• Journal of Computing Science and Engineering
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• v.4 no.4
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• pp.291-312
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• 2010

The last decades a large amount of research has been done in the genomics domain which has and is generating terabytes, if not exabytes, of information stored globally in a very fragmented way. Different databases use different ways of storing the same data, resulting in undesired redundancy and restrained information transfer. Adding to this, keeping the existing databases consistent and data integrity maintained is mainly left to human intervention which in turn is very costly, both in time and money as well as error prone. Identifying a fixed conceptual dictionary in the form of a conceptual model thus seems crucial. This paper presents an effort to integrate the mutational data from the established genomic data source HGMD into a conceptual model driven database HGDB, thereby providing useful lessons to improve the already existing conceptual model of the human genome.

• Journal of Life Science
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• v.21 no.8
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• pp.1067-1075
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• 2011

Coiled-coil domain-containing protein 98 (CCDC98) plays a role in G2/M DNA damage checkpoint pathways by recruiting breast cancer 1 (BRCA1)-A complex to the DNA-damaged sites. However, the molecular mechanism of CCDC98 on the DNA damage-induced G2/M checkpoint pathways is unclear. In this study, we identifed Wilms tumor 1-associating protein (WTAP) as a novel CCDC98-binding protein, using tandem affinity purification. We confirmed the association between CCDC98 and WTAP using in vivo and in vitro binding assays. We demonstrated that CCDC98 regulates cyclin B1 expression by affecting WTAP protein stability. Based on these results, we suggest that CCDC98 may act as a novel cell cycle regulator by regulating the expression level of cyclin B1.

• Molecules and Cells
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• v.44 no.2
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• pp.101-115
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• 2021

The INO80 chromatin remodeling complex has roles in many essential cellular processes, including DNA replication. However, the mechanisms that regulate INO80 in these processes remain largely unknown. We previously reported that the stability of Ino80, the catalytic ATPase subunit of INO80, is regulated by the ubiquitin proteasome system and that BRCA1-associated protein-1 (BAP1), a nuclear deubiquitinase with tumor suppressor activity, stabilizes Ino80 via deubiquitination and promotes replication fork progression. However, the E3 ubiquitin ligase that targets Ino80 for proteasomal degradation was unknown. Here, we identified the C-terminus of Hsp70-interacting protein (CHIP), the E3 ubiquitin ligase that functions in cooperation with Hsp70, as an Ino80-interacting protein. CHIP polyubiquitinates Ino80 in a manner dependent on Hsp70. Contrary to our expectation that CHIP degrades Ino80, CHIP instead stabilizes Ino80 by extending its half-life. The data suggest that CHIP stabilizes Ino80 by inhibiting degradative ubiquitination. We also show that CHIP works together with BAP1 to enhance the stabilization of Ino80, leading to its chromatin binding. Interestingly, both depletion and overexpression of CHIP compromise replication fork progression with little effect on fork stalling, as similarly observed for BAP1 and Ino80, indicating that an optimal cellular level of Ino80 is important for replication fork speed but not for replication stress suppression. This work therefore idenitifes CHIP as an E3 ubiquitin ligase that stabilizes Ino80 via nondegradative ubiquitination and suggests that CHIP and BAP1 act in concert to regulate Ino80 ubiquitination to fine-tune its stability for efficient DNA replication.

• Journal of Gynecologic Oncology
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• v.29 no.6
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• pp.93.1-93.11
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• 2018

