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Yong Cai, Xiwen Li, Runmiao Wang, Qing Yang, Peng Li, Hao Hu
Currently, the chemical fingerprint comparison and analysis is mainly based on professional equipment and software, it's expensive and inconvenient. This study aims to integrate QR (Quick Response) code with quality data and mobile intelligent technology to develop a convenient query terminal for tracing quality in the whole industrial chain of TCM (traditional Chinese medicine). Three herbal medicines were randomly selected and their chemical two-dimensional barcode (2D) barcodes fingerprints were constructed...
2016: PloS One
Laura Brueckner, Joris van Arensbergen, Waseem Akhtar, Ludo Pagie, Bas van Steensel
BACKGROUND: Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest. The assay combines a previously reported multiplexing strategy based on barcoded randomly integrated reporters with Gal4-mediated tethering. We applied the assay to Drosophila heterochromatin protein 1a (HP1a), which is mostly known as a repressive protein but has also been linked to transcriptional activation...
2016: Epigenetics & Chromatin
Anders Bjørnsgaard Aas, Marie Louise Davey, Håvard Kauserud
The formation of chimeric sequences can create significant methodological bias in PCR-based DNA metabarcoding analyses. During mixed-template amplification of barcoding regions, chimera formation is frequent and well documented. However, profiling of fungal communities typically uses the more variable rDNA region ITS. Due to a larger research community, tools for chimera detection have been developed mainly for the 16S/18S markers. However, these tools are widely applied to the ITS region without verification of their performance...
October 24, 2016: Molecular Ecology Resources
Davin Edric V. Adao, Ace O. Dela Serna, Maria Luz B. Belleza, Nicole R. Bolo, Windell L. Rivera
Blastocystis sp. is a commonly reported enteric protistan parasite in faecal specimens with a worldwide distribution afflicting both humans and a wide range of animals. The aim of this study is to characterize the subtypes (STs) of Blastocystis sp. isolates from asymptomatic individuals in an urban community in Pateros, Metro Manila, Philippines. The 600-bp small subunit ribosomal RNA (SSU rRNA) barcoding region of Blastocystis sp. isolates was amplified and sequenced using the primers RD5 and BhRDr. Subtypes were identified by uploading the sequences onto the Basic Local Alignment and Search Tool (BLAST) websites, the Blastocystis Subtype (18S) and Sequence Typing (MLST) Database and by construction of a phylogenetic tree...
October 1, 2016: Annals of Parasitology
Jahir Orozco, Elisa Villa, Carmem-Lara Manes, Linda K Medlin, Delphine Guillebault
Harmful algal blooms (HABs) are becoming more frequent as climate changes, with tropical species moving northward. Monitoring programs detecting the presence of toxic algae before they bloom are of paramount importance to protect aquatic ecosystems, aquaculture, human health and local economies. Rapid and reliable species identification methods using molecular barcodes coupled to biosensor detection tools have received increasing attention over the past decade as an alternative to the impractical standard microscopic counting-based techniques...
December 1, 2016: Talanta
Abdolbaset Ghorbani, Barbara Gravendeel, Sugirthini Selliah, Shahin Zarré, Hugo de Boer
Tubers of terrestrial orchids are harvested and traded from the eastern Mediterranean to the Caspian Sea for the traditional product Salep. Over-exploitation of wild populations and increased middle-class prosperity have escalated prices for Salep, causing overharvesting, depletion of native populations and providing an incentive to expand harvesting to untapped areas in Iran. Limited morphological distinctiveness among traded Salep tubers renders species identification impossible, making it difficult to establish which species are targeted and affected the most...
October 21, 2016: Molecular Ecology Resources
Stefan Schmidt, Andreas Taeger, Jérôme Morinière, Andrew Liston, Stephan M Blank, Katja Kramp, Manfred Kraus, Olga Schmidt, Erik Heibo, Marko Prous, Tommi Nyman, Tobias Malm, Julie Stahlhut
The 'Symphyta' is a paraphyletic assemblage at the base of the order Hymenoptera, comprising 14 families and about 8,750 species. All have phytophagous larvae, except for the Orussidae, which are parasitoids. This study presents and evaluates the results of DNA barcoding of approximately 5,360 specimens of 'Symphyta', mainly adults, and 4,362 sequences covering 1,037 species were deemed of suitable quality for inclusion in the analysis. All extant families are represented, except for the Anaxyelidae. The majority of species and specimens are from Europe, but approximately 38% of the species and 13% of the specimens are of non-European origin...
