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The main objective of this work is to contribute to the understanding of the grafting of nitrogen and amino surface functional groups on polymers by means of plasmas containing nitrogen and hydrogen. For this purpose, many aspects of plasma surface modification were studied. In the frame of this work, a new, UHV-sealed plasma reactor system was put into operation. The system is special for its clean reaction environment and the possibility to perform quasi in situ XPS measurements. A comparison of the UHV system to a fine vacuum reactor showed that a clean reaction environment is mandatory for reproducible plasma processing and efficient nitrogen and amino functionalisation. A key motivation for the present work was the observation that the non-coating plasma processes reported in literature fail to graft primary amino groups on polymer surfaces with densities that significantly exceed 3 - 4% NH2/C. In order to investigate this phenomenon in detail, this work followed two experimental tracks: On the one hand, a broad systematic study of plasma processing parameters was performed. On the other, the surface diagnostics methods used for the quantification of amino groups were critically reviewed. For this, a numerical algorithm was developed to reconstruct the element depth profile from angle-resolved XPS data. In the scope of the process parameter study, cw and pulsed microwave (MW) plasma excitation was compared to radio-frequency (RF) excitation. The home-built MW source was studied and optimised with respect to ignition behaviour and power efficiency. The performance of the MW and RF plasmas in polymer surface modifications was studied in various gas mixtures containing NH3 and H,, or N2 and H,. Also the differences of glow and afterglow processing of polymers were investigated. Large variations of the nitrogen and primary amino grafting efficiencies were obtained. They triggered a number of new ideas for the underlying reaction mechanisms. Special attendance was devoted to the selectivity of the functionalisation processes for primary amino groups. Nitrogen-containing discharges that were rich in hydrogen achieved selectivities up to 100%. The upper limit of 3 - 4% amino groups on the surface, however, was not passed. Angle-resolved XPS measurements revealed a systematic problem for the definition of a surface density, which is capable of explaining the upper limit for amino groups. It is either due to a limited labelling depth of amino groups by the applied TFBA derivatisation reaction, or to a limited functionalisation depth of the plasma process. One very efficient nitrogen-grafting plasma process that was developed on polystyrene was applied to seven other unfluorinated polymers. The similarity of the resulting functionalisation demonstrated a good transfer-ability of plasma surface functionalisation processes. Plasma treatments of polymer surfaces, especially in hydrogen-containing gases, are known to be generally followed by uncontrollable oxidation phenomena. The properties of plasma-functionalised polymer surfaces were therefore studied in conjunction with ageing effects. Quasi in situ XPS analysis allowed to distinguish the influence of oxygen contamination during the plasma process from post-process oxidation due to contact of plasma-treated samples to atmospheric oxygen. The surface modification experiments were accompanied by several gas phase diagnostic techniques. In the scope of this work, the UHV reactor system was equipped with optical emission spectroscopy (OES), two-photon absorption laser-induced fluorescence (TALIF), and tunable diode laser absorption spectroscopy (TDLAS). A separate plasma source was setup to perform an absolute quantification of the vacuum-ultra-violet (VUV) emission intensity of hydrogen-containing MW-excited plasmas. The techniques were evaluated with respect to their contribution to an understanding of the plasma processing of polymers. The rich experimental data allowed to suggest new reaction mechanisms for the grafting of nitrogen- and amino functional groups. Surface passivation experiments in H, plasmas of nitrogen-functionalised surfaces initiated a re-evaluation and an extension of the mechanism of selective etching [1]. Together with two other new reaction mechanisms, a hypothetical reaction scheme was suggested. It was studied by the help of two numerical models for heterogenous reactions of radicals with the surface. In order to avoid the complexity of the fragmentation process of NH,, the models were restricted to discharges in N, and H9. Despite the sparse information on the composition of the gas phase, the data of two experimental series showed a very particular phenomenology that allowed a first test of the model. The test supports the newly-suggested reaction mechanisms. Especially the role of NH2 attachment to open reaction sites for the grafting of amino groups was emphasised. A more stringent test of the model is left to future experiments with extended gas phase diagnostic means.
We improved our previous model of tracheal tube preparation and examined the effects of oral treatment of rats with carbocisteine (CCS) and its interaction with bronchial epithelium. The model permitted isometric or isotonic measurements of smooth muscle contraction or relaxation in cannulated or tracheal ring preparations, with or without epithelium. We found that oral treatment with carbocisteine and not preincubation of preparations in vitro, diminished sensitivity of preparations without epithelium to carbachol (EC50, -log(M) values: IN -luminary perfusion, -EP, controls vs. CCS: 5.8±0.06 vs. 5.5±0.09, p<0.005; OUT - serosal perfusion, -EP, controls vs. CCS: 5.9±0.06 vs. 5.6±0.05, p<0.005), while the sensitivity to aminophylline, degree of shortening, and the velocity of contraction of rat tracheal rings stimulated by 10-6M carbachol was not affected. Normal sensitivity to carbachol stimulation was re-established if preparations were preincubated with capsaicin. We conclude that carbocisteine has small inhibitory effects on the sensitivity to carbachol of the rat tracheal smooth muscle denuded of epithelium. Described model is valuable for examining the effects of bronchial epithelium on bronchial smooth muscle contraction.
In the thesis the reason for the low breeding success of white rhinos in captivity was investigated and solutions suggested. It was also investigated how to improve management of free ranging populations. It was establish whether female white rhinoceros choose their mates and, if so, which factors influence their choice. The study also seeks to establish whether there is any relationship between androgens, environmental factors and mating activity. The study was carried between March 1997 and May 1999 on a private game farm in South Africa. The study animals enjoyed conditions similar to those enjoyed by free-ranging populations. A non-invasive endocrine monitoring technique was developed to assess the androgen concentrations in faeces of male white rhinos. The body and horn size of adult males was measured, the concentration of testosterone in their faeces determined, and the characteristics of their territories investigated. All of these factors were then set in relation to their reproductive success. The reproductive success was established by genetic analysis of fatherhood using AFLP methods. The quality of male territories was described by vegetation structure, tree and grass species composition, the availability of frequently foraged or selected grass species as well as the nutritional composition of the forage. In addition, the influence of seasonal rainfall, presence of receptive females and territorial activity on androgen metabolite concentrations was established.
The present experimental work investigates plasma turbulence in the edge region of magnetized high-temperature plasmas. A main topic is the turbulent dynamics parallel to the magnetic field, where hitherto only a small data basis existed, especially for very long scale lengths in the order of ten of meters. A second point of special interest is the coupling of the dynamics parallel and perpendicular to the magnetic field. This anisotropic turbulent dynamics is investigated by two different approaches. Firstly, spatially and temporally high-resolution measurements of fluctuating plasma parameters are investigated by means of two-point correlation analysis. Secondly, the propagation of signals externally imposed into the turbulent plasma background is studied. For both approaches, Langmuir probe arrays were utilized for diagnostic purposes. The main findings can be summarized as follows: Greatly elongated fluctuation structures exist in plasma edge turbulence. The structures are aligned along the confining magnetic field (k|| = 0). The correlation degree of fluctuations for a short connection length of 0.75m is greater than 80%. For much longer connection lengths of 23m and 66m, the correlation degree is reduced to approximately 40%. A conceptual interpretation of these observations is the coexistence of two different fluctuation components. One component has a correlation length parallel to the magnetic field below 20m and the other component a correlation length greater than 70m. Sine signals in the frequency range 1-100 kHz were injected into the turbulent plasma background. The propagation parallel and perpendicular to the magnetic field of the signals was studied. In poloidal direction, an asymmetry is observed, that can be explained by a copropagation of the signal with the background E × B-rotation of the plasma. The signal propagation parallel to the magnetic field shows no such asymmetry. As an advanced approach, spatio-temporal wave patters were injected into the edge plasma. The waves launched that way can be seen as test waves' in a turbulent background. The coupling strength of the imposed wave patterns to the background turbulence relies on the match of the imposed waves to the dynamics of turbulent structures. If the propagation direction of the imposed waves is parallel to the propagation direction of the background plasma, improved coupling is observed. This finding underlines the importance of the background plasma rotation for future attempts of controlling the plasma edge turbulence. Further optimization of frequency and wave vector of the imposed waves is probably a promising approach for achieving a significant and systematic influence of turbulence. Taking into account the present experimental state-of-the-art, for a deeper insight into the mechanism of the plasma edge turbulence of magnetized high-temperature plasmas a joint effort of numerical modeling and experimental results is a valuable approach. Such a cooperation should cover the explanation of the correlation observations as well as the experiments on signal injection into background turbulence. A quantitative comparison between the results presented in this work and a dedicated numerical drift wave simulation would be a significant step forward to a better understanding of plasma edge turbulence.
The role of large-scale fluctuation structures in electrostatic
drift-wave-type plasma turbulence is highlighted. In particular,
well-defined laboratory experiments allow one to study the
dynamics of drift wave mode structures as well as `eddies' in
drift wave turbulence. In the present paper we discuss the
mutual relationships between observations made in linear
magnetic geometry, purely toroidal geometry and magnetic
confinement. The simplest structure, a saturated, nonlinear
drift mode, is the starting point for a Ruelle-Takens-Newhouse
transition route to chaos and weakly developed turbulence. Both
spectral and phase space analysis are applied to characterize in
detail the transition scenario, which is enforced due to an
increased drive by the plasma equilibrium state. In addition to
direct multi-probe observation, statistical approaches are most
revealing for the systematic study of the spatiotemporal
dynamics in fully developed drift wave turbulence. In
particular, the propagation of large-scale `eddy' structures is
traced by conditional statistics methods. Finally, the control
of drift wave turbulence by spatiotemporal synchronization is
discussed.
Until today most social, historical and cultural studies of the American postwar era have contributed to the myth of a relatively homogeneous society and culture. Even though they understood these years as a turning point for modern American society, they failed to encompass the polyvalence and heterogeneity of American society. Focussing mostly on white and middle class males, these studies formed a onedimensional picture of sociocultural conformity, a picture in which issues of gender, race and class were largely absent. Crossing the boundaries of feminist, cultural and historical studies this dissertation starts from identifying the gaps and problems in current academic research. Those sociopolitical structures that affected non-white women are then juxtaposed with the dominant postwar discourse of womanhood. The literary texts by women of color show them grappling with the conflicting demands of socioecnomic realities and pervasive role definitions. On the surface these literary interventions seemed to submit to dominant ideologies while opposing them at the same time. Thus they are both anticipatory and antagonistic. The dissent and criticism in writings by women of color seem to have become a catalyst for the deep social transformations in the following decades.
Studies of stroke in experimental animals have demonstrated the neuroprotective efficacy of a variety of interventions; however, most such strategies have failed to show clinical benefits in aged humans. One possible explanation for this discrepancy between animal and clinical studies may be the role that age plays in the recovery of the brain following insult. For example, the poor functional recovery of aged rats after stroke may be caused by a decline in brain plasticity. Although the incidence of ischemic stroke increases dramatically with advancing age, relatively few studies have been conducted on aged animals, which would mimic most closely the context in which stroke occurs in humans. We have shown that, at one week following stroke, there was vigorous expression of MAP1B and its mRNA, as well as MAP2 protein, in the border zone adjacent to the infarct of 3 month- and 20 month-old male Sprague Dawley rats. Hypothesis: The decline in brain plasticity is caused by an age-related decline in the upregulation of factors promoting brain plasticity (MAP1B, ßAPP) and an age-related increase in astroglial scaring and in the expression of neurotoxins such as beta amyloid. Methods: Focal cerebral ischemia was produced by reversible occlusion of the right middle cerebral artery in 3- and 20-month-old male Sprague Dawley rats. The functional outcome was assessed in neurobehavioral tests at 3, 7, 14, and 28 days post-stroke. At these time points, brains were removed and analyzed for markers of (i) brain plasticity (microtubule-associated protein 1B, MAP1B, secreted forms of fi-amyloid precursor protein); (ii) neurogenesis (BrdU-positive cells, doublecortin, nestin); (iii) neurotoxicity (B-amyloid aggregates); (iv) inflammation (microglia, astrocytes, oligodendrocytes, endothelial cells). Results: (1) There was a non-significant tendency for blood pressure to be higher in old than in young rats. By post-stroke day 3 the infarct volume covered about 15% of the cortical neurons in young and 28% in aged rats. By day 7, infarct volumes were roughly equal in the two age groups. (2) Cell counting showed increases in the number of BrdU-positive cells in the infarcted area of old rats at day 3 post-stroke. This increase became even more dramatic at day 7 post-stroke in aged rats. There was no significant contribution of apoptosis to cell death. (3) Behaviorally, young rats recovered gradually and reached a maximum of 90% of baseline performance at day 14, post-stroke while the aged rats recovered only to a maximum of 70% of pre-surgery performance by week 2 post-stroke, and remained at that level. (4) The temporal pattern of recovery correlated well with the expression of growth-associated phenotype of ßAPP as well as with MAP1B accumulation in varicosities along axons (an indicator of growth) in cortical areas affected by stroke and was at maximum between days 14 to 28 in young rats. In contrast, aged rats showed delayed (day 28) and reduced axonal remodelling as well as a delayed (day 28) expression of growth-associated ßAPP. Instead, the neurotoxic carboxy-terminal form of ßAPP steadily accumulated over time and reached a maximum at day 14 in aged rats as compared to 28d for the young rats. Nestin, a marker for immature neurons, overlapped with BrdU-labelled cells at day 7 post-stroke in corpus callosum and at the infarct border in both young and aged rats, suggesting increased stroke-induced neurogenesis. (5) In young rats there was a gradual activation of both microglia and astrocytes that peaked by days 14 to 28 with the formation of a glial scar. In contrast, aged rats showed an accelerated astrocytic and microglial reaction that peaked in week 1 post-stroke. We also noted a strong activation of oligodendrocytes at early stages of infarct development in all rats that persisted in aged rats. Evolution of astrocytic and microglial reactivity closely paralled the time course of scar formation in both young and aged rats and coincided with the stagnation in the recovery rate of aged rats. Conclusions: The time course of functional recovery in young rats correlated well with the expression of plasticity proteins such as MAP1B and ßAPP while an early and persistent expression of the neuro toxic fragment AB in conjunction with a delayed expression of MAP1B and ßAPP may impede functional recovery in aged rats. The results also suggest that a temporally anomalous glial reaction to cerebral ischemia in aged rats leads to the premature formation of scar tissue that impedes functional recovery to stroke.
