Identification of Fasciola Species Isolates from Nghe An Province, Vietnam, Based on ITS1 Sequence of Ribosomal DNA Using a Simple PCR-RFLP Method

Fascioliasis—a disease caused by Fasciola spp. (Platyhelminthes: Trematoda: Digenea)—is considered as the most important helminthic infection of bovine, sheep, and buffalo in Vietnam. The aim of this study is to detect the genotype of Fasciola spp. isolated from bovine and buffalo in the Nghe An province, central Vietnam, using PCR-RFLP and sequence analysis of the first nuclear ribosomal internal transcribed spacer (ITS1). Adult Fasciola spp. were isolated from bile ducts of bovine and buffalo in Nghe An province, Vietnam. Overall, 96 adult flukes from livers of slaughtered animals were collected from abattoirs of different areas. They included 7 samples from infected bovine and 89 samples from infected buffalo. 96/96 samples were identified as Fasciola species by ITS1 of rDNA. In this study, a PCR-RFLP method was used to distinguish between F. hepatica and F. gigantica in ITS1 of rDNA (680 bp) with RsaI restriction enzyme. RFLP pattern with RsaI produced a consistent pattern of 360, 100, and 60 bp fragments in F. hepatica, whereas F. gigantica worms had a profile of 360, 170, and 60 bp in size, respectively. The results showed that using PCR-RFLP based on the first internal transcribed spacers (ITS1) of the ribosomal RNA revealed that 93 out of 96 isolates were of Fasciola gigantica type, whereas three isolates presented an intermediate Fasciola. In the present study, F. gigantica and intermediate form were coexisting in bovine and buffalo in the Nghe An province of central Vietnam, whereas F. hepatica was not detected.

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Phylogenetic Relationships of Local Durian Species based on Morphological Characteristics and PCR-RFLP Analysis of the Ribosomal Internal Transcribed Spacer (ITS) DNA

Biosaintifika Journal of Biology & Biology Education ◽

10.15294/biosaintifika.v8i3.6748 ◽

2016 ◽

Vol 8 (3) ◽

pp. 362

Author(s):

Fidia Fibriana ◽

Lutfia Nur Hadiyanti

Keyword(s):

Phylogenetic Relationships ◽

Internal Transcribed Spacer ◽

Morphological Characteristics ◽

Biology Education ◽

Rflp Analysis ◽

Restriction Pattern ◽

Internal Transcribed Spacers ◽

Central Java ◽

Pcr Rflp ◽

Pcr Products

In this study, twenty local durian accessions obtained from Central Java in situ collection were characterized using the morphological characteristics and the restriction patterns which generated from the region spanning the internal transcribed spacers ITS LEU and ITS 4. Morphological characteristics of durian leaf, stem, tree, and fruit showed variations for the different accessions, whereas polymerase chain reaction (PCR) products of ribosomal DNA region showed a low length of variation. The size of the PCR products and the restriction analyses with the restriction endonucleases Bsp1431yielded a restriction pattern for each accessions. The results of this study can be utilized by local durian farmers as a preliminary reference for durian propagation. The data obtained need to be supported by further research using the other molecular markers to obtain more accurate data. The clear identity of durian species can help the management of propagation systems by farmers to get superior local durian.How to CiteFibriana, F., & Hadiyanti, L. N. (2016). Phylogenetic Relationships of Local Durian Species based on Morphological Characteristics and PCR-RFLP Analysis of the Ribosomal Internal Transcribed Spacer (ITS) DNA. Biosaintifika: Journal of Biology & Biology Education, 8(3), 362-370.

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Parasite hybridization in African Macrogyrodactylus spp. (Monogenea, Platyhelminthes) signals historical host distribution

Parasitology ◽

10.1017/s0031182010000302 ◽

2010 ◽

Vol 137 (10) ◽

pp. 1585-1595 ◽

Cited By ~ 27

Author(s):

MAXWELL BARSON ◽

IVA PŘIKRYLOVÁ ◽

MAARTEN P. M. VANHOVE ◽

TINE HUYSE

Keyword(s):

