• Microbiology and Biotechnology Letters
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• v.27 no.6
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• pp.440-445
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• 1999

In order to investigate structure-antibiotic activity relationships of brevinin-1 and thanatin containing Rana box composed of basic loop formed by disulfide bridge in their arboxy terminus, thanatin, brevinin 1 and their analogues (T-B1, T-B2 and B-T) in which their Rana box sequence exchanged was designed and synthesized by the solid phase method using Fmoc-chemistry. The basic sequence of Rana box of thanatin had more significant effect on both antibacterial and antifungal activity than that of brevinin 1. The tail sequence (QRM) of thanatin was found to be important in its antibacterial and antifungal activity. Rana box sequence of brevinin-1 did not have a significant effect on its antitumor and phospholipid vesicle-aggregating activities. Brevinin-1 showed stronger $\alpha$-helical structure in the membrane-mimicking environment such as SDS micelle than thanatin. A remarkable increase in a-helicity of bervinin-1 plays more important role in antibiotic activity than that of thanatin. Furthermore, antibacterial activity of thanatin against E. coli resulted from the disruptive effect against the outer cell membrane of E. coli.

• KIISE Transactions on Computing Practices
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• v.22 no.1
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• pp.32-37
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• 2016

In model-based testing using sequence diagrams, test cases are automatically derived from the sequence diagrams. For the generation of test cases, scenarios need to be found for representing as a sequence diagram, and to extract test paths satisfying the test coverage. However, it is hard to automatically extract test paths from the sequence diagram because a sequence diagram represents loop, opt, and alt information using CombinedFragments. To resolve this problem, we propose a transformation process that transforms a sequence diagram into an activity diagram which represents scenarios as a type of control flows. In addition, we generate test cases from the activity diagram by applying a test coverage concept. Finally, we present a case study for test cases generation from a sequence diagram.

• Journal of Plant Biology
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• v.38 no.3
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• pp.259-266
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• 1995

To investigate how the dyad symmetry region (DSR) and the distance between vir box and -35 sequence of the virE promoter plays a role in virE gene expression, two mutants were constructed by base substitution and insertional mutagenesis. The base substitutional mutation, a AAlongrightarrowCG substitution at positions -39 and -40 on the DSR, showed the level of $\beta$-galactosidase activity approximately 91% of the wild type virE promoter activity. Therefore, the native structure of the DSR seems to be not essential for virE expression. The insertional mutation, constructed by inserting 8 bp ClaI linker between -49 and -50, displayed the $\beta$-galactosidase activity at 12% of the native virE promoter activity. However, this striking reduction appears to be not caused by destruction of the native DSR structure, but by shifting the vir box far from putative -35 sequence.

• Journal of Microbiology and Biotechnology
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• v.9 no.3
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• pp.276-281
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• 1999

In order to determine the functional region of the antifungal protein (AFP) isolated from Aspergillus giganteus responsible for growth inhibitory activity and the promotion of phospholipid vesicle aggregation, overlapping peptides covering the complete sequence of AFP were synthesized. The antibiotic activity against bacterial, fungal, and tumor cells, and the vesicle-aggregation activity of the synthetic peptides were investigated. The AFP functional sequence responsible for antibiotic and vesicle-aggregation activity was determined to be located within the region between AFP residues 19 to 32. AFP (19-32) exhibited an a-helical conformation in a cell membrane-like environment. AFP (19-32) displayed potent antibiotic activity against bacterial, fungal, and tumor cells without peptide toxicity as indicated by hemolysis. Accordingly, AFP (19-32) could be used as a good model for the design of effective antibiotic agents with powerful antibiotic activity yet without any cytotoxic effects against the host organism.

• Journal of Microbiology and Biotechnology
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• v.14 no.5
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• pp.1022-1030
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• 2004

The gene encoding Aquifex pyrophilus (Apy) DNA polymerase was cloned and sequenced. The Apy DNA polymerase gene consists of 1,725 bp coding for a protein with 574 amino acid residues. The deduced amino acid sequence of Apy DNA. polymerase showed a high sequence homology to Escherichia coli DNA polymerase I-like DNA polymerases. It was deduced by amino acid sequence alignment that Apy DNA polymerase, like the Klenow fragment, has only the two domains, the $3'{\rightarrow}5'$ exonuclease domain and the $5'{\rightarrow}3'$ polymerase domain, containing the characteristic motifs. The Apy DNA polymerase gene was expressed under the control of T7lac promoter on the expression vector pET-22b(+) in E. coli. The expressed enzyme was purified by heat treatment, and Cibacron blue 3GA and $UNO^{TM}$ Q column chromatographies. The optimum pH of the purified enzyme was 7.5, and the optimal concentrations of KCl and $Mg^{2+}$ were 20 mM and 3 mM, respectively. Apy DNA polymerase contained a double strand-dependent $3'{\rightarrow}5'$ proofreading exonuclease activity, but lacked any detectable $5'{\rightarrow}3'$ exonuclease activity, which is consistent with its amino acid sequence. The somewhat lower thermostability of Apy DNA polymerase than the growth temperature of A. pyrophilus was analyzed by the comparison of amino acid composition and pressure effect.

