• Biomolecules & Therapeutics
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• 제27권3호
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• pp.302-310
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• 2019

Melanoma cells have been shown to respond to BRAF inhibitors; however, intrinsic and acquired resistance limits their clinical application. In this study, we performed RNA-Seq analysis with BRAF inhibitor-sensitive (A375P) and -resistant (A375P/Mdr with acquired resistance and SK-MEL-2 with intrinsic resistance) melanoma cell lines, to reveal the genes and pathways potentially involved in intrinsic and acquired resistance to BRAF inhibitors. A total of 546 differentially expressed genes (DEGs), including 239 up-regulated and 307 down-regulated genes, were identified in both intrinsic and acquired resistant cells. Gene ontology (GO) analysis revealed that the top 10 biological processes associated with these genes included angiogenesis, immune response, cell adhesion, antigen processing and presentation, extracellular matrix organization, osteoblast differentiation, collagen catabolic process, viral entry into host cell, cell migration, and positive regulation of protein kinase B signaling. In addition, using the PAN-THER GO classification system, we showed that the highest enriched GOs targeted by the 546 DEGs were responses to cellular processes (ontology: biological process), binding (ontology: molecular function), and cell subcellular localization (ontology: cellular component). Ingenuity pathway analysis (IPA) network analysis showed a network that was common to two BRAF inhibitorresistant cells. Taken together, the present study may provide a useful platform to further reveal biological processes associated with BRAF inhibitor resistance, and present areas for therapeutic tool development to overcome BRAF inhibitor resistance.

• Genomics & Informatics
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• 제6권3호
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• pp.153-156
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• 2008

Complex diseases such as stroke and cancer have two or more genetic loci and are affected by environmental factors that contribute to the diseases. Due to the complex characteristics of these diseases, identifying candidate genes requires a system-level analysis of the following: gene ontology, pathway, and interactions. A database and user interface, termed StrokeBase, was developed; StrokeBase provides queries that search for pathways, candidate genes, candidate SNPs, and gene networks. The database was developed by using in silico data mining of HGNC, ENSEMBL, STRING, RefSeq, UCSC, GO, HPRD, KEGG, GAD, and OMIM. Forty candidate genes that are associated with cerebrovascular disease were selected by human experts and public databases. The networked cerebrovascular disease gene maps also were developed; these maps describe genegene interactions and biological pathways. We identified 1127 genes, related indirectly to cerebrovascular disease but directly to the etiology of cerebrovascular disease. We found that a protein-protein interaction (PPI) network that was associated with cerebrovascular disease follows the power-law degree distribution that is evident in other biological networks. Not only was in silico data mining utilized, but also 250K Affymetrix SNP chips were utilized in the 320 control/disease association study to generate associated markers that were pertinent to the cerebrovascular disease as a genome-wide search. The associated genes and the genes that were retrieved from the in silico data mining system were compared and analyzed. We developed a well-curated cerebrovascular disease-associated gene network and provided bioinformatic resources to cerebrovascular disease researchers. This cerebrovascular disease network can be used as a frame of systematic genomic research, applicable to other complex diseases. Therefore, the ongoing database efficiently supports medical and genetic research in order to overcome cerebrovascular disease.

• 제어로봇시스템학회논문지
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• 제11권10호
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• pp.851-856
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• 2005

The DNA and protein data of diverse species have been daily discovered and deposited in the public archives according to each established format. Database systems in the public archives provide not only an easy-to-use, flexible interface to the public, but also in silico analysis tools of unidentified sequence data. Of such in silico analysis tools, multiple sequence alignment [1] methods relying on pairwise alignment and Smith-Waterman algorithm [2] enable us to identify unknown DNA, protein sequences or phylogenetic relation among several species. However, in the existing multiple alignment method as the number of sequences increases, the runtime increases exponentially. In order to remedy this problem, we adopted a parallel processing suffix tree algorithm that is able to search for common subsequences at one time without pairwise alignment. Also, the cross-matching subsequences triggering inexact-matching among the searched common subsequences might be produced. So, the cross-matching masking process was suggested in this paper. To identify the function of the clusters generated by suffix tree clustering, BLAST was combined with a clustering tool. Our clustering and annotating tool is summarized as the following steps: (1) construction of suffix tree; (2) masking of cross-matching pairs; (3) clustering of gene sequences and (4) annotating gene clusters by BLAST search. The system was successfully evaluated with 22 gene sequences in the pyrubate pathway of bacteria, clustering 7 clusters and finding out representative common subsequences of each cluster

• Journal of Microbiology and Biotechnology
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• 제31권7호
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• pp.933-941
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• 2021

