scholarly journals DNA Isolation: A Method for Improving the Efficiency of DNA Extraction From Clotted Blood Samples

2021 ◽  
Vol 1 (2) ◽  
pp. 44-47
Author(s):  
Bobby Rianto Adi Putra
Keyword(s):  
Dna Extraction ◽  
Ball Bearing ◽  
Dna Isolation ◽  
Genome Research ◽  
Salting Out ◽  
Blood Samples ◽  
Blood Clots ◽  
Safe Technique ◽  
Yield And Purity

In generally, the genome research of high DNA extraction from clotted blood produced a low quality. The aim of this study is to develop a simple and safe technique to dispering the blood clots by the ball bearing metal shots. The yield and purity of DNA obtained by three steps were significantly different (P < 0.0001), with a higher yield in the modified salting-out method. The salting-out method is simple, efficient and economical for DNA isolation from old clotted blood samples.

scholarly journals Improving DNA extraction quality by the salting‐out method to prepare blood samples for real‐time PCR. (LB124)

2014 ◽  
Vol 28 (S1) ◽  
Author(s):  
Natalia Araujo ◽  
Bruno Carmona ◽  
Glaucia Regina Nogueira ◽  
Marcor Ferreira Minicucci ◽  
Sandro Conde
Keyword(s):  
Real Time ◽  
Dna Extraction ◽  
Real Time Pcr ◽  
Salting Out ◽  
Blood Samples

scholarly journals ALLELE FREQUENCY, HETEROZIGOSITY, AND ALLELE MIGRATION IN JAVANESE AND MADURESE POPULATION IN MALANG AND MADURA, EAST JAVA INDONESIA

2017 ◽  
Vol 17 (1) ◽  
pp. 43
Author(s):  
Nikmatul Iza
Keyword(s):  
Allele Frequency ◽  
Dna Extraction ◽  
Pcr Amplification ◽  
Polyacrylamide Gel ◽  
Salting Out ◽  
Blood Samples ◽  
Band Profile ◽  
Program Software

FREKUENSI ALEL, HETEROZIGOSITAS DAN MIGRASI ALEL PADA POPULASI ETNIS JAWA DAN MADURA DI MALANG DAN MADURA,  JAWA TIMUR, INDONESA ABSTRAKPenelitian ini bertujuan untuk menentukan frekuensi alel, heterozigositas, dan migrasi alel pada populasi etnis Jawa dan Madura berdasarkan penanda 13 CODIS. Metode yang digunakan dalam penelitian ini adalah (1) Pengambilan sampel darah dari 5 populasi yang terdiri dari 3 populasi etnis jawa dan 2 populasi etnis Madura; (2) Isolasi DNA dari sampel darah dilakukan dengan menggunakan metode salting out; (3) Amplifikasi PCR dengan menggunakan 13 CODIS  yang terdiri dari TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D21S11 dan divisualisasi dengan elektroforesis gel polyacrylamid 8%; serta (4) Profil pita dianalisis dengan program QuantityOne dan variasi pola pita DNA dianalisis dengan menggunakan program software GENEPOP package versi 4.2 yang akan digunakan untuk menentukan frekuensi alel, heterozigositas, dan migrasi alel. Hasil penelitian menunjukkan bahwa (1) Pada populasi etnis Jawa frekuensi alel yang memiliki keragaman tertinggi terdapat pada lokus D21S11 dengan jumlah alel sebanyak enam, lokus VWA dengan jumlah alel sebanyak lima, dan lokus FGA, TH01, D13S317, D16S539 dengan jumlah alel sebanyak empat yang digunakan sebagai penanda. Populasi etnis Madura memiliki frekuensi alel dengan keragaman tertinggi terdapat pada lokus TH01, D13S317, dan D21S11 dengan jumlah alel sebanyak lima dan lokus FGA dengan jumlah alel sebanyak empat. (2) Nilai heterozigositas populasi etnis Madura I (90.38%) dan populasi etnis Madura II (86.54%) lebih tinggi dibandingkan dengan populasi etnis Jawa I (67.69%), populasi etnis Jawa II (83.03%), maupun populasi etnis Jawa III (70.77%) dan (3) Migrasi alel pada populasi etnis Jawa sebesar 0.085% dan pada populasi etnis Madura sebesar 0.081%.Kata kunci: Frekuensi Alel, Heterozigositas, Migrasi Alel, 13 CODIS, Etnis Jawa dan Madura ALLELE FREQUENCY, HETEROZIGOSITY, AND ALLELE MIGRATION IN JAVANESE AND MADURESE POPULATION IN MALANG AND MADURA, EAST JAVA INDONESIA ABSTRACTThe aim of this study is to determine the frequency of alleles, heterozygosity, and allele migration in Javanese and Madurese population use 13 CODIS. The methods used in this study were (1) blood samples from five population consist three population of Javanese ethnic and two population of Madurese ethnic, (2) DNA extraction from blood samples by salting out method, (3) PCR amplification use 13 CODIS were TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D21S11 and visualized by 8% polyacrylamide gel (4) The band profile was analyzed by using QuantityOne software and variations in the pattern of DNA bands were analyzed by using GENEPOP software version 4.2 package to determine the frequency of alleles, heterozygosity, and allele migration. The results showed that (1) The population of Javanese allele frequency that has the highest diversity found in the locus D21S11 with a number of alleles of six, locus VWA by the number of alleles of five, and the locus FGA, TH01, D13S317, and D16S539 with a number of alleles of four  which is used as a marker. The populations of Madurese allele frequency that has the highest diversity found in the locus TH01, D13S317, and D21S11 with a number of alleles of five and locus FGA with a number of alleles of four, (2) Value of heterozygosity populations of Madurese I (90.38 %) and populations of Madurese II (86.54%) was higher than the population of Javanese I (67.69%), the population of Javanese II (83.03%), as well as the population of Javanese III (70.77%) and (3) There has been a migration of alleles in population Javanese of 0.085% and population Madurese of 0.081%.Keywords: Allele Frequency, Heterozigosity, Allele Migration, 13 CODIS,       Javanese and Madurese ethnic.

