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We present a Green's function based treatment of the effects of electron-phonon coupling on transport through a molecular quantum dot in the quantum limit. Thereby we combine an incomplete variational Lang-Firsov approach with a perturbative calculation of the electron-phonon self energy in the framework of generalised Matsubara Green functions and a Landauer-type transport description. Calculating the ground-state energy, the dot single-particle spectral function and the linear conductance at finite carrier density, we study the low-temperature transport properties of the vibrating quantum dot sandwiched between metallic leads in the whole electron-phonon coupling strength regime. We discuss corrections to the concept of an anti-adiabatic dot polaron and show how a deformable quantum dot can act as a molecular switch.
In classical Drude theory the conductivity is determined by the mass of the propagating particles and the mean free path between two scattering events. For a quantum particle this simple picture of diffusive transport loses relevance if strong correlations dominate the particle motion. We study a situation where the propagation of a fermionic particle is possible only through creation and annihilation of local bosonic excitations. This correlated quantum transport process is outside the Drude picture, since one cannot distinguish between free propagation and intermittent scattering. The characterization of transport is possible using the Drude weight obtained from the f-sum rule, although its interpretation in terms of free mass and mean free path breaks down. For the situation studied we calculate the Green's function and Drude weight using a Green's functions expansion technique, and discuss their physical meaning.
A quantum kinetic approach is presented to investigate the energy relaxation of dense strongly coupled two-temperature plasmas. We derive a balance equation for the mean total energy of a plasma species including a quite general expression for the transfer rate. An approximation scheme is used leading to an expression of the transfer rates for systems with coupled modes relevant for the warm dense matter regime. The theory is then applied to dense beryllium plasmas under conditions such as realized in recent experiments. Special attention is paid to the influence of correlation and quantum effects on the relaxation process.
In order to clarify the physics of the crossover from a spin-density-wave (SDW) Mott insulator to a charge-density-wave (CDW) Peierls insulator in one-dimensional (1D) systems, we investigate the Hubbard-Holstein Hamiltonian at half filling within a density matrix renormalisation group (DMRG) approach. Determining the spin and charge correlation exponents, the momentum distribution function, and various excitation gaps, we confirm that an intervening metallic phase expands the SDW-CDW transition in the weak-coupling regime.
We discuss a numerical method to study electron transport in mesoscopic devices out of equilibrium. The method is based on the solution of operator equations of motion, using efficient Chebyshev time propagation techniques. Its peculiar feature is the propagation of operators backwards in time. In this way the resource consumption scales linearly with the number of states used to represent the system. This allows us to calculate the current for non-interacting electrons in large one-, two- and three-dimensional lead-device configurations with time-dependent voltages or potentials. We discuss the technical aspects of the method and present results for an electron pump device and a disordered system, where we find transient behaviour that exists for a very long time and may be accessible to experiments.
Because of some disadvantages of chemical disinfection in dental practice (especially denture cleaning), we investigated the effects of physical methods on Candida albicans biofilms. For this purpose, the antifungal efficacy of three different low-temperature plasma devices (an atmospheric pressure plasma jet and two different dielectric barrier discharges (DBDs)) on Candida albicans biofilms grown on titanium discs in vitro was investigated. As positive treatment controls, we used 0.1% chlorhexidine digluconate (CHX) and 0.6% sodium hypochlorite (NaOCl). The corresponding gas streams without plasma ignition served as negative treatment controls. The efficacy of the plasma treatment was determined evaluating the number of colony-forming units (CFU) recovered from titanium discs. The plasma treatment reduced the CFU significantly compared to chemical disinfectants. While 10 min CHX or NaOCl exposure led to a CFU log10 reduction factor of 1.5, the log10 reduction factor of DBD plasma was up to 5. In conclusion, the use of low-temperature plasma is a promising physical alternative to chemical antiseptics for dental practice.
Behavior of a porous particle in a radiofrequency plasma under pulsed argon ion beam bombardment
(2010)
The behavior of a single porous particle with a diameter of 250 μm levitating in a radiofrequency (RF) plasma under pulsed argon ion beam bombardment was investigated. The motion of the particle under the action of the ion beam was observed to be an oscillatory motion. The Fourier-analyzed motion is dominated by the excitation frequency of the pulsed ion beam and odd higher harmonics, which peak near the resonance frequency. The appearance of even harmonics is explained by a variation of the particles's charge depending on its position in the plasma sheath. The Fourier analysis also allows a discussion of neutral and ion forces. The particle's charge was derived and compared with theoretical estimates based on the orbital motion-limited (OML) model using also a numerical simulation of the RF discharge. The derived particle's charge is about 7–15 times larger than predicted by the theoretical models. This difference is attributed to the porous structure of the particle.
