scholarly journals Genetic Characterization and Real-Time PCR Detection of Burkholderia glumae, a Newly Emerging Bacterial Pathogen of Rice in the United States

Plant Disease ◽  
2006 ◽  
Vol 90 (5) ◽  
pp. 603-610 ◽  
Author(s):  
Ronald J. Sayler ◽  
Richard D. Cartwright ◽  
Yinong Yang
Keyword(s):  
United States ◽  
Sequence Analysis ◽  
Real Time ◽  
Real Time Pcr ◽  
Acid Methyl Ester ◽  
The United States ◽  
Its Sequence ◽  
Burkholderia Glumae ◽  
Rdna Its ◽  
Its Sequence Analysis

Panicle blight of rice (Oryza sativa), caused by the bacterium Burkholderia glumae, is one of the most important new diseases in rice production areas of the southern United States. In this study, pathogenic strains were isolated from diseased panicles in Arkansas rice fields and examined using the Biolog GN microplate system, whole cell fatty acid methyl ester analysis (FAME), rep-polymerase chain reaction (PCR) genomic DNA fingerprinting, and 16S–23S ribosomal DNA (rDNA) intergenic transcribed spacer (ITS) sequence analysis. The B. glumae isolates from Arkansas can be divided into two major groups, but their genetic diversity was relatively low as revealed by 16S–23S rDNA ITS sequence analysis. Since no practical method existed, up to now, for testing the presence of B. glumae in rice seeds, we have developed in this study a real-time PCR method that is effective in detecting and identifying the pathogen in seed lots and in whole plants. The specific PCR primers were designed based on the 16S–23S rDNA ITS sequence of several representative isolates from Arkansas and Japan. This method is highly sensitive, rapid, and reliable, and has great potential for analyzing large numbers of samples without the need for DNA extraction or agarose gel electrophoresis. Although vertical resistance has not been observed among tested rice cultivars, LM-1 and Drew exhibited considerable resistance to B. glumae infection based on disease lesion size and the bacterial growth in planta.

rDNA ITS Sequence Analysis of Different Cultivar Variety of Cornus officinalis

2010 ◽  
Vol 30 (1) ◽  
pp. 72-75
Author(s):  
Sui-Qing CHEN ◽  
Cheng-Xue PAN ◽  
Xiao-Lei LU ◽  
Li-Li WANG
Keyword(s):  
Sequence Analysis ◽  
Its Sequence ◽  
Rdna Its ◽  
Cornus Officinalis ◽  
Its Sequence Analysis

scholarly journals Ulva armoricana(Ulvales, Chlorophyta) from the coasts of Brittany (France). II. Nuclear rDNA ITS sequence analysis

1998 ◽  
Vol 33 (1) ◽  
pp. 81-86 ◽  
Author(s):  
G. Coat ◽  
P. Dion ◽  
M.-C. Noailles ◽  
B. De Reviers ◽  
J.-M. Fontaine ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Its Sequence ◽  
Nuclear Rdna ◽  
Rdna Its ◽  
Its Sequence Analysis ◽  
Ulva Armoricana

Differentiation ofDendrobiumSpecies used as ”Huangcao Shihu” by rDNA ITS Sequence Analysis

Planta Medica ◽  
2006 ◽  
Vol 72 (1) ◽  
pp. 89-92 ◽  
Author(s):  
Hong Xu ◽  
Zhengtao Wang ◽  
Xiaoyu Ding ◽  
Kaiya Zhou ◽  
Luoshan Xu
Keyword(s):  
Sequence Analysis ◽  
Its Sequence ◽  
Rdna Its ◽  
Its Sequence Analysis

scholarly journals Development and validation of a direct real-time PCR assay for Mycobacterium bovis and implementation into the United States national surveillance program

2016 ◽  
Author(s):  
Philip E Dykema ◽  
Kevin D Stokes ◽  
Nadine R Beckwith ◽  
James W Mungin ◽  
Lizhe Xu ◽  
...  
Keyword(s):  
United States ◽  
Real Time ◽  
Mycobacterium Bovis ◽  
Real Time Pcr ◽  
The United States ◽  
Surveillance Program ◽  
United States Department ◽  
Mycobacterial Culture ◽  
Development And Validation ◽  
Probe Set

