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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
21

Entwicklung einer monolithisch integrierten 2,44 GHz Phasenregelschleife in der LFoundry 150nm-CMOS Technologie

Scheibe, Niko 25 November 2010 (has links) (PDF)
Die Spezifikationen und Toleranzbereiche heutiger Hochgeschwindigkeitsdatenübertragungstechnologien nehmen immer weiter an Komplexität, aufgrund der steigenden Informationsmenge, zu. Zur Verarbeitung von Daten in Frequenzbereichen oberhalb von einem Gigahertz sind Referenzsignale notwendig, welche ein äußerst geringes Phasenrauschen aufweisen um benachbarte Kanäle nicht zu beeinflussen. Diese Referenzsignale werden in Mischerschaltungen zur Modulation oder Demodulation zwischen radio frequency (RF)- und intermediate frequency (IF)-Signalen verwendet. Die benötigte Signalform ist eine Sinusschwingung, die nicht durch digitale Schaltungsblöcke erzeugt werden kann. Daher ist die Notwendigkeit von analogen LC-Oszillatoren gegeben. Die Erzeugung von höchst stabilen und hochfrequenten Signalen war lange Zeit teuren Silizium-Germanium-Technologien vorbehalten. Jedoch erfordert der steigende Integrationsgrad und der hart umkämpfte Markt, die Entwicklung von RF-Schaltungen in günstigen CMOS-Technologien. In Zusammenarbeit mit der Landshut Silicon Foundry soll dazu eine monolithisch integrierte Phase-Locked Loop (PLL) mit einer mittleren Ausgangsfrequenz von 2,44 GHz und einem Phasenrauschen kleiner -115 dBc/Hz bei einem Abstand von 1 MHz vom Träger entwickelt werden. Dabei wird das Hauptaugenmerk auf den Kern der PLL gelegt, welcher einen spannungsgesteuerten Oszillator, einen Phasen-/Frequenzdetektor, eine Ladungspumpe, einen Schleifenfilter und einen Frequenzteiler beinhaltet. Außerdem sollen Testszenarien vorgestellt werden, um die Eigenschaften der gefertigten PLL zu bestimmen und zu vergleichen.
22

Entwicklung einer monolithisch integrierten 2,44 GHz Phasenregelschleife in der LFoundry 150nm-CMOS Technologie

Scheibe, Niko 30 August 2010 (has links)
Die Spezifikationen und Toleranzbereiche heutiger Hochgeschwindigkeitsdatenübertragungstechnologien nehmen immer weiter an Komplexität, aufgrund der steigenden Informationsmenge, zu. Zur Verarbeitung von Daten in Frequenzbereichen oberhalb von einem Gigahertz sind Referenzsignale notwendig, welche ein äußerst geringes Phasenrauschen aufweisen um benachbarte Kanäle nicht zu beeinflussen. Diese Referenzsignale werden in Mischerschaltungen zur Modulation oder Demodulation zwischen radio frequency (RF)- und intermediate frequency (IF)-Signalen verwendet. Die benötigte Signalform ist eine Sinusschwingung, die nicht durch digitale Schaltungsblöcke erzeugt werden kann. Daher ist die Notwendigkeit von analogen LC-Oszillatoren gegeben. Die Erzeugung von höchst stabilen und hochfrequenten Signalen war lange Zeit teuren Silizium-Germanium-Technologien vorbehalten. Jedoch erfordert der steigende Integrationsgrad und der hart umkämpfte Markt, die Entwicklung von RF-Schaltungen in günstigen CMOS-Technologien. In Zusammenarbeit mit der Landshut Silicon Foundry soll dazu eine monolithisch integrierte Phase-Locked Loop (PLL) mit einer mittleren Ausgangsfrequenz von 2,44 GHz und einem Phasenrauschen kleiner -115 dBc/Hz bei einem Abstand von 1 MHz vom Träger entwickelt werden. Dabei wird das Hauptaugenmerk auf den Kern der PLL gelegt, welcher einen spannungsgesteuerten Oszillator, einen Phasen-/Frequenzdetektor, eine Ladungspumpe, einen Schleifenfilter und einen Frequenzteiler beinhaltet. Außerdem sollen Testszenarien vorgestellt werden, um die Eigenschaften der gefertigten PLL zu bestimmen und zu vergleichen.
23