Clarias Gariepinus ◽

Internal Transcribed Spacers ◽

Nuclear Ribosomal Dna ◽

Hybrid Origin ◽

Its2 Region ◽

Rrna Gene ◽

Intermediate Form ◽

Its1 Sequence ◽

Haptoral Sclerite ◽

Partial 18S

SUMMARYMacrogyrodactylus spp. from the gills of Clarias gariepinus in Zimbabwe and Kenya, and C. anguillaris in Senegal were identified using haptoral sclerite morphology and by sequencing the nuclear ribosomal DNA internal transcribed spacers (ITS) 1 and 2, partial 18S and the complete 5·8S rRNA gene. A molecular phylogeny was constructed using all sequenced Macrogyrodactylus species to date. Based on morphology, Macrogyrodactylus congolensis, M. heterobranchii, M. clarii, and M. karibae were identified, with one specimen from Zimbabwe displaying morphological features that were intermediate between M. heterobranchii and M. clarii. In the intermediate form, the partial 18S and ITS1 sequence was identical to that of M. clarii while the remaining ITS1 and complete ITS2 region was almost identical to M. heterobranchii as was the partial cox1 fragment, thus strongly suggesting a hybrid origin. At present, the catfish host of M. heterobranchii and M. clarii do not co-occur in southern Zimbabwe; this hybridization event is therefore proof of historical sympatry of both fish species.

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Abundance, composition and natural infection of Anopheles mosquitoes from two malaria-endemic regions of Colombia

Biomédica ◽

10.7705/biomedica.v37i0.3553 ◽

2017 ◽

Vol 37 ◽

pp. 98 ◽

Cited By ~ 4

Author(s):

Carolina Montoya ◽

Priscila Bascuñán ◽

Julián Rodríguez-Zabala ◽

Margarita M. Correa

Keyword(s):

Ribosomal Rna ◽

Internal Transcribed Spacer ◽

Fragment Length Polymorphism ◽

Natural Infection ◽

Small Subunit ◽

Anopheles Mosquitoes ◽

Pcr Rflp ◽

Para Determinar ◽

Valle Del Cauca ◽

Restriction Fragment Length

Introducción. En Colombia hay tres especies de mosquitos Anopheles implicadas como vectores primarios en la transmisión de la malaria o paludismo; sin embargo, el rol local de algunas especies de Anopheles aún debe determinarse.Objetivo. Determinar la abundancia, la composición y la infección natural de mosquitos anofelinos con Plasmodium spp. en dos regiones endémicas de malaria en Colombia.Materiales y métodos. Se recolectaron mosquitos del género Anopheles usando los métodos de recolección con cebo humano y en reposo en corrales de ganado vacuno, en nueve localidades de dos regiones endémicas para malaria en Colombia. Los especímenes se identificaron morfológicamente y se confirmaron por reacción en cadena de la polimerasa (PCR) de los polimorfismos en la longitud de los fragmentos de restricción (Restriction Fragment Length Polymorphism, RFLP) en el espaciador intergénico ribosómico nuclear 2 (Internal Transcribed Spacer, ITS-2) (PCR-RFLP-ITS2). Los especímenes se procesaron y analizaron mediante ELISA y PCR anidada basada en la subunidad pequeña del ARN ribosómico (small subunit ribosomal RNA, ssrRNA) para determinar la infección por Plasmodium.Resultados. Se recolectaron 1.963 mosquitos Anopheles correspondientes a nueve especies. Anopheles nuneztovari fue la especie predominante (53,5 %), seguida por A. darlingi (34,5 %), A. triannulatus s.l. (6 %) y por otras especies (≈5,9 %). Tres especies se encontraron naturalmente infectadas con Plasmodium spp.: A. darlingi, A. nuneztovari y A. triannulatus s.l.Conclusiones. La infección natural de A. darlingi y A. nuneztovari indica que estos vectores primarios siguen siendo actores principales en la transmisión de malaria en las localidades estudiadas de los departamentos del Valle del Cauca y Chocó. Además, el espécimen A. triannulatus s.l. infectado, recolectado en corrales de animales de la localidad estudiada en el departamento de Córdoba, indica que existe la necesidad de estudios futuros para establecer la importancia epidemiológica de esta especie dada su abundancia y comportamiento antropofílico oportunista.

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Additional data for a new Theileria sp. from China based on the sequences of ribosomal RNA internal transcribed spacers

Experimental Parasitology ◽

10.1016/j.exppara.2012.11.023 ◽

2013 ◽

Vol 133 (2) ◽

pp. 217-221 ◽

Cited By ~ 6

Author(s):

Junlong Liu ◽

Guiquan Guan ◽

Zhijie Liu ◽

Aihong Liu ◽

Miling Ma ◽

...

