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Institute
- Institut für Biochemie und Biologie (63)
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Cargo transport by molecular motors is ubiquitous in all eukaryotic cells and is typically driven cooperatively by several molecular motors, which may belong to one or several motor species like kinesin, dynein or myosin. These motor proteins transport cargos such as RNAs, protein complexes or organelles along filaments, from which they unbind after a finite run length. Understanding how these motors interact and how their movements are coordinated and regulated is a central and challenging problem in studies of intracellular transport. In this thesis, we describe a general theoretical framework for the analysis of such transport processes, which enables us to explain the behavior of intracellular cargos based on the transport properties of individual motors and their interactions. Motivated by recent in vitro experiments, we address two different modes of transport: unidirectional transport by two identical motors and cooperative transport by actively walking and passively diffusing motors. The case of cargo transport by two identical motors involves an elastic coupling between the motors that can reduce the motors’ velocity and/or the binding time to the filament. We show that this elastic coupling leads, in general, to four distinct transport regimes. In addition to a weak coupling regime, kinesin and dynein motors are found to exhibit a strong coupling and an enhanced unbinding regime, whereas myosin motors are predicted to attain a reduced velocity regime. All of these regimes, which we derive both by analytical calculations and by general time scale arguments, can be explored experimentally by varying the elastic coupling strength. In addition, using the time scale arguments, we explain why previous studies came to different conclusions about the effect and relevance of motor-motor interference. In this way, our theory provides a general and unifying framework for understanding the dynamical behavior of two elastically coupled molecular motors. The second mode of transport studied in this thesis is cargo transport by actively pulling and passively diffusing motors. Although these passive motors do not participate in active transport, they strongly enhance the overall cargo run length. When an active motor unbinds, the cargo is still tethered to the filament by the passive motors, giving the unbound motor the chance to rebind and continue its active walk. We develop a stochastic description for such cooperative behavior and explicitly derive the enhanced run length for a cargo transported by one actively pulling and one passively diffusing motor. We generalize our description to the case of several pulling and diffusing motors and find an exponential increase of the run length with the number of involved motors.
One of the most exciting predictions of Einstein's theory of gravitation that have not yet been proven experimentally by a direct detection are gravitational waves. These are tiny distortions of the spacetime itself, and a world-wide effort to directly measure them for the first time with a network of large-scale laser interferometers is currently ongoing and expected to provide positive results within this decade. One potential source of measurable gravitational waves is the inspiral and merger of two compact objects, such as binary black holes. Successfully finding their signature in the noise-dominated data of the detectors crucially relies on accurate predictions of what we are looking for. In this thesis, we present a detailed study of how the most complete waveform templates can be constructed by combining the results from (A) analytical expansions within the post-Newtonian framework and (B) numerical simulations of the full relativistic dynamics. We analyze various strategies to construct complete hybrid waveforms that consist of a post-Newtonian inspiral part matched to numerical-relativity data. We elaborate on exsisting approaches for nonspinning systems by extending the accessible parameter space and introducing an alternative scheme based in the Fourier domain. Our methods can now be readily applied to multiple spherical-harmonic modes and precessing systems. In addition to that, we analyze in detail the accuracy of hybrid waveforms with the goal to quantify how numerous sources of error in the approximation techniques affect the application of such templates in real gravitational-wave searches. This is of major importance for the future construction of improved models, but also for the correct interpretation of gravitational-wave observations that are made utilizing any complete waveform family. In particular, we comprehensively discuss how long the numerical-relativity contribution to the signal has to be in order to make the resulting hybrids accurate enough, and for currently feasible simulation lengths we assess the physics one can potentially do with template-based searches.
