Search results for "Barco"

DNA barcoding for species assignment: the case of Mediterranean marine fishes

2014

Background: DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI) constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity. Methodology/Principal Findings: A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes…

Molecular analysis of the fungal community associated with phyllosphere and carposphere of fruit crops

Evaluation of criteria for species delimitation of bagworm moths (Lepidoptera: Psychidae)

2014

Accurate identification of species is fundamental for biological research and necessary for species conservation. DNA bar- coding is particularly useful when identification using morphological characteristics is laborious and/or unreliable. However, bar- codes for species are dependent on the availability of reference sequences from correctly identified specimens. The traditional use of morphology to delimit the species boundaries of Finnish bagworm moths (Lepidoptera: Psychidae: Naryciinae: Dahliciini) is contro- versial because there is overlap in their morphological characteristics. In addition, there are no suitable molecular markers. We veri- fied the delimitation of seven out of eight…

Experiences from a wearable-mobile acquisition system for ambulatory assessment of diet and activity

2017

Public health trends are currently monitored and diagnosed based on large studies that often rely on pen-and-paper data methods that tend to require a large collection campaign. With the pervasiveness of smart-phones and -watches throughout the general population, we argue in this paper that such devices and their built-in sensors can be used to capture such data more accurately with less of an effort. We present a system that targets a pan-European and harmonised architecture, using smartphones and wrist-worn activity loggers to enable the collection of data to estimate sedentary behavior and physical activity, plus the consumption of sugar-sweetened beverages. We report on a unified pilot…

Re-Clustering tool using an Open-Reference method that improves OTU definition

2019

International audience; 1.Environmental microbial communities are now widely studied using metabarcoding approaches, thanks to the democratization of high‐throughput DNA sequencing technologies. The massive number of reads produced with these technologies requires bioinformatic solutions to be treated. A key step in the analysis is to cluster reads into Operational Taxonomic Units (or OTUs) and thus reduce the amount of data for downstream analyses. Due to the important impact of the clustering method on the quantity and quality of OTUs, finding an equilibrium between the reliability and time‐consuming nature of the chosen strategy is a real challenge. The present article proposes a new pos…

<strong>Identification of the nymphal stages of two European seed bugs, <em>L. equestris</em> and <em>L. simulans</em> …

2013

The genus Lygaeus Fabricius, 1794 includes more than fifty species, mainly distributed in the Old World regions, with 17 species known from the Palearctic (Pericart 2001; Wachmann et al. 2007), and only two from Central Europe, i.e., L . equestris (Linnaeus, 1758) and L . simulans Deckert, 1985 (Pericart 2001).

Detection of multiple species of humanParagonimusfrom Mexico using morphological data and molecular barcodes

2013

Paragonimus mexicanus is the causal agent of human paragonimiasis in several countries of the Americas. It is considered to be the only species of the genus present in Mexico, where it is responsible for human infection. Through the investigation of P. mexicanus specimens from several places throughout Mexico, we provide morphological, molecular and geographical evidence that strongly suggests the presence of at least three species from this genus in Mexico. These results raise questions regarding the diagnosis, treatment, prophylaxis and control of human paragonimiasis in Mexico. We also provide a brief discussion regarding biodiversity inventories and the convenience of providing molecula…

The ‘giant phyllosoma’ are larval stages of Parribacus antarcticus (Decapoda : Scyllaridae)

2014

Early reports on larval distributions are frustratingly obscure due to ambiguous identification of plankton samples. A particularly striking case is posed by the so-called ‘giant phyllosoma’ which attain 80 mm in total length and are among the largest larvae known in marine invertebrates. Based on the supposition that these giant larvae are produced by local species, Philip Robertson (1968) assigned them to Parribacus. In the present study, 12 phyllosoma larvae collected in the Coral Sea and corresponding to intermediate stages VI to IX are described in detail. The identity of these freshly caught specimens was confirmed as belonging to Parribacus antarcticus (Lund, 1793) by using DNA barco…

Molecular analysis ofPhytophthoradiversity in nursery-grown ornamental and fruit plants

2015

The genetic diversity of Phytophthora spp. was investigated in potted ornamental and fruit tree species. A metabarcoding approach was used, based on a semi-nested PCR with Phytophthora genus-specific primers targeting the ITS1 region of the rDNA. More than 50 ITS1 sequence types representing at least 15 distinct Phytophthora taxa were detected. Nine had ITS sequences that grouped them in defined taxonomic groups (P. nicotianae, P. citrophthora, P. meadii, P. taxon Pgchlamydo, P. cinnamomi, P. parvispora, P. cambivora, P. niederhauserii and P. lateralis) whereas three phylotypes were associated to two or more taxa (P. citricola taxon E or III; P. pseudosyringae, P. ilicis or P. nemorosa; and…

Whither the species? Phytophthora taxa, MOTUs and barcodes in the world of metagenomics

2015

The study of ecosystem diversity is being transformed by high throughput sequencing technology that allows an unparalleled depth of sampling of DNA barcode sequences. The opportunities are great at this fascinating interface of pathology, ecology, taxonomy and molecular biology but there are pitfalls. It is important to consider the potential for bias at all steps in the process from sampling through to data analysis. Increasingly Phytophthora diversity is being examined by metabarcoding of the PCR amplified rDNA ITS regions from soil, water or plant sample DNA. We have applied baiting and isolation, cloning and Sanger sequencing and Illumina MiSeq analysis to a time-series of filtered wate…