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molecular barcoding

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https://www.readbyqxmd.com/read/28734268/dna-barcoding-allows-identification-of-european-fanniidae-diptera-of-forensic-interest
#1
Andrzej Grzywacz, Dominika Wyborska, Marcin Piwczyński
In forensic entomology practice, species identification is a prerequisite for any further analysis of collected material. Although morphology-based taxonomy may be hindered by a range of factors, these are not obstacles for a molecular identification approach, so-called DNA barcoding. The Fanniidae are a dipteran family that is attracted to and breeds in decomposing animal carrion and dead human bodies. However, morphological identification of fanniids, both at adult and immature stages, is considered to be difficult, particularly for non-experts...
June 29, 2017: Forensic Science International
https://www.readbyqxmd.com/read/28717207/barcoding-utility-in-a-mega-diverse-cross-continental-genus-keeping-pace-with-cyrtodactylus-geckos
#2
Ian G Brennan, Aaron M Bauer, Ngo Van Tri, Yun-Yu Wang, Wen-Zhi Wang, Ya-Ping Zhang, Robert W Murphy
Over the past decade, DNA barcoding has become a staple of low-cost molecular systematic investigations. The availability of universal primers and subsidized sequencing projects (PolarBOL, SharkBOL, SpongeBOL) have driven this popularity, often without appropriate investigation into the utility of barcoding data for the taxonomic group of interest. Here, our primary aim is to determine the phylogenetic value of DNA barcoding (mitochondrial locus COI) within the gecko genus Cyrtodactylus. With >40 new species described since last systematic investigation, Cyrtodactylus represents one of the most diverse extant squamate genera, and their contemporary distribution spans the Indian subcontinent, eastward through Indochina, and into AustraloPapua...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716157/advances-and-challenges-in-barcoding-pathogenic-and-environmental-leptospira
#3
Vanina Guernier, Kathryn J Allan, Cyrille Goarant
Leptospirosis is a zoonotic bacterial disease of global importance. A large spectrum of asymptomatic animal hosts can carry the infection and contribute to the burden of human disease. Environmental sources of human contamination also point to the importance of a hydrotelluric reservoir. Leptospirosis can be caused by as many as 15 different pathogenic or intermediate Leptospira species. However, classification of these bacteria remains complicated through the use of both serological and genetic classification systems that show poor correlation...
July 18, 2017: Parasitology
https://www.readbyqxmd.com/read/28708379/chemical-genomics-structure-elucidation-and-in-vivo-studies-of-the-marine-derived-anticlostridial-ecteinamycin
#4
Thomas P Wyche, René F Ramos Alvarenga, Jeff S Piotrowski, Megan N Duster, Simone R Warrack, Gabriel Cornilescu, Travis J De Wolfe, Yanpeng Hou, Doug R Braun, Gregory A Ellis, Scott W Simpkins, Justin Nelson, Chad L Myers, James Steele, Hirotada Mori, Nasia Safdar, John L Markley, Scott Raymond Rajski, Tim S Bugni
A polyether antibiotic, ecteinamycin (1) was isolated from a marine Actinomadura sp., cultivated from the ascidian Ectein-ascidia turbinata. 13C-enrichment, high resolution NMR spectroscopy and molecular modeling enabled elucidation of the structure of 1 which was validated on the basis of comparisons with its recently reported crystal structure. Importantly, ec-teinamycin demonstrated potent activity against the toxigenic strain of Clostridium difficile NAP1/B1/027 (MIC = 59 ng/μL), as well as other toxigenic and non-toxigenic C...
