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N", "lastName": "Mwangi" }, { "creatorType": "author", "firstName": "J. M", "lastName": "Kinuthia" }, { "creatorType": "author", "firstName": "G. M", "lastName": "Maina" }, { "creatorType": "author", "firstName": "L. E", "lastName": "Agola" }, { "creatorType": "author", "firstName": "M. W", "lastName": "Mutuku" }, { "creatorType": "author", "firstName": "M. L", "lastName": "Steinauer" }, { "creatorType": "author", "firstName": "B. R", "lastName": "Agwanda" }, { "creatorType": "author", "firstName": "L.", "lastName": "Kigo" }, { "creatorType": "author", "firstName": "B. M", "lastName": "Mungbai" }, { "creatorType": "author", "firstName": "E. S", "lastName": "Loker" }, { "creatorType": "author", "firstName": "G. M", "lastName": "Mkoji" } ], "abstractNote": "SUMMARYRecent schistosomiasis control efforts in sub-Saharan Africa have focused nearly exclusively on treatment of humans with praziquantel. However, the extent to which wild mammals act as reservoirs for Schistosoma mansoni and therefore as sources of renewed transmission following control efforts is poorly understood. With the objective to study the role of small mammals as reservoir hosts, 480 animals belonging to 9 rodent and 1 insectivore species were examined for infection with schistosomes in Kisumu, in the Lake Victoria Basin, Kenya. Animals were collected from 2 sites: near the lakeshore and from Nyabera Marsh draining into the lake. A total of 65%), given their potentially vast population size, their impact on transmission needs further study. Reservoir hosts could perpetuate snail infections and favour renewed transmission to humans once control programmes have ceased.", "publicationTitle": "Parasitology", "publisher": "", "place": "", "date": "2010", "volume": "First View", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "1-10", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1017/S0031182010000041", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2011-03-05T05:30:18Z", "dateModified": "2011-03-05T05:30:18Z" } }, { "key": "APFV6DFN", "version": 1, "library": { "type": "group", "id": 40029, "name": "DNA Barcoding", "links": { "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/40029/items/APFV6DFN", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding/items/APFV6DFN", "type": "text/html" } }, "meta": { "createdByUser": { "id": 163381, "username": "aborisen", "name": "Alex Borisenko", "links": { "alternate": { "href": "https://www.zotero.org/aborisen", "type": "text/html" } } }, "creatorSummary": "Zurovcova et al.", "parsedDate": "2010", "numChildren": 0 }, "data": { "key": "APFV6DFN", "version": 1, "itemType": "journalArticle", "title": "\"DNA barcoding\" is of limited value for identifying adelgids (Hemiptera: Adelgidae) but supports traditional morphological taxonomy", "creators": [ { "creatorType": "author", "firstName": "M.", "lastName": "Zurovcova" }, { "creatorType": "author", "firstName": "J.", "lastName": "Havelka" }, { "creatorType": "author", "firstName": "P.", "lastName": "Stary" }, { "creatorType": "author", "firstName": "P.", "lastName": "Vechtova" }, { "creatorType": "author", "firstName": "D.", "lastName": "Chundelova" }, { "creatorType": "author", "firstName": "A.", "lastName": "Jarosova" }, { "creatorType": "author", "firstName": "L.", "lastName": "Kucerova" } ], "abstractNote": "The sequence diversity in the mitochondrial cytochrome-c oxidase I (COI) gene was evaluated as a tool for resolving differences among species of European adelgids collected from several localities across the Czech Republic. Members of 7 genera and 16 species were examined, and as outgroups, two species of Phylloxeridae were used. Sequence divergences within species were on average less than 0.15%, whereas divergences between species ranged from 0.0 to 4.12% for congeneric and to 13.24% for intergeneric comparisons. It is concluded that DNA barcoding of Adelgidae is a powerful tool for identifying genera, but at the species level it works only in those cases where there are no species complexes. Nevertheless, it can be used as a complement to traditional, morphological taxonomy.", "publicationTitle": "European Journal of Entomology", "publisher": "", "place": "", "date": "2010", "volume": "107", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "147-156", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "Times Cited: 0 Cited Reference Count: 46 English Article EUR J ENTOMOL 578QY", "tags": [ { "tag": "Adelgidae;" }, { "tag": "DNA" }, { "tag": "aphids;" }, { "tag": "barcoding" }, { "tag": "diptera;" }, { "tag": "diversity;" }, { "tag": "evolution;" }, { "tag": "gene-sequences;" }, { "tag": "identification;" }, { "tag": "insecta;" }, { "tag": "mega" }, { "tag": "primers;" }, { "tag": "software;" }, { "tag": "species" }, { "tag": "systematics;" } ], "collections": [], "relations": {}, "dateAdded": "2011-03-05T05:30:18Z", "dateModified": "2011-03-05T05:30:18Z" } }, { "key": "WM2BIT2G", "version": 1, "library": { "type": "group", "id": 40029, "name": "DNA Barcoding", "links": { "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/40029/items/WM2BIT2G", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding/items/WM2BIT2G", "type": "text/html" } }, "meta": { "createdByUser": { "id": 163381, "username": "aborisen", "name": "Alex Borisenko", "links": { "alternate": { "href": "https://www.zotero.org/aborisen", "type": "text/html" } } }, "creatorSummary": "Zuo et al.", "parsedDate": "2010", "numChildren": 0 }, "data": { "key": "WM2BIT2G", "version": 1, "itemType": "journalArticle", "title": "DNA Barcoding of Panax Species", "creators": [ { "creatorType": "author", "firstName": "Yunjuan", "lastName": "Zuo" }, { "creatorType": "author", "firstName": "Zhongjian", "lastName": "Chen" }, { "creatorType": "author", "firstName": "Katsuhiko", "lastName": "Kondo" }, { "creatorType": "author", "firstName": "Tsuneo", "lastName": "Funamoto" }, { "creatorType": "author", "firstName": "Jun", "lastName": "Wen" }, { "creatorType": "author", "firstName": "Shiliang", "lastName": "Zhou" } ], "abstractNote": "", "publicationTitle": "Planta Med", "publisher": "", "place": "", "date": "2010", "volume": "", "issue": "EFirst", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "TY - JOUR AN - 101055S00301250166", "tags": [], "collections": [], "relations": {}, "dateAdded": "2011-03-05T05:30:18Z", "dateModified": "2011-03-05T05:30:18Z" } }, { "key": "KUM6P8IC", "version": 1, "library": { "type": "group", "id": 40029, "name": "DNA Barcoding", "links": { "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/40029/items/KUM6P8IC", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding/items/KUM6P8IC", "type": "text/html" } }, "meta": { "createdByUser": { "id": 163381, "username": "aborisen", "name": "Alex Borisenko", "links": { "alternate": { "href": "https://www.zotero.org/aborisen", "type": "text/html" } } }, "creatorSummary": "Zuccarello", "parsedDate": "2009", "numChildren": 0 }, "data": { "key": "KUM6P8IC", "version": 1, "itemType": "journalArticle", "title": "Beyond Barcoding: Understanding Species' Reproductive Biology", "creators": [ { "creatorType": "author", "firstName": "J.", "lastName": "Zuccarello" } ], "abstractNote": "", "publicationTitle": "Phycologia", "publisher": "", "place": "", "date": "2009", "volume": "48", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "434", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "Times Cited: 0", "tags": [], "collections": [], "relations": {}, "dateAdded": "2011-03-05T05:30:18Z", "dateModified": "2011-03-05T05:30:18Z" } }, { "key": "GDT9ATC4", "version": 1, "library": { "type": "group", "id": 40029, "name": "DNA Barcoding", "links": { "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/40029/items/GDT9ATC4", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding/items/GDT9ATC4", "type": "text/html" } }, "meta": { "createdByUser": { "id": 163381, "username": "aborisen", "name": "Alex Borisenko", "links": { "alternate": { "href": "https://www.zotero.org/aborisen", "type": "text/html" } } }, "creatorSummary": "Zink and Barrowclough", "parsedDate": "2008", "numChildren": 0 }, "data": { "key": "GDT9ATC4", "version": 1, "itemType": "journalArticle", "title": "Mitochondrial DNA under siege in phylogeography", "creators": [ { "creatorType": "author", "firstName": "R. M", "lastName": "Zink" }, { "creatorType": "author", "firstName": "G. F", "lastName": "Barrowclough" } ], "abstractNote": "", "publicationTitle": "Molecular Ecology", "publisher": "", "place": "", "date": "2008", "volume": "17", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "2107-2121", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2011-03-05T05:30:18Z", "dateModified": "2011-03-05T05:30:18Z" } }, { "key": "R2RUB33V", "version": 1, "library": { "type": "group", "id": 40029, "name": "DNA Barcoding", "links": { "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/40029/items/R2RUB33V", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding/items/R2RUB33V", "type": "text/html" } }, "meta": { "createdByUser": { "id": 163381, "username": "aborisen", "name": "Alex