scholarly journals Identifikasi Simplisia yang Dijual sebagai Strychnos ligustrina Bl. di Pasar Tradisional Surabaya dengan Metode Random Amplified Polymorphic DNA (RAPD)

2005 ◽  
Vol 11 (1) ◽  
pp. 19-24
Author(s):  
Oeke Yunita ◽  
Angelica Kresnamurti
Keyword(s):  
Cetyltrimethylammonium Bromide ◽  
Molecular Level ◽  
Random Amplified Polymorphic Dna ◽  
Local Market ◽  
Chain Reaction ◽  
Banding Patterns ◽  
Traditional Market ◽  
Ctab Method ◽  
Polymerase Chain ◽  
Rapd Method

Authentication of Strychnos ligustrina Bl. had been performed at molecular level (DNA) with Random Amplified Polymorphic DNA (RAPD) method, based on the amplification of random DNA fragments by Polymerase Chain Reaction (PCR) with a single arbitrary primer. The aim of this research was obtaining similar banding patterns between DNA of plant Strychnos ligustrina Bl. and DNA of its lignum on local market. Strychnos ligustrina Bl. was determined by UPT Balai Konservasi Tumbuhan Kebun Raya Purwodadi and plants sold as Strychnos ligustrina Bl. were collected as lignum from traditional market at Wonokromo, Rungkut, Genteng, Benowo dan Pabean. DNA from these plants were extracted by modified Cetyltrimethylammonium bromide (CTAB) method and amplified by RAPD method. Amplification had been performed by primer OPO-4 had shown banding patterns on the gel electrophoresis which banding patterns were shown by Strychnos ligustrina Bl. and plants sold as Strychnos ligustrina Bl. on Benowo. Based on this early result, we assume that plants sold as Strychnos ligustrina Bl. on Benowo has closely genetic relationship with Strychnos ligustrina Bl.

scholarly journals Sources of Potential Errors in the Application of Random Amplified Polymorphic DNAs in Cucumber

HortScience ◽  
1996 ◽  
Vol 31 (2) ◽  
pp. 262-266 ◽  
Author(s):  
Jack Staub ◽  
Jeffery Bacher ◽  
Karl Poetter
Keyword(s):  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Inbred Lines ◽  
Sphaerotheca Fuliginea ◽  
Chain Reaction ◽  
Banding Patterns ◽  
Taq Dna Polymerase ◽  
Polymerase Chain ◽  
Stock Solutions ◽  
Pcr Conditions

The influence of tissue age, pathogen infestation, intrapopulation contamination, and polymerase chain reaction (PCR) conditions were assessed as sources of error in random amplified polymorphic DNA (RAPD) analysis. DNA from young, uninfected tissue provided the most consistent results. Plants infected with Sphaerotheca fuliginea Schl. (ex Fr.) Poll. showed variation in RAPD banding patterns compared to those of uninfected plants. Differences in banding patterns were detectable when DNA from two inbred lines were mixed at dilution ratios of ≤20:1 but not ≥50:1. Differing lots of commercially available 10× reaction buffer, MgCl2 stock solutions, and Taq DNA polymerase affected RAPD banding patterns and overall yield. For reproducibility of RAPD assays, it may be necessary to optimize reactions for specific lots of PCR reagents from either commercial or in-house sources.

scholarly journals Comparison of methods to extract PCR-amplifiable DNA from fruit, herbal and black teas

2021 ◽  
Vol 39 (No. 5) ◽  
pp. 410-417
Author(s):  
Eliška Čermáková ◽  
Kamila Zdeňková ◽  
Kateřina Demnerová ◽  
Jaroslava Ovesná
Keyword(s):  
Cetyltrimethylammonium Bromide ◽  
Deoxyribonucleic Acid ◽  
Dna Isolation ◽  
Extraction Procedure ◽  
Sample Analysis ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Optimal Protocol ◽  
Ctab Method ◽  
Polymerase Chain

The success of polymerase chain reaction (PCR) assay depends on template deoxyribonucleic acid (DNA) being sufficient with respect to both quantity and quality. Some biological materials contain compounds which inhibit the functioning of DNA polymerase and thus need to be removed as part of the DNA extraction procedure. The aim of the present experiments was to optimise the process of DNA isolation from various types of black, fruit and herbal teas. A comparison was made between two cetyltrimethylammonium bromide (CTAB)-based protocols and two commercially available DNA purification kits. The yield and integrity of the extracted DNA were monitored both spectrophotometrically and using agarose gel electrophoresis. The presence/absence of inhibitors in the DNA preparations was checked by running quantitative real-time PCRs. The optimal protocol was deemed to be the CTAB method described in ISO 21571:2005, so this method is recommended for the routine sample analysis of tea products.

scholarly journals Heavy metal-induced oxidative stress and DNA damage as shown by RAPD-PCR in leaves of Elodea canadensis

