Discovery of stable and variable differences in the Mycobacterium avium subsp. paratuberculosis type I, II, and III genomes by pan-genome microarray analysis

Mycobacterium avium subsp. paratuberculosis is an important animal pathogen widely disseminated in the environment that has also been associated with Crohn's disease in humans. Three M. avium subsp. paratuberculosis genomotypes are recognized, but genomic differences have not been fully described. To further investigate these potential differences, a 60-mer oligonucleotide microarray (designated the MAPAC array), based on the combined genomes of M. avium subsp. paratuberculosis (strain K-10) and Mycobacterium avium subsp. hominissuis (strain 104), was designed and validated. By use of a test panel of defined M. avium subsp. paratuberculosis strains, the MAPAC array was able to identify a set of large sequence polymorphisms (LSPs) diagnostic for each of the three major M. avium subsp. paratuberculosis types. M. avium subsp. paratuberculosis type II strains contained a smaller genomic complement than M. avium subsp. paratuberculosis type I and M. avium subsp. paratuberculosis type III genomotypes, which included a set of genomic regions also found in M. avium subsp. hominissuis 104. Specific PCRs for genes within LSPs that differentiated M. avium subsp. paratuberculosis types were devised and shown to accurately screen a panel (n = 78) of M. avium subsp. paratuberculosis strains. Analysis of insertion/deletion region INDEL12 showed deletion events causing a reduction in the complement of mycobacterial cell entry genes in M. avium subsp. paratuberculosis type II strains and significantly altering the coding of a major immunologic protein (MPT64) associated with persistence and granuloma formation. Analysis of MAPAC data also identified signal variations in several genomic regions, termed variable genomic islands (vGIs), suggestive of transient duplication/deletion events. vGIs contained significantly low GC% and were immediately flanked by insertion sequences, integrases, or short inverted repeat sequences. Quantitative PCR demonstrated that variation in vGI signals could be associated with colony growth rate and morphology.

Thematic patterning in English and Spanish: contrastive annotation of a bilingual newspaper corpus for liguistic and computational applications

Thematization is recognized as a fundamental phenomenon in the construction of messages and texts by di erent linguistic schools. This location within a text privileges the elements that guide the reader in the orientation and interpretation of discourse at di erent levels. Thematizing a linguistic unit by locating it in the rst-initial position of a clause, paragraph, or text, confers upon it a special status: a signal of the organizational strategy which characterizes di erent text types playing a role as a variable in the distinction of registers, text types and genres. However, in spite of the importance of the study of thematization for message and textual structuring, to date there are no linguistic studies that have undertook the task of validating its aspects in a comparative manner, either for linguistic or computational purposes. This study, therefore, lls a research gap by implementing a methodology based on contrastive corpus annotation, which allows to empirically validate aspects of the phenomenon of Thematization in English and Spanish, it also seeks to develop a bilingual English-Spanish comparable corpus of newspaper texts automatically annotated with thematic features at clausal and discourse levels. The empirically validated categories (Thematic Field and its elements: Textual Theme, Interpersonal Theme, PreHead and Head) are used to annotate a larger corpus of three newspaper genres news reports, editorials and letters to the editor in terms of thematic choices. This characterization, reveals interesting results, such as the use of genre-speci c strategies in thematic position. In addition, the thesis investigates the possibility to automate the annotation of thematic features in the bilingual corpus through the development of a set of JAVA rules implemented in GATE. It also shows the e cacy of this method in comparison with the manual annotation results...