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https://www.readbyqxmd.com/read/28304358/a-pelagic-microbiome-viruses-to-protists-from-a-small-cup-of-seawater
#1
Flavia Flaviani, Declan C Schroeder, Cecilia Balestreri, Joanna L Schroeder, Karen Moore, Konrad Paszkiewicz, Maya C Pfaff, Edward P Rybicki
The aquatic microbiome is composed of a multi-phylotype community of microbes, ranging from the numerically dominant viruses to the phylogenetically diverse unicellular phytoplankton. They influence key biogeochemical processes and form the base of marine food webs, becoming food for secondary consumers. Due to recent advances in next-generation sequencing, this previously overlooked component of our hydrosphere is starting to reveal its true diversity and biological complexity. We report here that 250 mL of seawater is sufficient to provide a comprehensive description of the microbial diversity in an oceanic environment...
March 17, 2017: Viruses
https://www.readbyqxmd.com/read/28303008/an-analysis-of-echinacea-chloroplast-genomes-implications-for-future-botanical-identification
#2
Ning Zhang, David L Erickson, Padmini Ramachandran, Andrea R Ottesen, Ruth E Timme, Vicki A Funk, Yan Luo, Sara M Handy
Echinacea is a common botanical used in dietary supplements, primarily to treat upper respiratory tract infections and to support immune function. There are currently thought to be nine species in the genus Echinacea. Due to very low molecular divergence among sister species, traditional DNA barcoding has not been successful for differentiation of Echinacea species. Here, we present the use of full chloroplast genomes to distinguish between all 9 reported species. Total DNA was extracted from specimens stored at the National Museum of Natural History, Smithsonian Institution, which had been collected from the wild with species identification documented by experts in the field...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28296890/re-establishment-of-species-from-synonymies-based-on-dna-barcoding-and-phylogenetic-analysis-using-diplopterygium-simulans-gleicheniaceae-as-an-example
#3
Jiang-Ping Shu, Hui Shang, Dongmei Jin, Hong-Jin Wei, Xi-Le Zhou, Hong-Mei Liu, Yu-Feng Gu, Ying Wang, Fa-Guo Wang, Hui Shen, Rui Zhang, Bayu Adjie, Yue-Hong Yan
Because synonymy treatment traditionally relies on morphological judgments, it usually causes many problems in species delimitation and in the biodiversity catalogue. For example, Diplopterygium simulans, which belongs to the Gleicheniaceae family, has been considered to be synonymous with D. glaucum or D. giganteum based mainly on the morphology of its pinna rachis and blade. In the absence of molecular evidence, these revisions remain doubtful. DNA barcoding, which is considered to be a powerful method for species-level identification, was employed to assess the genetic distance among 9 members of the Diplopterygium genus...
2017: PloS One
https://www.readbyqxmd.com/read/28296214/morphological-secondary-metabolite-and-its-rdna-variability-within-usnic-acid-containing-lichen-thalli-of-the-genus-xanthoparmelia-explored-at-the-local-scale-of-rock-outcrop-in-western-italian-alps
#4
Enrica Matteucci, Andrea Occhipinti, Rosanna Piervittori, Massimo E Maffei, Sergio E Favero-Longo
Lichen secondary metabolites (LSMs) are regarded with interest for valuable biological properties, but chemical variability among/within lichen taxa has been only fragmentarily characterized by advanced analytical techniques. Knowledge of variability at a local geographic scale has been particularly neglected, while it should address the collection of chemically homogeneous materials to test and exploit LSMs. Here we evaluated the chemical variability of 48 Xanthoparmelia specimens from two rock outcrops in Western Italian Alps, representative of nine morphotypes and sixteen rDNA ITS haplotypes...
March 11, 2017: Chemistry & Biodiversity
https://www.readbyqxmd.com/read/28293890/characterizing-dynamic-protein-protein-interactions-using-the-genetically-encoded-split-biosensor-assay-technique-split-tev
#5
Jan P Wintgens, Moritz J Rossner, Michael C Wehr
Dynamic protein-protein interactions (PPIs) are fundamental building blocks of cellular signaling and monitoring their regulation promotes the understanding of signaling in health and disease. Genetically encoded split protein biosensor assays, such as the split TEV method, have proved to be highly valuable when studying regulated PPIs in living cells. Split TEV is based on the functional complementation of two previously inactive TEV protease fragments fused to interacting proteins and provides a robust, sensitive and flexible readout to monitor PPIs both at the membrane and in the cytosol...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28290550/abseq-ultrahigh-throughput-single-cell-protein-profiling-with-droplet-microfluidic-barcoding
#6
Payam Shahi, Samuel C Kim, John R Haliburton, Zev J Gartner, Adam R Abate
Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and quantitate proteins in single cells at ultrahigh throughput. Like flow and mass cytometry, Abseq uses specific antibodies to detect epitopes of interest; however, unlike these methods, antibodies are labeled with sequence tags that can be read out with microfluidic barcoding and DNA sequencing...