The introduction of checkpoint inhibitors revolutionized immuno-oncology. The efficacy of traditional immunotherapeutics, like vaccines and immunostimulants was very limited due to persistent immune-escape strategies of cancer cells. Checkpoint inhibitors target these escape mechanisms and re-direct the immune system to anti-tumor toxicity. Phenomenal results have been reported in entities like melanoma, where no other therapy was able to demonstrate survival benefit, before the introduction of immunotherapeutics. The first experience in ovarian cancer (OC) was reported for nivolumab, a fully human anti-programmed cell death protein 1 (PD1) antibody, in 2015. While the data are extraordinary for a mono-immunotherapeutic agent and very promising, they do not match up to the revolutionary results in entities like melanoma. The key to exceptional treatment response in OC, could be the identification of the most immunogenic patients. We hypothyse that BRCA mutation could be a predictor of improved response in OC. The underlying DNA-repair-deficiancy should result in increased immunogenicity because of higher mutational load and more neoantigen presentation. This hypothesis was not tested to date and should be subject to future trials. The present article gives an overview of the immunologic background of checkpoint inhibition (CI). It presents current data on nivolumab and other checkpoint-inhibitors in solid tumors and OC specifically and depicts important topics in the management of this novel substance group, such as side effect control, diagnostic PD-1/programmed cell death-ligand 1 (PD-L1) expression assessment and management of pseudoprogression.

• Journal of Microbiology and Biotechnology
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• v.12 no.4
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• pp.649-656
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• 2002

Fibrinolytic microorganisms were screened from 42 samples of Korean fermented food (7 kinds of Chungook-jang, 14 kinds of commercial Doen-Jang, 5 kinds of home-made Doen-jang, and 16 kinds of Jeot-gal), 15 samples of Japanese fermented food (5 kinds of home-made soybean paste, and 10 kinds of Natto), and 19 samples of Indonesian fermented food (Tempe) as well as starters of Meju (500 microflora from Korea, and 22 from China). Initially, 11 isolates with strong fibrinolytic activity were selected for further characterization. The fibrinolytic activity of the 11 isolates ranged from 89 to 199% of standard plasmin. Four strains, M5l from Korean fermented food (Meju), I 1-1, I 1-4, and I 5-1 from Indonesian fermented food (Tempe), were chosen based on the degree of activity and reproducibility, and identified as Staphylococcus sciuri, Citrobacter or Enterobacter, Enterococcus faecalis, and Bacillus subtilis, respectively. The first two isolates are pathogenic stains while the latter two are considered as GRAS (Generally Recognized As Safe). Fibrinolytic activity of E. faecalis, characterized and designated as BRCA-5, reached a maximum, when the producer was cultivated in Ml7 broth supplemented with 1.0% glucose for 5 h at 37$^{\circ}C$ with shaking at 180 rpm. Compared to commercial fibrinolytic enzymes, the cell-free culture supernatant of 5. faecaiis BRCA-5 showed stronger activity than plasmin and streptokinase, but similar degree of specific activity as nattokinase and urokinase, aud it also demonstrated anticoagulant and antiplatelet activity ex vivo. These features of E. faecalis make it an attractive agent as a biomaterial for health-promoting foods.

• Nutrition Research and Practice
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• v.3 no.3
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• pp.185-191
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• 2009

The elevated level of circulating estradiol increases the risk of breast tumor development. To gain further insight into mechanisms involved in their actions, we investigated the molecular mechanisms of 4-hydroxyestradiol (4-$OHE_2$) to initiate and/or promote abnormal cell growth, and of $\alpha$- or $\gamma$-tocopherol to inhibit this process. MCF-10A, human breast epithelial cells were incubated with $0.1{\mu}M$ 4-$OHE_2$, either with or without $30{\mu}M$ tocopherols for 96 h. 4-$OHE_2$ caused the accumulation of intracellular ROS, while cellular GSH/GSSG ratio and MnSOD protein levels were decreased, indicating that there was an oxidative burden. 4-$OHE_2$ treatment also changed the levels of DNA repair proteins, BRCA1 and PARP-1. $\gamma$-Tocopherol suppressed the 4-$OHE_2$-induced increases in ROS, GSH/GSSG ratio, and MnSOD protein expression, while $\alpha$-tocopherol up-regulated BRCA1 and PARP-1 protein expression. In conclusion, 4-$OHE_2$ increases oxidative stress reducing the level of proteins related to DNA repair. Tocopherols suppressed oxidative stress by scavenging ROS or up-regulating DNA repair elements.

