How Irish Food Criticism Reflected and Helped Shape a Changing Nation, 1988-2008

The perception and practice of eating out are linked to larger socioeconomic patterns. Newspaper restaurant reviews provide evidence of these trends which can be traced along a specific timeline. The early 1980s in Ireland were a difficult time for restaurants due to high taxes on food, a national recession and a lack of positive restaurant reviews. The economic upturn in the following decade contributed to unprecedented developments in the restaurant industry. Dining out became a regular activity – fueled in part by restaurant criticism by Irish food journalists, which joined pre-existing theatre, music and book reviews as regular features in national newspapers. The restaurant scene was burgeoning as Irish society experienced a new self-confidence bolstered by the growing economy. Data from restaurant reviews published from 1988–2008 in three national newspapers reveals the Dublin-centric middle-class nature of dining reflected in critics’ reviews, alongside changes in Irish society

Wigner-Moyal description of free variable mass Klein-Gordon fields

A system of coupled kinetic transport equations for the Wigner distributions of a free variable mass Klein-Gordon field is derived. This set of equations is formally equivalent to the full wave equation for electromagnetic waves in nonlinear dispersive media, thus allowing for the description of broadband radiation-matter interactions and the associated instabilities. The standard results for the classical wave action are recovered in the short wavelength limit of the generalized Wigner-Moyal formalism for the wave equation.Comment: 9 pages, accepted for publication in Journal of Mathematical Physic

Regulation of phenylacetic acid uptake is σ54 dependent in Pseudomonas putida CA-3

<p>Abstract</p> <p>Background</p> <p>Styrene is a toxic and potentially carcinogenic alkenylbenzene used extensively in the polymer processing industry. Significant quantities of contaminated liquid waste are generated annually as a consequence. However, styrene is not a true xenobiotic and microbial pathways for its aerobic assimilation, via an intermediate, phenylacetic acid, have been identified in a diverse range of environmental isolates. The potential for microbial bioremediation of styrene waste has received considerable research attention over the last number of years. As a result the structure, organisation and encoded function of the genes responsible for styrene and phenylacetic acid sensing, uptake and catabolism have been elucidated. However, a limited understanding persists in relation to host specific regulatory molecules which may impart additional control over these pathways. In this study the styrene degrader <it>Pseudomonas putida </it>CA-3 was subjected to random mini-Tn<it>5 </it>mutagenesis and mutants screened for altered styrene/phenylacetic acid utilisation profiles potentially linked to non-catabolon encoded regulatory influences.</p> <p>Results</p> <p>One mutant, D7, capable of growth on styrene, but not on phenylacetic acid, harboured a Tn<it>5 </it>insertion in the <it>rpoN </it>gene encoding σ54. Complementation of the D7 mutant with the wild type <it>rpoN </it>gene restored the ability of this strain to utilise phenylacetic acid as a sole carbon source. Subsequent RT-PCR analyses revealed that a phenylacetate permease, PaaL, was expressed in wild type <it>P. putida </it>CA-3 cells utilising styrene or phenylacetic acid, but could not be detected in the disrupted D7 mutant. Expression of plasmid borne <it>paaL </it>in mutant D7 was found to fully restore the phenylacetic acid utilisation capacity of the strain to wild type levels. Bioinformatic analysis of the <it>paaL </it>promoter from <it>P. putida </it>CA-3 revealed two σ⁵⁴consensus binding sites in a non-archetypal configuration, with the transcriptional start site being resolved by primer extension analysis. Comparative analyses of genomes encoding phenylacetyl CoA, (PACoA), catabolic operons identified a common association among styrene degradation linked PACoA catabolons in <it>Pseudomonas </it>species studied to date.</p> <p>Conclusions</p> <p>In summary, this is the first study to report RpoN dependent transcriptional activation of the PACoA catabolon <it>paaL </it>gene, encoding a transport protein essential for phenylacetic acid utilisation in <it>P. putida </it>CA-3. Bioinformatic analysis is provided to suggest this regulatory link may be common among styrene degrading <it>Pseudomonads</it>.</p

Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models

Background: Many current gene prediction methods use only one model to represent proteincoding regions in a genome, and so are less likely to predict the location of genes that have an atypical sequence composition. It is likely that future improvements in gene finding will involve the development of methods that can adequately deal with intra-genomic compositional variation. Results: This work explores a new approach to gene-prediction, based on the Self-Organizing Map, which has the ability to automatically identify multiple gene models within a genome. The current implementation, named RescueNet, uses relative synonymous codon usage as the indicator of protein-coding potential. Conclusions: While its raw accuracy rate can be less than other methods, RescueNet consistently identifies some genes that other methods do not, and should therefore be of interest to geneprediction software developers and genome annotation teams alike. RescueNet is recommended for use in conjunction with, or as a complement to, other gene prediction methods