Neben der Frequenz eines cues ist es dessen Zuverlässigkeit, die Kindern hilft, die an sie gerichtete Sprache zu segmentieren, Worteinheiten zu erkennen sowie diese syntaktisch zu kategorisieren. Im Deutschen weist die Subsilbe „Langvokal+Konsonant+/t/“ (z.B. in fehlt, wohnt) zuverlässig auf eine -t-flektierte Verbform hin. Die in kindgerichteter Sprache höher frequente Subsilbe „Kurzvokal+Konsonant+/t/“ (z.B. in Feld, Hemd, fällt, rund) gibt hingegen keinen derartig eindeutigen Hinweis. Es wurde der Frage nachgegangen, inwiefern diese unterschiedlichen Zuverlässigkeiten und Frequenzen der Subsilben auf die Nomen-, Verb- und Verbflexionsverarbeitung einwirken. Drei Altersgruppen wurden untersucht: achtzehn Monate alte Kinder, drei- bis fünfjährige sprachunauffällige und -auffällige Kinder sowie erwachsene Sprecher. Einflüsse der unterschiedlichen Zuverlässigkeiten und Frequenzen der ausgewählten Subsilben konnten für alle Probandengruppen gefunden werden. Die Subsilbe stellt damit eine linguistische Größe dar, die in der frühen Sprachwahrnehmung als cue dienen sowie die Sprachverarbeitung Erwachsener lenken kann und auch für die Sprachdiagnostik und -therapie sprachauffälliger Kinder berücksichtigt werden sollte.
This thesis contains several theoretical studies on optomechanical systems, i.e. physical devices where mechanical degrees of freedom are coupled with optical cavity modes. This optomechanical interaction, mediated by radiation pressure, can be exploited for cooling and controlling mechanical resonators in a quantum regime. The goal of this thesis is to propose several new ideas for preparing meso- scopic mechanical systems (of the order of 10^15 atoms) into highly non-classical states. In particular we have shown new methods for preparing optomechani-cal pure states, squeezed states and entangled states. At the same time, proce-dures for experimentally detecting these quantum effects have been proposed. In particular, a quantitative measure of non classicality has been defined in terms of the negativity of phase space quasi-distributions. An operational al- gorithm for experimentally estimating the non-classicality of quantum states has been proposed and successfully applied in a quantum optics experiment. The research has been performed with relatively advanced mathematical tools related to differential equations with periodic coefficients, classical and quantum Bochner’s theorems and semidefinite programming. Nevertheless the physics of the problems and the experimental feasibility of the results have been the main priorities.
Complex networks have been successfully employed to represent different levels of biological systems, ranging from gene regulation to protein-protein interactions and metabolism. Network-based research has mainly focused on identifying unifying structural properties, including small average path length, large clustering coefficient, heavy-tail degree distribution, and hierarchical organization, viewed as requirements for efficient and robust system architectures. Existing studies estimate the significance of network properties using a generic randomization scheme - a Markov-chain switching algorithm - which generates unrealistic reactions in metabolic networks, as it does not account for the physical principles underlying metabolism. Therefore, it is unclear whether the properties identified with this generic approach are related to the functions of metabolic networks. Within this doctoral thesis, I have developed an algorithm for mass-balanced randomization of metabolic networks, which runs in polynomial time and samples networks almost uniformly at random. The properties of biological systems result from two fundamental origins: ubiquitous physical principles and a complex history of evolutionary pressure. The latter determines the cellular functions and abilities required for an organism’s survival. Consequently, the functionally important properties of biological systems result from evolutionary pressure. By employing randomization under physical constraints, the salient structural properties, i.e., the smallworld property, degree distributions, and biosynthetic capabilities of six metabolic networks from all kingdoms of life are shown to be independent of physical constraints, and thus likely to be related to evolution and functional organization of metabolism. This stands in stark contrast to the results obtained from the commonly applied switching algorithm. In addition, a novel network property is devised to quantify the importance of reactions by simulating the impact of their knockout. The relevance of the identified reactions is verified by the findings of existing experimental studies demonstrating the severity of the respective knockouts. The results suggest that the novel property may be used to determine the reactions important for viability of organisms. Next, the algorithm is employed to analyze the dependence between mass balance and thermodynamic properties of Escherichia coli metabolism. The thermodynamic landscape in the vicinity of the metabolic network reveals two regimes of randomized networks: those with thermodynamically favorable reactions, similar to the original network, and those with less favorable reactions. The results suggest that there is an intrinsic dependency between thermodynamic favorability and evolutionary optimization. The method is further extended to optimizing metabolic pathways by introducing novel chemically feasibly reactions. The results suggest that, in three organisms of biotechnological importance, introduction of the identified reactions may allow for optimizing their growth. The approach is general and allows identifying chemical reactions which modulate the performance with respect to any given objective function, such as the production of valuable compounds or the targeted suppression of pathway activity. These theoretical developments can find applications in metabolic engineering or disease treatment. The developed randomization method proposes a novel approach to measuring the significance of biological network properties, and establishes a connection between large-scale approaches and biological function. The results may provide important insights into the functional principles of metabolic networks, and open up new possibilities for their engineering.
