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As society paves its way towards device miniaturization and precision medicine, micro-scale actuation and guided transport become increasingly prominent research fields, with high potential impact in both technological and clinical contexts. In order to accomplish directed motion of micron-sized objects, as biosensors and drug-releasing microparticles, towards specific target sites, a promising strategy is the use of living cells as smart biochemically-powered carriers, building the so-called bio-hybrid systems. Inspired by leukocytes, native cells of living organisms efficiently migrating to critical targets as tumor tissue, an emerging concept is to exploit the amoeboid crawling motility of such cells as mean of transport for drug delivery applications.
In the research work described in this thesis, I synergistically applied experimental, computational and theoretical modeling approaches to investigate the behaviour and transport mechanism of a novel kind of bio-hybrid system for active transport at the micro-scale, referred to as cellular truck. This system consists of an amoeboid crawling cell, the carrier, attached to a microparticle, the cargo, which may ideally be drug-loaded for specific therapeutic treatments.
For the purposes of experimental investigation, I employed the amoeba Dictyostelium discoideum as crawling cellular carrier, being a renowned model organism for leukocyte migration and, in general, for eukaryotic cell motility. The performed experiments revealed a complex recurrent cell-cargo relative motion, together with an intermittent motility of the cellular truck as a whole. The evidence suggests the presence of cargoes on amoeboid cells to act as mechanical stimulus leading cell polarization, thus promoting cell motility and giving rise to the observed intermittent dynamics of the truck. Particularly, bursts in cytoskeletal polarity along the cell-cargo axis have been
found to occur in time with a rate dependent on cargo geometrical features, as particle diameter. Overall, the collected experimental evidence pointed out a pivotal role of cell-cargo interactions in the emergent cellular truck motion dynamics. Especially, they can determine the transport capabilities of amoeboid cells, as the cargo size significantly impacts the cytoskeletal activity and repolarization dynamics along the cell-cargo axis, the latter responsible for truck displacement and reorientation.
Furthermore, I developed a modeling framework, built upon the experimental evidence on cellular truck behaviour, that connects the relative dynamics and interactions arising at the truck scale with the actual particle transport dynamics. In fact, numerical simulations of the proposed model successfully reproduced the phenomenology of the cell-cargo system, while enabling the prediction of the transport properties of cellular trucks over larger spatial and temporal scales. The theoretical analysis provided a deeper understanding of the role of cell-cargo interaction on mass transport, unveiling in particular how the long-time transport efficiency is governed by the interplay between the persistence time of cell polarity and time scales of the relative dynamics stemming from cell-cargo interaction. Interestingly, the model predicts the existence of an optimal cargo size, enhancing the diffusivity of cellular trucks; this is in line with previous independent experimental data, which appeared rather counterintuitive and had no explanation prior to this study.
In conclusion, my research work shed light on the importance of cargo-carrier interactions in the context of crawling cell-mediated particle transport, and provides a prototypical, multifaceted framework for the analysis and modelling of such complex bio-hybrid systems and their perspective optimization.
The interaction between surfaces displaying end-grafted hydrophilic polymer brushes plays important roles in biology and in many wet-technological applications. The outer surfaces of Gram-negative bacteria, for example, are composed of lipopolysaccharide (LPS) molecules exposing oligo- and polysaccharides to the aqueous environment. This unique, structurally complex biological interface is of great scientific interest as it mediates the interaction of bacteria with neighboring bacteria in colonies and biofilms. The interaction between polymer-decorated surfaces is generally coupled to the distance-dependent conformation of the polymer chains. Therefore, structural insight into the interacting surfaces is a prerequisite to understand the interaction characteristics as well as the underlying physical mechanisms. This problem has been addressed by theory, but accurate experimental data on polymer conformations under confinement are rare, because obtaining perturbation-free structural insight into buried soft interfaces is inherently difficult.
