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https://www.readbyqxmd.com/read/29791787/dna-barcoding-of-microgastrine-parasitoid-wasps-hymenoptera-braconidae-using-high-throughput-methods-more-than-doubles-the-number-of-species-known-for-australia
#1
Erinn P Fagan-Jeffries, Steven J B Cooper, Terry Bertozzi, Tessa M Bradford, Andrew D Austin
The Microgastrinae are a hugely diverse subfamily of endoparasitoid wasps of lepidopteran caterpillars. They are important in agriculture as biological control agents, and play a significant ecological role in the regulation of caterpillar populations. Whilst the group has been the focus of intensive rearing and DNA barcoding studies in the Northern Hemisphere, the Australian fauna has received little attention. In total, 100 species have been described from or have been introduced into Australia, but the real species diversity for the region is clearly much larger than this...
May 23, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29791719/molecular-and-morphological-diversity-of-trebouxia-microalgae-in-sphaerothallioid-circinaria-spp-lichens
#2
Arántzazu Molins, Patricia Moya, Francisco J García-Breijo, José Reig-Armiñana, Eva Barreno
Three vagrant (Circinaria hispida, Circinaria gyrosa, Circinaria sp. 'paramerae') and one crustose (semi-vagrant, Circinaria sp.'oromediterranea') lichens growing in very continental areas in the Iberian Peninsula were selected to study the phycobiont diversity. Mycobiont identification was checked using nrITS DNA barcoding: Circinaria sp.'oromediterranea' and Circinaria sp. 'paramerae' formed a new clade. Phycobiont diversity was analyzed in 50 thalli of Circinaria spp. using nrITS DNA and LSU rDNA, with microalgae coexistence being found in all the species analyzed by Sanger sequencing...
May 23, 2018: Journal of Phycology
https://www.readbyqxmd.com/read/29791459/species-identification-and-connectivity-of-marine-amphipods-in-canada-s-three-oceans
#3
Astrid Tempestini, Søren Rysgaard, France Dufresne
Monitoring the distribution of marine biodiversity is a crucial step to better assess the impacts of global changes. Arctic marine fauna is dominated by amphipods in terms of abundance and biomass. These peracarids are an important marine order of crustaceans but the number of species found in the different Canadian oceans is currently unknown. Furthermore, most species are difficult to identify due to poor taxonomic descriptions and morphological convergence. The aim of this study was to assess the species diversity of marine amphipods in the three Canadian oceans using DNA barcoding...
2018: PloS One
https://www.readbyqxmd.com/read/29790906/bcseq-an-r-package-for-fast-sequence-mapping-in-high-throughput-shrna-and-crispr-screens
#4
Jiaxing Lin, Jeremy Gresham, Tongrong Wang, So Young Kim, James Alvarez, Jeffrey S Damrauer, Scott Floyd, Joshua Granek, Andrew Allen, Cliburn Chan, Jichun Xie, Kouros Owzar
Summary: CRISPR-Cas9 and shRNA high-throughput sequencing screens have abundant applications for basic and translational research. Methods and tools for the analysis of these screens must properly account for sequencing error, resolve ambiguous mappings among similar sequences in the barcode library in a statistically principled manner, and be computationally efficient. Herein we present bcSeq, an open source R package that implements a fast and parallelized algorithm for mapping high-throughput sequencing reads to a barcode library while tolerating sequencing error...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29788324/the-application-of-coi-gene-for-species-identification-of-forensically-important-muscid-flies-diptera-muscidae
#5
Lipin Ren, Wei Chen, Yanjie Shang, Fanming Meng, Lagabaiyila Zha, Yong Wang, Yadong Guo
Muscid Flies (Diptera: Muscidae) are of great forensic importance due to their wide distribution, ubiquitous and synanthropic nature. They are frequently neglected as they tend to arrive at the corpses later than the flesh flies and blow flies. Moreover, the lack of species-level identification also hinders investigation of medicolegal purposes. To overcome the difficulty of morphological identification, molecular method has gained relevance. Cytochrome c oxidase subunit I (COI) gene has been widely utilized...
