www.archive-org-2013.com » ORG » Q » QBOL

Choose link from "Titles, links and description words view":

Or switch to "Titles and links view".

    Archived pages: 34 . Archive date: 2013-12.

  • Title: QBOL
    Descriptive info: .. Development of a new diagnostic tool using DNA barcoding to identify quarantine organisms in support of plant health.. QBOL project has come to an end.. On 21 September 2012 the QBOL project ended officially.. Many results were obtained in the different work packages.. Read more.. Areas of expertise.. Barcoding of Arthropods.. Barcoding of Bacteria.. Barcoding of Fungi.. Barcoding of Nematodes.. Barcoding of Phytoplasmas.. Barcoding of Viruses.. DNA Banks.. Library/Database/Informatics.. Validation/Evaluation.. Dissemination.. Continue to.. About QBOL.. e-Newsletter.. Training courses.. Meeting 2012.. Links.. Contact.. About QBOL.. A consortium of.. 20 partners.. (universities, research institutes and phytosanitary organizations) from all over the world working together and sharing their research expertise  ...   QBOL makes collections harboring plantpathogenic quarantine organisms available.. Informative genes from selected species on the EU Directive and EPPO lists are DNA barcoded.. Sequences, together with taxonomic features, have been included in an internet-based.. Q-bank database.. More about QBOL.. Collaboration.. The QBOL consortium is collaborating with organizations, institutes and companies submitting specimens of quarantine organisms as well as submitting technical support.. More information.. Q-bank: the QBOL databases.. Within WP 9 ‘DNA barcode library / Database / Informatics’ six databases have been built for the different groups of organisms (fungi, arthropods, bacteria, nematodes, viruses and phytoplasmas).. This project is financed by.. DNA Barcoding.. Activities.. Q-lists.. Databases.. Collaboration.. Partners.. About Qbol..

    Original link path: /en/qbol.htm
    Open archive

  • Title: QBOL project has come to an end
    Descriptive info: News.. Published on.. December 4, 2012.. - By.. Plant Research International.. A summary with the results for each work package can be found under ‘Activities’ in the different work packages on this website.. All data obtained have been uploaded into the Q-bank database:.. www.. q-bank.. eu.. The total numbers of sequences obtained within the QBOL project are as follows:.. The developed Q-bank database, is freely accessible.. Tools are provided how to search the database and perform BLAST analyses or even multilocus and / or polyphasic identifications.. More information via.. Peter Bonants.. News..

    Original link path: /en/qbol/show/QBOL-project-has-come-to-an-end-1.htm
    Open archive

