scholarly journals Paramagnetic Cellulose DNA Isolation Improves DNA Yield and Quality Among Diverse Plant Taxa

2014 ◽  
Vol 2 (10) ◽  
pp. 1400048 ◽  
Author(s):  
Jackson R. Moeller ◽  
Nicholas R. Moehn ◽  
Donald M. Waller ◽  
Thomas J. Givnish
Keyword(s):  
Dna Isolation ◽  
Dna Yield ◽  
Yield And Quality ◽  
Diverse Plant

High Microsatellite and SNP Genotyping Success Rates Established in a Large Number of Genomic DNA Samples Extracted From Mouth Swabs and Genotypes

2006 ◽  
Vol 9 (4) ◽  
pp. 501-506 ◽  
Author(s):  
Josine L. Min ◽  
Nico Lakenberg ◽  
Margreet Bakker-Verweij ◽  
Eka Suchiman ◽  
Dorret I. Boomsma ◽  
...  
Keyword(s):  
Success Rate ◽  
Genomic Dna ◽  
Snp Genotyping ◽  
High Yield ◽  
Success Rates ◽  
Nucleotide Polymorphism ◽  
High Quality ◽  
Single Nucleotide ◽  
Dna Yield ◽  
Yield And Quality

AbstractIn this article, we present the genomic DNA yield and the microsatellite and single nucleotide polymorphism (SNP) genotyping success rates of genomic DNA extracted from a large number of mouth swab samples. In total, the median yield and quality was determined in 714 individuals and the success rates in 378,480 genotypings of 915 individuals. The median yield of genomic DNA per mouth swab was 4.1 μg (range 0.1–42.2 μg) and was not reduced when mouth swabs were stored for at least 21 months prior to extraction. A maximum of 20 mouth swabs is collected per participant. Mouth swab samples showed in, respectively, 89% for 390 microsatellites and 99% for 24 SNPs a genotyping success rate higher than 75%. A very low success rate of genotyping (0%–10%) was obtained for 3.2% of the 915 mouth swab samples using microsatellite markers. Only 0.005% of the mouth swab samples showed a geno-typing success rate lower than 75% (range 58%–71%) using SNPs. Our results show that mouth swabs can be easily collected, stored by our conditions for months prior to DNA extraction and result in high yield and high-quality DNA appropriate for genotyping with high success rate including whole genome searches using microsatellites or SNPs.

An efficient protocol for the isolation of fungal DNA for strains obtained from oil contaminated fields

2012 ◽  
Vol 2 (4) ◽  
pp. 162-165
Author(s):  
Bhavya Ravi ◽  
Madhulika Rai ◽  
Sandhya Mehrotra ◽  
Rajesh Mehrotra
Keyword(s):  
Contaminated Soils ◽  
Petroleum Hydrocarbons ◽  
Dna Isolation ◽  
Cost Effective ◽  
Industrial Applications ◽  
Glass Beads ◽  
Natural Ecosystem ◽  
Dna Yield ◽  
Genomic Study ◽  
Fungal Dna

A natural ecosystem contaminated with petroleum hydrocarbons is likely to favor the growth of taxonomically diverse microbes having the ability to degrade these organic compounds. They can be exploited for purposes like bioremediation of oil contaminated soils and to obtain enzymes like lipases having important industrial applications. In this paper, a novel “IBG” (Improved ‘Bust and Grab’) protocol has been reported for the isolation of fungal DNA from strains collected from oil contaminated fields. Conventional methods for DNA isolation from fungi require the use of enzymes, liquid nitrogen, glass beads etc. The method reported here circumvents the use of enzymes or glass beads and is cost effective and can be used while handling large number of samples. The DNA yield obtained by the IBG protocol is significant and of good quality. The good quality DNA isolated by IBG protocol can be used for the quick and cost effective isolation of fungal genomic DNA facilitating the genomic study of microbes obtained from oil contaminated fields.