Frequency control of auto-oscillations of the magnetization in spin Hall nano-oscillators

Hache, Toni 15 April 2021 (has links)
This thesis experimentally demonstrates four approaches of frequency control of magnetic auto-oscillations in spin Hall nano-oscillators (SHNOs). The frequency can be changed in the GHZ-range by external magnetic fields as shown in this work. This approach uses large electromagnets, which is inconvenient for future applications. The nonlinear coupling between oscillator power and frequency can be used to control the latter one by changing the applied direct current to the SHNO. The frequency can be controlled over a range of several 100 MHz as demonstrated in this thesis. The first part of the experimental chapter demonstrates the synchronization (injection-locking) between magnetic auto-oscillations and an external microwave excitation. The additionally applied microwave current generates a modulation of the effective magnetic field, which causes the interaction with the auto-oscillation. Both synchronize over a range of several 100 MHz. In this range, the auto-oscillation frequency can be controlled by the external stimulus. An increase of power and a decrease of line width is achieved in the synchronization range. This is explained by the increased coherence of the auto-oscillations. A second approach is the synchronization of auto-oscillations to an alternating magnetic field. This field is generated by a freestanding antenna, which is positioned above the SHNO. The second part of the experimental chapter introduces a bipolar concept of SHNOs and its experimental demonstration. In contrast to conventional SHNOs, bipolar SHNOs generate auto-oscillations for both direct current polarities and both directions of the external magnetic field. This is achieved by combining two ferromagnetic layers in an SHNO. The combination of two different ferromagnetic materials is used to switch between two frequency ranges in dependence of the direct current polarity since it defines the layer showing auto-oscillations. This approach can be used to change the frequency in the GHz-range by switching the direct current polarity. / Diese Arbeit demonstriert experimentell vier verschiedene Methoden der Frequenzkontrolle magnetischer Auto-Oszillationen in Spin Hall Nano-Oszillatoren (SHNOs). Durch externe magnetische Felder kann die Frequenz im GHz-Bereich geändert werden, wie es in dieser Arbeit gezeigt wird. Dies erfordert jedoch große Elektromagneten, deren Nutzung für zukünftige Anwendungen der SHNOs nicht geeignet sind. Aufgrund der nichtlinearen Kopplung zwischen Oszillatorleistung und Oszillatorfrequenz, lässt sich letztere durch den Versorgungsstrom beeinflussen. Dies ist typischerweise in einem Bereich von mehreren 100 MHz möglich, wie es an mehreren Stellen dieser Arbeit gezeigt wird. Im ersten Abschnitt des Ergebnisteils wird die Synchronisation der magnetischen Auto-Oszillationen zu einer externen Mikrowellenanregung demonstriert. Der zusätzlich eingespeiste Mikrowellenstrom erzeugt eine Modulation des effektiven Magnetfelds, was zur Wechselwirkung mit den Auto-Oszillationen führt. Diese synchronisieren über eine Frequenzdifferenz von mehreren 100 MHz. In diesem Bereich lässt sich die Frequenz der Auto-Oszillation mit der äußeren Frequenz steuern. Innerhalb des Synchronisationsbereichs wird außerdem eine Erhöhung der Leistung und eine Verringerung der Linienbreite der Auto-Oszillationen festgestellt. Dies wird mit einer Erhöhung der Kohärenz der Auto-Oszillationen erklärt. Neben der zusätzlichen Einspeisung eines Mikrowellenstroms können die Auto-Oszillationen auch zu einem magnetischen Wechselfeld synchronisieren, welches von einer frei beweglichen Antenne erzeugt wird, die über dem SHNO positioniert wird. Im zweiten Abschnitt des Ergebnisteils wird ein bipolares Konzept eines SHNO vorgestellt und seine Funktionsfähigkeit experimentell nachgewiesen. Im Vergleich zu konventionellen SHNOs erzeugen bipolare SHNOs Auto-Oszillationen für beide Polaritäten des elektrischen Versorgungsstroms und beide Richtungen des externen Magnetfelds. Dies wird durch die Kombination zweier ferromagnetischer Lagen in einem SHNO erreicht. Die Kombination unterschiedlicher ferromagnetischer Materialien kann genutzt werden, um die Mikrowellenfrequenz in Abhängigkeit der Stromrichtung zu ändern, da diese bestimmt in welcher Lage die Auto-Oszillationen erzeugt werden können. Durch eine geeignete Materialkombination kann die Frequenz im GHz-Bereich geändert werden, wenn die Strompolarität umgekehrt wird.
24