In this thesis, lipid membrane surfaces decorated with hydrophilic polymers of technological and biological relevance are investigated under controlled interaction conditions, i.e., at defined surface separations. For this purpose, dedicated sample architectures and experimental tools are developed. Via ellipsometry and neutron reflectometry pressure-distance curves and distance-dependent polymer conformations in terms of brush compression and reciprocative interpenetration are determined. Additional element-specific structural insight into the end-point distribution of interacting brushes is obtained by standing-wave x-ray fluorescence (SWXF).
The methodology is first established for poly[ethylene glycol] (PEG) brushes of defined length and grafting density. For this system, neutron reflectometry revealed pronounced brush interpenetration, which is not captured in common brush theories and therefore motivates rigorous simulation-based treatments. In the second step the same approach is applied to realistic mimics of the outer surfaces of Gram-negative bacteria: monolayers of wild type LPSs extracted from E. Coli O55:B5 displaying strain-specific O-side chains. The neutron reflectometry experiments yield unprecedented structural insight into bacterial interactions, which are of great relevance for the properties of biofilms.
Bacteria respond to changing environmental conditions by switching the global pattern of expressed genes. In response to specific environmental stresses the cell activates several stress-specific molecules such as sigma factors. They reversibly bind the RNA polymerase to form the so-called holoenzyme and direct it towards the appropriate stress response genes. In exponentially growing E. coli cells, the majority of the transcriptional activity is carried out by the housekeeping sigma factor, while stress responses are often under the control of alternative sigma factors. Different sigma factors compete for binding to a limited pool of RNA polymerase (RNAP) core enzymes, providing a mechanism for cross talk between genes or gene classes via the sharing of expression machinery. To quantitatively analyze the contribution of sigma factor competition to global changes in gene expression, we develop a thermodynamic model that describes binding between sigma factors and core RNAP at equilibrium, transcription, non-specific binding to DNA and the modulation of the availability of the molecular components.
Association of housekeeping sigma factor to RNAP is generally favored by its abundance and higher binding affinity to the core. In order to promote transcription by alternative sigma subunits, the bacterial cell modulates the transcriptional efficiency in a reversible manner through several strategies such as anti-sigma factors, 6S RNA and generally any kind of transcriptional regulators (e.g. activators or inhibitors). By shifting the outcome of sigma factor competition for the core, these modulators bias the transcriptional program of the cell. The model is validated by comparison with in vitro competition experiments, with which excellent agreement is found. We observe that transcription is affected via the modulation of the concentrations of the different types of holoenzymes, so saturated promoters are only weakly affected by sigma factor competition. However, in case of overlapping promoters or promoters recognized by two types of sigma factors, we find that even saturated promoters are strongly affected.
Active transcription effectively lowers the affinity between the sigma factor driving it and the core RNAP, resulting in complex cross talk effects and raising the question of how their in vitro measure is relevant in the cell. We also estimate that sigma factor competition is not strongly affected by non-specific binding of core RNAPs, sigma factors, and holoenzymes to DNA. Finally, we analyze the role of increased core RNAP availability upon the shut-down of ribosomal RNA transcription during stringent response. We find that passive up-regulation of alternative sigma-dependent transcription is not only possible, but also displays hypersensitivity based on the sigma factor competition. Our theoretical analysis thus provides support for a significant role of passive control during that global switch of the gene expression program and gives new insights into RNAP partitioning in the cell.
