• Journal of Microbiology and Biotechnology
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• 제18권11호
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• pp.1841-1847
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• 2008

Vibrio vulnificus is a causative agent of serious diseases in humans, resulting from the contact of wound with seawater or consumption of raw seafood. Several studies aimed at detecting V. vulnificus have targeted vvh as a representative virulence toxin gene belonging to the bacterium. In this study, we targeted the rpoS gene, a general stress regulator, to detect V. vulnificus. PCR specificity was identified by amplification of 8 V. vulnificus templates and by the loss of a PCR product with 36 non-V. vulnificus strains. The PCR assay had the 273-bp fragment and the sensitivity of 10 pg DNA from V. vulnificus. SYBR Green I-based real-time PCR assay targeting the rpoS gene showed a melting temperature of approximately $84^{\circ}C$ for the V. vulnificus strains. The minimum level of detection by real-time PCR was 2 pg of purified genomic DNA, or $10^3$ V. vulnificus cells from pure cultured broth and $10^3$ cells in 1 g of oyster tissue homogenates. These data indicate that real-time PCR is a sensitive, species-specific, and rapid method for detecting this bacterium, using the rpoS gene in pure cultures and in infected oyster tissues.

• Archives of Pharmacal Research
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• 제29권1호
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• pp.88-95
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• 2006

Analysis of molecular nature of mitochondrial DNA (mtDNA) could be powerful marker for anthropological studies of modern populations. While population genetic studies on mtDNA have been reported for several ethnic groups, no such study has been documented for the Korean population. We surveyed mtDNA polymorphisms in the HVS I of noncoding D-loop region and its upstream region from 430 unrelated healthy Korean population by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and direct sequencing analysis. PCR product with 2,790 bp spanning the specific mtDNA region (mt13715-16504) was subjected to RFLP analysis using 6 restriction enzyme (Hinf I, Hae III, Alu I, Dde I, Mbo I, Rsa I). On the PAUP analysis of PCR-RFLP results, 38 mtDNA haplotypes (Hap 1-38) were detected in the Korean populations, which were classified into 11 haplogroups (Grp 1-11) of related haplotypes encompassing all 38 haplotypes. In comparison of sequencing data with Anderson's reference sequence, the transition type was more prevalent than the transversion type. Insertions or deletions were not found. In addition, three of the polymorphic sites (A16240C, A16351G, G16384A) in HVS-I region are determined newly. The polymorphic sites were distributed randomly in the region, though the frequency at each site was variable. Thus, this research might be required for the genealogical study of Orientals.

• BMB Reports
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• 제37권2호
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• pp.206-212
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• 2004

The genes that are located within the odvp-6e/odv-e56 region of the Choristoneura fumiferana granulovirus (ChfuGV) were identified by sequencing the 11 kb BamHI restriction fragment on the ChfuGV genome. The global GC content that was calculated from the data obtained from this genomic region was 34.96%. The open-reading frames (ORFs), located within the odvp-6e/odv-e56 region, are presented and compared to the equivalent ORFs that are located at the same region in other GVs. This region is composed of 14 ORFs, including three ORFs that are unique to ChfuGV with no obvious homologues in other baculoviruses as well as eleven ORFs with homologues to granuloviral ORFs, such as granulin, CfORF2, pk-1, ie-1, odv-e18, p49, and odvp-6e/odv-e56. In this study, the conceptual products of seven major conserved ORFs (granulin, CfORF2, IE-1, ODV-E18, p49 and ODVP-6E/ODV-E56) were used in order to construct phylogenetic trees. Our results show that granuloviruses can be grouped in 2 distinct groups as follows: Group I; Choristoneura fumiferana granulovirus (ChfuGV), Cydia pomonella granulovirus (CpGV), Phthorimaea operculella granulovirus (PhopGV), and Adoxophyes orana granulovirus (AoGV). Group II; Xestia c-nigrum granulovirus (XcGV), Plutella xylostella granulovirus (PxGV), and Trichoplusia ni granulovirus (TnGV). The ChfuGV conserved proteins are most closely related to those of CpGV, PhopGV, and AoGV. Comparative studies, performed on gene arrangements within this region of genomes, demonstrated that three GVs from group I maintain similar gene arrangements.

