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Sample records for barcoding nemo dna-based

  1. Potential for DNA-based identification of Great Lakes fauna: match and mismatch between taxa inventories and DNA barcode libraries

    Science.gov (United States)

    Trebitz, Anett S.; Hoffman, Joel C.; Grant, George W.; Billehus, Tyler M.; Pilgrim, Erik M.

    2015-01-01

    DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to bioassessment and non-native species monitoring. The ability to assign species identities to DNA sequences found depends on the availability of comprehensive DNA reference libraries. Here, we compile inventories for aquatic metazoans extant in or threatening to invade the Laurentian Great Lakes and examine the availability of reference mitochondrial COI DNA sequences (barcodes) in the Barcode of Life Data System for them. We found barcode libraries largely complete for extant and threatening-to-invade vertebrates (100% of reptile, 99% of fish, and 92% of amphibian species had barcodes). In contrast, barcode libraries remain poorly developed for precisely those organisms where morphological identification is most challenging; 46% of extant invertebrates lacked reference barcodes with rates especially high among rotifers, oligochaetes, and mites. Lack of species-level identification for many aquatic invertebrates also is a barrier to matching DNA sequences with physical specimens. Attaining the potential for DNA-based identification of mixed-organism samples covering the breadth of aquatic fauna requires a concerted effort to build supporting barcode libraries and voucher collections. PMID:26199185

  2. A DNA-based registry for all animal species: the barcode index number (BIN system.

    Directory of Open Access Journals (Sweden)

    Sujeevan Ratnasingham

    Full Text Available Because many animal species are undescribed, and because the identification of known species is often difficult, interim taxonomic nomenclature has often been used in biodiversity analysis. By assigning individuals to presumptive species, called operational taxonomic units (OTUs, these systems speed investigations into the patterning of biodiversity and enable studies that would otherwise be impossible. Although OTUs have conventionally been separated through their morphological divergence, DNA-based delineations are not only feasible, but have important advantages. OTU designation can be automated, data can be readily archived, and results can be easily compared among investigations. This study exploits these attributes to develop a persistent, species-level taxonomic registry for the animal kingdom based on the analysis of patterns of nucleotide variation in the barcode region of the cytochrome c oxidase I (COI gene. It begins by examining the correspondence between groups of specimens identified to a species through prior taxonomic work and those inferred from the analysis of COI sequence variation using one new (RESL and four established (ABGD, CROP, GMYC, jMOTU algorithms. It subsequently describes the implementation, and structural attributes of the Barcode Index Number (BIN system. Aside from a pragmatic role in biodiversity assessments, BINs will aid revisionary taxonomy by flagging possible cases of synonymy, and by collating geographical information, descriptive metadata, and images for specimens that are likely to belong to the same species, even if it is undescribed. More than 274,000 BIN web pages are now available, creating a biodiversity resource that is positioned for rapid growth.

  3. Potential for DNA-based ID of Great Lakes fauna: Species inventories vs. barcode libraries

    Science.gov (United States)

    DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to biotic condition assessment and non-native species early-detection monitoring. However the abil...

  4. Potential for DNA-based identification of Great Lakes fauna: Match and mismatch between taxa inventories and DNA barcode libraries

    Science.gov (United States)

    DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to biotic condition assessment and non-native species early-detection monitoring. However, the abi...

  5. The NEMO-3 Experiment

    International Nuclear Information System (INIS)

    The NEMO-3 (Neutrino Ettore Majorana Observatory) experiment, located in the Modane Underground Laboratory, is currently searching for neutrinoless double beta decay (0νββ). The experiment has been taking data since 2003 with seven double beta isotopes and is scheduled to complete data acquisition in late 2010. Two neutrino double beta decay (2νββ) results for the main isotopes (7 kg of 100Mo and 1 kg of 82Se), new results for 150Nd, as well as results for 96Zr, 48Ca, 130Te and 116Cd are presented. NEMO-3 uses a unique technique that allows for the in situ measurement of background contamination. No evidence for neutrinoless double beta decay has been found to date. The data are also interpreted in terms of alternative models such as weak right-handed currents and Majoron emission.

  6. Genetic barcodes

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Heinz -Ulrich G

    2015-08-04

    Herein are described multicolor FISH probe sets termed "genetic barcodes" targeting several cancer or disease-related loci to assess gene rearrangements and copy number changes in tumor cells. Two, three or more different fluorophores are used to detect the genetic barcode sections thus permitting unique labeling and multilocus analysis in individual cell nuclei. Gene specific barcodes can be generated and combined to provide both numerical and structural genetic information for these and other pertinent disease associated genes.

  7. Comprehensive DNA barcode coverage of North American birds

    OpenAIRE

    Kerr, Kevin C. R.; Mark Y Stoeckle; Carla J. Dove; Weigt, Lee A.; Charles M. Francis; Hebert, Paul D. N.

    2007-01-01

    DNA barcoding seeks to assemble a standardized reference library for DNA-based identification of eukaryotic species. The utility and limitations of this approach need to be tested on well-characterized taxonomic assemblages. Here we provide a comprehensive DNA barcode analysis for North American birds including 643 species representing 93% of the breeding and pelagic avifauna of the USA and Canada. Most (94%) species possess distinct barcode clusters, with average neighbour-joining bootstrap ...

  8. NEMO-O$\

    CERN Document Server

    Aiello, S

    2008-01-01

    The NEMO (NEutrino Mediterranean Observatory) Collaboration installed, 25 km E offshore the port of Catania (Sicily) at 2000 m depth, an underwater laboratory to perform long-term tests of prototypes and new technologies for an underwater high energy neutrino km$^3$-scale detector in the Mediterranean Sea. In this framework the collaboration deployed and successfully operated for about two years, starting form January 2005, an experimental apparatus for on-line monitoring of deep-sea noise. The station was equipped with 4 hydrophones and it is operational in the range 30 Hz - 43 kHz. This interval of frequencies matches the range suitable for the proposed acoustic detection technique of high energy neutrinos. Hydrophone signals were digitized underwater at 96 kHz sampling frequency and 24 bits resolution. A custom software was developed to record data on high resolution 4-channels digital audio file. This paper deals with the data analysis procedure and first results on the determination of sea noise sound pr...

  9. Unicolor woven barcode; Unicolor nuno barcode

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-03-01

    Development was made on a woven barcode system of single and inconspicuous color of thermal light emission infrared ray detecting system. This is a new barcode system to detect characteristic infrared ray of 4.5 {mu}m from polyacrylonitrile fiber constituting the barcode when it is heated to 70 degrees C. Codes can normally be read in 0.7 second. Differing from transparent barcode made with fluorescent color, the new barcode can be made into a thread, which resulted in realizing a woven barcode. This woven barcode could be applied in different and new ways utilizing its inconspicuousness, in addition to applicability to simplification of control in uniform rental and linen supply operations subject to repeated washing. (translated by NEDO)

  10. NEMO-Nordic : A NEMO based ocean modelling configuration for Baltic & North Seas

    Science.gov (United States)

    Hordoir, Robinson; Schimanke, Semjon; Axell, Lars; Gröger, Matthias; Dieterich, Christian; Liu, Ye; Höglund, Anders; Kuznetsov, Ivan; Ljungemyr, Patrik; Nygren, Petter; Jönsson, Anette; Meier, Markus

    2015-04-01

    Based on the NEMO ocean engine, three regional setups for the North Sea and Baltic Sea domain have been developed : the NEMO-Nordic configuration is declined in an operational setup, a stand-alone version used for climate and process studies, and a NEMO-Nordic-RCA4 atmosphere/ocean coupled configuration used for downscalling climate scenarios. We give a brief overview of the options chosen within the NEMO engine to design the configurations. Based on the results provided by each of the three configurations, we also provide an assessment of the strengths and weaknesses of NEMO-Nordic. Finally, a validation of the configurations is provided based on an extensive comparison between in-situ measurements and model results for temperature, salinity, sea-ice extent, sea level and mean circulation.

  11. The NEMO project: A status report

    Energy Technology Data Exchange (ETDEWEB)

    Taiuti, M., E-mail: Mauro.Taiuti@ge.infn.i [INFN Sezione di Genova, Via Dodecaneso 33, 16146 Genova (Italy); Dipartimento di Fisica, Universita di Genova, Via Dodecaneso 33, 16146 Genova (Italy); Aiello, S. [INFN Sezione di Catania, Via S. Sofia 64, 95123 Catania (Italy); Ameli, F. [INFN Sezione di Roma 1, P.le A. Moro 2, 00185 Roma (Italy); Amore, I. [Laboratori Nazionali del Sud INFN, Via S. Sofia 62, 95123 Catania (Italy); Dipartimento di Fisica e Astronomia, Universita di Catania, Via S. Sofia 64, 95123 Catania (Italy); Anghinolfi, M. [INFN Sezione di Genova, Via Dodecaneso 33, 16146 Genova (Italy); Anzalone, A. [Laboratori Nazionali del Sud INFN, Via S. Sofia 62, 95123 Catania (Italy); Barbarino, G. [INFN Sezione di Napoli, Via Cintia, 80126 Napoli (Italy); Dipartimento di Scienze Fisiche, Universita di Napoli, Via Cintia, 80126 Napoli (Italy); Battaglieri, M. [INFN Sezione di Genova, Via Dodecaneso 33, 16146 Genova (Italy); Bazzotti, M. [INFN Sezione di Bologna, V.le Berti Pichat 6/2, 40127 Bologna (Italy); Dipartimento di Fisica, Universita di Bologna, V.le Berti Pichat 6/2, 40127 Bologna (Italy); Bersani, A. [INFN Sezione di Genova, Via Dodecaneso 33, 16146 Genova (Italy); Beverini, N. [INFN Sezione di Pisa, Polo Fibonacci, Largo B. Pontecorvo 3, 56127 Pisa (Italy); Dipartimento di Fisica, Universita di Pisa, Polo Fibonacci, Largo B. Pontecorvo 3, 56127 Pisa (Italy); Biagi, S. [INFN Sezione di Bologna, V.le Berti Pichat 6/2, 40127 Bologna (Italy); Dipartimento di Fisica, Universita di Bologna, V.le Berti Pichat 6/2, 40127 Bologna (Italy); Bonori, M. [INFN Sezione di Roma 1, P.le A. Moro 2, 00185 Roma (Italy); Dipartimento di Fisica, Universita di Roma La Sapienza, P.le A. Moro 2, 00185 Roma (Italy); Bouhdaef, B. [INFN Sezione di Pisa, Polo Fibonacci, Largo B. Pontecorvo 3, 56127 Pisa (Italy); Dipartimento di Fisica, Universita di Pisa, Polo Fibonacci, Largo B. Pontecorvo 3, 56127 Pisa (Italy)

    2011-01-21

    The latest results and the activities towards the construction of a km{sup 3} Cherenkov neutrino detector carried out by the NEMO Collaboration are described. Long-term exploration of a 3500 m deep-sea site close to the Sicilian coast has shown that it is optimal for the installation of the detector. The NEMO Phase-1 project has validated several technologies proposed for the construction of the km{sup 3} detector on a test site at 2000 m depth. The new infrastructure on the candidate Capo Passero site set up as part of the Phase-2 project will provide the possibility to test detector components at 3500 m depth.

  12. Spectral modeling of scintillator for the NEMO-3 and SuperNEMO detectors

    OpenAIRE

    Argyriades, J.; Arnold, R.; Augier, C.; Baker, J.; Barabash, A. S.; Bongrand, M.; Broudin-Bay, G.; Brudanin, V. B.; Caffrey, A. J.; Cebrián, S; Chapon, A.; Chauveau, E.; Dafni, Th.; Daraktchieva, Z.; iaz, J. D

    2010-01-01

    We have constructed a GEANT4-based detailed software model of photon transport in plastic scintillator blocks and have used it to study the NEMO-3 and SuperNEMO calorimeters employed in experiments designed to search for neutrinoless double beta decay. We compare our simulations to measurements using conversion electrons from a calibration source of $\\rm ^{207}Bi$ and show that the agreement is improved if wavelength-dependent properties of the calorimeter are taken into account. In this arti...

  13. Insect Barcode Information System

    Science.gov (United States)

    Pratheepa, Maria; Jalali, Sushil Kumar; Arokiaraj, Robinson Silvester; Venkatesan, Thiruvengadam; Nagesh, Mandadi; Panda, Madhusmita; Pattar, Sharath

    2014-01-01

    Insect Barcode Information System called as Insect Barcode Informática (IBIn) is an online database resource developed by the National Bureau of Agriculturally Important Insects, Bangalore. This database provides acquisition, storage, analysis and publication of DNA barcode records of agriculturally important insects, for researchers specifically in India and other countries. It bridges a gap in bioinformatics by integrating molecular, morphological and distribution details of agriculturally important insects. IBIn was developed using PHP/My SQL by using relational database management concept. This database is based on the client– server architecture, where many clients can access data simultaneously. IBIn is freely available on-line and is user-friendly. IBIn allows the registered users to input new information, search and view information related to DNA barcode of agriculturally important insects.This paper provides a current status of insect barcode in India and brief introduction about the database IBIn. Availability http://www.nabg-nbaii.res.in/barcode PMID:24616562

  14. New Results from the NEMO 3 Experiment

    CERN Document Server

    Tretyak, V I

    2008-01-01

    NEMO 3 is a currently running experiment to search for the neutrinoless double beta decay and to study the two-neutrino double beta decay with 10kg of enriched isotopes. On the basis of the first two years of data taking, a limit on the neutrinoless decay $T_{1/2}^{0\

  15. Insect Barcode Information System

    OpenAIRE

    Pratheepa, Maria; Jalali, Sushil Kumar; Arokiaraj, Robinson Silvester; Venkatesan, Thiruvengadam; Nagesh, Mandadi; Panda, Madhusmita; Pattar, Sharath

    2014-01-01

    Insect Barcode Information System called as Insect Barcode Informática (IBIn) is an online database resource developed by the National Bureau of Agriculturally Important Insects, Bangalore. This database provides acquisition, storage, analysis and publication of DNA barcode records of agriculturally important insects, for researchers specifically in India and other countries. It bridges a gap in bioinformatics by integrating molecular, morphological and distribution details of agriculturally ...

  16. Using DNA barcoding to assess Caribbean reef fish biodiversity: expanding taxonomic and geographic coverage.

    Directory of Open Access Journals (Sweden)

    Lee A Weigt

    Full Text Available This paper represents a DNA barcode data release for 3,400 specimens representing 521 species of fishes from 6 areas across the Caribbean and western central Atlantic regions (FAO Region 31. Merged with our prior published data, the combined efforts result in 3,964 specimens representing 572 species of marine fishes and constitute one of the most comprehensive DNA barcoding "coverages" for a region reported to date. The barcode data are providing new insights into Caribbean shorefish diversity, allowing for more and more accurate DNA-based identifications of larvae, juveniles, and unknown specimens. Examples are given correcting previous work that was erroneous due to database incompleteness.

  17. The SuperNEMO tracking detector

    CERN Document Server

    Cascella, M

    2015-01-01

    The SuperNEMO detector will search for neutrinoless double beta decay at the Modane Underground Laboratory on the French-Italian border. This decay mode, if observed, would be proof that the neutrino is its own antiparticle, would constitute evidence for total lepton number violation, and could allow a measurement of the absolute neutrino mass. The SuperNEMO experiment is designed to reach a half-life sensitivity of $10^{26}$ years corresponding to an effective Majorana neutrino mass of $50-100~$meV. The SuperNEMO detector design allows complete topological reconstruction of the double beta decay event enabling excellent levels of background rejection. In the event of a discovery, such topological measurements will be vital in determining the nature of the lepton number violating process. This reconstruction will be performed by a gaseous tracking detector, consisting of 2034 drift cells per module operated in Geiger mode. The tracker of the Demonstrator Module is currently under construction in the UK. This ...

  18. Spectral modeling of scintillator for the NEMO-3 and SuperNEMO detectors

    CERN Document Server

    Argyriades, J; Augier, C; Baker, J; Barabash, A S; Bongrand, M; Broudin-Bay, G; Brudanin, V B; Caffrey, A J; Cebrián, S; Chapon, A; Chauveau, E; Dafni, Th; Daraktchieva, Z; iaz, J D; Durand, D; Egorov, V G; Evans, J J; Fatemi-Ghomi, N; Flack, R; Basharina-Freshville, A; Fushimi, K-I; Garrido, X; Gómez, H; Guillon, B; Holin, A; Holy, K; Horkey, J J; Hubert, Ph; Hugon, C; Iguaz, F J; Irastorza, I G; Ishihara, N; Jackson, C M; Jullian, S; Kanamaru, S; Kauer, M; Kochetov, O I; Konovalov, S I; Kovalenko, V E; Lalanne, D; Lang, K; ere, Y Lemi; Lutter, G; Luzón, G; Mamedov, F; Marquet, Ch; Martin-Albo, J; Mauger, F; Monrabal, F; Nachab, A; Nasteva, I; Nemchenok, I B; Nguyen, C H; Nova, F; Novella, P; Ohsumi, H; Pahlka, R B; Perrot, F; Piquemal, F; Povinec, P P; Richards, B; Ricol, J S; Riddle, C L; Rodriguez, A; Saakyan, R; Sarazin, X; Sedgbeer, J K; Serra, L; Simard, L; Šimkovic, F; Shitov, Yu A; Smolnikov, A A; Soldner-Rembold, S; Štekl, I; Sugaya, Y; Sutton, C S; Szklarz, G; Tamagawa, Y; Thomas, J; Thompson, R; Timkin, V V; Tretyak, V I; Tretyak, Vl I; Umatov, V I; ala, L V; Vanyushin, I A; Vasiliev, R; Vorobel, V; Vylov, Ts; Waters, D; Yahlali, N; Žukauskas, A

    2010-01-01

    We have constructed a GEANT4-based detailed software model of photon transport in plastic scintillator blocks and have used it to study the NEMO-3 and SuperNEMO calorimeters employed in experiments designed to search for neutrinoless double beta decay. We compare our simulations to measurements using conversion electrons from a calibration source of $\\rm ^{207}Bi$ and show that the agreement is improved if wavelength-dependent properties of the calorimeter are taken into account. In this article, we briefly describe our modeling approach and results of our studies.

  19. Spectral modeling of scintillator for the NEMO-3 and SuperNEMO detectors

    International Nuclear Information System (INIS)

    We have constructed a GEANT4-based detailed software model of photon transport in plastic scintillator blocks and have used it to study the NEMO-3 and SuperNEMO calorimeters employed in experiments designed to search for neutrinoless double beta decay. We compare our simulations to measurements using conversion electrons from a calibration source of 207Bi and show that the agreement is improved if wavelength-dependent properties of the calorimeter are taken into account. In this article, we briefly describe our modeling approach and results of our studies.

  20. A comparative signaling cost analysis of Macro Mobility scheme in NEMO (MM-NEMO) with mobility management protocol

    International Nuclear Information System (INIS)

    NEMO BSP is an upgraded addition to Mobile IPv6 (MIPv6). As MIPv6 and its enhancements (i.e. HMIPv6) possess some limitations like higher handoff latency, packet loss, NEMO BSP also faces all these shortcomings by inheritance. Network Mobility (NEMO) is involved to handle the movement of Mobile Router (MR) and it's Mobile Network Nodes (MNNs) during handoff. Hence it is essential to upgrade the performance of mobility management protocol to obtain continuous session connectivity with lower delay and packet loss in NEMO environment. The completion of handoff process in NEMO BSP usually takes longer period since MR needs to register its single primary care of address (CoA) with home network that may cause performance degradation of the applications running on Mobile Network Nodes. Moreover, when a change in point of attachment of the mobile network is accompanied by a sudden burst of signaling messages, ''Signaling Storm'' occurs which eventually results in temporary congestion, packet delays or even packet loss. This effect is particularly significant for wireless environment where a wireless link is not as steady as a wired link since bandwidth is relatively limited in wireless link. Hence, providing continuous Internet connection without any interruption through applying multihoming technique and route optimization mechanism in NEMO are becoming the center of attention to the current researchers. In this paper, we propose a handoff cost model to compare the signaling cost of MM-NEMO with NEMO Basic Support Protocol (NEMO BSP) and HMIPv6.The numerical results shows that the signaling cost for the MM-NEMO scheme is about 69.6 % less than the NEMO-BSP and HMIPv6

  1. DNA-based human karyotype

    Energy Technology Data Exchange (ETDEWEB)

    Mayall, B.H.; Carrano, A.V.; Moore, C.H. II; Ashworth, L.K.; Bennett, D.E.; Mendelsohn, M.L.

    1984-01-01

    Image cytometry and computer analysis are used to determine the relative DNA content and the DNA-based centromeric index of the 24 chromosomes of the human karyotype. A two-step procedure is used. Chromosomes of cells in metaphase first are stained with quinacrine and identified visually by their fluorescent Q-band patterns. They then are stained for DNA using gallocyanin-chrome alum. The chromosome images are scanned and recorded as digital values of optical density by an CYDAC image cytometric microscope system, CYDAC. The digital images are processed by computer to measure for each chromosome the relative DNA stain contents of the whole chromosome and of the p and q arms and the DNA-based centromeric index. About ten cells are analyzed for each of the donors, who are phenotypically normal men and women. The chromosome measurements are pooled by chromosome type for each donor and are compared among donors. The means of the chromosome measurements give the DNA-based human karyotype. Analysis of the DNA-based data shows that some chromosomes or portions of chromosomes vary significantly among donors. These variants do not correlate with detectable morphologic polymorphisms, such as Q- or C-band variants; thus they represent new and otherwise undetectable chromosome polymorphisms whose genetic basis and clinical significance are yet to be determined. 54 references, 1 figure, 3 tables.

  2. DNA-based hybrid catalysis

    NARCIS (Netherlands)

    Rioz-Martínez, Ana; Roelfes, Gerard

    2015-01-01

    In the past decade, DNA-based hybrid catalysis has merged as a promising novel approach to homogeneous (asymmetric) catalysis. A DNA hybrid catalysts comprises a transition metal complex that is covalently or supramolecularly bound to DNA. The chiral microenvironment and the second coordination sphe

  3. [Forced Oscillations of DNA Bases].

    Science.gov (United States)

    Yakushevich, L V; Krasnobaeva, L A

    2016-01-01

    This paper presents the results of the studying of forced angular oscillations of the DNA bases with the help of the mathematical model consisting of two coupled nonlinear differential equations that take into account the effects of dissipation and the influence of an external periodic field. The calculation results are illustrated for sequence of gene encoding interferon alpha 17 (IFNA 17). PMID:27192830

  4. NEMO: Network Mobility in IPv6 (NEMO: movilidad de redes en IPv6)

    OpenAIRE

    Bernardos, Carlos J.; Soto, Ignacio; Calderón, María; Dirk, Hugo von; Riou, Enmmanuel

    2005-01-01

    Nowadays, users request Internet access in more and more heterogeneous scenarios. In particular a need to access the Internet from mobile platforms, like trains, buses or planes, has appeared. A new working group has been formed within the IETF (Internet Engineering Task Force) NEMO WG (NEtwork MObility Working Group) whose main goal is to provide mechanisms allowing the management of the mobility of a network as a whole, enabling that network to change its point of attachment to an ...

  5. DNA barcoding for species assignment: the case of Mediterranean marine fishes.

    Directory of Open Access Journals (Sweden)

    Monica Landi

    Full Text Available BACKGROUND: DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity. METHODOLOGY/PRINCIPAL FINDINGS: A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes to assign species from query sequences. We tested query sequences against 1 a reference library of ranked DNA barcodes from the neighbouring North East Atlantic, and 2 the public databases BOLD and GenBank. In the first case, a reference library comprising DNA barcodes with reliability grades for 146 fish species was used as diagnostic dataset to screen 486 query DNA sequences from fish specimens collected in the central basin of the Mediterranean Sea. Of all query sequences suitable for comparisons 98% were unambiguously confirmed through complete match with reference DNA barcodes. In the second case, it was possible to assign species to 83% (BOLD-IDS and 72% (GenBank of the sequences from the Mediterranean. Relatively high intraspecific genetic distances were found in 7 species (2.2%-18.74%, most of them of high commercial relevance, suggesting possible cryptic species. CONCLUSION/SIGNIFICANCE: We emphasize the discriminatory power of COI barcodes and their application to cases requiring species level resolution starting from query sequences. Results highlight the value of public reference libraries of reliability grade-annotated DNA barcodes, to identify species from different geographical origins. The ability to assign species with high precision from DNA

  6. Barcode uses and abuses

    Energy Technology Data Exchange (ETDEWEB)

    KEENEN,MARTHA JANE; NUSBAUM,ANNA W.

    2000-05-18

    Barcodes are something that everybody sees every day; so common as to be taken for granted and normally unnoticed. Readable, no one reads them. They are used to allow machines to identify a wide variety of non-electronic, real life objects. Barcode is one of the earliest types of what is now called ``Automatic Identification and Data Capture'' (AIDC), meaning ``data was transmitted into whatever system by something other than typing or hand-writing.'' There are 18 technologies, broken down into six categories--biometrics, electromagnetic, magnetic, optical, Smart Cards, Touch--included in the AIDC concept. Many are used jointly with or as adjuncts to a basic barcode system of some type. All are based on assignment of a unique identifier to the object, usually a number. The uniqueness presumption makes barcode systems very applicable and appropriate to the nuclear information management venue as they inherently comply with the Nuclear Quality Assurance (NQA-1) requirements. Barcode systems belong to the optical category of AIDC. It is very old in usage as these technologies go, having first been patented in 1949. It astonished me, in researching this paper, to find that there are over 250 types of barcode (symbologies), each with its own specialized attributes, though only a few dozen are in active use. The initial uses were in the early 1950s and diversity of use is ever increasing as people find new ways to make this versatile old technology work. To what else could it be applied, in the future? This paper attempts to answer this.

  7. Recent Developments of NEMO: Detection of Solar Eruptions Characteristics

    CERN Document Server

    Podladchikova, Olena; Leontiev, Pavel; Van der Linden, Ronald

    2011-01-01

    The recent developments in space instrumentation for solar observations and telemetry have caused the necessity of advanced pattern recognition tools for the different classes of solar events. The Extreme ultraviolet Imaging Telescope (EIT) of solar corona on-board SOHO spacecraft has uncovered a new class of eruptive events which are often identified as signatures of Coronal Mass Ejection (CME) initiations on solar disk. It is evident that a crucial task is the development of an automatic detection tool of CMEs precursors. The Novel EIT wave Machine Observing (NEMO) (http://sidc.be/nemo) code is an operational tool that detects automatically solar eruptions using EIT image sequences. NEMO applies techniques based on the general statistical properties of the underlying physical mechanisms of eruptive events on the solar disc. In this work, the most recent updates of NEMO code - that have resulted to the increase of the recognition efficiency of solar eruptions linked to CMEs - are presented. These updates pro...

  8. Brain endothelial TAK1 and NEMO safeguard the neurovascular unit

    Science.gov (United States)

    Ridder, Dirk A.; Wenzel, Jan; Müller, Kristin; Töllner, Kathrin; Tong, Xin-Kang; Assmann, Julian C.; Stroobants, Stijn; Weber, Tobias; Niturad, Cristina; Fischer, Lisanne; Lembrich, Beate; Wolburg, Hartwig; Grand’Maison, Marilyn; Papadopoulos, Panayiota; Korpos, Eva; Truchetet, Francois; Rades, Dirk; Sorokin, Lydia M.; Schmidt-Supprian, Marc; Bedell, Barry J.; Pasparakis, Manolis; Balschun, Detlef; D’Hooge, Rudi; Löscher, Wolfgang; Hamel, Edith

    2015-01-01

    Inactivating mutations of the NF-κB essential modulator (NEMO), a key component of NF-κB signaling, cause the genetic disease incontinentia pigmenti (IP). This leads to severe neurological symptoms, but the mechanisms underlying brain involvement were unclear. Here, we show that selectively deleting Nemo or the upstream kinase Tak1 in brain endothelial cells resulted in death of endothelial cells, a rarefaction of brain microvessels, cerebral hypoperfusion, a disrupted blood–brain barrier (BBB), and epileptic seizures. TAK1 and NEMO protected the BBB by activating the transcription factor NF-κB and stabilizing the tight junction protein occludin. They also prevented brain endothelial cell death in a NF-κB–independent manner by reducing oxidative damage. Our data identify crucial functions of inflammatory TAK1–NEMO signaling in protecting the brain endothelium and maintaining normal brain function, thus explaining the neurological symptoms associated with IP. PMID:26347470

  9. Multfilm "V poiskah Nemo" delajet detei ubiitsami rõbok

    Index Scriptorium Estoniae

    2004-01-01

    Animafilm "Kalapoeg Nemo" : režissöör Andrew Stanton : Ameerika Ühendriigid 2003. Filmi vaatamise järgselt on tuhanded lapsed lasknud oma akvaariumikalad vabadusse, põhjustades sellega nende huku või keskkonnaprobleeme

  10. Brain endothelial TAK1 and NEMO safeguard the neurovascular unit

    OpenAIRE

    Ridder, Dirk A.; Wenzel, Jan; Müller, Kristin; Töllner, Kathrin; Tong, Xin-Kang; Assmann, Julian C; Stroobants, Stijn; Weber, Tobias; Niturad, Cristina; Fischer, Lisanne; Lembrich, Beate; Wolburg, Hartwig; Grand'Maison, Marilyn; Papadopoulos, Panayiota; Korpos, Eva

    2015-01-01

    Inactivating mutations of the NF-κB essential modulator (NEMO), a key component of NF-κB signaling, cause the genetic disease incontinentia pigmenti (IP). This leads to severe neurological symptoms, but the mechanisms underlying brain involvement were unclear. Here, we show that selectively deleting Nemo or the upstream kinase Tak1 in brain endothelial cells resulted in death of endothelial cells, a rarefaction of brain microvessels, cerebral hypoperfusion, a disrupted blood–brain barrier (BB...

  11. PORFIDO on the NEMO Phase 2 tower

    Energy Technology Data Exchange (ETDEWEB)

    Ciaffoni, Orlando; Cordelli, Marco; Habel, Roberto; Martini, Agnese; Trasatti, Luciano [INFN-Laboratori Nazionali di Frascati, Via E. Fermi 40, I-00044 Frascati (RM) (Italy)

    2014-11-18

    We have designed and built an underwater measurement system, PORFIDO (Physical Oceanography by RFID Outreach) to gather oceanographic data from the Optical Modules of a neutrino telescope with a minimum of disturbance to the main installation. PORFIDO is composed of a sensor glued to the outside of an Optical Module, in contact with seawater, and of a reader placed inside the sphere, facing the sensor. Data are transmitted to the reader through the glass by RFID and to shore in real time for periods of years. The sensor gathers power from the radio frequency, thus eliminating the need for batteries or connectors through the glass. We have deployed four PORFIDO probes measuring temperatures with the NEMO-KM3Net-Italy Phase 2 tower in april 2013. The four probes are operative and are transmitting temperature data from 3500 m depth.

  12. PORFIDO on the NEMO Phase 2 tower

    International Nuclear Information System (INIS)

    We have designed and built an underwater measurement system, PORFIDO (Physical Oceanography by RFID Outreach) to gather oceanographic data from the Optical Modules of a neutrino telescope with a minimum of disturbance to the main installation. PORFIDO is composed of a sensor glued to the outside of an Optical Module, in contact with seawater, and of a reader placed inside the sphere, facing the sensor. Data are transmitted to the reader through the glass by RFID and to shore in real time for periods of years. The sensor gathers power from the radio frequency, thus eliminating the need for batteries or connectors through the glass. We have deployed four PORFIDO probes measuring temperatures with the NEMO-KM3Net-Italy Phase 2 tower in april 2013. The four probes are operative and are transmitting temperature data from 3500 m depth

  13. Low power electronics for NEMO detector

    International Nuclear Information System (INIS)

    For the realization of the submarine detector NEMO it is necessary to design an acquisition system which is able to capture the signals coming from photo-multipliers (PMs) of the optical modules (OMs) and to satisfy several specifications: low power consumption; few submarine interconnections for reliability and simplicity of the deployment; flexibility of the system; minimum dead time; high dynamic range; accuracy in order to have good resolution. Here we present a Very Large Scale Integration full-custom solution for the OMs according to the requirements. It foresees to use a switched capacitor analog memory, a trigger and single photon classification system, a PLL and a control unit able to manage the different operation states of the whole system. For such a system we foresee a power dissipation not higher than 200-300 mV in each OM, 20 bit dynamic range and a dead time of about 0.1%

  14. Measurement of double-beta-decay—experiments TGV and NEMO

    Science.gov (United States)

    Štekl, I.

    2001-06-01

    A description of the aim and present status of the experiments NEMO and TGV are presented. The NEMO collaboration developed the detector NEMO-2 to investigate double-beta ( ββ) decay of 100Mo, 116Cd, 82Se and 96Zr. The results obtained for the above mentioned isotopes are given. The new detector NEMO-3, which is approximately 20 times larger than NEMO-2, is under construction. The NEMO-3 detector should allow the study of 0 νββ decays of 100Mo (or other isotopes) with half-life ˜10 25years, corresponding to neutrino masses of 0.1- 0.3 eV. The TGV I collaboration has studied the ββ decay of 48Ca. The result T 2 νββ1/2=(4.2 +3.3-1.3)×10 19 years has been found. Experiment TGV II is devoted to measurement of the ββ decay (β +β +, β +/ EC, EC/ EC) of 106Cd, particularly the 2 νEC/EC mode.

  15. Measurement of double-beta-decay--experiments TGV and NEMO

    International Nuclear Information System (INIS)

    A description of the aim and present status of the experiments NEMO and TGV are presented. The NEMO collaboration developed the detector NEMO-2 to investigate double-beta (ββ) decay of 100Mo, 116Cd, 82Se and 96Zr. The results obtained for the above mentioned isotopes are given. The new detector NEMO-3, which is approximately 20 times larger than NEMO-2, is under construction. The NEMO-3 detector should allow the study of 0νββ decays of 100Mo (or other isotopes) with half-life ∼1025 years, corresponding to neutrino masses of 0.1-0.3 eV. The TGV I collaboration has studied the ββ decay of 48Ca. The result T2νββ1/2=(4.2+3.3-1.3)x1019 years has been found. Experiment TGV II is devoted to measurement of the ββ decay (β+β+, β+/EC, EC/EC) of 106Cd, particularly the 2νEC/EC mode. (author)

  16. Research on Barcode Image Binarization in Barcode Positioning System

    Directory of Open Access Journals (Sweden)

    Dongli Li

    2012-09-01

    Full Text Available Aiming at the disadvantages of the traditional positioning technology, barcode positioning system is introduced in this paper. Based on Otsu method, a novel barcode image binarization is put forward by comparing varieties of image binarization methods domestically and abroad. Moreover, we have a systematic research on histogram and binarization mechanism, and also give the calculation of histogram and derive a formula of Otsu method. Finally, the histogram and binarization of one-dimensional barcode image are realized with the specific examples. After experiments for scanned barcode image, the result has demonstrated effectiveness of the method.

  17. Analyzing mosquito (Diptera: culicidae diversity in Pakistan by DNA barcoding.

    Directory of Open Access Journals (Sweden)

    Muhammad Ashfaq

    Full Text Available BACKGROUND: Although they are important disease vectors mosquito biodiversity in Pakistan is poorly known. Recent epidemics of dengue fever have revealed the need for more detailed understanding of the diversity and distributions of mosquito species in this region. DNA barcoding improves the accuracy of mosquito inventories because morphological differences between many species are subtle, leading to misidentifications. METHODOLOGY/PRINCIPAL FINDINGS: Sequence variation in the barcode region of the mitochondrial COI gene was used to identify mosquito species, reveal genetic diversity, and map the distribution of the dengue-vector species in Pakistan. Analysis of 1684 mosquitoes from 491 sites in Punjab and Khyber Pakhtunkhwa during 2010-2013 revealed 32 species with the assemblage dominated by Culex quinquefasciatus (61% of the collection. The genus Aedes (Stegomyia comprised 15% of the specimens, and was represented by six taxa with the two dengue vector species, Ae. albopictus and Ae. aegypti, dominant and broadly distributed. Anopheles made up another 6% of the catch with An. subpictus dominating. Barcode sequence divergence in conspecific specimens ranged from 0-2.4%, while congeneric species showed from 2.3-17.8% divergence. A global haplotype analysis of disease-vectors showed the presence of multiple haplotypes, although a single haplotype of each dengue-vector species was dominant in most countries. Geographic distribution of Ae. aegypti and Ae. albopictus showed the later species was dominant and found in both rural and urban environments. CONCLUSIONS: As the first DNA-based analysis of mosquitoes in Pakistan, this study has begun the construction of a barcode reference library for the mosquitoes of this region. Levels of genetic diversity varied among species. Because of its capacity to differentiate species, even those with subtle morphological differences, DNA barcoding aids accurate tracking of vector populations.

  18. Data transmission and acquisition in NEMO

    International Nuclear Information System (INIS)

    A comprehensive system for data transmission and acquisition has been developed for an 'a la NEMO' underwater neutrino telescope based on Cerenkov light detection using photomultipliers (PMTs) as sensors. Signals generated by each sensor are triggered, sampled and tagged by an electronics board, called Front End Module (FEM). Data streams from up to eight FEMs located on one tower floor are collected by a concentration board called Floor Control Module (FCM) and sent to a twin FCM board-located at the onshore station and plugged into an interface machine (FCM Interface, or FCMI) via a PCI bus-through a DWDM-compliant optical fiber and using a self-synchronous serial protocol. All sensor data reach the onshore lab through FCMI where they are made available to subsequent elaboration processes, such as time-wise alignment and muon track event-triggering. To meet requirements of the latter, onshore data unpacking is carried out with respect to their topological origin. The system promised, and keeps on showing, very light charges on power consumption and infrastructure complexity, while having recently proved to behave at high performance levels in its optical part

  19. Data transmission and acquisition in NEMO

    Energy Technology Data Exchange (ETDEWEB)

    Bunkheila, G. [Istituto Nazionale di Fisica Nucleare (INFN), sez. Roma 1, Marconi Building, University of Rome ' La Sapienza' , P.le Aldo Moro 2 - 00185 (Italy)]. E-mail: gabriele.bunkheila@gmail.com

    2006-11-15

    A comprehensive system for data transmission and acquisition has been developed for an 'a la NEMO' underwater neutrino telescope based on Cerenkov light detection using photomultipliers (PMTs) as sensors. Signals generated by each sensor are triggered, sampled and tagged by an electronics board, called Front End Module (FEM). Data streams from up to eight FEMs located on one tower floor are collected by a concentration board called Floor Control Module (FCM) and sent to a twin FCM board-located at the onshore station and plugged into an interface machine (FCM Interface, or FCMI) via a PCI bus-through a DWDM-compliant optical fiber and using a self-synchronous serial protocol. All sensor data reach the onshore lab through FCMI where they are made available to subsequent elaboration processes, such as time-wise alignment and muon track event-triggering. To meet requirements of the latter, onshore data unpacking is carried out with respect to their topological origin. The system promised, and keeps on showing, very light charges on power consumption and infrastructure complexity, while having recently proved to behave at high performance levels in its optical part.

  20. Measurement of double beta decay - experiments TGV and NEMO

    International Nuclear Information System (INIS)

    TGV and NEMO, two international collaboration projects are described. The TGV project deals with the double beta decay of 48Ca. In 1998, this project was augmented with the examination of the double beta decay of 106Cd - the β+β+, β+/EC, and EC/EC modes. The main objective of this experiment consists in recording the 2νEC/EC mode (0+ → 0+, ground state), giving rise to the emission of 2 gamma quanta of roughly 21 keV. The NEMO project deals with 100Mo. The main objective of the NEMO-3 experiment consists in the measurement of the half-life of the neutrinoless double decay of this nuclide (about 1025 years)

  1. 77 FR 12764 - POSTNET Barcode Discontinuation

    Science.gov (United States)

    2012-03-02

    ... are as follows: * * * * * d. Barcoded Discount--Flats. The barcoded discount applies to BPM flats that... Barcoded Bound Printed Matter The barcode discount applies only to BPM flat-size pieces that bear an... mailing of 50 or more flat-size pieces or part of a presort price mailing of at least 300 BPM...

  2. Expanding the substantial interactome of NEMO using protein microarrays.

    Directory of Open Access Journals (Sweden)

    Beau J Fenner

    Full Text Available Signal transduction by the NF-kappaB pathway is a key regulator of a host of cellular responses to extracellular and intracellular messages. The NEMO adaptor protein lies at the top of this pathway and serves as a molecular conduit, connecting signals transmitted from upstream sensors to the downstream NF-kappaB transcription factor and subsequent gene activation. The position of NEMO within this pathway makes it an attractive target from which to search for new proteins that link NF-kappaB signaling to additional pathways and upstream effectors. In this work, we have used protein microarrays to identify novel NEMO interactors. A total of 112 protein interactors were identified, with the most statistically significant hit being the canonical NEMO interactor IKKbeta, with IKKalpha also being identified. Of the novel interactors, more than 30% were kinases, while at least 25% were involved in signal transduction. Binding of NEMO to several interactors, including CALB1, CDK2, SAG, SENP2 and SYT1, was confirmed using GST pulldown assays and coimmunoprecipitation, validating the initial screening approach. Overexpression of CALB1, CDK2 and SAG was found to stimulate transcriptional activation by NF-kappaB, while SYT1 overexpression repressed TNFalpha-dependent NF-kappaB transcriptional activation in human embryonic kidney cells. Corresponding with this finding, RNA silencing of CDK2, SAG and SENP2 reduced NF-kappaB transcriptional activation, supporting a positive role for these proteins in the NF-kappaB pathway. The identification of a host of new NEMO interactors opens up new research opportunities to improve understanding of this essential cell signaling pathway.

  3. Expanding the substantial interactome of NEMO using protein microarrays.

    LENUS (Irish Health Repository)

    Fenner, Beau J

    2010-01-01

    Signal transduction by the NF-kappaB pathway is a key regulator of a host of cellular responses to extracellular and intracellular messages. The NEMO adaptor protein lies at the top of this pathway and serves as a molecular conduit, connecting signals transmitted from upstream sensors to the downstream NF-kappaB transcription factor and subsequent gene activation. The position of NEMO within this pathway makes it an attractive target from which to search for new proteins that link NF-kappaB signaling to additional pathways and upstream effectors. In this work, we have used protein microarrays to identify novel NEMO interactors. A total of 112 protein interactors were identified, with the most statistically significant hit being the canonical NEMO interactor IKKbeta, with IKKalpha also being identified. Of the novel interactors, more than 30% were kinases, while at least 25% were involved in signal transduction. Binding of NEMO to several interactors, including CALB1, CDK2, SAG, SENP2 and SYT1, was confirmed using GST pulldown assays and coimmunoprecipitation, validating the initial screening approach. Overexpression of CALB1, CDK2 and SAG was found to stimulate transcriptional activation by NF-kappaB, while SYT1 overexpression repressed TNFalpha-dependent NF-kappaB transcriptional activation in human embryonic kidney cells. Corresponding with this finding, RNA silencing of CDK2, SAG and SENP2 reduced NF-kappaB transcriptional activation, supporting a positive role for these proteins in the NF-kappaB pathway. The identification of a host of new NEMO interactors opens up new research opportunities to improve understanding of this essential cell signaling pathway.

  4. First results from the NEMO Phase-1 experiment

    International Nuclear Information System (INIS)

    The NEMO prototype detector, called 'NEMO Phase-1', has been successfully operated at 2000 m depth from December 2006 to May 2007. The apparatus comprises a Junction Box and a Mini-Tower hosting 16 optical sensors. Preliminary results are presented. Positions of the optical sensors in the Mini-Tower were reconstructed through the acoustic positioning system with a high level accuracy. Environmental parameters were analyzed. From data corresponding to a live time of 11.3 h, atmospheric muon tracks have been reconstructed and their angular distributions were measured and compared with Monte Carlo simulations.

  5. Development of quantum device simulator NEMO-VN1

    International Nuclear Information System (INIS)

    We have developed NEMO-VN1 (NanoElectronic MOdelling), a new modelling tool that simulates a wide variety of quantum devices including Quantum Dot (QD), Resonant Tunneling Diode (RTD), Resonant Tunneling Transistor (RTT), Single Electron Transistor (SET), Molecular FET (MFET), Carbon Nanotube FET (CNTFET), Spin FET (SPINFET). It has a collection of models that allow user to trade off between calculation speed and accuracy. NEMO-VN1 also includes a graphic user interface of Matlab that enables parameter entry, calculation control, intuitive display of calculation results, and in-situ data analysis methods.

  6. Neutrino Physics without Neutrinos: Recent results from the NEMO-3 experiment and plans for SuperNEMO

    CERN Document Server

    CERN. Geneva

    2015-01-01

    The observation of neutrino oscillations has proved that neutrinos have mass. This discovery has renewed and strengthened the interest in neutrinoless double beta decay experiments which provide the only practical way to determine whether neutrinos are Majorana or Dirac particles. The recently completed NEMO-3 experiment, located in the Laboratoire Souterrain de Modane in the Frejus Tunnel, was an experiment searching for neutrinoless double beta decays using a powerful technique for detecting a two-electron final state by employing an apparatus combining tracking, calorimetry, and the time-of-flight measurements. We will present latest results from NEMO-3 and will discuss the status of SuperNEMO, the next generation experiment that will exploit the same experimental technique to extend the sensitivity of the current search.

  7. DNA Barcoding of Marine Metazoa

    Science.gov (United States)

    Bucklin, Ann; Steinke, Dirk; Blanco-Bercial, Leocadio

    2011-01-01

    More than 230,000 known species representing 31 metazoan phyla populate the world's oceans. Perhaps another 1,000,000 or more species remain to be discovered. There is reason for concern that species extinctions may outpace discovery, especially in diverse and endangered marine habitats such as coral reefs. DNA barcodes (i.e., short DNA sequences for species recognition and discrimination) are useful tools to accelerate species-level analysis of marine biodiversity and to facilitate conservation efforts. This review focuses on the usual barcode region for metazoans: a ˜648 base-pair region of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Barcodes have also been used for population genetic and phylogeographic analysis, identification of prey in gut contents, detection of invasive species, forensics, and seafood safety. More controversially, barcodes have been used to delimit species boundaries, reveal cryptic species, and discover new species. Emerging frontiers are the use of barcodes for rapid and increasingly automated biodiversity assessment by high-throughput sequencing, including environmental barcoding and the use of barcodes to detect species for which formal identification or scientific naming may never be possible.

  8. Measurement of double beta decay - experiments TGV and NEMO

    International Nuclear Information System (INIS)

    The group of experimentalists of FNSPE CTU Prague takes part in two experiments connected with double beta (ββ) decay - TGV and NEMO. Both experimental set-ups are placed in the Modane underground laboratory (France). Experiment TGV has two phases. TGV I is a measurement of ββ decay of 48Ca (β-β-) and TGV II is a measurement with 106Cd (EC/EC, β+β+, β+/EC). The design and performances of the TGV I apparatus have been already detailed elsewhere. Measurements of the ββ decay of 48Ca have been started in August of 1996. The processing of the experimental data (still in progress), covering almost one year exposition (8700 hours), led to the following value of the half-life of 2νββ of 48Ca, T1/2 (4.2-1.3+3.3) . 1019 years and to an estimate of a limit on the half-life of 0νββ of 48Ca, T1/2 > 1.5 . 1021 years (90% CL). The aim of the project TGV II is the measurement of ββ decay of 106Cd particularly 2νEC/EC mode. This decay, up to now not measured, is characterized by the emission of two X-rays with energy approx. 23 keV. Project should give also information on the other modes - β+β+, β+/EC and EC/EC accompanied by the emission of a Majoron. TGV II is based on new spectrometer consisting of 32 HPGe detectors similar to the TGV I spectrometer. The background measurement is now in progress. The start of measurement with 106Cd is planned from the end of 2000. FNSPE CTU also participates in NEMO collaboration. The goal of the experiment NEMO-3 is to be sensitive to a 0.1 eV Majorana neutrino mass by looking for the 0νββ process of 100Mo. Two prototypes NEMO-1 and NEMO-2 have been built. The NEMO-2 gave (after 6 years of data taking) physical results for 2νββdecay of 100Mo, 116Cd, 82Se and 96Zr. The installation of NEMO-3 detector started in the Modane underground laboratory and should be ready in summer 2000. (author)

  9. Research on Barcode Image Binarization in Barcode Positioning System

    OpenAIRE

    Dongli Li; Weijun Zhang

    2012-01-01

    Aiming at the disadvantages of the traditional positioning technology, barcode positioning system is introduced in this paper. Based on Otsu method, a novel barcode image binarization is put forward by comparing varieties of image binarization methods domestically and abroad. Moreover, we have a systematic research on histogram and binarization mechanism, and also give the calculation of histogram and derive a formula of Otsu method. Finally, the histogram and binarization of one-dimensional ...

  10. DNA barcoding of the Lemnaceae, a family of aquatic monocots

    Directory of Open Access Journals (Sweden)

    Wang Wenqin

    2010-09-01

    Full Text Available Abstract Background Members of the aquatic monocot family Lemnaceae (commonly called duckweeds represent the smallest and fastest growing flowering plants. Their highly reduced morphology and infrequent flowering result in a dearth of characters for distinguishing between the nearly 38 species that exhibit these tiny, closely-related and often morphologically similar features within the same family of plants. Results We developed a simple and rapid DNA-based molecular identification system for the Lemnaceae based on sequence polymorphisms. We compared the barcoding potential of the seven plastid-markers proposed by the CBOL (Consortium for the Barcode of Life plant-working group to discriminate species within the land plants in 97 accessions representing 31 species from the family of Lemnaceae. A Lemnaceae-specific set of PCR and sequencing primers were designed for four plastid coding genes (rpoB, rpoC1, rbcL and matK and three noncoding spacers (atpF-atpH, psbK-psbI and trnH-psbA based on the Lemna minor chloroplast genome sequence. We assessed the ease of amplification and sequencing for these markers, examined the extent of the barcoding gap between intra- and inter-specific variation by pairwise distances, evaluated successful identifications based on direct sequence comparison of the "best close match" and the construction of a phylogenetic tree. Conclusions Based on its reliable amplification, straightforward sequence alignment, and rates of DNA variation between species and within species, we propose that the atpF-atpH noncoding spacer could serve as a universal DNA barcoding marker for species-level identification of duckweeds.

  11. Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices

    Science.gov (United States)

    Yan, Hao; Labean, Thomas H.; Feng, Liping; Reif, John H.

    2003-07-01

    The programmed self-assembly of patterned aperiodic molecular structures is a major challenge in nanotechnology and has numerous potential applications for nanofabrication of complex structures and useful devices. Here we report the construction of an aperiodic patterned DNA lattice (barcode lattice) by a self-assembly process of directed nucleation of DNA tiles around a scaffold DNA strand. The input DNA scaffold strand, constructed by ligation of shorter synthetic oligonucleotides, provides layers of the DNA lattice with barcode patterning information represented by the presence or absence of DNA hairpin loops protruding out of the lattice plane. Self-assembly of multiple DNA tiles around the scaffold strand was shown to result in a patterned lattice containing barcode information of 01101. We have also demonstrated the reprogramming of the system to another patterning. An inverted barcode pattern of 10010 was achieved by modifying the scaffold strands and one of the strands composing each tile. A ribbon lattice, consisting of repetitions of the barcode pattern with expected periodicity, was also constructed by the addition of sticky ends. The patterning of both classes of lattices was clearly observable via atomic force microscopy. These results represent a step toward implementation of a visual readout system capable of converting information encoded on a 1D DNA strand into a 2D form readable by advanced microscopic techniques. A functioning visual output method would not only increase the readout speed of DNA-based computers, but may also find use in other sequence identification techniques such as mutation or allele mapping.

  12. Extending NEMO for ensemble data assimilation on supercomputers with the parallel data assimilation framework PDAF

    OpenAIRE

    Nerger, Lars; Kirchgessner, Paul

    2014-01-01

    The NEMO model is a state-of-the-art ocean circulation model. For data assimilation applications with ensemble Kalman filters like the SEEK filter, e.g. for operational ocean forecasting, NEMO is typically run separately from the assimilation algorithm. Thus, NEMO is used to generate a set of restart files on disks that hold the ensemble of model forecasts providing the error covariance matrix information for the ensemble Kalman filter. These files need to be read by a separate assimilation p...

  13. A Tunnel Compress Scheme for Multi-Tunneling in PMIPv6-based Nested NEMO

    OpenAIRE

    Youn-Hee Han; Hyo-Beom Lee; Min-Soo Woo; Sung-Gi Min

    2010-01-01

    In nested NEMO, a multi-tunneling causes a pinball routing problem. Several solutions proposed tosolve the pinball routing problem in NEMO BSP cannot be used at PMIPv6-based NEMO due todifferent environment such as no route optimization with CN. We propose a tunnel compress scheme formulti-tunneling in PMIPv6-based NEMO. The scheme consists of two parts: the first part is an interdomainor wired Internet part. The other is an intra part of nested mobile networks. In the inter-domainpart, singl...

  14. Tamper-indicating barcode and method

    Energy Technology Data Exchange (ETDEWEB)

    Cummings, Eric B.; Even, Jr., William R.; Simmons, Blake A.; Dentinger, Paul Michael

    2005-03-22

    A novel tamper-indicating barcode methodology is disclosed that allows for detection of alteration to the barcode. The tamper-indicating methodology makes use of a tamper-indicating means that may be comprised of a particulate indicator, an optical indicator, a deformable substrate, and/or may be an integrated aspect of the barcode itself. This tamper-indicating information provides greater security for the contents of containers sealed with the tamper-indicating barcodes.

  15. UK low-background infrastructure for delivering SuperNEMO

    CERN Document Server

    Liu, Xin Ran

    2015-01-01

    SuperNEMO is a next generation neutrinoless double beta decay experiment with a design capability to reach a half-life sensitivity of $10^{26}$ years corresponding to an effective Majorana neutrino mass of $\\langle m_{\\beta\\beta} \\rangle$ $<$ 50 - 100 meV. To achieve this sensitivity, stringent radio-purity requirements are imposed resulting in an equally stringent screening programme. Dedicated facilities have been established in the UK for screening and selection of detector construction materials. Gamma ray spectroscopy using high-purity germanium (HPGe) detectors has been the standard method for the measurement of material contamination. A low-background facility has been established at Boulby Underground Laboratory. The first results from the 2 current HPGe detector are shown. Radon is one of the most critical backgrounds for SuperNEMO and most other low background experiments. It can enter the detector either through diffusion, contamination during construction or emanation from the detector material...

  16. NEMO 3 double beta decay experiment: latest results

    CERN Document Server

    Barabash, A S

    2008-01-01

    The double beta decay experiment NEMO~3 has been taking data since February 2003. The aim of this experiment is to search for neutrinoless decay and investigate two neutrino double beta decay in seven different enriched isotopes ($^{100}$Mo,$^{82}$Se, $^{48}$Ca, $^{96}$Zr, $^{116}$Cd, $^{130}$Te and $^{150}$Nd). After analysis of the data corresponding to 693 days, no evidence for $0\

  17. OpenDA-NEMO framework for ocean data assimilation

    Science.gov (United States)

    van Velzen, Nils; Altaf, Muhammad Umer; Verlaan, Martin

    2016-05-01

    Data assimilation methods provide a means to handle the modeling errors and uncertainties in sophisticated ocean models. In this study, we have created an OpenDA-NEMO framework unlocking the data assimilation tools available in OpenDA for use with NEMO models. This includes data assimilation methods, automatic parallelization, and a recently implemented automatic localization algorithm that removes spurious correlations in the model based on uncertainties in the computed Kalman gain matrix. We have set up a twin experiment where we assimilate sea surface height (SSH) satellite measurements. From the experiments, we can conclude that the OpenDA-NEMO framework performs as expected and that the automatic localization significantly improves the performance of the data assimilation algorithm by successfully removing spurious correlations. Based on these results, it looks promising to extend the framework with new kinds of observations and work on improving the computational speed of the automatic localization technique such that it becomes feasible to include large number of observations.

  18. The data acquisition and transport design for NEMO Phase 2

    Energy Technology Data Exchange (ETDEWEB)

    Simeone, Francesco, E-mail: francesco.simeone@roma1.infn.it [Istituto Nazionale di Fisica Nucleare, Sez. Roma 1 (Italy); Universita di Roma Sapienza (Italy)

    2012-11-11

    Many high energy physics experiments (Auger, IceCube, NEMO, Km3Net) currently taking data or planned in the near future consist of big and sparse detectors that acquire a huge amount of data. This kind of topology requires the ability to acquire physics information in different places of the detector and correlate them using the occurrence time, usually with a sub-ns precision. The architecture described here provides a real-time data transport layer, used to implement the data acquisition system for the NEMO experiment, and consists of a synchronous link with fixed and deterministic latency. The system clock, distributed at every level of the apparatus, has been derived by the signals provided by a GPS receiver during the operating configuration. The aim of this contribution is to give an overview of the NEMO electronic system: the underwater electronics sample signals from photomultipliers and acquires slow-control data from both oceanographic instruments and dedicated sensors, allowing to monitor the operational conditions of the apparatus. The whole data are sent to the laboratory through a fully bi-directional fiber optic link. On-shore the data are received by dedicated boards that distribute them to the first-level trigger and to the slow-control system. A description of the different stages of data acquisition and transport will be given.

  19. Barcode scanner for ring dosemeters

    International Nuclear Information System (INIS)

    A barcode scanner for circular bar codes was developed as an additional module for a dosimeter-reader manufactured in the USA. The new scanner had to fulfill all existing interface specifications (power supply, serial interface) to be integrated seamlessly into the existing instrument. The size of the barcode reader had to be compact enough to fit into the instrument without the need for additional external components. The barcode scanner has been realized using image processing technology. The system is designed in a way to fulfill all the functions of the 'old' laser barcode scanner (decoding of linear codes) plus the additional function of decoding circular barcodes in parallel. The system consists of CCD (charge coupled device) camera, infrared illumination, image processing hardware (frame grabber) and computer. The computer runs an image processing software developed in C. The result of the development effort is a fully functional prototype that is to be adapted for serial production (with minor modifications) by the US-manufacturer. (author)

  20. 2D Barcode for DNA Encoding

    Directory of Open Access Journals (Sweden)

    Elena Purcaru

    2011-09-01

    Full Text Available The paper presents a solution for endcoding/decoding DNA information in 2D barcodes. First part focuses on the existing techniques and symbologies in 2D barcodes field. The 2D barcode PDF417 is presented as starting point. The adaptations and optimizations on PDF417 and on DataMatrix lead to the solution – DNA2DBC – DeoxyriboNucleic Acid Two Dimensional Barcode. The second part shows the DNA2DBC encoding/decoding process step by step. In conclusions are enumerated the most important features of 2D barcode implementation for DNA.

  1. 2D Barcode for DNA Encoding

    CERN Document Server

    Purcaru, Elena

    2012-01-01

    The paper presents a solution for endcoding/decoding DNA information in 2D barcodes. First part focuses on the existing techniques and symbologies in 2D barcodes field. The 2D barcode PDF417 is presented as starting point. The adaptations and optimizations on PDF417 and on DataMatrix lead to the solution - DNA2DBC - DeoxyriboNucleic Acid Two Dimensional Barcode. The second part shows the DNA2DBC encoding/decoding process step by step. In conclusions are enumerated the most important features of 2D barcode implementation for DNA.

  2. Statistical Approaches for DNA Barcoding

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Matz, M.

    2006-01-01

    The use of DNA as a tool for species identification has become known as "DNA barcoding" (Floyd et al., 2002; Hebert et al., 2003; Remigio and Hebert, 2003). The basic idea is straightforward: a small amount of DNA is extracted from the specimen, amplified and sequenced. The gene region sequenced...... is chosen so that it is nearly identical among individuals of the same species, but different between species, and therefore its sequence, can serve as an identification tag for the species ("DNA barcode"). By matching the sequence obtained from an unidentified specimen ("query" sequence) to the database...

  3. Measurement of the background in the NEMO 3 double beta decay experiment

    CERN Document Server

    Argyriades, J; Augier, C; Baker, J; Barabash, A S; Bongrand, M; Broudin-Bay, G; Brudanin, V B; Caffrey, A J; Chapon, A; Chauveau, E; Daraktchieva, Z; Durand, D; Egorov, V G; Fatemi-Ghomi, N; Flack, R; Freshville, A; Guillon, B; Hubert, Ph; Jullian, S; Kauer, M; King, S; Kochetov, O I; Konovalov, S I; Kovalenko, V E; Lalanne, D; Lang, K; Lemi`ere, Y; Lutter, G; Mamedov, F; Marquet, Ch; Martín-Albo, J; Mauger, F; Nachab, A; Nasteva, I; Nemchenok, I B; Nova, F; Novella, P; Ohsumi, H; Pahlka, R B; Perrot, F; Piquemal, F; Reyss, J L; Ricol, J S; Saakyan, R; Sarazin, X; Simard, L; Shitov, Yu A; Smolnikov, A A; Snow, S; Söldner-Rembold, S; Stekl, I; Sutton, C S; Szklarz, G; Thomas, J; Timkin, V V; Tretyak, V I; Tretyak, Vl I; Umatov, V I; Vàla, L; Vanyushin, I A; Vasiliev, V A; Vorobel, V; Vylov, Ts

    2009-01-01

    In the double beta decay experiment NEMO~3 a precise knowledge of the background in the signal region is of outstanding importance. This article presents the methods used in NEMO~3 to evaluate the backgrounds resulting from most if not all possible origins. It also illustrates the power of the combined tracking-calorimetry technique used in the experiment.

  4. Detection potential to point-like neutrino sources with the NEMO-km3 telescope

    OpenAIRE

    Distefano, C.

    2006-01-01

    The NEMO Collaboration is conducting an R&D activity towards the construction of a Mediterranean km3 neutrino telescope. In this work, we present the results of Monte Carlo simulation studies on the capability of the proposed NEMO telescope to detect and identify point-like sources of high energy muon neutrinos.

  5. Measurement of the background in the NEMO 3 double beta decay experiment

    International Nuclear Information System (INIS)

    In the double beta decay experiment NEMO 3 a precise knowledge of the background in the signal region is of outstanding importance. This article presents the methods used in NEMO 3 to evaluate the backgrounds resulting from most if not all possible origins. It also illustrates the power of the combined tracking-calorimetry technique used in the experiment.

  6. Renzo Piano's NEMO. Example of integration. Decentralization of technical spaces; Renzo's Piano NEMO. Voorbeeld van integratie. Sterke decentralisatie van technische ruimten

    Energy Technology Data Exchange (ETDEWEB)

    Zeiler, W. [Installatietechnologie, Technische Universiteit Eindhoven, Eindhoven (Netherlands)

    2007-11-15

    At the time of the opening of Nemo, which was designed by the architect Renzo Piano, it was immediately the largest 'science center' of the Netherlands with 300,000 visitors annually. It started under the name NewMetropolis and is now called Nemo. Fitting in the installations requires closer collaboration between the architect and the advisor.(mk) [Dutch] Bij opening was het door de architect Renzo Piano ontworpen Nemo direct het grootste 'science-center' van Nederland met jaarlijks ruim 300.000 bezoekers. Het begon onder de naam NewMetropolis en heet nu Nemo. De inpassing van de installaties vroeg om een nauwe samenwerking tussen architect en adviseur.

