Facile and rapid DNA extraction and purification from food matrices using IFAST (immiscible filtration assisted by surface tension)

The Analyst ◽  
2012 ◽  
Vol 137 (17) ◽  
pp. 4023 ◽  
Author(s):  
Lindsay N. Strotman ◽  
Guangyun Lin ◽  
Scott M. Berry ◽  
Eric A. Johnson ◽  
David J. Beebe
Keyword(s):  
Surface Tension ◽  
Dna Extraction ◽  
Extraction And Purification ◽  
Food Matrices

A comparison of DNA extraction and purification methods to detect Escherichia coli O157:H7 in cattle manure

2003 ◽  
Vol 54 (2) ◽  
pp. 165-175 ◽  
Author(s):  
Teegan Trochimchuk ◽  
John Fotheringham ◽  
Edward Topp ◽  
Heidi Schraft ◽  
Kam Tin Leung
Keyword(s):  
Escherichia Coli ◽  
Dna Extraction ◽  
Cattle Manure ◽  
Escherichia Coli O157 ◽  
Extraction And Purification ◽  
Purification Methods

scholarly journals Improved Method for DNA Extraction and Purification from Tetrahymena pyriformis

2019 ◽  
Vol 2 (2) ◽  
pp. 40
Author(s):  
Ezzouhra El Maaiden ◽  
Youssef El Kharrassi ◽  
Abdel Khalid Essamadi ◽  
Khadija Moustaid ◽  
Boubker Nasser
Keyword(s):  
Dna Extraction ◽  
Sodium Dodecyl ◽  
Model Organism ◽  
Tetrahymena Pyriformis ◽  
Pyrrolidine Dithiocarbamate ◽  
Restriction Enzyme Digestion ◽  
Chelex 100 ◽  
Extraction And Purification ◽  
Ammonium Pyrrolidine Dithiocarbamate ◽  
Triton X

Tetrahymena pyriformis (protozoa) is intensely investigated as a model organism, offering numerous advantages in comprehensive and multidisciplinary studies using morphologic or molecular methods. Since DNA extraction is a vital step of any molecular experiment, here a new mixed surfactant (Sodium dodecyl sulfate (SDS) 20%/Triton X-100) was adopted for effective DNA extraction from Tetrahymena pyriformis under an easy, fast protocol. The efficiency of this technique was then compared with three widely-used alternative techniques, namely the Chelex 100 matrix, Ammonium pyrrolidine dithiocarbamate (APD) complex and SDS–chloroform methods. DNA extraction was analyzed by pulsed-field gel electrophoresis, spectral measurement, fluorometry (Qubit), restriction enzyme digestion, and polymerase chain reaction. Data analysis revealed that the quantity and quality of the recovered DNA varied depending on the applied DNA extraction method. The new method (SDS 20%/Triton X-100) was the most efficient for extracting DNA from Tetrahymena pyriformis with high integrity and purity, affordable cost, less time, and suitability for molecular applications.

scholarly journals Effects of DNA Extraction and Purification Methods on Real-Time Quantitative PCR Analysis of Roundup Ready Soybean

2009 ◽  
Vol 92 (4) ◽  
pp. 1136-1144 ◽  
Author(s):  
Tigst Demeke ◽  
Indira Ratnayaka ◽  
Anh Phan
Keyword(s):  
Real Time ◽  
Dna Extraction ◽  
Quantitative Pcr ◽  
Real Time Pcr ◽  
Roundup Ready ◽  
Dna Recovery ◽  
Real Time Quantitative Pcr ◽  
Extraction And Purification ◽  
Purification Methods ◽  
Accuracy And Repeatability

Abstract The quality of DNA affects the accuracy and repeatability of quantitative PCR results. Different DNA extraction and purification methods were compared for quantification of Roundup Ready (RR) soybean (event 40-3-2) by real-time PCR. DNA was extracted using cetylmethylammonium bromide (CTAB), DNeasy Plant Mini Kit, and Wizard Magnetic DNA purification system for food. CTAB-extracted DNA was also purified using the Zymo (DNA Clean & Concentrator 25 kit), Qtip 100 (Qiagen Genomic-Tip 100/G), and QIAEX II Gel Extraction Kit. The CTAB extraction method provided the largest amount of DNA, and the Zymo purification kit resulted in the highest percentage of DNA recovery. The Abs260/280 and Abs260/230 ratios were less than the expected values for some of the DNA extraction and purification methods used, indicating the presence of substances that could inhibit PCR reactions. Real-time quantitative PCR results were affected by the DNA extraction and purification methods used. Further purification or dilution of the CTAB DNA was required for successful quantification of RR soybean. Less variability of quantitative PCR results was observed among experiments and replications for DNA extracted and/or purified by CTAB, CTAB+Zymo, CTAB+Qtip 100, and DNeasy methods. Correct and repeatable results for real-time PCR quantification of RR soybean were achieved using CTAB DNA purified with Zymo and Qtip 100 methods.

scholarly journals Rapid and Simple Detection of Trichosporon asahii by Optimized Colony PCR

