scholarly journals Comparative account of DNA extraction protocols in some freshwater prawns of Genus Macrobrachium (Bate, 1868) (Family Palaemonidae) from Jammu waters for PCR based applications

2019 ◽  
Vol 12 (3) ◽  
pp. 1201-1206 ◽  
Author(s):  
Raman Jasrotia ◽  
Seema Langer
Keyword(s):  
Dna Extraction ◽  
Muscle Tissue ◽  
Genomic Dna ◽  
Uv Spectrophotometry ◽  
High Concentration ◽  
Salting Out ◽  
Basic Step ◽  
Tissue Samples ◽  
Inter Simple Sequence Repeats ◽  
High Yields

Genetic variations among prawns act as an important tool to characterize and differentiate between the species. Molecular and phylogenetic analysis of shrimps and prawns like any other organism rely on high yields of pure and better quality genomic DNA. In this regard isolation of DNA is the first and basic step. In spite of the availability of many protocols of DNA extraction from animal tissues, it is difficult to ascertain that which one would provide desired results for prawn tissue. In the present study, three different techniques of DNA isolation i.e., salting out, phenol-chloroform and Qiagen DNA extraction kit were performed and compared for their yield. Cephalothoracic tissue and muscle tissue of pleopods were used for isolation. Tissue samples from fresh specimens as well as from alcohol preserved specimens were employed for extraction. The quantity (µg/ml) and quality of isolated DNA were determined by UV spectrophotometry and agarose gel electrophoresis. Results showed that Phenol-chloroform method with slight modifications obtained higher yield of genomic DNA as compared to other methods. The present work also revealed that among fresh specimens cephalotoracic tissue yielded high concentration DNA than muscle tissue. However, among alcohol preserved specimens, the concentration of DNA was higher in muscle tissue of pleopods. The high quality DNA was then subjected to randomly amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) analysis. The DNAs produced clear, sharp and reproducible PCR (Polymerse chain reaction) product pattern.

scholarly journals Single Lysis-Salting Out Method of Genomic DNA Extraction From Dried Blood Spots

2016 ◽  
Vol 30 (6) ◽  
pp. 1009-1012 ◽  
Author(s):  
Muntaj Shaik ◽  
Devaraju Kuramkote Shivanna ◽  
Mahesh Kamate ◽  
Vedamurthy AB ◽  
Kruthika-Vinod TP
Keyword(s):  
Dna Extraction ◽  
Genomic Dna ◽  
Dried Blood Spots ◽  
Salting Out ◽  
Genomic Dna Extraction ◽  
Blood Spots

scholarly journals Novel kit for efficient extraction of long-segment genomic DNA by nanodisk adsorption

2019 ◽  
Vol 1 (1) ◽  
pp. 4-5
Author(s):  
Siqi Wu ◽  
Zhaofang Han ◽  
Hesong Qiu
Keyword(s):  
Molecular Biology ◽  
Dna Extraction ◽  
High Purity ◽  
Genomic Dna ◽  
Extraction Methods ◽  
Biochemical Properties ◽  
High Efficacy ◽  
Tissue Samples ◽  
Efficient Extraction ◽  
Total Dna

The acquisition of complete DNA is usually the first and most critical step in many basic molecular biology applications. Isolation of complete total DNA from tissue samples is related to different physical and biochemical properties of tissue. Long fragments of DNA are easily degraded and fragmented, which poses a challenge for extracting complete long fragments of DNA. By comparing several different extraction methods and verifying the concentration and length of extracted DNA, it is proved that the kit we used has high  efficacy. We provide tissue kit DNA extraction for long fragments and obtain long fragments of high purity DNA from almost any type of tissue, especially muscle and blood tissues.

Genomic DNA isolation from old needles of Cedrus deodara (Roxb.) G.Don and amplification of nuclear microsatellite markers

2015 ◽  
Vol 38 (3) ◽  
pp. 215-217
Author(s):  
Akhilesh Kumar ◽  
Santan Barthwal ◽  
Harish Ginwal
Keyword(s):  
Dna Extraction ◽  
Genomic Dna ◽  
High Concentration ◽  
Cedrus Deodara ◽  
Closely Related Species ◽  
Genomic Dna Isolation ◽  
Ctab Method ◽  
Nuclear Microsatellite ◽  
High Concentrations ◽  
Simple Sequence

A reliable and modified protocol based on the CTAB method was developed for DNA extraction from old needles of Cedrus deodara (Roxb.) G.Don. The presence of high concentrations of polysaccharides, polyphenols and other secondary metabolites in C. deodara needles poses problem in getting good quality DNA fit for PCR applications. used 2.5% PVP for removal of phenolics compound and apply high concentration of sodium chloride to removes polysaccharides. Oils was removed by centrifugation. The yield of extracted DNA was ranged from 35 to 130 µg/100mg fresh weight of the needles with absorbance ratio (A260/A280) ranged from 1.82 to 2.0. DNA extracted by modified protocol gives positive amplification with PCR using Nuclear Simple Sequence Repeat (SSR) markers. This modified protocol can be used in genomic DNA extraction from closely related species of C. deodara.

