scholarly journals DNA Barcode-Based PCR-RFLP and Diagnostic PCR for Authentication of Jinqian Baihua She (Bungarus Parvus)

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Xiaolei Li ◽  
Weiping Zeng ◽  
Jing Liao ◽  
Zhenbiao Liang ◽  
Shuhua Huang ◽  
...  
Keyword(s):  
Fragment Length Polymorphism ◽  
Dna Barcode ◽  
Specific Primers ◽  
Diagnostic Pcr ◽  
Pcr Rflp ◽  
Restriction Sites ◽  
Specific Restriction ◽  
Polymerase Chain ◽  
Coi Sequences ◽  
Species Specific

We established polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and diagnostic PCR based on cytochrome C oxidase subunit I (COI) barcodes ofBungarus multicinctus, genuine Jinqian Baihua She (JBS), and adulterant snake species. The PCR-RFLP system utilizes the specific restriction sites ofSpeI andBstEII in the COI sequence ofB. multicinctusto allow its cleavage into 3 fragments (120 bp, 230 bp, and 340 bp); the COI sequences of the adulterants do not contain these restriction sites and therefore remained intact after digestion withSpeI andBstEII (except for that ofZaocys dhumnades, which could be cleaved into a 120 bp and a 570 bp fragment). For diagnostic PCR, a pair of species-specific primers (COI37 and COI337) was designed to amplify a specific 300 bp amplicon from the genomic DNA ofB. multicinctus; no such amplicons were found in other allied species. We tested the two methods using 11 commercial JBS samples, and the results demonstrated that barcode-based PCR-RFLP and diagnostic PCR both allowed effective and accurate authentication of JBS.

Molecular and morphological discrimination betweenTylospora fibrillosaandTylospora asterophoramycorrhizae

1999 ◽  
Vol 77 (1) ◽  
pp. 11-21 ◽  
Author(s):  
Ursula Eberhardt ◽  
Lutz Walter ◽  
Ingrid Kottke
Keyword(s):  
Fragment Length Polymorphism ◽  
Pcr Primers ◽  
Morphological Identification ◽  
Chain Reaction ◽  
Specific Primers ◽  
Specific Pcr ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Species Specific ◽  
First Time

Among the mycorrhizal types of spruce, Tylospora-type mycorrhizae are the most constant and abundant. Two species of the genus Tylospora occur in Europe, Tylospora fibrillosa and Tylospora asterophora. Mycorrhizae of T. asterophora are described in detail for the first time. Sequences of the internal transcribed spacer (ITS) of the ribosomal genes were obtained from T. fibrillosa and T. asterophora mycorrhizae, sporocarps, and cultured mycelium. Discrimination and identification of the two species by ITS polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) are discussed in the light of inter- and intra-specific variability. Species-specific PCR primers were designed to distinguish both species. Molecular screening of Tylospora-type mycorrhizae from field material led to unambiguous results, whereas morphological identification is likely to fail because of great similarity even at the microscopic level.Key words: Tylospora asterophora, Tylospora fibrillosa, ectomycorrhizae, taxon specific primers (TSOPs), ITS sequences.

PCR-based molecular discrimination betweenMaritrema eroliaeandProbolocoryphe uca(Digenea: Microphallidae) in Kuwait Bay

2013 ◽  
Vol 88 (2) ◽  
pp. 177-182
Author(s):  
W.Y. Al-Kandari ◽  
S.A. Al-Bustan ◽  
M. Alnaqeeb ◽  
A.M. Isaac
Keyword(s):  
Fragment Length Polymorphism ◽  
Pcr Amplification ◽  
Direct Pcr ◽  
Specific Primers ◽  
Kuwait Bay ◽  
Future Studies ◽  
Larval Stages ◽  
Marine Snails ◽  
Pcr Rflp ◽  
Species Specific

