By implementing the rolled-up microfabrication method based on strain engineering, several systems are investigated within the contents of this thesis. The structural morphing of planar geometries into three-dimensional structures opens up many doors for the creation of unique material configurations and devices. An exploration into several novel microsystems, encompassing various scientific subjects, is made and methods for on-chip integration of these devices are presented. The roll-up of a metal and oxide allows for a cylindrical hollow-core structure with a cladding layer composed of a multilayer stack, plasmonic metamaterial. This structure can be used as a platform for a number of optical metamaterial devices. By guiding light radially through this structure, a theoretical investigation into the system makeup of a rolled-up hyperlens, is given. Using the same design, but rather propagating light parallel to the cylinder, a novel device known as a metamaterial optical fiber is defined. This fiber allows light to be guided classically and plasmonically within a single device. These fibers are developed experimentally and are integrated into preexisting on-chip structures and characterized. A system known as lab-in-a-tube is introduced. The idea of lab-in-a-tube combines various rolled-up components into a single all-encompassing biosensor that can be used to detect and monitor single bio-organisms. The first device specifically tailored to this system is developed, flexible split-wall microtube resonator sensors. A method for the capturing of embryonic mouse cells into on-chip optical resonators is introduced. The sensor can optically detect, via photoluminescence, living cells confined within the resonator through the compression and expansion of a nanogap built within its walls. The rolled-up fabrication method is not limited to the well-investigated systems based on the roll-up from semiconductor material or from a photoresist layer. A new approach, relying on the delamination of polymers, is presented. This offers never-before-realized microscale structures and configurations. This includes novel magnetic configurations and flexible fluidic sensors which can be designed for on-chip and roving detector applications.

During mitosis, adherent animal cells undergo a drastic shape change, from essentially flat to round, in a process known as mitotic cell rounding (MCR). The aim of this thesis was to critically examine the physical and biological basis of MCR. The experimental part of this thesis employed a combined optical microscope-atomic force microscope (AFM) setup in conjunction with flat tipless cantilevers to analyze cell mechanics, shape and volume. To this end, two AFM assays were developed: the constant force assay (CFA), which applies constant force to cells and measures the resultant height, and the constant height assay (CHA), which confines cell height and measures the resultant force. These assays were deployed to analyze the shape and mechanical properties of single cells trans-mitosis. The CFA results showed that cells progressing through mitosis could increase their height against forces as high as 50 nN, and that higher forces can delay mitosis in HeLa cells. The CHA results showed that mitotic cells confined to ~50% of their normal height can generate forces around 50-100 nN without disturbing mitotic progression. Such forces represent intracellular pressures of at least 200 Pascals and cell surface tensions of around 10 nN/µm. Using the CHA to compare mitotic cell rounding with induced cell rounding, it was observed that the intracellular pressure of mitotic cells is at least 3-fold higher than rounded interphase cells. To investigate the molecular basis of the mechanical changes inherent in mitotic cell rounding, inhibitors and toxins were used to pharmacologically dissect the role of candidate cellular processes. These results implicated the actomyosin cortex and osmolyte transporters, the most prominent of which is the Na+/H+ exchanger, in the maintenance of mechanical properties and intracellular hydrostatic pressure. Observations on blebbing cells under the cantilever supported the idea that the actomyosin cortex is required to sustain hydrostatic pressure and direct this pressure into cell shape changes. To gain further insight into the relationship between actomyosin activity and intracellular pressure, dynamic perturbation experiments were conducted. To this end, the CHA was used to evaluate the pressure and volume of mitotic cells before, during and after dynamic perturbations that included tonic shocks, influx of specific inhibitors, and exposure to pore-forming toxins. When osmotic pressure gradients were depleted, pressure and volume decreased. When the actomyosin cytoskeleton was abolished, cell volume increased while rounding pressure decreased. Conversely, stimulation of actomyosin cortex contraction triggered an increase in rounding pressure and a decrease in volume. Taken together, the dynamic perturbation results demonstrated that the actomyosin cortex contracts against an opposing intracellular pressure and that this relationship sets the surface tension, pressure and volume of the cell. The discussion section of this thesis provides a comprehensive overview of the physical basis of MCR by amalgamating the experimental results of this thesis with the literature. Additionally, the biochemal signaling pathways and proteins that drive MCR are collated and discussed. An exhaustive and unprecedented synthesis of the literature on cell rounding (approx. 750 papers as pubmed search hits on “cell rounding”, April 2012) reveals that the spread-to-round transition can be thought of in terms of a surface tension versus adhesion paradigm, and that cell rounding can be physically classified into four main modes, of which one is an MCR-like category characterized by increased actomyosin cortex tension and diminution of focal adhesions. The biochemical pathways and signaling patterns that correspond with these four rounding modes are catalogued and expounded upon in the context of the relevant physiology. This analysis reveals cell rounding as a pertinent topic that can be leveraged to yield insight into core principles of cell biophysics and tissue organization. It furthermore highlights MCR as a model problem to understand the adhesion versus cell surface tension paradigm in cells and its fundamentality to cell shape, mechanics and physiology.

