• KSBB Journal
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• v.24 no.4
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• pp.410-414
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• 2009

Single-nucleotide polymorphisms (SNPs) are the DNA sequences difference among the same species in the level of nucleic acids and are widely applied in clinical fields such as personalized medicine. The routine and labor-intensive methods to determine SNPs are performing the sequence homology search by using BLAST and navigating the trace of chromatogram files generated by high-throughput DNA sequencing machine by using Chromas program. In this paper, we developed SNPchaser, a web-based program for detecting SNPs substitution and heterozygosity existence, to improve the labor-intensive method in determining SNPs. SNPchaser performed sequence alignment and visualized the suspected region of SNPs by using user's reference sequence, AB1 files, and positional information of SNPs. It simultaneously provided the results of sequences alignment and chromatogram of relevant area of SNPs to user. In addition, SNPchaser can easily determine existence of heterozygosity in SNPs area. SNPchaser is freely accessible via the web site http://www.bioinformatics.ac.kr/SNPchaser and the source codes are available for academic research purpose.

• Journal of the Korean Institute of Gas
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• v.16 no.6
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• pp.7-16
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• 2012

Combustion Toxic Effects among several factors of risk encountered during fire are important in the evacuation and final survival, and they are broader and fatal than the direct damages caused by flame. Most studies on fire toxicity until the present are limited to fatality, mainly deaths by fire through pathological research. In this study, it is conducted as a fundamental experiment to address 3 principles of animal experiment and to provide an alternative test to animal testing that is regulated by national building codes and it was conducted through approval by the animal testing ethics committee. Hence, in this study average time of activity stop was measured after directly inhaling toxic gases (HCN) to laboratory animals (mice) through gas toxicity test (KS F 2271) for major asphyxiating gases(HCN) which are produced during fire combustion. effects of Combustion toxic gases on body were quantitatively analyzed through changes in internal organs and hematological analysis, and electrophoresis of a single cell of these laboratory animals. Biological conclusion of combustion toxicology is drawn through approaches (pathological examination, blood test, blood biochemical test, electrophoresis analysis of single cell) which could not confirmed in existing gas toxicity test.

• BMB Reports
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• v.39 no.3
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• pp.284-291
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• 2006

In this study, the cDNA of a new peptide from the venom of the scorpion, Buthotus saulcyi, was cloned and sequenced. It codes for a 64 residues peptide (Bsaul1) which shares high sequence similarity with depressant insect toxins of scorpions. The differences between them mainly appear in the loop1 which connects the $\beta$-strand1 to the $\alpha$-helix and seems to be functionally important in long chain scorpion neurotoxins. This loop is three amino acids longer in Bsaul1 compared to other depressant toxins. A comparative amino acid sequence analysis done on Bsaul1 and some of $\alpha$-, $\beta$-, excitatory and depressant toxins of scorpions showed that Bsaul1 contains all the residues which are highly conserved among long chain scorpion neurotoxins. Structural model of Bsaul1 was generated using Ts1 (a $\beta$-toxin that competes with the depressant insect toxins for binding to $Na^+$ channels) as template. According to the molecular model of Bsaul1, the folding of the polypeptide chain is being composed of an anti-parallel three-stranded $\beta$-sheet and a stretch of $\alpha$-helix, tightly bound by a set of four disulfide bridges. A striking similarity in the spatial arrangement of some critical residues was shown by superposition of the backbone conformation of Bsaul1 and Ts1.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.2
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• pp.1073-1075
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• 2013

Background: In normal cells, activated epidermal growth factor receptor (EGFR) molecules are subjected to ubiquitination-mediated proteasome degradation pathway by c-Cbl, an ubiquitin ligase that checks uncontrolled proliferation. Hence expression of wild type c-Cbl molecule is essential to keep this degradation machinery in a functional state. Loss of expression or function of c-Cbl may consequently lead to sustained activation of EGFR and promote carcinogenesis, loss of function mutations in the c-Cbl gene already being reported in lung and hematopoietic cancers. However, the genetic status of c-Cbl in oral squamous cell carcinoma (OSCC) is not known. Hence in the present study we investigated the genomic DNA isolated from OSCC tissue biopsy samples for mutations in the RING finger domain coding region of c-Cbl gene, which has also been reported to be most frequently mutated in other cancers. Materials and Methods: Total genomic DNA isolated from thirty two post surgical OSCC tissue samples were amplified using primers flanking the exon 8 of c-Cbl gene that codes for the RING finger domain. The PCR amplicons were then resolved in a 1.2% agarose gel, purified and subjected to direct sequencing to screen for mutations. Results: The sequencing data of the thirty two OSCC samples did not identify mutations in the RING finger domain coding region of c-Cbl gene. Conclusions: To the best of our knowledge, this is the first time that the genetic status of c-Cbl gene in OSCC samples has been investigated. The present data indicates that genetic alteration of RING finger domain coding region of c-Cbl gene is relatively infrequent in OSCC samples.

• Journal of Radiation Protection and Research
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• v.48 no.1
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• pp.44-51
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• 2023

Background: Aptamers are currently being used in various fields including medical treatments due to their characteristics of selectively binding to specific molecules. Due to their special characteristics, the aptamers are expected to be used to remove radionuclides from a large amount of liquid radioactive waste generated during the decommissioning of nuclear power plants. The radiological effects on the aptamers should be evaluated to ensure their integrity for the application of a radionuclide removal technique. Materials and Methods: In this study, Monte Carlo N-Particle transport code version 6 (MCNP6) and Monte Carlo damage simulation (MCDS) codes were employed to evaluate the radiological effects on the aptamers. MCNP6 was used to evaluate the secondary electron spectrum and the absorbed dose in a medium. MCDS was used to calculate the DNA damage by using the secondary electron spectrum and the absorbed dose. Binding experiments were conducted to indirectly verify the results derived by MCNP6 and MCDS calculations. Results and Discussion: Damage yields of about 5.00×10^-4 were calculated for 100 bp aptamer due to the radiation dose of 1 Gy. In experiments with radioactive materials, the results that the removal rate of the radioactive ⁶⁰Co by the aptamer is the same with the non-radioactive ⁵⁹Co prove the accuracy of the previous DNA damage calculation. Conclusion: The evaluation results suggest that only very small fraction of significant number of the aptamers will be damaged by the radioactive materials in the liquid radioactive waste.

