scholarly journals The detection of Plasmodiophora brassicae using loop-mediated isothermal DNA amplification

2014 ◽  
Vol 67 (4) ◽  
pp. 59-66 ◽  
Author(s):  
Joanna Kaczmarek ◽  
Witold Irzykowski ◽  
Adam Burzyński ◽  
Małgorzata Jędryczka
Keyword(s):  
Oilseed Rape ◽  
Visual Detection ◽  
Plasmodiophora Brassicae ◽  
Detection System ◽  
Screening Method ◽  
Dna Amplification ◽  
Good Alternative ◽  
Strand Displacement ◽  
Ctab Method ◽  
Vegetable Brassicas

<em>Plasmodiophora brassicae</em>, the cause of clubroot, is a very serious problem preventing from successful and profitable cultivation of oilseed rape in Poland. The pathogen was found in all main growing areas of oilseed rape; it also causes considerable problems in growing of vegetable brassicas. The aim of this work was to elaborate fast, cheap and reliable screening method to detect <em>P. brassicae</em>. To achieve this aim the Loop-mediated isothermal DNA amplification (LAMP) technique has been elaborated. The set of three primer pairs was designed using LAMP software. The detection was performed with the GspSSD polymerase, isolated from bacteria <em>Geobacillus</em> sp., with strand displacement activity. DNA extraction from clubbed roots obtained from farmers’ fields of oilseed rape infected by <em>P. brassicae</em> was done using a modified CTAB method. The reaction was performed for 60 min at 62<sup>o</sup>C. The visual detection was done using CFX96 Real Time PCR Detection System (BioRad) or Gerie II Amplicatior (Optigen). The detection with LAMP proved its usefulness; it was easy, fast and accurate and independent of plant age. The detection limit was 5 spores per 1 µl of the spore suspension, so LAMP was less sensitive than quantitative PCR tests reported in the literature. However, the method is cheap and simple, so it is a good alternative, when it comes to practical use and the assessment of numerous samples.

scholarly journals Biosensors Based on Isothermal DNA Amplification for Bacterial Detection in Food Safety and Environmental Monitoring

Sensors ◽  
2021 ◽  
Vol 21 (2) ◽  
pp. 602
Author(s):  
Sandra Leonardo ◽  
Anna Toldrà ◽  
Mònica Campàs
Keyword(s):  
Food Safety ◽  
Environmental Monitoring ◽  
Rolling Circle Amplification ◽  
Dna Amplification ◽  
Isothermal Amplification ◽  
In Situ Monitoring ◽  
Strand Displacement ◽  
Strand Displacement Amplification ◽  
Bacterial Detection ◽  
Efficient Detection

The easy and rapid spread of bacterial contamination and the risk it poses to human health makes evident the need for analytical methods alternative to conventional time-consuming laboratory-based techniques for bacterial detection. To tackle this demand, biosensors based on isothermal DNA amplification methods have emerged, which avoid the need for thermal cycling, thus facilitating their integration into small and low-cost devices for in situ monitoring. This review focuses on the breakthroughs made on biosensors based on isothermal amplification methods for the detection of bacteria in the field of food safety and environmental monitoring. Optical and electrochemical biosensors based on loop mediated isothermal amplification (LAMP), rolling circle amplification (RCA), recombinase polymerase amplification (RPA), helicase dependent amplification (HDA), strand displacement amplification (SDA), and isothermal strand displacement polymerisation (ISDPR) are described, and an overview of their current advantages and limitations is provided. Although further efforts are required to harness the potential of these emerging analytical techniques, the coalescence of the different isothermal amplification techniques with the wide variety of biosensing detection strategies provides multiple possibilities for the efficient detection of bacteria far beyond the laboratory bench.

scholarly journals COBAS AMPLICOR: fully automated RNA and DNA amplification and detection system for routine diagnostic PCR

1996 ◽  
Vol 42 (12) ◽  
pp. 1915-1923 ◽  
Author(s):  
N DiDomenico ◽  
H Link ◽  
R Knobel ◽  
T Caratsch ◽  
W Weschler ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Internal Control ◽  
Detection System ◽  
Dna Amplification ◽  
Cross Reactivity ◽  
Diagnostic Pcr ◽  
Thermal Cycler ◽  
Paramagnetic Microparticles ◽  
Rna And Dna ◽  
Single Reaction

Abstract The COBAS AMPLICOR system automates amplification and detection of target nucleic acids, making diagnostic PCR routine for a variety of infectious diseases. The system contains a single thermal cycler with two independently regulated heating/cooling blocks, an incubator, a magnetic particle washer, a pipettor, and a photometer. Amplified products are captured on oligonucleotide-coated paramagnetic microparticles and detected with use of an avidin-horseradish peroxidase (HRP) conjugate. Concentrated solutions of amplicon or HRP were pipetted without detectable carryover. Amplified DNA was detected with an intraassay CV of &lt; 4.5%; the combined intraassay CV for amplification and detection was &lt; 15%. No cross-reactivity was observed when three different target nucleic acids were amplified in a single reaction and detected with three target-specific capture probes. The initial COBAS AMPLICOR menu includes qualitative tests for diagnosing infections with Chlamydia trachomatis, Neisseria gonorrhoeae, Mycobacterium tuberculosis, and hepatitis C virus. All tests include an optional Internal Control to provide assurance that specimens are successfully amplified and detected.

