5,261 research outputs found
Defining operational taxonomic units using DNA barcode data
No full textThe scale of diversity of life on this planet is a significant challenge for any scientific programme hoping to produce a complete catalogue, whatever means is used. For DNA barcoding studies, this difficulty is compounded by the realization that any chosen barcode sequence is not the gene 'for' speciation and that taxa have evolutionary histories. How are we to disentangle the confounding effects of reticulate population genetic processes? Using the DNA barcode data from meiofaunal surveys, here we discuss the benefits of treating the taxa defined by barcodes without reference to their correspondence to 'species', and suggest that using this non-idealist approach facilitates access to taxon groups that are not accessible to other methods of enumeration and classification. Major issues remain, in particular the methodologies for taxon discrimination in DNA barcode data
The sense of a beginning : Bakhtinian dialogic criticism on 'the gospel' in Mark.
No full textContemporary literary approaches have caused paradigm shifts in Biblical Studies in the last two decades as it appears in a great deal of Markan studies using narrative, reader-response, deconstructive, feminist, and new historicist approaches. However, literary studies on the Gospel of Mark have not taken into account theoretical questions underlying those approaches. As a result biblical critics are driven by new trends without ever having a chance to examine the critical baggage of the approaches. Consequently, there is a gap of communication between the old and the new one. Therefore this thesis is an attempt to meet the need of enhancing the quality of critical endeavour in biblical studies. In the light of most recent competing critical theories of literature, the first contribution of this thesis is the methodological finding that Bakhtinian dialogic criticism contains the most profound philosophical and practical foundations for solving some crucial theoretical problems in contemporary literary theories. It is a critique to a Saussurian linguistic system of language which becomes the very foundation of modern and postmodern literary criticism. Bakhtinian literary theory shifts the foundation of literary criticism on linguistic signs into the creative activity of the socio-cultural production of human communication. The shift into socio-cultural reality of language communication makes the notion of 'genre' very important to unlock the problem of text and context in literary studies. Since the Gospel of Mark has fascinated most literary critics in Biblical Studies, the problem of 'genre' of this gospel is chosen as the focus of this study. Secondly, as no agreement is reached as to what 'genre' the Gospel of Mark belongs, this thesis makes its contribution to the discussion by locating the problem of 'genre' of Mark in the context of genre theories and argues that the Bakhtinian suggestion to find genre in the socio-cultural sphere by analysing artistic intercourse between narrative agents in Mark has freed the competing analysis from the unresolved problem between the kerygmatic (content oriented) approach and the analogical (form oriented) approach. To achieve finding 'genre' in the socio-cultural sphere, this thesis focuses on Bakhtinian analysis of the process of artistic intercourse between narrative agents. The narrative communicative interrelationships between narrative agents is constructed in this thesis as a 'stereophonic' Bakhtinian model of dialogic communication. This model is an original contribution of this thesis for revising the traditional two dimensional model of narrative communication. Based on this dialogical model of communication, a special role is given to the Bakhtinian 'author-creator' in the realization process of genre through the interaction of polyphonic voices. Through the interaction of voices of the author-artist and the hero we are led to discover a relatively stable type of portraying and controlling reality in Mark, known as the genre of Roman 'satire'. The closest literary affinity is Satyrica by Petronius. This narrative strategy of 'satire' in Mark has its root in the prophetic discourse of the Old Testament which is saturating the speech of the narrator, John the Immerser, the centurion, the people, and even Jesus. Finally, the whole search for Markan 'genre' culminates in the analysis of the realization of genre through the analysis of Bakhtinian chronotope. The reality of the genre of Mark is its social reality that is in its role as dpxrj/ 'beginning'. As the Gospel of Mark proclaims itself as 'a beginning', it defines its claim of socio-cultural 'authority' in early Christianity. It is this 'sense of beginning' which enables the narrating and the narrated world of Mark to interact dialogically
The promise of a DNA taxonomy
No full textNot only is the number of described species a very small proportion of the estimated extant number of taxa, but it also appears that all concepts of the extent and boundaries of 'species' fail in many cases. Using conserved molecular sequences it is possible to define and diagnose molecular operational taxonomic units (MOTU) that have a similar extent to traditional 'species'. Use of a MOTU system not only allows the rapid and effective identification of most taxa, including those not encountered before, but also allows investigation of the evolution of patterns of diversity. A MOTU approach is not without problems, particularly in the area of deciding what level of molecular difference defines a biologically relevant taxon, but has many benefits. Molecular data are extremely well suited to re-analysis and meta-analysis, and data from multiple independent studies can be readily collated and investigated by using new parameters and assumptions. Previous molecular taxonomic efforts have focused narrowly. Advances in high-throughput sequencing methodologies, however, place the idea of a universal, multi-locus molecular barcoding system in the realm of the possible
A conserved set of maternal genes? Insights from a molluscan transcriptome
No full textThe early animal embryo is entirely reliant on maternal gene products for a ‘jump-start’ that transforms a transcriptionally inactive embryo into a fully functioning zygote. Despite extensive work on model species, it has not been possible to perform a comprehensive comparison of maternally-provisioned transcripts across the Bilateria because of the absence of a suitable dataset from the Lophotrochozoa. As part of an ongoing effort to identify the maternal gene that determines left-right asymmetry in snails, we have generated transcriptome data from 1 to 2-cell and ~32-cell pond snail (Lymnaea stagnalis) embryos. Here, we compare these data to maternal transcript datasets from other bilaterian metazoan groups, including representatives of the Ecydysozoa and Deuterostomia. We found that between 5 and 10% of all L. stagnalis maternal transcripts (~300-400 genes) are also present in the equivalent arthropod (Drosophila melanogaster), nematode (Caenorhabditis elegans), urochordate (Ciona intestinalis) and chordate (Homo sapiens, Mus musculus, Danio rerio) datasets. While the majority of these conserved maternal transcripts (“COMATs”) have housekeeping gene functions, they are a non-random subset of all housekeeping genes, with an overrepresentation of functions associated with nucleotide binding, protein degradation and activities associated with the cell cycle. We conclude that a conserved set of maternal transcripts and their associated functions may be a necessary starting point of early development in the Bilateria. For the wider community interested in discovering conservation of gene expression in early bilaterian development, the list of putative COMATs may be useful resource