AbstractMicrophallid trematodes are common parasites in marine snails and crustacean hosts at Kuwait Bay. The larval stages of two microphallids,Maritrema eroliaeandProbolocoryphe uca, are difficult to differentiate morphologically. In this study, two PCR-based techniques were established for quick and accurate discrimination between the larval stages of the two microphallid species, employing restriction fragment length polymorphism (PCR-RFLP) and species-specific primers. Both techniques utilized nucleotide differences in the second internal transcribed region (ITS2) of the ribosomal DNA (rDNA) in the two species. For the PCR-RFLP technique, restriction enzymeAvaII was selected and it generated different restriction profiles among the two microphallids. In addition, species-specific primers were prepared for each microphallid species that amplified distinctive fragments. Both techniques showed that the larval stages of the two microphallid species can be identified accurately. However, direct PCR amplification using species-specific primers was more advantageous than the PCR-RFLP technique since it allowed rapid and specific discrimination between the two species. This technique provides a useful tool that can be used in future studies for the study of the distribution of microphallid species and their definitive hosts at different localities of Kuwait Bay.

scholarly journals Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Analysis of Mitochondrial cytb Gene from Species of Dairy Interest

2005 ◽  
Vol 88 (1) ◽  
pp. 128-135 ◽  
Author(s):  
Irene Lanzilao ◽  
Francesca Burgalassi ◽  
Silvia Fancelli ◽  
Mario Settimelli ◽  
Renato Fani
Keyword(s):  
Polymerase Chain Reaction ◽  
Restriction Fragment Length Polymorphism ◽  
Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Cytb Gene ◽  
Chain Reaction ◽  
Specific Restriction ◽  
Polymerase Chain ◽  
Species Specific ◽  
Restriction Fragment Length

Abstract Species identification plays an important role in food allergy prevention and food substitution detection that can reduce the commercial value of a product. For these reasons, many molecular methods have been developed to determine species origin; among them, polymerase chain reaction (PCR)-based methods were successfully applied to processed or unprocessed foodstuffs. An updated PCR-RFLP (restriction fragment length polymorphism) method of the cytb gene was developed for the identification of the 4 species of main interest in the dairy industry (Bos, Ovis, Capra, Bubalus). The comparative analysis of the 92 cytb sequences available in the database belonging to the 4 species allowed identification of 2 highly conserved regions, which were used to design 2 oligonucleotides for the PCR amplification of a 275 base-pair (bp) cytb fragment. The in silico analysis allowed identification of a set of species-specific restriction endonucleases (HaeIII, TaqI, and MwoI), which generated easily analyzable species-specific restriction profiles of the 275 bp cytb DNA fragment. The system was developed for both purified DNA and DNA extracted from meat or dairy products and finally tested on mixed samples, indicating its applicability to foodstuffs.

scholarly journals Survey of mutations in prolificacy genes in Santa Ines and Morada Nova sheep

2017 ◽  
Vol 69 (4) ◽  
pp. 1047-1053
Author(s):  
G.M.L. Holanda ◽  
J.C. Oliveira ◽  
D.M.F. Silva ◽  
S.S.N. Rocha ◽  
V. Pandolfi ◽  
...  
Keyword(s):  
Restriction Site ◽  
Fragment Length Polymorphism ◽  
Nucleotide Sequencing ◽  
Chain Reaction ◽  
Specific Primers ◽  
Pcr Rflp ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Santa Inês ◽  
Restriction Fragment Length

ABSTRACT Polymorphisms in the BMP-15 gene related to Galway (FecXG) and Inverdale (FecXI) and in the BMPR-1B gene known as Booroola (FecB) mutations were investigated using the Polymerase Chain Reaction - Restriction Fragment Length Polymorphism (PCR-RFLP) method, on sheep from the breeds Santa Inês (n= 574) and Morada Nova (n=282). DNA was extracted and amplified through PCR with specific primers that introduced a restriction site in association with the mutation. The PCR products were submitted to endonucleases. The experiment found no FecXG and FecXI mutations. Six samples of animals with multiple offspring/birth history presented polymorphism for FecB similar to control samples, but this pattern was not confirmed by nucleotide sequencing. Although the absence of these mutations in the studied breeds, other factors related to prolificacy should be investigated to explain the inherent prolificity mechanisms.

scholarly journals Identification of Carnobacterium Species by Restriction Fragment Length Polymorphism of the 16S-23S rRNA Gene Intergenic Spacer Region and Species-Specific PCR

2004 ◽  
Vol 70 (8) ◽  
pp. 4468-4477 ◽  
Author(s):  
Cinta Rachman ◽  
Petia Kabadjova ◽  
Rosica Valcheva ◽  
Hervé Prévost ◽  
Xavier Dousset
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Intergenic Spacer ◽  
Specific Primers ◽  
Intergenic Spacer Region ◽  
Pcr Rflp ◽  
Species Specific ◽  
Restriction Fragment Length

