• Animal cells and systems
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• v.4 no.2
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• pp.181-186
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• 2000

The expression of $p21^{WAF1/ClP1/SDl1}$, one of the cyclin-dependent kinase inhibitors, is regulated by a variety of transcription factors including p53 and STAT. Heat shock induces the expression of p21 in a temperature- and time-dependent manner. Although the p21 induction by heat shock has been reported to be controlled by p53, a p53-independent mechanism Is also involved. To understand the p53-independent regulation of heat shock-induced p21 expression, we searched the promoter region of p21 gene and found one or two heat shock element (HSE)-like sequences in human, rat, and mouse. Electromobility shift assay (EMSA) showed that heat shock factor (HSF) could bind to these HSE-like sequences In response to heat shock, even though to a lesser extent than to HSE. In addition, p21 promoter deletion analysis revealed that heat shock activated a p21 deletion promoter construct containing the HSE-like sequences but lacking p53-binding sites, but not a promoter construct containing neither HSE-like sequences nor the p53-responsive element. Furthermore, the p21 induction by heat shook was significantly inhibited in confluent cells in which heat shock-induced HSF activation was reduced. These results suggest that the transcriptional regulation of p21 by heat shock may be mediated through activation and binding to HSE-like sequences of HSF.

• Journal of Ginseng Research
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• v.41 no.2
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• pp.144-150
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• 2017

Background: The presence of gross deletions in the human immunodeficiency virus nef gene ($g{\Delta}nef$) is associated with long-term nonprogression of infected patients. Here, we investigated how quickly genetic defects in the nef gene are associated with Korean Red Ginseng (KRG) intakein 10 long-term slow progressors. Methods: This study was divided into three phases over a 20-yr period; baseline, KRG intake alone, and KRG plus highly active antiretroviral therapy (ART). nef gene amplicons were obtained using reverse transcription polymerase chain reaction (PCR) and nested PCR from 10 long-term slow progressors (n = 1,396), and nested PCR from 36 control patients (n = 198), and 28 ART patients (n = 157), and these were then sequenced. The proportion of $g{\Delta}nef$, premature stop codons, and not in-frame insertion or deletion of a nucleotide was compared between three phases, control, and ART patients. Results: The proportion of defective nef genes was significantly higher in on-KRG patients (15.6%) than in baseline (5.7%), control (5.6%), on-KRG plus ART phase (7.8%), and on-ART patients (6.6%; p < 0.01). Small in-frame deletions or insertions were significantly more frequent among patients treated with KRG alone compared with controls (p < 0.01). Significantly fewer instances of genetic defects were detected in samples taken during the KRG plus ART phase (7.8%; p < 0.01). The earliest defects detected were $g{\Delta}nef$ and small in-frame deletions after 7 mo and 67 mo of KRG intake, respectively. Conclusion: KRG treatment might induce genetic defects in the nef gene. This report provides new insight into the importance of genetic defects in the pathogenesis of AIDS.

• Korean Journal of Veterinary Research
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• v.41 no.2
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• pp.189-195
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• 2001

Single base substitution and deletion mutation have been introducted into the verotoxin 2 (VT2)A subunit gene from O157:H7 isolates to reduce cytotoxicity of VT2 and the cytotoxicity between wild type toxin and mutant toxoid were compared. A M13-derived recombinant plasmid pEP19RF containing a 940bp EcoRI-PstI fragment of VT2A gene was constructed for oligonucleotide-directed mutagenesis. The duoble mutant pDOEX was constructed by point and deletion mutation of two different highly conserved regions of VT2A encoding active site cleft of enzymatic domain. The key residue, Glu 167(GAA) and the pentamer(WGRIS) consisting of the enzymatic domain were replaced by ASP(GAC) and completely deleted in nucleotide sequence analysis of mutant, respectively. In the comparision of vero cell cytotoxicity between wide type toxin and toxoid from mutant, the wild type toxin expressed cytotoxicity in dilution of $10^{-6}$, but the toxid from mutant did not show cytotoxicity to vero cells.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.19 no.2
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• pp.365-371
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• 2015

CB tree represents the binary trie by a compact binary sequence. However, retrieval time grows fast since the more keys stored in the trie, longer the binary sequences are. In addition it is inefficient for frequent key insertion/deletion. HCB tree is a hierarchical CB tree consisting of small binary tries. However it can not avoid shift operations and have to scan an additional table to refer child or parent trie. In order to improve retrieval performance and avoid shift operations when keys are inserted or deleted, we in this paper represent each separated trie by a full binary trie and then assign the unique identifier to it. Finally the theoretical evaluations show that both the proposed approach and HCB tree provides better than CB tree for key retrieval. The proposed approach shows the highest performance in case of key insertion/deletion and moreover requires only 71%~89% of storage as compared with CB tree.