Keyword(s):

Ribosomal Rna ◽

Additional Data ◽

Internal Transcribed Spacers

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Six group I introns and three internal transcribed spacers in the chloroplast large subunit ribosomal RNA gene of the green alga Chlamydomonas eugametos

Journal of Molecular Biology ◽

10.1016/0022-2836(91)90713-g ◽

1991 ◽

Vol 218 (2) ◽

pp. 293-311 ◽

Cited By ~ 29

Author(s):

Monique Turmel ◽

Jean Boulanger ◽

Murray N. Schnare ◽

Michael W. Gray ◽

Claude Lemieux

Keyword(s):

Green Alga ◽

Ribosomal Rna ◽

Large Subunit ◽

Internal Transcribed Spacers ◽

Group I Introns ◽

Ribosomal Rna Gene ◽

Group I ◽

Chlamydomonas Eugametos ◽

Large Subunit Ribosomal Rna

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Group I Intron Versus its Sequences in Phylogeny of Cetrarioid Lichens

The Lichenologist ◽

10.1006/lich.1999.0231 ◽

1999 ◽

Vol 31 (5) ◽

pp. 441-449 ◽

Cited By ~ 9

Author(s):

Arne Thell

Keyword(s):

Ribosomal Rna ◽

Internal Transcribed Spacer ◽

Phylogenetic Trees ◽

Group I Intron ◽

Ribosomal Genes ◽

Its Sequences ◽

Its Sequence ◽

Ribosomal Rna Gene ◽

18S Ribosomal Rna Gene ◽

Group I

AbstractPhylogenetic trees based on group I intron sequences and on internal transcribed spacer (ITS) sequences of mycobiont ribosomal genes were calculated and compared. Eight cetrarioid and four non-cetrarioid species of the Parmeliaceae were compared. The phylogeny based on group I intron sequences is partly congruent with the ITS sequence phylogeny. Group I intron sequences are presumably less informative for infragenic studies. The introns have a length of 214–233 nucleotides, and differ at up to 33% of the bases between species. All introns analysed are located between the positions 1516 and 1517 of the fungal 18S ribosomal RNA gene. Cetrarioid lichens form a non-homogeneous group within the Parmeliaceae according to both group I intron and ITS sequences.

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Application of PCR-RFLP and MASA Analyses on 18S Ribosomal RNA Gene Sequence for the Identification of Three Ginseng Drugs.

Biological and Pharmaceutical Bulletin ◽

10.1248/bpb.20.765 ◽

1997 ◽

Vol 20 (7) ◽

pp. 765-769 ◽

Cited By ~ 30

Author(s):

Hirotoshi FUSHIMI ◽

Katsuko KOMATSU ◽

Masaharu ISOBE ◽

Tsuneo NAMBA

Keyword(s):

Ribosomal Rna ◽

Gene Sequence ◽

Ribosomal Rna Gene ◽

18S Ribosomal Rna ◽

18S Ribosomal Rna Gene ◽

Pcr Rflp

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Combining Natural Language Processing and Metabarcoding to Reveal Pathogen-Environment Associations

10.1101/2020.09.02.280578 ◽

2020 ◽

Author(s):

David C. Molik ◽

DeAndre Tomlinson ◽

Shane Davitt ◽

Eric L. Morgan ◽

Benjamin Roche ◽

...

Keyword(s):