ABSTRACT The genus Carnobacterium is currently divided into the following eight species: Carnobacterium piscicola, C. divergens, C. gallinarum, C. mobile, C. funditum, C. alterfunditum, C. inhibens, and C. viridans. An identification tool for the rapid differentiation of these eight Carnobacterium species was developed, based on the 16S-23S ribosomal DNA (rDNA) intergenic spacer region (ISR). PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of this 16S-23S rDNA ISR was performed in order to obtain restriction profiles for all of the species. Three PCR amplicons, which were designated small ISR (S-ISR), medium ISR (M-ISR), and large ISR (L-ISR), were obtained for all Carnobacterium species. The L-ISR sequence revealed the presence of two tRNA genes, tRNAAla and tRNAIle, which were separated by a spacer region that varied from 24 to 38 bp long. This region was variable among the species, allowing the design of species-specific primers. These primers were tested and proved to be species specific. The identification method based on the 16S-23S rDNA ISR, using PCR-RFLP and specific primers, is very suitable for the rapid low-cost identification and discrimination of all of the Carnobacterium species from other phylogenetically related lactic acid bacteria.

scholarly journals CYP27B1 Gene Polymorphism rs10877012 in Patients Diagnosed with Colorectal Cancer

Nutrients ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 998
Author(s):  
Maria Latacz ◽  
Jadwiga Snarska ◽  
Elżbieta Kostyra ◽  
Konrad Wroński ◽  
Ewa Fiedorowicz ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Vitamin D ◽  
Fragment Length Polymorphism ◽  
Intestinal Cells ◽  
Chain Reaction ◽  
The Third ◽  
Pcr Rflp ◽  
Study Population ◽  
Polymerase Chain ◽  
Peripheral Leukocytes

Colorectal cancer (CRC) is the third most commonly occurring cancer worldwide. Intestinal cells are CYP27B1 gene expression sites and, as a consequence, they are capable of converting pro-vitamin D into the active paracrine and autocrine forms. It was demonstrated that rs10877012 polymorphism in the CYP27B1 gene influenced the circulating vitamin D level. This provided a rationale for determining the role that this polymorphism plays in the risk of developing colon cancer. In this study, we investigated the association of rs10877012 (T/G) polymorphism in the CYP27B1 gene with CRC susceptibility. The study population (n = 325) included CRC patients (n = 106) and healthy controls (n = 219). DNA was extracted from peripheral leukocytes and analyzed for the CYP27B1 polymorphism using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. We found an association between the presence of the T allele at the polymorphic site (odds ratio (OR) = 2.94; 95% CI 1.77–4.86; p < 0.0001) and a decreased CRC incidence.

scholarly journals Associations of biochemical changes and maternal traits with mutation 1843 (C>T) in the RYR1 gene as a common cause for porcine stress syndrome

2016 ◽  
Vol 19 (2) ◽  
pp. 75-80 ◽  
Author(s):  
ZT Popovski ◽  
B Tanaskovska ◽  
E Miskoska-Milevska ◽  
S Andonov ◽  
S Domazetovska
Keyword(s):  
Fragment Length Polymorphism ◽  
Protein Product ◽  
Biochemical Changes ◽  
Chain Reaction ◽  
Maternal Characteristics ◽  
Stress Syndrome ◽  
Pcr Rflp ◽  
Porcine Stress Syndrome ◽  
Heterozygous Carriers ◽  
Polymerase Chain

AbstractStress syndrome is usually caused by a mutation in theryanodine receptorgene(ryr1) and it is widely studied in humans and swine populations. The protein product of this gene plays a crucial role in the regulation of calcium transport in muscle cells. A G>T mutation in the humanryr1gene, which results in the replacement of a conserved arginine at position 614 where a leucine occurs at the same position as the previously identified Arg→Cys mutation reported in all cases of porcine stress syndrome (PSS). Porcine stress syndrome affects biochemical pathways in stress-susceptible individuals during a stress episode and some biochemical parameters that were used as markers for diagnostic purposes. Also, PSS has remarkable influence on the maternal characteristics of sows. This study dealt with different genotypes for PSS and its association with possible biochemical changes and maternal traits of sows. Seventy-three reproductive sows genotyped for PSS by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) were included in this survey. Sixty of them were stress-free (NN), 11 were heterozygous carriers (Nn) and two animals were homozygous (nn) for the 1843 (C>T) mutation. Significant differences in non stress induced animals with different PSS genotypes were found in the values of creatine phoshokinase (CPK), lactate dehydrogenase (LDH), alkaline phosphatase (AP) and aspartate aminotransferase (AST). Regarding the maternal traits, our study showed that stress susceptible animals (nn) have an increased number of stillborn piglets and a reduced number of newborn piglets compared with heterozygous and normal animals.

