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  • 1
    Electronic Resource
    Electronic Resource
    The immunodiagnostic potential of Echinococcus granulosus adult-worm antigens in human cystic echinococcosis (1996)
    Springer
    Parasitology research 83 (1996), S. 90-92 
    Details
    ISSN: 1432-1955
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Echinococcus granulosus adult-worm antigens were characterised for assessment of their immunodiagnostic potential for human cystic echinococcosis (CE). The analysis of worm extracts by enzyme-linked immunosorbent assay (ELISA) showed a sensitivity of 83% for CE, which is comparable with data obtained for cyst-fluid-based serodiagnostic tests. Immunoprecipitation of in vitro-translated E. granulosus worm mRNA revealed a range of low-molecular-weight antigenic proteins (12–45 kDa) recognised by human CE sera. E. granulosus adult worms may provide an additional or alternative source to metacestode material for the isolation of both native and recombinant antigens to be considered for the serodiagnosis of human echinococcosis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004360050215
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Assessing sequence variation in the internal transcribed spacers of ribosomal DNA within and among members of the Contracaecum osculatum complex (Nematoda: Ascaridoidea: Anisakidae) (2000)
    Springer
    Parasitology research 86 (2000), S. 677-683 
    Details
    ISSN: 1432-1955
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The anisakid nematodes of seals from different geographical origins, previously identified as Contracaecum osculatum A, C. osculatum B, C. osculatum C, C. osculatum D, C. osculatum E and C. osculatum baicalensis by multilocus enzyme electrophoresis, were characterised using a DNA approach. The first and second internal transcribed spacers (ITS-1, ITS-2) of ribosomal DNA (rDNA) were individually amplified by polymerase chain reaction (PCR) and analysed by single-strand conformation polymorphism (SSCP) and sequencing. SSCP analyses allowed the unequivocal differentiation of all taxa except C. osculatum D from C. osculatum E. While C. osculatum D and C. osculatum E had identical ITS sequences, each of the other four taxa had distinct sequences, with interspecific differences ranging from 0.3% to 2.3%. C. osculatum C was genetically the most distinct taxon with respect to all other members of the species complex.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00008551
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  • 3
    Electronic Resource
    Electronic Resource
    Relationships among some ascaridoid nematodes based on ribosomal DNA sequence data (2000)
    Springer
    Parasitology research 86 (2000), S. 738-744 
    Details
    ISSN: 1432-1955
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The nuclear ribosomal DNA (rDNA) region spanning the first (ITS-1) and second (ITS-2) internal transcribed spacers was sequenced for 15 taxa of ascaridoid nematodes. The length of the ITS-1 and ITS-2 sequences in the 15 taxa ranged from 392–500 bp and 240–348 bp, respectively. While nucleotide variation of 0–2.9% in the ITS-1 and/or ITS-2 sequences was detected within taxa where multiple samples were sequenced, significantly higher level of nucleotide difference (9.4–66.6%) was detected between the taxa, except for Ascaris suum and A. lumbricoides whose taxonomic status remains uncertain. These interspecific differences were linked with the considerable size differences (0–108 bp) in the rDNA spacers. Phenograms based on the genetic differences among the 15 taxa showed some concordance with previous classification schemes derived from morphological data.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00008561
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  • 4
    Electronic Resource
    Electronic Resource
    Detection of sequence variation in parasite ribosomal DNA by electrophoresis in agarose gels supplemented with a DNA-intercalating agent (1998)
    Weinheim : Wiley-Blackwell
    Electrophoresis 19 (1998), S. 671-674 
    Details
    ISSN: 0173-0835
    Keywords: Ascarid ; Ribosomal DNA ; Internal transcribed spacer (ITS) ; Sequence variation ; Agarose gels ; DNA-intercalating agent ; Resolver Gold™ ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: This study evaluated the use of a commercially available DNA intercalating agent (Resolver Gold™) in agarose gels for the direct detection of sequence variation in ribosomal DNA (rDNA). This agent binds preferentially to AT sequence motifs in DNA. Regions of nuclear rDNA, known to provide genetic markers for the identification of species of parasitic ascarid nematodes (order Ascaridida), were amplified by polymerase chain reaction (PCR) and subjected to electrophoresis in standard agarose gels versus gels supplemented with Resolver Gold. Individual taxa examined could not be distinguished reliably based on the size of their amplicons in standard agarose gels, whereas they could be readily delineated based on mobility using Resolver Gold-supplemented gels. The latter was achieved because of differences (approximately 0.1-8.2%) in the AT content of the fragments among different taxa, which were associated with significant interspecific differences (approximately 11-39%) in the rDNA sequences employed. There was a tendency for fragments with higher AT content to migrate slower in supplemented agarose gels compared with those of lower AT content. The results indicate the usefulness of this electrophoretic approach to rapidly screen for sequence variability within or among PCR-amplified rDNA fragments of similar sizes but differing AT contents. Although evaluated on rDNA of parasites, the approach has potential to be applied to a range of genes of different groups of infectious organisms.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150190511
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  • 5
    Electronic Resource
    Electronic Resource
    Single-strand conformation polymorphism (SSCP)-based mutation scanning approaches to fingerprint sequence variation in ribosomal DNA of ascaridoid nematodes (1998)
    Weinheim : Wiley-Blackwell
    Electrophoresis 19 (1998), S. 1366-1373 
    Details
    ISSN: 0173-0835
