• Journal of Microbiology and Biotechnology
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• 제18권6호
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• pp.1081-1089
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• 2008

A novel ginsenoside-hydrolyzing ${\beta}$-glucosidase was purified from Paecilomyces Bainier sp. 229 by a combination of Q-Sepharose FF, phenyl-Sepharose CL-4B, and CHT ceramic hydroxyapatite column chromatography. The purified enzyme was a monomeric protein with a molecular mass estimated to be 115 kDa. The optimal enzyme activity was observed at pH 3.5 and $60^{\circ}C$. It was highly stable within pH 3-9 and at temperatures lower than $55^{\circ}C$. The enzyme was specific to ${\beta}$-glucoside. The order of enzyme activities against different types of ${\beta}$-glucosidic linkages was ${\beta}$-(1-6)>${\beta}$-(1-2)>${\beta}$-(1-4). The enzyme converted ginsenoside Rb1 to CK specifically and efficiently. An 84.3% amount of ginsenoside Rb1, with an initial concentration of 2 mM, was converted into CK in 24 h by the enzyme at $45^{\circ}C$ and pH 3.5. The hydrolysis pathway of ginsenoside Rb1 by the enzyme was $Rb1{\to}Rd{\to}F2{\to}CK$. Five tryptic peptide fragments of the enzyme were identified by a newly developed de novo sequencing method of post-source decay (PSD) matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. By comparing the five identified peptide sequences with the NCBI database, this purified ${\beta}$-glucosidase proves to be a new protein that has not been reported before.

• Journal of Microbiology and Biotechnology
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• 제16권6호
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• pp.911-920
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• 2006

[ $CD8^+$ ] T Iymphocytes with the cytotoxic activity and capability to release various cytokines are the major players in immune responses against viral infection and cancer. To identify the proteins specific to resting or activated human CD8$^+$ T cells, human CD8$^+$ T cells were activated with anti-CD3+anti-CD28 mAb in the presence of IL-2. The solubilized proteins from resting and activated human CD8$^+$ T cells were separated by high-resolution two-dimensional polyacrylamide gel electrophoresis, and their proteomes were analyzed. Proteomic analysis of resting and activated T cells resulted in identification of 35 proteins with the altered expression. Mass spectrometry coupled with Profound and SWISS-PROT database analysis revealed that these identified proteins are to be functionally associated with cell proliferation, metabolic pathways, antigen presentation, and intracellular signal transduction pathways. We also identified six unknown proteins predicted from genomic DNA sequences specific to resting or activated CD8$^+$ T cells. Protein network studies and functional characterization of these novel proteins may provide new insight into the signaling transduction pathway of CD8$^+$ T cell activation.

• Toxicological Research
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• 제32권4호
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• pp.289-300
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• 2016

Non-genotoxic carcinogens are substances that induce tumorigenesis by non-mutagenic mechanisms and long term rodent bioassays are required to identify them. Recent studies have shown that transcription profiling can be applied to develop early identifiers for long term phenotypes. In this study, we used rat liver expression profiles from the NTP (National Toxicology Program, Research Triangle Park, USA) DrugMatrix Database to construct a gene classifier that can distinguish between non-genotoxic carcinogens and other chemicals. The model was based on short term exposure assays (3 days) and the training was limited to oxidative stressors, peroxisome proliferators and hormone modulators. Validation of the predictor was performed on independent toxicogenomic data (TG-GATEs, Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System, Osaka, Japan). To build our model we performed Random Forests together with a recursive elimination algorithm (VarSelRF). Gene set enrichment analysis was employed for functional interpretation. A total of 770 microarrays comprising 96 different compounds were analyzed and a predictor of 54 genes was built. Prediction accuracy was 0.85 in the training set, 0.87 in the test set and increased with increasing concentration in the validation set: 0.6 at low dose, 0.7 at medium doses and 0.81 at high doses. Pathway analysis revealed gene prominence of cellular respiration, energy production and lipoprotein metabolism. The biggest target of toxicogenomics is accurately predict the toxicity of unknown drugs. In this analysis, we presented a classifier that can predict non-genotoxic carcinogenicity by using short term exposure assays. In this approach, dose level is critical when evaluating chemicals at early time points.

• Asian Pacific Journal of Cancer Prevention
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• 제14권11호
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• pp.6347-6350
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• 2013

Post-transplant lymphoproliferative disorder (PTLD) is a common complication of therapeutic immunosuppression after organ transplantation. Gene expression profile facilitates the identification of biological difference between Epstein-Barr virus (EBV) positive and negative PTLDs. Previous studies mainly implemented variance/regression analysis without considering unaccounted array specific factors. The aim of this study is to investigate the gene expression difference between EBV positive and negative PTLDs through partial least squares (PLS) based analysis. With a microarray data set from the Gene Expression Omnibus database, we performed PLS based analysis. We acquired 1188 differentially expressed genes. Pathway and Gene Ontology enrichment analysis identified significantly over-representation of dysregulated genes in immune response and cancer related biological processes. Network analysis identified three hub genes with degrees higher than 15, including CREBBP, ATXN1, and PML. Proteins encoded by CREBBP and PML have been reported to be interact with EBV before. Our findings shed light on expression distinction of EBV positive and negative PTLDs with the hope to offer theoretical support for future therapeutic study.

