scholarly journals Molecular identification of Atlantic goliath grouper Epinephelus itajara (Lichtenstein, 1822) (Perciformes: Epinephelidae) and related commercial species applying multiplex PCR

2016 ◽  
Vol 14 (3) ◽  
Author(s):  
Júnio S. Damasceno ◽  
Raquel Siccha-Ramirez ◽  
Claudio Oliveira ◽  
Fernando F. Mendonça ◽  
Arthur C. Lima ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Cost Effective ◽  
Molecular Techniques ◽  
Forensic Identification ◽  
Correct Identification ◽  
Western Atlantic ◽  
Endangered Fish ◽  
Critically Endangered Species ◽  
Goliath Grouper ◽  
Species Specific

ABSTRACT The Atlantic goliath grouper, Epinephelus itajara , is a critically endangered species, threatened by illegal fishing and the destruction of its habitats. A number of other closely related grouper species found in the western Atlantic are also fished intensively. While some countries apply rigorous legislation, illegal harvesting followed by the falsification of fish products, which impedes the correct identification of the species, is a common practice, allowing the catch to be marketed as a different grouper species. In this case, molecular techniques represent an important tool for the monitoring and regulation of fishery practices, and are essential for the forensic identification of a number of different species. In the present study, species-specific primers were developed for the Cytochrome Oxidase subunit I gene, which were applied in a multiplex PCR for the simultaneous identification of nine different species of Epinephelidae: Epinephelus itajara , E. quinquefasciatus , E. morio , Hyporthodus flavolimbatus , H. niveatus , Mycteroperca acutirostris , M. bonaci , M. marginata , and M. microlepis . Multiplex PCR is a rapid, reliable and cost-effective procedure for the identification of commercially-valuable endangered fish species, and may represent a valuable tool for the regulation and sustainable management of fishery resources.

scholarly journals Species-Specific Identification of Human Adenoviruses by a Multiplex PCR Assay

2000 ◽  
Vol 38 (11) ◽  
pp. 4114-4120 ◽  
Author(s):  
WanHong Xu ◽  
Mike C. McDonough ◽  
Dean D. Erdman
Keyword(s):  
Multiplex Pcr ◽  
Human Adenovirus ◽  
Cost Effective ◽  
Pcr Assay ◽  
Multiplex Pcr Assay ◽  
Amplicon Size ◽  
Species Specific ◽  
Fiber Gene ◽  
Amplification Reaction

A multiplex PCR assay was developed by using primers to the fiber gene that could differentiate human adenovirus (Ad) species A through F in a single amplification reaction. The assay correctly identified the species of all 49 recognized Ad prototype strains as well as 180 geographically and temporally diverse Ad field isolates. Ad serotype 6 (Ad6) (species C), Ad16 (species B), Ad31 (species A), and Ad40 and Ad41 (species F) could also be distinguished by amplicon size within each respective species. In comparison, a previously described Ad species-specific multiplex PCR assay that used primers to the Ad hexon gene gave equivocal results with several serotypes of species B, whereas our multiplex assay amplified all species B serotypes equally well. Our multiplex PCR assay will permit rapid, accurate, and cost-effective classification of Ad isolates.

scholarly journals Biotyping and Antimicrobial Susceptibility of Enterococcus faecalis and E. faecium Isolated from Urine and Stool Samples

2021 ◽  
Vol 13 (10) ◽  
Author(s):  
Gülşah Tollu ◽  
Ismail Hakkı Ekin
Keyword(s):  
Multiplex Pcr ◽  
Antimicrobial Susceptibility ◽  
Animal Health ◽  
Molecular Techniques ◽  
Penicillin G ◽  
Clinical Approach ◽  
Biochemical Tests ◽  
Specific Primers ◽  
Stool Samples ◽  
Species Specific