Since available phosphate (Pi) resources in soil are limited, symbiotic interactions between plant roots and arbuscular mycorrhizal (AM) fungi are a widespread strategy to improve plant phosphate nutrition. The repression of AM symbiosis by a high plant Pi-status indicates a link between Pi homeostasis signalling and AM symbiosis development. This assumption is supported by the systemic induction of several microRNA399 (miR399) primary transcripts in shoots and a simultaneous accumulation of mature miR399 in roots of mycorrhizal plants. However, the physiological role of this miR399 expression pattern is still elusive and offers the question whether other miRNAs are also involved in AM symbiosis. Therefore, a deep sequencing approach was applied to investigate miRNA-mediated posttranscriptional gene regulation in M. truncatula mycorrhizal roots. Degradome analysis revealed that 185 transcripts were cleaved by miRNAs, of which the majority encoded transcription factors and disease resistance genes, suggesting a tight control of transcriptional reprogramming and a downregulation of defence responses by several miRNAs in mycorrhizal roots. Interestingly, 45 of the miRNA-cleaved transcripts showed a significant differentially regulated between mycorrhizal and non-mycorrhizal roots. In addition, key components of the Pi homeostasis signalling pathway were analyzed concerning their expression during AM symbiosis development. MtPhr1 overexpression and time course expression data suggested a strong interrelation between the components of the PHR1-miR399-PHO2 signalling pathway and AM symbiosis, predominantly during later stages of symbiosis. In situ hybridizations confirmed accumulation of mature miR399 in the phloem and in arbuscule-containing cortex cells of mycorrhizal roots. Moreover, a novel target of the miR399 family, named as MtPt8, was identified by the above mentioned degradome analysis. MtPt8 encodes a Pi-transporter exclusively transcribed in mycorrhizal roots and its promoter activity was restricted to arbuscule-containing cells. At a low Pi-status, MtPt8 transcript abundance inversely correlated with a mature miR399 expression pattern. Increased MtPt8 transcript levels were accompanied by elevated symbiotic Pi-uptake efficiency, indicating its impact on balancing plant and fungal Pi-acquisition. In conclusion, this study provides evidence for a direct link of the regulatory mechanisms of plant Pi-homeostasis and AM symbiosis at a cell-specific level. The results of this study, especially the interaction of miR399 and MtPt8 provide a fundamental step for future studies of plant-microbe-interactions with regard to agricultural and ecological aspects.
