Evaluation of methods for isolation of DNA for polymerase chain reaction (PCR)-based identification of pathogenic bacteria from pure cultures and water samples

2008 ◽  
Vol 58 (5) ◽  
pp. 995-999 ◽  
Author(s):  
K. Horáková ◽  
H. Mlejnková ◽  
P. Mlejnek
Keyword(s):  
Polymerase Chain Reaction ◽  
Water Samples ◽  
Pathogenic Bacteria ◽  
Pcr Amplification ◽  
Bacterial Suspension ◽  
Chain Reaction ◽  
Alkaline Lysis ◽  
Bacterial Dna ◽  
Pure Cultures ◽  
Polymerase Chain

Polymerase chain reaction (PCR) provides a reliable detection of pathogenic bacteria in water samples. However, this method can be adversely influenced by the purity of the DNA template. This is a particularly important obstacle when the bacterial DNA is directly extracted from water samples. In this study we compared the suitability of 8 different methods for isolation of bacterial DNA from pure cultures and 10 different methods for isolation of DNA from water samples. The quality of extracted DNA was assessed by PCR amplification of target sequences derived from uid (E. coli and Shigella sp.), tuf (Enterococcus sp.) and hns (Salmonella sp.). Results indicated that there are differences among the methods tested and only a few of them gave satisfactory results. The method based on alkaline lysis of bacterial suspension, which was developed in our laboratory, seemed to be efficient enough for the detection of bacteria from pure cultures. Detection of bacteria directly from water samples was more difficult. The modified method developed by Slusarenko was found as the best of the tested methods.

scholarly journals DETEKSI Liberibacter spp. PADA JERUK SIAM BERGEJALA KLOROSIS DISERTAI BERCAK HITAM DENGAN Polymerase Chain Reaction

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Iliana Iliana ◽  
Rahmawati Rahmawati ◽  
Agus Rachmat ◽  
Mukarlina Mukarlina ◽  
Latiffah Zakaria
Keyword(s):  
Polymerase Chain Reaction ◽  
Plasmid Dna ◽  
Pathogenic Bacteria ◽  
Chain Reaction ◽  
16S Rdna Gene ◽  
Bacterial Dna ◽  
Leaf Sampling ◽  
Bacterial Plasmid ◽  
Polymerase Chain ◽  
Citrus Leaves

Liberibacter bacteria are one of the pathogenic bacteria in citrus plants. Siam Citrus Plant in Setapok Village, Singkawang City, suspected to be infected with Liberibacter spp. bacteria by showing patterns of symptoms of chlorosis accompanied by patches. This study aims to detect Liberibacter spp. on Siam Citrus leaves with symptomatic chlorosis with patches. Leaf sampling uses the roaming method in one of the citrus plantations in Setapok Village, Singkawang City. Detection of Liberibacter spp. done by PCR (Polymerase Chain Reaction) technique. Detection of bacterial DNA through several stages namely, isolation of bacterial plasmid DNA, 16S rDNA gene amplification with a thermocycler machine, and visualization using a set of electrophoresis devices. Electrophoresis results show the presence of DNA band lines, with a size of around 1100 bp for OI1 and OI2c primers, and DNA bands of 703 bp for A2 and J5 specifics. The results showed that there were Liberibacter spp. in the symptomatic chlorosis of Siam Citrus leaves accompanied by patches.

scholarly journals Amplification of human beta-actin gene by the reverse transcriptase-polymerase chain reaction: implications for assessment of RNA from formalin-fixed, paraffin-embedded material.

1996 ◽  
Vol 44 (10) ◽  
pp. 1205-1207 ◽  
Author(s):  
A Dakhama ◽  
V Macek ◽  
J C Hogg ◽  
R G Hegele
Keyword(s):  
Polymerase Chain Reaction ◽  
Pcr Amplification ◽  
Housekeeping Gene ◽  
Chain Reaction ◽  
Viral Genomes ◽  
Negative Results ◽  
Beta Actin ◽  
Target Nucleic Acid ◽  
Formalin Fixed Paraffin Embedded ◽  
Polymerase Chain

The polymerase chain reaction (PCR) is a powerful method that allows enzymatic amplification of rate target nucleic acid sequences. It has been applied to the amplification of viral genomes from paraffin-embedded pathology specimens. However, interpretation of negative results requires amplification of a housekeeping gene such as beta-actin. In the present study we used specific oligonucleotide primers previously designed to amplify both the genomic DNA and the mRNA transcript from paraffin-embedded tissue. These products have predicted sizes of 250 BP and 154 BP, respectively, but our results showed that PCR amplification only (without reverse transcription) unexpectedly generated the 154-BP product. Further investigation of the nature of this product demonstrated that it originated from the amplification of DNA, not RNA. We conclude that the 154-BP product generated by these primers cannot be exclusively considered as beta-actin RNA product and should not be used to assess successful extraction of RNA, to ascertain its integrity, or to normalize for the total amount of RNA assayed by RT-PCR from paraffin-embedded tissue.

scholarly journals A Self-Contained Portable Polymerase-Chain-Reaction System Integrated with Electromagnetic Mini-Actuators for Bi-Directional Fluid Transport

2011 ◽  
Vol 27 (3) ◽  
pp. 357-364
Author(s):  
B. T. Chia ◽  
S.-A. Yang ◽  
M.-Y. Cheng ◽  
C.-W. Lin ◽  
Y.-J. Yang
Keyword(s):  
Polymerase Chain Reaction ◽  
Fluid Transport ◽  
Point Of Care ◽  
Reaction System ◽  
Thermal Characteristics ◽  
Pcr Amplification ◽  
Chain Reaction ◽  
Rapid Temperature ◽  
Small Footprint ◽  
Polymerase Chain