Serbian Tertiary ultrapotassic province is part of widespread but not voluminous basaltic magmatism in Serbia. Two principal groups of ultrapotassic rocks are recognized; the lamproite affinity group (LAG) and the kamafugite affinity group (KAG). My results demonstrate three dominant low-pressure evolutional processes: magma mixing and fractional crystallization, analcimization and heteromorphism. The two suites of ultrapotassic rocks show large ranges of Sr and Nd isotopic values but a restricted variation of Pb isotopes. LAG is characterized by wide ranges of Sr and Nd isotopes (87Sr/86Sri 0.70735- 0.71299, 143Nd/144Ndi 0.51251-0.51216). KAG is isotopically homogeneous with a limited range of Sr-Nd isotopes (87Sr/86Sri 0.70599-0.70674, 143Nd/144Ndi 0.51263-0.51256). The Pb isotope compositions of both groups are similar (206Pb/204Pb 18.581-18.832, 207Pb/204Pb 15.624-15.696 and 208Pb/204Pb 38.744-38.987), and fall within the pelagic sediment field resembling Mesozoic flysch sediments from the Vardar ophiolitic composite suture zone. Highly variable Sr and Nd isotopic signatures of primitive-LAG rocks correlate with REE fractionation and enrichment of the HFSE. I explain this correlation using vein+wall-rock melting model, invoking the presence of different metasomatic domains (veins with phlogopite, Cpx and F-apatite) that are out of isotopic equilibrium with the peridotite wall rock. Relatively uniform Sr and Nd isotopic data of KAG rocks, similar trace element patterns and small but regular variations of HFSE ratios, indicate different degrees of melting of a relatively homogeneously metasomatized mantle source. Geochemical modelling implies the role of phlogopite, apatite and Ti-oxide in their mantle source.
Challenge of immunized mice with H. pylori induces protective gastric inflammation that is histologically indistinguishable from chronic H. pylori-associated gastritis in non-immune mice. To identify mechanisms of protective immunity gene expression in the gastric tissue from infected mice and mice vaccinated prior to challenge was compared by DNA array analysis. Message RNA was used to screen over 10,000 murine genes. Major Histocompatibility Complex antigens and IFN-γ dependent GTP binding proteins were strongly upregulated in both infected and immunized/challenged mice compared to naive controls. Differences in gene expression were also observed in novel T cell genes, which were exclusively upregulated in immunized/challenged mice. Both IFN I and II associated genes like the IFN-a/ßreceptor or IFN dependent transcription factors mIRF-1 and ISGF3 were also predominantly expressed in this group. These results were confirmed for several candidate genes by semi-quantitative RT-PCR. Additionally, H. pylori-stimulation of CD4+ T cells from immune mice induced significantly more IFN-γ production than stimulation of cells from infected mice. The present study provides evidence that the inflammatory infiltrate that arises in the gastric mucosa when immunized mice are challenged with H. pylori is associated with specific T cells sets and protein families that are distinct from those present in Helicobacter-associated chronic inflammation. Gene array profiles and in vitro assays indicate that immunized mice are more readily poised than infected mice to promote IFN-γ production and IFN related events and thus promote a strong proinflammatory THi response. This study supports recent findings that an immune response dominated by THi cytokines is essential for protection from H. pylori infection. This insight could facilitate the choice of the appropriate adjuvants for the development of vaccines against H. pylori, which are efficient and safe for use in humans. The mechanisms by which THi cells induce protective immunity or reduce Helicobacter colonization remain poorly understood and will be subject of future research.
Within the scope of this work, a versatile large linear magnetised plasma experiment was designed, constructed, and subsequently put into operation. The magnetised plasma was used to investigate the dispersion of whistler waves (circular polarised electromagnetic waves) with regard to the influence of the plasma boundaries. After a brief review over electromagnetic plasma waves and the three discharge modes of a helicon source, the experimental device and the diagnostic tools are explained in detail. Great attention is devoted to the identification of a reliable, calibrated magnetic fluctuation probe design. To the understanding of dynamical phenomena in ionospheric plasmas, whistler wave measurements in laboratory experiments may contribute significantly because of the ability to vary plasma parameters and to do measurements with high spatial and temporal resolution. However, the boundaries of laboratory experiments change the dispersion behaviour of whistler waves significantly if compared to the unbounded ionospheric situation. The influence of the plasma boundary is studied in the present work on three different levels of increasing complexity. First, a high density, small wavelength regime is established to make the effect of the boundary negligible. Measurements are in full agreement with whistler wave theory for unbounded plasma geometry. Measurements below the ion cyclotron frequency reveal the strong influence of the ion dynamics on whistler wave propagation, but are not straightforward to interpret in terms of dispersion theory. Second, the other limit case is examined: bounded plasma helicon modes. These waves are, mathematically speaking, eigenfunctions of the plasma-boundary system and are of great practical importance for high density plasma discharges, the helicon source. Careful measurements of the equilibrium plasma parameters as well as the magnetic fluctuation profiles of the helicon source are done in all three modes of operation, the capacitive, inductive, and helicon wave sustained mode. The first two modes are fairly well understood and the measurements are consistent with existing models. The high density helicon mode, however, is still a scientific case. The measurements partially confirm existing assumptions. It is demonstrated that the plasma production is detached from the antenna edge region. Moreover, it is shown that the plasma parameters are self-consistently determined by the antenna geometry and the discharge parameters according to basic helicon wave theory. Finally, it is ruled out that the plasma density is the control parameter determining the transition point into the high density helicon mode. The measurements rather suggest that the rf power density is the important value. As a third aspect, whistler waves in an intermediate wavelength regime are studied and the transition from unbounded to bounded plasma wave dispersion is systematically investigated. It is shown both experimentally and numerically that the wave dispersion in a plasma filled metal waveguide cannot be determined solely from wave vector measurements parallel to the magnetic field. For a correct description, the perpendicular mode profile has to be correctly taken into account. In contrast to simple helicon wave theory, it is demonstrated that the perpendicular mode profile is not only determined by the conducting vessel boundaries alone but the entire plasma-boundary system has to be considered as a unity. To summarise, this work has contributed to a better understanding of the physics of the propagation of whistler waves, where the particular role of metal boundaries acting as wave guides was highlighted. This basic science approach to the waves' dynamics is believed to be of significance in the course of the scientific debate on the physics principles of helicon discharges.
Two main aspects concerning drift wave dynamics in linear, magnetized plasma devices are addressed in the work: In part I of the thesis, drift waves are studied in a helicon plasma. The plasma parameter regime is characterized by comparably high collision frequencies and comparably high plasma-p exceeding the electron-ion mass ratio. Single Langmuir probes and a poloidal probe array are used for spatiotemporal studies of drift waves as well as for characterization of background plasma parameters. The main goals are the identification of a low-frequency instability and its major destabilization mechanisms. All experimentally observed features of the instability were found to be consistent with drift waves. A new code, based on a non-local cylindrical linear model for the drift wave dispersion, was used to gain more insight into the dominating destabilzation mechanisms, and also into dependencies of mode frequencies and growth rates on different parameters. In the experiment and in the numerical model, poloidal mode structures were found to be sheared. Part II of the thesis reports about mode-selective spatiotemporal synchronization of drift wave dynamics in a low-P plasma. Active control of the fluctuations is achieved by driving a preselected drift mode to the expense of other modes and broadband turbulence. It is demonstrated that only if a resonance between the driver signal and the drift waves in both space and time is reached, the driver has a strong influence on the drift wave dynamics. The synchronization effect is qualitatively well reproduced in a numerical simulation based on a Hasegawa-Wakatani model.
Low-pressure plasmas offer a unique possibility of confinement, control and
fine tailoring of particle properties. Hence, dusty plasmas have grown
into a vast field and new applications of plasma-processed dust particles
are emerging. There is demand for particles with special properties and
for particle-seeded composite materials. For example, the stability of
luminophore particles could be improved by coating with protective Al2O3
films which are deposited by a PECVD process using a metal-organic precursor gas.
Alternatively, the interaction between plasma and injected micro-disperse powder
particles can also be used as a diagnostic tool for the study of plasma surface
processes. Two examples will be provided: the interaction of micro-sized (SiO2)
grains confined in a radiofrequency plasma with an external ion beam as well as
the effect of a dc-magnetron discharge on confined particles during deposition
have been investigated.
Severe trauma results in alterations in immune functions, correlated with a dysbalanced cytokine synthesis. This imbalance endangers severely injured patients for post-traumatic complications such as MODS, liver failure, renal dysfunction and ARDS. IL-10, a powerful immunosuppressive cytokine, plays a central role in the immune response after severe trauma. The relevance of IL-10 for single and multiple organ failure was studied in a prospective study at a level I trauma center. Blood was systematically obtained from a total of 118 severely injured [median (IQR) ISS=34 (27-34)] patients. IL-10 plasma levels were measured by ELISA. Patients showed elevated IL-10 levels throughout the whole observation period of 5 days. IL-10 plasma levels rose rapidly after trauma and gradually declined towards day 5. Patients who developed complications demonstrated significantly elevated IL-10 levels compared with patients who did not. The odds of developing MODS were 9.6 times greater in patients with IL-10 plasma levels higher than 124 pg/mL 6 hours after arrival at the ICU. Multivariate analysis showed that IL-10 plasma levels >124 pg/mL at time-point 6h, severe head injury and an arterial pH <7.34 were simultaneously significant predictors of the development of MODS in severely injured patients. The dynamic with rapid increase and gradual decline in IL-10 plasma levels indicated that IL-10 is a marker of the initial damage to the organism caused by trauma, rather than a marker of somatic dysregulations.
The present work consists of four parts, containing experimental data obtained from analysis of 'Bacillus subtilis' specific and general defense strategies against reactive oxygen species. In the first part, the peroxide and superoxide stress stimulons ob 'B. subtilis' were analyzed by means of transcriptomics and proteomics. Oxidative stress responsive genes were classified into two groups: the gene expression pattern was either similar after both stresses or the genes primarily responded to one stimulus. The high induction observed for members of the PerR-regulon after both stimuli supported the assumption that activation of the peroxide specific PerR-regulon represented the primary stress response after superoxide and peroxide stress. The second part focuses on protein carbonylation in 'B. subtilis' wild-type and 'sigB' mutant cells. The introduction of carbonyl groups into amino acid side chains of proteins represents one possible form of protein modification after attack by reactive oxygen species. Carbonyl groups are readily detectable and the observed amounts can thus serve as an indicator for the severity of protein damage. The resultsdemonstrate clearly that 'B. subtilis' proteins are susceptible to hydrogen peroxide (H2O2) mediated carbonylation damage. The application of low concentrations of H2O2 prior to the exposure to otherwise lethal levels of peroxide reduced markedly the degree of protein carbonylation, which also held true for glucose starved cells. Artificial preloading with general stress proteins resulted in a lower level of protein carbonylation when cells were subjected to oxidative stress, but no differences were detected between wild-type and 'sigB' mutant cells. In the third part, strains with mutations in genes encoding general stress proteins were screenedfor decreased resistance after H2O2 challenge. It was demonstrated that resistance to H2O2 challenge. It was demonstrated that resistance to H2O2 after transient heat treatment, likewise to conditions of glucose starvation, was at least partly mediated by the sB-dependent general stress response. The screening of mutants in sB-controlled genes revealed an important role for the deoxyribonucleic acid (DNA)-binding protein Dps in the context of sB-mediated resistance to oxidative stress underlining previous reports. Therefore, the experimental strategy opens a global view on the importance of DNA integrity in 'B. subtilis' under conditions of oxidative stress. The fourth part includes analysis of a 'B. subtilis' thioredoxin conditional mutant. The thiol-disulfide oxidoreductase TrxA is an essential protein in 'B. subtilis' that is suggested to be involved in maintaining the cytoplasmic thiol-disulfide state even under conditions of oxidative stress. To investigate the physiological role of TrxA, growth experiments and two-dimensional gel electrophoresis were carried out with exponentially growing cells that were depleted of TrxA. The observations indicate that TrxA essentially involved in the re-reduction of phosphoadenosyl phosphosulfate reductase CysH within the sulfate assimilation pathway of 'B. subtilis'.
The insulin dependent type 1 diabetes mellitus (IDDM) and the metabolic syndrome are complex human diseases. Both diseases are heterogeneous, genetically inherited and do not follow a simple Mendelian single-locus pattern. The analysis of complex human diseases is complicated both by genetic heterogeneity and by environmental factors. One way to overcome the problem of genetic heterogeneity in humans may be to cluster patients by kinship. It was shown by analysis of maternal lines of type 1 diabetics using mitochondrial DNA that 89% of maternal lines are related to each other. Moreover, an alternative to the genetic differential analysis of complex mammalian diseases is the use of animal models. The availability of inbred animal models closely resembling the human disease is an essential component of genetic investigations in this field, as shown in the results of this work. These findings do not only underscore the utility of the congenic and subcongenic approach in differentially analyzing complex traits, but also show that candidate genes can be identified and that chromosomal exchange can variously influence the phenotype, leading to sub-phenotypes which may be representative for human beings. Furthermore, it will also be possible to locate the syntenic region in the human genome and congenic and subcongenic strains can also be used to study interactions between chromosomal regions and various selected environmental conditions. In this way, it may be possible to learn which region can be influenced by environmental factors and to which extent, an undertaking which will require prospective projects.
Colossal magneto-resistance manganites are characterized by a complex interplay of charge, spin, orbital and lattice degrees of freedom. Formulating microscopic models for these compounds aims at meeting two conflicting objectives: sufficient simplification without excessive restrictions on the phase space. We give a detailed introduction to the electronic structure of manganites and derive a microscopic model for their low-energy physics. Focusing on short-range electron–lattice and spin–orbital correlations we supplement the modelling with numerical simulations.
This work studies different alternatives for parallelization of ground-state DMRG, with a focus on shared memory multiprocessor systems. Exploiting the parallelism in the dominant part of a DMRG calculation (diagonalization of the superblock Hamiltonian), speedups of 5 to 6 on 8-CPU machines can be achieved. A performance analysis gives hints as to which machine is best siuted for the task. The parallelized DMRG code is then applied to current problems in theoretical solid state physics with electronics, bosonic and spin degrees of freedom. Stripe-like modulations of the hole density in the ground state of doped Hubbard with cylindrical boundary conditions are idenficied in the thermodynamic limit using extrapolation techniques. In the 1D Holstein model of spinless fermions at half filling, Luttinger parameters and the charge structure factor are determinde in order to derive the phase diagram that had previously been established only on small lattices. For the 1D half-filled Holstein-Hubbard model, a finite size analysisof spine and charge excitation gaps in the relevant sectors (Mott insulator, Peierls band insulator and bipolaronic Peierls insulator) is able to yield the phase diagram as well. Finally, is the Heisenberg spin chain with dynamical phonons is considered as a relevant model for a spin-Peierls transition in Copper Germanate. Using DMRG, the relation between singlet-triplet excitation gap and dynamical dimeriaztion is calculated for the first time.