scholarly journals A Rapid and Inexpensive Method of DNA Extraction from Palmyra Palm (Borassus flabellifer)

2019 ◽  
pp. 1-5
Author(s):  
Soni Kumari ◽  
Ruby Rani ◽  
Jitesh Kumar ◽  
Ravi Ranjan Kumar ◽  
Tushar Ranjan
Keyword(s):  
Dna Extraction ◽  
Dna Isolation ◽  
Pcr Amplification ◽  
Tween 20 ◽  
Inexpensive Method ◽  
Rapid Procedure ◽  
Dna Yield ◽  
Lysis Buffer ◽  
Yield And Purity ◽  
Different Levels

Aims: The study aims to highlight the simple optimisation, inexpensive and rapid procedure for DNA isolation from tough leaves (Palmyra palm) without compromising the yield and purity of DNA. Study Design: Leaf of palmyra palm (Borassus flabellifer) was used to conduct the experiment followed by laboratory analysis, DNA extraction and PCR amplification. Results and Discussion: The results showed that different buffers examined for the extraction of DNA provided significantly different levels of yield and purity. DNA isolated by lysis buffers C showed satisfactory amplifications in PCR. The fingerprint we obtained by using the DNA extracted by these buffers provided higher resolution than those using buffers. Conclusion: This study suggests that grinding of Palmyra palm leaves with sterile sand or cover slips and inclusion of SDS, Tween 20, and NaCl (1.4 M) in the lysis buffer without the costly use of liquid nitrogen, PVP and β mercaptoethanol, provides a DNA yield of sufficient purity, suitable for PCR amplification and subsequent use.

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

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.