March 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28290255/feeding-by-leucopis-argenticollis-and-leucopis-piniperda-diptera-chamaemyiidae-from-the-western-usa-on-adelges-tsugae-hemiptera-adelgidae-in-the-eastern-usa
#7
K Motley, N P Havill, A L Arsenault-Benoit, A E Mayfield, D S Ott, D Ross, M C Whitmore, K F Wallin
Leucopis argenticollis (Zetterstedt) and Leucopis piniperda (Malloch) are known to feed on the lineage of Adelges tsugae Annand that is native to western North America, but it is not known if they will survive on the lineage that was introduced from Japan to the eastern USA. In 2014, western Leucopis spp. larvae were brought to the laboratory and placed on A. tsugae collected in either Washington (North American A. tsugae lineage) or Connecticut (Japanese lineage). There were no significant differences in survival or developmental times between flies reared on the two different adelgid lineages...
March 14, 2017: Bulletin of Entomological Research
https://www.readbyqxmd.com/read/28290215/genetic-assessment-of-leech-species-from-yak-bos-grunniens-in-the-tract-of-northeast-india
#8
Nilkantha Chatterjee, Bishal Dhar, Debasis Bhattarcharya, Sourabh Deori, Juwar Doley, Joken Bam, Pranab J Das, Asit K Bera, Sitangshu M Deb, Ningthoujam Neelima Devi, Rajesh Paul, Sorokhaibam Malvika, Sankar Kumar Ghosh
Yak is an iconic symbol of Tibet and high altitudes of Northeast India. It is highly cherished for milk, meat, and skin. However, yaks suffer drastic change in milk production, weight loss, etc, when infested by parasites. Among them, infestation by leeches is a serious problem in the Himalayan belt of Northeast India. The parasite feeds on blood externally or from body orifices, like nasopharynx, oral, rectum, etc. But there has been limited data about the leech species infesting the yak in that region because of the difficulties in morphological identification due to plasticity of the body, changes in shape, and surface structure and thus, warrants for the molecular characterization of leech...
March 14, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28287980/constructing-dna-barcode-sets-based-on-particle-swarm-optimization
#9
Bin Waang, Xuedong Zheng, Shihua Zhou, Changjun Zhou, Xiaopeng Wei, Qiang Zhang, Ziqi Wei
Following the completion of the human genome project, a large amount of high-throughput bio-data was generated. To analyze these data, massively parallel sequencing, namely next-generation sequencing, was rapidly developed. DNA barcodes are used to identify the ownership between sequences and samples when they are attached at the beginning or end of sequencing reads. Constructing DNA barcode sets provides the candidate DNA barcodes for this application. To increase the accuracy of DNA barcode sets, a particle swarm optimization (PSO) algorithm has been modified and used to construct the DNA barcode sets in this paper...
March 7, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28287390/species-of-philometra-nematoda-philometridae-from-fishes-off-the-mediterranean-coast-of-africa-with-a-description-of-philometra-rara-n-sp-from-hyporthodus-haifensis-and-a-molecular-analysis-of-philometra-saltatrix-from-pomatomus-saltatrix
#10
František Moravec, Amira Chaabane, Lassad Neifar, Delphine Gey, Jean-Lou Justine
Two gonad-infecting species of Philometra Costa, 1845 (Nematoda, Philometridae) were recorded for the first time from marine perciform fishes off Tunisia and Libya: Philometra rara n. sp. from the rare, deep-water Haifa grouper Hyporthodus haifensis (Serranidae) off Libya and Philometra saltatrix Ramachandran, 1973 from the bluefish Pomatomus saltatrix (Pomatomidae) off Tunisia. Identification of both fish species was confirmed by molecular barcoding. Light and scanning electron microscope studies of Ph. rara n...
2017: Parasite: Journal de la Société Française de Parasitologie
https://www.readbyqxmd.com/read/28287117/barcode-extension-for-analysis-and-reconstruction-of-structures
#11
Cameron Myhrvold, Michael Baym, Nikita Hanikel, Luvena L Ong, Jonathan S Gootenberg, Peng Yin
Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure...
March 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/28287089/corrigendum-an-automated-approach-to-prepare-tissue-derived-spatially-barcoded-rna-sequencing-libraries
#12
Anders Jemt, Fredrik Salmén, Anna Lundmark, Annelie Mollbrink, José Fernández Navarro, Patrik L Ståhl, Tülay Yucel-Lindberg, Joakim Lundeberg
No abstract text is available yet for this article.
March 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28284548/relationships-between-metal-compartmentalization-and-biomarkers-in-earthworms-exposed-to-field-contaminated-soils
#13
Léa Beaumelle, Mickaël Hedde, Franck Vandenbulcke, Isabelle Lamy
Partitioning tissue metal concentration into subcellular compartments reflecting toxicologically available pools may provide good descriptors of the toxicological effects of metals on organisms. Here we investigated the relationships between internal compartmentalization of Cd, Pb and Zn and biomarker responses in a model soil organism: the earthworm. The aim of this study was to identify metal fractions reflecting the toxic pressure in an endogeic, naturally occurring earthworm species (Aporrectodea caliginosa) exposed to realistic field-contaminated soils...