  • Title: Barcoding of Arthropods
    Descriptive info: Barcoding of Arthropods.. In this work package 198 species of Q-arthropods have been divided into two priority groups.. Objectives:.. To generate from 5-10 barcode sequences (COI and ITS) for about 100 species of Q arthropods (priority 1), and about 50 closely related species.. To reach this aim we will :.. Establish a prioritized list of all Q arthropods relevant for the EU to be barcoded, plus a list of the related species that could be misidentified.. Collect all Q arthropods and nominated associated species, each from a variety of localities and/or crop hosts.. Develop reliable DNA extraction procedures for larvae and adults.. Develop and test primers for PCR amplification of the two proposed genes (COI & ITS) for all species of Q arthropods and nominated associated species.. Collect DNA barcode sequence data for the two proposed genes (COI & ITS) for all species of Q arthropods and nominated associated species.. Test the usefulness of this dataset together with independently generated data in BOLD for accurate identification of the Q arthropods.. Task.. Task 3.. 1 Sampling of species.. 2 Selection of barcode genes and regions.. 3 DNA extractions and generation of protocols for amplification of barcode regions.. 4 Generation of Barcode sequences.. Deliverables.. D 3.. 1 List of selected Q- arthropods and non-Q congeneric species (Month 6).. 2 List of barcode regions for selected Q-arthropods (Month 6).. 3 Three protocols for DNA extraction for selected Q-arthropods (Month 12).. 4 List of protocols for amplification of 2 barcode regions for all taxonomic groups (Month 18).. 5 About 3000 Barcode sequences of the Q-arthropods (Month 30).. 6 Providing diagnostic tool (including any current limitations) (Month 36).. 7 Detailed contingency plan for WP3 (Month 6).. Results.. The lists have been erected based on the economic value of the Q-arthropods, their availability and their habitat, trying to  ...   sequenced for a total of about 1300 sequences with an average of 16 COI and 8 ITS sequences per species.. 20 species were included that are not yet considered quarantine species, though they represent a threat to Europe.. This priority 3 list was established during the project.. Including these species makes this identification tool more adapted to European needs.. For these species, a total of ca.. 200 sequences with an average of 7 COI and 3 ITS sequences per species were obtained.. Instead of the 50 out group species initially proposed (i.. e.. species that are congeneric of or could be confused with the Q-arthropods), 128 species were sequenced, producing about 1300 sequences with an average of 7 COI and 4 ITS sequences per species.. To improve the representativeness of the Q-bank database of arthropods (i.. include Q-arthropod species included on priority 1 and 2 lists but not yet available or increase intraspecific variability for better identification), 334 COI sequences mostly produced by USDA and mined from GenBank have been added to our sequence library.. All sequences were carefully validated before inclusion in the Q-bank database (detection of contamination and pseudo genes).. Altogether, about 5300 sequences have been generated during the project and 334 sequences have been mined from Genbank.. The database now includes ca.. 5600 COI and ITS barcodes for 153 species of Q-arthropods (ca.. 77% of the priority 1 and 2 lists), 20 species of arthropods that are considered a serious threat for Europe and 140 out group species, far surpassing the original aim.. All specimens have been identified by taxonomists, vouchers in INRA and LNPV Montpellier.. Jean-Yves Rasplus.. View profile.. WP Coordinator: INRA (Partner 6).. INRA, LU, ACW and CIP.. Barcoding of Bacteria.. Barcoding of Fungi.. Barcoding of Nematodes.. Barcoding of Phytoplasmas.. Barcoding of Viruses.. DNA Banks.. Library/Database/Informatics.. Validation/Evaluation.. Dissemination..

    Original link path: /en/qbol/Activities/Barcoding-of-Arthropods.htm
    Open archive