• Korean Journal of Microbiology
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• v.40 no.1
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• pp.7-11
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• 2004

eIF5B is a translation initiation factor that delivers Met-$tRNA^{Met}$ to AUG start codon and subsequently joins the small and large ribosomes. In order to study the function of eIF5B encoded by FUN12, we constructed FUN12 which lacked 5' end of its sequence. We found that this construct lacking almost all of its promoter in pRS plasmid partially complemented slow growth phenotype of fun12 deletion strain. Interestingly, this construct expressed N-terminally truncated eIF5B and its expression level was about 5% of that of wild type eIF5B. Low amount of the eIF5B expressed additionally in fun12 deletion strain played a direct role as a limiting factor for its growth. This limiting factor eIF5B in those strains also modulates activities of overall translation in vitro.

• Journal of Microbiology
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• v.37 no.4
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• pp.256-262
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• 1999

Latent membrane protein 1 (LMP1) of the Epstein-Barr virus (EBV) is an integral membrane protein with six transmembrane domains, which is essential for EBV-induced B cell transformation. LMP1 functions as a constitutively active tumor necrosis factor receptor (TNFR) like membrane receptor, whose signaling requires recruitment of TNFR-associated factors (TRAFs) and leads to NF-${\kappa}B$ activation. NF-${\kappa}B$ activation by LMP1 is critical for B cell transformation and has been linked to many phenotypic changes associated with EBV-induced B cell transformation. Deletion analysis has identified two NF-${\kappa}B$ activation regions in the carboxy terminal cytoplasmic domains of LMP1, termed CTAR1 (residues 194-232) and CTAR2 (351-386). The membrane proximal C-terminal domain was precisely mapped to a PXQXT motif (residues 204-208) involved in TRAF binding as well as NF-${\kappa}B$ activation. In this study, we dissected the CTAR2 region, which is the major NF-${\kappa}B$ signaling effector of LMP1, to determine a minimal functional sequence. A series of LMP1 mutant constructs systematically deleted for the CTAR2 region were prepared, and NF-${\kappa}B$ activation activity of these mutants were assessed by transiently expressing them in 293 cells and Jurkat T cells. The NF-${\kappa}B$ activation domain of CTAR2 appears to reside in a stretch of 6 amino acids (residues 379-384) at the end of the carboxy terminus.

• Korean Journal of Plant Tissue Culture
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• v.25 no.4
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• pp.237-243
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• 1998

To understand the tissue specific expression pattern of S RNase genes associated with self-incompatibility in L. peruvianum, two promoter regions of $S_{11}$ and $S_{12}$ RNase genes were compared. Homologous sequences between two S RNase gene promoters were found within 300 bp upstream of transcription start site. Moreover short direct repeat sequences within $S_{11}$ RNase gene promoter existed in the vicinity of 350-500 bp upstream of transcription start site. To identify whether the unique promoter sequences of $S_{11}$ RNase gene confer the tissue specific expression, six deletion fragments for $S_{11}$ genomic gene promoter constructed by PCR were fused to $\beta$-glucuronidase gene, and introduced into various tissues of L. peruvianum by microprojectile bombardment. Transient expression assays indicated that $S_{11}$ RNase gene promoter contained the positive and negative regulatory sequences, which can control the floral tissue-specific expression in L. peruvianum.

• Plant Breeding and Biotechnology
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• v.6 no.4
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• pp.413-425
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• 2018

