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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
Jedsada Sukantamala, Kong-Wah Sing, Narong Jaturas, Raxsina Polseela, John-James Wilson
Certain species of Phlebotomine sandflies (Diptera: Psychodidae) are vectors of the protozoa which causes leishmaniasis. Sandflies are found breeding in enclosed places like caves. Thailand is a popular tourist destination, including for ecotourism activities like caving, which increases the risk of contact between tourists and sandflies. Surveillance of sandflies is important for monitoring this risk but identification of species based on morphology is challenged by phenotypic plasticity and cryptic diversity...
October 19, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Sundar Poovitha, Nithaniyal Stalin, Raju Balaji, Madasamy Parani
The genus Hibiscus L. includes several taxa of medicinal value and species used for the extraction of natural dyes. These applications require the use of authentic plant materials. DNA barcoding is a molecular method for species identification, which helps in reliable authentication by using one or more DNA barcode marker. In this study, we have collected 44 accessions, representing 16 species of Hibiscus, distributed in the southern peninsular India, to evaluate the discriminatory power of the two core barcodes rbcLa and matK together with the suggested additional regions trnH-psbA and ITS2...
September 14, 2016: Genome Génome / Conseil National de Recherches Canada
Muhammad Ashfaq, Paul D N Hebert
Many of the arthropod species that are important pests of agriculture and forestry are impossible to discriminate morphologically throughout all of their life stages. Some cannot be differentiated at any life stage. Over the past decade, DNA barcoding has gained increasing adoption as a tool to both identify known species and to reveal cryptic taxa. Although there has not been a focused effort to develop a barcode library for them, reference sequences are now available for 77% of the 409 species of arthropods documented on major pest databases...
August 30, 2016: Genome Génome / Conseil National de Recherches Canada
E Leyva-Cruz, L Vásquez-Yeomans, L Carrillo, M Valdez-Moreno
In the waters surrounding Banco Chinchorro in the Mexican Caribbean are spawning and nursery areas for many types of fish. In this natural environment, as opposed to under controlled laboratory conditions, it is almost impossible to link an individual egg to the adult that laid it. This makes identifying the species of the eggs difficult. However, DNA barcodes have made this easier. In the present study, 300 eggs were processed for molecular analysis, from which 139 sequences were obtained. We identified 42 taxa (33 species with their binomial names), 35 genera, and 24 families...
May 17, 2016: Genome Génome / Conseil National de Recherches Canada
Guozhu Zhao, Guohua Yin, Arati A Inamdar, Jing Luo, Ning Zhang, Ill Yang, Brian Buckley, Joan W Bennett
Super Storm Sandy provided an opportunity to study filamentous fungi (molds) associated with winter storm damage. We collected 36 morphologically distinct fungal isolates from flooded buildings. By combining traditional morphological and cultural characters with an analysis of ITS sequences (the fungal DNA barcode), we identified 24 fungal species that belong to 8 genera: Penicillium (12 species), Fusarium (4 species), Aspergillus (3 species), Trichoderma (2 species), and one species each of Metarhizium, Mucor, Pestalotiopsis, and Umbelopsis...
October 17, 2016: Indoor Air
Dhikra Souidenne, Isabelle Florent, Marc Dellinger, Mohamed Salah Romdhane, Philippe Grellier, Hidetaka Furuya
Dicyemids are common parasites found in the kidneys of many cephalopods. Species identification previously relied on old species descriptions containing considerable confusions, casting doubt on taxonomy and identification. Detailed morphological description and genotyping of all developmental stages are required for an exact taxonomy. To this end, we undertook the redescription of the dicyemid Dicyemennea eledones (Wagener, 1857), infecting the cephalopod Eledone cirrhosa (Lamarck). Samples were collected off Concarneau in the Bay of Biscay, France, and off La Goulette in the Gulf of Tunis, Tunisia...
November 2016: Systematic Parasitology
Ashley Daily, Erin D Kennedy, Leslie A Fierro, Jenica Huddleston Reed, Michael Greene, Warren W Williams, Heather V Evanson, Regina Cox, Patrick Koeppl, Ken Gerlach
BACKGROUND AND OBJECTIVE: Accurately recording vaccine lot number, expiration date, and product identifiers, in patient records is an important step in improving supply chain management and patient safety in the event of a recall. These data are being encoded on two-dimensional (2D) barcodes on most vaccine vials and syringes. Using electronic vaccine administration records, we evaluated the accuracy of lot number and expiration date entered using 2D barcode scanning compared to traditional manual or drop-down list entry methods...
October 11, 2016: Vaccine
Steven D Leavitt, Theodore L Esslinger, Pradeep K Divakar, Ana Crespo, H Thorsten Lumbsch
Molecular data provide unprecedented insight into diversity of lichenized fungi, although morphologically cryptic species-level lineages circumscribed from sequence data often remain undescribed even in well-studies groups. Using diagnostic characters from DNA sequence data and support from the multispecies coalescent model, we formally describe a total of eleven new species and resurrect two others in the hyperdiverse lichen-forming fungal family Parmeliaceae. These include: four in the genus Melanelixia - M...
November 2016: Fungal Biology
Sanja Vickovic, Patrik L Ståhl, Fredrik Salmén, Sarantis Giatrellis, Jakub Orzechowski Westholm, Annelie Mollbrink, José Fernández Navarro, Joaquin Custodio, Magda Bienko, Lesley-Ann Sutton, Richard Rosenquist, Jonas Frisén, Joakim Lundeberg
Single-cell transcriptome analysis overcomes problems inherently associated with averaging gene expression measurements in bulk analysis. However, single-cell analysis is currently challenging in terms of cost, throughput and robustness. Here, we present a method enabling massive microarray-based barcoding of expression patterns in single cells, termed MASC-seq. This technology enables both imaging and high-throughput single-cell analysis, characterizing thousands of single-cell transcriptomes per day at a low cost (0...
October 14, 2016: Nature Communications
L M Oliveira, T Knebelsberger, M Landi, P Soares, M J Raupach, F O Costa
A large-scale comprehensive reference library of DNA barcodes for European marine fishes was assembled, allowing the evaluation of taxonomic uncertainties and species genetic diversity that were otherwise hidden in geographically restricted studies. A total of 4118 DNA barcodes were assigned to 358 species generating 366 Barcode Index Numbers (BIN). Initial examination revealed as much as 141 BIN discordances (more than one species in each BIN). After implementing an auditing and five-grade (A-E) annotation protocol, the number of discordant species BINs was reduced to 44 (13% grade E), while concordant species BINs amounted to 271 (78% grades A and B) and 14 other had insufficient data (grade D)...
October 14, 2016: Journal of Fish Biology
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