  7. The DNA-based human karyotype.

    Science.gov (United States)

    Mayall, B H; Carrano, A V; Moore, D H; Ashworth, L K; Bennett, D E; Mendelsohn, M L

    1984-07-01

    Image cytometry and computer analysis are used to determine the relative DNA content and the DNA-based centromeric index of the 24 chromosomes of the human karyotype. A two-step procedure is used. Chromosomes of cells in metaphase first are stained with quinacrine and identified visually by their fluorescent Q-band patterns. They then are stained for DNA using gallocyanin-chrome alum. The chromosome images are scanned and recorded as digital values of optical density by an CYDAC image cytometric microscope system, CYDAC. The digital images are processed by computer to measure for each chromosome the relative DNA stain contents of the whole chromosome and of the p and q arms and the DNA-based centromeric index. About ten cells are analyzed for each of the donors, who are phenotypically normal men and women. The chromosome measurements are pooled by chromosome type for each donor and are compared among donors. The means of the chromosome measurements give the DNA-based human karyotype. Analysis of the DNA-based data shows that some chromosomes or portions of chromosomes vary significantly among donors. These variants do not correlate with detectable morphologic polymorphisms, such as Q- or C-band variants; thus they represent new and otherwise undetectable chromosome polymorphisms whose genetic basis and clinical significance are yet to be determined. PMID:6205836

  8. Study of the background neutron and gamma components of the ββ(0ν) decay in the NEMO2 prototype detector. Consequences for the NEMO3 detector

    International Nuclear Information System (INIS)

    Neutrinoless double beta decay ββ(0ν) is a test of physics beyond the Standard Model by involving the existence of a massive Majorana neutrino (ν = ν-bar). To try to observe such a process with a sensitivity of 0.1 eV on the neutrino effective mass (ν>), NEMO collaboration build the NEMO3 detector, able to measure half-lives greater than 1024 years, corresponding to a few detected events per year. For that, it is necessary to know and master all background sources. This work was first dedicated to the study of external (to the double beta source) background with crossing electrons recorded with NEMO2 prototype detector and then to the simulation of this background in NEMO3 detector. Comparison between NEMO2 data and results of gamma and neutron simulations for different shieldings, with and without neutron source, has allowed to determine background contributions of radon, thoron, 208Tl contaminations in materials, photon flux produced in laboratory and neutrons. This study, which has required improvements in the MICAP neutron simulation code by developing a photon generator, proved that radiative capture of fast neutrons thermalized in the detector was the source of events in the energy domain of the ββ(0ν) signal. In order to reach the required sensitivity on ν> mass, it has been shown that both a neutron shielding and magnetic field are necessary for NEMO3 detector. (author)

  9. Nano-electromechanical oscillators (NEMOs) for RF technologies.

    Energy Technology Data Exchange (ETDEWEB)

    Wendt, Joel Robert; Czaplewski, David A.; Gibson, John Murray (Argonne National Laboratory, Argonne, IL); Webster, James R.; Carton, Andrew James; Keeler, Bianca Elizabeth Nelson; Carr, Dustin Wade; Friedmann, Thomas Aquinas; Tallant, David Robert; Boyce, Brad Lee; Sullivan, John Patrick; Dyck, Christopher William; Chen, Xidong (Cedarville University, Cedarville, OH)

    2004-12-01

    Nano-electromechanical oscillators (NEMOs), capacitively-coupled radio frequency (RF) MEMS switches incorporating dissipative dielectrics, new processing technologies for tetrahedral amorphous carbon (ta-C) films, and scientific understanding of dissipation mechanisms in small mechanical structures were developed in this project. NEMOs are defined as mechanical oscillators with critical dimensions of 50 nm or less and resonance frequencies approaching 1 GHz. Target applications for these devices include simple, inexpensive clocks in electrical circuits, passive RF electrical filters, or platforms for sensor arrays. Ta-C NEMO arrays were used to demonstrate a novel optomechanical structure that shows remarkable sensitivity to small displacements (better than 160 fm/Hz {sup 1/2}) and suitability as an extremely sensitive accelerometer. The RF MEMS capacitively-coupled switches used ta-C as a dissipative dielectric. The devices showed a unipolar switching response to a unipolar stimulus, indicating the absence of significant dielectric charging, which has historically been the major reliability issue with these switches. This technology is promising for the development of reliable, low-power RF switches. An excimer laser annealing process was developed that permits full in-plane stress relaxation in ta-C films in air under ambient conditions, permitting the application of stress-reduced ta-C films in areas where low thermal budget is required, e.g. MEMS integration with pre-existing CMOS electronics. Studies of mechanical dissipation in micro- and nano-scale ta-C mechanical oscillators at room temperature revealed that mechanical losses are limited by dissipation associated with mechanical relaxation in a broad spectrum of defects with activation energies for mechanical relaxation ranging from 0.35 eV to over 0.55 eV. This work has established a foundation for the creation of devices based on nanomechanical structures, and outstanding critical research areas that need

  10. The natural emissions model (NEMO): Description, application and model evaluation

    Science.gov (United States)

    Liora, Natalia; Markakis, Konstantinos; Poupkou, Anastasia; Giannaros, Theodore M.; Melas, Dimitrios

    2015-12-01

    The aim of this study is the application and evaluation of a new computer model used for the quantification of emissions coming from natural sources. The Natural Emissions Model (NEMO) is driven by the meteorological data of the mesoscale numerical Weather Research and Forecasting (WRF) model and it estimates particulate matter (PM) emissions from windblown dust, sea salt aerosols (SSA) and primary biological aerosol particles (PBAPs). It also includes emissions from Biogenic Volatile Organic Compounds (BVOCs) from vegetation; however, this study focuses only on particle emissions. An application and evaluation of NEMO at European scale are presented. NEMO and the modelling system consisted of WRF model and the Comprehensive Air Quality Model with extensions (CAMx) were applied in a 30 km European domain for the year 2009. The computed domain-wide annual PM10 emissions from windblown dust, sea salt and PBAPs were 0.57 Tg, 20 Tg and 0.12 Tg, respectively. PM2.5 represented 6% and 33% of emitted windblown dust and sea salt, respectively. Natural emissions are characterized by high geographical and seasonal variations; windblown dust emissions were the highest during summer in the southern Europe and SSA production was the highest in Atlantic Ocean during the cold season while in Mediterranean Sea the highest SSA emissions were found over the Aegean Sea during summer. Modelled concentrations were compared with surface station measurements and showed that the model captured fairly well the contribution of the natural sources to PM levels over Europe. Dust concentrations correlated better when dust transport events from Sahara desert were absent while the simulation of sea salt episodes led to an improvement of model performance during the cold season.

  11. Construction and commissioning of the SuperNEMO detector tracker

    Science.gov (United States)

    Cascella, Michele

    2016-07-01

    The SuperNEMO detector will search for neutrinoless double beta decay at the Modane Underground Laboratory; the detector design allows complete topological reconstruction of the decay event enabling excellent levels of background rejection and, in the event of a discovery, the ability to determine the nature of the lepton number violating process. In order to demonstrate the feasibility of the full experiment, we are building a Demonstrator Module containing 7 kg of 82Se, with an expected sensitivity of |mββ | first results from the surface commissioning of one section of the Demonstrator Module tracker.

  12. Self-registering spread-spectrum barcode method

    Energy Technology Data Exchange (ETDEWEB)

    Cummings, Eric B.; Even Jr., William R.

    2004-11-09

    A novel spread spectrum barcode methodology is disclosed that allows a barcode to be read in its entirety even when a significant fraction or majority of the barcode is obscured. The barcode methodology makes use of registration or clocking information that is distributed along with the encoded user data across the barcode image. This registration information allows for the barcode image to be corrected for imaging distortion such as zoom, rotation, tilt, curvature, and perspective.

  13. Communication: Electron ionization of DNA bases.

    Science.gov (United States)

    Rahman, M A; Krishnakumar, E

    2016-04-28

    No reliable experimental data exist for the partial and total electron ionization cross sections for DNA bases, which are very crucial for modeling radiation damage in genetic material of living cell. We have measured a complete set of absolute partial electron ionization cross sections up to 500 eV for DNA bases for the first time by using the relative flow technique. These partial cross sections are summed to obtain total ion cross sections for all the four bases and are compared with the existing theoretical calculations and the only set of measured absolute cross sections. Our measurements clearly resolve the existing discrepancy between the theoretical and experimental results, thereby providing for the first time reliable numbers for partial and total ion cross sections for these molecules. The results on fragmentation analysis of adenine supports the theory of its formation in space. PMID:27131520

  14. DNA-Based Applications in Nanobiotechnology

    Directory of Open Access Journals (Sweden)

    Khalid M. Abu-Salah

    2010-01-01

    Full Text Available Biological molecules such as deoxyribonucleic acid (DNA have shown great potential in fabrication and construction of nanostructures and devices. The very properties that make DNA so effective as genetic material also make it a very suitable molecule for programmed self-assembly. The use of DNA to assemble metals or semiconducting particles has been extended to construct metallic nanowires and functionalized nanotubes. This paper highlights some important aspects of conjugating the unique physical properties of dots or wires with the remarkable recognition capabilities of DNA which could lead to miniaturizing biological electronics and optical devices, including biosensors and probes. Attempts to use DNA-based nanocarriers for gene delivery are discussed. In addition, the ecological advantages and risks of nanotechnology including DNA-based nanobiotechnology are evaluated.

  15. Barcoding poplars (Populus L. from western China.

    Directory of Open Access Journals (Sweden)

    Jianju Feng

    Full Text Available BACKGROUND: Populus is an ecologically and economically important genus of trees, but distinguishing between wild species is relatively difficult due to extensive interspecific hybridization and introgression, and the high level of intraspecific morphological variation. The DNA barcoding approach is a potential solution to this problem. METHODOLOGY/PRINCIPAL FINDINGS: Here, we tested the discrimination power of five chloroplast barcodes and one nuclear barcode (ITS among 95 trees that represent 21 Populus species from western China. Among all single barcode candidates, the discrimination power is highest for the nuclear ITS, progressively lower for chloroplast barcodes matK (M, trnG-psbK (G and psbK-psbI (P, and trnH-psbA (H and rbcL (R; the discrimination efficiency of the nuclear ITS (I is also higher than any two-, three-, or even the five-locus combination of chloroplast barcodes. Among the five combinations of a single chloroplast barcode plus the nuclear ITS, H+I and P+I differentiated the highest and lowest portion of species, respectively. The highest discrimination rate for the barcodes or barcode combinations examined here is 55.0% (H+I, and usually discrimination failures occurred among species from sympatric or parapatric areas. CONCLUSIONS/SIGNIFICANCE: In this case study, we showed that when discriminating Populus species from western China, the nuclear ITS region represents a more promising barcode than any maternally inherited chloroplast region or combination of chloroplast regions. Meanwhile, combining the ITS region with chloroplast regions may improve the barcoding success rate and assist in detecting recent interspecific hybridizations. Failure to discriminate among several groups of Populus species from sympatric or parapatric areas may have been the result of incomplete lineage sorting, frequent interspecific hybridizations and introgressions. We agree with a previous proposal for constructing a tiered barcoding system in

  16. An entropy-based persistence barcode

    OpenAIRE

    Chintakunta, Harish; Gentimis, Thanos; González Díaz, Rocío; Jiménez Rodríguez, María José; Krim, Hamid

    2015-01-01

    In persistent homology, the persistence barcode encodes pairs of simplices meaning birth and death of homology classes. Persistence barcodes depend on the ordering of the simplices (called a filter) of the given simplicial complex. In this paper, we define the notion of “minimal” barcodes in terms of entropy. Starting from a given filtration of a simplicial complex K, an algorithm for computing a “proper” filter (a total ordering of the simplices preserving the partial ordering imposed by the...

  17. Barcoding of soil microarthropods in Kobbefjord

    DEFF Research Database (Denmark)

    Krogh, Paul Henning; Wirta, Helena; Roslin, Tomas;

    2013-01-01

    Since it was proposed to identity species by small sequences of DNA with e.g. less than 1000 bp (base pairs) popularized by the term barcode, monitoring of biodiversity has included barcoding (Hebert et al. 2003, Hogg and Hebert 2004 and Rougerie et al. 2009). It is now a rapidly increasing...... collectively endeavour supported by the infrastructure of the iBOL project (the International Barcode of Life project)....

  18. The Practical Evaluation of DNA Barcode Efficacy*

    OpenAIRE

    Spouge, John L.; Mariño-Ramírez, Leonardo

    2012-01-01

    This chapter describes a workflow for measuring the efficacy of a barcode in identifying species. First, assemble individual sequence databases corresponding to each barcode marker. A controlled collection of taxonomic data is preferable to GenBank data, because GenBank data can be problematic, particularly when comparing barcodes based on more than one marker. To ensure proper controls when evaluating species identification, specimens not having a sequence in every marker database should be ...

  19. Choosing and Using a Plant DNA Barcode

    OpenAIRE

    Hollingsworth, Peter M.; Graham, Sean W.; Little, Damon P.

    2011-01-01

    The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the ...

  20. NEMO: A Mission to Explore and Return Samples from Europa's Oceans

    Science.gov (United States)

    Powell, James R.; Paniagua, John C.; Maise, George

    2004-02-01

    The NEMO [Nuclear Europa Mobile Ocean] mission would explore and return samples and possible life forms from Europa's sub-surface oceans to Earth. The NEMO spacecraft would land on Europa two years after leaving Earth, using a compact bi-modal NTP engine. NEMO'S small nuclear reactor melt probe would then melt a channel through the multi-km ice sheet to the ocean, which a small robotic submarine would explore, transmitting data by sonic link and optical fiber to the spacecraft for relay to Earth. After its exploration, the submarine would rejoin the melt probe for return to the NEMO spacecraft. Using electricity from the bi-modal MITEE engine, fresh H2 propellant would be manufactured by electrolysis of melt water from surface ice. NEMO would then hop to a new site, exploring ten sites in a year before returning with samples and life forms to Earth, six years after it left. The design and performance of the NEMO spacecraft, MITEE engine, melt probe, and submarine are described. The probe and submarine use existing reactor technology. A NEMO mission could launch shortly after 2013 AD.

  1. 2D Barcode for DNA Encoding

    OpenAIRE

    Elena Purcaru; Cristian Toma

    2012-01-01

    The paper presents a solution for endcoding/decoding DNA information in 2D barcodes. First part focuses on the existing techniques and symbologies in 2D barcodes field. The 2D barcode PDF417 is presented as starting point. The adaptations and optimizations on PDF417 and on DataMatrix lead to the solution – DNA2DBC – DeoxyriboNucleic Acid Two Dimensional Barcode. The second part shows the DNA2DBC encoding/decoding process step by step. In conclusions are enumerated the most important features ...

  2. DNA barcoding for the identification of sand fly species (Diptera, Psychodidae, Phlebotominae in Colombia.

    Directory of Open Access Journals (Sweden)

    María Angélica Contreras Gutiérrez

    Full Text Available Sand flies include a group of insects that are of medical importance and that vary in geographic distribution, ecology, and pathogen transmission. Approximately 163 species of sand flies have been reported in Colombia. Surveillance of the presence of sand fly species and the actualization of species distribution are important for predicting risks for and monitoring the expansion of diseases which sand flies can transmit. Currently, the identification of phlebotomine sand flies is based on morphological characters. However, morphological identification requires considerable skills and taxonomic expertise. In addition, significant morphological similarity between some species, especially among females, may cause difficulties during the identification process. DNA-based approaches have become increasingly useful and promising tools for estimating sand fly diversity and for ensuring the rapid and accurate identification of species. A partial sequence of the mitochondrial cytochrome oxidase gene subunit I (COI is currently being used to differentiate species in different animal taxa, including insects, and it is referred as a barcoding sequence. The present study explored the utility of the DNA barcode approach for the identification of phlebotomine sand flies in Colombia. We sequenced 700 bp of the COI gene from 36 species collected from different geographic localities. The COI barcode sequence divergence within a single species was <2% in most cases, whereas this divergence ranged from 9% to 26.6% among different species. These results indicated that the barcoding gene correctly discriminated among the previously morphologically identified species with an efficacy of nearly 100%. Analyses of the generated sequences indicated that the observed species groupings were consistent with the morphological identifications. In conclusion, the barcoding gene was useful for species discrimination in sand flies from Colombia.

  3. Nemo-3 experiment assets and limitations. Perspective for the double {beta} physics; Experience Nemo 3 avantage et limitations. Prospective pour la physique double {beta}

    Energy Technology Data Exchange (ETDEWEB)

    Augier, C

    2005-06-15

    After an introduction to this report in Chapter 1, I present a status of our knowledge in neutrino physics in Chapter 2. Then, I detail in Chapter 3 all the choices made for the design and realisation of the NEMO 3 detector for the research of double beta decay process. Performance of the detector is presented, concerning both the capacity of the detector to identify the backgrounds and the ability to study all the {beta}{beta} process. I also explain the methods chosen by the NEMO collaboration to reduce the radon activity inside the detector and to make this background negligible today. This chapter, which is written in English, is the 'Technical report of the NEMO 3 detector' and forms an independent report for the NEMO collaborators. I finish this report in Chapter 4 with a ten years prospect for experimental projects in physics, with both the SuperNEMO project and its experiment program, and also by comparing the most interesting experiments, CUORE and GERDA, showing as an example the effect of nuclear matrix elements on the neutrino effective mass measurement. (author)

  4. Excited state dynamics of DNA bases

    Czech Academy of Sciences Publication Activity Database

    Kleinermanns, K.; Nachtigallová, Dana; de Vries, M. S.

    2013-01-01

    Roč. 32, č. 2 (2013), s. 308-342. ISSN 0144-235X R&D Projects: GA ČR GAP208/12/1318 Grant ostatní: National Science Foundation(US) CHE-0911564; NASA(US) NNX12AG77G; Deutsche Forschungsgemeinschaft(DE) SFB 663; Deutsche Forschungsgemeinschaft(DE) KI 531-29 Institutional support: RVO:61388963 Keywords : DNA bases * nucleobases * excited state * dynamics * computations * gas phase * conical intersections Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.920, year: 2013

  5. 76 FR 34871 - Mobile Barcode Promotion

    Science.gov (United States)

    2011-06-15

    ... mailpieces contain a two-dimensional mobile (also known as a ``QR'' barcode) barcode that is readable by... in the Code of Federal Regulations. See 39 CFR 111.1. List of Subjects in 39 CFR Part 111.... Mires, Chief Counsel, Legislative. BILLING CODE 7710-12-P...

  6. 77 FR 26185 - POSTNET Barcode Discontinuation

    Science.gov (United States)

    2012-05-03

    ... March 2, 2012, the Postal Service published a proposed rule in the Federal Register (77 FR 12764-12769... Discount--Flats. The barcoded discount applies to BPM flats that meet the requirements for automation flats... discount applies only to BPM flat-size pieces that bear an Intelligent Mail barcode encoded with...

  7. DNA Barcoding Investigations Bring Biology to Life

    Science.gov (United States)

    Musante, Susan

    2010-01-01

    This article describes how DNA barcoding investigations bring biology to life. Biologists recognize the power of DNA barcoding not just to teach biology through connections to the real world but also to immerse students in the exciting process of science. As an investigator in the Program for the Human Environment at Rockefeller University in New…

  8. Nemo:. a Project for a KM3 Underwater Detector for Astrophysical Neutrinos in the Mediterranean Sea

    Science.gov (United States)

    Amore, I.; Aiello, S.; Ambriola, M.; Ameli, F.; Anghinolfi, M.; Anzalone, A.; Barbarino, G.; Barbarito, E.; Battaglieri, M.; Bellotti, R.; Beverini, N.; Bonori, M.; Bouhadef, B.; Brescia, M.; Cacopardo, G.; Cafagna, F.; Capone, A.; Caponetto, L.; Castorina, E.; Ceres, A.; Chiarusi, T.; Circella, M.; Cocimano, R.; Coniglione, R.; Cordelli, M.; Costa, M.; Cuneo, S.; D'Amico, A.; de Bonis, G.; de Marzo, C.; de Rosa, G.; de Vita, R.; Distefano, C.; Falchini, E.; Fiorello, C.; Flaminio, V.; Fratini, K.; Gabrielli, A.; Galeotti, S.; Gandolfi, E.; Giacomelli, G.; Giorgi, F.; Grimaldi, A.; Habel, R.; Leonora, E.; Lonardo, A.; Longo, G.; Lo Presti, D.; Lucarelli, F.; Maccioni, E.; Margiotta, A.; Martini, A.; Masullo, R.; Megna, R.; Migneco, E.; Mongelli, M.; Montaruli, T.; Morganti, M.; Musumeci, M. S.; Nicolau, C. A.; Orlando, A.; Osipenko, M.; Osteria, G.; Papaleo, R.; Pappalardo, V.; Petta, C.; Piattelli, P.; Raia, G.; Randazzo, N.; Reito, S.; Ricco, G.; Riccobene, G.; Ripani, M.; Rovelli, A.; Ruppi, M.; Russo, G. V.; Russo, S.; Sapienza, P.; Sedita, M.; Shirokov, E.; Simeone, F.; Sipala, V.; Spurio, M.; Taiuti, M.; Terreni, G.; Trasatti, L.; Urso, S.; Valente, V.; Vicini, P.

    The status of the project is described: the activity on long term characterization of water optical and oceanographic parameters at the Capo Passero site candidate for the Mediterranean km3 neutrino telescope; the feasibility study; the physics performances and underwater technology for the km3; the activity on NEMO Phase 1, a technological demonstrator that has been deployed at 2000 m depth 25 km offshore Catania; the realization of an underwater infrastructure at 3500 m depth at the candidate site (NEMO Phase 2).

  9. NEMO: A Project for a km$^3$ Underwater Detector for Astrophysical Neutrinos in the Mediterranean Sea

    CERN Document Server

    Amore, I; Ambriola, M; Ameli, F; Anghinolfi, M; Anzalone, A; Barbarino, G; Barbarito, E; Battaglieri, M; Bellotti, R; Beverini, N; Bonori, M; Bouhadef, B; Brescia, M; Cacopardo, G; Cafagna, F; Capone, A; Caponetto, L; Castorina, E; Ceres, A; Chiarusi, T; Circella, M; Cocimano, R; Coniglione, R; Cordelli, M; Costa, M; Cuneo, S; D'Amico, A; De Bonis, G; De Marzo, C; De Rosa, G; De Vita, R; Distefano, C; Falchini, E; Fiorello, C; Flaminio, V; Fratini, K; Gabrielli, A; Galeotti, S; Gandolfi, E; Giacomelli, G; Giorgi, F; Grimaldi, A; Habel, R; Leonora, E; Lonardo, A; Longo, G; Lo Presti, D; Lucarelli, F; Maccioni, E; Margiotta, A; Martini, A; Masullo, R; Megna, R; Migneco, E; Mongelli, M; Montaruli, T; Morganti, M; Musumeci, M S; Nicolau, C A; Orlando, A; Osipenko, M; Osteria, G; Papaleo, R; Pappalardo, V; Petta, C; Piattelli, P; Raia, G; Randazzo, N; Reito, S; Ricco, G; Riccobene, G; Ripani, M; Rovelli, A; Ruppi, M; Russo, G V; Russo, S; Sapienza, P; Sedita, M; Shirokov, E; Simeone, F; Sipala, V; Spurio, M; Taiuti, M; Terreni, G; Trasatti, L; Urso, S; Valente, V; Vicini, P

    2007-01-01

    The status of the project is described: the activity on long term characterization of water optical and oceanographic parameters at the Capo Passero site candidate for the Mediterranean km$^3$ neutrino telescope; the feasibility study; the physics performances and underwater technology for the km$^3$; the activity on NEMO Phase 1, a technological demonstrator that has been deployed at 2000 m depth 25 km offshore Catania; the realization of an underwater infrastructure at 3500 m depth at the candidate site (NEMO Phase 2).

  10. A DNA barcode for land plants.

    Science.gov (United States)

    2009-08-01

    DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants. PMID:19666622

  11. A DNA barcode for land plants

    Science.gov (United States)

    Hollingsworth, Peter M.; Forrest, Laura L.; Spouge, John L.; Hajibabaei, Mehrdad; Ratnasingham, Sujeevan; van der Bank, Michelle; Chase, Mark W.; Cowan, Robyn S.; Erickson, David L.; Fazekas, Aron J.; Graham, Sean W.; James, Karen E.; Kim, Ki-Joong; Kress, W. John; Schneider, Harald; van AlphenStahl, Jonathan; Barrett, Spencer C.H.; van den Berg, Cassio; Bogarin, Diego; Burgess, Kevin S.; Cameron, Kenneth M.; Carine, Mark; Chacón, Juliana; Clark, Alexandra; Clarkson, James J.; Conrad, Ferozah; Devey, Dion S.; Ford, Caroline S.; Hedderson, Terry A.J.; Hollingsworth, Michelle L.; Husband, Brian C.; Kelly, Laura J.; Kesanakurti, Prasad R.; Kim, Jung Sung; Kim, Young-Dong; Lahaye, Renaud; Lee, Hae-Lim; Long, David G.; Madriñán, Santiago; Maurin, Olivier; Meusnier, Isabelle; Newmaster, Steven G.; Park, Chong-Wook; Percy, Diana M.; Petersen, Gitte; Richardson, James E.; Salazar, Gerardo A.; Savolainen, Vincent; Seberg, Ole; Wilkinson, Michael J.; Yi, Dong-Keun; Little, Damon P.

    2009-01-01

    DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF–atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants. PMID:19666622

  12. The natural radioactivity background of the NEMO 2 detector

    International Nuclear Information System (INIS)

    Using Monte-Carlo simulation methods, we performed a study of the different sources of background of the NEMO 2 detector, nowadays at the Modane Underground Laboratory, designed for the search of double beta decay of 100-Mo. The experimental set-up consists of a thin foil (50 microns), source of double beta decay, placed at the center of a drift chamber. This tracking detector has at each side a wall of scintillators, used for time and energy information. This work includes the study of the external and internal sources of background. The source of external background is due to the glasses used in the photomultiplier tubes. The calculation for the external background is compatible with only this source. The internal background is due to natural radioisotopes contaminations in the central foil. The counting rates as well as the shapes of the experimental spectra are well reproduced by the simulations. (author)

  13. DNA-based control of protein activity.

    Science.gov (United States)

    Engelen, W; Janssen, B M G; Merkx, M

    2016-03-01

    DNA has emerged as a highly versatile construction material for nanometer-sized structures and sophisticated molecular machines and circuits. The successful application of nucleic acid based systems greatly relies on their ability to autonomously sense and act on their environment. In this feature article, the development of DNA-based strategies to dynamically control protein activity via oligonucleotide triggers is discussed. Depending on the desired application, protein activity can be controlled by directly conjugating them to an oligonucleotide handle, or expressing them as a fusion protein with DNA binding motifs. To control proteins without modifying them chemically or genetically, multivalent ligands and aptamers that reversibly inhibit their function provide valuable tools to regulate proteins in a noncovalent manner. The goal of this feature article is to give an overview of strategies developed to control protein activity via oligonucleotide-based triggers, as well as hurdles yet to be taken to obtain fully autonomous systems that interrogate, process and act on their environments by means of DNA-based protein control. PMID:26812623

  14. GeNemo: a search engine for web-based functional genomic data.

    Science.gov (United States)

    Zhang, Yongqing; Cao, Xiaoyi; Zhong, Sheng

    2016-07-01

    A set of new data types emerged from functional genomic assays, including ChIP-seq, DNase-seq, FAIRE-seq and others. The results are typically stored as genome-wide intensities (WIG/bigWig files) or functional genomic regions (peak/BED files). These data types present new challenges to big data science. Here, we present GeNemo, a web-based search engine for functional genomic data. GeNemo searches user-input data against online functional genomic datasets, including the entire collection of ENCODE and mouse ENCODE datasets. Unlike text-based search engines, GeNemo's searches are based on pattern matching of functional genomic regions. This distinguishes GeNemo from text or DNA sequence searches. The user can input any complete or partial functional genomic dataset, for example, a binding intensity file (bigWig) or a peak file. GeNemo reports any genomic regions, ranging from hundred bases to hundred thousand bases, from any of the online ENCODE datasets that share similar functional (binding, modification, accessibility) patterns. This is enabled by a Markov Chain Monte Carlo-based maximization process, executed on up to 24 parallel computing threads. By clicking on a search result, the user can visually compare her/his data with the found datasets and navigate the identified genomic regions. GeNemo is available at www.genemo.org. PMID:27098038

  15. The neotype barcode of the cotton aphid (Hemiptera: Aphididae: Aphis gossypii Glover, 1877) and a proposal for type barcodes

    Science.gov (United States)

    A type barcode is a DNA barcode unequivocally tied to an authoritatively identified specimen, preferably the primary type specimen. Type barcodes are analogous, albeit subordinate, to type specimens, providing a stable reference to which other barcodes can be compared. We here designate and describe...

  16. Measurement of 130Te double beta decay process in the NEMO-3 experiment- R and D of SuperNEMO project: study of the BiPo detector

    International Nuclear Information System (INIS)

    This thesis contains 2 parts: data analysis of the NEMO-3 experiment data and a study of a BiPo detector for the SuperNEMO project. NEMO-3 is searching for neutrinoless double beta decay process 2β0ν using direct detection of the 2 emitted electrons by a tracking detector coupled to a calorimeter. I completely studied the backgrounds in several analysis channels and gave the most accurate measurement of the allowed process with neutrinos emission for 130Te: T2ν(1/2) equals (6.1 ± 1.2 (stat) ± 0.6 (syst)) 1020 years. This result allows a good knowledge of the ultimate 2β2ν background for 2β0ν process research and helps to constrain or check the theoretical calculations of nuclear matrix elements, which have to be known with a good precision to determine the neutrino effective mass in case of 2β0ν observation. From NEMO-3 data, I also gave a limit on this effective neutrino massββ 130Te: T0ν(1/2) > 6.3 1022 years. Due to the low mass of 130Te contained in NEMO-3 (454 g), this result is not competitive with the limit recently published by CUORICINO for this isotope: T0ν(1/2) > 3.0 1024 years and mββ 0ν(1/2) > 1026 years, using the NEMO-3 detection principle but improving efficiency, radio-purity, energy resolution and reducing backgrounds. This background will be then limited by natural radioactive contaminations inside the source foils. Thus the SuperNEMO specifications concerning the source foil radio-purity are very high: A(208Tl) 214Bi) 208Tl and 214Bi contaminations, using identification of the Bi → Po chains. Foil source to measure is put between two scintillator planes allowing energy and time measurements. I studied BiPo-1 prototype, showed its technical feasibility, validated the principle and determined the sensitivity of the source measurement compared to backgrounds. Data analysis of BiPo-1 showed the possibility to measure 5 μBq/kg of 208Tl with the final BiPo. This result is not so far from SuperNEMO requirements and already shows a

  17. 2D Barcode Ticketing System

    OpenAIRE

    Salguero Piñeyro, Alejandro Raul

    2011-01-01

    The aim of this project is to generate a tool for companies who needs to control the attendance to their events. This could be done using an automated system composed by a web server, which will contain the events manager, connected to a database where the attendance data will be stored. The people interested in assisting at the events, will be provided with a unique two-dimensional barcode with which they will be able to authenticate themselves at the entrance of the event. To do this, Andro...

  18. A DNA barcode for land plants

    OpenAIRE

    Hollingsworth, Peter M.; Forrest, Laura L.; Spouge, John L.; Hajibabaei, Mehrdad; Ratnasingham, Sujeevan; van der Bank,Michelle; Chase, Mark W.; Cowan, Robyn S; Erickson, David L.; Fazekas, Aron J.; Graham, Sean W.; James, Karen E.; Kim, Ki-Joong; Kress, W. John; Schneider, Harald

    2009-01-01

    DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF–atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer). Based on assessments of recoverability, sequence quali...

  19. DNA Bar-Coding for Phytoplasma Identification

    DEFF Research Database (Denmark)

    Makarova, Olga; Contaldo, Nicoletta; Paltrinieri, Samanta;

    2013-01-01

    Phytoplasma identi fi cation has proved dif fi cult due to their inability to be maintained in vitro. DNA barcoding is an identi fi cation method based on comparison of a short DNA sequence with known sequences from a database. A DNA barcoding tool has been developed for phytoplasma identi fi...... cation. While other sequencebased methods may be well adapted to identification of particular strains of phytoplasmas, often they cannot be used for the simultaneous identification of phytoplasmas from different groups. The phytoplasma DNA barcoding protocol in this chapter, based on the tuf and 16Sr...

  20. From NEMO1D and NEMO3D to OMEN: Moving Towards Atomistic 3-D Quantum Transport in Nano-scale Semiconductors

    OpenAIRE

    Klimeck, Gerhard; Luisier, Mathieu

    2008-01-01

    Lessons learned in 15 years of NEMO development starting from quantitative and predictive resonant tunneling diode (RTD) to multi-million atom electronic structure modeling and the path for OMEN are laid out. The recent OMEN capabilities enable realistically large 3D atomistic nano-scale device simulation.

  1. Quantitative phenotyping via deep barcode sequencing

    OpenAIRE

    SMITH, ANDREW M.; Heisler, Lawrence E.; Mellor, Joseph; Kaper, Fiona; Thompson, Michael J.; Chee, Mark; Roth, Frederick P.; Giaever, Guri; Nislow, Corey

    2009-01-01

    Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or “Bar-seq,” outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied...

  2. Efficient alignment-free DNA barcode analytics

    OpenAIRE

    Kuksa, Pavel; Pavlovic, Vladimir

    2009-01-01

    Background In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient ...

  3. NEMO: A mission to search for and return to Earth possible life forms on Europa

    Science.gov (United States)

    Powell, Jesse; Powell, James; Maise, George; Paniagua, John

    2005-07-01

    The Nuclear Europa Mobile Ocean (NEMO) mission would land on the surface of Europa, and deploy a small, lightweight melt probe powered by a compact nuclear reactor to melt down through the multi-kilometer ice sheet. After reaching the sub-surface ocean, a small nuclear Autonomous Underwater Vehicle (AUV) would deploy to explore the sub-ice ocean. After exploration and sample collection, the AUV would return to the probe and melt back to the lander. The lander would have replenished its H2 propellant by electrolysis of H2O ice, and then hop to a new site on Europa to repeat the probe/AUV process. After completing the mission, the NEMO spacecraft would return to Earth with its collected samples. The NEMO melt probe and AUV utilize enriched U-235 fuel and conventional water reactor technology. The lander utilizes a compact nuclear thermal propulsion (NTP) engine based on the 710tungsten/UO2 cermet fuel and high-temperature H2 propellant. The compact nuclear reactors in both the NEMO melt probe and AUV drive a steam power cycle, generating over 10 kW(e) for use in each. Each nuclear reactor's operating lifetime is several years. With its high-mobility and long-duration mission, NEMO provides an ideal platform for life detection experiments.

  4. DNA based computing for understanding complex shapes.

    Science.gov (United States)

    Ullah, A M M Sharif; D'Addona, Doriana; Arai, Nobuyuki

    2014-03-01

    This study deals with a computing method called DNA based computing (DBC) that takes inspiration from the Central Dogma of Molecular Biology. The proposed DBC uses a set of user-defined rules to create a DNA-like sequence from a given piece of problem-relevant information (e.g., image data) in a dry-media (i.e., in an ordinary computer). It then uses another set of user-defined rules to create an mRNA-like sequence from the DNA. Finally, it uses the genetic code to translate the mRNA (or directly the DNA) to a protein-like sequence (a sequence of amino acids). The informational characteristics of the protein (entropy, absence, presence, abundance of some selected amino acids, and relationships among their likelihoods) can be used to solve problems (e.g., to understand complex shapes from their image data). Two case studies ((1) fractal geometry generated shape of a fern-leaf and (2) machining experiment generated shape of the worn-zones of a cutting tool) are presented elucidating the shape understanding ability of the proposed DBC in the presence of a great deal of variability in the image data of the respective shapes. The implication of the proposed DBC from the context of Internet-aided manufacturing system is also described. Further study can be carried out in solving other complex computational problems by using the proposed DBC and its derivatives. PMID:24447435

  5. Recommendations for Using Barcode in Hospital Process

    Science.gov (United States)

    Hachesu, Peyman Rezaei; Zyaei, Leila; Hassankhani, Hadi

    2016-01-01

    Background: Lack of attention to the proper barcode using leads to lack of use or misuse in the hospitals. The present research aimed to investigate the requirements and barrier for using barcode technology and presenting suggestions to use it. Methods: The research is observational-descriptive. The data was collected using the designed checklist which its validity was assessed. This check list consists of two parts: “Requirements” and “barrier” of using the barcodes. Research community included 10 teaching hospitals and a class of 65 participants included people in the hospitals. The collected data was analyzed using descriptive statistics. Results: Required changes of workflow processes in the hospital and compliance them with the hospital policy are such requirements that had been infringed in the 90 % of hospitals. Prioritization of some hospital processes for barcoding, system integration with Hospital Information system (HIS), training of staff and budgeting are requirements for the successful implementation which had been infringed in the 80% of hospitals. Dissatisfaction with the quality of barcode labels and lacks of adequate scanners both whit the rate of 100 %, and the lack of understanding of the necessary requirements for implementation of barcodes as 80% were the most important barrier. Conclusion: Integrate bar code system with clinical workflow should be considered. Lack of knowledge and understanding toward the infrastructure, inadequate staff training and technologic problems are considered as the greatest barriers. PMID:27482137

  6. Scanning-time evaluation of Digimarc Barcode

    Science.gov (United States)

    Gerlach, Rebecca; Pinard, Dan; Weaver, Matt; Alattar, Adnan

    2015-03-01

    This paper presents a speed comparison between the use of Digimarc® Barcodes and the Universal Product Code (UPC) for customer checkout at point of sale (POS). The recently introduced Digimarc Barcode promises to increase the speed of scanning packaged goods at POS. When this increase is exploited by workforce optimization systems, the retail industry could potentially save billions of dollars. The Digimarc Barcode is based on Digimarc's watermarking technology, and it is imperceptible, very robust, and does not require any special ink, material, or printing processes. Using an image-based scanner, a checker can quickly scan consumer packaged goods (CPG) embedded with the Digimarc Barcode without the need to reorient the packages with respect to the scanner. Faster scanning of packages saves money and enhances customer satisfaction. It reduces the length of the queues at checkout, reduces the cost of cashier labor, and makes self-checkout more convenient. This paper quantifies the increase in POS scanning rates resulting from the use of the Digimarc Barcode versus the traditional UPC. It explains the testing methodology, describes the experimental setup, and analyzes the obtained results. It concludes that the Digimarc Barcode increases number of items per minute (IPM) scanned at least 50% over traditional UPC.

  7. Status and first results of the NEMO Phase-2 tower

    Science.gov (United States)

    Chiarusi, T.; Aiello, S.; Ameli, F.; Anghinolfi, M.; Barbarino, G.; Barbarito, E.; Barbato, F.; Beverini, N.; Biagi, S.; Bouhadef, B.; Bozza, C.; Cacopardo, G.; Calamai, M.; Calì, C.; Capone, A.; Caruso, F.; Ceres, A.; Circella, M.; Cocimano, R.; Coniglione, R.; Costa, M.; Cuttone, G.; D'Amato, C.; D'Amato, V.; D'Amico, A.; DeBonis, G.; De Luca, V.; Deniskina, N.; De Rosa, G.; Distefano, C.; Fermani, P.; Flaminio, V.; Fusco, L. A.; Garufi, F.; Giordano, V.; Giovanetti, G.; Gmerk, A.; Grasso, R.; Grella, G.; Hugon, C.; Imbesi, M.; Kulikovsky, V.; Larosa, G.; Lattuada, D.; Leonora, E.; Litrico, P.; Lonardo, A.; Longhitano, F.; Lo Presti, D.; Maccioni, E.; Margiotta, A.; Martini, A.; Masullo, R.; Migliozzi, P.; Migneco, E.; Miraglia, A.; Mollo, C.; Mongelli, M.; Morganti, M.; Musico, P.; Musumeci, M.; Nicolau, C. A.; Orlando, A.; Papaleo, R.; Pellegrino, C.; Pellegriti, M. G.; Perrina, C.; Piattelli, P.; Pugliatti, C.; Pulvirenti, S.; Raffaelli, F.; Randazzo, N.; Riccobene, G.; Rovelli, A.; Sanguineti, M.; Sapienza, P.; Sgura, I.; Simeone, F.; Sipala, V.; Spurio, M.; Speziale, F.; Spitaleri, A.; Taiuti, M.; Terreni, G.; Trasatti, L.; Trovato, A.; Ventura, C.; Vicini, P.; Viola, S.; Vivolo, D.

    2014-03-01

    In March 2013, the NEMO Phase 2 tower has been successfully installed in the Capo Passero site, at a depth of 3500 m and 80 km off from the southern coast of Sicily. The unfurled tower is 450 m high; it is composed of 8 mechanical floors, for a total amount of 32 PMTs and various instruments for environmental measurements. The tower positioning is achieved by an acoustic system. The tower is continuously acquiring and transmitting all the measured signals to shore. Data reduction is completely performed in the Portopalo shore station by a dedicated computing facility connected to the persistent storage system at LNS, in Catania. Results from the last 9 months of acquisition will be presented. In particular, the analyzed optical rates, showing stable and low baseline values, are compatible with the contribution mainly of 40K light emission, with a small percentage of light bursts due to bioluminescence. These features reveal the optimal nature of the Capo Passero abyssal site to host a km3-sized Neutrino Telescope.

  8. Status and first results of the NEMO Phase-2 tower

    International Nuclear Information System (INIS)

    In March 2013, the NEMO Phase 2 tower has been successfully installed in the Capo Passero site, at a depth of 3500 m and 80 km off from the southern coast of Sicily. The unfurled tower is 450 m high; it is composed of 8 mechanical floors, for a total amount of 32 PMTs and various instruments for environmental measurements. The tower positioning is achieved by an acoustic system. The tower is continuously acquiring and transmitting all the measured signals to shore. Data reduction is completely performed in the Portopalo shore station by a dedicated computing facility connected to the persistent storage system at LNS, in Catania. Results from the last 9 months of acquisition will be presented. In particular, the analyzed optical rates, showing stable and low baseline values, are compatible with the contribution mainly of 40K light emission, with a small percentage of light bursts due to bioluminescence. These features reveal the optimal nature of the Capo Passero abyssal site to host a km3-sized Neutrino Telescope

  9. NEMO 2 - Be aware: Wind and solar are coming

    Energy Technology Data Exchange (ETDEWEB)

    Lund, P. [Helsinki Univ. of Technology, Otaniemi (Finland)

    1996-12-31

    Finnish research and development is well placed with respect to new renewable energy technologies in that there exists considerable expertise in specialized areas. For example, over 20 % of all power transmission equipment and generators used in wind energy systems world-wide are manufactured in Finland, while advanced instruments for monitoring wind speed are also highly regarded internationally. Moreover, unique wind technology for complex windy and freezing conditions have been developed. Finland has a 10 % share in the European photovoltaic market, and has competitive advantages in photovoltaic systems and applications, thin film solar cells, and automated electronic controlling systems. A unique solar energy storage system based on hydrogen technology demonstrates skills on overcoming the summer-winter syndrome of large-scale solar energy utilization. The annual turnover of the Finnish industries on solar and wind energy has increased from 5 million ECU in 1988 to almost 50 million ECU in 1996. The national R and D and D from 1988 onwards has played an important role in this context. Most of the research and development into new and renewable energy technologies in Finland has been carried out through the Advanced New Energy Systems and Technologies Research Programme (NEMO2) of Tekes

  10. Review paper of gateway selection schemes for MANET of NEMO (MANEMO)

    International Nuclear Information System (INIS)

    The fast growth of Internet applications brings with it new challenges for researchers to provide new solutions that guarantee better Internet access for mobile hosts and networks. The globally reachable, Home-Agent based, infrastructure Network Mobility (NEMO) and the local, multi-hop, and infrastructure-less Mobile Ad hoc Network (MANET) developed by Internet Engineering Task Force (IETF) support different topologies of the mobile networks. A new architecture was proposed by combining both topologies to obtain Mobile Ad Hoc NEMO (MANEMO). However, the integration of NEMO and MANET introduces many challenges such as network loops, sub-optimal route, redundant tunnel problem, absence of communication without Home Agent reachability, and exit router selection when multiple Exit Routers to the Internet exist. This paper aims to review the different proposed models that could be used to implement the gateway selection mechanism and it highlights the strengths as well as the limitations of these approaches

  11. NEMO5: Achieving High-end Internode Communication for Performance Projection Beyond Moore's Law

    CERN Document Server

    Andrawis, Robert; Charles, James; Fang, Jianbin; Fonseca, Jim; He, Yu; Klimeck, Gerhard; Jiang, Zhengping; Kubis, Tillmann; Mejia, Daniel; Lemus, Daniel; Povolotskyi, Michael; Rubiano, Santiago Alonso Perez; Sarangapani, Prasad; Zeng, Lang

    2015-01-01

    Electronic performance predictions of modern nanotransistors require nonequilibrium Green's functions including incoherent scattering on phonons as well as inclusion of random alloy disorder and surface roughness effects. The solution of all these effects is numerically extremely expensive and has to be done on the world's largest supercomputers due to the large memory requirement and the high performance demands on the communication network between the compute nodes. In this work, it is shown that NEMO5 covers all required physical effects and their combination. Furthermore, it is also shown that NEMO5's implementation of the algorithm scales very well up to about 178176CPUs with a sustained performance of about 857 TFLOPS. Therefore, NEMO5 is ready to simulate future nanotransistors.

  12. Extrapolation of NEMO technique to future generation of 2β-decay experiments

    International Nuclear Information System (INIS)

    Possibilities of NEMO technique for future neutrinoless double-beta-decay experiments are discussed. Main idea is to have a realistic project with planned sensitivity for half-life on the level of approximately (1-2)x1026 y (sensitivity to neutrino mass is about (0.05--0.1) eV). It is demonstrated that this can be achieved using improved NEMO technique to investigate 100 kg of 82Se. Possible improvements of NEMO technique and background conditions are discussed. Scheme of future SUPERNEMO detector and main characteristics of experiment are presented. Such detector can be used also to investigate 0νββ decay in 100Mo, 130Te and 116Cd with sensitivity up to approximately (5-10)x1025 y (or with sensitivity to neutrino mass about 0.1 eV). (author)

  13. Measurement of radon diffusion through shielding foils for the SuperNEMO experiment

    Energy Technology Data Exchange (ETDEWEB)

    Mamedov, F; Cermak, P; Smolek, K; Stekl, I, E-mail: fadahat.mamedov@utef.cvut.cz [Institute of experimental and applied physics, CTU in Prague, Horska 3a/22, 128 00 Prague 2 (Czech Republic)

    2011-01-15

    An apparatus developed for the measurement of radon diffusion through thin foils for the SuperNEMO project is presented. The goal of the SuperNEMO collaboration is to construct a new generation detector for the search for neutrinoless double-beta decay (0{nu}{beta}{beta}) with 100 kg of enriched isotope as the source. At present, the collaboration is carrying out R and D in order to suppress significantly intrinsic background including that caused by radon. The description of the apparatus, data analysis method, as well as the results obtained in the measurement of radon diffusion through several types of thin foils, glue and sealant suitable for shielding in the SuperNEMO detector are discussed.

  14. Monte Carlo simulation studies of the timing calibration accuracy required by the NEMO underwater neutrino telescope

    International Nuclear Information System (INIS)

    The results of Monte Carlo simulation studies of the timing calibration accuracy required by the NEMO underwater neutrino telescope are presented. The NEMO Collaboration is conducting a long term R and D activity toward the installation of a km3 apparatus in the Mediterranean Sea. An optimal site has been found and characterized at 3500 m depth off the Sicilian coast. Monte Carlo simulation shows that the angular resolution of the telescope remains approximately unchanged if the offset errors of timing calibration are less than 1 ns. This value is tolerable because the apparatus performance is not significantly changed when such inaccuracies are added to the other sources of error (e.g., the accuracy position of optical modules). We also discuss the optical background rate effect on the angular resolution of the apparatus and we compare the present version of the NEMO telescope with a different configuration.

  15. Exploring the Leaf Beetle Fauna (Coleoptera: Chrysomelidae of an Ecuadorian Mountain Forest Using DNA Barcoding.

    Directory of Open Access Journals (Sweden)

    Birthe Thormann

    Full Text Available Tropical mountain forests are hotspots of biodiversity hosting a huge but little known diversity of insects that is endangered by habitat destruction and climate change. Therefore, rapid assessment approaches of insect diversity are urgently needed to complement slower traditional taxonomic approaches. We empirically compare different DNA-based species delimitation approaches for a rapid biodiversity assessment of hyperdiverse leaf beetle assemblages along an elevational gradient in southern Ecuador and explore their effect on species richness estimates.Based on a COI barcode data set of 674 leaf beetle specimens (Coleoptera: Chrysomelidae of 266 morphospecies from three sample sites in the Podocarpus National Park, we employed statistical parsimony analysis, distance-based clustering, GMYC- and PTP-modelling to delimit species-like units and compared them to morphology-based (parataxonomic species identifications. The four different approaches for DNA-based species delimitation revealed highly similar numbers of molecular operational taxonomic units (MOTUs (n = 284-289. Estimated total species richness was considerably higher than the sampled amount, 414 for morphospecies (Chao2 and 469-481 for the different MOTU types. Assemblages at different elevational levels (1000 vs. 2000 m had similar species numbers but a very distinct species composition for all delimitation methods. Most species were found only at one elevation while this turnover pattern was even more pronounced for DNA-based delimitation.Given the high congruence of DNA-based delimitation results, probably due to the sampling structure, our study suggests that when applied to species communities on a regionally limited level with high amount of rare species (i.e. ~50% singletons, the choice of species delimitation method can be of minor relevance for assessing species numbers and turnover in tropical insect communities. Therefore, DNA-based species delimitation is confirmed as a

  16. Withaferin A disrupts ubiquitin-based NEMO reorganization induced by canonical NF-κB signaling

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, Shawn S. [McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, 6159 Wisconsin Institute for Medical Research, 1111 Highland Avenue, Madison, WI 53705 (United States); Medical Scientist Training Program, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705 (United States); Cellular and Molecular Biology Program, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705 (United States); Oberley, Christopher [McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, 6159 Wisconsin Institute for Medical Research, 1111 Highland Avenue, Madison, WI 53705 (United States); Hooper, Christopher P. [McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, 6159 Wisconsin Institute for Medical Research, 1111 Highland Avenue, Madison, WI 53705 (United States); Cellular and Molecular Biology Program, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705 (United States); Grindle, Kreg [Department of Medicine, Division of Hematology and Oncology, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705 (United States); Wuerzberger-Davis, Shelly [McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin-Madison, 6159 Wisconsin Institute for Medical Research, 1111 Highland Avenue, Madison, WI 53705 (United States); Wolff, Jared [Department of Medicine, Division of Hematology and Oncology, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI 53705 (United States); and others

    2015-02-01

    The NF-κB family of transcription factors regulates numerous cellular processes, including cell proliferation and survival responses. The constitutive activation of NF-κB has also emerged as an important oncogenic driver in many malignancies, such as activated B-cell like diffuse large B cell lymphoma, among others. In this study, we investigated the impact and mechanisms of action of Withaferin A, a naturally produced steroidal lactone, against both signal-inducible as well as constitutive NF-κB activities. We found that Withaferin A is a robust inhibitor of canonical and constitutive NF-κB activities, leading to apoptosis of certain lymphoma lines. In the canonical pathway induced by TNF, Withaferin A did not disrupt RIP1 polyubiquitination or NEMO–IKKβ interaction and was a poor direct IKKβ inhibitor, but prevented the formation of TNF-induced NEMO foci which colocalized with TNF ligand. While GFP-NEMO efficiently formed TNF-induced foci, a GFP-NEMO{sup Y308S} mutant that is defective in binding to polyubiquitin chains did not form foci. Our study reveals that Withaferin A is a novel type of IKK inhibitor which acts by disrupting NEMO reorganization into ubiquitin-based signaling structures in vivo. - Highlights: • Withaferin A, a NF-κB inhibitor, disrupts signaling induced NEMO localization, a novel point of inhibition. • NEMO can be localized to distinct signaling foci after treatment with TNF. • ABC-type DLCBL cells can be sensitized to apoptosis after treatment with Withaferin A.

  17. NEMO. Netherlands Energy demand MOdel. A top-down model based on bottom-up information

    International Nuclear Information System (INIS)

    The title model links energy use to other production factors, (physical) production, energy prices, technological trends and government policies. It uses a 'putty-semiputty' vintage production structure, in which new investments, adaptations to existing capital goods (retrofit) and 'good-housekeeping' are discerned. Price elasticities are relatively large in the long term and small in the short term. Most predictions of energy use are based on either econometric models or on 'bottom-up information', i.e. disaggregated lists of technical possibilities for and costs of saving energy. Typically, one predicts more energy-efficiency improvements using bottom-up information than using econometric ('top-down') models. We bridged this so-called 'energy-efficiency gap' by designing our macro/meso model NEMO in such a way that we can use bottom-up (micro) information to estimate most model parameters. In our view, reflected in NEMO, the energy-efficiency gap arises for two reasons. The first is that firms and households use a fairly high discount rate of 15% when evaluating the profitability of energy-efficiency improvements. The second is that our bottom-up information ('ICARUS') for most economic sectors does not (as NEMO does) take account of the fact that implementation of new, energy-efficient technology in capital stock takes place only gradually. Parameter estimates for 19 sectors point at a long-term technological energy efficiency improvement trend in Netherlands final energy use of 0.8% per year. The long-term price elasticity is estimated to be 0.29. These values are comparable to other studies based on time series data. Simulations of the effects of the oil price shocks in the seventies and the subsequent fall of oil prices show that the NEMO's price elasticities are consistent with historical data. However, the present pace at which new technologies become available (reflected in NEMO) appears to be lower than in the seventies and eighties. This suggests that it

  18. Strategy of HPGe screening measurements in the SuperNEMO experiment

    International Nuclear Information System (INIS)

    SuperNEMO is a double beta decay experiment that will use a tracko-calorimeter technique. The goal is to reach a sensitivity of T1/2(0ν)>1026 y corresponding to an effective Majorana neutrino mass of 0.04-0.11 eV with 100 kg of 82Se. The general strategy of the HPGe screening measurements is described for the materials of the SuperNEMO demonstrator, regarding their radiopurity and their location. The two platforms, PRISNA and LSM, used for this screening are also briefly described

  19. QR Codes in the Library: "It's Not Your Mother's Barcode!"

    Science.gov (United States)

    Dobbs, Cheri

    2011-01-01

    Barcode scanning has become more than just fun. Now libraries and businesses are leveraging barcode technology as an innovative tool to market their products and ideas. Developed and popularized in Japan, these Quick Response (QR) or two-dimensional barcodes allow marketers to provide interactive content in an otherwise static environment. In this…

  20. 75 FR 56922 - Implementation of the Intelligent Mail Package Barcode

    Science.gov (United States)

    2010-09-17

    ... 111 Implementation of the Intelligent Mail Package Barcode AGENCY: Postal Service TM . ACTION: Advance... Intelligent Mail package barcodes (IMpb), no later than January of 2011; and expects to require the mandatory...Standards@usps.gov , with a subject line of ``Intelligent Mail Package Barcode comments.'' Faxed...

  1. Performance Optimization of NEMO Oceanic Model at High Resolution

    Science.gov (United States)

    Epicoco, Italo; Mocavero, Silvia; Aloisio, Giovanni

    2014-05-01

    The NEMO oceanic model is based on the Navier-Stokes equations along with a nonlinear equation of state, which couples the two active tracers (temperature and salinity) to the fluid velocity. The code is written in Fortan 90 and parallelized using MPI. The resolution of the global ocean models used today for climate change studies limits the prediction accuracy. To overcome this limit, a new high-resolution global model, based on NEMO, simulating at 1/16° and 100 vertical levels has been developed at CMCC. The model is computational and memory intensive, so it requires many resources to be run. An optimization activity is needed. The strategy requires a preliminary analysis to highlight scalability bottlenecks. It has been performed on a SandyBridge architecture at CMCC. An efficiency of 48% on 7K cores (the maximum available) has been achieved. The analysis has been also carried out at routine level, so that the improvement actions could be designed for the entire code or for the single kernel. The analysis highlighted for example a loss of performance due to the routine used to implement the north fold algorithm (i.e. handling the points at the north pole of the 3-poles Grids): indeed an optimization of the routine implementation is needed. The folding is achieved considering only the last 4 rows on the top of the global domain and by applying a rotation pivoting on the point in the middle. During the folding, the point on the top left is updated with the value of the point on bottom right and so on. The current version of the parallel algorithm is based on the domain decomposition. Each MPI process takes care of a block of points. Each process can update its points using values belonging to the symmetric process. In the current implementation, each received message is placed in a buffer with a number of elements equal to the total dimension of the global domain. Each process sweeps the entire buffer, but only a part of that computation is really useful for the

  2. Botany without borders: barcoding in focus.

    Science.gov (United States)

    Kane, Nolan C; Cronk, Quentin

    2008-12-01

    This recent meeting, held on the campus of the University of British Columbia, attracted 1200 delegates and a vast array of talks, but was notable for a remarkable showing of talks and posters on DNA barcoding in plants, spread through many sessions. The Canadian Centre for DNA Barcoding defines barcoding as 'species identification and discovery through the analysis of short, standardized gene regions known as DNA barcodes'. This approach is somewhat controversial in animals (Rubinoff et al., 2006), although it has been shown to be useful and reliable in many metazoan taxa (Meyer & Paulay 2005; Hajibabaei et al., 2007), in which the mitochondrial cytochrome oxidase I (COI) gene is used. However, in land plants, COI evolves far too slowly to be useful, and there is no obvious single universal alternative (Fazekas et al., 2008).Genes that work well in one taxon may perform poorly in other taxa. Additionally, some perfectly good plant species,reproductively isolated and morphologically and ecologically distinct, are too young to show much sequence divergence at most loci. Nevertheless, as we saw at this conference, progress has been made towards identifying genes that serve many of the functions of DNA barcodes, at least in some plant taxa. PMID:19067801

  3. BARCODE DEKODET : En diskursanalyse av byutviklingsdebatten om utbyggingsprosjektet Barcode i Bjørvika

    OpenAIRE

    2009-01-01

    Denne oppgaven handler om "byutviklingsdebatten om Barcode". Utbyggingsprosjektet Barcode ble kåret til vinner av en arkitektkonkurranse for fire tomter i Bjørvika våren 2003. Disse tomtene ligger like sør for sporområdet på Oslo Sentralstasjon. Da utbyggerne for tomtene, Oslo S Utvikling, kom med et nytt reguleringsforslag for området der byggehøydene økes i tråd med Barcode-prinsippet, kom det inn usedvanlig mange kritiske reaksjoner til PBE. Dette var kimen til byutviklingsdebatten om Barc...

  4. Plant DNA barcoding in China

    Institute of Scientific and Technical Information of China (English)

    De-Zhu LI; Jian-Quan LIU; Zhi-Duan CHEN; Hong WANG; Xue-Jun GE; Shi-Liang ZHOU; Lian-Ming GAO; Cheng-Xin FU; Shi-Lin CHEN

    2011-01-01

    @@ Identification is the keystone of biology (Bell, 1986).However, to biologists and students of biology, the total numbers of species that must be identified far outnumber the names commonly used in English, Chinese, or other living languages.In addition, the identification cues vary greatly between different taxonomical groups.Even for the taxonomists with long training and experience, it is difficult to remember all specific terms for a given group, e.g., Orchidaceae or Poaceae, without help of floristic books or monographs.It takes much time and effort to train a taxonomist, at a time when fewer and fewer young students are interested in this "classical" and "out-of-style", but extremely important, discipline.Many students elect to learn the more "advanced'' and "modem" biological disciples like molecular biology and biochemistry.Thus, in China and therest of the world, taxonomists are themselves becoming "endangered".The rise of the DNA barcoding is expected to mitigate, at least in part, this dilemma.

  5. From Barcode to QR Code Applications

    Directory of Open Access Journals (Sweden)

    László Várallyai

    2012-12-01

    Full Text Available This paper shows the Zsohár Horticulture Company in Nagyrákos, how they want to change their barcode identification system to QR code. They cultivate herbaceous, perpetual decorational plants, rock-garden, flower-bed and swamp perpetuals, decorational grasses and spices. A part of the perpetuals are evergreens, but most of them has special organs - such as onions, thick-, bulbous roots, "winter-proof" buds - so they can survive winter. In the first part of the paper I introduce the different barcode standards, how can it be printed and how can it be read. In the second part of the paper I give details about the quick response code (QR code and the two-dimensional (2D barcode. Third part of this paper illustrates the QR code usability in agriculture focused on the gardening.

  6. Determining Lineage Pathways from Cellular Barcoding Experiments

    Directory of Open Access Journals (Sweden)

    Leïla Perié

    2014-02-01

    Full Text Available Cellular barcoding and other single-cell lineage-tracing strategies form experimental methodologies for analysis of in vivo cell fate that have been instrumental in several significant recent discoveries. Due to the highly nonlinear nature of proliferation and differentiation, interrogation of the resulting data for evaluation of potential lineage pathways requires a new quantitative framework complete with appropriate statistical tests. Here, we develop such a framework, illustrating its utility by analyzing data from barcoded multipotent cells of the blood system. This application demonstrates that the data require additional paths beyond those found in the classical model, which leads us to propose that hematopoietic differentiation follows a loss of potential mechanism and to suggest further experiments to test this deduction. Our quantitative framework can evaluate the compatibility of lineage trees with barcoded data from any proliferating and differentiating cell system.

  7. A Tunnel Compress Scheme for Multi-Tunneling in PMIPv6-based Nested NEMO

    Directory of Open Access Journals (Sweden)

    Youn-Hee Han

    2010-11-01

    Full Text Available In nested NEMO, a multi-tunneling causes a pinball routing problem. Several solutions proposed tosolve the pinball routing problem in NEMO BSP cannot be used at PMIPv6-based NEMO due todifferent environment such as no route optimization with CN. We propose a tunnel compress scheme formulti-tunneling in PMIPv6-based NEMO. The scheme consists of two parts: the first part is an interdomainor wired Internet part. The other is an intra part of nested mobile networks. In the inter-domainpart, single IP-in-IP tunnel is created by connecting an innermost entry point with an outermost exitpoint in original multi-tunnels. As the same way used in the inter-domain part, single IP-in-IP tunnel iscreated from the outermost exit point and an innermost exit point in original multi-tunnels. In theproposed scheme, IP-in-IP encapsulated packets are forwarded using host-based routing withoutmodifying the outer header. The information to compress multi-tunnels is piggybacked at the PMIPv6signaling.

  8. Design and Experimental Evaluation of a Vehicular Network Based on NEMO and MANET

    Directory of Open Access Journals (Sweden)

    Santa José

    2010-01-01

    Full Text Available Abstract Mobile Ad hoc Network (MANET routing protocols and Network Mobility (NEMO Basic Support are considered key technologies for vehicular networks. MANEMO, that is, the combination of MANET (for infrastructureless communications and NEMO (for infrastructure-based communications offers a number of benefits, such as route optimization or multihoming. With the aim of assessing the benefits of this synergy, this paper presents a policy-based solution to distribute traffic among multiple paths to improve the overall performance of a vehicular network. An integral vehicular communication testbed has been developed to carry out field trials. First, the performance of the Optimized Link State Routing protocol (OLSR is evaluated in a vehicular network with up to four vehicles. To analyze the impact of the vehicles' position and movement on network performances, an integrated evaluation environment called AnaVANET has been developed. Performance results have been geolocated using GPS information. Second, by switching from NEMO to MANET, routes between vehicles are optimized, and the final performance is improved in terms of latency and bandwidth. Our experimental results show that the network operation is further improved with simultaneous usage of NEMO and MANET.

  9. Advanced energy systems and technologies (NEMO 2). Final report 1993-1998

    International Nuclear Information System (INIS)

    NEMO2 has been the major Finnish energy research programme on advanced energy systems and technologies during 1993-1998. The main objective of the programme has been to support industrial technology development but also to increase the utilisation of wind and solar energy in Finland. The main technology fields covered are wind and solar energy. In addition, the programme has supported projects on energy storage and other small-scale energy technologies such as fuel cells that support the main technology fields chosen. NEMO2 is one of the energy research programmes of the Technology Development Centre of Finland (TEKES). The total R and D funding over the whole programme period was FIM 130 million (ECU 22 million). The public funding of the total programme costs has been 43 %. The industrial participation has been strong. International co-operation has been an important aspect in NEMO2: the programme has stimulated 24 EU-projects and participation in several IEA co-operative tasks. International funding adds nearly 20 % to the NEMO2 R and D funding. (orig.)

  10. NEMO educational kit on micro-optics at the secondary school

    Science.gov (United States)

    Flores-Arias, M. T.; Bao-Varela, Carmen

    2014-07-01

    NEMO was the "Network of Excellence in Micro-Optics" granted in the "Sixth Framework Program" of the European Union. It aimed at providing Europe with a complete Micro-Optics food-chain, by setting up centers for optical modeling and design; measurement and instrumentation; mastering, prototyping and replication; integration and packaging and reliability and standardization. More than 300 researchers from 30 groups in 12 countries participated in the project. One of the objectives of NEMO was to spread excellence and disseminate knowledge on micro-optics and micro-photonics. To convince pupils, already from secondary school level on, about the crucial role of light and micro-optics and the opportunities this combination holds, several partners of NEMO had collaborate to create this Educational Kit. In Spain the partner involved in this aim was the "Microoptics and GRIN Optics Group" at the University of Santiago of Compostela (USC). The educational kits provided to the Secondary School were composed by two plastic cards with the following microoptical element: different kinds of diffractive optical elements or DOES and refractive optical elements or ROEs namely arrays of micro-lenses. The kit also included a DVD with a handbook for performing the experiments as well as a laser pointer source. This kit was distributed free of charge in the countries with partners in NEMO. In particular in Spain was offered to around 200 Secondary School Centers and only 80 answered accepting evaluate the kit.

  11. Advanced energy systems and technologies (NEMO 2). Final report 1993-1998

    Energy Technology Data Exchange (ETDEWEB)

    Lund, P.; Konttinen, P. [eds.

    1998-12-31

    NEMO2 has been the major Finnish energy research programme on advanced energy systems and technologies during 1993-1998. The main objective of the programme has been to support industrial technology development but also to increase the utilisation of wind and solar energy in Finland. The main technology fields covered are wind and solar energy. In addition, the programme has supported projects on energy storage and other small-scale energy technologies such as fuel cells that support the main technology fields chosen. NEMO2 is one of the energy research programmes of the Technology Development Centre of Finland (TEKES). The total R and D funding over the whole programme period was FIM 130 million (ECU 22 million). The public funding of the total programme costs has been 43 %. The industrial participation has been strong. International co-operation has been an important aspect in NEMO2: the programme has stimulated 24 EU-projects and participation in several IEA co-operative tasks. International funding adds nearly 20 % to the NEMO2 R and D funding. (orig.)

  12. BiPo: A dedicated radiopurity detector for the SuperNEMO experiment

    Energy Technology Data Exchange (ETDEWEB)

    Gómez, H., E-mail: gomez@lal.in2p3.fr [Laboratoire de l' Accélérateur Linéaire, Centre Scientifique d' Orsay, Batiment 200 - BP34, 91898 Orsay Cedex (France)

    2013-08-01

    New generation experiments in Astroparticle Physics need to operate under really restrictive background conditions, which implies the use of highly radiopure materials for the experimental setup construction. For this reason, the screening of the materials with enough sensitivity has become a challenge that sometimes cannot be achieved with standard techniques like Germanium detector spectroscopy. BiPo is a dedicated detector that will operate in the Canfranc Underground Laboratory, designed to measure the radiopurity, mainly of the ββ sources of the SuperNEMO experiment, by the detection of BiPo events. It also has been recently considered to measure other elements of the SuperNEMO experimental setup. It is composed of two modules with 40 optical lines each, that register the energy and the time of the emitted particles. The well-known features of the BiPo events (delayed coincidence between an electron and an α particle) facilitate the discrimination of other background events that could entangle the expected signal. In addition, the geometry of the detector, with an active area of around 3.6 m{sup 2}, has been optimized to reach the sensitivity levels required for the SuperNEMO source foils in the shortest time possible. Main features of the detector, present status and prospects, and its crucial role inside the SuperNEMO schedule will be presented.

