scholarly journals An Improved Procedure of the Metagenomic DNA Extraction from Saline Soil, Sediment and Salt

2016 ◽  
Vol 60 ◽  
pp. 38-45
Author(s):  
Fereshteh Jookar Kashi
Keyword(s):  
Dna Extraction ◽  
Extraction Method ◽  
Large Scale ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Skim Milk ◽  
Community Analysis ◽  
Functional Genes ◽  
Dna Extraction Method ◽  
Gradient Gel Electrophoresis ◽  
Direct Dna Extraction

A new modified protocol has been developed for extracting pure community inhibitors-free DNA from saline soils, sediments and salts. Amplification of DNA from soil and sediment is often inhibited by copurified contaminants. A rapid, inexpensive, large-scale DNA extraction method involving minimal purification has been developed that is applicable to saline samples. Using a widely used a newly modified direct DNA extraction method proposed in this report, DNA was extracted from samples of Urmia Lake in diverse geological location in Iran and quantity of the DNA were examined. We developed an improved method to extract DNA include the combination of physical, chemical and mechanical lysis methods from saline samples. In the earlier reports, skim milk as an adsorption competitor was added to buffer DNA extract. In current study, we added skim milk to buffer DNA extraction. The results showed that skim milk was useful as an additive for extract DNA from saline samples. This method is applicable to molecular community analysis of saline samples which strongly adsorb DNA. The methods appear to have wide applicability in investigating molecular diversity and exploring functional genes from the total DNA. The extracted DNA was used to successfully amplify 16SrRNA region and functional genes. The amplicons were suitable for further applications such as diversity based analysis by denaturing gradient gel electrophoresis (DGGE) and cloning library.

scholarly journals Effect of DNA Extraction Method on the Apparent Microbial Diversity of Soil

2010 ◽  
Vol 76 (10) ◽  
pp. 3378-3382 ◽  
Author(s):  
Özgül İnceoǧlu ◽  
Eelco F. Hoogwout ◽  
Patrick Hill ◽  
Jan Dirk van Elsas
Keyword(s):  
Extraction Method ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Agricultural Soils ◽  
Extraction Methods ◽  
The Novel ◽  
Soil Dna ◽  
Dna Extraction Method ◽  
Gradient Gel Electrophoresis ◽  
Novel Method ◽  
Microbial Groups

ABSTRACT Four extraction methods, including a novel one, were compared for their efficiencies in producing DNA from three contrasting agricultural soils. Molecular analyses (PCR-denaturing gradient gel electrophoresis [DGGE] and clone libraries) focusing on different microbial groups were used as assessment criteria. Per soil, the DNA yields differed between extraction methods. Clear effects of method on apparent richness and community structure were found. Actinobacterial diversity based on soil DNA produced by two divergent methods revealed that a hitherto-undescribed group was obtained by the novel method.

scholarly journals Comparative investigation of DNA extraction methods in black gram (Vigna mungo (L.)

2019 ◽  
Author(s):  
M. . Prakash ◽  
B. . Priyadharshini ◽  
M. . Vignesh ◽  
R. . Anandan
Keyword(s):  
Dna Extraction ◽  
Extraction Method ◽  
Large Scale ◽  
Dna Isolation ◽  
Extraction Methods ◽  
Comparative Investigation ◽  
Black Gram ◽  
Dna Extraction Method ◽  
Ctab Method ◽  
Dna Extraction Methods

Isolation of intact, double stranded, pure and non- contaminated genomic DNA is prerequisite for large scale genotyping analysis including DNA-banks. Three methods of DNA isolation (Dellaporta, CTAB and Hi-PurAg DNA isolation kits) from 25 black gram genotypes were compared in terms of the yield, purity, integrity, and stability of extracted DNA. Purity and quantification of isolated DNA samples was confirmed by using the UV nano-spectrophotometer at OD260/280 and the same is confirmed based by agarose gel electrophoresis. The CTAB method showed the best results followed by Hi-PurAg and Dellaporta method. The CTAB DNA extraction method was found to be the most efficient DNA extraction method, capable of providing high quality, pure and stable DNA and could be used for various molecular related works. All the 25 black gram genotypes for this research gave good yield of DNA from the established modified CTAB protocol.

