scholarly journals VALIDATION OF PCR-RFLP TESTING METHOD TO DETECT PORCINE CONTAMINATION IN CHICKEN NUGGET

2012 ◽  
Vol 12 (3) ◽  
pp. 302-307 ◽  
Author(s):  
Tri Joko Raharjo ◽  
Winda Cahyaningtyas ◽  
Surajiman Surajiman ◽  
Istini Istini ◽  
Deni Pranowo
Keyword(s):  
Mitochondrial Dna ◽  
Rflp Analysis ◽  
Cytb Gene ◽  
Dna Fragments ◽  
Gene Fragment ◽  
Chicken Nugget ◽  
Testing Method ◽  
Pcr Product ◽  
Pcr Rflp ◽  
Dna Fragment

PCR-RFLP technique to detect porcine contamination in chicken nugget has been developed and validated in this research. Various concentrations of pork were fortified during preparation of the nugget. DNA was then isolated from the nugget followed by PCR employed primers which targeted a 359 bp cytB gene fragment of mitochondrial DNA. For RFLP, the PCR product was digested by means of BamHI and BseDI enzymes. Cutting DNA fragments from nugget containing pork using BseDI enzyme produced DNA fragment with size 228 and 131 bp, while cutting with BamHI enzyme produce DNA fragments with sizes 244 and 115 bp. All of these fragments were not present in RFLP analysis of pork-free nugget. The method shows good specificity and precision and could detect porcine contamination in the nugget up to 5%. The method has been applied to test commercial nugget. Four brand of Halal-labeled commercial nugget as well as four brand of non labeled one gave negative porcine contamination.

Identification of tuna species (Thunnini tribe) by PCR-RFLP analysis of mitochondrial DNA fragments

2015 ◽  
Vol 27 (3) ◽  
pp. 301-313 ◽  
Author(s):  
Kunhua Xu ◽  
Junli Feng ◽  
Xuting Ma ◽  
Xiao Wang ◽  
Dan Zhou ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Rflp Analysis ◽  
Dna Fragments ◽  
Pcr Rflp

scholarly journals Genotyping of bacteria belonging to the former Erwinia genus by PCR-RFLP analysis of a recA gene fragment

Microbiology ◽  
2002 ◽  
Vol 148 (2) ◽  
pp. 583-595 ◽  
Author(s):  
Małgorzata Waleron ◽  
Krzysztof Waleron ◽  
Anna J Podhajska ◽  
Ewa Łojkowska
Keyword(s):  
Geographic Origin ◽  
Rflp Analysis ◽  
Erwinia Carotovora ◽  
Pcr Primers ◽  
Reca Gene ◽  
Gene Fragment ◽  
Erwinia Tracheiphila ◽  
Pcr Product ◽  
Pcr Rflp ◽  
Erwinia Stewartii

Genotypic characterization, based on the analysis of restriction fragment length polymorphism of the recA gene fragment PCR product (recA PCR-RFLP), was performed on members of the former Erwinia genus. PCR primers deduced from published recA gene sequences of Erwinia carotovora allowed the amplification of an approximately 730 bp DNA fragment from each of the 19 Erwinia species tested. Amplified recA fragments were compared using RFLP analysis with four endonucleases (AluI, HinfI, TasI and Tru1I), allowing the detection of characteristic patterns of RFLP products for most of the Erwinia species. Between one and three specific RFLP groups were identified among most of the species tested (Erwinia amylovora, Erwinia ananas, Erwinia cacticida, Erwinia cypripedii, Erwinia herbicola, Erwinia mallotivora, Erwinia milletiae, Erwinia nigrifluens, Erwinia persicina, Erwinia psidii, Erwinia quercina, Erwinia rhapontici, Erwinia rubrifaciens, Erwinia salicis, Erwinia stewartii, Erwinia tracheiphila, Erwinia uredovora, Erwinia carotovora subsp. atroseptica, Erwinia carotovora subsp. betavasculorum, Erwinia carotovora subsp. odorifera and Erwinia carotovora subsp. wasabiae). However, in two cases, Erwinia chrysanthemi and Erwinia carotovora subsp. carotovora, 15 and 18 specific RFLP groups were detected, respectively. The variability of genetic patterns within these bacteria could be explained in terms of their geographic origin and/or wide host-range. The results indicated that PCR-RFLP analysis of the recA gene fragment is a useful tool for identification of species and subspecies belonging to the former Erwinia genus, as well as for differentiation of strains within E. carotovora subsp. carotovora and E. chrysanthemi.

scholarly journals Genetic diversity of Ongole Grade, Aceh, and Sumbawa cattle based on polymorphism on ND-5 fragment mitochondrial DNA using PCR-RFLP technique

2019 ◽  
Vol 20 (3) ◽  
pp. 783-788
Author(s):  
SUTARNO SUTARNO ◽  
SYARIFA ZAHRAH ◽  
OKID PARAMA ASTIRIN ◽  
ELISA HERAWATI ◽  
AHMAD DWI SETYAWAN
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Relationship ◽  
Livestock Breeding ◽  
Pcr Product ◽  
Pcr Rflp ◽  
Initial Improvement ◽  
Total Dna ◽  
Dna Fragment ◽  
Haplotypes Diversity