1. "Sole or Whole" – Quilting the Racialized Subject Calgary feminist and scholar Aruna Srivastava tackles the complex question of what it means to be "mixed-race/mixedblood/halfbreed/mestizo/hybrid/hyphenated?" in her editorial to Hyphe Nation (1996). In response to her question, this study of contemporary African-Canadian literature suggests that mixed-race Canadians are often constructed as the Other in Canadian society. In consequence, constructions of "racial hybridity" in African-Canadian literature usually aim at carving out a space that doesnt marginalize "racial" mixing but eviscerates restrictive Manichean constructions of identity in order to promulgate concepts of wholeness and self-definition. In consequence, African-Canadian mixed-race writers create hybrid identities that are infinite, multilayered, fragmented and yet whole. They reflect the processes of shifting, overlapping and re-creation in the process of creating identity and can hence be read as representations of complex, de-central, non-hierarchical identities. They are quilting multidimensional racialized subjects. 2. Signifying the In-Between: "Race", "Racial Hybridity" and Questions of Belonging "Race" is not a biological category. Rather it represents a social construction predicated upon the interpretation of difference. It was designed to establish, justify or perpetuate hegemonic social structures and is adherent to the principle of white supremacy. Contemporary "race" theory often neglects the experiences of racially mixed individuals because it fails to offer flexible models of identity in which bi- and multiracial people find themselves represented. This thesis argues in favor of a poetics of difference that accepts and recognizes the heterogeneity of subjectivities while taking into consideration the various dimensions of class, gender, sexuality and ethnicity. Accordingly, constructions of racial hybridity in contemporary African-Canadian literature demonstrate that racism must be acknowledged as an ideology in which people believe and upon which people act. Thus identities often bear the stamp of various histories of resistance and domination, while tackling the question of belonging and re-defining Canadianness. 3. African-Canadian Borderlands References to interracial contacts and the existence of bi- and multiracial people have been omitted from the official founding narratives of the Canadian nation. African-Canadian writers have therefore been successful chroniclers of the past and filled blanks in Canadian historiography in order to shed light on hitherto repressed or erased knowledge. Part of this process is also the inscription of the mixed-race experience into Canadas past. Along this line, bi- and multiracial Canadians often criticize that the state-proclaimed policy of multiculturalism fails to take their manifold racial and ethnic subjectivities into account. 4. "From Sole to Whole" – African-Canadian Mixed-Race Poetics Mixed-race characters in US-American literature often appear in the literary motif of the "tragic mulatto" and it is often implicitly suggested that the bi- or multiracial protagonist is categorized as black. In contrast, African-Canadian constructions of racial hybridity less frequently adhere to the stereotype of the "tragic mulatto" and leave more space for employing alternative modes of racial and ethnic identification. Canadian writers of mixed descent have created a mixed-race poetics that calls attention to contexts, relationships, intersections and wholes. They encourage sites of inclusiveness, incessant shifting and discontinuity in the process of constructing identities. Nevertheless, modes of identification among racially hybrid writers in Canada vary, ranging from detesting whiteness to claiming a Black Nationalist stance. In general, however, they support the idea of fluid and flexible identities. The answer to the initial question of Srivastava is hence given by a vast variety of African-Canadian subject positions. An essentially "black" or "racially mixed" Canadian subject does not exist. Instead, constructions of racial hybridity in African-Canadian literature offer a holistic view of identity and aim at re-conceptualizing the various senses of self and community in Canada. This strategy provides a significant means of self-empowerment and self-reclamation – making racially mixed African-Canadians "whole" instead of "sole".
“Za Hranetsiu” – “Beyond the Border”: Constructions of Identities in Ukrainian-Canadian Literature
(2010)
Grounded in the literary and cultural studies, the dissertation “Za Hranetsiu” – “Beyond the Border”: Constructions of Identities in Ukrainian-Canadian Literature answers the question how identities of different Ukrainian immigrants and their offspring have been constructed, continuously developed and transformed in contemporary Canadian literature. The study simultaneously presents a discussion of postmodern identities, a concise historical survey of Ukrainian immigration to Canada in the nineteenth and twentieth centuries, and an overall picture of the exceptionally substantial body of Ukrainian-Canadian literature. Detailed literary analyses focus on seven Ukrainian-Canadian works: Sons of the Soil (1939-45/1959) by Illia Kiriak, Yellow Boots (1954) by Vera Lysenko, A Letter to My Son (1981) by George Ryga, The Green Library (1996) by Janice Kulyk Keefer, The Doomed Bridegroom: A Memoir (1998) by Myrna Kostash, Kalyna’s Song (2003) by Lisa Grekul, and The Ladies’ Lending Library (2007) by Janice Kulyk Keefer.
