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박지하(Jiha Park),이상남(Sangnam Lee),노성수(Seongsoo Roh),김용현(Yonghyun Kim),서부일(Buil Seo) 한국한의학연구원 2010 한국한의학연구원논문집 Vol.16 No.1
Objectives & Method : We investigated toxicity, poisoning symptoms, poisoning treatment and prevention against poisoning of mind-tranquilizing herbal medicines(安神藥) in order to use herbal medicines accurately. Result : Cinnabaris(朱砂), Zizyphi Spinosae Semen(酸棗仁), Polygalae Radix(遠志), Ganoderma(靈芝) and Polygoni Multiflori Ramulus(夜交藤) may give rise to some side effects or toxic symptoms in mind-tranquilizing herbal medicines(安神藥). The representative methods of poisoning treatment in western medicines are washing out the stomach, promotion of vomiting, causing diarrhea, supplies of grape sugar and symptomatic treatment, etc. The representative methods of poisoning treatment in oriental medicine take advantage of herbs. And Oriental medical doctor should meet symptoms as patients call for attention. In order to prevent against poisoning of mind-tranquilizing herbal medicines(安神藥), the patients should keep usage, dosage and notes and oriental medical doctors should do processing drugs. Conclusion : We should pay attention to clinical using of Cinnabaris(朱砂), Zizyphi Spinosae Semen(酸棗仁), Polygalae Radix(遠志), Ganoderma(靈芝) and Polygoni Multiflori Ramulus(夜交藤) in mind-tranquilizing herbal medicines(安神藥).
hiPathDB: a human-integrated pathway database with facile visualization
Yu, Namhee,Seo, Jihae,Rho, Kyoohyoung,Jang, Yeongjun,Park, Jinah,Kim, Wan Kyu,Lee, Sanghyuk Oxford University Press 2012 Nucleic acids research Vol.40 No.d1
<P>One of the biggest challenges in the study of biological regulatory networks is the systematic organization and integration of complex interactions taking place within various biological pathways. Currently, the information of the biological pathways is dispersed in multiple databases in various formats. hiPathDB is an integrated pathway database that combines the curated human pathway data of NCI-Nature PID, Reactome, BioCarta and KEGG. In total, it includes 1661 pathways consisting of 8976 distinct physical entities. hiPathDB provides two different types of integration. The pathway-level integration, conceptually a simple collection of individual pathways, was achieved by devising an elaborate model that takes distinct features of four databases into account and subsequently reformatting all pathways in accordance with our model. The entity-level integration creates a single unified pathway that encompasses all pathways by merging common components. Even though the detailed molecular-level information such as complex formation or post-translational modifications tends to be lost, such integration makes it possible to investigate signaling network over the entire pathways and allows identification of pathway cross-talks. Another strong merit of hiPathDB is the built-in pathway visualization module that supports explorative studies of complex networks in an interactive fashion. The layout algorithm is optimized for virtually automatic visualization of the pathways. hiPathDB is available at http://hiPathDB.kobic.re.kr.</P>
Transcriptional Analysis of the iagB within Salmonella Pathogenicity Island 1 (SPI1)
Lim, Sangyong,Choi, Jihae,Kim, Dongho,Seo, Ho Seong The Korean Society for Microbiology 2016 Journal of Bacteriology and Virology Vol.46 No.3
HilA is a central regulator of Salmonella pathogenicity island 1 (SPI1), which is necessary for host invasion by Salmonella and induction of gastroenteritis. The iagB lies downstream of hilA and is thought to be co-transcribed with hilA, but iagB expression has not yet been analyzed directly. In this study, iagB expression in various mutant strains was measured to determine whether the expression pattern was similar to that of hilA. A ${\beta}$-galactosidase assay revealed that iagB expression was greater under shaking than standing culture condition. iagB expression was decreased in relA/spoT and ihfB mutants but not in luxS mutant, in line with previous reports on hilA expression. The hilA and iagB mRNA levels decreased by approximately 2-fold in arcA mutant grown aerobically and increased by approximately 10-fold in fnr mutant grown anaerobically. Although the fold changes in hilA and iagB mRNA level differed in hfq mutant strain, the patterns of time- and Hfq-dependent regulation were similar for both genes. Thus, iagB and hilA exhibited similar expression patterns in various mutational backgrounds and under different growth condition.