  13. Surface Wave Effects in the NEMO Ocean Model: Forced and Coupled Experiments

    CERN Document Server

    Breivik, Øyvind; Bidlot, Jean-Raymond; Balmaseda, Magdalena Alonso; Janssen, Peter A E M

    2015-01-01

    The NEMO general circulation ocean model is extended to incorporate three physical processes related to ocean surface waves, namely the surface stress (modified by growth and dissipation of the oceanic wave field), the turbulent kinetic energy flux from breaking waves, and the Stokes-Coriolis force. Experiments are done with NEMO in ocean-only (forced) mode and coupled to the ECMWF atmospheric and wave models. Ocean-only integrations are forced with fields from the ERA-Interim reanalysis. All three effects are noticeable in the extra-tropics, but the sea-state dependent turbulent kinetic energy flux yields by far the largest difference. This is partly because the control run has too vigorous deep mixing due to an empirical mixing term in NEMO. We investigate the relation between this ad hoc mixing and Langmuir turbulence and find that it is much more effective than the Langmuir parameterization used in NEMO. The biases in sea surface temperature as well as subsurface temperature are reduced, and the total oce...

  14. Long term monitoring of the optical background in the Capo Passero deep-sea site with the NEMO tower prototype

    OpenAIRE

    Adrián-Martínez, S.; Aiello, S.; Ameli, F.; Anghinolfi, M.; Ardid, M.; Barbarino, G.; Barbarito, E.; Barbato, F. C. T.; Beverini, N.(INFN, Sezione di Pisa, Pisa, Italy); Biagi, S.; Biagioni, A.; Bouhadef, B.; Bozza, C.; Cacopardo, G.; M. Calamai

    2015-01-01

    The NEMO Phase-2 tower is the first detector which was operated underwater for more than one year at the "record" depth of 3500 m. It was designed and built within the framework of the NEMO (NEutrino Mediterranean Observatory) project. The 380 m high tower was successfully installed in March 2013 80 km offshore Capo Passero (Italy). This is the first prototype operated on the site where the italian node of the KM3NeT neutrino telescope will be built. The installation and operation of the NEMO...

  15. Long term monitoring of the optical background in the Capo Passero deep-sea site with the NEMO tower prototype

    OpenAIRE

    Adrián-Martínez, S.; Aiello, S.; Ameli, F.; Anghinolfi, M.; Ardid, M.; Barbarino, G.; Barbarito, E.; Barbato, F. C. T.; Beverini, N.(INFN, Sezione di Pisa, Pisa, Italy); Biagi, S.; Biagioni, A.; Bouhadef, B.; Bozza, C.; Cacopardo, G.; M. Calamai

    2016-01-01

    The NEMO Phase-2 tower is the first detector which was operated underwater for more than 1 year at the “record” depth of 3500 m. It was designed and built within the framework of the NEMO (NEutrino Mediterranean Observatory) project. The 380 m high tower was successfully installed in March 2013 80 km offshore Capo Passero (Italy). This is the first prototype operated on the site where the Italian node of the KM3NeT neutrino telescope will be built. The installation and operation of the NEMO P...

  16. Adapting NEMO for use as the UK operational storm surge forecasting model

    Science.gov (United States)

    Furner, Rachel; Williams, Jane; Horsburgh, Kevin; Saulter, Andrew

    2016-04-01

    The United Kingdom is an area vulnerable to damage due to storm surges, particularly the East Coast which suffered losses estimated at over £1 billion during the North Sea surge event of the 5th and 6th December 2013. Accurate forecasting of storm surge events for this region is crucial to enable government agencies to assess the risk of overtopping of coastal defences so they can respond appropriately, minimising risk to life and infrastructure. There has been an operational storm surge forecast service for this region since 1978, using a numerical model developed by the National Oceanography Centre (NOC) and run at the UK Met Office. This is also implemented as part of an ensemble prediction system, using perturbed atmospheric forcing to produce an ensemble surge forecast. In order to ensure efficient use of future supercomputer developments and to create synergy with existing operational coastal ocean models the Met Office and NOC have begun a joint project transitioning the storm surge forecast system from the current CS3X code base to a configuration based on the Nucleus for European Modelling of the Ocean (NEMO). This work involves both adapting NEMO to add functionality, such as allowing the drying out of ocean cells and changes allowing NEMO to run efficiently as a two-dimensional, barotropic model. As the ensemble surge forecast system is run with 12 members 4 times a day computational efficiency is of high importance. Upon completion this project will enable interesting scientific comparisons to be made between a NEMO based surge model and the full three-dimensional baroclinic NEMO based models currently run within the Met Office, facilitating assessment of the impact of baroclinic processes, and vertical resolution on sea surface height forecasts. Moving to a NEMO code base will also allow many future developments to be more easily used within the storm surge model due to the wide range of options which currently exist within NEMO or are planned for

  17. Dual resolution two-dimensional color barcode

    Science.gov (United States)

    Fan, Zhigang; Zhao, Yonghui; Wang, Shenge; Ding, Hengzhou

    2013-03-01

    In this paper, a QR code is presented with a dual resolution structure. It contains a high resolution layer that is coded in luminance and is in consistency with the conventional QR code, and a low resolution layer providing additional error checking information, that is coded in chrominance and is robust to blurring. The proposed QR code is compatible to its underlying conventional black and white barcode as it can be read by their decoders. Its advantage is additional reliability when a color decoder is used. In particular, it enhances the decoding accuracy for devices such as mobile devices for barcodes printed in small sizes.

  18. Modelling turbulent vertical mixing sensitivity using a 1-D version of NEMO

    Directory of Open Access Journals (Sweden)

    G. Reffray

    2014-08-01

    Full Text Available Through two numerical experiments, a 1-D vertical model called NEMO1D was used to investigate physical and numerical turbulent-mixing behaviour. The results show that all the turbulent closures tested (k + l from Blanke and Delecluse, 1993 and two equation models: Generic Lengh Scale closures from Umlauf and Burchard, 2003 are able to correctly reproduce the classical test of Kato and Phillips (1969 under favourable numerical conditions while some solutions may diverge depending on the degradation of the spatial and time discretization. The performances of turbulence models were then compared with data measured over a one-year period (mid-2010 to mid-2011 at the PAPA station, located in the North Pacific Ocean. The modelled temperature and salinity were in good agreement with the observations, with a maximum temperature error between −2 and 2 °C during the stratified period (June to October. However the results also depend on the numerical conditions. The vertical RMSE varied, for different turbulent closures, from 0.1 to 0.3 °C during the stratified period and from 0.03 to 0.15 °C during the homogeneous period. This 1-D configuration at the PAPA station (called PAPA1D is now available in NEMO as a reference configuration including the input files and atmospheric forcing set described in this paper. Thus, all the results described can be recovered by downloading and launching PAPA1D. The configuration is described on the NEMO site (http://www.nemo-ocean.eu/Using-NEMO/Configurations/C1D_PAPA. This package is a good starting point for further investigation of vertical processes.

  19. Integrated Taxonomy and DNA Barcoding of Alpine Midges (Diptera: Chironomidae).

    Science.gov (United States)

    Montagna, Matteo; Mereghetti, Valeria; Lencioni, Valeria; Rossaro, Bruno

    2016-01-01

    Rapid and efficient DNA-based tools are recommended for the evaluation of the insect biodiversity of high-altitude streams. In the present study, focused principally on larvae of the genus Diamesa Meigen 1835 (Diptera: Chironomidae), the congruence between morphological/molecular delimitation of species as well as performances in taxonomic assignments were evaluated. A fragment of the mitochondrial cox1 gene was obtained from 112 larvae, pupae and adults (Diamesinae, Orthocladiinae and Tanypodinae) that were collected in different mountain regions of the Alps and Apennines. On the basis of morphological characters 102 specimens were attributed to 16 species, and the remaining ten specimens were identified to the genus level. Molecular species delimitation was performed using: i) distance-based Automatic Barcode Gap Discovery (ABGD), with no a priori assumptions on species identification; and ii) coalescent tree-based approaches as the Generalized Mixed Yule Coalescent model, its Bayesian implementation and Bayesian Poisson Tree Processes. The ABGD analysis, estimating an optimal intra/interspecific nucleotide distance threshold of 0.7%-1.4%, identified 23 putative species; the tree-based approaches, identified between 25-26 entities, provided nearly identical results. All species belonging to zernyi, steinboecki, latitarsis, bertrami, dampfi and incallida groups, as well as outgroup species, are recovered as separate entities, perfectly matching the identified morphospecies. In contrast, within the cinerella group, cases of discrepancy arose: i) the two morphologically separate species D. cinerella and D. tonsa are neither monophyletic nor diagnosable exhibiting low values of between-taxa nucleotide mean divergence (0.94%); ii) few cases of larvae morphological misidentification were observed. Head capsule color is confirmed to be a valid character able to discriminate larvae of D. zernyi, D. tonsa and D. cinerella, but it is here better defined as a color gradient

  20. Raman Barcode for Counterfeit Drug Product Detection.

    Science.gov (United States)

    Lawson, Latevi S; Rodriguez, Jason D

    2016-05-01

    Potential infiltration of counterfeit drug products-containing the wrong or no active pharmaceutical ingredient (API)-into the bona fide drug supply poses a significant threat to consumers worldwide. Raman spectroscopy offers a rapid, nondestructive avenue to screen a high throughput of samples. Traditional qualitative Raman identification is typically done with spectral correlation methods that compare the spectrum of a reference sample to an unknown. This is often effective for pure materials but is quite challenging when dealing with drug products that contain different formulations of active and inactive ingredients. Typically, reliable identification of drug products using common spectral correlation algorithms can only be made if the specific product under study is present in the library of reference spectra, thereby limiting the scope of products that can be screened. In this paper, we introduce the concept of the Raman barcode for identification of drug products by comparing the known peaks in the API reference spectrum to the peaks present in the finished drug product under study. This method requires the transformation of the Raman spectra of both API and finished drug products into a barcode representation by assigning zero intensity to every spectral frequency except the frequencies that correspond to Raman peaks. By comparing the percentage of nonzero overlap between the expected API barcode and finished drug product barcode, the identity of API present can be confirmed. In this study, 18 approved finished drug products and nine simulated counterfeits were successfully identified with 100% accuracy utilizing this method. PMID:27043140

  1. DNA barcoding and phylogenetic relationships in Timaliidae.

    Science.gov (United States)

    Huang, Z H; Ke, D H

    2015-01-01

    The Timaliidae, a diverse family of oscine passerine birds, has long been a subject of debate regarding its phylogeny. The mitochondrial cytochrome c oxidase subunit I (COI) gene has been used as a powerful marker for identification and phylogenetic studies of animal species. In the present study, we analyzed the COI barcodes of 71 species from 21 genera belonging to the family Timaliidae. Every bird species possessed a barcode distinct from that of other bird species. Kimura two-parameter (K2P) distances were calculated between barcodes. The average genetic distance between species was 18 times higher than the average genetic distance within species. The neighbor-joining method was used to construct a phylogenetic tree and all the species could be discriminated by their distinct clades within the phylogenetic tree. The results indicate that some currently recognized babbler genera might not be monophyletic, with the COI gene data supporting the hypothesis of polyphyly for Garrulax, Alcippe, and Minla. Thus, DNA barcoding is an effective molecular tool for Timaliidae species identification and phylogenetic inference. PMID:26125793

  2. The use of DNA barcode for identifying species of Oxysarcodexia Townsend (Diptera: Sarcophagidae): A preliminary survey.

    Science.gov (United States)

    Madeira, Tais; Souza, Carina M; Cordeiro, Juliana; Thyssen, Patricia J

    2016-09-01

    Oxysarcodexia is one of the Neotropical richest genera within the Sarcophagidae family. Medical, veterinary and forensic importance of these flies are due to their association with corpses, cases of myiasis in humans and domestic animals, and being pathogen carriers. Regarding morphological identification, molecular techniques, especially the DNA-based ones, arise as useful alternatives or complementary methodologies for species identification. Thus, in this study we aimed to investigate the potential of the COI marker (barcode region) to delimit Oxysarcodexia species in comparison with the morphological identification criteria. A COI fragment was amplified and the length of the sequences after alignment were of 648bp (149 parsimoniously informative variable sites). According to the Neighbor-Joining phylogenetic tree, specimens of the same morphological species were clustered in monophyletic clades (82-100% bootstrap branch support). Species-level resolution thus achieved was successful, despite low interspecific divergence (1.8-2.3%) and since interspecific variation was higher than intraspecific divergence (0.1-1.2%). Therefore, the use of COI barcode sequences supports differentiation and identification of the Oxysarcodexia species studied. PMID:27260665

  3. Barcode server: a visualization-based genome analysis system.

    Directory of Open Access Journals (Sweden)

    Fenglou Mao

    Full Text Available We have previously developed a computational method for representing a genome as a barcode image, which makes various genomic features visually apparent. We have demonstrated that this visual capability has made some challenging genome analysis problems relatively easy to solve. We have applied this capability to a number of challenging problems, including (a identification of horizontally transferred genes, (b identification of genomic islands with special properties and (c binning of metagenomic sequences, and achieved highly encouraging results. These application results inspired us to develop this barcode-based genome analysis server for public service, which supports the following capabilities: (a calculation of the k-mer based barcode image for a provided DNA sequence; (b detection of sequence fragments in a given genome with distinct barcodes from those of the majority of the genome, (c clustering of provided DNA sequences into groups having similar barcodes; and (d homology-based search using Blast against a genome database for any selected genomic regions deemed to have interesting barcodes. The barcode server provides a job management capability, allowing processing of a large number of analysis jobs for barcode-based comparative genome analyses. The barcode server is accessible at http://csbl1.bmb.uga.edu/Barcode.

  4. Barcode Server: A Visualization-Based Genome Analysis System

    Science.gov (United States)

    Mao, Fenglou; Olman, Victor; Wang, Yan; Xu, Ying

    2013-01-01

    We have previously developed a computational method for representing a genome as a barcode image, which makes various genomic features visually apparent. We have demonstrated that this visual capability has made some challenging genome analysis problems relatively easy to solve. We have applied this capability to a number of challenging problems, including (a) identification of horizontally transferred genes, (b) identification of genomic islands with special properties and (c) binning of metagenomic sequences, and achieved highly encouraging results. These application results inspired us to develop this barcode-based genome analysis server for public service, which supports the following capabilities: (a) calculation of the k-mer based barcode image for a provided DNA sequence; (b) detection of sequence fragments in a given genome with distinct barcodes from those of the majority of the genome, (c) clustering of provided DNA sequences into groups having similar barcodes; and (d) homology-based search using Blast against a genome database for any selected genomic regions deemed to have interesting barcodes. The barcode server provides a job management capability, allowing processing of a large number of analysis jobs for barcode-based comparative genome analyses. The barcode server is accessible at http://csbl1.bmb.uga.edu/Barcode. PMID:23457606

  5. Application of PDF417 symbology for 'DNA Barcoding'.

    Science.gov (United States)

    Kumar, N Pradeep; Rajavel, A R; Jambulingam, P

    2008-05-01

    DNA sequences consisting of about 600 base pairs of the 5' region of the cytochrome c oxidase subunit 1 (COI) gene has been proposed as DNA Barcodes for taxonomical identification of species in different animals. We evaluated the application of two-dimensional barcodes for 'DNA Barcoding'. 'PDF417' symbology was applied to convert DNA Barcode sequences already proposed [N. Pradeep Kumar, A.R. Rajavel, R. Natarajan, P. Jambulingam, DNA Barcodes can distinguish species of Indian mosquitoes (Diptera: Culicidae). J. Med. Entomol. 77 (2007) 1-7.] for 10 different species of mosquitoes prevalent in India. Decoding of these digital images using 2-D scanner and a suitable software reproduced the input DNA sequences unchanged. This analysis indicated the utility of PDF417 for 'DNA Barcoding', which could be of definite use for taxonomic documentation of animals. PMID:18282635

  6. How stable are the mutagenic tautomers of DNA bases?

    Directory of Open Access Journals (Sweden)

    Brovarets’ O. O.

    2010-02-01

    Full Text Available Aim. To determine the lifetime of the mutagenic tautomers of DNA base pairs through the investigation of the physicochemical mechanisms of their intramolecular proton transfer. Methods. Non-empirical quantum chemistry, the analysis of the electron density by means of Bader’s atom in molecules (AIM theory and physicochemical kinetics were used. Results. Physicochemical character of the transition state of the intramolecular tautomerisation of DNA bases was investigated, the lifetime of mutagenic tautomers was calculated. Conclusions. The lifetime of the DNA bases mutagenic tautomers by 3–10 orders exceeds typical time of DNA replication in the cell (~103 s. This fact confirms that the postulate, on which the Watson-Crick tautomeric hypothesis of spontaneous transitions grounds, is adequate. The absence of intramolecular H-bonds in the canonical and mutagenic tautomeric forms determine their high stability

  7. Defining operational taxonomic units using DNA barcode data

    OpenAIRE

    Blaxter, Mark; Mann, Jenna; Chapman, Tom; Thomas, Fran; Whitton, Claire; Floyd, Robin; Abebe, Eyualem

    2005-01-01

    The scale of diversity of life on this planet is a significant challenge for any scientific programme hoping to produce a complete catalogue, whatever means is used. For DNA barcoding studies, this difficulty is compounded by the realization that any chosen barcode sequence is not the gene 'for' speciation and that taxa have evolutionary histories. How are we to disentangle the confounding effects of reticulate population genetic processes? Using the DNA barcode data from meiofaunal surveys, ...

  8. One-dimensional barcode reading: an information theoretic approach

    OpenAIRE

    Houni, Karim; Sawaya, Wadih; Delignon, Yves

    2008-01-01

    In the convergence context of identification technology and information-data transmission, the barcode found its place as the simplest and the most pervasive solution for new uses, especially within mobile commerce, bringing youth to this long-lived technology. From a communication theory point of view, a barcode is a singular coding based on a graphical representation of the information to be transmitted. We present an information theoretic approach for 1D image-based barcode reading analysi...

  9. iBarcode.org: web-based molecular biodiversity analysis

    OpenAIRE

    Hajibabaei Mehrdad; Singer Gregory AC

    2009-01-01

    Abstract Background DNA sequences have become a primary source of information in biodiversity analysis. For example, short standardized species-specific genomic regions, DNA barcodes, are being used as a global standard for species identification and biodiversity studies. Most DNA barcodes are being generated by laboratories that have an expertise in DNA sequencing but not in bioinformatics data analysis. Therefore, we have developed a web-based suite of tools to help the DNA barcode research...

  10. A DNA mini-barcode for land plants.

    Science.gov (United States)

    Little, Damon P

    2014-05-01

    Small portions of the barcode region - mini-barcodes - may be used in place of full-length barcodes to overcome DNA degradation for samples with poor DNA preservation. 591,491,286 rbcL mini-barcode primer combinations were electronically evaluated for PCR universality, and two novel highly universal sets of priming sites were identified. Novel and published rbcL mini-barcode primers were evaluated for PCR amplification [determined with a validated electronic simulation (n = 2765) and empirically (n = 188)], Sanger sequence quality [determined empirically (n = 188)], and taxonomic discrimination [determined empirically (n = 30,472)]. PCR amplification for all mini-barcodes, as estimated by validated electronic simulation, was successful for 90.2-99.8% of species. Overall Sanger sequence quality for mini-barcodes was very low - the best mini-barcode tested produced sequences of adequate quality (B20 ≥ 0.5) for 74.5% of samples. The majority of mini-barcodes provide correct identifications of families in excess of 70.1% of the time. Discriminatory power noticeably decreased at lower taxonomic levels. At the species level, the discriminatory power of the best mini-barcode was less than 38.2%. For samples believed to contain DNA from only one species, an investigator should attempt to sequence, in decreasing order of utility and probability of success, mini-barcodes F (rbcL1/rbcLB), D (F52/R193) and K (F517/R604). For samples believed to contain DNA from more than one species, an investigator should amplify and sequence mini-barcode D (F52/R193). PMID:24286499

  11. DNA-based Artificial Nanostructures: Fabrication, Properties, and Applications

    OpenAIRE

    Sun, Young; Kiang, Ching-Hwa

    2005-01-01

    Table of Content 1. Introduction 2. DNA fundamentals 3. Attachment of DNA to surface 4. Fabrication of nanostructures using DNA 4.1 Nanostructures of pure DNA 4.2 DNA-based assembly of metal nanoparticles 4.3 Construction of semiconductor particle arrays using DNA 4.4 DNA-directed nanowires 4.5 DNA-functionalized carbon nanotubes 4.6 Field-transistor based on DNA 4.7 Nanofabrication using artificial DNA 5. DNA-based nanostructures as biosensors 6. Properties of DNA-linked gold nanoparticles 6...

  12. Measurement of the atmospheric muon flux with the NEMO Phase-1 detector

    Science.gov (United States)

    Aiello, S.; Ameli, F.; Amore, I.; Anghinolfi, M.; Anzalone, A.; Barbarino, G.; Battaglieri, M.; Bazzotti, M.; Bersani, A.; Beverini, N.; Biagi, S.; Bonori, M.; Bouhadef, B.; Brunoldi, M.; Cacopardo, G.; Capone, A.; Caponetto, L.; Carminati, G.; Chiarusi, T.; Circella, M.; Cocimano, R.; Coniglione, R.; Cordelli, M.; Costa, M.; D'Amico, A.; De Bonis, G.; De Marzo, C.; De Rosa, G.; De Ruvo, G.; De Vita, R.; Distefano, C.; Falchini, E.; Flaminio, V.; Fratini, K.; Gabrielli, A.; Galatà, S.; Gandolfi, E.; Giacomelli, G.; Giorgi, F.; Giovanetti, G.; Grimaldi, A.; Habel, R.; Imbesi, M.; Kulikovsky, V.; Lattuada, D.; Leonora, E.; Lonardo, A.; Lo Presti, D.; Lucarelli, F.; Marinelli, A.; Margiotta, A.; Martini, A.; Masullo, R.; Migneco, E.; Minutoli, S.; Morganti, M.; Musico, P.; Musumeci, M.; Nicolau, C. A.; Orlando, A.; Osipenko, M.; Papaleo, R.; Pappalardo, V.; Piattelli, P.; Piombo, D.; Raia, G.; Randazzo, N.; Reito, S.; Ricco, G.; Riccobene, G.; Ripani, M.; Rovelli, A.; Ruppi, M.; Russo, G. V.; Russo, S.; Sapienza, P.; Sciliberto, D.; Sedita, M.; Shirokov, E.; Simeone, F.; Sipala, V.; Spurio, M.; Taiuti, M.; Trasatti, L.; Urso, S.; Vecchi, M.; Vicini, P.; Wischnewski, R.

    2010-05-01

    The NEMO Collaboration installed and operated an underwater detector including prototypes of the critical elements of a possible underwater km 3 neutrino telescope: a four-floor tower (called Mini-Tower) and a Junction Box. The detector was developed to test some of the main systems of the km 3 detector, including the data transmission, the power distribution, the timing calibration and the acoustic positioning systems as well as to verify the capabilities of a single tridimensional detection structure to reconstruct muon tracks. We present results of the analysis of the data collected with the NEMO Mini-Tower. The position of photomultiplier tubes (PMTs) is determined through the acoustic position system. Signals detected with PMTs are used to reconstruct the tracks of atmospheric muons. The angular distribution of atmospheric muons was measured and results compared to Monte Carlo simulations.

  13. NEMO: Extraction and normalization of organization names from PubMed affiliation strings

    CERN Document Server

    Jonnalagadda, Siddhartha

    2011-01-01

    We propose NEMO, a system for extracting organization names in the affiliation and normalizing them to a canonical organization name. Our parsing process involves multi-layered rule matching with multiple dictionaries. The system achieves more than 98% f-score in extracting organization names. Our process of normalization that involves clustering based on local sequence alignment metrics and local learning based on finding connected components. A high precision was also observed in normalization. NEMO is the missing link in associating each biomedical paper and its authors to an organization name in its canonical form and the Geopolitical location of the organization. This research could potentially help in analyzing large social networks of organizations for landscaping a particular topic, improving performance of author disambiguation, adding weak links in the co-author network of authors, augmenting NLM's MARS system for correcting errors in OCR output of affiliation field, and automatically indexing the P...

  14. Measurement of the atmospheric muon flux with the NEMO Phase-1 detector

    CERN Document Server

    Aiello, S; Amore, I; Anghinolfi, M; Anzalone, A; Barbarino, G; Battaglieri, M; Bazzotti, M; Bersani, A; Beverini, N; Biagi, S; Bonori, M; Bouhadef, B; Brunoldi, M; Cacopardo, G; Capone, A; Caponetto, L; Carminati, G; Chiarusi, T; Circella, M; Cocimano, R; Coniglione, R; Cordelli, M; Costa, M; D'Amico, A; De Bonis, G; De Marzo, C; 1,; De Rosa, G; De Ruvo, G; De Vita, R; Distefano, C; Falchini, E; Flaminio, V; Fratini, K; Gabrielli, A; Galatà, S; Gandolfi, E; Giacomelli, G; Giorgi, F; Giovanetti, G; Grimaldi, A; Habel, R; Imbesi, M; Kulikovsky, V; Lattuada, D; Leonora, E; Lonardo, A; Presti, D Lo; Lucarelli, F; Marinelli, A; Margiotta, A; Martini, A; Masullo, R; Migneco, E; Minutoli, S; Morganti, M; Musico, P; Musumeci, M; Nicolau, C A; Orlando, A; Osipenko, M; Papaleo, R; Pappalardo, V; Piattelli, P; Piombo, D; Raia, G; Randazzo, N; Reito, S; Ricco, G; Riccobene, G; Ripani, M; Rovelli, A; Ruppi, M; Russo, G V; Russo, S; Sapienza, P; Sciliberto, D; Sedita, M; Shirokov, E; Simeone, F; Sipala, V; Spurio, M; Taiuti, M; Trasatti, L; Urso, S; Vecchi, M; Vicini, P; Wischnewski, R

    2009-01-01

    The NEMO Collaboration installed and operated an underwater detector including prototypes of the critical elements of a possible underwater km3 neutrino telescope: a four-floor tower (called Mini-Tower) and a Junction Box. The detector was developed to test some of the main systems of the km3 detector, including the data transmission, the power distribution, the timing calibration and the acoustic positioning systems as well as to verify the capabilities of a single tridimensional detection structure to reconstruct muon tracks. We present results of the analysis of the data collected with the NEMO Mini-Tower. The position of photomultiplier tubes (PMTs) is determined through the acoustic position system. Signals detected with PMTs are used to reconstruct the tracks of atmospheric muons. The angular distribution of atmospheric muons was measured and results compared with Monte Carlo simulations.

  15. Development of high performance and very low radioactivity scintillation counters for the SuperNEMO calorimeter

    International Nuclear Information System (INIS)

    SuperNEMO is a next generation double beta decay experiment which will extend the successful 'tracko-calo' technique employed in NEMO 3. The main characteristic of this type of detector is to identify not only double beta decays, but also to measure its own background components. The project aims to reach a sensitivity up to 1026 years on the half-life of 82Se. One of the main challenge of the Research and Development is to achieve an unprecedented energy resolution for the electron calorimeter, better than 8 % FWHM at 1 MeV. This thesis contributes to improve scintillators and photomultipliers performances and reduce their radioactivity, including in particular the development of a new photomultiplier in collaboration with Photonis. (author)

  16. Atmospheric muons in the NEMO Phase 1 detector at the Catania test site

    International Nuclear Information System (INIS)

    The NEMO Collaboration is involved in a long term R and D activity towards the construction of a km3 telescope in the Mediterranean sea. It has dedicated special efforts in the development of technologies for a km3 detector and in the search, characterization and monitoring of a deep sea site adequate for the installation of the Mediterranean km3. Now the NEMO Collaboration is involved in the Phase 1 of the project, planning to install a fully equipped deep-sea facility to test prototypes and develop new technologies for the detector. A full Monte Carlo simulation has been performed to analyse the response of a reduced-size detector to the passage of atmospheric muons. Preliminary steps of the simulation are presented in this work

  17. The trigger and data acquisition for the NEMO-Phase 2 tower

    International Nuclear Information System (INIS)

    In the framework of the Phase 2 of the NEMO neutrino telescope project, a tower with 32 optical modules is being operated since march 2013. A new scalable Trigger and Data Acquisition System (TriDAS) has been developed and extensively tested with the data from this tower. Adopting the all-data-to-shore concept, the NEMO TriDAS is optimized to deal with a continuous data-stream from off-shore to on-shore with a large bandwidth. The TriDAS consists of four computing layers: (i) data aggregation of isochronal hits from all optical modules; (ii) data filtering by means of concurrent trigger algorithms; (iii) composition of the filtered events into post-trigger files; (iv) persistent data storage. The TriDAS implementation is reported together with a review of dedicated on-line monitoring tools

  18. The Barcode of Life Data Portal: bridging the biodiversity informatics divide for DNA barcoding.

    Directory of Open Access Journals (Sweden)

    Indra Neil Sarkar

    Full Text Available With the volume of molecular sequence data that is systematically being generated globally, there is a need for centralized resources for data exploration and analytics. DNA Barcode initiatives are on track to generate a compendium of molecular sequence-based signatures for identifying animals and plants. To date, the range of available data exploration and analytic tools to explore these data have only been available in a boutique form--often representing a frustrating hurdle for many researchers that may not necessarily have resources to install or implement algorithms described by the analytic community. The Barcode of Life Data Portal (BDP is a first step towards integrating the latest biodiversity informatics innovations with molecular sequence data from DNA barcoding. Through establishment of community driven standards, based on discussion with the Data Analysis Working Group (DAWG of the Consortium for the Barcode of Life (CBOL, the BDP provides an infrastructure for incorporation of existing and next-generation DNA barcode analytic applications in an open forum.

  19. DNA barcoding as a screening tool for cryptic diversity

    DEFF Research Database (Denmark)

    Huemer, Peter; Karsholt, Ole; Mutanen, Marko

    2014-01-01

    We explore the potential value of DNA barcode divergence for species delimitation in the genus Caryocolum Gregor & Povolný, 1954 (Lepidoptera, Gelechiidae), based on data from 44 European species (including 4 subspecies). Low intraspecific divergence of the DNA barcodes of the mtCOI (cytochrome c...... oxidase 1) gene and/or distinct barcode gaps to the nearest neighbor support species status for all examined nominal taxa. However, in 8 taxa we observed deep splits with a maximum intraspecific barcode divergence beyond a threshold of 3%, thus indicating possible cryptic diversity. The taxonomy of these...

  20. Measurement of the atmospheric muon flux at 3500 m depth with the NEMO Phase-2 detector

    Science.gov (United States)

    Distefano, C.; Aiello, S.; Ameli, F.; Anghinolfi, M.; Barbarino, G.; Barbarito, E.; Barbato, F.; Beverini, N.; Biagi, S.; Bouhadef, B.; Bozza, C.; Cacopardo, G.; Calamai, M.; Calì, C.; Capone, A.; Caruso, F.; Ceres, A.; Chiarusi, T.; Circella, M.; Cocimano, R.; Coniglione, R.; Costa, M.; Cuttone, G.; D'Amato, C.; D'Amico, A.; De Bonis, G.; De Luca, V.; Deniskina, N.; De Rosa, G.; Di Capua, F.; Fermani, P.; Flaminio, V.; Fusco, L. A.; Garufi, F.; Giordano, V.; Gmerk, A.; Grasso, R.; Grella, G.; Hugon, C.; Imbesi, M.; Kulikovskiy, V.; Larosa, G.; Lattuada, D.; Leismueller, K. P.; Leonora, E.; Litrico, P.; Lonardo, A.; Longhitano, F.; Lo Presti, D.; Maccioni, E.; Margiotta, A.; Martini, A.; Masullo, R.; Migliozzi, P.; Migneco, E.; Miraglia, A.; Mollo, C. M.; Mongelli, M.; Morganti, M.; Musico, P.; Musumeci, M.; Nicolau, C. A.; Orlando, A.; Papaleo, R.; Pellegrino, C.; Pellegriti, M. G.; Perrina, C.; Piattelli, P.; Pugliatti, C.; Pulvirenti, S.; Orselli, A.; Raffaelli, F.; Randazzo, N.; Riccobene, G.; Rovelli, A.; Sanguineti, M.; Sapienza, P.; Sciacca, V.; Sgura, I.; Simeone, F.; Sipala, V.; Speziale, F.; Spina, M.; Spitaleri, A.; Spurio, M.; Stellacci, S. M.; Taiuti, M.; Terreni, G.; Trasatti, L.; Trovato, A.; Ventura, C.; Vicini, P.; Viola, S.; Vivolo, D.

    2016-07-01

    In March 2013, the Nemo Phase-2 tower was successfully deployed at 80 km off-shore Capo Passero (Italy) at 3500 m depth. The tower operated continuously until August 2014. We present the results of the atmospheric muon analysis from the data collected in 411 days of live time. The zenith-angle distribution of atmospheric muons was measured and results compared with Monte Carlo simulations. The associated depth intensity relation was then measured and compared with previous measurements and theoretical predictions.

  1. The Nanoelectronic Modeling Tool NEMO 5: Capabilities, Validation, and Application to Sb-Heterostructures

    OpenAIRE

    Steiger, Sebastian; Povolotskyi, Michael; Park, Hong Hyun; Kubis, Tillmann; Hegde, Ganesh; Haley, Benjamin; Rodwell, Mark; Klimeck, Gerhard

    2011-01-01

    Modeling and simulation take an important role in the exploration and design optimization of novel devices. As the downscaling of electronic devices continues, the description of interfaces, randomness, and disorder on an atomistic level gains importance and continuum descriptions lose their validity. Often a full-band description of the electronic structure is needed to model the interaction of different valleys and nonparabolicity effects. NEMO 5 [1] is a modeling tool that addresses these ...

  2. Measurement of the atmospheric muon flux with the NEMO Phase-1 detector

    OpenAIRE

    Aiello, S.; Ameli, F.; Amore, I.; Anghinolfi, M.; Anzalone, A.; Barbarino, G.; Battaglieri, M.; Bazzotti, M.; Bersani, A.; Beverini, N.(INFN, Sezione di Pisa, Pisa, Italy); Biagi, S.; Bonori, M.; Bouhadef, B.; Brunoldi, M.; Cacopardo, G.

    2009-01-01

    The NEMO Collaboration installed and operated an underwater detector including prototypes of the critical elements of a possible underwater km3 neutrino telescope: a four-floor tower (called Mini-Tower) and a Junction Box. The detector was developed to test some of the main systems of the km3 detector, including the data transmission, the power distribution, the timing calibration and the acoustic positioning systems as well as to verify the capabilities of a single tridimensional detection s...

  3. Measurement of the atmospheric muon depth intensity relation with the NEMO Phase-2 tower

    OpenAIRE

    Aiello, S.; Ameli, F.; Anghinolfi, M.; Barbarino, G.; Barbarito, E.; Barbato, F.; Beverini, N.(INFN, Sezione di Pisa, Pisa, Italy); Biagi, S.; Bouhadef, B.; Bozza, C.; Cacopardo, G.; M. Calamai; Calì, C.; A. Capone; Caruso, F.

    2014-01-01

    The results of the analysis of the data collected with the NEMO Phase-2 tower, deployed at 3500 m depth about 80 km off-shore Capo Passero (Italy), are presented. Cherenkov photons detected with the photomultipliers tubes were used to reconstruct the tracks of atmospheric muons. Their zenith-angle distribution was measured and the results compared with Monte Carlo simulations. An evaluation of the systematic effects due to uncertainties on environmental and detector parameters is also include...

  4. Probing New Physics Models of Neutrinoless Double Beta Decay with SuperNEMO

    CERN Document Server

    Arnold, R; Baker, J; Barabash, A S; Basharina-Freshville, A; Bongrand, M; Brudanin, V; Caffrey, A J; Cebrián, S; Chapon, A; Chauveau, E; Dafni, Th; Deppisch, F F; Diaz, J; Durand, D; Egorov, V; Evans, J J; Flack, R; Fushima, K-I; Irastorza, I García; Garrido, X; Gómez, H; Guillon, B; Holin, A; Holy, K; Horkey, J J; Hubert, Ph; Hugon, C; Iguaz, F J; Ishihara, N; Jackson, C M; Jullian, S; Kauer, M; Kochetov, O; Konovalov, S I; Kovalenko, V; Lamhamdi, T; Lang, K; Lutter, G; Luzón, G; Mamedov, F; Marquet, Ch; Mauger, F; Monrabal, F; Nachab, A; Nasteva, I; Nemchenok, I; Nguyen, C H; Nomachi, M; Nova, F; Ohsumi, H; Pahlka, R B; Perrot, F; Piquemal, F; Povinec, P P; Richards, B; Ricol, J S; Riddle, C L; Rodríguez, A; Saakyan, R; Sarazin, X; Sedgbeer, J K; Serra, L; Shitov, Yu; Simard, L; Šimkovic, F; Söldner-Rembold, S; Štekl, I; Sutton, C S; Tamagawa, Y; Thomas, J; Timkin, V; Tretyak, V; Tretyak, Vl I; Umatov, V I; Vanyushin, I A; Vasiliev, R; Vasiliev, V; Vorobel, V; Waters, D; Yahlali, N; Žukauskas, A

    2010-01-01

    The possibility to probe new physics scenarios of light Majorana neutrino exchange and right-handed currents at the planned next generation neutrinoless double beta decay experiment SuperNEMO is discussed. Its ability to study different isotopes and track the outgoing electrons provides the means to discriminate different underlying mechanisms for the neutrinoless double beta decay by measuring the decay half-life and the electron angular and energy distributions.

  5. Development and Testing of Nemo Metal Sealing Seat for Subsea Ball Valves

    OpenAIRE

    Rusten, Torgeir

    2010-01-01

    This report is the result of a master's thesis project for the Master of Science degree in engineering at the Norwegian University of Science and Technology (NTNU). The project was carried out in collaboration with Nemo Engineering AS which is company that provides EPC (Engineering Procurement Construction) solutions for subsea oil and gas systems. The master project is a continuation of a preface project carried out by the candidate during fall 2009 which again was a continuation of a develo...

  6. Bar-code automated waste tracking system

    International Nuclear Information System (INIS)

    The Bar-Code Automated Waste Tracking System was designed to be a site-Specific program with a general purpose application for transportability to other facilities. The system is user-friendly, totally automated, and incorporates the use of a drive-up window that is close to the areas dealing in container preparation, delivery, pickup, and disposal. The system features ''stop-and-go'' operation rather than a long, tedious, error-prone manual entry. The system is designed for automation but allows operators to concentrate on proper handling of waste while maintaining manual entry of data as a backup. A large wall plaque filled with bar-code labels is used to input specific details about any movement of waste

  7. Barcoding of fresh water fishes from Pakistan.

    Science.gov (United States)

    Karim, Asma; Iqbal, Asad; Akhtar, Rehan; Rizwan, Muhammad; Amar, Ali; Qamar, Usman; Jahan, Shah

    2016-07-01

    DNA bar-coding is a taxonomic method that uses small genetic markers in organisms' mitochondrial DNA (mt DNA) for identification of particular species. It uses sequence diversity in a 658-base pair fragment near the 5' end of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene as a tool for species identification. DNA barcoding is more accurate and reliable method as compared with the morphological identification. It is equally useful in juveniles as well as adult stages of fishes. The present study was conducted to identify three farm fish species of Pakistan (Cyprinus carpio, Cirrhinus mrigala, and Ctenopharyngodon idella) genetically. All of them belonged to family cyprinidae. CO1 gene was amplified. PCR products were sequenced and analyzed by bioinformatic software. Conspecific, congenric, and confamilial k2P nucleotide divergence was estimated. From these findings, it was concluded that the gene sequence, CO1, may serve as milestone for the identification of related species at molecular level. PMID:25980661

  8. Bar-code automated waste tracking system

    Energy Technology Data Exchange (ETDEWEB)

    Hull, T.E.

    1994-10-01

    The Bar-Code Automated Waste Tracking System was designed to be a site-Specific program with a general purpose application for transportability to other facilities. The system is user-friendly, totally automated, and incorporates the use of a drive-up window that is close to the areas dealing in container preparation, delivery, pickup, and disposal. The system features ``stop-and-go`` operation rather than a long, tedious, error-prone manual entry. The system is designed for automation but allows operators to concentrate on proper handling of waste while maintaining manual entry of data as a backup. A large wall plaque filled with bar-code labels is used to input specific details about any movement of waste.

  9. Machine Learning : for Barcode Detection and OCR

    OpenAIRE

    Fridolfsson, Olle

    2015-01-01

    Machine learning can be utilized in many different ways in the field of automatic manufacturing and logistics. In this thesis supervised machine learning have been utilized to train a classifiers for detection and recognition of objects in images. The techniques AdaBoost and Random forest have been examined, both are based on decision trees. The thesis has considered two applications: barcode detection and optical character recognition (OCR). Supervised machine learning methods are highly app...

  10. Barcode Payment System in Trusted Mobile Devices

    OpenAIRE

    Vibha Kaw Raina

    2012-01-01

    Mobile payment is an application of mobile commerce which facilitates mobile commerce transactions by providing the mobile customer with a convenient means to pay. Many mobile payment methods have been proposed and implemented like user friendly, customer centric, merchant centric where security concerns are highly addressed. This paper proposes a mobile payment model with barcodes for mobile users to improve mobile user experience in mobile payment. Unlike other existing mobile payment syste...

  11. Modelling the Clinical Risk: RFID vs Barcode

    OpenAIRE

    Lecce, Vincenzo Di; Calabrese, Marco; Quarto, Alessandro; Dario, Rita

    2010-01-01

    In this chapter the improvement resulted by RFID-based modelling for the clinical risk management has been discussed. The comparison between barcode-based healthcare systems and RFID technologies has shown the possibilities for a significant process reengineering which would represent an essential key to efficacy and efficiency increase in personalized healthcare services. In this view, the new model is centred around the idea of patient as an active element in the clinical process, thus over...

  12. BEST: Barcode Enabled Sequencing of Tetrads

    OpenAIRE

    Scott, Adrian C.; Ludlow, Catherine L.; Cromie, Gareth A.; Dudley, Aimée M.

    2014-01-01

    Tetrad analysis is a valuable tool for yeast genetics, but the laborious manual nature of the process has hindered its application on large scales. Barcode Enabled Sequencing of Tetrads (BEST)1 replaces the manual processes of isolating, disrupting and spacing tetrads. BEST isolates tetrads by virtue of a sporulation-specific GFP fusion protein that permits fluorescence-activated cell sorting of tetrads directly onto agar plates, where the ascus is enzymatically digested and the spores are di...

  13. Advancing taxonomy and bioinventories with DNA barcodes.

    Science.gov (United States)

    Miller, Scott E; Hausmann, Axel; Hallwachs, Winnie; Janzen, Daniel H

    2016-09-01

    We use three examples-field and ecology-based inventories in Costa Rica and Papua New Guinea and a museum and taxonomic-based inventory of the moth family Geometridae-to demonstrate the use of DNA barcoding (a short sequence of the mitochondrial COI gene) in biodiversity inventories, from facilitating workflows of identification of freshly collected specimens from the field, to describing the overall diversity of megadiverse taxa from museum collections, and most importantly linking the fresh specimens, the general museum collections and historic type specimens. The process also flushes out unexpected sibling species hiding under long-applied scientific names, thereby clarifying and parsing previously mixed collateral data. The Barcode of Life Database has matured to an essential interactive platform for the multi-authored and multi-process collaboration. The BIN system of creating and tracking DNA sequence-based clusters as proxies for species has become a powerful way around some parts of the 'taxonomic impediment', especially in entomology, by providing fast but testable and tractable species hypotheses, tools for visualizing the distribution of those in time and space and an interim naming system for communication.This article is part of the themed issue 'From DNA barcodes to biomes'. PMID:27481791

  14. Promise and Challenge of DNA Barcoding in Venus Slipper (Paphiopedilum).

    Science.gov (United States)

    Guo, Yan-Yan; Huang, Lai-Qiang; Liu, Zhong-Jian; Wang, Xiao-Quan

    2016-01-01

    Orchidaceae are one of the largest families of flowering plants, with over 27,000 species described and all orchids are listed in CITES. Moreover, the seedlings of orchid species from the same genus are similar. The objective of DNA barcoding is rapid, accurate, and automated species identification, which may be used to identify illegally traded endangered species from vegetative specimens of Paphiopedilum (Venus slipper), a flagship group for plant conservation with high ornamental and commercial values. Here, we selected eight chloroplast barcodes and nrITS to evaluate their suitability in Venus slippers. The results indicate that all tested barcodes had no barcoding gap and the core plant barcodes showed low resolution for the identification of Venus slippers (18.86%). Of the single-locus barcodes, nrITS is the most efficient for the species identification of the genus (52.27%), whereas matK + atpF-atpH is the most efficient multi-locus combination (28.97%). Therefore, we recommend the combination of matK + atpF-atpH + ITS as a barcode for Venus slippers. Furthermore, there is an upper limit of resolution of the candidate barcodes, and only half of the taxa with multiple samples were identified successfully. The low efficiency of these candidate barcodes in Venus slippers may be caused by relatively recent speciation, the upper limit of the barcodes, and/or the sampling density. Although the discriminatory power is relatively low, DNA barcoding may be a promising tool to identify species involved in illegal trade, which has broad applications and is valuable for orchid conservation. PMID:26752741

  15. Advanced energy systems and technologies research in Finland. NEMO-2 Programme Annual Report 1996-1997

    International Nuclear Information System (INIS)

    Advanced energy technologies were linked to the national energy research in the beginning of 1988 when energy research was reorganised in Finland. The Ministry of Trade and Industry established several energy research programmes and NEMO was one of them. Major objectives of the programme were to assess the potential of new energy systems for the national energy supply system and to promote industrial activities. Within the NEMO 2 programme for the years 1993-1998, research was focused on a few promising technological solutions. In the beginning of 1995, the national energy research activities were passed on to the Technology Development Centre TEKES. The NEMO 2 programme is directed towards those areas that have particular potential for commercial exploitation or development. Emphasis is placed particularly on solar and wind energy, as well as supporting technologies, such as energy storage and hydrogen technology. Resources have been focused on three specific areas: arctic wind technology, wind turbine components, and the integration of solar energy into applications (including thin film solar cells). In Finland, the growth of the new energy technology industry is concentrated on these areas. The turnover of the Finnish industry has been growing considerably due to the national research activities and support of technology development. The sales have increased more than 10 times compared with the year 1987 and is now over 300 million FIM. The support to industries and their involvement in the program has grown considerably. In this report, the essential research projects of the programme during 1996-1997 are described. The total funding for these projects was about 30 million FIM per year, of which the TEKES's share was about 40 per cent. The programme consists of 10 research projects, some 15 joint development projects, and 9 EU projects. In case the research projects and joint development projects are acting very closely, the description of the project is

  16. Advanced energy systems and technologies research in Finland. NEMO-2 Programme Annual Report 1996-1997

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-10-01

    Advanced energy technologies were linked to the national energy research in the beginning of 1988 when energy research was reorganised in Finland. The Ministry of Trade and Industry established several energy research programmes and NEMO was one of them. Major objectives of the programme were to assess the potential of new energy systems for the national energy supply system and to promote industrial activities. Within the NEMO 2 programme for the years 1993-1998, research was focused on a few promising technological solutions. In the beginning of 1995, the national energy research activities were passed on to the Technology Development Centre TEKES. The NEMO 2 programme is directed towards those areas that have particular potential for commercial exploitation or development. Emphasis is placed particularly on solar and wind energy, as well as supporting technologies, such as energy storage and hydrogen technology. Resources have been focused on three specific areas: arctic wind technology, wind turbine components, and the integration of solar energy into applications (including thin film solar cells). In Finland, the growth of the new energy technology industry is concentrated on these areas. The turnover of the Finnish industry has been growing considerably due to the national research activities and support of technology development. The sales have increased more than 10 times compared with the year 1987 and is now over 300 million FIM. The support to industries and their involvement in the program has grown considerably. In this report, the essential research projects of the programme during 1996-1997 are described. The total funding for these projects was about 30 million FIM per year, of which the TEKES`s share was about 40 per cent. The programme consists of 10 research projects, some 15 joint development projects, and 9 EU projects. In case the research projects and joint development projects are acting very closely, the description of the project is

  17. DNA barcoding: species delimitation in tree peonies

    Institute of Scientific and Technical Information of China (English)

    ZHANG JinMei; WANG JianXiu; XIA Tao; ZHOU ShiLiang

    2009-01-01

    Delimitations of species are crucial for correct and precise identification of taxa. Unfortunately "spe-cies" is more a subjective than an objective concept in taxonomic practice due to difficulties in re-vealing patterns of infra- or inter-specific variations. Molecular phylogenetic studies at the population level solve this problem and lay a sound foundation for DNA barcoding. In this paper we exemplify the necessity of adopting a phylogenetic concept of species in DNA barcoding for tree peonies (Paeonia sect. Moutan). We used 40 samples representing all known populations of rare and endangered species and several populations of widely distributed tree peonies. All currently recognized species and majorbvariants have been included in this study. Four chloroplast gene fragments, I.e. ndhF, rps16-trnQ, trnL.F and trnS-G (a total of 5040 characters, 96 variable and 69 parsimony-informative characters) and one variable and single-copy nuclear GPAT gene fragment (2093-2197 bp, 279 variable and 148 parsi-mony-informative characters) were used to construct phylogenetic relationships among the taxa. The evolutionary lineages revealed by the nuclear gene and the chloroplast genes are inconsistent with the current circumscriptions of P. Decomposita, P. Jishanensis, P. Qiui, and P. Rockii based on morphology. The inconsistencies come from (1) significant chloroplast gene divergence but little nuclear GPAT gene divergence among population systems of P. Decomposita + P. Rockii, and (2) well-diverged nuclear GPAT gene but little chloroplast gene divergence between P. Jishanensis and P. Qiui. The incongruence of the phylogenies based on the chloroplast genes and the nuclear GPAT gene is probably due to the chloro-plast capture event in evolutionary history, as no reproductive barriers exist to prevent inter-specific hybridization. We also evaluated the suitability of these genes for use as DNA barcodes for tree peonies. The variability of chloroplast genes among well

  18. Multilocus inference of species trees and DNA barcoding.

    Science.gov (United States)

    Mallo, Diego; Posada, David

    2016-09-01

    The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree-gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent.This article is part of the themed issue 'From DNA barcodes to biomes'. PMID:27481787

  19. Dissecting host-associated communities with DNA barcodes.

    Science.gov (United States)

    Baker, Christopher C M; Bittleston, Leonora S; Sanders, Jon G; Pierce, Naomi E

    2016-09-01

    DNA barcoding and metabarcoding methods have been invaluable in the study of interactions between host organisms and their symbiotic communities. Barcodes can help identify individual symbionts that are difficult to distinguish using morphological characters, and provide a way to classify undescribed species. Entire symbiont communities can be characterized rapidly using barcoding and especially metabarcoding methods, which is often crucial for isolating ecological signal from the substantial variation among individual hosts. Furthermore, barcodes allow the evolutionary histories of symbionts and their hosts to be assessed simultaneously and in reference to one another. Here, we describe three projects illustrating the utility of barcodes for studying symbiotic interactions: first, we consider communities of arthropods found in the ant-occupied domatia of the East African ant-plant Vachellia (Acacia) drepanolobium; second, we examine communities of arthropod and protozoan inquilines in three species of Nepenthes pitcher plant in South East Asia; third, we investigate communities of gut bacteria of South American ants in the genus Cephalotes Advances in sequencing and computation, and greater database connectivity, will continue to expand the utility of barcoding methods for the study of species interactions, especially if barcoding can be approached flexibly by making use of alternative genetic loci, metagenomes and whole-genome data.This article is part of the themed issue 'From DNA barcodes to biomes'. PMID:27481780

  20. Complementing morphological classification of Anguilliform leptocephali with DNA barcoding

    Directory of Open Access Journals (Sweden)

    Alessandra Anibaldi

    2015-10-01

    The highly consistent results obtained revealed a good performance of COI barcoding as a diagnostic method for the identification of these larvae, but the limited number of leptocephali species annotated in the reference databases for barcode (Barcode of Life Data Systems and GenBank allowed to validate only partially the morphological analysis. Moreover two species, Gnathophis mystax and Facciolella sp., showed unexpected outcomes. The data obtained in this work represent the first results of a wider project aimed at the creation of a new barcode database for the assessment of leptocephali diversity in the Mediterranean Sea (Barcoding of the Adriatic Leptocephali [BAL], contributing to the knowledge of these unusual larvae and of their adult forms.

  1. Identification of herbal medicinal materials using DNA barcodes

    Institute of Scientific and Technical Information of China (English)

    Ming LI; Hui CAO; Paul Pui-Hay BUT; pang-Chui SHAW

    2011-01-01

    Herbal medicinal materials have been used worldwide for centuries to maintain health and to treat disease. However, adulteration of herbal medicines remains a major concern of users and industry for reasons of safety and efficacy. Identification of herbal medicinal materials by DNA technology has been widely applied,started from the mid-1990s. In recent years, DNA barcoding of global plant species using four standard barcodes (rbcL, matK, trnH-psbA and ITS) has been a major focus in the fields of biodiversity and conservation. These DNA barcodes can also be used as reliable tools to facilitate the identification of herbal medicinal materials for the safe use of herbs, quality control, and forensic investigation. Many studies have applied these DNA barcodes for the identification of herbal medicinal species and their adulterants. The present article reviews efforts in the identification of herbal medicinal materials using the standard DNA barcodes and other DNA sequence-based markers.

  2. Identification of Indian crocodile species through DNA barcodes.

    Science.gov (United States)

    Meganathan, P R; Dubey, Bhawna; Jogayya, Kothakota Naga; Haque, Ikramul

    2013-07-01

    The biodiversity of India includes three crocodile species, Crocodylus palustris, Crocodylus porosus, and Gavialis gangeticus, whose status is threatened due to bushmeat crisis and illegal hunting. The crocodilian conservation management requires novel techniques to help forensic analysts to reveal species identity. DNA barcoding is a species identification technique, where a partial cytochrome c oxidase subunit 1 gene is used as a marker for species identification. Herein, the DNA barcoding technique is evaluated for three Indian crocodiles by analyzing an approximately 750-bp barcode region. The alignment result shows interspecific variations between sequences for discrimination of the three Indian crocodiles leading to species identification. The phylogenetic analyses also substantiate the established crocodilian relationships, which add further advantage to use this DNA barcoding approach for Indian crocodiles. This study provides preliminary evidences for the use of DNA barcoding technique in the identification of Indian crocodile species. PMID:23718785

  3. [Screening potential DNA barcode regions of genus Papaver].

    Science.gov (United States)

    Zhang, Shuang; Liu, Yu-jing; Wu, Yan-sheng; Cao, Ying; Yuan, Yuan

    2015-08-01

    DNA barcoding is an effective technique in species identification. To determine the candidate sequences which can be used as DNA barcode to identify in Papaver genus, five potential sequences (ITS, matK, psbA-trnH, rbcL, trnL-trnF) were screened. 69 sequences were downloaded from Genbank, including 21 ITS sequences, 10 matK sequences, 8 psbA-trnH sequences, 14 rbcL sequences and 16 trnL-trnF sequences. Mega 6.0 was used to analysis the comparison of sequences. By the methods of calculating the distances in intraspecific and interspecific divergences, evaluating DNA barcoding gap and constructing NJ and UPMGA phylogenetic trees. The sequence trnL-trnF performed best. In conclusion, trnL-trnF can be considered as a novel DNA barcode in Papaver genus, other four sequences can be as combination barcode for identification. PMID:26677693

  4. Identifying Chinese species of Gammarus (Crustacea: Amphipoda) using DNA barcoding

    Institute of Scientific and Technical Information of China (English)

    Zhong-e HOU; Zhu LI; Shu-qiang LI

    2009-01-01

    Using a standard cytochrome c oxidase I sequence, DNA barcoding has been shown to be effective to distinguish known species and to discover cryptic species. Here we assessed the efficiency of DNA barcoding for the amphipod genus Gammarus from China. The maximum intraspecific divergence for widespread species, Gammarus lacustris, was 3.5%, and mean interspecific divergence reached 21.9%. We presented a conservative benchmark for determining provisional species using maximum intraspecific divergence of Gammarus lacustris. Thirty-one species possessed distinct barcode clusters. Two species were comprised of highly divergent clades with strong neighbor-joining bootstrap values, and likely indicated the presence of cryptic species. Although DNA barcoding is effective, future identification of species of Gammarus should incorporate DNA barcoding and morphological detection[Current Zoology 55(2):158-164,2009].

  5. Gold Nanoparticles-Based Barcode Analysis for Detection of Norepinephrine.

    Science.gov (United States)

    An, Jeung Hee; Lee, Kwon-Jai; Choi, Jeong-Woo

    2016-02-01

    Nanotechnology-based bio-barcode amplification analysis offers an innovative approach for detecting neurotransmitters. We evaluated the efficacy of this method for detecting norepinephrine in normal and oxidative-stress damaged dopaminergic cells. Our approach use a combination of DNA barcodes and bead-based immunoassays for detecting neurotransmitters with surface-enhanced Raman spectroscopy (SERS), and provides polymerase chain reaction (PCR)-like sensitivity. This method relies on magnetic Dynabeads containing antibodies and nanoparticles that are loaded both with DNA barcords and with antibodies that can sandwich the target protein captured by the Dynabead-bound antibodies. The aggregate sandwich structures are magnetically separated from the solution and treated to remove the conjugated barcode DNA. The DNA barcodes are then identified by SERS and PCR analysis. The concentration of norepinephrine in dopaminergic cells can be readily detected using the bio-barcode assay, which is a rapid, high-throughput screening tool for detecting neurotransmitters. PMID:27305769

  6. [Hydrophidae identification through analysis on Cyt b gene barcode].

    Science.gov (United States)

    Liao, Li-xi; Zeng, Ke-wu; Tu, Peng-fei

    2015-08-01

    Hydrophidae, one of the precious traditional Chinese medicines, is generally drily preserved to prevent corruption, but it is hard to identify the species of Hydrophidae through the appearance because of the change due to the drying process. The identification through analysis on gene barcode, a new technique in species identification, can avoid the problem. The gene barcodes of the 6 species of Hydrophidae like Lapemis hardwickii were aquired through DNA extraction and gene sequencing. These barcodes were then in sequence alignment and test the identification efficency by BLAST. Our results revealed that the barcode sequences performed high identification efficiency, and had obvious difference between intra- and inter-species. These all indicated that Cyt b DNA barcoding can confirm the Hydrophidae identification. PMID:26790288

  7. DNA barcoding to fishes: current status and future directions.

    Science.gov (United States)

    Bhattacharya, Manojit; Sharma, Ashish Ranjan; Patra, Bidhan Chandra; Sharma, Garima; Seo, Eun-Min; Nam, Ju-Suk; Chakraborty, Chiranjib; Lee, Sang-Soo

    2016-07-01

    DNA barcoding appears to be a promising approach for taxonomic identification, characterization, and discovery of newer species, facilitating biodiversity studies. It helps researchers to appreciate genetic and evolutionary associations by collection of molecular, morphological, and distributional data. Fish DNA barcoding, based on the sequencing of a uniform area of Cytochrome C Oxidase type I (COI) gene, has received significant interest as an accurate tool for species identification, authentication, and phylogenetic analysis. The aim of this review article was to investigate recent global status, approaches, and future direction of DNA barcoding in fisheries sectors. We have tried to highlight its possible impacts, complications, and validation issues at species levels for biodiversity analysis. Moreover, an effort has been put forward to understand issues related to various marker genes associated with barcode process as primer sequences and have concluded barcode promotion as an indispensable tool of molecular biology for the development of taxonomic support systems. PMID:26057011

  8. Decoding of PDF417 barcode in Identity Authentication Based on LabVIEW

    Directory of Open Access Journals (Sweden)

    Qian Song

    2013-06-01

    Full Text Available Two dimensional barcode had widely applied in identity authentication. In this paper, the symbol structure of PDF417 barcode was introduced, and the image processing methods used in PDF417 barcode recognition were researched. A quick and effective method to calculate the width of the unit module in PDF417 barcode was proposed, and a recognition and decoding system of PDF417 barcode based on software development platform of the LabVIEW virtual instrument was designed and implemented. The system could process and analyze the images containing PDF417 barcode collected by camera in real time, and achieve the fast and omnibearing decoding of the barcode.

  9. DNA Barcoding and the International Barcode of Life Project in China

    Institute of Scientific and Technical Information of China (English)

    CHE Jing; HUANG Dawei; LI Dezhu; MA Juncai; ZHANG Yaping

    2010-01-01

    @@ 1.Scientific and Social Benefits of DNA Barcoding Along with the accelerated global trade and climate change,the needs for sustainable development and for understanding biodiversity are increasing.Rapid and accurate species identification and sustainable utility of biodiversity resources have become a great need for the world.

  10. Charge Transport across DNA-Based Three-Way Junctions.

    Science.gov (United States)

    Young, Ryan M; Singh, Arunoday P N; Thazhathveetil, Arun K; Cho, Vincent Y; Zhang, Yuqi; Renaud, Nicolas; Grozema, Ferdinand C; Beratan, David N; Ratner, Mark A; Schatz, George C; Berlin, Yuri A; Lewis, Frederick D; Wasielewski, Michael R

    2015-04-22

    DNA-based molecular electronics will require charges to be transported from one site within a 2D or 3D architecture to another. While this has been shown previously in linear, π-stacked DNA sequences, the dynamics and efficiency of charge transport across DNA three-way junction (3WJ) have yet to be determined. Here, we present an investigation of hole transport and trapping across a DNA-based three-way junction systems by a combination of femtosecond transient absorption spectroscopy and molecular dynamics simulations. Hole transport across the junction is proposed to be gated by conformational fluctuations in the ground state which bring the transiently populated hole carrier nucleobases into better aligned geometries on the nanosecond time scale, thus modulating the π-π electronic coupling along the base pair sequence. PMID:25822073

  11. Progress of DNA-based Methods for Species Identification

    Institute of Scientific and Technical Information of China (English)

    HU Zhen; ZHANG Su-hua; WANG Zheng; BIAN Ying-nan; LI Cheng-tao

    2015-01-01

    Species identification of biological samples is widely used in such fields as forensic science and food industry. A variety of accurate and reliable methods have been developed in recent years. The cur-rent reviewshows common target genes and screening criteria suitable for species identification, and de-scribed various DNA-based molecular biology methods about species identification. Additionally, it dis-cusses the future development of species identification combined with real-time PCR and sequencing technologies.

  12. ANALYTICAL APPROACH OF COST-EFFECTIVE AND SECURE SIP-BASED MOBILITY MANAGEMENT SCHEME FOR NEMO ENVIRONMENTS

    Directory of Open Access Journals (Sweden)

    Chulhee Cho

    2014-12-01

    Full Text Available The mobile Virtual Private Network (MVPN of the Internet Engineering Task Force (IETF is not designed to support NEtwork MObility (NEMO and is not suitable for real-time applications. Therefore, architecture and protocols to support VPN in NEMO are needed. In this paper, we propose a cost-effective and secure mobility management scheme (SeSIP that is based on session initiation protocol (SIP and designed for real-time applications with VPN. Our scheme to support MVPN in NEMO enables the session to be well maintained during movement of the entire network. Further, in order to reduce the authentication delay time in handoff operations, the signaling time which occurs to maintain the session is shortened through our proposed handoff scheme which adopts authentication using HMAC-based one-time password (HOTP. Our performance analysis results show our proposed scheme provides improvement in average handoff performance time relative to existing schemes.

  13. NEMO-SN1 observatory developments in view of the European Research Infrastructures EMSO and KM3NET

    International Nuclear Information System (INIS)

    NEMO-SN1 (Western Ionian Sea off Eastern Sicily), the first real-time multiparameter observatory operating in Europe since 2005, is one of the nodes of the upcoming European ESFRI large-scale research infrastructure EMSO (European Multidisciplinary Seafloor Observatory), a network of seafloor observatories placed at marine sites on the European Continental Margin. NEMO-SN1 constitutes also an important test-site for the study of prototypes of Kilometre Cube Neutrino Telescope (KM3NeT), another European ESFRI large-scale research infrastructure. Italian resources have been devoted to the development of NEMO-SN1 facilities and logistics, as with the PEGASO project, while the EC project ESONET-NoE is funding a demonstration mission and a technological test. EMSO and KM3NeT are presently in the Preparatory Phase as projects funded under the EC-FP7.

  14. NEMO-SN1 observatory developments in view of the European Research Infrastructures EMSO and KM3NET

    Energy Technology Data Exchange (ETDEWEB)

    Favali, Paolo, E-mail: emsopp@ingv.i [Istituto Nazionale di Geofisica e Vulcanologia (INGV), Sect. Roma 2, Via di Vigna Murata 605, 00143 Roma (Italy); Beranzoli, Laura [Istituto Nazionale di Geofisica e Vulcanologia (INGV), Sect. Roma 2, Via di Vigna Murata 605, 00143 Roma (Italy); Italiano, Francesco [Istituto Nazionale di Geofisica e Vulcanologia (INGV), Sect. Palermo, Via Ugo La Malfa 153, 90146 Palermo (Italy); Migneco, Emilio; Musumeci, Mario; Papaleo, Riccardo [Istituto Nazionale di Fisica Nucleare (INFN), Laboratori Nazionali del Sud, Via di S. Sofia 62, 95125 Catania (Italy)

    2011-01-21

    NEMO-SN1 (Western Ionian Sea off Eastern Sicily), the first real-time multiparameter observatory operating in Europe since 2005, is one of the nodes of the upcoming European ESFRI large-scale research infrastructure EMSO (European Multidisciplinary Seafloor Observatory), a network of seafloor observatories placed at marine sites on the European Continental Margin. NEMO-SN1 constitutes also an important test-site for the study of prototypes of Kilometre Cube Neutrino Telescope (KM3NeT), another European ESFRI large-scale research infrastructure. Italian resources have been devoted to the development of NEMO-SN1 facilities and logistics, as with the PEGASO project, while the EC project ESONET-NoE is funding a demonstration mission and a technological test. EMSO and KM3NeT are presently in the Preparatory Phase as projects funded under the EC-FP7.

