• Title, Summary, Keyword: Strain specificity

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Development of Strain-specific PCR Primers Based on a DNA Probe Fu12 for the Identification of Fusobacterium nucleatum subsp. nucleatum ATCC $25586^T$

  • Kim Hwa-Sook;Song Soo Keun;Yoo So Young;Jin Dong Chun;Shin Hwan Seon;Lim Chae Kwang;Kim Myong Soo;Kim Jin-Soo;Choe Son-Jin;Kook Joong-Ki
    • Journal of Microbiology
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    • v.43 no.4
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    • pp.331-336
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    • 2005
  • The objective of this study was to assess the strain-specificity of a DNA probe, Fu12, for Fusobacterium nucleatum subsp. nucleatum ATCC $25586^T$ (F. nucleatum ATCC $25586^T$), and to develop sets of strain-specific polymerase chain reaction (PCR) primers. Strain-specificity was tested against 16 strains of F. nucleatum and 3 strains of distinct Fusobacterium species. Southern blot hybridization revealed that the Fu12 reacted exclusively with the HindIII-digested genomic DNA of F. nucleatum ATCC $25586^T$. The results of PCR revealed that three pairs of PCR primers, based on the nucleotide sequence of Fu12, generated the strain-specific amplicons from F. nucleatum ATCC $25586^T$. These results suggest that the DNA probe Fu12 and the three pairs of PCR primers could be useful in the identification of F. nucleatum ATCC $25586^T$, especially with regard to the determination of the authenticity of the strain.

Isolation of Novel Pseudomonas diminuta KAC-1 Strain Producing Glutaryl 7-Aminocephalosporanic Acid Acylase

  • Kim, Dae-Weon;Kang, Sang-Mo;Yoon, Ki-Hong
    • Journal of Microbiology
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    • v.37 no.4
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    • pp.200-205
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    • 1999
  • 7-Aminocephalosporanic acid (7-ACA) is the initial compound in preparation of cephalosporin antibiotics widely used in clinical treatment. Bacteria producing glutaryl 7-ACA acylase, which convert cephalosporin C to 7-ACA, has been screened in soil samples. A bacterial strain exhibiting high glutaryl 7-ACA acylase activity, designated KAC-1, was isolated and identified as a strain of Pseudomonas diminuta by characterizing its morphological and physiological properties. The screening procedures include culturing on enrichment media containing glutaric acid, glutamate, and glutaryl 7-aminocephalosporanic acid as selective carbon sources. To enhance enzyme production, optimal cultivation conditions were investigated. This strain grew optimally at pH 7 to 9 and in temperatures of 20 to 40 C, but acylase production was higher when the strain was grown at 25 C. Glutaric acid, glutamate and glucos also acted as inducers for acylase production. In a jar fermenter culture, P. diminuta KAC-1 produce acylase in a growth-associated manner. The substrate specificity of KAC-1 acylase by cell extract showed that this enzyme had specificity toward glutaryl 7-ACA, glutaryl 7-ADCA, but not cephalosporin C.

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Diagnostic Potential of Strain Ratio Measurement and a 5 Point Scoring Method for Detection of Breast Cancer: Chinese Experience

  • Parajuly, Shyam Sundar;Lan, Peng Yu;Yun, Ma Bu;Gang, Yang Zhi;Hua, Zhuang
    • Asian Pacific Journal of Cancer Prevention
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    • v.13 no.4
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    • pp.1447-1452
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    • 2012
  • Aim: To evaluate the differential diagnostic potential of lesion stiffness assessed by the sonoelastographic strain index ratio (SR) and elastographic color scoring system (UE) for breast lesions. Materials and Methods: Three hundred and forty two breast masses (158 benign and 184 malignant) from 325 consecutive patients (mean age 44.2 years; range 16-81)who had been scheduled for a sonographically guided core biopsy were examined proposed by Itoh et al, with scoring 1-3=benign and 4-5=malignant. Strain and area ratios of each lesion were calculated within the same machine. Histological diagnosis was used as the reference standard. The area under the curve (AUC) and cut-off point were obtained by receiver operating curve and the cross table Fischer Test was carried out for assessing diagnostic value. Sensitivity, specificity, PPV, NPV, accuracy and false-discovery rates were compared. Results: The mean strain ratios for benign and malignant lesions were 1.87 and 7.9 respectively. (P<0.0001). When a cutoff point of 3.54 was used, SR had a sensitivity of 94.6%, a specificity 94.3%, a PPV of 95.1%, an NPV of 93.7% and an accuracy of 94.4%. The AUC values were 0.90 for the 5 point scoring system (UE) and 0.96 for the strain index ratio. The overall diagnostic performance was SR method was better (P<0.05). Conclusions: Strain ratio measurement could be another effective predictor in elastography imaging besides 5 the point scoring system for differential diagnosis of breast lesions.

