Colour in English: from metonymy to metaphor

Colour words abound with figurative meanings, expressing much more than visual signals. Some of these figurative properties are well known; in English, for example, black is associated with EVIL and blue with DEPRESSION. Colours themselves are also described in metaphorical terms using lexis from other domains of experience, such as when we talk of deep blue, drawing on the domain of spatial position. Both metaphor and colour are of central concern to semantic theory; moreover, colour is recognised as a highly productive metaphoric field. Despite this, comparatively few works have dealt with these topics in unison, and even those few have tended to focus on Basic Colour Terms (BCTs) rather than including non-BCTs. This thesis addresses the need for an integrated study of both BCTs and non-BCTs, and provides an overview of metaphor and metonymy within the semantic area of colour. Conducted as part of the Mapping Metaphor project, this research uses the unique data source of the Historical Thesaurus of English (HT) to identify areas of meaning that share vocabulary with colour and thus point to figurative uses. The lexicographic evidence is then compared to current language use, found in the British National Corpus (BNC) and the Corpus of Contemporary American (COCA), to test for currency and further developments or changes in meaning. First, terms for saturation, tone and brightness are discussed. This lexis often functions as hue modifiers and is found to transfer into COLOUR from areas such as LIFE, EMOTION, TRUTH and MORALITY. The evidence for cross-modal links between COLOUR with SOUND, TOUCH and DIMENSION is then presented. Each BCT is discussed in turn, along with a selection of non-BCTs, where it is revealed how frequently hue terms engage in figurative meanings. This includes the secondary BCTs, with the only exception being orange, and a number of non-BCTs. All of the evidence discussed confirms that figurative uses of colour originate through a process of metonymy, although these are often extended into metaphor.

Towards in silico IBV vaccine design: defining the role of polymorphism in viral attenuation

The gammacoronavirus, Infectious Bronchitis Virus (IBV), is a respiratory pathogen of chickens. IBV is a constant threat to poultry production as established vaccines are often ineffective against emerging strains. This requires constant and rapid vaccine production by a process of viral attenuation by egg passage, but the essential forces leading to attenuation in the virus have not yet been characterised. Knowledge of these factors will lead to the development of more effective, rationally attenuated, live vaccines and reduction of the mortality and morbidity caused by this pathogen. M41 CK strain was egg passaged four times many years ago at Houghton Poultry Research Station and stored as M41-CK EP4 (stock virus at The Pirbright Institute since 1992). It was the first egg passage to have its genome pyrosequenced and was therefore used as the baseline reference. The overall aim of this project was to analyse deep sequence data obtained from four IBV isolates (called A, A1, C and D) each originating from the common M41-CK EP4 (ep4) and independently passaged multiple times in embryonated chicken eggs (figure 1.1). Highly polymorphic encoding regions of the IBV genome were then identified which are likely involved in the attenuation process through the formation of independent SNPs and/or SNP clusters. This was then used to direct targeted investigation of SNPs during the attenuation process of the four IBV passages. A previously generated deep sequence dataset was used as a preliminary map of attenuation for one virulent strain of IBV. This investigation showed the nucleocapsid and spike as two highly polymorphic encoding regions within the IBV genome with the highest proportion of SNPs compared to encoding region size. This analysis then led to more focussed studies of the nucleocapsid and spike encoding region with the ultimate aim of mapping key attenuating regions and nucleotide positions. The 454 pyrosequencing data and further investigation of nucleocapsid and spike encoding regions have identified the SNPs present at the same nucleotide positions within analysed A, A1, C and D isolates. These SNPs probably play a crucial role in viral attenuation and universal vaccine production but it is not clear if independent SNPs are also involved in loss of virulence. The majority of SNPs accumulated at different nucleotide positions without further continuation in Sanger sequenced egg passages presenting S2 subunit (spike) and nucleocapsid as polymorphic encoding regions which in nature remain highly conserved.