Blood storage at 4°C—factors involved in DNA yield and quality

2006 ◽  
Vol 147 (6) ◽  
pp. 290-294 ◽  
Author(s):  
Andrea J. Richardson ◽  
Niro Narendran ◽  
Robyn H. Guymer ◽  
Hien Vu ◽  
Paul N. Baird
Keyword(s):  
Blood Storage ◽  
Dna Yield ◽  
Yield And Quality

Comparison of commercial DNA extraction kits for isolation and purification of bacterial and eukaryotic DNA from PAH-contaminated soils

2011 ◽  
Vol 57 (8) ◽  
pp. 623-628 ◽  
Author(s):  
Nagissa Mahmoudi ◽  
Greg F. Slater ◽  
Roberta R. Fulthorpe
Keyword(s):  
Dna Extraction ◽  
Contaminated Soils ◽  
Dna Isolation ◽  
Extraction Process ◽  
Organic Carbon Content ◽  
Soil Dna ◽  
Isolation And Purification ◽  
Dna Yield ◽  
Pcr Products ◽  
Eukaryotic Dna

Molecular characterization of the microbial populations of soils and sediments contaminated with polycyclic aromatic hydrocarbons (PAHs) is often a first step in assessing intrinsic biodegradation potential. However, soils are problematic for molecular analysis owing to the presence of organic matter, such as humic acids. Furthermore, the presence of contaminants, such as PAHs, can cause further challenges to DNA extraction, quantification, and amplification. The goal of our study was to compare the effectiveness of four commercial soil DNA extraction kits (UltraClean Soil DNA Isolation kit, PowerSoil DNA Isolation kit, PowerMax Soil DNA Isolation kit, and FastDNA SPIN kit) to extract pure, high-quality bacterial and eukaryotic DNA from PAH-contaminated soils. Six different contaminated soils were used to determine if there were any biases among the kits due to soil properties or level of contamination. Extracted DNA was used as a template for bacterial 16S rDNA and eukaryotic 18S rDNA amplifications, and PCR products were subsequently analyzed using denaturing gel gradient electrophoresis (DGGE). We found that the FastDNA SPIN kit provided significantly higher DNA yields for all soils; however, it also resulted in the highest levels of humic acid contamination. Soil texture and organic carbon content of the soil did not affect the DNA yield of any kit. Moreover, a liquid–liquid extraction of the DNA extracts found no residual PAHs, indicating that all kits were effective at removing contaminants in the extraction process. Although the PowerSoil DNA Isolation kit gave relatively low DNA yields, it provided the highest quality DNA based on successful amplification of both bacterial and eukaryotic DNA for all six soils. DGGE fingerprints among the kits were dramatically different for both bacterial and eukaryotic DNA. The PowerSoil DNA Isolation kit revealed multiple bands for each soil and provided the most consistent DGGE profiles among replicates for both bacterial and eukaryotic DNA.

scholarly journals To beat or not to beat a tick: Comparison of DNA extraction methods from ticks (Ixodes scapularis)

2015 ◽  
Author(s):  
Alyssa D Ammazzalorso ◽  
Christine P Zolnik ◽  
Thomas J Daniels ◽  
Sergios-Orestis Kolokotronis
Keyword(s):  
Dna Extraction ◽  
Disease Transmission ◽  
Dna Isolation ◽  
Ixodes Scapularis ◽  
Genetic Material ◽  
The United States ◽  
Qualitative Assessment ◽  
Single Individual ◽  
Cross Sectional ◽  
Dna Yield

Background. Blacklegged ticks (Ixodes scapularis) are important disease vectors in the United States, known to transmit a variety of pathogens to humans, including bacteria, protozoa, and viruses. Their importance as a disease vector necessitates reliable and comparable methods for extracting microbial DNA from ticks. Furthermore, to explore the population genetics or genomics of this tick, appropriate DNA extraction techniques are needed for both the vector and its microbes. Although a few studies have investigated different methods of DNA isolation from ticks, they are limited in the number and types of DNA extraction and lack species-specific quantification of DNA yield. Methods. Here we determined the most efficient and consistent method of DNA extraction from two different developmental stages of I. scapularis – nymph and adult - that are the most important for disease transmission. We used various methods of physical disruption of the hard, chitinous exoskeleton, as well as commercial and non-commercial DNA isolation kits. To gauge the effectiveness of these methods we quantified the DNA yield and confirmed the DNA quality via PCR of both tick and microbial genetic material. Results. DNA extraction using the Thermo GeneJET Genomic DNA Purification kit resulted in the highest DNA yields and the strongest, most consistent PCR amplification. We also found that physical disruption of the tick exoskeleton was most effective using cross-sectional cutting compared to any type of bead-beating matrices used. Storing ticks at -80°C resulted in considerably higher DNA yields than those from ticks stored in ethanol. Discussion. We contrasted a variety of readily available methods of DNA extraction from single individual blacklegged ticks and presented the results through a quantitative and qualitative assessment.