July 14, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28706316/description-of-pseudacrobeles-pseudacrobeles-curvatus-sp-n-cephalobidae-rhabditida-in-south-korea
#5
Jiyeon Kim, Taeho Kim, Joong-Ki Park
Pseudacrobeles (Pseudacrobeles) curvatus sp. n. was collected from potato fields in Gyeongsangnam-do, South Korea. The new species shares morphological characters typical of the genus Pseudacrobeles, including three lateral incisures that fade posteriorly near the phasmid openings. The new species differs from other Pseudacrobeles species by its smaller body size and a comparatively shorter corpus relative to the isthmus length. In this study, we provide a comparison of morphometrics and diagnostic features of Pseudacrobeles species and molecular sequence data from the D2-D3 regions of the 28S ribosomal DNA (rDNA) and ITS1-5...
June 2017: Journal of Nematology
https://www.readbyqxmd.com/read/28688979/remarkable-richness-of-trypanosomes-in-tsetse-flies-glossina-morsitans-morsitans-and-glossina-pallidipes-from-the-gorongosa-national-park-and-niassa-national-reserve-of-mozambique-revealed-by-fluorescent-fragment-length-barcoding-fflb
#6
Herakles A Garcia, Carla M F Rodrigues, Adriana C Rodrigues, Dagmar L Pereira, Carlos L Pereira, Erney P Camargo, P B Hamilton, Marta M G Teixeira
Trypanosomes of African wild ungulates transmitted by tsetse flies can cause human and livestock diseases. However, trypanosome diversity in wild tsetse flies remains greatly underestimated. We employed FFLB (fluorescent fragment length barcoding) for surveys of trypanosomes in tsetse flies (3086) from the Gorongosa National Park (GNP) and Niassa National Reserve (NNR) in Mozambique (MZ), identified as Glossina morsitans morsitans (GNP/NNR=77.6%/90.5%) and Glossina pallidipes (22.4%/9.5%). Trypanosomes were microscopically detected in 8...
July 5, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28687754/dna-barcoding-studies-on-thrips-in-india-cryptic-species-and-species-complexes
#7
Kaomud Tyagi, Vikas Kumar, Devkant Singha, Kailash Chandra, Boni Amin Laskar, Shantanu Kundu, Rajasree Chakraborty, Sumantika Chatterjee
Thrips are one of the major sucking pest and vector of plant viruses causing huge economic loss in agriculture. The accurate identification of thrips is crucial for effective pest management strategies. However, morphology based identification has limitations and warrants integration of molecular data. We attempted the largest DNA barcoding initiative on 370 sequences of 89 thrips morphospecies including 104 novel sequences from 39 morphospecies, including the type specimens of four species. The results of multiple species delimitation methods (BIN, ABGD, GMYC and bPTP) were consistent for 73 species (82%) with their morphological identifications...
July 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28687070/massively-parallel-nanowell-based-single-cell-gene-expression-profiling
#8
Leonard D Goldstein, Ying-Jiun Jasmine Chen, Jude Dunne, Alain Mir, Hermann Hubschle, Joseph Guillory, Wenlin Yuan, Jingli Zhang, Jeremy Stinson, Bijay Jaiswal, Kanika Bajaj Pahuja, Ishminder Mann, Thomas Schaal, Leo Chan, Sangeetha Anandakrishnan, Chun-Wah Lin, Patricio Espinoza, Syed Husain, Harris Shapiro, Karthikeyan Swaminathan, Sherry Wei, Maithreyan Srinivasan, Somasekar Seshagiri, Zora Modrusan
BACKGROUND: Technological advances have enabled transcriptome characterization of cell types at the single-cell level providing new biological insights. New methods that enable simple yet high-throughput single-cell expression profiling are highly desirable. RESULTS: Here we report a novel nanowell-based single-cell RNA sequencing system, ICELL8, which enables processing of thousands of cells per sample. The system employs a 5,184-nanowell-containing microchip to capture ~1,300 single cells and process them...
July 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28675688/whole-mitochondrial-genome-capture-from-fecal-samples-and-museum-preserved-specimens
#9
Tom van der Valk, Frida Lona Durazo, Love Dalén, Katerina Guschanski
Population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. The use of non-invasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 non-invasively collected fecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee...