Adhesion of biological cells to their environment is mediated by two-dimensional clusters of specific adhesion molecules which are assembled in the plasma membrane of the cells. Due to the activity of the cells or external influences, these adhesion sites are usually subject to physical forces. In recent years, the influence of such forces on the stability of cellular adhesion clusters was increasingly investigated. In particular, experimental methods that were originally designed for the investigation of single bond rupture under force have been applied to investigate the rupture of adhesion clusters. The transition from single to multiple bonds, however, is not trivial and requires theoretical modelling. Rupture of biological adhesion molecules is a thermally activated, stochastic process. In this work, a stochastic model for the rupture and rebinding dynamics of clusters of parallel adhesion molecules under force is presented. In particular, the influence of (i) a constant force as it may be assumed for cellular adhesion clusters is investigated and (ii) the influence of a linearly increasing force as commonly used in experiments is considered. Special attention is paid to the force-mediated cooperativity of parallel adhesion bonds. Finally, the influence of a finite distance between receptors and ligands on the binding dynamics is investigated. Thereby, the distance can be bridged by polymeric linker molecules which tether the ligands to a substrate.
Die Fusion von Membranen ist ein entscheidender Prozeß bei der Entwicklung von Zellen im Körper. Beispielsweise ist sie eine der Voraussetzungen bei der Befruchtung einer Eizelle durch ein Spermium oder für das Eindringen von Viren in eine Zelle. Membranfusion ist auch notwendig für den Stofftransport in die Zelle hinein oder aus ihr heraus. Die Membranfusion ist daher auch von praktischen Interesse auf den Gebieten der Pharmazeutik und des 'Bioengineering'. Oft muss eine Membran mit der infiziertin Zelle fusionieren, um ein Medikament an sein Zeil zu bringen. Deshalb ist ein Verständnis der Membranfusion von großem Interesse für die Entwicklung von gezielten und effizienten Methoden des 'drug delivery'. Dasselbe gilt für die gezielte Zufuhr von Genen bei der Gentherapie. Obwohl die Membranfusion schon vor nahezu 200 Jahren von dem deutschen Biologen und Mediziner Johannes Müller beobachtet wurde, liegt ein vollständiges Verständnis des Fusionsprozesses von Zellen und (Modell-) Membranen auch heute noch in weiter Ferne. Allerdings hat im letzten Jahrzehnt das Interesse für dieses Forschungsgebiet stark zugenommen. Wissenschaftler der unterschiedlichsten Disziplinen arbeiten daran, die Mechanismen der Membranfusion aufzudecken. Biologen untersuchen Proteine, die die Fusion auslösen, Chemiker entwickeln Moleküle, die die Fusion erleichtern, und Physiker versuchen die Antriebsmechanismen der Membranfusion zu verstehen. Neue Mikroskopietechniken und die hohe Rechenleistung moderner Computer helfen die molekulare und die makroskopische Welt der Membranfusion in einem Bild zusammenzufügen. Für unsere Untersuchungen haben wir Modellmembranen, die aus Lipiddoppelschichten bestehen, benutzt. Diese Membranen formen sogenannte Vesikel oder Liposomen, abgeschlossene Membrane, in denen eine bestimmte Menge an Flüssigkeit enthalten ist. Indem wir Rezeptoren in die Membran einbringen, schaffen wir funkionalisierte Vesikel, die sich differenzieren, kooperieren und selektiv reagieren können. Wir benutzen positiv geladene wasserlösliche Ionen, um Wechselwirkungen zwischen den Vesikeln zu vermitteln, und lassen die Rezeptoren und die Ionen den Fusionsprozess auslösen. Die Wechselwirkungen werden unter dem Mikroskop durch spezielle Mikromechanischn Gerätz Mikromechinerien kontrolliert. Mit Hilfe einer sehr schnellen digitale Bildaufnahmetechnik ist es uns gelungen, die Fusion unserer Modellmembranen aufzunehmen und in Echtzeit zu dokumentieren mit einer Auflösung von 50 µs. Unsere Messungen können vergleichen werden mit Computersimulationen des Fusionsprozesses. Diese Simulationen untersuchen Prozesse, die zwischen 0.1 und 1 Mikrosekunde dauern. Eine Herausforderung für die Zukunft wird es sein, die Lücke zwischen den in Experimenten (50µs) und den in Simulationen zugänglichen Zeitskalen von beiden Seiten her zu schließen.