  15. Design of 240,000 orthogonal 25mer DNA barcode probes

    OpenAIRE

    Xu, Qikai; Schlabach, Michael R.; Hannon, Gregory J.; Elledge, Stephen J.

    2009-01-01

    DNA barcodes linked to genetic features greatly facilitate screening these features in pooled formats using microarray hybridization, and new tools are needed to design large sets of barcodes to allow construction of large barcoded mammalian libraries such as shRNA libraries. Here we report a framework for designing large sets of orthogonal barcode probes. We demonstrate the utility of this framework by designing 240,000 barcode probes and testing their performance by hybridization. From the ...

  16. Design of a Thin-Film Infrared Barcode on a Flexible Substrate

    Energy Technology Data Exchange (ETDEWEB)

    Dale Kotter; Brian Monicelli; Glenn Boreman

    2004-02-01

    We report the design, fabrication and characterization of an infrared barcode. This barcode is composed of a bilayer of titanium and amorphous silicon on a flexible Kapton substrate. Information encoded in the barcode shows high contrast when viewed with an infrared imaging system in the 8 to 12 m spectral region. The barcode information is concealed under visible viewing conditions, i.e., the barcode appears as an untreated, uniform metal sheet to a detector of visible radiation (400 to 700nm).

  17. Density functional calculations of planar DNA base-pairs

    CERN Document Server

    Machado, M V T; Artacho, E; Sánchez-Portál, D; Soler, J M; Machado, Maider; Ordejon, Pablo; Artacho, Emilio; Sanchez-Portal, Daniel; Soler, Jose M.

    1999-01-01

    We present a systematic Density Functional Theory (DFT) study of geometries and energies of the nucleic acid DNA bases (guanine, adenine, cytosine and thymine) and 30 different DNA base-pairs. We use a recently developed linear-scaling DFT scheme, which is specially suited for systems with large numbers of atoms. As a first step towards the study of large DNA systems, in this work: (i) We establish the reliability of the approximations of our method (including pseudopotentials and basis sets) for the description of the hydrogen-bonded base pairs, by comparing our results with those of former calculations. We show that the interaction energies at Hartree-Fock geometries are in very good agreement with those of second order M{ø}ller-Plesset (MP2) perturbation theory (the most accurate technique that can be applied at present for system of the sizes of the base-pairs). (ii) We perform DFT structural optimizations for the 30 different DNA base-pairs, only three of which had been previously studied with DFT. Our ...

  18. Identifying Fishes through DNA Barcodes and Microarrays.

    Directory of Open Access Journals (Sweden)

    Marc Kochzius

    Full Text Available BACKGROUND: International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. METHODOLOGY/PRINCIPAL FINDINGS: This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S, cytochrome b (cyt b, and cytochrome oxidase subunit I (COI for the identification of 50 European marine fish species by combining techniques of "DNA barcoding" and microarrays. In a DNA barcoding approach, neighbour Joining (NJ phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the "position of label" effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90% renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. CONCLUSIONS/SIGNIFICANCE: Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.

  19. Pokretanje doma za starije i nemoćne u Požeško-slavonskoj županiji

    OpenAIRE

    Asančaić, Ana; Plazibat, Olga; Vukoja, Ivan; Vukoja, Marko

    2015-01-01

    Poslovni pothvat izgradnje doma za starije i nemoćne osobe u Požeško-slavonskoj županiji temelji se na demografskom trendu starenja stanovništva i povećanog iseljavanja mladih. Uočena je povećana potreba za odgovarajućim oblicima smještaja starijih i nemoćnih osoba, koji bi korisnike zadovoljavali kvalitetom sadržaja. Na osnovi Porterovog modela pet konkurentskih snaga pokazalo se da je industrija usluge smještaja u dom umjereno atraktivna; za ulazak novih pothvata, zbog prijetnje od ulaska n...

  20. From Barcode to QR Code Applications

    OpenAIRE

    László Várallyai

    2012-01-01

    This paper shows the Zsohár Horticulture Company in Nagyrákos, how they want to change their barcode identification system to QR code. They cultivate herbaceous, perpetual decorational plants, rock-garden, flower-bed and swamp perpetuals, decorational grasses and spices. A part of the perpetuals are evergreens, but most of them has special organs - such as onions, thick-, bulbous roots, "winter-proof" buds - so they can survive winter. In the first part of the paper I introduce the different ...

  1. Measuring and Test Equipment through barcode technology

    Energy Technology Data Exchange (ETDEWEB)

    Crockett, J.D.; Carr, C.C.

    1993-06-01

    Over the past several years, the use, trace methodology, and documentation of Measuring and Test Equipment has become a major concern. Current regulations are forcing companies to develop new policies, providing use history and traceability of Measuring and Test Equipment. The US Department of Energy and Environmental Organizations are driving Westinghouse Hanford Company to comply with the more stringent environmental guidelines and recent modifications in Department of Energy Orders. This paper discusses how the Fast Flux Test Facility at Westinghouse Hanford Company overcame these obstacles by using a computerized system through barcode technology.

  2. Evaluation of QoS supported in Network Mobility NEMO environments

    International Nuclear Information System (INIS)

    Network mobility basic support (NEMO BS) protocol is an entire network, roaming as a unit which changes its point of attachment to the Internet and consequently its reachability in the network topology. NEMO BS doesn't provide QoS guarantees to its users same as traditional Internet IP and Mobile IPv6 as well. Typically, all the users will have same level of services without considering about their application requirements. This poses a problem to real-time applications that required QoS guarantees. To gain more effective control of the network, incorporated QoS is needed. Within QoS-enabled network the traffic flow can be distributed to various priorities. Also, the network bandwidth and resources can be allocated to different applications and users. Internet Engineering Task Force (IETF) working group has proposed several QoS solutions for static network such as IntServ, DiffServ and MPLS. These QoS solutions are designed in the context of a static environment (i.e. fixed hosts and networks). However, they are not fully adapted to mobile environments. They essentially demands to be extended and adjusted to meet up various challenges involved in mobile environments. With existing QoS mechanisms many proposals have been developed to provide QoS for individual mobile nodes (i.e. host mobility). In contrary, research based on the movement of the whole mobile network in IPv6 is still undertaking by the IETF working groups (i.e. network mobility). Few researches have been done in the area of providing QoS for roaming networks. Therefore, this paper aims to review and investigate (previous /and current) related works that have been developed to provide QoS in mobile network. Consequently, a new proposed scheme will be introduced to enhance QoS within NEMO environment, achieving by which seamless mobility to users of mobile network node (MNN)

  3. [Rifampicin-resistant Mycobacterium bovis BCG strain isolated from an infant with NEMO mutation].

    Science.gov (United States)

    Çavuşoğlu, Cengiz; Edeer Karaca, Neslihan; Azarsız, Elif; Ulusoy, Ezgi; Kütükçüler, Necil

    2015-04-01

    It is well known that disseminated Mycobacterium bovis BCG infection is developed after BCG vaccination in infants with congenital cellular immune deficiencies such as mutations in genes along the interleukin (IL)-12/interferon (IFN)-γ pathway and mutations in nuclear factor-kB essential modulator (NEMO). In this report, a rifampicin-resistant M.bovis BCG strain isolated from an infant with NEMO defect was presented. An 8-month-old male infant with NEMO defect admitted to the pediatric outpatient clinic of our hospital with fever, generalized lymphadenopathy and hepatosplenomegaly. Microscopic examination of the smears prepared from lymph node and liver biopsy specimens revealed abundant amount (3+) of acid-fast bacilli (AFB). Rifampicin-susceptible Mycobacterium tuberculosis complex (MTC) was detected by real-time PCR (GeneXpert MTB/RIF; Cepheid, USA) in the samples. The growth of mycobacteria was determined on the 20th day of culture performed in MGIT960 system (Becton Dickinson, USA). The isolate was identified as M.bovis BCG by GenoType MTBC kit (Hain Lifescience, Germany) and defined as M.bovis BCG [SIT 482 (BOV_1)] by spoligotyping. In the primary anti-tuberculosis drug susceptibility test performed by MGIT960 system, the isolate was found susceptible to rifampicin (RIF), isoniazid (INH), streptomycin (STM) and ethambutol (EMB). Then anti-tuberculosis treatment was started to the patient. However, the patient at the age of 2 years, re-admitted to the hospital with the complaint of hepatosplenomegaly. Smear of spontaneously draining abscess material obtained from subcutaneous nodules revealed intensive AFB positivity (3+) once again. In the present instance RIF-resistant MTC was detected with GeneXpert system in the specimen. The growth of mycobacteria was determined on the 13th day of culture and isolate was identified as M.bovis BCG. The present isolate was found susceptible to INH, STM and EMB but resistant to RIF. A mutation in the rpoB gene (codon 531, S

  4. The optical modules of the phase-2 of the NEMO project

    Science.gov (United States)

    Aiello, S.; Leonora, E.; Ameli, F.; Anghinolfi, M.; Anzalone, A.; Barbarino, G.; Barbarito, E.; Barbato, F.; Bersani, A.; Beverini, N.; Biagi, S.; Bonori, M.; Bouhadef, B.; Bozza, C.; Cacopardo, G.; Capone, A.; Caruso, F.; Ceres, A.; Chiarusi, T.; Circella, M.; Cocimano, R.; Coniglione, R.; Cordelli, M.; Costa, M.; D'Amico, A.; De Asmundis, R.; De Bonis, G.; De Rosa, G.; De Vita, R.; Distefano, C.; Fermani, P.; Flaminio, V.; Fusco, L. A.; Garufi, F.; Giordano, V.; Giovanetti, G.; Grella, G.; Grimaldi, A.; Habel, R.; Imbesi, M.; Kulikovsky, V.; Lattuada, D.; Leotta, G.; Lonardo, A.; Longhitano, F.; Lo Presti, D.; Maccioni, E.; Margiotta, A.; Marinelli, A.; Martini, A.; Masullo, R.; Maugeri, F.; Migliozzi, P.; Migneco, E.; Minutoli, S.; Miraglia, A.; Mollo, C.; Mongelli, M.; Morganti, M.; Musico, P.; Musumeci, M.; Nicolau, C. A.; Orlando, A.; Papaleo, R.; Pappalardo, V.; Pellegrino, C.; Perrina, C.; Piattelli, P.; Pugliatti, C.; Pulvirenti, S.; Raffaelli, F.; Raia, G.; Randazzo, N.; Riccobene, G.; Rovelli, A.; Russo, A.; Russo, G. V.; Sapienza, P.; Sciliberto, D.; Sedita, M.; Sgura, I.; Shirokov, E.; Simeone, F.; Sipala, V.; Sollima, C.; Spina, M.; Spurio, M.; Stefani, F.; Taiuti, M.; Terreni, G.; Trasatti, L.; Trovato, A.; Vicini, P.; Viola, S.; Vivolo, D.

    2013-07-01

    A 13-inch Optical Module (OM) containing a large-area (10-inch) photomultiplier was designed as part of Phase-2 of the NEMO project. An intense R&D activity on the photomultipliers, the voltage supply boards, the optical coupling as well as the study of the influences of the Earth's magnetic field has driven the choice of each single component of the OM. Following a well-established production procedure, 32 OMs were assembled and their functionality tested. The design, the testing and the production phases are thoroughly described in this paper.

  5. Measurement of the atmospheric muon depth intensity relation with the NEMO Phase-2 tower

    CERN Document Server

    Aiello, S; Anghinolfi, M; Barbarino, G; Barbarito, E; Barbato, F; Beverini, N; Biagi, S; Bouhadef, B; Bozza, C; Cacopardo, G; Calamai, M; Calì, C; Capone, A; Caruso, F; Ceres, A; Chiarusi, T; Circella, M; Cocimano, R; Coniglione, R; Costa, M; Cuttone, G; D'Amato, C; D'Amico, A; De Bonis, G; De Luca, V; Deniskina, N; De Rosa, G; Di Capua, F; Distefano, C; Fermani, P; Fusco, L A; Garufi, F; Giordano, V; Gmerk, A; Grasso, R; Grella, G; Hugon, C; Imbesi, M; Kulikovskiy, V; Larosa, G; Lattuada, D; Leismueller, K P; Leonora, E; Litrico, P; Lonardo, A; Longhitano, F; Presti, D Lo; Maccioni, E; Margiotta, A; Martini, A; Masullo, R; Migliozzi, P; Migneco, E; Miraglia, A; Mollo, C M; Mongelli, M; Morganti, M; Musico, P; Musumeci, M; Nicolau, C A; Orlando, A; Papaleo, R; Pellegrino, C; Pellegriti, M G; Perrina, C; Piattelli, P; Pugliatti, C; Pulvirenti, S; Orselli, A; Raffaelli, F; Randazzo, N; Riccobene, G; Rovelli, A; Sanguineti, M; Sapienza, P; Sciacca, V; Sgura, I; Simeone, F; Sipala, V; Speziale, F; Spina, M; Spitaleri, A; Spurio, M; Stellacci, S M; Taiuti, M; Terreni, G; Trasatti, L; Trovato, A; Ventura, C; Vicini, P; Viola, S; Vivolo, D

    2014-01-01

    The results of the analysis of the data collected with the NEMO Phase-2 tower, deployed at 3500 m depth about 80 km off-shore Capo Passero (Italy), are presented. Cherenkov photons detected with the photomultipliers tubes were used to reconstruct the tracks of atmospheric muons. Their zenith-angle distribution was measured and the results compared with Monte Carlo simulations. An evaluation of the systematic effects due to uncertainties on environmental and detector parameters is also included. The associated depth intensity relation was evaluated and compared with previous measurements and theoretical predictions. With the present analysis, the muon depth intensity relation has been measured up to 13 km of water equivalent.

  6. The optical modules of the phase-2 of the NEMO project

    International Nuclear Information System (INIS)

    A 13-inch Optical Module (OM) containing a large-area (10-inch) photomultiplier was designed as part of Phase-2 of the NEMO project. An intense R and D activity on the photomultipliers, the voltage supply boards, the optical coupling as well as the study of the influences of the Earth's magnetic field has driven the choice of each single component of the OM. Following a well-established production procedure, 32 OMs were assembled and their functionality tested. The design, the testing and the production phases are thoroughly described in this paper

  7. A generic approach to explicit simulation of uncertainty in the NEMO ocean model

    Directory of Open Access Journals (Sweden)

    J.-M. Brankart

    2015-05-01

    Full Text Available In this paper, a generic implementation approach is presented, with the aim of transforming a deterministic ocean model (like NEMO into a probabilistic model. With this approach, several kinds of stochastic parameterizations are implemented to simulate the non-deterministic effect of unresolved processes, unresolved scales and unresolved diversity. The method is illustrated with three applications, showing that uncertainties can produce a major effect in the circulation model, in the ecosystem model, and in the sea ice model. These examples show that uncertainties can produce an important effect in the simulations, strongly modifying the dynamical behaviour of these three components of ocean systems.

  8. The km sup 3 Mediterranean neutrino observatory - the NEMO.RD project

    CERN Document Server

    De Marzo, C N

    2001-01-01

    The NEMO.RD Project is a feasibility study of a km sup 3 underwater telescope for high energy astrophysical neutrinos to be located in the Mediterranean Sea. Results on various issues of this project are presented on: i) Monte Carlo simulation study of the capabilities of various arrays of phototubes in order to determine the detector geometry that can optimize performance and cost; ii) oceanographic survey of various sites in search of the optimal one; iii) feasibility study of mechanics, deployment, connections and maintenance of such a detector. Parameters of a site near Capo Passero, Sicily, where depth, transparency and other water parameters seem optimal are shown.

  9. Hypohidrotic ectodermal dysplasia and immunodeficiency with coincident NEMO and EDA Mutations

    Directory of Open Access Journals (Sweden)

    Michael D. Keller

    2011-11-01

    Full Text Available Ectodermal dysplasias (ED are uncommon genetic disorders resulting in abnormalities in ectodermally-derived structures. Though many ED-associated genes have been described, the NF-κB Essential Modulator (NEMO encoded by the IKBKG gene is unique in that mutations also result in severe humoral and cellular immunologic defects. We describe three unrelated kindreds with defects in both EDA and IKBKG resulting from an X-chromosome crossover. This demonstrates the importance of thorough immunologic consideration of patients with ED even when an EDA etiology is confirmed, and raises the possibility of a specific phenotype arising from coincident mutations in EDA and IKBKB.

  10. DNA-Based Authentication of Botanicals and Plant-Derived Dietary Supplements: Where Have We Been and Where Are We Going?

    Science.gov (United States)

    Coutinho Moraes, Denise F; Still, David W; Lum, Michelle R; Hirsch, Ann M

    2015-06-01

    Herbal medicines and botanicals have long been used as sole or additional medical aids worldwide. Currently, billions of dollars are spent on botanicals and related products, but minimal regulation exists regarding their purity, integrity, and efficacy. Cases of adulteration and contamination have led to severe illness and even death in some cases. Identifying the plant material in botanicals and phytomedicines using organoleptic means or through microscopic observation of plant parts is not trivial, and plants are often misidentified. Recently, DNA-based methods have been applied to these products because DNA is not changed by growth conditions unlike the chemical constituents of many active pharmaceutical agents. In recent years, DNA barcoding methods, which are used to identify species diversity in the Tree of Life, have been also applied to botanicals and plant-derived dietary supplements. In this review, we recount the history of DNA-based methods for identification of botanicals and discuss some of the difficulties in defining a specific bar code or codes to use. In addition, we describe how next generation sequencing technologies have enabled new techniques that can be applied to identifying these products with greater authority and resolution. Lastly, we present case histories where dietary supplements, decoctions, and other products have been shown to contain materials other than the main ingredient stipulated on the label. We conclude that there is a fundamental need for greater quality control in this industry, which if not self-imposed, that may result from legislation. PMID:25856442

  11. DNA barcodes effectively identify the morphologically similar Common Opossum (Didelphis marsupialis) and Virginia Opossum (Didelphis virginiana) from areas of sympatry in Mexico.

    Science.gov (United States)

    Cervantes, Fernando A; Arcangeli, Jésica; Hortelano-Moncada, Yolanda; Borisenko, Alex V

    2010-12-01

    Two morphologically similar species of opossum from the genus Didelphis-Didelphis virginiana and Didelphis marsupialis-cooccur sympatrically in Mexico. High intraspecific variation complicates their morphological discrimination, under both field and museum conditions. This study aims to evaluate the utility and reliability of using DNA barcodes (short standardized genome fragments used for DNA-based identification) to distinguish these two species. Sequences of the cytochrome c oxidase subunit I (Cox1) mitochondrial gene were obtained from 12 D. marsupialis and 29 D. virginiana individuals and were compared using the neighbor-joining (NJ) algorithm with Kimura's two-parameter (K2P) model of nucleotide substitution. Average K2P distances were 1.56% within D. virginiana and 1.65% in D. marsupialis. Interspecific distances between D. virginiana and D. marsupialis varied from 7.8 to 9.3% and their barcode sequences formed distinct non-overlapping clusters on NJ trees. All sympatric specimens of both species were effectively discriminated, confirming the utility of Cox1 barcoding as a tool for taxonomic identification of these morphologically similar taxa. PMID:21271858

  12. DNA barcoding identifies Argentine fishes from marine and brackish waters.

    Directory of Open Access Journals (Sweden)

    Ezequiel Mabragaña

    Full Text Available BACKGROUND: DNA barcoding has been advanced as a promising tool to aid species identification and discovery through the use of short, standardized gene targets. Despite extensive taxonomic studies, for a variety of reasons the identification of fishes can be problematic, even for experts. DNA barcoding is proving to be a useful tool in this context. However, its broad application is impeded by the need to construct a comprehensive reference sequence library for all fish species. Here, we make a regional contribution to this grand challenge by calibrating the species discrimination efficiency of barcoding among 125 Argentine fish species, representing nearly one third of the known fauna, and examine the utility of these data to address several key taxonomic uncertainties pertaining to species in this region. METHODOLOGY/PRINCIPAL FINDINGS: Specimens were collected and morphologically identified during crusies conducted between 2005 and 2008. The standard BARCODE fragment of COI was amplified and bi-directionally sequenced from 577 specimens (mean of 5 specimens/species, and all specimens and sequence data were archived and interrogated using analytical tools available on the Barcode of Life Data System (BOLD; www.barcodinglife.org. Nearly all species exhibited discrete clusters of closely related haplogroups which permitted the discrimination of 95% of the species (i.e. 119/125 examined while cases of shared haplotypes were detected among just three species-pairs. Notably, barcoding aided the identification of a new species of skate, Dipturus argentinensis, permitted the recognition of Genypterus brasiliensis as a valid species and questions the generic assignment of Paralichthys isosceles. CONCLUSIONS/SIGNIFICANCE: This study constitutes a significant contribution to the global barcode reference sequence library for fishes and demonstrates the utility of barcoding for regional species identification. As an independent assessment of alpha

  13. Environmental barcoding reveals massive dinoflagellate diversity in marine environments.

    Directory of Open Access Journals (Sweden)

    Rowena F Stern

    Full Text Available BACKGROUND: Dinoflagellates are an ecologically important group of protists with important functions as primary producers, coral symbionts and in toxic red tides. Although widely studied, the natural diversity of dinoflagellates is not well known. DNA barcoding has been utilized successfully for many protist groups. We used this approach to systematically sample known "species", as a reference to measure the natural diversity in three marine environments. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we assembled a large cytochrome c oxidase 1 (COI barcode database from 8 public algal culture collections plus 3 private collections worldwide resulting in 336 individual barcodes linked to specific cultures. We demonstrate that COI can identify to the species level in 15 dinoflagellate genera, generally in agreement with existing species names. Exceptions were found in species belonging to genera that were generally already known to be taxonomically challenging, such as Alexandrium or Symbiodinium. Using this barcode database as a baseline for cultured dinoflagellate diversity, we investigated the natural diversity in three diverse marine environments (Northeast Pacific, Northwest Atlantic, and Caribbean, including an evaluation of single-cell barcoding to identify uncultivated groups. From all three environments, the great majority of barcodes were not represented by any known cultured dinoflagellate, and we also observed an explosion in the diversity of genera that previously contained a modest number of known species, belonging to Kareniaceae. In total, 91.5% of non-identical environmental barcodes represent distinct species, but only 51 out of 603 unique environmental barcodes could be linked to cultured species using a conservative cut-off based on distances between cultured species. CONCLUSIONS/SIGNIFICANCE: COI barcoding was successful in identifying species from 70% of cultured genera. When applied to environmental samples, it revealed a

  14. Real-time multi-barcode reader for industrial applications

    Science.gov (United States)

    Zafar, Iffat; Zakir, Usman; Edirisinghe, Eran A.

    2010-05-01

    The advances in automated production processes have resulted in the need for detecting, reading and decoding 2D datamatrix barcodes at very high speeds. This requires the correct combination of high speed optical devices that are capable of capturing high quality images and computer vision algorithms that can read and decode the barcodes accurately. Such barcode readers should also be capable of resolving fundamental imaging challenges arising from blurred barcode edges, reflections from possible polyethylene wrapping, poor and/or non-uniform illumination, fluctuations of focus, rotation and scale changes. Addressing the above challenges in this paper we propose the design and implementation of a high speed multi-barcode reader and provide test results from an industrial trial. To authors knowledge such a comprehensive system has not been proposed and fully investigated in existing literature. To reduce the reflections on the images caused due to polyethylene wrapping used in typical packaging, polarising filters have been used. The images captured using the optical system above will still include imperfections and variations due to scale, rotation, illumination etc. We use a number of novel image enhancement algorithms optimised for use with 2D datamatrix barcodes for image de-blurring, contrast point and self-shadow removal using an affine transform based approach and non-uniform illumination correction. The enhanced images are subsequently used for barcode detection and recognition. We provide experimental results from a factory trial of using the multi-barcode reader and evaluate the performance of each optical unit and computer vision algorithm used. The results indicate an overall accuracy of 99.6 % in barcode recognition at typical speeds of industrial conveyor systems.

  15. DNA Barcoding Identifies Argentine Fishes from Marine and Brackish Waters

    Science.gov (United States)

    Mabragaña, Ezequiel; Díaz de Astarloa, Juan Martín; Hanner, Robert; Zhang, Junbin; González Castro, Mariano

    2011-01-01

    Background DNA barcoding has been advanced as a promising tool to aid species identification and discovery through the use of short, standardized gene targets. Despite extensive taxonomic studies, for a variety of reasons the identification of fishes can be problematic, even for experts. DNA barcoding is proving to be a useful tool in this context. However, its broad application is impeded by the need to construct a comprehensive reference sequence library for all fish species. Here, we make a regional contribution to this grand challenge by calibrating the species discrimination efficiency of barcoding among 125 Argentine fish species, representing nearly one third of the known fauna, and examine the utility of these data to address several key taxonomic uncertainties pertaining to species in this region. Methodology/Principal Findings Specimens were collected and morphologically identified during crusies conducted between 2005 and 2008. The standard BARCODE fragment of COI was amplified and bi-directionally sequenced from 577 specimens (mean of 5 specimens/species), and all specimens and sequence data were archived and interrogated using analytical tools available on the Barcode of Life Data System (BOLD; www.barcodinglife.org). Nearly all species exhibited discrete clusters of closely related haplogroups which permitted the discrimination of 95% of the species (i.e. 119/125) examined while cases of shared haplotypes were detected among just three species-pairs. Notably, barcoding aided the identification of a new species of skate, Dipturus argentinensis, permitted the recognition of Genypterus brasiliensis as a valid species and questions the generic assignment of Paralichthys isosceles. Conclusions/Significance This study constitutes a significant contribution to the global barcode reference sequence library for fishes and demonstrates the utility of barcoding for regional species identification. As an independent assessment of alpha taxonomy, barcodes provide

  16. DNA Barcode Authentication of Saw Palmetto Herbal Dietary Supplements

    OpenAIRE

    Little, Damon P.; Jeanson, Marc L.

    2013-01-01

    Herbal dietary supplements made from saw palmetto (Serenoa repens; Arecaceae) fruit are commonly consumed to ameliorate benign prostate hyperplasia. A novel DNA mini–barcode assay to accurately identify [specificity = 1.00 (95% confidence interval = 0.74–1.00); sensitivity = 1.00 (95% confidence interval = 0.66–1.00); n = 31] saw palmetto dietary supplements was designed from a DNA barcode reference library created for this purpose. The mini–barcodes were used to estimate the frequency of mis...

  17. BEST: Barcode Enabled Sequencing of Tetrads

    Science.gov (United States)

    Scott, Adrian C.; Ludlow, Catherine L.; Cromie, Gareth A.; Dudley, Aimée M.

    2014-01-01

    Tetrad analysis is a valuable tool for yeast genetics, but the laborious manual nature of the process has hindered its application on large scales. Barcode Enabled Sequencing of Tetrads (BEST)1 replaces the manual processes of isolating, disrupting and spacing tetrads. BEST isolates tetrads by virtue of a sporulation-specific GFP fusion protein that permits fluorescence-activated cell sorting of tetrads directly onto agar plates, where the ascus is enzymatically digested and the spores are disrupted and randomly arrayed by glass bead plating. The haploid colonies are then assigned sister spore relationships, i.e. information about which spores originated from the same tetrad, using molecular barcodes read during genotyping. By removing the bottleneck of manual dissection, hundreds or even thousands of tetrads can be isolated in minutes. Here we present a detailed description of the experimental procedures required to perform BEST in the yeast Saccharomyces cerevisiae, starting with a heterozygous diploid strain through the isolation of colonies derived from the haploid meiotic progeny. PMID:24836713

  18. Barcode Payment System in Trusted Mobile Devices

    Directory of Open Access Journals (Sweden)

    Vibha Kaw Raina

    2012-11-01

    Full Text Available Mobile payment is an application of mobile commerce which facilitates mobile commerce transactions by providing the mobile customer with a convenient means to pay. Many mobile payment methods have been proposed and implemented like user friendly, customer centric, merchant centric where security concerns are highly addressed. This paper proposes a mobile payment model with barcodes for mobile users to improve mobile user experience in mobile payment. Unlike other existing mobile payment systems, the proposed payment solution provides distinct advantages to support buy-and-sale products and services based on 2D Barcodes. The aim of this work is to integrate a model of payment with the financial services, including payment and banking ones, based on two primary capabilities: the use of computational resources of a trusted mobile device and the establishment of a user controlled channel with the customer’s bank. The proposed architecture is characterized bank-centric, since the bank acts consultatively, informatively and protectively for the end user and it offers flexibility, adaptability and continuous extendibility to open technologies.

  19. DNA-based Simultaneous Identification of Three Terminalia Species Targeting Adulteration

    Science.gov (United States)

    Sharma, Sonal; Shrivastava, Neeta

    2016-01-01

    Background: Various parts of three Terminalia species, namely, Terminalia arjuna (stem bark), Terminalia bellirica (fruit), and Terminalia chebula (fruit) are widely known for their therapeutic principles and other commercial values. However, stem bark of T. bellirica and T. chebula along with Terminalia tomentosa are reported as adulterants of T. arjuna. Correct botanical identification is very critical for safe and effective herbal drugs. DNA-based identification approaches are advancing the conventional methods and sometime proved more beneficial. Objective: The purpose of the study was to develop polymerase chain reaction (PCR) method using internal transcribed spacer (ITS) region to ascertain the identity of T. arjuna herbal material as well as detection of mixing of other three Terminalia species. Materials and Methods: DNA from stem barks samples were isolated and subjected to ITS region amplification and sequencing. Sequences were compared for polymorphic nucleotides determination to develop species-specific primers. Final primers were selected on the basis of in silico analysis and experimentally validated. PCR assays for botanical identification of Terminalia species were developed. Sensitivity testing and assay validation were also performed. Results: The PCR assays developed for Terminalia species were resulted in definite amplicons of the corresponding species. No cross-reactivity of the primers was detected. Sensitivity was found enough to amplify as low as 2 ng of DNA. Mixing of DNA in various concentrations for validation also proved the sensitivity of assay to detect original botanicals in the mixture. The developed methods proved very specific and sensitive to authenticate Arjuna bark to develop evidence-based herbal medicines. SUMMARY Internal transcribed spacer-based species-specific polymerase chain reaction.(PCR) assays were developed to authenticate Terminalia arjuna stem bark and to identify substitution/adulteration of Terminalia bellirica

  20. Quantum interference in DNA bases probed by graphene nanoribbons

    Science.gov (United States)

    Jeong, Heejeong; Seul Kim, Han; Lee, Sung-Hoon; Lee, Dongho; Hoon Kim, Yong; Huh, Nam

    2013-07-01

    Based on first-principles nonequilibrium Green's function calculations, we demonstrate quantum interference (QI) effects on the tunneling conductance of deoxyribonucleic acid bases placed between zigzag graphene nanoribbon electrodes. With the analogy of QI in hydrocarbon ring structures, we hypothesize that QI can be well preserved in the π-π coupling between the carbon-based electrode and a single DNA base. We demonstrate indications of QI, such as destructively interfered anti-resonance or Fano-resonance, that affect the variation of tunneling conductance depending on the orientation of a base. We find that guanine, with a 10-fold higher transverse conductance, can be singled out from the other bases.

  1. A DNA Barcode Library for Korean Chironomidae (Insecta: Diptera) and Indexes for Defining Barcode Gap

    OpenAIRE

    Kim, Sungmin; Song, Kyo-Hong; Ree, Han-Il; Kim, Won

    2011-01-01

    Non-biting midges (Diptera: Chironomidae) are a diverse population that commonly causes respiratory allergies in humans. Chironomid larvae can be used to indicate freshwater pollution, but accurate identification on the basis of morphological characteristics is difficult. In this study, we constructed a mitochondrial cytochrome c oxidase subunit I (COI)-based DNA barcode library for Korean chironomids. This library consists of 211 specimens from 49 species, including adults and unidentified l...

  2. Study of tracking detector of NEMO experiment - Simulation of the measurement of the ultra low 208Tl radioactivity in the source foils used as neutrinoless double beta decay emitters in NEMO experiment

    International Nuclear Information System (INIS)

    The purpose of NEMO3 experiment is the research of the neutrinoless double beta decay. This low energy process can sign the massive and Majorana nature of neutrino. This experiment with a very low radioactive background and containing 10 kg of enriched isotopes, studies mainly 100Mo. Installed at the Frejus underground laboratory, NEMO3 is a cylindrical detector which consists in very thin central source foils in a tracking detector made up of vertical drift cells operating in Geiger mode in a calorimeter and in a suitable shielding. This thesis is divided in two different parts. The first part is a full study of the features of the tracking detector. With a prototype composed of 9 drift cells we characterised the longitudinal and transverse reconstruction of position of the ionisation created by a LASER. With the first 3 modules under operation we used radioactive external neutron sources to measure the transverse resolution of ionisation position in a drift cell for high energy electrons. To study the vertex reconstruction on the source foil, sources of 207Bi which produced conversion electrons, were used inside the 3 modules. The second part of this thesis we show with simulations that we can measure with NEMO3 detector itself, the ultra low level of contamination in 208Tl of the source foil which comes from the natural radioactive chain of thorium. Using electron-photons channels we can obtain the 208Tl activity in the sources. With an analysis on the energy and on the time of flight of particles, NEMO3 is able to reach a sensitivity of 20μBq/kg after only 2 months of measurement. This sensitivity is the maximum 208Tl activity which we accepted for the sources in the NEMO3 proposal. (author)

  3. DNA barcoding in animal species: progress, potential and pitfalls.

    Science.gov (United States)

    Waugh, John

    2007-02-01

    Despite 250 years of work in systematics, the majority of species remains to be identified. Rising extinction rates and the need for increased biological monitoring lend urgency to this task. DNA sequencing, with key sequences serving as a "barcode", has therefore been proposed as a technology that might expedite species identification. In particular, the mitochondrial cytochrome c oxidase subunit 1 gene has been employed as a possible DNA marker for species and a number of studies in a variety of taxa have accordingly been carried out to examine its efficacy. In general, these studies demonstrate that DNA barcoding resolves most species, although some taxa have proved intractable. In some studies, barcoding provided a means of highlighting potential cryptic, synonymous or extinct species as well as matching adults with immature specimens. Higher taxa, however, have not been resolved as accurately as species. Nonetheless, DNA barcoding appears to offer a means of identifying species and may become a standard tool. PMID:17226815

  4. DNA barcoding of Jamaican bats: implications to Neotropical biodiversity.

    Science.gov (United States)

    K Lim, Burton; Arcila Hernandez, Lina Maria

    2016-07-01

    We report on the first comprehensive DNA barcoding survey of bats from Jamaica and compare the genetic variation to similar species on South America and Central America. Bats comprise the majority of mammalian diversity in typical lowland forest in the Neotropics, but the Caribbean is one noticeable geographic gap in the International Barcode of Life reference database. Of the 20 known species reported from Jamaica, half were DNA barcoded and were genetically distinct with interspecific variation ranging from 17 to 33%. By contrast, intraspecific variation ranged from 0 to 0.5% indicating that the barcode gap was sufficient in differentiating bat species diversity in Jamaica. The low levels of intraspecific divergence indicate that the populations within each species are relatively homogeneous across the island. There were, however, several cases of high sequence divergence for widely distributed species that occur on both the Caribbean islands and the continental mainland, which warrant further taxonomic study. PMID:27158792

  5. DNA barcoding Satyrine butterflies (Lepidoptera: Nymphalidae) in China.

    Science.gov (United States)

    Yang, Mingsheng; Zhai, Qing; Yang, Zhaofu; Zhang, Yalin

    2016-07-01

    We investigated the effectiveness of the standard 648 bp mitochondrial COI barcode region in discriminating among Satyrine species from China. A total of 214 COI sequences were obtained from 90 species, including 34 species that have never been barcoded. Analyses of genetic divergence show that the mean interspecific genetic divergence is about 16-fold higher than within species, and little overlap occurs between them. Neighbour-joining (NJ) analyses showed that 48 of the 50 species with two or more individuals, including two cases with deep intraspecific divergence (>3%), are monophyletic. Furthermore, when our sequences are combined with the conspecific sequences sampled from distantly geographic regions, the "barcoding gap" still exists, and all related species are recovered to be monophyletic in NJ analysis. Our study demonstrates that COI barcoding is effective in discriminating among the satyrine species of China, and provides a reference library for their future molecular identification. PMID:26017046

  6. VEHICLE IDENTIFICATION TASK SOLUTION BY WINDSCREEN MARKING WITH A BARCODE

    Directory of Open Access Journals (Sweden)

    A. Levterov

    2012-01-01

    Full Text Available The vehicle identification means are considered and the present-day traffic requirements are set. The vehicle automatic identification method concerned with barcode use is proposed and described.

  7. Illumination Compensation for 2-D Barcode Recognition Basing Morphologic

    Directory of Open Access Journals (Sweden)

    Jian-Hua Li

    2013-04-01

    Full Text Available Improvement of image quality has been highly demanded in digital imaging systems. This study presents a novel illumination normalization approach for 2-D barcode recognition under varying lighting conditions. MMs (Morphological transformations are employed to original images using big scale multiple SEs (structuring elements. Then we make use of entropy to fuse images. The performance of proposed methodology is illustrated through the processing of images with different kinds of 2-D barcodes under different backgrounds. The experimental results show that this approach can process different kinds of 2-D barcodes under varying lighting conditions adaptively. Compared with other conventional methods, our proposed approach does a better job in processing 2-D barcode under non-uniform illumination.

  8. Topological mapping and navigation in indoor environment with invisible barcode

    International Nuclear Information System (INIS)

    This paper addresses the localization and navigation problem using invisible two dimensional barcodes on the floor. Compared with other methods using natural/artificial landmark, the proposed localization method has great advantages in cost and appearance, since the location of the robot is perfectly known using the barcode information after the mapping is finished. We also propose a navigation algorithm which uses the topological structure. For the topological information, we define nodes and edges which are suitable for indoor navigation, especially for large area having multiple rooms, many walls and many static obstacles. The proposed algorithm also has an advantage that errors occurred in each node are mutually independent and can be compensated exactly after some navigation using barcode. Simulation and experimental results were performed to verify the algorithm in the barcode environment, and the result showed an excellent performance. After mapping, it is also possible to solve the kidnapped case and generate paths using topological information

  9. Topological mapping and navigation in indoor environment with invisible barcode

    Energy Technology Data Exchange (ETDEWEB)

    Huh, Jin Wook [Agency for Defense Development, Daejeon (Korea, Republic of); Chung, Woong Sik [Microrobot, Seoul (Korea, Republic of); Chung, Wan Kyun [Pohang University of Science and Technology, Pohang (Korea, Republic of)

    2006-09-15

    This paper addresses the localization and navigation problem using invisible two dimensional barcodes on the floor. Compared with other methods using natural/artificial landmark, the proposed localization method has great advantages in cost and appearance, since the location of the robot is perfectly known using the barcode information after the mapping is finished. We also propose a navigation algorithm which uses the topological structure. For the topological information, we define nodes and edges which are suitable for indoor navigation, especially for large area having multiple rooms, many walls and many static obstacles. The proposed algorithm also has an advantage that errors occurred in each node are mutually independent and can be compensated exactly after some navigation using barcode. Simulation and experimental results were performed to verify the algorithm in the barcode environment, and the result showed an excellent performance. After mapping, it is also possible to solve the kidnapped case and generate paths using topological information.

  10. Fused number representation systems and their barcode applications

    Science.gov (United States)

    Agaian, Sarkis

    2010-01-01

    In this paper we focus on: a) enhancing the performance of existing barcode systems and b) building a barcode system for mobile applications. First we introduce a new concept of generating a parametric number representation system by fusing a number of representation systems that use multiplication, addition, and other operations. Second we show how one can generate a secure, reliable, and high capacity color barcode by using the fused system. The representation, symbols, and colors may be used as encryption keys that can be encoded into barcodes, thus eliminating the direct dependence on cryptographic techniques. To supply an extra layer of security, the fused system also allows one to encrypt given data using different types of encryption methods. In addition, this fused system can be used to improve image processing applications and cryptography.

  11. Application Research of QRCode Barcode in Validation of Express Delivery

    Science.gov (United States)

    Liu, Zhihai; Zeng, Qingliang; Wang, Chenglong; Lu, Qing

    The barcode technology has become an important way in the field of information input and identify automatically. With the outstanding features of big storage capacity, secure, rich encoding character set and fast decoding, the two-dimensional(2D) QRcode(Quick Response Barcode) has become an important choice of commerce barcode. The development of wireless communications technology and the popularization and application of mobile device has set the foundation of 2D barcode used in business. In this paper, the characteristics and the compositions of 2D QRcode are described, the secure validation workflows and contents of QRcode in goods express delivery are discussed, the encoding process of QRcode is showed, and the system framework is analyzed and established. At last, the system compositions and functions of each part are discussed.

  12. Novel DNA barcodes for detection, idenfication and tracking of stachybotrys and chaetomium species

    DEFF Research Database (Denmark)

    Lewinska, Anna Malgorzata; Nielsen, Jakob Birkedal; Peuhkuri, Ruut Hannele;

    2014-01-01

    Detection and identification of indoor fungi in water-damaged buildings is crucial for preventi and control of fungal growth. This study focuses on a molecular method called DNA barcoding. evaluates commonly used sequences in DNA barcoding for fungal species identification Chaetomium and...... Stachybotrys. The existing DNA barcodes: ITS, SSU, LSU, B-TUB, CMD, RP and TEF-1α do not give satisfying species resolution to be considered as DNA barcodes for the two genera. Therefore, novel barcodes for them are needed. Barcode potentials, such as HOG1 a NAHA, were identified using bioinformatics and are...

  13. DNA Barcoding of Catfish: Species Authentication and Phylogenetic Assessment

    OpenAIRE

    Wong, Li Lian; Peatman, Eric; Lu, Jianguo; Kucuktas, Huseyin; He, Shunping; Zhou, Chuanjiang; Na-Nakorn, Uthairat; Liu, Zhanjiang

    2011-01-01

    As the global market for fisheries and aquaculture products expands, mislabeling of these products has become a growing concern in the food safety arena. Molecular species identification techniques hold the potential for rapid, accurate assessment of proper labeling. Here we developed and evaluated DNA barcodes for use in differentiating United States domestic and imported catfish species. First, we sequenced 651 base-pair barcodes from the cytochrome oxidase I (COI) gene from individuals of ...

  14. Wolbachia and DNA Barcoding Insects: Patterns, Potential, and Problems

    OpenAIRE

    M. Alex Smith; Claudia Bertrand; Kate Crosby; Eveleigh, Eldon S.; Jose Fernandez-Triana; Fisher, Brian L.; Jason Gibbs; Mehrdad Hajibabaei; Winnie Hallwachs; Katharine Hind; Jan Hrcek; Da-Wei Huang; Milan Janda; Janzen, Daniel H.; Yanwei Li

    2012-01-01

    Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Us...

  15. A DNA Barcoding Approach to Characterize Pollen Collected by Honeybees

    OpenAIRE

    Andrea Galimberti; Fabrizio De Mattia; Ilaria Bruni; Daniela Scaccabarozzi; Anna Sandionigi; Michela Barbuto; Maurizio Casiraghi; Massimo Labra

    2014-01-01

    In the present study, we investigated DNA barcoding effectiveness to characterize honeybee pollen pellets, a food supplement largely used for human nutrition due to its therapeutic properties. We collected pollen pellets using modified beehives placed in three zones within an alpine protected area (Grigna Settentrionale Regional Park, Italy). A DNA barcoding reference database, including rbcL and trnH-psbA sequences from 693 plant species (104 sequenced in this study) was assembled. The datab...

  16. Graded core/shell semiconductor nanorods and nanorod barcodes

    Science.gov (United States)

    Alivisatos, A. Paul; Scher, Erik C.; Manna, Liberato

    2010-12-14

    Graded core/shell semiconductor nanorods and shaped nanorods are disclosed comprising Group II-VI, Group III-V and Group IV semiconductors and methods of making the same. Also disclosed are nanorod barcodes using core/shell nanorods where the core is a semiconductor or metal material, and with or without a shell. Methods of labeling analytes using the nanorod barcodes are also disclosed.

  17. Magnetic phase diagrams of barcode-type nanostructures

    International Nuclear Information System (INIS)

    The magnetic configurations of barcode-type magnetic nanostructures consisting of alternate ferromagnetic and nonmagnetic layers arranged within a multilayer nanotube structure are investigated as a function of their geometry. Based on a continuum approach we have obtained analytical expressions for the energy which lead us to obtain phase diagrams giving the relative stability of characteristic internal magnetic configurations of the barcode-type nanostructures.

  18. SURVEY ON INFORMATION HIDING TECHNIQUES USING QR BARCODE

    Directory of Open Access Journals (Sweden)

    Manoj S. Rewatkar

    2014-05-01

    Full Text Available Nowadays, the information processing system plays crucial part in the internet. Online information security has become the top priority in all sectors. Failing to provide online information security may cause loss of critical information or someone may use or distribute such information for malicious purpose. Recently QR barcodes have been used as an effective way to securely share information. This paper presents the survey on information hiding techniques which can share high security information over network using QR barcode.

  19. Hypermarket Competition and the Diffusion of Retail Checkout Barcode Scanning

    OpenAIRE

    Beck, Jonathan; Grajek, Michal; Wey, Christian

    2005-01-01

    This paper presents a set of panel data to study the diffusion of retail checkout barcode scanning in ten European countries over the period 1981-1996. Estimates from a standard diffusion model suggest that countries differ most in the long-run diffusion level of barcode scanning and less in timing or diffusion speed. We present evidence that the emergence of hypermarkets raises competitive intensity and use hypermarket data, among other variables, in a pooled estimation. Results suggest that...

  20. Biodegradable porous silicon barcode nanowires with defined geometry

    OpenAIRE

    Chiappini, Ciro; Liu, Xuewu; Fakhoury, Jean Raymond; Ferrari, Mauro

    2010-01-01

    Silicon nanowires are of proven importance in diverse fields such as energy production and storage, flexible electronics, and biomedicine due to the unique characteristics emerging from their one-dimensional semiconducting nature and their mechanical properties. Here we report the synthesis of biodegradable porous silicon barcode nanowires by metal assisted electroless etch of single crystal silicon with resistivity ranging from 0.0008 Ω-cm to 10 Ω-cm. We define the geometry of the barcode na...

  1. Barcode van DNA. Democratisering van de taxonomie door digitaal identificatiesysteem

    OpenAIRE

    Bakker, F.T.

    2011-01-01

    Het herkennen van biologische soorten aan de hand van een gestandaardiseerde DNA-barcode heeft de laatste tijd een enorme vlucht genomen. Gedreven door aan de ene kant de biodiversiteitscrises en de mogelijke global change, en aan de andere kant zowel razendsnelle technologische vooruitgang als ook het vooruitzicht dat niet genoeg klassieke taxonomen worden opgeleid voor de nabije toekomst, lijkt DNA-barcoding zich een strategische plek te veroveren op huidige, al dan niet toegepaste, biodive...

  2. Magnetic phase diagrams of barcode-type nanostructures

    OpenAIRE

    Leighton, B; O.J Suarez; Landeros, P.; Escrig, J.

    2010-01-01

    The magnetic configurations of barcode-type magnetic nanostructures consisting of alternate ferromagnetic and nonmagnetic layers arranged within a multilayer nanotube structure are investigated as a function of their geometry. Based on a continuum approach we have obtained analytical expressions for the energy which lead us to obtain phase diagrams giving the relative stability of characteristic internal magnetic configurations of the barcode-type nanostructures.

  3. Magnetic phase diagrams of barcode-type nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Leighton, B; Escrig, J [Departamento de Fisica, Universidad de Santiago de Chile (USACH), Avenida Ecuador 3493, 917-0124 Santiago (Chile); Suarez, O J; Landeros, P, E-mail: juan.escrig@usach.c [Departamento de Fisica, Universidad Tecnica Federico Santa Maria, Avenida Espana 1680, Casilla 110 V, 2340000 Valparaiso (Chile)

    2009-09-23

    The magnetic configurations of barcode-type magnetic nanostructures consisting of alternate ferromagnetic and nonmagnetic layers arranged within a multilayer nanotube structure are investigated as a function of their geometry. Based on a continuum approach we have obtained analytical expressions for the energy which lead us to obtain phase diagrams giving the relative stability of characteristic internal magnetic configurations of the barcode-type nanostructures.

  4. A comparative analysis of DNA barcode microarray feature size

    OpenAIRE

    Ammar, Ron; SMITH, ANDREW M.; Heisler, Lawrence E.; Giaever, Guri; Nislow, Corey

    2009-01-01

    Background Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density), but this increase in resolution can compromise sensitivity. Results We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarray platfor...

  5. Filling the gap - COI barcode resolution in eastern Palearctic birds

    OpenAIRE

    Koblik Eugeny A; Red'kin Yaroslav A; Kalyakin Mikhail V; Birks Sharon M; Kerr Kevin CR; Hebert Paul DN

    2009-01-01

    Abstract Background The Palearctic region supports relatively few avian species, yet recent molecular studies have revealed that cryptic lineages likely still persist unrecognized. A broad survey of cytochrome c oxidase I (COI) sequences, or DNA barcodes, can aid on this front by providing molecular diagnostics for species assignment. Barcodes have already been extensively surveyed in the Nearctic, which provides an interesting comparison to this region; faunal interchange between these regio...

  6. Illumination Compensation for 2-D Barcode Recognition Basing Morphologic

    OpenAIRE

    Jian-Hua Li; Yi-Wen Wang; Yi Chen; Meng Zhang

    2013-01-01

    Improvement of image quality has been highly demanded in digital imaging systems. This study presents a novel illumination normalization approach for 2-D barcode recognition under varying lighting conditions. MMs (Morphological transformations) are employed to original images using big scale multiple SEs (structuring elements). Then we make use of entropy to fuse images. The performance of proposed methodology is illustrated through the processing of images with different kinds of 2-D barcode...

  7. Comparative study of Barcode, QR-code and RFID System

    OpenAIRE

    Trupti Lotlikar; Rohan Kankapurkar; Anand Parekar; Akshay Mohite

    2013-01-01

    Wireless sensors are standard measurement tools equipped with transmitters to convert signals from process control instruments into a radio transmission. The radio signal is interpreted by a receiver which then converts the wireless signal to a specific, desired output, such as an analog current or data analysis via computer software. The paper gives a brief on wireless sensors and their types like Barcode, QR code, RFID along with their characteristics and working components. The Barcode is ...

  8. A comparative analysis of DNA barcode microarray feature size

    OpenAIRE

    Smith Andrew M; Ammar Ron; Heisler Lawrence E; Giaever Guri; Nislow Corey

    2009-01-01

    Abstract Background Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density), but this increase in resolution can compromise sensitivity. Results We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarra...

  9. DNA barcoding of Gaultheria L.in China (Ericaceae: Vaccinioideae)

    Institute of Scientific and Technical Information of China (English)

    He REN; Lu LU; Hong WANG; De-Zhu LI

    2011-01-01

    Four DNA barcoding loci,chloroplast loci rbcL,matK,trnH-psbA,and nuclear locus internal transcribed spacer (ITS),were tested for the accurate discrimination of the Chinese species of Gaultheria by using intraspecific and interspecific pairwise P-distance,Wilcoxon signed rank test,and tree-based analyses.This study included 186 individuals from 89 populations representing 30 species.For all individuals,single locus markers showed high levels of sequencing universality but were ineffective for species resolvability.Polymerase chain reaction amplification and sequencing were successful for all four loci.Both ITS and matK showed significantly higher levels of interspecific species delimitation than rbcL and trnH-psbA.A combination ofmatK and ITS was the most efficient DNA barcode among all studied regions,however,they do not represent an appropriate candidate barcode for Chinese Gaultheria,by which only 11 out of 30 species can be separated.Loci rbcL,matK,and trnH-psbA,which were recently proposed as universal plant barcodes,have a very poor capacity for species separation for Chinese Gaultheria.DNA barcodes may be reliable tools to identify the evolutionary units of this group,so further studies are needed to develop more efficient DNA barcodes for Gaultheria and other genera with complicated evolutionary histories.

  10. DNA-Based Identification and Chemical Characteristics of Hypnea musciformis from Coastal Sites in Ghana

    OpenAIRE

    Marcel Tutor Ale; Kristian Barrett; Gloria Naa Dzama Addico; Nanna Rhein-Knudsen; Amoako Atta deGraft-Johnson; Meyer, Anne S.

    2016-01-01

    This work reveals new, important insights about the influence of broad spatial variations on the phylogenetic relationship and chemical characteristics of Ghanaian Hypnea musciformis—a carrageenan-containing red seaweed. DNA barcoding techniques alleviate the difficulty for accurate morphological identification. COI barcode sequences of the Ghanaian H. musciformis showed <0.7% intraspecies divergence, indicating no distinct phylogenetic variation, suggesting that they actually belong to th...

  11. DNA barcoding of Pedicularis L.(Orobanchaceae): Evaluating four universal barcode loci in a large and hemiparasitic genus

    Institute of Scientific and Technical Information of China (English)

    Wen-Bin YU; pan-Hui HUANG; Richard H. REE; Min-Lu LIU; De-Zhu LI; Hong WANG

    2011-01-01

    One application ofDNA barcoding is species identification based on sequences of a short and standardized DNA region.In plants,various DNA regions,alone or in combination,have been proposed and investigated,but consensus on a universal plant barcode remains elusive.In this study,we tested the utility of four candidate barcoding regions (rbcL,matK,trnH-psbA,and internal transcribed spacer (ITS)) as DNA barcodes for discriminating species in a large and hemiparasitic genus Pedicularis (Orobanchaceae).Amplification and sequencing was successful using single primer pairs for rbcL,trnH-psbA,and ITS,whereas two primer pairs were required for matK.Patterns of sequence divergence commonly showed a “barcoding gap”,that is,a bimodal frequency distribution of pairwise distances representing genetic diversity within and between species,respectively Considering primer universality,ease of amplification and sequencing,and performance in discriminating species,we found the most effective single-region barcode for Pedicularis to be ITS,and the most effective two-region barcode to be rbcL +ITS.Both discriminated at least 78% of the 88 species and correctly identified at least 89% of the sequences in our sample,and were effective in placing unidentified samples in known species groups.Our results suggest that DNA barcoding has the potential to aid taxonomic research in Pedicularis,a species-rich cosmopolitan clade much in need of revision,as well as ecological studies in its center of diversity,the Hengduan Mountains region of China.

  12. A Rewritable, Random-Access DNA-Based Storage System

    Science.gov (United States)

    Tabatabaei Yazdi, S. M. Hossein; Yuan, Yongbo; Ma, Jian; Zhao, Huimin; Milenkovic, Olgica

    2015-09-01

    We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing read-only methods that require decoding the whole file in order to read one data fragment. Our system is based on new constrained coding techniques and accompanying DNA editing methods that ensure data reliability, specificity and sensitivity of access, and at the same time provide exceptionally high data storage capacity. As a proof of concept, we encoded parts of the Wikipedia pages of six universities in the USA, and selected and edited parts of the text written in DNA corresponding to three of these schools. The results suggest that DNA is a versatile media suitable for both ultrahigh density archival and rewritable storage applications.

  13. Magnetic Propulsion of Microswimmers with DNA-Based Flagellar Bundles.

    Science.gov (United States)

    Maier, Alexander M; Weig, Cornelius; Oswald, Peter; Frey, Erwin; Fischer, Peer; Liedl, Tim

    2016-02-10

    We show that DNA-based self-assembly can serve as a general and flexible tool to construct artificial flagella of several micrometers in length and only tens of nanometers in diameter. By attaching the DNA flagella to biocompatible magnetic microparticles, we provide a proof of concept demonstration of hybrid structures that, when rotated in an external magnetic field, propel by means of a flagellar bundle, similar to self-propelling peritrichous bacteria. Our theoretical analysis predicts that flagellar bundles that possess a length-dependent bending stiffness should exhibit a superior swimming speed compared to swimmers with a single appendage. The DNA self-assembly method permits the realization of these improved flagellar bundles in good agreement with our quantitative model. DNA flagella with well-controlled shape could fundamentally increase the functionality of fully biocompatible nanorobots and extend the scope and complexity of active materials. PMID:26821214

  14. Spectroscopic investigation on the telomeric DNA base sequence repeat

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Telomeres are protein-DNA complexes at the terminals of linear chromosomes, which protect chromosomal integrity and maintain cellular replicative capacity.From single-cell organisms to advanced animals and plants,structures and functions of telomeres are both very conservative. In cells of human and vertebral animals, telomeric DNA base sequences all are (TTAGGG)n. In the present work, we have obtained absorption and fluorescence spectra measured from seven synthesized oligonucleotides to simulate the telomeric DNA system and calculated their relative fluorescence quantum yields on which not only telomeric DNA characteristics are predicted but also possibly the shortened telomeric sequences during cell division are imrelative fluorescence quantum yield and remarkable excitation energy innerconversion, which tallies with the telomeric sequence of (TTAGGG)n. This result shows that telomeric DNA has a strong non-radiative or innerconvertible capability.``

  15. Oxidative DNA base modifications as factors in carcinogenesis

    International Nuclear Information System (INIS)

    Reactive oxygen species can cause extensive DNA modifications including modified bases. Some of the DNA base damage has been found to possess premutagenic properties. Therefore, if not repaired, it can contribute to carcinogenesis. We have found elevated amounts of modified bases in cancerous and precancerous tissues as compared with normal tissues. Most of the agents used in anticancer therapy are paradoxically responsible for induction of secondary malignancies and some of them may generate free radicals. The results of our experiments provide evidence that exposure of cancer patients to therapeutic doses of ionizing radiation and anticancer drugs cause base modifications in genomic DNA of lymphocytes. Some of these base damages could lead to mutagenesis in critical genes and ultimately to secondary cancers such as leukemias. This may point to an important role of oxidative base damage in cancer initiation. Alternatively, the increased level of the modified base products may contribute to genetic instability and metastatic potential of tumor cells. (author)

  16. JPEG color barcode images analysis: A camera phone capture channel model with auto-focus

    Directory of Open Access Journals (Sweden)

    Keng T. Tan

    2009-12-01

    Full Text Available As camera phones have permeated into our everyday lives, two dimensional (2D barcode has attracted researchers and developers as a cost-effective ubiquitous computing tool. A variety of 2D barcodes and their applications have been developed. Often, only monochrome2D barcodes are used due to their robustness in an uncontrolled operating environment of camera phones. However, we are seeing an emerging use of color 2D barcodes for camera phones. Nonetheless, using a greater multitude of colors introduces errors that can negatively affect the robustness of barcode reading. This is especially true when developing a 2D barcode for camera phones which capture and store these barcode images in the baselineJPEG format. This paper presents one aspect of the errors introduced by such camera phones by modeling the camera phone capture channel for JPEG color barcode images wherein there is camera auto-focus.

  17. Modelling of Camera Phone Capture Channel for JPEG Colour Barcode Images

    Science.gov (United States)

    Tan, Keng T.; Ong, Siong Khai; Chai, Douglas

    As camera phones have permeated into our everyday lives, two dimensional (2D) barcode has attracted researchers and developers as a cost-effective ubiquitous computing tool. A variety of 2D barcodes and their applications have been developed. Often, only monochrome 2D barcodes are used due to their robustness in an uncontrolled operating environment of camera phones. However, we are seeing an emerging use of colour 2D barcodes for camera phones. Nonetheless, using a greater multitude of colours introduces errors that can negatively affect the robustness of barcode reading. This is especially true when developing a 2D barcode for camera phones which capture and store these barcode images in the baseline JPEG format. This paper present one aspect of the errors introduced by such camera phones by modelling the camera phone capture channel for JPEG colour barcode images.

  18. Ab initio Study of Naptho-Homologated DNA Bases

    Energy Technology Data Exchange (ETDEWEB)

    Sumpter, Bobby G [ORNL; Vazquez-Mayagoitia, Alvaro [ORNL; Huertas, Oscar [Universitat de Barcelona; Fuentes-Cabrera, Miguel A [ORNL; Orozco, Modesto [Institut de Recerca Biomedica, Parc Cientific de Barcelona, Barcelona, Spain; Luque, Javier [Universitat de Barcelona

    2008-01-01

    Naptho-homologated DNA bases have been recently used to build a new type of size expanded DNA known as yyDNA. We have used theoretical techniques to investigate the structure, tautomeric preferences, base-pairing ability, stacking interactions, and HOMO-LUMO gaps of the naptho-bases. The structure of these bases is found to be similar to that of the benzo-fused predecessors (y-bases) with respect to the planarity of the aromatic rings and amino groups. Tautomeric studies reveal that the canonical-like form of naptho-thymine (yyT) and naptho-adenine (yyA) are the most stable tautomers, leading to hydrogen-bonded dimers with the corresponding natural nucleobases that mimic the Watson-Crick pairing. However, the canonical-like species of naptho-guanine (yyG) and naptho-cytosine (yyC) are not the most stable tautomers, and the most favorable hydrogen-bonded dimers involve wobble-like pairings. The expanded size of the naphto-bases leads to stacking interactions notably larger than those found for the natural bases, and they should presumably play a dominant contribution in modulating the structure of yyDNA duplexes. Finally, the HOMO-LUMO gap of the naptho-bases is smaller than that of their benzo-base counterparts, indicating that size-expansion of DNA bases is an efficient way of reducing their HOMO-LUMO gap. These results are examined in light of the available experimental evidence reported for yyT and yyC.

  19. First results of the search of neutrinoless double beta decay with the NEMO 3 detector

    CERN Document Server

    Arnold, R; Baker, J; Barabash, A; Broudin, G; Brudanin, V; Caffrey, A J; Caurier, E; Egorov, V; Errahmane, K; Etienvre, A I; Guyonnet, J L; Hubert, F; Hubert, P; Jollet, C; Jullian, S; Kochetov, O; Kovalenko, V; Konovalov, S; Lalanne, D; Leccia, F; Longuemare, C; Lutter, G; Marquet, C; Mauger, F; Nowacki, F; Ohsumi, H; Piquemal, F; Reyss, J L; Saakyan, R; Sarazin, X; Simard, L; Simkovic, F; Shitov, Y; Smolnikov, A A; Stekl, I; Suhonen, J; Sutton, C S; Szklarz, G; Thomas, J; Timkin, V; Tretyak, V; Umatov, V; Vàla, L; Vanyushin, I A; Vasilyev, V; Vorobel, V; Vylov, T D

    2005-01-01

    The NEMO 3 detector, which has been operating in the Frejus underground laboratory since February 2003, is devoted to the search for neutrinoless double beta decay (bb0nu). Half-lives of the two neutrino double beta decays (bb2nu) have been measured for 100Mo and 82Se. After 389 effective days of data collection from February 2003 until September 2004 (Phase I), no evidence for neutrinoless double beta decay was found from ~7kg of 100Mo and ~1 kg of 82Se. The corresponding lower limits for the half-lives are 4.6 x 10^23 years for 100Mo and 1.0 x10^23 years for 82Se (90% C.L.). Depending on the nuclear matrix elements calculation, limits for the effective Majorana neutrino mass are < 1.7-4.9 eV for 82Se

  20. Feasibility studies for a Mediterranean Neutrino Observatory - The NEMO.RD Project

    Energy Technology Data Exchange (ETDEWEB)

    De Marzo, C.; Ambriola, M.; Bellotti, R.; Cafagna, F.; Calicchio, M.; Ciacio, F.; Circella, M.; Montaruli, T.; Falchieri, D.; Gabrielli, A.; Gandolfi, E.; Masetti, M.; Vitullo, C.; Zanarini, G.; Habel, R.; Usai, I.; Aiello, S.; Burrafato, G.; Caponetto, L.; Costanzo, E.; LoPresti, D.; Pappalardo, L.; Petta, C.; Randazzo, N.; Russo, G. V.; Troia, O.; Barna, R.; D' Amico, V.; De Domenico, E.; De Pasquale, D.; Giacobbe, S.; Italiano, A.; Migliardo, F.; Salvato, G.; Trafiro, A.; Trimarchi, M.; Ameli, F.; Bonori, M.; Bottai, S.; Capone, A.; Desiati, P.; Massa, F.; Masullo, R.; Salusti, E.; Vicini, M.; Coniglione, R.; Migneco, E.; Piattelli, P.; Riccobene, R.; Sapienza, P.; Cordelli, M.; Trasatti, L.; Valente, V.; De Marchis, G.; Piccari, L.; Accerboni, E.; Mosetti, R.; Astraldi, M.; Gasparini, G. P.; Ulzega, A.; Orru, P

    2000-06-01

    The NEMO.RD Project is a feasibility study of a km{sup 3} underwater telescope for high energy astrophysical neutrinos to be located in the Mediterranean Sea. At present this study concerns: i) Monte Carlo simulation study of the capabilities of various arrays of phototubes in order to determine the detector geometry that can optimize performance and cost; ii) design of low power consumption electronic cards for data acquisition and transmission to shore; iii) feasibility study of mechanics, deployment, connection and maintenance of such a detector in collaboration with petrol industries having experience of undersea operations; iv) oceanographic exploration of various sites in search for the optimal one. A brief report on the status of points i) and iv) is presented here.