Well-known trade mark protection: confusion in EU and Japan
No full textIn this thesis concerning the protection of well-known trade marks against confusion in the European Community Trade Mark (CTM) and Japanese trademark systems, the author critically considers the difficulties in comprehensively defining ‘well-known trade mark’ in the relevant international trade mark instruments. After critical analysis of various definitions of both ‘trade mark’ and ‘well-known trade mark’, she undertakes a comparison of the definitions of the parallel concepts of ‘trade mark of repute’ and ‘syuchi-syohyo’, and also undertakes an assessment as to the extent to which these trade marks are protected against confusion and kondo in the CTM and Japanese systems, respectively. It is concluded that the protection of well- known trade marks against confusion in the CTM and Japan cannot be said to be completely clear, and the author identifies some areas for legal refor
Second-generation environmental sequencing unmasks marine metazoan biodiversity
No full textBiodiversity is of crucial importance for ecosystem functioning, sustainability and resilience, but the magnitude and organization of marine diversity at a range of spatial and taxonomic scales are undefined. In this paper, we use second-generation sequencing to unmask putatively diverse marine metazoan biodiversity in a Scottish temperate benthic ecosystem. We show that remarkable differences in diversity occurred at microgeographical scales and refute currently accepted ecological and taxonomic paradigms of meiofaunal identity, rank abundance and concomitant understanding of trophic dynamics. Richness estimates from the current benchmarked Operational Clustering of Taxonomic Units from Parallel UltraSequencing analyses are broadly aligned with those derived from morphological assessments. However, the slope of taxon rarefaction curves for many phyla remains incomplete, suggesting that the true alpha diversity is likely to exceed current perceptions. The approaches provide a rapid, objective and cost-effective taxonomic framework for exploring links between ecosystem structure and function of all hitherto intractable, but ecologically important, communities
The Gospel on the Margins: The Ideological Function of the Patristic Tradition on the Evangelist Mark
No full textIn spite of the virtually unanimous patristic opinion that the evangelist Mark was the interpreter of Peter, one of the most prestigious apostolic founding figures in Christian memory, the Gospel of Mark was mostly neglected in the patristic period. Not only is the text of Mark the least well represented of the canonical Gospels in terms of the number of patristic citations, commentaries and manuscripts, the explicit comments about the evangelist Mark reveal some ambivalence about its literary or theological value. In my survey of the reception of Mark from Papias of Hierapolis until Clement of Alexandria, I will argue that the reason why the patristic writers were hesitant to embrace the Gospel of Mark was that they perceived the text to be amenable to the Christological beliefs and social praxis of rival Christian factions. The patristic tradition about Mark may have little historical basis, but it had an important ideological function in appropriating the text in the name of an apostolic authority from the margins or periphery
prot4EST: translating expressed sequence tags from neglected genomes
No full textThe genomes of an increasing number of species are being investigated through generation of expressed sequence tags (ESTs). However, ESTs are prone to sequencing errors and typically define incomplete transcripts, making downstream annotation difficult. Annotation would be greatly improved with robust polypeptide translations. Many current solutions for EST translation require a large number of full-length gene sequences for training purposes, a resource that is not available for the majority of EST projects
Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes
No full textComparisons between the genomes of the closely related nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal high rates of rearrangement, with a bias towards within-chromosome events. To assess whether this pattern is true of nematodes in general, we have used genome sequence to compare two nematode species that last shared a common ancestor approximately 300 million years ago: the model C. elegans and the filarial parasite Brugia malayi
The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus
No full textABSTRACT: BACKGROUND: Anguillicola crassus is an economically and ecologically important parasitic nematode of eels. The native range of A. crassus is in East Asia, where it infects Anguilla japonica, the Japanese eel. A. crassus was introduced into European eels, Anguilla anguilla, 30 years ago. The parasite is more pathogenic in its new host than in its native one, and is thought to threaten the endangered An. anguilla across its range. The molecular bases for the increased pathogenicity of the nematodes in their new hosts is not known. RESULTS: A reference transcriptome was assembled for A. crassus from Roche 454 pyrosequencing data. Raw reads (756,363 total) from nematodes from An. japonica and An. anguilla hosts were filtered for likely host contaminats and ribosomal RNAs. The remaining 353,055 reads were assembled into 11,372 contigs of a high confidence assembly (spanning 6.6 Mb) and an additional 21,153 singletons and contigs of a lower confidence assembly (spanning an additional 6.2 Mb). Roughly 55% of the high condence assembly contigs were annotated with domain- or protein sequence similarity derived functional information. Sequences conserved only in nematodes, or unique to A. crassus were more likely to have secretory signal peptides. Thousands of high quality single nucleotide polymorphisms were identified, and coding polymorphism was correlated with diffrential expression between individual nematodes. Transcripts identfied as being under positive selection were enriched in peptidases. Enzymes involved in energy metabolism were enriched in the set of genes differentially expressed between European and Asian A. crassus. CONCLUSIONS: The reference transcriptome of A. crassus is of high quality, and will serve as a basis for future work on the invasion biology of this important parasite. The polymorphisms identied will provide a key tool set for analysis of population structure and identication of genes likely to be involved in increased pathogenicity in European eel hosts. The identication of peptidases under positive selection is a first step in this programme
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