Natural Language Processing ◽

Natural Language ◽

Cryptococcus Neoformans ◽

Language Processing ◽

Ribosomal Rna ◽

Internal Transcribed Spacer ◽

De Novo ◽

Ecological Niches ◽

Sequence Read Archive ◽

Ncbi Sequence Read Archive

AbstractCryptococcus neoformans is responsible for life-threatening infections that primarily affect immunocompromised individuals and has an estimated worldwide burden of 220,000 new cases each year—with 180,000 resulting deaths—mostly in sub-Saharan Africa. Surprisingly, little is known about the ecological niches occupied by C. neoformans in nature. To expand our understanding of the distribution and ecological associations of this pathogen we implement a Natural Language Processing approach to better describe the niche of C. neoformans. We use a Latent Dirichlet Allocation model to de novo topic model sets of metagenetic research articles written about varied subjects which either explicitly mention, inadvertently find, or fail to find C. neoformans. These articles are all linked to NCBI Sequence Read Archive datasets of 18S ribosomal RNA and/or Internal Transcribed Spacer gene-regions. The number of topics was determined based on the model coherence score, and articles were assigned to the created topics via a Machine Learning approach with a Random Forest algorithm. Our analysis provides support for a previously suggested linkage between C. neoformans and soils associated with decomposing wood. Our approach, using a search of single-locus metagenetic data, gathering papers connected to the datasets, de novo determination of topics, the number of topics, and assignment of articles to the topics, illustrates how such an analysis pipeline can harness large-scale datasets that are published/available but not necessarily fully analyzed, or whose metadata is not harmonized with other studies. Our approach can be applied to a variety of systems to assert potential evidence of environmental associations.Author SummaryOur finding that C. neoformans is associated with decomposing wood is reinforced by the general literature on C. neoformans and its close congeneric relatives and warrants further investigation. This work demonstrates the potential utility of pairing Natural Language Processing (NLP) with single-locus metagenetic data for the study of Neglected Tropical Diseases. We present a novel method to study the ecological niches of rare pathogens that leverages the immense amount of data available to researchers in the NCBI Sequence Read Archive (SRA)combined with a text-mining analysis based on Natural Language Processing. We demonstrate that text processing, noun identification, and verb identification can play an important role in analyzing a large corpus of documents together with metagenetic data. Forging this connection requires access to all of the available ecological 18S ribosomal RNA and Internal Transcribed Spacer NCBI SRA datasets. These datasets use metabarcoding to query taxonomic diversity in eukaryotic organisms, and in the case of the Internal Transcribed Spacer, they specifically target Fungi. The presence of specific species is inferred when diagnostic 18S or ITS gene region sequences are found in the SRA data. We searched for C. neoformans in all 18S and ITS datasets available and gathered all associated journal articles that either cite the SRA data accessions or are cited in the SRA data accessions.Published metagenetic data often have associated metadata including: latitude and longitude, temperature, and other physical characteristics describing the conditions in which the metagenetic sample was collected. These metadata are not always be presented in consistent formats, so harmonizing study methods may be needed to appropriately compare metagenetic data as commonly required in metanalysis studies. We present an analysis which takes as input articles associated with SRA datasets that were found to contain evidence of C. neoformans. We apply NLP methods to this corpus of articles to describe the niche of C. neoformans. Our results reinforce the current understanding of C. neoformans’s niche, indicating the pertinence of employing a NLP analysis to identify the niche of an organism. This approach could further the description of virtually any other organism that routinely appears in metagenetic surveys, especially pathogens, whose ecological niches are unknown or poorly understood.Optional Striking ImageCryptococcus neoformans cells budding. Image Provided Courtesy of Felipe H. Santiago-Tirado, colored by Kristina Davis, CC-BY 4.0

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First Report of Musk Thistle Rust (Puccinia carduorum) in California and Nevada

Plant Disease ◽

10.1094/pdis.2002.86.7.814b ◽

2002 ◽

Vol 86 (7) ◽

pp. 814-814 ◽

Cited By ~ 5

Author(s):

D. M. Woods ◽

M. J. Pitcairn ◽

D. G. Luster ◽

W. L. Bruckart

Keyword(s):

Ribosomal Rna ◽

Dna Sequences ◽

Internal Transcribed Spacer ◽

East Coast ◽

Rust Fungus ◽

The United States ◽

Rust Disease ◽

Carduus Nutans ◽

Its1 And Its2 ◽

Spacer Dna

Musk thistle, Carduus nutans L., is an introduced weed of pastures, rangelands, and natural areas in much of North America. Puccinia carduorum Jacky, an autoecious rust fungus from Turkey, has been evaluated for biological control of musk thistle since 1978, including a field study near Blacksburg, VA, from 1987 to 1990. After release of the fungus in Virginia, rusted musk thistle was found in eight eastern states by 1992, in Missouri by 1994 (1), and in Oklahoma by 1997 (2). A rust disease was discovered on musk thistle near Mt. Shasta, CA, on 22 September 1998, and near Mogul, NV, on 12 August 1999. The pathogen was identified as P. carduorum on the basis of pathogenicity on musk thistle and urediniospore morphology (ovate spores, 21 μm diameter, three germ pores equatorial in location, and echinulations over the upper two-thirds to three-quarters of urediniospores). Ribosomal RNA internal transcribed spacer DNA sequences (ITS1 and ITS2) were identical to those from the isolate obtained after the field release in Virginia, verifying that the California isolate is P. carduorum. The initial California infestation was observed on a few plants late in the season, and by September 2000, nearly 100% of plants were infected. The occurrence of P. carduorum in California is apparently the result of natural, unaided spread of the fungus on musk thistle from the East Coast of the United States. References: (1) A. B. A. M. Baudoin and W. L. Bruckart. Plant Dis. 80:1193, 1996. (2) L. J. Littlefield et al. Plant Dis. 82:832, 1998.

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