Carbon dioxide (CO2) is one of the most important factors of the Earth’s carbon cycle. Peatlands are well-known to be a long term sink for atmospheric carbon dioxide. Under changing environmental conditions, the carbon balance and hence the CO2 fluxes can be significantly changed, and peatlands may even become a significant atmospheric carbon source. To be able to predict the changes in climatic conditions and their effects on ecosystems, it is important to understand the contemporary CO2 exchange of the ecosystems. Many studies on peatland CO2 fluxes have been conducted in the boreal zone of North America and Scandinavia. Still little scientific evidence is available from peatland ecosystems of boreal Russia. This dissertation presents the detailed investigation of CO2 dynamics and the relevant processes and environmental factors from the boreal peatland site Ust-Pojeg (61°56'N, 50°13'E) in Komi Republic, northwest Russia. On the small spatial scale (microform), the investigated peatland was characterised by high variability in vegetation composition and coverage as well as in water table level which resulted in large variability in CO2 fluxes not only between the microform types but also within one microform type. The cumulative flux over the investigation period for the different microforms ranged from strong CO2 sources to CO2 sinks. An area-weighted estimate for the entire peatland showed that it was a CO2 source for the investigation period, which was characterised by average conditions in terms of precipitation and temperature. The CO2 fluxes were measured at different scales: by the closed chamber method at the microform scale and by the eddy covariance technique at the ecosystem scale. Three different upscaling methods were used to compare the fluxes. Irrespective of the upscaling methods, the discrepancies between the estimates based on the upscaled chamber measurements and estimates based on measurements by the eddy covariance technique were high. The high spatial heterogeneity of the vegetation and the water table level and thus of the CO2 fluxes were recognised as reasons for high potential errors when upscaling CO2 fluxes from the microform to the ecosystem level. Large discrepancies were also observed in comparison between measured CO2 fluxes and CO2 estimates based on the mechanistic ecosystem model LPJ-GUESS. Insufficient model forcing may have led to errors in the timing of the onset and the end of the growing season, and the modelled vegetation did not always reproduce the observed vegetation. These two factors may have led to the discrepancies in the model-measurement comparison. Although the closed chamber technique is widely used for measurements of CO2 fluxes between ecosystems and the atmosphere, the errors which might occur during the measurement itself or which are associated with the used measurement devices as well as the flux calculation from chamber-based CO2 concentration data are still under discussion. The study showed that the CO2 fluxes measured by the closed chamber method can be overestimated during low-turbulence nighttime conditions and can be seriously biased by inappropriate application of linear regression for the flux calculation. The methodological studies were conducted at the boreal peatland Salmisuo in eastern Finland (62°46'N, 30°58'E). The methods developed in this dissertation could contribute significantly to improved CO2 flux estimates. VI
Electromagnetic Drift Waves
(2010)
In the rf-plasma of the linear magnetized VINETA experiment, different types of low-frequency waves are observed. The emphasis in this work is on the interaction mechanism between drift waves on the one and kinetic Alfven waves on the other hand. In the peaked density profile of the plasma column drift waves occur as modulation of the plasma density. As gradient driven instability, they draw their energy from the radial density gradients. Alfven waves as magnetic field fluctuations are stable in the present configuration. They are launched by a magnetic excitation antenna. Parallel conduction currents in the plasma are common to both wave phenoma. A B-dot probe as standard diagnostic tool is used to detect the fluctuating magnetic fields of both wave types. The challenge are the small induced voltages due to the low wave frequency. The probe design with an integrated amplifier close to the probe head takes this into acount. The developed B-dot probe is mounted to different positioning systems to characterize both wave phenomena. For Alfven waves, the dispersion relation is recorded experimentally. It is found to be in good agreement with the prediction of the Hall-MHD theory with included resistive term, accounting for the cold collisional plasma. The fluctuating magnetic field pattern is recorded with azimuthal scans. The current density is obained by Amperes law. It is concentrated in helically twisted current filaments. For the unstable drift waves, similar investigations are done with simultaneously recorded density fluctuations. In the azimuthal plane, the locations of the parallel current filaments and the fluctuating density are found to be in phase, supporting the predicted drive of parallel currents by pressure gradients. A mutual influence of the two wave types is observed in an interaction experiment. Assuming parallel currents as coupling quantity, an interpretation of the experimental findings is given based on the linear theory of drift waves.