ABSTRACTIn this paper, the development of a portable polymerase chain reaction (PCR) device is presented. Integrating electromagnetic mini-actuators for bi-directional fluid transport, the proposed device, whose dimension is 67mm × 66mm × 25mm, can be fully operated with a 5V DC voltage. The device consists of four major parts: A disposable channel chip in which PCR mixture is manipulated and reacted, a heater chip which generates different temperature zones for PCR reaction, a linear actuator array for pumping PCR mixture, and a circuit module for controlling and driving the system. The advantages of the device include the rapid temperature responses associated with continuous-flow-type PCR devices, as well as the programmable thermal cycling associated with chamber-type PCR devices. The thermal characteristics are measured and discussed. PCR amplification is successfully performed for the 122 bp segment of MCF-7/adr cell line. Due to its small footprint, this self-contained system potentially can be employed for point-of-care (POC) applications.

scholarly journals Method Comparison of DNA Isolation and Quantification for Fish and Seafood Authenticity Determination

2018 ◽  
Vol 13 (3) ◽  
pp. 115
Author(s):  
Dwiyitno Dwiyitno ◽  
Stefan Hoffman ◽  
Koen Parmentier ◽  
Chris Van Keer
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Extraction ◽  
Dna Isolation ◽  
Blue Mussel ◽  
Pcr Amplification ◽  
Amplification Efficiency ◽  
Chain Reaction ◽  
Seafood Products ◽  
Polymerase Chain ◽  
Commercial Kit

Fish and seafood products has been commonly targeted for fraudulent activities. For that reason, authentication of fish and seafood products is important to protect consumers from fraudulent and adulteration practices, as well as to implement traceability regulation. From the viewpoint of food safety, authenticity is beneficial to protect public from serious food poisoning incidents, such as due to ingestion of toxic species. Since DNA based identification depends on the nucleic acid polymerase chain reaction (PCR), the quantity and quality/purity of DNA will contribute significantly to the species authentication. In the present study, different DNA extraction and purification methods (3 classical methods and one commercial kit) were compared to produce the better isolated DNA for PCR amplification. Additionally, different methods for the estimation of DNA concentration and purity which is essential for PCR amplification efficiency were also evaluated. The result showed that classical DNA extraction methods (based on TNES-Urea) yielded a higher amount of DNA (11.30-323.60 ng/g tissue) in comparison to commercial kit/Wizard Promega (5.70-83.45 ng/g tissue). Based on the purity of DNA extract (A260/280), classical DNA extraction method produced relatively similar on DNA quality to the commercial kit (1.79-2.12). Interestingly, all classical methods produced DNA with A260/280 ratio of more than 2.00 on the blue mussel, in contrast with commercial kit. The commercial kit also produced better quality of DNA compared to the classical methods, showing the higher efficiency in PCR amplification. NanoDrop is promising as cheap, robust and safe UV-spectrophotometer method for DNA quantification, as well as the purity evaluation.Keywords: seafood authenticity, DNA isolation, polymerase chain reaction, NanoDrop, Picogreen

Detection of Genetically Modified Coho Salmon Using Polymerase Chain Reaction (PCR) Amplification

2002 ◽  
Vol 50 (11) ◽  
pp. 3161-3164 ◽  
Author(s):  
Saad Masri ◽  
Heidi Rast ◽  
Teresa Ripley ◽  
Delano James ◽  
Margaret Green ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Coho Salmon ◽  
Genetically Modified ◽  
Pcr Amplification ◽  
Chain Reaction ◽  
Polymerase Chain

scholarly journals Diversity ofLeptospiraspp. in Rats and Environment from Urban Areas of Sarawak, Malaysia

2017 ◽  
Vol 2017 ◽  
pp. 1-8 ◽  
Author(s):  
Chai Fung Pui ◽  
Lesley Maurice Bilung ◽  
Kasing Apun ◽  
Lela Su’ut
Keyword(s):  
Polymerase Chain Reaction ◽  
Water Samples ◽  
Urban Areas ◽  
Environmental Samples ◽  
Soil Samples ◽  
Chain Reaction ◽  
Prevalence Studies ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Soil And Water

Various prevalence studies onLeptospirain animals and humans, as well as environmental samples, had been conducted worldwide, including Malaysia. However, limited studies have been documented on the presence of pathogenic, intermediate, and saprophyticLeptospirain selected animals and environments. This study was therefore conducted to detectLeptospiraspp. in rats, soil, and water from urban areas of Sarawak using the polymerase chain reaction (PCR) method. A total of 107 rats, 292 soil samples, and 324 water samples were collected from April 2014 to February 2015. PathogenicLeptospirawas present in 5.6% (6/107) of rats, 11.6% (34/292) of soil samples, and 1.9% (6/324) of water samples. IntermediateLeptospirawas present in 2.7% (8/292) of soil samples and 1.9% (6/324) of water samples. SaprophyticLeptospirawas present in 10.3% (11/107) of rats, 1.4% (4/292) of soil samples, and 0.3% (1/324) of water samples. From this study, 76Leptospiraspp. were isolated. Based on DNA sequencing, the dominantLeptospiraspp. circulating in urban areas of Sarawak are pathogenicLeptospira noguchii, intermediateLeptospira wolffiiserovar Khorat, and saprophyticLeptospira meyeri, respectively. Overall, this study provided important surveillance data on the prevalence ofLeptospiraspp. from rats and the environment, with dominant local serovars in urban areas of Sarawak.

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