scholarly journals DNA extraction and pattern of crab and macrobentos from North Sumatran mangrove forest, Indonesia

2021 ◽  
Vol 912 (1) ◽  
pp. 012046
Author(s):  
A M Harahap ◽  
M Basyuni ◽  
I E Susetya
Keyword(s):  
Dna Extraction ◽  
Mangrove Forest ◽  
Morphological Analysis ◽  
Animal Species ◽  
Pcr Amplification ◽  
Sequencing Analysis ◽  
Chain Reaction ◽  
Mangrove Ecosystems ◽  
Polymerase Chain ◽  
North Sumatra

Abstract Mangrove forest ecosystem is one of the most productive and unique ecosystems that serves to protect coastal areas from various disturbances, as well as provide habitat for various animal species. The large number of crab species and macrobentos in mangrove ecosystems results in frequent errors in the naming of species that have similarities in morphological features. This problem can be solved through a comprehensive approach by combining morphological analysis with genetic analysi.This study aims to report a DNA extraction and PCR amplification prior was used for the identification of crab and macrozoobentos from mangrove forest, North Sumatra. Primer 16S has a conserved area so it is appropriately used in Polymerase Chain Reaction (PCR) and sequencing analysis to determine taxonomy, phylogeny and diversity between specie. Visualization of PCR amplification results with primer16S from crab samples and macrobentos resulting a low DNA band with a size of 206 bp and a high of 678bp

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 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 Genetic Identification of Eggs Purportedly From the Extinct Labrador Duck (Camptorhynchus Labradorius)

The Auk ◽  
2007 ◽  
Vol 124 (3) ◽  
pp. 962-968
Author(s):  
Glen Chilton ◽  
Michael D. Sorenson
Keyword(s):  
Dna Extraction ◽  
Pcr Amplification ◽  
Genetic Identification ◽  
Somateria Mollissima ◽  
Chain Reaction ◽  
Additional Information ◽  
Breeding Grounds ◽  
The Common ◽  
Polymerase Chain ◽  
And Control

Abstract Material extracted from inside the shells of nine purported Labrador Duck (Camptorhynchus labradorius) eggs was subjected to DNA extraction and polymerase chain reaction (PCR) amplification. For each egg, partial sequences of one to three mitochondrial genes (12S, ND2, and control region) were compared with sequences derived from a Labrador Duck specimen and representatives of several other waterfowl species. Sequences from six eggs were consistent with those of the Red-breasted Merganser (Mergus serrator), whereas the sequences from one egg was most consistent with that of the Common Eider (Somateria mollissima). The remaining two eggs yielded sequences consistent with that of the Mallard (Anas platyrhynchos) or a domestic duck. Regrettably, none of the eggs provided additional information about the breeding grounds of the extinct Labrador Duck. To our knowledge, this is the first report of DNA extraction and amplification from old eggshells of birds. Identification génétique d'œufs présumés provenir de l'espèce disparue Camptorhynchus labradorius

scholarly journals Amplification of human beta-actin gene by the reverse transcriptase-polymerase chain reaction: implications for assessment of RNA from formalin-fixed, paraffin-embedded material.

1996 ◽  
Vol 44 (10) ◽  
pp. 1205-1207 ◽  
Author(s):  
A Dakhama ◽  
V Macek ◽  
J C Hogg ◽  
R G Hegele
Keyword(s):  
Polymerase Chain Reaction ◽  
Pcr Amplification ◽  
Housekeeping Gene ◽  
Chain Reaction ◽  
Viral Genomes ◽  
Negative Results ◽  
Beta Actin ◽  
Target Nucleic Acid ◽  
Formalin Fixed Paraffin Embedded ◽  
Polymerase Chain

The polymerase chain reaction (PCR) is a powerful method that allows enzymatic amplification of rate target nucleic acid sequences. It has been applied to the amplification of viral genomes from paraffin-embedded pathology specimens. However, interpretation of negative results requires amplification of a housekeeping gene such as beta-actin. In the present study we used specific oligonucleotide primers previously designed to amplify both the genomic DNA and the mRNA transcript from paraffin-embedded tissue. These products have predicted sizes of 250 BP and 154 BP, respectively, but our results showed that PCR amplification only (without reverse transcription) unexpectedly generated the 154-BP product. Further investigation of the nature of this product demonstrated that it originated from the amplification of DNA, not RNA. We conclude that the 154-BP product generated by these primers cannot be exclusively considered as beta-actin RNA product and should not be used to assess successful extraction of RNA, to ascertain its integrity, or to normalize for the total amount of RNA assayed by RT-PCR from paraffin-embedded tissue.

scholarly journals A Self-Contained Portable Polymerase-Chain-Reaction System Integrated with Electromagnetic Mini-Actuators for Bi-Directional Fluid Transport

2011 ◽  
Vol 27 (3) ◽  
pp. 357-364
Author(s):  
B. T. Chia ◽  
S.-A. Yang ◽  
M.-Y. Cheng ◽  
C.-W. Lin ◽  
Y.-J. Yang
Keyword(s):  
Polymerase Chain Reaction ◽  
Fluid Transport ◽  
Point Of Care ◽  
Reaction System ◽  
Thermal Characteristics ◽  
Pcr Amplification ◽  
Chain Reaction ◽  
Rapid Temperature ◽  
Small Footprint ◽  
Polymerase Chain

ABSTRACTIn this paper, the development of a portable polymerase chain reaction (PCR) device is presented. Integrating electromagnetic mini-actuators for bi-directional fluid transport, the proposed device, whose dimension is 67mm × 66mm × 25mm, can be fully operated with a 5V DC voltage. The device consists of four major parts: A disposable channel chip in which PCR mixture is manipulated and reacted, a heater chip which generates different temperature zones for PCR reaction, a linear actuator array for pumping PCR mixture, and a circuit module for controlling and driving the system. The advantages of the device include the rapid temperature responses associated with continuous-flow-type PCR devices, as well as the programmable thermal cycling associated with chamber-type PCR devices. The thermal characteristics are measured and discussed. PCR amplification is successfully performed for the 122 bp segment of MCF-7/adr cell line. Due to its small footprint, this self-contained system potentially can be employed for point-of-care (POC) applications.

scholarly journals Suitability of different tissue fixatives for subsequent PCR analysis of Cysticercus ovis

2012 ◽  
Vol 49 (2) ◽  
pp. 67-70 ◽  
Author(s):  
M. Kolesárová ◽  
R. Herich ◽  
M. Levkut ◽  
J. Čurlík ◽  
M. Levkut
Keyword(s):  
Retrospective Studies ◽  
Pcr Amplification ◽  
Pcr Analysis ◽  
Chain Reaction ◽  
Fresh Tissue ◽  
Carnoy’S Solution ◽  
Negative Results ◽  
Pcr Product ◽  
Polymerase Chain ◽  
Cysticercus Ovis

AbstractPCR amplification of specific DNA regions is a powerful tool for retrospective studies, but not all preservation or fixation methods render DNA that is suitable for subsequent amplification. Several factors affect sensitivity of polymerase chain reaction (PCR) amplification. There were reported the effects of commonly used fixation solutions — 10 % neutral buffered formalin, 20 % neutral buffered formalin and Carnoy’s solution and the efficiency of PCR amplification in fresh tissue and paraffin (or wax) embedded samples of Cysticercus ovis. DNA from samples was isolated and PCR product of 1300 bp was amplified. Results indicated that the samples fixed in Carnoy’s solution produced reliable amplification of desired fragments. The samples that were fixed in 10 % and 20 % neutral buffered formalin brought negative results.

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