• Asian Pacific Journal of Cancer Prevention
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• 제13권5호
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• pp.1787-1791
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• 2012

Objective: The p53 tumor suppressor pathway plays an important role in gastric cancer (GC) development. Auto-regulatory feedback control of p53 expression is critical to maintaining proper tumor suppressor function. So far, several studies between p53 Arg72Pro polymorphism and GC have generated controversial and inconclusive results. Methods: To better assess the purported relationship, we performed a meta-analysis of 19 publications. Eligible studies were identified by searching the Pubmed database. Odds ratios (ORs) with 95% confidence intervals (CIs) were estimated to assess any link. Results: Overall, a significant association was detected between the p53 Arg72Pro polymorphism and GC risk (Pro-allele vs. Arg-allele: OR = 1.05, 95%CI = 1.01-1.08; Pro/Pro vs. Arg/Arg: OR = 1.13, 95%CI = 1.04-1.22). Moreover, on stratified analysis by race, significantly increased risk was found for Asian populations (Pro-allele vs. Arg-allele: OR = 1.06, 95%CI = 1.02-1.10; Pro/Pro vs. Arg/Arg: OR = 1.16, 95%CI = 1.07-1.26; Pro/Pro+Pro/Arg vs. Arg/Arg: OR = 1.58, 95%CI = 1.09-2.27). Conclusions: Our study provided evidence that the p53 72Pro allele may increase GC risk in Asians. Future studies with larger sample size are warranted to further confirm this association in more detail.

• 한국멀티미디어학회논문지
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• 제16권9호
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• pp.1089-1097
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• 2013

초기 증상을 가진 재가 치매 환자부터 심각한 증상을 가져 병원에 있는 치매 환자까지 다양한 형태로 발생되고 있으나 환자의 위치와 생활 패턴을 고려한 시스템에 대한 연구는 미흡한 실정이다. 본 논문에서는 치매 환자의 일정에 따른 안전반경과 현 위치의 행동 상태 정보를 등록하여 지도 기반의 위치 표출 및 위험문자 알림서비스를 제공하는 치매 환자 가족을 위한 안드로이드 기반의 치매 환자 관리 어플리케이션을 개발한다. 치매환자의 행동 상태를 정상적인 상태와 이탈 및 배회인 비정상적인 상태로 분류한다. 이탈은 환자가 환자의 일정에 등록되어 있는 위치의 안전반경 범위에 있지 않을 경우에, 배회는 한 번 지나온 위치를 반복하는 경우일 때 설정된다. 본 어플리케이션은 환자 위치 전송, 사용자 정보, 환자 일정 및 안전반경 등록, 이동위치 및 행동 상태 등록, 이동경로 표출 및 알림, 구조 요청 모듈로 구성된다. 치매 환자의 가족은 본 앱을 사용하여 환자의 이동 위치 알림서비스와 환자가 안전 반경을 이탈하거나 배회 행동을 할 경우 위험 알림서비스 및 구조요청 서비스를 제공받을 수 있다.

• Genomics & Informatics
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• 제9권4호
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• pp.143-151
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• 2011

In this study, we propose a novel, intuitive method of constructing an expression quantitative trait (eQT) network that is related to the metabolic syndrome using LOD scores and peak loci for selected eQTs, based on the concept of gene-gene interactions. We selected 49 eQTs that were related to insulin resistance. A variance component linkage analysis was performed to explore the expression loci of each of the eQTs. The linkage peak loci were investigated, and the "support zone" was defined within boundaries of an LOD score of 0.5 from the peak. If one gene was located within the "support zone" of the peak loci for the eQT of another gene, the relationship was considered as a potential "directed causal pathway" from the former to the latter gene. SNP markers under the linkage peaks or within the support zone were searched for in the database to identify the genes at the loci. Two groups of gene networks were formed separately around the genes IRS2 and UGCGL2. The findings indicated evidence of networks between genes that were related to the metabolic syndrome. The use of linkage analysis enabled the construction of directed causal networks. This methodology showed that characterizing and locating eQTs can provide an effective means of constructing a genetic network.