Peatlands cover only about 3% of the terrestrial surface but are significant players in the global carbon (C) cycle and the climate system, since they store roughly one quarter of the global soil carbon (C) and are among the largest natural sources of methane (CH4). Since the resulting feedbacks on the climate system are uncertain, research efforts aim at identifying key processes and quantifying the C exchange from ecosystem to regional and global scales. To identify peatland ecosystem dynamics requires analysis of yet different scales. The key scale for their C dynamics is the microform scale, which is the smallest entity of the system. To estimate ecosystem dynamics, up-scaling from the microform scale is needed. Up-scaling demands (1) a correct estimation of the spatial heterogeneity and (2) the correct aggregation. In this thesis, the traditional spatial weighting of microform fluxes by the microform distribution is evaluated by (1) analyzing the flux calculation procedure, (2) investigating the effect of the resolution of the landcover maps on the up-scaling and by (3) cross-evaluating the up-scaling result with the directly measured ecosystem flux. Eventually, it is evaluated how these dynamics are considered in a mechanistic ecosystem model (LPJ-WHyMe). CH4 fluxes were measured on the microform scale with the closed chamber technique and on the ecosystem scale with the eddy covariance (EC) technique. The quantification of microform fluxes relies on the correct flux calculation. Since only few gas samples are taken during the closure period, traditionally the linear regression is applied when calculating CH4 fluxes from chamber measurements. Still, the chamber itself affects the diffusion gradient between peat and chamber atmosphere resulting in a theoretically non-linear concentration increase in the chamber. Using data with six data points per measurement from different microform types it is tested whether the linear or exponential regression fits the data better. In the majority of cases, the linear regression fits best. However, the exponential concentration change might still not be detectable resulting in an underestimation of the ’real‘ flux and the test of different techniqes to estimate the slope of a non-linear function with small sample amounts is recommended. To define the spatial heterogeneity of the peatland surface, the application of remote sensing techniques offer the advantage of supplying area-wide information with less uncertainty when compared to vegetation mapping along transects. However, the required resolution to resolve the microform distribution is <1m which in this study was derived from near-aerial photography. Besides for up-scaling, the resulting high-resolution landcover map was used in combination with a footprint model to analyze (1) the effect of landcover on the directly measured ecosystem flux and (2) its spatial representativeness. It was shown that fluctuations of the measured ecosystem flux over periods of several days could be explained by changes of the landcover composition in the source area of the EC measurements. The estimated budget was slightly biased towards the higher emissions from lawns which could be corrected. Still, the seasonal ecosystem CH4 budget was higher than the estimate derived from the up-scaling of microform fluxes. This is most likely due to an underestimation of microform fluxes by the chamber technique. Generally, the budget estimate derived from EC measurements was more accurate, i.e., characterized by less uncertainty than the up-scaled estimate. The developed approach depends on (1) identification and accurate measurements of all relevant microform types and (2) on spatial information which should be smaller than the footprint size of the EC measurements and available on the scale relevant for the studied process, i.e., the microform scale. The demonstrated effect of microform dynamics on the ecosystem flux highlights the importance of dealing with spatial heterogeneity of ecosystems in mechanistic modelling. For example, in LPJ-WHyMe, the ecosystem flux is simulated with mean input variables as water table level. To investigate its model performance, flux data from the rather homogeneous peatland margin and the more heterogeneous peatland centre were compared with the model output. At the homogeneous peatland margin, the ecosystem flux was clearly dominated (with a contribution of 91%) by one microform flux. In this case, one water table level as input variable could be used to estimate the ecosystem flux. However, for a heterogeneous site such as the peatland centre in this study, only one mean water table would simulate a mean microform flux but not the ecosystem flux. Consequently, it is recommended to incorporate at least one high-emitting and one low-emitting microform type in the model to increase the model performance.
The focus of this thesis is the engineering and analysis of the enantioselectivity of esterases using 3-phenylbutyric acid (3-PBA) as model substrate. An ultra high throughput assay for identification of enantioselective esterases has been developed, based on the combination of in vivo selection and flow cytometry. The in vivo selection medium consists of a couple of pseudo-enantiomers of 3-PBA; one enantiomer is coupled to glycerol (GE), and hydrolysis of this substrate will enable cell survival. The other enantiomer is coupled to the toxin 2,3-dibromopropanol (BE), the hydrolysis of this substrate will cause cell death. Thus, cell survival is a function of the enantioselectivity of the enzyme expressed. The pseudo-enantiomeric substrates are structurally similar to allow selection for enantioselectivity instead of selection for enzyme substrate affinity. Next, esterase BS2 was chosen as negative control to establish the selection system since it hydrolyses both pseudo-enantiomers with low enantioselectivity (E~3 and 1, respectively). High enantioselective esterases towards 3-PBA: esterases PestE and CL1 (E > 100, both (R)-selective) were identified in a screening and used as positive controls. Further, the hyperthermophilic esterase PestE was crystallized. After elucidation of the enzyme structure, the high enantioselectivity of the enzyme towards 3-PBA could be explained by molecular modelling. The optimal concentration of the pseudo-enantiomeric substrates was set to be 5 mM for GE (higher concentrations were toxic) and 20 mM for BE (lower concentrations did not completely inhibit bacterial growth). The in vivo selection system was established together with the identification of a flow cytometric method to differentiate bacterial physiological status. The combination of Syto9 and PI was chosen as staining technique, because it allowed differentiation of the viable and the dead cell populations, and of these from the background. After viability detection by flow cytometry was established, esterases PestE and BS2 were cultivated in selection ((R)-GE and (S)-BE) and anti-selection medium ((S)-GE and (R)-BE). Clear differences in the culture viability depending on the enantioselectivity of the enzyme expressed appeared: cells expressing the (R)-enantioselective PestE could proliferate in selection medium, but could not proliferate in anti-selection medium. Cells expressing the non-selective BS2 did not grow in any media. Further, cultures