A theoretical investigation of protein recruitment during the DNA damage response and of the dynamics of DNA replication

In this thesis, three interrelated theoretical investigations on the cell-biological topics of DNA double strand break response and DNA replication are presented. The first investigation is concerned with the recruitment of DNA double strand break response proteins to DNA damage sites. In the second, necessary conditions for the appearance of multiple steady states and oscillations in generic protein complex assembly networks are identified. Lastly in the third investigation, the mechanisms underlying the genome-scale organization of DNA replication are analyzed. It is known from experiment that the recruitment of the pathway-independent double strand break response protein NBS1 qualitatively changes its dynamics beyond a certain damage density, from damage density dependent to damage density independent. A minimal computer model of the recruitment of NBS1 (contained in the MRN complex) and several interacting proteins is developed and compared to experimental data. It becomes evident from the model that the change in dynamics can be interpreted a consequence of the shifting importance of two different MRN binding interactions. At low damage densities, binding in the wider damage site vicinity dominates, while at higher damage densities, binding directly to the damaged double strand ends becomes more important. Next, generic protein recruitment/protein complex assembly networks are investigated to find the prerequisites of complex dynamical effects such as multistability and oscillation. It is shown that if the networks are limited to association and dissociation reactions and if the protein numbers are conserved for the indivisible “elementary” proteins participating, then at least four such elementary protein species must be present for multistability or oscillations to appear. A rigorous mathematical proof is given that networks with only three elementary species cannot have multiple steady states. DNA replication in mammals and humans is qualitatively different from the well-understood replication process in simpler eukaryotes such as yeast. Reliable patterns exist in the organization of replication on the scale of chromosomes and chromosome segments, while the microscopic dynamics are known to be stochastic. A stochastic computer model is presented that incorporates the minimal set of model ingredients necessary to reproduce these dynamical properties. The ingredients are a fast-diffusing limiting factor, induced firing of origins depending on proximity to replication forks, a constant replication fork speed that is reduced during early S-phase and the initiation of replication in euchromatic DNA. Results are consistent with experimental data and the literature, making the model presented here one of the best-benchmarked replication models in existence. A combination of model results with a three-dimensional DNA conformation obtained from a Monte Carlo model shows that chromatin packing is a main cause of the microscopy patterns observed during mammalian DNA replication. The theoretical investigations presented in this thesis combine methods of physics and applied mathematics with problems from the field of cell-biology. Thus, due to this inherently interdisciplinary character, this thesis is of interest to a readership of both, physicists and biologists

Senescence

The book "Senescence" is aimed to describe all the phenomena related to aging and senescence of all forms of life on Earth, i.e. plants, animals and the human beings. The book contains 36 carefully reviewed chapters written by different authors, aiming to describe the aging and senescent changes of living creatures, i.e. plants and animals

Stochastical analysis of finite point sampling of 3D chromatin fiber in interphase cell nuclei

Investigation of 3D chromatin structure in interphase cell nuclei is important for the understanding of genome function. For a reconstruction of the 3D architecture of the human genome, systematic fluorescent in situ hybridization in combination with 3D confocal laser scanning microscopy is applied. The position of two or three genomic loci plus the overall nuclear shape were simultaneously recorded, resulting in statistical series of pair and triple loci combinations probed along the human chromosome 1 q-arm. For interpretation of statistical distributions of geometrical features (e.g. distances, angles, etc.) resulting from finite point sampling experiments, a Monte-Carlo-based approach to numerical computation of geometrical probability density functions (PDFs) for arbitrarily-shaped confined spatial domains is developed. Simulated PDFs are used as bench marks for evaluation of experimental PDFs and quantitative analysis of dimension and shape of probed 3D chromatin regions. Preliminary results of our numerical simulations show that the proposed numerical model is capable to reproduce experimental observations, and support the assumption of confined random folding of 3D chromatin fiber in interphase cell nuclei