scholarly journals A protocol for good quality genomic DNA isolation from formalin-fixed paraffin-embedded tissues without using commercial kits

2021 ◽  
Author(s):  
Fazlur Rahman Talukdar ◽  
Irena Abramovic ◽  
Cyrille Cuenin ◽  
Christine Carreira ◽  
Nitin Gangane ◽  
...  
Keyword(s):  
Dna Isolation ◽  
Middle Income ◽  
Dna Yield ◽  
Genomic Dna Isolation ◽  
Novel Approach ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Commercial Kits ◽  
Formalin Fixed

DNA isolation from formalin fixed paraffin embedded (FFPE) tissues for molecular analysis has become a frequent procedure in cancer research. However, the yield or quality of the isolated DNA is often compromised, and commercial kits are used to overcome this to some extent. We developed a new protocol (IARCp) to improve better quality and yield of DNA from FFPE tissues without using any commercial kit. To evaluate the IARCp performance, we compared the quality and yield of DNA with two commercial kits, namely NucleoSpin DNA FFPE XS (MN) and QIAamp DNA Micro (QG) isolation kit. Total DNA yield for QG ranged from 120.0 to 282.0 ng (mean 216.5 ng), for MN: 213.6 to 394.2 ng (mean 319.1 ng), and with IARCp the yield was much higher ranging from 775.5 to 1896.9 ng (mean 1517.8 ng). Moreover, IARCp has also performed well in qualitative assessments. Overall, IARCp represents a novel approach to DNA isolation from FFPE which results in good quality and significant amounts of DNA suitable for many downstream genome-wide and targeted molecular analyses. Our proposed protocol does not require the use of any commercial kits for isolating DNA from FFPE tissues, making it suitable to implement in low-resource settings such as low and middle-income countries (LMICs).

Efficient DNA isolation from moroccan arar tree [Tetraclinis articulata (Vahl) Masters] leaves and optimization of the rapd-pcr molecular technique. Extraction efficace de l’ADN des feuilles du thuya de berberie (Tetraclinis articulata (Vahl) masters) et optimisation de la technique moléculaire rapd-pcr

2010 ◽  
Vol 35 ◽  
pp. 97-106
Author(s):  
Salaheddine Bakkali Yakhlef ◽  
Imane Guenoun ◽  
Benaîssa Kerdouh ◽  
Noureddine Hamamouch ◽  
Mohamed Abourouh
Keyword(s):  
Dna Extraction ◽  
Genomic Dna ◽  
Dna Isolation ◽  
Molecular Genetic Analysis ◽  
Molecular Technique ◽  
High Quality ◽  
Fresh Tissue ◽  
Dna Yield ◽  
Tetraclinis Articulata ◽  
Rapd Pcr