A previous work developed and identified a new omega-5 gliadin deficient wheat line named O-free by crossing Keumkang and Olgeuru, which is nutritionally quite meaningful in that omega-5 gliadin is one of the known wheat allergens. To verify the characteristics of the O-free, we performed RNA sequencing (RNAseq) analysis of the O-free and the two parent lines (Keumkang and Olgeuru). The results of the similarity analysis with the ESTs for gliadins and glutenins showed that the O-free ESTs had no similarity with the omega-5 gliadin sequences but had similarity to other gliadins and glutenins. Furthermore, mapping results between the raw RNAseq data from the O-free and the omega-5 gliadin sequence showed a clear deletion of the N-terminal sequences which are an important signature of omega-5 gliadin. We also designed specific PCR primers that could identify omega-5 gliadin in the genomic DNA. The results showed that no omega-5 gliadin fragments were detected in the O-free. According to these results, we confirmed that the deficiency of omega-5 gliadin in the O-free is not caused by post-transcriptional or post-translational regulations such as epigenetic phenomena but by a simple deletion in the chromosome. Furthermore, we showed that the low-molecular weight glutenin subunit (LMW-GS) gene in the O-free had a single nucleotide polymorphism (SNP) causing a premature stop codon, resulting in a truncated polypeptide. We expect that the O-free line may serve as an excellent source of wheat that could prevail in the hypo-allergen wheat market, which has recently gained interest world-wide.

• BMB Reports
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• v.54 no.6
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• pp.317-322
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• 2021

CCCTC-binding factor (CTCF), a zinc finger protein, is a transcription factor and regulator of chromatin structure. Forebrain excitatory neuron-specific CTCF deficiency contributes to inflammation via enhanced transcription of inflammation-related genes in the cortex and hippocampus. However, little is known about the long-term effect of CTCF deficiency on postnatal neurons, astrocytes, or microglia in the hippocampus of adult mice. To address this, we knocked out the Ctcf gene in forebrain glutamatergic neurons (Ctcf cKO) by crossing Ctcf-floxed mice with Camk2a-Cre mice and examined the hippocampi of 7.5-10-month-old male mice using immunofluorescence microscopy. We found obvious neuronal cell death and reactive gliosis in the hippocampal cornu ammonis (CA)1 in 7.5-10-month-old cKO mice. Prominent rod-shaped microglia that participate in immune surveillance were observed in the stratum pyramidale and radiatum layer, indicating a potential increase in inflammatory mediators released by hippocampal neurons. Although neuronal loss was not observed in CA3, and dentate gyrus (DG) CTCF depletion induced a significant increase in the number of microglia in the stratum oriens of CA3 and reactive microgliosis and astrogliosis in the molecular layer and hilus of the DG in 7.5-10-month-old cKO mice. These results suggest that long-term Ctcf deletion from forebrain excitatory neurons may contribute to reactive gliosis induced by neuronal damage and consequent neuronal loss in the hippocampal CA1, DG, and CA3 in sequence over 7 months of age.

• Clinical and Experimental Reproductive Medicine
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• v.31 no.2
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• pp.105-110
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• 2004

Objectives: Despite severe oligospermia, males with Y chromosome microdeletion can achieve conception through ICSI (Intracytoplasmic Sperm Injection). However, ICSI may not only result in the transmission of microdeletions but also the expansion of deletion to the offspring. The purpose of this study was to screen vertical transmission, expansion of microdeletions and de novo deletion in male fetuses conceived by ICSI. Materials and Methods: A total of 32 ICSI treated patients with their 33 (a case of twin) male fetuses conceived by ICSI were used to make this study group. Sequence-tagged sites (STSs)-based PCR analyses were performed on genomic DNA isolated from peripheral blood of fathers and from the amniocytes of male fetuses. Ten primer pairs namely, sY134, sY138, MK5, sY152, sY147, sY254, sY255, SPGY1, sY269 and sY158 were used. The samples with deletions were verified at least three times. Results: We detected a frequency of 12.5% (4 of the 32 patients) of microdeletions in ICSI patients. In 4 patients with detected deletions, two patients have proven deletions on single STS marker and their male fetuses have the identical deletion in this region. Another two patients have two and three deletions, but their male fetuses have more than 3 deletions which include deletions to their father's. Meanwhile, seven male fetuses, whose fathers were analyzed to have all 10 STS markers present, have deletions present in at least one or more of the markers. Conclusions: Although the majority of deletions on the Y chromosome are believed to arise de novo, in some cases a deletion has been transmitted from the fertile father to the infertile patient. In other cases the deletion was transmitted through ICSI treatment, it is likely that one sperm cell is injected through the oocyte's cytoplasm and fertilization can be obtained from spermatozoa. Our tests for deletion were determined by PCR and our results show that the ICSI treatment may lead to vertical transmission, expansion and de novo Y chromosome microdeletions in male fetuses. Because the sample group was relatively small, one should be cautious in analyzing these data. However, it is important to counsel infertile couples contemplating ICSI if the male carries Y chromosomal microdeletions.