containing mixtures of BS2/PestE or BS2/CL1 expressing cells were incubated in selection and anti-selection medium, and the viable clones were detected by flow cytometry analysis, sorted out and plated on agar. When the mixtures were incubated in selection medium, enrichment of the (R)-selective enzyme (PestE or CL1) over the non-selective enzyme (BS2) was observed. When the enzyme mixtures were incubated in anti-selection medium, very few colonies grew on agar, indicating that cell survival was a function of enzyme enantioselectivity. The successfully developed assay was used to identify variants with increased enantioselectivity in a mutant library of esterase PFEI (E ~ 3, (R)-selective) created by saturation mutagenesis. After library expression, 108 clones were in vivo selected and analyzed by flow cytometry. The viable cells were sorted out and plated on agar. The 28 resulting colonies were transferred to one microtiterplate and their activity and enantioselectivity (Eapp) was investigated using p-nitrophenyl derivatives. Four interesting mutants were identified: Table 1. Enantioselectivity of the in vivo selected mutants. Mutant Eapp[a]Etrue[b]Etrue[c]Etrue[d]Etrue[e] Mutations C4 80 4 4 3 1 V121I, F198G, V225A E7 >100 2 n.d. 3 n.d. V121S E8 2 25 16 50 >100 V121S, F198G, V225A F5 5 13 15 18 80 F121I, F198C [a] with separate (R)- or (S)-enantiomers of p-nitrophenyl-3-phenylbutanoate. [b] towards GE with cell lysate or [c] pure enzyme. [d] towards Et-3-PB with cell lysate or [e] pure enzyme. n.d. not determined. The mutants were purified and activity and enantioselectivity were determined in kinetic resolutions towards Et-3-PB and GE (Table 1). Mutants identified as highly enantioselective in the Eapp-assay (C4 and E7) were low selective in kinetic resolutions. On the contrary, mutants E8 and F5, which showed low enantioselectivity towards p-nitrophenyl-3-phenylbutanoate, hydrolyzed the 3-phenylbutyric esters with good to excellent enantioselectivities. This confirms that Eapp values can differ much from Etrue values as “you get what you screen for”, and supports that the here described method is very suitable for identification of enantioselective esterases. In this PhD thesis a novel strategy for identification of enantioselective esterases has been developed. This method allows a very high throughput (≥ 108 mutants/day) and opens the bottleneck of variant analysis, which exists in protein engineering technology.
Parsimonious Histograms
(2010)
The dissertation is concerned with the construction of data driven histograms. Histograms are the most elementary density estimators at all. However, they require the specification of the number and width of the bins. This thesis provides two new construction methods delivering adaptive histograms where the required parameters are determined automatically. Both methods follow the principle of parsimony, i.e. the histograms are solutions of predetermined optimization problems. In both cases, but under different aspects, the number of bins is minimized. The dissertation presents the algorithms that solve the optimization problems and illustrates them by a number of numerical experiments. Important properties of the estimators are shown. Finally, the new developed methods are compared with standard methods by an extensive simulation study. By means of synthetic samples of different size and distribution the histograms are evaluated by special performance criteria. As one main result, the proposed methods yield histograms with considerably fewer bins and with an excellent ability of peak detection.
This thesis presents the results of experimental investigations of the vertical and lateral properties of polyelectrolyte multilayer films (PEMs) adsorbed on a solid support. PEMs are a new class of organic thin films based on self-assembly layer-by-layer (LbL) processes of oppositely charged polyelectrolytes (charged polymers). The LbL assembly technique allows precise control of film thickness within a few nanometers and makes PEM systems especially interesting for technical applications. Thin films are prepared by alternating exposure of a hydrophilic substrate to solutions of oppositely charged polyelectrolytes. In this work, synthetic polycation poly (allylamine hydrochloride) (PAH) and polyanion poly (styrene sulfonate) (PSS) have been used. Range and amplitude of the electrostatic force during PEM build-up, has been shielded by use of high salt concentration in the deposition solution. As a foundation of any theory, role of non-elecrostatic (secondary) forces is explored. Four complementary methods have been combined to investigate the properties and composition of PEMs. X-ray reflectivity is sensitive to electron density gradients, and therefore provides information about film thickness, average electron density and interfacial roughness between materials of different electron densities (like PEM and air). Neutrons are the unique probe that is sensitive to the internal order of the multilayers (scattering length density variation) due to selective deuteration of the layers (PSS replaced by PSS_d). Therefore neutron reflectivity at V6 beamline, at the research reactor BER II, Helmholtz Centre for Materials and Energy (former Hahn-Meitner-Institute), was used in this work. Ultraviolet-visible (UV-Vis) light induces the characteristic absorption peak of polyelectrolytes and metallic nanoparticles, therefore with UV-Vis absorption spectroscopy is possible to probe the aggregation of metallic nanoparticles embedded into PEM by measuring their absorption spectra (imaginary part of the refraction index). Atomic force microscopy (AFM) allows to observe lateral structures at nano-level and to obtain surface topology of the films. Application of only small forces (pN) is achieved by use of a intermittent contact (tapping) mode in air. Summarizing the main results, the unambiguous parametrization of the investigated system for neutron reflectivity measurements enables to obtain detailed information about internal interfaces. New approach for polyelectrolyte multilayer architectures consisting of thick protonated and deuterated blocks can be used in order to distinguish different zones of the thin film growth which can be described as precursor and core zones. Thus, almost no bound water is found in precursor layers at 0% relative humidity, which suggests that water is mobile and the precursor layer is not in the glassy state like in the central zone of the PEM. Swelling behaviour of the PEMs (reversibility of the swelling) can be understood in terms of equilibrium reactions. Explored influence of temperature and type of salt used during preparation contributes to a better understanding of the formation of PEMs. The dependence of the film thickness on preparation temperature, concentration and the type of salt can be described by the hydrophobic nature of the effect. Experimental observations demonstrate that it is possible to decrease both the range and the amplitude of the electrostatic force by using an ion concentration of at least 0.1 mol/L in the solution. The role of secondary interactions such as hydrophobic attraction of the chains that can overcome electrostatic repulsion and become the major contributing factor for the layer formation and resulting structures is emphasized.