 English.  Molecular genetic analysis of Arar tree [Tetraclinis articulata (Vahl) Masters] is often limited by the availability of fresh tissue and an efficient and reliable protocol for high quality genomic DNA extraction. In this study, two DNA extraction protocols were specifically developed for extracting high quality genomic DNA from Arar tree leaves: modified QIAgen DNA Kit and protocol developed by Ouenzar et al. (1998). DNA yield and purity were monitored by gel electrophoresis and by determining absorbance at UV (A260/A280 and A260/A230). Both ratios were between 1.7 and 2.0, indicating that the presence of contaminating metabolites was minimal. The DNA yield obtained ranged between 20 to 40 µg/g of plant materiel. The Ouenzar and collaborators protocol gave higher yield but was more time consuming compared to QIAgen Kit. However, both techniques gave DNA of good quality that is amenable to RAPD-PCR reactions.Additionally, restriction digestion and PCR analyses of the obtained DNA showed its compatibility with downstream applications. Randomly Amplified Polymorphic DNA profiling from the isolated DNA was optimized to produce scorable and clear amplicons. The presented protocols allow easy and high quality DNA isolation for genetic diversity studies within Arar tree.Français.  Les analyses en génétique moléculaire chez le thuya de Berberie [Tetraclinis articulata (Vahl) Masters] sont souvent limitées par la disponibilité du matériel végétal frais et le temps nécessaire pour l’extraction l’ADN ainsi que par sa qualité. Dans cette étude, deux protocoles d’extraction, à partir des feuilles du thuya, de l’ADN génomique de haute qualité, ont été développés : le Kit Qiagen et le protocole mis au point par Ouenzar et al. (1998) modifiés. La qualité et la quantité de l’ADN sont évaluées par électrophorèse sur gel d’agarose et par la mesure de l’absorbance en UV à (A260/A280) et (A260/A230). Ces deux rapports varient entre 1,7 et 2,0 indiquant la faible fréquence des métabolites contaminants. Le rendement d’ADN varie entre 20 et 40 µg/g du matériel végétal. Le protocole de Ouenzar et collaborateurs donne le meilleur rendement d’ADN mais nécessite plus de temps. Néanmoins, les deux protocoles donnent un ADN de bonne qualité utilisable dans les réactions RAPD-PCR. En outre, la restriction enzymatique et l’analyse PCR de l’ADN obtenu ont montré sa compatibilité avec les applications moléculaires ultérieures. Les paramètres intervenant dans les réactions RAPD ont été optimisés. Les protocoles présentés permettent l’extraction facile de l’ADN de haute qualité nécessaire pour des études de la diversité génétique au sein du thuya.

scholarly journals High quality DNA from human papillomavirus (HPV) for PCR/RFLPs

2005 ◽  
Vol 48 (1) ◽  
pp. 37-40 ◽  
Author(s):  
Denise Wanderlei-Silva ◽  
Mariana Nobre ◽  
Rosa Silva Gonzaga ◽  
Luciana Silva Viana ◽  
Eduardo Ramalho Neto
Keyword(s):  
Dna Isolation ◽  
Electrophoretic Pattern ◽  
Virus Genome ◽  
Clinical Samples ◽  
Chain Reaction ◽  
Papilloma Virus ◽  
Dna Yield ◽  
Cheap Method ◽  
Polymerase Chain ◽  
Late Region

The analysis of DNA in clinical samples for a secure diagnostic has become indispensable nowadays. Techniques approaching isolation of high molecular weigth DNA of HPV could lead to efficient amplification and early clinical diagnosis of the virus DNA by PCR (polymerase chain reaction). We describe a fast, non-toxical, efficient and cheap method for DNA isolation of human papilloma virus (HPV) from cervical smears using guanidine (DNAzol solution). A 450 bp DNA band correponding to the late region (L1) of the virus genome was detected by PCR, showing that the DNAzol extraction soluction generated a good viral DNA yield. The electrophoretic pattern after digestion with restriction endonucleases (RFLPs/PCR) revealed the predominance of HPV-16 and HPV-33 in the samples from the State of Alagoas, Brazil.

scholarly journals Antifreeze Solution Improves DNA Recovery by Preserving the Integrity of Pathogen-Infected Blood and Other Tissues

2000 ◽  
Vol 7 (6) ◽  
pp. 945-946 ◽  
Author(s):  
Diana Sara Leal-Klevezas ◽  
Irma Olivia Martı́nez-Vázquez ◽  
Baltazar Cuevas-Hernández ◽  
Juan Pablo Martı́nez-Soriano
Keyword(s):  
Dna Extraction ◽  
Freeze Drying ◽  
Microscopic Analysis ◽  
Infected Blood ◽  
Dna Recovery ◽  
Dna Yield ◽  
Yield And Quality ◽  
Field Samples ◽  
Protease Treatment ◽  
Novel Method

ABSTRACT Preserving blood samples for shipping and later DNA extraction has been performed by cooling, freezing, drying, freeze-drying, and protease treatment, among other methods. Most methods to preserve field samples for further DNA extraction do not prevent cellular and DNA damage or are useful only in preserving them for short periods. This report introduces a novel method for blood and tissue that allows preservation in freezing temperatures for a prolonged period of time. The solution reported here (20% ethylene glycol-propylene glycol) preserves cells and tissues integrity, as judged by microscopic analysis, and improves DNA yield and quality.

Sign in / Sign up

Export Citation Format

Share Document