2019 ◽  
Vol 2019 ◽  
pp. 1-9
Author(s):  
Dequan Zhang ◽  
Xuelian Lu ◽  
Yong Liao ◽  
Zhikuan Xia ◽  
Zhuoying Peng ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Intergenic Spacer ◽  
Glass Beads ◽  
Clinical Samples ◽  
Trichosporon Asahii ◽  
Colony Pcr ◽  
Extraction And Purification ◽  
Simple Detection ◽  
Mock Infection ◽  
Species Specific

Trichosporon asahii is the major pathogen causing invasive trichosporonosis. Conventional methods of its detection are time-consuming or costly and often require complex DNA extraction and purification steps, which hinders rapid clinical diagnosis. In this study, we evaluated colony PCR, which directly uses colonies or trace clinical samples as the template for amplification, for rapid detection of T. asahii infection. Four methods, namely, direct colony, freeze-thaw, glass beads, and enzymolysis, were compared to select the best DNA extraction strategy. We subsequently designed and screened species-specific primers targeting the intergenic spacer 1 (IGS1) of the ribosomal DNA of T. asahii and used them to detect mock infection clinical samples. The species-specific colony PCR based on glass beads proved advantageous, with short procedure time (154.8 ± 0.6 min), good sensitivity (detection limit, 102 CFU/mL), and specificity for T. asahii, indicating that this method can be used for the rapid and simple identification of clinical samples of T. asahii infection.

scholarly journals Innovative Methods for Soil DNA Purification Tested in Soils with Widely Differing Characteristics

2008 ◽  
Vol 74 (9) ◽  
pp. 2902-2907 ◽  
Author(s):  
Marketa Sagova-Mareckova ◽  
Ladislav Cermak ◽  
Jitka Novotna ◽  
Kamila Plhackova ◽  
Jana Forstova ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Soil Ph ◽  
Vegetation Cover ◽  
Organic Matter Content ◽  
Clay Content ◽  
Matter Content ◽  
Soil Dna ◽  
Innovative Methods ◽  
Soil Dna Extraction ◽  
Extraction And Purification

ABSTRACT Seven methods of soil DNA extraction and purification were tested in a set of 14 soils differing in bedrock, texture, pH, salinity, moisture, organic matter content, and vegetation cover. The methods introduced in this study included pretreatment of soil with CaCO3 or purification of extracted DNA by CaCl2. The performance of innovated methods was compared to that of the commercial kit Mo Bio PowerSoil and the phenol-chloroform-based method of D. N. Miller, J. E. Bryant, E. L. Madsen, and W. C. Ghiorse (Appl. Environ. Microbiol. 65:4715-4724, 1999). This study demonstrated significant differences between the tested methods in terms of DNA yield, PCR performance, and recovered bacterial diversity. The differences in DNA yields were correlated to vegetation cover, soil pH, and clay content. The differences in PCR performances were correlated to vegetation cover and soil pH. The innovative methods improved PCR performance in our set of soils, in particular for forest acidic soils. PCR was successful in 95% of cases by the method using CaCl2 purification and in 93% of cases by the method based on CaCO3 pretreatment, but only in 79% by Mo Bio PowerSoil, for our range of soils. Also, the innovative methods recovered a higher percentage of actinomycete diversity from a subset of three soils. Recommendations include the assessment of soil characteristics prior to selecting the optimal protocol for soil DNA extraction and purification.

scholarly journals Comparative Different DNA Isolation Protocols from Ziziphus spina-christi (L.) Leaves through RAPD and ISSR Markers

2016 ◽  
Vol 8 (6) ◽  
pp. 49
Author(s):  
Fatemeh Bina ◽  
Zabihollah Zamani ◽  
Vahideh Nazeri ◽  
Daryush Talei
Keyword(s):  
Dna Extraction ◽  
Genomic Analysis ◽  
Restriction Enzymes ◽  
Fruit Trees ◽  
Issr Markers ◽  
Plant Tissues ◽  
Extraction And Purification ◽  
High Level ◽  
Rapd And Issr

<p>Genomic analysis of plants relies on high quantity and quality of pure DNA. Extraction and purification of DNA from woody and medicinal plants, such as fruit trees present a great challenge due to accumulation of a large amount of co-purify with DNA, including polysaccharides, polyphenols and proteins. Therefore, it is necessary to optimize the extraction protocols to reduce these compounds to the lowest level. A study was conducted to compare six DNA extraction and precipitation methods for genomic analysis in<em> Ziziphus spina-christi</em> (L.) plant tissues. The results showed significant differences in DNA contents among the six methods. Quantity and quality of extracted genomic DNAs were compared by employing the spectrophotometer, Nano-Drop, agarose gel electrophoresis, digestion by restriction enzymes and polymerase chain reaction (PCR) methods and molecular marker such as RAPD and ISSR. The method of Vroh Bi et al., provided the best results (208.89 ng/μL) in terms of quantity and quality of DNA, and Doyle and Doyle method as second method for leaves sample were chosen. According to the results, the method of Bi et al. is recommended for DNA extraction from plant tissues having high level of polysaccharides and phenol compounds.</p>

A quantitative analysis of DNA extraction and purification from compost

2003 ◽  
Vol 54 (1) ◽  
pp. 37-45 ◽  
Author(s):  
Michael Howeler ◽  
William C Ghiorse ◽  
Larry P Walker
Keyword(s):  
Quantitative Analysis ◽  
Dna Extraction ◽  
Extraction And Purification
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