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ResearcherID
- J-8841-2015 (1)
Due to the earth´s rotation around itself and the sun, rhythmic daily and seasonal changes in illumination, temperature and many other environmental factors occur. Adaptation to these environmental rhythms presents a considerable advantage to survival. Thus, almost all living beings have developed a mechanism to time their behavior in accordance. This mechanism is the endogenous clock. If it fulfills the criteria of (1) entraining to zeitgebers (2) free-running behavior with a period of ~ 24 hours (3) temperature compensation, it is also referred to as “circadian clock”. Well-timed behavior is crucial for eusocial insects, which divide their tasks among different behavioral castes and need to respond to changes in the environment quickly and in an orchestrated fashion. Circadian rhythms have thus been studied and observed in many eusocial species, from ants to bees. The underlying mechanism of this clock is a molecular feedback loop that generates rhythmic changes in gene expression and protein levels with a phase length of approximately 24 hours. The properties of this feedback loop are well characterized in many insects, from the fruit fly Drosophila melanogaster, to the honeybee Apis mellifera. Though the basic principles and components of this loop are seem similar at first glance, there are important differences between the Drosophila feedback loop and that of hymenopteran insects, whose loop resembles the mammalian clock loop. The protein PERIOD (PER) is thought to be a part of the negative limb of the hymenopteran clock, partnering with CRYPTOCHROME (CRY). The anatomical location of the clock-related neurons and the PDF-network (a putative in- and output mediator of the clock) is also well characterized in Drosophila, the eusocial honeybee as well as the nocturnal cockroach Leucophea maderae. The circadian behavior, anatomy of the clock and its molecular underpinnings were studied in the carpenter ant Camponotus floridanus, a eusocial insect Locomotor activity recordings in social isolation proved that the majority of ants could entrain to different LD cycles, free-ran in constant darkness and had a temperature-compensated clock with a period slightly shorter than 24 hours. Most individuals proved to be nocturnal, but different types of activity like diurnality, crepuscularity, rhythmic activity during both phases of the LD, or arrhythmicity were also observed. The LD cycle had a slight influence on the distribution of these activities among individuals, with more diurnal ants at shorter light phases. The PDF-network of C. floridanus was revealed with the anti-PDH antibody, and partly resembled that of other eusocial or nocturnal insects. A comparison of minor and major worker brains, only revealed slight differences in the number of somata and fibers crossing the posterior midline. All in all, most PDF-structures that are conserved in other insects where found, with numerous fibers in the optic lobes, a putative accessory medulla, somata located near the proximal medulla and many fibers in the protocerebrum. A putative connection between the mushroom bodies, the optic lobes and the antennal lobes was found, indicating an influence of the clock on olfactory learning. Lastly, the location and intensity of PER-positive cell bodies at different times of a 24 hour day was established with an antibody raised against Apis mellifera PER. Four distinct clusters, which resemble those found in A. mellifera, were detected. The clusters could be grouped in dorsal and lateral neurons, and the PER-levels cycled in all examined clusters with peaks around lights on and lowest levels after lights off.
In summary, first data on circadian behavior and the anatomy and workings of the clock of C. floridanus was obtained. Firstly, it´s behavior fulfills all criteria for the presence of a circadian clock. Secondly, the PDF-network is very similar to those of other insects. Lastly, the location of the PER cell bodies seems conserved among hymenoptera. Cycling of PER levels within 24 hours confirms the suspicion of its role in the circadian feedback loop.
One of the most significant technological advances in history was driven by the utilization of a new material class: semiconductors.
Its most important application being the transistor, which is indispensable in our everyday life. The technological advance in the semiconductor industry, however, is about to slow down. Making transistors ever smaller to increase the performance and trying to reduce and deal with the dissipative heat will soon reach the limits dictated by quantum mechanics with Moore himself, predicting the death of his famous law in the next decade.
A possible successor for semiconductor transistors is the recently discovered material class of topological insulators. A material which in its bulk is insulating but has topological protected metallic surface states or edge states at its boundary. Their electrical transport characteristics include forbidden backscattering and spin-momentum-locking with the spin of the electron being perpendicular to its momentum. Topological insulators therefore offer an opportunity for high performance devices with low dissipation, and applications in spintronic where data is stored and processed at the same point.
