Open Access (OA) publishing – myths, choices and costs

Discussions and enquiries concerning open access journals and the best way to support the associated costs of OA publishing have increased over the last 12‐18 months at the University of Strathclyde. Much of this discussion has taken place with individual academics or at departmental level, rather than at an institutional level. The Information Services Directorate has participated in some of these interchanges, and is aware that the Library, in particular, is identified by many as being the most likely source of funding and/or possible coordinator of any decision to tackle this matter should a central support policy be put in place. Whilst ISD agree that its field of responsibility should include some involvement with OA publishing, not least due to the support and management of the institutional repository, it is concerned that many of the views being expressed by colleagues elsewhere are showing some evidence that the real workings of the OA enterprise in the wider arena are misunderstood, specifically on the matter of cost. This discussion paper attempts to clear‐up some of the myths and provide an objective assessment of the options this institution may wish to consider

Molecular helminthology in the Rockies

A report on the Keystone Symposium on Molecular Helminthology, Copper Mountain, Colorado, USA, 9-13 April 2005

Commentary on 'a Reflexive Account of Reusing Qualitative Data: Beyond Primary/secondary Dualism' (Libby Bishop)

[No abstract][No keywords]

Operon conservation and the evolution of trans-splicing in the phylum Nematoda

The nematode Caenorhabditis elegans is unique among model animals in that many of its genes are cotranscribed as polycistronic pre-mRNAs from operons. The mechanism by which these operonic transcripts are resolved into mature mRNAs includes trans-splicing to a family of SL2-like spliced leader exons. SL2-like spliced leaders are distinct from SL1, the major spliced leader in C. elegans and other nematode species. We surveyed five additional nematode species, representing three of the five major clades of the phylum Nematoda, for the presence of operons and the use of trans-spliced leaders in resolution of polycistronic pre-mRNAs. Conserved operons were found in Pristionchus pacificus, Nippostrongylus brasiliensis, Strongyloides ratti, Brugia malayi, and Ascaris suum. In nematodes closely related to the rhabditine C. elegans, a related family of SL2-like spliced leaders is used for operonic transcript resolution. However, in the tylenchine S. ratti operonic transcripts are resolved using a family of spliced leaders related to SL1. Non-operonic genes in S. ratti may also receive these SL1 variants. In the spirurine nematodes B. malayi and A. suum operonic transcripts are resolved using SL1. Mapping these phenotypes onto the robust molecular phylogeny for the Nematoda suggests that operons evolved before SL2-like spliced leaders, which are an evolutionary invention of the rhabditine lineage

Toward 959 nematode genomes

The sequencing of the complete genome of the nematode Caenorhabditis elegans was a landmark achievement and ushered in a new era of whole-organism, systems analyses of the biology of this powerful model organism. The success of the C. elegans genome sequencing project also inspired communities working on other organisms to approach genome sequencing of their species. The phylum Nematoda is rich and diverse and of interest to a wide range of research fields from basic biology through ecology and parasitic disease. For all these communities, it is now clear that access to genome scale data will be key to advancing understanding, and in the case of parasites, developing new ways to control or cure diseases. The advent of second-generation sequencing technologies, improvements in computing algorithms and infrastructure and growth in bioinformatics and genomics literacy is making the addition of genome sequencing to the research goals of any nematode research program a less daunting prospect. To inspire, promote and coordinate genomic sequencing across the diversity of the phylum, we have launched a community wiki and the 959 Nematode Genomes initiative (www.nematodegenomes.org/). Just as the deciphering of the developmental lineage of the 959 cells of the adult hermaphrodite C. elegans was the gateway to broad advances in biomedical science, we hope that a nematode phylogeny with (at least) 959 sequenced species will underpin further advances in understanding the origins of parasitism, the dynamics of genomic change and the adaptations that have made Nematoda one of the most successful animal phyla

Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes

BACKGROUND: Comparisons 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. RESULTS: An 83 kb region flanking the gene for Bm-mif-1 (macrophage migration inhibitory factor, a B. malayi homolog of a human cytokine) was sequenced. When compared to the complete genome of C. elegans, evidence for conservation of long-range synteny and microsynteny was found. Potential C. elegans orthologs for II of the 12 protein-coding genes predicted in the B. malayi sequence were identified. Ten of these orthologs were located on chromosome I, with eight clustered in a 2.3 Mb region. While several, relatively local, intrachromosomal rearrangements have occurred, the order, composition, and configuration of two gene clusters, each containing three genes, was conserved. Comparison of B. malayi BAC-end genome survey sequence to C. elegans also revealed a bias towards intrachromosome rearrangements. CONCLUSIONS: We suggest that intrachromosomal rearrangement is a major force driving chromosomal organization in nematodes, but is constrained by the interdigitation of functional elements of neighboring genes

Ther varom mid j hia: Tracing linguistic diffusion in the history of Norwegian using kernel density estimation

AbstractTracing the diffusion of linguistic innovations in space from historical sources is challenging. The complexity of the datasets needed in combination with the noisy reality of historical language data mean that it has not been practical until recently. However, bigger historical corpora with richer spatial and temporal information allow us to attempt it. This paper presents an investigation into changes affecting first person non-singular pronouns in the history of Norwegian: first, individual changes affecting the dual (vit&gt;mit) and plural (vér&gt;mér), followed by loss of the dual-plural distinction by merger into either form or replacement of both by Danish-Swedishvi. To create dynamic spatial visualisations of these changes, the use of kernel density estimation is proposed. This term covers a range of statistical tools depending on the kernel function. The paper argues for a Gaussian kernel in time and an adaptive uniform (k-nearest neighbours) kernel in space, allowing uncertainty or multiple localisation to be incorporated into calculations. The results for this dataset allow us to make a link between Modern Norwegian dialectological patterns and language use in the Middle Ages; they also exemplify different types of diffusion process in the spread of linguistic innovations.</jats:p