scholarly journals Advancing traceability using DNA sequence on seafood product: fraudulence in shrimp crackers

2020 ◽  
Vol 21 (12) ◽  
Author(s):  
Mala Nurilmala ◽  
YOGHI AJITAMA ◽  
AGOES M. JACOEB ◽  
AFKAR RONA INDARWATI ◽  
RONI NUGRAHA
Keyword(s):  
Dna Sequence ◽  
Control Method ◽  
Gc Content ◽  
Pcr Primers ◽  
Morphological Characters ◽  
Coi Gene ◽  
Universal Primers ◽  
Unidentified Species ◽  
Polymerase Chain ◽  
Seafood Product

Abstract. Nurilmala M, Atjitama Y, Jacob AM, Indarwati AR, Nugraha R. 2020. Advancing traceability using DNA sequence on seafood product: fraudulence in shrimp crackers. Biodiversitas 21: 5650-5656. Shrimp crackers are snacks made from starch with the addition of shrimp and other ingredients. Authentication of shrimp crackers becomes a quality control method in line with its traceability since the morphological characters are not recognized in those products. The failure of the authentication will lead to adulteration of shrimp products. The study aimed to design shrimp-specific polymerase chain reaction (PCR) primers by and used them to authenticate shrimp cracker products to assure their traceability. The primers were designed from cytochrome oxidase subunit I (COI) gene with a GC content of 50% and a melting temperature of 57 °C. The amplicon had a length of 613 bp. Fourteen shrimp crackers having DNA concentrations 0.3 to 8.1 ng/µL were evaluated. Eight out of fourteen DNA samples were successfully amplified using the specific primer and could be visualized on the agarose gel at 500-750 bp. Those DNA samples were identified belonging to shrimp species, namely Litopenaeus vannamei, Metapenaeus ensis, and Fenneropenaeus merguiensis with 95% to 100% identity. Meanwhile, the other six DNA samples underwent PCR using universal primers. One sample was amplified and identified as fish (Sphyraena flavicauda). These results indicate illegal substitution of shrimp using unidentified species occurred in shrimp crackers.

scholarly journals Molecular enrichment for detection of S. aureus in recreational waters

2012 ◽  
Vol 66 (11) ◽  
pp. 2305-2310 ◽  
Author(s):  
F. Valeriani ◽  
S. Giampaoli ◽  
L. Buggiotti ◽  
G. Gianfranceschi ◽  
V. Romano Spica
Keyword(s):  
Pcr Primers ◽  
Molecular Techniques ◽  
Universal Primers ◽  
Recreational Water ◽  
Recreational Waters ◽  
Low Concentrations ◽  
Microbiological Methods ◽  
Microbiological Parameters ◽  
Specific Amplification ◽  
Polymerase Chain

The identification of rapid methods for the control of recreational water and of aquatic environments with similar characteristics is necessary to provide adequate levels of health safety for users. Molecular techniques have been proposed in recent years as a viable alternative to traditional microbiological methods, as they offer various advantages and are less time consuming than traditional tests. An innovative protocol based on molecular enrichment that allows the identification of low concentrations of Staphylococcus aureus in recreational water has been developed. The method is based on the specific amplification of prokaryotic genomic DNA by the usage of universal primers for 23S rDNA; subsequently, a second amplification step is performed with specific real-time polymerase chain reaction (PCR) primers and probe. This approach shows sensitivity levels similar to those observed with microbiological tests, with the additional benefits of the specificity typical of nucleic acids techniques. This methodology is easily applicable also to other microbiological parameters, representing an important milestone in hygiene monitoring by the detection of specific pollution indicators.

Automated DNA sequencing methods involving polymerase chain reaction.

1989 ◽  
Vol 35 (11) ◽  
pp. 2196-2201 ◽  
Author(s):  
L J McBride ◽  
S M Koepf ◽  
R A Gibbs ◽  
W Salser ◽  
P E Mayrand ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequencing ◽  
Dna Sequence ◽  
Sequence Data ◽  
Identification Accuracy ◽  
Universal Primers ◽  
Chain Reaction ◽  
Universal Primer ◽  
Polymerase Chain ◽  
Primer Sequence

Abstract Polymerase chain reaction (PCR) as a method for preparing DNA templates has been used for several DNA sequencing applications. An in situ procedure for directly sequencing PCR products by the dideoxy-termination method has been developed by using fluorophore-labeled sequencing primers. Completed sequence reactions were combined and loaded into a single electrophoretic lane of a fluorescence-based DNA sequence analyzer. DNA targets devoid of a universal primer sequence could be sequenced with labeled universal primers by incorporating a universal primer sequence into the PCR product. With this method, the sequence of a 351-bp region in the bacteriophage lambda genome was fully analyzed in a single lane with automatic base identification accuracy of greater than 99%. An unknown sequence, 1.7 kb long, also was sequenced by this procedure, in combination with a "PCR gene walking" strategy. Comparison of the 1110 bases in overlapping sequence data from both strands yielded only two single-base ambiguities. Automated DNA sequence analysis of the highly polymorphic HLA-DQA-1 (alpha) region in the human genome can be performed with this simple methodology. Use of this PCR-sequencing method to analyze DNA extracted from a one-month-old blood sample from an individual who is heterozygous at this locus allowed unambiguous assignment of genotype.