scholarly journals Identifikasi Keragaman Gen DGAT1 serta Asosiasinya terhadap Karakteristik Karkas dan Sifat Perlemakan Domba

2019 ◽  
Vol 6 (2) ◽  
pp. 259
Author(s):  
Asep Gunawan ◽  
Ratna Sholatia Harahap ◽  
Kasita Listyarini ◽  
Cece Sumantri
Keyword(s):  
Polymerase Chain Reaction ◽  
Single Nucleotide Polymorphism ◽  
Fragment Length Polymorphism ◽  
Nucleotide Polymorphism ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
Dgat1 Gene ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Restriction Fragment Length

ABSTRAK Karakteristik karkas dan sifat perlemakan pada daging domba dikontrol oleh banyak gen salah satunya gen DGAT1 (Diacylglycerol Acyltransferasel 1). Penelitian ini bertujuan mengidentifikasi SNP (Single Nucleotide Polymorphism) gen DGAT1 pada titik mutasi g.8539 C>T dan asosiasinya terhadap karakteristik karkas dan sifat perlemakan pada domba Indonesia. Total sampel domba yang digunakan sebanyak 150 buah terdiri dari 35 sampel domba compass agrinak (DCA), 36 sampel domba barbados cross (DBC), 41 sampel domba komposit garut (DKG), 20 sampel domba ekor gemuk (DEG), dan 18 sampel domba ekor tipis (DET). Karakteristik karkas dan sifat perlemakan diukur dari domba jantan berumur 10-12 bulan. Identifikasi keragaman DGAT1|ALuI dianalisis dengan metode PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism). Hasil keragaman gen DGAT1 bersifat polimorfik dalam DET dan DEG, sedangkan DCA, DBC, dan DKG bersifat monomorfik. Dua genotipe disebut CC dan  CT ditemukan dalam DET dan DEG. Titik mutasi gen DGAT1 berasosiasi (P<0.05) dengan karakteristik karkas, yaitu bobot dan panjang karkas. Selain itu, keragaman gen DGAT1 juga berasosiasi signifikan (P<0.05) dengan asam lemak jenuh, yaitu asam stearat (C18:0) dan asam arakidat (C20:0) dan asam lemak tak jenuh tunggal, yaitu asam oleat (C18:1n9c). Gen DGAT1 memiliki kontribusi dalam karakteristik karkas dan komposisi asam lemak pada domba.Kata Kunci: domba, gen DGAT1, karakteristik karkas, PCR-RFLP, sifat perlemakan                                                              ABSTRACT            Characteristic of carcass and fatness traits of sheep is regulated by many genes such as DGAT1 (Diacylglycerol Acyltransferasel 1) gene. The research was aimed to investigate SNP (Single Nucleotide Polymorphism) of DGAT1 and its association with characteristic of carcass and fatness traits in Indonesian sheep. A total sample of sheeps used 150 rams of 10–12 months consisted 35 samples of compas agrinak sheep (CAS), 36 of barbados cross (BCS), 41 of garut composite (GCS), 20  of javanese fat tailed (JFT), and 18 of javanese thin tailed (JTT). Identification variant of DGAT1|ALuI were performed by PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism). The results of polymorphism of DGAT1 were found in JTT and JFT. However, SNP of DGAT1 in CAS, BCS and GCS were monomorfic. Two genotype namely CC and CT were found in JTT and JFT populations. A SNP of the DGAT1 was associated (P<0.05) with characteristic of carcass, including weight and length of carcass. The variant of DGAT1 was associated too with saturated fatty acids (SFA) including stearic acid (C18:0) and arachidic acid (C20:0), and mono unsaturated fatty acid (MUFA) including oleic acid (C18:1n9c). The DGAT1 gene was contribute to characteristic carcass and fatty acid composition in sheep.Keywords: DGAT1 gene, characteristic carcass, fatness traits, PCR-RFLP, sheep

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