The Regulation of Segmentation Clock Period in Zebrafish

Herrgen, Leah 08 December 2008 (has links) (PDF)
Oscillations are present at many different levels of biological organization. The cell cycle that directs the division of individual cells, the regular depolarization of neurons in the sinu-atrial node which underlies the regular beating of the heart, the circadian rhythms that govern the daily activity cycles of virtually all organisms, and the clocks that make entire populations of fireflies flash on and off in unison feature as prominent examples of biological clocks. During development, biological clocks regulate the patterning of growing tissues, as is the case in vertebrate somitogenesis, and potentially also in vertebrate limb outgrowth and axial segmentation of invertebrate embryos. During vertebrate segmentation, the embryonic axis is subdivided along its anterior-posterior axis into epithelial spheres of cells called somites. This rhythmic process is thought to be driven by a multicellular oscillatory gene network, the so-called segmentation clock. Oscillations of hairy and enhancer of split gene products have been proposed to constitute the core clockwork in individual cells, and these oscillators are coupled to each other by Delta-Notch intercellular signaling. The interaction of the segmentation clock with a posteriorly-moving arrest wavefront then translates the temporal information encoded by the clock into a spatial pattern of segments. In the framework of this Clock and Wavefront model, segment length is determined by both clock period and arrest wavefront velocity. How the period of the segmentation clock is regulated is presently unknown, and understanding the mechanism of period setting might yield insight into the nature and function of the segmentation clock. In this study, two different but complementary approaches were pursued to investigate how period is regulated in the zebrafish segmentation clock. First, it has been reported that zebrafish mind bomb (mib) mutant embryos form somites more slowly than their wt siblings, suggesting that Mib might be implicated in period setting. Mib is an E3 ubiquitin ligase required for ubiquitination and endocytosis of the Notch ligand Delta, and Notch signaling is impaired in mutants with defective Mib. It has been suggested that the mechanistic basis for the requirement of Delta endocytosis in Notch signaling is a need for Delta to enter a particular endocytic compartment, potentially a recycling endosome, in a ubiquitin-dependent manner, where its signaling ability might be established or amplified by an as yet unknown posttranslational modification. In the present study, Delta trafficking through the endocytic pathway was analyzed in the PSM of wt and mib embryos through colocalization studies with endocytic markers. The rationale of this approach was that if Delta gained access to a particular endocytic compartment through Mib-dependent endocytosis, the presence of Delta in this compartment would be expected to be reduced in mutants with defective Mib, thereby revealing the compartment’s identity. However, no qualitative changes in colocalization with different endocytic markers could be detected in mib mutants, and the methods available did not allow for quantification of colocalization in wt or mutant backgrounds. However, Delta colocalized with 13 markers of recycling endosomes, consistent with the hypothesis that these are functionally important in Notch signaling. More refined techniques will be necessary for a quantitative analysis of normal as compared to impaired Delta trafficking. A genetic approach to period regulation proved to be successful for the Drosophila circadian clock, where the identification of period mutants advanced the understanding of the clock’s genetic circuitry. This motivated a screen for period mutants of the segmentation clock, which was carried out by measuring somitogenesis period, segment length and arrest wavefront velocity in a pool of candidate mutants. A subset of Delta-Notch mutants, and embryos treated with a small-molecule inhibitor that impairs Notch signaling, displayed correlated increases in somitogenesis period and segment length, while there was no detectable change in arrest wavefront velocity. Combined, these findings suggested that segmentation clock period is increased in experimental conditions with impaired Delta-Notch signaling. Using a theoretical description of the segmentation clock as an array of coupled phase oscillators, the delay in the coupling and the autonomous frequency of individual cells were estimated from the direction and magnitude of the period changes. The mutants presented here are the first candidates for segmentation clock period mutants in any vertebrate. The nature of the molecular lesions in these mutants, all of which affect genes implicated in intercellular Delta-Notch signaling, suggests that communication between oscillating PSM cells is a key factor responsible for setting the period of the segmentation clock.
25

