요인 등에 관해 벌채업무 담당 공무원 그룹과 목재벌채 실행그룹을 대상으로 한 설문조사 분석결과, 기준 벌기령은 벌채업무 담당그룹 만이 소나무(3.13)와 삼나무(3.05)의 벌기령이 적정하다는 인식을 보였고 기타 수종의 벌기령은 하향 조정해야 한다는 의견을 보였다. 개벌면적에 대해서는 1 벌구 5 ha 이내, 최대 합계면적 30 ha 한도 기준에 대해서는 벌채 업자와 산림법인 그룹만이 현행보다 확대가 필요하다는 인식을 나타냈다. 현행 벌채제도에 대한 활성화 요인으로는 벌채면적의 확대, 시설지원, 기술교육의 강화, 장비지원 확대, 행정 간소화, 다양한 혜택 부여 등이 제시되었는데, 기술교육 강화가 집단 간의 인식 차이에서 유의수준이 가장 낮게 나타났다.