Monday, December 12, 2016

Monday reads

Although it is not long ago that I posted some new publications, there are a few more:

Inle (Inlay) Lake, an ancient lake of Southeast Asia, is located at the eastern part of Myanmar, surrounded by the Shan Mountains. Detailed information on fish fauna in and around the lake has long been unknown, although its outstanding endemism was reported a century ago.
Based on the fish specimens collected from markets, rivers, swamps, ponds and ditches around Inle Lake as well as from the lake itself from 2014 to 2016, we recorded a total of 948 occurrence data (2120 individuals), belonging to 10 orders, 19 families, 39 genera and 49 species. Amongst them, 13 species of 12 genera are endemic or nearly endemic to the lake system and 17 species of 16 genera are suggested as non-native. The data are all accessible from the document "A dataset of Inle Lake fish fauna and its distribution", as well as DNA barcoding data (mitochondrial COI) for all species being available from the DDBJ/EMBL/GenBank (Accession numbers: LC189568-LC190411). Live photographs of almost all the individuals and CT/3D model data of several specimens are also available at the graphical fish biodiversity database. The information can benefit the clarification, public concern and conservation of the fish biodiversity in the region.

Epidemics of mosquito-borne viral infections such as dengue, chikungunya, West Nile and Rift Valley fevers in neighbouring countries and risk of introduction of exotic vectors into Iran have placed this country at a significant risk for these mosquito-borne diseases.
After the first dengue case reported in Iran in 2008, active entomological surveillance of Aedes albopictus (Skuse) and Ae. aegypti (Linnaeus) were conducted in May/Jun, Sep, and Oct/Nov, 2008-2014. Based on occurrence of dengue cases and the presence of potential entry sides including ports and boarder gates, 121 sites in eight provinces were monitored for mosquito vectors. Larval collections were carried out using droppers or dippers and adult collections with CDC light traps, human landing catches, aspirator and Pyrethrum spray space catches.
A total of 8,186 larvae and 3,734 adult mosquitoes were collected belonging to 23 Culicinae species, including 13 of the genus Culex, 1 Culiseta, 1 Uranotaenia, and 8 of the genus Aedes. Five Aedes albopictus larvae were identified from the Sistan & Baluchestan province bordering Pakistan in 2009. In 2013, seven Ae. albopictus adult mosquitoes were also collected in a coastal locality near the city of Chabahar in the same province.
The detection of larvae and adults of this species in different parts of this province reveal its probable establishment in southeast Iran, which has implications for public health and requires active entomological surveillance as well as the implementation of vector control to prevent the further spread of this critical vector.

Medically important ticks (Acari: Ixodidae) are often difficult to identify morphologically. A standardized, molecular approach using a 658 base pair DNA barcode sequence (from the 5' region of the mitochondrial cytochrome c oxidase subunit I gene) was evaluated for its effectiveness in discriminating ticks in North America, with an emphasis on Canadian ticks. DNA barcodes were generated for 96 of 154 specimens representing 26 ixodid species. A genetic cluster analysis was performed on the barcode sequences, which separated specimens into haplogroups closely corresponding with morphologically identified species. The tree topology was further supported by a BIN analysis. COI sequences generated were found to have a mean maximum intraspecific divergence of 1.59% and a mean nearest neighbour divergence of 12.8%, indicating a significant "barcode gap". This study also revealed possible cryptic diversity among specimens morphologically identified as Ixodes soricis and Ixodes texanus. A PCR-based test for Borrelia burgdorferi determined that 18.1% of Lyme-competent ticks in this study were positive. This study is also the first to record a B. burgdorferi-positive exoskeleton. In conclusion, DNA barcoding is a powerful tool that clinicians can use to determine the identification of tick specimens which can help them to suggest whether an attached tick is a potential health risk.

We describe a high-resolution melting (HRM) analysis method that is rapid, reproducible, and able to identify reference strains and further 40 clinical isolates of Aspergillus fumigatus (14), A. lentulus (3), A. terreus (7), A. flavus (8), A. niger (2), A. welwitschiae (4), and A. tubingensis (2). Asp1 and Asp2 primer sets were designed to amplify partial sequences of the Aspergillus benA (beta-tubulin) genes in a closed-, single-tube system. Human placenta DNA, further Aspergillus (3), Candida (9), Fusarium (6), and Scedosporium (2) nucleic acids from type strains and clinical isolates were also included in this study to evaluate cross reactivity with other relevant pathogens causing invasive fungal infections. The barcoding capacity of this method proved to be 100% providing distinctive binomial scores; 14, 34, 36, 35, 25, 15, 26 when tested among species, while the within-species distinction capacity of the assay proved to be 0% based on the aligned thermodynamic profiles of the Asp1, Asp2 melting clusters allowing accurate species delimitation of all tested clinical isolates. The identification limit of this HRM assay was also estimated on Aspergillus reference gDNA panels where it proved to be 10-102 genomic equivalents (GE) except the A. fumigatus panel where it was 103 only. Furthermore, misidentification was not detected with human genomic DNA or with Candida, Fusarium, and Scedosporium strains. Our DNA barcoding assay introduced here provides results within a few hours, and it may possess further diagnostic utility when analyzing standard cultures supporting adequate therapeutic decisions.

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