Compact few-cycle mid-wave and long-wave infrared OPCPA / based on a Cr:ZnS front-end

Fürtjes, Pia Johanna 27 November 2023 (has links)
Die Weiterentwicklung von Ultrakurzimpulslaserquellen hat die Horizonte für Wissenschaft, Medizin und Industrie stetig erweitert. Ultrakurze Impulsdauern und hohe Energien erzeugen Spitzenleistungen auf der Gigawatt-Skala, deren zeitliche und spektrale Charakteristik ideale Voraussetzungen für nichtlineare zeitaufgelöste Spektroskopie und ultraschnelle nichtlineare Optik bieten. Die Untersuchung von Molekülschwingungen im sogenannten Fingerabdrucksbereich (engl. fingerprint region) und die effiziente lasergetriebene Erzeugung von Hohen-Harmonischen- und Röntgenimpulsen benötigen Laserquellen im mittleren bis langwelligen Infrarot. Da oberhalb einer Wellenlänge von 4 μm keine Festkörperlaserquellen existieren, hat sich optische parametrische Verstärkung zur Schlüsseltechnik in diesem Wellenlängenbereich entwickelt. In dieser Arbeit werden Laserimpulse oberhalb von 4 μm Wellenlänge mittels optischer parametrischer Verstärkung gestreckter Impulse erzeugt, deren Energien den Micro- bis Millijoule Bereich bei einer Kilohertz-Wiederholrate erreichen. Die Pumpwellenlänge von 2 μm ist vorteilhaft gegenüber den üblicherweise verwendeten Pumpen im nahen Infraroten und erlaubt zur Generation der Eingangsspektren besonders innovative kompakte Laserarchitekturen. Es werden zwei Systeme im mittleren und langwelligen Infrarot entwickelt basierend auf einem Cr:ZnS Eingangslaser, die bisherigen Systemen in Energie und Spitzenleistungen überlegen sind. Während sich die Laserquelle im mittleren Infraroten durch seine Durchstimmbarkeit auszeichnet, wird mit den langwelligen infraroten Impulsen erstmals einen nichtlineare Absorptionsmessung an Wasser durchgeführt. / The progress in the development of ultrafast laser sources has opened up new horizons in science, medicine and industry. Pulses of ultrashort duration and high energy reach gigawatt peak power which offer ideal conditions for time-resolved nonlinear absorption spectroscopy and ultrafast nonlinear optics. The investigation of vibrational states of biomolecules in the so-called fingerprint region and strong-field experiments aiming for the generation of high-harmonics or x-rays quest for such laser sources in the mid- to long-infrared spectral range. Due to the lack of existing solid state lasers beyond 4 μm, optical parametric amplification has emerged as the key technique to generate adequate infrared pulses. In this work, optical parametric chirped pulse amplification (OPCPA) is the key technique used to generate 100 μJ-level energy pulses at kHz repetition rate beyond 4 μm. In this context, novel front-end architectures are designed, tailored to compactness and to exploit the advantages of 2 μm pumped OPCPA over the typically used near-infrared drivers around 1 μm. The novel front-end based on a femtosecond Cr:ZnS oscillator emitting 30 fs pulses at 2.4 μm provides the necessary spectral components for the 2 μm pump and the signal. Two OPCPA systems in the mid-wave infrared (MWIR) and long-wave infrared (LWIR) spectral region, superior in terms of pulse energy and peak power compared with existing systems, are developed. While the tunability of the first system is unique, the second system is used to for the first time demonstrate a nonlinear transmission experiment in water by direct excitation of the L2 libration.
26

