• Journal of Ginseng Research
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• 제43권4호
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• pp.572-579
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• 2019

Background: Panax ginseng has been used in traditional medicine to strengthen the body and mental well-being of humans for thousands of years. Many elite ginseng cultivars have been developed, and ginseng cultivation has become well established during the last century. However, heat stress poses an important threat to the growth and sustainable production of ginseng. Efforts have been made to study the effects of high temperature on ginseng physiology, but knowledge of the molecular responses to heat stress is still limited. Methods: We sequenced the transcriptomes (RNA-Seq) of two ginseng cultivars, Chunpoong (CP) and Yunpoong (YP), which are sensitive and resistant to heat stress, respectively, after 1- and 3-week heat treatments. Differential gene expression and gene ontology enrichment along with profiled chlorophyll contents were performed. Results: CP is more sensitive to heat stress than YP and exhibited a lower chlorophyll content than YP. Moreover, heat stress reduced the chlorophyll content more rapidly in CP than in YP. A total of 329 heat-responsive genes were identified. Intriguingly, genes encoding chlorophyll a/b-binding proteins, WRKY transcription factors, and fatty acid desaturase were predominantly responsive during heat stress and appeared to regulate photosynthesis. In addition, a genome-wide scan of photosynthetic and sugar metabolic genes revealed reduced transcription levels for ribulose 1,5-bisphosphate carboxylase/oxygenase under heat stress, especially in CP, possibly attributable to elevated levels of soluble sugars. Conclusion: Our comprehensive genomic analysis reveals candidate loci/gene targets for breeding and functional studies related to developing high temperature-tolerant ginseng varieties.

• Journal of Animal Science and Technology
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• 제64권6호
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• pp.1144-1172
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• 2022

Salmonella enterica serovar Typhimurium isolate HJL777 is a virulent bacterial strain in pigs. The high rate of salmonella infection are at high risk of non-typhoidal salmonella gastroenteritis development. Salmonellosis is most common in young pigs. We investigated changes in gut microbiota and biological function in piglets infected with salmonella via analysis of rectal fecal metagenome and intestinal transcriptome using 16S rRNA and RNA sequencing. We identified a decrease in Bacteroides and increase in harmful bacteria such as Spirochaetes and Proteobacteria by microbial community analysis. We predicted that reduction of Bacteroides by salmonella infection causes proliferation of salmonella and harmful bacteria that can cause an intestinal inflammatory response. Functional profiling of microbial communities in piglets with salmonella infection showed increasing lipid metabolism associated with proliferation of harmful bacteria and inflammatory responses. Transcriptome analysis identified 31 differentially expressed genes. Using gene ontology and Innate Immune Database analysis, we identified that BGN, DCN, ZFPM2 and BPI genes were involved in extracellular and immune mechanisms, specifically salmonella adhesion to host cells and inflammatory responses during infection. We confirmed alterations in gut microbiota and biological function during salmonella infection in piglets. Our findings will help prevent disease and improve productivity in the swine industry.

• Journal of Ginseng Research
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• 제46권1호
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• pp.39-53
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• 2022

Ginsenoside Rb₁ (Rb₁), one of the most important ingredients in Panax ginseng Meyer, has been confirmed to have favorable activities, including reducing antioxidative stress, inhibiting inflammation, regulating cell autophagy and apoptosis, affecting sugar and lipid metabolism, and regulating various cytokines. This study reviewed the recent progress on the pharmacological effects and mechanisms of Rb₁ against cardiovascular and nervous system diseases, diabetes, and their complications, especially those related to neurodegenerative diseases, myocardial ischemia, hypoxia injury, and traumatic brain injury. This review retrieved articles from PubMed and Web of Science that were published from 2015 to 2020. The molecular targets or pathways of the effects of Rb₁ on these diseases are referring to HMGB1, GLUT4, 11β-HSD1, ERK, Akt, Notch, NF-κB, MAPK, PPAR-γ, TGF-β1/Smad pathway, PI3K/mTOR pathway, Nrf2/HO-1 pathway, Nrf2/ARE pathway, and MAPK/NF-κB pathway. The potential effects of Rb₁ and its possible mechanisms against diseases were further predicted via Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and disease ontology semantic and enrichment (DOSE) analyses with the reported targets. This study provides insights into the therapeutic effects of Rb₁ and its mechanisms against diseases, which is expected to help in promoting the drug development of Rb₁ and its clinical applications.