Borisenko", "links": { "alternate": { "href": "https://www.zotero.org/aborisen", "type": "text/html" } } }, "creatorSummary": "Zimmermann et al.", "parsedDate": "2008", "numChildren": 0 }, "data": { "key": "R2RUB33V", "version": 1, "itemType": "journalArticle", "title": "DNA damage in preserved specimens and tissue samples: a molecular assessment", "creators": [ { "creatorType": "author", "firstName": "J.", "lastName": "Zimmermann" }, { "creatorType": "author", "firstName": "M.", "lastName": "Hajibabaei" }, { "creatorType": "author", "firstName": "D. C", "lastName": "Blackburn" }, { "creatorType": "author", "firstName": "J.", "lastName": "Hanken" }, { "creatorType": "author", "firstName": "E.", "lastName": "Cantin" }, { "creatorType": "author", "firstName": "J.", "lastName": "Posfai" }, { "creatorType": "author", "firstName": "T. C", "lastName": "Evans" } ], "abstractNote": "The extraction of genetic information from preserved tissue samples or museum specimens is a fundamental component of many fields of research, including the Barcode of Life initiative, forensic investigations, biological studies using scat sample analysis, and cancer research utilizing formaldehyde-fixed, paraffin-embedded tissue. Efforts to obtain genetic information from these sources are often hampered by an inability to amplify the desired DNA as a consequence of DNA damage. Previous studies have described techniques for improved DNA extraction from such samples or focused on the effect of damaging agents - such as light, oxygen or formaldehyde - on free nucleotides. We present ongoing work to characterize lesions in DNA samples extracted from preserved specimens. The extracted DNA is digested to single nucleosides with a combination of DNase I, Snake Venom Phosphodiesterase, and Antarctic Phosphatase and then analyzed by HPLC-ESI-TOF-MS. We present data for moth specimens that were preserved dried and pinned with no additional preservative and for frog tissue samples that were preserved in either ethanol, or formaldehyde, or fixed in formaldehyde and then preserved in ethanol. These preservation methods represent the most common methods of preserving animal specimens in museum collections. We observe changes in the nucleoside content of these samples over time, especially a loss of deoxyguanosine. We characterize the fragmentation state of the DNA and aim to identify abundant nucleoside lesions. Finally, simple models are introduced to describe the DNA fragmentation based on nicks and double-strand breaks.", "publicationTitle": "Frontiers in Zoology", "publisher": "", "place": "", "date": "2008", "volume": "5", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "Times Cited: 2 Cited Reference Count: 37 English Article FRONT ZOOL 371KP", "tags": [ { "tag": "PCR;" }, { "tag": "ancient" }, { "tag": "bases;" }, { "tag": "degradation" }, { "tag": "depurination;" }, { "tag": "dna;" }, { "tag": "endocyclic" }, { "tag": "formaldehyde;" }, { "tag": "formalin;" }, { "tag": "groups;" }, { "tag": "imino" }, { "tag": "nucleotide-sequence;" }, { "tag": "probe;" }, { "tag": "real-time" } ], "collections": [], "relations": {}, "dateAdded": "2011-03-05T05:30:18Z", "dateModified": "2011-03-05T05:30:18Z" } }, { "key": "TAJG6AG9", "version": 1, "library": { "type": "group", "id": 40029, "name": "DNA Barcoding", "links": { "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/40029/items/TAJG6AG9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding/items/TAJG6AG9", "type": "text/html" } }, "meta": { "createdByUser": { "id": 163381, "username": "aborisen", "name": "Alex Borisenko", "links": { "alternate": { "href": "https://www.zotero.org/aborisen", "type": "text/html" } } }, "creatorSummary": "Zhou et al.", "parsedDate": "2010", "numChildren": 0 }, "data": { "key": "TAJG6AG9", "version": 1, "itemType": "journalArticle", "title": "Ephemeroptera, Plecoptera, and Trichoptera fauna of Churchill (Manitoba, Canada): insights into biodiversity patterns from DNA barcoding", "creators": [ { "creatorType": "author", "firstName": "X.", "lastName": "Zhou" }, { "creatorType": "author", "firstName": "L. M.", "lastName": "Jacobus" }, { "creatorType": "author", "firstName": "R. E.", "lastName": "DeWalt" }, { "creatorType": "author", "firstName": "S. J.", "lastName": "Adamowicz" }, { "creatorType": "author", "firstName": "P. D. N.", "lastName": "Hebert" } ], "abstractNote": "", "publicationTitle": "Journal of the North American Benthological