scholarly journals Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?

2017 ◽  
Vol 36 (1) ◽  
pp. 162-177 ◽  
Author(s):  
Valentin Vasselon ◽  
Isabelle Domaizon ◽  
Frédéric Rimet ◽  
Maria Kahlert ◽  
Agnès Bouchez
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Extraction Methods ◽  
Dna Extraction Methods

Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

2015 ◽  
Vol 16 (2) ◽  
pp. 459-469 ◽  
Author(s):  
Cristina Gamba ◽  
Kristian Hanghøj ◽  
Charleen Gaunitz ◽  
Ahmed H. Alfarhan ◽  
Saleh A. Alquraishi ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Ancient Dna ◽  
High Throughput Sequencing ◽  
Extraction Methods ◽  
Dna Extraction Methods

scholarly journals Monitoring of four DNA extraction methods upstream of high-throughput sequencing of Anisakidae nematodes

2014 ◽  
Vol 102 ◽  
pp. 69-72 ◽  
Author(s):  
Y. Seesao ◽  
C. Audebert ◽  
V. Verrez-Bagnis ◽  
S. Merlin ◽  
M. Jérôme ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Extraction Methods ◽  
Dna Extraction Methods

Comparison of High-throughput and Manual DNA Extraction Methods for the Qualitative and Quantitative Analysis of MON810 Maize

2014 ◽  
Vol 28 (3) ◽  
pp. 232-249 ◽  
Author(s):  
Katarzyna Grelewska-Nowotko ◽  
Jarosław Nowosielski ◽  
Magdalena Żurawska-Zajfert ◽  
Paweł Częstobor Czembor ◽  
Sławomir Sowa
Keyword(s):  
Quantitative Analysis ◽  
Dna Extraction ◽  
High Throughput ◽  
Extraction Methods ◽  
Qualitative And Quantitative Analysis ◽  
Qualitative And Quantitative ◽  
Dna Extraction Methods ◽  
Mon810 Maize

scholarly journals Comparison of different DNA extraction methods from hair root follicles to genotype Finnish Landrace boars with the Illumina PorcineSNP60 BeadChip

2008 ◽  
Vol 20 (2) ◽  
pp. 143 ◽  
Author(s):  
A. SIRONEN ◽  
P. UIMARI ◽  
J. VILKKI
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Extraction Methods ◽  
Sequence Information ◽  
Hair Root ◽  
Tissue Samples ◽  
Preparation Methods ◽  
Large Populations ◽  
Recent Developments ◽  
Dna Extraction Methods

Recent developments in sequencing methods have enabled whole genome sequencing of several species and the available sequence information has allowed the development of high throughput genotyping chips. However, these genotyping methods require high quality DNA. The possibility to genotype samples based on DNA from non-invasive sources would permit retrospective genotyping of previously collected samples and also facilitate the analysis of large populations e.g. for genomic selection. In this study we have developed and evaluated different DNA preparation methods from porcine hair root follicles for high throughput genotyping with the PorcineSNP60 Genotyping BeadChip (Illumina). We describe a method for DNA extraction from porcine hair root samples, which produces results from high throughput genotyping with the same high degree of accuracy as previously reported for DNA extracted from sperm, blood or tissue samples. This method was used for the genotyping of 273 hair follicle samples. When the DNA concentration was > 30 ng/ìl all samples had the same high call rate ( > 99%) as sperm samples confirming the robustness of this DNA extraction method for high throughput genotyping. Our data also establishes the suitability of the PorcineSNP60 BeadChip for genotyping the Finnish Landrace population.;

scholarly journals Towards high–throughput analyses of fecal samples from wildlife

2020 ◽  
pp. 171-183
Author(s):  
C. Sarabia ◽  
I. Salado ◽  
A. Cornellas ◽  
A. Fernández-Gil ◽  
C. Vilà ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Low Cost ◽  
Molecular Ecology ◽  
Extraction Methods ◽  
Success Rates ◽  
Sample Collection ◽  
Field Sampling ◽  
Fecal Samples