Properties of sequence-tagged-site primer sets influencing repeatability

Genome ◽  
2000 ◽  
Vol 43 (1) ◽  
pp. 47-52 ◽  
Author(s):  
A Vanichanon ◽  
N K Blake ◽  
J M Martin ◽  
L E Talbert
Keyword(s):  
Genomic Dna ◽  
Standard Procedure ◽  
Gc Content ◽  
Pcr Primers ◽  
Gene Identification ◽  
Sequence Information ◽  
Chain Reaction ◽  
Sequence Tagged Site ◽  
Polymerase Chain ◽  
Primer Sets

The polymerase chain reaction (PCR) has become a standard procedure in plant genetics, and is the basis for many emerging genomics approaches to mapping and gene identification. One advantage of PCR is that sequence information for primer sets can be exchanged between laboratories, obviating the need for exchange and maintenance of biological materials. Repeatability of primer sets, whereby the same products are amplified in different laboratories using the same primer set, is important to successful exchange and utilization. We have developed several hundred sequence-tagged site (STS) primer sets for wheat and barley. The ability of the primer sets to generate reproducible amplifications in other laboratories has been variable. We wished to empirically determine the properties of the primer sets that most influenced repeatability. A total of 96 primer sets were tested with four genomic DNA samples on each of four thermocyclers. All major bands were repeatable across all four thermocyclers for approximately 50% of the primer sets. Characteristics most often associated with differences in repeatability included primer GC content and 3'-end stability of the primers. The propensity for primer-dimer formation was not a factor in repeatability. Our results provide empirical direction for the development of repeatable primer sets. Key words: STS-PCR primers, wheat, barley.

A Multiplex PCR Assay Mediated by Universal Primers for the Detection of Adulterated Meat in Mutton

2019 ◽  
Vol 82 (2) ◽  
pp. 325-330 ◽  
Author(s):  
WANWAN LIU ◽  
XIAONAN WANG ◽  
JING TAO ◽  
BANGSHENG XI ◽  
MAN XUE ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Detection System ◽  
Meat Products ◽  
Pcr Primers ◽  
Rapid Identification ◽  
Food Samples ◽  
Detection Sensitivity ◽  
Universal Primers ◽  
Multiplex Pcr Assay ◽  
Multiple Pcr

ABSTRACT This study aimed to establish a multiplex PCR detection system mediated by “universal primers,” which would be able to determine whether mutton meat contained nonmutton ingredients from rats, foxes, and ducks. Based on the sequence variation of specific mitochondrial genes, nine different multiplex PCR primers were designed, and four kinds of meat products were rapidly identified by electrophoresis using an optimized multiplex PCR system based on the molecular weight differences of the amplified products. Multiplex PCR applications optimized for meat food source from food samples for testing was used to verify the accuracy of the identification method. The results showed that the primers in multiple PCR system mediated by universal primers could be used for the rapid identification of rat, fox, duck, and sheep meat in mutton products, and the detection sensitivity could reach 0.05 ng/μL. The identification of food samples validated the practical value of this method. Therefore, a multiplex PCR system mediated by universal primers was established, which can be used to quickly identify the origin of animal ingredients from rats, foxes, and ducks in mutton products.

Are Tetranychus macfarlanei Baker & Pritchard and Tetranychus malaysiensis Ehara (Acari: Tetranychidae) one species? Morphological and molecular evidences for synonymy between these two spider mite species and a note on invasiveness of T. macfarlanei on okra and eggplant in India

2017 ◽  
Vol 22 (4) ◽  
pp. 467
Author(s):  
Mahran Zeity ◽  
Nagappa Srinivas ◽  
Chinnamade Channegowde Gowda
Keyword(s):  
Spider Mite ◽  
Morphological Characters ◽  
Molecular Data ◽  
Mite Species ◽  
Coi Gene ◽  
High Similarity ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
High Degree ◽  
Degree Of Similarity

Study of morphological characters of Tetranychus macfarlanei Baker & Pritchard and Tetranychus malaysiensis Ehara revealed high similarity by comparing all the important characters in addition to the characters pointed out by Ehara to separate those two species. Molecular phylogeny of seven Indian populations of T. macfarlanei and one population of T. malaysiensis from Philippines along with few distantly related species of Tetranychus was attempted. High degree of similarity between these two species at mitochondrial COI gene (96%) as well as ITS2 (rDNA) (96–99%) region was evident. Based on both morphological features and molecular data, T. malaysiensis is proposed as a junior synonym of T. macfarlanei based on ICZN’s law of priority. Also more female characters are prompted in this study to distinctly discriminate T. macfarlanei from its most resembling species, Tetranychus ludeni Zacher. Tetranychus macfarlanei has emerged as a pest of several cultivated crop plants in India. 

scholarly journals A strategy to detect and isolate an intron-containing gene in the presence of multiple processed pseudogenes