Abstract. Sutarno, Zahrah S, Astirin OP, Herawati E, Setyawan AD. 2019. Genetic diversity of Ongole Grade, Aceh, and Sumbawa cattle based on polymorphism on ND-5 fragment mitochondrial DNA using PCR-RFLP technique. Biodiversitas 20: 783-788. Genetic diversity is the basis of livestock breeding because it can be used as an initial improvement in livestock quality through artificial selection. This study aims to determine polymorphism in ND-5 fragment of mitochondrial DNA in Ongole Grade, Aceh, and Sumbawa cattle and their genetic diversity. The total DNA from the blood of the local cattle was extracted using the Wizard genomic DNA purification system from Promega and amplified using the PCR technique. The PCR product was then digested with HindIII enzyme using the RFLP technique to detect polymorphism. The genetic diversity of the Ongole Grade, Aceh, and Sumbawa cattle was analyzed using the formula from Nei and its genetic relationship was evaluated with the 2.02i NTSYSpc version program. Our findings showed there were polymorphisms in the ND-5 fragment of mitochondrial DNA. Digestion with HindIII restriction enzyme produces two types of haplotypes. Haplotype B is a 453 bp-sized DNA fragment that is not truncated by the HindIII enzyme, and haplotype A is a DNA fragment cut by HindIII enzyme into two with fragments of 336 bp and 117 bp. Polymorphism was found in Ongole Grade cattle, but not in Sumbawa and Aceh cattle. Haplotypes diversity in ND-5 fragments of mitochondrial DNA of Ongole Grade was 0.6250 while Sumbawa and Aceh cattle displayed no diversity of haplotypes. The genetic relationship shows that Sumbawa cattle belonged to the same cluster with Ongole Grade but separated from Aceh cattle.

Identification of Hake Species (MerlucciusGenus) Using Sequencing and PCR−RFLP Analysis of Mitochondrial DNA Control Region Sequences

2001 ◽  
Vol 49 (11) ◽  
pp. 5108-5114 ◽  
Author(s):  
Javier Quinteiro ◽  
Rodrigo Vidal ◽  
Mónica Izquierdo ◽  
Carmen G. Sotelo ◽  
María José Chapela ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Rflp Analysis ◽  
Mitochondrial Dna Control Region ◽  
Control Region Sequences ◽  
Pcr Rflp

PCR-based genetic identification of marlin and other billfish

1998 ◽  
Vol 49 (5) ◽  
pp. 383 ◽  
Author(s):  
B. H. Innes ◽  
P. M. Grewe ◽  
R. D. Ward
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Test ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Genetic Identification ◽  
Dna Molecule ◽  
Pcr Rflp ◽  
D Loop ◽  
Specific Variation ◽  
Species Specific

A genetic test was developed for the identification of the six species of billfish found in Australian waters (black marlin, Indo–Pacific blue marlin, striped marlin, Indo–Pacific sailfish, shortbill spearfish and broadbill swordfish). The test was based on the PCR–RFLP analysis of a 1400 bp region of the mitochondrial DNA molecule, the d-loop, using four restriction enzymes (Hinf I, Rsa I and Sau3A I andTaq I). A total of 33 composite haplotypes were observed among 160 fish; all were species-specific. Three of the species—black marlin, striped marlin and broadbill swordfish—showed sufficient intra-specific variation to be useful in population structure analyses.

scholarly journals Mitochondrial DNA Mutation Detection by Electrospray Mass Spectrometry

2007 ◽  
Vol 53 (2) ◽  
pp. 195-203 ◽  
Author(s):  
Yun Jiang ◽  
Thomas A Hall ◽  
Steven A Hofstadler ◽  
Robert K Naviaux
Keyword(s):  
Mass Spectrometry ◽  
Mitochondrial Dna ◽  
Rflp Analysis ◽  
Endocrine Disorders ◽  
Ion Cyclotron Resonance ◽  
Accurate Identification ◽  
Mtdna Mutations ◽  
Fticr Ms ◽  
Pcr Rflp ◽  
Mtdna Variants

Abstract Background: Mitochondrial DNA (mtDNA) mutations cause a large spectrum of clinically important neurodegenerative, neuromuscular, cardiovascular, and endocrine disorders. We describe the novel application of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR MS) to the rapid and accurate identification of pathogenic mtDNA variants. Methods: In a blinded study, we used ESI-FTICR MS to analyze 24 unrelated samples of total cellular DNA containing 12 mtDNA variants and compared the results with those obtained by conventional PCR-restriction fragment length polymorphism (PCR-RFLP) analysis and gel electrophoresis. Results: From the 24-sample blinded panel, we correctly identified 12 of the samples as bearing an mtDNA variant and found the remaining 12 samples to have no pathogenic variants. The correlation coefficient between the 2 methods for mtDNA variant detection was 1.0; there were no false positives or false negatives in this sample set. In addition, the ESI-FTICR method identified 4 single-nucleotide polymorphisms (SNP) that had previously been missed by standard PCR-RFLP analysis. Conclusions: ESI-FTICR MS is a rapid, sensitive, and accurate method for the identification and quantification of mtDNA mutations and SNPs.

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