Optical parametric oscillators for precision IR spectroscopy and metrology

Kovalchuk, Evgeny 21 May 2008 (has links)
In der vorliegenden Doktorarbeit wird ein Dauerstrich Optisch Parametrischer Oszillator (cw OPO) vorgestellt, der speziell für die hochauflösende Dopplerfreie Molekülspektroskopie und Metrologie entwickelt wurde. Der kontrollierte Zugang zu jeder beliebigen Wellenlänge im breiten Emissionsspektrum von OPOs wie auch das präzise Abstimmen seiner Ausgangsfrequenz über zu untersuchende molekulare und atomare Übergänge stellten lange Zeit Probleme dar, deren Lösung die Grundzielsetzung dieser Arbeit war. Das im Laufe dieser Arbeit entwickelte System hat diese Ziele vollständig erreicht, was durch verschiedene Messungen und Anwendungen demonstriert wurde. Zu diesem Zweck wurde ein neues OPO-Design mit einem Intracavity-Etalon entwickelt und aufgebaut, wobei der OPO auf dem Konzept eines einfach-resonanten cw OPOs mit resonanter Pumpwelle basiert. Die OPO-Ausgangsstrahlung zeigt sehr gute Langzeitstabilität und Spektraleigenschaften, welche durch direkte Frequenzvergleichsmessungen mit einem optischen Methan-Frequenzstandard im Infraroten bestimmt wurden. Eine Idler-Linienbreite von 12 kHz und ein Modensprung-freier Betrieb des OPOs über einen Zeitraum von einigen Tagen wurde beobachtet. Außerdem wurde gezeigt, dass ein OPO zu einer hochstabilen optischen Referenz phasengelockt und somit seine Frequenz sehr genau kontrolliert und durchgestimmt werden kann. Als erste erfolgreiche Anwendung eines OPOs in der Dopplerfreien Spektroskopie wurde ein Aufbau zur Frequenz-Modulationsspektroskopie in Methan realisiert. Weiterhin, wurde der entwickelte cw OPO mit einem femtosekunden optischen Frequenzkamm kombiniert, um eine neue Idee für eine kohärente Verbindung zwischen dem sichtbaren und dem infraroten Spektralbereich zu realisieren. Als erste Demonstration dieser Technologie wurde ein direkter absoluter Frequenzvergleich zwischen einem Jod-stabilisierten Laser bei 532 nm und einem Methan-stabilisierten Laser bei 3390 nm durchgeführt. / This thesis presents a continuous-wave optical parametric oscillator (cw OPO), specially developed for high-resolution Doppler-free molecular spectroscopy and metrology. The basic objective was to solve the long-standing problem of controlled access to any desired wavelength in the wide emission range of OPOs, including the ability to precisely tune the output frequency over the molecular and atomic transitions of interest. The system implemented during this work fully achieves these goals and its performance was demonstrated in various measurements and applications. For this aim, a new design for the OPO cavity with an intracavity etalon was implemented, extending the concept of a cw singly resonant OPO with resonated pump wave. The newly developed device demonstrates very good long-term stability and spectral properties, which were determined in direct beat frequency measurements with a methane infrared optical frequency standard. Thus, an idler radiation linewidth of 12 kHz and mode-hop-free operation of the OPO over several days were observed. Furthermore, it was shown that an OPO can be phase locked to a highly stable optical reference and thus much more precisely controlled and tuned. As the first successful application of OPOs in Doppler-free spectroscopy, a frequency modulation spectroscopy setup for detection of sub-Doppler resonances in methane was implemented. Furthermore, the developed cw OPO was integrated with a femtosecond optical frequency comb to realize a new concept for a coherent link between the visible and infrared spectral ranges. As a first demonstration of this technique, a direct absolute frequency comparison between an iodine stabilized laser at 532 nm and a methane stabilized laser at 3390 nm was performed.
27