A central point of this thesis is the investigation of surface structure and surface forces, which are created by single layers of linear polyelectrolytes (PE). In detail, the properties of cationic poly(allylamine)hydrochloride (PAH) and poly-l-lysine (PLL) and anionic sodium poly(styrene sulfonate) (PSS) are determined, which have been physisorbed onto oppositely charged silica surfaces in presence of a predefined salt concentration IAds. For these investigations, a new averaging method for colloidal probe (CP) force profiles is developed, which leads to an ultimate force resolution of 1 pN after the data processing, (signal to noise ratio of > 1000). Furthermore, a new kind of tapping mode imaging is presented (so called colloidal probe tapping mode, CPTM), which uses a CP instead of a sharp tip and hence which allows to resolve lateral inhomogeneously distributed surface forces. The basics to understand such-like obtained tapping mode images are developed. For adsorption from salt-free solution (IAds = 0) the dominance of an electrostatic double layer repulsion is observed, which is commonly attributed to the adsorption of the PE chains into a rather flat and compact layer and which is in full agreement with theoretical predictions and enormous experimental data available in literature. However, even a small addition of salt to the deposition solution (i.e. IAds > 1 mM NaCl) introduces a new contribution to the surface force, which is attributed to PE chains that are non-flatly physisorbed. Using scaling considerations, it is shown for all investigated PE that this non-flat conformation can be described by brush-like chain adsorption (cf. Section 3.3.5); other conformations like mushroom or pancake are excluded (cf. Section 5.3). Interestingly, these non-flatly physisorbed chains combine properties of neutral and PE brushes: (i) The force is very well described by the theory of Alexander and de Gennes (AdG, cf. Section 5.4). By fitting the AdG force law to the data, it is possible to determine the (brush) thickness L of the PE layer and the average distance s between brush-like physisorbed chains. Although the chains are charged the electrostatic contribution to the surface forces is too small to be noticeable (cf. Section 5.4.2). (ii) The thickness L of this PE layer is much larger compared to the compact layer (observed for salt-free adsorption) and is also subject to a pronounced swelling and shrinking if the bulk salt concentration I is decreased or increased, respectively. Surprisingly, all measurements indicate that L follows a scaling law known for salted end-grafted PE brushes, i.e. L ~ N (I s^2)^(-1/3) (with N denoting the degree of polymerization). Furthermore, the osmotic brush phase is never observed in the experiments, but chain stretching up to 1 / 3 of the contour length is regularly achieved. CPTM imaging applied to PSS shows that the brush-like physisorbed chains are not homogenously distributed over the surface, but form brush domains which coexist with flatly physisorbed chains (cf. sections 5.5 and 5.6). This clearly shows that PSS generally physisorbs in two distinct phases, which differ in conformation (flat vs. brush) and the surface force caused (electrostatic vs. steric repulsion). The force profile of the two phase system is in good approximation simply the superposition of a steric and an electrostatic repulsion, whereby their respective contribution to the composed force profile is given by their area fraction. The quantitative analysis reveals that L and s of the brush phase are independent on IAds. This is remarkable, as a change in IAds is known to induce a continuous transition between a stretched (low IAds) and coiled chain conformation (high IAds) in the deposition solution (cf. [Fleer1993, Yashiro2002]). Hence, one can conclude that the conformation in solution does not necessarily correspond to the conformation after adsorption. It is also shown that the area fraction A of the brush domains strongly depends on N and IAds. For example, for constant N the scaling relation A ~ sqrt(IAds) is determined, which is very similar to the common observation that the surface coverage %Gamma of adsorbed PE layers increases also with %Gamma ~ sqrt(IAds) [Schmitt1996, Cosgrove1986, Ahrens2001, Yim2000, Gopinadhan2007, Cornelson2010]. This suggest that brush-like physisorbed PE chains are responsible for the increase in %Gamma. In fact, Section 5.6 shows that the mass of the brush phase is approx. 0.5 mg/m² which is comparable to the increase in %Gamma reported in literature for IAds = 1 M NaCl [Cosgrove1986, Schmitt1996, Ahrens2001]. As a change in IAds does not affect L and s, but solely the brush area fraction A, it is argued in Section 5.6 that an increase in IAds can be understood as a phase transition from the (disordered) flat phase towards the (ordered and extended) brush phase. Here, further theoretical considerations would be desirable.