May 17, 2018: Journal of Medical Entomology
https://www.readbyqxmd.com/read/29786943/integrating-a-comprehensive-dna-barcode-reference-library-with-a-global-map-of-yews-taxus-l-for-forensic-identification
#6
Jie Liu, Richard I Milne, Michael Möller, Guang-Fu Zhu, Lin-Jiang Ye, Ya-Huang Luo, Jun-Bo Yang, Moses Cheloti Wambulwa, Chun-Neng Wang, De-Zhu Li, Lian-Ming Gao
Rapid and accurate identification of endangered species is a critical component of bio-surveillance and conservation management, and potentially policing illegal trades. However, this is often not possible using traditional taxonomy, especially where only small or pre-processed parts of plants are available. Reliable identification can be achieved via a comprehensive DNA barcode reference library, accompanied by precise distribution data. However, these require extensive sampling at spatial and taxonomic scales, which has rarely been achieved for cosmopolitan taxa...
May 22, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29785925/comparison-of-two-genotyping-methods-for-distinguishing-recrudescence-from-reinfection-in-antimalarial-drug-efficacy-effectiveness-trials
#7
Joseph R M Fulakeza, Rachel L Banda, Trancizeo R Lipenga, Dianne J Terlouw, Standwell C Nkhoma, Eva Maria Hodel
Genotyping of allelic variants of Plasmodium falciparum merozoite surface proteins 1 and 2 ( msp-1 and msp-2 ), and the glutamate-rich protein is the gold standard for distinguishing reinfections from recrudescences in antimalarial drug trials. We compared performance of the recently developed 24-single-nucleotide polymorphism (SNP) Barcoding Assay against msp-1 and msp-2 genotyping in a cluster-randomized effectiveness trial of artemether-lumefantrine and dihydroartemisinin-piperaquine in Malawi. Rates of recrudescence and reinfection estimated by the two methods did not differ significantly (Fisher's exact test; P = 0...
May 21, 2018: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29784414/source-attribution-profiling-of-five-species-of-amanita-mushrooms-from-four-european-countries-by-high-resolution-liquid-chromatography-mass-spectrometry-combined-with-multivariate-statistical-analysis-and-dna-barcoding
#8
Daniel Jansson, Arthur Wolterink, Leonie Bergwerff, Patrick Hough, Kris Geukens, Crister Åstot
Source attribution profiling of five species of Amanita mushrooms from four European countries was performed using Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS) combined with multivariate statistical analysis. Initially, species determination was carried out morphologically and was verified by DNA-analysis. This data was then combined with chemical profiling, generated from LC-HRMS full scan analysis. The untargeted data was processed and the 720 most abundant peaks in the LC-HRMS chromatogram were used to build a multivariate PLS-DA model...
August 15, 2018: Talanta
https://www.readbyqxmd.com/read/29784069/first-molecular-phylogeny-of-agrilus-coleoptera-buprestidae-the-largest-genus-on-earth-with-dna-barcode-database-for-forestry-pest-diagnostics
#9
I Kelnarova, E Jendek, V V Grebennikov, L Bocak
All more than 3000 species of Agrilus beetles are phytophagous and some cause economically significant damage to trees and shrubs. Facilitated by international trade, Agrilus species regularly invade new countries and continents. This necessitates a rapid identification of Agrilus species, as the first step for subsequent protective measures. This study provides the first DNA reference library for ~100 Agrilus species from the Northern Hemisphere based on three mitochondrial markers: cox1-5' (DNA barcode fragment), cox1-3', and rrnL...
May 22, 2018: Bulletin of Entomological Research
https://www.readbyqxmd.com/read/29783865/flow-cytometry-based-epitope-binning-using-competitive-binding-profiles-for-the-characterization-of-monoclonal-antibodies-against-cellular-and-soluble-protein-targets
#10
Brian M Chan, Anita Badh, Kelly A Berry, Stephanie A Grauer, Chadwick T King
A key step in the therapeutic antibody drug discovery process is early identification of diverse candidate molecules. Information comparing antibody binding epitopes can be used to classify antibodies within a large panel, guiding rational lead molecule selection. We describe a novel epitope binning method utilizing high-throughput flow cytometry (HTFC) that leverages cellular barcoding or spectrally distinct beads to multiplex samples to characterize antibodies raised against cell membrane receptor or soluble protein targets...