The topological insulator Bi\(_2\)Se\(_3\) and related compounds offer relatively high energy band gaps and a rather simple band structure with a single dirac cone at the gamma point of the Brillouin zone. These characteritics make them ideal candidates to study the topological surface state in electrical transport experiments and explore its physics.
The interaction of synaptic proteins orchestrate the function of one of the most complex organs, the brain. The multitude of molecular elements influencing neurological correlations makes imaging processes complicated since conventional fluorescence microscopy methods are unable to resolve structures beyond the diffraction-limit.
The implementation of super-resolution fluorescence microscopy into the field of neuroscience allows the visualisation of the fine details of neural connectivity. The key element of my thesis is the super-resolution technique dSTORM (direct Stochastic Optical Reconstruction Microscopy) and its optimisation as a multi-colour approach. Capturing more than one target, I aim to unravel the distribution of synaptic proteins with nanometer precision and set them into a structural and quantitative context with one another. Therefore dSTORM specific protocols are optimized to serve the peculiarities of particular neural samples.
In one project the brain derived neurotrophic factor (BDNF) is investigated in primary, hippocampal neurons. With a precision beyond 15 nm, preand post-synaptic sites can be identified by staining the active zone proteins bassoon and homer. As a result, hallmarks of mature synapses can be exhibited. The single molecule sensitivity of dSTORM enables the measurement of endogenous BDNF and locates BDNF granules aligned with glutamatergic pre-synapses. This data proofs that hippocampal neurons are capable of enriching BDNF within the mature glutamatergic pre-synapse, possibly influencing synaptic plasticity.
The distribution of the metabotropic glutamate receptor mGlu4 is investigated in physiological brain slices enabling the analysis of the receptor in its natural environment. With dual-colour dSTORM, the spatial arrangement of the mGlu4 receptor in the pre-synaptic sites of parallel fibres in the molecular layer of the mouse cerebellum is visualized, as well as a four to six-fold increase in the density of the receptor in the active zone compared to the nearby environment. Prior functional measurements show that metabotropic glutamate receptors influence voltage-gated calcium channels and proteins that are involved in synaptic vesicle priming. Corresponding dSTORM data indeed suggests that a subset of the mGlu4 receptor is correlated with the voltage-gated calcium channel Cav2.1 on distances around 60 nm.
These results are based on the improvement of the direct analysis of localisation data. Tools like coordinated based correlation analysis and nearest neighbour analysis of clusters centroids are used complementary to map protein connections of the synapse. Limits and possible improvements of these tools are discussed to foster the quantitative analysis of single molecule localisation microscopy data.
Performing super-resolution microscopy on complex samples like brain slices benefits from a maximised field of view in combination with the visualisation of more than two targets to set the protein of interest in a cellular context. This challenge served as a motivation to establish a workflow for correlated structured illumination microscopy (SIM) and dSTORM. The development of the visualisation software coSIdSTORM promotes the combination of these powerful super-resolution techniques even on separated setups. As an example, synapses in the cerebellum that are affiliated to the parallel fibres and the dendrites of the Purkinje cells are identified by SIM and the protein bassoon of those pre-synapses is visualised threedimensionally with nanoscopic precision by dSTORM.
In this work I placed emphasis on the improvement of multi-colour super-resolution imaging and its analysing tools to enable the investigation of synaptic proteins. The unravelling of the structural arrangement of investigated proteins supports the building of a synapse model and therefore helps to understand the relation between structure and function in neural transmission processes.
Chronic Obstructive Pulmonary Disease (COPD) exacerbations are a considerable reason for increased morbidity and mortality in patients. Infections with influenza virus (H1N1), respiratory syncytial virus (RSV) or nontypeable Haemophilus influenzae (NTHi) are important triggers of exacerbations. To date, no treatments are available which can stop the progression of COPD. Novel approaches are urgently needed. Pre-clinical models of the disease are crucial for the development of novel therapeutic options.