• 대한한의학방제학회지
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• 제32권1호
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• pp.11-28
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• 2024

Objectives : GunRyeong-Tang(GRT) is a traditional herbal prescription that combines Oryeongsan and Sagunja-tang. This study employed network analysis methods on the components of GRT and target genes related to diabetes complications to predict the improvement effects of GRT on diabetes complications. Methods : The collection of active compounds of GRT and related target genes involved the utilization of public databases and the PubChem database. We selected diabetes complication-related genes using GeneCards and confirmed their correlation through comparative analysis with the target genes of GRT. We constructed a network using Cytoscape 3.9.1 and conducted topological analysis. To predict the mechanism, we performed functional enrichment analysis based on Gene Ontology (GO) biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Results : Through network analysis, 234 active compounds and 1361 related genes were collected from GRT. A total of 9,136 genes related to diabetes complications were collected, and 1,039 target genes overlapping with the components of GRT were identified. The core genes of this network were TP53, INS, AKT1, ALB, and EGFR. In addition, GRT significantly reduced the H9c2 cell size and the expression of myocardial hypertrophy biomarkers (ANP, BNP), which were increased by high glucose (HG). Conclusions : Through this study, we were able to predict the activity and mechanism of action of GRT on diabetes and diabetic complications, and confirmed the potential of GRT as a treatment for diabetes complications through the effect of GRT on improving myocardial hypertrophy for diabetic cardiomyopathy.

• 대한방사선치료학회지
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• 제18권1호
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• pp.7-12
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• 2006

