• Journal of Life Science
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• v.12 no.2
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• pp.219-225
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• 2002

The organization of eukayotic chromatin into specific conformation that are associated with transcription, replication, reapir and other nuclear processes are achieved via a series of DNA-protein interaction. These interactions are mediated by a range of DNA-binding domains such as SAP domain et at. By searching S. pombe genomic DNA database, we have found a gene named SAPuvs (SAP UV Sensitive) whose amino acid sequence is in part similar to SAP domain of Arabidopsis poly (ADP-ribose) polymerase and Ku7O. Knock-out cell of S. pombe SAPuvs gene was constructed using Ura4 as a selection marker. Survival analysis of knock-out cell indicated that treatment with UV significantly reduces the survival compared to wild type cell. Potentiation of MMS-induced cytotoxicity by 3AB post-treatment was observed in wild type cells, but not in knock-out cells. These data suggested that the protein encoded by SAPuvs gene is associated with chromatin reorganization during DNA repair.

• Journal of Microbiology
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• v.41 no.1
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• pp.28-33
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• 2003

Pycnogenol (PYC) is believed to have potential as a therapeutic agent against free radical-mediated oxidative stress. It is important, therefore, to understand the interactions between PYC and cellular defenses against oxidative stress. Toward this end, we analyzed the survival rates on the gene expression responses of E. coli sod katG mutants to PYC after pre-treatment of PQ or H$_2$O$_2$-mediated stress under aerobic conditions. We identified SOD induced by PYC, but not HP1 in sod hate mutants. A striking result was the PYC induction of SOD with antioxidant property in single katG mutant cells, particularly MnSOD and CuZnSOD. These inductions were further increased with oxidative stress, while HP1 was not induced in these conditions. The effects of pycnogenol treatment on these cells depend in part on its concentration on the stress response. Protective effects of PYC exposure which affected gene expression in cells were consistent with cell survival rates. Our results demonstrate that pycnogenol may alter the stress response gene expression in a specific manner such as SOXRS because PYC induction of single mutant only worked under increased PQ stress. All together our data indicate that SOD activity is essential for the cellular defense against PQ-mediated oxidative stress, suggesting that PYC may not be effective as an antioxidant in only oxidative stress conditions. On the other hand, it was expected that PYC may play a role as a pro-oxidant and if it is available for use, it should be evaluated carefully.

• The Journal of the Korean bone and joint tumor society
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• v.3 no.1
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• pp.9-17
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• 1997

Resistance to combination chemotherapy remains challenge in the treatment of osteosarcoma. One of the mechanisms of multiple drug resistance is an increased expression of the multidrug resistance gene(mdr1). Expression of the P-glycoprotein(mdr-1 gene product) was studied immunohistochemically and the mdr-1 gene by in situ hybridization in 33 osteosarcomas relating to various prognostic factors. Thirty cases out of 33 osteosarcomas(90.9%) showed positive cytoplasmic reactions with P-glycoprotein and nineteen instances(57.6%) were strong positive(2+). The older(>20 years) and female patients revealed more intense immunohistochemical reactions rather than those of the younger and male patients. Osteoblastic and chondroblastic osteosarcomas revealed more strong immunohistochemical reactions compared to fibroblastic types. There were no significant staining differences between the type of bony involvement, Broder's grade and the presence of necrosis. On follow-up, the mean survival rate was decreased in the strong positive group, however, this was not statistically significant. In situ hybridization for mdr-1 gene revealed positive signals in 22 cases out of 29 osteosarcomas(75.9%). Chemotherapy was done in 15 cases out of 28 patients(53.6%). The results of immunohistochemistry and in situ hybridization were not correlated with the protocols for chemotherapy. However, this result should be confirmed by a larger scale study about mdr1 mRNA expression.