Characteristics of ustilago maydis virus of SH14 killer strain isolated in Korea

  • Hwang, Seon-Hee;Jung, Cheong-Hwan;Yie, Se-Won
    • Journal of Microbiology
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    • v.33 no.2
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    • pp.154-159
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    • 1995
  • SH-14, a novel killer strain of Ustilago maydis was isolated in Korea. It has been reported in other papers that the toxin specificity and double-stranded RNA pattern of SH-14 strain were different from other laboratory strains. In this paper, we analyzed the biochemical characteristics of U. maydis SH-14 virus. Three distinctive peaks were isolated from CsCl density gradient, designated as top (T), intermediate (I) and bottom (B) components. We found that the densities of each components, 1.285, 1.408 g/cm$\^$3/, respectively, are very similar to those of other strains. As previously reported by the analysis of dsRNA in each component, the dsRNA segments are separately encapsidated. Capsid protein of SH-14 virus consists of two proteins about 70 Kd shown by SDS-PAGE analysis. Electron microscopic examination of the virus particles revealed that UmV particles are very similar in size and morphology to all isolates as well as all lab-strains. In order to test immunological cross reactivity of UmV, werstern bolt analysis was carriedout with antiserum against A8 virus. All capsid protein had positive reaction against A8 antibody which indicated that UmV are immunologically cross-reactive with all isolates from Korea. The results presented in this paper may show that UmV isolated from SH-14 strain has very similar biochemical characteristics to those of other UmV. However, the difference in the toxin specificity and the molecular weight of toxin protein from the SH-14 strain has us to conclude that U. maydis SH-14 strain is a new killer type.

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Substrate Specificity of the Macrolide-Phosphotransferase K (마크로라이드-포스포트란스페라제 K의 기질 특이성)

  • Kim, Sook-Kyung;Oh, Tae-Gwon;Baek, Moon-Chang;Kim, Byong-Kak;Choi, Eung-Chil
    • YAKHAK HOEJI
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    • v.41 no.4
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    • pp.530-532
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    • 1997
  • The MICs of various macrolide, lincosamide and streptogramin B antibiotics against highly erythromycin-resistant Escherichia coli 209K strain were evaluated. E. coli 209K showed high MICs against 14-membered macrolides and the relatively weaker resistance to 16-membered macrolides, lincosamides and streptogramin B. The macrolide-phosphotransferase K from E. coli 209K showed greater substrate specificity to the 14-membered macrolide antibiotics than to the 16-membered macrolide antibiotics, lincosamide and streptogramin B. Therefore, it was considered that the high resistance was due to the macrolide-phosphotransferase K.

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Purification of Cholesterol Esterase from Aeromoans SP. (Aeromoans SP.가 생산하는 콜레스테롤 에스테라아제의 정제)

  • 박부길;이해익
    • KSBB Journal
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    • v.5 no.1
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    • pp.19-23
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    • 1990
  • A cholesterol esterase-producing microorganism, strain CES 506, isolated from soil was identified as Aeromonas sp. This strain produce about 0.023 units of cholesterol esterase per ml of culture broth. The cholesterol esterase produced by this strain was purified, 370 fold to homogeneity in an overall yield of 24% from culture broth. The apparent molecular weight was 64, 000, as estimated by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The enzyme showed a high substrate specificity for cholesterylpalmitate and the Km value for the hydrolysis of cholesterylpalmitate by this enzyme were 0.15mM.

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Detection and Quantification of Toxin-Producing Microcystis aeruginosa Strain in Water by NanoGene Assay

  • Lee, Eun-Hee;Cho, Kyung-Suk;Son, Ahjeong
    • Journal of Microbiology and Biotechnology
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    • v.27 no.4
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    • pp.808-815
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    • 2017
  • We demonstrated the quantitative detection of a toxin-producing Microcystis aeruginosa (M. aeruginosa) strain with the laboratory protocol of the NanoGene assay. The NanoGene assay was selected because its laboratory protocol is in the process of being transplanted into a portable system. The mcyD gene of M. aeruginosa was targeted and, as expected, its corresponding fluorescence signal was linearly proportional to the mcyD gene copy number. The sensitivity of the NanoGene assay for this purpose was validated using both dsDNA mcyD gene amplicons and genomic DNAs (gDNA). The limit of detection was determined to be 38 mcyD gene copies per reaction and 9 algal cells/ml water. The specificity of the assay was also demonstrated by the addition of gDNA extracted from environmental algae into the hybridization reaction. Detection of M. aeruginosa was performed in the environmental samples with environmentally relevant sensitivity (${\sim}10^5$ algal cells/ml) and specificity. As expected, M. aeruginosa were not detected in nonspecific environmental algal gDNA over the range of $2{\times}10^0$ to $2{\times}10^7$ algal cells/ml.

Strain-specific Detection of Kimchi Starter Leuconostoc mesenteroides WiKim33 using Multiplex PCR

  • Lee, Moeun;Song, Jung Hee;Park, Ji Min;Chang, Ji Yoon
    • Journal of the Korean Society of Food Culture
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    • v.34 no.2
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    • pp.208-216
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    • 2019
  • Leuconostoc spp. are generally utilized as kimchi starters, because these strains are expected to have beneficial effects on kimchi fermentation, including improvement of sensory characteristics. Here, we developed a detection method for verifying the presence of the kimchi starter Leuconostoc mesenteroides WiKim33, which is used for control of kimchi fermentation. A primer set for multiplex polymerase chain reaction was designed based on the nucleotide sequence of the plasmids in strain WiKim33, and their specificity was validated against 45 different strains of Leuconostoc spp. and 30 other strains. Furthermore, the starter strain consistently tested positive, regardless of the presence of other bacterial species in starter kimchi during the fermentation period. Our findings showed that application of a strain-specific primer set for strain WiKim33 presented a rapid, sensitive, and specific method for detection of this kimchi starter strain during natural kimchi fermentation.