    Keywords: Ascaridoids ; Ribosomal DNA ; Second internal transcribed spacer (ITS-2) ; Polymerase chain reaction-linked single-strand conformation polymorphism ; Dideoxy fingerprinting ; Restriction endonuclease fingerprinting ; Parasite identification ; Sequence variation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: In this study, we assessed single-strand conformation polymorphism (SSCP)-based approaches for their capacity to fingerprint sequence variation in ribosomal DNA (rDNA) of ascaridoid nematodes of veterinary and/or human health significance. The second internal transcribed spacer region (ITS-2) of rDNA was utilised as the target region because it is known to provide species-specific markers for this group of parasites. ITS-2 was amplified by PCR from genomic DNA derived from individual parasites and subjected to analysis. Direct SSCP analysis of amplicons from seven taxa (Toxocara vitulorum, Toxocara cati, Toxocara canis, Toxascaris leonina, Baylisascaris procyonis, Ascaris suum and Parascaris equorum) showed that the single-strand (ss) ITS-2 patterns produced allowed their unequivocal identification to species. While no variation in SSCP patterns was detected in the ITS-2 within four species for which multiple samples were available, the method allowed the direct display of four distinct sequence types of ITS-2 among individual worms of T. cati. Comparison of SSCP/sequencing with the methods of dideoxy fingerprinting (ddF) and restriction endonuclease fingerprinting (REF) revealed that also ddF allowed the definition of the four sequence types, whereas REF displayed three of four. The findings indicate the usefulness of the SSCP-based approaches for the identification of ascaridoid nematodes to species, the direct display of sequence variation in rDNA and the detection of population variation. The ability to fingerprint microheterogeneity in ITS-2 rDNA using such approaches also has implications for studying fundamental aspects relating to mutational change in rDNA.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150190828
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  • 6
    Electronic Resource
    Electronic Resource
    Polymerase chain reaction-linked single-strand conformation polymorphism of ribosomal DNA to fingerprint parasites (1997)
    Weinheim : Wiley-Blackwell
    Electrophoresis 18 (1997), S. 1564-1566 
    Details
    ISSN: 0173-0835
    Keywords: Parasitic nematodes ; Polymerase chain reaction-linked single-strand conformation polymorphism ; Species identification ; Second internal transcribed spacer ; Ribosomal DNA ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: To overcome limitations of the morphological identification of some parasites (and their different developmental stages) to species, we have established a polymerase chain reaction-linked single-strand conformation polymorphism technique (PCR-SSCP) utilizing the second internal transcribed spacer (ITS-2) of ribosomal (r)DNA. This spacer was specifically chosen in the study of strongylid and ascarid nematodes because it is known to provide reliable species markers. The ITS-2 from individual parasites was amplified by PCR, then denatured and subjected to electrophoresis on a mutation detection enhancement (MDE) (nondenaturing) gel matrix. PCR-SSCP analysis showed that the single-strand ITS-2 patterns produced allowed the accurate identification of species. The method also allowed the display of (low-level) variation in patterns within some species between different geographical isolates. These findings demonstrate the usefulness of PCR-SSCP of ITS-2 for the identification of nematode species and indicate its potential for resolving variation in the ITS-2 sequence within species.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150180913
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  • 7
    Electronic Resource
    Electronic Resource
    Analysis of sequence homogenisation in rDNA arrays of Haemonchus contortus by denaturing gradient gel electrophoresis (1998)
    Weinheim : Wiley-Blackwell
    Electrophoresis 19 (1998), S. 2391-2395 
    Details
    ISSN: 0173-0835
    Keywords: Haemonchus contortus ; Internal transcribed spacer ; Ribosomal DNA ; Denaturing gradient gel electrophoresis ; Mutations ; pre-rRNA structure ; Concerted evolution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Testing different theories of concerted evolution experimentally has been hampered mainly due to the lack of appropriate model systems and technical limitations. In this study, we employed a denaturing gradient gel electrophoresis (DGGE) approach for the display and definition of nucleotide variations in the second internal transcribed spacer (ITS-2) of ribosomal DNA (rDNA) of the parasitic nematode, Haemonchus contortus. The ITS-2 was amplified from individual adult nematodes by PCR and subjected to DGGE. Of the 94 individuals (representing nine different populations) analysed, 13 different DGGE profiles were displayed. Eighteen bands representing those profiles were excised and sequenced. Sequencing defined 13 different types of ITS-2 with 12 nucleotide variations (4 transitions, 5 transversions, 1 insertion and 2 deletions) which could be related to particular positions of the predicted secondary structure for the ITS-2 pre-rRNA. The results showed that individuals of interbreeding populations of H. contortus can have rDNA arrays that are partially or fully homogenised for different sequence variants (despite interindividual variation), suggesting that the homogenisation process is driven mainly by intrachromosomal exchange. The findings also demonstrated the capacity of the DGGE-sequencing strategy to quantify the frequency of ITS-2 sequence types within individual nematodes from different populations without the need for cloning or Southern blot procedures. This has important implications for studying the mechanisms of sequence homogenisation in rDNA and pre-rRNA processing as well as for elucidating speciation events and population differentation at the molecular level.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150191405
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  • 8
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    A communal catalogue reveals Earth’s multiscale microbial diversity (2017)
    Nature Research
    In:  Nature, 551 (7681). pp. 457-463.
    Details
    Publication Date: 2020-02-06
    Description: Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1038/nature24621
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    OceanRep: Article in a Scientific Journal - peer-reviewed
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