• Proceedings of the KSRS Conference
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• v.2
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• pp.627-630
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• 2006

Sequential Pattern Mining is the mining approach which addresses the problem of discovering the existent maximal frequent sequences in a given databases. In the daily and scientific life, sequential data are available and used everywhere based on their representative forms as text, weather data, satellite data streams, business transactions, telecommunications records, experimental runs, DNA sequences, histories of medical records, etc. Discovering sequential patterns can assist user or scientist on predicting coming activities, interpreting recurring phenomena or extracting similarities. For the sake of that purpose, the core of sequential pattern mining is finding the frequent sequence which is contained frequently in all data sequences. Beside the discovery of frequent itemsets, sequential pattern mining requires the arrangement of those itemsets in sequences and the discovery of which of those are frequent. So before mining sequences, the main task is checking if one sequence is a subsequence of another sequence in the database. In this paper, we implement the subsequence matching method as the preprocessing step for sequential pattern mining. Matched sequences in our implementation are the normalized sequences as the form of number chain. The result which is given by this method is the review of matching information between input mapped sequences.

• Korean Journal of Remote Sensing
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• v.22 no.5
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• pp.457-462
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• 2006

Sequential Pattern Mining is the mining approach which addresses the problem of discovering the existent maximal frequent sequences in a given databases. In the daily and scientific life, sequential data are available and used everywhere based on their representative forms as text, weather data, satellite data streams, business transactions, telecommunications records, experimental runs, DNA sequences, histories of medical records, etc. Discovering sequential patterns can assist user or scientist on predicting coming activities, interpreting recurring phenomena or extracting similarities. For the sake of that purpose, the core of sequential pattern mining is finding the frequent sequence which is contained frequently in all data sequences. Beside the discovery of frequent itemsets, sequential pattern mining requires the arrangement of those itemsets in sequences and the discovery of which of those are frequent. So before mining sequences, the main task is checking if one sequence is a subsequence of another sequence in the database. In this paper, we implement the subsequence matching method as the preprocessing step for sequential pattern mining. Matched sequences in our implementation are the normalized sequences as the form of number chain. The result which is given by this method is the review of matching information between input mapped sequences.

• Natural Product Sciences
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• v.17 no.2
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• pp.65-79
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• 2011

Reactive oxygen species potentially cause damage to cellular components including lipids, protein and DNA; this oxidative damage plays a key role in the pathogenesis of neurodegenerative disease, cardiovascular disease, metabolic disease and cancer. On the basis of the oxidative stress hypothesis, a number of studies have been performed to search for an efficient and safe antioxidant. Although in vitro studies have provided promising results, only a limited number of natural and synthetic antioxidants have been developed for clinical application due to their low efficacy and side-effects. Thus, the discovery of new antioxidants with marked efficacy and safety has attracted worldwide attention in recent decades. Since plants are recognized as important sources of natural antioxidants, our research has focused on the discovery of new naturally occurring antioxidants from medicinal plants. The purpose of this review is to open a new prospect in the field of search for natural antioxidants from medicinal plants by summarizing our recent findings. Using in vitro bioassay systems such as 2,2-diphenyl-1-picrylhydrazyl, superoxide radical scavenging tests and lipid peroxidation models, we have tested over than 350 species of medicinal plants for their antioxidant activity and selected several of them for further investigation. During the research on the discovery of effective natural antioxidants from the medicinal plants selected, we have isolated several new and known antioxidant compounds that include stilbene glycosides, phenolic glycosides, flavonoids, oligostilbenes, and coumarins. Our results suggest that the presence of antioxidant compounds in the medicinal plants might be associated with the traditional use to treat inflammation, cardiovascular disease and various chronic diseases.

• BMB Reports
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• v.53 no.6
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• pp.299-310
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• 2020

Chronic liver disease progresses through several stages, fatty liver, steatohepatitis, cirrhosis, and eventually, it leads to hepatocellular carcinoma (HCC) over a long period of time. Since a large proportion of patients with HCC are accompanied by cirrhosis, it is considered to be an important factor in the diagnosis of liver cancer. This is because cirrhosis leads to an irreversible harmful effect, but the early stages of chronic liver disease could be reversed to a healthy state. Therefore, the discovery of biomarkers that could identify the early stages of chronic liver disease is important to prevent serious liver damage. Biomarker discovery at liver cancer and cirrhosis has enhanced the development of sequencing technology. Next generation sequencing (NGS) is one of the representative technical innovations in the biological field in the recent decades and it is the most important thing to design for research on what type of sequencing methods are suitable and how to handle the analysis steps for data integration. In this review, we comprehensively summarized NGS techniques for identifying genome, transcriptome, DNA methylome and 3D/4D chromatin structure, and introduced framework of processing data set and integrating multi-omics data for uncovering biomarkers.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.5
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• pp.650-657
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• 2018