2020 ◽  
Vol 3 (1) ◽  
pp. 14
Author(s):  
Dilek Demirezen Yilmaz ◽  
Nuri Ercan ◽  
Fahriye Sumer Ercan
Keyword(s):  
Heavy Metals ◽  
Dna Damage ◽  
Random Amplified Polymorphic Dna ◽  
Antioxidant Response ◽  
Elodea Canadensis ◽  
Chain Reaction ◽  
Banding Patterns ◽  
Dna Damages ◽  
Rapd Pcr ◽  
Polymerase Chain

The objective of the study was to evaluate the antioxidant response and DNA damage of heavy metals (Cd, Cu and Cr) in Elodea canadensis. Superoxide dismutase (SOD), catalase (CAT), Glutathione reductase (GR) and lipid peroxidation levels of leaves of Elodea canadensis which was exposed to different concentrations of heavy metals (Cd: 2, 5, 10, 15, 25 ppb; Cu: 200, 500, 1000, 2500 ppb and Cr: 1, 3, 10, 15, 25 ppb) in a hydroponic culture were determined spectrophotometrically. The highest induction in SOD and CAT activities were determined at highest concentration of heavy metals. The Random Amplified Polymorphic DNA Polymerase Chain Reaction (RAPD-PCR) technique was used to investigate the variation of DNA banding patterns of samples that exposed to different concentrations of heavy metals. Changing in band intensity and the gain and loss of bands were demonstrated the genotoxic effect of heavy metals. Bioaccumulation, oxidative responses and DNA damages were shown that Elodea canadensis represents a useful bioindicator.

scholarly journals DNA Extraction from Several Cacti

HortScience ◽  
2000 ◽  
Vol 35 (6) ◽  
pp. 1124-1126 ◽  
Author(s):  
Candelario Mondragon-Jacobo ◽  
Natalia Doudareva ◽  
Bruce P. Bordelon
Keyword(s):  
Dna Extraction ◽  
Pcr Amplification ◽  
Hexadecyltrimethylammonium Bromide ◽  
Digestion Time ◽  
Chain Reaction ◽  
High Quality ◽  
Banding Patterns ◽  
Extraction Buffer ◽  
Ctab Method ◽  
Polymerase Chain

A method for extraction of high quality DNA from four Opuntia sp. and other cacti using a hexadecyltrimethylammonium bromide (CTAB) method is described. These plants typically contain high levels of mucilages, complex polysaccharide compounds that bind water, thus preventing DNA extraction by common miniprep methods. The method involves adjusting the amount of tissue used according to species and age, followed by processing in an extraction buffer to separate coarse material. Extended centrifugation and digestion time in a separation buffer with CTAB (2%) was used. Exposing tissue to both buffers maintained polysaccharides in solution and allowed easier recovery of the aqueous phase that contains the DNA. We found that 5-8 g were needed to obtain up to 153 μg·g-1 of DNA from tender tissue. Old tissue yielded 26% less. Extraction of DNA from 5-g samples of tender tissue of the ornamental cacti Stenocereus sp., Cleistocactus sp., and Echinocereus sp. was successful. For these species, average yields ranged from 25 to 53 μg per sample. The DNA obtained was suitable for polymerase chain reaction (PCR) amplification, producing clear, distinctive, and reproducible banding patterns useful for a variety of applications.

scholarly journals RANDOM AMPLIFIED POLYMORPHIC DNA (RAPDs) DETECTS PATTERNS OF GENETIC DIVERSITY IN DIPLOID MUSA ACUMINATA COLLA

HortScience ◽  
1992 ◽  
Vol 27 (6) ◽  
pp. 660b-660
Author(s):  
Robert L. Jarret
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Geographic Origin ◽  
Morphological Characteristics ◽  
Principal Component ◽  
Chain Reaction ◽  
Banding Patterns ◽  
Random Primers ◽  
Pcr Products ◽  
Polymerase Chain

Patterns of diversity among thirty diploid clones of banana (Musa acuminata Colla.), collected in Papua New Guinea and the surrounding islands between 1987 and 1989, were examined genetically using the polymerase chain reaction (PCR) and random primers, to detect random amplified polymorphic DNA (RAPDs). PCR products were visualized on ethidium bromide stained agarose gels. Twenty of 60 random primers examined detected RAPDS in CTAB-extracted genomic DNA. Banding patterns ranged from very simple (1 or 2 bands/gel) to very complex (more than 20 bands/gel). All 30 Musa clones were distinguishable from each other based on their unique RAPD banding pattern. Principal component analysis (PCA) revealed several clusters of closely related clones within the materials examined. However, these clusterings were not correlated with either the geographic origin or the morphological characteristics of the clones. A role of the use of RAPDs in germplasm characterization is discussed.

scholarly journals Characterization of Xanthomonas axonopodis pv. phaseoli isolates