May 1, 2018: SLAS Discovery
https://www.readbyqxmd.com/read/29783021/a-hyper-diverse-genus-of-acanthocephalans-revealed-by-tree-based-and-non-tree-based-species-delimitation-methods-ten-cryptic-species-of-neoechinorhynchus-in-middle-american-freshwater-fishes
#11
Carlos Daniel Pinacho-Pinacho, Martín García-Varela, Ana L Sereno-Uribe, Gerardo Pérez-Ponce de León
The genus Neoechinorhynchus represents a hyper-diverse group of acanthocephalans, parasites of fresh and brackish water fish and freshwater turtles, with approximately 116 species described worldwide. Forty-nine species have been recorded in the Americas, nine of them in Middle America. Even though species delimitation methods using DNA sequences have been rarely used for parasitic helminths, the genetic library for species of Neoechinorhynchus has grown in the past few years, enhancing the possibility of using these methods for inferring evolutionary relationships and for establishing more robust species boundaries...
May 18, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29782489/systematic-identification-of-factors-mediating-accelerated-mrna-degradation-in-response-to-changes-in-environmental-nitrogen
#12
Darach Miller, Nathan Brandt, David Gresham
Cellular responses to changing environments frequently involve rapid reprogramming of the transcriptome. Regulated changes in mRNA degradation rates can accelerate reprogramming by clearing or stabilizing extant transcripts. Here, we measured mRNA stability using 4-thiouracil labeling in the budding yeast Saccharomyces cerevisiae during a nitrogen upshift and found that 78 mRNAs are subject to destabilization. These transcripts include Nitrogen Catabolite Repression (NCR) and carbon metabolism mRNAs, suggesting that mRNA destabilization is a mechanism for targeted reprogramming of the transcriptome...
May 21, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29781987/retrospective-microrna-sequencing-complementary-dna-library-preparation-protocol-using-formalin-fixed-paraffin-embedded-rna-specimens
#13
Olivier Loudig, Christina Liu, Thomas Rohan, Iddo Z Ben-Dov
-Archived, clinically classified formalin-fixed paraffin-embedded (FFPE) tissues can provide nucleic acids for retrospective molecular studies of cancer development. By using non-invasive or pre-malignant lesions from patients who later develop invasive disease, gene expression analyses may help identify early molecular alterations that predispose to cancer risk. It has been well described that nucleic acids recovered from FFPE tissues have undergone severe physical damage and chemical modifications, which make their analysis difficult and generally requires adapted assays...
May 5, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29780268/filling-the-bins-of-life-report-of-an-amphibian-and-reptile-survey-of-the-tanintharyi-tenasserim-region-of-myanmar-with-dna-barcode-data
#14
Daniel G Mulcahy, Justin L Lee, Aryeh H Miller, Mia Chand, Myint Kyaw Thura, George R Zug
Despite threats of species extinctions, taxonomic crises, and technological advances in genomics and natural history database informatics, we are still distant from cataloguing all of the species of life on earth. Amphibians and reptiles are no exceptions; in fact new species are described nearly every day and many species face possible extinction. The number of described species continues to climb as new areas of the world are explored and as species complexes are examined more thoroughly. The use of DNA barcoding provides a mechanism for rapidly estimating the number of species at a given site and has the potential to record all of the species of life on Earth...
2018: ZooKeys
https://www.readbyqxmd.com/read/29779722/the-impact-of-using-an-intravenous-workflow-management-system-ivwms-on-cost-and-patient-safety
#15
Alex C Lin, Yihong Deng, Hilal Thaibah, John Hingl, Jonathan Penm, Marianne F Ivey, Mark Thomas
PURPOSE: The aim of this study was to determine the financial costs associated with wasted and missing doses before and after the implementation of an intravenous workflow management system (IVWMS) and to quantify the number and the rate of detected intravenous (IV) preparation errors. METHOD: A retrospective analysis of the sample hospital information system database was conducted using three months of data before and after the implementation of an IVWMS System (DoseEdge® ) which uses barcode scanning and photographic technologies to track and verify each step of the preparation process...