October 21, 2016: Molecular Ecology Resources
Joanne E Littlefair, Elizabeth L Clare
Society faces the complex challenge of supporting biodiversity and ecosystem functioning, while ensuring food security by providing safe traceable food through an ever-more-complex global food chain. The increase in human mobility brings the added threat of pests, parasites, and invaders that further complicate our agro-industrial efforts. DNA barcoding technologies allow researchers to identify both individual species, and, when combined with universal primers and high-throughput sequencing techniques, the diversity within mixed samples (metabarcoding)...
September 2, 2016: Genome Génome / Conseil National de Recherches Canada
Vernon G Thomas, Robert H Hanner, Alex V Borisenko
Managing invasive alien species in Canada requires reliable taxonomic identification as the basis of rapid-response management. This can be challenging, especially when organisms are small and lack morphological diagnostic features. DNA-based techniques, such as DNA barcoding, offer a reliable, rapid, and inexpensive toolkit for taxonomic identification of individual or bulk samples, forensic remains, and even environmental DNA. Well suited for this requirement, they could be more broadly deployed and incorporated into the operating policy and practices of Canadian federal departments and should be authorized under these agencies' articles of law...
July 19, 2016: Genome Génome / Conseil National de Recherches Canada
Saroj Rajvanshi, Kirti Choudhary, Nirupama Agrawal
The protein encoding zone of Mitochondrial DNA region (inherited from single lineage) seems most suitable and effective for taxonomic, systematic, ecological, evolutionary, DNA barcoding, cryptic species and population studies, exploiting nucleotide/amino acid datasets (1D/2D/3D conformational level). Nowadays, expeditious computerized methods are in trend for analyzing genetic material to demonstrate variations at various levels of protein structures. Structural proteomics have implemented here for genetic identification, differentiation and relationship of species from information rich data of mt COI gene of the family Diplostomidae with inclusion of molecular tools...
October 17, 2016: Experimental Parasitology
Christoph Baldow, Lars Thielecke, Ingmar Glauche
The availability of several methods to unambiguously mark individual cells has strongly fostered the understanding of clonal developments in hematopoiesis and other stem cell driven regenerative tissues. While cellular barcoding is the method of choice for experimental studies, patients that underwent gene therapy carry a unique insertional mark within the transplanted cells originating from the integration of the retroviral vector. Close monitoring of such patients allows accessing their clonal dynamics, however, the early detection of events that predict monoclonal conversion and potentially the onset of leukemia are beneficial for treatment...
2016: PloS One
Vazrick Nazari, B Christian Schmidt, Sean Prosser, Paul D N Hebert
Analysis of the DNA barcode region of the cytochrome c oxidase 1 gene from a specimen of the extinct Jamaican sunset moth, Urania sloanus, places this species as a sister to the Central American U. fulgens. We found that all Urania F. species were closely related (<2.8% maximum divergence at COI), with the Cuban endemic U. boisduvalii appearing as sister to the rest. The low divergence in DNA barcodes and genitalic structures indicate that the Cuban U. poeyi and eastern Brazilian U. brasiliensis are geographic segregates of U...
2016: PloS One
Guilhem Sommeria-Klein, Lucie Zinger, Pierre Taberlet, Eric Coissac, Jérôme Chave
The DNA present in the environment is a unique and increasingly exploited source of information for conducting fast and standardized biodiversity assessments for any type of organisms. The datasets resulting from these surveys are however rarely compared to the quantitative predictions of biodiversity models. In this study, we simulate neutral taxa-abundance datasets, and artificially noise them by simulating noise terms typical of DNA-based biodiversity surveys. The resulting noised taxa abundances are used to assess whether the two parameters of Hubbell's neutral theory of biodiversity can still be estimated...
October 20, 2016: Scientific Reports
Aleksandra Biedrzycka, Alvaro Sebastian, Magdalena Migalska, Helena Westerdahl, Jacek Radwan
Characterisation of highly duplicated genes, such as genes of the major histocompatibility complex (MHC), where multiple loci often co-amplify, has until recently been hindered by insufficient read depths per amplicon. Here we used ultra-deep Illumina sequencing to resolve genotypes at exon 3 of MHC class I genes in the sedge warbler (Acrocephalus schoenobaenus). We sequenced 24 individuals in two replicates and used this data, as well as a simulated dataset, to test the effect of amplicon coverage (range: 500-20 000 reads per amplicon) on the repeatability of genotyping using four different genotyping approaches...
