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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
#1
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/29782489/systematic-identification-of-factors-mediating-accelerated-mrna-degradation-in-response-to-changes-in-environmental-nitrogen
#2
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
#3
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/29774786/comparison-of-three-molecular-methods-for-species-identification-of-the-family-cichlidae-in-kwan-phayao-thailand
#4
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
#5
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
#6
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
#7
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
https://www.readbyqxmd.com/read/29767359/simultaneous-multiplexed-detection-of-rna-and-protein-on-the-nanostring-%C3%A2-ncounter-%C3%A2-platform
#8
Sarah Warren
The NanoString nCounter Analysis System uses a digital fluorescent barcode technology that allows for direct multiplexed measurement of gene expression (mRNA), DNA, and protein. The technology uses molecular barcodes and single-molecule imaging to detect and count unique mRNA and protein targets in a single reaction. nCounter-based detection is enzyme-free (no amplification of mRNA is required), fully automated, and allows simultaneous detection of up to 770 mRNA and 30 protein targets from multiple sample types...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29765686/phylogeography-of-hydrothermal-vent-stalked-barnacles-a-new-species-fills-a-gap-in-the-indian-ocean-dispersal-corridor-hypothesis
#9
Hiromi Kayama Watanabe, Chong Chen, Daniel P Marie, Ken Takai, Katsunori Fujikura, Benny K K Chan
Phylogeography of animals provides clues to processes governing their evolution and diversification. The Indian Ocean has been hypothesized as a 'dispersal corridor' connecting hydrothermal vent fauna of Atlantic and Pacific oceans. Stalked barnacles of the family Eolepadidae are common associates of deep-sea vents in Southern, Pacific and Indian oceans, and the family is an ideal group for testing this hypothesis. Here, we describe Neolepas marisindica sp. nov. from the Indian Ocean, distinguished from N. zevinae and N...
April 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29762744/forensically-relevant-blow-flies-in-lebanon-survey-and-identification-using-molecular-markers-diptera-calliphoridae
#10
Salman Shayya, Régis Debruyne, André Nel, Dany Azar
Calliphoridae are among the first insects associated to decomposing animal remains. We have collected 1,841 specimens of three calliphorid genera: Calliphora, Lucilia, and Chrysomya, from different Lebanese localities as a first step in implementing a database of insects of forensic relevance for the country. Blow-flies are crucial for the estimation of the postmortem interval. DNA-based identification is a rapid and accurate method, often used for morphologically similar species, especially for immatures or incomplete specimens...
May 12, 2018: Journal of Medical Entomology
https://www.readbyqxmd.com/read/29757522/evidence-of-natural-wolbachia-infections-and-molecular-identification-of-field-populations-of-culex-pipiens-complex-diptera-culicidae-mosquitoes-in-western-turkey
#11
Burçin Morçiçek, Belgin Gocmen Taskin, Ersin Doğaç, Taylan Doğaroğlu, Vatan Taskin
Establishing reliable risk projection information about the distribution pattern of members of the Culex pipiens complex is of particular interest, as these mosquitoes are competent vectors for certain disease-causing pathogens. Wolbachia, a maternally inherited bacterial symbiont, are distributed in various arthropod species and can induce cytoplasmic incompatibility, i.e., reduced egg hatch, in certain crosses. It is being considered as a tool for population control of mosquito disease vectors. The Aegean region is characterized by highly populated, rural, and agricultural areas and is also on the route of the migratory birds...
June 2018: Journal of Vector Ecology: Journal of the Society for Vector Ecology
https://www.readbyqxmd.com/read/29755504/molecular-identification-of-shark-meat-from-local-markets-in-southern-brazil-based-on-dna-barcoding-evidence-for-mislabeling-and-trade-of-endangered-species
#12
Fernanda Almerón-Souza, Christian Sperb, Carolina L Castilho, Pedro I C C Figueiredo, Leonardo T Gonçalves, Rodrigo Machado, Larissa R Oliveira, Victor H Valiati, Nelson J R Fagundes
Elasmobranchs, the group of cartilaginous fishes that include sharks and rays, are especially vulnerable to overfishing due to low fecundity and late sexual maturation. A significant number of elasmobranch species are currently overexploited or threatened by fisheries activities. Additionally, several recent reports have indicated that there has been a reduction in regional elasmobranch population sizes. Brazil is an important player in elasmobranch fisheries and one of the largest importers of shark meat. However, carcasses entering the shark meat market have usually had their fins and head removed, which poses a challenge to reliable species identification based on the morphology of captured individuals...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29736329/from-water-striders-to-water-bugs-the-molecular-diversity-of-aquatic-heteroptera-gerromorpha-nepomorpha-of-germany-based-on-dna-barcodes
#13
Nadine Havemann, Martin M Gossner, Lars Hendrich, Jèrôme Morinière, Rolf Niedringhaus, Peter Schäfer, Michael J Raupach
With about 5,000 species worldwide, the Heteroptera or true bugs are the most diverse taxon among the hemimetabolous insects in aquatic and semi-aquatic ecosystems. Species may be found in almost every freshwater environment and have very specific habitat requirements, making them excellent bioindicator organisms for water quality. However, a correct determination by morphology is challenging in many species groups due to high morphological variability and polymorphisms within, but low variability between species...