목 적: 방사선사로서 근무부서에 따라 보건복지부령 제349호에 따른 '방사선관계종사자'와 원자력법 제2조 21항의 '방사선 작업종사자'로 분류되고 있다. 따라서 방사선관계종사자와 방사선작업종사자에 따른 법률, 시행령, 시행규칙을 분석하여 방사선관계 법 개정 시 체계적으로 구축하는데 도움을 주고자 한다. 2차, 3차 의료기관에서는 보건복지부와 과학기술부에서 이중규제를 받으므로 의료기관에서의 방사선관계법 적용에 관하여 보건복지부로 이관하여 법적용이 이루어지도록 하고자 한다. 대상 및 방법: 방사선사에 관하여 의료기사 등에 관한 법률 시행령 시행규칙과 방사선관계 종사자에 관하여는 진단용방사선발생장치의 안전관리에 관한 규칙 그리고 방사선작업종사자에 관하여 원자력법 시행령 시행규칙을 수집하여 근무부서에 따른 명칭, 유효선량한도, 보수교육 및 교육 훈련, 방사선사의 건강진단 시기, 방사선구역, 방사선안전관리책임자 자격기준, 방사선 기기의 검사 시기 등을 비교 분석하였다. 결 과: 방사선사 중에서도 진단방사선과에 근무하는 경우에는 의료법에 의해 '방사선관계종사자'라는 명칭을 사용하고 있으며, 방사선종양학과나 핵의학과에 근무하는 방사선사는 원자력법에 의해 '방사선작업종사자'라는 명칭을 사용하고 있다. 유효선량한도는 연간 20 mSv로 동일하지만 방사선관계종사자의 경우는 피폭선량관리센터를 구축 중에 있는 반면, 방사선작업종사자의 피폭선량은 2002년 국가방사선작업종사자 안전관리센터를 발족하여 현재 시행 중에 있다. 방사선사 보수교육은 연간 8시간 이상 받게 되어 있으며, 방사선관계종사자는 진단용 방사선 안전관리책임자의 자체교육훈련으로 실시하는 반면에 방사선작업종사자는 작업종사전 교육 훈련을 20시간, 정기적 교육 훈련을 매년 6시간 이상이며, 건강진단 시기는 진단용 방사선발생장치의 안전관리에 관한 규칙에서 방사선관계종사자는 2년마다 실시하고 있으며, 원자력법 시행규칙에 의한 방사선작업종사자는 매년 실시하고 있다. 진단용방사선발생장치를 설치한 장소 중 외부방사선량이 1주당 $300{\mu}Sv$ 이상인 곳을 '방사선구역'으로 설정하고 있는 반면에 외부 방사선량률이 $400{\mu}Sv$을 초과하는 구역을 '방사선관리구역'으로 설정하고 있다. 임신이 확인된 여성의 방사선작업종사자는 임신이 확인된 시점부터 출산 시까지 하복부 표면에서의 등가선량한도를 2 mSv로 명시되어 있는데, 임신이 확인된 여성의 방사선관계종사자의 선량한도는 누락되어 있다. 결 론: 방사선사로서 근무 환경에 따라 방사선관계종사자나 방사선작업종사자의 명칭과 방사선구역이나 방사선관리구역의 용어, 그리고 건강진단 시기의 통일과 외부방사선량률에 대한 수치도 통일되어야 할 것이다. 방사선사 보수교육과 방사선작업종사자의 정기적 교육 훈련이 따로 관리되고 있지만 방사선작업종사자의 정기적 교육 훈련이 더 엄격하게 진행되므로, 부서 관의 협력으로 방사선사 보수교육에 합산하는 방안이 필요할 것이다. 임신이 확인된 방사선관계종사자의 피폭관리도 새로이 반영되어야 할 것이다. 따라서 업무의 특성상 사용되는 특별한 용어 외에 공통적으로 사용되는 용어의 통일은 반드시 필요하며, 방사선분야의 법, 시행령, 시행규칙, 고시 등의 개정 시 반드시 방사선 관련 부서의 해당기관과 합의하여 개정되어야 할 것이고, 대한방사선사협회에서는 방사선사에 대한 법률을 구체적이고 체계적으로 명시할 필요성이 있다고 생각된다.

• Journal of Acupuncture Research
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• 제37권2호
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• pp.128-135
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• 2020

Background: Classical acupuncture is being used in the treatment of rheumatoid arthritis (RA). To explore the biological response to acupuncture, a network-based analysis was performed on gene expression data collected from an animal model of RA treated with acupuncture. Methods: Gene expression data were obtained from published microarray studies on blood samples from rats with collagen induced arthritis (CIA) and non-CIA rats, both treated with manual acupuncture. The weighted gene co-expression network analysis was performed to identify gene clusters expressed in association with acupuncture treatment time and RA status. Gene ontology and pathway analyses were applied for functional annotation and network visualization. Results: A cluster of 347 genes were identified that differentially downregulated expression in association with acupuncture treatment over time; specifically in rats with CIA with module-RA correlation at 1 hour after acupuncture (-0.27; p < 0.001) and at 34 days after acupuncture (-0.33; p < 0.001). Functional annotation showed highly significant enrichment of porphyrin-containing compound biosynthetic processes (p < 0.001). The network-based analysis also identified a module of 140 genes differentially expressed between CIA and non-CIA in rats (p < 0.001). This cluster of genes was enriched for antigen processing and presentation of exogenous peptide antigen (p < 0.001). Other functional gene clusters previously reported in earlier studies were also observed. Conclusion: The identified gene expression networks and their hub-genes could help with the understanding of mechanisms involved in the pathogenesis of RA, as well understanding the effects of acupuncture treatment of RA.