In order to establish pre-clinical models which mimic aspects of human COPD exacerbations, mice were exposed to cigarette smoke (CS) and additionally infected with H1N1, RSV and/or NTHi. Clinically relevant treatments such as the corticosteroids Fluticasone propionate and Dexamethasone, the phosphodiesterase-4 (PDE-4) inhibitor Roflumilast and the long-acting muscarinic receptor antagonist Tiotropium were tested in the established models. Furthermore, a novel treatment approach using antibodies (Abs) directed against IL-1α, IL-1β or IL-1R1 was examined in the established CS/H1N1 model. Levels of IFN-γ, IL-1β, IL-2, IL-6, KC, TNF-α, RANTES, IL-17, MCP-1, MIP 1α and MIP-1β were measured in lung homogenate. Numbers of total cells, neutrophils and macrophages were assessed in bronchoalveolar lavage (BAL) fluid. Hematoxylin- and eosin- (H&E-) stained lung slices were analyzed to detect pathological changes. Quantitative polymerase-chain-reaction (qPCR) was used to investigate gene expression of ICAM-1 and MUC5 A/C. The viral/bacterial load was investigated in lung homogenate or BAL fluid. In addition to the in vivo studies, the effects of the above mentioned treatments were investigated in vitro in H1N1, RSV or NTHi-infected (primary) human bronchial epithelial cells using submerged or air-liquid-interface (ALI) cell culture systems.
Four pre-clinical models (CS/H1N1, CS/RSV, CS/NTHi, CS/H1N1/NTHi) were established depicting clinically relevant aspects of COPD exacerbations such as increased inflammatory cells and cytokines in the airways and impaired lung function.
In the CS/H1N1 model, Tiotropium improved lung function and was superior in reducing inflammation in comparison to Fluticasone or Roflumilast. Moreover, Fluticasone increased the loss of body-weight, levels of IL-6, KC and TNF-α and worsened lung function. In CS/RSV-exposed mice Tiotropium but not Fluticasone or Roflumilast treatment reduced neutrophil numbers and IL-6 and TNF α levels in the lung. The viral load of H1N1 and RSV was significantly elevated in CS/virus-exposed mice and NCI-H292 cells after Fluticasone and Dexamethasone treatment. The results from these studies demonstrate that Tiotropium has anti-inflammatory effects on CS/virus-induced inflammation and might help to explain the observed reduction of exacerbation rates in Tiotropium-treated COPD patients. Furthermore, the findings from this work indicate that treatment with Fluticasone or Dexamethasone might not be beneficial to reduce inflammation in the airways of COPD patients and supports clinical studies that link treatment with corticosteroids to an increased risk for pneumonia.
Testing of anti-IL-1α, anti-IL-1β or anti-IL-1R1 Abs in the CS/H1N1 model suggests that, in line with clinical data, antagonization of IL-1β is not sufficient to reduce pulmonary inflammation and indicates a predominant role of IL-1α in CS/virus-induced airway inflammation. In line with the in vivo findings, anti-IL-1α but not anti-IL-1β Abs reduced levels of TNF-α and IL-6 in H1N1-infected primary human bronchial epithelial ALI cell culture. Blocking the IL-1R1 provided significant inhibitory effects on inflammatory cells in vivo but was inferior compared to inhibiting both its soluble ligands IL-1α and IL-1β. Concomitant usage of Abs against IL-1α/IL-1β revealed strong effects and reduced total cells, neutrophils and macrophages. Additionally, levels of KC, IL-6, TNF-α, MCP-1, MIP-1α and MIP-1β were significantly reduced and ICAM-1 mRNA expression was attenuated. These results suggest that combined inhibition of IL-1α/IL-1β might be beneficial to reduce inflammation and exacerbations in COPD patients. Moreover, combined targeting of both IL-1α/IL-1β might be more efficient compared to inhibition of the IL-1R1.
As in the CS/virus models, corticosteroid treatment failed to reduce inflammatory cells in the CS/NTHi and CS/H1N1/NTHi models, increased the loss of body-weight and the bacterial load. Furthermore, Roflumilast administration had no significant effects on cell counts or cytokines. However, it improved compliance in the CS/NTHi model. Treatment with Azithromycin reduced the bacterial load in the CS/NTHi model and reduced numbers of total cells, neutrophils, macrophages and levels of KC and TNF-α in the CS/H1N1/NTHi model.