Calcium (Ca2+) ist ein in eukaryotischen Zellen allgegenwärtiger sekundärer Botenstoff. Durch Inositoltrisphosphat (IP3) ausgelöste Ca2+-Signale von IP3-Rezeptoren (IP3Rs) sind eines der universellsten Zell Signalübertragungssysteme. Ca2+ Signale sind fundamental stochastisch. Dennoch hat sich die Modellierung dieser Ca2+-Signale bisher stark auf deterministische Ansätze mit gewöhnlichen Differentialgleichungen gestützt. Diese wurden als Ratengleichungen etabliert und beruhen auf räumlich gemitteltem Ca2+ Werten. Diese Ansätze vernachlässigen Rauschen und Zufall. In dieser Dissertation präsentieren wir ein stochastisches Modell zur Erzeugung von Ca2+ Spikes in Form einer linearen Zustands-Kette. Die Anzahl offener Cluster ist die Zustandsvariable und Erholung von negativem Feedback wird berücksichtigt. Wir identifizieren einen Ca2+ Spike mit dem ersten Erreichen eines kritischen Zustands und sein Interspike Intervall mit der first-passage time (FPT) zu diesem Zustand. Dafür entwickeln wir einen allgemeinen mathematischen Rahmen zur analytischen Berechnung von FPTs auf solch einer Kette. Wir finden z.B. einen allgemein verringerten CV, der ein deutliches Minimum in Abhängigkeit der Zustandskettenlänge N aufweist. Dies nennen wir resonante Länge. Danach ergänzen wir positives Feedback und wenden das Modell auf verschiedene Zelltypen an. Es erfasst alle verfügbaren allgemeinen Beobachtungen zu Ca2+ Signalvorgängen. Es erlaubt uns Einblicke in den Zusammenhang von Agonistenstärke und Puffraten. Auch werden einzelne Ca2+ Spikes in Purkinje Neuronen, welche eine Rolle für Lernen und Erinnerung spielen, als stochastisches reaction-diffusion Model in einer 3D Dornenfortsatz Geometrie modelliert. Ataxia, eine Krankheit, die zum Verlust der Feinmotorik führt, wird auf defekte IP3R zurückgeführt, die abnormale Ca2+ Spikes erzeugen. Dieser Zustand wird ebenfalls untersucht und es wird ein Weg zur Wiederherstellung normaler Ca2+ Spikes vorgeschlagen. / Calcium (Ca2+) is a ubiquitous 2nd messenger molecule in all eukaryotic cells. Inositol trisphosphate (IP3)-induced Ca2+ signalling via IP3 receptors (IP3Rs) is one of the most universal signalling systems used by cells to transmit information. Ca2+ signalling is noisy and a fundamentally stochastic system. Yet, modelling of IP3-induced Ca2+ signalling has relied heavily on deterministic approaches with ordinary differential equations in the past, established as rate equations using spatially averaged Ca2+. These approaches neglect the defining features of Ca2+ signalling, noise and fluctuations. In this thesis, we propose a stochastic model of Ca2+ spike generation in terms of a linear state chain with the number of open clusters as its state variable, also including recovery from negative feedback. We identify a Ca2+ spike with reaching a critical state for the first time, and its interspike interval with the first passage time to that state. To this end, a general mathematical framework for analytically computing first-passage times of such a linear chain is developed first. A substantially reduced CV with a pronounced minimum, dependent on the chain length N, termed resonant length, are found. Positive feedback is then included into the model, and it is applied directly to various cell types. The model is fundamentally stochastic and successfully captures all available general observations on Ca2+ signalling. Also, we specifically study single Ca2+ spikes in spines of Purkinje neurons, assumed to be important for motor learning and memory, using MCell to simulate a reaction-diffusion system in a complex 3D Purkinje spine geometry. The model successfully reproduces experimentally findings on properties of Ca2+ spikes. Ataxia, a pathological condition resulting in, e.g., a loss of fine motor control, assumed to be caused by malfunctioning IP3Rs, is modelled and a possible way of recovery is suggested.