Abattoir surveillance for bovine tuberculosis, which consists of identifying and submitting granulomas for histopathology and mycobacterial culture was the primary means for detecting new cases in the United States. Mycobacterial culture is expensive, labor intensive and identifies cases weeks after slaughter, hampering trace back efforts. To address this inefficiency, the United States Department of Agriculture replaced culture with real-time PCR for screening granulomas. The objectives of this paper were to describe the development and validation of this PCR as well as the performance of the assay during the first year of implementation. Using archived culture and histologically positive tissue, the sensitivity was 0.96 (95% CI: 0.89, 0.99) for the Mycobacterium tuberculosis complex primer-probe set and 0.89 (95% CI: 0.80, 0.95) for the Mycobacterium bovis specific primer-probe set. Specificity, estimated during by side by side testing was 0.998 (95% CI: 0.994, 1.000). After implementation, 6124 samples over 54 weeks were tested and all 36 histopathology positive samples were detected including 2 additional cases initially misclassified by histopathology. It appeared that specificity may have declined during post validation testing with 47/6086 signaling positive but not confirmed by either histopathology or culture. While PCR implementation has significantly improved the efficiency of the US slaughter surveillance program, careful attention must be paid to prevent and address cross contamination in the laboratory.

Classification of Rhizoctonia spp. using rDNA-ITS sequence analysis supports the genetic basis of the classical anastomosis grouping

Mycoscience ◽  
2008 ◽  
Vol 49 (2) ◽  
pp. 93-114 ◽  
Author(s):  
Michal Sharon ◽  
Baruch Sneh ◽  
Shiro Kuninaga ◽  
Mitsuro Hyakumachi ◽  
Shigeo Naito
Keyword(s):  
Sequence Analysis ◽  
Genetic Basis ◽  
Its Sequence ◽  
Rdna Its ◽  
Its Sequence Analysis

scholarly journals Mycobiota of maize seeds revealed by rDNA ‐ ITS sequence analysis of samples with varying storage times

2018 ◽  
Vol 7 (6) ◽  
pp. e00609 ◽  
Author(s):  
Hui‐Qin Xing ◽  
Jian‐Cang Ma ◽  
Bing‐Liang Xu ◽  
Shu‐Wu Zhang ◽  
Jin Wang ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Its Sequence ◽  
Rdna Its ◽  
Maize Seeds ◽  
Its Sequence Analysis ◽  
Storage Times

scholarly journals Development and validation of a direct real-time PCR assay for Mycobacterium bovis and implementation into the United States national surveillance program

2016 ◽  
Author(s):  
Philip E Dykema ◽  
Kevin D Stokes ◽  
Nadine R Beckwith ◽  
James W Mungin ◽  
Lizhe Xu ◽  
...  
Keyword(s):  
United States ◽  
Real Time ◽  
Mycobacterium Bovis ◽  
Real Time Pcr ◽  
The United States ◽  
Surveillance Program ◽  
United States Department ◽  
Mycobacterial Culture ◽  
Development And Validation ◽  
Probe Set

Abattoir surveillance for bovine tuberculosis, which consists of identifying and submitting granulomas for histopathology and mycobacterial culture was the primary means for detecting new cases in the United States. Mycobacterial culture is expensive, labor intensive and identifies cases weeks after slaughter, hampering trace back efforts. To address this inefficiency, the United States Department of Agriculture replaced culture with real-time PCR for screening granulomas. The objectives of this paper were to describe the development and validation of this PCR as well as the performance of the assay during the first year of implementation. Using archived culture and histologically positive tissue, the sensitivity was 0.96 (95% CI: 0.89, 0.99) for the Mycobacterium tuberculosis complex primer-probe set and 0.89 (95% CI: 0.80, 0.95) for the Mycobacterium bovis specific primer-probe set. Specificity, estimated during by side by side testing was 0.998 (95% CI: 0.994, 1.000). After implementation, 6124 samples over 54 weeks were tested and all 36 histopathology positive samples were detected including 2 additional cases initially misclassified by histopathology. It appeared that specificity may have declined during post validation testing with 47/6086 signaling positive but not confirmed by either histopathology or culture. While PCR implementation has significantly improved the efficiency of the US slaughter surveillance program, careful attention must be paid to prevent and address cross contamination in the laboratory.

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