July 4, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28671248/generic-relationships-among-molluginaceae-inferred-from-a-molecular-phylogenetic-analysis-of-the-matk-gene
#10
M A Ali, J Lee, F Al-Hemaid
The family Molluginaceae (order Caryophyllales) is considered polyphyletic based on the photosynthetic pathway, C4 evolution, and phylogeny of the family. This inference was made based on photosynthetic, anatomical, and molecular datasets. The generic circumscription of this family has greatly been changed owing to the placement of several of its genera into the Caryophyllaceae, Microteaceae, Lophiocarpaceae, and Limeaceae families. However, the generic relationships are largely unknown. By virtue of high substitution rates within the species and the ability to resolve the phylogenetic position of morphologically very closely related species and species complexes, the matK gene has emerged as one of the potential chloroplast DNA molecular markers in plant molecular phylogenetics and DNA barcoding studies...
June 29, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28654351/zz-z0-the-new-system-of-sex-chromosomes-in-eigenmannia-aff-trilineata-teleostei-gymnotiformes-sternopygidae-characterized-by-molecular-cytogenetics-and-dna-barcoding
#11
Cristian Araya-Jaime, Nadayca T Bonani Mateussi, Ricardo Utsunomia, Guilherme J Costa-Silva, Claudio Oliveira, Fausto Foresti
The cytogenetic characteristics of Eigenmannia aff. trilineata were analyzed by basic and molecular cytogenetics, applying fluorescent in situ hybridization, with 18S and 5S rDNA and U2 snRNA probes. The species revealed a kind of polymorphism associated to ZZ/Z0 type sex chromosomes, with 2n = 32 (8m+2sm+22a, NF = 42) in all males under analysis, whereas females evidenced 2n = 31 (8m+1sm+22a, NF = 40). C-banding showed constitutive heterochromatin restricted to the pericentromeric region of all chromosomes and single-nucleolus organized regions on pair 11...
June 27, 2017: Zebrafish
https://www.readbyqxmd.com/read/28651582/intra-and-inter-isolate-variation-of-ribosomal-and-protein-coding-genes-in-pleurotus-implications-for-molecular-identification-and-phylogeny-on-fungal-groups
#12
Xiao-Lan He, Qian Li, Wei-Hong Peng, Jie Zhou, Xue-Lian Cao, Di Wang, Zhong-Qian Huang, Wei Tan, Yu Li, Bing-Cheng Gan
BACKGROUND: The internal transcribed spacer (ITS), RNA polymerase II second largest subunit (RPB2), and elongation factor 1-alpha (EF1α) are often used in fungal taxonomy and phylogenetic analysis. As we know, an ideal molecular marker used in molecular identification and phylogenetic studies is homogeneous within species, and interspecific variation exceeds intraspecific variation. However, during our process of performing ITS, RPB2, and EF1α sequencing on the Pleurotus spp., we found that intra-isolate sequence polymorphism might be present in these genes because direct sequencing of PCR products failed in some isolates...
June 26, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28650462/haplotype-phasing-of-whole-human-genomes-using-bead-based-barcode-partitioning-in-a-single-tube
#13
Fan Zhang, Lena Christiansen, Jerushah Thomas, Dmitry Pokholok, Ros Jackson, Natalie Morrell, Yannan Zhao, Melissa Wiley, Emily Welch, Erich Jaeger, Ana Granat, Steven J Norberg, Aaron Halpern, Maria C Rogert, Mostafa Ronaghi, Jay Shendure, Niall Gormley, Kevin L Gunderson, Frank J Steemers
Haplotype-resolved genome sequencing promises to unlock a wealth of information in population and medical genetics. However, for the vast majority of genomes sequenced to date, haplotypes have not been determined because of cumbersome haplotyping workflows that require fractions of the genome to be sequenced in a large number of compartments. Here we demonstrate barcode partitioning of long DNA molecules in a single compartment using "on-bead" barcoded tagmentation. The key to the method that we call "contiguity preserving transposition" sequencing on beads (CPTv2-seq) is transposon-mediated transfer of homogenous populations of barcodes from beads to individual long DNA molecules that get fragmented at the same time (tagmentation)...
