Ultra-fast PCR method for the distinguishing between Miichthys miiuy and Sciaenops ocellatus

2021 ◽  
Author(s):  
Yewon Hong ◽  
Jung Ju Kim ◽  
Yeon-Cheol Yu ◽  
Hyung Soo Kim ◽  
Guiim Moon ◽  
...  
Keyword(s):  
Sciaenops Ocellatus ◽  
Pcr Method ◽  
Miichthys Miiuy

scholarly journals Identification and determination of toxin genes of Vibrio strains causing hemorrhagic disease on red drum (Sciaenops ocellatus) using PCR method

2020 ◽  
Author(s):  
Nguyen Quang Linh ◽  
Yen Thi Hai Pham ◽  
Tram Duy Quynh Nguyen
Keyword(s):  
16S Rrna ◽  
Digestive Tract ◽  
Dna Sequences ◽  
Haplotype Diversity ◽  
Red Drum ◽  
Nucleotide Sequences ◽  
Sciaenops Ocellatus ◽  
Hemorrhagic Disease ◽  
Toxin Genes ◽  
Pcr Method

Abstract Data were collected from 30 strains of Vibrio and sampled on different organs (brain, hemorrhagic site and digestive tract) of Sciaenops ocellatus infection. The results showed that the nucleotide sequences 16S rRNA region are highly similar to those of V. alginolyticus, V. azureus, V. fluvialis and V. orientalis which is published on Genebank, ranging from 98.05 to 100 %. The digestive tract has the most common Vibrio strains (V. alginolyticus, V. azureus and V. fluvialis). Thereout, 25 of 30 strains of Vibrio contained 1 to 3 toxin genes, except V. parahaemolyticus. Six parameters were used to measure the DNA polymorphism of 33 homologous DNA sequences in this Vibrio bacteria population. The results indicated that number of separate polymorphic sites (S), total number of mutant sites (Eta), number of haplotype (h), haplotype diversity (Hd), average number of nucleotide differences (k), nucleotide diversity (Pi) were 98 (S), 103 (Eta), 9 (h), 0.887 ± 0.032 (Hd), 25.789 (k) and 17.980x10-3 ± 0.003 (Pi), respectively (P < 0,05). The G+C content above 1434 sites positions of nucleotide sequences accounted for 0.542. The phylogenetic tree showed that these strains are divided into six groups. As observed, the appearance of isolated Vibrio on 3 organs of fish (S. ocellatus) hemorrhagic are V. azureus (27,67 %), V. alginolyticus (50 %), V. orientalis (6,67 %) and V. fluvialis (16,67 %). Through this result, we found that the diversity of Vibrio species that appeared on the red drum was used in the 16S rRNA region and the presence of toxin genes in these Vibrio species.

Identification and authentication of commercial mi-iuy croaker (Miichthys miiuy) products by two PCR-based methods

2020 ◽  
Author(s):  
tae sun kang
Keyword(s):  
Economic Value ◽  
Cost Effective ◽  
Cross Reactivity ◽  
Duplex Pcr ◽  
Consensus Sequences ◽  
Pcr Product ◽  
Otolithes Ruber ◽  
Pcr Method ◽  
First Time ◽  
Miichthys Miiuy

Mi-iuy croaker (Miichthys miiuy) is one of the most important ingredients of Korean cuisine and thus has the highest economic value. However, the similar morphological traits among croaker fish belonging to family Sciaenidae are often exploited for seafood fraud. In this study, M. miiuy-specific primer set was designed and further improved by the development of a rapid and cost-effective duplex PCR method. The specificity of M. miiuy-specific duplex PCR was tested using 22 seafood species, and no cross-reactivity was observed. The sensitivity of the PCR assay was found to be 0.1 ng/µL. For the first time, labeling compliance of 43 commercial m-iuy croaker products was verified using both full DNA barcoding and M. miiuy-specific duplex PCR methods. For species identification, BOLDSYSTEMS and GenBank database were screened with the consensus sequences of each PCR product as a query. This identification result was further confirmed using the M. miiuy-specific duplex PCR method. The findings of this study revealed that principal species substituted were law croaker (Pseudotolithus senegallus, n=4), bigeye croaker (Micropogonias megalops, n=3), whitemouth croaker (Micropogonias furnieri, n=1), and tigertoothed croaker (Otolithes ruber, n=1). A significant percentage (21%) of mislabeling was present in commercial mi-iuy products sold on the South Korea market.

scholarly journals Identification and determination of toxin genes of Vibrio strains causing hemorrhagic disease on red drum (Sciaenops ocellatus) using PCR method