October 19, 2016: Molecular Ecology Resources
Séverine Fourdrilis, Patrick Mardulyn, Olivier J Hardy, Kurt Jordaens, António Manuel de Frias Martins, Thierry Backeljau
We report the presence of mitochondrial DNA (mtDNA) hyperdiversity in the marine periwinkle Melarhaphe neritoides (Linnaeus, 1758), the first such case among marine gastropods. Our dataset consisted of concatenated 16S-COI-Cytb gene fragments. We used Bayesian analyses to investigate three putative causes underlying genetic variation, and estimated the mtDNA mutation rate, possible signatures of selection and the effective population size of the species in the Azores archipelago. The mtDNA hyperdiversity in M...
2016: PeerJ
Alba Ardura, Elvira Morote, Marc Kochzius, Eva Garcia-Vazquez
Mid-trophic pelagic fish are essential components of marine ecosystems because they represent the link between plankton and higher predators. Moreover, they are the basis of the most important fisheries resources; for example, in African waters. In this study, we have sampled pelagic fish larvae in the Eastern Atlantic Ocean along a latitudinal gradient between 37°N and 2°S. We have employed Bongo nets for plankton sampling and sorted visually fish and fish larvae. Using the cytochrome oxidase I gene (COI) as a DNA barcode, we have identified 44 OTUs down to species level that correspond to 14 families, with Myctophidae being the most abundant...
2016: PeerJ
Nhu Nguyen, Else C Vellinga, Thomas D Bruns, Peter Kennedy
The genus Suillus represents one of the most recognizable groups of mushrooms in conifer forests throughout the Northern Hemisphere. Although for decades the genus has been relatively well defined morphologically, previous molecular phylogenetic assessments have provided important yet preliminary insights into its evolutionary history. Here we present the first large-scale phylogenetic study of the boundaries of each species in the genus Suillus based on the most current internal transcribed spacer (ITS) barcode sequences available in public databases, as well as sequencing of 224 vouchered specimens and cultures, 15 of which were type specimens from North America...
October 19, 2016: Mycologia
Maria Desterro Santos, Maria Esther Fonseca-Boiteux, Leonardo Silva Boiteux, Paulo Eduardo Câmara, Jose Carmine Dianese
Nine Phyllachora species found on hosts belonging to the family Myrtaceae native to the Brazilian Cerrado were described and illustrated. We sequenced nuc rDNA internal transcribed spacer barcode regions for representatives of seven species and conducted phylogenetic analyses, which provided strong support for four new species that we describe as Phyllachora cerradensis, P. ermidensis, P. furnasensis, and P. myrciariae Catacauma nigerrimum was recombined into P. nigerrima, and a key to the common Phyllachora species on myrtaceous hosts from the Brazilian Cerrado was also included...
October 19, 2016: Mycologia
Mahsa Jalali, Ye Yu, Kaichen Xu, Ray J H Ng, Zhaogang Dong, Liancheng Wang, Saman Safari Dinachali, Minghui Hong, Joel K W Yang
Color printing with plasmonic resonators can overcome limitations in pigment-based printing approaches. While layering in pigment-based prints results in familiar color mixing effects, the color effects of stacking plasmonic resonator structures have not been investigated. Here, we demonstrate an experimental strategy to fabricate a 3-tiered complex superlattice of nanostructures with multiple sets of building blocks. Laser interference lithography was used to fabricate the nanostructures and a thin-layer of aluminum was deposited to introduce plasmonic colors...
October 19, 2016: Nanoscale
Boris A Levin, Evgeniy Simonov, Michael P Matveyev, Oleg N Artaev, Namig J Mustafayev, Andrey N Pashkov, Haikaz R Roubenyan
Spirlins of the genus Alburnoides are widespread fishes, which taxonomy has been rapidly developing in recent years. Mitochondrial cytochrome c oxidase subunit I (COI) was used as DNA barcode marker to create a reference dataset of Caucasian Alburnoides and to test its barcoding efficiency. All four previously known Caucasian species of Alburnoides were confirmed as valid species with high genetic distances to sister species as well confirmed as Caucasian endemics. Alburnoides samiii, previously known from Sefidroud basin (Iran), was discovered in Transcaucasia...
October 19, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
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