1989 ◽  
Vol 86 (17) ◽  
pp. 6691-6695 ◽  
Author(s):  
B Davies ◽  
S Feo ◽  
E Heard ◽  
M Fried
Keyword(s):  
Ribosomal Protein ◽  
Recombinant Dna ◽  
Single Gene ◽  
Ribosomal Protein Gene ◽  
Pcr Primers ◽  
Pcr Product ◽  
Dna Libraries ◽  
Processed Pseudogenes ◽  
Polymerase Chain ◽  
Genomic Dna Sequence

We have devised a strategy that utilizes the polymerase chain reaction (PCR) for the detection and isolation of intron-containing genes in the presence of an abundance of processed pseudogenes. The method depends on the genomic DNA sequence between the PCR primers spanning at least one intron in the gene of interest, resulting in the generation of a larger intron-containing PCR product in addition to the smaller PCR product amplified from the intronless pseudogenes. A unique intron probe isolated from the larger PCR product is used for the detection of intron-containing clones from recombinant DNA libraries that also contain pseudogene clones. This method has been used successfully for the selective isolation of an intron-containing rat L19 ribosomal protein gene in the presence of multiple pseudogenes. Analysis of a number of mammalian ribosomal protein multigene families by PCR indicates that they all contain only a single gene with introns.

Detection ofErwinia amylovorain plant material using novel polymerase chain reaction (PCR) primers

2001 ◽  
Vol 29 (1) ◽  
pp. 35-43 ◽  
Author(s):  
R. K. Taylor ◽  
P. J. Guilford ◽  
R. G. Clark ◽  
C. N. Hale ◽  
R. L. S. Forster
Keyword(s):  
Polymerase Chain Reaction ◽  
Plant Material ◽  
Pcr Primers ◽  
Chain Reaction ◽  
Polymerase Chain

DNA sequence of the androgen receptor in prostatic tumor cell lines and tissue specimens assessed by means of the polymerase chain reaction

The Prostate ◽  
1993 ◽  
Vol 22 (1) ◽  
pp. 11-22 ◽  
Author(s):  
Zoran Culig ◽  
Helmut Klocker ◽  
Johannes Eberle ◽  
Felizia Kaspar ◽  
Alfred Hobisch ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Androgen Receptor ◽  
Tumor Cell ◽  
Dna Sequence ◽  
Cell Lines ◽  
Tumor Cell Lines ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Prostatic Tumor ◽  
Tissue Specimens

Two new species of the genus Flavoperla (Plecoptera: Perlidae) from Guangxi, China

Zootaxa ◽  
2021 ◽  
Vol 5032 (2) ◽  
pp. 247-261
Author(s):  
RAORAO MO ◽  
JINJUN CAO ◽  
GUOQUAN WANG ◽  
WEIHAI LI ◽  
DÁVID MURÁNYI
Keyword(s):  
New Species ◽  
Dna Sequence ◽  
Southern China ◽  
Morphological Characters ◽  
Sequence Comparisons ◽  
Autonomous Region ◽  
Guangxi Zhuang Autonomous Region ◽  
Taxonomic Relationships ◽  
Two New Species

Two new species, Flavoperla retusata Mo, Li & Wang, sp. nov. and F. yangi Mo, Li & Murányi, sp. nov. are proposed from the Guangxi Zhuang Autonomous Region of southern China. Distinctness of the new species is based on morphological characters and DNA sequence comparisons with their closest known relative, F. galerispina Mo, Wang & Li, 2020. The taxonomic relationships of the two new species and related congeners are discussed.  

MSX1, PAX9, and TGFA Contribute to Tooth Agenesis in Humans

2004 ◽  
Vol 83 (9) ◽  
pp. 723-727 ◽  
Author(s):  
A.R. Vieira ◽  
R. Meira ◽  
A. Modesto ◽  
J.C. Murray
Keyword(s):  
Dna Sequence ◽  
Cleft Lip ◽  
Dna Analysis ◽  
Ethnically Diverse ◽  
Tooth Agenesis ◽  
Single Strand Conformational Polymorphism ◽  
Coding Regions ◽  
Cleft Lip Palate ◽  
Transmission Distortion ◽  
Polymerase Chain

In this study, we sought to determine the association between tooth agenesis and DNA sequence variation in the genes MSX1 and PAX9 in an ethnically diverse human population. Since cleft lip/palate is also associated with both tooth agenesis and the gene TGFA, we included TGFA in the analysis as well. Cheek swab samples were obtained for DNA analysis from 116 case/parent trios. Probands had at least one developmentally missing tooth, excluding third molars. Genotyping was performed by single-strand conformational polymorphism or kinetic polymerase chain-reaction assays. Transmission distortion of the marker alleles and DNA sequence analysis was performed. Results showed that tooth agenesis is associated with markers of the genes MSX1 and TGFA. No mutations were found in MSX1 or PAX9 coding regions. There were statistically significant data suggesting that MSX1 interacts with PAX9. These findings suggest that MSX1, PAX9, and TGFA play a role in isolated dental agenesis.

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