  • Title: Barcoding of Bacteria
    Descriptive info: In this work package the work focussed on the Q-species within the genera Ralstonia, Xylella, Clavibacter and Xanthomonas.. Objectives.. To maintain and expand existing collection with relevant bacterial isolates (collection strains and recent field isolates).. To unravel the taxonomic and phylogenetic identity of quarantine bacteria in support of EU regulation.. To collect barcode data including genetic variation, inclusiveness and exclusiveness for the selected scope of Q-bacteria.. To generate barcode sequences from a selected set of regions and for a selected set of relevant quarantine bacteria.. To develop reliable routine DNA extraction protocols.. To develop robust primers for PCR amplification of the barcode gene regions in the different taxa.. Tasks.. Task 4.. 1 Selection of target organisms and composition of the relevant working collection.. 2 Selection of barcode target regions.. 3 DNA isolation and DNA bank.. 4 Generation of Barcode sequences, evaluation and deposit in QBOL database.. 5 Generation of protocols for generation and evaluation of bacterial barcodes.. D 4.. 1 List of selected bacterial Q-organisms (Month 6).. 2 List of barcode regions for selected bacterial Q-organisms (Month 12).. 3 Protocols for amplification of 4 barcode regions (Month 18).. 4 Three protocols for DNA extraction and DNA bank (Month 20).. 5 At least 3000 Barcode sequences of selected regions for the bacterial Q-organisms selected (Month 34).. 6 A correct delineation of the Q-bacteria belonging to Xanthomonas, Clavibacter, Xylella fastidiosa and Ralstonia solanacearum in support of decision making on regulated bacterial pests (Month 34).. 7 At least 3 scientific papers on taxonomic aspects of Xanthomonas  ...   evaluated for their performance as a barcode region.. Finally a decision scheme was published to lead the end-user through the identification process.. This scheme clearly shows when to use which barcoding genes.. Extensive sequencing also confirmed the taxonomic position of most of the target Q bacteria (within.. Ralstonia, Xylella, Clavibacter michiganensis and the Xanthomonas.. species) and also supports recent proposals for the taxonomic division of the Ralstonia solanacearum complex.. On the other hand, our research also revealed that some Q-pathogens are represented by heterogeneous strains (e.. g.. X.. axonopodis pvs.. dieffenbachiae, phaseoli and allii.. ).. Their classification under the same Q-pathovar name is questionable and needs further investigation by sequencing more genomic domains and performing host range experiments on plants.. Within.. Clavibacter.. , the three.. Q- C.. michiganensis.. subspecies are identified by the gyrB-based barcode.. Also many non-pathogenic strains of the species (look-a-likes) were included in the study.. In total, the QBOL working collection increased to 1,008 strains and 3,667 sequences have been generated.. Based on these sequences and on other strain characteristics (such as host, geographic origin and symptom type) a subset of reference strains has been identified for the end-users.. The barcodes have been deposited in the Q-bank bacteria database and the strains are stored and available from the certified public service culture collections BCCM-LMG (BE), NCPPB (UK), and CFBP (FR).. Under the initiative of ILVO, these culture collections collaborate on a reference collection of plant health-affecting bacteria.. Martine Maes.. WP Coordinator: VLAGEW (ILVO) (Partner 3).. VLAGEW (ILVO), LM-UGent, ACW and CIP..

    Original link path: /en/qbol/Activities/Barcoding-of-Bacteria.htm
    Open archive

  • Title: Barcoding of Fungi
    Descriptive info: In this work package a short list of 19 Q-species were selected for barcoding.. To generate barcode sequences from a selected set of genetic regions and for a selected set of relevant/quarantine and related fungi.. To reach this aim we will:.. Establish a prioritized list of all phytopathogenic fungi relevant for the EU to be barcoded.. Maintain and expand existing collection(s) with relevant fungal isolates.. Produce data to be used as a decision basis for the choice of 3 fungi barcode genes and regions.. Evaluate existing or develop new reliable DNA extraction procedures.. Develop robust primers for PCR amplification of the fungal barcode gene regions.. Collect barcode data including intra- and interspecies genetic variation on the fungal barcode regions.. Task 2.. 1 Selection of targets.. 2 Selection of barcode regions.. 3 DNA extractions.. 4 Generation of protocols for amplification of barcode regions.. 5 Generation of Barcode sequences.. D 2.. 1 List of available fungal Q-organisms and related species (Month 6).. 2 List of potential barcode regions for selected fungal Q-organisms – five candidate loci (Month 6), workable list of barcode regions – two loci (Month 15).. 3 Three protocols for DNA extraction for selected fungal Q-organisms (Month 12).. 4  ...   some species it was difficult to obtain larger numbers of isolates per quarantine species.. This work package succeeded to make available to the Q-bank database: 791 sequences for 193 strains from 25 quarantine species; as well as 6107 sequences from 1145 strains of 612 related species.. Of these sequences, 360 sequences for 81 species were extracted from studies in peer-reviewed journals (mainly for the related species of the unculturable obligate biotroph genera.. Melampsora, Puccinia and Thecaphora.. For each species of quarantine importance in the Q-bank database, hyperlinks to EPPO and EU Council Directive documents are provided.. A field “Diagnostic locus for identification in Q-bank” is present for each quarantine species to help the end-user to determine which locus is needed for identification in the database and polyphasic identifications are possible per genus group.. A molecular decision scheme showing the route to an identification starting with DNA isolation and amplification of the internal transcribed spacers (ITS) of the nrRNA operon as primary barcode is provided on the.. Q-bank fungi website.. A link to MycoBank, a database for the taxonomy of fungal names, is also provided for each species.. Ewald Groenewald.. WP Coordinator: KNAW-CBS (Partner 9).. KNAW-CBS, PRI, FERA and CIP..