July 2018: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/29774898/chiroptical-methods-in-a-wide-wavelength-range-for-obtaining-ln-3-complexes-with-circularly-polarized-luminescence-of-practical-interest
#16
Marcin Górecki, Luca Carpita, Lorenzo Arrico, Francesco Zinna, Lorenzo Di Bari
We studied enantiopure chiral trivalent lanthanide (Ln3+ = La3+, Sm3+, Eu3+, Gd3+, Tm3+, and Yb3+) complexes with two fluorinated achiral tris(β-diketonate) ligands (HFA = hexafluoroacetylacetonate and TTA = 2-thenoyltrifluoroacetonate), incorporating a chiral bis(oxazolinyl)pyridine (PyBox) unit as a neutral ancillary ligand, by the combined use of optical and chiroptical methods, ranging from UV to IR both in absorption and circular dichroism (CD), and including circularly polarized luminescence (CPL). Ultimately, all the spectroscopic information is integrated into a total and a chiroptical super-spectrum, which allows one to characterize a multidimensional chemical space, spanned by the different Ln3+ ions, the acidity and steric demand of the diketone and the chirality of the PyBox ligand...
May 18, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29774786/comparison-of-three-molecular-methods-for-species-identification-of-the-family-cichlidae-in-kwan-phayao-thailand
#17
Dutrudi Panprommin, Kanyanat Soontornprasit, Tanapat Pangeson
The species diversity of cichlids was investigated in Kwan Phayao from August 2016 to May 2017. Four cichlid species were found, including Oreochromis niloticus, Oreochromis mossambicus, Coptodon rendalli and Coptodon zillii. Due to similar characterizations, it is very difficult to identify each species. Three molecular methods were used to distinguish these four species. DNA barcodes or partial cytochrome c oxidase I (COI) gene sequences were amplified by PCR and sequenced. In Oreochromis sp. and Coptodon sp...
May 18, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29773077/aedes-vittatus-in-spain-current-distribution-barcoding-characterization-and-potential-role-as-a-vector-of-human-diseases
#18
Alazne Díez-Fernández, Josué Martínez-de la Puente, Santiago Ruiz, Rafael Gutiérrez-López, Ramón Soriguer, Jordi Figuerola
BACKGROUND: Aedes vittatus is currently found in Africa, Asia and Europe, where it acts as a vector of pathogens causing animal and human diseases (e.g. chikungunya, Zika and dengue). Like other Aedes species, Ae. vittatus is able to breed in artificial containers. The ECDC has recently highlighted the need for molecular tools (i.e. barcoding characterization) that enable Aedes species to be identified in entomological surveys. RESULTS: We sampled mosquito larvae and adults in southern Spain and used a molecular approach to amplify and sequence a fragment of the cytochrome c oxidase subunit 1 gene (barcoding region) of the mosquitoes...
May 18, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29769836/a-revision-of-the-cleptoparasitic-bee-genus-epeolus-latreille-for-nearctic-species-north-of-mexico-hymenoptera-apidae
#19
Thomas M Onuferko
Herein, the cleptoparasitic (cuckoo) bee genus Epeolus (Hymenoptera: Apidae) is revised for species occurring in North America, north of Mexico, and an updated checklist of all species known to occur in Canada and the United States of America is provided with comprehensive descriptions, diagnoses, and a single dichotomous key (using the same couplets for both sexes) to aid in their identification. To increase their recognition among North American naturalists, English common names are also proposed for all North American Epeolus ...
2018: ZooKeys
https://www.readbyqxmd.com/read/29769698/mutation-screening-using-formalin-fixed-paraffin-embedded-tissues-a-stratified-approach-according-to-dna-quality
#20
Francesco Cucco, Alexandra Clipson, Hannah Kennedy, Joe Sneath Thompson, Ming Wang, Sharon Barrans, Moniek van Hoppe, Eguzkine Ochoa Ruiz, Josh Caddy, Debbie Hamid, Thomas Cummin, Cathy Burton, Andrew J Davies, Peter Johnson, Ming-Qing Du
DNA samples from formalin-fixed paraffin-embedded tissues are highly degraded with variable quality, and this imposes a big challenge for targeted sequencing due to false positives, largely caused by PCR errors and cytosine deamination. To eliminate false positives, a common practice is to validate the detected variants by Sanger sequencing or perform targeted sequencing in duplicate. Technically, PCR errors could be removed by molecular barcoding of template DNA prior to amplification as in the HaloPlexHS design...
May 16, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
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