High–throughput sequencing offers new possibilities in molecular ecology and conservation studies. However, its potential has not yet become fully exploited for noninvasive studies of free–ranging animals, such as those based on feces. High–throughput sequencing allows sequencing of short DNA fragments and could allow simultaneous genotyping of a very large number of samples and markers at a low cost. The application of high throughput genotyping to fecal samples from wildlife has been hindered by several labor–intensive steps. We evaluate alternative protocols which could allow higher throughput for two of these steps: sample collection and DNA extraction. Two different field sampling and seven different DNA extraction methods are tested here on grey wolf (Canis lupus) feces. There was high variation in genotyping success rates. The field sampling method based on surface swabbing performed much worse than the extraction from a fecal fragment. In addition, there is a lot of room for improvement in the DNA extraction step. Optimization of protocols can lead to very much more efficient, cheaper and higher throughput noninvasive monitoring. Selection of appropriate markers is still of paramount importance to increase genotyping success.

scholarly journals A comparison of DNA extraction methods for high-throughput DNA analyses

2016 ◽  
Vol 17 (4) ◽  
pp. 721-729 ◽  
Author(s):  
Lauren M. Schiebelhut ◽  
Sarah S. Abboud ◽  
Liza E. Gómez Daglio ◽  
Holly F. Swift ◽  
Michael N Dawson
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Extraction Methods ◽  
Dna Analyses ◽  
Dna Extraction Methods

OPTIMIZATION OF DNA EXTRACTION METHODS FROM BIOLOGICAL MATERIALS OF HONEY BEES IN A DIFFERENT METAMOTPHOSIS PHASE

2016 ◽  
Vol 52 ◽  
pp. 171-176
Author(s):  
M. Palkina ◽  
O. Metlitska
Keyword(s):  
Ion Exchange ◽  
Dna Extraction ◽  
Honey Bees ◽  
Biological Material ◽  
Exchange Resin ◽  
Ion Exchange Resin ◽  
Extraction Methods ◽  
Chelex 100 ◽  
Drone Brood ◽  
Dna Extraction Methods

The aim of the research – adaptation, optimization and using of existing DNA extraction methods from bees’ biological material with the reagent «Chelex-100" under complex economic conditions of native laboratories, which will optimize labour costs and improve the economic performance of DNA extraction protocol. Materials and methods. In order to conduct the research the samples of honey bees’ biological material: queen pupae exuviae, larvae of drone brood, some adult bees’ bodies (head and thorax) were selected. Bowl and drone brood were obtained from the experimental bee hives of Institute of Apiculture nd. a. P. I. Prokopovich of NAAS. DNA extraction from biosamples of Apis mellifera ssp. was carried out using «Chelex-100®» ion exchange resin in different concentrations and combinations. Before setting tests for determination of quantitative and quality indexes, dilution of DNA samples of the probed object was conducted in ratio 1:40. The degree of contamination with protein and polysaccharide fractions (OD 260/230), quantitative content of DNA (OD 260/280) in the extracted tests were conducted using spectrophotometer of «Biospec – nano» at the terms of sample volume in 2 µl and length of optical way in 0,7 mm [7]. Verification of DNA samples from biological material of bees, isolated by «Chelex-100®», was conducted after cold keeping during 24 hours at 20°C using PСR with primaries to the fragment of gene of quantitative trait locus (QTL) Sting-2 of next structure [8]:  3' – CTC GAC GAG ACG ACC AAC TTG – 5’; 3' – AAC CAG AGT ATC GCG AGT GTT AC – 5’ Program of amplification: 94 °C – 5 minutes – 1 cycle; 94 °C – 1 minute, 57°C – 1 minute, 72 °C – 2 minutes – 30 cycles; elongation after 72°C during 2 minutes – 1 cycle. The division of obtained amplicons was conducted by gel electrophoresis at a low current – 7 µÀ, in 1,5 % agarose gel (Sigma ®) in TAE buffer [7]. The results. At the time of optimization of DNA isolation methods, according to existing methods of foreign experts, it was found optimal volume of ion exchange resin solution was in the proposed concentration: instead of 60 µl of solution used 120 µl of «Chelex-100®», time of incubation was also amended from 30 minutes to 180 minutes [9]. The use of the author's combination of method «Chelex-100®» with lysis enzymes, proteinase K and detergents (1M dithiothreitol), as time of incubation was also amended, which was reduced to 180 minutes instead of the proposed 12 hours [10]. Changes in quality characteristics of obtained DNA in samples after reduction in incubation time were not found. Conclusions. The most economical method of DNA isolation from bees’ biological material is 20% solution of «Chelex-100» ion exchange resin with the duration of the incubation period of 180 minutes. It should also be noted that the best results can be obtained from exuviae, selected immediately after the queen’s exit from bowl, that reduces the likelihood of DNA molecules destruction under the influence of nucleases activation, but not later than 12 hours from release using the technology of isolated obtain of queens.

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