• Journal of Microbiology
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• v.45 no.1
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• pp.34-40
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• 2007

In budding yeast, G2/M transition is tightly correlated with bud morphogenesis regulated by Swel and septin that plays as a scaffold to recruits protein components. BNI5 isolated as a suppressor for septin defect is implicated in septin organization and cytokinesis. The mechanism by which Bni5 regulates normal septin function is not completely understood. Here, we show that Bni5 phosphorylation is required for mitotic entry regulated by Swel pathway. Bni5 modification was evident from late mitosis to G1 phase, and CIP treatment in vitro of affinity-purified Bni5 removed the modification, indicative of phosphorylation on Bni5. The phosphorylation-deficient mutant of BNI5 (bni5-4A) was defective in both growth at semi-restrictive temperature and suppression of septin defect. Loss of Bni5 phosphorylation resulted in abnormal bud morphology and cell cycle delay at G2 phase, as evidenced by the formation of elongated cells with multinuclei. However, deletion of Swel completely eliminated the elongated-bud phenotypes of both bni5 deletion and bni5-4A mutants. These results suggest that the bud morphogenesis and mitotic entry are positively regulated by phosphorylation-dependent function of Bni5 which is under the control of Swel morphogenesis pathway.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.41-41
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• 2003

Small conductance calcium-activated potassium channels (or SKCa channels) are potassium selective, voltage-independent, and activated by intracellular calcium concentration. These channels play important roles in excitable cells such as neuron in the central nervous system (Vergara et al., 1998). The activity of SKCa channels underlies the slow afterhyperpolarization that inhibits neuronal cell firing (Hille, 1991; Vergara et al.,1998). Until now, N-terminal region of rSK2 isn't characterized. To study the role of N-terminus, we constructed the N-terminal deletion mutant and characterized by electrophysiological means. Interestingly, N-terminal deletion mutant be trafficked to membrane couldn't evoke any ionic currents. Thus, N-terminal region has a role in functional rSK2 channel formation. To elucidate the function of N-terminal region, (His)6-conjugated protein was purified and filtrated by affinity column chromatography. Surprisingly, N-terminal region was shown in tetramer size that was supported by cross-linking result. Thus, we predicted that N-terminal region might be involved in the tetramerization of rSK2.

• Molecules and Cells
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• v.41 no.8
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• pp.753-761
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• 2018

Tumor necrosis factor receptor-associated factor 6 (TRAF6) is identified as a signaling adaptor protein that regulates bone metabolism, immunity, and the development of several tissues. Therefore, its functions are closely associated with multiple diseases. TRAF6 is also involved in the regulation of hematopoiesis under steady-state conditions, but the role of TRAF6 in modulating hematopoietic stem and progenitor cells (HSPCs) during the developmental stages remains unknown. Here, we report that the deletion of TRAF6 in hematopoietic lineage cells resulted in the upregulation of HSPCs in the fetal liver at the prenatal period. However, in the early postnatal period, deletion of TRAF6 drastically diminished HSPCs in the bone marrow (BM), with severe defects in BM development and extramedullary hematopoiesis in the spleen being identified. In the analysis of adult HSPCs in a BM reconstitution setting, TRAF6 played no significant role in HSPC homeostasis, albeit it affected the development of T cells. Taken together, our results suggest that the role of TRAF6 in regulating HSPCs is altered in a spatial and temporal manner during the developmental course of mice.

• Journal of Microbiology and Biotechnology
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• v.29 no.3
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• pp.401-409
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• 2019

Heat-resistant microbial hosts are required for bioprocess development using high cell density cultivations at the industrial scale. We report that the thermotolerance of Escherichia coli can be enhanced by overexpressing ybeD, which was known to encode a hypothetical protein of unknown function. In the wild-type E. coli BL21(DE3), ybeD transcription level increased over five-fold when temperature was increased from $37^{\circ}C$ to either $42^{\circ}C$ or $46^{\circ}C$. To study the function of ybeD, a deletion strain and an overexpression strain were constructed. At $46^{\circ}C$, in comparison to the wild type, the ybeD-deletion reduced cell growth half-fold, and the ybeD-overexpression promoted cell growth over two-fold. The growth enhancement by ybeD-overexpression was much more pronounced at $46^{\circ}C$ than $37^{\circ}C$. The ybeD-overexpression was also effective in other E. coli strains of MG1655, W3110, DH10B, and BW25113. These findings reveal that ybeD gene plays an important role in enduring high-temperature stress, and that ybeD-overexpression can be a prospective strategy to develop thermotolerant microbial hosts.