Background: Enterococci are one of the opportunistic pathogenic microorganisms that can cause significant problems for human and animal health. Enterococcus faecium seems to be more resistant to antibiotics than E. faecalis. It is thought that pathogenic E. faecium can develop antibiotic resistance very quickly, and the ability to transfer this feature is considered to be an important health risk. Objectives: This study aimed to determine the prevalence, biotypes, and in vitro antimicrobial susceptibility of E. faecalis and E. faecium strains isolated from 267 routine urine and stool samples that were brought to the microbiology laboratory of Regional Training and Research Hospital of Van, with permission of the patients. Methods: In the present study, enterococci using species-specific primers to examine E. faecalis and E. faecium multiplex PCR technique was applied. Biotyping of the isolates was used to identify them as E. faecalis and E. faecium by molecular techniques, and antibiotic susceptibility of all samples was examined, as well. Results: The isolates were identified by multiplex PCR using species-specific primers for E. faecalis and E. faecium. Biotyping based on 13 biochemical tests showed that 72.5%, 12.5%, and 15% of E. faecalis strains were of biotypes I, II, and III, respectively, whereas E. faecium strains could be divided into biotype I (10%), biotype II (12.5%), biotype III (27.5%), and biotype IV (50%). Additionally, all E. faecalis strains were found to be susceptible to penicillin G and imipenem. On the other hand, 95% of the E. faecalis strains were found to be resistant to clindamycin, 77.5% to tetracycline and trimethoprim/sulfamethoxazole, 42.5% to erythromycin, 32.5% to gentamicin, and 17.5% to ciprofloxacin. Of E. faecium strains, 37.5% were found to be resistant to clindamycin, 32.5% to penicillin G, 27.5% to erythromycin and imipenem, 20% to ciprofloxacin, 17.5% to tetracycline and trimethoprim/sulfamethoxazole, 15% to gentamicin, and 5% to vancomycin. Conclusions: In conclusion, the identification of E. faecalis and E. faecium strains by PCR is reliable and faster than biochemical tests. Additionally, the results of antimicrobial susceptibility tests may provide important contributions to the clinical approach.

Molecular identification of some Hoplolaimus species from the USA based on duplex PCR, multiplex PCR and PCR-RFLP analysis

Nematology ◽  
2009 ◽  
Vol 11 (3) ◽  
pp. 471-480 ◽  
Author(s):  
Robert Robbins ◽  
Allen Szalanski ◽  
Chang-Hwan Bae
Keyword(s):  
Multiplex Pcr ◽  
Dna Sequences ◽  
Rflp Analysis ◽  
Pcr Primers ◽  
Interspecific Variation ◽  
Molecular Techniques ◽  
Specific Pcr ◽  
Pcr Multiplex ◽  
Pcr Rflp ◽  
Species Specific

AbstractTwo different molecular approaches, a multiplex PCR and PCR-RFLP of ITS-rDNA, were developed for the identification of Hoplolaimus species. DNA sequences of H. columbus, H. galeatus, H. concaudajuvencus, H. magnistylus, H. seinhorsti and three undescribed Hoplolaimus species were used to design species-specific primers. Three reverse species-specific PCR primers for H. columbus, H. galeatus and H. magnistylus were developed using the ITS1 region exhibiting interspecific variation. Three species-specific PCR primers in combination with the forward primer, Hoc-1f, produced distinct amplicons of 580 bp for H. columbus, 120 bp for H. galeatus and 340 bp for H. magnistylus. We successfully identified each of three species by multiplex PCR when all three were mixed in a single PCR reaction. Restriction enzyme digests of the PCR amplicon using HaeIII and RsaI permitted discrimination of H. columbus, H. galeatus, H. magnistylus, H. concaudajuvencus, H. sp. 1, H. sp. 2 and H. sp. 3 from each other. These results suggest that these molecular techniques allow for rapid, easy and reliable identification of Hoplolaimus species.

scholarly journals Conversion of sequence-characterized amplified region (SCAR) bands into high-throughput DNA markers based on RAPD technique for detection of the stem nematode Ditylenchus dipsaci in crucial plant hosts

2008 ◽  
Vol 53 (No. 3) ◽  
pp. 97-104 ◽  
Author(s):  
M. Zouhar ◽  
M. Marek ◽  
O. Douda ◽  
J. Mazáková ◽  
P. Ryšánek
Keyword(s):  
Cost Effective ◽  
Healthy Plant ◽  
Host Preferences ◽  
Sequence Characterized Amplified Region ◽  
Detection And Identification ◽  
Plant Hosts ◽  
Cost Effective Technique ◽  
Ditylenchus Dipsaci ◽  
Species Specific ◽  
Template Dna