Society", "publisher": "", "place": "", "date": "2010", "volume": "29", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "814-837", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2011-03-05T05:30:18Z", "dateModified": "2011-03-05T05:30:18Z" } }, { "key": "GZHTEJBK", "version": 1, "library": { "type": "group", "id": 40029, "name": "DNA Barcoding", "links": { "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/40029/items/GZHTEJBK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding/items/GZHTEJBK", "type": "text/html" } }, "meta": { "createdByUser": { "id": 163381, "username": "aborisen", "name": "Alex Borisenko", "links": { "alternate": { "href": "https://www.zotero.org/aborisen", "type": "text/html" } } }, "creatorSummary": "Zhou et al.", "parsedDate": "2009", "numChildren": 0 }, "data": { "key": "GZHTEJBK", "version": 1, "itemType": "journalArticle", "title": "Towards a comprehensive barcode library for arctic life - Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada", "creators": [ { "creatorType": "author", "firstName": "Xin", "lastName": "Zhou" }, { "creatorType": "author", "firstName": "Sarah", "lastName": "Adamowicz" }, { "creatorType": "author", "firstName": "Luke", "lastName": "Jacobus" }, { "creatorType": "author", "firstName": "R Edward", "lastName": "DeWalt" }, { "creatorType": "author", "firstName": "Paul", "lastName": "Hebert" } ], "abstractNote": "BACKGROUND:This study reports progress in assembling a DNA barcode reference library for Ephemeroptera, Plecoptera, and Trichoptera (\"EPTs\") from a Canadian subarctic site, which is the focus of a comprehensive biodiversity inventory using DNA barcoding. These three groups of aquatic insects exhibit a moderate level of species diversity, making them ideal for testing the feasibility of DNA barcoding for routine biotic surveys. We explore the correlation between the morphological species delineations, DNA barcode-based haplotype clusters delimited by a sequence threshold (2%), and a threshold-free approach to biodiversity quantification–phylogenetic diversity.RESULTS:A DNA barcode reference library is built for 112 EPT species for the focal region, consisting of 2277 COI sequences. Close correspondence was found between EPT morphospecies and haplotype clusters as designated using a standard threshold value. Similarly, the shapes of taxon accumulation curves based upon haplotype clusters were very similar to those generated using phylogenetic diversity accumulation curves, but were much more computationally efficient.CONCLUSION:The results of this study will facilitate other lines of research on northern EPTs and also bode well for rapidly conducting initial biodiversity assessments in unknown EPT faunas.", "publicationTitle": "Frontiers in Zoology", "publisher": "", "place": "", "date": "2009", "volume": "6", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "30", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2011-03-05T05:30:18Z", "dateModified": "2011-03-05T05:30:18Z" } }, { "key": "4F46DQHU", "version": 1, "library": { "type": "group", "id": 40029, "name": "DNA Barcoding", "links": { "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/40029/items/4F46DQHU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding/items/4F46DQHU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 163381, "username": "aborisen", "name": "Alex Borisenko", "links": { "alternate": { "href": "https://www.zotero.org/aborisen", "type": "text/html" } } }, "creatorSummary": "Zhou", "parsedDate": "2009", "numChildren": 0 }, "data": { "key": "4F46DQHU", "version": 1, "itemType": "journalArticle", "title": "The larvae of Chinese Hydropsychidae (Insecta: Trichoptera), Part I: Arctopsyche shimianensis, Parapsyche sp A, and Diplectrona obscura", "creators": [ { "creatorType": "author", "firstName": "X.", "lastName": "Zhou" } ], "abstractNote": "DNA sequence libraries (mitochondrial COI barcode and nuclear 28S D2) are built for Chinese caddisflies, a fauna largely under-studied. These independent DNA sequences are used to associate larvae and adults of Chinese Hydropsychidae. As the first part of the result of this work, Arctopsyche shimianensis Gui and Yang, 2000 and Parapsyche sp. A are associated with their adults across both gene markers. Probable association is also made for Diplectrona obscura Ulmer, 1930. Larval descriptions and illustrations are provided for all three species for the first time.", "publicationTitle": "Zootaxa", "publisher": "", "place": "", "date": "2009", "volume": "", "issue": "2174", "section": "", "partNumber": "", "partTitle": "", "pages": "1-17", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "Times