Statistical properties and scaling of the Lyapunov exponents in stochastic systems

Zillmer, Rüdiger January 2003 (has links)
Die vorliegende Arbeit umfaßt drei Abhandlungen, welche allgemein mit einer stochastischen Theorie für die Lyapunov-Exponenten befaßt sind. Mit Hilfe dieser Theorie werden universelle Skalengesetze untersucht, die in gekoppelten chaotischen und ungeordneten Systemen auftreten. <br /> <br /> Zunächst werden zwei zeitkontinuierliche stochastische Modelle für schwach gekoppelte chaotische Systeme eingeführt, um die Skalierung der Lyapunov-Exponenten mit der Kopplungsstärke ('coupling sensitivity of chaos') zu untersuchen. Mit Hilfe des Fokker-Planck-Formalismus werden Skalengesetze hergeleitet, die von Ergebnissen numerischer Simulationen bestätigt werden. <br /> <br /> Anschließend wird gezeigt, daß 'coupling sensitivity' im Fall gekoppelter ungeordneter Ketten auftritt, wobei der Effekt sich durch ein singuläres Anwachsen der Lokalisierungslänge äußert. Numerische Ergebnisse für gekoppelte Anderson-Modelle werden bekräftigt durch analytische Resultate für gekoppelte raumkontinuierliche Schrödinger-Gleichungen. Das resultierende Skalengesetz für die Lokalisierungslänge ähnelt der Skalierung der Lyapunov-Exponenten gekoppelter chaotischer Systeme. <br /> <br /> Schließlich wird die Statistik der exponentiellen Wachstumsrate des linearen Oszillators mit parametrischem Rauschen studiert. Es wird gezeigt, daß die Verteilung des zeitabhängigen Lyapunov-Exponenten von der Normalverteilung abweicht. Mittels der verallgemeinerten Lyapunov-Exponenten wird der Parameterbereich bestimmt, in welchem die Abweichungen von der Normalverteilung signifikant sind und Multiskalierung wesentlich wird. / This work incorporates three treatises which are commonly concerned with a stochastic theory of the Lyapunov exponents. With the help of this theory universal scaling laws are investigated which appear in coupled chaotic and disordered systems. <br /> <br /> First, two continuous-time stochastic models for weakly coupled chaotic systems are introduced to study the scaling of the Lyapunov exponents with the coupling strength (coupling sensitivity of chaos). By means of the the Fokker-Planck formalism scaling relations are derived, which are confirmed by results of numerical simulations. <br /> <br /> Next, coupling sensitivity is shown to exist for coupled disordered chains, where it appears as a singular increase of the localization length. Numerical findings for coupled Anderson models are confirmed by analytic results for coupled continuous-space Schrödinger equations. The resulting scaling relation of the localization length resembles the scaling of the Lyapunov exponent of coupled chaotic systems. <br /> <br /> Finally, the statistics of the exponential growth rate of the linear oscillator with parametric noise are studied. It is shown that the distribution of the finite-time Lyapunov exponent deviates from a Gaussian one. By means of the generalized Lyapunov exponents the parameter range is determined where the non-Gaussian part of the distribution is significant and multiscaling becomes essential.
28