Objective: The study investigated the biological functions and mechanisms for controlling cashmere growth of Liaoning cashmere goat by ovarian carcinoma immunoreactive antigen-like protein 2 (OCIAD2) and decorin (DCN) genes. Methods: cDNA library of Liaoning cashmere goat was constructed in early stages. OCIAD2 and DCN genes related to cashmere growth were identified by homology analysis comparison. The expression location of OCIAD2 and DCN genes in primary and secondary hair follicles (SF) was performed using in situ hybridization. The expression of OCIAD2 and DCN genes in primary and SF was performed using real-time polymerase chain reaction (PCR). Results: In situ hybridization revealed that OCIAD2 and DCN were expressed in the inner root sheath of Liaoning cashmere goat hair follicles. Real-time quantitative PCR showed that these genes were highly expressed in SF during anagen, while these genes were highly expressed in primary hair follicle in catagen phase. Melatonin (MT) inhibited the expression of OCIAD2 and promoted the expression of DCN. Insulin-like growth factors-1 (IGF-1) inhibited the expression of OCIAD2 and DCN, while fibroblast growth factors 5 (FGF5) promoted the expression of these genes. MT and IGF-1 promoted OCIAD2 synergistically, while MT and FGF5 inhibited the genes simultaneously. MT+IGF-1/MT+FGF5 inhibited DCN gene. RNAi technology showed that OCIAD2 expression was promoted, while that of DCN was inhibited. Conclusion: Activation of bone morphogenetic protein (BMP) signaling pathway up-regulated OCIAD2 expression and stimulated SF to control cell proliferation. DCN gene affected hair follicle morphogenesis and periodic changes by promoting transforming growth $factor-{\beta}$ ($TGF-{\beta}$) and BMP signaling pathways. OCIAD2 and DCN genes have opposite effects on $TGF-{\beta}$ signaling pathway and inhibit each other to affect the hair growth.

• Interdisciplinary Bio Central
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• v.2 no.3
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• pp.8.1-8.5
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• 2010

Introduction: Recently identified human homologues of ALKB protein have shown the activity of DNA damaging drugs, used for cancer therapy. Bioinformatics study of hABH2 and hABH3 had led to the discovery of a novel DNA repair mechanism. Very little is known about structure and function of hABH4, one of the members of this superfamily. Therefore, in present study we are intended to predict its structure and function through various bioinformatics tools. Materials and Methods: Modeling was done with modeler 9v7 to predict the 3D structure of the hABH4 protein. This model was validated with the program Procheck using Ramachandran plot statistics and was submitted to PMDB with ID PM0076284. The 3d2GO server was used to predict the functions. Residues at protein ligand and protein RNA binding sites were predicted with 3dLigandSite and KYG programs respectively. Results and Discussion: 3-D model of hABH4, ALKBH4.B99990003.pdb was predicted and evaluated. Validation result showed that 96.4 % residues lies in favored and additional allowed region of Ramachandran plot. Ligand binding residues prediction showed four Ligand clusters, having 24 ligands in cluster 1. Importantly, conserved pattern of Glu196-X-Pro198- Xn-His254 in the functional domain was detected. DNA and RNA binding sites were also predicted in the model. Conclusion and Prospects: The predicted and validated model of human homologue hABH4 resulted from this study may unveil the mechanism of DNA damage repair in human and accelerate the research on designing of appropriate inhibitors aiding in chemotherapy and cancer related diseases.

• Parasites, Hosts and Diseases
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• v.45 no.1 s.141
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• pp.1-9
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• 2007

The endosymbionts of 4 strains of Acanthamoeba(KA/E9, KA/E21, KA/E22, and KA/E23) isolated from the infected corneas of Korean patients were characterized via orcein stain, transmission electron microscopic examination, and 16S rDNA sequence analysis. Double membrane-bound, rod-shaped endosymbionts were distributed randomly throughout both the trophozoites and cysts of each of Acanthamoeba isolates. The endosymbionts of KA/E9, KA/E22, and KA/E23 were surrounded by electron-translucent areas. No lacunae-like structures were observed in the endosymbionts of KA/E21, the bacterial cell walls of which were studded with host ribosomes. Comparative analyses of the 16S rDNA sequences showed that the endosymbionts of KA/E9, KA/E22 and KA/E23 were closely related to Caedibacter caryophilus, whereas the KA/E21 endosymbiont was assigned to the Cytophaga-Flavobacterium-Bacteroides(CFB) phylum. In the 4 strains of Acanthamoeba, the hosts of the endosymbionts were identified as belonging to the Acanthamoeba castellanii complex, which corresponds to the T4 genotype. Acanthamoeba KA/E21 evidenced characteristics almost identical to those of KA/E6, with the exception of the existence of endosymbionts. The discovery of these endosymbionts from Acanthamoeba may prove essential to future studies focusing on interactions between the endosymbionts and the amoebic hosts.