    Original link path: /en/qbol/Activities/Barcoding-of-Fungi.htm
    Open archive

  • Title: Barcoding of Nematodes
    Descriptive info: In this work package a base list of 32 nematode species was created for which barcodes needed to be collected.. To generate barcode sequences from a selected set of genetic regions and for a selected set of relevant quarantine nematodes.. Establish a prioritized list of all phytopathogenic nematodes relevant for the EU to be barcoded.. Produce data to be used as a decision basis for the choice of 2-3 nematode barcode genes and regions.. Compare and validate reliable DNA extraction procedures.. Develop robust primers for PCR amplification of the nematode barcode gene regions.. Collect barcode data including intra- and interspecies genetic variation on the nematode barcode regions.. Task 5.. D 5.. 1 List of selected nematode Q-organisms (Month 6).. 2 List of barcode regions for selected nematode Q-organisms (Month 12).. 3 Two protocols for DNA extraction for selected nematodes Q-organisms (Month 12).. 4 List of protocols for generic amplification of barcode regions (Month 18).. 5 About 1600 Barcode sequences of the selected nematode Q-organisms (Month 36).. 6 Detailed contingency plan for WP5 (Month 6).. This list contained all quarantine nematodes as well as a number of close relatives.. In addition, 43 nematodes species  ...   methods, and the best two methods were selected for further use.. Primers were developed for the amplification of six potential barcoding regions: the small subunit (SSU) ribosomal RNA gene, the D1-D2 and D2-D3 regions of the large subunit (LSU) ribosomal RNA gene, the second intragenic spacer region (IGS2) of the ribosomal RNA cassette, a fragment of the RNA polymerase II gene and the mitochondrial cytochrome oxidase c subunit 1 (COI) and subunit 2 (COII) genes.. A subset of nematode species was assigned to assess both the inter- and intra-species variation of these potential barcode regions and based on these results the SSU, LSU, COI and COII genes were chosen for sequencing in the remaining nematode species.. A total of 1600 sequences for up to 58 species, distributed over the various priority groups, was promised in the project.. For each priority group the required amount of sequences was generated and in some cases well surpassed.. Of all generated sequences, 1683 were of a high enough quality for inclusion in the.. Q-Bank nematodes database.. , originating from a total of 121 species.. Juerg Frey.. WP Coordinator: ACW (Partner 5).. ACW, PRI, VLAGEW (ILVO).. INRA and CIP..

    Original link path: /en/qbol/Activities/Barcoding-of-Nematodes.htm
    Open archive

