• The Korean Journal of Physiology and Pharmacology
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• v.13 no.5
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• pp.343-348
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• 2009

53BP1 is an important genome stability regulator, which protects cells against double-strand breaks. Following DNA damage, 53BP1 is rapidly recruited to sites of DNA breakage, along with other DNA damage response proteins, including ${\gamma}$-H2AX, MDC1, and BRCA1. The recruitment of 53BP1 requires a tandem Tudor fold which associates with methylated histones H3 and H4. It has already been determined that the majority of DNA damage response proteins are phosphorylated by ATM and/or ATR after DNA damage, and then recruited to the break sites. 53BP1 is also phosphorylated at several sites, like other proteins after DNA damage, but this phosphorylation is not critically relevant to recruitment or repair processes. In this study, we evaluated the functions of phosphor-53BP1 and the role of the BRCT domain of 53BP1 in DNA repair. From our data, we were able to detect differences in the phosphorylation patterns in Ser25 and Ser1778 of 53BP1 after neocarzinostatin-induced DNA damage. Furthermore, the foci formation patterns in both phosphorylation sites of 53BP1 also evidenced sizeable differences following DNA damage. From our results, we concluded that each phosphoryaltion site of 53BP1 performs different roles, and Ser1778 is more important than Ser25 in the process of DNA repair.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.6
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• pp.2917-2922
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• 2014

Background: The p53-binding protein 1 (TP53BP1) gene may be involved in the development of cancer through disrupting DNA repair. However, investigation of associations between TP53BP1 rs2602141 A/C polymorphism and cancer have yielded contradictory and inconclusive outcomes. We therefore performed a meta-analysis to evaluate the association between the TP53BP1 rs2602141 A/C polymorphism and cancer susceptibility. Materials and Methods: Published literature from PubMed, Medline, the Cochrane Library, EMbase, Web of Science, Google (scholar), CBMDisc, Chongqing VIP database, and CNKI database were retrieved. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using fixed or random-effects models. Publication bias was estimated using funnel plots, Begg's and Egger's test. Results: A total of seven studies (3,018 cases and 5,548 controls) were included in the meta-analysis. Our results showed that the genotype distribution of TP53BP1 rs2602141 A/C was not associated with cancer risk overall. However, on subgroup analysis, we found that TP53BP1 rs2602141 A/C was associated with cancer risk within an allele model (A vs C, OR=1.14, 95%CI: 1.01-1.29) and a codominant model (AA vs CC, OR=1.36, 95%CI: 1.06-1.74) in Asians rather than in Caucasians. Subgroup analysis by cancer type, genotype, and with or without adjustment for controls showed no significant association. Conclusions: The findings suggested an association between rs2602141 A/C polymorphism in TP53BP1 gene and increased risk of cancer in Asians.

• Korean Journal of Plant Taxonomy
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• v.53 no.1
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• pp.47-53
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• 2023

We have determined the complete chloroplast genome of Erigeron Canadensis isolated in Korea. The circular chloroplast genome of E. canadensis is 152,767 bp long and has four subregions: 84,317 bp of large single-copy and 18,446 bp of small single-copy regions are separated by 25,004 bp of inverted repeat regions including 133 genes (88 protein-coding genes, eight rRNAs, and 37 tRNAs). The chloroplast genome isolated in Korea differs from the Chinese isolate by 103 single-nucleotide polymorphisms (SNPs) and 47 insertions and deletion (INDEL) regions, suggesting different invasion sources of E. canadensis in Korea and China. A nucleotide diversity analysis revealed that the trend of the nucleotide diversity of E. canadensis followed that of 11 Erigeron chloroplasts, except for three peaks. The phylogenetic tree showed that our E. canadensis chloroplast is clustered with E. canadensis reported from China. Erigeron canadensis can be a good target when attempting to understand genetic diversity of invasive species.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.6
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• pp.2631-2634
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• 2014

Background: p53 gene is a well-known tumor suppressor gene that has several polymorphisms in both its exons and introns. It has been suggested that intron 3 16 bp duplication polymorphism may affect the gene function resulting in reduction or suppression of p53 anti tumor activity. In most case control studies a duplicated allele has been noticeably more frequent in cases rather than controls but there are also conflicting results. The aim of this study was to assess the association of intron 3 16 bp duplication polymorphism of p53 with breast cancer risk among Iranian-Azeri population. We also analyzed the clinicopathological information of patients as an epidemiological description of breast cancer in the north-west of Iran. Materials and Methods: This case-control study was performed on 221 breast cancer patients and 170 controls. Genomic DNA was extracted from peripheral blood samples and tumor tissues. p53 PIN3 genotype was determined using electrophoresis of PCR products on 8% non-denaturing polyacrylamide gels and silver staining. Results: In the control and case groups, respectively, 62.9% and 61.1% had no 16 bp insertion (A1A1 genotype), 7.1% and 7.7% had insertion in both p53 alleles (A2A2) and 30% and 31.2% were heterozygous (A1A2). There was no significant difference between genotype frequencies as well as allelic frequencies in two case and control groups. Conclusions: According to the result of the present study, the intron 3 16 bp duplication polymorphism of p53 could not be assessed as a marker of risk factor for predisposition to breast cancer in Azeri population. However, a high frequency of A2 allele (22.1%) in our population suggested that intron 3 16 bp duplication polymorphism may be a valuable marker for study in other cancers with well designed large groups.

