• 대한골관절종양학회지
• /
• 제6권4호
• /
• pp.143-151
• /
• 2000

목적 : p53 종양억제 유전자는 사람의 암에서 변형이 가장 많이 발견되는 유전자로 유잉 육종에서 p53 유전자의 변형을 관찰하고자 하였다. 재료 및 방법 : 유잉육종 환자 35례의 파라핀 블록을 사용하였으며, 유전자의 결핍과 p53 유전자의 염기서열의 변형을 관찰하였다. 결과 : 정성적인 중합효소 연쇄반응을 이용한 p53의 4-9번까지의 유전자검사중 2례에서 동일성의 유전자 결핍이 관찰되었으며, exon 5-8의 유전자 중합효소 연쇄반응에서는 3례에서 missense 점돌연변이가 관찰되었다. 결론 : 이상의 결과로 p53은 유전적으로 적은 부분에서 유잉육종에 관여하는 것으로 관찰 되었다.

• Molecules and Cells
• /
• 제19권1호
• /
• pp.114-123
• /
• 2005

Nitropyrene, the predominant nitropolycyclic hydrocarbon found in diesel exhaust, is a mutagenic and tumorigenic environmental pollutant that requires metabolic activation via nitroreduction and ring oxidation. In order to determine the role of ring oxidation in the mutagenicity of 1-nitropyrene, its oxidative metabolites, 1-nitropyrene 4,5-oxide and 1-nitropyrene 9,10-oxide, were synthesized and their mutation spectra were determined in the coding region of hprt gene of CHO cells by a PCR amplification of reverse-transcribed hprt mRNA, followed by a DNA sequence analysis. A comparison of the two metabolites for mutation frequencies showed that 1-nitropyrene 9,10-oxide was 2-times higher than 1-nitropyrene 4,5-oxide. The mutation spectrum for 1-nitropyrene 4,5-oxide was base substitutions (33/49), one base deletions (11/49) and exon deletions (5/49). In the case of 1-nitropyrene 9,10-oxide, base substitutions (27/50), one base deletions (15/50), and exon deletions (8/50) were observed. Base substitutions were distributed randomly throughout the hprt gene. The majority of the base substitutions in mutant from 1-nitropyrene 4,5-oxide treated cells were $A{\rightarrow}G$ transition (15/33) and $G{\rightarrow}A$ transition (8/33). The predominant base substitution, $A{\rightarrow}G$ transition (11/27) and $G{\rightarrow}A$ transition (8/27), were also observed in mutant from 1-nitropyrene 9,10-oxide treated cells. The mutation at the site of adenine and guanine was consistent with the previous results, where the sites of DNA adduct formed by these compounds were predominant at the sites of purines. A comparison of the mutational patterns between 1-nitropyrene 4,5-oxide and 1-nitropyrene 9,10-oxide showed that there were no significant differences in the overall mutational spectrum. These results indicate that each oxidative metabolite exhibits an equal contribution to the mutagenicity of 1-nitropyrene, and ring oxidation of 1-nitropyrene is an important metabolic pathway to the formation of significant lethal DNA lesions.

• Journal of Microbiology and Biotechnology
• /
• 제26권9호
• /
• pp.1636-1642
• /
• 2016

Phenalamide is a bioactive secondary metabolite produced by Myxococcus stipitatus. We identified a 56 kb phenalamide biosynthetic gene cluster from M. stipitatus DSM 14675 by genomic sequence analysis and mutational analysis. The cluster is comprised of 12 genes (MYSTI_04318- MYSTI_04329) encoding three pyruvate dehydrogenase subunits, eight polyketide synthase modules, a non-ribosomal peptide synthase module, a hypothetical protein, and a putative flavin adenine dinucleotide-binding protein. Disruption of the MYSTI_04324 or MYSTI_04325 genes by plasmid insertion resulted in a defect in phenalamide production. The organization of the phenalamide biosynthetic modules encoded by the fifth to tenth genes (MYSTI_04320-MYSTI_04325) was very similar to that of the myxalamid biosynthetic gene cluster from Stigmatella aurantiaca Sg a15, as expected from similar backbone structures of the two substances. However, the loading module and the first extension module of the phenalamide synthase encoded by the first to fourth genes (MYSTI_04326-MYSTI_04329) were found only in the phenalamide biosynthetic gene cluster from M. stipitatus DSM 14675.