In conclusion, the established CS/H1N1, CS/RSV, CS/NTHi, CS/H1N1/NTHi models depict clinically relevant aspects of human COPD exacerbations in mice and provide the opportunity to investigate underlying disease mechanisms and to test novel therapies.
Imagine a technology that automatically creates a full 3D thermal model of an environment and detects temperature peaks in it. For better orientation in the model it is enhanced with color information. The current state of the art for analyzing temperature related issues is thermal imaging. It is relevant for energy efficiency but also for securing important infrastructure such as power supplies and temperature regulation systems. Monitoring and analysis of the data for a large building is tedious as stable conditions need to be guaranteed for several hours and detailed notes about the pose and the environment conditions for each image must be taken. For some applications repeated measurements are necessary to monitor changes over time. The analysis of the scene is only possible through expertise and experience.
This thesis proposes a robotic system that creates a full 3D model of the environment with color and thermal information by combining thermal imaging with the technology of terrestrial laser scanning. The addition of a color camera facilitates the interpretation of the data and allows for other application areas. The data from all sensors collected at different positions is joined in one common reference frame using calibration and scan matching. The first part of the thesis deals with 3D point cloud processing with the emphasis on accessing point cloud data efficiently, detecting planar structures in the data and registering multiple point clouds into one common coordinate system. The second part covers the autonomous exploration and data acquisition with a mobile robot with the objective to minimize the unseen area in 3D space. Furthermore, the combination of different modalities, color images, thermal images and point cloud data through calibration is elaborated. The last part presents applications for the the collected data. Among these are methods to detect the structure of building interiors for reconstruction purposes and subsequent detection and classification of windows. A system to project the gathered thermal information back into the scene is presented as well as methods to improve the color information and to join separately acquired point clouds and photo series.
A full multi-modal 3D model contains all the relevant geometric information about the recorded scene and enables an expert to fully analyze it off-site. The technology clears the path for automatically detecting points of interest thereby helping the expert to analyze the heat flow as well as localize and identify heat leaks. The concept is modular and neither limited to achieving energy efficiency nor restricted to the use in combination with a mobile platform. It also finds its application in fields such as archaeology and geology and can be extended by further sensors.
Genetic foundation of unrivaled survival strategies - Of water bears and carnivorous plants -
(2018)
All living organisms leverage mechanisms and response systems to optimize reproduction, defense, survival, and competitiveness within their natural habitat. Evolutionary theories such as the universal adaptive strategy theory (UAST) developed by John Philip Grime (1979) attempt to describe how these systems are limited by the trade-off between growth, maintenance and regeneration; known as the universal three-way trade-off. Grime introduced three adaptive strategies that enable organisms to coop with either high or low intensities of stress (e.g., nutrient deficiency) and environmental disturbance (e.g., seasons). The competitor is able to outcompete other organisms by efficiently tapping available resources in environments of low intensity stress and disturbance (e.g., rapid growers). A ruderal specism is able to rapidly complete the life cycle especially during high intensity disturbance and low intensity stress (e.g., annual colonizers). The stress tolerator is able to respond to high intensity stress with physiological variability but is limited to low intensity disturbance environments. Carnivorous plants like D. muscipula and tardigrades like M. tardigradum are two extreme examples for such stress tolerators. D. muscipula traps insects in its native habitat (green swamps in North and South Carolina) with specialized leaves and thereby is able to tolerate nutrient deficient soils. M. tardigradum on the other side, is able to escape desiccation of its terrestrial habitat like mosses and lichens which are usually covered by a water film but regularly fall completely dry. The stress tolerance of the two species is the central study object of this thesis. In both cases, high througput sequencing data and methods were used to test for transcriptomic (D. muscipula) or genomic adaptations (M. tardigradum) which underly the stress tolerance. A new hardware resource including computing cluster and high availability storage system was implemented in the first months of the thesis work to effectively analyze the vast amounts of data generated for both projects. Side-by-side, the data management resource TBro [14] was established together with students to intuitively approach complex biological questions and enhance collaboration between researchers of several different disciplines. Thereafter, the unique trapping abilities of D. muscipula were studied using a whole transcriptome approach. Prey-dependent