Topological interactions between ring polymers: Implications for chromatin loops

Chromatin looping is a major epigenetic regulatory mechanism in higher eukaryotes. Besides its role in transcriptional regulation, chromatin loops have been proposed to play a pivotal role in the segregation of entire chromosomes. The detailed topological and entropic forces between loops still remain elusive. Here, we quantitatively determine the potential of mean force between the centers of mass of two ring polymers, i.e. loops. We find that the transition from a linear to a ring polymer induces a strong increase in the entropic repulsion between these two polymers. On top, topological interactions such as the non-catenation constraint further reduce the number of accessible conformations of close-by ring polymers by about 50%, resulting in an additional effective repulsion. Furthermore, the transition from linear to ring polymers displays changes in the conformational and structural properties of the system. In fact, ring polymers adopt a markedly more ordered and aligned state than linear ones. The forces and accompanying changes in shape and alignment between ring polymers suggest an important regulatory function of such a topology in biopolymers. We conjecture that dynamic loop formation in chromatin might act as a versatile control mechanism regulating and maintaining different local states of compaction and order.Comment: 12 pages, 11 figures. The article has been accepted by The Journal Of Chemical Physics. After it is published, it will be found at http://jcp.aip.or

Modelling of Interphase Chromosomes : From Genome Function to Spatial Organization

Genome function in higher eukaryotes involves major changes in the spatial organization of the chromatin fiber. Nevertheless, our understanding of chromatin folding is remarkably limited. Experimental results suggest that chromatin loops not only impact transcriptional regulation but also act as a major epigenetic mechanism, playing a pivotal role in the observed compartmentalization of chromosomes. However, a unified description of chromatin folding comprising various experimental results is still lacking. After showing that the theory of compact polymers is inconsistent with experimental data, we develop a new model for chromatin based on probabilistic formation of loops. This Random-Loop-Model correctly describes folding into a confined sub-space of the nucleus as well as the observed cell-to-cell variation, suggesting a close relation between expression-dependent compaction and local variations in the looping probabilities. We find that formation of loops is highly beneficial for the nucleus to maintain order and to accomplish entropy-driven segregation of chromosomes. A dynamic model is proposed, showing that the formation of loops can be accomplished solely on the basis of diffusional motion without invoking active mechanisms. Such a dynamic model provides a unified explanatory framework of chromatin folding, yielding testable predictions, which for the first time consistently explain many experimental findings

Conformational properties of compact polymers

Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact conformations on a cubic LxLxL lattice with different occupancy fractions by modifying a recently proposed algorithm. The system sizes studied extend up to N=256000 monomers, going well beyond the limits of older publications on compact polymers. We analyze several conformational properties of these polymers, including segment correlations and screening of excluded volume. Most importantly we propose a scaling law for the end-to-end distance distribution and analyze the moments of this distribution. It shows universality with respect to different occupancy fractions, i.e. system densities. We further analyze the distance distribution between intrachain segments, which turns out to be of great importance for biological experiments. We apply these new findings to the problem of chromatin folding inside interphase nuclei and show that -- although chromatin is in a compacted state -- the classical theory of compact polymers does not explain recent experimental results

Influence of surface albedo inhomogeneities on remote sensing of optical thin cirrus cloud mikrophysics

Cirrus clouds play an important role in atmospheric chemistry and climate, but they are complicated to handle mostly due to the complex non-spherical shape of the particles and their spatial inhomogeneity which causes major problems in remote sensing of cirrus from satellite platforms. Therefore spectral measurements of solar radiation are applied on the new research aircraft for atmospheric research and earth observation of the german science community HALO (High Altitude and LOng range research aircraft)

Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization

Chromatin folding inside the interphase nucleus of eukaryotic cells is done on multiple scales of length and time. Despite recent progress in understanding the folding motifs of chromatin, the higher-order structure still remains elusive. Various experimental studies reveal a tight connection between genome folding and function. Chromosomes fold into a confined subspace of the nucleus and form distinct territories. Chromatin looping seems to play a dominant role both in transcriptional regulation as well as in chromatin organization and has been assumed to be mediated by long-range interactions in many polymer models. However, it remains a crucial question which mechanisms are necessary to make two chromatin regions become co-located, i.e. have them in spatial proximity. We demonstrate that the formation of loops can be accomplished solely on the basis of diffusional motion. The probabilistic nature of temporary contacts mimics the effects of proteins, e.g. transcription factors, in the solvent. We establish testable quantitative predictions by deriving scale-independent measures for comparison to experimental data. In this Dynamic Loop (DL) model, the co-localization probability of distant elements is strongly increased compared to linear non-looping chains. The model correctly describes folding into a confined space as well as the experimentally observed cell-to-cell variation. Most importantly, at biological densities, model chromosomes occupy distinct territories showing less inter-chromosomal contacts than linear chains. Thus, dynamic diffusion-based looping, i.e. gene co-localization, provides a consistent framework for chromatin organization in eukaryotic interphase nuclei

Tree mortality submodels drive simulated long-term forest dynamics: assessing 15 models from the stand to global scale

Models are pivotal for assessing future forest dynamics under the impacts of changing climate and management practices, incorporating representations of tree growth, mortality, and regeneration. Quantitative studies on the importance of mortality submodels are scarce. We evaluated 15 dynamic vegetation models (DVMs) regarding their sensitivity to different formulations of tree mortality under different degrees of climate change. The set of models comprised eight DVMs at the stand scale, three at the landscape scale, and four typically applied at the continental to global scale. Some incorporate empirically derived mortality models, and others are based on experimental data, whereas still others are based on theoretical reasoning. Each DVM was run with at least two alternative mortality submodels. Model behavior was evaluated against empirical time series data, and then, the models were subjected to different scenarios of climate change. Most DVMs matched empirical data quite well, irrespective of the mortality submodel that was used. However, mortality submodels that performed in a very similar manner against past data often led to sharply different trajectories of forest dynamics under future climate change. Most DVMs featured high sensitivity to the mortality submodel, with deviations of basal area and stem numbers on the order of 10–40% per century under current climate and 20–170% under climate change. The sensitivity of a given DVM to scenarios of climate change, however, was typically lower by a factor of two to three. We conclude that (1) mortality is one of the most uncertain processes when it comes to assessing forest response to climate change, and (2) more data and a better process understanding of tree mortality are needed to improve the robustness of simulated future forest dynamics. Our study highlights that comparing several alternative mortality formulations in DVMs provides valuable insights into the effects of process uncertainties on simulated future forest dynamics

Konzeption einer Produkterfolgsrechnung für Planung und Kontrolle

Konzeption einer Produkterfolgsrechnung für Planung und Kontrolle. - Frankfurt am Main u.a. : Lang, 1982. - IX, 286 S. - Zugl.: Augsburg, Univ., Diss. - (Beiträge zum Rechnungs-, Finanz- und Revisionswesen ; 7