Mapping genes within a YAC by computer-assisted interpretation of partial restriction digestions.

Partial restriction digestion is used to map restriction sites and the location of genes within yeast artificial chromosomes (YACs). Locus-specific probes are hybridised to the partially digested YAC DNA and the fragments to which they hybridise are compared with the pattern of partial digestion products that include each map region. A least squares criterion is presented which allows for error in fragment length determination. This rapidly defines the most likely location of a marker within the restriction map and permits the combination of results from digestions with different restriction enzymes. Approximate confidence intervals may be assigned to gene locations, and tests of goodness-of-fit of the data may be performed. Since the number of erroneously matched fragments increases in proportion to the square of the number of sites, denser maps are not necessarily more informative. Simulations indicate that the optimal number of internal restriction sites given typical experimental error (1% of YAC length) is about five sites; the associated broad support interval (on average one third of YAC length) may be reduced by combining results from different enzyme digestions. Application of a computer implementation of this model to experimental data showed that the model fitted well, and estimates of location were found to be consistent with other evidence.

Incidence of Anoplocephala perfoliata in horses examined at an Irish abattoir.

The intestinal tracts of 363 horses were examined after slaughter at a horse abattoir. The presence or absence of Anoplocephala perfoliata and the sites of attachment were recorded. A total of 51 per cent of the horses had A perfoliata attached to the mucosa of the ileocaecal junction and/or to the caecal mucosa; 5 per cent of the horses had A perfoliata attached only to the mucosa of the ileocaecal junction, 24 per cent had A perfoliata attached only to the caecal mucosa and 22 per cent of the horses had A perfoliata attached at both sites. The degree of infestation did not appear to be influenced by the season or by the age, breed or source of origin of the horses. The lesions at the sites of attachment included congestion, oedema, ulceration, diphtheresis, mucosal thickening, eosinophil infiltration and fibroplasia. The severity of the lesions was exacerbated by increasing numbers of worms.

Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes.

Codon usage data has been compiled for 110 yeast genes. Cluster analysis on relative synonymous codon usage revealed two distinct groups of genes. One group corresponds to highly expressed genes, and has much more extreme synonymous codon preference. The pattern of codon usage observed is consistent with that expected if a need to match abundant tRNAs, and intermediacy of tRNA-mRNA interaction energies are important selective constraints. Thus codon usage in the highly expressed group shows a higher correlation with tRNA abundance, a greater degree of third base pyrimidine bias, and a lesser tendency to the A+T richness which is characteristic of the yeast genome. The cluster analysis can be used to predict the likely level of gene expression of any gene, and identifies the pattern of codon usage likely to yield optimal gene expression in yeast.