Greenhouse and field experiments with winter oilseed rape cultivars resistant to Plasmodiophora brassicae Wor.

2017 ◽  
Vol 92 ◽  
pp. 60-69 ◽  
Author(s):  
Veronika Řičařová ◽  
Jan Kazda ◽  
Petr Baranyk ◽  
Pavel Ryšánek
Keyword(s):  
Oilseed Rape ◽  
Field Experiments ◽  
Plasmodiophora Brassicae ◽  
Winter Oilseed Rape

scholarly journals History of Oilseed Rape Cropping and Geographic Origin Affect the Genetic Structure of Plasmodiophora brassicae Populations

2014 ◽  
Vol 104 (5) ◽  
pp. 532-538 ◽  
Author(s):  
Becke Strehlow ◽  
Friederike de Mol ◽  
Christine Struck
Keyword(s):  
Oilseed Rape ◽  
Plasmodiophora Brassicae ◽  
Gene Diversity ◽  
Spatial Scales ◽  
Field Isolate ◽  
Geographic Origin ◽  
Fixation Index ◽  
Common Disease ◽  
Geographic Differentiation ◽  
Soilborne Pathogen

The soilborne pathogen Plasmodiophora brassicae causes clubroot on Brassica crops, a common disease in many oilseed rape growing regions. Here, we investigate genetic diversity and geographic differentiation of P. brassicae populations from different regions in Germany. We compared three regions that differ in oilseed rape cropping history, oilseed rape acreage, and incidence of clubroot. These regions were either spatially separated or separated by the former inner German border. Plasmodiophora isolates were collected from 59 fields (29, 17, and 13 fields per region, respectively) and 174 amplified fragment length polymorphism (AFLP) markers were analyzed. Every field isolate showed a unique genotype pattern; that is, no genotype was shared among the regions and different fields. The mean gene diversity was 0.27, suggesting that P. brassicae is a genetically diverse species. The comparison of indexes (gene diversity, genotypic diversity, and linkage disequilibrium) between the regions does not support our hypotheses that cropping history, oilseed rape acreage, and incidence of clubroot affect these estimates. Principal component analysis (PCA), fixation index (FST), and generalized linear model (GLM) were suitable to specify regional differences. PCA revealed two clusters of isolates based on the geographic origin of the isolates and FST showed that these clusters were highly differentiated. Hypotheses about association of genotypes with different spatial scales were tested with GLM: the region, reflecting the cropping history, and the individual field had a significant effect on the AFLP pattern. We propose that individual field isolates represent a discrete population and that geographic differentiation results from low levels of gene flow due to the limited dispersal of this soilborne pathogen and from localized selection pressure as unifying force on the genotypes.

scholarly journals Visual detection of glial cell line-derived neurotrophic factor based on a molecular translator and isothermal strand-displacement polymerization reaction

2015 ◽  
pp. 1889
Author(s):  
Jing Cai ◽  
Li-Yong Zhang ◽  
Tao Xing ◽  
Li-Xin Du ◽  
Qing-Min Li ◽  
...  
Keyword(s):  
Cell Line ◽  
Glial Cell ◽  
Neurotrophic Factor ◽  
Visual Detection ◽  
Polymerization Reaction ◽  
Strand Displacement

Visual detection system of powder mixing equipment based on PLC

2021 ◽  
Author(s):  
Ce Fang ◽  
Qian Wang ◽  
Zizheng Weng
Keyword(s):  
Visual Detection ◽  
Detection System ◽  
Powder Mixing

scholarly journals Visual detection of gene mutations based on isothermal strand-displacement polymerase reaction and lateral flow strip

2012 ◽  
Vol 31 (1) ◽  
pp. 310-315 ◽  
Author(s):  
Yuqing He ◽  
Kang Zeng ◽  
Sanquan Zhang ◽  
Anant S. Gurung ◽  
Meenu Baloda ◽  
...  
Keyword(s):  
Visual Detection ◽  
Gene Mutations ◽  
Lateral Flow ◽  
Strand Displacement ◽  
Lateral Flow Strip

The Error Analysis about Gauge Visual Detection System between High Signals and Contact Net

2012 ◽  
Vol 522 ◽  
pp. 347-350
Author(s):  
Xi Lin Zhu ◽  
Yong Yu ◽  
Qiang Wei ◽  
Xiang Zou ◽  
Chen Jun Huang
Keyword(s):  
Image Processing ◽  
Error Analysis ◽  
System Design ◽  
Visual Detection ◽  
Imaging System ◽  
Detection System ◽  
Systematic Errors ◽  
Lighting Conditions ◽  
Specific Impact

t is need to experiment to verify the correctness and validity of various stages in system design after gauge visual detection system designing between high signals and contact net. Then it does error analysis from lighting conditions, camera resolution, binocular imaging system installation structure, camera out of synchronized, noise and subsequent image processing operations, etc. It analysis the systematic errors principle and specific impact, then identifies specific improvements.

OCCURRENCE AND SURVIVAL OF PLASMODIOPHORA BRASSICAE IN FINNISH TURNIP RAPE AND OILSEED RAPE FIELDS

2013 ◽  
pp. 627-632
Author(s):  
M. Rastas ◽  
S. Latvala ◽  
A. Hannukkala
Keyword(s):  
Oilseed Rape ◽  
Plasmodiophora Brassicae ◽  
Turnip Rape
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