Ginsenoside Rg4 is a rare ginsenoside that is naturally found in ginseng, and exhibits a wide range of biological activities including antioxidant and anti-inflammatory properties in several cell types. The purpose of this study was to use an in vivo model of hair follicle (HF)-mimic based on a human dermal papilla (DP) spheroid system prepared by three-dimensional (3D) culture and to investigate the effect of Rg4 on the hair-inductive properties of DP cells. Treatment of the DP spheroids with Rg4 (20 to 50 ㎍/ml) significantly increased the viability and size of the DP spheres in a dose-dependent manner. Rg4 also increased the mRNA and protein expression of DP signature genes that are related to hair growth including ALP, BMP2, and VCAN in the DP spheres. Analysis of the signaling molecules and luciferase reporter assays further revealed that Rg4 induces the activation of phosphoinositide 3-kinase (PI3K)/AKT and the inhibitory phosphorylation of GSK3β, which activates the WNT/β-catenin signaling pathway. These results correlated with not only the increased nuclear translocation of β-catenin following the treatment of the DP spheres with Rg4 but also the significant elevation of mRNA expression of the downstream target genes of the WNT/β-catenin pathway including WNT5A, β-catenin, and LEF1. In conclusion, these results demonstrated that ginsenoside Rg4 promotes the hair-inductive properties of DP cells by activating the AKT/GSK3β/β-catenin signaling pathway in DP spheres, suggesting that Rg4 could be a potential natural therapy for hair growth.

• Journal of Ginseng Research
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• 제33권3호
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• pp.212-218
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• 2009

인삼으로부터 뽑은 PgCYP 유전자와 표지유전자인 NPTII 유전자를 함유하고 있는 Agrobacterium tumefaciens GV3101균주를 이용하여 담배 잎절편과 공동배양한 후 MS 기본배지에 kanamycin 100 $\mu$g/ml, cefotaxime 500 $\mu$g/l, BA 2 mg/l와 NAA 0.2 mg/l가 첨가된 선발배지에 치상하여 4주 후 항생제가 첨가된 기본배지에서 발근시켰다. 생존한 선발체의 잎을 이용하여 PCR 반응으로 도입유전자의 삽입여부를 확인하였다. 또한 선발된 형질전환체를 이용하여 RT-PCR을 실시하여 PgCYP 유전자가 담배식물에 안정적으로 도입되어 전사되고 있음을 확인하였다.

• 한국해양바이오학회지
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• 제15권2호
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• pp.33-40
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• 2023

This study aimed to investigate the immunomodulatory function of Pyropia yezoensis hydrothermal (water) extract (PYWE) in comparison to the group treated only with lipopolysaccharides (LPS) in RAW264.7 cells. LPS is known to be an inflammatory mediator that activates macrophages, leading to the secretion of nitric oxide (NO), inducible nitric oxide synthase (iNOS), tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6) as defense responses. Through enzyme-linked immunoassay and western blot analyses, it was observed that PYWE increased the expression levels of NO, iNOS, TNF-α, and IL-6 in RAW264.7 cells in a dose-dependent manner, although to a lesser extent compared with the group treated with LPS alone. In addition, the study examined the mitogen-activated protein kinases (MAPKs) pathway, which regulates various cellular activities, including gene expression, mitosis, cell differentiation, transformation, survival, and death. The western blot analysis confirmed that PYWE also regulated the MAPKs pathway. Furthermore, the expression levels of immunomodulatory-related factors increased in the group treated with PYWE compared with the control group. Even though the effects of PYWE were usually less strong than those of LPS, the effects of PYWE increased with increasing doses compared to the control group. This suggests that PYWE could be used to control the immune system.

• Tuberculosis and Respiratory Diseases
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• 제56권5호
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• pp.450-464
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• 2004