• 한국잠사학회:학술대회논문집
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• 한국잠사학회 1997년도 Progress and Future Development of Sericultural Science and Technology 40th Anniversary Commemoration Symposium
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• pp.23-49
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• 1997

This is a progress report of rice biotechnology including development of gene transformation system, gene cloning and molecular mapping in rice. The scope of the research was focused on the connection between conventional breeding and biotech-researches. Plant transformation via Agrobacterium or particle bombardment was developed to introduce one or several genes to recommended rice cultivars. Two chimeric genes containing a maize ribosome inactivating protein gene (RIP) and a gerbicide resistant gene (bar) were introduced to Nipponbare, a Japonica cultivar, and transmitted to Korean cultivars. The homozygous progenies of herbicide resistant transgenic plant showed good fertility and agronomic characters. To explore the genetic resourses in rice, over 8,000 cDNA clones from immature rice seed have been isolated and sequenced. About 13% of clones were identified as enzymes related to metabolic pathway. Among them, twenty clones have high homology with genes encoding enzymes in the photorespiratory carbon cycle reaction. Up to now about 100 clones were fully sequenced and registered at EMBL and GenBank. For the mapping of quantitative tarits loci (QTL) and eternal recombinant inbred population with 164 F13 lines (MGRI) was developed from a cross between Milyang 23 and Gihobyeo, Korean rice cultivars. After construction of fully saturated RFLP and AFLP map, quantitative traits using MGRI population were analyzed and integrated into the molecular map. Eighty seven loci were determined with 27 QTL characters including yield and yield components on rice chromosomes. Map based cloning was also tried to isolate semi-dwarf (sd-1) gene in rice. A DNA probe, RG 109, the most tightly linked to sd-1 gene was used to screen from bacterial artifical chromosome (BAC) libraries and five over lapping clones presumably containing sd-1 gene were isolated. Rice genetic database including results of biotech reasearch and classical genetics is provided at Korea Rice Genome Server which is accessible with world wide web (www) browser. The server provides rice cDNA sequences and map informations linked with phenotypic images.

• Journal of Animal Science and Technology
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• 제63권4호
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• pp.854-863
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• 2021

Weaning induces physiological changes in intestinal development that affect pigs' growth performance and susceptibility to disease. As a posttranscriptional regulator, microRNAs (miRNAs) regulate cellular homeostasis during intestinal development. We performed small RNA expression profiling in the small intestine of piglets before weaning (BW), 1 week after weaning (1W), and 2 weeks after weaning (2W) to identify weaning-associated differentially expressed miRNAs. We identified 38 differentially expressed miRNAs with varying expression levels among BW, 1W, and 2W. Then, we classified expression patterns of the identified miRNAs into four types. ssc-miR-196a and ssc-miR-451 represent pattern 1, which had an increased expression at 1W and a decreased expression at 2W. ssc-miR-499-5p represents pattern 2, which had an increased expression at 1W and a stable expression at 2W. ssc-miR-7135-3p and ssc-miR-144 represent pattern 3, which had a stable expression at 1W and a decreased expression at 2W. Eleven miRNAs (ssc-miR-542-3p, ssc-miR-214, ssc-miR-758, ssc-miR-4331, ssc-miR-105-1, ssc-miR-1285, ssc-miR-10a-5p, ssc-miR-4332, ssc-miR-503, ssc-miR-6782-3p, and ssc-miR-424-5p) represent pattern 4, which had a decreased expression at 1W and a stable expression at 2W. Moreover, we identified 133 candidate targets for miR-196a using a target prediction database. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the target genes were associated with 19 biological processes, 4 cellular components, 8 molecular functions, and 7 KEGG pathways, including anterior/posterior pattern specification as well as the cancer, PI3K-Akt, MAPK, GnRH, and neurotrophin signaling pathways. These findings suggest that miRNAs regulate the development of the small intestine during the weaning process in piglets by anterior/posterior pattern specification as well as the cancer, PI3K-Akt, MAPK, GnRH, and neurotrophin signaling pathways.

• 턱관절균형의학회지
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• 제10권1호
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• pp.12-20
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• 2020

Objectives: Tourette syndrome (TS) is a disease that occurs evenly in many social classes. Despite the long experience of drug treatment, the preference is low due to various side effects. The aim of this study was to discover herbal medicine resources through network pharmacology analysis predicted to be useful for Tourette syndrome. Methods: We used Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) to identify herbal medicines that can be used for TS by using network pharmacology research methods and to predict the mechanism of action. After evaluating compounds of each identified herb, molecular target proteins and mechanisms of action were analyzed, focusing on compounds that are likely to exhibit clinical activity in consideration of the pharmacokinetic parameters of these individual compounds. Results: Fifty nine ingredients such as atropine, veraguensin, and nuciferin among the compounds contained in 48 types of medicinal herbs such as Daturae Flos (洋金花), Salviae Radix (丹参), and Nelumbinis Plumula (蓮子心) act on the D(2) dopamine receptor, which is a protein involved in the development of TS. It has been found that atropine, veraguensin, and nuciferin are highly likely to exhibit activity by acting on the G protein-coupled receptor signaling pathway. Conclusions: It can be used in conjunction with non-invasive treatment means such as FCST Yinyang Balancing Appliance with herbal therapy to bring about a significant therapeutic effect, and it will be possible to develop a treatment that can replace drug therapy used in Western medicine.