Cited: 0", "tags": [], "collections": [], "relations": {}, "dateAdded": "2011-03-05T05:30:18Z", "dateModified": "2011-03-05T05:30:18Z" } }, { "key": "49TTG88M", "version": 1, "library": { "type": "group", "id": 40029, "name": "DNA Barcoding", "links": { "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/40029/items/49TTG88M", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding/items/49TTG88M", "type": "text/html" } }, "meta": { "createdByUser": { "id": 163381, "username": "aborisen", "name": "Alex Borisenko", "links": { "alternate": { "href": "https://www.zotero.org/aborisen", "type": "text/html" } } }, "creatorSummary": "Zhang and Savolainen", "parsedDate": "2009", "numChildren": 0 }, "data": { "key": "49TTG88M", "version": 1, "itemType": "journalArticle", "title": "BPSI2.0: a C/C++ interface program for species identification via DNA barcoding with a BP-neural network by calling the Matlab engine", "creators": [ { "creatorType": "author", "firstName": "A. B", "lastName": "Zhang" }, { "creatorType": "author", "firstName": "P.", "lastName": "Savolainen" } ], "abstractNote": "BP-Species Identification (BPSI2.0) is a computer program that performs species identification by training a Back-Propagation Neural Network. A short DNA barcoding segment is used as input for training a three-layer BP network. The trained network can assign an unknown query sequence to a known species in the user's database, and provide the corresponding subvector value of the output vector as a relative probability value.", "publicationTitle": "Molecular Ecology Resources", "publisher": "", "place": "", "date": "2009", "volume": "9", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "104-106", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "Times Cited: 1", "tags": [], "collections": [], "relations": {}, "dateAdded": "2011-03-05T05:30:18Z", "dateModified": "2011-03-05T05:30:18Z" } }, { "key": "2K78QGHH", "version": 1, "library": { "type": "group", "id": 40029, "name": "DNA Barcoding", "links": { "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/40029/items/2K78QGHH", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding/items/2K78QGHH", "type": "text/html" } }, "meta": { "createdByUser": { "id": 163381, "username": "aborisen", "name": "Alex Borisenko", "links": { "alternate": { "href": "https://www.zotero.org/aborisen", "type": "text/html" } } }, "creatorSummary": "Zhang", "parsedDate": "2010", "numChildren": 0 }, "data": { "key": "2K78QGHH", "version": 1, "itemType": "journalArticle", "title": "Exploiting formalin-preserved fish specimens for resources of DNA barcoding", "creators": [ { "creatorType": "author", "firstName": "J.", "lastName": "Zhang" } ], "abstractNote": "With the development of the DNA barcoding project, a large number of specimens are required to establish the library of reference barcode. Formalin-fixed samples from museums provide a potential resource for it. However, recovery of DNA and amplification of the target gene from formalin-fixed samples are challenging. In this study, a hot alkali pre-treatment accompanied by the use of cetyltrimethylammonium bromide (CTAB) method was employed for DNA recovery from formalin-preserved samples, with the purpose of pursuing the optimal condition for high quantity and quality of DNA and minimizing PCR inhibition. Meanwhile, a semi-nested PCR-based method was developed to enhance the efficacy of amplification. This advanced protocol was demonstrated to be reliable and effective. Even for 23-year-old samples, genomic DNA could be extracted, and COI gene was correctly sequenced.", "publicationTitle": "Molecular Ecology Resources", "publisher": "", "place": "", "date": "2010", "volume": "10", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "935-941", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2011-03-05T05:30:18Z", "dateModified": "2011-03-05T05:30:18Z" } }, { "key": "JNCFH9IR", "version": 1, "library": { "type": "group", "id": 40029, "name": "DNA Barcoding", "links": { "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/40029/items/JNCFH9IR", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding/items/JNCFH9IR", "type": "text/html" } }, "meta": { "createdByUser": { "id": 163381, "username": "aborisen", "name": "Alex Borisenko", "links": { "alternate": { "href": "https://www.zotero.org/aborisen", "type": "text/html" } } }, "creatorSummary": "Zapata and Robertson", "parsedDate": "2006", "numChildren": 0 }, "data": { "key": "JNCFH9IR", "version": 1, "itemType": "journalArticle", "title": "How many species