• Genomics & Informatics
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• v.17 no.4
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• pp.40.1-40.9
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• 2019

While studies aimed at detecting and analyzing indels or single nucleotide polymorphisms within human genomic sequences have been actively conducted, studies on detecting long insertions/deletions are not easy to orchestrate. For the last 10 years, the availability of long read data of human genomes from PacBio or Nanopore platforms has increased, which makes it easier to detect long insertions/deletions. However, because long read data have a critical disadvantage due to their relatively high cost, many next generation sequencing data are produced mainly by short read sequencing machines. Here, we constructed programs to detect so-called unmapped regions (UMRs, where no reads are mapped on the reference genome), scanned 40 Korean genomes to select UMR long deletion candidates, and compared the candidates with the long deletion break points within the genomes available from the 1000 Genomes Project (1KGP). An average of about 36,000 UMRs were found in the 40 Korean genomes tested, 284 UMRs were common across the 40 genomes, and a total of 37,943 UMRs were found. Compared with the 74,045 break points provided by the 1KGP, 30,698 UMRs overlapped. As the number of compared samples increased from 1 to 40, the number of UMRs that overlapped with the break points also increased. This eventually reached a peak of 80.9% of the total UMRs found in this study. As the total number of overlapped UMRs could probably grow to encompass 74,045 break points with the inclusion of more Korean genomes, this approach could be practically useful for studies on long deletions utilizing short read data.

• The Korean Journal of Cytopathology
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• v.12 no.2
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• pp.73-80
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• 2001

The prevalence of Epstein-Barr virus(EBV) in the uterine cervix was investigated to define the possible etiologic role in cervical carcinogenesis. The viral genotyping and LMP-1 30bp deletion were also stooled. The materials included 169 uterine cervical swabs(152 within normal limits, 12 atypical squamous cells of uncertain significance, 3 low grade intraepithelial lesions, and 2 high grade squamous intraepithelial lesion) and 104 uterine cervical tissues obtained from hysterectomy specimens(32 carcinoma in situ, 9 microinvasive squamous cell carcinomas, 37 invasive squamous cell carcinomas, 7 adenocarcinomas, 7 adenosquamous carcinomas, and 12 cervicitis). EBV detected by PCR for EBNA-1 was positive in 52(56.5%) of 92 invasive and noninvasive cervical carcinomas, and 80(48.8%) of 164 inflammatory or normal cervices. The viruses detected in carcinomas were all type A, and LMP-1 30bp deletion form was more frequent in premalignant and malignant cervical lesions than in nonneoplastic cervices. From the above results, it may be concluded that EBV is one of common viruses detected in uterine cervix of Korean women, and type A virus and LMP-1 30bp deletion form may have a role in cervical carcinogenesis.

• Journal of Plant Biotechnology
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• v.4 no.4
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• pp.143-150
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• 2002

