Polyphyly in widespread serovars and using genomic proximity to choose the best reference genome for bioinformatics analyses.

is the most common cause of gastroenteritis in the world. Over the past 5 years, whole-genome analysis has led to the high-resolution characterization of clinical and foodborne responsible for typhoid fever, foodborne illness or contamination of the agro-food chain. Whole-genome analyses are simplified by the availability of high-quality, complete genomes for mapping analysis and for calculating the pairwise distance between genomes, but unfortunately some difficulties may still remain.

Estimating selection on nonsynonymous mutations.

The distribution of mutational effects on fitness is of fundamental importance for many aspects of evolution. We develop two methods for characterizing the fitness effects of deleterious, nonsynonymous mutations, using polymorphism data from two related species. These methods also provide estimates of the proportion of amino acid substitutions that are selectively favorable, when combined with data on between-species sequence divergence.

The detection of shared and ancestral polymorphisms.

There is increasing evidence that closely related species contain many polymorphisms that were present in their common ancestral species. Use of a more distant relative as an outgroup increases the ability to detect such ancestral polymorphisms. We describe a method for further improving estimates of the fraction of polymorphisms that are ancestral, and illustrate this with reference to data on Drosophila pseudoobscura and D.

Time-temperature profiles of chilled ready-to-eat foods in school catering and probabilistic analysis of Listeria monocytogenes growth.

The purpose of this study was to evaluate the chill chain in school catering by monitoring time-temperature profiles. Chilled ready-to-eat foods have been chosen as subject of this study because of their high risk due to their production, storage and distribution steps, separated in time, followed by consumption without any further thermal treatment. In order to integrate the effects of storage duration and storage temperature, a quantitative criterion, namely "TTE" or "Time-Temperature Equivalent", was proposed.