The present work is a paleolimnological orientated approach to refine and improve the indicator ability of freshwater ostracods from Holocene and Late glacial deposits in northeast Germany. The thesis follows two different approaches, one utilizes quantitative paleoenvironmental analysis, while the other evaluates ecological investigations of living specimens to extend the potential indicator group. For the first time quantitative ostracod analysis are carried out for a lacustrine basin (lake Krakower See) and a near-shore locality (Pudagla lowland) in the study area. The ecological investigation of living ostracods comprises 96 localities. The evaluation focused on environmental variables, which explain significantly the species composition. A canonical correspondence analysis identified at least four environmental parameters - water temperature, conductivity, pH-value, and mean water depth – which have an effect on ostracod assemblages. An extended analysis, which included only a subset of lake sites, revealed also that the former three environmental parameters affect the ostracod lake fauna, whereas the water temperature is the dominant factor. A temperature-transfer function could be regressed and calculated from the given trainingset by a weighted average model. These estimates can now be use in future paleolimnological investigations in northeast Germany to quantify the paleotemperature.
First-principle path integral Monte Carlo simulations were performed in order to analyze correlation effects in complex electron-hole plasmas, particularly with regard to the appearance of excitonic bound states. Results are discussed in relation to exciton formation in unconventional semiconductors with large electron hole mass asymmetry.
Collisional absorption of dense fully ionized plasmas in strong high-frequency laser fields is investigated in the non-relativistic case. Quantum statistical methods are used as well as molecular dynamics simulations. In the quantum statistical expressions for the electrical current density and the electron-ion collision frequency–valid for arbitrary field strength–strong correlations are taken into account. In addition, molecular dynamic simulations were performed to calculate the heating of dense plasmas in laser fields. Comparisons with the analytic results for different plasma parameters are given. Isothermal plasmas as well as two-temperature plasmas are considered.
We investigate the equilibration of nonideal plasmas from initial states where each species has already established a Maxwellian distribution, but the species temperatures and the chemical composition are not in equilibrium. On the basis of quantum kinetic equations, we derive hydrodynamic balance equations for the species densities and temperatures. The coupled density-temperature relaxation is then given in terms of the energy transfer between the subsystems and the population kinetics. We use the Landau-Spitzer approach for the energy transfer rates and a system of rate equations to describe the nonequilibrium plasma composition. Nonideality corrections are included in the rate coefficients and as potential energy contributions in the temperature equations on the simplest level of a Debye shift.
The relaxation of nonideal two-temperature plasmas is investigated with a kinetic approach. First the energy transfer between the electrons and ions is described using different approximations: the energy transfer through classical collisions (Landau-Spitzer approach) is reviewed; quantum diffraction and strong collisions are included by applying the quantum Boltzmann equation; the influence of collective modes is considered on the basis of the Lenard-Balescu equation (coupled modes) and with the Fermi-Golden-Rule approach (independent electron and ion modes). Finally, the evolution of the species temperature is investigated. In nonideal plasmas, changes in the correlation energy have to be taken into account during the relaxation. It is demonstrated that ionic correlations can significantly influence the relaxation particularly the evolution of the ion temperature).
A highly stereoselective recombinant alcohol dehydrogenase aus 'Pseudomonas fluorescens' DSM50106
(2005)
The alcohol dehydrogenase was biochemically characterized. A broad range of arylaliphatic ketones is efficiently reduced to the corresponding optically active (R)-alcohols by a recombinant alcohol dehydrogenase (PF-ADH) produced by overexpression in 'Escherichia coli'. PF-ADH shows high activity and stereoselectivity in the reduction of acetophenone and various derivatives (45-99%), as well as in the reduction of 3-oxy-butyric acid methyl ester and 3-oxy-butyric acid methyl ester and 3-oxy-hexanoic acid ethyl ester (>99%). The highest activity was observed between 10 and 20°C. The copfactor NADH can be efficiently recycled by the addition of 10-20% of iso-propanol. A flow-through-polarimetry-based assay to determine oxidoreductase activity and stereoselectivity is described.
The triple-trap mass spectrometer ISOLTRAP at ISOLDE/CERN has demonstrated the feasibility of mass spectrometry of in-trap-decay product ions. This novel technique gives access to radionuclides, which are not produced directly at ISOL-type radioactive ion beam facilities. As a proof of principle, the in-trap decay of 37K+ has been investigated in a Penning trap filled with helium buffer gas. The half-life of the mother nuclide was confirmed and the recoiling 37Ar+ daughter ion was contained within the trap. The ions of either the mother or the daughter nuclide were transferred to a precision Penning trap, where their mass was determined.
About 30 % of epileptic patients are non-responsive to multidrug antiepileptic therapy. One of non-responsiveness in epilepsy hypothesis claims that non-responsiveness occurs because of reduced access of antiepileptic drugs to their targets, as a result of increased efflux of antiepileptic drugs away from these targets. Transporters believed to be involved in non-responsiveness in epilepsy are mainly but not exclusively the members of the ABC superfamily including P-gp (MDR1, ABCB1), MRP1 (ABCC1), MRP2 (ABCC2) and others. These proteins are normally found in the blood-brain barrier and the blood-cerebrospinal fluid barrier where they function as protectors. There is emerging evidence that P-gp, MRP1 and MRP2 are up-regulated in epileptogenic brain tissue. The risk of non-responsiveness could be related also to the MDR1 or MRP2 gene polymorphisms. We hypothesised that changes in expression and function of multidrug transporters involved in non-responsiveness of epilepsy might be detectable not only in the brain but also in other tissues such as lymphocytes. Therefore we evaluated the expression of MDR1, MRP1 and MRP2 and function of P-gp in lymphocytes in patients with epilepsy and healthy subjects. Three groups of epileptic patients and 15 healthy subjects as a control group were included in the study. The patients’ group was defined as follows: Monotherapy – patients treated with carbamazepine monotherapy, without seizures - corresponded to group responders. Combined therapy – patients after monotherapy (two different medicines have been tried) and combined therapy (two trials of combined therapy), not free of seizures. Monotherapy and combined therapy groups each embraced 15 patients. Neurosurgery – patients who had undergone neurosurgery, afterwards were or were not additionally treated with carbamazepine, with or without seizures. This group comprised 24 patients. Combined therapy and neurosurgery groups composed the group of non-responders. The mRNA expression of MRP1, MRP2 and MDR1 by means of quantitative real-time PCR as well as MRP2 and P-gp protein content by Western blot in lymphocytes was measured. For P-gp functional analysis rhodamine efflux from lymphocytes and natural killer (NK) cells was performed. The influence of the polymorphisms C3435T, G2677T/A in the MDR1 gene and C24T, G1249A, C3972T in the MRP2 gene for the transporters expression, function and their association with non-responsive epilepsy phenotype was investigated. Our results showed that MRP1 expression in lymphocytes was significantly lower in epileptics than in healthy subjects. Non-responders had lower MRP1 mRNA content in lymphocytes than responders. We did not find any difference in MRP2 expression between epileptics and healthy volunteers. MRP2 mRNA levels in lymphocytes were higher in non-responders than in responders. However, at protein level epileptic patients had significantly lower MRP2 content in lymphocytes than controls. MRP2 protein content did not differ in responders and non-responders. There was no reliable correlation between MRP2 mRNA expression and MRP2 protein content in lymphocytes. Epileptics had significantly lower MDR1 expression in lymphocytes than healthy individuals. MDR1 expression was decreasing according to the consumption of antiepileptic drugs and seizures frequency: patients after neurosurgery had significantly lower MDR1 expression than patients after combined therapy and monotherapy. MDR1 expression was significantly lower in non-responders than in responders. At protein level epileptics had lower P-gp content than controls. Detected P-gp amount in lymphocytes did not differ between responders and non-responders. Rhodamine efflux from lymphocytes and NK cells did not differ significantly between epileptics and healthy subjects, but it was higher in patients after neurosurgery than in patients after monotherapy. Rhodamine efflux from NK cells, which are known to express the highest levels of P-gp, was significantly higher in non-responders than in responders. In this study, we showed that MRP1 mRNA expression in lymphocytes was significantly correlated to its expression in the brain. We detected also a significant co-correlation between MRP1 expression in the hippocampus and MDR1 expression in lymphocytes. We found no evidence regarding the impact of the MDR1 polymorphisms on mRNA expression, P-gp content and rhodamine efflux from lymphocytes. Our data showed lack of evidence regarding the impact of the MRP2 polymorphisms on mRNA expression and protein content. We did not detect any association between MDR1 or MRP2 polymorphisms and non-responsiveness in epilepsy or epilepsy in the main. In conclusion, our results suggest that lymphocytes are an appropriate surrogate for studies on changes of multidrug transporters expression in epilepsy. Lymphocytes as an easily accessible tissue might serve as a marker for responsiveness to antiepileptic drug therapy in epilepsy studies.
The biodiversity of marine microorganisms opens a promising potential for the discovery of new technical enzymes. During this study a characterization of marine microorganisms, isolated from Arctic or Antarctic ice, sea water or sediment from the ocean was performed based on a comprehensive strain collection at the Alfred-Wegener-Institut für Polar- und Meeresforschung. These marine psychrophilic bacteria indicated a wide spectrum of extracellular cold-active enzymes. 16S rRNA sequencing revealed that many of these psychrophilic bacteria represent new species. Characterization of selected isolates by means of transmission electron or raster electron microscopy showed remarkably pleomorphic cellular structures throughout their growth. The major part of this thesis focuses on a marine Antarctic, psychrophilic bacterium (strain ANT/505) isolated from sea ice covered surface water from the Southern Ocean, which was identified to express a very uncommon enzymatic activity for the marine environment, namely a pectinolytic activity. The sequencing of the 16S rRNA of isolate ANT/505 and biochemical tests indicated a taxonomical affiliation to the specie Pseudoalteromonas haloplanktis. The supernatant of this bacterial isolate showed after growth on citrus pectin three different pectinolytic activities. By activity screening of a genomic DNA library of isolate ANT/505 in Escherichia coli, two different pectinolytic clones could be isolated. Subcloning and sequencing revealed two open reading frames of 1671 and 1968 nt corresponding to proteins of 68 and 75 kDa. The deduced amino acid sequence of the two orfs showed homology to pectate lyases from Erwinia chrysanthemi and Aspergillus nidulans. The pectate lyases contain signal peptides of 17 and 26 amino acids length that were correctly processed after overexpression in E. coli BL21. Both enzymes were purified by anionic exchange chromatography. Maximal enzymatic activities for both pectate lyases were observed at a temperature of 30°C and a pH range of 9-10. The Km values of both lyases for pectate and citrus pectin were 1 g⋅l-1 and 5 g⋅l-1, respectively. Calcium was required for activity on pectic substrates, while the addition of 1 mM ethylenediaminetetraacetic acid (EDTA) resulted in complete inhibition of the enzymes. These two cold-adapted enzymes represent the first pectate lyases isolated and characterized from a marine bacterium. Further cloning and sequence analyses revealed that PelA from P. haloplanktis is an exceptionally big bifunctional enzyme featuring pectate lyase and pectin methylesterase activity. The deduced amino acid sequence of the pectin methylesterase domain showed homology to group I pectin methylesterases from Erwinia chrysanthemi and Erwinia carotovora. The pectin methylesterase domain of PelA was found to show highest homology to a potential pectin methylesterase from Saccharophagus degradans strain MD2-40. Maximum pectin methylesterase activity of PelA was detected at a pH of 7.5 and a maximum temperature of 30°C. This cold-adapted enzyme revealed high remaining pectin methylesterase activity at low temperatures around 5°C and was quickly unstabilized at temperatures above 45°C. The analysis of the localization of the two pectinolytic genes on the genome of P. haloplanktis ANT/505 revelaed that these pectinase genes are expressed from independent cistrons, which are not clustered but located at distant positions on chromosome I of the P. haloplanktis genome. It was found that the transcription of both pectinase genes is induced by the presence of pectin. By means of primer extension the promoter regions of both cistrons were detected.
Recent geochemical and mineralogical alteration processes in tropical coastal sediments of Vietnam
(2006)
The dissertation contains two main parts: (i) Syn-sedimentary hydrodynamic processes & relationship with elemental distribution, clay matter, (ii) Short-term mineral alteration during early diagenes. Samples were taken from the uppermost one metre (<50 year old in RRD, < 300 y old in south central VN). In part one, three principal hydrodynamic factors can be revealed based on End-Member Modelling Algorithm (EMMA), for the polymodal grain-size distribution patterns in coastline of VN (i) Accumulation factor: accumulation of terrigenous sediments linked with a grain size separation (distance dependence), (ii) Erosion factor: synsedimentary erosion by wave activities, (iii) Aeolian factor: deposition from neighbour sand bar by wind (typically only for low sedimentation rate, like in South Central Coast but not to detect in RRD). Distributions of clay matter and chemical elements in the coastal sediments in Vietnam are strongly influenced by hydrodynamic forces (distance from the coastline). In part two, particle-wise analysis by TEM allowed to determined four main mixed layer series: di-Vermiculite/Smectite-ml, Kaolinite/ Expandable-ml, Illite/Smectite-ml, Chlorite/Saponite-ml. Three principal mineral alteration processes can be detected in coastal sediments during early diagenesis: Dissolution, Smectitization, Kaolinitization, based on XRD (CSD, peak area) & TEM-EDX (particle morphology, chemical formula, polytype, particle frequency). Dissolution process of clay matter is typically in the coastal alkaline condition. It is a function of diagenetic time. Dissolution begins with a higher degree of dislocation and is followed by step-wise delamination & dissolution of the first stacks Smectitization (mirrored in diVS-ml series) alters mica-like structures (illite, dioctahedral vermiculite) to smectitic structures (Beidellite, Montmorillonite). Smectitization process occurs in group-wise layer by layer transforming mechanism (mica-like layer to smectitic layer). Each step is indicated by a gauss-like distribution of the octahedral layer charge with K as trigger. Kaolinitization of KE series alters smectitic structure (beidellite, smectitic KE-ml) to kaolinitic structure (kaolinitic KE-ml, kaolinite) "interlayer by interlayer" transformation of KE-ml series is comparable to kaolinitization mechanism discussed by Dudek et al. (2006).OH- groups in ambient could be the trigger. Mangroves biota influences the sediments in two main pathways: Nutrients supply & trapping function (clay matter, heavy metals)Interaction of active root-layer: intensification of dissolution, smectitization & kaolinitization: uptake of K, Na by mangrove root is possible trigger Human activities like shrimp cultivation have stopped the influences of the former active roots.Besides, erosion process related to water discharge gives rise to dispersion of clay species & heavy metals => more toxic for ecosystem.
