• Bioinformatics and Biosystems
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• v.2 no.2
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• pp.71-74
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• 2007

Cell phenotypes are determined by groups of functionally related genes. Microarray profiling of gene expression provides us response of cellular state to its perturbation. Several methods for uncovering a cellular network show reliable network reconstruction. In this study, we present reconstruction of genetic regulatory network of inflammation bowel disease in human peripheral blood mononuclear cell. The microarray based on Affymetrix Gene Chip Human Genome U133 Array Set HG-U133A is processed and applied network reconstruction algorithm, ARACNe. As a result, we will show that inferred network composed of 450 nodes and 2017 edges is roughly scale-free network and hierarchical organization. The major hub, CCNL2 (cyclin A2), in inferred network is shown to be associated with inflammatory function as well as apoptotic function.

• BMB Reports
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• v.52 no.1
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• pp.5-12
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• 2019

Organismal aging is accompanied by a host of progressive metabolic alterations and an accumulation of senescent cells, along with functional decline and the appearance of multiple diseases. This implies that the metabolic features of cell senescence may contribute to the organism's metabolic changes and be closely linked to age-associated diseases, especially metabolic syndromes. However, there is no clear understanding of senescent metabolic characteristics. Here, we review key metabolic features and regulators of cellular senescence, focusing on mitochondrial dysfunction and anabolic deregulation, and their link to other senescence phenotypes and aging. We further discuss the mechanistic involvement of the metabolic regulators mTOR, AMPK, and GSK3, proposing them as key metabolic switches for modulating senescence.

• BMB Reports
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• v.56 no.1
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• pp.24-31
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• 2023

Urological cancers such as kidney, bladder, prostate, and testicular cancers are the most common types of cancers worldwide with high mortality and morbidity. To date, traditional cell lines and animal models have been broadly used to study pre-clinical applications and underlying molecular mechanisms of urological cancers. However, they cannot reflect biological phenotypes of real tissues and clinical diversities of urological cancers in vitro system. In vitro models cannot be utilized to reflect the tumor microenvironment or heterogeneity. Cancer organoids in three-dimensional culture have emerged as a promising platform for simulating tumor microenvironment and revealing heterogeneity. In this review, we summarize recent advances in prostate and kidney cancer organoids regarding culture conditions, advantages, and applications of these cancer organoids.

• BMB Reports
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• v.30 no.3
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• pp.167-172
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• 1997

The yeast Saccharomyces cerevisiae, mutant CH117, shows a drug-hypersensitivity (dhs) to cycloheximide, bleomycin, actinomycin D, 5-fluorouracil. nystatin, nigericin and several other antibiotics. CH 117 was also temperature-sensitive (ts). being unable to grow at $37^{\circ}C$ and secreted more invertase and acid phosphatase into the medium than the parent yeast. CH117 grows very slowly and the cell shape is somewhat larger and more sensitive to zymolyase than the wild type cells. Light microscopic and electron microscopic observation also revealed abnormality of the mutant cell wall. These characteristics indicate that CH117 has a defect in an essential component of the cell surface and that the cell wall which performs barrier functions has become leaky in the mutant. We screened a genomic library of wild type yeast for clones that can complement the mutation of CH117. A plasmid, pCHX1, with an insert of 3.6 kilobases (kbs) could complement the dhs and ts of CH117. Deletion and subcloning of the 3.6 kb insert showed that a gene for the complementation of mutant phenotypes was located in 1.9 kbs Puvll-Hindlll fragment.

• BMB Reports
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• v.37 no.1
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• pp.83-92
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• 2004

As a result of the enormous amount of information that has been collected with E. coli over the past half century (e.g. genome sequence, mutant phenotypes, metabolic and regulatory networks, etc.), we now have detailed knowledge about gene regulation, protein activity, several hundred enzyme reactions, metabolic pathways, macromolecular machines, and regulatory interactions for this model organism. However, understanding how all these processes interact to form a living cell will require further characterization, quantification, data integration, and mathematical modeling, systems biology. No organism can rival E. coli with respect to the amount of available basic information and experimental tractability for the technologies needed for this undertaking. A focused, systematic effort to understand the E. coli cell will accelerate the development of new post-genomic technologies, including both experimental and computational tools. It will also lead to new technologies that will be applicable to other organisms, from microbes to plants, animals, and humans. E. coli is not only the best studied free-living model organism, but is also an extensively used microbe for industrial applications, especially for the production of small molecules of interest. It is an excellent representative of Gram-negative commensal bacteria. E. coli may represent a perfect model organism for systems biology that is aimed at elucidating both its free-living and commensal life-styles, which should open the door to whole-cell modeling and simulation.