Extraction of Genomic DNA from Inner Bark of Cedrus deodara (Roxb.) G. Don for RAPD Study

2017 ◽  
Vol 40 (1) ◽  
pp. 25-27
Author(s):  
Akhilesh Kumar ◽  
◽  
Santan Barthwal ◽  
H.S. Ginwal ◽  
◽  
...  
Keyword(s):  
Sodium Chloride ◽  
Dna Extraction ◽  
Genomic Dna ◽  
Rapd Markers ◽  
High Concentration ◽  
High Quality ◽  
Cedrus Deodara ◽  
Remote Areas ◽  
Inner Bark ◽  
Random Amplification

Genomic DNA extraction from forestry tree species require young leaf samples to obtain high-quality DNA for molecular based study. For some study, leaf samples must be collected from remote areas and are difficult to transport long distances. We developed alternative method of DNA extraction from inner bark of Cedrus deodara. We used 2.5% PVP for removal of phenolic compound and apply high concentration of sodium chloride to removes polysaccharides. Extracted DNA gives positive amplification with PCR using random amplification of polymorphic DNA (RAPD) markers.

A rapid salting out method for DNA extraction from buccal swabs

2012 ◽  
Vol 31 (12) ◽  
pp. 1370-1374
Author(s):  
Wei-feng ZHU ◽  
Da-ya LUO ◽  
Shuo TU ◽  
Xia-li ZHANG ◽  
Ke-min JIE ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Salting Out ◽  
Buccal Swabs

Optimization of genomic DNA extraction from formalin-fixed fish specimens

2013 ◽  
Vol 19 (6) ◽  
pp. 1068-1073
Author(s):  
Xiaolan KONG ◽  
Zuozhi CHEN ◽  
Lin LIN ◽  
Chunhou LI ◽  
Peiwen LIANG
Keyword(s):  
Dna Extraction ◽  
Genomic Dna ◽  
Genomic Dna Extraction ◽  
Formalin Fixed

Extraction of DNA from a Wide Range of Objects by Treatment with Ammonium Salts

2020 ◽  
Vol 36 (6) ◽  
pp. 98-106
Author(s):  
E.I. Levitin ◽  
B.V. Sviridov ◽  
O.V. Piksasova ◽  
T.E. Shustikova
Keyword(s):  
Dna Extraction ◽  
Dna Isolation ◽  
Tissue Samples ◽  
New Approach ◽  
Cell Wall Disruption ◽  
Wide Range ◽  
Low Salt ◽  
Mammalian Blood ◽  
Plasmid Extraction ◽  
Two Hybrid

Currently, simple, rapid, and efficient techniques for DNA isolation from a wide range of organisms are in demand in biotechnology and bioinformatics. A key (and often limiting) step is the cell wall disruption and subsequent DNA extraction from the disintegrated cells. We have developed a new approach to DNA isolation from organisms with robust cell walls. The protocol includes the following steps: treatment of cells or tissue samples with ammonium acetate followed by cell lysis in low-salt buffer with the addition of SDS. Further DNA extraction is carried out according to standard methods. This approach is efficient for high-molecular native DNA isolation from bacteria, ascomycetes, yeast, and mammalian blood; it is also useful for express analysis of environmental microbial isolates and for plasmid extraction for two-hybrid library screening. express method for DNA isolation; ammonium salt treatment (в русских ключевых такой порядок), osmotic breakage of cells This study was financially supported by the NRC "Kurchatov Institute"-GOSNIIGENETIKA Kurchatov Genomic Center.

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.

scholarly journals Validating DNA Extraction Protocols for Bentonite Clay

mSphere ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Katja Engel ◽  
Sara Coyotzi ◽  
Melody A. Vachon ◽  
Jennifer R. McKelvie ◽  
Josh D. Neufeld
Keyword(s):  
Microbial Community ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Dna Extraction ◽  
Genomic Dna ◽  
Bentonite Clay ◽  
Dna Recovery ◽  
Blocking Agents ◽  
Clay Matrix ◽  
Microbial Dna

ABSTRACT Bentonite clay is an integral component of the engineered barrier system of deep geological repositories (DGRs) that are planned for the long-term storage of high-level radioactive waste. Although nucleic acid extraction and analysis can provide powerful qualitative and quantitative data reflecting the presence, abundance, and functional potential of microorganisms within DGR materials, extraction of microbial DNA from bentonite clay is challenging due to the low biomass and adsorption of nucleic acids to the charged clay matrix. In this study, we used quantitative PCR, gel fingerprinting, and high-throughput sequencing of 16S rRNA gene amplicons to assess DNA extraction efficiency from natural MX-80 bentonite and the same material “spiked” with Escherichia coli genomic DNA. Extraction protocols were tested without additives and with casein and phosphate as blocking agents. Although we demonstrate improved DNA recovery by blocking agents at relatively high DNA spiking concentrations, at relatively low spiking concentrations, we detected a high proportion of contaminant nucleic acids from blocking agents that masked sample-specific microbial profile data. Because bacterial genomic DNA associated with casein preparations was insufficiently removed by UV treatment, casein is not recommended as an additive for DNA extractions from low-biomass samples. Instead, we recommend a kit-based extraction protocol for bentonite clay without additional blocking agents, as tested here and validated with multiple MX-80 bentonite samples, ensuring relatively high DNA recoveries with minimal contamination. IMPORTANCE Extraction of microbial DNA from MX-80 bentonite is challenging due to low biomass and adsorption of nucleic acid molecules to the charged clay matrix. Blocking agents improve DNA recovery, but their impact on microbial community profiles from low-biomass samples has not been characterized well. In this study, we evaluated the effect of casein and phosphate as blocking agents for quantitative recovery of nucleic acids from MX-80 bentonite. Our data justify a simplified framework for analyzing microbial community DNA associated with swelling MX-80 bentonite samples within the context of a deep geological repository for used nuclear fuel. This study is among the first to demonstrate successful extraction of DNA from Wyoming MX-80 bentonite.

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