scholarly journals Genetic diversity and comparative study of genomic DNA extraction protocols in Tamarix L. species

Caryologia ◽  
2021 ◽  
Vol 74 (2) ◽  
pp. 131-139
Author(s):  
Xiao Cheng ◽  
Xiaoling Hong ◽  
Majid Khayatnezhad ◽  
Fazal Ullah
Keyword(s):  
Genetic Diversity ◽  
Dna Extraction ◽  
Genomic Dna ◽  
Species Group ◽  
Proteinase K ◽  
Amplification Efficiency ◽  
Nrdna Its ◽  
Dna Extraction Method ◽  
Dna Contents

The genus Tamarix  consists of about 54 species that mainly grow in saline areas of deserts and semi-deserts. This genus is chemically characterized by the presence of tannins, flavonoids, anthocyanins and essential oils which interfere with the extraction of pure genomic DNA. Thus it is necessary to optimize extraction protocols to minimize the influence of these compounds to the lowest level. The present study compares the efficiency of five different approaches to extract total genomic DNA in Tamarix species, showing significant differences in the extracted DNA contents and quality,by using  Kit (DNP TM Kit), CTAB DNA extraction method by Murray and Thompson, Sahu et al., Nalini et al. and Bi et al., for the extraction of DNA from Tamarix species. Our results showed significant differences in DNA contents between these five methods. The quantity and quality of extracted genomic DNA were checked by the spectrophotometer, Nano-Drop and and agarose gel electrophoresis analysis. Finally, a PCR-based method was also applied to verify the amplification efficiency for two molecular markers (ITS and ISSR).. In the present study, the genetic diversity of 96 Tamarix individuals species and 8 populations were studied using 10 ISSR markerswhile for nrDNA ITS 8 species samples were used. The method of Nalini et al., provided best results (207 ng/μL) in terms of quantity and quality ofDNA. Our results proposed that this method could be effective for plants with the same polysaccharides, proteins and polyphenols components. The advantage of this method is simple and fast as it does not involve time consuming steps such as incubation at higher temperatures, and also do not requires expensive chemicals such as proteinase K, liquid nitrogen. ,. The success of this method in obtaining high-quality genomic DNA has been demonstrated in the Tamarix species group and the reliability of this method has been discussed.

scholarly journals Total Genomic DNA Extraction Studies from Seaweeds

2020 ◽  
Vol 4 (1) ◽  
pp. 10
Author(s):  
Made Pharmawati ◽  
Wildan Mujahidul Basyar ◽  
Ida Ayu Astarini
Keyword(s):  
Dna Extraction ◽  
Genomic Dna ◽  
Extraction Method ◽  
Genetic Improvement ◽  
Food Industry ◽  
Carotenoid Biosynthesis ◽  
Marine Resources ◽  
Basic Requirement ◽  
Dna Extraction Method

One of marine resources that has high value is seaweed.  Seaweed is a carrageenan producer used in the food industry. Seaweed contains many minerals, vitamins and proteins that are useful for health. Carotenoids are pigments found in seaweed that function as antioxidants.   The genes involved in carotenoid biosynthesis have been studied and provide opportunities for genetic improvement of seaweed.  DNA is a basic requirement in molecular analysis. Therefore, a suitable method of DNA extraction from seaweed is needed.  The aim of this research was to investigate DNA extraction method from several seaweed species and test the DNA quality through PCR-RAPD.  Seaweed samples were collected from Pantai Bumi Perkemahan Taman Nasional Bali Barat and DNA was extracted using Doyle and Doyle’s method with modifications.  PCR-RAPD was conducted using primer UBC127 and OPD 11 to test the quality of DNA.  Results showed that 3 hours incubation in 60ºC had the best result of DNA extraction.  However, the quality of DNA was low, as indicated by inconsistent PCR-RAPD products.   Further optimization in DNA extraction is needed to obtain high quality DNA for genetic analysis.

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 Optimized protocol to isolate high quality genomic DNA from different tissues of a palm species

Hoehnea ◽  
2019 ◽  
Vol 46 (2) ◽  
Author(s):  
Marília Souza Lucas ◽  
Carolina da Silva Carvalho ◽  
Giovane Böerner Hypolito ◽  
Marina Corrêa Côrtes
Keyword(s):  
Dna Extraction ◽  
Genomic Dna ◽  
Dna Isolation ◽  
Molecular Techniques ◽  
Tissue Type ◽  
High Quality ◽  
Optimized Protocol ◽  
Palm Species ◽  
Different Tissues

ABSTRACT The application of molecular techniques to tackle ecological and evolutionary questions requires genomic DNA in good quality and quantity. The quality of the isolated DNA, however, can be influenced by the tissue type and the way the sample was conserved and manipulated. Therefore, customizing protocols to improve the DNA isolation and locus amplification is crucial. We optimized a cheap and manual protocol of DNA extraction and microsatellites amplification using five different tissues of a palm species of the brazilian Atlantic Forest. We successfully extracted DNA from all five tissue types. Leaf, stem, and endocarp of non-dispersed seeds presented the highest rates of successful DNA extraction and microsatellite amplification; whereas root, endocarp of dispersed seeds, and embryo showed the lowest quality and quantity. Based on these results, we discussed the implications of using different tissues for studies about seed dispersal, pollination, and population genetics.