  • Title: Barcoding of Phytoplasmas
    Descriptive info: In this work package a prioritized list of all phytopathogenic phytoplasms relevant for the EU to be barcoded was established.. To generate barcode sequences from a selected set of genetic regions and for a selected set of relevant/quarantine phytoplasms.. Establish a prioritized list of all phytopathogenic phytoplasms relevant for the EU to be barcoded.. Maintain and expand existing collection with relevant phytoplasma isolates.. Produce data to be used as a decision basis for the choice of 3 phytoplasma barcode genes and regions.. Develop reliable DNA extraction procedures.. Develop robust primers for PCR amplification of the phytoplasma barcode gene regions.. Collect barcode data including intra- and interspecies genetic variation on the phytoplasma barcode regions (3 regions).. Task 7.. 1 Availability collections and taxonomic data from non-partners.. 2 Maintenance and expansion of collection at UB and INRA.. 3 Selection of targets.. 4 Selection of barcode regions.. 5 DNA extractions.. 6 Generation of protocols for amplification of barcode regions.. 7 Generation of Barcode sequences.. D 7.. 1 Access to non-partners collections and taxonomic expertise and information for selected Q-organisms.. Seven named non-partners will be contacted (Month 6).. 2 Collection of all relevant phytoplasms from about 30 taxonomic groups (Month 6).. 3 List of selected phytoplasma Q-organisms (Month 6).. 4 List of barcode regions for selected phytoplasma Q-organisms (Month 9).. 5 Protocols  ...   as DNA.. Colleagues and collections were contacted worldwide for specific strains throughout the project, for instance after publication of interesting new phytoplasma strains.. The COST0807 network was mainly used for obtaining new strains.. As the list of ‘Candidatus Phytoplasma’ species is constantly expanding we are still trying to include these in the collection/database though our international contacts.. Several DNA extraction methods were evaluated in the project for their effectiveness to extract phytoplasma DNA from infected host material and two methods have been recommended that work for most plant species/phytoplasmas.. Phytoplasma barcode regions 16S, tuf and SecA were selected to be used as DNA barcodes.. Tuf and SecA regions are 400-600 bp whereas the 16S region is app.. 1.. 8 kb, however, also a smaller region of the 5’ end of 18S has been selected for quick identification of phytoplasmas.. Barcode data from the 3 regions have been collected during the project.. Until now, more than 460 barcodes have been produced from approximately 200 phytoplasma strains.. These barcodes enable good separation between phytoplasma groups and are thus ideal for identification of phytoplasmas, including quarantine organisms.. Thus, a very efficient, sensitive and specific method for phytoplasma identification has been developed using a generic PCR followed by barcode sequencing.. Mogens Nicolaisen.. WP Coordinator: UA (Partner 7).. UA, UB, INRA and CIP..

    Original link path: /en/qbol/Activities/Barcoding-of-Phytoplasmas.htm
    Open archive

  • Title: Barcoding of Viruses
    Descriptive info: Since viruses don’t contain a generic barcode gene, it was decided to sequence the whole genome of viruses in this work package using Next Generation Sequence Technology.. The objective of this WP is to develop a DNA barcoding method for identification of high priority viruses present in the EU Plant Health Directive and EPPO Plant Health lists of quarantine pathogens.. In order to achieve this aim we will:.. Develop reliable nucleic acid (DNA&RNA) extraction procedures.. Develop standard operating procedures for identification of viruses including extraction, PCR amplification, sequencing and database searching.. Task 6.. 1 Selection and acquisition of targets.. 2 Nucleic acid extraction.. 3 Generic primer sets.. 4 Genome sequencing.. 5 Generation and validation of Barcode sequences.. 6 Development and publication of complete protocols.. D 6.. 1 List of selected quarantine viruses (Month 6).. 2 A recommended protocol for nucleic acid extraction for virus infected plant material (Month 9).. 3 Quarantine viruses (at least two Nepoviruses, Ilarviruses and Criniviruses) acquired by the consortium for primer testing (Month 12).. 4 Validation data for published (Nepovirus, Ilarvirus Sadawaviruses, Begomoviruses, Tospoviruses and Crinivirus primer sets) and newly designed (three of Torradovirus, Comovirus or Rhabdovirus) generic primer sets with quarantine viruses (Month 18).. 5 Validated barcode and meta data available for Nepovirus, Ilarvirus, Sadawaviruses, Begomoviruses, Tospoviruses and Crinivirus primers and three of Torradovirus, Comovirus or Rhabdovirus on the project/sequence database (Month 30).. 6 Complete barcode identification methods written and available for Nepovirus, Ilarvirus, Sadawaviruses, Begomoviruses, Tospoviruses and Crinivirus primers and three of Torradovirus, Comovirus or Rhabdovirus genera (Month 30).. 7 Genomic  ...   extraction process have reduced the cost of viral genome sequencing.. Genome sequence data have been produced for a range of viruses including:.. Arracacha virus B, oca strain, Potato black ringspot virus, Potato virus T, Potato yellowing virus, Tomato infectious chlorosis virus, Chrysanthemum stem necrosis virus, Iris yellow spot virus, Tomato torrado virus, Tomato marchitez virus, Potato yellow vein virus and Tomato chocolate virus.. A number of different RNA extraction methods have been tested and used to successfully produce virus genome sequence.. It was discovered that to maximise virus sequence recovery and thus minimise sequencing cost total RNA extraction of plants containing virus is not the best approach.. Methods have been developed within the consortium to purify virus RNA away from plant RNA.. These methods have been being compared to determine the optimum method for a particular sample type.. These methods include double stranded RNA isolation, small interfering RNA isolation, partial virus purification prior to RNA isolation, subtractive hybridisation and the use of capture probes.. Results suggest that no one method is optimal for all samples.. The optimum methods for viral genome sequencing, along with advice on accessing this technology have now been published as part of the QBOL project.. The methods were used to sequence in total 46 viruses and have been instrumental in the diagnosis of a number of novel diseases including the discovery of watercress white vein virus causing damage to the production of watercress and maize lethal necrosis devastating the 2012 Kenyan maize crop.. Neil Boonham.. WP Coordinator: CSL (Partner 2).. FERA, PRI and CIP..