  1. Feasibility studies for a Mediterranean Neutrino Observatory - The NEMO.RD Project

    International Nuclear Information System (INIS)

    The NEMO.RD Project is a feasibility study of a km3 underwater telescope for high energy astrophysical neutrinos to be located in the Mediterranean Sea. At present this study concerns: i) Monte Carlo simulation study of the capabilities of various arrays of phototubes in order to determine the detector geometry that can optimize performance and cost; ii) design of low power consumption electronic cards for data acquisition and transmission to shore; iii) feasibility study of mechanics, deployment, connection and maintenance of such a detector in collaboration with petrol industries having experience of undersea operations; iv) oceanographic exploration of various sites in search for the optimal one. A brief report on the status of points i) and iv) is presented here

  2. Design and assembly of the optical modules for phase-2 of the NEMO project

    International Nuclear Information System (INIS)

    The NEMO collaboration team has undertaken a Phase-2 project, which aims at the realization and installation of a new infrastructure at the Capo Passero (Italy) deep-sea site at a depth of 3500 m. With this objective in mind, a fully equipped tower with 8-storey hosting two optical modules at each end is under construction. Following a well established procedure, 32 optical modules have been assembled. The optical module consists of a large area photomultiplier tube enclosed in a pressure resistant glass sphere with a diameter of 13 in. The photomultiplier is a R7081 type, produced by Hamamatsu, with a photocathode area with a diameter of 10 in. and 10 dynodes. Mechanical and optical contacts between the front of the photomultiplier tube and the glass surface are ensured by an optical bi-component silicone gel. A mu-metal cage is used to shield the photomultiplier against the influence of the Earth's magnetic field

  3. Measurement of the atmospheric muon depth intensity relation with the NEMO Phase-2 tower

    Science.gov (United States)

    Aiello, S.; Ameli, F.; Anghinolfi, M.; Barbarino, G.; Barbarito, E.; Barbato, F.; Beverini, N.; Biagi, S.; Bouhadef, B.; Bozza, C.; Cacopardo, G.; Calamai, M.; Calí, C.; Capone, A.; Caruso, F.; Ceres, A.; Chiarusi, T.; Circella, M.; Cocimano, R.; Coniglione, R.; Costa, M.; Cuttone, G.; D'Amato, C.; D'Amico, A.; De Bonis, G.; De Luca, V.; Deniskina, N.; De Rosa, G.; Di Capua, F.; Distefano, C.; Fermani, P.; Flaminio, V.; Fusco, L. A.; Garufi, F.; Giordano, V.; Gmerk, A.; Grasso, R.; Grella, G.; Hugon, C.; Imbesi, M.; Kulikovskiy, V.; Larosa, G.; Lattuada, D.; Leismueller, K. P.; Leonora, E.; Litrico, P.; Lonardo, A.; Longhitano, F.; Lo Presti, D.; Maccioni, E.; Margiotta, A.; Martini, A.; Masullo, R.; Migliozzi, P.; Migneco, E.; Miraglia, A.; Mollo, C. M.; Mongelli, M.; Morganti, M.; Musico, P.; Musumeci, M.; Nicolau, C. A.; Orlando, A.; Papaleo, R.; Pellegrino, C.; Pellegriti, M. G.; Perrina, C.; Piattelli, P.; Pugliatti, C.; Pulvirenti, S.; Orselli, A.; Raffaelli, F.; Randazzo, N.; Riccobene, G.; Rovelli, A.; Sanguineti, M.; Sapienza, P.; Sciacca, V.; Sgura, I.; Simeone, F.; Sipala, V.; Speziale, F.; Spina, M.; Spitaleri, A.; Spurio, M.; Stellacci, S. M.; Taiuti, M.; Terreni, G.; Trasatti, L.; Trovato, A.; Ventura, C.; Vicini, P.; Viola, S.; Vivolo, D.

    2015-06-01

    The results of the analysis of the data collected with the NEMO Phase-2 tower, deployed at 3500 m depth about 80 km off-shore Capo Passero (Italy), are presented. Čerenkov photons detected with the photomultipliers tubes were used to reconstruct the tracks of atmospheric muons. Their zenith-angle distribution was measured and the results compared with Monte Carlo simulations. An evaluation of the systematic effects due to uncertainties on environmental and detector parameters is also included. The associated depth intensity relation was evaluated and compared with previous measurements and theoretical predictions. With the present analysis, the muon depth intensity relation has been measured up to 13 km of water equivalent.

  4. Development realization and test of an electronic data acquisition board for the NEMO experiment

    Energy Technology Data Exchange (ETDEWEB)

    Caponetto, L. [Istituto Nazionale di Fisica Nucleare, Sezione di Catania (Italy); Gabrielli, A.; Gandolfi, E. [Dipartimento di Fisica, Universita degli studi di Bologna, Bologna (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Bologna (Italy); Giorgi, F.M. [Dipartimento di Fisica, Universita degli studi di Bologna, Bologna (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Bologna (Italy)], E-mail: giorgi@bo.infn.it; Lo Presti, D. [Dipartimento di Fisica, Universita degli studi di Catania, Catania (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Catania (Italy); Randazzo, N. [Istituto Nazionale di Fisica Nucleare, Sezione di Catania (Italy)

    2008-10-21

    The development, realization and test of an electronic data acquisition-board for the NEutrino Mediterranean Observatory (NEMO) collaboration are described. The collaboration is involved in R and D of a deep underwater km{sup 3} scale Cherenkov neutrino telescope in the southern Ionian Sea. Thousands of Optical Modules (OM), spread over the entire volume and supported by a three-dimensional structure, constitute the sensitive part of the detector. Each OM is equipped by a Photo-Multiplier Tube (PMT) and an electronic circuit for data acquisition and transmission (DAQ board). This work tries to point out the possible benefits of a hybrid solution based on an analog Application Specific Integrated Circuit (ASIC) employed for the analog acquisition, and a Field Programmable Gate Array (FPGA), a digital programmable Integrated Circuit (IC) which manages the acquisition and the data transmission.

  5. Development realization and test of an electronic data acquisition board for the NEMO experiment

    International Nuclear Information System (INIS)

    The development, realization and test of an electronic data acquisition-board for the NEutrino Mediterranean Observatory (NEMO) collaboration are described. The collaboration is involved in R and D of a deep underwater km3 scale Cherenkov neutrino telescope in the southern Ionian Sea. Thousands of Optical Modules (OM), spread over the entire volume and supported by a three-dimensional structure, constitute the sensitive part of the detector. Each OM is equipped by a Photo-Multiplier Tube (PMT) and an electronic circuit for data acquisition and transmission (DAQ board). This work tries to point out the possible benefits of a hybrid solution based on an analog Application Specific Integrated Circuit (ASIC) employed for the analog acquisition, and a Field Programmable Gate Array (FPGA), a digital programmable Integrated Circuit (IC) which manages the acquisition and the data transmission.

  6. A VLSI ASIC front end for the optical module of the NEMO underwater neutrino detector

    International Nuclear Information System (INIS)

    The work described here has been developed in the context of the NEMO Collaboration with the aim of studying and designing a front-end electronics for the Optical Modules, which contains the telescope optical sensors, as a full-custom Very Large Scale Integration (VLSI) Application Specific Integrated Circuit (ASIC). The solution has a multitude of advantages. The most important are low power consumption and the pre-analysis and suitable reduction of data to be transferred to the shore station for acquisition. A detailed description of the chosen architecture and the design principles of the blocks, that carry out the specialized function required by this architecture, will be given. The chips produced will be described and the test measurements performed will be shown

  7. Proposal, development and test of an analog front-end electronic board for Nemo telescope

    CERN Document Server

    Caponetto, L; Gandolfi, E; Giorgi, F M; Lo Presti, D; Randazzo, N

    2007-01-01

    The NEMO collaboration is involved in the R&D of the main technologies for the project of a km3 scale underwater neutrino telescope. The proposed detector is made up of thousands of Optical Modules (hereafter OM), spread over the entire volume for Cˇ erenkov light detection. Each OMis equipped with a photo multiplier tube (PMT) and an electronic circuit for data acquisition and transmission (DAQ-Board). This work points out the possible benefits of a hybrid solution based on an analog ASIC (Application Specific Integrated Circuit) employed for the analog signal acquisition and an FPGA (Field Programmable Gate Array), a digital programmable IC (Integrated Circuit) which performs the data acquisition and the data transmission.

  8. Nemo-like kinase is a novel regulator of spinal and bulbar muscular atrophy.

    Science.gov (United States)

    Todd, Tiffany W; Kokubu, Hiroshi; Miranda, Helen C; Cortes, Constanza J; La Spada, Albert R; Lim, Janghoo

    2015-01-01

    Spinal and bulbar muscular atrophy (SBMA) is a progressive neuromuscular disease caused by polyglutamine expansion in the androgen receptor (AR) protein. Despite extensive research, the exact pathogenic mechanisms underlying SBMA remain elusive. In this study, we present evidence that Nemo-like kinase (NLK) promotes disease pathogenesis across multiple SBMA model systems. Most remarkably, loss of one copy of Nlk rescues SBMA phenotypes in mice, including extending lifespan. We also investigated the molecular mechanisms by which NLK exerts its effects in SBMA. Specifically, we have found that NLK can phosphorylate the mutant polyglutamine-expanded AR, enhance its aggregation, and promote AR-dependent gene transcription by regulating AR-cofactor interactions. Furthermore, NLK modulates the toxicity of a mutant AR fragment via a mechanism that is independent of AR-mediated gene transcription. Our findings uncover a crucial role for NLK in controlling SBMA toxicity and reveal a novel avenue for therapy development in SBMA. PMID:26308581

  9. Hypohidrotic ectodermal dysplasia and immunodeficiency with coincident NEMO and EDA mutations.

    Science.gov (United States)

    Keller, Michael D; Petersen, Maureen; Ong, Peck; Church, Joseph; Risma, Kimberly; Burham, Jon; Jain, Ashish; Stiehm, E Richard; Hanson, Eric P; Uzel, Gulbu; Deardorff, Matthew A; Orange, Jordan S

    2011-01-01

    Ectodermal dysplasias (ED) are uncommon genetic disorders resulting in abnormalities in ectodermally derived structures. Many ED-associated genes have been described, of which ectodysplasin-A (EDA) is one of the more common. The NF-κB essential modulator (NEMO encoded by the IKBKG gene) is unique in that mutations result in severe humoral and cellular immunologic defects in addition to ED. We describe three unrelated kindreds with defects in both EDA and IKBKG resulting from X-chromosome crossover. This demonstrates the importance of thorough immunologic consideration of patients with ED even when an EDA etiology is confirmed, and raises the possibility of a specific phenotype arising from coincident mutations in EDA and IKBKG. PMID:22566850

  10. ycf1, the most promising plastid DNA barcode of land plants

    OpenAIRE

    Wenpan Dong; Chao Xu; Changhao Li; Jiahui Sun; Yunjuan Zuo; Shuo Shi; Tao Cheng; Junjie Guo; Shiliang Zhou

    2015-01-01

    A DNA barcode is a DNA fragment used to identify species. For land plants, DNA fragments of plastid genome could be the primary consideration. Unfortunately, most of the plastid candidate barcodes lack species-level resolution. The identification of DNA barcodes of high resolution at species level is critical to the success of DNA barcoding in plants. We searched the available plastid genomes for the most variable regions and tested the best candidates using both a large number of tree specie...

  11. SBVLC:Secure Barcode-based Visible Light Communication for Smartphones

    OpenAIRE

    Zhang, Bingsheng; Ren, Kui; Xing, Guoliang; Fu, Xinwen; Wang, Cong

    2016-01-01

    2D barcodes have enjoyed a significant penetration rate in mobile applications. This is largely due to the extremely low barrier to adoption – almost every camera-enabled smartphone can scan 2D barcodes. As an alternative to NFC technology, 2D barcodes have been increasingly used for security-sensitive mobile applications including mobile payments and personal identification. However, the security of barcode-based communication in mobile applications has not been systematically studied. Due t...

  12. Patterns of DNA Barcode Variation in Canadian Marine Molluscs

    Science.gov (United States)

    Layton, Kara K.S.; Martel, André L.; Hebert, Paul DN.

    2014-01-01

    Background Molluscs are the most diverse marine phylum and this high diversity has resulted in considerable taxonomic problems. Because the number of species in Canadian oceans remains uncertain, there is a need to incorporate molecular methods into species identifications. A 648 base pair segment of the cytochrome c oxidase subunit I gene has proven useful for the identification and discovery of species in many animal lineages. While the utility of DNA barcoding in molluscs has been demonstrated in other studies, this is the first effort to construct a DNA barcode registry for marine molluscs across such a large geographic area. Methodology/Principal Findings This study examines patterns of DNA barcode variation in 227 species of Canadian marine molluscs. Intraspecific sequence divergences ranged from 0–26.4% and a barcode gap existed for most taxa. Eleven cases of relatively deep (>2%) intraspecific divergence were detected, suggesting the possible presence of overlooked species. Structural variation was detected in COI with indels found in 37 species, mostly bivalves. Some indels were present in divergent lineages, primarily in the region of the first external loop, suggesting certain areas are hotspots for change. Lastly, mean GC content varied substantially among orders (24.5%–46.5%), and showed a significant positive correlation with nearest neighbour distances. Conclusions/Significance DNA barcoding is an effective tool for the identification of Canadian marine molluscs and for revealing possible cases of overlooked species. Some species with deep intraspecific divergence showed a biogeographic partition between lineages on the Atlantic, Arctic and Pacific coasts, suggesting the role of Pleistocene glaciations in the subdivision of their populations. Indels were prevalent in the barcode region of the COI gene in bivalves and gastropods. This study highlights the efficacy of DNA barcoding for providing insights into sequence variation across a broad

  13. International Barcode of Life: Evolution of a global research community.

    Science.gov (United States)

    Adamowicz, Sarah J

    2015-05-01

    The 6th International Barcode of Life Conference (Guelph, Canada, 18-21 August 2015), themed Barcodes to Biomes, showcases the latest developments in DNA barcoding research and its diverse applications. The meeting also provides a venue for a global research community to share ideas and to initiate collaborations. All plenary and contributed abstracts are being published as an open-access special issue of Genome. Here, I use a comparison with the 3rd Conference (Mexico City, 2009) to highlight 10 recent and emerging trends that are apparent among the contributed abstracts. One of the outstanding trends is the rising proportion of abstracts that focus upon multiple socio-economically important applications of DNA barcoding, including studies of agricultural pests, quarantine and invasive species, wildlife forensics, disease vectors, biomonitoring of ecosystem health, and marketplace surveys evaluating the authenticity of seafood products and medicinal plants. Other key movements include the use of barcoding and metabarcoding approaches for dietary analyses-and for studies of food webs spanning three or more trophic levels-as well as the spread of next-generation sequencing methods in multiple contexts. In combination with the rising taxonomic and geographic scope of many barcoding iniatives, these developments suggest that several important questions in biology are becoming tractable. "What is this specimen on an agricultural shipment?", "Who eats whom in this whole food web?", and even "How many species are there?" are questions that may be answered in time periods ranging from a few years to one or a few decades. The next phases of DNA barcoding may expand yet further into prediction of community shifts with climate change and improved management of biological resources. PMID:26444714

  14. NEMO on the shelf: assessment of the Iberia–Biscay–Ireland configuration

    Directory of Open Access Journals (Sweden)

    C. Maraldi

    2013-08-01

    Full Text Available This work describes the design and validation of a high-resolution (1/36° ocean forecasting model over the "Iberian–Biscay–Irish" (IBI area. The system has been set-up using the NEMO model (Nucleus for European Modelling of the Ocean. New developments have been incorporated in NEMO to make it suitable to open- as well as coastal-ocean modelling. In this paper, we pursue three main objectives: (1 to give an overview of the model configuration used for the simulations; (2 to give a broad-brush account of one particular aspect of this work, namely consistency verification; this type of validation is conducted upstream of the implementation of the system before it is used for production and routinely validated; it is meant to guide model development in identifying gross deficiencies in the modelling of several key physical processes; and (3 to show that such a regional modelling system has potential as a complement to patchy observations (an integrated approach to give information on non-observed physical quantities and to provide links between observations by identifying broader-scale patterns and processes. We concentrate on the year 2008. We first provide domain-wide consistency verification results in terms of barotropic tides, transports, sea surface temperature and stratification. We then focus on two dynamical subregions: the Celtic shelves and the Bay of Biscay slope and deep regions. The model–data consistency is checked for variables and processes such as tidal currents, tidal fronts, internal tides and residual elevation. We also examine the representation in the model of a seasonal pattern of the Bay of Biscay circulation: the warm extension of the Iberian Poleward Current along the northern Spanish coast (Navidad event in the winter of 2007–2008.

  15. NEMO on the shelf: assessment of the Iberia-Biscay-Ireland configuration

    Science.gov (United States)

    Maraldi, C.; Chanut, J.; Levier, B.; Ayoub, N.; De Mey, P.; Reffray, G.; Lyard, F.; Cailleau, S.; Drévillon, M.; Fanjul, E. A.; Sotillo, M. G.; Marsaleix, P.; Mercator Research, the; Development Team

    2013-08-01

    This work describes the design and validation of a high-resolution (1/36°) ocean forecasting model over the "Iberian-Biscay-Irish" (IBI) area. The system has been set-up using the NEMO model (Nucleus for European Modelling of the Ocean). New developments have been incorporated in NEMO to make it suitable to open- as well as coastal-ocean modelling. In this paper, we pursue three main objectives: (1) to give an overview of the model configuration used for the simulations; (2) to give a broad-brush account of one particular aspect of this work, namely consistency verification; this type of validation is conducted upstream of the implementation of the system before it is used for production and routinely validated; it is meant to guide model development in identifying gross deficiencies in the modelling of several key physical processes; and (3) to show that such a regional modelling system has potential as a complement to patchy observations (an integrated approach) to give information on non-observed physical quantities and to provide links between observations by identifying broader-scale patterns and processes. We concentrate on the year 2008. We first provide domain-wide consistency verification results in terms of barotropic tides, transports, sea surface temperature and stratification. We then focus on two dynamical subregions: the Celtic shelves and the Bay of Biscay slope and deep regions. The model-data consistency is checked for variables and processes such as tidal currents, tidal fronts, internal tides and residual elevation. We also examine the representation in the model of a seasonal pattern of the Bay of Biscay circulation: the warm extension of the Iberian Poleward Current along the northern Spanish coast (Navidad event) in the winter of 2007-2008.

  16. NEMO on the shelf: assessment of the Iberia-Biscay-Ireland configuration

    Directory of Open Access Journals (Sweden)

    C. Maraldi

    2013-01-01

    Full Text Available The Iberia-Biscay-Ireland (IBI system serves one of the 7 MyOcean "Monitoring and Forecasting Centres". A high resolution simulation covering the IBI region is set-up over July 2007–February 2009. The NEMO (Nucleus for European Modelling of the Ocean model is used with a 1/36° horizontal resolution and 50 z-levels in the vertical. New developments have been incorporated in NEMO to make it suitable to open- as well as coastal-ocean modelling. In this paper, we pursue three main objectives: (1 give an overview of the model configuration used for the simulations; (2 give a broad-brush account of one particular aspect of this work, namely consistency verification; this type of validation is conducted upstream of the implementation of the system before it is used for production and routinely validated; it is meant to guide model development in identifying gross deficiencies in the modelling of several key physical processes; (3 show that such a regional modelling system has potential as a complement to patchy observations (an integrated approach to give information on non-observed physical quantities and to provide links between observations by identifying broader-scale patterns and processes. We concentrate on the year 2008. We first provide domain-wide consistency verification results in terms of barotropic tides, transports, sea surface temperature and stratification. We then focus on two dynamical sub-regions: the Celtic shelves and the Bay of Biscay slope and deep regions. The model-data consistency is checked for variables and processes such as tidal currents, tidal fronts, internal tides, residual elevation. We also examine the representation in the model of a seasonal pattern of the Bay of Biscay circulation: the warm extension of the Iberian Poleward Current along the northern Spanish coast (Navidad event in winter 2007–2008.

  17. Nemo-like kinase (NLK) expression in osteoblastic cells and suppression of osteoblastic differentiation

    International Nuclear Information System (INIS)

    Mitogen-activated protein kinases (MAPKs) regulate proliferation and differentiation in osteoblasts. The vertebral homologue of nemo, nemo-like kinase (NLK), is an atypical MAPK that targets several signaling components, including the T-cell factor/lymphoid enhancer factor (TCF/Lef1) transcription factor. Recent studies have shown that NLK forms a complex with the histone H3-K9 methyltransferase SETDB1 and suppresses peroxisome proliferator-activated receptor (PPAR)-gamma:: action in the mesenchymal cell line ST2. Here we investigated whether NLK regulates osteoblastic differentiation. We showed that NLK mRNA is expressed in vivo in osteoblasts at embryonic day 18.5 (E18.5) mouse calvariae. By using retrovirus vectors, we performed forced expression of NLK in primary calvarial osteoblasts (pOB cells) and the mesenchymal cell line ST2. Wild-type NLK (NLK-WT) suppressed alkaline phosphatase activity and expression of bone marker genes such as alkaline phosphatase, type I procollagen, runx2, osterix, steopontin and osteocalcin in these cells. NLK-WT also decreased type I collagen protein expression in pOB and ST2 cells. Furthermore, mineralized nodule formation was reduced in pOB cells overexpressing NLK-WT. In contrast, kinase-negative form of NLK (NLK-KN) did not suppress or partially suppress ALP activity and bone marker gene expression in pOB and ST2 cells. NLK-KN did not suppress nodule formation in pOB cells. In addition to forced expression, suppression of endogenous NLK expression by siRNA increased bone marker gene expression in pOB and ST2 cells. Finally, transcriptional activity analysis of gene promoters revealed that NLK-WT suppressed Wnt1 activation of TOP flash promoter and Runx2 activation of the osteocalcin promoter. Taken together, these results suggest that NLK negatively regulates osteoblastic differentiation.

  18. Nemo-like kinase (NLK) expression in osteoblastic cells and suppression of osteoblastic differentiation

    Energy Technology Data Exchange (ETDEWEB)

    Nifuji, Akira, E-mail: nifuji-a@tsurumi-u.ac.jp [Transcriptome profiling group, National Institute of Radiological Sciences, Chiba (Japan); Department of Pharmacology, Tsurumi University School of Dental Medicine, Yokohama (Japan); Ideno, Hisashi [Transcriptome profiling group, National Institute of Radiological Sciences, Chiba (Japan); Ohyama, Yoshio [Department of Molecular Pharmacology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo (Japan); Takanabe, Rieko; Araki, Ryoko; Abe, Masumi [Transcriptome profiling group, National Institute of Radiological Sciences, Chiba (Japan); Noda, Masaki [Department of Molecular Pharmacology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo (Japan); Shibuya, Hiroshi [Department of Molecular Cell Biology, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, Tokyo (Japan)

    2010-04-15

    Mitogen-activated protein kinases (MAPKs) regulate proliferation and differentiation in osteoblasts. The vertebral homologue of nemo, nemo-like kinase (NLK), is an atypical MAPK that targets several signaling components, including the T-cell factor/lymphoid enhancer factor (TCF/Lef1) transcription factor. Recent studies have shown that NLK forms a complex with the histone H3-K9 methyltransferase SETDB1 and suppresses peroxisome proliferator-activated receptor (PPAR)-gamma:: action in the mesenchymal cell line ST2. Here we investigated whether NLK regulates osteoblastic differentiation. We showed that NLK mRNA is expressed in vivo in osteoblasts at embryonic day 18.5 (E18.5) mouse calvariae. By using retrovirus vectors, we performed forced expression of NLK in primary calvarial osteoblasts (pOB cells) and the mesenchymal cell line ST2. Wild-type NLK (NLK-WT) suppressed alkaline phosphatase activity and expression of bone marker genes such as alkaline phosphatase, type I procollagen, runx2, osterix, steopontin and osteocalcin in these cells. NLK-WT also decreased type I collagen protein expression in pOB and ST2 cells. Furthermore, mineralized nodule formation was reduced in pOB cells overexpressing NLK-WT. In contrast, kinase-negative form of NLK (NLK-KN) did not suppress or partially suppress ALP activity and bone marker gene expression in pOB and ST2 cells. NLK-KN did not suppress nodule formation in pOB cells. In addition to forced expression, suppression of endogenous NLK expression by siRNA increased bone marker gene expression in pOB and ST2 cells. Finally, transcriptional activity analysis of gene promoters revealed that NLK-WT suppressed Wnt1 activation of TOP flash promoter and Runx2 activation of the osteocalcin promoter. Taken together, these results suggest that NLK negatively regulates osteoblastic differentiation.

  19. Radon emanation based material measurement and selection for the SuperNEMO double beta experiment

    International Nuclear Information System (INIS)

    The SuperNEMO Demonstrator experiment aims to study the neutrinoless double beta decay of 7 kg of 82Se in order to reach a limit on the light Majorana neutrino mass mechanism T1/2 (ββ0ν) > 6.5 1024 years (90%CL) equivalent to a mass sensitivity mββ < 0.20 - 0.40 eV (90%CL) in two years of data taking. The detector construction started in 2014 and its installation in the Laboratoire Souterrain de Modane (LSM) is expected during the course of 2015. The remaining level of 226Ra (238U chain) in the detector components can lead to the emanation of 222Rn gas. This isotope should be controlled and reduced down to the level of a 150 µBq/m3 in the tracker chamber of the detector to achieve the physics goals. Besides the HPGe selection of the detector materials for their radiopurity, the most critical materials have been tested and selected in a dedicated setup facility able to measure their 222Rn emanation level. The operating principle relies on a large emanation tank (0.7m3) that allows measuring large material surfaces or large number of construction pieces. The emanation tank is coupled to an electrostatic detector equipped with a silicon diode to perform the alpha spectroscopy of the gas it contains and extract the 222Rn daughters. The transfer efficiency and the detector efficiency have been carefully calibrated through different methods. The intrinsic background of the system allows one to measure 222Rn activities down to 3 mBq, leading to a typical emanation sensitivity of 20 µBq/m2/day for a 30 m2 surface sample. Several construction materials have been measured and selected, such as nylon and aluminized Mylar films, photomultipliers and tracking of the SuperNEMO Demonstrator

  20. Q-Bank Phytoplasma: A DNA Barcoding Tool for Phytoplasma Identification

    DEFF Research Database (Denmark)

    Contaldo, Nicoletta; Paltrinieri, Samanta; Makarova, Olga;

    2015-01-01

    DNA barcoding is an identification method based on comparison of a short DNA sequence with known sequences from a database. A DNA barcoding tool has been developed for phytoplasma identification. This phytoplasma DNA barcoding protocol based on the tuf gene has been shown to identify phytoplasmas...

  1. Efficient replication bypass of size-expanded DNA base pairs in bacterial cells

    OpenAIRE

    Delaney, James C.; GAO, JIANMIN; Liu, Haibo; Shrivastav, Nidhi; Essigmann, John M.; Kool, Eric T.

    2009-01-01

    Supersize me! Size-expanded DNA bases (xDNA) are able to encode natural DNA sequences in replication. In vitro experiments with a DNA polymerase show nucleotide incorporation opposite the xDNA bases with correct pairing. In vivo experiments using E. coli show that two xDNA bases (xA and xC, see picture) encode the correct replication partners.

  2. Efficiency of ITS Sequences for DNA Barcoding in Passiflora (Passifloraceae)

    Science.gov (United States)

    Giudicelli, Giovanna Câmara; Mäder, Geraldo; de Freitas, Loreta Brandão

    2015-01-01

    DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using “best match” and “best close match” methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1) region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species. PMID:25837628

  3. Increasing global participation in genetics research through DNA barcoding.

    Science.gov (United States)

    Adamowicz, Sarah J; Steinke, Dirk

    2015-12-01

    DNA barcoding--the sequencing of short, standardized DNA regions for specimen identification and species discovery--has promised to facilitate rapid access to biodiversity knowledge by diverse users. Here, we advance our opinion that increased global participation in genetics research is beneficial, both to scientists and for science, and explore the premise that DNA barcoding can help to democratize participation in genetics research. We examine publication patterns (2003-2014) in the DNA barcoding literature and compare trends with those in the broader, related domain of genomics. While genomics is the older and much larger field, the number of nations contributing to the published literature is similar between disciplines. Meanwhile, DNA barcoding exhibits a higher pace of growth in the number of publications as well as greater evenness among nations in their proportional contribution to total authorships. This exploration revealed DNA barcoding to be a highly international discipline, with growing participation by researchers in especially biodiverse nations. We briefly consider several of the challenges that may hinder further participation in genetics research, including access to training and molecular facilities as well as policy relating to the movement of genetic resources. PMID:26642251

  4. A comparative analysis of DNA barcode microarray feature size

    Directory of Open Access Journals (Sweden)

    Smith Andrew M

    2009-10-01

    Full Text Available Abstract Background Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density, but this increase in resolution can compromise sensitivity. Results We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarray platform. The barcodes used in this study are the well-characterized set derived from the Yeast KnockOut (YKO collection used for screens of pooled yeast (Saccharomyces cerevisiae deletion mutants. We treated these pools with the glycosylation inhibitor tunicamycin as a test compound. Three generations of barcode microarrays at 30, 8 and 5 μm features sizes independently identified the primary target of tunicamycin to be ALG7. Conclusion We show that the data obtained with 5 μm feature size is of comparable quality to the 30 μm size and propose that further shrinking of features could yield barcode microarrays with equal or greater resolving power and, more importantly, higher density.

  5. Assessment of candidate plant DNA barcodes using the Rutaceae family

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention.Here,seven regions (psbA-trnH,matK,ycf5,rpoC1,rbcL,ITS2,and ITS) with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the family Rutaceae.To evaluate each barcode’s utility for species authentication,PCR amplification efficiency,genetic divergence,and barcoding gaps were assessed.We found that the ITS2 region exhibited the highest inter-specific divergence,and that this was significantly higher than the intra-specific variation in the "DNA barcoding gap" assessment and Wilcoxon two-sample tests.The ITS2 locus had the highest identification efficiency among all tested regions.In a previous study,we found that ITS2 was able to discriminate a wide range of plant taxa,and here we confirmed that ITS2 was also able to discriminate a number of closely related species.Therefore,we propose that ITS2 is a promising candidate barcode for plant species identification.

  6. Automation and workflow considerations for embedding Digimarc Barcodes at scale

    Science.gov (United States)

    Rodriguez, Tony; Haaga, Don; Calhoon, Sean

    2015-03-01

    The Digimarc® Barcode is a digital watermark applied to packages and variable data labels that carries GS1 standard GTIN-14 data traditionally carried by a 1-D barcode. The Digimarc Barcode can be read with smartphones and imaging-based barcode readers commonly used in grocery and retail environments. Using smartphones, consumers can engage with products and retailers can materially increase the speed of check-out, increasing store margins and providing a better experience for shoppers. Internal testing has shown an average of 53% increase in scanning throughput, enabling 100's of millions of dollars in cost savings [1] for retailers when deployed at scale. To get to scale, the process of embedding a digital watermark must be automated and integrated within existing workflows. Creating the tools and processes to do so represents a new challenge for the watermarking community. This paper presents a description and an analysis of the workflow implemented by Digimarc to deploy the Digimarc Barcode at scale. An overview of the tools created and lessons learned during the introduction of technology to the market are provided.

  7. Efficiency of ITS Sequences for DNA Barcoding in Passiflora (Passifloraceae

    Directory of Open Access Journals (Sweden)

    Giovanna Câmara Giudicelli

    2015-04-01

    Full Text Available DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using “best match” and “best close match” methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1 region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species.

  8. Measurement of the Thallium 208 and Bismuth 214 radiopurities of a molybdenum foil with the NEMO detector

    International Nuclear Information System (INIS)

    The NEMO 2 detector consists of a tracking volume to reconstruct electron trajectories associated with plastic scintillators. The purpose of the R and D is to aid in studies of neutrinoless double β decay. Using the first nine months of data from the NEMO 2 detector, a method of measurement of the 208Tl and 214Bi radiopurities is presented. These isotopes contribute to the background in the 3 MeV region corresponding to the Q of 2β(0ν) for molybdenum. The channel 1e1γ is used. Monte Carlo simulations with GEANT give the corresponding efficiencies. Radiopurities for a standard Molybdenum foil and for two high purity molybdenum samples have been measured. The results are in good agreement with γ-spectroscopy measurements using an HPGe crystal. 2000 hours of data yields a sensitivity of .3 events/min/kg

  9. On line monitoring of the power control and engineering parameters systems of the NEMO Phase-2 tower

    International Nuclear Information System (INIS)

    The NEMO Collaboration is presently carrying out an intense activity on 'NEMO Phase-2' project for the realization of an underwater infrastructure on the deep-sea site of Capo Passero including a fully instrumented 16 storey tower. In this paper the design of the electrical power control system and of a system for the monitoring of some engineering parameters, useful to study the dynamical behavior of the structure, are presented. The proposed architecture is strongly modular and flexible. The entire architecture is described with a special focus on the electrical parameters monitoring, protection system and on the sensors fusion algorithm implemented to deduce the attitude through Micro Electro-Mechanical Systems (MEMS) accelerometers and magnetometer sensors.

  10. Oceanographic conditions in the NEMO region during the KM3NeT project (April 2006-May 2009)

    Energy Technology Data Exchange (ETDEWEB)

    Sparnocchia, Stefania, E-mail: stefania.sparnocchia@ismar.cnr.i [CNR-Istituto di Scienze Marine, Viale R. Gessi 2, 34123 Trieste (Italy); Pietro Gasparini, Gian; Schroeder, Katrin; Borghini, Mireno [CNR-Istituto di Scienze Marine, Forte S. Teresa, 19036 Pozzuolo di Lerici (Italy)

    2011-01-21

    An intense observational activity was conducted in the NEMO region, western Ionian Sea, 40 nm south-east of Capo Passero (Sicily), in the framework of the KM3NeT project. Several oceanographic cruises were performed from 2006 to 2009 and current measurements carried out. The new data describe the present status of the deep layer and its evolution after the occurrence of a notable change that affected the Eastern Mediterranean water masses and circulation during the 1990's. In particular, they evidence the presence of a newly formed water mass in the abyssal layer of the Ionian Sea, coming likely from the Adriatic. Deep currents in the region are quite energetic, as already known, and highly variable both spatially and in strength. They are organized in a cyclonic circuit, with a prevalent north-west direction corresponding to the NEMO site.

  11. Oceanographic conditions in the NEMO region during the KM3NeT project (April 2006-May 2009)

    International Nuclear Information System (INIS)

    An intense observational activity was conducted in the NEMO region, western Ionian Sea, 40 nm south-east of Capo Passero (Sicily), in the framework of the KM3NeT project. Several oceanographic cruises were performed from 2006 to 2009 and current measurements carried out. The new data describe the present status of the deep layer and its evolution after the occurrence of a notable change that affected the Eastern Mediterranean water masses and circulation during the 1990's. In particular, they evidence the presence of a newly formed water mass in the abyssal layer of the Ionian Sea, coming likely from the Adriatic. Deep currents in the region are quite energetic, as already known, and highly variable both spatially and in strength. They are organized in a cyclonic circuit, with a prevalent north-west direction corresponding to the NEMO site.

  12. DNA Barcoding and Pharmacovigilance of Herbal Medicines.

    Science.gov (United States)

    de Boer, Hugo J; Ichim, Mihael C; Newmaster, Steven G

    2015-07-01

    Pharmacovigilance of herbal medicines relies on the product label information regarding the ingredients and the adherence to good manufacturing practices along the commercialisation chain. Several studies have shown that substitution of plant species occurs in herbal medicines, and this in turn poses a challenge to herbal pharmacovigilance as adverse reactions might be due to adulterated or added ingredients. Authentication of constituents in herbal medicines using analytical chemistry methods can help detect contaminants and toxins, but are often limited or incapable of detecting the source of the contamination. Recent developments in molecular plant identification using DNA sequence data enable accurate identification of plant species from herbal medicines using defined DNA markers. Identification of multiple constituent species from compound herbal medicines using amplicon metabarcoding enables verification of labelled ingredients and detection of substituted, adulterated and added species. DNA barcoding is proving to be a powerful method to assess species composition in herbal medicines and has the potential to be used as a standard method in herbal pharmacovigilance research of adverse reactions to specific products. PMID:26076652

  13. Study of radon and thoron by electrostatic collection and gamma spectrometry in the double beta decay NEMO experiment

    International Nuclear Information System (INIS)

    This work is part of the NEMO (Neutrino Ettore Majorana Observatory) experiment that is looking for an extremely rare radioactivity: the double beta decay without neutrino emission. Such process could prove the Majorana nature of the neutrino and could give an estimation of its absolute mass. The particularity of this experiment, currently running in the Modane underground laboratory (LSM), is the extreme weak signal (for T1/2∼1024 years, a few events per year). It requires therefore very stringent conditions on all components of the background among which the level of radon and thoron activity. After a reminding of the general properties of radon and thoron as well as their influence on the NEMO data, this thesis focuses on the detection of these radioactive gases using the technique of electrostatic collection. The radon and/or the thoron daughters are collected by an electrostatic field on the surface of a silicon diode, where their characteristic alphas are detected. We have shown that the detection efficiencies are strongly influenced by the experimental conditions and that sensitivity around 1 mBq/m3 can be achieved for the radon in a gas. A series of measures through low background gamma spectrometer allowed us to understand the origin of the radon background, and thus showing that better sensitivity could be obtained by increasing the detection volume and by carrying out a strict selection of non-radioactive materials. For the thoron gas, which had never been studied before, the detection efficiencies have been found very low as a consequence of the short periods involved. Therefore, a continuous monitoring of the level of thoron in the NEMO gas is excluded, which underlines the importance for the NEMO experimental device to be able to control its own background. (author)

  14. CAR-TO-CAR AND CAR-TO-INFRASTRUCTURE COMMUNICATION SYSTEM BASED ON NEMO AND MANET IN IPv6

    OpenAIRE

    Ernst, Thierry; De La Fortelle, Arnaud

    2006-01-01

    A communication system is required for Intelligent Transportation Systems (ITS) applications. Given that vehicles will count by hundred millions and have a life expectancy of ten years or more and also that technologies are always involving, we believe that the communication system must be based on IPv6 and its associated protocols in order to scale and meet future needs. Recent work at the IETF and particularly on NEMO (Network Mobility) and MANET (ad-hoc networking) clearly support this bel...

  15. Photocleavable DNA barcode-antibody conjugates allow sensitive and multiplexed protein analysis in single cell

    Science.gov (United States)

    Agasti, Sarit S.; Liong, Monty; Peterson, Vanessa M.; Lee, Hakho; Weissleder, Ralph

    2012-01-01

    DNA barcoding is an attractive technology as it allows sensitive and multiplexed target analysis. However, DNA barcoding of cellular proteins remains challenging, primarily because barcode amplification and readout techniques are often incompatible with the cellular microenvironment. Here, we describe the development and validation of a photocleavable DNA barcode-antibody conjugate method for rapid, quantitative and multiplexed detection of proteins in single live cells. Following target binding, this method allows DNA barcodes to be photoreleased in solution, enabling easy isolation, amplification and readout. As a proof of principle, we demonstrate sensitive and multiplexed detection of protein biomarkers in a variety of cancer cells. PMID:23092113

  16. DNA barcoding as a means for identifying medicinal plants of Pakistan

    International Nuclear Information System (INIS)

    DNA barcoding involves the generation of DNA sequencing data from particular genetic regions in an organism and the use of these sequence data to identify or 'barcode' that organism and distinguish it from other species. Here, DNA barcoding is being used to identify several medicinal plants found in Pakistan and distinguished them from other similar species. Several challenges to the successful implementation of plant DNA barcoding are presented and discussed. Despite these challenges, DNA barcoding has the potential to uniquely identify medicinal plants and provide quality control and standardization of the plant material supplied to the pharmaceutical industry. (author)

  17. A Concealed Barcode Identification System Using Terahertz Time-domain Spectroscopy

    Science.gov (United States)

    Guan, Yu; Yamamoto, Manabu; Kitazawa, Toshiyuki; Tripathi, Saroj R.; Takeya, Kei; Kawase, Kodo

    2015-03-01

    We present a concealed terahertz barcode/chipless tag to achieve remote identification through an obstructing material using terahertz radiation. We show scanned terahertz reflection spectral images of barcodes concealed by a thick obstacle. A concealed and double- side printed terahertz barcode structure is proposed, and we demonstrate that our design has better performance in definition than a single-side printed barcode using terahertz time-domain spectroscopy. This technique combines the benefits of a chipless tag to read encoded information covered by an optically opaque material with low cost and a simple fabrication process. Simulations are also described, along with an explanation of the principle of the terahertz barcode identification system.

  18. The properties of small Ag clusters bound to DNA bases

    Science.gov (United States)

    Soto-Verdugo, Víctor; Metiu, Horia; Gwinn, Elisabeth

    2010-05-01

    We study the binding of neutral silver clusters, Agn (n=1-6), to the DNA bases adenine (A), cytosine (C), guanine (G), and thymine (T) and the absorption spectra of the silver cluster-base complexes. Using density functional theory (DFT), we find that the clusters prefer to bind to the doubly bonded ring nitrogens and that binding to T is generally much weaker than to C, G, and A. Ag3 and Ag4 make the stronger bonds. Bader charge analysis indicates a mild electron transfer from the base to the clusters for all bases, except T. The donor bases (C, G, and A) bind to the sites on the cluster where the lowest unoccupied molecular orbital has a pronounced protrusion. The site where cluster binds to the base is controlled by the shape of the higher occupied states of the base. Time-dependent DFT calculations show that different base-cluster isomers may have very different absorption spectra. In particular, we find new excitations in base-cluster molecules, at energies well below those of the isolated components, and with strengths that depend strongly on the orientations of planar clusters with respect to the base planes. Our results suggest that geometric constraints on binding, imposed by designed DNA structures, may be a feasible route to engineering the selection of specific cluster-base assemblies.

  19. DNA-based nanoparticle composite materials for EMI shielding

    Science.gov (United States)

    Zang, De Yu; Grote, James

    2012-03-01

    Composite materials, such as polymer-matrix containing conductive fillers, are very attractive for shielding electromagnetic interference (EMI) due to their high shielding efficiency and seamlessness, processability, flexibility, light-weight and low-cost. Here, we report a development of novel, DNA-based EMI-shielding materials (DESM), consisting of DNA and metal nanoparticles. It has been shown that a thin DESM layer (typically ~30 - 50 μm) could block EMI radiations up to 60 dB effectively over an RF frequency range from KHz to tens GHz, exhibiting excellent EMI shielding efficiency. A wide selection of metal nanoparticle fillers for DESM has been tested for their performance in EMI shielding efficiency. Among them, silver and carbon-based nanoparticles have demonstrated the best performance and were selected for further investigation. The silver-doped DESM films could be also non-conductive while their EMI shielding efficiency is still well-preserved. The nonconductive DESM could have a great potential in the microelectronics industries for EMI shielding on electronic devices and circuit boards.

  20. Applications of nanoparticles for DNA based rabies vaccine.

    Science.gov (United States)

    Shah, Muhammad Ali A; Khan, Sajid Umar; Ali, Zeeshan; Yang, Haowen; Liu, Keke; Mao, Lanlan

    2014-01-01

    Rabies is a fatal encephalomyelitis. Most cases occur in developing countries and are transmitted by dogs. The cell culture vaccines as associated with high cost; therefore, have not replaced the unsafe brain-derived vaccines. In the developing countries these brain-derived rabies vaccines still can be seen in action. Moreover, there will be a need for vaccines against rabies-related viruses against which classical vaccines are not always effective. The worldwide incidence of rabies and the inability of currently used vaccination strategies to provide highly potent and cost-effective therapy indicate the need for alternate control strategies. DNA vaccines have emerged as the safest vaccines and best remedy for complicated diseases like hepatitis, HIV, and rabies. A number of recombinant DNA vaccines are now being developed against several diseases such as AIDS and malaria. Therefore, it can be a valuable alternative for the production of cheaper rabies vaccines against its larger spectrum of viruses. In this review we report published data on DNA-based immunization with sequences encoding rabies with special reference to nanotechnology. PMID:24730305

  1. Electron accommodation dynamics in the DNA base thymine

    International Nuclear Information System (INIS)

    The dynamics of electron attachment to the DNA base thymine are investigated using femtosecond time-resolved photoelectron imaging of the gas phase iodide-thymine (I−T) complex. An ultraviolet pump pulse ejects an electron from the iodide and prepares an iodine-thymine temporary negative ion that is photodetached with a near-IR probe pulse. The resulting photoelectrons are analyzed with velocity-map imaging. At excitation energies ranging from −120 meV to +90 meV with respect to the vertical detachment energy (VDE) of 4.05 eV for I−T, both the dipole-bound and valence-bound negative ions of thymine are observed. A slightly longer rise time for the valence-bound state than the dipole-bound state suggests that some of the dipole-bound anions convert to valence-bound species. No evidence is seen for a dipole-bound anion of thymine at higher excitation energies, in the range of 0.6 eV above the I−T VDE, which suggests that if the dipole-bound anion acts as a “doorway” to the valence-bound anion, it only does so at excitation energies near the VDE of the complex

  2. Currency verification by a 2D infrared barcode

    International Nuclear Information System (INIS)

    Nowadays all the National Central Banks are continuously studying innovative anti-counterfeiting systems for banknotes. In this note, an innovative solution is proposed, which combines the potentiality of a hylemetric approach (methodology conceptually similar to biometry), based on notes' intrinsic characteristics, with a well-known and consolidated 2D barcode identification system. In particular, in this note we propose to extract from the banknotes a univocal binary control sequence (template) and insert an encrypted version of it in a barcode printed on the same banknote. For a more acceptable look and feel of a banknote, the superposed barcode can be stamped using IR ink that is visible to near-IR image sensors. This makes the banknote verification simpler. (technical design note)

  3. S-K Smartphone Barcode Reader for the Blind

    Science.gov (United States)

    Tekin, Ender; Vásquez, David; Coughlan, James M.

    2014-01-01

    We describe a new smartphone app called BLaDE (Barcode Localization and Decoding Engine), designed to enable a blind or visually impaired user find and read product barcodes. Developed at The Smith-Kettlewell Eye Research Institute, the BLaDE Android app has been released as open source software, which can be used for free or modified for commercial or non-commercial use. Unlike popular commercial smartphone apps, BLaDE provides real-time audio feedback to help visually impaired users locate a barcode, which is a prerequisite to being able to read it. We describe experiments performed with five blind/visually impaired volunteer participants demonstrating that BLaDE is usable and that the audio feedback is key to its usability. PMID:25602592

  4. DNA条形码技术%DNA barcode technology

    Institute of Scientific and Technical Information of China (English)

    马英; 鲁亮

    2012-01-01

    DNA条形码是一种利用短的DNA序列对物种进行鉴定的技术.文中简略介绍了DNA条形码的背景知识和原理,举例说明其在物种分类、鉴定及遗传多样性等方面的广泛应用研究,并讨论了该技术在生物分类应用中可能存在的一些问题.%DNA barcode is a diagnostic technique in which short DNA sequences can be used for species identification. In this article, the background knowledge and principles of DNA barcode were reviewed simply. Also illustrated application research on classification, identification and genetic diversity in species and some existed problems of DNA barcode.

  5. Long term monitoring of the optical background in the Capo Passero deep-sea site with the NEMO tower prototype

    Science.gov (United States)

    Adrián-Martínez, S.; Aiello, S.; Ameli, F.; Anghinolfi, M.; Ardid, M.; Barbarino, G.; Barbarito, E.; Barbato, F. C. T.; Beverini, N.; Biagi, S.; Biagioni, A.; Bouhadef, B.; Bozza, C.; Cacopardo, G.; Calamai, M.; Calì, C.; Calvo, D.; Capone, A.; Caruso, F.; Ceres, A.; Chiarusi, T.; Circella, M.; Cocimano, R.; Coniglione, R.; Costa, M.; Cuttone, G.; D'Amato, C.; D'Amico, A.; De Bonis, G.; De Luca, V.; Deniskina, N.; De Rosa, G.; di Capua, F.; Distefano, C.; Enzenhöfer, A.; Fermani, P.; Ferrara, G.; Flaminio, V.; Fusco, L. A.; Garufi, F.; Giordano, V.; Gmerk, A.; Grasso, R.; Grella, G.; Hugon, C.; Imbesi, M.; Kulikovskiy, V.; Lahmann, R.; Larosa, G.; Lattuada, D.; Leismüller, K. P.; Leonora, E.; Litrico, P.; Llorens Alvarez, C. D.; Lonardo, A.; Longhitano, F.; Lo Presti, D.; Maccioni, E.; Margiotta, A.; Marinelli, A.; Martini, A.; Masullo, R.; Migliozzi, P.; Migneco, E.; Miraglia, A.; Mollo, C. M.; Mongelli, M.; Morganti, M.; Musico, P.; Musumeci, M.; Nicolau, C. A.; Orlando, A.; Orzelli, A.; Papaleo, R.; Pellegrino, C.; Pellegriti, M. G.; Perrina, C.; Piattelli, P.; Pugliatti, C.; Pulvirenti, S.; Raffaelli, F.; Randazzo, N.; Real, D.; Riccobene, G.; Rovelli, A.; Saldaña, M.; Sanguineti, M.; Sapienza, P.; Sciacca, V.; Sgura, I.; Simeone, F.; Sipala, V.; Speziale, F.; Spitaleri, A.; Spurio, M.; Stellacci, S. M.; Taiuti, M.; Terreni, G.; Trasatti, L.; Trovato, A.; Ventura, C.; Vicini, P.; Viola, S.; Vivolo, D.

    2016-02-01

    The NEMO Phase-2 tower is the first detector which was operated underwater for more than 1 year at the "record" depth of 3500 m. It was designed and built within the framework of the NEMO (NEutrino Mediterranean Observatory) project. The 380 m high tower was successfully installed in March 2013 80 km offshore Capo Passero (Italy). This is the first prototype operated on the site where the Italian node of the KM3NeT neutrino telescope will be built. The installation and operation of the NEMO Phase-2 tower has proven the functionality of the infrastructure and the operability at 3500 m depth. A more than 1 year long monitoring of the deep water characteristics of the site has been also provided. In this paper the infrastructure and the tower structure and instrumentation are described. The results of long term optical background measurements are presented. The rates show stable and low baseline values, compatible with the contribution of ^{40}K light emission, with a small percentage of light bursts due to bioluminescence. All these features confirm the stability and good optical properties of the site.

  6. Long term monitoring of the optical background in the Capo Passero deep-sea site with the NEMO tower prototype

    International Nuclear Information System (INIS)

    The NEMO Phase-2 tower is the first detector which was operated underwater for more than 1 year at the ''record'' depth of 3500 m. It was designed and built within the framework of the NEMO (NEutrino Mediterranean Observatory) project. The 380 m high tower was successfully installed in March 2013 80 km offshore Capo Passero (Italy). This is the first prototype operated on the site where the Italian node of the KM3NeT neutrino telescope will be built. The installation and operation of the NEMO Phase-2 tower has proven the functionality of the infrastructure and the operability at 3500 m depth. A more than 1 year long monitoring of the deep water characteristics of the site has been also provided. In this paper the infrastructure and the tower structure and instrumentation are described. The results of long term optical background measurements are presented. The rates show stable and low baseline values, compatible with the contribution of 40K light emission, with a small percentage of light bursts due to bioluminescence. All these features confirm the stability and good optical properties of the site. (orig.)

  7. Long term monitoring of the optical background in the Capo Passero deep-sea site with the NEMO tower prototype

    CERN Document Server

    Adrián-Martínez, S; Ameli, F; Anghinolfi, M; Ardid, M; Barbarino, G; Barbarito, E; Barbato, F C T; Beverini, N; Biagi, S; Biagioni, A; Bouhadef, B; Bozza, C; Cacopardo, G; Calamai, M; Calí, C; Calvo, D; Capone, A; Caruso, F; Ceres, A; Chiarusi, T; Circella, M; Cocimano, R; Coniglione, R; Costa, M; Cuttone, G; D'Amato, C; D'Amico, A; De Bonis, G; De Luca, V; Deniskina, N; De Rosa, G; di Capua, F; Distefano, C; Enzenhöfer, A; Fermani, P; Ferrara, G; Flaminio, V; Fusco, L A; Garufi, F; Giordano, V; Gmerk, A; Grasso, R; Grella, G; Hugon, C; Imbesi, M; Kulikovskiy, V; Lahmann, R; Larosa, G; Lattuada, D; Leismüller, K P; Leonora, E; Litrico, P; Alvarez, C D Llorens; Lonardo, A; Longhitano, F; Presti, D Lo; Maccioni, E; Margiotta, A; Marinelli, A; Martini, A; Masullo, R; Migliozzi, P; Migneco, E; Miraglia, A; Mollo, C M; Mongelli, M; Morganti, M; Musico, P; Musumeci, M; Nicolau, C A; Orlando, A; Orzelli, A; Papaleo, R; Pellegrino, C; Pellegriti, M G; Perrina, C; Piattelli, P; Pugliatti, C; Pulvirenti, S; Raffaelli, F; Randazzo, N; Real, D; Riccobene, G; Rovelli, A; Saldaña, M; Sanguineti, M; Sapienza, P; Sciacca, V; Sgura, I; Simeone, F; Sipala, V; Speziale, F; Spitaleri, A; Spurio, M; Stellacci, S M; Taiuti, M; Terreni, G; Trasatti, L; Trovato, A; Ventura, C; Vicini, P; Viola, S; Vivolo, D

    2015-01-01

    The NEMO Phase-2 tower is the first detector which was operated underwater for more than one year at the "record" depth of 3500 m. It was designed and built within the framework of the NEMO (NEutrino Mediterranean Observatory) project. The 380 m high tower was successfully installed in March 2013 80 km offshore Capo Passero (Italy). This is the first prototype operated on the site where the italian node of the KM3NeT neutrino telescope will be built. The installation and operation of the NEMO Phase-2 tower has proven the functionality of the infrastructure and the operability at 3500 m depth. A more than one year long monitoring of the deep water characteristics of the site has been also provided. In this paper the infrastructure and the tower structure and instrumentation are described. The results of long term optical background measurements are presented. The rates show stable and low baseline values, compatible with the contribution of 40K light emission, with a small percentage of light bursts due to bio...

  8. Long term monitoring of the optical background in the Capo Passero deep-sea site with the NEMO tower prototype

    Energy Technology Data Exchange (ETDEWEB)

    Adrian-Martinez, S.; Ardid, M.; Llorens Alvarez, C.D.; Saldana, M. [Universitat Politecnica de Valencia, Instituto de Investigacion para la Gestion Integrada de las Zonas Costeras, Gandia (Spain); Aiello, S.; Giordano, V.; Leonora, E.; Longhitano, F.; Randazzo, N.; Sipala, V.; Ventura, C. [INFN Sezione Catania, Catania (Italy); Ameli, F.; Biagioni, A.; De Bonis, G.; Fermani, P.; Lonardo, A.; Nicolau, C.A.; Simeone, F.; Vicini, P. [INFN Sezione Roma, Rome (Italy); Anghinolfi, M.; Hugon, C.; Musico, P.; Orzelli, A.; Sanguineti, M. [INFN Sezione Genova, Genoa (Italy); Barbarino, G.; Barbato, F.C.T.; De Rosa, G.; Di Capua, F.; Garufi, F.; Vivolo, D. [INFN Sezione Napoli, Naples (Italy); Dipartimento di Scienze Fisiche Universita di Napoli, Naples (Italy); Barbarito, E. [INFN Sezione Bari, Bari (Italy); Dipartimento Interateneo di Fisica Universita di Bari, Bari (Italy); Beverini, N.; Calamai, M.; Maccioni, E.; Marinelli, A.; Terreni, G. [INFN Sezione Pisa, Polo Fibonacci, Pisa (Italy); Dipartimento di Fisica Universita di Pisa, Polo Fibonacci, Pisa (Italy); Biagi, S.; Cacopardo, G.; Cali, C.; Caruso, F.; Cocimano, R.; Coniglione, R.; Costa, M.; Cuttone, G.; D' Amato, C.; De Luca, V.; Distefano, C.; Gmerk, A.; Grasso, R.; Imbesi, M.; Kulikovskiy, V.; Larosa, G.; Lattuada, D.; Leismueller, K.P.; Litrico, P.; Migneco, E.; Miraglia, A.; Musumeci, M.; Orlando, A.; Papaleo, R.; Pulvirenti, S.; Riccobene, G.; Rovelli, A.; Sapienza, P.; Sciacca, V.; Speziale, F.; Spitaleri, A.; Trovato, A.; Viola, S. [INFN Laboratori Nazionali del Sud, Catania (Italy); Bouhadef, B.; Flaminio, V.; Raffaelli, F. [INFN Sezione Pisa, Polo Fibonacci, Pisa (Italy); Bozza, C.; Grella, G.; Stellacci, S.M. [INFN Gruppo Collegato di Salerno, Fisciano (Italy); Dipartimento di Fisica Universita di Salerno, Fisciano (Italy); Calvo, D.; Real, D. [CSIC-Universitat de Valencia, IFIC-Instituto de Fisica Corpuscular, Valencia (Spain); Capone, A.; Masullo, R.; Perrina, C. [INFN Sezione Roma, Rome (Italy); Dipartimento di Fisica Universita ' ' Sapienza' ' , Rome (Italy); Ceres, A.; Circella, M.; Mongelli, M.; Sgura, I. [INFN Sezione Bari, Bari (Italy); Chiarusi, T. [INFN Sezione Bologna, Bologna (Italy); D' Amico, A. [INFN Laboratori Nazionali del Sud, Catania (Italy); Nikhef, Science Park, Amsterdam (Netherlands); Deniskina, N.; Migliozzi, P.; Mollo, C.M. [INFN Sezione Napoli, Naples (Italy); Enzenhoefer, A.; Lahmann, R. [Friedrich-Alexander-Universitaet Erlangen-Nuernberg, Erlangen Centre for Astroparticle Physics, Erlangen (Germany); Ferrara, G. [INFN Laboratori Nazionali del Sud, Catania (Italy); Dipartimento di Fisica e Astronomia Universita di Catania, Catania (Italy); Fusco, L.A.; Margiotta, A.; Pellegrino, C.; Spurio, M. [INFN Sezione Bologna, Bologna (Italy); Dipartimento di Fisica ed Astronomia Universita di Bologna, Bologna (Italy); Lo Presti, D.; Pugliatti, C. [INFN Sezione Catania, Catania (Italy); Dipartimento di Fisica e Astronomia Universita di Catania, Catania (Italy); Martini, A.; Trasatti, L. [INFN Laboratori Nazionali di Frascati, Frascati (Italy); Morganti, M. [INFN Sezione Pisa, Polo Fibonacci, Pisa (Italy); Accademia Navale di Livorno, Livorno (Italy); Pellegriti, M.G. [INFN Laboratori Nazionali del Sud, Catania (IT); Piattelli, P. [INFN Laboratori Nazionali del Sud, Catania (IT); Taiuti, M. [INFN Sezione Genova, Genoa (IT); Dipartimento di Fisica Universita di Genova, Genoa (IT)

    2016-02-15

    The NEMO Phase-2 tower is the first detector which was operated underwater for more than 1 year at the ''record'' depth of 3500 m. It was designed and built within the framework of the NEMO (NEutrino Mediterranean Observatory) project. The 380 m high tower was successfully installed in March 2013 80 km offshore Capo Passero (Italy). This is the first prototype operated on the site where the Italian node of the KM3NeT neutrino telescope will be built. The installation and operation of the NEMO Phase-2 tower has proven the functionality of the infrastructure and the operability at 3500 m depth. A more than 1 year long monitoring of the deep water characteristics of the site has been also provided. In this paper the infrastructure and the tower structure and instrumentation are described. The results of long term optical background measurements are presented. The rates show stable and low baseline values, compatible with the contribution of {sup 40}K light emission, with a small percentage of light bursts due to bioluminescence. All these features confirm the stability and good optical properties of the site. (orig.)

  9. The changing epitome of species identification - DNA barcoding.

    Science.gov (United States)

    Ajmal Ali, M; Gyulai, Gábor; Hidvégi, Norbert; Kerti, Balázs; Al Hemaid, Fahad M A; Pandey, Arun K; Lee, Joongku

    2014-07-01

    The discipline taxonomy (the science of naming and classifying organisms, the original bioinformatics and a basis for all biology) is fundamentally important in ensuring the quality of life of future human generation on the earth; yet over the past few decades, the teaching and research funding in taxonomy have declined because of its classical way of practice which lead the discipline many a times to a subject of opinion, and this ultimately gave birth to several problems and challenges, and therefore the taxonomist became an endangered race in the era of genomics. Now taxonomy suddenly became fashionable again due to revolutionary approaches in taxonomy called DNA barcoding (a novel technology to provide rapid, accurate, and automated species identifications using short orthologous DNA sequences). In DNA barcoding, complete data set can be obtained from a single specimen irrespective to morphological or life stage characters. The core idea of DNA barcoding is based on the fact that the highly conserved stretches of DNA, either coding or non coding regions, vary at very minor degree during the evolution within the species. Sequences suggested to be useful in DNA barcoding include cytoplasmic mitochondrial DNA (e.g. cox1) and chloroplast DNA (e.g. rbcL, trnL-F, matK, ndhF, and atpB rbcL), and nuclear DNA (ITS, and house keeping genes e.g. gapdh). The plant DNA barcoding is now transitioning the epitome of species identification; and thus, ultimately helping in the molecularization of taxonomy, a need of the hour. The 'DNA barcodes' show promise in providing a practical, standardized, species-level identification tool that can be used for biodiversity assessment, life history and ecological studies, forensic analysis, and many more. PMID:24955007

  10. Counting animal species with DNA barcodes: Canadian insects.

    Science.gov (United States)

    Hebert, Paul D N; Ratnasingham, Sujeevan; Zakharov, Evgeny V; Telfer, Angela C; Levesque-Beaudin, Valerie; Milton, Megan A; Pedersen, Stephanie; Jannetta, Paul; deWaard, Jeremy R

    2016-09-01

    Recent estimates suggest that the global insect fauna includes fewer than six million species, but this projection is very uncertain because taxonomic work has been limited on some highly diverse groups. Validation of current estimates minimally requires the investigation of all lineages that are diverse enough to have a substantial impact on the final species count. This study represents a first step in this direction; it employs DNA barcoding to evaluate patterns of species richness in 27 orders of Canadian insects. The analysis of over one million specimens revealed species counts congruent with earlier results for most orders. However, Diptera and Hymenoptera were unexpectedly diverse, representing two-thirds of the 46 937 barcode index numbers (=species) detected. Correspondence checks between known species and barcoded taxa showed that sampling was incomplete, a result confirmed by extrapolations from the barcode results which suggest the occurrence of at least 94 000 species of insects in Canada, a near doubling from the prior estimate of 54 000 species. One dipteran family, the Cecidomyiidae, was extraordinarily diverse with an estimated 16 000 species, a 10-fold increase from its predicted diversity. If Canada possesses about 1% of the global fauna, as it does for known taxa, the results of this study suggest the presence of 10 million insect species with about 1.8 million of these taxa in the Cecidomyiidae. If so, the global species count for this fly family may exceed the combined total for all 142 beetle families. If extended to more geographical regions and to all hyperdiverse groups, DNA barcoding can rapidly resolve the current uncertainty surrounding a species count for the animal kingdom. A newly detailed understanding of species diversity may illuminate processes important in speciation, as suggested by the discovery that the most diverse insect lineages in Canada employ an unusual mode of reproduction, haplodiploidy.This article is part of the

  11. Use of rbcL and trnL-F as a two-locus DNA barcode for identification of NW-European ferns: an ecological perspective.

    Directory of Open Access Journals (Sweden)

    G Arjen de Groot

    Full Text Available Although consensus has now been reached on a general two-locus DNA barcode for land plants, the selected combination of markers (rbcL + matK is not applicable for ferns at the moment. Yet especially for ferns, DNA barcoding is potentially of great value since fern gametophytes--while playing an essential role in fern colonization and reproduction--generally lack the morphological complexity for morphology-based identification and have therefore been underappreciated in ecological studies. We evaluated the potential of a combination of rbcL with a noncoding plastid marker, trnL-F, to obtain DNA-identifications for fern species. A regional approach was adopted, by creating a reference database of trusted rbcL and trnL-F sequences for the wild-occurring homosporous ferns of NW-Europe. A combination of parsimony analyses and distance-based analyses was performed to evaluate the discriminatory power of the two-region barcode. DNA was successfully extracted from 86 tiny fern gametophytes and was used as a test case for the performance of DNA-based identification. Primer universality proved high for both markers. Based on the combined rbcL + trnL-F dataset, all genera as well as all species with non-equal chloroplast genomes formed their own well supported monophyletic clade, indicating a high discriminatory power. Interspecific distances were larger than intraspecific distances for all tested taxa. Identification tests on gametophytes showed a comparable result. All test samples could be identified to genus level, species identification was well possible unless they belonged to a pair of Dryopteris species with completely identical chloroplast genomes. Our results suggest a high potential of the combined use of rbcL and trnL-F as a two-locus cpDNA barcode for identification of fern species. A regional approach may be preferred for ecological tests. We here offer such a ready-to-use barcoding approach for ferns, which opens the way for answering a

  12. A diffractive barcode using diffusion-dot lines to form intersected bright bars with different orientations

    Science.gov (United States)

    Lih Yeh, Sheng; Lin, Shyh Tsong; Wu, Ming Wei

    2010-11-01

    Conventional barcodes can perform well for the data management of commercial products, but they cannot be used for anti-counterfeiting. Therefore, this paper will propose a new barcode with macro- and micro-anti-counterfeiting features. A barcode image for a conventional barcode is composed of parallel bars with different widths, whereas a barcode image for the new barcode is composed of intersected bars with different orientations. Codes for the proposed barcode are composed of bright bars along four possible orientations only. The proposed barcode pattern possesses many parallel diffusion-dot lines. Because diffusion-dot lines can diffract a laser beam to form different bright bar arrangements corresponding to different codes, the proposed barcode is called a 'diffractive barcode' here. There are brightness and length differences between the bars in a bright bar image and the differences are difficult to counterfeit, so the macrofeatures can be used for anti-counterfeiting. On the other hand, because the appearances of the diffusion dots are special and they cannot be reproduced, the microfeatures can be used for anti-counterfeiting. Moreover, both the encoding and decoding work of the diffractive barcode are easy.