changes of the transcriptional landscape as well as individual tissue-specific aspects of the whole plant were studied. The analysis revealed that non-stimulated traps of D. muscipula exhibit the expected hallmarks of any typical leaf but operates evolutionary conserved stress-related pathways including defense-associated responses when digesting prey. An integrative approach, combining proteome and transcriptome data further enabled the detailed description of the digestive cocktail and the potential nutrient uptake machinery of the plant. The published work [25] as well as a accompanying video material (https://www.eurekalert.org/pub_releases/ 2016-05/cshl-fgr042816.php; Video credit: Sönke Scherzer) gained global press coverage and successfully underlined the advantages of D. muscipula as experimental system to understand the carnivorous syndrome. The analysis of the peculiar stress tolerance of M. tardigradum during cryptobiosis was carried out using a genomic approach. First, the genome size of M. tardigradum was estimated, the genome sequenced, assembled and annotated. The first draft of M. tardigradum and the workflow used to established its genome draft helped scrutinizing the first ever released tardigrade genome (Hypsibius dujardini) and demonstrated how (bacterial) contamination can influence whole genome analysis efforts [27]. Finally, the
M. tardigradum genome was compared to two other tardigrades and all species present in the current release of the Ensembl Metazoa database. The analysis revealed that tardigrade genomes are not that different from those of other Ecdysozoa. The availability of the three genomes allowed the delineation of their phylogenetic position within the Ecdysozoa and placed them as sister taxa to the nematodes. Thereby, the comparative analysis helped to identify evolutionary trends within this metazoan lineage. Surprisingly, the analysis did not reveal general mechanisms (shared by all available tardigrade genomes) behind the arguably most peculiar feature of tardigrades; their enormous stress tolerance. The lack of molecular evidence for individual tardigrade species (e.g., gene expression data for M. tardigradum) and the non-existence of a universal experimental framework which enables hypothesis testing withing the whole phylum Tardigrada, made it nearly impossible to link footprints of genomic adaptations to the unusual physiological capabilities. Nevertheless, the (comparative) genomic framework established during this project will help to understand how evolution tinkered, rewired and modified existing molecular systems to shape the remarkable phenotypic features of tardigrades.
The goal of this work is to improve the understanding of adsorption-induced deformation in nanoporous (and in particular microporous) materials in order to explore its potential for material characterization and provide guidelines for related technical applications such as adsorption-driven actuation. For this purpose this work combines in-situ dilatometry measurements with in-depth modeling of the obtained adsorption-induced strains. A major advantage with respect to previous studies is the combination of the dilatometric setup and a commercial sorption instrument resulting in high quality adsorption and strain isotherms. The considered model materials are (activated and thermally annealed) carbon xerogels, a sintered silica aerogel, a sintered hierarchical structured porous silica and binderless zeolites of type LTA and FAU; this selection covers micro-, meso- and macroporous as well as ordered and disordered model materials.
All sample materials were characterized by scanning electron microscopy, gas adsorption and sound velocity measurements. In-situ dilatometry measurements on mesoporous model materials were performed for the adsorption of N2 at 77 K, while microporous model materials were also investigated for CO2 adsorption at 273 K, Ar adsorption at 77 K and H2O adsorption at 298 K. Within this work the available in-situ dilatometry setup was revised to improve resolution and reproducibility of measurements of small strains at low relative pressures, which are of particular relevance for microporous materials.
The obtained experimental adsorption and strain isotherms of the hierarchical structured porous silica and a micro-macroporous carbon xerogel were quantitatively analyzed based on the adsorption stress model; this approach, originally proposed by Ravikovitch and Neimark, was extended for anisotropic pore geometries within this work. While the adsorption in silica mesopores could be well described by the classical and analytical theory of Derjaguin, Broekhoff and de Boer, the adsorption in carbon micropores required for comprehensive nonlocal density functional theory calculations. To connect adsorption-induced stresses and strains, furthermore mechanical models for the respective model materials were derived. The resulting theoretical framework of adsorption, adsorption stress and mechanical model was applied to the experimental data yielding structural and mechanical information about the model materials investigated, i.e., pore size or pore size distribution, respectively, and mechanical moduli of the porous matrix and the nonporous solid skeleton. The derived structural and mechanical properties of the model materials were found to be consistent with independent measurements and/or literature values. Noteworthy, the proposed extension of the adsorption stress model proved to be crucial for the correct description of the experimental data.
