Agrobacterium tumefaciens is a phytopathogen which is known to be the causal agent of crown gall disease in dicotyledonous plants. Virulent Agrobacterium strains are always carrier of a tumor... Show moreAgrobacterium tumefaciens is a phytopathogen which is known to be the causal agent of crown gall disease in dicotyledonous plants. Virulent Agrobacterium strains are always carrier of a tumor-inducing (Ti) plasmid. As a result of the expression of Vir proteins, a section of this plasmid termed the T-DNA is transferred via a type four secretion system (T4SS) as a T-strand to the recipient cell where it can integrate into the genomic DNA of the recipient cell. In this thesis the prerequisites of T-DNA circle formation using yeast as a model were assayed. It was found that the homologous repair (HR) protein Rad52 is of importance to the formation of T-DNA circles. In addition to this, the effects of double strand break (DSB) induction on the efficiency of T-DNA integration via the HR pathway in yeast and the role the nucleosome occupancy of the target locus has on DSB induction were assayed. It was found that a decrease in the nucleosome occupancy of a target locus had no measurable impact on the efficiency of T-DNA integration at this locus. However, the combined translocation of nuclease proteins aimed at the target locus and T-strands during AMT greatly facilitated HR-mediated integration of T-DNA. Show less
This thesis, titled __Genetic and pharmacogenetic determinants of cardiovascular disease__ is divided in three sections. In section one the genetic determinants of coronary restenosis are explored.... Show moreThis thesis, titled __Genetic and pharmacogenetic determinants of cardiovascular disease__ is divided in three sections. In section one the genetic determinants of coronary restenosis are explored. In the first genome-wide association study on this condition, in the GENetic DEterminants of Restenosis study, we describe a novel locus on chromosome 12 possibly associated with restenosis. Furthermore, by using several analysis tools on this data, we describe multiple biological pathways and genes that are likely associated with restenosis. In section two, we focus on genetic factors involved in three other (cardio)vascular diseases. We explore the role of DNA repair genes in myocardial infarction and stroke and the genetic determinants of dialysis shunt failure. Section three is on pharmacogenetics. In particular, we were interested in genetic variation involved in aspirin and clopidogrel resistance. We validated two genetic polymorphisms associated with recurrent thrombotic events during treatment with these agents in patients with an acute myocardial infarction. Genetic research is a fast developing field of research. By increasing our knowledge on the molecular background of diseases, genetics potentially could lead to more personalized treatment in the near future. Show less
To protect the genome, cells have evolved a diverse set of pathways designed to sense, signal, and repair multiple types of DNA damage. To assess the degree of coordination and crosstalk among... Show moreTo protect the genome, cells have evolved a diverse set of pathways designed to sense, signal, and repair multiple types of DNA damage. To assess the degree of coordination and crosstalk among these pathways, we systematically mapped changes in the cell's genetic network across a panel of different DNA-damaging agents, resulting in ~1,800,000 differential measurements. Each agent was associated with a distinct interaction pattern, which, unlike single-mutant phenotypes or gene expression data, has high statistical power to pinpoint the specific repair mechanisms at work. The agent-specific networks revealed roles for the histone acetyltranferase Rtt109 in the mutagenic bypass of DNA lesions and the neddylation machinery in cell-cycle regulation and genome stability, while the network induced by multiple agents implicates Irc21, an uncharacterized protein, in checkpoint control and DNA repair. Our multiconditional genetic interaction map provides a unique resource that identifies agent-specific and general DNA damage response pathways. Show less