2008 ◽  
Vol 34 (3) ◽  
pp. 228-231 ◽  
Author(s):  
Willian Mário de Carvalho Nunes ◽  
Maria Júlia Corazza ◽  
Silvana Aparecida Crestes Dias de Souza ◽  
Siu Mui Tsai ◽  
Eiko Eurya Kuramae
Keyword(s):  
Xanthomonas Campestris ◽  
Random Amplified Polymorphic Dna ◽  
Hypersensitive Reaction ◽  
Chain Reaction ◽  
Xanthomonas Axonopodis ◽  
Paulo State ◽  
Total Dna ◽  
Polymerase Chain ◽  
Bacterial Plant Pathogen

A simple, quick and easy protocol was standardized for extraction of total DNA of the bacteria Xanthomonas axonopodis pv. phaseoli. The DNA obtained by this method had high quality and the quantity was enough for the Random Amplified Polymorphic DNA (RAPD) reactions with random primers, and Polymerase Chain Reaction (PCR) with primers of the hypersensitivity and pathogenicity gene (hrp). The DNA obtained was free of contamination by proteins or carbohydrates. The ratio 260nm/380nm of the DNA extracted ranged from 1.7 to 1.8. The hrp gene cluster is required by bacterial plant pathogen to produce symptoms on susceptible hosts and hypersensitive reaction on resistant hosts. This gene has been found in different bacteria as well as in Xanthomonas campestris pv. vesicatoria (9). The primers RST21 and RST22 (9) were used to amplify the hrp gene of nine different isolates of Xanthomonas axonopodis pv. phaseoli from Botucatu, São Paulo State, Brazil, and one isolate, "Davis". PCR amplified products were obtained in all isolates pathogenic to beans.

Polymerase chain reaction based mapping of rye involving repeated DNA sequences

Genome ◽  
1992 ◽  
Vol 35 (4) ◽  
pp. 621-626 ◽  
Author(s):  
Peter M. Rogowsky ◽  
Ken W. Shepherd ◽  
Peter Langridge
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
Chromosome 1 ◽  
Repeated Dna ◽  
Chain Reaction ◽  
Pcr Marker ◽  
Banding Patterns ◽  
Repeated Dna Sequences ◽  
Cereal Rye ◽  
Polymerase Chain

A novel type of polymerase chain reaction (PCR) marker was developed for the mapping of cereal rye (Secale cereale). Primer pairs were synthesized targeting the insertion sites of three individual copies of the R173 family of rye specific repeated DNA sequences. While one primer was derived from a sequence within the respective R173 element, the second primer corresponded to a flanking region. The complex banding patterns obtained in rye allowed not only the mapping of the three R173 elements to certain chromosome regions of 1RS (the short arm of rye chromosome 1) but also the mapping of an additional 3–10 easily identifiable bands per primer pair to other rye chromosomes. Linkage mapping of a polymorphic 1R band derived from three rye cultivars demonstrated the presence of nonallelic, dominant markers in two independent crosses. Because of the high copy number of the R173 family (15 000 copies per diploid rye genome), its dispersion over the entire length of all chromosomes and the high number of markers obtained per primer pair, PCR markers based on the R173 family provide an almost unlimited source for well-spaced markers in rye mapping.Key words: polymerase chain reaction, mapping, repetitive DNA sequences, wheat, rye.

scholarly journals Genetic variation between susceptible and non-susceptible snails to Schistosoma infection using random amplified polymorphic DNA analysis (RAPDs)

1999 ◽  
Vol 41 (5) ◽  
pp. 291-295 ◽  
Author(s):  
Abdel-Hamid Zaki ABDEL-HAMID ◽  
Jeanne Blanco de MOLFETTA ◽  
Vania FERNANDEZ ◽  
Vanderlei RODRIGUES
Keyword(s):  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Polyacrylamide Gel Electrophoresis ◽  
Genome Comparison ◽  
Gene Products ◽  
Chain Reaction ◽  
High Molecular Weight Dna ◽  
Polymerase Chain ◽  
Or Gene ◽  
Host Parasite

Susceptibility of snails to infection by certain trematodes and their suitability as hosts for continued development has been a bewildering problem in host-parasite relationships. The present work emphasizes our interest in snail genetics to determine what genes or gene products are specifically responsible for susceptibility of snails to infection. High molecular weight DNA was extracted from both susceptible and non-susceptible snails within the same species Biomphalaria tenagophila. RAPD was undertaken to distinguish between the two types of snails. Random primers (10 mers) were used to amplify the extracted DNA by the polymerase chain reaction (PCR) followed by polyacrylamide gel electrophoresis (PAGE) and silver staining. The results suggest that RAPD represents an efficient means of genome comparison, since many molecular markers were detected as genetic variations between susceptible and non-susceptible snails.

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