Furthermore, it could be shown that the adsorption-induced deformation of disordered mesoporous aero-/xerogel structures follows qualitatively the same mechanisms obtained for the ordered hierarchical structured porous silica. However, respective quantitative modeling proved to be challenging due to the ill-shaped pore geometry of aero-/xerogels; good agreement between model and experiment could only be achieved for the filled pore regime of the adsorption isotherm and the relative pressure range of monolayer formation. In the intermediate regime of multilayer formation a more complex model than the one proposed here is required to correctly describe stress related to the curved adsorbate-adsorptive interface. Notably, for micro-mesoporous carbon xerogels it could be shown that micro- and mesopore related strain mechanisms superimpose one another.
The strain isotherms of the zeolites were only qualitatively evaluated. The result for the FAU type zeolite is in good agreement with other experiments reported in literature and the theoretical understanding derived from the adsorption stress model. On the contrary, the strain isotherm of the LTA type zeolite is rather exceptional as it shows monotonic expansion over the whole relative pressure range. Qualitatively this type of strain isotherm can also be explained by the adsorption stress model, but a respective quantitative analysis is beyond the scope of this work.
In summary, the analysis of the model materials' adsorption-induced strains proved to be a suitable tool to obtain information on their structural and mechanical properties including the stiffness of the nonporous solid skeleton. Investigations on the carbon xerogels modified by activation and thermal annealing revealed that adsorption-induced deformation is particularly suited to analyze even small changes of carbon micropore structures.
In this dissertation the electronic and high-energy optical properties of thin nanoscale
films of the magnetic topological insulator (MTI) (V,Cr)y(BixSb1-x)2-yTe3 are studied
by means of X-ray photoelectron spectroscopy (XPS) and electron energy-loss
spectroscopy (EELS). Magnetic topological insulators are presently of broad interest
as the combination of ferromagnetism and spin-orbit coupling in these materials
leads to a new topological phase, the quantum anomalous Hall state (QAHS), with
dissipation less conduction channels. Determining and controlling the physical
properties of these complex materials is therefore desirable for a fundamental understanding
of the QAHS and for their possible application in spintronics. EELS can
directly probe the electron energy-loss function of a material from which one can
obtain the complex dynamic dielectric function by means of the Kramers-Kronig
transformation and the Drude-Lindhard model of plasmon oscillations.
The XPS core-level spectra in (V,Cr)y(BixSb1-x)2-yTe3 are analyzed in detail with
regards to inelastic background contributions. It is shown that the spectra can be
accurately described based on the electron energy-loss function obtained from an
independent EELS measurement. This allows for a comprehensive and quantitative
analysis of the XPS data, which will facilitate future core-level spectroscopy studies
in this class of topological materials. From the EELS data, furthermore, the bulk and
surface optical properties were estimated, and compared to ab initio calculations
based on density functional theory (DFT) performed in the GW approximation
for Sb2Te3. The experimental results show a good agreement with the calculated
complex dielectric function and the calculated energy-loss function. The positions of
the main plasmon modes reported here are expected to be generally similar in other
materials in this class of nanoscale TI films. Hence, the present work introduces
EELS as a powerful method to access the high-energy optical properties of TI
thin films. Based on the presented results it will be interesting to explore more
systematically the effects of stoichiometry, magnetic doping, film thickness and
surface morphology on the electron-loss function, potentially leading to a better
understanding of the complex interplay of structural, electronic, magnetic and
optical properties in MTI nanostructures.
Coherent Multidimensional Spectroscopy in Molecular Beams and Liquids Using Incoherent Observables
(2018)
The aim of the present work was to implement an experimental approach that enables coherent two-dimensional (2D) electronic spectroscopy of samples in various states of matter. For samples in the liquid phase, a setup was realized that utilizes the sample fluorescence for the acquisition of 2D spectra. Whereas the liquid-phase approach has been established before, coherent 2D spectroscopy on gaseous samples in a molecular beam as developed in this work is in fact a new method. It employs for the first time cations in a time-of-flight mass spectrometer for signal detection and was used to obtain the first ion-selective 2D spectra of a molecular-beam sample. Additionally, a new acquisition concept was developed in this thesis that significantly decreases measurement times in 2D spectroscopy using optimized sparse sampling and a compressed-sensing reconstruction algorithm.