• 한국결정학회지
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• 제13권1호
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• pp.21-24
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• 2002

Cholesterol crotonate(CH₃CH = CHCOOC/sub 27/H/sub 45/)의 분자 및 결정 구조를 X-선 회절법으로 연구하였다. 결정은 P2₁, a = 13.446(4) , b = 11.802(3) , c = 18.782(5) , β = 103.99(2)°, Z = 4이다. 회절 반점들의 세기는 흑연 단색화 장치가 있는 Enraf-Nonius CAD-4 diffractometei로 얻었으며 (2θ/sub max/ = 25°, Mo-Kα X선(λ= 0.7107 )을 사용하였다. 분자 구조는 직접법으로 풀었으며, 최소자승법으로 정밀화하였고, 최종신뢰도 R값은 1604개의 회절 반점에 대하여 0.092이었다. 화합물의 결정 구조는 cholesterol ethylcarbonate, propylcarbonate, crotylcarbonate등의 결정 구조와 isostructure로, 분자들은 monolayer를 이루면서 쌓여 있으며, monolayer 중심부에서는 A 분자의 cholesteryl ring system들끼리, B 분자의 cholesterol ring system과 분자 B의 C(17)-side chain들이 서로 촘촘히 쌓여있다. 층(layer)들 사이에는 crotonate tail들과 분자 A의 C(17)-side chain들이 느슨하게 모여있다. 결정은 cholesteric phase를 갖는 liquid crystalline state을 보여주고 있다.

• Animal cells and systems
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• 제2권2호
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• pp.259-267
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• 1998

A deletion of one out of the two copies of 9-bp repeat sequence (CCCCCTCTA), between the cytochrome oxidase II and Iysine tranfer RNA (COII/$tRNA^{Lys}$) genes in human mitochondrial DNA (mtDNA) has been used as a polymorphic anthropological marker for people of east Asian origin, and to lesser extent, Pacific and African populations. We searched for the 9-bp deletion of the intergenic COII/$tRNA^{Lys}$ Lys region in two Korean populations (175 from Seoul and 38 from Cheju) and examine the distibution of this deletion in world populations. The 9-bp deletion was detected directly by electrophoresis of the polymerase chain reaction (PCR)-amplified nucleotide(nt) 8211-8310 mtDNA fragment. The frequencies of the 9-bp deletion were significantly different between the Seoul (16%) and Cheju (8%) populations. Examination of data from the world populations suggests a geographic gradient. The frequency reaches its highest values in some Pacific island populations and decreases along the southeast Asia-Siberia transect. In spite of this geographic gradient, Mongoloid populations including Korean, Chinese, Japanese, and Mongolian populations were relatively homo-geneous with regard to the 9-bp deletion type of the intergenic COII/$tRNA^{Lys}$ region. These results indicate Koreans are genetically related to northeast Asian populations, and have a maternal mongoloid ancestry. Therefore, the 9-bp deletion of the intergenic COII/$tRNA^{Lys}$ region will provide significant information to elucidate the historical patterns of migration of the Mongoloids.

• 한국통신학회논문지
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• 제34권10A호
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• pp.760-768
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• 2009

본 논문에서는 선박에 적용할 e-네비게이션을 위한 HR(high rate)-WPAN(Wireless Personal Area Network) 시스템에 대한 전송 파라미터를 분석하여 최적 전송파라미터 선택방식을 제시한다. 본 논문에서는 IEEE 802.15.3 CSMA/CA기반의 HR-WPAN을 SAN(Ship Area Network)에 적용할 경우에 고려되어야하는 에너지 효율성 측면에서의 전송파라미터들을 분석하고 에너지를 절약할 수 있는 전송파라미터 결정방식에 대하여 각 선박환경별로 분석하여 제안한다. 특히 SAN환경에서 무선채널의 경로손실(path loss)을 결정하는 가장 큰 파라미터인 선박의 다양한 재질을 고려하여 각 HR-WPAN의 전송파라미터별로 에너지 소모량을 분석하여 파라미터 선택방안을 제시한다. 시뮬레이션 결과 선박환경에 따라서 전송률 선택방식, 전송전력 조절 방식 및 데이터 분할크기의 적절한 선택에 따라 에너지 효율성능이 결정됨을 보였다.

• Journal of Microbiology and Biotechnology
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• 제13권2호
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• pp.282-286
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• 2003

The purpose of this study was to isolate a specific DNA probe for the strain ATTC 25611 of the species Prevotella intermedia by using a new rapid screening mothod. The whole-genomic DNA of P. intermedia ATCC 25611 was isolated and purified. The HindIII-digested genomic DNAs from the strain were cloned by the random cloning method. To screen the strain-specific DNA probe, inverted dot blot hybridization tests were performed. In this assay, 20 ng of recombinant plasmids containing the HindIII-digested genomic DNA fragment were boiled and blotted onto a nylon membrane, and hybridized with digoxigenin-dUTP labeled genomic DNAs in a concentration of 100 ng/ml. Southern blot analysis was performed in order to confirm the results of the inverted dot blot hybridization tests. The data showed that a Pi34 probe (2.1 kbp; 1 out of 32 probes) was specific for P. intermedia strain ATCC 25611 and could be useful for the detection and identification of the strain, particularly in epidemiological studies of periodontal disease.