June 26, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28645767/assessing-the-potential-of-rad-sequencing-to-resolve-phylogenetic-relationships-within-species-radiations-the-fly-genus-chiastocheta-diptera-anthomyiidae-as-a-case-study
#14
Tomasz Suchan, Anahí Espíndola, Sereina Rutschmann, Brent C Emerson, Kevin Gori, Christophe Dessimoz, Nils Arrigo, Michał Ronikier, Nadir Alvarez
Determining phylogenetic relationships among recently diverged species has long been a challenge in evolutionary biology. Cytoplasmic DNA markers, which have been widely used, notably in the context of molecular barcoding, have not always proved successful in resolving such phylogenies. However, with the advent of next-generation-sequencing technologies and associated techniques of reduced genome representation, phylogenies of closely related species have been resolved at a much higher detail in the last couple of years...
June 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28642581/molecular-methods-to-detect-spodoptera-frugiperda-in-ghana-and-implications-for-monitoring-the-spread-of-invasive-species-in-developing-countries
#15
Matthew J W Cock, Patrick K Beseh, Alan G Buddie, Giovanni Cafá, Jayne Crozier
Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) is a polyphagous pest indigenous throughout the Americas, which recently appeared in Africa, first reported from São Tomé, Nigeria, Bénin and Togo in 2016, and which we now report from Ghana. This species is recognised to comprise two morphologically identical but genetically distinct strains or species in the Americas, and we found both to be present in Ghana. We discuss possible routes of entry to Africa, of which the likeliest is adults and/or egg masses transported on direct commercial flights between the Americas and West Africa, followed by dispersal by adult flight within Africa...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642488/biomimetic-molecular-signaling-using-dna-walkers-on-microparticles
#16
Tulsi Ram Damase, Adam Spencer, Bamidele Samuel, Peter B Allen
We report the release of catalytic DNA walkers from hydrogel microparticles and the detection of those walkers by substrate-coated microparticles. This might be considered a synthetic biology analog of molecular signal release and reception. One type of particles was coated with components of a DNA one-step strand displacement (OSD) reaction to release the walker. A second type of particle was coated with substrate (or "track") for the molecular walker. We distinguish these particle types using fluorescence barcoding: we synthesized and distinguished multiple particle types with multicolor fluorescence microscopy and automated image analysis software...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28637924/vp4-and-vp7-specific-antibodies-mediate-heterotypic-immunity-to-rotavirus-in-humans
#17
Nitya Nair, Ningguo Feng, Lisa K Blum, Mrinmoy Sanyal, Siyuan Ding, Baoming Jiang, Adrish Sen, John M Morton, Xiao-Song He, William H Robinson, Harry B Greenberg
Human rotaviruses (RVs) are the leading cause of severe diarrhea in young children worldwide. The molecular mechanisms underlying the rapid induction of heterotypic protective immunity to RV, which provides the basis for the efficacy of licensed monovalent RV vaccines, have remained unknown for more than 30 years. We used RV-specific single cell-sorted intestinal B cells from human adults, barcode-based deep sequencing of antibody repertoires, monoclonal antibody expression, and serologic and functional characterization to demonstrate that infection-induced heterotypic immunoglobulins (Igs) primarily directed to VP5*, the stalk region of the RV attachment protein, VP4, are able to mediate heterotypic protective immunity...
June 21, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28634359/infections-of-horses-and-shrews-with-bornaviruses-in-upper-austria-a-novel-endemic-area-of-borna-disease
#18
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/28629429/linked-read-sequencing-resolves-complex-genomic-rearrangements-in-gastric-cancer-metastases
#19
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/28623498/minimal-barcode-distance-between-two-water-mite-species-from-madeira-island-a-cautionary-tale
#20
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
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