2020 ◽  
Author(s):  
Nguyen Quang Linh ◽  
Yen Thi Hai Pham ◽  
Tram Duy Quynh Nguyen
Keyword(s):  
16S Rrna ◽  
Digestive Tract ◽  
Dna Sequences ◽  
Haplotype Diversity ◽  
Red Drum ◽  
Nucleotide Sequences ◽  
Sciaenops Ocellatus ◽  
Hemorrhagic Disease ◽  
Toxin Genes ◽  
Pcr Method

Abstract Data were isolated from 30 strains of Vibrio and sampled on different organs (brain, hemorrhagic site and digestive tract) of Sciaenops ocellatus infection. The results showed that nucleotide sequences 16S rRNA region are highly, similar to those of V. alginolyticus, V. azureus, V. fluvialis and V. orientalis is published on Genebank, ranging from 98.05 to 100 %. The digestive tract has the most common Vibrio strains (V. alginolyticus, V. azureus and V. fluvialis). Thereout, 25 of 30 strains of Vibrio contained 1 to 3 toxin genes, excepted V. parahaemolyticus. Six parameters were used to measure the DNA polymorphism of 33 homologous DNA sequences in this Vibrio bacteria population. The results indicated number of separate polymorphic sites (S), total number of mutant sites (Eta), number of haplotype (h), haplotype diversity (Hd), average number of nucleotide differences (k), nucleotide diversity (Pi) were 98 (S) 103 (Eta), 9 (h), 0.887 ± 0.032 (Hd), 25.789 (k) and 17.980x10-3 ± 0.003 (Pi), respectively (P < 0,05). The G+C content above 1434 sites positions of nucleotide sequences accounts for 0.542. The phylogenetic tree showed that these strains are divided into six groups. As observed, the appearance of isolated Vibrio on 3 organs of fish (S. ocellatus) hemorrhagic are V. azureus (27,67 %), V. alginolyticus (50 %), V. orientalis (6,67 %) and V. fluvialis (16,67 %). Through this result, we found that the diversity of Vibrio species that appeared on the red drum was used in the 16S rRNA region and the presence of toxin genes in these Vibrio species.

scholarly journals The identification and determination of toxin genes of Vibrio strains causing hemorrhagic disease on red drum (Sciaenops ocellatus) using PCR method

2020 ◽  
Author(s):  
Nguyen Quang Linh ◽  
Yen Thi Hai Pham ◽  
Tram Duy Quynh Nguyen
Keyword(s):  
16S Rrna ◽  
Digestive Tract ◽  
Dna Sequences ◽  
Haplotype Diversity ◽  
Red Drum ◽  
Nucleotide Sequences ◽  
Sciaenops Ocellatus ◽  
Hemorrhagic Disease ◽  
Toxin Genes ◽  
Pcr Method

Abstract Data were collected from 30 strains of Vibrio and sampled on different organs (brain, hemorrhagic site and digestive tract) of Sciaenops ocellatus infection. The results showed that the nucleotide sequences 16S rRNA region are highly similar to those of V. alginolyticus, V. azureus, V. fluvialis, V. natriengens and V. orientalis, which were published on Genbank and other, ranging from 98.05 to 100 %. The digestive tract has the most common Vibrio strains (V. alginolyticus [16] V. azureus [7] and V. fluvialis). Thereout, 25 of 30 strains of Vibrio contained from 1 to 3 toxin genes, except for V. parahaemolyticus. Six parameters were used to measure the DNA polymorphism of 33 homologous DNA sequences in this Vibrio bacteria population. The results indicated that the number of separate polymorphic sites (S), the total number of mutant sites (Eta), the number of haplotype (h), the haplotype diversity (Hd), the average number of nucleotide differences (k), the nucleotide diversity (Pi) were 98 (S), 103 (Eta), 9 (h), 0.887 ± 0.032 (Hd), 25.789 (k) and 17.980x10-3 ± 0.003 (Pi), respectively (P < 0,05). The G+C contentover 1434 sites positions of nucleotide sequences accounted for 0.542. The phylogenetic tree showed that these strains are divided into six groups. As observed, the appearance of isolated Vibrio on 3 organs of fish (S. ocellatus) which are hemorrhagic include V. azureus (27,67 %), V. alginolyticus (50 %), V. orientalis (6,67 %) and V. fluvialis (16,67 %). Through this result, it is found that the diversity of Vibrio species that appeared on the red drum was used in the 16S rRNA region and the presence of toxin genes in these Vibrio species.