연구배경 : FHIT 유전자의 homozygous deletion과 이와 관련된 mRNA 발현 이상, 단백질의 발현 결손은 폐암에서 매우 높은 빈도로 관찰되고 있다. 일부 연구에 의하면 FHIT 유전자를 폐암 세포 내에 이입시켰을 때 apoptosis가 유발되었고, 세포 주기의 이상 소견이 관찰되었으며, 종양형성 능력이 억제됨이 관찰되었다. 하지만 아직까지 FHIT 단백질의 기능에 대한 지식은 미진한 상태이다. 본 연구에서는 FHIT 유전자를 폐암 세포에 이입시켰을 때 유발되는 apoptosis의 기전을 규명하고자 하였다. 방 법 : FHIT 유전자가 결손된 NCI-H358 세포주에 FHIT 유전자를 stable transfection 시킨 후, cisplatin 혹은 paclitaxel을 가하고 apoptosis가 항진되어 나타나는가를 DAPI staining과 flow cytometry로 관찰해 보았다. 또한 이 과정에서 나타나는 caspase system의 변화와 Bcl-2 family의 변화를 Western blotting으로 조사해 보았다. 결 과 : FHIT를 발현시킨 세포에서는 cisplatin 혹은 paclitaxel을 투여하였을 때 유의하게 생존율이 감소하였으며, 이는 apoptosis 증가에 의한 것으로 확인 되었다. 이 과정에서 FHIT가 발현된 세포는 caspase-3, caspase-7의 활성화가 유의하게 증가되었으며, Bcl-2와 Bcl-xL 발현은 유의하게 감소하고 Bax와 Bad 발현은 유의하게 증가하였다. 결 론 : FHIT가 발현된 폐암 세포에 항암제를 투여하였을 때 유의하게 증가한 apoptosis는 caspase system과 Bcl-2 family의 활성화와 관련되어 있다.

• International Journal of Industrial Entomology and Biomaterials
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• 제36권1호
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• pp.15-24
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• 2018

N-glycosylation is an important posttranslational modification that results in a variety of biological activities, structural stability, and protein-protein interactions. There are still many mysteries in the structure and function of N-glycans, and detailed elucidation is necessary. Baculovirus expression system (BES) is widely used to produce recombinant glycoproteins, but it is not suitable for clinical use due to differences in N-glycan structure between insects and mammals. It is necessary to develop adequate model glycoproteins for analysis to efficiently alter the insect-type N-glycosylation pathway to human type. The previous research shows the recombinant alpha 1-acid glycoprotein (${\alpha}1AGP$) secreted from silkworm cultured cells or larvae is highly glycosylated and expected to be an excellent research candidate for the glycoprotein analysis expressed by BES. Therefore, we improved the ${\alpha}1AGP$ to be a better model for studying glycosylation. The modified ${\alpha}1AGP$ (${\alpha}1AGP{\Delta}$) recombinant protein was successfully expressed and purified by using BES, however, the expression level in silkworm cultured cells and larvae were lower than that of the ${\alpha}1AGP$. Subsequently, we confirmed the detailed profile of N-glycan on the ${\alpha}1AGP{\Delta}$ by LS/MS analysis the N-glycan structure at each glycosylation site. These results indicated that the recombinant ${\alpha}1AGP{\Delta}$ could be usable as a better model glycoprotein of N-glycosylation research in BES.

• 방사선산업학회지
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• 제5권1호
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• pp.1-5
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• 2011

Since proteomics can be employed to compare changes in the expression levels of many proteins under particular genetic and environmental conditions, using mass spectrometry to establish radiation stimulon, we performed two-dimensional gel electrophoresis and identified E. coli proteins whose expressions are affected by high dose of ionizing radiation. After exposure to 3 kGy, it was found that 6 proteins involved in carbon and energy metabolism were reduced. Although 4 of 7 protein spots showing a significant increase in expression level were neither identified nor classified, uridine phosphorylase (Udp), superoxide dismutase (SodB), and thioredoxin-dependent thiol peroxidase (Bcp) were proven to be up-regulated after irradiation. This suggests that E. coli subjected to high doses of radiation (3 kGy) may operate a defense system that is able to detoxify reactive oxygen species and stimulate the salvage pathway of nucleotide synthesis to replenish damaged DNA.

• 한국발생생물학회지:발생과생식
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• 제16권2호
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• pp.129-135
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• 2012

선행연구에서 본 연구자는 IEX-1 단백질이 난소 암세포에서 세포사멸(apoptosis)을 유도하는 기능을 수행함을 확인하였으나, 세포사멸과 세포생존의 여러 단계에서 어떠한 신호전달 체계로 IEX-1이 작용하는지는 정확히 알지 못하고 있다. 따라서 IEX-1 단백질과 결합하는 새로운 단백질을 찾기 위해 yeast two-hybrid system을 이용하였다. 그 결과 IEX-1이 여러 다양한 인간 암 세포에서 세포사멸을 유도하는 CATHEPSIN B 단백질과 결합함을 밝혔다. 본 연구에서는 리소좀 프로테아제의 일원인 CATHEPSIN B 단백질과 IEX-1 단백질의 결합을 면역침강법과 western blot 분석으로 확인하였다. 그러므로 이 결과들을 통해서 IEX-1과 CATHEPSIN B는 세포 내에서 서로의 기능에 영향을 미칠 것으로 예상되며, 세포사멸을 유도하는 IEX-1 단백질이 lysosome-mediated apoptotic pathway에 관여할 가능성을 시사한다.