In this thesis, different speciation processes were studied that were involved in the origin of V. stagnina and its closest relatives. Phylogenetic analyses of the CHS intron showed that... Show moreIn this thesis, different speciation processes were studied that were involved in the origin of V. stagnina and its closest relatives. Phylogenetic analyses of the CHS intron showed that hybridization and polyploidisation played an important role during speciation and that Viola stagnina is one of the parental species of the alloploid species V. canina, V. lactea and V. pumila and the parental species of the autotetraploid V. elatior. The analyses also confirmed that the closest relatives of V. stagnina were the other arosulate violets V. canina, V. elatior, V. pumila and V. lactea. In an attempt to settle a debate among Dutch botanists about the taxonomic status of V. stagnina var. lacteoides, the morphological and genetic variation within V. stagnina were studied using AFLP, morphometrics analyses, a common garden experiment, and a crossing experiment. The genetic and morphological differences found support for the recognition of the infraspecific taxon V. stagnina var. lacteoides. The nomenclatural studies carried out resulted in a recommendation to formally reject the ambiguous name V. persicifolia for the European Fen Violet and use the name V. stagnina, instead. To bring the common name into line with the usage in Belgium, it is also recommended to change the Dutch common name from Melkviooltje into Vals melkviooltje. Show less
To date, 128 mycobacterial species have been characterised, ranging from non-pathogenic to pathogenic for humans. Molecular methods contributed significantly to the identification of the species,... Show moreTo date, 128 mycobacterial species have been characterised, ranging from non-pathogenic to pathogenic for humans. Molecular methods contributed significantly to the identification of the species, replacing conventional laborious methods. In this thesis, the design and application of a genus-specific real-time PCR, for the rapid detection of non-tuberculous mycobacteria in clinical materials, was described. The technique was extremely useful for the rapid detection of the slowgrowing Mycobacterium species. Addition of species-specific probes to the ITS assay, identified M. haemophilum to be present in previously undiagnosed skin inflammation and resulted in the recognition of M. haemophilum as the second most common mycobacterial species causing lymphadenitis. Subsequent Amplified Fragment Length Polymorphism analysis of M. haemophilum isolates showed this species to posses an extremely low mutation rate. Also, M. haemophilum lymphadenitis cases are suspected to have a common source, most likely piped water, in contrast to M. avium infections, which appear to originate from variable environmental sources as was underscribed by Restriction Fragment Length Polymorphism analysis. Contamination with saprophytic mycobacterial DNA is problematic for the current NTM detection in clinical materials. This and other bottlenecks in the molecular diagnostics of NTM were addressed in this thesis as well. Show less
In a surveillance study in Jakarta, Indonesia, 88 typhoid and 26 paratyphoid fever patients were identified by blood culture. Risk factors for transmission of typhoid fever were mainly intra... Show moreIn a surveillance study in Jakarta, Indonesia, 88 typhoid and 26 paratyphoid fever patients were identified by blood culture. Risk factors for transmission of typhoid fever were mainly intra-household factors (poor hand-washing hygiene, recent household contacts), whereas paratyphoid was mainly contracted through street food. In an additional study, street vendors observed poorer hand-washing and food-handling hygiene compared to food handlers in restaurants, and had higher bacterial loads in dishwater. Further host factor-studies in (para)typhoid patients revealed that polymorphisms in genes encoding pro-inflammatory cytokines (IFN-_, IL1A/B, IL1R1, TNFRSF1A, CASP1 and CRP) were not associated with susceptibility to typhoid fever, and might therefore at most be associated with severity of disease. An association was found of typhoid fever and a polymorphism in the PARK2/PACRG proteasome-mediated protein degradation pathway through ubiquitination, similar to infection with Mycobacterium leprae. Also an association between genotypes in the Cystic Fibrosis Transmembrane Conductance Regulator (the affected protein in Cystic Fibrosis) and susceptibility to typhoid fever was found, suggesting a decreased adherence potential of S. typhi to intestinal mucosal cells with these polymorphisms. Finally, bacterial characteristics were compared by use of AFLP and biochemical/antibiotic susceptibility profiles, showing very homogeneous S. typhi and S. paratyphi A strains circulating in the study area. Show less
