The nucleosome core particle is at the lowest level of DNA compaction, a mechanism that enables the DNA to fit inside the cell nucleus. Multiple nucleosomes, connected to each other like beads on a...Show moreThe nucleosome core particle is at the lowest level of DNA compaction, a mechanism that enables the DNA to fit inside the cell nucleus. Multiple nucleosomes, connected to each other like beads on a string, can stack tightly together to form the chromatin fiber. The compact form of this structure hinders external proteins and enzymes from accessing the nucleosomal DNA and using them in fundamental DNA processes. Nucleosome breathing is a process in which access is facilitated by the transient unwrapping of the nucleosome, thereby exposing the otherwise occluded DNA. This thesis investigates the nucleosome breathing mechanism in a dinucleosome system, a sub-structure of the chromatin fiber where two identical nucleosomes with varying DNA sequence are connected by a piece of linker DNA of varying length. The accessibility of the nucleosomal binding sites is modelled through a statistical model, expressing the breathing process in terms of the adsorption energy of the binding sites and the elasticity of the bent DNA in a dinucleosome configuration. The elastic energy of the bent linker DNA and nucleosomal DNA during the breathing process is estimated through a Monte-Carlo simulation. The results make clear that binding sites in such a dinucleosome structure are much more accessible than binding sites in a mononucleosome. Our findings show that the length of the linker DNA and the sequence of the nucleosomes are a determining factor of the dinucleosome configuration, thereby suggesting that these parameters play an important role in regulating the accessibility of higher order structures such as the chromatin fiber.Show less
This research focuses on improving the accessibility of archaeology in the Netherlands. The motives for this research are both to create more awareness and support for archaeology and to meet the...Show moreThis research focuses on improving the accessibility of archaeology in the Netherlands. The motives for this research are both to create more awareness and support for archaeology and to meet the needs of people that are interested in archaeology. This topic is addressed by analysing blogs and social networking sites. Additionally, it is examined whether these digital communication methods can help reach non-traditional audiences, particularly to engage the more difficult to reach target group of young adults. To be able to answer the research questions, questionnaires were set up for three target groups: bloggers, blog readers and young adults. A total number of 1.174 respondents have provided for many new insights regarding the use of blogs and social networking sites in archaeology, which messages need to be communicated and in which ways they can be communicated. Among other things, it has appeared that there are still some significant differences in the preferences of blog readers and the content that bloggers mainly blog about: most blog readers prefer to read about specific archaeological regions, excavations and sites, while most bloggers blog about personal opinions on archaeological matters. Blogs and social networking sites can contribute to making archaeology more accessible for a wider public and reaching out to young adults by incorporating and listening to the preferences, ideas, needs and wishes of the audiences they reach and of young adults themselves. Specifically regarding young adults, there are several approaches that can be applied in order to reach them. This requires depending less on the technology of blogs and social media and requires more of a focus on the content and message.Show less