The non-natural substances in commonly used UV protection creams such as TiO2, are known to have a photocatalytic side effect, which is very harmful to human skin. This study presents some properties of clays and clays minerals concerning UV protection potential, which can be very helpful for the development of new UV protection cream generation. Clays and clay minerals are demonstrated that they have potential to absorb UV-radiation. The structures of clay particles in cream were shown to be dependent on the layer charge of clay minerals. The total amount of Fe2C>3 in chemical composition of clay plays a key role in determining the UV-absorption ability of the clay matter. Moreover, the UV-absorption ability also depends on the expandable or non- expandable property of the clay. The studies were also performed on the mixtures of wool-wax-alcohol cream and nanosuspension obtained by the extraction of fungi mass Ganoderma pfeifferi by using plantacare together with clay. The combination of clays and nanosuspension increased its UV-absorption ability. The skin model test was performed in vivo in mouse ears with skin flora Escherichia coli and infectious bacteria Staphylococcus aureus in order to determine the effects of cream samples on skin under UV irradiation and skin infection. From the results of characterization of clays and clay minerals properties in UV protection cream, this study also brings some ideas about products designing.
Although the benefit of expedient antibiotic therapy remains unquestioned, little is known about the effects that are unrelated to their antimicrobial property but which the antibiotics may exert upon the septic microcirculation. Impairment of intestinal microcirculation has been recognized as an important factor in the pathogenesis of the septic syndrome (intestine = ¡°motor¡± of multiple organ failure). To examine the effects of various antibiotics on microcirculation is justified by the fact that one of major features of sepsis is disturbance of microcirculation. However, monitoring of pharmacological effects on intestinal blood flow is nearly impossible during acute therapy in humans and requires sophisticated equipment when applied to experimental animals. Therefore, the aim of this study was to evaluate the effects of common antibiotics on intestinal microcirculation using intravital microscopy (IVM) and on the release of the cytokines in septic and endotoxemic rats. In a first series of experiments we induced sepsis by using colon ascendens stent peritonitis (CASP) model in the rat (16 hours prior microscopy). We evaluated the effects of common antibiotics on intestinal microcirculation using intravital microscopy (functional capillary density (FCD) and leukocyte-endothelial interactions) and on the release of the cytokines TNF-¥á, IL-1©¬, IL-6 and IL-10. Metronidazole (MET) (10 mg/kg); imipenem (IMI) (20 mg/kg); tobramycin (TOB) (25 mg/kg); vancomycin (VAN) (70 mg/kg); and erythromycin (ERY) (5 mg/kg) were given intravenously 16 hours following sepsis induction. To differentiate antimicrobial from anti-inflammatory effects we performed a second series of experiments using endotoxin (LPS, i. v.) and intravital microscopic examination was performed 2 hours later. Cytokine release was estimated at the end of the experiments. In the CASP model, acute administration of metronidazole was associated with an improvement of markers of the intestinal microcirculation in septic rats (CASP). Our study showed that vancomycin stimulated leukocyte rolling, while erythromycin prevented the activation of leukocyte-endothelial interaction in postcapillary intestinal venules (V1) that occurred within 16 hours after CASP. TNF-¥á release in untreated CASP rats was twice as high in comparison to all antibiotic-treated CASP rats, except in CASP rats treated with tobramycin. Key findings of the present study are that MET and ERY were more potent than other antibiotics in improving the intestinal microcirculation in the CASP model. Protective effects of metronidazole, erythromycin and vancomycin upon the microcirculation were found in LPS model. The administration of MET or VAN or ERY led to significantly higher FCD values within the longitudinal muscular layers. Metronidazole and erythromycin significantly reduced the n umber of sticking leukocytes within the V1-venules of LPS-challenged animals. Leukocyte rolling flux was significant increased within the V1- and V3-venules of the endotoxemic rats treated with VAN. Some antibiotics showed immuno-modulatory effects: MET or IMI or VAN treated LPS rats showed increased IL-10 levels; while ERY treated LPS rats showed decreased IL-1©¬ and increased IL-6 concentrations. In conclusion, metronidazole and erythromycin exerted a positive influence upon the intestinal perfusion not only within septic microcirculation (anti-bacterial effect) but also in a pathogenically independent manner (anti-inflammatory effect); vancomycin had only anti-inflammatory actions in the endotoxin model without bacterial infection. Imipenem and tobramycin had no effect on intestinal microcirculation in septic and endotoxemic rats. The clinical usefulness of studies such as this is that they could provide important information about possible side effects or indicate some potential beneficial effects of the antibiotics. They can influence not only microcirculation but also inflammatory processes by some mechanisms that are probably unrelated to their antibiotic effect. However, these effects may be particularly relevant to the intestinal microcirculation which plays an essential role in the development of multi-organ failure in the instance of sepsis.
The toluene-degrading and solvent-tolerant strain Pseudomonas putida DOT-T1E was investigated with respect to its suitability and economic efficiency as biocatalyst in aqueous-organic two-phase systems with aliphatic solvents as organic phase (Rojas et al. 2004, chapter 4 and 5) and to its adaptive responses to the solvent decanol. The adaptive changes on the level of cell morphology (chapter 2), membrane fatty acids and permeability (chapter 3), as well as energetics and surface properties (chapter 5) of P. putida DOT-T1E have been investigated in order to ascertain information about the strain's suitability for two-phase biotransformation systems (chapter 4). The morphological adaptation to the presence of solvents was observable in changes of the cell size of P. putida DOT-T1E. Those changes were dependent on the cellular activity and occurred only after addition of non-lethal solvent concentrations. The cells reacted to the presence of organic solvents by decreasing the ratio between surface and volume of the cells and therefore reducing their relative surfaces (chapter 2). The cell surface and especially the cytoplasmic membrane are the major targets for toxic effects of membrane-active compounds like solvents. The mechanism of the cis-trans isomerisation of unsaturated fatty acids counteracts the fluidizing effect of solvents by increase the ordering of the membrane and therefore its rigidity. By comparing the responses of the cells to a series of stress factors (like solvents), a direct correlation between the activation of this mechanism and the well investigated K+-uptake pumps was observed (chapter 3). Huertas et al. (1998) reported that this strain tolerated concentrations of heptane, propylbenzene, octanol, and toluene of at least 10 % (vol/vol). 1-decanol is, in comparison to toluene, less hazardous and volatile, and it possesses good extraction properties for the desired fine chemical products. In further investigations of possible biotechnological processes, it was discovered that decanol is also a more suitable solvent as organic phase (chapter 4). Although the cells of P. putida DOT-T1E needed additional energy for their adaptation to the presence of the solvent decanol, they were able to maintain or activate their electron transport phosphorylation allowing homeostasis of ATP level and energy charge in the presence of the solvent, at the price of a reduced growth yield. On the other hand, significantly enhanced cell hydrophobicities converging with more negative cell surface charges were observed in cells grown in the presence of 1-decanol (chapter 5). It is however important to note that all the cell’s properties observed are closely linked to each other since they are all part of the adaptive response of the cells. It can be concluded that the easy adaptability and good growth properties of Pseudomonas putida DOT-T1E in the presence of the organic solvent 1-decanol make this system an excellent candidate for two-phase fermentation processes. Moreover, the absence of differences in the energetics of the bacteria during exposure to 1-decanol as compared to bacteria that grew in the absence of 1-decanol, support that this organism can be used for the industrial production of fine chemicals in an economically sound manner.
For many years, rangeland ecologists have debated about whether the state of semi-arid and arid rangelands is the expression of an ecological equilibrium or non-equilibrium dynamics reached in response to grazing livestock. Since the problem has been considered at different spatial scales, it is recognised that the competing concepts of equilibrium and non-equilibrium dynamics need to be integrated. Furthermore, the role of environmental variables as vegetation driving factors has long been ignored in the discussion on grazing effects on ecosystems. Present thesis, examines the dependence of plant communities on environmental in particular site-ecological conditions in three ecosystems of Western Mongolia established along a precipitation gradient to detect the vegetation-driving ecological factors involved. Furthermore, grazing impact is exemplary assessed in a desert steppe at additional spatial scales of plant communities and population. At the landscape level, a classification of plant communities in dependence on environmental conditions is carried out. Additionally, the investigations focused on the impact of grazing on soil and on the occurrence of grazing-mediated plant communities. Data were sampled along an altitudinal gradient between 1150 m to 3050 m a.s.l. from arid lowland with desert steppe via semi-arid mountain steppe to humid alpine belt. Within each altitudinal belt, data sampling was carried out along grazing gradients, established from grazing hot spots to areas distant from them. By means of an environmentally based vegetation classification, factors with highest explanation values for largest variation in vegetation were identified and considered as most responsible for vegetation patterns. To validate and affirm the classification, three different statistical methods are applied: environmentally adjusted table work of vegetation relevés supported by cluster analysis of species distribution, detrended correspondence analysis of vegetation data separately from environmental data, and the principle component analysis of only environmental data. Vegetation-driving factors change along the altitudinal gradient from abiotic forces in the desert steppe, as e.g. altitude and soil texture, to abiotic and biotic forces in the alpine belt represented by soil texture, soil nutrients and grazing. Vegetation and soil of all ecosystems respond to grazing but with different patterns and to a different extent. While desert steppe does not indicate grazing communities, mountain steppe demonstrates grazing communities at fertilised sites and alpine belt at nutrients depleted sites. Thus, the grazing sensitiveness of the ecosystems is assumed to be linked with plant productivity and the role of vegetation as site-determining factor (Chapter 2). To examine grazing impact at lower spatial scales on desert steppe as the ecosystem with lowest grazing sensitiveness at the landscape scale, at community scale the total number of species, the total vegetation cover, the percentage of annual species, the cover of annual species, and properties of soil nutrient along gradients of grazing intensity within three different communities were assessed. Vegetation parameters respond to grazing in different ways, and the responses of the same parameters vary between plant communities. Correlations with grazing intensity indicate only partly statistical significance. Significant correlations of grazing intensity with concentrations of soil nutrient point to eutrophication in two communities. A comparison of vegetation and soil properties refers to a greater indirect influence of grazing via increased soil nutrients than the direct effect on vegetation (Chapter 4). At the population level, data about stand density, aboveground biomass, individual plant weight, and the proportion of flowering plants of the dominant dwarf semi-shrub Artemisia xerophytica were collected along a grazing gradient. Soil data were used to distinguish between grazing and edaphic influences. All parameters of Artemisia xerophytica reflect the assumed gradient of grazing intensity up to 800 m distance from the grazing hot spot. As grazing pressure decreases, plant density and total biomass per plot increase. The average shrub weight, an indicator of plant vitality, is related to both: distance from the grazing hot spot and stand density, which may be explained by additional intraspecific competition at higher densities. At a longer distance, these effects are masked by variations in soil parameters determining water availability, leading to quite similar degradation forms. These results are in contrast to other studies carried out at the scale of plant communities which did not detect significant changes along a grazing gradient. One explanation is the different map scale: the study took place only within a single plant community comparing populations of one species (Chapter 3). The comparative study demonstrates that even arid desert steppes of western Mongolia display equilibrial and non-equilibrial properties, depending on the observational scale: while no grazing mediated plant communities could be identified at the landscape scale as predicted by the non-equlilibrium model, at the community level vegetation parameters imply an intermediate position between equilibrium and non-equilibrium system. At the population level, the results clearly reflect the grazing gradient as predicted by the equilibrium model (Chapter 4). As a consequence, the assessment of vegetation dynamics and grazing impact in rangelands requires a multiple-scale approach that duly considers different vegetation properties responding differently to grazing, climatic and edaphic variability at different spatial scales. It is further suggested, that future research should draw comparisons between landscapes that co-evolved with herbivory, and those that did without (Chapter 4).
The thesis contains 6 chapter and mentions about the influences of sea level change, climate, tectonic into the sedimentary process. The results show that late Pleistocene facies mostly are weathered facies which content gibbsite-kaolinite, limonite. In transgression, facies assemblage includes lagoon, tidal and estuary. The composition are in-situ reworked minerals like illite, gypsum. In regression, facies are shallow marine, prodelta, delta front, distributary lobe, swamp, tidal and beach, channel infill, flood plain, lake. Abundant minerals are named like smectite, illite, chlorite, quartz, feldspar, rock fragments, gypsum.Gypsum is the evaporited mineral easily to be formed in coastal environment of Red River Delta. It is a good indicative mineral for distinguishing the deposits formed in dry season of monsoon regions. Smectite is good indicative mineral for sea environment which mostly related with the transference and low accumulation and new formed in climate with wet and dry periods. Kaolinite-gibbsite is an indicator of strong chemical weathering with high precipitation. The stratigraphy can be divide into trangressive systems tract (10-8.5 cal. kyr BP) and highstand systems tract with aggradational-progradational parasequence set (8.5-6.5 cal. kyr BP) and progradational parasequence set (6.5 cal. kyr BP-today, with subsets 6.5-4.0; 4.0-1.5; and 1.5-0.0 cal. kyr BP). The subsidence process which reflex in accumulation rate regarded to not only sea level change, tectonics but also human impact - dyke build plays the main role to increased sedimentary thickness. The influence of source variation and climate change are recorded on mineral composition. In late Pleistocene, materials are chemical weathering authigenic components during warm/wet climate. In transgression, dominated materials are reworked terrigenous and chemical weathering components during warm/dry and cool/wet climate. In regression, materials are low maturity, suffered by physical weathering transported from surrounding mountains during 3 warm/dry or wet - cool/dry or wet big climate cycles.