女貞子와 ?寄生이 난소적출로 유발된 흰쥐의 골다공증 치료효과에 미치는 영향
이상윤(Sangyun Lee),서부일(Buil Seo),박지하(Jiha Park),노성수(Seongsoo Roh),김대준(Daejun Kim) 한국한의학연구원 2011 한국한의학연구원논문집 Vol.17 No.1
Objectives : The present study had been undertaken to investigate the effects of Ligustri Lucidi Fructus Extract and Vici Herba Extract on treatment of osteoporosis in ovariectomized rats. Method : In this experiment, the rats were ovariectomized. Rats were individually administered by water extract from Ligustri Lucidi Fructus or Vici Herba(dose:1㎖/100g, 2times/day). The levels of bone mineral density, serum components, urinary components, bony components, body weight and uterus weight were measured. Results : The levels of spinal and femoral bone mineral density(BMD) were significantly increased in comparison with OVX group at 8 weeks after administration in Vici Herba group. The levels of serum osteocalcin showed significant decrease in comparison with OVX group at 4 weeks after administration in Ligustri Lucidi Fructus and Vici Herba group. The levels of serum ALP and phosphorus showed significant decrease in comparison with OVX group at 4, 8 weeks in after administration in Ligustri Lucidi Fructus and Vici Herba group. The levels of urinary deoxypyridinoline showed significant decrease in comparison with OVX group in Ligustri Lucidi Fructus group. The levels of fibula-tibial ash weight showed significant increase in comparison with OVX group after administration in Ligustri Lucidi Fructus group. The levels of body weight were significantly decreased in comparison with OVX group at 4 weeks after administration in Ligustri Lucidi Fructus group and at 4, 8 weeks after administration in Vici Herba group. The levels of uterus weight were not significantly increased in comparison with OVX group in Ligustri Lucidi Fructus and Vici Herba group. Conclusion : Reviewing these experimetal results, it appeared that Ligustri Lucidi Fructus and Vici Herba had efficacy on treatment of osteoporosis.
GARNET – gene set analysis with exploration of annotation relations
Rho, Kyoohyoung,Kim, Bumjin,Jang, Youngjun,Lee, Sanghyun,Bae, Taejeong,Seo, Jihae,Seo, Chaehwa,Lee, Jihyun,Kang, Hyunjung,Yu, Ungsik,Kim, Sunghoon,Lee, Sanghyuk,Kim, Wan Kyu BioMed Central 2011 BMC bioinformatics Vol.12 No.suppl1
<P><B>Background</B></P><P>Gene set analysis is a powerful method of deducing biological meaning for an a priori defined set of genes. Numerous tools have been developed to test statistical enrichment or depletion in specific pathways or gene ontology (GO) terms. Major difficulties towards biological interpretation are integrating diverse types of annotation categories and exploring the relationships between annotation terms of similar information.</P><P><B>Results</B></P><P>GARNET (Gene Annotation Relationship NEtwork Tools) is an integrative platform for gene set analysis with many novel features. It includes tools for retrieval of genes from annotation database, statistical analysis & visualization of annotation relationships, and managing gene sets. In an effort to allow access to a full spectrum of amassed biological knowledge, we have integrated a variety of annotation data that include the GO, domain, disease, drug, chromosomal location, and custom-defined annotations. Diverse types of molecular networks (pathways, transcription and microRNA regulations, protein-protein interaction) are also included. The pair-wise relationship between annotation gene sets was calculated using kappa statistics. GARNET consists of three modules - <I>gene set manager</I>, <I>gene set analysis</I> and <I>gene set retrieval</I>, which are tightly integrated to provide virtually automatic analysis for gene sets. A dedicated viewer for annotation network has been developed to facilitate exploration of the related annotations.</P><P><B>Conclusions</B></P><P>GARNET (gene annotation relationship network tools) is an integrative platform for diverse types of gene set analysis, where complex relationships among gene annotations can be easily explored with an intuitive network visualization tool (http://garnet.isysbio.org/ or http://ercsb.ewha.ac.kr/garnet/).</P>
Yu, Namhee,Yong, Seunghui,Kim, Hong Kwan,Choi, Yoon‐,La,Jung, Yeonjoo,Kim, Doyeon,Seo, Jihae,Lee, Ye Eun,Baek, Daehyun,Lee, Jinseon,Lee, Seungjae,Lee, Jong Eun,Kim, Jaesang,Kim, Jhingook,Lee, Sa John Wiley and Sons Inc. 2019 MOLECULAR ONCOLOGY Vol.13 No.6
<P>The roles of miRNAs in lung cancer have not yet been explored systematically at the genome scale despite their important regulatory functions. Here, we report an integrative analysis of miRNA and mRNA sequencing data for matched tumor–normal samples from 109 Korean female patients with non‐small‐cell lung adenocarcinoma (LUAD). We produced miRNA sequencing (miRNA‐Seq) and RNA‐Seq data for 48 patients and RNA‐Seq data for 61 additional patients. Subsequent differential expression analysis with stringent criteria yielded 44 miRNAs and 2322 genes. Integrative gene set analysis of the differentially expressed miRNAs and genes using miRNA–target information revealed several regulatory processes related to the cell cycle that were targeted by tumor suppressor miRNAs (TSmiR). We performed colony formation assays in A549 and NCI‐H460 cell lines to test the tumor‐suppressive activity of downregulated miRNAs in cancer and identified 7 novel TSmiRs (miR‐144‐5p, miR‐218‐1‐3p, miR‐223‐3p, miR‐27a‐5p, miR‐30a‐3p, miR‐30c‐2‐3p, miR‐338‐5p). Two miRNAs, miR‐30a‐3p and miR‐30c‐2‐3p, showed differential survival characteristics in the Tumor Cancer Genome Atlas (TCGA) LUAD patient cohort indicating their prognostic value. Finally, we identified a network cluster of miRNAs and target genes that could be responsible for cell cycle regulation. Our study not only provides a dataset of miRNA as well as mRNA sequencing from the matched tumor–normal samples, but also reports several novel TSmiRs that could potentially be developed into prognostic biomarkers or therapeutic RNA drugs.</P>