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  1. Article ; Online: Identification of individual root-knot nematodes using low coverage long-read sequencing.

    Sellers, Graham S / Jeffares, Daniel C / Lawson, Bex / Prior, Tom / Lunt, David H

    PloS one

    2021  Volume 16, Issue 12, Page(s) e0253248

    Abstract: Root-knot nematodes (RKN; genus Meloidogyne) are polyphagous plant pathogens of great economic importance to agriculturalists globally. These species are small, diverse, and can be challenging for accurate taxonomic identification. Many of the most ... ...

    Abstract Root-knot nematodes (RKN; genus Meloidogyne) are polyphagous plant pathogens of great economic importance to agriculturalists globally. These species are small, diverse, and can be challenging for accurate taxonomic identification. Many of the most important crop pests confound analysis with simple genetic marker loci as they are polyploids of likely hybrid origin. Here we take a low-coverage, long-read genome sequencing approach to characterisation of individual root-knot nematodes. We demonstrate library preparation for Oxford Nanopore Technologies Flongle sequencing of low input DNA from individual juveniles and immature females, multiplexing up to twelve samples per flow cell. Taxonomic identification with Kraken 2 (a k-mer-based taxonomic assignment tool) is shown to reliably identify individual nematodes to species level, even within the very closely related Meloidogyne incognita group. Our approach forms a robust, low-cost, and scalable method for accurate RKN species diagnostics.
    MeSH term(s) Animals ; DNA, Helminth/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Plant Diseases/genetics ; Plant Diseases/parasitology ; Tylenchoidea/classification ; Tylenchoidea/genetics
    Chemical Substances DNA, Helminth
    Language English
    Publishing date 2021-12-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0253248
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Assay validation for identification of hereditary nonpolyposis colon cancer-causing mutations in mismatch repair genes MLH1, MSH2, and MSH6.

    Hegde, Madhuri / Blazo, Maria / Chong, Belinda / Prior, Tom / Richards, Carolyn

    The Journal of molecular diagnostics : JMD

    2005  Volume 7, Issue 4, Page(s) 525–534

    Abstract: Hereditary nonpolyposis colon cancer (HNPCC, Online Mendelian Inheritance in Man (OMIM) 114500) is an autosomal dominant disorder that is genetically heterogeneous because of underlying mutations in mismatch repair genes, primarily MLH1, MSH2, and MSH6. ... ...

    Abstract Hereditary nonpolyposis colon cancer (HNPCC, Online Mendelian Inheritance in Man (OMIM) 114500) is an autosomal dominant disorder that is genetically heterogeneous because of underlying mutations in mismatch repair genes, primarily MLH1, MSH2, and MSH6. One challenge to correctly diagnosing HNPCC is that the large size of the causative genes makes identification of mutations both labor intensive and expensive. We evaluated the usefulness of denaturing high performance liquid chromatography (DHPLC) for scanning mismatch repair genes (MLH1, MSH2, and MSH6) for point mutations, small deletions, and insertions. Our assay consisted of 51 sets of primers designed to amplify all exons of these genes. All polymerase chain reaction reactions were amplified simultaneously using the same reaction conditions in a 96-well format. The amplified products were analyzed by DHPLC across a range of optimum temperatures for partial fragment denaturation based on the melting profile of each specific fragment. DNA specimens from 23 previously studied HNPCC patients were analyzed by DHPLC, and all mutations were correctly identified and confirmed by sequence analysis. Here, we present our validation studies of the DHPLC platform for HNPCC mutation analysis and compare its merits with other scanning technologies. This approach provides greater sensitivity and more directed molecular analysis for clinical testing in HNPCC.
    MeSH term(s) Base Pair Mismatch/genetics ; Chromatography, High Pressure Liquid ; Colorectal Neoplasms, Hereditary Nonpolyposis/genetics ; DNA Mutational Analysis ; DNA Repair/genetics ; DNA-Binding Proteins/genetics ; Genetic Testing/methods ; Humans ; MutS Homolog 2 Protein/genetics ; Mutation/genetics ; Polymorphism, Genetic/genetics ; Reproducibility of Results ; Sensitivity and Specificity
    Chemical Substances DNA-Binding Proteins ; G-T mismatch-binding protein ; MSH2 protein, human (EC 3.6.1.3) ; MutS Homolog 2 Protein (EC 3.6.1.3)
    Language English
    Publishing date 2005-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 2000060-1
    ISSN 1943-7811 ; 1525-1578
    ISSN (online) 1943-7811
    ISSN 1525-1578
    DOI 10.1016/S1525-1578(10)60584-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5146: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article: Phylogeny, diversity, and species delimitation in some species of the Xiphinema americanum-group complex (Nematoda: Longidoridae), as inferred from nuclear and mitochondrial DNA sequences and morphology

    Gutiérrez-Gutiérrez, Carlos / Cantalapiedra-Navarrete, Carolina / Decraemer, Wilfrida / Vovlas, Nicola / Prior, Tom / Rius, Juan E. Palomares / Castillo, Pablo

    European journal of plant pathology. 2012 Nov., v. 134, no. 3

    2012  

    Abstract: During nematode surveys in southern Spain and Italy 14 populations of Xiphinema species tentatively identified as Xiphinema americanum-group were detected. Morphological and morphometrical studies identified three new species and six known Xiphinema ... ...