• Tuberculosis and Respiratory Diseases
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• v.44 no.3
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• pp.534-546
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• 1997

Background : The p53 and retinoblastoma(Rb) tumor suppressor genes are associated with the pathogenesis of several types of human cancer. Substantial proportion of the primary lung cancers or cell lines have been reported to have the p53 and/or the Rb gene mutations. But, so far there is no report on the analysis of the Rb gene polymorphism as one of the genetic susceptibility marker. This study was undertaken to establish the gene frequencies of the polymorphic genotypes of the p53 and Rb genes in Koreans to evaluate the possible involvement of these genotypes as a risk factor of lung cancer. Methods : In this study 145 controls without previous and present tumor history and 128 lung cancer patients were subjected to analysis. The two intragenic polymorphisms of the p53 gene(exon 4/ AccII, intron 6/MspI) and one intron 17/XbaI polymorphism of the Rb gene were analysed by the method of polymersae chain reaction- restriction fragment length polymorphisms(PCR-RFLPs). The genotype of the intron 3/16 bp repeat polymorphism of p53 was determined by PCR and direct gel electrophoresis. Results : There were no significant differences in the genotype distributions of the p53 gene between lung cancer patients and controls. But heterozygotes(Arg/Pro) of the exon 4/AccII polymorphisms were slightly over-represented than controls, especially in the Kreyberg type I cancer, which was known to be associated with smoking. The intron 3/16 bp duplication and the intron 6/MspI polymorphisms were in complete linkage disequilibrium. About 95% of the individuals were homozygotes of the common alleles both in the 16 duplication and MspI polymorphisms, and no differences were deteced in the genotype distributions between lung cancer patients and controls. Overall genotype distributions of the Rb gene polymorphisms between lung cancer patients and controls were not significantly different However, the genotype distributions in the Kreyberg type I cancer were significantly different from those of controls(p = 0.0297) or adenocarcinomas(p = 0.0008). It was noticeable that 73.4% of the patients with adenocarcinomas were heterozygotes(r1/r2) whereas 39.2% of the Kreyberg type I cancer were heterozygous at this polymorphisms. In the lung cancer patients, significant differences were also noted between the high dose smokers and low dose smokers including non-smokers(p = 0.0258). The relative risk to Kreyberg type I cancer was significantly reduced in the individuals with the genotype of r1/r2(odds ratio = 0.46, 95% C.I. = 0.25-0.86, p = 0.0124). The combined genotype distribution of the exon 4 AccII of the p53 and the intron 17 Rb gene polymorphisms in Kreyberg type I cancers were significantly different from dose of controls or adenocarcinomas. The highest odds ratio were observed in the individuals with the genotypes of Arg/Pro and r2/r2(odds ratio = 1.97,95% C.I. = 0.84-4.59) and lowest one was in the patients with Arg/Arg, r1/r2 genotype(odds ratio = 0.54, 95% C.I. = 0.25-1.14). Conclusion : The p53 and the Rb gene polymorphisms modulate the risk of smoking induced lung cancer development in Koeans. However, the exact mechanism of risk modulation by these polymorphism remains to be determined. For more discrete clarification of associations between specific genotypes and lung cancer risk, the evaluations of these polymorphisms in other ethnics and more number of patients will be needed.

• Journal of Aquaculture
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• v.11 no.3
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• pp.327-335
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• 1998

Amplification of brook trout growth hormone cDNA using polymerase chain reactiono (PCR) produced a nucleotide of 1,120 bp which contained the 5'non-coding region (13bp), an open reading frame (ORF) coding a growth hormone polypeptide consisting of 210 amino acids (630 bp), and a 3'non-coding region (477 bp). In open reading frame s signal peptide of 22 amino acid and 2 potential disulfide bond sites deduced by 4 cysteine residues were obser-bed. Brook trout growth hormone has 97.1%, 94.8%, 94.3%, 91.9%, 66.2%, 63.5%, 62.9%, 62.3%, 53.8% and 48.1% amino acid identity with that of Atlantic salmon, chum salmon, rainbow trout, coho salmon, tuna, tilapia, yellow tail, carp, flounder and eel, respectively.

