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  • Computational Methods, Massively Parallel (Deep) Sequencing, Genomics  (1)
  • connectivity  (1)
  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Hydrobiologia 422-423 (2000), S. 85-97 
    ISSN: 1573-5117
    Keywords: ecological integrity ; running waters ; fish ecology ; extended serial discontinuity concept ; connectivity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Current ecological theories and concepts describe running waters as four-dimensional systems, their longitudinal, lateral and vertical linkages, interactions and exchange processes varying over time and over different scales. According to Ward & Stanford's (1983) extended serial discontinuity concept (ESDC), along a three-reach river, model the relative strength of the longitudinal pathways is highest in the constrained headwaters, vertical interactions reach their maximum in the braided middle course and lateral connectivity plays the major role in alluvial floodplain rivers. The present paper examines the general tenets of the ESDC from a fundamental fish ecology perspective. Specifically, it focuses on the degree to which the spatial/temporal connectivity requirements of fish communities or key fish species along a schematic longitudinal river course are compatible with the underlying principles of the ESDC and whether these requirements provide basic criteria for assessing the ecological integrity of running waters. From the fish ecological perspective, the examples provided here demonstrate a principle agreement with the concept of the four-dimensional nature of running waters, whose key functional and structural elements are spatial/temporal fluvial dynamics, disturbances, connectivity, succession and ecotones. Fish are particularly useful indicators of the temporally variable connectivities on the full range of scales at the three spatial dimensions. As far as the habitat requirements of typical species/developmental stages are concerned, two major modifications of the ESDC are needed. In constrained headwaters, in addition to longitudinal connectivity, the crucial importance of the vertical pathway river/bed sediments for reproduction must be emphasized. Also, in addition to lateral connectivity, longitudinal connectivity remains a vital basis for potamal fish communities in alluvial braided and meandering zones.
    Type of Medium: Electronic Resource
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  • 2
    Publication Date: 2014-08-15
    Description: Next-generation sequencing (NGS) technologies enable new insights into the diversity of virus populations within their hosts. Diversity estimation is currently restricted to single-nucleotide variants or to local fragments of no more than a few hundred nucleotides defined by the length of sequence reads. To study complex heterogeneous virus populations comprehensively, novel methods are required that allow for complete reconstruction of the individual viral haplotypes. Here, we show that assembly of whole viral genomes of ~8600 nucleotides length is feasible from mixtures of heterogeneous HIV-1 strains derived from defined combinations of cloned virus strains and from clinical samples of an HIV-1 superinfected individual. Haplotype reconstruction was achieved using optimized experimental protocols and computational methods for amplification, sequencing and assembly. We comparatively assessed the performance of the three NGS platforms 454 Life Sciences/Roche, Illumina and Pacific Biosciences for this task. Our results prove and delineate the feasibility of NGS-based full-length viral haplotype reconstruction and provide new tools for studying evolution and pathogenesis of viruses.
    Keywords: Computational Methods, Massively Parallel (Deep) Sequencing, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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