keyword
MENU ▼
Read by QxMD icon Read
search

barcoding

keyword
https://www.readbyqxmd.com/read/28330205/dna-record-of-some-traditional-small-millet-landraces-in-india-and-nepal
#1
Subramanyam Ragupathy, Shanmughanandhan Dhivya, Kirit Patel, Abiran Sritharan, Kathirvelu Sambandan, Hom Gartaula, Ramalingam Sathishkumar, Kamal Khadka, Balasubramanian C Nirmala, A Nirmala Kumari, Steven G Newmaster
Despite the extensive use of small millet landraces as an important source of nutrition for people living in semi-arid regions, they are presently marginalized and their diversity and distribution are threatened at a global scale. Local farmers have developed ancient breeding programs entrenched in traditional knowledge (TK) that has sustained rural cultures for thousands of years. The convention on biological diversity seeks fair and equitable sharing of genetic resources arising from local knowledge and requires signatory nations to provide appropriate policy and legal framework to farmers' rights over plant genetic resources and associated TK...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329763/the-allosteric-inhibitor-abl001-enables-dual-targeting-of-bcr-abl1
#2
Andrew A Wylie, Joseph Schoepfer, Wolfgang Jahnke, Sandra W Cowan-Jacob, Alice Loo, Pascal Furet, Andreas L Marzinzik, Xavier Pelle, Jerry Donovan, Wenjing Zhu, Silvia Buonamici, A Quamrul Hassan, Franco Lombardo, Varsha Iyer, Michael Palmer, Giuliano Berellini, Stephanie Dodd, Sanjeev Thohan, Hans Bitter, Susan Branford, David M Ross, Timothy P Hughes, Lilli Petruzzelli, K Gary Vanasse, Markus Warmuth, Francesco Hofmann, Nicholas J Keen, William R Sellers
Chronic myeloid leukaemia (CML) is driven by the activity of the BCR-ABL1 fusion oncoprotein. ABL1 kinase inhibitors have improved the clinical outcomes for patients with CML, with over 80% of patients treated with imatinib surviving for more than 10 years. Second-generation ABL1 kinase inhibitors induce more potent molecular responses in both previously untreated and imatinib-resistant patients with CML. Studies in patients with chronic-phase CML have shown that around 50% of patients who achieve and maintain undetectable BCR-ABL1 transcript levels for at least 2 years remain disease-free after the withdrawal of treatment...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28327913/the-use-of-oxford-nanopore-native-barcoding-for-complete-genome-assembly
#3
Sion C Bayliss, Vicky L Hunt, Maho Yokoyama, Harry A Thorpe, Edward J Feil
Background: The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short-read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short-read data...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28325987/new-and-poorly-known-palaearctic-fungus-gnats-diptera-sciaroidea
#4
Jukka Salmela, Levente-Péter Kolcsár
BACKGROUND: Fungus gnats (Sciaroidea) are a globally species rich group of lower Diptera. In Europe, Fennoscandian peninsula in particular holds a notable diversity, ca. 1000 species, of which 10 % are still unnamed. Fungus gnats are predominantly terrestrial insects, but some species dwell in wetland habitats. NEW INFORMATION: Eight new fungus gnat species, belonging to the families Keroplatidae (Orfelia boreoalpina Salmela sp.n.) and Mycetophilidae (Sciophila holopaineni Salmela sp...
2017: Biodiversity Data Journal
https://www.readbyqxmd.com/read/28325970/making-the-most-of-your-host-the-metrosideros-feeding-psyllids-hemiptera-psylloidea-of-the-hawaiian-islands
#5
Diana M Percy
The Hawaiian psyllids (Psylloidea, Triozidae) feeding on Metrosideros (Myrtaceae) constitute a remarkable radiation of more than 35 species. This monophyletic group has diversified on a single, highly polymorphic host plant species, Metrosideros polymorpha. Eleven Metrosideros-feeding species included in the Insects of Hawaii by Zimmerman are redescribed, and an additional 25 new species are described. Contrary to previous classifications that placed the Metrosideros-feeders in two genera, Trioza Foerster, 1848 and Kuwayama Crawford, 1911, all 36 named species are placed in Pariaconus Enderlein, 1926; and the relationship of this genus to other Pacific taxa within the family Triozidae, and other Austro-Pacific taxa feeding on host plants in Myrtaceae is clarified...
2017: ZooKeys
https://www.readbyqxmd.com/read/28325121/dna-extraction-and-barcode-identification-of-development-stages-of-forensically-important-flies-in-the-czech-republic
#6
Tereza Olekšáková, Martina Žurovcová, Vanda Klimešová, Miroslav Barták, Hana Šuláková
Several methods of DNA extraction, coupled with 'DNA barcoding' species identification, were compared using specimens from early developmental stages of forensically important flies from the Calliphoridae and Sarcophagidae families. DNA was extracted at three immature stages - eggs, the first instar larvae, and empty pupal cases (puparia) - using four different extraction methods, namely, one simple 'homemade' extraction buffer protocol and three commercial kits. The extraction conditions, including the amount of proteinase K and incubation times, were optimized...
March 21, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28320321/evolution-of-group-i-introns-in-porifera-new-evidence-for-intron-mobility-and-implications-for-dna-barcoding
#7
Astrid Schuster, Jose V Lopez, Leontine E Becking, Michelle Kelly, Shirley A Pomponi, Gert Wörheide, Dirk Erpenbeck, Paco Cárdenas
BACKGROUND: Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarians, placozoans and one annelid species. Within demosponges, group I and group II introns are present in six families. Based on different insertion sites within the cox1 gene and secondary structures, four types of group I and two types of group II introns are known, which can harbor up to three encoding homing endonuclease genes (HEG) of the LAGLIDADG family (group I) and/or reverse transcriptase (group II)...
March 20, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28304358/a-pelagic-microbiome-viruses-to-protists-from-a-small-cup-of-seawater
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
keyword
keyword
75802
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"