Hairy switches and oscillators - reconstructing the zebrafish segmentation clock

Oswald, Annelie 26 May 2014 (has links) (PDF)
Formation of segments during vertebrate embryogenesis is regulated by a biological clock. Models and experimental data indicate that the core of this clock consists of a cell- autonomous single cell oscillator. This oscillator likely involves a genetic feedback loop of transcriptional repressors belonging to the hairy gene family. In zebrafish, three her genes, her1, hes6 and her7, have been identified as core oscillator components. The main purpose of this project was to study the molecular mechanism of the hairy gene negative feedback oscillator in single cells. To determine whether a single cell oscillator is part of the zebrafish segmentation clock, a cell dissociation protocol was established to track the expression of Her1 ex vivo. Upon dissociation, Her1 expression continued to oscillate for up to three cycles. The period of oscillations was significantly slower than that of the segmentation clock, but appears to speed up in the presence of serum. To test whether the hairy gene interactions are sufficient to generate oscillations in single cells, a protocol was established that uses synthetic biology principles to design, construct and characterize hairy gene networks in yeast. First a library of network parts, containing hairy genes, promoters and Her binding sites was generated and subsequently assembled into simple devices to test their functionality in yeast. The three core oscillator components, Her1, Hes6 and Her7, were characterized and optimized for expression in yeast. In the SWITCH-OFF assay, the Her1 protein, modified with a MigED yeast repressor domain, was found to function as a transcriptional repressor in yeast, while Hes6 with the same modification can not. The dissociation of segmentation clock cells provides the first direct evidence that single cell oscillators exist in zebrafish. In this system, oscillator dynamics can be studied without the interactions of higher level clock components. In parallel, establishing a yeast chassis for hairy gene networks provides a novel technique to directly test predicted oscillator mechanisms by constructing them ’bottom up’.
29

Hairy switches and oscillators - reconstructing the zebrafish segmentation clock

Oswald, Annelie 30 January 2014 (has links)
Formation of segments during vertebrate embryogenesis is regulated by a biological clock. Models and experimental data indicate that the core of this clock consists of a cell- autonomous single cell oscillator. This oscillator likely involves a genetic feedback loop of transcriptional repressors belonging to the hairy gene family. In zebrafish, three her genes, her1, hes6 and her7, have been identified as core oscillator components. The main purpose of this project was to study the molecular mechanism of the hairy gene negative feedback oscillator in single cells. To determine whether a single cell oscillator is part of the zebrafish segmentation clock, a cell dissociation protocol was established to track the expression of Her1 ex vivo. Upon dissociation, Her1 expression continued to oscillate for up to three cycles. The period of oscillations was significantly slower than that of the segmentation clock, but appears to speed up in the presence of serum. To test whether the hairy gene interactions are sufficient to generate oscillations in single cells, a protocol was established that uses synthetic biology principles to design, construct and characterize hairy gene networks in yeast. First a library of network parts, containing hairy genes, promoters and Her binding sites was generated and subsequently assembled into simple devices to test their functionality in yeast. The three core oscillator components, Her1, Hes6 and Her7, were characterized and optimized for expression in yeast. In the SWITCH-OFF assay, the Her1 protein, modified with a MigED yeast repressor domain, was found to function as a transcriptional repressor in yeast, while Hes6 with the same modification can not. The dissociation of segmentation clock cells provides the first direct evidence that single cell oscillators exist in zebrafish. In this system, oscillator dynamics can be studied without the interactions of higher level clock components. In parallel, establishing a yeast chassis for hairy gene networks provides a novel technique to directly test predicted oscillator mechanisms by constructing them ’bottom up’.
30