Investigation of duck plague virus in hoar areas of Bangladesh

2020 ◽  
Vol 26 (1-2) ◽  
pp. 73-78
Author(s):  
A Hossen ◽  
MH Rahman ◽  
MZ Ali ◽  
MA Yousuf ◽  
MZ Hassan ◽  
...  
Keyword(s):  
Cytopathic Effect ◽  
Clinical Sample ◽  
Chorioallantoic Membrane ◽  
Clinical Samples ◽  
Isolation And Identification ◽  
Duck Plague Virus ◽  
Pcr Method ◽  
Polymerase Chain ◽  
The Individual ◽  
Free Ranging

Duck plague (DP) is the most important infectious disease of geese, ducks and free-ranging water birds. The present study was conducted to determine the prevalence of duck plague virus followed by isolation and identification. For these purposes, a total of 155 cloacal swabs samples were collected randomly from duck of different haor areas of Bangladesh including 45 (41 surveillance and 4 clinical) samples from Netrokona; 42 (40 surveillance and 2 clinical) samples from Kishoregonj; 30 samples from Brahmanbaria and 38 samples from Sunamganj. The samples were processed and pooled (1:5 ratio) for initial screening of target polymerase gene of duck plague virus by polymerase chain reaction (PCR) method. All the samples of a positive pool were then tested individually for identifying the individual positive samples. The result showed that out of 155 samples, 41 (26.45%) were found positive in which 17 were from Netrokona, where 15 (36.58%) were from surveillance samples and 2 (50%) were from clinical sample; 16 were from Kishoregonj, where 14 (35%) were from surveillance samples and 2 (100%) were from clinical sample; 2 (6.6%) were from Brahmanbaria and 5 (13.15%) were from Sunamganj. These positive samples were inoculated into 9-10 days embryonated duck eggs (EDE) through chorioallantoic membrane (CAM) route for the isolation of virus. The EDE died earlier was also chilled, and in a similar way, the CAMs were collected and again performed PCR for id entification of virus. Out of 41 PCR positive samples, 26 samples were isolated and reconfirmed by PCR. Subsequently, DPV was isolated in primary duck embryo fibroblasts cell culture and confirmed by observing cytopathic effect (CPE). Bang. J. Livs. Res. Vol. 26 (1&2), 2019: P. 73-78

Diagnosis of helicobacter pylori infection: problems and prospects

2020 ◽  
pp. 54-59
Author(s):  
A. S. Molostova ◽  
N. S. Gladyshev ◽  
A. V. Svarval ◽  
R. S. Ferman ◽  
A. B. Karasyova ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Urease Activity ◽  
Diagnostic Methods ◽  
Study Group ◽  
Biochemical Method ◽  
Antimicrobial Drugs ◽  
Non Invasive ◽  
Number Of Patients ◽  
Pcr Method ◽  
Positive Results

(HP) infection was performed using invasive and non-invasive methods. The study group consisted of 95 patients with dyspepsia. HP infection was detected in 47 patients (49.4 %). The expediency of using a set of diagnostic methods for detecting HP (PCR, immunochromatographic, bacteriological and method for determining urease activity) is proved. Most often (100 %) in patients HP infection was detected in biopsies using the PCR method. Somewhat less frequently it was detected when examining biopsies with an invasive biochemical method (AMA RUT Reader) (82 %) and fecal immunochromatographic method (83 %). Despite the fact that helicobacteriosis was detected bacteriologically in a small number of patients (24 %), this method is of particular value, since it allows you to assess the sensitivity to antimicrobial drugs and probiotics, and does not give false positive results.

WEEDS IN POTATO CULTURE AND THEIR OUTCOME IN SPREADING OF Alternaria spp.

2018 ◽  
Vol 17 (6) ◽  
pp. 159-166
Author(s):  
Halina Kurzawińska ◽  
Stanisław Mazur ◽  
Małgorzata Nadziakiewicz ◽  
Jacek Nawrocki
Keyword(s):  
Chenopodium Album ◽  
Potato Cultivar ◽  
Cirsium Arvense ◽  
Potato Plants ◽  
Potato Culture ◽  
Rapd Pcr ◽  
Microscopic Features ◽  
Weed Infestation ◽  
Pcr Method ◽  
Potato Crops

The aim of this study was to determine whether the weeds accompanying potato crops can be a source of Alternaria spp. causing Alternaria leaf blight and to determine the genetic similarities of Alternaria alternata isolates infecting selected weeds: Chenopodium album, Cirsium arvense and tested potato cultivar. Three-year field experiment was conducted on the potato cultivar ‘Vineta N’. The isolates were classified into different species on the basis of macro- and microscopic features. In each year of the study, A. alternata dominated among the isolated fungi colonizing the leaves of potato plants and the selected weeds. The genetic similarities of A. alternata isolates was determined by the RAPD-PCR method. Tested genetic forms of A. alternata were closely related; only small differences in the pattern of the separated amplification products was evidenced. The dominance of A. alternata on the weeds accompanying potato crops suggests that if weed infestation is extensive, the pathogen is very likely to spread and its population to increase.

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