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https://www.readbyqxmd.com/read/28635635/identifying-bird-remains-using-ancient-dna-barcoding
#1
Love Dalén, Vendela K Lagerholm, Johan A A Nylander, Nick Barton, Zbigniew M Bochenski, Teresa Tomek, David Rudling, Per G P Ericson, Martin Irestedt, John R Stewart
Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28634359/infections-of-horses-and-shrews-with-bornaviruses-in-upper-austria-a-novel-endemic-area-of-borna-disease
#2
Herbert Weissenböck, Zoltán Bagó, Jolanta Kolodziejek, Barbara Hager, Günter Palmetzhofer, Ralf Dürrwald, Norbert Nowotny
Borna disease, a lethal infection with Borna disease virus-1 (BoDV-1), was diagnosed in four horses from Upper Austria in 2015 and 2016. All cases occurred in winter (two cases in February 2015 and two cases in December 2016), and the maximal distance of the affected stables was 17 km. To demonstrate whether the causative agent was also harbored by its reservoir host, the bicolored white-toothed shrew (Crocidura leucodon), 28 shrews from this geographic area were collected in 2015 and investigated for the presence of BoDV-1...
June 21, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/28633080/disruptive-non-disruptive-applications-of-crispr-cas9
#3
REVIEW
Jonathan L Schmid-Burgk
The bacterial type II Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR Associated (Cas) systems, and in particular Streptococcus pyogenes CRISPR-Cas9, have been broadly applied to edit the genome of bacterial and eukaryotic cells. Cas9, which is an RNA-guided programmable nuclease, is a powerful tool for disrupting protein-coding genes. Cas9 cleaves target sites to generate a double-strand break (DSB) that is repaired via an error-prone repair process, leading to insertion/deletion mutations and gene knockouts...
June 17, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28631933/a-salt-reduction-smartphone-app-supports-lower-salt-food-purchases-for-people-with-cardiovascular-disease-findings-from-the-saltswitch-randomised-controlled-trial
#4
Helen Eyles, Rebecca McLean, Bruce Neal, Yannan Jiang, Robert N Doughty, Rachael McLean, Cliona Ni Mhurchu
Background SaltSwitch is an innovative smartphone application (app) that enables shoppers to scan the barcode of a packaged food and receive an immediate, interpretive, traffic light nutrition label on the screen, along with suggestions for lower salt alternatives. Our aim was to determine the effectiveness of SaltSwitch to support people with cardiovascular disease to make lower salt food choices. Design Six-week, two-arm, parallel, randomised controlled trial in Auckland, New Zealand (2 weeks baseline and 4 weeks intervention)...
January 1, 2017: European Journal of Preventive Cardiology
https://www.readbyqxmd.com/read/28630464/rapid-monoisotopic-cisplatin-based-barcoding-for-multiplexed-mass-cytometry
#5
Ryan L McCarthy, Duncan H Mak, Jared K Burks, Michelle C Barton
Mass cytometry presents an exceptional opportunity to interrogate the biology of highly heterogeneous cell populations, owing to the ability to collect highly parametric proteomic data at a single cell level. However, sample-to-sample variability, due to antibody staining and/or instrument sensitivity, can introduce substantial artifacts into the data, which can in turn lead to erroneous conclusions. This variability can be eliminated by sample barcoding which enables samples to be pooled, stained and run simultaneously...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28629531/survey-of-traditional-dai-medicine-reveals-species-confusion-and-potential-safety-concerns-a-case-study-on-radix-clerodendri-japonicum
#6
Bao-Zhong Duan, Hai-Lan Fang, Xi-Wen Li, Lin-Fang Huang, Wang Ping, Shi-Lin Chen
The adulteration of herbal products is a threat to consumer safety. In the present study, we surveyed the species composition of commercial Radix Clerodendri Japonicum products using DNA barcoding as a supervisory method. A reference database for plant-material DNA-barcode was successfully constructed with 48 voucher samples from 12 Clerodendrum species. The database was used to identify 27 Radix Clerodendri Japonicum decoction piece samples purchased from drug stores and hospitals. The DNA sequencing results revealed that only 1 decoction piece (3...
June 2017: Chinese Journal of Natural Medicines
https://www.readbyqxmd.com/read/28629429/linked-read-sequencing-resolves-complex-genomic-rearrangements-in-gastric-cancer-metastases
#7
Stephanie U Greer, Lincoln D Nadauld, Billy T Lau, Jiamin Chen, Christina Wood-Bouwens, James M Ford, Calvin J Kuo, Hanlee P Ji
BACKGROUND: Genome rearrangements are critical oncogenic driver events in many malignancies. However, the identification and resolution of the structure of cancer genomic rearrangements remain challenging even with whole genome sequencing. METHODS: To identify oncogenic genomic rearrangements and resolve their structure, we analyzed linked read sequencing. This approach relies on a microfluidic droplet technology to produce libraries derived from single, high molecular weight DNA molecules, 50 kb in size or greater...