March 8, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28284194/clonocalc-and-clonoplot-immune-repertoire-analysis-from-raw-files-to-publication-figures-with-graphical-user-interface
#14
Anke Fähnrich, Moritz Krebbel, Normann Decker, Martin Leucker, Felix D Lange, Kathrin Kalies, Steffen Möller
BACKGROUND: Next generation sequencing (NGS) technologies enable studies and analyses of the diversity of both T and B cell receptors (TCR and BCR) in human and animal systems to elucidate immune functions in health and disease. Over the last few years, several algorithms and tools have been developed to support respective analyses of raw sequencing data of the immune repertoire. These tools focus on distinct aspects of the data processing and require a strong bioinformatics background...
March 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28281309/bayesian-species-identification-under-the-multispecies-coalescent-provides-significant-improvements-to-dna-barcoding-analyses
#15
Ziheng Yang, Bruce Rannala
DNA barcoding methods use a single locus (usually the mitochondrial COI gene) to assign unidentified specimens to known species in a library based on a genetic distance threshold that distinguishes between-species divergence from within-species diversity. Recently developed species delimitation methods based on the multispecies coalescent (MSC) model offer an alternative approach to individual assignment using either single-locus or multi-loci sequence data. Here we use simulations to demonstrate three features of an MSC method implemented in the program bpp...
March 9, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28280591/correction-to-dna-barcoding-uncovers-cryptic-diversity-in-50-of-deep-sea-antarctic-polychaetes
#16
Madeleine J Brasier, Helena Wiklund, Lenka Neal, Rachel Jeffreys, Katrin Linse, Henry Ruhl, Adrian G Glover
[This corrects the article DOI: 10.1098/rsos.160432.].
January 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28278695/dna-barcoding-and-genetic-diversity-analyses-of-fishes-of-kaladan-river-of-indo-myanmar-biodiversity-hotspot
#17
Anindya Sundar Barman, Mamta Singh, Pramod Kumar Pandey
Species are considered as a fundamental unit of biodiversity. Therefore, the prerequisite for biodiversity management and conservation is to know the number of species one is dealing with. Consequently, the need of the present study was conceptualized, which dealt with the comprehensive molecular appraisal of Kaladan's Fish fauna. A total of 291 specimens representing 49 species, 28 genera, 11 families, and 4 orders, were collected from 11 sampling stations situated along the main Kaladan River and its four major tributaries, i...
February 16, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28278693/dna-barcoding-revises-a-misidentification-on-mossy-frog-new-record-and-distribution-extension-of-theloderma-corticale-boulenger-1903-amphibia-anura-rhacophoridae
#18
Huayuan Huang, Zening Chen, Zhonghui Wei, Rongping Bu, Zhengjun Wu
As an endangered animal group, mossy frog (genus Theloderma) has attracted the attention of biologists and wildlife conservationists. Clarifying the taxonomic status and distribution of each species in Theloderma is important to determine the conservation status for each species, establish appropriate conservation strategies and probe the speciation process. Recently, we discovered a medium-sized species of mossy frog of the genus Theloderma in April 2015 during municipal surveys of amphibians in Dayao Mountain of Jinxiu...
February 16, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28270824/advances-of-community-level-plant-dna-barcoding-in-china
#19
Nancai Pei, Bufeng Chen, W J Kress
DNA barcoding is a commonly used bio-technology in multiple disciplines including biology, environmental science, forensics and inspection, etc. Forest dynamic plots provide a unique opportunity to carry out large-scale, comparative, and multidisciplinary research for plant DNA barcoding. The paper concisely reviewed four previous progresses in China; specifically, species discrimination, community phylogenetic reconstruction, phylogenetic community structure exploration, and biodiversity index evaluation. Further, we demonstrated three major challenges; specifically, building the impetus to generate DNA barcodes using multiple plant DNA markers for all woody species at forest community levels, analyzing massive DNA barcoding sequence data, and promoting theoretical innovation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28267567/safety-assessment-of-mushrooms-in-dietary-supplements-by-combining-analytical-data-with-in-silico-toxicology-evaluation
#20
Karen M VanderMolen, Jason G Little, Vincent P Sica, Tamam El-Elimat, Huzefa A Raja, Nicholas H Oberlies, Timothy R Baker, Catherine Mahony
Despite growing popularity in dietary supplements, many medicinal mushrooms have not been evaluated for their safe human consumption using modern techniques. The multifaceted approach described here relies on five key principles to evaluate the safety of non-culinary fungi for human use: (1) identification by sequencing the nuclear ribosomal internal transcribed spacer (ITS) region (commonly referred to as ITS barcoding), (2) screening an extract of each fungal raw material against a database of known fungal metabolites, (3) comparison of these extracts to those prepared from grocery store-bought culinary mushrooms using UHPLCPDA-ELS-HRMS, (4) review of the toxicological and chemical literature for each fungus, and (5) evaluation of data establishing presence in-market...
March 4, 2017: Food and Chemical Toxicology
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