Proteomic signatures select the physiology state of the cell. By using 2-D technique, proteome signature of Bacillus subtilis under different stresses and starvations are analyzed. Consequently, a proteomic map of Bacillus subtilis in non-growing phase was created. The ammonium and tryptophan as well as phenol and catechol stress are analyzed using both of proteomics and transcriptomics. And the proteomic map represents a good application in the prediction of the mode of action of phenol and catechol stress.
In the present thesis, a systematic study of beam driven Alfvén eigenmodes in high-density and low-temperature plasmas of the W7-AS stellarator is performed. The device went out of operation in 2002 and the study is based on stored experimental data. Alfvén instabilities can roughly be divided into ideal MHD Alfvén eigenmodes and those existing due to kinetic effects. The spectrum of ideal MHD Alfvén waves in toroidal fusion devices consists of a continuum of stable waves that are strongly localized. Weakly damped, discrete eigenmodes can exist in gaps of the continuous spectrum which are formed by plasma inhomogeneities and the coupling of Alfvén continua. This allows an identification of ideal MHD Alfvén eigenmodes in terms of their frequency and mode numbers. Kinetic effects can modify this spectrum and cause additional types of eigenmodes, the kinetic Alfvén eigenmodes (KAE) and energetic particle modes (EPM). The goal of this thesis is twofold: (I) identification and description of fast particle driven Alfvén instabilities in W7-AS, and (II) study of energetic particle losses induced by Alfvén instabilities. The reconstruction of the ideal MHD plasma equilibrium for each discharge with sufficient accuracy is the very foundation of all subsequent steps. This is achieved, based on measured plasma parameter profiles that are further refined by validating them to the measurements of other, independent plasma diagnostics. The applied scheme is inspired by an approach of Integrated Data Analysis (IDA) to combine different diagnostic data and provide combined uncertainties. After mode number analysis and eigenmode identification, the theoretically expected, linear growth rate of the instability is calculated where possible, and the various contributions of the fast particle drive to the instability of the mode are identified. Alfvénic activity recorded by the Mirnov diagnostic is analyzed, which consists of a set of spatially distributed coils that measure magnetic fluctuations. On W7-AS, the probes are arranged in three poloidal arrays at different toroidal positions. The spacing between the probes is non-equidistant. In addition, the signals of one probe array are digitized with a different sample rate. These characteristics prohibit the straight-forward use of standard tools available for harmonic analysis. Instead, a new tool has been developed and thoroughly tested. It is a multi-dimensional extension of the Lomb periodogram, able to provide reliable time-resolved frequency and mode number spectra in the case of uneven datapoint spacing. Numerical studies of this periodogram show a good performance with respect to mode number resolution given the low number of available probes, and robustness against perturbations of the signal. Only two of the probe arrays can be used for the analysis of eigenmodes with frequencies >70 kHz, such that for high-frequency phenomena insufficient information about the mode numbers is available. A total of 133 different Alfvén eigenmodes is studied in discharges from different experimental campaigns. A restriction to discharges from various high-beta campaigns with neutral beam heating is required to allow for a realistic reconstruction of plasma equilibrium and velocity distribution functions of energetic particles. The discharges are characterized by high density, ne = 5 x 1019 m-3 to 2.5 x 1020 m-3 at relatively low temperatures of Te = Ti = 150 ... 600 eV. Alfvén eigenmodes often appear transiently in the startup phase of these discharges, where density and heating power are being ramped up. Occasionally, Alfvén eigenmodes are seen in the stationary, high-beta phase in the presence of considerable neutral beam heating. Most of the Alfvén eigenmodes are successfully classified as ideal MHD eigenmodes. 19 global, 47 toroidicity-induced and 8 ellipticity-induced Alfvén eigenmodes (GAEs, TAEs, and EAEs, respectively) are unambiguously identified by their mode numbers and frequencies. Excellent agreement between experimentally observed mode number spectra and theoretically calculated eigenmode structure is shown for a TAE example. Additional 13 events are found to have frequencies inside the EAE gap and could possibly be EAEs. Evidence for high-frequency Alfvén eigenmodes (mirror- and helicity-induced Alfvén eigenmodes) is seen, but can not be proven rigorously due to uncertain mode numbers and the complexity of the Alfvén continuum. The remaining 41 Alfvén eigenmodes can not be classified to be one of the above cases. Reasons are either high frequencies, mode numbers obscured by far-field effects, or mode numbers that could not be related to ideal MHD Alfvén eigenmodes. A selection of these shows indications of strong non-linear wave-particle interactions and are assumed to be EPMs. Kinetic Alfvén eigenmodes are not expected to exist in the experimental conditions that were studied. The radially resolved velocity distribution function is used to describe the parameter regimes in which the modes are observed in terms of the dimensionless parameters vb/vA (beam velocity normalized to the Alfvén velocity) and ßfast/ßth, where beta is the ratio of plasma pressure to magnetic pressure. The first parameter describes through which of the possible resonance velocities particles can interact with the eigenmode. A peculiarity of the fast particle dynamics in fusion devices is that they can resonantly interact with Alfvén eigenmodes through sideband resonances even if v < vA. The second parameter describes the energy content of the destabilizing fast particle population compared to the potentially stabilizing thermal plasma component. These parameters contain relevant information about the instability of an eigenmode and such diagrams are given for all observed modes. In addition to that, the expected linear growth rate of gap modes is calculated based on a theoretical model that extends the ideal MHD by a perturbative, drift-kinetic description of the energy exchange between waves and circulating particles, neglecting the effects of trapped particles. For the discharges under consideration the thermal electron speed is comparable to vA and the electrons provide a significant Landau damping contribution. Due to strong density gradients near the plasma boundary in most of the discharges, the thermal ions can provide a small drive via the spatial inhomogeneity which does not overcome the electron damping, however. The drive by spatial inhomogeneity of thermal ions requires a certain propagation direction of the mode and is equally stabilizing for opposite mode numbers. The fast particles also contribute to the growth rate via spatial inhomogeneity, velocity gradients and velocity anisotropy terms are negligible in W7-AS. Most of the observed GAE or EAE modes have negative mode numbers, which correspond to a propagation direction for which the spatial inhomogeneity of thermal and beam ions is predicted to be stabilizing. A fast particle drive of these modes is not confirmed, whereas the TAEs are found to be strongly destabilized by neutral beam injection. The distribution of plasma parameters for discharges showing TAEs in terms of the dimensionless stability parameters suggests an instability threshold that is qualitatively confirmed by an exploration of the parameter space with the theoretical model. Wave-induced, resonant losses of energetic ions scale linearly with the wave amplitude. To identify them, correlations between ion loss probe signals and wave amplitudes are searched, where correlation times in the order of the slowing-down time of energetic particles are expected. Significant correlations can be established only exceptionally for 3 of the identified ideal MHD Alfvén eigenmodes. Those Alfvén eigenmodes, however, which are assumed to be EPMs frequently show severe losses of energetic ions that are visible in the time traces of the plasma energy as well.
The Gram-positive bacterium Bacillus licheniformis is an important industrial host for the production of enzymes. Genomic DNA arrays and proteomics are being used to investigate the physiology of this bacterium. A genome-wide transcriptional profiling analysis of the adaptation of B. licheniformis to phosphate starvation shows more than 100 induced genes. Most of strongly induced genes belong to the putative Pho regulon. The data of the transcriptome analysis have been verified by the analysis of the extracellular and cytoplasmic proteome. The main response of B. licheniformis to glucose starvation was a switch to the usage of alternative carbon sources. In addition, B. licheniformis seems to be using other organic substances like amino acids and lipids as carbon sources when subjected to glucose starvation. This was indicated by the induction of a high number of genes the proteins of which are involved in amino acid and lipid degradation. During nitrogen starvation genes necessary for the recruitment of nitrogen from alternative sources were induced, e.g. genes for nitrate and nitrite assimilation, several proteases and peptidases. Both starvation conditions led to a down-regulation of the transcription of most vegetative genes and subsequently to a reduced synthesis of the corresponding proteins. Only a few genes were induced by both starvation conditions like yvyD, citA and the methylcitrate shunt genes mmgD, mmgE and yqiQ. Data of this study use to better understand the physiology of this bacterium during fermentation processes and thus to identify and circumvent bottlenecks of B. licheniformis based bioprocesses. In addition, the phytase promoter was tested for the construction of an alternative phosphate regulated expression system for B. licheniformis.
The thesis contains 6 studies and mentions the validation and comparison of several methods for measuring body composition and assessing nutritional status in different groups of pediatric patients. It also deals with the effects of infant formulas supplemented with nucleotides on the growth and body composition of healthy term and preterm babies. The first study shows that BMI-standard deviation score and %BF have a moderate agreement in classifying the nutritional status. The second study done in preterm neonates points out that bioelectrical impedance provides only insignificant information on fat-free mass (FFM) compared to anthropometry. The third study validates published prediction equations and develops a new equation in a group of children with Crohn's disease. The equation of Schaefer et al. is the best to predict FFM. The accuracy of a prediction equation is influenced by weight, height and age other than impedance index alone. The fourth study indicates that impedance index is better than weight, height squared as the predictor for estimating FFM. Addition of weight improves the predictive accuracy of prediction equations. The fifth study shows that birth weight centiles gives a rough estimation of nutritional status. Weight-for-length ratio shows the best correlation with fat mass. The last study shows that weight gain and gain in lean mass are higher in the standard formula group than in the groups nourished with nucleotides or breast milk.
Synthesis and evaluation of pseudosaccharin amine derivatives as potential elastase inhibitions
(2006)
Elastase is a serine protease which by definition is able to solubilize elastin by hydrolytic cleavage.Human Leukocyte Elastase, HLE (EC 3.4.21.37), is involved in deseases such as adult respiatory distress syndrome, pulmonary emphysema, smoking related chronic bronchitits, ischemic-reperfusion injury and rheumatoid arthritis. Hence, the elastase inhibitors have clinical utility in these diseases. Heterocyclic compounds are one of the most important classes of the elastase inhibitiors. In the present work different pseudosaccharin amine derivatives were synthesized and tested against the elastase. The synthesis of pseudosaccharin amine dervatives was carried out from the amines and(1,1-dioxobenzo[d]isothiazol-3-ylsulfanyl)acetonitrile in different solvents. Futhermore, the pseudosaccharin amines were obtained by refluxing the thiosaccarinates in absolute acetic acid. The reaction of 3-ethoxybenzo[d]isothiazole 1,1-dioxide with different amines in dioxane under reflux resulted into the desired pseudosaccharin amine derivatives in higher yields. Pseudosaccharin chloride was also used in the synthesis of these derivatives.A detail study of the synthesis of pseudosaccharin amine dervatives from the above differnt routes is described. Peptides were also synthesized by using the mixed anhydride method. The ester, acid, amide and peptide derivatives were tested against the Porcine Pancreatic Elastase (PPE) and Human Leukocyte Elastase (HLE). The esters were found to be the reversible inhibitors of HLE. The process of the PPE inhibion by cyanomethyl(2S)-2-(1,1-dioxobenzo[d]isothiazol-3-ylamino)-3-methylbutanoate was studied. Michaelis-Menten curve and Lineweaver-Burk double reciprocal plot were constructed in order to study the kinetic of this reaction. The compounds showing high inhibition of HLE were further stuied for determination of their inhibitory constant(Ki). The esters were found to be the higly active compounds against HLE. The cyanomethyl(2S)-2-(1,1-dioxobenzo[d]isothiazol-3-ylamino)-3-methylbutanoate and cyanomethyl(2S,3S)-2-(1,1-dioxobenzo[d]isothiazol-3-ylamino)-3-methylpentanoate showed the competitive reversible inhibition of HLE.The cyanomethyl(2S,3S)-2-(1,1-dioxobenzo[d]isothiazol-3-ylamino)-3-methylpentanoate is highly potent inhibitor of HLE. The possible mechanism of inhibition of elastase by these compounds is discussed. Molecular modelling of some of the ester derivatives is also discussed.
A fluorescent lamp driven with an 'instant start electronic control gear' starts in a glow mode. In the glow mode, which lasts typically for tens of milliseconds, the cathode fall exceeds hundreds of volts. This causes high energy ion bombardment of the electrode which heats the electrode, and induces a transition from glow to arc mode. In the arc mode the electrode emits thermionically and the cathode fall drops to the 12 – 15 V range. Unfortunately, the high energy ion bombardment during the glow mode leads also to intense sputtering of electrode material, including tungsten as well as emitter. Thus, instant started fluorescent lamps often suffer from early failures due to coil fracture. Therefore, the investigation of tungsten erosion during instant start is necessary and was the main goal of this work.
The density of neutral atomic tungsten is determined by laser-induced fluorescence (LIF) and optical emission spectroscopy measurements (OES). Investigations are performed on a low-pressure argon dc discharge and on commercial fluorescent lamps. To include the entire temperature profile along the electrode the diffuse and spot operation modes of the dc lamp are studied experimentally and theoretically. The measured dependencies of the cathode temperature along the coil on the discharge and heating parameters are compared with the calculated results. For the first time the tungsten erosion during instant start of commercial fluorescent lamps was experimentally investigated in this work. The erosion process could be related to sputtering. A reconstruction of the temporal evolution of the absolute tungsten population density of the ground state during the glow mode was presented. The sputtered tungsten density increases immediately with the ignition, reaches a maximum where the discharge contracts at the end of the glow mode, and decreases some milliseconds before the glow-to-arc transition takes place. The maximum tungsten density was observed within a region of a few hundred micrometers only located at the discharge attachment point. The main result achieved in this work is that during the whole glow mode tungsten is sputtered. Therefore, the lifetime of instant started fluorescent lamps can be enhanced by reducing the duration of the glow mode. Additionally, the need for the application of different types of diagnostics for the observation of lamp ignition was shown due to different results of LIF, AAS and OES: The observation of excited tungsten atoms by OES shows the maximum emission signal at the glow-to-arc transition whereas by LIF and AAS measurements of tungsten atoms in the ground state the maximum density is found during the whole glow mode. This can be explained by the fact that the intensity of the spontaneous emitted light is related not only to the density but also to the degree of excitation.
The interaction of partially ionized plasmas with an electromagnetic field is investigated using quantum statistical methods. A general statistical expression for the current density of a plasma in an electromagnetic field is presented and considered in the high field regime. Expressions for the collisional absorption are derived and discussed. Further, partially ionized plasmas are considered. Plasma Bloch equations for the description of bound-free transitions are given and the absorption coefficient as well as rate coefficients for multiphoton ionization are derived and numerical results are presented.