Deciphering the entire protein complement of a living cell together with the elucidation of dynamic processes on protein level are the main goals of proteomics as it is used today. To achieve this goal, namely the elucidation of dynamic processes of the entire bacterial cell, we have developed strategies and distinct workflows to cover the most proteins in different subcellular localizations in bacteria together with a stable isotopes labeling approach to follow temporal and spatial changes in different proteomic subfractions. In this work, it has been shown that the use of mass spectrometry based in vivo quantitation techniques and the application of subcellular and chromatographic fractionation has lead to a new level of qualitative and quantitative proteomics data. Emphasizing on the studies revealing the dynamics of the bacterial physiology on a time resolved base, both spatial and temporal processes can be monitored to obtain knowledge on physiological processes in a depth that has not been reached before in comparable global studies.
This thesis contains results from transcriptome studies on different aspects of host-pathogen interactions. First, liver gene expression profiles from a murine chronic stress model served to elucidate aspects of the influence of stress on metabolism and immune response state. Chronic stress in female BALB/c mice was shown to lead to a hypermetabolic syndrome including induction of gluconeogenesis, hypercholesteremia, and loss of essential amino acids, to the induction of the acute phase response, but also of immune suppressive pathways and to the repression of hepatic antigen presentation. Increased leukocyte trafficking, increased oxidative stress together with counter-regulatory gene expression changes, and an induction of apoptosis were detected. The influence of intra-venous infection on the host kidney gene expression was analyzed in another murine model using the wild type strain Staphylococcus aureus RN1HG and its isogenic sigB mutant. Gene expression profiling indicated a highly reproducible host kidney response to infection. The comparison of infected with non-infected samples revealed a strong inflammatory reaction of kidney tissue, e. g. Toll-like receptor signaling, complement system, antigen presentation, interferon and IL-6 signaling. However, the results of this study did not provide any hints for differences in the pathomechanism of the S. aureus strains RN1HG and ΔsigB, since the host response did not differ between infections with the two strains analyzed. Effects of SigB might be transient, only apparent at earlier time points, or might also be compensated for in the in vivo infection by the interlaced pattern of other regulators. SigB might possess only to a lesser extent characteristics attributed to virulence factors and might act in vivo more like a virulence modulator and fine tune bacterial reactions. In addition to the analysis of tissue samples, different in vitro models were furthermore studied. The third part of this thesis focuses on bone-marrow derived macrophages (BMM) of the two mouse strains BALB/c and C57BL/6, which are described in literature to exhibit genetically determined differences in their reaction to infection. Expression profiling was performed on control and IFN-γ treated samples from a serum-free cultivation system and revealed mainly induction of gene expression after treatment of BMM with IFN-γ. Gene expression changes confirmed known IFN-γ effects like induction of immunoproteasome, antigen presentation, interferon signaling related genes, GTPase/GBPs, and inducible NO synthase. IFN-γ dependent gene expression changes were highly similar in BALB/c and C57BL/6 BMM. Considering gene expression differences between BMM of both strains, a similar expression trend was visible on the level of untreated controls as well as after IFN-γ treatment. Differentially expressed genes between BMM of both strains included immune-relevant genes as well as genes linked to cell death, but the coverage of functional groups was limited. The bronchial epithelial cell line S9 was used as an in vitro model system for the infection with S. aureus RN1HG. The fourth chapter in this thesis includes S9 cell gene expression signatures 2.5 h and 6.5 h after start of infection. At the early time point, only 40 genes were differentially expressed, which nevertheless indicated a beginning pro-inflammatory response, e. g. induction of cytokines (IL-6, IFN-β, LIF) or prostaglandin-endoperoxide synthase 2 (PTGS2), but also counter-regulatory processes, e. g. induction of CD274. The host cell response was dramatically aggravated at the later 6.5 h time point. Differential expression was detected for 1196 genes. These included induced cytokines, pattern recognition receptor signaling, antigen presentation, and genes involved in immune defense (e. g. GBPs, MX, APOL). Negative effects on growth and proliferation were even more enhanced in comparison to the early time point, and signs for apoptotic processes were revealed. Finally, the last chapter addresses amongst others the pathogen’s expression profile in the S9 cell in vitro infection model at the two time points 2.5 h and 6.5 h after start of infection by tiling array gene expression analysis. The pathogen expression profiling revealed the activity of the SaeRS two-component system in internalized staphylococci. Partly dependent on SaeRS, the induction of adhesins (e. g. fnbAB, clfAB), toxins (hlgBC, lukDE, hla), and immune evasion genes (e. g. chp, eap) was observed. Furthermore, expression changes of metabolic genes were recorded (gene induction of amino acid biosynthesis, TCA cycle, gluconeogenesis; gene repression of glycolysis, purine biosynthesis, tRNA synthetases). Expression analysis recorded a distinct bacterial expression program, which supported literature results of a specific, bacterial strain and host cell line dependent transcriptional adaptation of the pathogen.
