scholarly journals Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

2015 ◽  
Vol 5 (11) ◽  
pp. 2252-2266 ◽  
Author(s):  
Jullien M. Flynn ◽  
Emily A. Brown ◽  
Frédéric J. J. Chain ◽  
Hugh J. MacIsaac ◽  
Melania E. Cristescu
Keyword(s):  
Molecular Identification ◽  
Environmental Samples ◽  
Clustering Methods ◽  
Identification Of Species

scholarly journals Molecular identification of species in Juglandaceae: A tiered method

2011 ◽  
Vol 49 (3) ◽  
pp. 252-260 ◽  
Author(s):  
Xiao-Guo XIANG ◽  
Jing-Bo ZHANG ◽  
An-Ming LU ◽  
Rui-Qi LI
Keyword(s):  
Molecular Identification ◽  
Identification Of Species

Molecular identification of species and ploidy of Carassius fishes in Lake Biwa, using mtDNA and microsatellite multiplex PCRs

2014 ◽  
Vol 61 (2) ◽  
pp. 169-175 ◽  
Author(s):  
Tappei Mishina ◽  
Mikumi Takada ◽  
Hirohiko Takeshima ◽  
Mitsunori Nakano ◽  
Ryoichi Tabata ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Lake Biwa ◽  
Multiplex Pcrs ◽  
Identification Of Species ◽  
Microsatellite Multiplex

Genisys and computer-assisted identification of nematodes

Nematology ◽  
2000 ◽  
Vol 2 (1) ◽  
pp. 17-30 ◽  
Author(s):  
Jack Milton ◽  
Renaud Fortuner ◽  
Jim Diederich
Keyword(s):  
Present Article ◽  
Molecular Identification ◽  
Large Scale ◽  
Computer Assisted ◽  
Identification System ◽  
Base De Données ◽  
Expert User ◽  
Identification Of Species ◽  
Computer Identification ◽  
Meloidogyne Species

AbstractIdentification of species for the study of biodiversity in the phylum Nemata is defined as being able to identify any of the 12 000 described species of nematodes, and being able to recognise when the specimen under study belongs to a species unknown to science. Moreover, this large-scale identification must be done by biologists who are not expert taxonomists. It is argued that printed identification aids are too rigid and unreliable, and molecular identification aid is too limited, to be used in this context. Only computer identification tools are flexible, reliable, and general enough to give a non-taxonomist the possibility to identify any species. However, a review of existing tools and approaches shows that they fall short of reaching this objective. The functionality of a general identification system that could overcome the problems and difficulties encountered in the use of computerised tools is then described. This system (which has been described by the authors in several articles under the name of Genisys) would include a general database with all the characters from all the published descriptions of nematodes species and a set of integrated identification tools. Some of these tools would export the data into formats usable by existing identification and systematics tools. Other tools would have to be developed to support new approaches. A guidance tool would help the non-expert user by suggesting the successive computerised tools to be used during an identification session or by directing the user to other approaches, such as molecular identification in the case of heteroderids or some Meloidogyne species. L’identification des espèces pour l’étude de la biodiversité dans le phylum Nemata est définie comme la possibilité d’identifier n’importe laquelle des 12 000 espèces décrites du groupe et d’être capable de reconnaître que le spécimen étudié appartient à une espèce non encore décrite. En outre, ce type d’identification à grande échelle doit pouvoir être pratiqué par des biologistes qui ne sont pas des taxinomistes. Il est montré que les aides imprimées à l’identification sont trop rigides et trop peu fiables et que l’identification moléculaire est encore de portée trop limitée pour être utilisables dans ce contexte. Seuls les outils d’identification assistée par ordinateur sont suffisamment flexibles, fiables et généraux pour permettre à un non taxinomiste d’accomplir les identifications définies plus haut. Pourtant, une revue des outils existants et des approches utilisées montre qu’ils sont incapables d’atteindre l’objectif fixé. La fonctionnalité d’un système d’identification général capable de résoudre les problèmes soulevés par l’utilisation d’outils informatisés est ensuite décrite. Ce système (décrit par les auteurs du présent article sous le nom de Genisys) doit comprendre une base de données avec tous les caractères inclus dans les descriptions publiées des espèces connues et un ensemble d’outils d’identification intégrés. L’un de ces outils devrait permettre d’exporter les données sous des formats utilisables par les outils existants d’identification et de systématique. D’autres outils devraient être développés pour mettre en œuvre de nouvelles approches. Un outil de guidage aiderait le non-spécialiste en lui suggérant les outils informatiques à utiliser successivement dans le cadre d’une session d’identification ou en le dirigeant vers d’autres approches telles que l’identification moléculaire dans le cas de certains Hétérodérides et d’espèces de Meloidogyne.

scholarly journals The molecular identification of Zanthoxylum armatum DC of Pakistan based on DNA barcoding