Based on distributions of local Green's functions we present a stochastic approach to disordered systems. specifically we address Anderson localisation and cluster effects in binary alloys. Taking Anderson localisation of Holstein polarons as an example we discuss how this stochastic approach can be used for the investigation of interacting disordered systems.
1,1-Bis(trimethylsilyloxy)ketene acetals represent useful synthetic building blocks which can be regarded as masked carboxylic acid dianions. In recent years, a number of cyclization reactions of 1,1-bis(trimethylsilyloxy)ketene acetals have been reported. Functionalized maleic anhydrides represent important synthetic building blocks, which have been employed, for example, in the synthesis of γ-alkylidenebutenolides, maleimides, 5-alkylidene-5H-pyrrol-2-ones. Substituted maleic anhydrides are available by Michael reaction of nucleophiles with parent maleic anhydride and subsequent halogenation and elimination. Oxalyl chloride is an important synthetic tool for the synthesis of O-heterocycles. 3-hydroxymaleic (1-3) anhydrides were synthesised by one-pot cyclization of 1,1-bis(trimethylsilyloxy)ketene acetals with oxalyl chloride using TMSOTf as a catalyst. The Me3SiOTf mediated reaction of 1,1-bis(trimethylsilyloxy)ketene acetals with 3-silyloxyalk-2-en-1-ones, such as (4), afforded 5-ketoacids, such as (5). Treatment of the latter with TFA in CH2Cl2 afforded pyran-2-ones, such as (6-8). It has been found that 1,1-bis(trimethylsilyloxy)ketene acetals can behave as dinucleophile. Functionalized benzo-azoxabicyclo[3.3.1]nonanones (9-12), were prepared by regio- and diastereoselective condensation of 1,1-bis(silyloxy)ketene acetals with isoquinolinium and quinolinium salts and subsequent regioselective and stereospecific iodolactonization. Our next target was the reaction of silyl ketene acetals with pyrazine and quinoxaline. These reactions provide a facile access to a variety of 2,3-benzo-1,4-diaza-7-oxabicyclo[4.3.0]non-2-en-6-ones and 1,4-diaza-7-oxabicyclo[4.3.0]non-2-en-6-ones (13-14). The second part of my research work was concentrated on bis(silyl enol ethers). The TiCl4-mediated [3+3] cyclization of 2,4-bis(trimethylsilyloxy)penta-1,3-diene with 3-silyloxyalk-2-en-1-ones afforded 2-acetylphenols (15), which were transformed into functionalized chromones (16). The Me3SiOTf-mediated condensation of the latter with 1,3-bis(silyl enol ethers) and subsequent domino ′retro-Michael–aldol–lactonization′ reaction afforded 7-hydroxy-6H-benzo[c]chromen-6-ones (17-18). With regard to our on going investigation with bis(silyl enol ethers), we significantly extended the preparative scope of the methodology. We have successfully developed regioselective cyclizations of unsymmetrical 1,1-diacylcyclopentanes, such as 1-acetyl-1-formylcyclopentane, and also studied cyclizations of 2,2-diacetylindane, 1,1-diacetylcyclopent-3-ene and 3,3-dimethylpentane-2,4-dione. In addition, the mechanism of the domino process was studied. We have synthesised spiro[5.4]decenones (19) and that were transfored into bicyclo[4.4.0]deca-1,4-dien-3-ones (20-21), by domino ′Elimination–Double-Wagner-Meerwein-Rearrangement′ reactions. The Lewis acid mediated domino ′[3+3]-cyclization-homo-Michael′ reaction of 1,3-bis-silyl enol ethers with unsymmetrical 1,1-diacylcyclopentanes, such as 1-acetyl-1-formylcyclopentane, allows an efficient one-pot synthesis of functionalized salicylates containing a halogenated side-chain (22-23). A great variety of substitution patterns have been realized by variation of the starting materials and of the Lewis acid. The mechanism of the domino process was studied.
Expression of the T cell regulatory molecule ICOS (CD278) and LICOS (CD275) on human blood cells
(2006)
Expression of the T cell regulatory molecule ICOS (CD278) and LICOS (CD275) on human blood cells Summary General bacterial infections, which can lead to the clinical picture of sepsis, are a major concern in intensive care units (ICU) and mortality remains high. Recent data have shown that, besides an overreaction of the immune system, also immunosuppression also plays a role in the pathogenesis of sepsis. Immunosuppression has been documented in patients with polytrauma, stroke and burn wounds, which all confer a high risk of severe bacterial infection. Moreover, it has been shown that T cells have an important role in sepsis. A shift of a Th1 dominated T cell response towards a Th2 response has been described as a potential mechanism of immune suppression in patients with sepsis. One of the molecules on the surface of T cells that is involved in the Th2-mediated immune response is the Inducible Costimulator of T cells (ICOS). Its ligand, LICOS, is expressed on the surface of B cells and monocytes. ICOS ligation induces the production of anti-inflammatory cytokines, especially of IL-10. However, nothing is known about the expression of ICOS on T cells and that of LICOS on APCs in patients with severe trauma and stroke. Therefore, in the present study, in a first step, a recombinant human LICOS-Ig fusion protein was generated, which was then used as an antigen for the generation of anti-LICOS monoclonal antibodies. In three fusion experiments, 5,000 primay clones were screened and a single hybridoma was obtained, which produced monoclonal antibodies that specifically reacted with recombinant LICOS, both in form of the LICOS-Ig fusion protein and on the surface of a cell line transfected with a full-length LICOS transgene. Since, it turned out that the antibodies did not bind with high affinity to wild type LICOS, as it is expressed on primary human blood cells, phenotypic analyses were carried out with another anti-LICOS monoclonal antibody, which had become commercially available. Next, the expression of HLA-DR, CD86, LICOS, and ICOS, on the surface of monocytes (CD14+), B cells (CD19+) and T cells (CD3+, CD4+) in whole blood was measured by flow cytometry. Six patients with severe trauma and nine stroke patients were compared with 32 healthy donors. On CD14+ monocytes from healthy donors, the expression levels of HLA-DR and CD86 were over 90%, while the expression of LICOS was much lower (7,5%). In critically ill patients, HLA-DR, CD86 and LICOS expression were strongly reduced. CD86 and HLA-DR were co-regulated, while HLA-DR and LICOS were not. In healthy donors, virtually all B cells expressed HLA-DR and the majority of them co-expressed LICOS (72%), while only a small fraction were CD86+ (14%). After trauma and stroke, HLA-DR, as well as LICOS expression on these cells remained normal; CD86 had a tendency towards being downregulated in most of the trauma patients, while most of the stroke patients exhibited normal CD86+ levels. The levels of HLA-DR and LICOS on T cells in trauma and stroke patients were low and very similar to those of healthy donors. The fraction of CD3+ T lymphocytes or their CD4+ subpopulation, which expressed measurable levels of ICOS (64% and 48%, respectively), did not change after stoke or trauma. However, within the ICOS+ T cell population two subpopulations could be distinguished: ICOSbright and ICOSdim T cells. Interestingly, the ICOSbright subpopulation, but not the ICOSdim and ICOSnegative subpopulations, was markedly increased in all trauma patients and in most of the stroke patients. Given that CD86 was co-regulated with HLA-DR on monocytes it appears that, similar to HLA-DR, CD86 expression could discriminate between patients with a low and high risk of sepsis. In contrast, because of its low basal expression on monocytes and its low signal-noise ratio, LICOS expression levels are not informative. Since ICOS expression on T cells is tightly connected to IL-10 secretion, the high proportion of ICOS bright cells in critically ill patients might contribute to the high IL-10 serum concentrations, which have been reported to be linked to immunosuppression in these patients.
SUMMARY To date, Staphylococcus aureus is the most common cause of nosocomial infections and the species is becoming increasingly resistant to antibiotics. Beyond this, S. aureus colonises the nasal mucosa of circa 35% of the healthy population, so-called carriers. Importantly, S. aureus nasal carriage is a major risk factor for the development of S. aureus infections, which are commonly caused by the colonising strain. This underlines the importance of host factors for the outcome of S. aureus-host interactions. Despite the clinical importance of nasal carriage, little is known about humoral immune responses triggered by colonisation. Therefore, this thesis was focussed on the anti-staphylococcal antibody responses of S. aureus carriers and noncarriers. Staphylococcal superantigens (SAgs) served as indicator antigens for our studies. SAgs are virulence factors with extraordinary variability in the species S aureus and act as extremely potent T cell mitogens. To date, 19 different SAg gene loci are known in the species S. aureus, but molecular-epidemiological studies on the distribution of these genes are limited. Therefore, we established five multiplex PCRs for the detection of all known SAgs. With this robust and high-throughput technique we analysed the SAg gene patterns of more than 300 isolates, including 107 nasal isolates of S. aureus carriers and 88 blood culture isolates of hospital patients from Western Pomerania. The SAg gene patterns were highly heterogeneous, which can be explained by their localisation on mobile genetic elements (MGE), such as genomic islands, pathogenicity islands, phages and plasmids. Most isolates (~80%) harboured SAg genes, on average five to six, and SAgs of the enterotoxin gene cluster (egc) were by far the most prevalent. Additionally, we observed a strict correlation between the presence of SAg genes and the T cell mitogenic potency of clinical isolates. SAg-encoding MGEs can be distributed by two distinct mechanisms: horizontal transfer by bacteriophages and vertical transmission to daughter cells. To investigate the distribution of SAg genes within the S. aureus population, we determined the clonal relationship of our isolates by spa genotyping. Interestingly, SAg-gene encoding MGEs were not randomly distributed, but rather closely linked to clonal lineages. Each clonal lineage was characterised by defined combinations of SAg genes. These data suggest that the simultaneous assessment of virulence gene profiles and the genetic background strongly enhances the discriminatory power of genetic investigations into the mechanisms of S. aureus virulence. Indeed, the comparison of virulence genes within each clonal complex indicated a role in invasiveness for some MGEs, e.g. the exfoliative toxin D-encoding pathogenicity island, while rendering it unlikely for SAgs. It is known that neutralising serum antibodies against the SAgs SEA, SEB, SEC, SED and TSST-1 are frequently present in healthy individuals. However, the neutralising antibody profiles against more recently described SAgs or complex SAg cocktails as secreted by clinical isolates had not been determined so far. Therefore, we screened more than 100 sera for their SAg neutralising capacity with a neutralisation assay. We observed a marked heterogeneity and surprisingly large “gaps” in the neutralising capacity. Interestingly, the egc SAgs were inhibited only rarely (5-10%), whereas between 32 and 86% of the tested sera neutralised “classical” SAgs. This “egc gap” in the SAg-neutralising antibody profiles of healthy individuals was unexpected, since egc SAgs are by far the most prevalent SAgs. We could demonstrate that the “egc gap” is probably not due to different T cell activating properties of egc SAgs compared to classical SAgs, but rather to a differential regulation of SAg gene expression. S. aureus carriers have an increased risk of developing an S. aureus bacteraemia, which is in most cases caused by the colonising strain. Intriguingly, a large prospective clinical trial revealed a considerably higher mortality in noncarriers with invasive S. aureus strains compared to carriers with invasive disease. To explain these paradoxical findings, we hypothesised that in carriers partial immunity against the colonising strain may contribute to their improved outcome. We used SAgs as strain-specific indicator antigens. Importantly, sera from persistent carriers neutralised SAgs of their colonising strain with significantly higher efficiency than sera from noncarriers. This antibody response was strain-specific, since the antibody response of carriers against other SAgs did not differ from that of noncarriers. Thus, colonisation with S. aureus confers a strong and strain-specific antibody response against staphylococcal SAgs. We suggest that in carriers neutralising antibodies directed against SAgs and other staphylococcal virulence factors confer partial protection during systemic infections. This could explain the better prognosis of carriers with S. aureus bacteraemia compared to noncarriers. Moreover, our data imply that the key to understanding the pathogenesis of S. aureus disease may lie in the identification of host factors rather than bacterial factors. Such host factors could be the immune status and gene polymorphisms that contribute to colonisation, susceptibility to infection and outcome of infection. Finally, while the treatment of S. aureus bacteraemia with pooled immunoglobulins was performed in the past without significant success, our findings on strain-specific antibody profiles suggest that therapies with customised cocktails of monoclonal antibodies could have a higher efficacy.
Vegetation dynamics on abandoned terraces of Sicily: the course and driving factors of succession
(2007)
Secondary succession processes have been widely studied in Europe for some agroecosystems, but not for terraced ones. The first part of the present study focuses on a description of the plant communities involved in secondary succession processes on Sicily (Italy) a) from a floristic and structural point of view and b) from a species diversity point of view. In order to obtain these results, 129 vegetation relevés (sensu Braun-Blanquet) were made on abandoned terraces in five of the main terraced areas of Siciliy: 1) the Aeolian Islands, 2) Pantelleria Island, 3) Mt. Etna, 4) the Palermo Mts. and 5) the Hyblaean Plateau. Only abandoned vineyards or grain crop fields were selected as sample plots, always 50 m2-sized. The results of biodiversity evaluation by t-tests and ANOVA showed that vascular plant diversity is linked to disturbance regime and to abiotic factors (especially geological substrate). Especially grazing increases species richness. Moreover, it was found that on limestone species richness is higher than on volcanic substrates. Vegetation relevés were also analysed with DCA and TWINSPAN. The resulting 14 sample plot groups (= clusters) were then used to check the dynamic relations. From a floristic point of view, plant communities involved in secondary succession processes on Sicilian terraces are quite different between and within the five study areas. This is mainly due to different substrate and bioclimatic conditions. Moreover, vegetation is strongly influenced by abandonment age and disturbance status. If no disturbance biases succession, then plant communities evolve rather rapidly (30-50 years) to maquis communities. If frequent fires or intense grazing occur, secondary succession is blocked in a "steady state". The second part of the present study focuses on the colonization mechanisms of old fields by woody species. In a first section, the existence of 1) the neighbourhood effect and 2) the safe-site effect are checked by analyzing 51 transect relevés, made up of 357 subplot relevés (1x1m). The transects were made in target fields 1) with older neighbour (i.e. old succession stage characterized by maquis communities) and 2) with older neighbour absent within a 100 m-distance. All woody species individuals were counted, recording if they grew within the influence of a potential safe site (former crop plants of vine and the terrace wall base). Data evaluation by Kruskal-Wallis ANOVA and Mann-Whitney Rank Sum confirmed the existence of the two effects. Moreover, it was shown that animals as dispersal vectors strongly influence these effects. For the neighbourhood effect, seed dispersal distance is the crucial point, while for the safe site effect 1) passive facilitation (i.e. animals tend to create heterogeneous seed rain patterns because they frequent certain microhabitats more often than others) and 2) active facilitation (i.e. the positive influence of an existing woody or herbaceous plant individual on the establishment or the growth of another one) are crucial. The second section describes the performance of establishment of Quercus ilex L. in different microsites of terraced old fields. In November 2004, acorns were buried on a North-facing slope and on a South-facing slope in five different microsites: 1) under vine plants, 2) at wall bases, 3) under the canopies of isolated shrubs, 4) between small rock accumulations and 5) in open spaces (i.e. outside of any of the previously named microsites). In monthly checks, seedling emergence, survival, height and leaf number were recorded. Moreover, in April and July were measured air temperature and air humidity in the different microsites. Overall emergence rate was 52.4% (n = 1,020). More seedlings emerged on the South-facing slope (S; 59.8%) than on the North-facing slope (N; 45.0%). Emergence was higher when acorns were buried under vine plants and at the wall base than in other microsites of the old fields. At the end of the experiment (September 2006), 45.3% of all emerged seedlings were still alive (29.2% on N, 58.9% on S). Survival was higher in general on the South-facing slope, and higher under vine plants and at the wall base than in the open spaces of the old fields. From literature, it is known that seed vitality, seed germination and seedling survival of Quercus ilex are favoured by shady, wet and fresh conditions. The temperature and air humidity measurements showed that at the wall base, under vine plants and under isolated shrubs environmental conditions are milder than in open spaces. However, even if temperature and relative air humidity seem to play an important role for Quercus ilex seedling emergence and survival, they did not unambiguously explain the differences between the safe site types. A factor of major importance is probably soil moisture. As a last part, the present study discusses what does the obtained results mean for terrace landscape conservation and biodiversity management.
