Spatial and temporal dynamics of the RNA silencing response

In this thesis we studied various aspects of siRNA mediated silencing. siRNA mediated silencing is initiated by the introduction of dsRNA, transgenes and viral infection. Our first goal was to study the ability of the core pathway of RNA silencing to explain transgene and dsRNA induced silencing. To that extend we developed and studied concise models of the RNA silencing pathway. Secondly, we investigated the efficacy of RNA silencing to reduce viral infections, and added a replicating RNA virus. While we initially studied antiviral silencing within the cell, we extended our study to tissue level dynamics and symptom development in plants. Finally, we added virus encoded silencing suppressors and studied the effect and capability of the different silencing suppressors. We found that the available knowledge about the RNA silencing pathway was not sufficient to explain transgene induced silencing. We proposed mechanisms that could result in transgene induced silencing and recently the existence of these mechanisms has been confirmed experimentally. Our detailed model of both intra- and inter-cellular dynamics gives an explanation for the observed patterns on plant leaves that occur during viral infection. These patterns can have the form of local spots, concentric circles, or resemble mosaic-like patterns. We have shown that models studies are indispensable to understand complex cellular pathways. On the one hand we have shown that the generally accepted pathway of RNA silencing was insufficient to explain the experimental findings on transgene induced silencing it was supposed to explain. On the other hand we have shown that the interaction of RNA silencing and viral growth is indeed able to generate infection patterns for which the link to RNA silencing was still tentative.