<i>Ditylenchus dipsaci</i>, the stem nematode, is a migratory endoparasite of over 500 species of angiosperms. The main method of <i>D. dipsaci</i> control is crop rotation, but the presence of morphologically indistinguishable host races with different host preferences makes rotation generally ineffective. Therefore, a sensitive, rapid, reliable, as well as cost effective technique is needed for identification of <i>D. dipsaci</i> in biological samples. This study describes the development of species-specific pairs of PCR oligonucleotides for detection and identification of the <i>D. dipsaci</i> stem nematode in various plant hosts. Designed DIT-2 primer pair specifically amplified a fragment of 325 bp, while DIT-5 primer pair always produced a fragment of 245 bp in all <i>D. dipsaci</i> isolates. Two developed SCAR primer pairs were further tested using template DNA extracted from a collection of twelve healthy plant hosts; no amplification was however observed. The developed PCR protocol has proved to be quite sensitive and able to specifically detect <i>D. dipsaci</i> in artificially infested plant tissues.

scholarly journals Current and Future Pathotyping Platforms for Plasmodiophora brassicae in Canada

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1446
Author(s):  
Heather H. Tso ◽  
Leonardo Galindo-González ◽  
Stephen E. Strelkov
Keyword(s):  
Crop Production ◽  
Plasmodiophora Brassicae ◽  
Cost Effective ◽  
Turnaround Time ◽  
Molecular Techniques ◽  
Differential Set ◽  
Management Plans ◽  
Increased Sensitivity ◽  
Phenotypic Methods ◽  
Important Disease

Clubroot, caused by Plasmodiophora brassicae, is one of the most detrimental threats to crucifers worldwide and has emerged as an important disease of canola (Brassica napus) in Canada. At present, pathotypes are distinguished phenotypically by their virulence patterns on host differential sets, including the systems of Williams, Somé et al., the European Clubroot Differential set, and most recently the Canadian Clubroot Differential set and the Sinitic Clubroot Differential set. Although these are frequently used because of their simplicity of application, they are time-consuming, labor-intensive, and can lack sensitivity. Early, preventative pathotype detection is imperative to maximize productivity and promote sustainable crop production. The decreased turnaround time and increased sensitivity and specificity of genotypic pathotyping will be valuable for the development of integrated clubroot management plans, and interest in molecular techniques to complement phenotypic methods is increasing. This review provides a synopsis of current and future molecular pathotyping platforms for P. brassicae and aims to provide information on techniques that may be most suitable for the development of rapid, reliable, and cost-effective pathotyping assays.

Centroceras gasparrinii subsp. minor subsp. nov. (Ceramiaceae, Rhodophyta) in the North Adriatic Sea (Mediterranean): molecular and morphological characterization

Phytotaxa ◽  
2019 ◽  
Vol 415 (4) ◽  
pp. 233-239
Author(s):  
MARION A. WOLF ◽  
ALESSANDRO BUOSI ◽  
ABDUL-SALAM F. JUHMANI ◽  
ADRIANO SFRISO
Keyword(s):  
Morphological Characterization ◽  
Type Locality ◽  
Correct Identification ◽  
Cortical Cells ◽  
Western Atlantic ◽  
Gland Cells ◽  
The North ◽  
Red Algal ◽  
Long Time ◽  
The 19Th Century