    Abstract During nematode surveys in southern Spain and Italy 14 populations of Xiphinema species tentatively identified as Xiphinema americanum-group were detected. Morphological and morphometrical studies identified three new species and six known Xiphinema americanum-group species, viz.: Xiphinema parabrevicolle n. sp., Xiphinema parapachydermum n. sp., Xiphinema paratenuicutis n. sp., Xiphinema duriense, Xiphinema incertum, Xiphinema opisthohysterum, Xiphinema pachtaicum, Xiphinema rivesi, and Xiphinema santos. The Xiphinema americanum-group is the most difficult Xiphinema species group for diagnosis since the morphology is very conservative and morphometric characters often overlap. This group includes vectors of several important plant pathogenic viruses that cause significant damage to a wide range of agricultural crops. Molecular characterisation of these species using D2-D3 expansion regions of 28S rRNA, 18S rRNA, ITS1-rRNA and the protein-coding mitochondrial gene, cytochrome oxidase c subunit 1 was carried out and maximum likelihood and Bayesian inference analysis were used to reconstruct phylogenetic relationships among these species and with other Xiphinema americanum-group species.
    Keywords Xiphinema ; crops ; cytochrome-c oxidase ; genes ; new species ; nucleotide sequences ; phylogeny ; ribosomal RNA ; surveys ; viruses ; Italy ; Spain
    Language English
    Dates of publication 2012-11
    Size p. 561-597.
    Publishing place Springer-Verlag
    Document type Article
    ZDB-ID 1196520-4
    ISSN 0929-1873
    ISSN 0929-1873
    DOI 10.1007/s10658-012-0039-9
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 1151: Show issues

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  4. Book: Plundering sons

    Prior, Tom / Wannan, Bill / Nunn, H

    a pictorial history of Australian bushranging

    1966  

    Keywords Australia
    Language English
    Size 183 p., illus.
    Publisher Lansdowne Press
    Publishing place Melbourne
    Document type Book
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: Phylogeny, diversity, and species delimitation in some species of the Xiphinema americanum-group complex (Nematoda: Longidoridae), as inferred from nuclear and mitochondrial DNA sequences and morphology

    Gutiérrez-Gutiérrez, Carlos / Cantalapiedra-Navarrete, Carolina / Decraemer, Wilfrida / Vovlas, Nicola / Prior, Tom / Rius, Juan E. Palomares / Castillo, Pablo

    European journal of plant pathology

    Volume v. 134,, Issue no. 3

    Abstract: During nematode surveys in southern Spain and Italy 14 populations of Xiphinema species tentatively identified as Xiphinema americanum-group were detected. Morphological and morphometrical studies identified three new species and six known Xiphinema ... ...

    Abstract During nematode surveys in southern Spain and Italy 14 populations of Xiphinema species tentatively identified as Xiphinema americanum-group were detected. Morphological and morphometrical studies identified three new species and six known Xiphinema americanum-group species, viz.: Xiphinema parabrevicolle n. sp., Xiphinema parapachydermum n. sp., Xiphinema paratenuicutis n. sp., Xiphinema duriense, Xiphinema incertum, Xiphinema opisthohysterum, Xiphinema pachtaicum, Xiphinema rivesi, and Xiphinema santos. The Xiphinema americanum-group is the most difficult Xiphinema species group for diagnosis since the morphology is very conservative and morphometric characters often overlap. This group includes vectors of several important plant pathogenic viruses that cause significant damage to a wide range of agricultural crops. Molecular characterisation of these species using D2-D3 expansion regions of 28S rRNA, 18S rRNA, ITS1-rRNA and the protein-coding mitochondrial gene, cytochrome oxidase c subunit 1 was carried out and maximum likelihood and Bayesian inference analysis were used to reconstruct phylogenetic relationships among these species and with other Xiphinema americanum-group species.
    Keywords new species ; phylogeny ; genes ; nucleotide sequences ; cytochrome-c oxidase ; viruses ; surveys ; ribosomal RNA ; crops ; Xiphinema
    Language English
    Document type Article
    ISSN 0929-1873
    Database AGRIS - International Information System for the Agricultural Sciences and Technology

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