• Molecules and Cells
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• v.37 no.9
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• pp.691-698
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• 2014

SCYL1-BP1 is thought to function in the p53 pathway through Mdm2 and hPirh2, and mutations in SCYL1-BP1 are associated with premature aging syndromes such as Geroderma Osteodysplasticum; however, these mechanisms are unclear. Here, we report significant alterations in miRNA expression levels when SCYL1-BP1 expression was inhibited by RNA interference in HEK293T cells. We functionally characterized the effects of potential kernel miRNA-target genes by miRNA-target network and protein-protein interaction network analysis. Importantly, we showed the diminished SCYL1-BP1 dramatically reduced the expression levels of EEA1, BMPR2 and BRCA2 in HEK293T cells. Thus, we infer that SCYL1-BP1 plays a critical function in HEK293T cell development and directly regulates miRNA-target genes, including, but not limited to, EEA1, BMPR2, and BRCA2, suggesting a new strategy for investigating the molecular mechanism of SCYL1-BP1.

• Korean Journal of Microbiology
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• v.53 no.1
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• pp.58-60
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• 2017

Halioglobus sp. RR3-57 was isolated from a biofilter of a seawater recirculating aquaculture system and its complete genome sequence was obtained using the PacBio RS II platform. Two circular contigs were assembled and considered as a chromosome and a plasmid (size of 4,847,776 bp and 155,799 bp, and G+C content of 57.5% and 53.2%, respectively). Genomic analysis showed RR3-57 had 18 denitrification-related genes and an incomplete prophage.

• Journal of Life Science
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• v.16 no.7 s.80
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• pp.1158-1163
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• 2006

Bisphenol A (BPA), 2,2-bis(4-hydroxyphenyl) propane, has been widely used as a monomer for production of epoxy resins and polycarbonate plastics, and final products of BPA include adhesives, protective coatings, paints, optical lens, building materials, compact disks and other electrical parts. Since BPA is a toxic chemical to elicit acute cell cytotoxicity and chronic endocrine disrupting activity, the degradation of BPA has been focused during last decades. To overcome the problem of photo-, and chemical-degradation of BPA, in this study, a bacterium that is able to biodegrade BPA, was isolated. The bacterium, isolated froln the soil of plastic factory, was identified as Acinetobacter calcoaceticus (strain BP-2) based on physiological and 16S rDNA sequencing analysis. A. calcoaceticus BP-2 was able to grow in the presence of $1140{\mu}g\;ml^{-1}$ BPA. Biodegradation experiments showed that BP-2 mineralized BPA via 4-hydroxybenzoic acid and 4-hydroxyacetophenone, and average degradation rate was $53.3{\mu}g\;ml^{-1}\;day^{-1}$ under optimal conditions (pH 7 and $30^{\circ}C$). In high density resting cell $(3.5g-dcw.1^{-1})$ experiments, the maximal degradation rate was increased to $89.7{\mu}g\;ml^{-1}\;h^{-1}$. Our results suggest that BP-2 has high potential as a catalyst for practical BPA bioremediation.

• Korean Journal of Plant Taxonomy
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• v.53 no.1
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• pp.32-37
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• 2023

Spiraea prunifolia f. simpliciflora Nakai is a perennial shrub widely used for horticultural and medicinal purposes. We simultaneously obtained the complete plastid genome (plastome) and nuclear ribosomal gene transcription units, 45S nuclear ribosomal DNA (nrDNA) and 5S nrDNA of S. prunifolia f. simpliciflora, using Illumina short-read data. The plastome is 155,984 bp in length with a canonical quadripartite structure consisting of 84,417 bp of a large single-copy region, 18,887 bp of a short single-copy region, and 26,340 bp of two inverted repeat regions. Overall, a total of 113 genes (79 protein-coding genes, 30 tRNAs, and four rRNAs) were annotated in the plastome. The 45S nrDNA transcription unit is 5,848 bp in length: 1,809 bp, 161 bp, and 3,397 bp for 18S, 5.8S, and 26S, respectively, and 261 bp and 220 bp for internal transcribed spacer (ITS) 1 and ITS 2 regions, respectively. The 5S nrDNA unit is 512 bp, including 121 bp of 5S rRNA and 391 bp of intergenic spacer regions. Phylogenetic analyses showed that the genus Spiraea was monophyletic and sister to the clade of Sibiraea angustata, Petrophytum caespitosum and Kelseya uniflora. Within the genus Spiraea, the sections Calospira and Spiraea were monophyletic, but the sect. Glomerati was nested within the sect. Chamaedryon. In the sect. Glomerati, S. prunifolia f. simpliciflora formed a subclade with S. media, and the subclade was sister to S. thunbergii and S. mongolica. The close relationship between S. prunifolia f. simpliciflora and S. media was also supported by the nrDNA phylogeny, indicating that the plastome and nrDNA sequences assembled in this study belong to the genus Spiraea. The newly reported complete plastome and nrDNA transcription unit sequences of S. prunifolia f. simpliciflora provide useful information for further phylogenetic and evolutionary studies of the genus Spiraea, as well as the family Rosaceae.