  13. A diffractive barcode using diffusion-dot lines to form intersected bright bars with different orientations

    International Nuclear Information System (INIS)

    Conventional barcodes can perform well for the data management of commercial products, but they cannot be used for anti-counterfeiting. Therefore, this paper will propose a new barcode with macro- and micro-anti-counterfeiting features. A barcode image for a conventional barcode is composed of parallel bars with different widths, whereas a barcode image for the new barcode is composed of intersected bars with different orientations. Codes for the proposed barcode are composed of bright bars along four possible orientations only. The proposed barcode pattern possesses many parallel diffusion-dot lines. Because diffusion-dot lines can diffract a laser beam to form different bright bar arrangements corresponding to different codes, the proposed barcode is called a 'diffractive barcode' here. There are brightness and length differences between the bars in a bright bar image and the differences are difficult to counterfeit, so the macrofeatures can be used for anti-counterfeiting. On the other hand, because the appearances of the diffusion dots are special and they cannot be reproduced, the microfeatures can be used for anti-counterfeiting. Moreover, both the encoding and decoding work of the diffractive barcode are easy

  14. Reliable DNA barcoding performance proved for species and island populations of comoran squamate reptiles.

    Directory of Open Access Journals (Sweden)

    Oliver Hawlitschek

    Full Text Available In the past decade, DNA barcoding became increasingly common as a method for species identification in biodiversity inventories and related studies. However, mainly due to technical obstacles, squamate reptiles have been the target of few barcoding studies. In this article, we present the results of a DNA barcoding study of squamates of the Comoros archipelago, a poorly studied group of oceanic islands close to and mostly colonized from Madagascar. The barcoding dataset presented here includes 27 of the 29 currently recognized squamate species of the Comoros, including 17 of the 18 endemic species. Some species considered endemic to the Comoros according to current taxonomy were found to cluster with non-Comoran lineages, probably due to poorly resolved taxonomy. All other species for which more than one barcode was obtained corresponded to distinct clusters useful for species identification by barcoding. In most species, even island populations could be distinguished using barcoding. Two cryptic species were identified using the DNA barcoding approach. The obtained barcoding topology, a Bayesian tree based on COI sequences of 5 genera, was compared with available multigene topologies, and in 3 cases, major incongruences between the two topologies became evident. Three of the multigene studies were initiated after initial screening of a preliminary version of the barcoding dataset presented here. We conclude that in the case of the squamates of the Comoros Islands, DNA barcoding has proven a very useful and efficient way of detecting isolated populations and promising starting points for subsequent research.

  15. ISBN and QR Barcode Scanning Mobile App for Libraries

    OpenAIRE

    Graham McCarthy; Sally Wilson

    2011-01-01

    This article outlines the development of a mobile application for the Ryerson University Library. The application provides for ISBN barcode scanning that results in a lookup of library copies and services for the book scanned, as well as QR code scanning. Two versions of the application were developed, one for iOS and one for Android. The article includes some details on the free packages used for barcode scanning functionality. Source code for the Ryerson iOS and Android applications are fre...

  16. Application bar-code system for solid radioactive waste management

    International Nuclear Information System (INIS)

    Solid radioactive wastes are generated from the post-irradiated fuel examination facility, the irradiated material examination facility, the research reactor, and the laboratories at KAERI. A bar-code system for a solid radioactive waste management of a research organization became necessary while developing the RAWMIS(Radioactive Waste Management Integration System) which it can generate personal history management for efficient management of a waste, documents, all kinds of statistics. This paper introduces an input and output application program design to do to database with data in the results and a stream process of a treatment that analyzed the waste occurrence present situation and data by bar-code system

  17. S-K Smartphone Barcode Reader for the Blind

    OpenAIRE

    Tekin, Ender; Vásquez, David; Coughlan, James M.

    2013-01-01

    We describe a new smartphone app called BLaDE (Barcode Localization and Decoding Engine), designed to enable a blind or visually impaired user find and read product barcodes. Developed at The Smith-Kettlewell Eye Research Institute, the BLaDE Android app has been released as open source software, which can be used for free or modified for commercial or non-commercial use. Unlike popular commercial smartphone apps, BLaDE provides real-time audio feedback to help visually impaired users locate ...

  18. DNA barcoding, phylogenetic relationships and speciation of snappers (genus Lutjanus)

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The phylogenetic relationships of 13 snapper species from the South China Sea have been established using the combined DNA sequences of three full-length mitochondrial genes (COI, COII and CYTB) and two partial nuclear genes (RAG1, RAG2). The 13 species (genus Lutjanus) were selected after DNA barcoding 72 individuals, representing 20 species. Our study suggests that although DNA barcoding aims to develop species identification systems, it may also be useful in the construction of phylogenies by aiding the selection of taxa. Combined mitochondrial and nuclear gene data has an advantage over an individual dataset because of its higher resolving power.

  19. Barcoding of live human PBMC for multiplexed mass cytometry*

    OpenAIRE

    Mei, Henrik E; Leipold, Michael D.; Schulz, Axel Ronald; Chester, Cariad; Maecker, Holden T.

    2015-01-01

    Mass cytometry is developing as a means of multiparametric single cell analysis. Here, we present an approach to barcoding separate live human PBMC samples for combined preparation and acquisition on a CyTOF® instrument. Using six different anti-CD45 antibody (Ab) conjugates labeled with Pd104, Pd106, Pd108, Pd110, In113, and In115, respectively, we barcoded up to 20 samples with unique combinations of exactly three different CD45 Ab tags. Cell events carrying more than or less than three dif...

  20. DNA Barcodes for Marine Biodiversity: Moving Fast Forward?

    Directory of Open Access Journals (Sweden)

    Adriana E. Radulovici

    2010-03-01

    Full Text Available ‘Biodiversity’ means the variety of life and it can be studied at different levels (genetic, species, ecosystem and scales (spatial and temporal. Last decades showed that marine biodiversity has been severely underestimated at all levels. In order to investigate diversity patterns and underlying processes, there is a need to know what species live in the marine environment. An emerging tool for species identification, DNA barcoding can reliably assign unknown specimens to known species, also flagging potential cryptic species and genetically distant populations. This paper will review the role of DNA barcoding for the study of marine biodiversity at the species level.

  1. DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads.

    Directory of Open Access Journals (Sweden)

    Chodon Sass

    Full Text Available Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL, and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS, were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.

  2. Barcoding of live human PBMC for multiplexed mass cytometry*

    Science.gov (United States)

    Mei, Henrik E.; Leipold, Michael D.; Schulz, Axel Ronald; Chester, Cariad; Maecker, Holden T.

    2014-01-01

    Mass cytometry is developing as a means of multiparametric single cell analysis. Here, we present an approach to barcoding separate live human PBMC samples for combined preparation and acquisition on a CyTOF® instrument. Using six different anti-CD45 antibody (Ab) conjugates labeled with Pd104, Pd106, Pd108, Pd110, In113, and In115, respectively, we barcoded up to 20 samples with unique combinations of exactly three different CD45 Ab tags. Cell events carrying more than or less than three different tags were excluded from analyses during Boolean data deconvolution, allowing for precise sample assignment and the electronic removal of cell aggregates. Data from barcoded samples matched data from corresponding individually stained and acquired samples, at cell event recoveries similar to individual sample analyses. The approach greatly reduced technical noise and minimizes unwanted cell doublet events in mass cytometry data, and reduces wet work and antibody consumption. It also eliminates sample-to-sample carryover and the requirement of instrument cleaning between samples, thereby effectively reducing overall instrument runtime. Hence, CD45-barcoding facilitates accuracy of mass cytometric immunophenotyping studies, thus supporting biomarker discovery efforts, and should be applicable to fluorescence flow cytometry as well. PMID:25609839

  3. High universality of matK primers for barcoding gymnosperms

    Institute of Scientific and Technical Information of China (English)

    Yan LI; Lian-Ming GAO; RAM C.POUDEL; De-Zhu Li; Alan FORREST

    2011-01-01

    DNA barcoding is a tool to provide rapid and accurate taxonomic identification using a standard DNA region. A two-marker combination of rnatK+rbcL was formally proposed as the core barcode for land plants by the Consortium for the Barcode of Life Plant Working Group. However, there are currently no barcoding primers for matK showing high universality in gymnosperms. We used 57 gymnosperm species representing 40 genera, 11families and four subclasses to evaluate the universality of nine candidate matK primers and one rbcL primer in this study. Primer (1F/724R) of rbcL is proposed here as a universal primer for gymnosperms due to high universality. One of the nine candidate matK primers (Gym_F1A/Gym_R1A) is proposed as the best "universal" matK primer for gynnosperms because of high polymerase chain reaction success and routine generation of high quality bidirectional sequences. A specific matK primer for Ephedra was newly designed in this study, which performed well on the sampled species. The primers proposed here for rbcL and matK can be easily and successfully amplified for most gymnosperms.

  4. The interaction field in arrays of ferromagnetic barcode nanowires

    International Nuclear Information System (INIS)

    A theoretical model and an experimental approach to the identification of the interaction field in ferromagnetic barcode nanowires are described and applied to electrodeposited Ni/Au cylindrical barcode arrays. Elementary hysteresis loops of individual magnetic segments in these barcode nanowires are considered as superpositions of fully irreversible and locally reversible magnetization processes, whose distributions of switching fields are experimentally identified by first order reversal curve measurements. Non-interacting major hysteresis loops of the arrays are computed as superpositions of several elementary loops by considering the distributions of switching fields as probability density functions. The interaction field is then computed from the condition that the geometric transformation of the experimental major hysteresis loop into the Preisach operative plane be well approximated by this non-interacting hysteresis loop. Experimental interaction field values are compared with those obtained by numerical micromagnetic computations and a very good agreement is obtained on extended Ni/Au barcode arrays. The simple and accurate phenomenological model for the interaction field in multisegmented ferromagnetic nanowire arrays proposed here provides an insight into the morphology of these magnetic nanomaterials, as quantitative information about individual nano-objects may be extracted from macroscopic measurements of their arrays

  5. DNA Barcode Authentication of Saw Palmetto Herbal Dietary Supplements

    Science.gov (United States)

    Little, Damon P.; Jeanson, Marc L.

    2013-01-01

    Herbal dietary supplements made from saw palmetto (Serenoa repens; Arecaceae) fruit are commonly consumed to ameliorate benign prostate hyperplasia. A novel DNA mini–barcode assay to accurately identify [specificity = 1.00 (95% confidence interval = 0.74–1.00); sensitivity = 1.00 (95% confidence interval = 0.66–1.00); n = 31] saw palmetto dietary supplements was designed from a DNA barcode reference library created for this purpose. The mini–barcodes were used to estimate the frequency of mislabeled saw palmetto herbal dietary supplements on the market in the United States of America. Of the 37 supplements examined, amplifiable DNA could be extracted from 34 (92%). Mini–barcode analysis of these supplements demonstrated that 29 (85%) contain saw palmetto and that 2 (6%) supplements contain related species that cannot be legally sold as herbal dietary supplements in the United States of America. The identity of 3 (9%) supplements could not be conclusively determined. PMID:24343362

  6. Prospects for discriminating Zingiberaceae species in India using DNA barcodes

    Institute of Scientific and Technical Information of China (English)

    Meenakshi Ramaswamy Vinitha; Unnikrishnan Suresh Kumar; Kizhakkethil Aishwarya; Mamiyil Sabu; George Thomas

    2014-01-01

    We evaluated nine plastid (matK, rbcL, rpoC1, rpoB, rpl36-rps8, ndhJ, trnL-F, trnH-psbA, accD) and two nuclear (ITS and ITS2) barcode loci in family Zingiberaceae by analyzing 60 accessions of 20 species belonging to seven genera from India. Bidirectional sequences were recovered for every plastid locus by direct sequencing of polymerase chain reaction (PCR) amplicons in al the accessions tested. However, only 35 (58%) and 40 accessions (66%) yielded ITS and ITS2 sequences, respectively, by direct sequencing. In different bioinformatics analyses, matK and rbcL consistently resolved 15 species (75%) into monophyletic groups and five species into two para-phyletic groups. The 173 ITS sequences, including 138 cloned sequences from 23 accessions, discriminated only 12 species (60%), and the remaining species were entered into three paraphyletic groups. Phylogenetic and genealogic analyses of plastid and ITS sequences imply the possible occurrence of natural hybridizations in the evolutionary past in giving rise to species paraphyly and intragenomic ITS heterogeneity in the species tested. The results support using matK and rbcL loci for barcoding Zingiberaceae members and highlight the poor utility of ITS and the highly regarded ITS2 in barcoding this family, and also caution against proposing ITS loci for barcoding taxa based on limited sampling.

  7. Clinical Validation of Quantum Dot Barcode Diagnostic Technology.

    Science.gov (United States)

    Kim, Jisung; Biondi, Mia J; Feld, Jordan J; Chan, Warren C W

    2016-04-26

    There has been a major focus on the clinical translation of emerging technologies for diagnosing patients with infectious diseases, cancer, heart disease, and diabetes. However, most developments still remain at the academic stage where researchers use spiked target molecules to demonstrate the utility of a technology and assess the analytical performance. This approach does not account for the biological complexities and variabilities of human patient samples. As a technology matures and potentially becomes clinically viable, one important intermediate step in the translation process is to conduct a full clinical validation of the technology using a large number of patient samples. Here, we present a full detailed clinical validation of Quantum Dot (QD) barcode technology for diagnosing patients infected with Hepatitis B Virus (HBV). We further demonstrate that the detection of multiple regions of the viral genome using multiplexed QD barcodes improved clinical sensitivity from 54.9-66.7% to 80.4-90.5%, and describe how to use QD barcodes for optimal clinical diagnosis of patients. The use of QDs in biology and medicine was first introduced in 1998 but has not reached clinical care. This study describes our long-term systematic development strategy to advance QD technology to a clinically feasible product for diagnosing patients. Our "blueprint" for translating the QD barcode research concept could be adapted for other nanotechnologies, to efficiently advance diagnostic techniques discovered in the academic laboratory to patient care. PMID:27035744

  8. Untangling taxonomy: a DNA barcode reference library for Canadian spiders.

    Science.gov (United States)

    Blagoev, Gergin A; deWaard, Jeremy R; Ratnasingham, Sujeevan; deWaard, Stephanie L; Lu, Liuqiong; Robertson, James; Telfer, Angela C; Hebert, Paul D N

    2016-01-01

    Approximately 1460 species of spiders have been reported from Canada, 3% of the global fauna. This study provides a DNA barcode reference library for 1018 of these species based upon the analysis of more than 30,000 specimens. The sequence results show a clear barcode gap in most cases with a mean intraspecific divergence of 0.78% vs. a minimum nearest-neighbour (NN) distance averaging 7.85%. The sequences were assigned to 1359 Barcode index numbers (BINs) with 1344 of these BINs composed of specimens belonging to a single currently recognized species. There was a perfect correspondence between BIN membership and a known species in 795 cases, while another 197 species were assigned to two or more BINs (556 in total). A few other species (26) were involved in BIN merges or in a combination of merges and splits. There was only a weak relationship between the number of specimens analysed for a species and its BIN count. However, three species were clear outliers with their specimens being placed in 11-22 BINs. Although all BIN splits need further study to clarify the taxonomic status of the entities involved, DNA barcodes discriminated 98% of the 1018 species. The present survey conservatively revealed 16 species new to science, 52 species new to Canada and major range extensions for 426 species. However, if most BIN splits detected in this study reflect cryptic taxa, the true species count for Canadian spiders could be 30-50% higher than currently recognized. PMID:26175299

  9. Testing four barcoding markers for species identification of Potamogetonaceae

    Institute of Scientific and Technical Information of China (English)

    Zhi-Yuan DU; Alitong QIMIKE; Chun-Feng YANG; Jin-Ming CHEN; Qing-Feng WANG

    2011-01-01

    The pondweeds (Potamogetonaceae) are among the most important plant groups in the aquatic environment. Owing to their high morphological and ecological diversity, species identification of this aquatic family remains problematic. DNA barcoding involves sequencing a standard DNA region and has been shown to be a powerful tool for species identification. In the present study, we tested four barcoding markers (rbcL, matK, internal transcribed spacer (ITS), and trnH-psbA) in 15 Potamogeton species and two Stuckenia species, representing most species of the Potamogetonaceae in China. The results show that all four regions can distinguish and support the newly proposed genera of Stuckenia from Potamogeton. Using ITS and trnH-psbA, significant interspecific genetic variability was shown. However, intraspecific genetic variability of trnH-psbA is high and so it is not suitable for barcoding in Potamogetonaceae. The ITS and matK regions showed good discrimination. However, matK was not easy to sequence using universal primers. The best performing single locus was ITS, making it a potentially useful DNA barcode in Potamogetonaceae.

  10. The interaction field in arrays of ferromagnetic barcode nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Clime, L [NRC, Industrial Materials Institute, 75 de Mortagne Boulevard, Boucherville, J4B 6Y4 (Canada); Zhao, S Y [NRC, Industrial Materials Institute, 75 de Mortagne Boulevard, Boucherville, J4B 6Y4 (Canada); Chen, P [Research Center for Applied Sciences, Academia Sinica 128 Section 2, Academia Rd, Nankang, Taipei 11529, Taiwan (China); Normandin, F [NRC, Industrial Materials Institute, 75 de Mortagne Boulevard, Boucherville, J4B 6Y4 (Canada); Roberge, H [NRC, Industrial Materials Institute, 75 de Mortagne Boulevard, Boucherville, J4B 6Y4 (Canada); Veres, T [NRC, Industrial Materials Institute, 75 de Mortagne Boulevard, Boucherville, J4B 6Y4 (Canada)

    2007-10-31

    A theoretical model and an experimental approach to the identification of the interaction field in ferromagnetic barcode nanowires are described and applied to electrodeposited Ni/Au cylindrical barcode arrays. Elementary hysteresis loops of individual magnetic segments in these barcode nanowires are considered as superpositions of fully irreversible and locally reversible magnetization processes, whose distributions of switching fields are experimentally identified by first order reversal curve measurements. Non-interacting major hysteresis loops of the arrays are computed as superpositions of several elementary loops by considering the distributions of switching fields as probability density functions. The interaction field is then computed from the condition that the geometric transformation of the experimental major hysteresis loop into the Preisach operative plane be well approximated by this non-interacting hysteresis loop. Experimental interaction field values are compared with those obtained by numerical micromagnetic computations and a very good agreement is obtained on extended Ni/Au barcode arrays. The simple and accurate phenomenological model for the interaction field in multisegmented ferromagnetic nanowire arrays proposed here provides an insight into the morphology of these magnetic nanomaterials, as quantitative information about individual nano-objects may be extracted from macroscopic measurements of their arrays.

  11. Measuring and test equipment control through bar-code technology

    International Nuclear Information System (INIS)

    Over the past several years, the use, tracking, and documentation of measuring and test equipment (M ampersand TE) has become a major issue. New regulations are forcing companies to develop new policies for providing use history, traceability, and accountability of M ampersand TE. This paper discusses how the Fast Flux Test Facility (FFTF), operated by Westinghouse Hanford Company and located at the Hanford site in Rich- land, Washington, overcame these obstacles by using a computerized system exercising bar-code technology. A data base was developed to identify M ampersand TE containing 33 separate fields, such as manufacturer, model, range, bar-code number, and other pertinent information. A bar-code label was attached to each piece of M ampersand TE. A second data base was created to identify the employee using the M ampersand TE. The fields contained pertinent user information such as name, location, and payroll number. Each employee's payroll number was bar coded and attached to the back of their identification badge. A computer program was developed to automate certain tasks previously performed and tracked by hand. Bar-code technology was combined with this computer program to control the input and distribution of information, eliminate common mistakes, electronically store information, and reduce the time required to check out the M ampersand TE for use

  12. A retrospective approach to testing the DNA barcoding method.

    Directory of Open Access Journals (Sweden)

    David G Chapple

    Full Text Available A decade ago, DNA barcoding was proposed as a standardised method for identifying existing species and speeding the discovery of new species. Yet, despite its numerous successes across a range of taxa, its frequent failures have brought into question its accuracy as a short-cut taxonomic method. We use a retrospective approach, applying the method to the classification of New Zealand skinks as it stood in 1977 (primarily based upon morphological characters, and compare it to the current taxonomy reached using both morphological and molecular approaches. For the 1977 dataset, DNA barcoding had moderate-high success in identifying specimens (78-98%, and correctly flagging specimens that have since been confirmed as distinct taxa (77-100%. But most matching methods failed to detect the species complexes that were present in 1977. For the current dataset, there was moderate-high success in identifying specimens (53-99%. For both datasets, the capacity to discover new species was dependent on the methodological approach used. Species delimitation in New Zealand skinks was hindered by the absence of either a local or global barcoding gap, a result of recent speciation events and hybridisation. Whilst DNA barcoding is potentially useful for specimen identification and species discovery in New Zealand skinks, its error rate could hinder the progress of documenting biodiversity in this group. We suggest that integrated taxonomic approaches are more effective at discovering and describing biodiversity.

  13. Measurement of double beta decay of 100Mo to excited states in the NEMO 3 experiment

    International Nuclear Information System (INIS)

    The double beta decay of 100Mo to the 01+ and 21+ excited states of 100Ru is studied using the NEMO 3 data. After the analysis of 8024 h of data the half-life for the two-neutrino double beta decay of 100Mo to the excited 01+ state is measured to be T1/2(2ν)=[5.7-0.9+1.3(stat.)+/-0.8(syst.)]x1020 y. The signal-to-background ratio is equal to 3. Information about energy and angular distributions of emitted electrons is also obtained. No evidence for neutrinoless double beta decay to the excited 01+ state has been found. The corresponding half-life limit is T1/2(0ν)(0+->01+)>8.9x1022 y (at 90% C.L.). The search for the double beta decay to the 21+ excited state has allowed the determination of limits on the half-life for the two neutrino mode T1/2(2ν)(0+->21+)>1.1x1021 y (at 90% C.L.) and for the neutrinoless mode T1/2(0ν)(0+->21+)>1.6x1023 y (at 90% C.L.)

  14. Measurement of double beta decay of 100Mo to excited states in the NEMO 3 experiment

    CERN Document Server

    Arnold, R; Baker, J; Barabash, A S; Bongrand, M; Broudin, G; Brudanin, V; Caffrey, A J; Egorov, V; Etienvre, A I; Fatemi-Ghomi, N; Hubert, F; Hubert, P; Jerie, J; Jollet, C; Jullian, S; King, S; Kochetov, O; Konovalov, S I; Kovalenko, V; Lalanne, D; Lamhamdi, T; Leccia, F; Lemière, Y; Longuemare, C; Lutter, G; Marquet, C; Mauger, F; Nachab, A; Ohsumi, H; Perrot, F; Piquemal, F; Reyss, J L; Ricol, J S; Saakyan, R; Sarazin, X; Shitov, Y; Simard, L; Simkovic, F; Smolnikov, A; Stekl, I; Suhonen, J; Sutton, C S; Szklarz, G; Söldner-Rembold, S; Thomas, J; Timkin, V; Tretyak, V; Umatov, V; Vanyushin, I A; Vasilev, V; Vorobel, V; Vylov, T; Vàla, L; Hubert, Ph.; Marquet, Ch.; Shitov, Yu.; Vylov, Ts.

    2007-01-01

    The double beta decay of 100Mo to the 0^+_1 and 2^+_1 excited states of 100Ru is studied using the NEMO 3 data. After the analysis of 8024 h of data the half-life for the two-neutrino double beta decay of 100Mo to the excited 0^+_1 state is measured to be T^(2nu)_1/2 = [5.7^{+1.3}_{-0.9}(stat)+/-0.8(syst)]x 10^20 y. The signal-to-background ratio is equal to 3. Information about energy and angular distributions of emitted electrons is also obtained. No evidence for neutrinoless double beta decay to the excited 0^+_1 state has been found. The corresponding half-life limit is T^(0nu)_1/2(0^+ --> 0^+_1) > 8.9 x 10^22 y (at 90% C.L.). The search for the double beta decay to the 2^+_1 excited state has allowed the determination of limits on the half-life for the two neutrino mode T^(2nu)_1/2(0^+ --> 2^+_1) > 1.1 x 10^21 y (at 90% C.L.) and for the neutrinoless mode T^(0nu)_1/2(0^+ --> 2^+_1) > 1.6 x 10^23 y (at 90% C.L.).

  15. Performance and results of the high-resolution biogeochemical model PELAGOS025 within NEMO

    Directory of Open Access Journals (Sweden)

    I. Epicoco

    2015-12-01

    Full Text Available The present work aims at evaluating the scalability performance of a high-resolution global ocean biogeochemistry model (PELAGOS025 on massive parallel architectures and the benefits in terms of the time-to-solution reduction. PELAGOS025 is an on-line coupling between the physical ocean model NEMO and the BFM biogeochemical model. Both the models use a parallel domain decomposition along the horizontal dimension. The parallelisation is based on the message passing paradigm. The performance analysis has been done on two parallel architectures, an IBM BlueGene/Q at ALCF (Argonne Leadership Computing Facilities and an IBM iDataPlex with Sandy Bridge processors at CMCC (Euro Mediterranean Center on Climate Change. The outcome of the analysis demonstrated that the lack of scalability is due to several factors such as the I/O operations, the memory contention, the load unbalancing due to the memory structure of the BFM component and, for the BlueGene/Q, the absence of a hybrid parallelisation approach.

  16. Nuclear initiated NF-κB signaling: NEMO and ATM take center stage

    Institute of Scientific and Technical Information of China (English)

    Shigeki Miyamoto

    2011-01-01

    A large body of literature describes elaborate NF-κB signaling networks induced by inflammatory and immune signals.Decades of research has revealed that transcriptionally functional NF-κB dimers are activated by two major pathways,canonical and non-canonical.Both pathways involve the release of NF-κB dimers from inactive cytoplasmic complexes to cause their nuclear translocation to modulate gene expression programs and biological responses.NF-κB is also responsive to genotoxic agents; however,signal communication networks that are initiated in the nucleus following DNA damage induction are less defined.Evidence in the literature supports the presence of such signaling pathways induced by multiple distinct genotoxic agents,resulting in the activation of cytoplasmic IKK complex.An example is a pathway that involves the DNA damage-responsive kinase ataxia telangiectasia mutated(ATM)and a series of post-translational modifications of NF-κB essential modulator(NEMO)in the nucleus of a genotoxinexposed cell.Recent evidence also suggests that this nuclear-initiated NF-κB signaling pathway plays significant physiological and pathological roles,particularly in lymphocyte development and human cancer progression.This review will summarize these new developments,while identifying significant unanswered questions and providing new hypotheses that may be addressed in future studies.

  17. Comparison of Functional Protein Transduction Domains Using the NEMO Binding Domain Peptide

    Directory of Open Access Journals (Sweden)

    Paul Robbins

    2010-01-01

    Full Text Available Protein transduction domains (PTDs, both naturally occurring and synthetic, have been extensively utilized for intracellular delivery of biologically active molecules both in vitro and in vivo. However, most comparisons of transduction efficiency have been performed using fluorescent markers. To compare efficiency of functional protein transduction, a peptide derived from IkB kinase ß (IKKß that prevents formation of an active IKK complex was used as a biologically active cargo. This peptide, termed NEMO Binding Domain (NBD, is able to block activation of the transcriptional factor NF-κB by IKK, but not basal NF-κB activity. Our results demonstrate that Antp and Tat PTDs were most effective for delivery of NBD for inhibition of NF-kB activation compared to other PTD-NBD in both Hela and 293 cells, however, at higher concentrations (100 µM, the Antp-NBD as well as the FGF-NBD peptide caused significant cellular toxicity. In contrast to the cell culture results, delivery of NBD using 8K (octalysine and 6R (six arginine were the most effect in blocking inflammation following local, footpad delivery in a KLH-induced DTH murine model of inflammatory arthritis. These results demonstrate differences between PTDs for delivery of a functional cargo between cell types.

  18. A Test of Seven Candidate Barcode Regions from the Plastome in Picea (Pinaceae)

    Institute of Scientific and Technical Information of China (English)

    Jin-Hua Ran; Pei-Pei Wang; Hui-Juan Zhao; Xiao-Quan Wang

    2010-01-01

    DNA barcoding, as a tool for species discrimination, has been used efficiently in animals, algae and fungi, but there are still debates on which DNA region(s) can be used as the standard barcode(s) for land plants. Gymnosperms, especially conifers, are important components of forests, and there is an urgent need for them to be identified through DNA barcoding because of their high frequency of collection in the field. However, the feasibility of DNA barcoding in gymnosperms has not been examined based on a dense species sampling. Here we selected seven candidate DNA barcodes from the plastome (matK, rbcL, rpoB, rpoC1, atpF-atpH, psbA-trnH, and psbK-psbl) to evaluate their suitability in Picea (spruce). The results showed that none of them or their different combinations has sufficient resolution for spruce species, although matK+rbcL might be used as a two-locus barcode. The low efficiency of these candidate barcodes in Picea might be caused by the paternal inheritance of the chloroplast genome, long generation time, recent radiation, and frequent inter-specific hybridization aided by wind pollination. Some of these factors could also be responsible for the difficulties in barcoding other plant groups. Furthermore, the potential of the nuclear LEAFY gene as a land plant barcode was discussed.

  19. DNA barcoding of sigmodontine rodents: identifying wildlife reservoirs of zoonoses.

    Directory of Open Access Journals (Sweden)

    Lívia Müller

    Full Text Available Species identification through DNA barcoding is a tool to be added to taxonomic procedures, once it has been validated. Applying barcoding techniques in public health would aid in the identification and correct delimitation of the distribution of rodents from the subfamily Sigmodontinae. These rodents are reservoirs of etiological agents of zoonoses including arenaviruses, hantaviruses, Chagas disease and leishmaniasis. In this study we compared distance-based and probabilistic phylogenetic inference methods to evaluate the performance of cytochrome c oxidase subunit I (COI in sigmodontine identification. A total of 130 sequences from 21 field-trapped species (13 genera, mainly from southern Brazil, were generated and analyzed, together with 58 GenBank sequences (24 species; 10 genera. Preliminary analysis revealed a 9.5% rate of misidentifications in the field, mainly of juveniles, which were reclassified after examination of external morphological characters and chromosome numbers. Distance and model-based methods of tree reconstruction retrieved similar topologies and monophyly for most species. Kernel density estimation of the distance distribution showed a clear barcoding gap with overlapping of intraspecific and interspecific densities < 1% and 21 species with mean intraspecific distance < 2%. Five species that are reservoirs of hantaviruses could be identified through DNA barcodes. Additionally, we provide information for the description of a putative new species, as well as the first COI sequence of the recently described genus Drymoreomys. The data also indicated an expansion of the distribution of Calomys tener. We emphasize that DNA barcoding should be used in combination with other taxonomic and systematic procedures in an integrative framework and based on properly identified museum collections, to improve identification procedures, especially in epidemiological surveillance and ecological assessments.

  20. Identification of North Sea molluscs with DNA barcoding.

    Science.gov (United States)

    Barco, Andrea; Raupach, Michael J; Laakmann, Silke; Neumann, Hermann; Knebelsberger, Thomas

    2016-01-01

    Sequence-based specimen identification, known as DNA barcoding, is a common method complementing traditional morphology-based taxonomic assignments. The fundamental resource in DNA barcoding is the availability of a taxonomically reliable sequence database to use as a reference for sequence comparisons. Here, we provide a reference library including 579 sequences of the mitochondrial cytochrome c oxidase subunit I for 113 North Sea mollusc species. We tested the efficacy of this library by simulating a sequence-based specimen identification scenario using Best Match, Best Close Match (BCM) and All Species Barcode (ASB) criteria with three different threshold values. Each identification result was compared with our prior morphology-based taxonomic assignments. Our simulation resulted in 87.7% congruent identifications (93.8% when excluding singletons). The highest number of congruent identifications was obtained with BCM and ASB and a 0.05 threshold. We also compared identifications with genetic clustering (Barcode Index Numbers, BINs) computed by the Barcode of Life Datasystem (BOLD). About 68% of our morphological identifications were congruent with BINs created by BOLD. Forty-nine sequences were clustered in 16 discordant BINs, and these were divided in two classes: sequences from different species clustered in a single BIN and conspecific sequences divided in more BINs. Whereas former incongruences were probably caused by BOLD entries in need of a taxonomic update, the latter incongruences regarded taxa requiring further investigations. These include species with amphi-Atlantic distribution, whose genetic structure should be evaluated over their entire range to produce a reliable sequence-based identification system. PMID:26095230

  1. DNA barcode detects high genetic structure within neotropical bird species.

    Directory of Open Access Journals (Sweden)

    Erika Sendra Tavares

    Full Text Available BACKGROUND: Towards lower latitudes the number of recognized species is not only higher, but also phylogeographic subdivision within species is more pronounced. Moreover, new genetically isolated populations are often described in recent phylogenies of Neotropical birds suggesting that the number of species in the region is underestimated. Previous COI barcoding of Argentinean bird species showed more complex patterns of regional divergence in the Neotropical than in the North American avifauna. METHODS AND FINDINGS: Here we analyzed 1,431 samples from 561 different species to extend the Neotropical bird barcode survey to lower latitudes, and detected even higher geographic structure within species than reported previously. About 93% (520 of the species were identified correctly from their DNA barcodes. The remaining 41 species were not monophyletic in their COI sequences because they shared barcode sequences with closely related species (N = 21 or contained very divergent clusters suggestive of putative new species embedded within the gene tree (N = 20. Deep intraspecific divergences overlapping with among-species differences were detected in 48 species, often with samples from large geographic areas and several including multiple subspecies. This strong population genetic structure often coincided with breaks between different ecoregions or areas of endemism. CONCLUSIONS: The taxonomic uncertainty associated with the high incidence of non-monophyletic species and discovery of putative species obscures studies of historical patterns of species diversification in the Neotropical region. We showed that COI barcodes are a valuable tool to indicate which taxa would benefit from more extensive taxonomic revisions with multilocus approaches. Moreover, our results support hypotheses that the megadiversity of birds in the region is associated with multiple geographic processes starting well before the Quaternary and extending to more recent

  2. Detection of Avian Influenza Virus by Fluorescent DNA Barcode-based Immunoassay with Sensitivity Comparable to PCR

    DEFF Research Database (Denmark)

    Cao, Cuong; Dhumpa, Raghuram; Bang, Dang Duong;

    2010-01-01

    In this paper, a coupling of fluorophore-DNA barcode and bead-based immunoassay for detecting avian influenza virus (AIV) with PCR-like sensitivity is reported. The assay is based on the use of sandwich immunoassay and fluorophore-tagged oligonucleotides as representative barcodes. The detection...... involves the sandwiching of the target AIV between magnetic immunoprobes and barcode-carrying immunoprobes. Because each barcode-carrying immunoprobe is functionalized with a multitude of fluorophore-DNA barcode strands, many DNA barcodes are released for each positive binding event resulting in...

  3. Application of the digital watermarking technique in 2D barcode certificate anti-counterfeit systems

    Science.gov (United States)

    Chen, MuSheng; Lin, ShunDa

    2011-06-01

    At present, two dimensional barcode has been used in many fields. The safety of information in barcode is important, so this article brings up an effective two dimensional barcode encryption technology to assure it. Either two-dimensional barcode or digital watermarking technique is one of the most important parts and research focuses in anti-counterfeit fields. This paper designs and realizes a whole set of certificate administration system based on QRcode. On this platform the digital watermarking technique based on the spatial domain is used to encrypt the two dimensional barcode. The combination of two dimensional barcode and digital watermarking can improve the security and secrecy of personal information, and realize real anti-counterfeit certificates.

  4. Amelioration of Chronic Murine Colitis by Peptide-Mediated Transduction of the IκB Kinase Inhibitor NEMO Binding Domain Peptide1

    OpenAIRE

    Davé, Shaival H.; Tilstra, Jeremy S.; Matsuoka, Katsuyoshi; Li, Fengling; Karrasch, Thomas; Uno, Jennifer K.; Sepulveda, Antonia R; Jobin, Christian; Baldwin, Albert S.; Paul D Robbins; Plevy, Scott E.

    2007-01-01

    The NF-κB family of transcription factors is a central regulator of chronic inflammation. The phosphorylation of IκB proteins by the IκB kinase (IKK) complex (IKKα, IKKβ, and NF-κB essential modulator or NEMO) is a key step in NF-κB activation. Peptides corresponding to the NEMO binding domain (NBD) of IKK blocks NF-κB activation without inhibiting basal NF-κB activity. In this report, we determined the effects of the IKK inhibitor peptide (NBD) in a model of spontaneously occurring chronic m...

  5. A Ranking System for Reference Libraries of DNA Barcodes: Application to Marine Fish Species from Portugal

    OpenAIRE

    Costa, Filipe O.; Landi, Monica; Martins, Rogelia; Costa, Maria H.; Costa, Maria E.; Carneiro, Miguel; Alves, Maria J.; Steinke, Dirk; Carvalho, Gary R.

    2012-01-01

    Background The increasing availability of reference libraries of DNA barcodes (RLDB) offers the opportunity to the screen the level of consistency in DNA barcode data among libraries, in order to detect possible disagreements generated from taxonomic uncertainty or operational shortcomings. We propose a ranking system to attribute a confidence level to species identifications associated with DNA barcode records from a RLDB. Here we apply the proposed ranking system to a newly generated RLDB f...

  6. Rapid DNA barcoding analysis of large datasets using the composition vector method

    OpenAIRE

    Chu, Ka Hou; Xu, Minli; Li, Chi Pang

    2009-01-01

    Background Sequence alignment is the rate-limiting step in constructing profile trees for DNA barcoding purposes. We recently demonstrated the feasibility of using unaligned rRNA sequences as barcodes based on a composition vector (CV) approach without sequence alignment (Bioinformatics 22:1690). Here, we further explored the grouping effectiveness of the CV method in large DNA barcode datasets (COI, 18S and 16S rRNA) from a variety of organisms, including birds, fishes, nematodes and crustac...

  7. DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability

    OpenAIRE

    Little, Damon P.

    2011-01-01

    For DNA barcoding to succeed as a scientific endeavor an accurate and expeditious query sequence identification method is needed. Although a global multiple-sequence alignment can be generated for some barcoding markers (e.g. COI, rbcL), not all barcoding markers are as structurally conserved (e.g. matK). Thus, algorithms that depend on global multiple-sequence alignments are not universally applicable. Some sequence identification methods that use local pairwise alignments (e.g. BLAST) are u...

  8. EM-Based joint symbol and blur estimation for 2D barcode

    OpenAIRE

    Dridi, Noura; Delignon, Yves; Sawaya, Wadih; Garnier, Christelle

    2011-01-01

    Decoding a severely blurred 2D barcode can be considered as a special case of blind image restoration issue. In this paper, we propose an appropriate system model which includes the original image with the particularities related to barcode, the blur and the observed image. We develop an unsupervised algorithm that jointly estimates the blur and detects the symbols using the maximum likelihood (ML) criterion. Besides, we show that when taking into account the spatial properties of the barcode...

  9. Site-specific recombinatorics: in situ cellular barcoding with the Cre Lox system

    OpenAIRE

    Weber, Tom S.; Dukes, Mark; Miles, Denise; Glaser, Stefan; Naik, Shalin; Duffy, Ken R.

    2016-01-01

    Cellular barcoding is a significant, recently developed, biotechnology tool that enables the familial identification of progeny of individual cells in vivo. Most existing approaches rely on ex vivo viral transduction of cells with barcodes, followed by adoptive transfer into an animal, which works well for some systems, but precludes barcoding cells in their native environment, such as those inside solid tissues. With a view to overcoming this limitation, we propose a new design for a genetic...

  10. SECURITY-EFFECTIVE LOCAL-LIGHTED AUTHENTICATION MECHANISM IN NEMO-BASED FAST PROXY MOBILE IPV6 NETWORKS

    OpenAIRE

    Illkyun Im; Jongpil Jeong

    2012-01-01

    This paper reinforced security under the network evaluation of wire/wireless integration of NEMO (NEwork MObility) supporting mobility and network-based PMIPv6 (Proxy Mobile IPv6). It also proposes SK-L2AM (Symmetric Key-Based Local-Lighted Authentication Mechanism) based on simple key which reduces code calculation and authentication delay costs. Moreover, fast handoff technique was also adopted to reduce handoff delay time in PMIPv6 and X-FPMIPv6 (eXtension of Fast Handoff for PMIPv6) was u...

  11. Failure of the Nemo trial: bumetanide is a promising agent to treat many brain disorders but not newborn seizures

    Directory of Open Access Journals (Sweden)

    Yehezkel eBen-Ari

    2016-04-01

    Full Text Available The diuretic bumetanide failed to treat acute seizures due to hypoxic ischemic encephalopathy (HIE in newborn babies and was associated with hearing loss (NEMO trial; 1. On the other hand, clinical and experimental observations suggest that the diuretic might provide novel therapy for many brain disorders including autistic spectrum disorder, schizophrenia, Rett syndrome and Parkinson disease. Here, we discuss the differences between the pathophysiology of severe recurrent seizures in the neonates and neurological and psychiatric disorders stressing the uniqueness of severe seizures in newborn in comparison to other disorders.

  12. Failure of the Nemo Trial: Bumetanide Is a Promising Agent to Treat Many Brain Disorders but Not Newborn Seizures.

    Science.gov (United States)

    Ben-Ari, Yehezkel; Damier, Philippe; Lemonnier, Eric

    2016-01-01

    The diuretic bumetanide failed to treat acute seizures due to hypoxic ischemic encephalopathy (HIE) in newborn babies and was associated with hearing loss (NEMO trial, Pressler et al., 2015). On the other hand, clinical and experimental observations suggest that the diuretic might provide novel therapy for many brain disorders including Autism Spectrum Disorders (ASD), schizophrenia, Rett syndrome, and Parkinson disease. Here, we discuss the differences between the pathophysiology of severe recurrent seizures in the neonates and neurological and psychiatric disorders stressing the uniqueness of severe seizures in newborn in comparison to other disorders. PMID:27147965

  13. Measurement of the two neutrino double beta decay half-life of Zr-96 with the NEMO-3 detector

    OpenAIRE

    Argyriades, J.; Arnold, R.; Augier, C.; Baker, J.; Barabash, A. S.; Basharina-Freshville, A.; Bongrand, M.; Broudin-Bay, G.; Brudanin, V.(Joint Institute for Nuclear Research, Dubna, Russia); Caffrey, A. J.; Chapon, A.; Chauveau, E.; Daraktchieva, Z.; Durand, D.; Egorov, V.

    2009-01-01

    Using 9.4 g of Zr-96 and 1221 days of data from the NEMO-3 detector corresponding to 0.031 kg yr, the obtained 2vbb decay half-life measurement is [2.35 +/- 0.14(stat) +/- 0.16(syst)] x 10^19 yr. Different characteristics of the final state electrons have been studied, such as the energy sum, individual electron energy, and angular distribution. The 2v nuclear matrix element is extracted using the measured 2vbb half-life and is 0.049 +/- 0.002. Constraints on 0vbb decay have also been set.

  14. Measurement of the beta beta Decay Half-Life of Te-130 with the NEMO-3 Detector

    OpenAIRE

    Arnold, R.; Augier, C.; Baker, J.; Barabash, A. S.; Basharina-Freshville, A.; Blondel, S.; Bongrand, M.; Broudin-Bay, G.; Brudanin, V.(Joint Institute for Nuclear Research, Dubna, Russia); Caffrey, A. J.; Chapon, A.; Chauveau, E.; Durand, D.; Egorov, V.; Flack, R.

    2011-01-01

    We report results from the NEMO-3 experiment based on an exposure of 1275 days with 661 g of Te-130 in the form of enriched and natural tellurium foils. The beta beta decay rate of Te-130 is found to be greater than zero with a significance of 7.7 standard deviations and the half-life is measured to be T-1/2(2v)=[7.0 +/- 0.9(stat) +/- 1: 1(syst)] x 10(20) yr. This represents the most precise measurement of this half- life yet published and the first real-time observation of this decay.

  15. Measurement of the Double Beta Decay Half-life of 130Te with the NEMO-3 Detector

    CERN Document Server

    Arnold, R; Baker, J; Barabash, A S; Basharina-Freshville, A; Blondel, S; Bongrand, M; Broudin-Bay, G; Brudanin, V; Caffrey, A J; Chapon, A; Chauveau, E; Durand, D; Egorov, V; Flack, R; Garrido, X; Grozier, J; Guillon, B; Hubert, Ph; Jackson, C M; Jullian, S; Kauer, M; Klimenko, A; Kochetov, O; Konovalov, S I; Kovalenko, V; Lalanne, D; Lamhamdi, T; Lang, K; Liptak, Z; Lutter, G; Mamedov, F; Marquet, Ch; Martin-Albo, J; Mauger, F; Mott, J; Nachab, A; Nemchenok, I; Nguyen, C H; Nova, F; Novella, P; Ohsumi, H; Pahlka, R B; Perrot, F; Piquemal, F; Reyss, J L; Richards, B; Ricol, J S; Saakyan, R; Sarazin, X; Shitov, Yu; Simard, L; Šimkovic, F; Smolnikov, A; Söldner-Rembold, S; Štekl, I; Suhonen, J; Sutton, C S; Szklarz, G; Thomas, J; Timkin, V; Torre, S; Tretyak, V I; Umatov, V; Vála, L; Vanyushin, I; Vasiliev, V; Vorobel, V; Vylov, T; Zukauskas, A

    2011-01-01

    This Letter reports results from the NEMO-3 experiment based on an exposure of 1275 days with 661g of 130Te in the form of enriched and natural tellurium foils. With this data set the double beta decay rate of 130Te is found to be non-zero with a significance of 7.7 standard deviations and the half-life is measured to be T1/2 = (7.0 +/- 0.9(stat) +/- 1.1(syst)) x 10^{20} yr. This represents the most precise measurement of this half-life yet published and the first real-time observation of this decay.

  16. Measurement of the Double Beta Decay Half-life of 130Te with the NEMO-3 Detector

    OpenAIRE

    Arnold, R.; Augier, C.; Baker, J.; Barabash, A. S.; Basharina-Freshville, A.; Blondel, S.; Bongrand, M.; Broudin-Bay, G.; Brudanin, V.(Joint Institute for Nuclear Research, Dubna, Russia); Caffrey, A. J.; Chapon, A.; Chauveau, E.; Durand, D.; Egorov, V.; Flack, R.

    2011-01-01

    This Letter reports results from the NEMO-3 experiment based on an exposure of 1275 days with 661g of 130Te in the form of enriched and natural tellurium foils. The double beta decay rate of 130Te is found to be greater than zero with a significance of 7.7 standard deviations and the half-life is measured to be T1/2 = (7.0 +/- 0.9(stat) +/- 1.1(syst)) x 10^{20} yr. This represents the most precise measurement of this half-life yet published and the first real-time observation of this decay.

  17. Measurement of the ββ decay half-life of 130Te with the NEMO-3 detector.

    Science.gov (United States)

    Arnold, R; Augier, C; Baker, J; Barabash, A S; Basharina-Freshville, A; Blondel, S; Bongrand, M; Broudin-Bay, G; Brudanin, V; Caffrey, A J; Chapon, A; Chauveau, E; Durand, D; Egorov, V; Flack, R; Garrido, X; Grozier, J; Guillon, B; Hubert, Ph; Hugon, C; Jackson, C M; Jullian, S; Kauer, M; Klimenko, A; Kochetov, O; Konovalov, S I; Kovalenko, V; Lalanne, D; Lamhamdi, T; Lang, K; Liptak, Z; Lutter, G; Mamedov, F; Marquet, Ch; Martin-Albo, J; Mauger, F; Mott, J; Nachab, A; Nemchenok, I; Nguyen, C H; Nova, F; Novella, P; Ohsumi, H; Pahlka, R B; Perrot, F; Piquemal, F; Reyss, J L; Richards, B; Ricol, J S; Saakyan, R; Sarazin, X; Simard, L; Simkovic, F; Shitov, Yu; Smolnikov, A; Söldner-Rembold, S; Stekl, I; Suhonen, J; Sutton, C S; Szklarz, G; Thomas, J; Timkin, V; Torre, S; Tretyak, V I; Umatov, V; Vála, L; Vanyushin, I; Vasiliev, V; Vorobel, V; Vylov, Ts; Zukauskas, A

    2011-08-01

    We report results from the NEMO-3 experiment based on an exposure of 1275 days with 661 g of (130)Te in the form of enriched and natural tellurium foils. The ββ decay rate of (130)Te is found to be greater than zero with a significance of 7.7 standard deviations and the half-life is measured to be T(½)(2ν) = [7.0 ± 0.9(stat) ± 1.1(syst)] × 10(20) yr. This represents the most precise measurement of this half-life yet published and the first real-time observation of this decay. PMID:21902318

  18. Measurement of the ββ Decay Half-Life of Te130 with the NEMO-3 Detector

    Science.gov (United States)

    Arnold, R.; Augier, C.; Baker, J.; Barabash, A. S.; Basharina-Freshville, A.; Blondel, S.; Bongrand, M.; Broudin-Bay, G.; Brudanin, V.; Caffrey, A. J.; Chapon, A.; Chauveau, E.; Durand, D.; Egorov, V.; Flack, R.; Garrido, X.; Grozier, J.; Guillon, B.; Hubert, Ph.; Hugon, C.; Jackson, C. M.; Jullian, S.; Kauer, M.; Klimenko, A.; Kochetov, O.; Konovalov, S. I.; Kovalenko, V.; Lalanne, D.; Lamhamdi, T.; Lang, K.; Liptak, Z.; Lutter, G.; Mamedov, F.; Marquet, Ch.; Martin-Albo, J.; Mauger, F.; Mott, J.; Nachab, A.; Nemchenok, I.; Nguyen, C. H.; Nova, F.; Novella, P.; Ohsumi, H.; Pahlka, R. B.; Perrot, F.; Piquemal, F.; Reyss, J. L.; Richards, B.; Ricol, J. S.; Saakyan, R.; Sarazin, X.; Simard, L.; Šimkovic, F.; Shitov, Yu.; Smolnikov, A.; Söldner-Rembold, S.; Štekl, I.; Suhonen, J.; Sutton, C. S.; Szklarz, G.; Thomas, J.; Timkin, V.; Torre, S.; Tretyak, V. I.; Umatov, V.; Vála, L.; Vanyushin, I.; Vasiliev, V.; Vorobel, V.; Vylov, Ts.; Zukauskas, A.

    2011-08-01

    We report results from the NEMO-3 experiment based on an exposure of 1275 days with 661 g of Te130 in the form of enriched and natural tellurium foils. The ββ decay rate of Te130 is found to be greater than zero with a significance of 7.7 standard deviations and the half-life is measured to be T1/22ν=[7.0±0.9(stat)±1.1(syst)]×1020yr. This represents the most precise measurement of this half-life yet published and the first real-time observation of this decay.

  19. DNA barcode goes two-dimensions: DNA QR code web server.

    Science.gov (United States)

    Liu, Chang; Shi, Linchun; Xu, Xiaolan; Li, Huan; Xing, Hang; Liang, Dong; Jiang, Kun; Pang, Xiaohui; Song, Jingyuan; Chen, Shilin

    2012-01-01

    The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR) code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications. PMID:22574113

  20. DNA barcode goes two-dimensions: DNA QR code web server.

    Directory of Open Access Journals (Sweden)

    Chang Liu

    Full Text Available The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications.

  1. Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species

    OpenAIRE

    Shilin Chen; Hui Yao; Jianping Han; Chang Liu; Jingyuan Song; Linchun Shi; Yingjie Zhu; Xinye Ma; Ting Gao; Xiaohui Pang; Kun Luo; Ying Li; Xiwen Li; Xiaocheng Jia; Yulin Lin

    2010-01-01

    BACKGROUND: The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL+matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over. METHODOLOGY/PRINCIPAL FINDINGS: Here, we compared seven candidate DNA barcod...

  2. DNA barcode information for the sugar cane moth borer Diatraea saccharalis.

    Science.gov (United States)

    Bravo, J P; Silva, J L C; Munhoz, R E F; Fernandez, M A

    2008-01-01

    We reviewed the use and relevance of barcodes for insect studies and investigated the barcode sequence of Diatraea saccharalis. This sequence has a high level of homology (99%) with the barcode sequence of the Crambidae (Lepidoptera). The sequence data can be used to construct relationships between species, allowing a multidisciplinary approach for taxonomy, which includes morphological, molecular and distribution data, all of which are essential for the understanding of biodiversity. The D. saccharalis barcode is a previously undescribed sequence that could be used to analyze Lepidoptera biology. PMID:18767242

  3. Applications of Barcode Images by Enhancing the Two-Dimensional Recognition Rate

    Directory of Open Access Journals (Sweden)

    Kun-Hsien Lin

    2012-07-01

    Full Text Available The paper not only proposed the latest Two-Dimensional Barcodes Image-processing Module, but also captured the smallest camera screens (320 240 with different focal distances and tried to find out “Finder Pattern” for positioning images. Further, use CROBU (Conversion Ratio of Basic Unit the thesis proposed to convert 2-D barcodes into 1-pixel ratio to match images before judging recognition rate of 2-D barcodes through matching. Normally speaking, 2-D barcodes are deciphered and recognized by software while the thesis recognizes 2-D barcodes and enhances implementation speed up to 10-cm accurate max. using image matching. The 2-D barcodes image-processing module the thesis proposed does capture and standardize image with complicated background or raw edge, which enhances 2-D barcodes recognition rate. The main point of this study is to construct a platform to manage or suggest nutrients human body needs. The Quick Response Code image of 2-D barcodes represents vitamin and calories information. 2-D barcodes taken instantly by MATLAB and CCD camera can be used to list nutrients from foods you eat recently and suggest what else you should eat for the purpose of health management.

  4. DNA barcode analysis of butterfly species from Pakistan points towards regional endemism

    Science.gov (United States)

    Ashfaq, Muhammad; Akhtar, Saleem; Khan, Arif M; Adamowicz, Sarah J; Hebert, Paul D N

    2013-01-01

    DNA barcodes were obtained for 81 butterfly species belonging to 52 genera from sites in north-central Pakistan to test the utility of barcoding for their identification and to gain a better understanding of regional barcode variation. These species represent 25% of the butterfly fauna of Pakistan and belong to five families, although the Nymphalidae were dominant, comprising 38% of the total specimens. Barcode analysis showed that maximum conspecific divergence was 1.6%, while there was 1.7–14.3% divergence from the nearest neighbour species. Barcode records for 55 species showed <2% sequence divergence to records in the Barcode of Life Data Systems (BOLD), but only 26 of these cases involved specimens from neighbouring India and Central Asia. Analysis revealed that most species showed little incremental sequence variation when specimens from other regions were considered, but a threefold increase was noted in a few cases. There was a clear gap between maximum intraspecific and minimum nearest neighbour distance for all 81 species. Neighbour-joining cluster analysis showed that members of each species formed a monophyletic cluster with strong bootstrap support. The barcode results revealed two provisional species that could not be clearly linked to known taxa, while 24 other species gained their first coverage. Future work should extend the barcode reference library to include all butterfly species from Pakistan as well as neighbouring countries to gain a better understanding of regional variation in barcode sequences in this topographically and climatically complex region. PMID:23789612

  5. DNA Barcode Goes Two-Dimensions: DNA QR Code Web Server

    OpenAIRE

    Chang Liu; Linchun Shi; Xiaolan Xu; Huan Li; Hang Xing; Dong Liang; Kun Jiang; Xiaohui Pang; Jingyuan Song; Shilin Chen

    2012-01-01

    The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three diff...

  6. A 1/16° eddying simulation of the global NEMO sea-ice-ocean system

    Science.gov (United States)

    Iovino, Doroteaciro; Masina, Simona; Storto, Andrea; Cipollone, Andrea; Stepanov, Vladimir N.

    2016-08-01

    Analysis of a global eddy-resolving simulation using the NEMO general circulation model is presented. The model has 1/16° horizontal spacing at the Equator, employs two displaced poles in the Northern Hemisphere, and uses 98 vertical levels. The simulation was spun up from rest and integrated for 11 model years, using ERA-Interim reanalysis as surface forcing. Primary intent of this hindcast is to test how the model represents upper ocean characteristics and sea ice properties. Analysis of the zonal averaged temperature and salinity, and the mixed layer depth indicate that the model average state is in good agreement with observed fields and that the model successfully represents the variability in the upper ocean and at intermediate depths. Comparisons against observational estimates of mass transports through key straits indicate that most aspects of the model circulation are realistic. As expected, the simulation exhibits turbulent behaviour and the spatial distribution of the sea surface height (SSH) variability from the model is close to the observed pattern. The distribution and volume of the sea ice are, to a large extent, comparable to observed values. Compared with a corresponding eddy-permitting configuration, the performance of the model is significantly improved: reduced temperature and salinity biases, in particular at intermediate depths, improved mass and heat transports, better representation of fluxes through narrow and shallow straits, and increased global-mean eddy kinetic energy (by ˜ 40 %). However, relatively minor weaknesses still exist such as a lower than observed magnitude of the SSH variability. We conclude that the model output is suitable for broader analysis to better understand upper ocean dynamics and ocean variability at global scales. This simulation represents a major step forward in the global ocean modelling at the Euro-Mediterranean Centre on Climate Change and constitutes the groundwork for future applications to short

  7. Security Issues for 2D Barcodes Ticketing Systems

    Directory of Open Access Journals (Sweden)

    Cristian Toma

    2011-03-01

    Full Text Available The paper presents a solution for endcoding/decoding access to the subway public transportation systems. First part of the paper is dedicated through section one and two to the most used 2D barcodes used in the market – QR and DataMatrix. The sample for DataMatrix is author propietary and the QR sample is from the QR standard [2]. The section three presents MMS and Digital Rights Management topics used for issuing the 2D barcodes tickets. The second part of the paper, starting with section four shows the architecture of Subway Ticketing Systems and the proposed procedure for the ticket issuing. The conclusions identify trends of the security topics in the public transportation systems.

  8. System Design Considerations In Bar-Code Laser Scanning

    Science.gov (United States)

    Barkan, Eric; Swartz, Jerome

    1984-08-01

    The unified transfer function approach to the design of laser barcode scanner signal acquisition hardware is considered. The treatment of seemingly disparate system areas such as the optical train, the scanning spot, the electrical filter circuits, the effects of noise, and printing errors is presented using linear systems theory. Such important issues as determination of depth of modulation, filter specification, tolerancing of optical components, and optimi-zation of system performance in the presence of noise are discussed. The concept of effective spot size to allow for impact of optical system and analog processing circuitry upon depth of modulation is introduced. Considerations are limited primarily to Gaussian spot profiles, but also apply to more general cases. Attention is paid to realistic bar-code symbol models and to implications with respect to printing tolerances.

  9. Magnetic micro-barcodes for molecular tagging applications

    International Nuclear Information System (INIS)

    We present proof-of-principle experiments and simulations that demonstrate a new biological assay technology in which microscopic tags carrying multi-bit magnetic codes are used to label probe biomolecules. It is demonstrated that these 'micro-barcode tags' can be encoded, transported using micro-fluidics and are compatible with surface chemistry. We also present simulations and experimental results which suggest the feasibility of decoding the micro-barcode tags using magnetoresistive sensors. Together, these results demonstrate substantial progress towards meeting the critical requirements of a magnetically encoded, high-throughput and portable biological assay platform. We also show that an extension of our technology could potentially be used to label libraries consisting of ∼104 distinct probe molecules, and could therefore have a strong impact on mainstream medical diagnostics.

  10. Development of barcode system for internal dose monitoring

    International Nuclear Information System (INIS)

    In Tarapur Atomic Power Station unit-3 and 4, which is 540 MWe pressurized heavy water reactor, tritium is produced in primary heat transport system and moderator system. Tritium is a major contributor to the internal dose. Internal dose contributes about 30% of the collective dose. Internal dose monitoring and its control are important to control the collective dose. Estimation of internal dose is done by analysis of bioassay samples of radiation workers. In a month, about 7000 bioassay samples are analysed for the internal dose assessment during normal operation, and about 12000 during the biennial shut down of the reactor. To enhance the sample preparation and counting performance, minimize the entry errors and reduce the processing time, barcode based label generation system was developed for the internal dose monitoring. This paper discusses about the use of barcode system in the internal dose monitoring at TAPS 3 and 4. (author)

  11. ISBN and QR Barcode Scanning Mobile App for Libraries

    Directory of Open Access Journals (Sweden)

    Graham McCarthy

    2011-04-01

    Full Text Available This article outlines the development of a mobile application for the Ryerson University Library. The application provides for ISBN barcode scanning that results in a lookup of library copies and services for the book scanned, as well as QR code scanning. Two versions of the application were developed, one for iOS and one for Android. The article includes some details on the free packages used for barcode scanning functionality. Source code for the Ryerson iOS and Android applications are freely available, and instructions are provided on customizing the Ryerson application for use in other library environments. Some statistics on the number of downloads of the Ryerson mobile app by users are included.

  12. Evaluating Ethanol-based Sample Preservation to Facilitate Use of DNA Barcoding in Routine Freshwater Biomonitoring Programs Using Benthic Macroinvertebrates

    Science.gov (United States)

    Molecular methods, such as DNA barcoding, have the potential in enhance biomonitoring programs worldwide. Altering routinely used sample preservation methods to protect DNA from degradation may pose a potential impediment to application of DNA barcoding and metagenomics for biom...

  13. DNA barcoding provides distinction between Radix Astragali and its adulterants

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Based on variable nuclear and/or organellar DNA sequences among vastly divergent species as well as morphologically indistinguishable species, DNA barcoding is widely applicable in species identification, biodiversity studies, forensic analyses, and authentication of medicinal plants. The roots of Astragalus membranaceus and A. membranaceus var. mongholica are commonly used as Radix Astragali in several Asian countries, including China, Japan, and Korea. However, in addition to the two species recorded in the Chinese Pharmacopoeia, there are twenty-three species from different genera including Astragalus, Oxytropis, Hedysarum, and Glycyrrhiza, which have been used as adulterants not only in trading markets but also by the herbal medicine industry. Therefore, a simple, reliable, and accurate classification method is important for distinguishing authentic Radix Astragali from its adulterants. In this study, we acquired data for 37 samples from four related genera within the family Fabaceae. Then we compared four candidate DNA barcoding markers using ITS, matK, rbcL, and coxI sequences from nuclear, chloroplast, and mitochondrial genomes, all commonly used for plants to identify genetic variations among genera, intraspecies, and interspecies. We observed higher divergences among genera and interspecies for ITS, which have the average Kimura 2-parameter distances of 4.5% and 14.1%, respectively, whereas matK was found to have sufficient divergence at the intraspecific level. Moreover, two indels detected in the matK sequence are useful for PCR studies in distinguishing Radix Astragali from its adulterants. This study suggests that the combined barcoding regions of ITS and matK are superior barcodes for Radix Astragali and further studies should focus on evaluating the applicability and accuracy of such combined markers for a wide range of traditional Chinese herbs.

  14. Neotropical bats: estimating species diversity with DNA barcodes.

    Directory of Open Access Journals (Sweden)

    Elizabeth L Clare

    Full Text Available DNA barcoding using the cytochrome c oxidase subunit 1 gene (COI is frequently employed as an efficient method of species identification in animal life and may also be used to estimate species richness, particularly in understudied faunas. Despite numerous past demonstrations of the efficiency of this technique, few studies have attempted to employ DNA barcoding methodologies on a large geographic scale, particularly within tropical regions. In this study we survey current and potential species diversity using DNA barcodes with a collection of more than 9000 individuals from 163 species of Neotropical bats (order Chiroptera. This represents one of the largest surveys to employ this strategy on any animal group and is certainly the largest to date for land vertebrates. Our analysis documents the utility of this tool over great geographic distances and across extraordinarily diverse habitats. Among the 163 included species 98.8% possessed distinct sets of COI haplotypes making them easily recognizable at this locus. We detected only a single case of shared haplotypes. Intraspecific diversity in the region was high among currently recognized species (mean of 1.38%, range 0-11.79% with respect to birds, though comparable to other bat assemblages. In 44 of 163 cases, well-supported, distinct intraspecific lineages were identified which may suggest the presence of cryptic species though mean and maximum intraspecific divergence were not good predictors of their presence. In all cases, intraspecific lineages require additional investigation using complementary molecular techniques and additional characters such as morphology and acoustic data. Our analysis provides strong support for the continued assembly of DNA barcoding libraries and ongoing taxonomic investigation of bats.

  15. DNA barcoding: complementing morphological identification of mosquito species in Singapore

    OpenAIRE

    Chan, Abigail; Chiang, Lee-Pei; Hapuarachchi, Hapuarachchige C; Tan, Cheong-Huat; Pang, Sook-Cheng; Lee, Ruth; Lee, Kim-Sung; Ng, Lee-Ching; Lam-Phua, Sai-Gek

    2014-01-01

    Background Taxonomy that utilizes morphological characteristics has been the gold standard method to identify mosquito species. However, morphological identification is challenging when the expertise is limited and external characters are damaged because of improper specimen handling. Therefore, we explored the applicability of mitochondrial cytochrome C oxidase subunit 1 (COI) gene-based DNA barcoding as an alternative tool to identify mosquito species. In the present study, we compared the ...

  16. Denture identification using unique identification authority of India barcode

    Science.gov (United States)

    Mahoorkar, Sudhindra; Jain, Anoop

    2013-01-01

    Over the years, various denture marking systems have been reported in the literature for personal identification. They have been broadly divided into surface marking and inclusion methods. In this technique, patient's unique identification number and barcode printed in the patient's Aadhaar card issued by Unique Identification Authority of India (UIDAI) are used as denture markers. This article describes a simple, quick, and economical method for identification of individual. PMID:23960418

  17. Barcode Annotations for Medical Image Retrieval: A Preliminary Investigation

    OpenAIRE

    Tizhoosh, Hamid R.