Author's correction DNA extraction from urea-preserved blood or blood clots for use in PCR

1995 ◽  
Vol 11 (4) ◽  
pp. 129 ◽  
Author(s):  
Annette Gelhaus ◽  
Britta Urban ◽  
Claude Pirmez
Keyword(s):  
Dna Extraction ◽  
Blood Clots

scholarly journals DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation

2017 ◽  
Author(s):  
Elizabeth Nacheva ◽  
Katya Mokretar ◽  
Aynur Soenmez ◽  
Alan M Pittman ◽  
Colin Grace ◽  
...  
Keyword(s):  
Substantia Nigra ◽  
Human Brain ◽  
Frontal Cortex ◽  
Genome Sequencing ◽  
Copy Number ◽  
Dna Isolation ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Whole Genome ◽  
Salting Out

AbstractPotential bias introduced during DNA isolation is inadequately explored, although it could have significant impact on downstream analysis. To investigate this in human brain, we isolated DNA from cerebellum and frontal cortex using spin columns under different conditions, and salting-out. We first analysed DNA using array CGH, which revealed a striking wave pattern suggesting primarily GC-rich cerebellar losses, even against matched frontal cortex DNA, with a similar pattern on a SNP array. The aCGH changes varied with the isolation protocol. Droplet digital PCR of two genes also showed protocol-dependent losses. Whole genome sequencing showed GC-dependent variation in coverage with spin column isolation from cerebellum. We also extracted and sequenced DNA from substantia nigra using salting-out and phenol / chloroform. The mtDNA copy number, assessed by reads mapping to the mitochondrial genome, was higher in substantia nigra when using phenol / chloroform. We thus provide evidence for significant method-dependent bias in DNA isolation from human brain, as reported in rat tissues. This may contribute to array “waves”, and could affect copy number determination, particularly if mosaicism is being sought, and sequencing coverage. Variations in isolation protocol may also affect apparent mtDNA abundance.

scholarly journals Method Comparison of DNA Isolation and Quantification for Fish and Seafood Authenticity Determination

2018 ◽  
Vol 13 (3) ◽  
pp. 115
Author(s):  
Dwiyitno Dwiyitno ◽  
Stefan Hoffman ◽  
Koen Parmentier ◽  
Chris Van Keer
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Extraction ◽  
Dna Isolation ◽  
Blue Mussel ◽  
Pcr Amplification ◽  
Amplification Efficiency ◽  
Chain Reaction ◽  
Seafood Products ◽  
Polymerase Chain ◽  
Commercial Kit

Fish and seafood products has been commonly targeted for fraudulent activities. For that reason, authentication of fish and seafood products is important to protect consumers from fraudulent and adulteration practices, as well as to implement traceability regulation. From the viewpoint of food safety, authenticity is beneficial to protect public from serious food poisoning incidents, such as due to ingestion of toxic species. Since DNA based identification depends on the nucleic acid polymerase chain reaction (PCR), the quantity and quality/purity of DNA will contribute significantly to the species authentication. In the present study, different DNA extraction and purification methods (3 classical methods and one commercial kit) were compared to produce the better isolated DNA for PCR amplification. Additionally, different methods for the estimation of DNA concentration and purity which is essential for PCR amplification efficiency were also evaluated. The result showed that classical DNA extraction methods (based on TNES-Urea) yielded a higher amount of DNA (11.30-323.60 ng/g tissue) in comparison to commercial kit/Wizard Promega (5.70-83.45 ng/g tissue). Based on the purity of DNA extract (A260/280), classical DNA extraction method produced relatively similar on DNA quality to the commercial kit (1.79-2.12). Interestingly, all classical methods produced DNA with A260/280 ratio of more than 2.00 on the blue mussel, in contrast with commercial kit. The commercial kit also produced better quality of DNA compared to the classical methods, showing the higher efficiency in PCR amplification. NanoDrop is promising as cheap, robust and safe UV-spectrophotometer method for DNA quantification, as well as the purity evaluation.Keywords: seafood authenticity, DNA isolation, polymerase chain reaction, NanoDrop, Picogreen

scholarly journals Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

2017 ◽  
Author(s):  
Taha Soliman ◽  
Sung-Yin Yang ◽  
Tomoko Yamazaki ◽  
Holger Jenke-Kodama
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Communities ◽  
Dna Extraction ◽  
Dna Isolation ◽  
Soil Microbial Communities ◽  
Next Generation ◽  
Microbial Composition ◽  
Okinawa Island ◽  
The Impact ◽  
Generation Sequencing

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil® DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin® Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA; P <0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.

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