Under natural conditions, most parts of northeastern Germany would be covered by forests that would be dominated by beech (Fagus sylvatica) and oak (Quercus robur and Q. petraea). However, today most of the wooded area is covered by artificial monocultures of pine forests. This form of cultivation was recognised to be the cause of instability against calamities of pests as well as severe storms therefore in the early eighties of the last century this knowledge was used to start the conversion of the forests towards more nature-like stands. The ecological effects of the forest conversion on the soil, the fauna and the flora have been investigated in a nation-wide project supported by the Federal Ministry of Education and Research (BMBF) in the project “Future-oriented forest management”. The present work has been accomplished within the scope of this project and is concerned about the effects that different aspects of forest conversion have on oribatid mites. The present work shall serve to answer a number of questions about the distribution of oribatid mites and their reaction to environmental changes. The investigation was carried out on 12 plots in two sampling areas. 7 plots were chosen in the Müritz NP and 5 in Eberswalde. In both areas plots were chosen that resemble the different stages of forest conversion: one medium aged pine plot in each area, two medium aged mixed plots with pines and beeches in the Müritz NP and one mixed plot in Eberswalde as well as one beech plot in each area. Furthermore, in the Müritz NP the chance arose to investigate the effects of different age stages of the stands on the oribatid mites. Therefore, an additional young pine plot and two old mixed plots have been sampled. In Eberswalde, on the other hand, another emphasis was laid on the effects of a different nutrient content in the soil. Here, an additional pine plot and mixed plot, respectively, of a higher trophotopic level was sampled. In Eberswalde, an additional sampling was done in three plots (a beech plot, a mixed plot and a pine plot) to investigate the horizontal distribution of the oribatid mites in these habitats. The data were used along with others to ecologically characterise the different species. The sampling took place from 2000 to 2002. Within the scope of the doctoral thesis, 392 samples were analysed. 122 samples from one year from the Müritz NP and 270 samples from three years from Eberswalde were analysed. Altogether 155,450 oribatid mites from 82 taxa were found in these samples. The ecological characterisation of the species revealed that the various species react quite differently to the investigated factors. Most species occur with different abundances in different forest types, but their abundance often varies also in comparable stands of both sampling areas. This indicates that they react to climatic effects as well as to biotic and abiotic factors. The forest conversion from pine forests to beech forests causes the abundance of oribatid mites to decrease, probably due to the change of the humus form from mor or mor-like moder in pine forests to mull in beech forests, that is accompanied by a decrease of the abundance of fungi, the main food source for most oribatid mites. Furthermore, the species composition changed. Species like Camisia spinifer, Adoristes ovatus or Acrogalumna longipluma that are typical for pine forests disappeared, while other species like Achipteria coleoptrata or Chamobates voigtsi immigrated in mixed stands after the introduction of beeches. The age of the stands proved to be another important factor. The overall abundance of oribatid mites was higher in the older stands than in the younger stands, while the percentage of juvenile oribatids decreased towards the older stands. Furthermore, the dominance structure became more uneven and shifted toward a higher percentage of fungivorous oppiid and suctobelbid mites. Especially on the old mixed plots, Oppiella nova reaches a dominance value of about 60 %. The nutrient content of the soil seems to be a relatively unimportant factor on the community level as no significant differences with regard to overall abundance and the dominance structure could be recorded. However, the Canonical Correspondence Analysis showed that the nutrient content of the soil does influence the distribution of species, at least with regard to their individual abundance. In summary, it can be said that the distribution of the oribatid species is influenced by many factors, and the stocking is only one of these factors. Nevertheless, a group of four species could be established, that can be used as indicators for the success of the forest conversion towards more nature-like deciduous forests: Achipteria coleoptrata, Autogneta longilamellata, Chamobates subglobulus and C. voigtsi.
Aging is a risk factor for stroke. Animal models of stroke have been widely used to study the pathophysiology of ischemic stroke, which in turn helped to develop numerous therapeutic strategies. Despite the considerable success of therapeutic strategies in animal models of ischemic stroke, almost all of them have been proved to be unsuccessful in the clinical trials. One of explanation is that data obtained from young animals may not fully resemble the effects of ischemic stroke in aged animals or elder patients, causing the discrepancy between animal experiments and clinical trials. To investigate these differences with regard to age, pathway specific gene arrays were used to identify and isolate differentially expressed genes in periinfarct following focal cerebral ischemia. The results from this study showed a persistent up-regulation of pro-apoptotic and inflammatory-related genes up to 14 days post stroke, a 50% reduction in the number of transcriptionally active stem cell-related genes and a decreased expression of genes with anti-oxidative capacity in aged rats. Also, it was observed that at day 3 post-stroke, the contralateral, healthy hemisphere of young rats is much more active at transcriptional level than that of the aged rats, especially at the level of stem cell- and hypoxia signaling associated genes. Next, protein levels between young and aged post-stroke rats in periinfarct were compared using proteomic tools. Among others, AnxA3 was identified as differentially regulated protein, but the expression of AnxA3 has no significant changes in periinfarct between these two age groups at day 3 and 14. Different from periinfarct, a strong upregulation of AnxA3 at day 3 in young rats plus a strengthened increase of AnxA3 at day 14 in aged rats using immunohistochemical quantification indicated a delayed microglial accumulation in infarct core of aged rats, suggesting that quick activation of microglia in infarct core of young rats might be beneficial for recovery. Colocalization with established microglial marker demonstrated that AnxA3 as a novel microglial marker is implicated in the microglial responses to the focal cerebral ischemia. In addition, it was found that AnxA3 positive microglial cells incorporated more proliferating cell marker BrdU. Third, the expression, localization and function of several transport proteins were investigated in young rats following focal ischemic stroke. P-gp staining was detected in endothelial cells of desintegrated capillaries and by day 14 in newly generated blood vessels. There was no significant difference, however, in the Mdr1a mRNA amount in the periinfarct region compared to the contralateral site. For Bcrp, a significant mRNA up-regulation was observed from day 3 to 14. This up-regulation was followed by the protein as confirmed by quantitative immunohistochemistry. Oatp2, located in the vascular endothelium, was also up-regulated at day 14. For Mrp5, an up-regulation was observed in neurons in the periinfarct region (day 14). In conclusion, reduced transcriptional activity in the healthy, contralateral sensorimotor cortex in conjunction with an early up-regulation of proapoptotic genes and a decreased expression of genes with anti-oxidative capacity in the ipsilateral sensorimotor cortex of aged rats, plus the delayed up-regulation of AnxA3 positive microglial cells in infarct core may contribute to diminished recovery in post-stroke old rats. In addition, it was demonstrated in this study that after stroke the transport proteins were up-regulated with a maximum at day 14, a time point that coincides with behavioral recuperation. The study further suggests Bcrp as a pronounced marker for the regenerative process and a possible functional role of Mrp5 in surviving neurons. This study provided several evidences for the different responses of young and aged rats using a focal ischemic stroke model. Understanding the effect of age is crucial for the development of relevant therapeutic drugs.
Abstract: Ischemic stroke is an aging disease and causes high mortality or long-term disability. The reduced neurological recovery in aging is possibly associated with impairment of angiogenesis and non-specific enhancement of inflammatory reaction. To check this hypotheses, those events were compared within young and elder animals brain at day 14 following focal ischemic stroke. Moreover, it is of importance to investigate also the potential therapies of indomethacin for prolonging the therapeutic window using aged animal models. The focus of present study was on neurobiological and neurological differences between young and old rats modulated by indomethacin daily treatment beginning at four hours post-ischemic episode. The effectiveness of indomethacin treatment in young and elder rats was probed using immunohistochemistry, oligonucleotide microarray, Real Time PCR and neurological evaluation. Our results provide insight of several age-independent positive consequences of Cox non-specific inhibition by indomethacin including increased NeuN positive surviving neurons, reduced infarct volume and enhanced neuroprotective response of innate immune system evidenced by increased Iba1 and Anx3 immunoreactivities in moderately activated microglia in periinfarction. From gene level we observed in both age groups downregulation of Mdk and Cxcl1 chemokines, and Id3 transcription factor which might modulate inflammatory response and facilitate repair. Other several findings showed age-dependent drug effect. Indomethacin had reduced efficacy in aged ischemic brain. From a total of 34 genes differential regulated, we observed 43% in young and only 28% of genes in aged have tendency toward age-matched sham expression level. In aged rats, indomethacin is ineffective in inhibiting phagocytic activity which is probably due to no expression changes of several cytokines like Tnfá and Cxcl4. Also, at protein level we observed no change of lysosomal ED1 immunoreactivity under treatment. On the other hand aging is characterized by no expression changes of Plau, Timp1, Timp2 and Col18a1 after treatment resulting in no improvement of angiogenesis. In young rats, conversely, drug administration decreased phagocytic activity by downregulating several cytotoxic cytokines such as Tnfá and Cxcl4. Moreover, the observable decrease of proteases like MMP10, Plau and MMP inhibitor Timp2 employed in matrix remodeling together with downregulation of Col18a1 expression after treatment might sustain angiogenesis in young rat ischemic brain. Indomethacin improves the motor-sensory performance in ischemic stroke rats as compared with age-matched untreated animals. Young rats fully recovered while aged showed important recuperation but did not achieve the preoperative level. In view of all this, indomethacin treatment might be consider as adjuvant therapy following ischemic stroke, even if aging blunts the positive effect of indomethacin on altered angiogenic-related gene expression. Because of the small number of rats, the results obtained from this study show only a tendency to significance and that further studies with more animals need to be statistically validated before firmly conclusions can be drawn. KEY WORDS: indomethacin; aging; microglia; angiogenesis; gene expression; microarray; neurological recovery; reversible middle cerebral artery occlusion.
Pretransplant Tolerance Induction Reduces the Islet Mass Required to Reverse Diabetes in NOD Mice
(2007)
Islet transplantation can restore normoglycemia in diabetic patients. However, its application is limited by the high number of islets required to reverse diabetes. As the mass and potency of most human islet preparations are marginal, a large impact on the applicability of islet transplantation is expected from the implementation of strategies that improve engraftment of these islet preparations. The roles of adaptive immunity and immunosuppression on islet engraftment are not well studied. Therefore, the effects of currently used immunosuppression with antilymphocyte serum, tacrolimus and sirolimus on islet engraftment were separated from their impact on immunity and diabetes reversal rates were compared after islet allotransplantation in immunosuppressed and chimeric, non-immunosuppressed NOD mice. Both strategies prevented rejection of islet allografts and reduced the frequency of donor-specific, IFN-gamma-secreting T cells. However, in order to achieve stable diabetes reversal with a probability of about 80% after islet allotransplantation in diabetic NOD mice, a fourfold higher islet mass (400 islets) was required in immunosuppressed recipients, compared with non-immunosuppressed recipients made tolerant pretransplant by induction of mixed hematopoietic chimerism (100 islets). The failure of immunosuppressed mice to become normoglycemic after low-dose islet transplantation primarily resulted from the inhibitory effects of tacrolimus combined with sirolimus on islet engraftment and not from the inhibitory effects of this combination on islet graft function. These data suggest that immunotherapeutic strategies that control adaptive immunity without interfering with islet neovascularization or other processes critical to islet engraftment are likely to improve the success rate of marginal mass human islet allografts.
Background: Due to the high number of immunosuppressed and other predisposed patients hospitals have to control and ensure the microbiological water quality. The origin for the occurrence of pathogenic microorganisms in water pipes is the formation of biofilm. Methods: For the permanent control of water safety a water safety plan (WSP) was realized as recommended by the WHO following the principle "search and destroy". The WSP is based on an established HACCP concept due to the special focus. The most important measures include the concept for sample taking depending on patient risk. 3 different categories) are distinguished: risk area1 (high infection risk), risk 2 (moderate infection risk), and risk area 3 (not increased infection risk). Additionally to the threshold value of the German law for the quality of drinking water (TrinkwV) three more limiting values were defined (warning, alert, and worst case) for immediate risk adapted reaction. Additional attention has to be focussed on lavatory sinks, which are an open bacterial reservoir. Therefore continuous disinfecting siphons were installed as part of the WSP in high risk areas. If extended technical equipment is not available, especially for immunocompromised patients the following measures are easy to realize: boiled (or sun exposed) water for nursing procedures as well alimentary use, no showering. Results: Comparing data over 3 years the microbial water quality was significantly improved resulting in no new case of nosocomial Legionella pneumoniae and decrease in neonatal sepsis. Conclusion: According to average situations with highly contaminated water system the management must be defined with implementation of water task force, immediate providing of special equipment, information of patients and staff and control of the water quality, an example for successful decontamination of the hospital within 24 hours is given.
