Chromosome Kissing and Chromosome Folding in Eukaryotic and Bacterial Cells

Das bakterielle und eukaryotische Genom wird durch ein differenziertes Zusammenspiel von dreidimensionaler (3D) Kompaktifizierung und Zellfunkionalitaet, beispielsweise bezueglich Genexpression, organisiert. Das Ziel dieser Arbeit ist es, solche Struktur- und Funktionszusammenhaenge zu untersuchen. Ich habe vier Schluesselmerkmale identifiziert, die einen grossen Einfluss auf die Architektur von Biopolymeren haben: Polymertopologie, (raeumlicher) Einschluss, Semiflexibilitaet und Fixierung. In einem Projekt meiner Doktorarbeit habe ich gezeigt, dass die 3D-Organisation der Synaptonemalen Komplexe (SK) waehrend der Meiose stark durch das Wechselspiel von raeumlichem Einschluss und doppelter Fixierung der SK-Enden beeinflusst wird. In einer anderen Kollaboration konnte gezeigt werden, dass die raeumlich Anordnung und Dynamik von Hefe-Chromosomen im Rahmen eines Rabl Models, basierend auf Einschluss, Fixierung und der entsprechenden Packungsdichte, beschrieben werden kann. Ein grosser Teil der Dissertation traegt zu einem besseren Verstaendnis der raeumlichen E. coli Chromosomorganisation und -segregation bei. Wir konnten zeigen, dass Sternpolymere mit zirkulaeren Armen, deren struktureller Aufbau dem des E. coli Chromosomes entspricht, einen Uebergang von sphaerischen zu flachen, gestreckten Strukturen durchlaufen, welcher es erleichtern koennte, das bakterielle Genom in einer gestreckten Huelle unterzubringen. Wir konnten den Nachweis liefern, dass die Kopplung von Chromosomentopologie und Einschluss relevant ist, um den Hang des bakterielle Chromosomes zu ueberwinden, sich zu mischen. Wir schlagen einen Mechanismus zur Bildung von Domaenen im E. coli Chromosom vor und testen diesen: Der Prozess der Kolokalisation von Transkriptionsfaktoren und deren Zielgenen, der die durch das regulative Transkriptionsnetzwerk definierte Kontrolle imitiert, kann die experimentell beobachtete, praezise Positionierung der genetischen Segmente erklaeren. Der hier definierte Rahmen zur Chromosomenanordnung erlaubt es ausserdem, die Segregation von E. coli Chromosomenpaaren waehrend der Zellteilung im Kontext von Volumenausschlusswechselwirkung, spezifischen Chromosomentopologien und geometrischen Einschraenkungen zu verstehen. Im Schulterschluss mit einer weiteren Kollaboration wurde eine Methode entwickelt, die die raeumliche Chromosomenorganisation aufloesen kann, indem sie den Chromatinstrang als Worm-like Chain modelliert und ein Ensemble von Chromatinstrukturen generiert, die Strukturrestriktionen basierend auf Chromosome Conformation Capture- oder Mikroskopiedaten konsistent abbilden

Conformational Temperature-Dependent Behavior of a Histone H2AX: A Coarse-Grained Monte Carlo Approach Via Knowledge-Based Interaction Potentials

Histone proteins are not only important due to their vital role in cellular processes such as DNA compaction, replication and repair but also show intriguing structural properties that might be exploited for bioengineering purposes such as the development of nano-materials. Based on their biological and technological implications, it is interesting to investigate the structural properties of proteins as a function of temperature. In this work, we study the spatial response dynamics of the histone H2AX, consisting of 143 residues, by a coarse-grained bond fluctuating model for a broad range of normalized temperatures. A knowledge-based interaction matrix is used as input for the residue-residue Lennard-Jones potential. A knowledge-based interaction matrix is used as input for the residue-residue Lennard-Jones potential. We find a variety of equilibrium structures including global globular configurations at low normalized temperature (T* = 0.014), combination of segmental globules and elongated chains (T* = 0.016,0.017), predominantly elongated chains (T* = 0.019,0.020), as well as universal SAW conformations at high normalized temperature (T* ≥= 0.023). The radius of gyration of the protein exhibits a non-monotonic temperature dependence with a maximum at a characteristic temperature (T-c* = 0.019) where a crossover occurs from a positive (stretching at T*≤T*c) thermal response on increasing T*