• Parasites, Hosts and Diseases
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• v.47 no.4
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• pp.337-344
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• 2009

In a previous study, we reported our discovery of Acanthamoeba contamination in domestic tap water; in that study, we determined that some Acanthamoeba strains harbor endosymbiotic bacteria, via our molecular characterization by mitochondrial DNA restriction fragment length polymorphism (Mt DNA RFLP). Five (29.4%) among 17 Acanthamoeba isolates contained endosymbionts in their cytoplasm, as demonstrated via orcein staining. In order to estimate their pathogenicity, we conducted a genetic characterization of the endosymbionts in Acanthamoeba isolated from domestic tap water via 16S rDNA sequencing. The endosymbionts of Acanthamoeba sp. KA/WP3 and KA/WP4 evidenced the highest level of similarity, at 97% of the recently published 16S rDNA sequence of the bacterium, Candidatus Amoebophilus asiaticus. The endosymbionts of Acanthamoeba sp. KA/WP8 and KA/WP12 shared a 97% sequence similarity with each other, and were also highly similar to Candidatus Odyssella thessalonicensis, a member of the $\alpha$-proteobacteria. The endosymbiont of Acanthamoeba sp. KA/WP9 exhibits a high degree of similarity (85-95%) with genus Methylophilus, which is not yet known to harbor any endosymbionts. This is the first report, to the best of our knowledge, to show that Methylophilus spp. can live in the cytoplasm of Acanthamoeba.

• Journal of Ginseng Research
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• v.43 no.1
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• pp.1-9
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• 2019

Background: Korean ginseng is an important cash crop in Asian countries. However, plant yield is reduced by pathogens. Among the Ilyonectria radicicola-species complex, I. mors-panacis is responsible for root-rot and replant failure of ginseng in Asia. The development of new methods to reveal the existence of the pathogen before cultivation is started is essential. Therefore, a quantitative real-time polymerase chain reaction method was developed to detect and quantify the pathogen in ginseng soils. Methods: In this study, a species-specific histone H3 primer set was developed for the quantification of I. mors-panacis. The primer set was used on DNA from other microbes to evaluate its sensitivity and selectivity for I. mors-panacis DNA. Sterilized soil samples artificially infected with the pathogen at different concentrations were used to evaluate the ability of the primer set to detect the pathogen population in the soil DNA. Finally, the pathogen was quantified in many natural soil samples. Results: The designed primer set was found to be sensitive and selective for I. mors-panacis DNA. In artificially infected sterilized soil samples, using quantitative real-time polymerase chain reaction the estimated amount of template was positively correlated with the pathogen concentration in soil samples ($R^2=0.95$), disease severity index ($R^2=0.99$), and colony-forming units ($R^2=0.87$). In natural soils, the pathogen was recorded in most fields producing bad yields at a range of $5.82{\pm}2.35pg/g$ to $892.34{\pm}103.70pg/g$ of soil. Conclusion: According to these results, the proposed primer set is applicable for estimating soil quality before ginseng cultivation. This will contribute to disease management and crop protection in the future.

• Applied Biological Chemistry
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• v.48 no.4
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• pp.345-351
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• 2005

To access the natural products of uncultured microorganisms, we constructed and screened the metagenomic DNA libraries by using a cosmid vector and DNA inserts isolated directly from soil. Initial screening of the libraries in Escherichia coli resulted in the isolation of several clones that produce a dark brown color when grown in LB medium. One of the positive clones, designed pYS85C, was transposon mutagenized and the DNA surrounding the transposon insertions in cosmids that no longer conferred the production of brown pigment to E. coli was sequenced. Annotation of the pYS85C sequence obtained from the transposon mutagenesis experiment indicated a single 393 amino acid open reading frame (ORF) with a molecular mass of about 44.5 kDa, predicted to be a 4-hydroxyphenylpyruvate dioxygenases (HPPDs), was responsible for the observed brown pigment. In a BLAST search against deposited sequence, the translated protein from this ORF showed moderate-level identity (>60%) to the other known HPPDs and was most conserved in the C-terminal region of the protein. These results show that genes involved in natural product synthesis can be cloned directly from soil DNA and expressed in a heterologous host, supporting the idea that this technology has the potential to provide novel natural products from the wealth of environmental microbial diversity and is a potentially important new tool for drug discovery.