• Korean Journal of Clinical Laboratory Science
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• v.43 no.3
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• pp.89-97
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• 2011

The Human Papilloma Virus (HPV) infection has been strongly associated with pathogenesis of uterine cervix carcinoma. HPV type 16, a causative agent of uterine cervix carcinoma, encodes the E6 and E7 oncogenes, expression of which is pivotal for malignant transformation and maintenance of malignant phenotypes. To develop a gene therapy for HPV-related carcinoma, We investigated the effect of E6 short-interfering RNA (E6 siRNA) on the expression of this oncogene and on the growth of HPV 16-related uterine cervix carcinoma cells. SiHa cells, a uterine cervix carcinoma cell line, which contain a single copy of HPV 16 integrated in the chromosome and express the E6 and E7 oncogenes. Before 24 hr of transfection, cells were seeded and transfected with control plasmid or E6 siRNA-expressing plasmid. The mRNA was analysed by reverse transcriptase polymerase chain reaction (RT-PCR). The cell growth rate was investigated by MTT method. The E6 mRNA level in SiHa cells was decreased in HPV 16 E6 siRNA-expression vector transfected cells and a decrease in the growth of these cells was also observed. From these results. it is evident that E6 siRNA played a role in suppression of growth of SiHa cells and has a fair chance as a candidate for gene specific therapy for HPV related uterine cervix carcinoma.

• Journal of Periodontal and Implant Science
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• v.28 no.2
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• pp.281-291
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• 1998

Chitosan is a biodegradable and non-toxic material with a molecular weight of 800-1,500Kd which can be obtained in various forms with extraordinary chemical structures and biological characteristics of which enables it to be used in many fields as a biomaterial. Ion irradiation is a useful tool to modify chemical structures and physical properties of high molecular weight polymers. The basic hypothesis of this study is that when surface properties of chitosan in a sponge form are modified with ion beam-irradiation and cell adhesion properties of chitosan would improve and thereby increase the regenerative ability of the damaged bone. The purpose of this study was to illuminate the changes in the cytocompatibility of chitosan sponges after ion beam-irradiation as a preliminary research. Argon($Ar^+$) ions were irradiated at doses of $5{\times}10^{13}$, $5{\times}10^{15}$ at 35 keV on surfaces of each sponges. Cell adhesion and activity of alkaline phosphatases were studied using rat fetal osteoblasts. The results of this study show hat ion beam-irradiation at optimal doses($5{\times}10^^{13}\;Ar^+\;ion/cm^2$) is a useful method to improve cytocompatibility without sacrificing cell viability and any changing cell phenotypes. These results show that ion beam-irradiated chitosan sponges can be further applied as carriers in tissue engineering and as bone filling materials.

• Molecules and Cells
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• v.45 no.9
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• pp.610-619
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• 2022

Cellular senescence plays a paradoxical role in tumorigenesis through the expression of diverse senescence-associated (SA) secretory phenotypes (SASPs). The heterogeneity of SA gene expression in cancer cells not only promotes cancer stemness but also protects these cells from chemotherapy. Despite the potential correlation between cancer and SA biomarkers, many transcriptional changes across distinct cell populations remain largely unknown. During the past decade, single-cell RNA sequencing (scRNA-seq) technologies have emerged as powerful experimental and analytical tools to dissect such diverse senescence-derived transcriptional changes. Here, we review the recent sequencing efforts that successfully characterized scRNA-seq data obtained from diverse cancer cells and elucidated the role of senescent cells in tumor malignancy. We further highlight the functional implications of SA genes expressed specifically in cancer and stromal cell populations in the tumor microenvironment. Translational research leveraging scRNA-seq profiling of SA genes will facilitate the identification of novel expression patterns underlying cancer susceptibility, providing new therapeutic opportunities in the era of precision medicine.

• Journal of Korean Foot and Ankle Society
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• v.27 no.3
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• pp.108-111
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• 2023

Anaplastic large cell lymphoma (ALCLs) are a group CD30-positive mature T-cell lymphomas, an uncommon subtype of non-Hodgkin lymphomas, characterized by diverse clinical and genetic features. Among the types of ALCL, anaplastic lymphoma kinase (ALK)-negative ALCL, though typically involves the lymph nodes, can infrequently invade other tissues. When soft tissue involvement occurs, it may mimic the clinical presentation of infectious diseases, leading to potential misdiagnosis. Therefore, a histological examination is necessary to differentiate between ALK-negative ALCL and similar phenotypes associated with infectious conditions. This paper reports a case of ALCL, initially misdiagnosed as an infection.

• Restorative Dentistry and Endodontics
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• v.48 no.2
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• pp.20.1-20.13
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• 2023

This mini-review was conducted to present an overview of the use of exosomes in regenerating the dentin-pulp complex (DPC). The PubMed and Scopus databases were searched for relevant articles published between January 1, 2013 and January 1, 2023. The findings of basic in vitro studies indicated that exosomes enhance the proliferation and migration of mesenchymal cells, as human dental pulp stem cells, via mitogen-activated protein kinases and Wingless-Int signaling pathways. In addition, they possess proangiogenic potential and contribute to neovascularization and capillary tube formation by promoting endothelial cell proliferation and migration of human umbilical vein endothelial cells. Likewise, they regulate the migration and differentiation of Schwann cells, facilitate the conversion of M1 pro-inflammatory macrophages to M2 anti-inflammatory phenotypes, and mediate immune suppression as they promote regulatory T cell conversion. Basic in vivo studies have indicated that exosomes triggered the regeneration of dentin-pulp-like tissue, and exosomes isolated under odontogenic circumstances are particularly strong inducers of tissue regeneration and stem cell differentiation. Exosomes are a promising regenerative tool for DPC in cases of small pulp exposure or for whole-pulp tissue regeneration.