scholarly journals Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples

2018 ◽  
Vol 2 ◽  
Author(s):  
Markus Majaneva ◽  
Ola H. Diserud ◽  
Shannon H.C. Eagle ◽  
Mehrdad Hajibabaei ◽  
Torbjørn Ekrem
Keyword(s):  
Dna Extraction ◽  
Extraction Method ◽  
Target Material ◽  
Cost Effective ◽  
Community Analysis ◽  
Extraction Methods ◽  
Dna Recovery ◽  
Dna Yield ◽  
Dna Extraction Method ◽  
Dna Metabarcoding

Characterisation of freshwater benthic biodiversity using DNA metabarcoding may allow more cost-effective environmental assessments than the current morphological-based assessment methods. DNA metabarcoding methods where sorting or pre-sorting of samples are avoided altogether are especially interesting, since the time between sampling and taxonomic identification is reduced. Due to the presence of non-target material like plants and sediments in crude samples, DNA extraction protocols become important for maximising DNA recovery and sample replicability. We sampled freshwater invertebrates from six river and lake sites and extracted DNA from homogenised bulk samples in quadruplicate subsamples, using a published method and two commercially available kits: HotSHOT approach, Qiagen DNeasy Blood & Tissue Kit and Qiagen DNeasy PowerPlant Pro Kit. The performance of the selected extraction methods was evaluated by measuring DNA yield and applying DNA metabarcoding to see if the choice of DNA extraction method affects DNA yield and metazoan diversity results. The PowerPlant Kit extractions resulted in the highest DNA yield and a strong significant correlation between sample weight and DNA yield, while the DNA yields of the Blood & Tissue Kit and HotSHOT method did not correlate with the sample weights. Metazoan diversity measures were more repeatable in samples extracted with the PowerPlant Kit compared to those extracted with the HotSHOT method or the Blood & Tissue Kit. Subsampling using Blood & Tissue Kit and HotSHOT extraction failed to describe the same community in the lake samples. Our study exemplifies that the choice of DNA extraction protocol influences the DNA yield as well as the subsequent community analysis. Based on our results, low specimen abundance samples will likely provide more stable results if specimens are sorted prior to DNA extraction and DNA metabarcoding, but the repeatability of the DNA extraction and DNA metabarcoding results was close to ideal in high specimen abundance samples.

scholarly journals Direct DNA extraction method of an obligate parasitic fungus from infected plant tissue

2015 ◽  
Vol 14 (4) ◽  
pp. 18546-18551 ◽  
Author(s):  
L. Liu ◽  
C.L. Wang ◽  
W.Y. Peng ◽  
J. Yang ◽  
M.Q. Lan ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Plant Tissue ◽  
Extraction Method ◽  
Infected Plant ◽  
Parasitic Fungus ◽  
Dna Extraction Method ◽  
Direct Dna Extraction

Sensitivity detection of Abacavir in human through SNP detection of HLA-B*5701 allele

2016 ◽  
Vol 5 (08) ◽  
pp. 4754
Author(s):  
Tanushree Mitra* ◽  
Shivshankar Kumdale ◽  
Sameer Chowdhary ◽  
Amol D. Raut
Keyword(s):  
Blood Sample ◽  
Dna Extraction ◽  
Genomic Dna ◽  
Extraction Method ◽  
Snp Detection ◽  
Dna Extraction Method ◽  
Sensitivity Detection

The main objective of this study was to make sure whether randomly taken 12 samples were sensitive to abacavir. The genomic DNA from 12 blood sample were extracted by phenol chloroform DNA extraction method, extracted genomic DNA were amplified and sequenced, thereafter SNPs were detected. Every sample had shown the presence of normal base at SNP position. This study indicated, those randomly taken 12 patients were sensitive to abacavir, so they can consume abacavir if they get infected with HIV.

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