Monday, November 7, 2016

Monday reads

Monday morning is my time for going through all my RSS feeds and read some of the more recent publications. A number of very interesting reads for me this morning which made me think that I might as well share a slection with all the blog readers. So, in case you haven't come across them, here are some:

DNA barcoding and health

Theileria spp. are tick-borne protozoan parasites that infect a wide range of wild and domestic animals. In this study, the utility of xenosurveillance of blood-fed specimens of Culiseta annulata for detecting the presence of piroplasms in livestock was investigated. Blood-fed mosquitoes were collected at Elmley National Nature Reserve, Kent, United Kingdom. All specimens were morphologically identified, and DNA barcoding was used to confirm the morphological identification. Both the vertebrate host species and Theileria genome was detected within the bloodmeal by real-time PCR. Sequencing was used to confirm the identity of all amplicons. In total, 105 blood-fed mosquitoes morphologically identified as Cs. annulata were collected. DNA barcoding revealed that 102 specimens were Cs. annulata (99%), while a single specimen was identified as Anopheles messeae. Two specimens could not be identified molecularly due to PCR amplification failure. Blood meal analysis revealed that Cs. annulata fed almost exclusively on cattle at the collection site (n = 100). The application of a pan-piroplasm PCR detected 16 positive samples (15.2%) and sequence analysis of the amplicons demonstrated that the piroplasms present in the blood meal belonged to the Theileria orientalis group. This study demonstrates how xenosurveillance can be applied to detecting pathogens in livestock and confirms the presence of Theileria species in livestock from the United Kingdom.

A reference 535 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI), acquired from specimens of An. neivai Howard, Dyar & Knab, 1913 from its type locality in Panama, was used as a tool for distinguishing this species from others in the subgenus Kerteszia. Comparisons with corresponding regions of COI between An. neivai and other species in the subgenus (An. bellator Dyar & Knab 1906, An. homunculus Komp 1937, An cruzii Dyar & Knab, 1908 and An. laneanus Corrêa & Cerqueira, 1944) produced K2P genetic distances of 8.3–12.6%, values well above those associated with intraspecific variation. In contrast, genetic distances among 55 specimens from five municipalities in the Colombian Pacific coastal state of Chocó were all within the range of 0–2.5%, with an optimized barcode threshold of 1.3%, the limit for unambiguous differentiation of An. neivai. Among specimens from the Chocó region, 18 haplotypes were detected, two of which were widely distributed over the municipalities sampled. The barcode sequence permits discrimination of An. neivai from sympatric species and indicates genetic variability within the species; aspects key to malaria surveillance and control as well as defining geographic distribution and dispersion patterns.

Plant exposures are among the most frequently reported cases to poison control centres worldwide. This is a growing condition due to recent societal trends oriented towards the consumption of wild plants as food, cosmetics, or medicine. At least three general causes of plant poisoning can be identified: plant misidentification, introduction of new plant-based supplements and medicines with no controls about their safety, and the lack of regulation for the trading of herbal and phytochemical products. Moreover, an efficient screening for the occurrence of plants poisonous to humans is also desirable at the different stages of the food supply chain: from the raw material to the final transformed product. A rapid diagnosis of intoxication cases is necessary in order to provide the most reliable treatment. However, a precise taxonomic characterization of the ingested species is often challenging. In this review, we provide an overview of the emerging DNA-based tools and technologies to address the issue of poisonous plant identification. Specifically, classic DNA barcoding and its applications using High Resolution Melting (Bar-HRM) ensure high universality and rapid response respectively, whereas High Throughput Sequencing techniques (HTS) provide a complete characterization of plant residues in complex matrices. The pros and cons of each approach have been evaluated with the final aim of proposing a general user's guide to molecular identification directed to different stakeholder categories interested in the diagnostics of poisonous plants.

High-Throughput Sequencing

Evaluating and Optimizing the Performance of Software Commonly Used for the Taxonomic Classification of DNA Metabarcoding Sequence Data
The taxonomic classification of DNA sequences has become a critical component of numerous ecological research applications; however, few studies have evaluated the strengths and weaknesses of commonly used sequence classification approaches. Further, the methods and software available for sequence classification are diverse, creating an environment in which it may be difficult to determine the best course of action and the tradeoffs made using different classification approaches. Here, we provide an in silico evaluation of three DNA sequence classifiers, the RDP Naïve Bayesian Classifier, RTAX and UTAX. Further, we discuss the results, merits and limitations of both the classifiers and our method of classifier evaluation. Our methods of comparison are simple, yet robust, and will provide researchers a methodological and conceptual foundation for making such evaluations in a variety of research situations. Generally, we found a considerable trade-off between accuracy and sensitivity for the classifiers tested, indicating a need for further improvement of sequence classification tools.

Invertebrates that impact human well-being

DNA barcoding for biosecurity: case studies from the UK plant protection program.
Since its conception, DNA barcoding has seen a rapid uptake within the research community. Nevertheless, as with many new scientific tools, progression towards the point of routine deployment within diagnostic laboratories has been slow. In this paper, we discuss the application of DNA barcoding in the Defra plant health diagnostic laboratories, where DNA barcoding is used primarily for the identification of invertebrate pests. We present a series of case studies that demonstrate the successful application of DNA barcoding but also reveal some potential limitations to expanded use. The regulated plant pest, Bursephalenchus xylophilus, and one of its vectors, Monochamus alternatus, were found in dining chairs. Some traded wood products are potentially high risk, allowing the movement of longhorn beetles; Trichoferus campestris, Leptura quadrifasciata, and Trichoferus holosericeus were found in a wooden cutlery tray, a railway sleeper, and a dining chair, respectively. An outbreak of Meloidogyne fallax was identified in Allium ampeloprasum and in three weed species. Reference sequences for UK native psyllids were generated to enable the development of rapid diagnostics to be used for monitoring following the release of Aphalara itadori as a biological control agent for Fallopia japonica.

We spend most of our lives inside homes, surrounded by arthropods that impact our property as pests and our health as disease vectors and producers of sensitizing allergens. Despite their relevance to human health and well-being, we know relatively little about the arthropods that exist in our homes and the factors structuring their diversity. Since previous work has been limited in scale by the costs and time associated with collecting arthropods and the subsequent morphological identification we used a DNA-based method for investigating the arthropod diversity in homes via high-throughput marker gene sequencing of home dust. Settled dust samples were collected by citizen scientists from both inside and outside more than 700 homes across the United States, yielding the first continental-scale estimates of arthropod diversity associated with our residences. We were able to document food webs and previously unknown geographic distributions of diverse arthropods-from allergen producers to invasive species and nuisance pests. Home characteristics, including the presence of basements, home occupants, and surrounding land-use, were more useful than climate parameters at predicting arthropod diversity in homes. These non-invasive, scalable tools and resultant findings not only provide the first continental-scale maps of household arthropod diversity, our analyses also provide valuable baseline information on arthropod allergen exposures and the distributions of invasive pests inside homes. This article is protected by copyright. All rights reserved.

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