June 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28624254/-of-corkscrews-and-barcodes
#8
EDITORIAL
P Assouly
No abstract text is available yet for this article.
June 14, 2017: Annales de Dermatologie et de Vénéréologie
https://www.readbyqxmd.com/read/28623498/minimal-barcode-distance-between-two-water-mite-species-from-madeira-island-a-cautionary-tale
#9
Ricardo García-Jiménez, Jose Luis Horreo, Antonio G Valdecasas
In this work, we compare morphological and molecular data in their ability to distinguish between species of water mites (Acari, Prostigmata, Hydrachnidia). We have focused on the two species of the genus Lebertia inhabiting the island of Madeira. While traditional morphological traits were initially sufficient to distinguish between these two species, the molecular data were more dependable on the kind of analysis carried out. Single arbitrary genetic distance (e.g. a K2P distance below 2%) may lead to the conclusion that the specimens under study belong to the same species...
June 16, 2017: Experimental & Applied Acarology
https://www.readbyqxmd.com/read/28622748/dna-barcoding-of-five-species-of-groupers-pisces-serranidae-off-visakhapatnam-central-eastern-coast-of-india
#10
Vaddiparti Iswarya Deepti, Sujatha Kandula, G D Khedkar
Grouper species of Epinephelus - E. epistictus, E. heniochus, E. latifasciatus, E. magniscuttis and E. radiatus exhibit overlapping colour pattern that often leads to misidentification in the field. Even the colour pattern of juveniles of these species in different size groups varies considerably with that of adults. DNA barcoding of these five species was carried out to reinforce our knowledge on existing taxonomic relationships derived based on morphological and biochemical genetic studies that were previously done from Indian waters...
June 16, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28622375/identification-of-benthic-diatoms-isolated-from-the-eastern-tidal-flats-of-the-yellow-sea-comparison-between-morphological-and-molecular-approaches
#11
Sung Min An, Dong Han Choi, Jung Ho Lee, Howon Lee, Jae Hoon Noh
Benthic diatoms isolated from tidal flats in the west coast of Korea were identified through both traditional morphological method and molecular phylogenetic method for methodological comparison. For the molecular phylogenetic analyses, we sequenced the 18S rRNA and the ribulose bisphosphate carboxylase large subunit coding gene, rbcL. Further, the comparative analysis allowed for the assessment of the suitability as a genetic marker for identification of closely related benthic diatom species and as potential barcode gene...
2017: PloS One
https://www.readbyqxmd.com/read/28620408/quality-control-of-the-traditional-patent-medicine-yimu-wan-based-on-smrt-sequencing-and-dna-barcoding
#12
Jing Jia, Zhichao Xu, Tianyi Xin, Linchun Shi, Jingyuan Song
Substandard traditional patent medicines may lead to global safety-related issues. Protecting consumers from the health risks associated with the integrity and authenticity of herbal preparations is of great concern. Of particular concern is quality control for traditional patent medicines. Here, we establish an effective approach for verifying the biological composition of traditional patent medicines based on single-molecule real-time (SMRT) sequencing and DNA barcoding. Yimu Wan (YMW), a classical herbal prescription recorded in the Chinese Pharmacopoeia, was chosen to test the method...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28620101/barcodes-show-family-trees-in-all
#13
Jonas Larsson
No abstract text is available yet for this article.
June 15, 2017: Blood
https://www.readbyqxmd.com/read/28616174/spatial-overlap-of-shark-nursery-areas-and-the-salmon-farming-industry-influences-the-trophic-ecology-of-squalus-acanthias-on-the-southern-coast-of-chile
#14
Juan Diego Gaitán-Espitia, Daniela Gómez, Alistair J Hobday, Ross Daley, Julio Lamilla, Leyla Cárdenas
Potential interactions between marine predators and humans arise in the southern coast of Chile where predator feeding and reproduction sites overlap with fisheries and aquaculture. Here, we assess the potential effects of intensive salmon aquaculture on food habits, growth, and reproduction of a common predator, the spiny dogfish-identified as Squalus acanthias via genetic barcoding. A total of 102 (89 females and 13 males) individuals were collected during winter and summer of 2013-2014 from the Chiloé Sea where salmon aquaculture activities are concentrated...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28613121/experiences-in-running-a-complex-electronic-data-capture-system-using-mobile-phones-in-a-large-scale-population-trial-in-southern-nepal
#15
Sarah Style, B James Beard, Helen Harris-Fry, Aman Sengupta, Sonali Jha, Bhim P Shrestha, Anjana Rai, Vikas Paudel, Meelan Thondoo, Anni-Maria Pulkki-Brannstrom, Jolene Skordis-Worrall, Dharma S Manandhar, Anthony Costello, Naomi M Saville
The increasing availability and capabilities of mobile phones make them a feasible means of data collection. Electronic Data Capture (EDC) systems have been used widely for public health monitoring and surveillance activities, but documentation of their use in complicated research studies requiring multiple systems is limited. This paper shares our experiences of designing and implementing a complex multi-component EDC system for a community-based four-armed cluster-Randomised Controlled Trial in the rural plains of Nepal, to help other researchers planning to use EDC for complex studies in low-income settings...