of shore fishes are there in the Tropical Eastern Pacific?", "creators": [ { "creatorType": "author", "firstName": "F. A", "lastName": "Zapata" }, { "creatorType": "author", "firstName": "D. R", "lastName": "Robertson" } ], "abstractNote": "", "publicationTitle": "Journal of Biogeography", "publisher": "", "place": "", "date": "2006", "volume": "34", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "38-51", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2011-03-05T05:30:18Z", "dateModified": "2011-03-05T05:30:18Z" } }, { "key": "B299IEMR", "version": 1, "library": { "type": "group", "id": 40029, "name": "DNA Barcoding", "links": { "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/40029/items/B299IEMR", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding/items/B299IEMR", "type": "text/html" } }, "meta": { "createdByUser": { "id": 163381, "username": "aborisen", "name": "Alex Borisenko", "links": { "alternate": { "href": "https://www.zotero.org/aborisen", "type": "text/html" } } }, "creatorSummary": "Zampieri et al.", "parsedDate": "2009", "numChildren": 0 }, "data": { "key": "B299IEMR", "version": 1, "itemType": "journalArticle", "title": "PCR primers specific for the genus Tuber reveal the presence of several truffle species in a truffle-ground", "creators": [ { "creatorType": "author", "firstName": "E.", "lastName": "Zampieri" }, { "creatorType": "author", "firstName": "A.", "lastName": "Mello" }, { "creatorType": "author", "firstName": "P.", "lastName": "Bonfante" }, { "creatorType": "author", "firstName": "C.", "lastName": "Murat" } ], "abstractNote": "Truffles are hypogeous Ascomycete fungi belonging to the genus Tuber and forming fruiting bodies highly prized for their taste and aroma. The identification of the genus Tuber and its species is important to investigate their ecology and avoid fraud in the food market. As genus-specific primers are not available, the aims of this work were (1) to assess the usefulness of the beta-tubulin gene as a DNA barcoding region for designing Tuber genus-specific primers, (2) to test the primers on a range of fruiting bodies, representing a large part of truffle biodiversity and (3) to check their ecological usefulness, applying them to truffle-ground soil. The new primers designed on the b-tubulin gene were specific to the Tuber genus in nested PCR. When applied to DNA from soils, they gave a positive signal for 23 of 32 soils. Phylogenetic analysis confirmed that the bands corresponded to Tuber and that at least five Tuber species were present in the truffle-ground. b-tubulin was found to be a good barcoding region for designing Tuber genus-specific primers, detecting a high Tuber diversity in a natural environment. These primers will be useful for understanding truffle ecology and for practical needs in plantation management.", "publicationTitle": "Fems Microbiology Letters", "publisher": "", "place": "", "date": "2009", "volume": "297", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "67-72", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "Times Cited: 1", "tags": [], "collections": [], "relations": {}, "dateAdded": "2011-03-05T05:30:18Z", "dateModified": "2011-03-05T05:30:18Z" } }, { "key": "G3WME5MS", "version": 1, "library": { "type": "group", "id": 40029, "name": "DNA Barcoding", "links": { "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/40029/items/G3WME5MS", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/dna_barcoding/items/G3WME5MS", "type": "text/html" } }, "meta": { "createdByUser": { "id": 163381, "username": "aborisen", "name": "Alex Borisenko", "links": { "alternate": { "href": "https://www.zotero.org/aborisen", "type": "text/html" } } }, "creatorSummary": "Zakharov et al.", "parsedDate": "2009", "numChildren": 0 }, "data": { "key": "G3WME5MS", "version": 1, "itemType": "journalArticle", "title": "Introgression as a likely cause of mtDNA paraphyly in two allopatric skippers (Lepidoptera: Hesperiidae)", "creators": [ { "creatorType": "author", "firstName": "E. V.", "lastName": "Zakharov" }, { "creatorType": "author", "firstName": "N. F.", "lastName": "Lobo" }, { "creatorType": "author", "firstName": "C.", "lastName": "Nowak" }, { "creatorType": "author", "firstName": "J. J.", "lastName": "Hellmann" } ], "abstractNote": "", "publicationTitle": "Heredity", "publisher": "", "place": "", "date": "2009", "volume": "102", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "590 - 599", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2011-03-05T05:30:18Z", "dateModified": "2011-03-05T05:30:18Z" } } ]