The Impact of Entropy on the Spatial Organization of Synaptonemal Complexes within the Cell Nucleus

We employ 4Pi-microscopy to study SC organization in mouse spermatocyte nuclei allowing for the three-dimensional reconstruction of the SC's backbone arrangement. Additionally, we model the SCs in the cell nucleus by confined, self-avoiding polymers, whose chain ends are attached to the envelope of the confining cavity and diffuse along it. This work helps to elucidate the role of entropy in shaping pachytene SC organization. The framework provided by the complex interplay between SC polymer rigidity, tethering and confinement is able to qualitatively explain features of SC organization, such as mean squared end-to-end distances, mean squared center-of-mass distances, or SC density distributions. However, it fails in correctly assessing SC entanglement within the nucleus. In fact, our analysis of the 4Pi-microscopy images reveals a higher ordering of SCs within the nuclear volume than what is expected by our numerical model. This suggests that while effects of entropy impact SC organization, the dedicated action of proteins or actin cables is required to fine-tune the spatial ordering of SCs within the cell nucleus

A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation

What physical mechanism leads to organization of a highly condensed and confined circular chromosome? Computational modeling shows that confinement-induced organization is able to overcome the chromosome's propensity to mix by the formation of topological domains. The experimentally observed high precision of separate subcellular positioning of loci (located on different chromosomal domains) in Escherichia coli naturally emerges as a result of entropic demixing of such chromosomal loops. We propose one possible mechanism for organizing these domains: regulatory control defined by the underlying E. coli gene regulatory network requires the colocalization of transcription factor genes and target genes. Investigating this assumption, we find the DNA chain to self-organize into several topologically distinguishable domains where the interplay between the entropic repulsion of chromosomal loops and their compression due to the confining geometry induces an effective nucleoid filament-type of structure. Thus, we propose that the physical structure of the chromosome is a direct result of regulatory interactions. To reproduce the observed precise ordering of the chromosome, we estimate that the domain sizes are distributed between 10 and 700 kb, in agreement with the size of topological domains identified in the context of DNA supercoiling

Medium Chain Acylcarnitines Dominate the Metabolite Pattern in Humans under Moderate Intensity Exercise and Support Lipid Oxidation

Background: Exercise is an extreme physiological challenge for skeletal muscle energy metabolism and has notable health benefits. We aimed to identify and characterize metabolites, which are components of the regulatory network mediating the beneficial metabolic adaptation to exercise

Mutation Bias Favors Protein Folding Stability in the Evolution of Small Populations

Mutation bias in prokaryotes varies from extreme adenine and thymine (AT) in obligatory endosymbiotic or parasitic bacteria to extreme guanine and cytosine (GC), for instance in actinobacteria. GC mutation bias deeply influences the folding stability of proteins, making proteins on the average less hydrophobic and therefore less stable with respect to unfolding but also less susceptible to misfolding and aggregation. We study a model where proteins evolve subject to selection for folding stability under given mutation bias, population size, and neutrality. We find a non-neutral regime where, for any given population size, there is an optimal mutation bias that maximizes fitness. Interestingly, this optimal GC usage is small for small populations, large for intermediate populations and around 50% for large populations. This result is robust with respect to the definition of the fitness function and to the protein structures studied. Our model suggests that small populations evolving with small GC usage eventually accumulate a significant selective advantage over populations evolving without this bias. This provides a possible explanation to the observation that most species adopting obligatory intracellular lifestyles with a consequent reduction of effective population size shifted their mutation spectrum towards AT. The model also predicts that large GC usage is optimal for intermediate population size. To test these predictions we estimated the effective population sizes of bacterial species using the optimal codon usage coefficients computed by dos Reis et al. and the synonymous to non-synonymous substitution ratio computed by Daubin and Moran. We found that the population sizes estimated in these ways are significantly smaller for species with small and large GC usage compared to species with no bias, which supports our prediction

La partecipazione dei cittadini: un manuale. Metodi partecipativi: protagonisti, opportunit\ue0 e limiti.

Si affrontano i metodi partecipativi, le organizzazioni nel mondo che promuovono la diffusione di una nuova governance partecipativa, ne studiano e sperimentano i metodi. Si affrontano i limiti di tali approcci e le opportunit\ue0 soprattutto nel miglioramento del rapporto di fiducia tra cittadini e istituzioni