Development of an Efficient Fungal DNA Extraction Method To Be Used in Random Amplified Polymorphic DNA–PCR Analysis To Differentiate Cyclopiazonic Acid Mold Producers

2008 ◽  
Vol 71 (12) ◽  
pp. 2497-2503 ◽  
Author(s):  
BEATRIZ SÁNCHEZ ◽  
MAR RODRÍGUEZ ◽  
EVA M. CASADO ◽  
ALBERTO MARTÍN ◽  
JUAN J. CÓRDOBA
Keyword(s):  
Dna Extraction ◽  
Extraction Method ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Cyclopiazonic Acid ◽  
Proteinase K ◽  
Vacuum System ◽  
Pcr Analysis ◽  
Dna Extraction Method ◽  
Rapd Pcr

A variety of previously established mechanical and chemical treatments to achieve fungal cell lysis combined with a semiautomatic system operated by a vacuum pump were tested to obtain DNA extract to be directly used in randomly amplified polymorphic DNA (RAPD)–PCR to differentiate cyclopiazonic acid–producing and –nonproducing mold strains. A DNA extraction method that includes digestion with proteinase K and lyticase prior to using a mortar and pestle grinding and a semiautomatic vacuum system yielded DNA of high quality in all the fungal strains and species tested, at concentrations ranging from 17 to 89 ng/μl in 150 μl of the final DNA extract. Two microliters of DNA extracted with this method was directly used for RAPD-PCR using primer (GACA)4. Reproducible RAPD fingerprints showing high differences between producer and nonproducer strains were observed. These differences in the RAPD patterns did not differentiate all the strains tested in clusters by cyclopiazonic acid production but may be very useful to distinguish cyclopiazonic acid producer strains from nonproducer strains by a simple RAPD analysis. Thus, the DNA extracts obtained could be used directly without previous purification and quantification for RAPD analysis to differentiate cyclopiazonic acid producer from nonproducer mold strains. This combined analysis could be adaptable to other toxigenic fungal species to enable differentiation of toxigenic and nontoxigenic molds, a procedure of great interest in food safety.

scholarly journals Comparative Analysis of Different DNA Extraction Methods and Preliminary Analysis of Genetic Diversity of Hedera nepalensis K. Koch. in Vietnam Based on GBSSI Marker

2019 ◽  
Vol 35 (1) ◽  
Author(s):  
Dinh Doan Long ◽  
Nguyen Xuan Bach ◽  
Nguyen Thi Thu Thao ◽  
Pham Thi Hong Nhung ◽  
Do Thi Le Hang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Extraction ◽  
Genomic Dna ◽  
Preliminary Analysis ◽  
Herbarium Specimens ◽  
Arnold Arboretum ◽  
Sprague Dawley ◽  
National Academy Of Sciences ◽  
Manihot Esculenta Crantz ◽  
Spacer Length