    2015-01-01

    This paper proposes to generate and to use barcodes to annotate medical images and/or their regions of interest such as organs, tumors and tissue types. A multitude of efficient feature-based image retrieval methods already exist that can assign a query image to a certain image class. Visual annotations may help to increase the retrieval accuracy if combined with existing feature-based classification paradigms. Whereas with annotations we usually mean textual descriptions, in this paper barco...

  18. A universal DNA mini-barcode for biodiversity analysis

    OpenAIRE

    Hebert Paul DN; Hickey Donal A; Landry Jean-François; Singer Gregory AC; Meusnier Isabelle; Hajibabaei Mehrdad

    2008-01-01

    Abstract Background The goal of DNA barcoding is to develop a species-specific sequence library for all eukaryotes. A 650 bp fragment of the cytochrome c oxidase 1 (CO1) gene has been used successfully for species-level identification in several animal groups. It may be difficult in practice, however, to retrieve a 650 bp fragment from archival specimens, (because of DNA degradation) or from environmental samples (where universal primers are needed). Results We used a bioinformatics analysis ...

  19. Patterns of DNA Barcode Variation in Canadian Marine Molluscs

    OpenAIRE

    Layton, Kara K. S.; Martel, André L.; Hebert, Paul D. N.

    2014-01-01

    BACKGROUND: Molluscs are the most diverse marine phylum and this high diversity has resulted in considerable taxonomic problems. Because the number of species in Canadian oceans remains uncertain, there is a need to incorporate molecular methods into species identifications. A 648 base pair segment of the cytochrome c oxidase subunit I gene has proven useful for the identification and discovery of species in many animal lineages. While the utility of DNA barcoding in molluscs has been demonst...

  20. Pooled‐matrix protein interaction screens using Barcode Fusion Genetics

    OpenAIRE

    Yachie, Nozomu; Petsalaki, Evangelia; Mellor, Joseph C.; Weile, Jochen; Jacob, Yves; Verby, Marta; Ozturk, Sedide B.; Li, Siyang; Cote, Atina G; Mosca, Roberto; Knapp, Jennifer J; Ko, Minjeong; Yu, Analyn; Gebbia, Marinella; Sahni, Nidhi

    2016-01-01

    Abstract High‐throughput binary protein interaction mapping is continuing to extend our understanding of cellular function and disease mechanisms. However, we remain one or two orders of magnitude away from a complete interaction map for humans and other major model organisms. Completion will require screening at substantially larger scales with many complementary assays, requiring further efficiency gains in proteome‐scale interaction mapping. Here, we report Barcode Fusion Genetics‐Yeast Tw...

  1. Magnetic Barcode Assay for Genetic Detection of Pathogens

    OpenAIRE

    Liong, Monty; Hoang, Anh N.; Chung, Jaehoon; Gural, Nil; Ford, Christopher B; Min, Changwook; Shah, Rupal R.; Ahmad, Rushdy; Fernandez-Suarez, Marta; Fortune, Sarah M.; Toner, Mehmet; Lee, Hakho; Weissleder, Ralph

    2013-01-01

    The task of rapidly identifying patients infected with Mycobacterium tuberculosis (MTB) in resource-constrained environments remains a challenge. A sensitive and robust platform that does not require bacterial isolation or culture is critical in making informed diagnostic and therapeutic decisions. Here we introduce a platform for the detection of nucleic acids based on a magnetic barcoding strategy. PCR-amplified mycobacterial genes are sequence-specifically captured on microspheres, labeled...

  2. Texture Features based Blur Classification in Barcode Images

    OpenAIRE

    Shamik Tiwari; Vidya Prasad Shukla; Sangappa Birada; Ajay Singh

    2013-01-01

    Blur is an undesirable phenomenon which appears as image degradation. Blur classification is extremely desirable before application of any blur parameters estimation approach in case of blind restoration of barcode image. A novel approach to classify blur in motion, defocus, and co-existence of both blur categories is presented in this paper. The key idea involves statistical features extraction of blur pattern in frequency domain and designing of blur classification system with feed forward ...

  3. Denture identification using unique identification authority of India barcode

    Directory of Open Access Journals (Sweden)

    Sudhindra Mahoorkar

    2013-01-01

    Full Text Available Over the years, various denture marking systems have been reported in the literature for personal identification. They have been broadly divided into surface marking and inclusion methods. In this technique, patient′s unique identification number and barcode printed in the patient′s Aadhaar card issued by Unique Identification Authority of India (UIDAI are used as denture markers. This article describes a simple, quick, and economical method for identification of individual.

  4. Blind Detection of Severely Blurred 1D Barcode

    OpenAIRE

    Dridi, Noura; Delignon, Yves; Sawaya, Wadih; Septier, François

    2010-01-01

    In this paper, we present a joint blind channel estimation and symbol detection for decoding a blurred and noisy 1D barcode captured image. From an information transmission point of view, we show that the channel impulse response, the noise power and the symbols can be efficiently estimated by taking into account the signal structure such as the cyclostationary property of the hidden Markov process to estimate. Based on the Expectation-Maximisation method, we show that the new algorithm offer...

  5. Denture identification using unique identification authority of India barcode

    OpenAIRE

    Sudhindra Mahoorkar; Anoop Jain

    2013-01-01

    Over the years, various denture marking systems have been reported in the literature for personal identification. They have been broadly divided into surface marking and inclusion methods. In this technique, patient′s unique identification number and barcode printed in the patient′s Aadhaar card issued by Unique Identification Authority of India (UIDAI) are used as denture markers. This article describes a simple, quick, and economical method for identification of individual.

  6. Identification and Typing of Human Enterovirus: A Genomic Barcode Approach

    OpenAIRE

    Chengguo Wei; Guoqing Wang; Xin Chen; Honglan Huang; Bin Liu; Ying Xu; Fan Li

    2011-01-01

    Identification and typing of human enterovirus (HEVs) are important to pathogen detection and therapy. Previous phylogeny-based typing methods are mainly based on multiple sequence alignments of specific genes in the HEVs, but the results are not stable with respect to different choices of genes. Here we report a novel method for identification and typing of HEVs based on information derived from their whole genomes. Specifically, we calculate the k-mer based barcode image for each genome, HE...

  7. SURVEY ON INFORMATION HIDING TECHNIQUES USING QR BARCODE

    OpenAIRE

    Manoj S. Rewatkar; Shital A. Raut

    2014-01-01

    Nowadays, the information processing system plays crucial part in the internet. Online information security has become the top priority in all sectors. Failing to provide online information security may cause loss of critical information or someone may use or distribute such information for malicious purpose. Recently QR barcodes have been used as an effective way to securely share information. This paper presents the survey on information hiding techniques which can share high...

  8. Detection Tuna and Processed Products Based Protein and DNA Barcoding

    OpenAIRE

    Nuring Wulansari; Mala Nurilamala; Nurjanah

    2015-01-01

    Tuna is the second largest fishery commodity in Indonesia after the shrimp. Since the high demand and the limited stock of tuna resulted in fraudulent chance. Authentication is required to meassure consumers regarding the accuracy of its labeling and food safety. In this study, the authentication was based on protein and DNA barcoding using cytochrome-b gene (cyt-b) of the mitochondrial DNA as the target of gene. Primer of cyt b gene was designed based on the tuna species. This...

  9. DNA barcoding for species Identification in prepared fishery products

    OpenAIRE

    ANNA MOTTOLA; PATRIZIA MARCHETTI; MARILISA BOTTARO; ANGELA DI PINTO

    2014-01-01

    Considering that seafood mislabeling has been widely reported throughout the world and that the authentication of food components is one of the key issues in food quality, the aim of this study was to use DNA barcoding to investigate the prevalence of mislabeling among fresh prepared fishery products from markets and supermarkets located in Apulia (SE Italy). The study reveals a high occurrence of species mislabeling (42%) in the prepared fillet products, further evidence of the need for incr...

  10. DNA barcoding and taxonomy: dark taxa and dark texts.

    Science.gov (United States)

    Page, Roderic D M

    2016-09-01

    Both classical taxonomy and DNA barcoding are engaged in the task of digitizing the living world. Much of the taxonomic literature remains undigitized. The rise of open access publishing this century and the freeing of older literature from the shackles of copyright have greatly increased the online availability of taxonomic descriptions, but much of the literature of the mid- to late-twentieth century remains offline ('dark texts'). DNA barcoding is generating a wealth of computable data that in many ways are much easier to work with than classical taxonomic descriptions, but many of the sequences are not identified to species level. These 'dark taxa' hamper the classical method of integrating biodiversity data, using shared taxonomic names. Voucher specimens are a potential common currency of both the taxonomic literature and sequence databases, and could be used to help link names, literature and sequences. An obstacle to this approach is the lack of stable, resolvable specimen identifiers. The paper concludes with an appeal for a global 'digital dashboard' to assess the extent to which biodiversity data are available online.This article is part of the themed issue 'From DNA barcodes to biomes'. PMID:27481786

  11. A DNA barcoding approach to characterize pollen collected by honeybees.

    Directory of Open Access Journals (Sweden)

    Andrea Galimberti

    Full Text Available In the present study, we investigated DNA barcoding effectiveness to characterize honeybee pollen pellets, a food supplement largely used for human nutrition due to its therapeutic properties. We collected pollen pellets using modified beehives placed in three zones within an alpine protected area (Grigna Settentrionale Regional Park, Italy. A DNA barcoding reference database, including rbcL and trnH-psbA sequences from 693 plant species (104 sequenced in this study was assembled. The database was used to identify pollen collected from the hives. Fifty-two plant species were identified at the molecular level. Results suggested rbcL alone could not distinguish among congeneric plants; however, psbA-trnH identified most of the pollen samples at the species level. Substantial variability in pollen composition was observed between the highest elevation locality (Alpe Moconodeno, characterized by arid grasslands and a rocky substrate, and the other two sites (Cornisella and Ortanella at lower altitudes. Pollen from Ortanella and Cornisella showed the presence of typical deciduous forest species; however in samples collected at Ortanella, pollen of the invasive Lonicera japonica, and the ornamental Pelargonium x hortorum were observed. Our results indicated pollen composition was largely influenced by floristic local biodiversity, plant phenology, and the presence of alien flowering species. Therefore, pollen molecular characterization based on DNA barcoding might serve useful to beekeepers in obtaining honeybee products with specific nutritional or therapeutic characteristics desired by food market demands.

  12. A DNA barcoding approach to characterize pollen collected by honeybees.

    Science.gov (United States)

    Galimberti, Andrea; De Mattia, Fabrizio; Bruni, Ilaria; Scaccabarozzi, Daniela; Sandionigi, Anna; Barbuto, Michela; Casiraghi, Maurizio; Labra, Massimo

    2014-01-01

    In the present study, we investigated DNA barcoding effectiveness to characterize honeybee pollen pellets, a food supplement largely used for human nutrition due to its therapeutic properties. We collected pollen pellets using modified beehives placed in three zones within an alpine protected area (Grigna Settentrionale Regional Park, Italy). A DNA barcoding reference database, including rbcL and trnH-psbA sequences from 693 plant species (104 sequenced in this study) was assembled. The database was used to identify pollen collected from the hives. Fifty-two plant species were identified at the molecular level. Results suggested rbcL alone could not distinguish among congeneric plants; however, psbA-trnH identified most of the pollen samples at the species level. Substantial variability in pollen composition was observed between the highest elevation locality (Alpe Moconodeno), characterized by arid grasslands and a rocky substrate, and the other two sites (Cornisella and Ortanella) at lower altitudes. Pollen from Ortanella and Cornisella showed the presence of typical deciduous forest species; however in samples collected at Ortanella, pollen of the invasive Lonicera japonica, and the ornamental Pelargonium x hortorum were observed. Our results indicated pollen composition was largely influenced by floristic local biodiversity, plant phenology, and the presence of alien flowering species. Therefore, pollen molecular characterization based on DNA barcoding might serve useful to beekeepers in obtaining honeybee products with specific nutritional or therapeutic characteristics desired by food market demands. PMID:25296114

  13. Bar-code technology applied to drug-use evaluation.

    Science.gov (United States)

    Zarowitz, B J; Petitta, A; Mlynarek, M; Touchette, M; Peters, M; Long, P; Patel, R

    1993-05-01

    Bar-code technology was used to determine: (1) patterns in histamine H2-receptor antagonist use and (2) the occurrence of adverse drug effects and drug interactions associated with the use of these agents in critically ill patients. Patients at Henry Ford Hospital (Detroit) receiving histamine H2-receptor antagonists over a two-month period were evaluated. Clinical information was collected in the intensive care units by using a bar-code system. The data-capture menu was based on drug-use-evaluation criteria for H2-receptor antagonists. Data collected in the scanning wands were uploaded into a computer database and were analyzed at the end of the study. Data were collected for 207 patients. Cimetidine was the predominant H2-receptor antagonist used, and the predominant indication was stress-ulcer prophylaxis. Dosing trends followed accepted guidelines for cimetidine dosage adjustment in renal and hepatic failure. Two drug interactions and six adverse drug reactions occurred. Pharmacists made 92 recommendations to the medical staff regarding modification in therapy, involving 32% of the patients. Data collection required an average of 10 minutes per day each for three pharmacists. H2-receptor antagonist use patterns were evaluated in intensive care units through the application of bar-code technology. The speed and efficiency of this automated tool facilitated collection of a large amount of data. PMID:8099468

  14. DNA barcoding in diverse educational settings: five case studies

    Science.gov (United States)

    Imondi, Ralph; James, Karen; Spencer, Diana; Steinke, Dirk

    2016-01-01

    Despite 250 years of modern taxonomy, there remains a large biodiversity knowledge gap. Most species remain unknown to science. DNA barcoding can help address this gap and has been used in a variety of educational contexts to incorporate original research into school curricula and informal education programmes. A growing body of evidence suggests that actively conducting research increases student engagement and retention in science. We describe case studies in five different educational settings in Canada and the USA: a programme for primary and secondary school students (ages 5–18), a year-long professional development programme for secondary school teachers, projects embedding this research into courses in a post-secondary 2-year institution and a degree-granting university, and a citizen science project. We argue that these projects are successful because the scientific content is authentic and compelling, DNA barcoding is conceptually and technically straightforward, the workflow is adaptable to a variety of situations, and online tools exist that allow participants to contribute high-quality data to the international research effort. Evidence of success includes the broad adoption of these programmes and assessment results demonstrating that participants are gaining both knowledge and confidence. There are exciting opportunities for coordination among educational projects in the future. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481792

  15. DNA barcoding in diverse educational settings: five case studies.

    Science.gov (United States)

    Henter, Heather J; Imondi, Ralph; James, Karen; Spencer, Diana; Steinke, Dirk

    2016-09-01

    Despite 250 years of modern taxonomy, there remains a large biodiversity knowledge gap. Most species remain unknown to science. DNA barcoding can help address this gap and has been used in a variety of educational contexts to incorporate original research into school curricula and informal education programmes. A growing body of evidence suggests that actively conducting research increases student engagement and retention in science. We describe case studies in five different educational settings in Canada and the USA: a programme for primary and secondary school students (ages 5-18), a year-long professional development programme for secondary school teachers, projects embedding this research into courses in a post-secondary 2-year institution and a degree-granting university, and a citizen science project. We argue that these projects are successful because the scientific content is authentic and compelling, DNA barcoding is conceptually and technically straightforward, the workflow is adaptable to a variety of situations, and online tools exist that allow participants to contribute high-quality data to the international research effort. Evidence of success includes the broad adoption of these programmes and assessment results demonstrating that participants are gaining both knowledge and confidence. There are exciting opportunities for coordination among educational projects in the future.This article is part of the themed issue 'From DNA barcodes to biomes'. PMID:27481792

  16. Identification and typing of human enterovirus: a genomic barcode approach.

    Directory of Open Access Journals (Sweden)

    Chengguo Wei

    Full Text Available Identification and typing of human enterovirus (HEVs are important to pathogen detection and therapy. Previous phylogeny-based typing methods are mainly based on multiple sequence alignments of specific genes in the HEVs, but the results are not stable with respect to different choices of genes. Here we report a novel method for identification and typing of HEVs based on information derived from their whole genomes. Specifically, we calculate the k-mer based barcode image for each genome, HEV or other human viruses, for a fixed k, 1barcode is defined in terms of the k-mer frequency distribution across the whole genome for all combinations of k-mers. A phylogenetic tree is constructed using a barcode-based distance and a neighbor-joining method among a set of 443 representative non-HEV human viruses and 395 HEV sequences. The tree shows a clear separation of the HEV viruses from all the non-HEV viruses with 100% accuracy and a separation of the HEVs into four distinct clads with 93.4% consistency with a multiple sequence alignment-based phylogeny. Our detailed analyses of the HEVs having different typing results by the two methods indicate that our results are in better agreement with known information about the HEVs.

  17. DNA barcoding birds: from field collection to data analysis.

    Science.gov (United States)

    Lijtmaer, Darío A; Kerr, Kevin C R; Stoeckle, Mark Y; Tubaro, Pablo L

    2012-01-01

    As of February 2011, COI DNA barcode sequences (a 648-bp segment of the 5' end of the mitochondrial gene cytochrome c oxidase I, the standard DNA barcode for animals) have been collected from over 23,000 avian specimens representing 3,800 species, more than one-third of the world's avifauna. Here, we detail the methodology for obtaining DNA barcodes from birds, covering the entire process from field collection to data analysis. We emphasize key aspects of the process and describe in more detail those that are particularly relevant in the case of birds. We provide elemental information about collection of specimens, detailed protocols for DNA extraction and PCR, and basic aspects of sequencing methodology. In particular, we highlight the primer pairs and thermal cycling profiles associated with successful amplification and sequencing from a broad range of avian species. Finally, we succinctly review the methodology for data analysis, including the detection of errors (such as contamination, misidentifications, or amplification of pseudogenes), assessment of species resolution, detection of divergent intraspecific lineages, and identification of unknown specimens. PMID:22684955

  18. Pooled-matrix protein interaction screens using Barcode Fusion Genetics.

    Science.gov (United States)

    Yachie, Nozomu; Petsalaki, Evangelia; Mellor, Joseph C; Weile, Jochen; Jacob, Yves; Verby, Marta; Ozturk, Sedide B; Li, Siyang; Cote, Atina G; Mosca, Roberto; Knapp, Jennifer J; Ko, Minjeong; Yu, Analyn; Gebbia, Marinella; Sahni, Nidhi; Yi, Song; Tyagi, Tanya; Sheykhkarimli, Dayag; Roth, Jonathan F; Wong, Cassandra; Musa, Louai; Snider, Jamie; Liu, Yi-Chun; Yu, Haiyuan; Braun, Pascal; Stagljar, Igor; Hao, Tong; Calderwood, Michael A; Pelletier, Laurence; Aloy, Patrick; Hill, David E; Vidal, Marc; Roth, Frederick P

    2016-01-01

    High-throughput binary protein interaction mapping is continuing to extend our understanding of cellular function and disease mechanisms. However, we remain one or two orders of magnitude away from a complete interaction map for humans and other major model organisms. Completion will require screening at substantially larger scales with many complementary assays, requiring further efficiency gains in proteome-scale interaction mapping. Here, we report Barcode Fusion Genetics-Yeast Two-Hybrid (BFG-Y2H), by which a full matrix of protein pairs can be screened in a single multiplexed strain pool. BFG-Y2H uses Cre recombination to fuse DNA barcodes from distinct plasmids, generating chimeric protein-pair barcodes that can be quantified via next-generation sequencing. We applied BFG-Y2H to four different matrices ranging in scale from ~25 K to 2.5 M protein pairs. The results show that BFG-Y2H increases the efficiency of protein matrix screening, with quality that is on par with state-of-the-art Y2H methods. PMID:27107012

  19. Universal Plant DNA Barcode Loci May Not Work in Complex Groups: A Case Study with Indian Berberis Species

    OpenAIRE

    Sribash Roy; Antariksh Tyagi; Virendra Shukla; Anil Kumar; Singh, Uma M.; Lal Babu Chaudhary; Bhaskar Datt; Bag, Sumit K.; Singh, Pradhyumna K.; Nair, Narayanan K.; Tariq Husain; Rakesh Tuli

    2010-01-01

    BACKGROUND: The concept of DNA barcoding for species identification has gained considerable momentum in animals because of fairly successful species identification using cytochrome oxidase I (COI). In plants, matK and rbcL have been proposed as standard barcodes. However, barcoding in complex genera is a challenging task. METHODOLOGY AND PRINCIPAL FINDINGS: We investigated the species discriminatory power of four reportedly most promising plant DNA barcoding loci (one from nuclear genome--ITS...

  20. Finding NEMO (novel electromaterial muscle oscillator): a polypyrrole powered robotic fish with real-time wireless speed and directional control

    Science.gov (United States)

    McGovern, Scott; Alici, Gursel; Truong, Van-Tan; Spinks, Geoffrey

    2009-09-01

    This paper presents the development of an autonomously powered and controlled robotic fish that incorporates an active flexural joint tail fin, activated through conducting polymer actuators based on polypyrrole (PPy). The novel electromaterial muscle oscillator (NEMO) tail fin assembly on the fish could be controlled wirelessly in real time by varying the frequency and duty cycle of the voltage signal supplied to the PPy bending-type actuators. Directional control was achieved by altering the duty cycle of the voltage input to the NEMO tail fin, which shifted the axis of oscillation and enabled turning of the robotic fish. At low speeds, the robotic fish had a turning circle as small as 15 cm (or 1.1 body lengths) in radius. The highest speed of the fish robot was estimated to be approximately 33 mm s-1 (or 0.25 body lengths s-1) and was achieved with a flapping frequency of 0.6-0.8 Hz which also corresponded with the most hydrodynamically efficient mode for tail fin operation. This speed is approximately ten times faster than those for any previously reported artificial muscle based device that also offers real-time speed and directional control. This study contributes to previously published studies on bio-inspired functional devices, demonstrating that electroactive polymer actuators can be real alternatives to conventional means of actuation such as electric motors.

  1. Use of fluorescence spectroscopy for quantitative investigations of ubiquitin interactions with the ubiquitin-binding domains of NEMO.

    Science.gov (United States)

    Dubosclard, Virginie; Fontan, Elisabeth; Agou, Fabrice

    2015-01-01

    Ubiquitin serves as a signal for a variety of cellular processes and its specific interaction with ubiquitin-binding domain (UBD) regulates key cellular events including protein degradation, cell-cycle control, DNA repair, and kinase activation. Several binding mechanisms for isolated UBDs have been reported in recent years. However, little is known about the mechanism through which proteins containing multiple-UBDs achieve specificity for a particular oligomer of polyUb. The NF-κB essential modulator (NEMO, also known IKKγ), which plays a key role in the NF-κB signaling pathway, belongs to the latter family of proteins since it contains two distal NOA (also known UBAN/CC2-LZ/NUB) and ZF UBDs, separated by an unstructured proline-rich linker of about 40 residues in length. Here, we show a new procedure for fast purification of this bipartite domain. We also describe the use of intrinsic fluorescence spectroscopy for quantitative investigations of ubiquitin interactions between two distal ubiquitin-binding domains of NEMO (NOA and ZF). This spectroscopic method has many advantages over other techniques like GST pulldown and Biacore's SPR for monitoring avid interactions between two UBDs, especially when UBDs are located at significant distance from each other within the protein. PMID:25736758

  2. Seamless Infrastructure Independent Multi Homed NEMO Handoff Using Effective and Timely IEEE 802.21 MIH Triggers

    Directory of Open Access Journals (Sweden)

    Zohra Slimane

    2012-07-01

    Full Text Available Handoff performance of NEMO BS protocol with existent improvement proposals is still not sufficient for real time and QoS-sensitive applications and further optimizations are needed. When dealing with single homed NEMO, handoff latency and packet loss become irreducible all optimizations included, so that it is impossible to meet requirements of the above applications. Then, How to combine the different Fast handoff approaches remains an open research issue and needs more investigation. In this paper, we propose a new Infrastructure independent handoff approach combining multihoming and intelligent Make-Before-Break Handoff. Based on required Handoff time estimation, L2 and L3 handoffs are initiated using effective and timely MIH triggers, reducing so the anticipation time and increasing the probability of prediction. We extend MIH services to provide tunnel establishment and switching beforelink break. Thus, the handoff is performed in background with no latency and no packet loss while pingpong scenario is almost avoided. In addition, our proposal saves cost and power consumption by optimizing the time of simultaneous use of multiple interfaces. We provide also NS2 simulation experiments identifying suitable parameter values used for estimation and validating the proposed model.

  3. Finding NEMO (novel electromaterial muscle oscillator): a polypyrrole powered robotic fish with real-time wireless speed and directional control

    International Nuclear Information System (INIS)

    This paper presents the development of an autonomously powered and controlled robotic fish that incorporates an active flexural joint tail fin, activated through conducting polymer actuators based on polypyrrole (PPy). The novel electromaterial muscle oscillator (NEMO) tail fin assembly on the fish could be controlled wirelessly in real time by varying the frequency and duty cycle of the voltage signal supplied to the PPy bending-type actuators. Directional control was achieved by altering the duty cycle of the voltage input to the NEMO tail fin, which shifted the axis of oscillation and enabled turning of the robotic fish. At low speeds, the robotic fish had a turning circle as small as 15 cm (or 1.1 body lengths) in radius. The highest speed of the fish robot was estimated to be approximately 33 mm s−1 (or 0.25 body lengths s−1) and was achieved with a flapping frequency of 0.6–0.8 Hz which also corresponded with the most hydrodynamically efficient mode for tail fin operation. This speed is approximately ten times faster than those for any previously reported artificial muscle based device that also offers real-time speed and directional control. This study contributes to previously published studies on bio-inspired functional devices, demonstrating that electroactive polymer actuators can be real alternatives to conventional means of actuation such as electric motors

  4. 支持多接口的NEMO实现与测试%IMPLEMENTATION AND TEST OF MULTIPLE INTERFACES-SUPPORTED NEMO

    Institute of Scientific and Technical Information of China (English)

    邱陆威; 高德云; 周华春

    2012-01-01

    Network Mobility ( NEMO) Basic Protocol is able to allow mobile nodes within sub-network to maintain continuity of the session when moving. Multiple care-of address (MCoA) protocol allows a mobile node to register multiple care-of addresses simultaneously. In this paper we integrate the protocols of NEMO and MCoA and study the implementation of the function of NEMO supported with multiple interfaces, and design the experiments to verify this function and analyse its performance test.%子网移动性(NEMO)基本支持协议可以让移动子网内部的节点在移动时依然保持会话的连续性,多转交地址协议(MCoA)允许一个移动节点同时注册多个转交地址.集成NEMO和MCoA协议,研究了支持多接口的NEMO功能的实现,并设计实验进行了功能验证和性能测试分析.

  5. DNA-Based Identification and Chemical Characteristics of Hypnea musciformis from Coastal Sites in Ghana

    DEFF Research Database (Denmark)

    Ale, Marcel Tutor; Barrett, Kristian; Addico, Gloria;

    2016-01-01

    This work reveals new, important insights about the influence of broad spatial variationson the phylogenetic relationship and chemical characteristics of Ghanaian Hypnea musciformis—acarrageenan-containing red seaweed. DNA barcoding techniques alleviate the difficulty for accurate morphological...... identification. COI barcode sequences of the Ghanaian H. musciformis showed <0.7% intraspecies divergence, indicating no distinct phylogenetic variation, suggesting that they actually belong to the same species. Thus, the spatial distribution of the sampling sites along the coast of Ghana did not influence the...

  6. Filling the gap - COI barcode resolution in eastern Palearctic birds

    Directory of Open Access Journals (Sweden)

    Koblik Eugeny A

    2009-12-01

    Full Text Available Abstract Background The Palearctic region supports relatively few avian species, yet recent molecular studies have revealed that cryptic lineages likely still persist unrecognized. A broad survey of cytochrome c oxidase I (COI sequences, or DNA barcodes, can aid on this front by providing molecular diagnostics for species assignment. Barcodes have already been extensively surveyed in the Nearctic, which provides an interesting comparison to this region; faunal interchange between these regions has been very dynamic. We explored COI sequence divergence within and between species of Palearctic birds, including samples from Russia, Kazakhstan, and Mongolia. As of yet, there is no consensus on the best method to analyze barcode data. We used this opportunity to compare and contrast three different methods routinely employed in barcoding studies: clustering-based, distance-based, and character-based methods. Results We produced COI sequences from 1,674 specimens representing 398 Palearctic species. These were merged with published COI sequences from North American congeners, creating a final dataset of 2,523 sequences for 599 species. Ninety-six percent of the species analyzed could be accurately identified using one or a combination of the methods employed. Most species could be rapidly assigned using the cluster-based or distance-based approach alone. For a few select groups of species, the character-based method offered an additional level of resolution. Of the five groups of indistinguishable species, most were pairs, save for a larger group comprising the herring gull complex. Up to 44 species exhibited deep intraspecific divergences, many of which corresponded to previously described phylogeographic patterns and endemism hotspots. Conclusion COI sequence divergence within eastern Palearctic birds is largely consistent with that observed in birds from other temperate regions. Sequence variation is primarily congruent with taxonomic boundaries

  7. DNA barcoding:species delimitation in tree peonies

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Delimitations of species are crucial for correct and precise identification of taxa.Unfortunately "spe-cies" is more a subjective than an objective concept in taxonomic practice due to difficulties in revealing patterns of infra-or inter-specific variations.Molecular phylogenetic studies at the population level solve this problem and lay a sound foundation for DNA barcoding.In this paper we exemplify the necessity of adopting a phylogenetic concept of species in DNA barcoding for tree peonies(Paeonia sect.Moutan).We used 40 samples representing all known populations of rare and endangered species and several populations of widely distributed tree peonies.All currently recognized species and major variants have been included in this study.Four chloroplast gene fragments,i.e.ndhF,rps16-trnQ,trnL-F and trnS-G(a total of 5040 characters,96 variable and 69 parsimony-informative characters) and one variable and single-copy nuclear GPAT gene fragment(2093?2197 bp,279 variable and 148 parsi-mony-informative characters) were used to construct phylogenetic relationships among the taxa.The evolutionary lineages revealed by the nuclear gene and the chloroplast genes are inconsistent with the current circumscriptions of P.decomposita,P.jishanensis,P.qiui,and P.rockii based on morphology.The inconsistencies come from(1) significant chloroplast gene divergence but little nuclear GPAT gene divergence among population systems of P.decomposita + P.rockii,and(2) well-diverged nuclear GPAT gene but little chloroplast gene divergence between P.jishanensis and P.qiui.The incongruence of the phylogenies based on the chloroplast genes and the nuclear GPAT gene is probably due to the chloro-plast capture event in evolutionary history,as no reproductive barriers exist to prevent inter-specific hybridization.We also evaluated the suitability of these genes for use as DNA barcodes for tree peonies.The variability of chloroplast genes among well-defined species or population systems of a

  8. Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species

    Science.gov (United States)

    Chen, Shilin; Yao, Hui; Han, Jianping; Liu, Chang; Song, Jingyuan; Shi, Linchun; Zhu, Yingjie; Ma, Xinye; Gao, Ting; Pang, Xiaohui; Luo, Kun; Li, Ying; Li, Xiwen; Jia, Xiaocheng; Lin, Yulin; Leon, Christine

    2010-01-01

    Background The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL + matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over. Methodology/Principal Findings Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level. Conclusions The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa. PMID:20062805

  9. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species.

    Directory of Open Access Journals (Sweden)

    Shilin Chen

    Full Text Available BACKGROUND: The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL+matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over. METHODOLOGY/PRINCIPAL FINDINGS: Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2 of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level. CONCLUSIONS: The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa.

  10. A Barcode-Free Combinatorial Screening Platform for Matrix Metalloproteinase Screening

    OpenAIRE

    Rane, Tushar D.; Zec, Helena C.; Wang, Tza-Huei

    2014-01-01

    Application of droplet microfluidics to combinatorial screening applications remains elusive because of the need for composition-identifying unique barcodes. Here we propose a barcode-free continuous flow droplet microfluidic platform to suit the requirements of combinatorial screening applications. We demonstrate robust and repeatable functioning of this platform with matrix metalloproteinase activity screening as a sample application.

  11. Magnetic NiFe/Au barcode nanowires with self-powered motion

    Science.gov (United States)

    Jeon, In Tak; Yoon, Seung Jae; Kim, Bong Gun; Lee, Ji Sung; An, Boo Hyun; Ju, Jae-Seon; Wu, Jun Hua; Kim, Young Keun

    2012-04-01

    NiFe/Au barcode nanowires were synthesized by pulsed electrodeposition using anodic aluminum oxide nanotemplate, comprising magnetic, catalytic, and optical segments, respectively. The self-powered motion of the BNWs due to the catalytic reaction was observed in aqueous H2O2. The approach demonstrates how sophistication in barcode nanoarchitecture can be used to synthesize a wide range of hybrid materials.

  12. Barcode haplotype variation in North American agroecosystem ladybird beetles (Coleoptera: Coccinellidae

    Science.gov (United States)

    DNA barcodes have proven invaluable in identifying and distinguishing insect pests, for example for determining the provenance of exotic invasives, but relatively few insect natural enemies have been barcoded. We used Folmer et al.’s universal invertebrate primers (1994), and those designed by Heber...

  13. Some 'ant'swers: Application of a layered barcode approach to problems in ant taxonomy.

    Science.gov (United States)

    Paknia, Omid; Bergmann, Tjard; Hadrys, Heike

    2015-11-01

    DNA barcoding has emerged as a routine tool in modern taxonomy. Although straightforward, this approach faces new challenges, when applied to difficult situation such as defining cryptic biodiversity. Ants are prime examples for high degrees of cryptic biodiversity due to complex population differentiation, hybridization and speciation processes. Here, we test the DNA barcoding region, cytochrome c oxidase 1 and two supplementary markers, 28S ribosomal DNA and long-wavelength rhodopsin, commonly used in ant taxonomy, for their potential in a layered, character-based barcoding approach across different taxonomic levels. Furthermore, we assess performance of the character-based barcoding approach to determine cryptic species diversity in ants. We found (i) that the barcode potential of a specific genetic marker varied widely among taxonomic levels in ants; (ii) that application of a layered, character-based barcode for identification of specimens can be a solution to taxonomical challenging groups; (iii) that the character-based barcoding approach allows us to differentiate specimens even within locations based on pure characters. In summary, (layered) character-based barcoding offers a reliable alternative for problematic species identification in ants and can be used as a fast and cost-efficient approach to estimate presence, absence or frequency of cryptic species. PMID:25712507

  14. Classification of sharks in the Egyptian Mediterranean waters using morphological and DNA barcoding approaches.

    Directory of Open Access Journals (Sweden)

    Marie Moftah

    Full Text Available The identification of species constitutes the first basic step in phylogenetic studies, biodiversity monitoring and conservation. DNA barcoding, i.e. the sequencing of a short standardized region of DNA, has been proposed as a new tool for animal species identification. The present study provides an update on the composition of shark in the Egyptian Mediterranean waters off Alexandria, since the latest study to date was performed 30 years ago, DNA barcoding was used in addition to classical taxonomical methodologies. Thus, 51 specimen were DNA barcoded for a 667 bp region of the mitochondrial COI gene. Although DNA barcoding aims at developing species identification systems, some phylogenetic signals were apparent in the data. In the neighbor-joining tree, 8 major clusters were apparent, each of them containing individuals belonging to the same species, and most with 100% bootstrap value. This study is the first to our knowledge to use DNA barcoding of the mitochondrial COI gene in order to confirm the presence of species Squalus acanthias, Oxynotus centrina, Squatina squatina, Scyliorhinus canicula, Scyliorhinus stellaris, Mustelus mustelus, Mustelus punctulatus and Carcharhinus altimus in the Egyptian Mediterranean waters. Finally, our study is the starting point of a new barcoding database concerning shark composition in the Egyptian Mediterranean waters (Barcoding of Egyptian Mediterranean Sharks [BEMS], http://www.boldsystems.org/views/projectlist.php?&#Barcoding%20Fish%20%28FishBOL%29.

  15. 76 FR 59504 - Intelligent Mail Package Barcode (IMpb) Implementation for Commercial Parcels

    Science.gov (United States)

    2011-09-27

    ... 111 Intelligent Mail Package Barcode (IMpb) Implementation for Commercial Parcels AGENCY: Postal... implementation of this final rule by requiring an Intelligent Mail package barcode (IMpb) for all commercial... the Federal Register (75 FR 56922- 56923), announcing plans to provide interim IMpb...

  16. The link between the Barents Sea and ENSO events reproduced by NEMO model

    Directory of Open Access Journals (Sweden)

    V. N. Stepanov

    2012-05-01

    Full Text Available An analysis of observational data in the Barents Sea along a meridian at 33°30´ E between 70°30´ and 72°30´ N has reported a negative correlation between El Niño/La Niña-Southern Oscillation (ENSO events and water temperature in the top 200 m: the temperature drops about 0.5 °C during warm ENSO events while during cold ENSO events the top 200 m layer of the Barents Sea is warmer. Results from 1 and 1/4-degree global NEMO models show a similar response for the whole Barents Sea. During the strong warm ENSO event in 1997–1998 an anticyclonic atmospheric circulation is settled over the Barents Sea instead of a usual cyclonic circulation. This change enhances heat loses in the Barents Sea, as well as substantially influencing the Barents Sea inflow from the North Atlantic, via changes in ocean currents. Under normal conditions along the Scandinavian peninsula there is a warm current entering the Barents sea from the North Atlantic, however after the 1997–1998 event this current is weakened.

    During 1997–1998 the model annual mean temperature in the Barents Sea is decreased by about 0.8 °C, also resulting in a higher sea ice volume. In contrast during the cold ENSO events in 1999–2000 and 2007–2008 the model shows a lower sea ice volume, and higher annual mean temperatures in the upper layer of the Barents Sea of about 0.7 °C.

    An analysis of model data shows that the Barents Sea inflow is the main source for the variability of Barents Sea heat content, and is forced by changing pressure and winds in the North Atlantic. However, surface heat-exchange with atmosphere can also play a dominant role in the Barents Sea annual heat balance, especially for the subsequent year after ENSO events.

  17. Novel non-peptide small molecules preventing IKKβ/NEMO association inhibit NF-κB activation in LPS-stimulated J774 macrophages.

    Science.gov (United States)

    De Falco, Francesca; Di Giovanni, Carmen; Cerchia, Carmen; De Stefano, Daniela; Capuozzo, Antonella; Irace, Carlo; Iuvone, Teresa; Santamaria, Rita; Carnuccio, Rosa; Lavecchia, Antonio

    2016-03-15

    Nuclear Factor-κB (NF-κB) is a transcription factor regulating several genes involved in important physiological and pathological processes. NF-κB has been found constitutively activated in many inflammatory/immune diseases. In addition, a positive correlation between persistent activation of NF-κB and tumor promotion has been demonstrated. Since the IKK (IκB kinase) activation is an indispensable component of all pro-inflammatory signaling pathways leading to NF-κB activation, considerable efforts have been done in order to develop novel anti-inflammatory therapeutics targeting IKK. Association of the IKK complex relies on critical interactions between the C-terminus NBD (NEMO binding domain) of the catalytic subunits IKKα and IKKβ, and the regulatory subunit NEMO (NF-κB Essential Modulator). Thus, this IKK/NEMO interacting region provides an attractive target to prevent the IKK complex formation and NF-κB activation. In this regard, we have identified non-peptide small molecule disruptors of IKKβ/NEMO complex through a structure-based virtual screening (SBVS) of the NCI chemical library. Phenothiazine 22 and its close analogues (22.2, 22.4 and 22.10) were able to reduce nitrite production and iNOS mRNA expression in J774 murine macrophages stimulated with LPS for 24h. These effects were associated with a reduced NF-κB/DNA binding activity as well as a decreased expression of phosphorylated IKKβ, IκBα and NF-κB/p65 in these cells. These observations suggest that compound 22 and its three structural analogues by inhibiting IKKβ/NEMO association mediate the blockage of NF-κB signaling pathway and may prove effective in treatment of diseases in which the IKK/NF-κB pathway is dysregulated. PMID:26776306

  18. Efficiency of DNA barcodes for species delimitation: A case in Pterygiella Oliv.(Orobanchaceae)

    Institute of Scientific and Technical Information of China (English)

    Li-Na DONG; Alexandra H. WORTLEY; Hong WANG; De-Zhu LI; Lu LU

    2011-01-01

    DNA barcoding is becoming an increasingly popular means to identify species. The obscure discrimination in the genus Pterygiella calls into question the re-assessment of the criterion for species delimitation. We collected 20 individuals, representing all five described species of this genus in its distributional range. The aim was to use three proposed barcode DNA regions (rbcL, matK, and ITS) to diagnose Pterygiella species, and examine which barcode is more suitable for discerning the congeneric and related species. The results showed that the core barcodes matK and rbcL were comparatively less effective. However, the ITS region, especially ITS-1and ITS-2, successfully identified all species in the genus. Furthermore, the secondary structure of ITS-2 RNA, especially compensatory base changes, appears complementary to classical primary sequence analysis for DNA barcoding.

  19. Dynamical downscaling of warming scenarios with NEMO-Nordic setup for the North Sea and Baltic Sea

    Science.gov (United States)

    Gröger, Matthias; Almroth Rosell, Elin; Anderson, Helén; Axell, Lars; Dieterich, Christain; Edman, Moa; Eilola, Kari; Höglund, Anders; Hordoir, Robinson; Hieronymus, Jenny; Karlsson, Bengt; Liu, Ye; Meier, Markus; Pemberton, Per; Saraiva, Sofia

    2016-04-01

    The North Sea and Baltic Sea constitute one of the most complex and challenging areas in the world. The oceanographic setting ranges from quasi open ocean conditions in the northern North Sea to more brackish conditions in the Baltic Sea which is also affected by sea ice in winter. The two seas are connected by narrow straits which sporadically allow the important inflow of salt and oxygen rich bottom waters into the Baltic Sea. For this, the high resolution regional model NEMO-Nordic has recently been developed. Here, the model is applied on hindcast simulations and used to downscale several climate warming scenarios. The model can be interactively coupled to the regional atmosphere model RCA4 by exchanging air sea fluxes of mass and energy (Wang et al., 2015). Comparison with well established models and newly compiled observational data sets (Bersch et al., 2013) indicates NEMO-Nordic performs well on climate relevant time scales. Emphasis is laid on thermal dynamics. Hindcast simulations demonstrate that simulated winter temperatures in the Baltic Sea can benefit from interactive air sea coupling by allowing interactive feedback loops to take place between the ocean and the atmosphere (Gröger et al. 2015). Likewise, a more realistic dynamical behaviour makes the interactive coupled model suitable for dynamic downscaling of climate warming scenarios. Depending on the driving global climate model and IPCC representative concentration pathway scenario NEMO-Nordic shows an average warming of the North Sea between 2 and 4 K at the end of the 21st century. However the warming pattern is spatially inhomogeneous showing strong east west gradients. Involved processes such as circulation changes and changes in radiative forcing will be discussed. Bersch, M., Gouretski, V., Sadikni, R., Hinrichs, I., 2013. Hydrographic climatology of the North Sea and surrounding regions. Centre for Earth System Research and Sustainability, University of Hamburg, www

  20. Building a DNA barcode reference library for the true butterflies (Lepidoptera of Peninsula Malaysia: what about the subspecies?

    Directory of Open Access Journals (Sweden)

    John-James Wilson

    Full Text Available The objective of this study was to build a DNA barcode reference library for the true butterflies of Peninsula Malaysia and assess the value of attaching subspecies names to DNA barcode records. A new DNA barcode library was constructed with butterflies from the Museum of Zoology, University of Malaya collection. The library was analysed in conjunction with publicly available DNA barcodes from other Asia-Pacific localities to test the ability of the DNA barcodes to discriminate species and subspecies. Analyses confirmed the capacity of the new DNA barcode reference library to distinguish the vast majority of species (92% and revealed that most subspecies possessed unique DNA barcodes (84%. In some cases conspecific subspecies exhibited genetic distances between their DNA barcodes that are typically seen between species, and these were often taxa that have previously been regarded as full species. Subspecies designations as shorthand for geographically and morphologically differentiated groups provide a useful heuristic for assessing how such groups correlate with clustering patterns of DNA barcodes, especially as the number of DNA barcodes per species in reference libraries increases. Our study demonstrates the value in attaching subspecies names to DNA barcode records as they can reveal a history of taxonomic concepts and expose important units of biodiversity.

  1. Building a DNA Barcode Reference Library for the True Butterflies (Lepidoptera) of Peninsula Malaysia: What about the Subspecies?

    Science.gov (United States)

    Wilson, John-James; Sing, Kong-Wah; Sofian-Azirun, Mohd

    2013-01-01

    The objective of this study was to build a DNA barcode reference library for the true butterflies of Peninsula Malaysia and assess the value of attaching subspecies names to DNA barcode records. A new DNA barcode library was constructed with butterflies from the Museum of Zoology, University of Malaya collection. The library was analysed in conjunction with publicly available DNA barcodes from other Asia-Pacific localities to test the ability of the DNA barcodes to discriminate species and subspecies. Analyses confirmed the capacity of the new DNA barcode reference library to distinguish the vast majority of species (92%) and revealed that most subspecies possessed unique DNA barcodes (84%). In some cases conspecific subspecies exhibited genetic distances between their DNA barcodes that are typically seen between species, and these were often taxa that have previously been regarded as full species. Subspecies designations as shorthand for geographically and morphologically differentiated groups provide a useful heuristic for assessing how such groups correlate with clustering patterns of DNA barcodes, especially as the number of DNA barcodes per species in reference libraries increases. Our study demonstrates the value in attaching subspecies names to DNA barcode records as they can reveal a history of taxonomic concepts and expose important units of biodiversity. PMID:24282514

  2. An Asiatic Chironomid in Brazil: morphology, DNA barcode and bionomics

    Science.gov (United States)

    Amora, Gizelle; Hamada, Neusa; Fusari, Lívia Maria; Andrade-Souza, Vanderly

    2015-01-01

    Abstract In most freshwater ecosystems, aquatic insects are dominant in terms of diversity; however, there is a disproportionately low number of records of alien species when compared to other freshwater organisms. The Chironomidae is one aquatic insect family that includes some examples of alien species around the world. During a study on aquatic insects in Amazonas state (Brazil), we collected specimens of Chironomidae that are similar, at the morphological level, to Chironomus kiiensis Tokunaga and Chironomus striatipennis Kieffer, both with distributions restricted to Asia. The objectives of this study were to provide morphological information on this Chironomus population, to investigate its identity using DNA barcoding and, to provide bionomic information about this species. Chironomus DNA barcode data were obtained from GenBank and Barcode of Life Data Systems (BOLD) and, together with our data, were analyzed using the neighbor-joining method with 1000 bootstrap replicates and the genetic distances were estimated using the Kimura-2-parameter. At the morphological level, the Brazilian population cannot be distinguished either from Chironomus striatipennis or Chironomus kiiensis, configuring a species complex but, at the molecular level our studied population is placed in a clade together with Chironomus striatipennis, from South Korea. Bionomic characteristics of the Brazilian Chironomus population differ from the ones of Chironomus kiiensis from Japan, the only species in this species complex with bionomic information available. The Brazilian Chironomus population has a smaller size, the double of the number of eggs and inhabits oligotrophic water, in artificial container. In the molecular analysis, populations of Chironomus striatipennis and Chironomus kiiensis are placed in a clade, formed by two groups: Group A (which includes populations from both named species, from different Asiatic regions and our Brazilian population) and Group B (with populations of

  3. Recent Results From Seafloor Instruments at the NeMO Observatory, Axial Volcano, Juan de Fuca Ridge

    Science.gov (United States)

    Chadwick, W. W.; Butterfield, D. A.; Embley, R. W.; Meinig, C.; Stalin, S. E.; Nooner, S. L.; Zumberge, M. A.; Fox, C. G.

    2002-12-01

    NeMO is a seafloor observatory at Axial Seamount, an active submarine volcano located on the Juan de Fuca Ridge (JdFR) in the NE Pacific. Axial Volcano was chosen for NeMO because it has the largest magma supply on the JdFR, and is therefore the best place to study volcanic events and the perturbations they cause to pre-existing hydrothermal systems. In fact, Axial volcano erupted in January 1998 and initially our field efforts were focused on mapping the new lava flows and documenting the impact of the eruption on the hydrothermal vents and biological communities. Since then, our emphasis has gradually shifted to long-term geophysical and geochemical monitoring of the volcano in anticipation of its next eruption. Recent results from seafloor monitoring instruments and recent geologic mapping will be presented, including the following: (1) NeMO Net, a state-of-the-art, two-way communication system currently deployed at Axial, which uses a moored surface buoy to link three instruments on the seafloor in near real-time to the internet. The buoy communicates with the seafloor instruments via acoustic modems and relays data to and from shore via the Orbcomm and Iridium satellite systems. The seafloor instruments include two Remote Access Samplers (RAS) located at two hydrothermal vents in the ASHES vent field, and a Bottom Pressure Recorder (BPR) located near the center of the caldera. The RAS samplers monitor temperature and chemistry at the vents and can take 48 fluid and particle samples over a year, but can also be commanded from shore to take a sample at any time in response to detected seismic or volcanic events. The BPR is monitoring vertical motion of the seafloor, looking for sudden inflation or deflation events that may signal the onset of an eruption or intrusion. Data from the three instruments is displayed on the web at http://www.pmel.noaa.gov/vents/nemo/realtime/. (2) Data from a RAS sampler that was deployed at Cloud vent in Axial caldera between 2001

  4. Nemo-like kinase regulates the expression of vascular endothelial growth factor (VEGF) in alveolar epithelial cells.

    Science.gov (United States)

    Ke, Hengning; Masoumi, Katarzyna Chmielarska; Ahlqvist, Kristofer; Seckl, Michael J; Rydell-Törmänen, Kristina; Massoumi, Ramin

    2016-01-01

    The canonical Wnt signaling can be silenced either through β-catenin-mediated ubiquitination and degradation or through phosphorylation of Tcf and Lef by nemo-like kinase (NLK). In the present study, we generated NLK deficient animals and found that these mice become cyanotic shortly before death because of lung maturation defects. NLK-/- lungs exhibited smaller and compressed alveoli and the mesenchyme remained thick and hyperplastic. This phenotype was caused by epithelial activation of vascular endothelial growth factor (VEGF) via recruitment of Lef1 to the promoter of VEGF. Elevated expression of VEGF and activation of the VEGF receptor through phosphorylation promoted an increase in the proliferation rate of epithelial and endothelial cells. In summary, our study identifies NLK as a novel signaling molecule for proper lung development through the interconnection between epithelial and endothelial cells during lung morphogenesis. PMID:27035511

  5. DNA barcodes for marine fungal identification and discovery

    Digital Repository Service at National Institute of Oceanography (India)

    Velmurugan, S.; Prasannakumar, C.; Manokaran, S.; AjithKumar, T.; Samkamaleson, A.; Palavesam, A.

    gene of fungi varied between 1548 bp and 22 kb, similar to the barcoding region within COX1 gene which ranged from 642 bp to 12.3 kb (Seifert et al. 2007; Seifert 2009). Only one COX1 gene was published for just one glomeromycotan species with a length... was observed within the com- plex group of Aspergillus niger (Geiser et al. 2007). Lang & Hijri (2009) reported a COX1 intron in Glomus diaphanum with a high sequence similarity to both a plant sequence and a Rhi- zopus oryzae COX1 intron. This intronmay result...

  6. A simple protocol for venom peptide barcoding in scorpions

    Directory of Open Access Journals (Sweden)

    Stephan Schaffrath

    2014-06-01

    Full Text Available Scorpion venoms contain many species-specific peptides which target ion channels in cell membranes. Without harming the scorpions, these peptides can easily be extracted and detected by MALDI-TOF mass spectrometry. So far, only few studies compared the venom of different species solely for taxonomic purposes. Here, we describe a very simple protocol for venom extraction and mass fingerprinting that was developed for peptide barcoding (venom code for species identification and facilitates reproducibility if sample preparation is performed under field conditions. This approach may serve as suitable basis for a taxonomy-oriented scorpion toxin database that interacts with MALDI-TOF mass spectra.

  7. Barcode of life: Advancing species identification and discovery

    Digital Repository Service at National Institute of Oceanography (India)

    Chandramohan, D.

    and (ii) possess greater range of phylogenetic signal than any other mitochondrial gene. The accumulated evidence now shows that these short DNA sequences can be a distinguishing feature from insects to birds. As a Linnaean binomial is an abbreviated... DNA as a model system. Gene 238, 195-210. 5. Simmons, R.B. and Weller,S.J. 2001. Utility and evolution of cytochrome b in insects.Mol. Phylogenet. Evol. 20, 196-210. Barcode of Life: Advancing Species Identification and Discovery ...

  8. Denture bar-coding: An innovative technique in forensic dentistry

    OpenAIRE

    Dineshshankar, Janardhanam; Venkateshwaran, Rajendran; J. Vidhya; Anuradha, R.; Mary, Gold Pealin; Pradeep, R.; Senthileagappan, A. R.

    2015-01-01

    Denture markers play an important role in forensic odontology and also in identifying a person. A number of methods are there for identifying dentures from a less expensive technique to a more expensive technique. Out of different denture markers, the bar-coding system is a way of collecting data from the mobile. Even a huge amount of data can be stored in that. It can be easily incorporated during acrylization of the denture and thus could be helpful in identification. This article reviews t...

  9. Bjørvika Barcode : storskala arkitektur og byrom

    OpenAIRE

    Kristoffersen, Aleksander Styrvold

    2012-01-01

    Bjørvika er et område som står fremfor en stor transformasjon, det skal bli Oslos nye bydel. Både kommunen og utviklerne ønsker seg noe eksepsjonelt ut av området. Alt skal være av høy estetisk kvalitet, som kan stå i stil med den nye Operaen. Etter at jernbanen frigjorde arealene sør for sporområdet, har grunneierne Oslo S Utvikling i samarbeid med kommunen, arkitekter, og andre fagpersoner utviklet disse arealene etter deres intensjoner og ønsker. Plan og bygningsetaten støtter Barcode fors...

  10. Automation of dosimeter issue using barcode and RWP software

    International Nuclear Information System (INIS)

    At Madras Atomic Power Station (MAPS) external dose measurement is done by thermoluminescent dosimeter (TLD) and direct reading dosimeter (DRD). During shut down periods large number of DRDs are to be issued to workers and after work these are to be received. For this manual entry of TLD numbers and DRD numbers are required in the online DRD issue programme. Manual entry can cause errors while entering TLD and DRD numbers. To avoid these errors and to reduce time taken for DRD transaction, barcodes were introduced on TLDs and DRDs at MAPS for the first time in Radiation Protection Programme from February 2005. (author)

  11. Denture barcoding in forensic dentistry: A future option

    Science.gov (United States)

    Basavanna, Jayaprakash Mugur; Jain, Abhishek; Misra, Sumit Kumar

    2016-01-01

    Neurodegenerative disorders are commonly seen in elderly individuals. Parkinson's disease (PD) is the most common example with memory loss, lack of logic, reasoning and analytical thinking. In this case report simple method of 2D Bar code technique of denture marking has been explained which will not only useful in patients with memory loss but it is very helpful in identifying the individuals in case of natural calamities like floods, earthquake, tornedo, state of unconsciousness and accidents. Such patients can be traced easily by denture barcoding. This technique is a major breakthrough in the field of forensic dentistry. PMID:27051224

  12. Denture barcoding in forensic dentistry: A future option.

    Science.gov (United States)

    Basavanna, Jayaprakash Mugur; Jain, Abhishek; Misra, Sumit Kumar

    2016-01-01

    Neurodegenerative disorders are commonly seen in elderly individuals. Parkinson's disease (PD) is the most common example with memory loss, lack of logic, reasoning and analytical thinking. In this case report simple method of 2D Bar code technique of denture marking has been explained which will not only useful in patients with memory loss but it is very helpful in identifying the individuals in case of natural calamities like floods, earthquake, tornedo, state of unconsciousness and accidents. Such patients can be traced easily by denture barcoding. This technique is a major breakthrough in the field of forensic dentistry. PMID:27051224

  13. EDA-ID and IP, two faces of the same coin: how the same IKBKG/NEMO mutation affecting the NF-κB pathway can cause immunodeficiency and/or inflammation.

    Science.gov (United States)

    Fusco, Francesca; Pescatore, Alessandra; Conte, Matilde Immacolata; Mirabelli, Peppino; Paciolla, Mariateresa; Esposito, Elio; Lioi, Maria Brigida; Ursini, Matilde Valeria

    2015-01-01

    Anhidrotic Ectodermal Dysplasia with ImmunoDeficiency (EDA-ID, OMIM 300291) and Incontinentia Pigmenti (IP, OMIM 308300) are two rare diseases, caused by mutations of the IKBKG/NEMO gene. The protein NEMO/IKKγ is essential for the NF-κB activation pathway, involved in a variety of physiological and cellular processes, such as immunity, inflammation, cell proliferation, and survival. A wide spectrum of IKBKG/NEMO mutations have been identified so far, and, on the basis of their effect on NF-κB activation, they are considered hypomorphic or amorphic (loss of function) mutations. IKBKG/NEMO hypomorphic mutations, reducing but not abolishing NF-κB activation, have been identified in EDA-ID and IP patients. Instead, the amorphic mutations, abolishing NF-κB activation by complete IKBKG/NEMO gene silencing, cause only IP. Here, we present an overview of IKBKG/NEMO mutations in EDA-ID and IP patients and describe similarities and differences between the clinical/immunophenotypic and genetic aspects, highlighting any T and B lymphocyte defect, and paying particular attention to the cellular and molecular defects that underlie the pathogenesis of both diseases. PMID:26269396

  14. Analysis of the data from the NEMO3 experiment and search for neutrinoless double beta decay - Study of systematic bias of the calorimeter and development of analysis tools

    International Nuclear Information System (INIS)

    The NEMO3 experiment was researching the neutrinoless double-β (0ndb) decay by using various sources of double beta decay isotopes (mainly 100Mo, 82Se, 116Cd and 130Te for about 10 kg in total). The detector was located in the underground laboratory of Modane (Italy) in the halfway point of the Frejus tunnel. This experiment demonstrated that the 'tracko-calo' technology is really competitive and, in addition, it gives new results for the 2-neutrinos double-β (2ndb) decay and the (0ndb) decays research. Moreover it opened an new way for its successor SuperNEMO, which aim is to reach a mass of 100 kg of 82Se (for a sensitivity of 1026 years). The main goal of the thesis is to measure the 2ndb and 0ndb decay of the 100Mo to the excited state 01+ of the 100Ru thanks to the whole NEMO3 data, with new original methods of analysis and through the development of the collaboration analysis software. The results obtained for the ground states (gs) and excited states 2ndb of the 100Mo are for the half-lives: T(2nbd, gs)=[7.05±0.01(stat)±0.54(syst)]*1018 years and T(2ndb, 01+)=[6.15±1.1(sta)±0.78]*1020 years. Those results are compatibles with the last ones published by the collaboration. For the 0ndb(01+), this work gave a half-life of T(0ndb, 01+) > 2.6*1023 years, improving significantly the last published results. Furthermore those methods also allowed to present a new and more exhaustive background noise model for this experiment. The second point of this work was to measure the systematics errors of the NEMO3 calorimeter, among others due to the wavelength of the NEMO3 calibration systems. This work was done using a new test bench based on LED. This bench also allowed to contribute to the development of the SuperNEMO calorimeter, especially in the time characteristic and the energy linearity measurement of the photomultiplier intended to the demonstrator of the experiments. (author)

  15. TAA Polyepitope DNA-Based Vaccines: A Potential Tool for Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Roberto Bei

    2010-01-01

    Full Text Available DNA-based cancer vaccines represent an attractive strategy for inducing immunity to tumor associated antigens (TAAs in cancer patients. The demonstration that the delivery of a recombinant plasmid encoding epitopes can lead to epitope production, processing, and presentation to CD8+ T-lymphocytes, and the advantage of using a single DNA construct encoding multiple epitopes of one or more TAAs to elicit a broad spectrum of cytotoxic T-lymphocytes has encouraged the development of a variety of strategies aimed at increasing immunogenicity of TAA polyepitope DNA-based vaccines. The polyepitope DNA-based cancer vaccine approach can (a circumvent the variability of peptide presentation by tumor cells, (b allow the introduction in the plasmid construct of multiple immunogenic epitopes including heteroclitic epitope versions, and (c permit to enroll patients with different major histocompatibility complex (MHC haplotypes. This review will discuss the rationale for using the TAA polyepitope DNA-based vaccination strategy and recent results corroborating the usefulness of DNA encoding polyepitope vaccines as a potential tool for cancer therapy.

  16. DNA-based stable isotope probing: a link between community structure and function

    Czech Academy of Sciences Publication Activity Database

    Uhlík, Ondřej; Ječná, K.; Leigh, M. B.; Macková, Martina; Macek, Tomáš

    2009-01-01

    Roč. 407, č. 12 (2009), s. 3611-3619. ISSN 0048-9697 Grant ostatní: GA MŠk(CZ) 2B08031 Institutional research plan: CEZ:AV0Z40550506 Keywords : DNA-based stable isotope probing * microbial diversity * bioremediation Subject RIV: EI - Biotechnology ; Bionics Impact factor: 2.905, year: 2009

  17. The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life.

    Science.gov (United States)

    Zhou, Xin; Frandsen, Paul B; Holzenthal, Ralph W; Beet, Clare R; Bennett, Kristi R; Blahnik, Roger J; Bonada, Núria; Cartwright, David; Chuluunbat, Suvdtsetseg; Cocks, Graeme V; Collins, Gemma E; deWaard, Jeremy; Dean, John; Flint, Oliver S; Hausmann, Axel; Hendrich, Lars; Hess, Monika; Hogg, Ian D; Kondratieff, Boris C; Malicky, Hans; Milton, Megan A; Morinière, Jérôme; Morse, John C; Mwangi, François Ngera; Pauls, Steffen U; Gonzalez, María Razo; Rinne, Aki; Robinson, Jason L; Salokannel, Juha; Shackleton, Michael; Smith, Brian; Stamatakis, Alexandros; StClair, Ros; Thomas, Jessica A; Zamora-Muñoz, Carmen; Ziesmann, Tanja; Kjer, Karl M

    2016-09-01

    DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between 'Barcode Index Numbers' (BINs) and 'species' that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description.This article is part of the themed issue 'From DNA barcodes to biomes'. PMID:27481793

  18. The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life

    Science.gov (United States)

    Frandsen, Paul B.; Holzenthal, Ralph W.; Beet, Clare R.; Bennett, Kristi R.; Blahnik, Roger J.; Bonada, Núria; Cartwright, David; Chuluunbat, Suvdtsetseg; Cocks, Graeme V.; Collins, Gemma E.; deWaard, Jeremy; Dean, John; Flint, Oliver S.; Hausmann, Axel; Hendrich, Lars; Hess, Monika; Hogg, Ian D.; Kondratieff, Boris C.; Malicky, Hans; Milton, Megan A.; Morinière, Jérôme; Morse, John C.; Mwangi, François Ngera; Pauls, Steffen U.; Gonzalez, María Razo; Rinne, Aki; Robinson, Jason L.; Salokannel, Juha; Shackleton, Michael; Smith, Brian; Stamatakis, Alexandros; StClair, Ros; Thomas, Jessica A.; Zamora-Muñoz, Carmen; Ziesmann, Tanja

    2016-01-01

    DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481793

  19. An integrated web medicinal materials DNA database: MMDBD (Medicinal Materials DNA Barcode Database

    Directory of Open Access Journals (Sweden)

    But Paul

    2010-06-01

    Full Text Available Abstract Background Thousands of plants and animals possess pharmacological properties and there is an increased interest in using these materials for therapy and health maintenance. Efficacies of the application is critically dependent on the use of genuine materials. For time to time, life-threatening poisoning is found because toxic adulterant or substitute is administered. DNA barcoding provides a definitive means of authentication and for conducting molecular systematics studies. Owing to the reduced cost in DNA authentication, the volume of the DNA barcodes produced for medicinal materials is on the rise and necessitates the development of an integrated DNA database. Description We have developed an integrated DNA barcode multimedia information platform- Medicinal Materials DNA Barcode Database (MMDBD for data retrieval and similarity search. MMDBD contains over 1000 species of medicinal materials listed in the Chinese Pharmacopoeia and American Herbal Pharmacopoeia. MMDBD also contains useful information of the medicinal material, including resources, adulterant information, medical parts, photographs, primers used for obtaining the barcodes and key references. MMDBD can be accessed at http://www.cuhk.edu.hk/icm/mmdbd.htm. Conclusions This work provides a centralized medicinal materials DNA barcode database and bioinformatics tools for data storage, analysis and exchange for promoting the identification of medicinal materials. MMDBD has the largest collection of DNA barcodes of medicinal materials and is a useful resource for researchers in conservation, systematic study, forensic and herbal industry.