Kanalrhodopsine (ChRs), lichtgesteuerte Ionenkanäle, vermitteln phototaktische Reaktionen in beweglichen Algen und sind als optogenetische Werkzeuge zur Manipulation der Zellaktivität mittels Lichts weit verbreitet. Viele Kationen- und Anionen-leitende ChRs (CCRs und ACRs) wurden aus kultivierbaren Chlorophyten- und Cryptophytenarten identifiziert. Die meisten mikrobiellen Organismen kann jedoch nicht kultiviert werden, was zu einem unvollständigen Bild der ChR-Vielfalt führt. Die Metagenomik öffnet die Tür für Erkenntnisse über die Verteilung von ChRs in unkultivierten Organismen. Diese Arbeit beschreibt die biophysikalische Charakterisierung von zwei Gruppen metagenomisch identifizierter ChRs. Die MerMAIDs (Metagenomically discovered marine, anion-conducting, and intensely desensitizing ChRs) sind eine neue ChR-Familie und zeigen nahezu komplette Photostrom-Inaktivierung unter Dauerlicht. Die Photoströme lassen sich durch einen Photozyklus erklären, der zur Akkumulation eines langlebigen und nicht-leitenden Photointermediats führt. Ein konserviertes Cystein ist für dieses Phänomen entscheidend, da seine Substitution zu einer stark reduzierten Inaktivierung führt. Die Prasinophyten ChRs, die große carboxyterminale Domänen aufweisen, wurden in großen, marinen Viren identifiziert, die sie von ihren beweglichen und einzelligen Grünalgen-Wirten durch lateralen Gentransfer übernommen haben. Heterolog exprimiert, sind die viralen ChRs nur nach Ergänzung von Transportsequenzen und carboxyterminaler Kürzung funktional. Die Grünalgen- und viralen ChRs sind Anionen-leitend mit nicht-inaktivierenden Photoströmen, wenn sie in Säugetierzellen exprimiert werden, obwohl die viralen Vertreter weniger leitfähig und zytotoxisch sind. Nichtsdestotrotz repräsentiert diese ChR-Gruppe die ersten Grünalgen- und Virus-ACRs. Diese Arbeit zeigt eine breite Verteilung der ACRs unter marinen mikrobiellen Organismen und die Bedeutung der Funktionsmetagenomik bei der Entdeckung neuer ChRs. / Channelrhodopsins (ChRs) are light-gated ion channels mediating phototactic responses in motile algae and widely used as optogenetic tools to manipulate cellular activity using light. Many cation- and anion-conducting ChRs (CCRs and ACRs) have been identified from culturable chlorophyte and cryptophyte species. However, most microbial organisms cannot be cultured, resulting in an incomplete view of the diversity of ChRs. Metagenomics opens the door to gather insights on the distribution of ChRs in uncultured organisms. Here, the biophysical characterization of two groups of metagenomically identified ChRs is described. The MerMAIDs (Metagenomically discovered marine, anion-conducting, and intensely desensitizing ChRs) represent a new ChR family with near-complete photocurrent desensitization under continuous illumination. The photocurrents can be explained by a single photocycle leading to the accumulation of a long-lived and non-conducting photointermediate. A conserved cysteine is critical for this phenomenon, as its substitution results in a strongly reduced desensitization. The prasinophyte ChRs, harboring large carboxy-terminal extensions, were identified in marine giant viruses that acquired them from their motile and unicellular green algal hosts via lateral gene transfer. Expressed in cell culture, the viral ChRs are only functional upon the addition of trafficking sequences and carboxy-terminal truncation. The green algal and viral ChRs are anion-conducting and display non-desensitizing photocurrents when expressed in mammalian cells, though the viral representatives are less conductive and cytotoxic. Nonetheless, this group of ChRs represents the first green algal and viral ACRs. This thesis highlights a broad distribution of ACRs among marine microbial organisms and the importance of functional metagenomics in discovering new ChRs.