Im Rahmen des ersten Teils der vorliegenden Doktorarbeit konnten zwei nicht-essentielle (rps15, rpl36) und fünf essentielle (rps3, rps16, rpl22, rpl23, rpl32) im Plastom von Nicotiana tabacum kodierte Proteine des plastidären Ribosoms bezüglich ihrer Essentialität charakterisiert werden. Diese Gene wurden durch gezielte Knockout-Experimente inaktiviert und die resultierenden Effekte untersucht. Die Ergebnisse lassen einen Rückschluss auf die Lokalisation der Gene der insgesamt sieben untersuchten ribosomalen Proteine zu, die im Plastom mehrerer parasitischer, Plastiden-besitzender Spezies nicht mehr nachweisbar sind. Im Fall von rps15 könnte tatsächlich ein Verlust des Genes stattgefunden haben, im Fall der restlichen Gene ist eher mit einem Transfer in den Nukleus zu rechnen (rpl36 ausgenommen). Dies würde bedeuten, dass die Geschwindigkeit der erfolgreichen Etablierung eines Gentransfers in vielen parasitischen Spezies gegenüber grünen Pflanzen stark erhöht ist. Alle in E. coli nicht-essentiellen Proteine mit Homologen in Plastiden (rps15, rpl33, rpl36) sind auch dort, trotz ~1,5 Milliarden Jahren getrennter Evolution, nicht essentiell. Dieses Ergebnis bestätigt den schon früher festgestellten hohen Konservierungsgrad der bakteriellen und plastidären Translationsmaschinerien. Die Phänotypen der KO-Pflanzen der nicht-essentiellen Gene (rps15, rpl36) weisen auf eine interessante Rolle von S15 während der Ribosomenassemblierung hin und im Fall von L36 auf eine wichtige funktionelle Rolle im Plastiden-Ribosomen sowie auf eine Involvierung der Plastidentranslation in der Generierung eines retrograden Signals, welches die Blattform zu beeinflussen im Stande ist. Des Weiteren konnte eine Verbindung der Translationsaktivität mit der Ausbildung von Seitentrieben hergestellt werden, die vermutlich auf veränderte Auxinsynthese im Chloroplast zurückzuführen ist. Aus dem Folgeprojekt, bei dem Doppel-KO-Pflanzen nicht-essentieller ribosomaler Proteine erzeugt wurden, lässt sich auf eine relativ große Plastizität der Architektur von Plastidenribosomen schließen. Im zweiten Teil der Arbeit konnte erfolgreich ein Hochdurchsatz-Screeningsystem zur semiquantitativen Analyse von 192 verschiedenen miRNAs aus Chlamydomonas reinhardtii etabliert werden. Es gelang durch die Untersuchung von 23 verschiedenen Wachstums- und Stressbedingungen sowie Entwicklungsstadien mehrere miRNAs zu identifizieren, die eine differenzielle Expression zeigen sowie unter allen untersuchten Bedingungen konstant bleibende miRNAs nachzuweisen. Dadurch konnten mehrere vielversprechende Kandidaten-miRNAs ausgemacht werden, die nun eingehender untersucht werden können.
Ziel der vorliegenden Arbeit war es, die Auswirkungen von Glucose- und Lipidtoxizität auf die Funktion der β-Zellen von Langerhans-Inseln in einem diabetesresistenten (B6.V-Lepob/ob, ob/ob) sowie diabetessuszeptiblen (New Zealand Obese, NZO) Mausmodell zu untersuchen. Es sollten molekulare Mechanismen identifiziert werden, die zum Untergang der β-Zellen in der NZO-Maus führen bzw. zum Schutz der β-Zellen der ob/ob-Maus beitragen. Zunächst wurde durch ein geeignetes diätetisches Regime in beiden Modellen durch kohlenhydratrestriktive Ernährung eine Adipositas(Lipidtoxizität) induziert und anschließend durch Fütterung einer kohlenhydrathaltigen Diät ein Zustand von Glucolipotoxizität erzeugt. Dieses Vorgehen erlaubte es, in der NZO-Maus in einem kurzen Zeitfenster eine Hyperglykämie sowie einen β-Zelluntergang durch Apoptose auszulösen. Im Vergleich dazu blieben ob/ob-Mäuse längerfristig normoglykämisch und wiesen keinen β-Zelluntergang auf. Die Ursache für den β-Zellverlust war die Inaktivierung des Insulin/IGF-1-Rezeptor-Signalwegs, wie durch Abnahme von phospho-AKT, phospho-FoxO1 sowie des β-zellspezifischen Transkriptionsfaktors PDX1 gezeigt wurde. Mit Ausnahme des Effekts einer Dephosphorylierung von FoxO1, konnten ob/ob-Mäuse diesen Signalweg aufrechterhalten und dadurch einen Verlust von β-Zellen abwenden. Die glucolipotoxischen Effekte wurden in vitro an isolierten Inseln beider Stämme und der β-Zelllinie MIN6 bestätigt und zeigten, dass ausschließlich die Kombination hoher Glucose und Palmitatkonzentrationen (Glucolipotoxizität) negative Auswirkungen auf die NZO-Inseln und MIN6-Zellen hatte, während ob/ob-Inseln davor geschützt blieben. Die Untersuchung isolierter Inseln ergab, dass beide Stämme unter glucolipotoxischen Bedingungen keine Steigerung der Insulinexpression aufweisen und sich bezüglich ihrer Glucose-stimulierten Insulinsekretion nicht unterscheiden. Mit Hilfe von Microarray- sowie immunhistologischen Untersuchungen wurde gezeigt, dass ausschließlich ob/ob-Mäuse nach Kohlenhydratfütterung eine kompensatorische transiente Induktion der β-Zellproliferation aufwiesen, die in einer nahezu Verdreifachung der Inselmasse nach 32 Tagen mündete. Die hier erzielten Ergebnisse lassen die Schlussfolgerung zu, dass der β-Zelluntergang der NZO-Maus auf eine Beeinträchtigung des Insulin/IGF-1-Rezeptor-Signalwegs sowie auf die Unfähigkeit zur β- Zellproliferation zurückgeführt werden kann. Umgekehrt ermöglichen der Erhalt des Insulin/IGF-1-Rezeptor-Signalwegs und die Induktion der β-Zellproliferation in der ob/ob-Maus den Schutz vor einer Hyperglykämie und einem Diabetes.
Theory of mRNA degradation
(2012)
One of the central themes of biology is to understand how individual cells achieve a high fidelity in gene expression. Each cell needs to ensure accurate protein levels for its proper functioning and its capability to proliferate. Therefore, complex regulatory mechanisms have evolved in order to render the expression of each gene dependent on the expression level of (all) other genes. Regulation can occur at different stages within the framework of the central dogma of molecular biology. One very effective and relatively direct mechanism concerns the regulation of the stability of mRNAs. All organisms have evolved diverse and powerful mechanisms to achieve this. In order to better comprehend the regulation in living cells, biochemists have studied specific degradation mechanisms in detail. In addition to that, modern high-throughput techniques allow to obtain quantitative data on a global scale by parallel analysis of the decay patterns of many different mRNAs from different genes. In previous studies, the interpretation of these mRNA decay experiments relied on a simple theoretical description based on an exponential decay. However, this does not account for the complexity of the responsible mechanisms and, as a consequence, the exponential decay is often not in agreement with the experimental decay patterns. We have developed an improved and more general theory of mRNA degradation which provides a general framework of mRNA expression and allows describing specific degradation mechanisms. We have made an attempt to provide detailed models for the regulation in different organisms. In the yeast S. cerevisiae, different degradation pathways are known to compete and furthermore most of them rely on the biochemical modification of mRNA molecules. In bacteria such as E. coli, degradation proceeds primarily endonucleolytically, i.e. it is governed by the initial cleavage within the coding region. In addition, it is often coupled to the level of maturity and the size of the polysome of an mRNA. Both for S. cerevisiae and E. coli, our descriptions lead to a considerable improvement of the interpretation of experimental data. The general outcome is that the degradation of mRNA must be described by an age-dependent degradation rate, which can be interpreted as a consequence of molecular aging of mRNAs. Within our theory, we find adequate ways to address this much debated topic from a theoretical perspective. The improvements of the understanding of mRNA degradation can be readily applied to further comprehend the mRNA expression under different internal or environmental conditions such as after the induction of transcription or stress application. Also, the role of mRNA decay can be assessed in the context of translation and protein synthesis. The ultimate goal in understanding gene regulation mediated by mRNA stability will be to identify the relevance and biological function of different mechanisms. Once more quantitative data will become available, our description allows to elaborate the role of each mechanism by devising a suitable model.