2018: PeerJ
https://www.readbyqxmd.com/read/29736197/xenomonitoring-of-mosquitoes-diptera-culicidae-for-the-presence-of-filarioid-helminths-in-eastern-austria
#14
Sarah Susanne Übleis, Claudia Cuk, Michaela Nawratil, Julia Butter, Ellen Schoener, Adelheid G Obwaller, Thomas Zechmeister, Georg G Duscher, Franz Rubel, Karin Lebl, Carina Zittra, Hans-Peter Fuehrer
Information on mosquito-borne filarioid helminths in Austria is scarce, but recent discoveries of Dirofilaria repens indicate autochthonous distribution of this parasite in Eastern Austria. In the current xenomonitoring study, more than 48,000 mosquitoes were collected in Eastern Austria between 2013 and 2015, using different sampling techniques and storage conditions, and were analysed in pools with molecular tools for the presence of filarioid helminth DNA. Overall, DNA of D. repens , Setaria tundra , and two unknown filarioid helminths were documented in twenty mosquito pools within the mitochondrial cox1 gene (barcode region)...
2018: Canadian Journal of Infectious Diseases & Medical Microbiology
https://www.readbyqxmd.com/read/29732322/a-case-study-on-the-labeling-of-bottarga-produced-in-sardinia-from-ovaries-of-grey-mullets-mugil-cephalus-and-mugil-capurrii-caught-in-eastern-central-atlantic-coasts
#15
Pierluigi Piras, Francesco Sardu, Domenico Meloni, Maria Vittoria Riina, Chiara Beltramo, Pier Luigi Acutis
The aim of this case study is to show how traditional and molecular methods can be employed to identify the Mugilidae species currently used in Sardinia (Italy) to produce the traditional bottarga for the processing of their ovaries. A total of six specimens of Mugil cephalus (n=3) and Mugil capurrii (n=3) were subjected to external morphology and meristic measurements. Subsequently, tissue samples of white muscle and ovaries from three individuals per species were underwent PCR-sequencing assay of mitochondrial DNA cytochrome oxidase subunit I ( COI )...
March 31, 2018: Italian Journal of Food Safety
https://www.readbyqxmd.com/read/29729674/dna-barcoding-and-real-time-pcr-detection-of-bactrocera-xanthodes-tephritidae-diptera-complex
#16
D Li, D W Waite, D N Gunawardana, B McCarthy, D Anderson, A Flynn, S George
Immature fruit fly stages of the family Tephritidae are commonly intercepted on breadfruit from Pacific countries at the New Zealand border but are unable to be identified to the species level using morphological characters. Subsequent molecular identification showed that they belong to Bactrocera xanthodes, which is part of a species complex that includes Bactrocera paraxanthodes, Bactrocera neoxanthodes and an undescribed species. To establish a more reliable molecular identification system for B. xanthodes, a reference database of DNA barcode sequences for the 5'-fragment of COI gene region was constructed for B...
May 6, 2018: Bulletin of Entomological Research
https://www.readbyqxmd.com/read/29722246/-research-progress-on-dna-barcoding-analysis-methods
#17
Qian Qian Yang, Su Wen Liu, Xiao Ping Yu
DNA barcode is a fragment of short DNA sequence from a standard part of the genome. DNA barcoding is an effective taxonomic method for species identification through analyzing the DNA barcodes. With the dramatic increasing of DNA barcode sequences, the analysis methods have developed rapidly, which promoted their applications in molecular identification for organisms. Since 2003, DNA barcoding has been widely used in species identification for animals, plants, fungi, etc. It has also robustly promoted the development of scientific disciplines, such as taxonomy, biodiversity science, and ecology...
March 2018: Ying Yong Sheng Tai Xue Bao, the Journal of Applied Ecology
https://www.readbyqxmd.com/read/29719474/a-revision-of-blanket-hermit-crabs-of-the-genus-paguropsis-henderson-1888-with-the-description-of-a-new-genus-and-five-new-species-crustacea-anomura-diogenidae
#18
Rafael Lemaitre, Dwi Listyo Rahayu, Tomoyuki Komai
For 130 years the diogenid genus Paguropsis Henderson, 1888 was considered monotypic for an unusual species, P. typica Henderson, 1888, described from the Philippines and seldom reported since. Although scantly studied, this species is known to live in striking symbiosis with a colonial sea anemone that the hermit can stretch back and forth like a blanket over its cephalic shield and part of cephalothoracic appendages, and thus the common name "blanket-crab". During a study of paguroid collections obtained during recent French-sponsored biodiversity campaigns in the Indo-West Pacific, numerous specimens assignable to Paguropsis were encountered...
2018: ZooKeys
https://www.readbyqxmd.com/read/29701068/corrigendum-molecular-identification-of-species-of-physalis-solanaceae-using-a-candidate-dna-barcode-the-chloroplast-psba-trnh-intergenic-region
#19
Shangguo Feng, Kaili Jiao, Yujia Zhu, Hongfen Wang, Mengying Jiang, Huizhong Wang
No abstract text is available yet for this article.
April 27, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29695263/dna-barcoding-of-morphologically-characterized-mosquitoes-belonging-to-the-subfamily-culicinae-from-sri-lanka
#20
Thilini Chathurika Weeraratne, Sinnathamby Noble Surendran, S H P Parakrama Karunaratne
BACKGROUND: Vectors of mosquito-borne diseases in Sri Lanka, except for malaria, belong to the subfamily Culicinae, which includes nearly 84% of the mosquito fauna of the country. Hence, accurate and precise species identification of culicine mosquitoes is a crucial factor in implementing effective vector control strategies. During the present study, a combined effort using morphology and DNA barcoding was made to characterize mosquitoes of the subfamily Culicinae for the first time from nine districts of Sri Lanka...
April 25, 2018: Parasites & Vectors
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