The study of bacterial-fungal interactions is essential to obtain a better understanding of terrestrial microbial ecology and may lie at the basis of novel applications in agriculture, food... Show moreThe study of bacterial-fungal interactions is essential to obtain a better understanding of terrestrial microbial ecology and may lie at the basis of novel applications in agriculture, food industry and human health. Nevertheless, the incentives, the genetic determinants and the mechanisms that underlie bacterial-fungal interactions are still poorly understood. Bacterial mycophagy is a trophic behaviour that takes place when bacteria obtain nutrients from living fungal hyphae, allowing the conversion of living fungal biomass into bacterial biomass (29). This trophic behavior was demonstrated for the first time for bacteria of the genus Collimonas, based on their ability to grow at the expenses of living fungal hyphae in a soil-like microcosm (28, 30). In this thesis I addressed the following research questions: (1) Which of the mechanisms putatively involved in Collimonas mycophagy are actually activated when Collimonas interact with a fungus (2) What is the fungal response to the presence of Collimonas bacteria? (3) What is the role played by plasmid pTer331, detected in the genome of the mycophagous bacterium C. fungivorans Ter331, in the ecology of this bacterium? Are the genes encoded on plasmid pTer331 involved in mycophagy? (4) Are the putative determinants of mycophagy uniformly distributed among Collimonas species? Show less
Total mesorectal excision (TME) is the standard treatment for rectal cancer, while transanal endoscopic microsurgery (TEM) is a recently introduced surgical approach for the treatment of rectal... Show moreTotal mesorectal excision (TME) is the standard treatment for rectal cancer, while transanal endoscopic microsurgery (TEM) is a recently introduced surgical approach for the treatment of rectal adenomas. Incorrect preoperative staging before TEM is a problem. Therefore the aim of this thesis was to identify molecular differences between rectal tumors of different stages, using gene expression profiling and genomic analysis. First protocols and data analysis algorithms for a new type of SNP array were developed. These studies showed that reliable LOH and copy number changes could be obtained from both frozen and paraffin embedded material. Consequently SNP arrays were used to type groups of TEM and TME treated samples. Five genomic events were found which could make a clear discrimination between adenomas and carcinomas. Early carcinomas treated by TEM, which were not recognized preoperatively as carcinomas, showed already carcinoma-associated aberrations. Analysis of tree core biopsies per patient showed a large degree of intra- tumor heterogeneity; although a good correlation was obtained between the biopsy with the largest number of aberrations and its corresponding tumor fraction. Gene expression array analysis was performed on the same samples as the SNP array series. A high concordance between chromosomal aberrations and changes in gene expression was observed. Finally a clinical application of these data is discussed in the preoperative staging of rectal tumours. Show less