• Genomics & Informatics
• /
• 제5권2호
• /
• pp.68-76
• /
• 2007

Due to the increasing interest in SNPs and mutational hot spots for disease traits, it is becoming more important to define and understand the relationship between SNPs and their flanking sequences. To study the effects of flanking sequences on SNPs, statistical approaches are necessary to assess bias in SNP data. In this study we mainly applied Markov chains for SNP sequences, particularly those located in intronic regions, and for analysis of in-del data. All of the pertaining sequences showed a significant tendency to generate particular SNP types. Most sequences flanking SNPs had lower complexities than average sequences, and some of them were associated with microsatellites. Moreover, many Alu repeats were found in the flanking sequences. We observed an elevated frequency of single-base-pair repeat-like sequences, mirror repeats, and palindromes in the SNP flanking sequence data. Alu repeats are hypothesized to be associated with C-to-T transition mutations or A-to-I RNA editing. In particular, the in-del data revealed an association between particular changes such as palindromes or mirror repeats. Results indicate that the mechanism of induction of in-del transitions is probably very different from that which is responsible for other SNPs. From a statistical perspective, frequent DNA lesions in some regions probably have effects on the occurrence of SNPs.

• Journal of Microbiology
• /
• 제45권1호
• /
• pp.58-63
• /
• 2007

In this study, the relative synonymous codon and amino acid usage biases of the broad-host range phage, KVP40, were investigated in an attempt to understand the structure and function of its proteins/protein-coding genes, as well as the role of its tRNAs. Synonymous codons in KVP40 were determined to be AT-rich at the third codon positions, and their variations are dictated principally by both mutational bias and translational selection. Further analysis revealed that the RSCU of KVP40 is distinct from that of its Vibrio hosts, V. cholerae and V. parahaemolyticus. Interestingly, the expression of the putative highly expressed genes of KVP40 appear to be preferentially influenced by the abundant host tRNA species, whereas the tRNAs expressed by KVP40 may be required for the efficient synthesis of all its proteins in a diverse array of hosts. The data generated in this study also revealed that KVP40 proteins are rich in low molecular weight amino acid residues, and that these variations are influenced primarily by hydropathy, mean molecular weight, aromaticity, and cysteine content.

• Molecules and Cells
• /
• 제39권6호
• /
• pp.460-467
• /
• 2016

Bacteriophytochromes are phytochrome-like light-sensing photoreceptors that use biliverdin as a chromophore. To study the biochemical properties of the Deinococcus radiodurans bacteriophytochrome (DrBphP) protein, two anti-DrBphP mouse monoclonal antibodies (2B8 and 3H7) were generated. Their specific epitopes were identified in our previous report. We present here fine epitope mapping of these two antibodies by using truncation and substitution of original epitope sequences in order to identify minimized epitope peptides. The previously reported original epitope sequences for 2B8 and 3H7 were truncated from both sides. Our analysis showed that the minimal peptide sequence lengths for 2B8 and 3H7 antibodies were nine amino acids (RDPLPFFPP) and six amino acids (PGEIEE), respectively. We further characterized these peptides in order to investigate their reactivity after single deletion and single substitution of the original peptides. We found that single-substituted 2B8 epitope (RDPLPAFPP) and dual-substituted 3H7 epitope (PGEIAD) showed significantly increased reactivity. These two antibodies with high reactivity for the short modified peptide sequences are valueble for developing new peptide tags for protein research.

• Journal of Microbiology and Biotechnology
• /
• 제16권4호
• /
• pp.569-575
• /
• 2006

The 530 stem-loop is a 46 nucleotide stem-loop structure found in all small-subunit ribosomal RNAs. Phylogenetic and mutational studies by others suggest the requirement for Watson-Crick interactions between the nucleotides 505-507 and 524-526 (530 pseudoknot), which are highly conserved. To examine the nature and functional significance of these interactions, a random mutagenesis experiment was conducted in which the nucleotides in the proposed pseudoknot were simultaneously mutated and functional mutants were selected and analyzed. Genetic analysis revealed that the particular nucleotide present at each position except 524 was not exclusively critical to the selection of functional mutants. It also indicated that basepairing interactions between the positions 505-507 and 524-526 were required for ribosomal function, and much weaker base-pairing interactions than those of the wild-type also allowed high ribosomal function. Our results support the hypothesis that the 530 pseudoknot structure may undergo a 'conformational switch' between folded and unfolded states during certain stages of the protein synthesis process by interacting with other ligands present in its environment.