2017: Global Health Action
https://www.readbyqxmd.com/read/28611392/targeted-sequencing-of-both-dna-strands-barcoded-and-captured-individually-by-rna-probes-to-identify-genome-wide-ultra-rare-mutations
#16
Qing Wang, Xu Wang, Pheobe S Tang, Grace M O'leary, Ming Zhang
Next Generation Sequencing (NGS) has been widely implemented in biological research and has made a profound impact on patient care. One of the essential NGS applications is to identify disease-causing sequence variants, where high coverage and accuracy are needed. Here, we reported a novel NGS pipeline, termed a Sequencing System of Digitalized Barcode Encrypted Single-stranded Library from Extremely Low (quality and quantity) DNA Input with Probe-based DNA Enrichment by RNA probes targeting DNA duplex (DEEPER-Seq)...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28611359/chloroplast-genomic-resource-of-paris-for-species-discrimination
#17
Yun Song, Shaojun Wang, Yuanming Ding, Jin Xu, Ming Fu Li, Shuifang Zhu, Naizhong Chen
Paris is famous in China for its medicinal value and has been included in the Chinese Pharmacopoeia. Inaccurate identification of these species could confound their effective exploration, conservation, and domestication. Due to the plasticity of the morphological characteristics, correct identification among Paris species remains problematic. In this regard, we report the complete chloroplast genome of P. thibetica and P. rugosa to develop highly variable molecular markers. Comparing three chloroplast genomes, we sought out the most variable regions to develop the best cpDNA barcodes for Paris...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28610586/genotyping-of-high-risk-anal-human-papillomavirus-hpv-ion-torrent-next-generation-sequencing-vs-linear-array
#18
Rebecca G Nowak, Nicholas P Ambulos, Lisa M Schumaker, Trevor J Mathias, Ruth A White, Jennifer Troyer, David Wells, Manhattan E Charurat, Søren M Bentzen, Kevin J Cullen
BACKGROUND: Our next generation sequencing (NGS)-based human papillomavirus (HPV) genotyping assay showed a high degree of concordance with the Roche Linear Array (LA) with as little as 1.25 ng formalin-fixed paraffin-embedded-derived genomic DNA in head and neck and cervical cancer samples. This sensitive genotyping assay uses barcoded HPV PCR broad-spectrum general primers 5+/6+ (BSGP)5+/6+ applicable to population studies, but it's diagnostic performance has not been tested in cases with multiple concurrent HPV infections...
June 13, 2017: Virology Journal
https://www.readbyqxmd.com/read/28610230/-i-lampetra-i-i-soljani-i-a-new-brook-lamprey-from-the-southern-adriatic-sea-basin-petromyzontiformes-petromyzontidae
#19
Pero Tutman, Jörg Freyhof, Jakov Dulčić, Branko Glamuzina, Matthias Geiger
Lampetra soljani, new species, is described from the lower Neretva River in the Adriatic Sea basin. Previously it was identified as L. zanandreai. Based on morphological similarity and mitochondrial genetic data, it is related to L. lanceolata and L. ninae from the Black Sea basin. Lampetra soljani is distinguished from all other species of Lampetra by having a marmorate flank pattern in live, fully grown ammocoetes, and in some adults (vs. plain colour pattern). Lampetra soljani is distinguished from other Lampetra species by having three velar tentacles, 54-57 trunk myomeres between the last branchial opening and the anus, no posterial teeth and a bicuspid middle endolateral tooth...
June 7, 2017: Zootaxa
https://www.readbyqxmd.com/read/28610228/pipunculidae-diptera-from-southern-iran-including-two-new-species-of-the-genus-i-tomosvaryella-i-acz%C3%A3-l
#20
Bahareh Majnon-Jahromi, Mehdi Gheibi, Majid Fallahzadeh, Christian Kehlmaier, Shahram Hesami
We provide data on the distribution of 23 big-headed fly species (Diptera: Brachycera: Pipunculidae) from Fars province, southern Iran. Two new species of the genus Tomosvaryella Aczél, T. angulata sp. nov. and T. pistacia sp. nov., are described and illustrated. The new species show a clear morphological affiliation to the T. congoana species-group that was hitherto only known from the Afrotropical region. Nine species recorded herein represent first records for Iran. The number of pipunculid species recorded from Iran is now raised to 30...
June 7, 2017: Zootaxa
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