    Original link path: /en/qbol/Activities/Barcoding-of-Viruses.htm
    Open archive

  • Title: DNA Banks
    Descriptive info: DNA of quarantine organisms is scarce.. Therefore in this work package an investigation in different protocols to store, transport and multiply DNA samples of these organisms was made.. To develop protocols for the correct storage and whole genome amplification (WGA) of extracted DNA and RNA samples.. To develop a DNA bank, containing DNA/RNA and/or WGA amplified material from selected quarantine and regulated plant pathogens and their taxonomically closely related species.. Task 8.. 1 Development protocols for correct storage of DNA samples.. 2 Development of whole genome amplification (WGA) protocols for groups of organisms.. 3 Development of DNA storage and transfer procedure of WGA amplified material.. 4 Development and implementation of prototype of DNA bank.. 5 Contingency plan.. D 8.. 1 Two protocols for correct storage of DNA samples (Month 12).. 2 Two protocols for WGA of DNA and RNA samples for the selected Q-organisms (Month 30).. 3 Two protocols for the storage and transfer of WGA amplified samples for the  ...   DNA/RNA samples and WGA products were investigated and tested (e.. filter, beads, other).. GenTegra was chosen as storage medium.. Four kits for whole genome amplification (WGA), a method to multiply DNA, were tested on a subset of organisms from each group (fungi, bacteria, arthropods, nematodes, viruses, phytoplasms).. The quality of the individual kits was assessed using different methods: TaqMan PCR, conventional PCR, sequence analysis and gel electrophoresis.. Based upon results obtained thus far a WGA kit was selected to be used for the rest of the project.. The samples for ring testing in the.. work package Validation.. were prepared and a prototype of DNA bank was established.. Several protocols have been evaluated and final protocols have been written.. Using these protocols NPPO’s can better handle DNA samples of rare specimen to be used as positive and negative controls in their molecular identification and detection assays.. WP Coordinator: PRI (Partner 1).. PRI, FERA, VLAGEW (ILVO), LM-UGent, ACW, INRA, UA, UB and KNAW-CBS..