• Preventive Nutrition and Food Science
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• v.15 no.4
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• pp.360-363
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• 2010

To enhance the expression and secretion of pediocin PA-1 from heterologous bacterial hosts, the promoter and deduced signal sequence (PS) of an $\alpha$-amylase gene from a Bifidobacterium adolescentis strain was fused with pediocin PA-1 structural and immunity genes (AB) and the resulting functions were evaluated in Escherichia coli. Two recombinant PCR products were created-one with just the deduced signal sequence and one with the sequence plus the Ser and Thr sequences that are the next two amino acids of the signal sequence. These two products, the PSAB (---AQA::KYY---) and PSABST (---AQA$\underline{ST}$::KYY---), respectively, were inserted into a TA cloning vector (yT&A) and named pPSAB, which was previously reported, and pPSABST. The two recombinant plasmid DNAs were transferred into E. coli JM109 and the transformants displayed antimicrobial activity, where the activity of E. coli JM109 (pPSAB) was stronger than that of E. coli JM109 (pPSABST), indicating that the ST amino acid residues were not necessary for secretion and might have even decreased the antimicrobial activity of recombinant pediocin PA-1.

• Journal of Radiation Industry
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• v.11 no.3
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• pp.145-149
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• 2017

The cel7A sequence variation was analyzed between the wild type (Lentinula edodes KACC42378) and its cellulase activity enhanced mutant LER277. LER277 was induced by using gamma ray radiation ($^{60}Co$) at the $LD_{99}$ dose (0.94 kGy). Cloning and sequencing results showed that the cel7A coding DNA sequence (CDS) of LER277 had five nucleotide substitutions ($T{\rightarrow}C$, 201, 285 and 744 nt; $A{\rightarrow}G$, 525 nt; $C{\rightarrow}T$, 540 nt) and one hexanucleotide repeat insertion (GGCACC, within 1375-1392 nt) compared to that of the wild type. The Five nucleotide substitutions did not change the deduced amino acids and the hexanucleotide insertion elongated the GT repeat in a serine/threonine/glycine-rich linker. These results suggest that the enhancement of the cellulase activity in LER277 partly stemmed from cel7A changes by which the GT repeat of the linker is elongated.

• Restorative Dentistry and Endodontics
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• v.24 no.4
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• pp.535-545
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• 1999

Crease of Streptococcus salivarius is believed to play a critical role in bacterial ecology and pH homeostasis in the mouth, and consequently affect the pathogenesis of dental caries and periodontal diseases. Expression of the urease gene is greatly enhanced by low p. f. excess of Carbohydrate, and faster growth. It was observed that urease activity of the strains of S. salivarius that exhibited no of low urease activity was not increased even in low pH condition. In this study, it was hypothesized that the urease gene of the strains is absent, defected, or greatly changed by genetic combination. In order to prove this hypothesis, chromosomes were obtained from 28 S. salivarius strains which had been isolated from normal teeth and carious lesions, subjected to polymerase chain reaction (PCR) using primers encoding highly conserved sequence from ureC, and then the obtained PCR products were compared. The results were as follows: 1. After PCR the strains generated either one of 0.54- and 1.3-kbp PCR products, or none. 2. All 16 strains having a higher urease activity(<50${\mu}mol/min/mg$) produced 0.54-kbp PCR products. 3. Twelve strains without urease activity and with a lower urease activity(<50${\mu}mol/min/mg$) yield either one of 0.54 and 1.3-kbp PCR products, or none. 4. The DNA sequence of the 0.54-kbp PCR product (pCAP-0.54) exhibited 95% identity to the ureC of S. salivarus 57.I; 30bp were found to be different, which led to difference of only 2 amino acids in the sequence. 5. The DNA sequence of the 1.3-kbp PCR product(pCAP-1.3) was found to be highly homologous to the aminopeptidase C gene of Streptococcus thermophilus. Overall results indicate that there are considerable variations of the urease genes from S. salivarus strains and the variations may affect the uncolytic activity of the bacteria directly of indirectly.

• Korean Journal of Microbiology
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• v.31 no.3
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• pp.208-213
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• 1993

The structural and functional roles of IGS element of T4 td intron in thymidylate synthase activity in vivo were investigated Site-directed mutagenesis was employed to crete mutations of IGS element of T4 td intron, When a U-G pari was changed to a U-C pari in the 5' splice site of P1 stem of td intron, the activity of thymidylate synthase was completely abolished whereas the wild type retained the normal activity of enzyme. When U at 12 position within IGS element was changed to C, the activity of thymidylate synthase was approximately 32% of that of the wild type. Comparison of enzyme activities suggests that IGS element within P1 structure is an essential requirement for splicing of td gene in vivo.

• Animal cells and systems
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• v.1 no.2
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• pp.345-350
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• 1997

The ${\beta}$-Lactoglobulin (BLG) gene expression is differentially regulated during development of the mammary tissues. Such differential regulation of the BLG gene expression can be reiterated in the cultured mammary HC11 cells. In the growing non-confluent HC11 cells, the BLG promoter activity was shown to be partially repressed by the upstream regulatory sequence. The repression was gradually diminished and switched to activation as the cells grew confluent. The differential regulation of the BLG promoter was controlled by the 5'-regulatory sequence located at the upstream of 205 bp. Electromobility shift assay showed that nuclear extract from HC11 cells differentially bound on the regulatory sequence, depending on the cell confluency, which was in accordance with the differential transcriptional activity. DNase I foot-print assay, however, revealed that all nuclear extracts presented the same foot-prints, regardless of confluency of HC11 cells. These results suggest that differential regulation BLG gene expression by the 5'-regulatory sequence may be accomplished by competitive and/or cooperative binding of differential regulatory factors on the same regulatory element.