Cilia and flagella are hair-like appendages of eukaryotic cells. They are actively bending structures that exhibit regular beat patterns and thereby play an important role in many different circumstances where motion on a cellular level is required. Most dramatic is the effect of nodal cilia whose vortical motion leads to a fluid flow that is directly responsible for establishing the left-right axis during embryological development in many vertebrate species, but examples range from the propulsion of single cells, such as the swimming of sperm, to the transport of mucus along epithelial cells, e.g. in the ciliated trachea. Cilia and flagella contain an evolutionary highly conserved structure called the axoneme, whose characteristic architecture is based on a cylindrical arrangement of elastic filaments (microtubules). In the presence of a chemical fuel (ATP), molecular motors (dynein) exert shear forces between neighbouring microtubules, leading to a bending of the axoneme through structural constraints. We address the following two questions: How can these organelles generate regular oscillatory beat patterns in the absence of a biochemical signal regulating the activity of the force generating elements? And how can the beat patterns be so different for apparently very similar structures? We present a theoretical description of the axonemal structure as an actively bending elastic cylinder, and show that in such a system bending waves emerge from a non-oscillatory state via a dynamic instability. The corresponding beat patterns are solutions to a set of coupled partial differential equations presented herein.

No description available.

No description available.

By implementing the rolled-up microfabrication method based on strain engineering, several systems are investigated within the contents of this thesis. The structural morphing of planar geometries into three-dimensional structures opens up many doors for the creation of unique material configurations and devices. An exploration into several novel microsystems, encompassing various scientific subjects, is made and methods for on-chip integration of these devices are presented. The roll-up of a metal and oxide allows for a cylindrical hollow-core structure with a cladding layer composed of a multilayer stack, plasmonic metamaterial. This structure can be used as a platform for a number of optical metamaterial devices. By guiding light radially through this structure, a theoretical investigation into the system makeup of a rolled-up hyperlens, is given. Using the same design, but rather propagating light parallel to the cylinder, a novel device known as a metamaterial optical fiber is defined. This fiber allows light to be guided classically and plasmonically within a single device. These fibers are developed experimentally and are integrated into preexisting on-chip structures and characterized. A system known as lab-in-a-tube is introduced. The idea of lab-in-a-tube combines various rolled-up components into a single all-encompassing biosensor that can be used to detect and monitor single bio-organisms. The first device specifically tailored to this system is developed, flexible split-wall microtube resonator sensors. A method for the capturing of embryonic mouse cells into on-chip optical resonators is introduced. The sensor can optically detect, via photoluminescence, living cells confined within the resonator through the compression and expansion of a nanogap built within its walls. The rolled-up fabrication method is not limited to the well-investigated systems based on the roll-up from semiconductor material or from a photoresist layer. A new approach, relying on the delamination of polymers, is presented. This offers never-before-realized microscale structures and configurations. This includes novel magnetic configurations and flexible fluidic sensors which can be designed for on-chip and roving detector applications.