A strong oxidative stress-inducible peroxidase promoter (referred to as SWPA2 promoter) was cloned from tell cultures of sweetpotato (Ipomoea batatas) and characterized in transgenic tobacco cultured cells in terms of biotechnological applications. Employing a transient expression assay in tobacco protoplasts, with five different 5'-deletion mutants of the SWPA2 promoter fused to the $\beta$-glucuronidase (GUS) reporter gene, the 1314 bp deletion mutant showed approximately 30 times higher GUS expression than the CaMV 35S promoter. The expression of GUS activity in suspension cultures of transgenic cells derived from transgenic tobacco leaves containing the -1314 bp SWPA2 promoter-GUS fusion was strongly expressed following 15 days of subculture compared to other deletion mutants, suggesting that the 1314 bp SWPA2 promoter will be biotechnologically useful for the development of transgenic cell lines engineered to produce key pharmaceutical proteins. In this respect, we developed transgenic cell lines such as tobacco (Nicotiana tabacum L. BY-2), ginseng (Panax ginseng) and Siberian ginseng (Acanthopanax senticosus) using a SWPA2 promoter to produce a human lactoferrin (hLf) and characterized the hLf production in cultured cells. The hLf production monitored by ELISA analysis in transgenic BY-2 cells was directly increased proportional to cell growth and reached a maximal level (up to 4.3% of total soluble protein) at the stationary phase in suspension cultures. The SWPA2 promoter should result in higher productivity and increased applications of plant cultured cells for the production of high-value recombinant proteins.

• Journal of Korean Society of Transportation
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• v.34 no.6
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• pp.570-579
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• 2016

This study proposes a concept of Stepwise Transfer Coefficient(STC) which implies greater transfer cost with increasing the number of transfers. Thus, the public transport information system provides the choice sets of travel routes by the consideration of not only transportation time but also the optimum number of transfers. However, path choice problems that involve STC are found to include non additive cost, which requires additional route enumeration works. Discussions on route enumeration in actual transportation networks is very complicated, thereby warranting a theoretical examination of route search considering STC. From these points of view, this study results in a probability based transit trip assignment model including STC. This research also uses incoming link based entire route deletion method. The entire route deletion method proposed herein simplifies construction of an aggregation of possible routes by theoretically supporting the process of enumeration of the different routes from origin to destination. Conclusively, the STC reflected route based logit model is proposed as a public transportation transit trip assignment model.

• Journal of Internet Computing and Services
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• v.18 no.1
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• pp.27-35
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• 2017

In near future, IoT data is expected to be a major portion of Big Data. Moreover, sensor data is expected to be major portion of IoT data, and its' research is actively carried out currently. However, processed results may not be trusted and used if outlier data is included in the processing of sensor data. Therefore, method for detection and deletion of those outlier data before processing is studied in this paper. Moreover, we used Spark which is memory based distributed processing environment for fast processing of big sensor data. The detection and deletion of outlier data consist of four stages, and each stage is implemented with Mapper and Reducer operation. The proposed method is compared in three different processing environments, and it is expected that the outlier detection and deletion performance is best in the distributed Spark environment as data volume is increasing.

• The Plant Pathology Journal
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• v.32 no.4
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• pp.281-289
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• 2016

The transcription cofactor Swi6 plays important roles in regulating vegetative growth and meiosis in Saccharomyces cerevisiae. Functions of Swi6 ortholog were also characterized in Fusarium graminearum which is one of the devastating plant pathogenic fungi. Here, we report possible role of FgSwi6 in the interaction between F. graminearum and Fusarium graminearum virus 1 (FgV1) strain DK21. FgV1 perturbs biological characteristics of host fungi such as vegetative growth, sporulation, pigmentation, and reduction of the virulence (hypovirulence) of its fungal host. To characterize function(s) of FgSWI6 gene during FgV1 infection, targeted deletion, over-expression, and complementation mutants were generated and further infected successfully with FgV1. Deletion of FgSwi6 led to severe reduction of vegetative growth even aerial mycelia while over-expression did not affect any remarkable alteration of phenotype in virus-free isolates. Virus-infected (VI) FgSWI6 deletion isolate exhibited completely delayed vegetative growth. However, VI FgSWI6 over-expression mutant grew faster than any other VI isolates. To verify whether these different growth patterns in VI isolates, viral RNA quantification was carried out using qRT-PCR. Surprisingly, viral RNA accumulations in VI isolates were similar regardless of introduced mutations. These results provide evidence that FgSWI6 might play important role(s) in FgV1 induced phenotype alteration such as delayed vegetative growth.