Staphylococcus aureus is a commensal colonizing 20-30% of the population as well as a pathogen causing diverse diseases ranging from skin infections via toxin mediated diseases to life threatening conditions. In its interplay with the human host, this microorganism resorts to an extensive repertoire of both membrane-bound and secreted virulence factors facilitating adhesion to, invasion of, and spreading into various host tissues. Among the numerous virulence factors produced by S. aureus are the staphylococcal superantigens (SAgs). They directly cross-link conserved regions of the T cell-receptor with MHC class II molecules (outside the peptide-binding cleft) on antigen presenting cells. This results in a strong stimulation of up to 20% of all T cells which respond with proliferation and massive cytokine release. Recently, the enterotoxin gene cluster (egc) located on a pathogenicity island was described. The egc-genes are the most prevalent SAg genes in commensal and invasive S. aureus isolates. However, they appear to cause toxic shock only very rarely and their presence is negatively correlated with severity of S. aureus sepsis. Therefore it was suggested that SAgs might differ in their pro-inflammatory potential. In addition to their superantigenicity, SAgs also act as conventional antigens and induce a specific antibody response. In contrast to non-egc SAgs, despite the high prevalence of egc SAgs, neutralizing antibodies against egc SAgs are very rare, even among carriers of egc-positive S. aureus strains. In order to find an explanation for this “egc-gap”, we have tested two non-exclusive hypotheses: (i) egc and non-egc SAgs have unique intrinsic properties and drive the immune response into different directions and (ii) egc and non-egc SAgs are released by S. aureus under different conditions, which shape the immune response to them. To test these hypotheses, we compared the effects of egc and non-egc SAgs on human blood cells. Their T cell-mitogenic potencies, the elicited cytokine profiles as well as their impact on gene expression were highly similar. Both egc and non-egc SAgs induced a very strong pro-inflammatory response. In contrast, the regulation of SAg release by S. aureus differed markedly between egc and non-egc SAgs. Egc-encoded proteins were secreted by S. aureus during exponential growth, while non-egc SAgs were released in the stationary phase. We conclude that the distinct biological behavior of egc and non-egc SAgs is not due to their intrinsic properties, which are very similar, but is caused by their differential release by S. aureus. Traditionally, S. aureus has not been considered as an intracellular pathogen but strong evidence emerged indicating that staphylococci can invade and persist in various cell types. Internalization might constitute a bacterial strategy to evade the host’s defense reactions and the action of antibiotics. The intracellular niche might thus constitute a reservoir for chronic or relapsing infections. Contrary to their potential importance, genome-wide functional genomics analyses of the adaptation reactions of S. aureus to the host cell environment are rare and so far confined to gene expression profiling. Investigations addressing the proteome of internalized S. aureus are still lacking due to the challenge of obtaining a sufficient number of infecting bacteria. The proteome of other pathogens such as Francisella tularensis has been characterized by classical 2-DE approaches. However, the number of bacteria required for such a 2-DE based approach is often exceeding the numbers available from in vivo infection models. Furthermore, this approach does not allow monitoring of time-dependent quantitative changes in protein levels. Here, a workflow allowing time-resolved analysis of internalized S. aureus by combining pulse-chase stable isotope labeling by amino acids in cell culture with high capacity cell sorting, on-membrane digestion, and high-sensitivity mass spectrometry is presented. This workflow permits detection and quantitative monitoring of several hundred staphylococcal proteins from as little as a few million internalized S. aureus cells. This approach has been used to reveal time-resolved changes in levels of proteins in S. aureus RN1HG upon internalization by human bronchial epithelial cells. Proteins involved in stress adaptation as well as protein folding and some components of the phosphotransferase system were upregulated in internalized staphylococci, whereas proteins of the purine biosynthesis pathway and tRNA aminoacylation were downregulated. Furthermore, regulatory adaptive responses of internalized S. aureus to the intracellular milieu were shown as global regulators displayed increased protein abundance levels compared to non-internalized bacteria. Taken together, we observed changes in levels of proteins with functions in protection against oxidative damage and adaptation of cell wall synthesis in internalized S. aureus.