  20. A smartphone-readable barcode assay for the detection and quantitation of pesticide residues.

    Science.gov (United States)

    Guo, Juan; Wong, Jessica X H; Cui, Caie; Li, Xiaochun; Yu, Hua-Zhong

    2015-08-21

    In this paper, we present a smartphone-readable barcode assay for the qualitative detection of methyl parathion residues, a toxic organophosphorus pesticide that is popularly used in agriculture worldwide. The detection principle is based on the irreversible inhibition of the enzymatic activity of acetylcholinesterase (AchE) by methyl parathion; AchE catalytically hydrolyzes acetylthiocholine iodine to thiocholine that in turn dissociates dithiobis-nitrobenzoate to produce a yellow product (deprotonated thio-nitrobenzoate). The yellow intensity of the product was confirmed to be inversely dependent on the concentration of the pesticide. We have designed a barcode-formatted assay chip by using a PDMS (polydimethylsiloxane) channel plate (as the reaction reservoir), situated under a printed partial barcode, to complete the whole barcode such that it can be directly read by a barcode scanning app installed on a smartphone. The app is able to qualitatively present the result of the pesticide test; the absence or a low concentration of methyl parathion results in the barcode reading as "-", identifying the test as negative for pesticides. Upon obtaining a positive result (the app reads a "+" character), the captured image can be further analyzed to quantitate the methyl parathion concentration in the sample. Besides the portability and simplicity, this mobile-app based colorimetric barcode assay compares favorably with the standard spectrophotometric method. PMID:26087169

  1. A DNA barcode library for North American Ephemeroptera: progress and prospects.

    Directory of Open Access Journals (Sweden)

    Jeffrey M Webb

    Full Text Available DNA barcoding of aquatic macroinvertebrates holds much promise as a tool for taxonomic research and for providing the reliable identifications needed for water quality assessment programs. A prerequisite for identification using barcodes is a reliable reference library. We gathered 4165 sequences from the barcode region of the mitochondrial cytochrome c oxidase subunit I gene representing 264 nominal and 90 provisional species of mayflies (Insecta: Ephemeroptera from Canada, Mexico, and the United States. No species shared barcode sequences and all can be identified with barcodes with the possible exception of some Caenis. Minimum interspecific distances ranged from 0.3-24.7% (mean: 12.5%, while the average intraspecific divergence was 1.97%. The latter value was inflated by the presence of very high divergences in some taxa. In fact, nearly 20% of the species included two or three haplotype clusters showing greater than 5.0% sequence divergence and some values are as high as 26.7%. Many of the species with high divergences are polyphyletic and likely represent species complexes. Indeed, many of these polyphyletic species have numerous synonyms and individuals in some barcode clusters show morphological attributes characteristic of the synonymized species. In light of our findings, it is imperative that type or topotype specimens be sequenced to correctly associate barcode clusters with morphological species concepts and to determine the status of currently synonymized species.

  2. ycf1, the most promising plastid DNA barcode of land plants.

    Science.gov (United States)

    Dong, Wenpan; Xu, Chao; Li, Changhao; Sun, Jiahui; Zuo, Yunjuan; Shi, Shuo; Cheng, Tao; Guo, Junjie; Zhou, Shiliang

    2015-01-01

    A DNA barcode is a DNA fragment used to identify species. For land plants, DNA fragments of plastid genome could be the primary consideration. Unfortunately, most of the plastid candidate barcodes lack species-level resolution. The identification of DNA barcodes of high resolution at species level is critical to the success of DNA barcoding in plants. We searched the available plastid genomes for the most variable regions and tested the best candidates using both a large number of tree species and seven well-sampled plant groups. Two regions of the plastid gene ycf1, ycf1a and ycf1b, were the most variable loci that were better than existing plastid candidate barcodes and can serve as a barcode of land plants. Primers were designed for the amplification of these regions, and the PCR success of these primers ranged from 82.80% to 98.17%. Of 420 tree species, 357 species could be distinguished using ycf1b, which was slightly better than the combination of matK and rbcL. For the well-sampled representative plant groups, ycf1b generally performed better than any of the matK, rbcL and trnH-psbA. We concluded that ycf1a or ycf1b is the most variable plastid genome region and can serve as a core barcode of land plants. PMID:25672218

  3. ycf1, the most promising plastid DNA barcode of land plants

    Science.gov (United States)

    Dong, Wenpan; Xu, Chao; Li, Changhao; Sun, Jiahui; Zuo, Yunjuan; Shi, Shuo; Cheng, Tao; Guo, Junjie; Zhou, Shiliang

    2015-01-01

    A DNA barcode is a DNA fragment used to identify species. For land plants, DNA fragments of plastid genome could be the primary consideration. Unfortunately, most of the plastid candidate barcodes lack species-level resolution. The identification of DNA barcodes of high resolution at species level is critical to the success of DNA barcoding in plants. We searched the available plastid genomes for the most variable regions and tested the best candidates using both a large number of tree species and seven well-sampled plant groups. Two regions of the plastid gene ycf1, ycf1a and ycf1b, were the most variable loci that were better than existing plastid candidate barcodes and can serve as a barcode of land plants. Primers were designed for the amplification of these regions, and the PCR success of these primers ranged from 82.80% to 98.17%. Of 420 tree species, 357 species could be distinguished using ycf1b, which was slightly better than the combination of matK and rbcL. For the well-sampled representative plant groups, ycf1b generally performed better than any of the matK, rbcL and trnH-psbA. We concluded that ycf1a or ycf1b is the most variable plastid genome region and can serve as a core barcode of land plants. PMID:25672218

  4. Prospects and Problems for Identification of Poisonous Plants in China using DNA Barcodes

    Institute of Scientific and Technical Information of China (English)

    XIE Lei; WANG YingWei; GUAN ShanYue; XIE LiJing; LONG Xin; SUN ChengYe

    2014-01-01

    ObjectivePoisonous plants are a deadly threat to public health in China. The traditional clinical diagnosis of the toxic plants isinefficient, fallible, and dependent upon experts. In this study, we tested the performance of DNA barcodes for identification of the most threatening poisonous plants in China. MethodsSeventy-four accessions of 27 toxic plant species in 22 genera and 17 families were sampled andthree DNA barcodes (matK,rbcL, and ITS) were amplified, sequenced and tested.Three methods, Blast,pairwise global alignment (PWG)distance, and Tree-Building were tested for discrimination power. ResultsThe primer universality of all the three markers was high. Except in the case of ITS for Hemerocallisminor, the three barcodes were successfully generated from all the selected species. Among the three methodsapplied, Blast showed the lowest discrimination rate,whereasPWGDistance and Tree-Building methods were equally effective. The ITS barcode showed highest discrimination rates using the PWG Distance and Tree-Building methods. When the barcodes were combined, discrimination rates were increased for the Blast method. ConclusionDNA barcoding technique provides us a fast tool for clinical identification of poisonous plants in China.We suggestmatK,rbcL, ITS used in combination as DNA barcodes for authentication of poisonous plants.

  5. DNA barcoding and minibarcoding as a powerful tool for feather mite studies.

    Science.gov (United States)

    Doña, Jorge; Diaz-Real, Javier; Mironov, Sergey; Bazaga, Pilar; Serrano, David; Jovani, Roger

    2015-09-01

    Feather mites (Astigmata: Analgoidea and Pterolichoidea) are among the most abundant and commonly occurring bird ectosymbionts. Basic questions on the ecology and evolution of feather mites remain unanswered because feather mite species identification is often only possible for adult males, and it is laborious even for specialized taxonomists, thus precluding large-scale identifications. Here, we tested DNA barcoding as a useful molecular tool to identify feather mites from passerine birds. Three hundred and sixty-one specimens of 72 species of feather mites from 68 species of European passerine birds from Russia and Spain were barcoded. The accuracy of barcoding and minibarcoding was tested. Moreover, threshold choice (a controversial issue in barcoding studies) was also explored in a new way, by calculating through simulations the effect of sampling effort (in species number and species composition) on threshold calculations. We found one 200-bp minibarcode region that showed the same accuracy as the full-length barcode (602 bp) and was surrounded by conserved regions potentially useful for group-specific degenerate primers. Species identification accuracy was perfect (100%) but decreased when singletons or species of the Proctophyllodes pinnatus group were included. In fact, barcoding confirmed previous taxonomic issues within the P. pinnatus group. Following an integrative taxonomy approach, we compared our barcode study with previous taxonomic knowledge on feather mites, discovering three new putative cryptic species and validating three previous morphologically different (but still undescribed) new species. PMID:25655349

  6. DNA barcoding for identification of 'Candidatus Phytoplasmas' using a fragment of the elongation factor Tu gene.

    Directory of Open Access Journals (Sweden)

    Olga Makarova

    Full Text Available BACKGROUND: Phytoplasmas are bacterial phytopathogens responsible for significant losses in agricultural production worldwide. Several molecular markers are available for identification of groups or strains of phytoplasmas. However, they often cannot be used for identification of phytoplasmas from different groups simultaneously or are too long for routine diagnostics. DNA barcoding recently emerged as a convenient tool for species identification. Here, the development of a universal DNA barcode based on the elongation factor Tu (tuf gene for phytoplasma identification is reported. METHODOLOGY/PRINCIPAL FINDINGS: We designed a new set of primers and amplified a 420-444 bp fragment of tuf from all 91 phytoplasmas strains tested (16S rRNA groups -I through -VII, -IX through -XII, -XV, and -XX. Comparison of NJ trees constructed from the tuf barcode and a 1.2 kbp fragment of the 16S ribosomal gene revealed that the tuf tree is highly congruent with the 16S rRNA tree and had higher inter- and intra- group sequence divergence. Mean K2P inter-/intra- group divergences of the tuf barcode did not overlap and had approximately one order of magnitude difference for most groups, suggesting the presence of a DNA barcoding gap. The use of the tuf barcode allowed separation of main ribosomal groups and most of their subgroups. Phytoplasma tuf barcodes were deposited in the NCBI GenBank and Q-bank databases. CONCLUSIONS/SIGNIFICANCE: This study demonstrates that DNA barcoding principles can be applied for identification of phytoplasmas. Our findings suggest that the tuf barcode performs as well or better than a 1.2 kbp fragment of the 16S rRNA gene and thus provides an easy procedure for phytoplasma identification. The obtained sequences were used to create a publicly available reference database that can be used by plant health services and researchers for online phytoplasma identification.

  7. Plant DNA barcodes can accurately estimate species richness in poorly known floras.

    Directory of Open Access Journals (Sweden)

    Craig Costion

    Full Text Available BACKGROUND: Widespread uptake of DNA barcoding technology for vascular plants has been slow due to the relatively poor resolution of species discrimination (∼70% and low sequencing and amplification success of one of the two official barcoding loci, matK. Studies to date have mostly focused on finding a solution to these intrinsic limitations of the markers, rather than posing questions that can maximize the utility of DNA barcodes for plants with the current technology. METHODOLOGY/PRINCIPAL FINDINGS: Here we test the ability of plant DNA barcodes using the two official barcoding loci, rbcLa and matK, plus an alternative barcoding locus, trnH-psbA, to estimate the species diversity of trees in a tropical rainforest plot. Species discrimination accuracy was similar to findings from previous studies but species richness estimation accuracy proved higher, up to 89%. All combinations which included the trnH-psbA locus performed better at both species discrimination and richness estimation than matK, which showed little enhanced species discriminatory power when concatenated with rbcLa. The utility of the trnH-psbA locus is limited however, by the occurrence of intraspecific variation observed in some angiosperm families to occur as an inversion that obscures the monophyly of species. CONCLUSIONS/SIGNIFICANCE: We demonstrate for the first time, using a case study, the potential of plant DNA barcodes for the rapid estimation of species richness in taxonomically poorly known areas or cryptic populations revealing a powerful new tool for rapid biodiversity assessment. The combination of the rbcLa and trnH-psbA loci performed better for this purpose than any two-locus combination that included matK. We show that although DNA barcodes fail to discriminate all species of plants, new perspectives and methods on biodiversity value and quantification may overshadow some of these shortcomings by applying barcode data in new ways.

  8. Effect of field deposition and pore size on Co/Cu barcode nanowires by electrodeposition

    International Nuclear Information System (INIS)

    We have studied the effect of an external magnetic field applied during electrodeposition of Co/Cu barcode nanowires in anodic aluminum oxide nanotemplates. The magnetic properties of the barcode nanowires were greatly enhanced for 50 nm pore diameter regardless of segment aspect ratio, but field deposition has little effect on the 200 nm nanowires. The magnetic improvement is correlated with a structural change, attributed to field modification of the growth habit of the barcode nanowires. A mechanism of growth subject to geometric confinement is proposed

  9. A bar-code reader for an alpha-beta automatic counting system - FAG

    International Nuclear Information System (INIS)

    A bar-code laser system for sample number reading was integrated into the FAG Alpha-Beta automatic counting system. The sample identification by means of an attached bar-code label enables unmistakable and reliable attribution of results to the counted sample. Installation of the bar-code reader system required several modifications: Mechanical changes in the automatic sample changer, design and production of new sample holders, modification of the sample planchettes, changes in the electronic system, update of the operating software of the system (authors)

  10. Effect of field deposition and pore size on Co/Cu barcode nanowires by electrodeposition

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Ji Ung [Department of Materials Science and Engineering, Korea University, Seoul 136-713 (Korea, Republic of); Wu, J.-H. [Research Institute of Engineering and Technology, Korea University, Seoul 136-713 (Korea, Republic of)]. E-mail: feitianshenhu@yahoo.com; Min, Ji Hyun [Department of Materials Science and Engineering, Korea University, Seoul 136-713 (Korea, Republic of); Lee, Ju Hun [Department of Materials Science and Engineering, Korea University, Seoul 136-713 (Korea, Republic of); Liu, H.-L. [Institute for Nano Science, Korea University, Seoul 136-713 (Korea, Republic of); Kim, Young Keun [Department of Materials Science and Engineering, Korea University, Seoul 136-713 (Korea, Republic of)]. E-mail: ykim97@korea.ac.kr

    2007-03-15

    We have studied the effect of an external magnetic field applied during electrodeposition of Co/Cu barcode nanowires in anodic aluminum oxide nanotemplates. The magnetic properties of the barcode nanowires were greatly enhanced for 50 nm pore diameter regardless of segment aspect ratio, but field deposition has little effect on the 200 nm nanowires. The magnetic improvement is correlated with a structural change, attributed to field modification of the growth habit of the barcode nanowires. A mechanism of growth subject to geometric confinement is proposed.

  11. Identification of Fabaceae plants using the DNA barcode matK.

    Science.gov (United States)

    Gao, Ting; Sun, Zhiying; Yao, Hui; Song, Jingyuan; Zhu, Yingjie; Ma, Xinye; Chen, Shilin

    2011-01-01

    In this study, we tested the applicability of the core DNA barcode MATK for identifying species within the Fabaceae family. Based on an evaluation of genetic variation, DNA barcoding gaps, and species discrimination power, MATK is a useful barcode for Fabaceae species. Of 1355 plant samples collected from 1079 species belonging to 409 diverse genera, MATK precisely identified approximately 80 % and 96 % of them at the species and genus levels, respectively. Therefore, our research indicates that the MATK region is a valuable marker for plant species within Fabaceae. PMID:20549596

  12. DNA barcoding of perennial fruit tree species of agronomic interest in the genus Annona (Annonaceae)

    OpenAIRE

    Larranaga, Nerea; Hormaza, José I.

    2015-01-01

    The DNA barcode initiative aims to establish a universal protocol using short genetic sequences to discriminate among animal and plant species. Although many markers have been proposed to become the barcode of plants, the Consortium for the Barcode of Life (CBOL) Plant Working Group recommended using as a core the combination of two portions of plastid coding region, rbcL and matK. In this paper, specific markers based on matK sequences were developed for 7 closely related Annona species of a...

  13. Bio-barcode gel assay for microRNA

    Science.gov (United States)

    Lee, Hyojin; Park, Jeong-Eun; Nam, Jwa-Min

    2014-02-01

    MicroRNA has been identified as a potential biomarker because expression level of microRNA is correlated with various cancers. Its detection at low concentrations would be highly beneficial for cancer diagnosis. Here, we develop a new type of a DNA-modified gold nanoparticle-based bio-barcode assay that uses a conventional gel electrophoresis platform and potassium cyanide chemistry and show this assay can detect microRNA at aM levels without enzymatic amplification. It is also shown that single-base-mismatched microRNA can be differentiated from perfectly matched microRNA and the multiplexed detection of various combinations of microRNA sequences is possible with this approach. Finally, differently expressed microRNA levels are selectively detected from cancer cells using the bio-barcode gel assay, and the results are compared with conventional polymerase chain reaction-based results. The method and results shown herein pave the way for practical use of a conventional gel electrophoresis for detecting biomolecules of interest even at aM level without polymerase chain reaction amplification.

  14. DNA barcoding for species Identification in prepared fishery products

    Directory of Open Access Journals (Sweden)

    ANNA MOTTOLA

    2014-06-01

    Full Text Available Considering that seafood mislabeling has been widely reported throughout the world and that the authentication of food components is one of the key issues in food quality, the aim of this study was to use DNA barcoding to investigate the prevalence of mislabeling among fresh prepared fishery products from markets and supermarkets located in Apulia (SE Italy. The study reveals a high occurrence of species mislabeling (42% in the prepared fillet products, further evidence of the need for increased traceability and assessment of the authenticity of food products. Given the increasing demand for transparency in the food industry and the enforcement of proper labeling have provided a driving force for the development of suitable analytical methodologies for species identification. There is therefore a great need to develop fast and reliable methods to identify meat species and to quantify their levels in seafood products, in order to ensure product quality and thus to protect consumers. The study provides further evidence that molecular investigations based on DNA barcoding may be one of the most powerful tools for the assessment of species identity, food traceability, safety and fraud.

  15. DNA barcoding as a tool for coral reef conservation

    Science.gov (United States)

    Neigel, J.; Domingo, A.; Stake, J.

    2007-09-01

    DNA Barcoding (DBC) is a method for taxonomic identification of animals that is based entirely on the 5' portion of the mitochondrial gene, cytochrome oxidase subunit I ( COI-5). It can be especially useful for identification of larval forms or incomplete specimens lacking diagnostic morphological characters. DBC can also facilitate the discovery of species and in defining “molecular taxonomic units” in problematic groups. However, DBC is not a panacea for coral reef taxonomy. In two of the most ecologically important groups on coral reefs, the Anthozoa and Porifera, COI-5 sequences have diverged too little to be diagnostic for all species. Other problems for DBC include paraphyly in mitochondrial gene trees and lack of differentiation between hybrids and their maternal ancestors. DBC also depends on the availability of databases of COI-5 sequences, which are still in early stages of development. A global effort to barcode all fish species has demonstrated the importance of large-scale coordination and is yielding promising results. Whether or not COI-5 by itself is sufficient for species assignments has become a contentious question; it is generally advantageous to use sequences from multiple loci.

  16. DNA barcoding of marine ornamental fishes from India.

    Science.gov (United States)

    Bamaniya, Dhaval C; Pavan-Kumar, A; Gireesh-Babu, P; Sharma, Niti; Reang, Dhalongsaih; Krishna, Gopal; Lakra, W S

    2016-09-01

    India has rich marine ornamental fish diversity with 400 fish species distributed in Gulf of Munnar/Palk Bay, Gulf of Kutch, and in reefs around Andaman & Nicobar and Lakshadweep Islands. Marine ornamental fish identification at the field level is very difficult because of their high diversity and profound changes in appearance during their developmental stages and camouflage. To facilitate ornamental fish trading with ease and in compliance with the biodiversity act, DNA barcoding technique could be used to accurately identify species. In this study, DNA barcodes were generated for 31 species of commercially important marine ornamental fishes from India. The average genetic distance (K2P model) within species, genus, and family was 0.446, 13.08, and 20.09%, respectively. Intraspecific variation has increased several folds (15-20 times) after including conspecific sequences from different geographical locations. The presence of allopatric lineages/cryptic species was observed in the Indo-pacific region. The NJ tree constructed based on K2P values showed distinct clusters shared by congeneric species specific to populations. PMID:25703851

  17. Imagining Sisyphus happy: DNA barcoding and the unnamed majority.

    Science.gov (United States)

    Blaxter, Mark

    2016-09-01

    The vast majority of life on the Earth is physically small, and is classifiable as micro- or meiobiota. These organisms are numerically dominant and it is likely that they are also abundantly speciose. By contrast, the vast majority of taxonomic effort has been expended on 'charismatic megabionts': larger organisms where a wealth of morphology has facilitated Linnaean species definition. The hugely successful Linnaean project is unlikely to be extensible to the totality of approximately 10 million species in a reasonable time frame and thus alternative toolkits and methodologies need to be developed. One such toolkit is DNA barcoding, particularly in its metabarcoding or metagenetics mode, where organisms are identified purely by the presence of a diagnostic DNA sequence in samples that are not processed for morphological identification. Building on secure Linnaean foundations, classification of unknown (and unseen) organisms to molecular operational taxonomic units (MOTUs) and deployment of these MOTUs in biodiversity science promises a rewarding resolution to the Sisyphean task of naming all the world's species.This article is part of the themed issue 'From DNA barcodes to biomes'. PMID:27481781

  18. New universal matK primers for DNA barcoding angiosperms

    Institute of Scientific and Technical Information of China (English)

    Jing YU; Jian-Hua XUE; Shi-Liang ZHOU

    2011-01-01

    The chloroplast maturase K gene (matK) is one of the most variable coding genes of angiosperms and has been suggested to be a "barcode" for land plants. However, matK exhibits low amplification and sequencing rates due to low universality of currently available primers and mononucleotide repeats. To resolve these technical problems, we evaluated the entire matK region to find a region of 600-800 bp that is highly variable, represents the best of all matK regions with priming sites conservative enough to design universal primers, and avoids the mononucleotide repeats. After careful evaluation, a region in the middle was chosen and a pair of primers named natK472F and matK1248R was designed to amplify and sequence the matK fragment of approximately 776 bp. This region encompasses the most variable sites, represents the entire matK region best, and also exhibits high amplification rates and quality of sequences. The universality of this primer pair was tested using 58 species from 47 families of angiosperm plants. The primers showed a strong amplification (93.1%) and sequencing (92.6%)successes in the species tested. We propose that the new primers will solve, in part, the problems encountered when using matK and promote the adoption of matK as a DNA barcode for angiosperms.

  19. Mosquitoes of eastern Amazonian Ecuador: biodiversity, bionomics and barcodes

    Directory of Open Access Journals (Sweden)

    Yvonne-Marie Linton

    2013-01-01

    Full Text Available Two snapshot surveys to establish the diversity and ecological preferences of mosquitoes (Diptera: Culicidae in the terra firme primary rain forest surrounding the Tiputini Biodiversity Station in the UNESCO Yasuní Biosphere Reserve of eastern Amazonian Ecuador were carried out in November 1998 and May 1999. The mosquito fauna of this region is poorly known; the focus of this study was to obtain high quality link-reared specimens that could be used to unequivocally confirm species level diversity through integrated systematic study of all life stages and DNA sequences. A total of 2,284 specimens were preserved; 1,671 specimens were link-reared with associated immature exuviae, all but 108 of which are slide mounted. This study identified 68 unique taxa belonging to 17 genera and 27 subgenera. Of these, 12 are new to science and 37 comprise new country records. DNA barcodes [658-bp of the mtDNA cytochrome c oxidase ( COI I gene] are presented for 58 individuals representing 20 species and nine genera. DNA barcoding proved useful in uncovering and confirming new species and we advocate an integrated systematics approach to biodiversity studies in future. Associated bionomics of all species collected are discussed. An updated systematic checklist of the mosquitoes of Ecuador (n = 179 is presented for the first time in 60 years.

  20. Magnetic Barcode Assay for Genetic Detection of Pathogens

    Science.gov (United States)

    Liong, Monty; Hoang, Anh N.; Chung, Jaehoon; Gural, Nil; Ford, Christopher B.; Min, Changwook; Shah, Rupal R.; Ahmad, Rushdy; Fernandez-Suarez, Marta; Fortune, Sarah M.; Toner, Mehmet; Lee, Hakho; Weissleder, Ralph

    2013-01-01

    The task of rapidly identifying patients infected with Mycobacterium tuberculosis (MTB) in resource-constrained environments remains a challenge. A sensitive and robust platform that does not require bacterial isolation or culture is critical in making informed diagnostic and therapeutic decisions. Here we introduce a platform for the detection of nucleic acids based on a magnetic barcoding strategy. PCR-amplified mycobacterial genes are sequence-specifically captured on microspheres, labeled by magnetic nanoprobes, and detected by nuclear magnetic resonance. All components are integrated into a single, small fluidic cartridge for streamlined on-chip operation. We use this platform to detect MTB and identify drug-resistance strains from mechanically processed sputum samples within 2.5 hours. The specificity of the assay is confirmed by a panel of clinically relevant non-MTB bacteria, and the clinical utility is demonstrated by the measurements in MTB-positive patient specimens. Combined with portable systems, the magnetic barcode assay holds promise to become a sensitive, high-throughput, and low-cost platform for point-of-care diagnostics. PMID:23612293

  1. Layer-by-layer growth of superparamagnetic, fluorescent barcode nanospheres

    International Nuclear Information System (INIS)

    We report a novel stepwise layer-by-layer synthesis strategy to achieve multi-component barcode nanospheres that contain magnetic nanoparticles (MNPs) as the core and quantum dots (QDs) of different emission colors in spatially separated silica layers as the shells, with QD-free silica layers as the insulation layers. This strategy offers the following unique features: (1) the location of the MNPs and the QDs in the silica spheres are separated spatially, so that no interference of the QD photoluminescence (PL) by the magnetic particles is observed; (2) the PL spectra of barcode nanospheres can be easily tuned through the ratio of different QDs loaded in each layer; (3) the size of the silica nanospheres can range from submicron (∼100 nm) to micrometers depending on the number of layers and the thickness of each layer; (4) QD stability is preserved by embedding the QDs covalently in the silica matrix; (5) fluorescence resonance energy transfer (FRET) between different colored QDs is avoided by isolating them into separated layers with a silica spacer layer

  2. Nested image steganography scheme using QR-barcode technique

    Science.gov (United States)

    Chen, Wen-Yuan; Wang, Jing-Wein

    2009-05-01

    In this paper, QR bar code and image processing techniques are used to construct a nested steganography scheme. There are two types of secret data (lossless and lossy) embedded into a cover image. The lossless data is text that is first encoded by the QR barcode; its data does not have any distortion when comparing with the extracted data and original data. The lossy data is a kind of image; the face image is suitable for our case. Because the extracted text is lossless, the error correction rate of QR encoding must be carefully designed. We found a 25% error correction rate is suitable for our goal. In image embedding, because it can sustain minor perceptible distortion, we thus adopted the lower nibble byte discard of the face image to reduce the secret data. When the image is extracted, we use a median filter to filter out the noise and obtain a smoother image quality. After simulation, it is evident that our scheme is robust to JPEG attacks. Compared to other steganography schemes, our proposed method has three advantages: (i) the nested scheme is an enhanced security system never previously developed; (ii) our scheme can conceal lossless and lossy secret data into a cover image simultaneously; and (iii) the QR barcode used as secret data can widely extend this method's application fields.

  3. Layer-by-layer growth of superparamagnetic, fluorescent barcode nanospheres

    Energy Technology Data Exchange (ETDEWEB)

    Wang Qiangbin [Biodesign Institute, Arizona State University, Tempe, AZ 85287 (United States); Liu Yan [Biodesign Institute, Arizona State University, Tempe, AZ 85287 (United States); Lin Chenxiang [Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287 (United States); Yan Hao [Biodesign Institute, Arizona State University, Tempe, AZ 85287 (United States)

    2007-10-10

    We report a novel stepwise layer-by-layer synthesis strategy to achieve multi-component barcode nanospheres that contain magnetic nanoparticles (MNPs) as the core and quantum dots (QDs) of different emission colors in spatially separated silica layers as the shells, with QD-free silica layers as the insulation layers. This strategy offers the following unique features: (1) the location of the MNPs and the QDs in the silica spheres are separated spatially, so that no interference of the QD photoluminescence (PL) by the magnetic particles is observed; (2) the PL spectra of barcode nanospheres can be easily tuned through the ratio of different QDs loaded in each layer; (3) the size of the silica nanospheres can range from submicron ({approx}100 nm) to micrometers depending on the number of layers and the thickness of each layer; (4) QD stability is preserved by embedding the QDs covalently in the silica matrix; (5) fluorescence resonance energy transfer (FRET) between different colored QDs is avoided by isolating them into separated layers with a silica spacer layer.

  4. Comparative study of Barcode, QR-code and RFID System

    Directory of Open Access Journals (Sweden)

    Trupti Lotlikar

    2013-09-01

    Full Text Available Wireless sensors are standard measurement tools equipped with transmitters to convert signals from process control instruments into a radio transmission. The radio signal is interpreted by a receiver which then converts the wireless signal to a specific, desired output, such as an analog current or data analysis via computer software. The paper gives a brief on wireless sensors and their types like Barcode, QR code, RFID along with their characteristics and working components. The Barcode is an optical machine-readable representation of data relating to the object to which it is attached. On the other hand the Radio-frequency identification (RFID is the use of a wireless non-contact system that uses radio-frequency electromagnetic fields to transfer data from a tag attached to an object, for the purposes of automatic identification and tracking. Quick response (QR codes are a very convenient way to display a small bit of information that is easily scanned and processed typically by mobile devices allowing physical items to almost become interactive, by providing information that is easily scanned like a website URL. Finally this paper will compare all the three technologies on various grounds like durability, cost, information capacity, read range etc. to determine best out of it.

  5. Application of DNA barcodes in Hedyotis L.(Spermacoceae, Rubiaceae)

    Institute of Scientific and Technical Information of China (English)

    Xing GUO; Mark P.SIMMONS; paul Pui-Hay BUT; Pang-Chui SHAW; Rui-Jiang WANG

    2011-01-01

    The potential application of DNA barcodes of plastid (matK, trnH-psbA, petD, and rbcL) and nuclear (internal transcribed spacer (ITS) of rDNA) DNA regions was investigated for 25 Hedyotis taxa. The ITS showed the best species discrimination by resolving 23 of the species as exclusive lineages with no shared alleles between any of the 24 distinct species (H. Assimilis and H. Mellii are not supported as distinct species based on our molecular and morphological data). Conversely, rbcL performed the worst and only resolved 10 of the species as exclusive lineages, and 10 species with shared alleles. Using ITS has the advantage of high PCR amplification success and it provides good intra- and interspecific variation distribution patterns. The most powerful plastid markers were petD and trnH-psbA, but we could amplify and sequence trnH-psbA for only 83% of the accessions sampled. Combination of ITS and petD performed extremely well, with all 24 of the distinct species resolved as exclusive lineages and no shared alleles between any of the distinct species. We therefore recommend ITS, or a combination of ITS and petD, as the standard DNA barcode in Hedyotis, but acknowledge that there are no shared alleles between distinct species for marK and rbcL combined.

  6. DNA barcoding of Dalbergia spp. from Western Ghats in India

    Directory of Open Access Journals (Sweden)

    R. M. Bhagwat

    2011-01-01

    Full Text Available (Abstract selected from presentation in National Conference on Biodiversity of Medicinal and Aromatic Plants: Collection, Characterization and Utilization, held at Anand, India during November 24-25, 2010  Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin-top:0in; mso-para-margin-right:0in; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0in; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin;} The Western Ghats (WG in India are well known for their rich and unique assemblage of flora and fauna, and are amongst the 25 biodiversity hotspots identified in the world. Dalbergia (family: Fabaceae is an important member of the WG flora; valued for decorative and often fragrant wood (rosewood, African blackwood, sisu and is rich in aromatic oils. There is taxonomic confusion with respect to several Dalbergia species as these often have more than one species names. Hence, the size of the Dalbergia genus remains disputed. DNA barcoding is modern biotechnological tool which can distinguish among species that look alike. It is also useful in medicinal formulations to identify adulterants. Although DNA barcoding is well established ly accepted barcode is still lacking in plants. Hence, the main objective of this study is to develop a unique barcode for quick, accurate and reliable species identification using the Dalbergia genus as a model system. Leaf samples from 15 accessions each, belonging to six

  7. Geohazards in the Western Ionian Sea: Insights from non-earthquake signals recorded by the NEMO-SN1 seafloor observatory

    OpenAIRE

    2014-01-01

    Seafloor instability resulting from both tectonics and volcanism affects the Western Ionian Sea. The NEutrino Mediterranean Observatory-Submarine Network 1 (NEMO-SN1), deployed 25 km offshore eastern Sicily at 2,100 m water depth, records a variety of signals for geophysical and environmental long-term monitoring, including non-earthquake seismic signals that provide insights into the area’s geohazards. The signals analyzed for this paper are: (1) seismic signals associated ...

  8. A comparison of sea surface temperatures in the Equatorial Pacific Nino regions with results from two early runs of the NEMO 1/12° Ocean Model

    OpenAIRE

    Webb, D.J.

    2016-01-01

    Sea surface temperature observations from the Nino regions of the Tropical Pacific are compared with results from two 1/12° runs of the NEMO global ocean model. The results show good agreement between the model and observations. There was some concern that the model surface temperatures were being strongly coupled to the actual temperatures via the surface boundary conditions. The near surface structure of the ocean was investigated, as were the individual surface flux terms, but no evi...

  9. A DNA barcoding approach to identify plant species in multiflower honey.

    Science.gov (United States)

    Bruni, I; Galimberti, A; Caridi, L; Scaccabarozzi, D; De Mattia, F; Casiraghi, M; Labra, M

    2015-03-01

    The purpose of this study was to test the ability of DNA barcoding to identify the plant origins of processed honey. Four multifloral honeys produced at different sites in a floristically rich area in the northern Italian Alps were examined by using the rbcL and trnH-psbA plastid regions as barcode markers. An extensive reference database of barcode sequences was generated for the local flora to determine the taxonomic composition of honey. Thirty-nine plant species were identified in the four honey samples, each of which originated from a mix of common plants belonging to Castanea, Quercus, Fagus and several herbaceous taxa. Interestingly, at least one endemic plant was found in all four honey samples, providing a clear signature for the geographic identity of these products. DNA of the toxic plant Atropa belladonna was detected in one sample, illustrating the usefulness of DNA barcoding for evaluating the safety of honey. PMID:25306350

  10. Revealing the hyperdiverse mite fauna of subarctic Canada through DNA barcoding.

    Directory of Open Access Journals (Sweden)

    Monica R Young

    Full Text Available Although mites are one of the most abundant and diverse groups of arthropods, they are rarely targeted for detailed biodiversity surveys due to taxonomic constraints. We address this gap through DNA barcoding, evaluating acarine diversity at Churchill, Manitoba, a site on the tundra-taiga transition. Barcode analysis of 6279 specimens revealed nearly 900 presumptive species of mites with high species turnover between substrates and between forested and non-forested sites. Accumulation curves have not reached an asymptote for any of the three mite orders investigated, and estimates suggest that more than 1200 species of Acari occur at this locality. The coupling of DNA barcode results with taxonomic assignments revealed that Trombidiformes compose 49% of the fauna, a larger fraction than expected based on prior studies. This investigation demonstrates the efficacy of DNA barcoding in facilitating biodiversity assessments of hyperdiverse taxa.

  11. DNA barcoding and the identification of tree frogs (Amphibia: Anura: Rhacophoridae).

    Science.gov (United States)

    Dang, Ning-Xin; Sun, Feng-Hui; Lv, Yun-Yun; Zhao, Bo-Han; Wang, Ji-Chao; Murphy, Robert W; Wang, Wen-Zhi; Li, Jia-Tang

    2016-07-01

    The DNA barcoding gene COI (cytochrome c oxidase subunit I) effectively identifies many species. Herein, we barcoded 172 individuals from 37 species belonging to nine genera in Rhacophoridae to test if the gene serves equally well to identify species of tree frogs. Phenetic neighbor joining and phylogenetic Bayesian inference were used to construct phylogenetic trees, which resolved all nine genera as monophyletic taxa except for Rhacophorus, two new matrilines for Liuixalus, and Polypedates leucomystax species complex. Intraspecific genetic distances ranged from 0.000 to 0.119 and interspecific genetic distances ranged from 0.015 to 0.334. Within Rhacophorus and Kurixalus, the intra- and interspecific genetic distances did not reveal an obvious barcode gap. Notwithstanding, we found that COI sequences unambiguously identified rhacophorid species and helped to discover likely new cryptic species via the synthesis of genealogical relationships and divergence patterns. Our results supported that COI is an effective DNA barcoding marker for Rhacophoridae. PMID:26004249

  12. Genetic identification of two species of Pleuronichthys byDNA barcoding

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hui; ZHANG Yan; GAO Tianxiang; LI Pengfei; XU Hanxiang

    2011-01-01

    DNA barcoding is a new method for biological taxonomy,offering the ability to identify species from fragments in any life-history stage.Pleuronichthys cornutus and P.japonicus are two morphologically similar species.Pleuronichthys japonicus has never been found previously in China.However,in this study,we identified both species using DNA barcoding (cytochrome c oxidase subunit I (COI)),the mtDNA control region and cytochrome b.The results reveal that:1) intraspecific variation in the DNA barcode is much less than interspecific variation; 2) the two morphologically similar species were placed into separate clades distinguishable by high bootstrap values; 3) COI barcodes are more powerful for identifying the two species than the other two mtDNA fragments.

  13. CRISPR-Barcoding for Intratumor Genetic Heterogeneity Modeling and Functional Analysis of Oncogenic Driver Mutations.

    Science.gov (United States)

    Guernet, Alexis; Mungamuri, Sathish Kumar; Cartier, Dorthe; Sachidanandam, Ravi; Jayaprakash, Anitha; Adriouch, Sahil; Vezain, Myriam; Charbonnier, Françoise; Rohkin, Guy; Coutant, Sophie; Yao, Shen; Ainani, Hassan; Alexandre, David; Tournier, Isabelle; Boyer, Olivier; Aaronson, Stuart A; Anouar, Youssef; Grumolato, Luca

    2016-08-01

    Intratumor genetic heterogeneity underlies the ability of tumors to evolve and adapt to different environmental conditions. Using CRISPR/Cas9 technology and specific DNA barcodes, we devised a strategy to recapitulate and trace the emergence of subpopulations of cancer cells containing a mutation of interest. We used this approach to model different mechanisms of lung cancer cell resistance to EGFR inhibitors and to assess effects of combined drug therapies. By overcoming intrinsic limitations of current approaches, CRISPR-barcoding also enables investigation of most types of genetic modifications, including repair of oncogenic driver mutations. Finally, we used highly complex barcodes inserted at a specific genome location as a means of simultaneously tracing the fates of many thousands of genetically labeled cancer cells. CRISPR-barcoding is a straightforward and highly flexible method that should greatly facilitate the functional investigation of specific mutations, in a context that closely mimics the complexity of cancer. PMID:27453044

  14. Adaptive Segmentation Method for 2-D Barcode Image Base on Mathematic Morphological

    Directory of Open Access Journals (Sweden)

    Jianhua Li

    2013-10-01

    Full Text Available Segmentation is a key process of 2-D barcode identification. In this study we propose a fast adaptive segmentation method that is based on morphological method which is suitable for kinds of 2-D barcode images with different scale, angle and sort. The algorithm is based on mathematical morphology, the basic idea of the algorithm is to use Multi-scale open reconstruction of mathematical morphology to transform the image continuously, then choose whether to terminate by the results of the adjacent image transformation and finally get the final segmentation results by further processing of the images obtain from termination.The proposed approach is applied in experiments on 2-D barcodes with complicated background. The results indicated that the proposed method is very effective in adaptively 2-D barcode image segmentation.

  15. DNA bases assembled on the Au(110)/electrolyte interface: A combined experimental and theoretical study

    DEFF Research Database (Denmark)

    Salvatore, Princia; Nazmutdinov, Renat R.; Ulstrup, Jens;

    2015-01-01

    Among the low-index single-crystal gold surfaces, the Au(110) surface is the most active toward molecular adsorption and the one with fewest electrochemical adsorption data reported. Cyclic voltammetry (CV), electrochemically controlled scanning tunneling microscopy (EC-STM), and density functional......, accompanied by a pair of strong voltammetry peaks in the double-layer region in acid solutions. Adsorption of the DNA bases gives featureless voltammograms with lower double-layer capacitance, suggesting that all the bases are chemisorbed on the Au(110) surface. Further investigation of the surface structures...... of the adlayers of the four DNA bases by EC-STM disclosed lifting of the Au(110) reconstruction, specific molecular packing in dense monolayers, and pH dependence of the A and G adsorption. DFT computations based on a cluster model for the Au(110) surface were performed to investigate the adsorption energy...

  16. Universal spectrum for DNA base CG frequency distribution in Takifugu rubripes (Puffer fish) genome

    CERN Document Server

    Selvam, A M

    2007-01-01

    The frequency distribution of DNA bases A, C, G, T exhibit fractal fluctuations, namely a zigzag pattern of an increase followed by a decrease of all orders of magnitude along the length of the DNA molecule. Selfsimilar fractal fluctuations are ubiquitous to space-time fluctuations of dynamical systems in nature. The power spectra of fractal fluctuations exhibit inverse power law form signifying long-range space-time correlations such that there is two-way communication between local (small-scale) and global (large-scale) perturbations. In this paper it is shown that DNA base CG frequency distribution in Takifugu rubripes (Puffer fish) Genome Release 4 exhibit universal inverse power law form of the statistical normal distribution consistent with a general systems theory model prediction of quantumlike chaos governing fractal space-time distributions. The model predictions are (i) quasicrystalline Penrose tiling pattern for the nested coiled structure thereby achieving maximum packing efficiency for the DNA m...

  17. A novel Lie algebra of the genetic code over the Galois field of four DNA bases.

    Science.gov (United States)

    Sánchez, Robersy; Grau, Ricardo; Morgado, Eberto

    2006-07-01

    Starting from the four DNA bases order in the Boolean lattice, a novel Lie Algebra of the genetic code is proposed. Here, the main partitions of the genetic code table were obtained as equivalent classes of quotient spaces of the genetic code vector space over the Galois field of the four DNA bases. The new algebraic structure shows strong connections among algebraic relationships, codon assignments and physicochemical properties of amino acids. Moreover, a distance defined between codons expresses a physicochemical meaning. It was also noticed that the distance between wild type and mutant codons tends to be small in mutational variants of four genes: human phenylalanine hydroxylase, human beta-globin, HIV-1 protease and HIV-1 reverse transcriptase. These results strongly suggest that deterministic rules in genetic code origin must be involved. PMID:16780898

  18. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

    OpenAIRE

    Schoch, C.L.; Seifert, K.A.; Huhndorf, S.; Robert, V.; Spouge, J L; Levesque, C.A.; W. Chen; Crous, P.W.; Boekhout, T.; Damm, U.; Hoog, de, R.; Eberhardt, U.; Groenewald, J.Z.; Groenewald, M.; Hagen, F.

    2012-01-01

    Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of thre...

  19. Secure Audio Forensic Marking Algorithm Using 2D Barcode in DWT-DFRNT Domain

    OpenAIRE

    Li(李, Li, 莉); JongWeon Kim

    2014-01-01

    We created a robust and secure forensic marking algorithm through the process of hiding information in a two-dimensional (2D) barcode and embedding it into the discrete wavelet transformation-discrete fractional random transformation (DWT-DFRNT) domain using the quantization technique. We hid information in the 2D barcode, encoded it with the block code that we developed, and then converted it through scrambling. The security of the algorithm was greatly improved by increasing the calculation...

  20. DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market.

    Science.gov (United States)

    Mishra, Priyanka; Kumar, Amit; Nagireddy, Akshitha; Mani, Daya N; Shukla, Ashutosh K; Tiwari, Rakesh; Sundaresan, Velusamy

    2016-01-01

    The past couple of decades have witnessed global resurgence of herbal-based health care. As a result, the trade of raw drugs has surged globally. Accurate and fast scientific identification of the plant(s) is the key to success for the herbal drug industry. The conventional approach is to engage an expert taxonomist, who uses a mix of traditional and modern techniques for precise plant identification. However, for bulk identification at industrial scale, the process is protracted and time-consuming. DNA barcoding, on the other hand, offers an alternative and feasible taxonomic tool box for rapid and robust species identification. For the success of DNA barcode, the barcode loci must have sufficient information to differentiate unambiguously between closely related plant species and discover new cryptic species. For herbal plant identification, matK, rbcL, trnH-psbA, ITS, trnL-F, 5S-rRNA and 18S-rRNA have been used as successful DNA barcodes. Emerging advances in DNA barcoding coupled with next-generation sequencing and high-resolution melting curve analysis have paved the way for successful species-level resolution recovered from finished herbal products. Further, development of multilocus strategy and its application has provided new vistas to the DNA barcode-based plant identification for herbal drug industry. For successful and acceptable identification of herbal ingredients and a holistic quality control of the drug, DNA barcoding needs to work harmoniously with other components of the systems biology approach. We suggest that for effectively resolving authentication challenges associated with the herbal market, DNA barcoding must be used in conjunction with metabolomics along with need-based transcriptomics and proteomics. PMID:26079154

  1. Speckle revisited: analysis of speckle noise in bar-code scanning systems

    Science.gov (United States)

    Marom, Emanuel; Kresic-Juric, Sasa; Bergstein, Leonard

    2001-06-01

    Laser beams used for bar-code scanning exhibit speckle noise generated by the roughness of the surface on which bar-codes are printed. Statistical properties of a photodetector signal that integrates a time-varying speckle pattern falling on its aperture are analyzed in detail. We derive simple closed form expressions for the auto-correlation function and power spectral density of the detector current for general form scanning beams with arbitrary field distributions. Theoretical calculations are illustrated by numerical simulations.

  2. Assessing DNA Barcoding as a Tool for Species Identification and Data Quality Control

    OpenAIRE

    Yong-Yi Shen; Xiao Chen; Murphy, Robert W.

    2013-01-01

    In recent years, the number of sequences of diverse species submitted to GenBank has grown explosively and not infrequently the data contain errors. This problem is extensively recognized but not for invalid or incorrectly identified species, sample mixed-up, and contamination. DNA barcoding is a powerful tool for identifying and confirming species and one very important application involves forensics. In this study, we use DNA barcoding to detect erroneous sequences in GenBank by evaluating ...

  3. Raising the Barcode Scanner: Technology and Productivity in the Retail Sector

    OpenAIRE

    Emek Basker

    2011-01-01

    Barcodes and barcode scanners transformed the grocery industry in the 1970s. I use store-level data from the 1972, 1977, and 1982 Census of Retail Trade, matched to data on store scanner installations, to estimate scanners' effect on labor productivity. I find that scanners increased a store's labor productivity, on average, by approximately 4.5 percent in the first few years. The effect was larger in stores carrying more packaged products, consistent with the presence of network externalitie...

  4. Investigation of the Mesenchymal Stem Cell Compartment by Means of a Lentiviral Barcode Library.

    Science.gov (United States)

    Bigildeev, A E; Cornils, K; Aranyossy, T; Sats, N V; Petinati, N A; Shipounova, I N; Surin, V L; Pshenichnikova, O S; Riecken, K; Fehse, B; Drize, N I

    2016-04-01

    The hematopoietic bone marrow microenvironment is formed by proliferation and differentiation of mesenchymal stem cells (MSCs). The MSC compartment has been less studied than the hematopoietic stem cell compartment. To characterize the structure of the MSC compartment, it is necessary to trace the fate of distinct mesenchymal cells. To do so, mesenchymal progenitors need to be marked at the single-cell level. A method for individual marking of normal and cancer stem cells based on genetic "barcodes" has been developed for the last 10 years. Such approach has not yet been applied to MSCs. The aim of this study was to evaluate the possibility of using such barcoding strategy to mark MSCs and their descendants, colony-forming units of fibroblasts (CFU-Fs). Adherent cell layers (ACLs) of murine long-term bone marrow cultures (LTBMCs) were transduced with a lentiviral library with barcodes consisting of 32 + 3 degenerate nucleotides. Infected ACLs were suspended, and CFU-F derived clones were obtained. DNA was isolated from each individual colony, and barcodes were analyzed in marked CFU-F-derived colonies by means of conventional polymerase chain reaction and Sanger sequencing. Barcodes were identified in 154 marked colonies. All barcodes appeared to be unique: there were no two distinct colonies bearing the same barcode. It was shown that ACLs included CFU-Fs with different proliferative potential. MSCs are located higher in the hierarchy of mesenchymal progenitors than CFU-Fs, so the presented data indicate that MSCs proliferate rarely in LTBMCs. A method of stable individual marking and comparing the markers in mesenchymal progenitor cells has been developed in this work. We show for the first time that a barcoded library of lentiviruses is an effective tool for studying stromal progenitor cells. PMID:27293094

  5. Identification of the vascular plants of Churchill, Manitoba, using a DNA barcode library

    OpenAIRE

    Kuzmina Maria L; Johnson Karen L; Barron Hannah R; Hebert Paul DN

    2012-01-01

    Abstract Background Because arctic plant communities are highly vulnerable to climate change, shifts in their composition require rapid, accurate identifications, often for specimens that lack diagnostic floral characters. The present study examines the role that DNA barcoding can play in aiding floristic evaluations in the arctic by testing the effectiveness of the core plant barcode regions (rbcL, matK) and a supplemental ribosomal DNA (ITS2) marker for a well-studied flora near Churchill, ...

  6. 真菌DNA条形码研究进展%Progress of fungal DNA barcode

    Institute of Scientific and Technical Information of China (English)

    张宇; 郭良栋

    2012-01-01

    DNA barcode uses a short gene sequence taken from standardized portions of the genome to identify species. Cytochrome oxidase I (COI), as an animal DNA barcode, has been successfully employed in the species identification. In plants a combination of chloroplast rbcL and matK genes has been accepted as basic DNA barcode. In fungi more genes have being screened and evaluated in all major lineages of fungi by mycologists all over the world. Recently, the internal transcribed spacer (ITS) has been recommended as primary DNA barcode of fungi in the Fourth International Barcode of Life Conference. This review summarized the recent progress of fungal DNA barcode, and pointed out the prospect of DNA barcode in future fungal studies.%DNA条形码(DNA barcode)是通过一段短的标准DNA片段实现物种的快速、准确和标准化鉴定.线粒体细胞色素C氧化酶亚基I (COI)基因作为动物的DNA条形码已广泛应用于物种鉴定中,在植物上已选定叶绿体rbcL和matK基因作为基本的DNA条形码.目前世界各国真菌学家正对不同的真菌类群进行不同基因片段的筛选与评价,并在第四届国际生命条形码大会上正式推荐了ITS作为真菌的首选DNA条形码.对国内外真菌DNA条形码的研究进展进行总结与分析,并展望真菌DNA条形码的应用前景.

  7. Reflex: intramolecular barcoding of long-range PCR products for sequencing multiple pooled DNAs

    OpenAIRE

    Casbon, James A; Slatter, Andrew F; Musgrave-Brown, Esther; Osborne, Robert J.; Lichtenstein, Conrad P.; Brenner, Sydney

    2013-01-01

    We present an intramolecular reaction, Reflex™, to derive shorter, sequencer-ready, daughter polymerase chain reaction products from a pooled population of barcoded long-range polymerase chain reaction products, whilst still preserving the cognate DNA barcodes. Our Reflex workflow needs only a small number of primer extension steps to rapidly enable uniform sequence coverage of long contiguous sequence targets in large numbers of samples at low cost on desktop next-generation sequencers.

  8. DNA barcodes from four loci provide poor resolution of taxonomic groups in the genus Crataegus

    OpenAIRE

    Zarrei, Mehdi; Talent, Nadia; Kuzmina, Maria; Lee, Jeanette; Lund, Jensen; Shipley, Paul R.; Stefanović, Saša; Dickinson, Timothy A.

    2015-01-01

    The leaves and fruits of some of the approximately 230 species of hawthorn (Crataegus) yield natural health products with significant therapeutic effects on symptoms of cardiovascular disease. DNA barcoding could be a valuable tool for authenticating these products, but only a small fraction of the 93 taxa that we examined were distinguished, even though all major clades and eight out of ten taxonomic sections of the genus were included. DNA barcoding as currently practised thus has limited u...

  9. Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections

    Science.gov (United States)

    Chambers, E. Anne; Hebert, Paul D. N.

    2016-01-01

    Background High rates of species discovery and loss have led to the urgent need for more rapid assessment of species diversity in the herpetofauna. DNA barcoding allows for the preliminary identification of species based on sequence divergence. Prior DNA barcoding work on reptiles and amphibians has revealed higher biodiversity counts than previously estimated due to cases of cryptic and undiscovered species. Past studies have provided DNA barcodes for just 14% of the North American herpetofauna, revealing the need for expanded coverage. Methodology/Principal Findings This study extends the DNA barcode reference library for North American herpetofauna, assesses the utility of this approach in aiding species delimitation, and examines the correspondence between current species boundaries and sequence clusters designated by the BIN system. Sequences were obtained from 730 specimens, representing 274 species (43%) from the North American herpetofauna. Mean intraspecific divergences were 1% and 3%, while average congeneric sequence divergences were 16% and 14% in amphibians and reptiles, respectively. BIN assignments corresponded with current species boundaries in 79% of amphibians, 100% of turtles, and 60% of squamates. Deep divergences (>2%) were noted in 35% of squamate and 16% of amphibian species, and low divergences (<2%) occurred in 12% of reptiles and 23% of amphibians, patterns reflected in BIN assignments. Sequence recovery declined with specimen age, and variation in recovery success was noted among collections. Within collections, barcodes effectively flagged seven mislabeled tissues, and barcode fragments were recovered from five formalin-fixed specimens. Conclusions/Significance This study demonstrates that DNA barcodes can effectively flag errors in museum collections, while BIN splits and merges reveal taxa belonging to deeply diverged or hybridizing lineages. This study is the first effort to compile a reference library of DNA barcodes for herpetofauna

  10. The role of DNA base excision repair in brain homeostasis and disease

    DEFF Research Database (Denmark)

    Akbari, Mansour; Morevati, Marya; Croteau, Deborah;

    2015-01-01

    Chemical modification and spontaneous loss of nucleotide bases from DNA are estimated to occur at the rate of thousands per human cell per day. DNA base excision repair (BER) is a critical mechanism for repairing such lesions in nuclear and mitochondrial DNA. Defective expression or function of p...... energy homeostasis, mitochondrial function and cellular bioenergetics, with especially strong influence on neurological function. Further studies in this area could lead to novel approaches to prevent and treat human neurodegenerative disease....

  11. Quantification of Plasmodiophora brassicae Using a DNA-Based Soil Test Facilitates Sustainable Oilseed Rape Production

    OpenAIRE

    Ann-Charlotte Wallenhammar; Albin Gunnarson; Fredrik Hansson; Anders Jonsson

    2016-01-01

    Outbreaks of clubroot disease caused by the soil-borne obligate parasite Plasmodiophora brassicae are common in oilseed rape (OSR) in Sweden. A DNA-based soil testing service that identifies fields where P. brassicae poses a significant risk of clubroot infection is now commercially available. It was applied here in field surveys to monitor the prevalence of P. brassicae DNA in field soils intended for winter OSR production and winter OSR field experiments. In 2013 in Scania, prior to plantin...

  12. Construction of a New Molecular Barcode for Discriminating Plants and Animals with a Close Genetic Relationship

    Institute of Scientific and Technical Information of China (English)

    HUANG Li; ZHAO Xiao-feng; ZHU Yi-peng; DONG Heng; XU Ning-ying; CAO Jia-shu

    2013-01-01

    DNA barcodes have been proposed as a shortcut to provide species identification and as a way to accelerate the discovery of new species. A number of candidate gene regions have been suggested as possible barcodes for animals and plants, but for the identification of recently diverged species and/or varieties with only a few genetic differences it has been reported to be problematic in some cases. This study selected widely cultivated cruciferous vegetables as the primary samples, after failure of discrimination of each species using current DNA barcodes, we performed the fluorescent amplified fragment length polymorphism (F-AFLP) and successfully discriminated each species, subspecies, variety and their cultivar in 74 samples. Then the non-qualitative results obtained from F-AFLP were transformed into two-dimensional barcodes image file of each cultivar via the PDF417 software. This method was also successfully applied to the discrimination of 17 Chinese indigenous pig breeds. The barcode we constructed which greatly reduces the information storage space is genotypes-specific, and can be conveniently decoded into the original data and thereby be conveniently shared and referred to. We believe that it is possible to construct a new data sharing molecular barcode system that could discriminate the subspecies, varieties, cultivars and even individuals with close genetic relationships.

  13. Cells Cultured on Core-Shell Photonic Crystal Barcodes for Drug Screening.

    Science.gov (United States)

    Fu, Fanfan; Shang, Luoran; Zheng, Fuyin; Chen, Zhuoyue; Wang, Huan; Wang, Jie; Gu, Zhongze; Zhao, Yuanjin

    2016-06-01

    The development of effective drug screening platforms is an important task for biomedical engineering. Here, a novel methacrylated gelatin (GelMA) hydrogel-encapsulated core-shell photonic crystal (PhC) barcode particle was developed for three-dimensional cell aggregation culture and drug screening. The GelMA shells of the barcode particles enable creation of a three-dimensional extracellular matrix (ECM) microenvironment for cell adhesion and growth, while the PhC cores of the barcode particles provide stable diffraction peaks that can encode different cell spheroids during culture and distinguish their biological response during drug testing. The applicability of this cell spheroids-on-barcodes platform was investigated by testing the cytotoxic effect of tegafur (TF), a prodrug of 5-fluorouracil (5-FU), on barcode particle-loaded liver HepG2 and HCT-116 colonic tumor cell spheroids. The cytotoxicity of TF against the HCT-116 tumor cell spheroids was enhanced in systems using cocultures of HepG2 and NIH-3T3 cells, indicating the effectiveness of this multiple cell spheroids-on-barcodes platform for drug screening. PMID:27214156

  14. Linking eggs and adults of Argulus spp. using mitochondrial DNA barcodes.

    Science.gov (United States)

    Feroz Khan, K; Sanker, G; Prasanna Kumar, C

    2014-12-10

    Abstract We have created barcode library for common Argulus spp. infecting Carassius auratus, which could also be used to identify premature forms of Argulus spp. even by non-professionals. Infected C. auratus was examined and purchased from ornamental fish-trading centers and the adult life stage of Argulus spp. was identified and DNA barcoded. The eggs of Argulus spp. were collected using bottle implants. The collected eggs are barcoded and precisely identified by matching with the adult sequences. Four species of adult Argulus spp. were identified, namely Argulus japonicus, Argulus indicus, Argulus siamensis, and Argulus foliaceus. Precise identification of egg samples was done by two different analyses, namely (i) BLAST analysis and (ii) phylogenetic clustering of adults and eggs. All egg samples including the control were precisely identified by BLAST analysis and the results are consistent with phylogenetic clustering of adult and egg's DNA barcodes. In order to establish the DNA barcode technology for the identification of all Argulus spp and its premature forms, the development of full-fledged barcode library that includes all species of this genus is very important for the benefit of ornamental fish industries. PMID:25492543

  15. 2D NMR barcoding and differential analysis of complex mixtures for chemical identification: the Actaea triterpenes.

    Science.gov (United States)

    Qiu, Feng; McAlpine, James B; Lankin, David C; Burton, Ian; Karakach, Tobias; Chen, Shao-Nong; Pauli, Guido F

    2014-04-15

    The interpretation of NMR spectroscopic information for structure elucidation involves decoding of complex resonance patterns that contain valuable molecular information (δ and J), which is not readily accessible otherwise. We introduce a new concept of 2D-NMR barcoding that uses clusters of fingerprint signals and their spatial relationships in the δ-δ coordinate space to facilitate the chemical identification of complex mixtures. Similar to widely used general barcoding technology, the structural information of individual compounds is encoded as a specifics pattern of their C,H correlation signals. Software-based recognition of these patterns enables the structural identification of the compounds and their discrimination in mixtures. Using the triterpenes from various Actaea (syn. Cimicifuga) species as a test case, heteronuclear multiple-bond correlation (HMBC) barcodes were generated on the basis of their structural subtypes from a statistical investigation of their δH and δC data in the literature. These reference barcodes allowed in silico identification of known triterpenes in enriched fractions obtained from an extract of A. racemosa (black cohosh). After dereplication, a differential analysis of heteronuclear single-quantum correlation (HSQC) spectra even allowed for the discovery of a new triterpene. The 2D barcoding concept has potential application in a natural product discovery project, allowing for the rapid dereplication of known compounds and as a tool in the search for structural novelty within compound classes with established barcodes. PMID:24673652

  16. Species delimitation in the green algal genus Codium (Bryopsidales) from Korea using DNA barcoding

    Institute of Scientific and Technical Information of China (English)

    LEE Hyung Woo; KIM Myung Sook

    2015-01-01

    Codium, one of the largest marine green algal genera, is difficult to delimit species boundary accurately based on morphological identification only. DNA barcoding is a powerful tool for discriminating species of seaweeds. The plastid elongation factor TU (tufA) is considered as maker to perform DNA barcoding of green algal species than rbcL gene due to universality and rapid evolution rate. We conducted DNA barcoding application to Codium specimens from the Jeju Island, Korea to overcome the limit of morphological identification and to confirm the species diversity. As a result of applying tufA marker, we newly generated fifty-five tufA barcodes to resolve eight species. TufA marker exhibited 6.1%–21.8% interspecific divergences, wider than the gap of rbcL exon 1, 3.5%–11.5%. Molecular analysis of rbcL exon 1 sequences of Codium revealed eight distinct species like tufA analysis separated in five phylogenetic groups. DNA barcoding of the genus Codium using tufA marker is more helpful to overcome the limit of morphological identification, and this is more potential to reveal cryptic species and to resolve the relationships among subspecies than rbcL analysis alone. The complement of tufA barcoding and rbcL analyses including morphology for the genus Codium in the northwestern Pacific will give much more reliable achievement for discovering species diversity and resolving the phylogenetic relationships.

  17. PiCode: A New Picture-Embedding 2D Barcode.

    Science.gov (United States)

    Chen, Changsheng; Huang, Wenjian; Zhou, Baojian; Liu, Chenchen; Mow, Wai Ho

    2016-08-01

    Nowadays, 2D barcodes have been widely used as an interface to connect potential customers and advertisement contents. However, the appearance of a conventional 2D barcode pattern is often too obtrusive for integrating into an aesthetically designed advertisement. Besides, no human readable information is provided before the barcode is successfully decoded. This paper proposes a new picture-embedding 2D barcode, called PiCode, which mitigates these two limitations by equipping a scannable 2D barcode with a picturesque appearance. PiCode is designed with careful considerations on both the perceptual quality of the embedded image and the decoding robustness of the encoded message. Comparisons with the existing beautified 2D barcodes show that PiCode achieves one of the best perceptual qualities for the embedded image, and maintains a better tradeoff between image quality and decoding robustness in various application conditions. PiCode has been implemented in the MATLAB on a PC and some key building blocks have also been ported to Android and iOS platforms. Its practicality for real-world applications has been successfully demonstrated. PMID:27249833

  18. DNA barcoding of populations of Fallopia multiflora, an indigenous herb in China.

    Science.gov (United States)

    Sun, X Q; Bai, M M; Yao, H; Guo, J L; Li, M M; Hang, Y Y

    2013-01-01

    Fallopia multiflora, locally known as Heshouwu, is one of the most important and widely used Chinese medicinal herbs. However, there is still considerable confusion concerning its different provenances. DNA barcoding is a recent aid to taxonomic identification and uses a short standardized DNA region to discriminate plant species. We assessed the applicability of 4 candidate DNA barcodes (matK, rbcL, psbA-trnH, and ITS2) to identify populations of F. multiflora. To our knowledge, this is the first attempt involving the plant kingdom to apply DNA barcoding at a level lower than species. Four DNA loci (matK, rbcL, psbA-trnH, and ITS2) of 105 samples, including the wild F. multiflora distributed in 17 provinces of China and 4 cultivated F. multiflora lines, were amplified by PCR and sequenced. The 4 loci were evaluated by PCR amplification for sequence quality, extent of genetic divergence, DNA barcoding gap, and the ability to discriminate between populations by BLAST1 and Nearest Distance. We found that psbA-trnH was the best barcode, with significant inter-population variability and best potential for identifying F. multiflora. The combination of loci gave better performance for distinguishing populations than a single locus. We recommend using matK + rbcL + psbA-trnH + ITS2 or psbA-trnH alone for this species. This research demonstrates the utility of DNA barcoding for geoherbalism identifications. PMID:24089097

  19. Identification of species within Tetrastigma (Miq.) Planch.(Vitaceae) based on DNA barcoding techniques

    Institute of Scientific and Technical Information of China (English)

    Yuan-Miao FU; Wei-Mei JIANG; Cheng-Xin FU

    2011-01-01

    Many species of Tetrastigma (Miq.) Planch. (Vitaceae) have long been used as medicinal plants in China, and some are endangered due to overexploitation. Although adulterants are often added to traditional Chinese medicines, there is no reliable or practical method for identifying them. In this study, we used four markers (rbcL, matK, trnH-psbA and internal transcribed spacer [ITS]) as DNA barcodes to test their ability to distinguish species of Tetrastigma. The results indicated that the best barcode was ITS, which showed significant inter-specific genetic variability, and thus its potential as a DNA barcode for identifying Tetrastigma. Multiple loci provided a greater ability to distinguish species than single loci. We recommend using the combined rbcL+matK+ITS barcode for the genus. Phylogenetic trees from each barcode were compared. Analyses using the unweighted pair group method with arithmetic mean discriminated an equal or greater percentage of resolvable species than did neighbor joining, maximum likelihood, or maximum parsimony analyses. Additionally, five medicinal species of Tetrastigma, especially T. Hemsleyanum, could be identified precisely using DNA barcoding.

  20. Correlation dynamics and enhanced signals for the identification of serial biomolecules and DNA bases

    International Nuclear Information System (INIS)

    Nanopore-based sequencing has demonstrated a significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multilayered graphene-based nanopore device architecture for the recognition of single biomolecules. Molecular detection and analysis can be accomplished through the detection of transverse currents as the molecule or DNA base translocates through the nanopore. To increase the overall signal-to-noise ratio and the accuracy, we implement a new ‘multi-point cross-correlation’ technique for identification of DNA bases or other molecules on the single molecular level. We demonstrate that the cross-correlations between each nanopore will greatly enhance the transverse current signal for each molecule. We implement first-principles transport calculations for DNA bases surveyed across a multilayered graphene nanopore system to illustrate the advantages of the proposed geometry. A time-series analysis of the cross-correlation functions illustrates the potential of this method for enhancing the signal-to-noise ratio. This work constitutes a significant step forward in facilitating fingerprinting of single biomolecules using solid state technology. (paper)