• 대한임상검사과학회지
• /
• 제44권2호
• /
• pp.75-80
• /
• 2012

Papillary thyroid carcinoma (PTC) is the most common thyroid cancer, accounting for 95% or more of malignancies in Korea. Recently, many thyroid cancers have been detected owing to the widespread use of ultrasonography in health surveillance. The objective of this study was to evaluate the association of known prognostic factors with the $BRAF^{V600E}$ mutation and its association features in Korean patients with papillary thyroid carcinomas. The $BRAF^{V600E}$ mutation was detected in 69.1% (256 of 370) of PTC cases. In univariate analysis, the $BRAF^{V600E}$ mutation was significantly associated with tumor size (p < 0.05) and sex. However, it was not significantly associated with other established risk factors, such as age, extrathyroidal extension, and lymph node metastasis. This finding supports the idea that the BRAF mutation plays a role in the early stage of PTC development. This relationship deserves further investigation to clarify whether $BRAF^{V600E}$ is a useful risk factor or prognostic marker for PTC.

• Genomics & Informatics
• /
• 제20권4호
• /
• pp.43.1-43.18
• /
• 2022

Atropa belladonna is a valuable medicinal plant and a commercial source of tropane alkaloids, which are frequently utilized in therapeutic practice. In this study, bioinformatic methodologies were used to examine the pattern of coding sequences and the factors that might influence codon usage bias in the chloroplast genome of Atropa belladonna and other nightshade genomes. The chloroplast engineering being a promising field in modern biotechnology, the characterization of chloroplast genome is very important. The results revealed that the chloroplast genomes of Nicotiana tabacum, Solanum lycopersicum, Capsicum frutescens, Datura stramonium, Lyciumbarbarum, Solanum melongena, and Solanum tuberosum exhibited comparable codon usage patterns. In these chloroplast genomes, we observed a weak codon usage bias. According to the correspondence analysis, the genesis of the codon use bias in these chloroplast genes might be explained by natural selection, directed mutational pressure, and other factors. GC12 and GC3S were shown to have no meaningful relationship. Further research revealed that natural selection primarily shaped the codon usage in A. belladonna and other nightshade genomes for translational efficiency. The sequencing properties of these chloroplast genomes were also investigated by investing the occurrences of palindromes and inverted repeats, which would be useful for future research on medicinal plants.

• Journal of Korean Neurosurgical Society
• /
• 제63권5호
• /
• pp.566-578
• /
• 2020

Objective : Radiation is known to induce autophagy in malignant glioma cells whether it is cytocidal or cytoprotective. Dexamethasone is frequently used to reduce tumor-associated brain edema, especially during radiation therapy. The purpose of the study was to determine whether and how dexamethasone affects autophagy in irradiated malignant glioma cells and to identify possible intervening molecular pathways. Methods : We prepared p53 mutant U373 and LN229 glioma cell lines, which varied by phosphatase and tensin homolog (PTEN) mutational status and were used to make U373 stable transfected cells expressing GFP-LC3 protein. After performing cell survival assay after irradiation, the IC₅₀ radiation dose was determined. Dexamethasone dose (10 μM) was determined from the literature and added to the glioma cells 24 hours before the irradiation. The effect of adding dexamethasone was evaluated by cell survival assay or clonogenic assay and cell cycle analysis. Measurement of autophagy was visualized by western blot of LC3-I/LC3-II and quantified by the GFP-LC3 punctuated pattern under fluorescence microscopy and acridine orange staining for acidic vesicle organelles by flow cytometry. Results : Dexamethasone increased cell survival in both U373 and LN229 cells after irradiation. It interfered with autophagy after irradiation differently depending on the PTEN mutational status : the autophagy decreased in U373 (PTEN-mutated) cells but increased in LN229 (PTEN wild-type) cells. Inhibition of protein kinase B (AKT) phosphorylation after irradiation by LY294002 reversed the dexamethasone-induced decrease of autophagy and cell death in U373 cells but provoked no effect on both autophagy and cell survival in LN229 cells. After ATG5 knockdown, radiation-induced autophagy decreased and the effect of dexamethasone also diminished in both cell lines. The diminished autophagy resulted in a partial reversal of dexamethasone protection from cell death after irradiation in U373 cells; however, no significant change was observed in surviving fraction LN229 cells. Conclusion : Dexamethasone increased cell survival in p53 mutated malignant glioma cells and increased autophagy in PTEN-mutant malignant glioma cell but not in PTEN-wildtype cell. The difference of autophagy response could be mediated though the phosphatidylinositol 3-kinase/AKT/mammalian target of rapamycin signaling pathway.