• Women's Health Nursing
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• v.26 no.4
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• pp.285-299
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• 2020

Purpose: This systematic review aims to identify factors associated with risk-reducing salpingo-oophorectomy (RRSO), including the uptake rate and decision timing, among women at high risk for hereditary breast and ovarian cancer (HBOC). Methods: We found 4,935 relevant studies using MEDLINE, Embase, CINAHL, and PsycINFO on July 6, 2020. Two authors screened the articles and extracted data. Twenty-four studies met the inclusion criteria. Quality assessment of articles was conducted using the Risk of Bias for Nonrandomized Studies tool. Results: Five types of factors were identified (demographic factors, clinical factors, family history of cancer, psychological factors, and objective cancer risk). The specific significant factors were older age, having child(ren), being a BRCA1/2 carrier, mastectomy history, perceived risk for ovarian cancer, and perceived advantages of RRSO, whereas objective cancer risk was not significant. The uptake rate of RRSO was 23.4% to 87.2% (mean, 45.2%) among high-risk women for HBOC. The mean time to decide whether to undergo RRSO after BRCA testing was 4 to 34 months. Conclusion: RRSO decisions are affected by demographic, clinical, and psychological factors, rather than objective cancer risk. Nonetheless, women seeking RRSO should be offered information about objective cancer risk. Even though decision-making for RRSO is a complex and multifaceted process, the psychosocial factors that may influence decisions have not been comprehensively examined, including family attitudes toward RRSO, cultural norms, social values, and health care providers' attitudes.

• 한국생물공학회:학술대회논문집
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• 2005.04a
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• pp.17-17
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• 2005

In this presentation, we will discuss several recent achievements developed in my laboratory for microarray-based diagnosis of human genetic mutations including HNF-1 and BRCA1 mutations. To determine the presence of the genetic mutations in a human sample, we prepared allele-specific oligonucleotide chips from selected mutation sites and generated target probes using a tow-step method for Cy-3 DNA $samples^{1)}$ or in vitro transcription of promoter-tagged PCR products for Cy-3 RNA $samples^{2)}$. Hybridization of the target probes to the chips successfully identified all of the genotypes for the tested sites. For more reliable diagnosis, we also employed single base extension (SBE) reaction and zip-code microarray technique for our strategy. Particularly we developed an efficient PNA zip-code microarray for the detection of $HNF-1{\alpha}$ $mutations^{3)}$. Using multiplex SBE reactions and zip-code strategy, we were able to correctly diagnose several mutation sites in exon 2 of $HNF-1{\alpha}$ with a wild-type and mutant including a MODY3 patient. These works represent successful applications of DNA microarray technology for the diagnosis of human genetic mutations.

• Journal of Korean Neurosurgical Society
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• v.59 no.6
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• pp.650-654
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• 2016

Intrathoracic meningoceles are relatively rare entities found in patients with neurofibromatosis type I (NF1). Given that both the BRCA1 and NF-1 genes are located on the same long arm of chromosome 17, one would expect concurrence of neurofibromatosis and breast cancer. However, incidence of such co-disorders is very rare in the literature. Here, the authors report a case of a 50-year-old female patient with NF-1 and concurrent cancer of the left breast, who had a huge bilobulated intrathoracic meningocele with thoracic dystrophic scoliosis, treated surgically via a posterior-only approach for the meningocele and spinal deformity in the same setting.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.1
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• pp.22-26
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• 2016

FANCJ is a DNA helicase which contributes genome stability by resolving G-quadruplex DNA from 5' to 3' direction. In addition to main ATPase helicase core, FANCJ has the protein binding region at its C-terminal part. BRCA1 and BLM are the binding partner of FANCJ and these protein-protein interactions contribute genomic stability and the proper response to replication stress. As the first attempt for studying FANCJ-BLM interaction, we prepared BLM binding region of FANCJ and characterized with CD and NMR spectroscopy. FANCJ (881-941) with N-ter 6xHis was purified as the oligomer. Secondary structure prediction based on CD data revealed that FANCJ (881-941) composed with ${\beta}$ sheet, turn and coils.$^1H-^{15}N$ HSQC spectra showed nonhomogeneous peak intensities with less number of peaks comparing than the number of amino acids in the construct. It indicated that optimization should be necessary for detailed further structural studies.