The Regulation of Segmentation Clock Period in Zebrafish

Herrgen, Leah 05 December 2008 (has links)
Oscillations are present at many different levels of biological organization. The cell cycle that directs the division of individual cells, the regular depolarization of neurons in the sinu-atrial node which underlies the regular beating of the heart, the circadian rhythms that govern the daily activity cycles of virtually all organisms, and the clocks that make entire populations of fireflies flash on and off in unison feature as prominent examples of biological clocks. During development, biological clocks regulate the patterning of growing tissues, as is the case in vertebrate somitogenesis, and potentially also in vertebrate limb outgrowth and axial segmentation of invertebrate embryos. During vertebrate segmentation, the embryonic axis is subdivided along its anterior-posterior axis into epithelial spheres of cells called somites. This rhythmic process is thought to be driven by a multicellular oscillatory gene network, the so-called segmentation clock. Oscillations of hairy and enhancer of split gene products have been proposed to constitute the core clockwork in individual cells, and these oscillators are coupled to each other by Delta-Notch intercellular signaling. The interaction of the segmentation clock with a posteriorly-moving arrest wavefront then translates the temporal information encoded by the clock into a spatial pattern of segments. In the framework of this Clock and Wavefront model, segment length is determined by both clock period and arrest wavefront velocity. How the period of the segmentation clock is regulated is presently unknown, and understanding the mechanism of period setting might yield insight into the nature and function of the segmentation clock. In this study, two different but complementary approaches were pursued to investigate how period is regulated in the zebrafish segmentation clock. First, it has been reported that zebrafish mind bomb (mib) mutant embryos form somites more slowly than their wt siblings, suggesting that Mib might be implicated in period setting. Mib is an E3 ubiquitin ligase required for ubiquitination and endocytosis of the Notch ligand Delta, and Notch signaling is impaired in mutants with defective Mib. It has been suggested that the mechanistic basis for the requirement of Delta endocytosis in Notch signaling is a need for Delta to enter a particular endocytic compartment, potentially a recycling endosome, in a ubiquitin-dependent manner, where its signaling ability might be established or amplified by an as yet unknown posttranslational modification. In the present study, Delta trafficking through the endocytic pathway was analyzed in the PSM of wt and mib embryos through colocalization studies with endocytic markers. The rationale of this approach was that if Delta gained access to a particular endocytic compartment through Mib-dependent endocytosis, the presence of Delta in this compartment would be expected to be reduced in mutants with defective Mib, thereby revealing the compartment’s identity. However, no qualitative changes in colocalization with different endocytic markers could be detected in mib mutants, and the methods available did not allow for quantification of colocalization in wt or mutant backgrounds. However, Delta colocalized with 13 markers of recycling endosomes, consistent with the hypothesis that these are functionally important in Notch signaling. More refined techniques will be necessary for a quantitative analysis of normal as compared to impaired Delta trafficking. A genetic approach to period regulation proved to be successful for the Drosophila circadian clock, where the identification of period mutants advanced the understanding of the clock’s genetic circuitry. This motivated a screen for period mutants of the segmentation clock, which was carried out by measuring somitogenesis period, segment length and arrest wavefront velocity in a pool of candidate mutants. A subset of Delta-Notch mutants, and embryos treated with a small-molecule inhibitor that impairs Notch signaling, displayed correlated increases in somitogenesis period and segment length, while there was no detectable change in arrest wavefront velocity. Combined, these findings suggested that segmentation clock period is increased in experimental conditions with impaired Delta-Notch signaling. Using a theoretical description of the segmentation clock as an array of coupled phase oscillators, the delay in the coupling and the autonomous frequency of individual cells were estimated from the direction and magnitude of the period changes. The mutants presented here are the first candidates for segmentation clock period mutants in any vertebrate. The nature of the molecular lesions in these mutants, all of which affect genes implicated in intercellular Delta-Notch signaling, suggests that communication between oscillating PSM cells is a key factor responsible for setting the period of the segmentation clock.

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