2020 ◽  
Vol 27 (2) ◽  
pp. 323-333
Author(s):  
Shakila Umer ◽  
Nayab Safdar ◽  
Khushi Muhammad
Keyword(s):  
Dna Barcoding ◽  
Molecular Identification ◽  
Sequence Similarity ◽  
Pcr Analysis ◽  
Dna Barcodes ◽  
Zanthoxylum Armatum ◽  
The Family ◽  
Plant Taxon ◽  
Identification Of Species ◽  
Zanthoxylum Bungeanum

Zanthoxylum armatum DC., belonged to the family Ruteacea, is a medicinal plant used to cure many diseases. DNA barcoding was used as a tool for molecular identification of Zanthoxylum armatum DC. species from Balakot Pakistan. In the present study four DNA barcodes including matk, rbcl, ITS and trnH-psbA were used. The sequenced data were analyzed by using BLASTn at NCBI, FASTA and Mega 7.0 software. During PCR analysis, 3 DNA barcodes ITS, rbcl and trnh-psbA were successfully amplified and showed the 100% sequencing success. Furthermore, these barcode markers showed 99-100% sequence similarity with the reference sequences at the BLASTn. The further analysis revealed the sequence similarity of investigating marker with Zanthoxylum armatum (MH016484.1), Zanthoxylum nitidum (FN599471.1) and Zanthoxylum bungeanum (MF097123.1) respectively. The current finding provides the basis for sequenced data of Z. armatum to be used in future for molecular discrimination among the plant species from Pakistan and it is concluded that combination of diverse kind of barcoding markers could be helpful in proper identification of species at lower taxonomic level. Bangladesh J. Plant Taxon. 27(2): 323-333, 2020 (December)

scholarly journals Identification of Species and Sources ofCryptosporidium Oocysts in Storm Waters with a Small-Subunit rRNA-Based Diagnostic and Genotyping Tool

2000 ◽  
Vol 66 (12) ◽  
pp. 5492-5498 ◽  
Author(s):  
Lihua Xiao ◽  
Kerri Alderisio ◽  
Josef Limor ◽  
Michael Royer ◽  
Altaf A. Lal
Keyword(s):  
New York ◽  
Sequence Analysis ◽  
Restriction Fragment Length Polymorphism ◽  
Environmental Samples ◽  
Fragment Length Polymorphism ◽  
Small Subunit ◽  
Storm Water ◽  
Small Subunit Rrna ◽  
Identification Of Species ◽  
Restriction Fragment Length

ABSTRACT The identification of Cryptosporidium oocysts in environmental samples is largely made by the use of an immunofluorescent assay. In this study, we have used a small-subunit rRNA-based PCR-restriction fragment length polymorphism technique to identify species and sources of Cryptosporidium oocysts present in 29 storm water samples collected from a stream in New York. A total of 12 genotypes were found in 27 positive samples; for 4 the species and probable origins were identified by sequence analysis, whereas the rest represent new genotypes from wildlife. Thus, this technique provides an alternative method for the detection and differentiation of Cryptosporidium parasites in environmental samples.

Molecular Identification of Species-Specific Adenovirus Causing Respiratory Tract Infections in Pediatric Patients at Benha University Hospital

2020 ◽  
Vol EJMM29 (4) ◽  
pp. 157-163
Author(s):  
Amal M. Matta ◽  
Somaya M. Desouky ◽  
Reem R. Abdel-Glil ◽  
Marwa S. Azab
Keyword(s):  
Tissue Culture ◽  
Respiratory Tract ◽  
Molecular Identification ◽  
Respiratory Tract Infections ◽  
Pediatric Patients ◽  
University Hospital ◽  
Gold Standard Method ◽  
Identification Of Species ◽  
Species Specific ◽  
Tract Infections

Background: Acute respiratory tract infections (ARTI) are a major threat in children all around the world. Adenovirus is one of the most important pathogens causing respiratory tract infections in children. Adenovirus (AdV) respiratory tract infections is caused mainly by species B, C and E. Accurate and rapid identification of AdV respiratory tract infection is important to avoid unnecessary antibiotic prescription and prevents AdV-related outbreaks. Objectives: This study aimed to identify the most prevalent species of adenovirus causing ARTI in pediatric patients hospitalized at Benha University Hospital which were diagnosed by tissue culture and direct immunofluorescence (DIF) test and compare them with polymerase chain reaction (PCR) as a gold standard method. Methodology: This study was conducted on 60 pediatric patients suffering from ARTI admitted to Benha University Hospitals. Adenovirus was detected by DIF test and isolated by tissue culture. Molecular identification of species- specific adenovirus was done by PCR. Results: Out of 60 cases, 35% were Adenovirus positive by PCR. AdV-B was the most prevalent identified species (76.2%) followed by AdV-C (19.0%) and AdV-E (4.8%). The sensitivity and the specificity of tissue culture and DIF test were 90.5%, 100%, 61.9%, 97.4%, respectively. Conclusion: AdV was encountered in one-third of admitted pediatric Egyptian patients with ARTI in Benha University Hospital. PCR was useful for rapid diagnosis of adenovirus infections with higher sensitivity than other methods.

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