Climate is the principal driving force of hydrological extremes like floods and attributing generating mechanisms is an essential prerequisite for understanding past, present, and future flood variability. Successively enhanced radiative forcing under global warming enhances atmospheric water-holding capacity and is expected to increase the likelihood of strong floods. In addition, natural climate variability affects the frequency and magnitude of these events on annual to millennial time-scales. Particularly in the mid-latitudes of the Northern Hemisphere, correlations between meteorological variables and hydrological indices suggest significant effects of changing climate boundary conditions on floods. To date, however, understanding of flood responses to changing climate boundary conditions is limited due to the scarcity of hydrological data in space and time. Exploring paleoclimate archives like annually laminated (varved) lake sediments allows to fill this gap in knowledge offering precise dated time-series of flood variability for millennia. During river floods, detrital catchment material is eroded and transported in suspension by fluid turbulence into downstream lakes. In the water body the transport capacity of the inflowing turbidity current successively diminishes leading to the deposition of detrital layers on the lake floor. Intercalated into annual laminations these detrital layers can be dated down to seasonal resolution. Microfacies analyses and X-ray fluorescence scanning (µ-XRF) at 200 µm resolution were conducted on the varved Mid- to Late Holocene interval of two sediment profiles from pre-alpine Lake Ammersee (southern Germany) located in a proximal (AS10prox) and distal (AS10dist) position towards the main tributary River Ammer. To shed light on sediment distribution within the lake, particular emphasis was (1) the detection of intercalated detrital layers and their micro-sedimentological features, and (2) intra-basin correlation of these deposits. Detrital layers were dated down to the season by microscopic varve counting and determination of the microstratigraphic position within a varve. The resulting chronology is verified by accelerator mass spectrometry (AMS) 14C dating of 14 terrestrial plant macrofossils. Since ~5500 varve years before present (vyr BP), in total 1573 detrital layers were detected in either one or both of the investigated sediment profiles. Based on their microfacies, geochemistry, and proximal-distal deposition pattern, detrital layers were interpreted as River Ammer flood deposits. Calibration of the flood layer record using instrumental daily River Ammer runoff data from AD 1926 to 1999 proves the flood layer succession to represent a significant time-series of major River Ammer floods in spring and summer, the flood season in the Ammersee region. Flood layer frequency trends are in agreement with decadal variations of the East Atlantic-Western Russia (EA-WR) atmospheric pattern back to 200 yr BP (end of the used atmospheric data) and solar activity back to 5500 vyr BP. Enhanced flood frequency corresponds to the negative EA-WR phase and reduced solar activity. These common links point to a central role of varying large-scale atmospheric circulation over Europe for flood frequency in the Ammersee region and suggest that these atmospheric variations, in turn, are likely modified by solar variability during the past 5500 years. Furthermore, the flood layer record indicates three shifts in mean layer thickness and frequency of different manifestation in both sediment profiles at ~5500, ~2800, and ~500 vyr BP. Combining information from both sediment profiles enabled to interpret these shifts in terms of stepwise increases in mean flood intensity. Likely triggers of these shifts are gradual reduction of Northern Hemisphere orbital summer forcing and long-term solar activity minima. Hypothesized atmospheric response to this forcing is hemispheric cooling that enhances equator-to-pole temperature gradients and potential energy in the troposphere. This energy is transferred into stronger westerly cyclones, more extreme precipitation, and intensified floods at Lake Ammersee. Interpretation of flood layer frequency and thickness data in combination with reanalysis models and time-series analysis allowed to reconstruct the flood history and to decipher flood triggering climate mechanisms in the Ammersee region throughout the past 5500 years. Flood frequency and intensity are not stationary, but influenced by multi-causal climate forcing of large-scale atmospheric modes on time-scales from years to millennia. These results challenge future projections that propose an increase in floods when Earth warms based only on the assumption of an enhanced hydrological cycle.