Though the ivy (Hedera nepalensis K. Koch.) has long been utilized in traditional medicine, its genome information is very limited. For plants, an effective method of DNA extraction is a very important step which greatly affects subsequent genetic analyses. In this study, four different methods of DNA extraction from dry leaves were used. A comparison of different protocols resulted in the yield of extracted DNA that ranged from 10.5 to 437.4 ng/μl and with a purity ranged from 1.8 to 2.2. Based on the PCR results of GBSSI gene, Gene JET Plant Genomic DNA Purification Mini Kit is the most optimal extraction method for Vietnam ivy’s dry leaves. A preliminary analysis of the phylogenetic tree based on the GBSSI marker showed that ivy growing in a number of northern mountainous provinces of Vietnam belonged to the H. nepalensis K. Koch species. The high - quality total DNA will allow us to amplify different DNA markers, providing valuable genetic information to preserve and develop medicinal resources in Vietnam. Keywords GBSSI, Hedera nepalensis K. Koch, DNA extraction. References [1] J. Ackerfield, J. Wen, A morphometric analysis of Hedera L. (the ivy genus, Araliaceae) and its taxonomic implications, Adansonia Sér. 24 (2002) 187-212.[2] U.S. National Plant Germplasm System, Taxon: Hedera nepalensis K. Koch, https://npgsweb.ars -grin.gov/gringlobal/taxonomydetail.aspx?id= 18567, 2019 (accessed 21 March 2019). [3] L. Jafri, S. Saleem, T.P. Kondrytuk, I.Q. Haq, N. Ullah, J.M. Pezzuto, B. Mirza, Hedera nepalensis K. Koch: A Novel Source of Natural Cancer Chemopreventive and Anticancerous Compounds, Phytotherapy Reserch. 30 (2016) 447-453.[4] S. Saleem, L. Jafri, I. Haq, L.C. Chang, D. Calderwood, B.D. Green, B. Mirza, Plants Fagonia cretica L. and Hedera nepalensis K. Koch contain natural compounds with potent dipeptidyl peptidase-4 (DPP-4) inhibitory activity, Journal of Ethnopharmacology. 156 (2014) 26-32.[5] W.J. Hashmi, H. Ismail, F. Mehmood, B. Mirza, Neuroprotective, antidiabetic and antioxidant effect of Hedera nepalensis and lupeol against STZ+ AlCl3 induced rats model, DARU: Journal of faculty of Pharmacy, Tehran University of Medical Sciences. 26 (2018) 179-190.[6] H. Ismail, A. Rasheed, I.U. Haq, L. Jafri, N. Ullah, E. Dilshad, M. Sajd, B. Mirza, Five indigenous plants of Pakistan with Antinociceptive, anti-inflammatory, antidepressant, and anticoagulant properties in Sprague Dawley rats, Evidence-based Complementary and alternative medicine 2017 (2017) 1-10.[7] A. Mitchell, J. Wen. Phylogenetic utility and evidence for multiple copies of granule-bound starch synthase I (GBSSI) in Araliaceae, Taxon 53 (2004) 29-44.[8] M.A. Saghai-Maroof, K.M. Soliman, R.A. Jorgensen, R.W.L. Allard, Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics, Proceeding of the National Academy of Sciences of the USA. 81 (1984) 8014-8018.[9] M. Elias, G.S. Mühlen, D. McKey, A.C. Roa, J. Tohme, Genetic diversity of traditional South American landraces of cassava (Manihot esculenta Crantz): an analysis using microsatellites, Economic Botany. 58 (2004) 242-256.[10] B.D. Lade, A.S. Patil, H.M. Paikrao, Efficient genomic DNA extraction protocol from medicinal rich Passiflora foetida containing high level of polysaccharide and polyphenol, Springerplus. 3 (2014) 1-7.[11] J.H. Cota-Sánchez, K. Remarchuk, K. Ubayasena, Ready-to-use DNA extracted with a CTAB method adapted for herbarium specimens and mucilaginous plant tissue, Plant Molecular Biology Reporter. 24 (2006) 161.[12] J. Zhang, J.M. Stewart, Economical and rapid method for extracting cotton genomic DNA, Journal of Cotton Science. 4 (2000) 193-201.[13] T. Li, H. Pan, Y. Feng, H. Li, Y. Zhao, Bioactivity-guided isolation of anticancer constituents from Hedera nepalensis K. Koch, South African Journal of Botany. 100 (2015) 87-93.[14] L. Jafri, S. Saleem, N. Ullah, B. Mirza, In vitro assessment of antioxidant potential and determination of polyphenolic compounds of Hedera nepalensis K. Koch, Arabian Journal of Chemistry. 10 (2017) S3699-S3706.[15] B. Ahmad, N. Munir, S. Bashir, S. Azam, I. Khan, M. Ayub, Biological screening of Hedera nepalensis, Journal of Medicinal Plants Research. 6 (2012) 5250-5257.[16] K.H.E. Koch, Hortus Dendrologicus, F. Schneider & Co., Berlin, 1985, pp 250.[17] A. Rehder, New species, varieties and combinations from the herbarim and the collections of the Arnold arboretum, Journal of the Arnold Arboretum. 4 (1923) 250.  

scholarly journals Evaluation of eight protocols for genomic DNA extraction of Hypostomus commersoni Valenciennes, 1836 (Loricariidae: Siluriformes)

2019 ◽  
Author(s):  
P. Mezzomo ◽  
A. A. Mielniczki-Pereira ◽  
T. L. Sausen ◽  
J. R. Marinho ◽  
R. L. Cansian
Keyword(s):  
Dna Extraction ◽  
Genetic Material ◽  
Proteinase K ◽  
Ocular Tissue ◽  
South American ◽  
Target Tissue ◽  
Sample Collection ◽  
High Concentration ◽  
Positive Spectrum

AbstractThe principle and the techniques applied in DNA extraction play a pivotal role in the obtention of a purified genetic material. The present study investigates the efficiency of eight protocols in the DNA extraction of Hypostomus commersoni, an essential component of South American freshwater ichthyofauna. The quality of samples was assessed through spectrophotometry, gel electrophoresis, and PCR-RAPD amplification. The efficiency of DNA extraction was influenced both by the method applied and the target-tissue of choice. Higher concentrations and yield of DNA were obtained from ocular tissue, with a positive spectrum of incubation in lysis buffer for up to 36 hours after sample collection, using fresh tissues and in the presence of a high concentration of Proteinase K (20 mg.ml-1). In these conditions, samples were successfully amplified. To date, there is no record of description for the parameters analyzed in this work, neither the description of RAPD markers for the species H. commersoni.

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