scholarly journals Rapid Identification ofHelicoverpa armigeraandHelicoverpa zea(Lepidoptera: Noctuidae) Using Ribosomal RNA Internal Transcribed Spacer 1

2015 ◽  
Vol 15 (1) ◽  
pp. 155 ◽  
Author(s):  
Omaththage P. Perera ◽  
Kerry C. Allen ◽  
Devendra Jain ◽  
Matthew Purcell ◽  
Nathan S. Little ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Rapid Identification ◽  
Lepidoptera Noctuidae

PCR Detection of Alternaria spp. in Processed Foods, Based on the Internal Transcribed Spacer Genetic Marker

2011 ◽  
Vol 74 (2) ◽  
pp. 240-247 ◽  
Author(s):  
MIGUELÁNGEL PAVÓN ◽  
ISABEL GONZÁLEZ ◽  
MARÍA ROJAS ◽  
NICOLETTE PEGELS ◽  
ROSARIO MARTÍN ◽  
...  
Keyword(s):  
Food Processing ◽  
Internal Transcribed Spacer ◽  
Rapid Identification ◽  
Food Samples ◽  
Pcr Analysis ◽  
Infant Food ◽  
Rrna Gene ◽  
Tomato Pulp ◽  
Pcr Method ◽  
Fungal Contaminants

The genus Alternaria is considered one of the most important fungal contaminants of vegetables, fruits, and cereals, producing several mycotoxins that can withstand food processing methods. Conventional methods for Alternaria identification and enumeration are laborious and time-consuming, and they might not detect toxigenic molds inactivated by food processing. In this study, a PCR method has been developed for the rapid identification of Alternaria spp. DNA in foodstuffs, based on oligonucleotide primers targeting the internal transcribed spacer (ITS) 1 and ITS2 regions of the rRNA gene. The specificity of the Alternaria-specific primer pair designed (Dir1ITSAlt–Inv1ITSAlt) was verified by PCR analysis of DNA from various Alternaria spp., and also from several fungal, bacterial, yeast, animal, and plant species. The detection limit of the method was 102 CFU/ml in viable culture, heated culture, or experimentally inoculated tomato pulp. The applicability of the method for detection of Alternaria spp. DNA in foodstuffs was assessed by testing several commercial samples. Alternaria DNA was detected in 100% of spoiled tomato samples, 8% of tomato products, and 36.4% of cereal-based infant food samples analyzed.

Group I Intron Versus its Sequences in Phylogeny of Cetrarioid Lichens

1999 ◽  
Vol 31 (5) ◽  
pp. 441-449 ◽  
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.

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

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

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

Plant Disease ◽  
2002 ◽  
Vol 86 (7) ◽  
pp. 814-814 ◽  
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.

Amanita mansehraensis, a new species in section Vaginatae from Pakistan

Phytotaxa ◽  
2019 ◽  
Vol 409 (4) ◽  
pp. 189-201 ◽  
Author(s):  
MALKA SABA ◽  
DANNY HAELEWATERS ◽  
MUHAMMAD FIAZ ◽  
ABDUL NASIR KHALID ◽  
DONALD H. PFISTER
Keyword(s):  
New Species ◽  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Large Subunit ◽  
Pine Forests ◽  
Evolutionary Relationships ◽  
Internal Transcribed Spacer Region ◽  
Bayesian Inferences ◽  
A New Species

A new species of Amanita subgenus Amanita sect. Vaginatae is described and illustrated based on material collected in pine forests in district Mansehra, Khyber Pakhtoonkhaw, Pakistan. Amanita mansehraensis is recognized by the presence of a light brown or light greyish olive pileus with strong brown or deep brown pileus center; non-appendiculate, rimose, sulcate or plicate striate pileus margin; subglobose to ellipsoid basidiospores; and a saccate volva. The internal transcribed spacer region (ITS) and large subunit of the nuclear ribosomal RNA gene (nrLSU) were used for the delimitation of this species based on sequence data. The evolutionary relationships of A. mansehraensis with other species of Amanita were inferred by means of Maximum Likelihood and Bayesian inferences of the nrLSU dataset and concatenated ITS+nrLSU dataset. Amanita mansehraensis is most closely related to A. brunneofuliginea, A. pseudovaginata, and the recently described A. glarea.

scholarly journals Viability of pathogenic dermatophytes during a 4-week treatment with 1% topical luliconazole for tinea pedis

2019 ◽  
Vol 58 (3) ◽  
pp. 401-403 ◽  
Author(s):  
Tomoyuki Iwanaga ◽  
Tsuyoshi Ushigami ◽  
Kazushi Anzawa ◽  
Takashi Mochizuki
Keyword(s):  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Copy Number ◽  
Tinea Pedis ◽  
Pathogenic Fungi ◽  
Topical Administration ◽  
Initial Visit ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Average Copy

Abstract The viability of pathogenic fungi in the scale was investigated during topical administration of 1% luliconazole (LLCZ). Thirteen tinea pedis patients found to be positive on KOH examination were assessed by mycological examinations and quantitative real-time polymerase chain reaction (PCR) targeted internal transcribed spacer (ITS) in ribosomal RNA gene at the initial visit and after 2 and 4 weeks of treatment. Assays showed that the average copy number of ITS DNA had significantly decreased to 22.9% at 2 weeks and 4.8% at 4 weeks compared with the initial visit. LLCZ topical treatment could defeat almost pathogenic dermatophytes in the scales within 4 weeks.

A new species and a new record of Xanthagaricus (Agaricaceae, Agaricales) from China

Phytotaxa ◽  
2018 ◽  
Vol 371 (4) ◽  
pp. 241 ◽  
Author(s):  
FENGJIAN WANG ◽  
LIANGLIANG QI ◽  
XIANGYU ZHOU ◽  
YU LI
Keyword(s):  
New Species ◽  
Molecular Analysis ◽  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
New Record ◽  
Morphological Features ◽  
The Other ◽  
Ribosomal Rna Gene ◽  
Micromorphological Characters ◽  
A New Species

Two species of Xanthagaricus discovered in Hubei Province of China are described based on the macro- and micromorphological features. Their identity is further supported by molecular analysis of the internal transcribed spacer (ITS) of the ribosomal RNA gene. The phylogeny obtained here showed that one of the Chinese species is nested in an exclusive clade which in combination with its striking morphological features, infers that it represents a new species, named X. ianthinus, while the other species is placed as a member in the X. epipastus clade. Descriptions are accompanied with illustrations of macro- and micromorphological characters and a discussion of related taxa is presented.

Ceriporia albomellea (Phanerochaetaceae, Basidiomycota), a new species from tropical China based on morphological and molecular evidences

Phytotaxa ◽  
2017 ◽  
Vol 298 (1) ◽  
pp. 20 ◽  
Author(s):  
YUAN YUAN ◽  
XIAO-HONG JI ◽  
FANG WU ◽  
JIA-JIA CHEN
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Morphological Characteristics ◽  
Molecular Evidence ◽  
Its Regions ◽  
Tropical China ◽  
A New Species

A new polypore, Ceriporia albomellea, collected from tropical China, is described and illustrated based on morphological characteristics and molecular evidence. It is characterized by thin, resupinate basidiome with a white subiculum, cottony margin, white to cinnamon-buff pores, clavate cystidia and oblong-ellipsoid basidiospores measured as 3.1–3.8 × 1.7–2 µm. Phylogenetic analysis based on the internal transcribed spacer (ITS) regions and nuclear large subunit (nLSU) ribosomal RNA gene regions supported C. albomellea as a distinctive species belonging to Ceriporia.

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