• Asian-Australasian Journal of Animal Sciences
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• v.30 no.3
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• pp.328-337
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• 2017

Objective: An experiment was conducted to determine the relationship between the KAP11.1 and the regulation wool fineness. Methods: In previous work, we constructed a skin cDNA library and isolated a full-length cDNA clone termed KAP11.1. On this basis, we conducted a series of bioinformatics analysis. Tissue distribution of KAP11.1 mRNA was performed using semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) analysis. The expression of KAP11.1 mRNA in primary and secondary hair follicles was performed using real-time PCR (real-time polymerase chain reaction) analysis. The expression location of KAP11.1 mRNA in primary and secondary hair follicles was performed using in situ hybridization. Results: Bioinformatics analysis showed that KAP11.1 gene encodes a putative 158 amino acid protein that exhibited a high content of cysteine, serine, threonine, and valine and has a pubertal mammary gland) structural domain. Secondary structure prediction revealed a high proportion of random coils (76.73%). Semi-quantitative RT-PCR showed that KAP11.1 gene was expressed in heart, skin, and liver, but not expressed in spleen, lung and kidney. Real time PCR results showed that the expression of KAP11.1 has a higher expression in catagen than in anagen in the primary hair follicles. However, in the secondary hair follicles, KAP11.1 has a significantly higher expression in anagen than in catagen. Moreover, KAP11.1 gene has a strong expression in inner root sheath, hair matrix, and a lower expression in hair bulb. Conclusion: We conclude that KAP11.1 gene may play an important role in regulating the fiber diameter.

• Korean Journal of Microbiology
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• v.38 no.4
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• pp.230-230
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• 2002

Class Ⅲ chitin synthases in filamentous fungi are important for hyphal growth and differentiation of several filamentous fungi. A genomic clone containing the full gene encoding Chs4, a class Ⅲ chitin synthase in Penicillium chrysogenum, was cloned by PCR screening and colony hybridization from the genomic library. Nucleotide sequence analysis and transcript mapping of chs4 revealed an open reading frame (ORF) that consisted of 5 exons and 4 introns and encoded a putative protein of 915 amino acids. Nucleotide sequence analysis of the 5′flanking region of the ORF revealed a potential TATA box and several binding sites for transcription activators. The putative transcription initiation site at -716 position was identified by primer extension and the expression of the chs4 during the vegetative growth was confirmed by Northern blot analysis. Amino acid sequence analysis of the Chs4 revealed at least 5 transmembrane helices and several sites for past-transnational modifications. Comparison of the amino acid sequence of Chs4 with those of other fungi showed a close relationship between P chrysogenum and genus Aspergillus.

• Journal of Plant Biotechnology
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• v.48 no.3
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• pp.139-147
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• 2021

Since whole-genome duplication (WGD) of diploid Chrysanthemum nankingense and de novo assembly whole-genome of C. seticuspe have been obtained, they have afforded to perceive the diversity evolution and gene discovery in the improved investigation of chrysanthemum breeding. The robust tools of high-throughput identification and analysis of gene function and expression produce their vast importance in chrysanthemum genomics. However, the gigantic genome size and heterozygosity are also mentioned as the major obstacles preventing the chrysanthemum breeding practices and functional genomics analysis. Nonetheless, some of technological contemporaries provide scientific efficient and promising solutions to diminish the drawbacks and investigate the high proficient methods for generous phenotyping data obtaining and system progress in future perspectives. This review provides valuable strategies for a broad overview about the high-throughput identification, and molecular analysis of gene function and expression in chrysanthemum. We also contribute the efficient proposition about specific protocols for considering chrysanthemum genes. In further perspective, the proper high-throughput identification will continue to advance rapidly and advertise the next generation in chrysanthemum breeding.

• Biomolecules & Therapeutics
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• v.30 no.1
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• pp.98-116
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• 2022

The small GTPase RhoA has been studied extensively for its role in actin dynamics. In this study, multiple bioinformatics tools were applied cooperatively to the microarray dataset GSE64714 to explore previously unidentified functions of RhoA. Comparative gene expression analysis revealed 545 differentially expressed genes in RhoA-null cells versus controls. Gene set enrichment analysis (GSEA) was conducted with three gene set collections: (1) the hallmark, (2) the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and (3) the Gene Ontology Biological Process. GSEA results showed that RhoA is related strongly to diverse pathways: cell cycle/growth, DNA repair, metabolism, keratinization, response to fungus, and vesicular transport. These functions were verified by heatmap analysis, KEGG pathway diagramming, and direct acyclic graphing. The use of multiple gene set collections restricted the leakage of information extracted. However, gene sets from individual collections are heterogenous in gene element composition, number, and the contextual meaning embraced in names. Indeed, there was a limit to deriving functions with high accuracy and reliability simply from gene set names. The comparison of multiple gene set collections showed that although the gene sets had similar names, the gene elements were extremely heterogeneous. Thus, the type of collection chosen and the analytical context influence the interpretation of GSEA results. Nonetheless, the analyses of multiple collections made it possible to derive robust and consistent function identifications. This study confirmed several well-described roles of RhoA and revealed less explored functions, suggesting future research directions.