Cilia and flagella are hair-like appendages of eukaryotic cells. They are actively bending structures that exhibit regular beat patterns and thereby play an important role in many different circumstances where motion on a cellular level is required. Most dramatic is the effect of nodal cilia whose vortical motion leads to a fluid flow that is directly responsible for establishing the left-right axis during embryological development in many vertebrate species, but examples range from the propulsion of single cells, such as the swimming of sperm, to the transport of mucus along epithelial cells, e.g. in the ciliated trachea. Cilia and flagella contain an evolutionary highly conserved structure called the axoneme, whose characteristic architecture is based on a cylindrical arrangement of elastic filaments (microtubules). In the presence of a chemical fuel (ATP), molecular motors (dynein) exert shear forces between neighbouring microtubules, leading to a bending of the axoneme through structural constraints. We address the following two questions: How can these organelles generate regular oscillatory beat patterns in the absence of a biochemical signal regulating the activity of the force generating elements? And how can the beat patterns be so different for apparently very similar structures? We present a theoretical description of the axonemal structure as an actively bending elastic cylinder, and show that in such a system bending waves emerge from a non-oscillatory state via a dynamic instability. The corresponding beat patterns are solutions to a set of coupled partial differential equations presented herein.

Ziel der vorgestellten Arbeit war die Synthese von Nucleolipiden zur Lipophilisierung von Oligonucleotiden sowie deren Untersuchung im Hinblick auf ihre Wechselwirkung und Duplex-Bildung an horizontalen Lipidmembranen und verschiedenen Phasengrenzen zur Entwicklung eines neuartigen Bio-Chips für die RNA/DNA-Analyse. Mit der Synthese N(3)-prenylierter und 2’,3’-O-ketalisierter Pyrimidinbasen Uridin und Methyluridin wurden Nucleolipid-Bausteine dargestellt, die auch als terminale Kopfgruppen eines Oligonucleotid-Dodecamers den lipophilen Charakter dieser Oligonucleotid-Sequenz erhöhten. Für den Einsatz solcher LONs (Lipo-Oligonucleotide) in einer vereinfachten RNA/DNA-Analytik wurde eine Vielzahl von Lipo-Oligonucleotiden mit diversen Nucleolipid-Kopfgruppen synthetisiert und auf ihr Einlagerungsverhalten in künstliche Lipid-Bilayer untersucht. Fluoreszenz-spektroskopische Untersuchungen zeigten, dass alle Lipo-Oligonucleotide in der Lage sind, sich in künstliche Lipid-Bilayer einzulagern. Abhängig von der Struktur, der Länge und der Anzahl der C-Atom-Ketten dieser lipophilen Anker-Bausteine wurden die Geschwindigkeit und die Festigkeit der Verankerung im Lipid-Bilayer beeinflusst. Des Weiteren wurde die Hybridisierung von LONs mit komplementären Oligomeren an Lipidmembranen untersucht. Es konnte gezeigt werden, dass die im Bilayer verankerten Lipo-Oligonucleotide mit komplementären Oligomeren DNA-Duplexe bilden. Die hybridisierte DNA wurde nicht nur über einen kovalent gebundenen Cy5-Fluorophor am Gegenstrang nachgewiesen, sondern auch über den DNA-Interkalator SYBR Green I (SG). Am Beispiel von zwei Lipo-Oligonucleotiden (LON 20 und 23), die sich schnell und fest in der Bilayermembran verankern, konnte eine spontane Akkumulation dieser LONs an CHCl3/H2O sowie H2O/n-Decan Grenzflächen direkt nach der Probenzugabe beobachtet werden. Diese und andere Ergebnisse stützen den Einsatz von Lipo-Oligonucleotiden als Ziel-Oligomere in einem neuartigen RNA/DNA-Nachweisverfahren an Phasengrenzen.