Centroceras Kützing is a small red algal genus with 18 currently accepted species (Guiry & Guiry 2019), characterized by simple filamentous thalli with erect axes arising from a prostrate system and di-trichotomous branching (Hommersand 1963). The characters used to distinguish species are primarily cortical filament morphology: shape and number of the acropetal cortical cells, shape of gland cells, and shape of spines (Won et al. 2009). The generitype C. clavulatum (C. Agardh) Montagne has been viewed for a long time as a highly variable and cosmopolitan species (Hommersand 1963). Molecular and detailed morphological analyses brought Barros-Barreto et al. (2006) to report that C. clavulatum may consist of a species complex and Won et al. (2009) confirmed this hypothesis identifying eight taxonomic entities phylogenetically segregated from genuine C. clavulatum. Seven of these entities were assigned to the following species: C. gasparrinii (Meneghini) Kützing, C. hommersandii Won, T.O. Cho & Fredericq, C. hyalacanthum Kützing, C. micracanthum Kützing, C. natalensis Won, T.O. Cho & Fredericq, C. rodmanii Won, T.O. Cho & Fredericq, and C. tetrachotomum Won, T.O. Cho & Fredericq, (Won et al. 2009). Centroceras gasparrinii, C. hyalacanthum, and C. micracanthum are three western Atlantic species listed as synonyms of C. clavulatum since the middle of the 19th century and resurrected from the ‘C. clavulatum complex’ by Won et al. (2009). In particular, two of these taxa were described from specimens of the Mediterranean Sea: C. gasparrinii (as Ceramium gasparrinii Meneghini, type locality Palermo, Italy) and C. micracanthum (reported with the synonym Centroceras leptacanthum Kützing, type locality Genoa, Italy). Therefore, the numerous Mediterranean records of C. clavulatum (e.g., Gómez Garreta et al. 2001; Verlaque 2001; Sfriso & Curiel 2007; Taşkýn et al. 2013) most probably belong to one of these two species and have to be re-examined for a correct identification and to understand the spatial distribution of the different taxa (Tsiamis et al. 2010). For this reason, in the last years in Greece (Tsiamis et al. 2010), Spain (Gallardo et al. 2016) and Morocco (Hassoun et al. 2018) accurate sampling and morphological analyses of specimens previously identified as C. clavulatum were conducted to determine their correct taxonomic identities. In all cases the recognized species was C. gasparrinii, which can be distinguished morphologically from the other ones previously known as C. clavulatum by the presence of ovoid gland cells and ovoid terminal acropetal cortical cells (Won et al. 2009). As reported by Tsiamis et al. (2010), Greek samples differed from those described by Won et al. (2009), in the smaller number of periaxial cells (10–12 against 13–19).

Duplex DNA barcoding allows accurate species determination of morphologically similar limpets (Patella spp.) from non-destructive sampling

2016 ◽  
Vol 97 (7) ◽  
pp. 1479-1482 ◽  
Author(s):  
Thomas J. Ashton ◽  
Meriem Kayoueche-Reeve ◽  
Andrew J. Blight ◽  
Jon Moore ◽  
David M. Paterson
Keyword(s):  
Dna Barcoding ◽  
Species Abundance ◽  
Microscopic Analysis ◽  
Cost Effective ◽  
Field Studies ◽  
Similar Species ◽  
Species Determination ◽  
Destructive Sampling ◽  
Species Specific ◽  
Non Destructive

Accurate discrimination of two morphologically similar species of Patella limpets has been facilitated by using qPCR amplification of species-specific mitochondrial genomic regions. Cost-effective and non-destructive sampling is achieved using a mucus swab and simple sample lysis and dilution to create a PCR template. Results show 100% concurrence with dissection and microscopic analysis, and the technique has been employed successfully in field studies. The use of highly sensitive DNA barcoding techniques such as this hold great potential for improving previously challenging field assessments of species abundance.

Effects of Carrier Material and Design on Microalgae Attachment for Biofuel Manufacturing: A Literature Review

2010 ◽  
Author(s):  
Yan Cui ◽  
Wenqiao Wayne Yuan ◽  
Zhijian Pei
Keyword(s):  
Free Energy ◽  
Large Scale ◽  
Cell Attachment ◽  
Cost Effective ◽  
Surface Wettability ◽  
Biofuel Production ◽  
Algae Biofuels ◽  
Attachment Strength ◽  
Species Specific ◽  
Continuous Use

Continuous use of petroleum derived fuels is widely recognized as unsustainable due to depleting supplies and the accumulation of greenhouse gases in the environment. Renewable, carbon neutral transport fuels are needed for environmental and economic sustainabilities. Algae have been demonstrated to be one of the most promising sources for biofuel production. However, large-scale algae production and harvesting for energy manufacturing are too costly using existing methods. The approach of growing algae on solid carriers is innovative and can potentially lead to cost-effective manufacturing of algae biofuels. As cells approach to the solid surface, many factors come in to influence microbial attachment such as the surface wettability, free energy, polarity, roughness and topography. Surface wettability plays an important role in the initial cell attachment. For further contact, surface free energy and polarity are more directly related to cell-substratum attachment strength. Surface roughness and texture are species-specific parameters and have been applied widely in attachment studies.

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