• 한국인삼전략화협의회:학술대회논문집
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• v.2003 no.09
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• pp.54-63
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• 2003

"Korea ginseng (Panax ginseng C.A Meyer) is an important medicinal plant. Its root has been used as an herbal medicine that provides resistance to stress and disease, and prevents exhaustion since the ancient time. Ginsenosides, glycosylated triterpene (saponin), are considered to be the main active compounds of the ginseng root. Despite of considerable commercial interests of ginsenosides, very little is known about the genes and their biochemical pathways for ginsenoside biosynthesis. This work will focus on the identification of genes involved in ginsenoside biosynthesis and the dissection of ginsenoside biosynthetic pathway using a functional genomics tool. Expression sequence tags (ESTs) provide a valuable tool to discovery the genes in secondary metabolite biosynthesis. We generated over 21,155 ginseng ESTs that is now sufficient to facilitate discovering the genes involved in ginsenoside biosynthesis such as oxidosqualene cyclase(OSC), cytochrome P450 and glycosyltransferase. With ESTs information, microarray technology will be used for the analysis of gene expression, and the identification of genes including transcription factors expressed in tissues under given experimental condition. Heterogous system such as yeast and plants will allow us to do the functional analysis. And selected ginseng hairy root which show variation in ginsenoside production will be used as a material for functional analysis of candidate gene. Functional genomics approach will successfully accelerate gene discovery, and also provide promises of metabolic engineering for the ginsenoside production."

• Korean Journal of Biological Psychiatry
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• v.1 no.1
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• pp.60-66
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• 1994

Advances in molecular biology have renewed hope for the discovery of disease relevant gene. The basic strategy is gene mapping and likely to have on important role in psychiatric research and practice. Recent linkage studies of chromosomal loci to psychiatric diseases shed light on the potential for new genetics in psychiatric science. This article reviews molecular application to psychiatrymethodological issues in genetic linkage, study of gene expression by analysis of mRNA, and current linkage studies in psychiatric diseases.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.39-40
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• 2000

Knowledge discovery has attracted increased attention in the biomedical industry in recent years is due to the increased availability of huge amount of biomedical data and the imminent need to turn such data into useful information and knowledge. In this talk, we discuss knowledge discovery techniques for gene expression analysis and MHC-peptide binding prediction in the context of discovering protein antigens and hot spots in these antigens.

• Molecular & Cellular Toxicology
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• v.3 no.4
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• pp.222-230
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• 2007

Some drugs may be limited in their clinical application due to their propensity towards their adverse effects. Toxicogenomic technology represents a useful approach for evaluating the toxic properties of new drug candidates early in the drug discovery process. Nitrofurantoin (NF) is clinical chemotherapeutic agent and antimicrobial and used to treatment of urinary tract infections. However, NF has been shown to result in pulmonary toxic effects. In this research, we revealed the changing expression gene profiles in BEAS-2B, human bronchial epithelial cell line, exposed to NF by using human oligonucleotide chip. Through the clustering analysis of gene expression profiles, we identified 136 up-regulated genes and 379 down-regulated genes changed by more than 2-fold by NF. This study identifies several interesting targets and functions in relation to NF-induced toxicity through a gene ontology analysis method including biological process, cellular components, molecular function and KEGG pathway.

• Biomolecules & Therapeutics
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• v.25 no.1
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• pp.57-68
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• 2017

Seven transmembrane receptors (7TMRs), also known as G protein-coupled receptors, are popular targets of drug development, particularly 7TMR systems that are activated by peptide ligands. Although many pharmaceutical drugs have been discovered via conventional bulk analysis techniques the increasing availability of structural and evolutionary data are facilitating change to rational, targeted drug design. This article discusses the appeal of neuropeptide-7TMR systems as drug targets and provides an overview of concepts in the evolution of vertebrate genomes and gene families. Subsequently, methods that use evolutionary concepts and comparative analysis techniques to aid in gene discovery, gene function identification, and novel drug design are provided along with case study examples.

• Genomics & Informatics
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• v.11 no.4
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• pp.191-199
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• 2013

High-throughput next-generation sequencing (NGS) technology produces a tremendous amount of raw sequence data. The challenges for researchers are to process the raw data, to map the sequences to genome, to discover variants that are different from the reference genome, and to prioritize/rank the variants for the question of interest. The recent development of many computational algorithms and programs has vastly improved the ability to translate sequence data into valuable information for disease gene identification. However, the NGS data analysis is complex and could be overwhelming for researchers who are not familiar with the process. Here, we outline the analysis pipeline and describe some of the most commonly used principles and tools for analyzing NGS data for disease gene identification.