• KSBB Journal
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• v.7 no.3
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• pp.155-160
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• 1992

To improve the nutritional quality of plant proteins, a synthetic gene, called HEAAE (high essential amino acid encoding)-DNA, was introduced and expressed in tobacco plants. The synthetic gene, which is 292 basepair-long, codes for a protein composed of about 80% essential amino acids. To improve its expression level in plants, Cauliflower Mosaic Virus (CaMV) 355 and CaMV duplicate 35S promoters which are known as strong promoters were used with Nopaline Synthase promoter as a control. Transformed and regenerated tobacco plants were subject to analysis for introduction and expression of this gene. Integration of the gene into the plant genome and its expression into mRNAs and its proteins have been demonstrated using Southern, northern blot analysis and amino acid analysis. The differences of expression levels among CaMV duplicate 35S, CaMV 35S and Nopaline Synthase promoters are significant in term of mRNAs, but not in terms of proteins.

• Microbiology and Biotechnology Letters
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• v.18 no.3
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• pp.317-321
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• 1990

The broad-host plasmid PAM $\beta_1$ of Streptococcus faecalis DS 5 which codes for erythromycin resistance and lactose utilization was transferred into L. casei M-3 (lac-mutant) by conjugation, but was not transferred by protoplast fusion and protoplast transformation. For conjugal transfer of plasmid PAM $\beta_1$ the method of membrane filter mating was more efficient than that of agar surface mating. The rate of acid production of transconjugant C-1, C-3 was similar to L. casei YIT 9018. The proteolytic activity of transconjugant C-3 was increased 20% higher than that of wild type. Plasmid PAM $\beta_1$ was detected by a11 of the transconjugants. The transconjugants expressed lactose ulitization and erythromycin resistance.

• The Korean Journal of Zoology
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• v.37 no.3
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• pp.304-310
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• 1994

Using in situ hybridization, we have mapped the anatomical localization of perikarya containing myNA that codes for sonadotropin releasing hormone (GnRH) in the brains of female frogs, R. dybowskii. DNA olisomers, with sequences complementary to the GnRH portion of pro-GnRH myNA sequence, were synthesized and hybridized to paraformaldehvde-fixed, sagittal sections of the whole brain stem. The distribution of the GnRH mRNA containing cell bodies was similar to that described for GnRH peptide by immunohistochemistrv. That is, cells containing GnRH mRNA were observed in the medial septal area, anterior preoptic area, ventromedial hvpothalamus and infundibular regions. However, another cell groups which contains GnRH mRNAs were also detected by in situ hybridization in the bed nucleus of hippocampal commissure, preoptic area, nucleus infundibularis dorsalis, mesencephalic nuclei and intermediolateral cell column of spinal cord areas. These results demonstrate the feasibility of using in situ hybridization as a strategy to study the distribution of GnRH neurons and the detection of GnRH gene expression in the vertebrates.

• BMB Reports
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• v.37 no.4
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• pp.474-479
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• 2004

The expressed sequence tag (EST) effort in Toxoplasma gondii has generated a substantial amount of gene information. To exploit this valuable resource, we chose to study tgd057, a novel gene identified by a large number of ESTs that otherwise show no significant match to known sequences in the database. Northern analysis showed that tgd057 is transcribed in this tachyzoite. The complete cDNA sequence of tgd057 is 1169 bp in length. Sequence analysis revealed that tgd057 possibly adopts two polyadenylation sites, utilizes the fourth in-frame ATG for translation initiation, and codes for a secretory protein. The longest open reading frame for the tgd057 gene was cloned and expressed as a recombinant protein (rd57) in Escherichia coli. Western analysis revealed that serum against rd57 recognized a molecule of ~21 kDa in the tachyzoite protein extract. This suggests that the tgd057 gene is expressed in vivo in the parasite.

• BMB Reports
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• v.36 no.6
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• pp.545-551
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• 2003

A cDNA of bovine brain glutamate dehydrogenase (GDH) was isolated from a cDNA library by recombinant PCR. The isolated cDNA has an open-reading frame of 1677 nucleotides, which codes for 559 amino acids. The expression of the recombinant bovine brain GDH enzyme was achieved in E. coli. BL21 (DE3) by using the pET-15b expression vector containing a T7 promoter. The recombinant GDH protein was also purified and characterized. The amino acid sequence was found 90% homologous to the human GDH. The molecular mass of the expressed GDH enzyme was estimated as 50 kDa by SDS-PAGE and Western blot using monoclonal antibodies against bovine brain GDH. The kinetic parameters of the expressed recombinant GDH enzymes were quite similar to those of the purified bovine brain GDH. The $K_m$ and $V_{max}$ values for $NAD^+$ were 0.1 mM and $1.08\;{\mu}mol/min/mg$, respectively. The catalytic activities of the recombinant GDH enzymes were inhibited by ATP in a concentration-dependent manner over the range of 10 - $100\;{\mu}M$, whereas, ADP increased the enzyme activity up to 2.3-fold. These results indicate that the recombinant-expressed bovine brain GDH that is produced has biochemical properties that are very similar to those of the purified GDH enzyme.