• Nuclear Engineering and Technology
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• v.54 no.4
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• pp.1439-1448
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• 2022

Background: We investigated the feasibility of in vitro radiosensitivity prediction with gene expression using deep learning. Methods: A microarray gene expression of the National Cancer Institute-60 (NCI-60) panel was acquired from the Gene Expression Omnibus. The clonogenic surviving fractions at an absorbed dose of 2 Gy (SF2) from previous publications were used to measure in vitro radiosensitivity. The radiosensitivity prediction model was based on the convolutional neural network. The 6-fold cross-validation (CV) was applied to train and validate the model. Then, the leave-one-out cross-validation (LOOCV) was applied by using the large-errored samples as a validation set, to determine whether the error was from the high bias of the folded CV. The criteria for correct prediction were defined as an absolute error<0.01 or a relative error<10%. Results: Of the 174 triplicated samples of NCI-60, 171 samples were correctly predicted with the folded CV. Through an additional LOOCV, one more sample was correctly predicted, representing a prediction accuracy of 98.85% (172 out of 174 samples). The average relative error and absolute errors of 172 correctly predicted samples were 1.351±1.875% and 0.00596±0.00638, respectively. Conclusion: We demonstrated the feasibility of a deep learning-based in vitro radiosensitivity prediction using gene expression.

• Journal of the Korean Data and Information Science Society
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• v.25 no.5
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• pp.1057-1067
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• 2014

Many genetic variants have been identified to be associated with complex diseases such as hypertension, diabetes and cancers throughout genome-wide association studies (GWAS). However, there still exist a serious missing heritability problem since the proportion explained by genetic variants from GWAS is very weak less than 10~15%. Gene-gene interaction study may be helpful to explain the missing heritability because most of complex disease mechanisms are involved with more than one single SNP, which include multiple SNPs or gene-gene interactions. This paper focuses on gene-gene interactions with the survival phenotype by extending the multifactor dimensionality reduction (MDR) method to the accelerated failure time (AFT) model. The standardized residual from AFT model is used as a residual score for classifying multiple geno-types into high and low risk groups and algorithm of MDR is implemented. We call this method AFT-MDR and compares the power of AFT-MDR with those of Surv-MDR and Cox-MDR in simulation studies. Also a real data for leukemia Korean patients is analyzed. It was found that the power of AFT-MDR is greater than that of Surv-MDR and is comparable with that of Cox-MDR, but is very sensitive to the censoring fraction.

• Journal of Microbiology and Biotechnology
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• v.28 no.10
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• pp.1736-1748
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• 2018

Brucella abortus can survive and replicate within host macrophages, and great efforts have been made to demonstrate the genes involved in pathogenicity, such as internalization, in Brucella research. Here, intracellular responses were compared between THP-1 macrophage cells stimulated with B. abortus wild-type and four mutants (C1, C10, C27, and C32) using microarray to demonstrate the role of genes related to intracellular survival and replication. These mutants were generated by deleting genes encoding BAB_RS13225 (4-hydrobenzoate 3-monooxygenase, PHBH), BAB_RS00455 (heme exporter protein cytochrome C, CcmC), BAB_RS03675 (exopolyphosphatase, PPX), and BAB_RS13225 (peptidase M24). The results showed that mutants C1 and C10 induced significant suppression of survival levels and cytokine expression relative to wild-type in the THP-1 macrophage cells. These findings suggest that the BAB_RS13225 and BAB_RS00455 genes play important roles in survival within human macrophages. Conversely, mutants C27 and C32 induced significantly higher survival level than wild-type in the cells inhibiting cellular signal transduction. It is assumed that the BAB_RS03675 and BAB_RS13225 genes play a role in cellular resistance to B. abortus. Therefore, the disrupted genes are involved in B. abortus intracellular growth, and especially in its survival, and they could be effective targets for understanding the intracellular bacterium, B. abortus.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.2
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• pp.569-573
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• 2012