• Mycobiology
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• 제45권4호
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• pp.401-408
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• 2017

Colletotrichum gloeosporioides is an economically important fungal pathogen causing substantial yield losses indifferent host plants. To understand the genetic diversity and molecular epidemiology of this fungus, we have developed a novel, high-resolution multi-locus microsatellite typing (MLMT) method. Bioinformatic analysis of C. gloeosporioides unannotated genome sequence yielded eight potential microsatellite loci, of which five, CG1 $(GT)_n$, CG2 $(GT1)_n$, CG3 $(TC)_n$, CG4 $(CT)_n$, and CG5 $(CT1)_n$ were selected for further study based on their universal amplification potential, reproducibility, and repeat number polymorphism. The selected microsatellites were used to analyze 31 strains of C. gloeosporioides isolated from 20 different host plants from India. All microsatellite loci were found to be polymorphic, and the approximate fragment sizes of microsatellite loci CG1, CG2, CG3, CG4, and CG5 were in ranges of 213-241, 197-227, 231-265, 209-275, and 132-188, respectively. Among the 31 isolates, 55 different genotypes were identified. The Simpson's index of diversity (D) values for the individual locus ranged from 0.79 to 0.92, with the D value of all combined five microsatellite loci being 0.99. Microsatellite data analysis revealed that isolates from Ocimum sanctum, Capsicum annuum (chili pepper), and Mangifera indica (mango) formed distinct clusters, therefore exhibited some level of correlation between certain genotypes and host. The developed MLMT method would be a powerful tool for studying the genetic diversity and any possible genotype-host correlation in C. gloeosporioides.

• International Journal of Industrial Entomology and Biomaterials
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• 제36권2호
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• pp.25-30
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• 2018

The larvae of Hermetia. illucens have a high probability of coming into contact with microorganisms such as bacteria and fungi. Therefore, the survival of H. illucens is primarily the protection of their own against microbial infection. This effect depends on the development of the innate immune system. Antimicrobial Peptides (AMPs) exhibit antimicrobial activity against other bacterial strains and can provide important data to understand the basis of the innate immunity of H. illucens. In this study, we injected larvae with Enterococcus. faecalis (gram-positive bacteria) and Serratia. marcescens as (gram-negative bacteria) to test the hypothesis that H. illucens is protected from infection by its immune-related gene expression repertoire. To identify the inducible immune-related genes, we performed and cataloged the transcriptomes by RNA-Seq analysis. We compared the transcriptomes of whole larvae and obtained a DNA fragment of 465 bp including the poly (A) tail by RACE as a novel H. illucens immune-related gene against bacteria. A novel target mRNA expression was higher in immunized larvae with E. faecalis and S. marcescens groups than non-immunized group. We expect our study to provide evidence that the global RNA-Seq approach allowed for the identification of a gene of interest which was further analyzed by quantitative RT-PCR, together with genes chosen from the available literature.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• 제18권1호
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• pp.39-47
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• 2015

Purpose: To determine clinically useful biochemical markers reflecting disease activity and/or gastrointestinal (GI) tract involvement in Henoch-$Sch{\ddot{o}}nlein$ purpura (HSP). Methods: A total of 185 children with HSP and 130 controls were included. Laboratory data indicating inflammation, standard coagulation, and activated coagulation were analyzed for the HSP patients, including measurements of the hemoglobin level, white blood cell (WBC) count, absolute neutrophil count (ANC), platelet count, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP) level, prothrombin time, activated partial thromboplastin time, and fibrinogen, D-dimer, and fibrin degradation product (FDP) levels. The clinical scores of the skin, joints, abdomen, and kidneys were assessed during the acute and convalescence phases of HSP. Results: The WBC count, ANC, ESR, and CRP, fibrinogen, D-dimer, and FDP levels were significantly higher in the acute phase compared with the convalescent phase of HSP (p<0.05). The total clinical scores were more strongly correlated with the D-dimer (r=0.371, p<0.001) and FDP (r=0.369, p<0.001) levels than with inflammatory markers, such as the WBC count (r=0.241, p=0.001), ANC (r=0.261, p<0.001), and CRP (r=0.260, p<0.001) levels. The patients with GI symptoms had significantly higher ANC (median [interquartile range], 7,138.0 [4,446.4-9,470.0] vs. 5,534.1 [3,263.0-8,153.5], p<0.05) and CRP (0.49 [0.15-1.38] vs. 0.23 [0.01-0.67], p<0.05), D-dimer (2.63 [1.20-4.09] vs. 1.75 [0.62-3.39]), and FDP (7.10 [0.01-13.65] vs. 0.10 [0.01-7.90], p<0.05) levels than those without GI symptoms. Conclusion: D-dimer and FDPs are more strongly associated with disease activity and more consistently reflect GI involvement than inflammatory markers during the acute phase of HSP.