Characteristic for the variant of 2D spectroscopy presented in this work is the usage of a phase-coherent sequence of four laser pulses in a fully collinear geometry for sample excitation. The pulse sequence was generated by a custom-designed pulse shaper that is capable of rapid scanning by changing the pulse parameters such as time delays and phases with the repetition rate of the laser. The sample's response was detected by monitoring incoherent observables that arise from the final-state population, for instance fluorescence or cations. Phase cycling, i.e., signal acquisition with different combinations of the relative phases of the excitation pulses, was applied to extract nonlinear signal contributions from the full signal during data analysis.
Liquid-phase 2D fluorescence spectroscopy was established with the laser dye cresyl violet as a sample molecule, confirming coherent oscillations previously observed in literature that are originating from vibronic coherences in specific regions of the 2D spectrum.
The data set of this experiment was used subsequently to introduce optimized sparse sampling in 2D spectroscopy. An optimization algorithm was implemented in order to find the best sampling pattern while taking only one quarter of the regular time-domain sampling points, thereby reducing the acquisition time by a factor of four. Signal recovery was based on a new and compact representation of 2D spectra using the von Neumann basis, which required about six times less coefficients than the Fourier basis to retain the relevant information. Successful reconstruction was shown by recovering the coherent oscillations in cresyl violet from a reduced data set.
Finally, molecular-beam coherent 2D spectroscopy was introduced with an investigation of ionization pathways in highly-excited nitrogen dioxide, revealing transitions to discrete auto-ionizing states as the dominant contribution to the ion signal. Furthermore, the advantage of the time-of-flight approach to obtain reactant and product 2D spectra simultaneously enabled the observation of distinct differences in the multiphoton-ionization response functions of the nitrogen dioxide cation and the nitrogen oxide ionic fragment.
The developed experimental techniques of this work will facilitate fast acquisition of 2D spectra for samples in various states of matter and permit reliable direct comparison of results. Therefore, they pave the way to study the properties of quantum coherences during photophysical processes or photochemical reactions in different environments.
Staphylococcus aureus asymptomatically colonises one third of the healthy human population, finding its niche in the nose and on skin. Apart from being a commensal, it is also an important opportunistic human pathogen capable of destructing tissue, invading host cells and killing them from within. This eventually contributes to severe hospital- and community-acquired infections. Methicillin-resistant Staphylococcus aureus (MRSA), resistant to commonly used antibiotics are protected when residing within the host cell.
This doctoral thesis is focused on the investigation of staphylococcal factors governing intracellular virulence and subsequent host cell death. To initiate an unbiased approach to conduct this study, complex S. aureus mutant pools were generated using transposon insertional mutagenesis. Genome-wide infection screens were performed using these S. aureus transposon mutant pools in vitro and in vivo, followed by analysis using Transposon insertion site deep sequencing (Tn-seq) technology.
Amongst several other factors, this study identified a novel regulatory system in S. aureus that controls pathogen-induced host cytotoxicity and intra-host survival. The primary components of this system are an AraC-family transcription regulator called Repressor of surface proteins (Rsp) and a virulence associated non-coding RNA, SSR42. Mutants within rsp exhibit enhanced intra-host survival in human epithelial cells and delayed host cytotoxicity. Global gene-expression profiling by RNA-seq demonstrated that Rsp controls the expression of SSR42, several cytotoxins and other bacterial factors directed against the host immune system. Rsp enhances S. aureus toxin response when triggered by hydrogen peroxide, an antimicrobial substance employed by neutrophils to destroy pathogens. Absence of rsp reduces S. aureus-induced neutrophil damage and early lethality during mouse pneumonia, but still permits blood stream infection. Intriguingly, S. aureus lacking rsp exhibited enhanced survival in human macrophages, which hints towards a Trojan horse-like phenomenon and could facilitate dissemination within the host.
Hence, Rsp emerged as a global regulator of bacterial virulence, which has an impact on disease progression with prolonged intra-cellular survival, delayed-lethality but allows disseminated manifestation of disease. Moreover, this study exemplifies the use of genome-wide approaches as useful resources for identifying bacterial factors and deduction of its pathogenesis.