• 생명과학회지
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• 제30권6호
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• pp.501-512
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• 2020

제주조릿대 잎은 항염, 해열 및 이뇨작용을 가지고 있어 위궤양, 목마름 및 토혈 치료를 위한 민간의약으로 사용되어 왔다. 본 저자들은 제주조리대 잎에서 분리한 피토케미칼 풍부 추출물(PRE)과 그 에틸아세테이트 분획물(EPRE)은 여러 위암 세포주에서 세포사멸을 유도하는 항암 효과가 있다고 보고한 바 있다. 본 연구는 EPRE의 세포사멸 유도 기전에 관여하는 분자표적들을 탐색하기 위하여 EPRE을 처리한 SNU-16 세포에서 mRNA와 microRNA (miRNA)의 프로파일 변화를 분석하였다. RNA sequencing 분석을 통해 총 2,875개의 차등적으로 발현되는 유전자들(DEGs)을 동정하였다. 유전자 온톨로지(GO)와 KEGG 경로 분석 결과, EPRE는 세포사멸, 유사 분열-활성화 단백질 키나제(MAPK) 및 염증 반응, 종양 괴사 인자(TNF) 신호 전달 및 암 경로에 관여하는 유전자들의 발현을 조절하는 것으로 나타났다. 단백질-단백질 상호 작용(PPI) 네트워크 분석으로 세포사멸 및 세포죽음과 관련된 유전자들 간의 상호작용들을 확인할 수 있었다. 그리고, miRNA sequencing 분석을 통해 총 27개의 차별적으로 발현되는 miRNAs (DEMs)를 동정하였다. GO와 KEGG 경로 분석 결과, EPRE는 세포주기, 세포사멸 및 tropomyosin-receptor-kinase (TRK) 수용체 신호 전달, 성장인자-β(TGF-β), 핵인자 κB (NF-κB) 및 암 경로에 관여하는 miRNAs의 발현을 조정하였다. 본 연구결과는 EPRE의 항암 효과의 근본적인 메커니즘에 대한 통찰력을 제공한다.

• Journal of Ginseng Research
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• 제38권4호
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• pp.278-288
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• 2014

Background: Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential. Methods: RNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, expression profiling was performed. Results: Assemblies were generated from ~85 million and ~77 million high-quality reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in public databases.We identified several candidate genes involved in ginsenoside biosynthesis. In addition, a large number of transcripts (17%) with different gene ontology designations were uniquely detected in adventitious roots compared to normal ginseng roots. Conclusion: This study will provide a comprehensive insight into the transcriptome of ginseng adventitious roots, and a way for successful transcriptome analysis and profiling of resource plants with less genomic information. The transcriptome profiling data generated in this study are available in our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use.

• Molecules and Cells
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• 제38권3호
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• pp.210-220
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• 2015

Athletic performance is an important criteria used for the selection of superior horses. However, little is known about exercise-related epigenetic processes in the horse. DNA methylation is a key mechanism for regulating gene expression in response to environmental changes. We carried out comparative genomic analysis of genome-wide DNA methylation profiles in the blood samples of two different thoroughbred horses before and after exercise by methylated-DNA immunoprecipitation sequencing (MeDIP-Seq). Differentially methylated regions (DMRs) in the pre-and post-exercise blood samples of superior and inferior horses were identified. Exercise altered the methylation patterns. After 30 min of exercise, 596 genes were hypomethy-lated and 715 genes were hypermethylated in the superior horse, whereas in the inferior horse, 868 genes were hypomethylated and 794 genes were hypermethylated. These genes were analyzed based on gene ontology (GO) annotations and the exercise-related pathway patterns in the two horses were compared. After exercise, gene regions related to cell division and adhesion were hypermethylated in the superior horse, whereas regions related to cell signaling and transport were hypermethylated in the inferior horse. Analysis of the distribution of methylated CpG islands confirmed the hypomethylation in the gene-body methylation regions after exercise. The methylation patterns of transposable elements also changed after exercise. Long interspersed nuclear elements (LINEs) showed abundance of DMRs. Collectively, our results serve as a basis to study exercise-based reprogramming of epigenetic traits.