Early diagnosis and better prognosis of ovarian cancer is still a challenge. Besides environmental risk factors, genetic factors have established a role in pathogenesis of ovarian cancer. Methods: A case-control and a prospective study design conducted in 224 ovarian cancer patients and 432 controls in Chinese population. MTHFR C677T genotyping was done by PCR-RFLP. Results: Patients with ovarian cancer is associated with a higher less number of delivery and less frequent oral contraceptive use. When potential confounding factors adjusted logistic regression analysis between cases and controls were performed, significant association was obtained for 677T/T genotype and ovarian cancer (OR=3.13, 95% CI=1.59-5.72). Cox regression survival analysis showed individuals carrying T/T genotype had significantly increased HR for death in ovarian cancer patients (HR=2.86, 95% CI=1.27-7.93). In conclusion, we observed that the MTHFR C677T polymorphism is associated with the susceptibility and survival of ovarian cancer in Chinese population.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.19
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• pp.8469-8474
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• 2014

Introduction: Recent studies have indicated that down-regulation of the suppressor of cytokine signaling-1 (SOCS-1) gene results in tumor formation and that SOCS-1 acts as a tumor suppressor gene. SOCS-1 has been also suggested to function as a tumor suppressor with colorectal cancer. Objectives: In the present study, we aimed to determine the association of SOCS-1 expression in colorectal cancer tissues with clinicopathologic characteristics immunohistochemically and also to identify its prognostic significance. Materials and Methods: SOCS-1 expression was studied immunohistochemically in 67 patients diagnosed with resected colorectal carcinomas and 30 control subjects. Results: SOCS-1 expression was found in 46.3% of tumor tissues and 46.7% of the control group. Statistical analyses did not establish any significant association between SOCS-1 expression and clinicopathologic characteristics. Also, no significant association with SOCS-1 expression was found using progression-free survival and overall survival analyses (p=0.326 and p=0.360, respectively). Conclusions: Our results show that SOCS-1 has no prognostic significance in colorectal cancer.

• Journal of Microbiology and Biotechnology
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• v.22 no.8
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• pp.1066-1076
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• 2012

Previous observations demonstrated that various immunosuppressive agents and their combination therapies can increase allograft survival rates. However, these treatments may have serious side effects and cannot substantially improve or prolong graft survival in acute graft-versus-host disease (GVHD). To improve the therapeutic potency of divalent immunoadhesins, we have constructed and produced several tetravalent forms of immunoadhesins comprising each of cytotoxic T-lymphocyte-associated antigen-4 (CTLA4), CD2, and lymphocyte activation gene-3 (LAG3). Flow cytometric and T cell proliferation analyses displayed that tetravalent immunoadhesins have a higher binding affinity and more potent efficacy than divalent immunoadhesins. Although all tetravalent immunoadhesins possess better efficacies, tetravalent forms of CTLA4-Ig and LAG3-Ig revealed higher inhibitory effects on T cell proliferation than tetravalent forms of TNFR2-Ig and CD2-Ig. In vitro mixed lymphocytes reaction (MLR) showed that combined treatment with tetravalent CTLA4-Ig and tetravalent LAG3-Ig was highly effective for inhibiting T cell proliferation in both human and murine allogeneic stimulation. In addition, both single tetravalent-form and combination treatments can prevent the lethality of murine acute GVHD. The results of this study demonstrated that co-blockade of the major histocompatibility complex class (MHC)II:T cell receptor (TCR) and CD28:B7 pathways by using tetravalent human LAG3-Ig and CTLA4-Ig synergistically prevented murine acute GVHD.

• The Korean Journal of Physiology and Pharmacology
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• v.18 no.1
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• pp.73-78
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• 2014

Cell death and survival are tightly controlled through the highly coordinated activation/inhibition of diverse signal transduction pathways to insure normal development and physiology. Imbalance between cell death and survival often leads to autoimmune diseases and cancer. Death receptors sense extracellular signals to induce caspase-mediated apoptosis. Acting upstream of CED-3 family proteases, such as caspase-3, Bcl-2 prevents apoptosis. Using short hairpin RNAs (shRNAs), we suppressed Bcl-2 expression in Jurkat T cells, and this increased TCR-triggered AICD and enhanced TNFR gene expression. Also, knockdown of Bcl-2 in Jurkat T cells suppressed the gene expression of FLIP, TNF receptor-associated factors 3 (TRAF3) and TRAF4. Furthermore, suppressed Bcl-2 expression increased caspase-3 and diminished nuclear factor kappa B (NF-${\kappa}B$) translocation.