    Original link path: /en/qbol/Activities/DNA-Banks.htm
    Open archive

  • Title: DNA barcode library / Database / Informatics
    Descriptive info: DNA barcode library / Database / Informatics.. The database (developed within the Dutch FES project, 2006-2010) has been further developed during the QBOL project in this work package.. To create a complex database structure including and interlinking the different organisms (fungi, arthropods, bacteria, nematodes, viruses and phytoplasmas) and associated data.. To develop a web based public Database system for correct taxonomic identification of relevant Quarantine plant pathogens.. The.. internet based system.. will allow online deposit of any data related to the pathogens or the host plants and will be automatically linked to other database systems systems such as Genbank, EMBL, BOLD and GBIF.. The online version will provide an unique identification system of the included organisms that could involve any scientific data considered of importance by the partners involved (morphological, physiological, molecular, etc).. Polyphasic identifications will be possible for any Internet user.. Task 9.. 1 Selection of fields to be included into the database for each group of organisms and associated functions and algorithms.. 2 Training and data entry.. 3 Testing databases, linking and the efficiency of identification tools.. 4 Last modifications and release of the system.. D 9.. 1 List of fields to be included into the Database for each  ...   for fungi, arthropods, bacteria, nematodes, viruses and phytoplasmas.. All groups have access to their databases via Citrix XenApp.. The total database Q-bank is freely accessible via.. Contacts with.. CBOL/BOLD.. EDIT.. , QBOL work packages,.. GBIFStrainInfo.. GenBank.. EMBL.. were taken at several occasions during the course of the project in order to import from and export data to the respective projects or databases.. A software module to export to and import from Genbank (and therefore EMBL) has been implemented.. In discussion with the curators of the database we continuously improved the Internet-based software to comply with the needs of the end-users during pairwise meetings.. Additional training was provided during the meetings with QBOL work package leaders and associated researchers.. Filling of the Q-bank databases has been done during last stages of the QBOL project and will continue even beyond the end of the project.. Publication of the created databases is now complete and internet visitors are regularly using the system.. Websites are therefore not restricted to the users participating in the QBOL project anymore.. Usage of the different databases are monitored by Google Analytics.. Vincent Robert.. WP Coordinator: KNAW-CBS (Partner 9).. KNAW-CBS, PRI, FERA, VLAGEW (ILVO), LM-UGent, ACW, INRA, UA and UB..

    Original link path: /en/qbol/Activities/LibraryDatabaseInformatics.htm
    Open archive

  • Title: Validation / Evaluation
    Descriptive info: Validation / Evaluation.. In the first part of the QBOL project a survey was set-up to find out wishes and expectations of possible end-users (scientists and technicians of NPPO’s) regarding the data to be generated by QBOL and stored into the Q-bank database.. To validate developed DNA barcoding protocols and to validate the use of DNA barcoding as a diagnostic tool.. Task 10.. 1 Validation/evaluation of the barcoding protocols.. 2 Validation/evaluation of diagnostic use of barcoding.. 3 Contingency plan.. D 10.. 1 Report of validation of DNA barcoding protocols (Month36).. 2 Report of evaluation of diagnostic use of DNA barcoding (Month 36).. 3 Scientific publication of results evaluation diagnostic use barcoding (provided that results and time allow this; Month 36).. 4 Detailed contingency plan for WP10 (Month 6).. Based on the end-users’ expectations, and on the queries submitted, the usability of the QBOL database has been improved.. Before the start of the test-performance study in this work package, the  ...   test has been performed with all samples before sending.. Obtained sequences in the homogeneity test served as standards for comparison with the outcome of the test-performance study.. 21 test packages (14 QBOL partners, 7 training sessions) were prepared providing partners and training session organizers with an instruction booklet including the EPPO standard, all DNA purification kits, primers and samples.. All results from the QBOL partners were analysed and evaluated in terms of.. Number of samples analysed and % of test correct used.. % Amplicons obtained.. % Consensus obtained.. % Consensus sequence of correct size.. % Primers trimmed.. Diagnostic sensitivity.. Diagnostic specificity.. Repeatability.. Robustness.. Pitfalls in the use of the EPPO standard, instruction booklet and the use of Q-bank databases have been identified and recommendations for future work have been made.. Bart van de Vossenberg.. WP Coordinator: PPS (Partner 11).. PPS, PRI, FERA, VLAGEW (ILVO), LM-UGent, ACW, INRA, UA, UB, CIP, NIB, SPA, LNPV, CAIQ, LU, CNPMF DAFS, INIA and US..

    Original link path: /en/qbol/Activities/ValidationEvaluation.htm
    Open archive


  • Archived pages: 34