Dense sensor event-related brain potentials were measured in participants with spider phobia, high anxiety sensitive individuals and non-fearful controls during viewing of medical emergency, spider and standard emotional (pleasant, unpleasant, neutral) pictures. Compared to non-fearful controls spider phobia participants showed a significantly enlarged late positive potential (LPP) during the encoding of phobia-relevant pictures whereas high anxiety sensitive individuals showed a significantly greater Early Posterior Negativity (EPN) during the encoding of medical emergency pictures and a significantly greater Late Positive Potential (LPP) during the encoding of highly arousing unpleasant visual material. Moreover, within group comparisons of the spider phobia group revealed comparable LPP evoked by spider pictures and emotional (unpleasant and pleasant) picture contents indicating that at the level of early stimulus evaluation, the effects of selective attention seem to be related to emotional relevance of the stimulus rather than reflecting a fear-specific response.
1. The study confirms an association between transverse arch dimensions and severity of ankyloglossia, which reflects relationship between molar difference and free tongue. 2. Molar difference in group A (complete and severe ankyloglossia cases) has high negative values (average -4.38) which was much smaller than the data from the literature concerning many different types of occlusion. 99 3. The exact relation between transverse arch dimension and severity of ankyloglossia needs further research.
Summary Prostate cancer (PCa) is the most common type of cancer found in men from western countries and is the leading cancer death next to lung cancer and colorectal cancer. Proteomic studies on PCa identified a number of differentially expressed proteins and some of them were reported as potential markers, but clinical application of these markers is mostly missing. Most of the expression profiling studies have been carried out on radical prostatectomy specimens, formalin-fixed paraffin-embedded (FFPE) tissue sections, serum, urine and prostate fluids. To define the protein expression pattern of prostate biopsies, in the present study we investigated biopsy samples from benign prostate hyperplasia (BPH) and PCa patients by two-dimensional gel electrophoresis (BPH n=11 and PCa n=12) and mass spectrometry to identify potential biomarkers which might distinguish the two clinical situations. 2-DE results revealed 88 protein spots expressed differentially among hyperplasia and cancer groups with statistical significance. Interesting spots were analyzed by MALDI-TOF-MS-MS and 79 different proteins identified. The important proteins identified included, Prohibitin and NDRG1 tumor suppressor proteins, HSPs, cytoskeletal proteins, enzymes like DDAH1 and ALDH2. Prohibitin expression was investigated in detail at mRNA level and protein level using immunohistochemistry on prostatectomized specimens. We found that the level of mRNA for prohibitin correlates with the increased amount of protein indicating the involvement of changes at transcriptional level. Furthermore, immunohistochemistry revealed no staining in BPH, moderate staining in prostate intraepithelial neoplasia (PIN) and strong staining in PCa. From the list of differentially proteins compared to PCa, TPD52 is over expressed in prostate cancer and also mRNA estimation by real-time PCR confirmed over expression of TPD52 at transcriptional level in cancer. TPD52 is a protein over expressed in prostate and breast cancer due to gene amplification but its exact physiological function is not investigated in detail. In the present study, we explored the responsiveness of LNCaP cells after dysregulation of TPD52 expression. Transfection of LNCaP cells with specific shRNA giving efficient knockdown of TPD52 resulted in a significant cell death of the carcinoma LNCaP cells. As evidenced by the activation of caspases (caspase-3 and -9) and by the loss of mitochondrial membrane potential, cell death occurs due to apoptosis. The disruption of the mitochondrial membrane potential indicates that TPD52 acts upstream of the mitochondrial apoptotic reaction. To study the effect of TPD52 expression on cell proliferation, LNCaP cells were either transfected with EGFP-TPD52 or a specific shRNA. EGFP-TPD52 overexpressing cells showed an increased proliferation rate whereas TPD52-depleted cells showed a reverse effect. Additionally, we demonstrated that the exogenous expression of TPD52 promotes cell migration via ávâ3 integrin in prostate cancer cells through the activation of protein kinase B (PKB/Akt) pathway. In an attempt to identify new interacting proteins for TPD52, GST pulldown assays provided evidence for the physical interaction between TPD52 and Prx1 in LNCaP cells. Further, immunoprecipitation results confirmed this interaction. Our results demonstrates that protein profiling and mRNA studies can be performed on prostate biopsies. Moreover, our study revealed a significant up-regulation of prohibitin in prostate cancer compared to BPH which may be a potential marker to distinguish PCa and BPH. From the results for functional characterization of TPD52, we conclude that TPD52 plays an important role in various molecular events particularly in morphological diversification and dissemination of PCa. It may be a promising target to investigate further in detail to develop new therapeutic strategies to treat PCa patients. Caspases represent a family of cysteine proteases that are regarded as central executioners of apoptotic cell death. Activation of caspase cascade is an essential prerequisite in the induction of apoptosis in cellular systems. So far, in many tumors caspases were shown to be downregulated while anti-apoptotic Bcl-2 is up-regulated. To get insight in their putative role in PCa progression we determined the expression of caspase-1, uncleaved caspases 3 and 6, cleaved (activated) caspases 3 and 6, caspase-9 and antiapoptotic protein Bcl-2 in benign prostate epithelium (BPE) and prostate carcinoma. In the current study 20 prostates were obtained from patients undergoing radical prostatectomy due to PCa. Paraffin embedded prostate whole mounts were cut at (4 µm) and investigated immunohistochemically using anti-mouse monoclonal antibodies directed against caspases 1 and 9, uncleaved caspases 3 and 6, cleaved caspases 3 and 6, and Bcl-2. In BPE all caspases were localized in the cytoplasm of glandular cells. Comparing BPE to PCa, no differences were found for caspase-1, uncleaved caspases 3 and 6 as well as caspase-9. Immunostaining for cleaved caspases 3 and 6, however, revealed a statistically significant reduction in PCa compared to non-neoplastic tissue. Whereas in BPE Bcl-2 protein was detected in the basal compartment of epithelial gland cells no immunostaining was seen in PCa. As our results show a decreased amount of activated caspases may be due to the alterations of posttranslational cleavage rather than expression of caspases 3 and 6. This suggests that the modification in their activation pathway could play an important role during PCa progression.
The study of sow reproduction traits is important in livestock science and production to increase animal survival and economic efficiency. This work deals with the detection of different effects on within-litter variance of birth weight by applying different statistical models with different distributional assumptions. The piglets within one litter were separated by sex. The trait of sow was formed from the sample variances of birth weights within litter separated by sex to consider the sex effect on mean birth weight. A linear mixed model (LMM) approach was fitted to the logarithmized sample variance and the sample standard deviation. A generalized linear mixed model with gamma distributed residuals and log-link function was applied to the untransformed sample variance. Appropriate weights were constructed to account for individual litter sizes. Models were compared by analysing data from Landrace and Large White. The estimates of heritability for the different traits ranged from 6-14%. The LMM for the weighted standard deviation of birth weights was identified as most suitable in terms of residual normality. Furthermore, the impact of piglets´ sex on birth weight variability was tested, but it was only proved for one practical dataset. Additionally, we analysed the influence of including or not including birth weights of stillborn piglets on the estimates of variance components of birth weight variability. With omitted stillborns the estimates of heritability resulted in about 2% higher values than in investigations of total born piglets. We were interested in the presence of the random boar effect on birth weight variability. The corresponding variance component was tested via restricted likelihood ratio test. Among others, the null distribution of the test statistic was approximated by parametric bootstrap simulations which were computational intensive. We picked up a two-parametric approach from literature and proposed a three-parametric approach to approximate the null distribution of the test statistic. We have analysed correlated data in balanced (simulated data) and unbalanced (empirical data) designs. The two-parametric approach using a scaled mixture of chisquare-distributions as well as a three-parametric approach, that uses a mixture of the point mass at zero and a gamma distribution, behaved most solid in all investigations and were most powerful in the simulation study.
The rapid neutron-capture or the r-process is responsible for the origin of about half of the neutron-rich atomic nuclei in the universe heavier than iron. For the calculation of the abundances of those nuclei, atomic masses are required as one of the input parameters with very high precision. In the present work, the masses of the neutron-rich Zn isotopes (A=71 to 81) lying in the r-process path have been measured in the ISOLTRAP experiment at ISOLDE/CERN. The mass of 81Zn has been measured directly for the first time. The half-lives of the nuclides ranged from 46.5 h (72Zn) down to 290 ms (81Zn). In case of all the nuclides, the relative mass uncertainty (∆m/m) achieved was in the order of 1E-8 corresponding to a 100-fold improvement in precision over previous measurements.
The WEGA stellarator is used to confine low temperature, overdense (densities exceeding the cut-off density of the heating wave) plasmas by magnetic fields in the range of B=50-500 mT. Microwave heating systems are used to ignite gas discharges using hydrogen, helium, neon or argon as working gases. The produced plasmas have been analyzed using Langmuir and emissive probes, a single-channel interferometer and ultra-high resolution Doppler spectroscopy. For a typical argon discharge in the low field operation, B=56 mT, the maximum electron density is n_e~10^18m^{-3} with temperatures in the range of T=4-12 eV. The plasma parameters are determined by using Langmuir probes and are cross-checked with interferometry. It is demonstrated within this work that the joint use of emissive probes and ultra-high resolution Doppler spectroscopy allows a precise measurement of the radial electric field. Here the floating potential measurements using emissive probes have been compared to measurements of the poloidal rotation of the plasma which is also linked to the radial electric field. In order to alter the plasma parameters a biasing probe setup has been used during this work. The focus of this work is on demonstrating the ability to modify the existing radial electric field in a plasma by using the biasing probe. This technique is in principle not new, as it has been around for decades. Looking at details, it turns out that describing low field operation WEGA argon plasmas in connection with biasing is not covered by the present set of theoretical approaches and experimental cognition. This work will commence with a basic approach and first establishes the diagnostic tools in a well-known discharge. Then the perturbation caused by the biasing probe is assessed. Following the characterization of the unperturbed plasmas, plasma states altered by the operation of the energized biasing probe will be characterized. It is demonstrated that modifying the existing radial electric field can be achieved and reliably diagnosed using spectroscopy and probe measurements. In order to verify the different approaches for determining the radial electric field the diagnostics are cross-checked against another whenever possible. During biasing the plasma two different stable plasma states have been found. Stable here refers to the state existing much longer than the confinement time for WEGA. The presence of a calorimetric limiter placed in the scrape-off layer has an impact on the type of the plasma state. The two observed plasma states differ in plasma parameter profiles, such as density, temperature, electric field and confined energy. The results are compared to two simple models. One model relies on the relevant atomic processes and a second one is based on neoclassical theory. Both models can be used to derive the particle and power flux from the plasma. The losses predicted by the atomic models can be tested using bolometry. It can be shown that both models agree well in the description of the particle balance of the electrons for large regions of the plasma. By comparing the models the neoclassical heat flux turns out to be small compared to the energy fluxes caused by atomic processes. For the reference discharge taking the energy flux due to the atomic processes and balancing it by the input microwave power is satisfying the energy balance, without the need for transport. For the biased discharges it turns out that neoclassical transport can be neglected as well, but the additional biasing power has to be taken into account. A simple model for the biasing power is motivated and tested. An agreement in the energy balance can be reached in this way as far as the models are applicable. The models also allow drawing conclusions on the amount of absorbed microwave power.
Mind the gap: Information gaps and bridging options in assessing in-situ conservation achievements
(2008)
The biodiversity crisis has gained political attention on a global level. The “2010 Target” of the Convention on Biological Diversity (CBD) aims to significantly reduce the loss of biodiversity by 2010. In order to achieve this, a network of representative and effectively managed protected areas is to be established. The effectiveness of protected areas thus represents one indicator for progress towards the CBD’s 2010 Target. However, indicators require information. The present study, in a first step, reviews the availability of open access long-term ecological data for assessing protected area effectiveness. This review shows two parallel – though contradictory – phenomena: data overkill and data scarcity. While the number of online databases providing open access data on biodiversity has grown tremendously, no long-term ecological data for a larger set of protected areas can be openly accessed. Reasons for this data scarcity are discussed. Based on this lack of information, in a second step, a method to bridge information gaps through social science research is aspired. An innovative Conservation Success Framework is developed, which defines and relates conservation needs, conservation capacity and conservation actions, its three main components. The basic assumption is that conservation can only be successful where the conservation capacity exists that is required to implement the conservation actions determined by the conservation needs. The framework was used to develop open and closed questionnaires for application in two Mexican biosphere reserves, the Sierra Gorda and the Sierra de Manantlán. As "conservation success" is often immeasurable in protected areas in practice due to unspecific conservation objectives the term is for the case studies substituted by “conservation achievements”, i.e. clearly noticeable effects from conservation actions. Overall, almost 60 interviews were conducted with different stakeholder groups. The gained information is validated through social science research techniques, such as triangulation of perspectives and active and passive observation. Based on this, conservation needs are identified and conservation capacities summarised and discussed for both case study sites. Implemented conservation actions addressing identified conservation needs and conservation capacity constraints are then analysed. In addition, noticeable effects from conservation actions on the state of biodiversity at case study sites, i.e. the conservation achievements, are described. Where locally available, non-open access data (as opposing open access data) are used to verify the findings from the social science research. Identified conservation achievements at both case study sites are evident both from quantitative information (for example forest cover increase according to non-open access data) and qualitative information (for example perceived change in the occurrence of illegal activities according to interviews). In addition, rather “intangible” indicators that can only be revealed through qualitative surveys are identified for both sites. This study thus highlights the crucial importance of integrating different types of data, ecological and socio-economic, as well as quantitative and qualitative ones. The present study concludes with a series of recommendations 1) to local practitioners at the two case study sites, and 2) to the international conservation community. Local practitioners may benefit from the present study because its results provide for each site a) an overview of existing conservation needs and implemented conservation actions; b) an easy way to identify action gaps; c) a baseline to identify progress indicators; and d) an overview of diverse perspectives on the current effectiveness of the biosphere reserves. These benefits are considered of particular importance as they can be influential in the revision of the site’s management plans, which both are now approximately ten years old and will soon be revised. The international conservation community will not be able to make a clear statement in the year 2010 about the effectiveness of protected areas on a global level due to a lack of information and transparency. However, the year 2010 should not be considered an end point for measuring progress in in-situ conservation; instead protected area quality standards must be created, effectiveness evaluations institutionalised and efforts to foster regular reporting must continue. Consequently, a scheme of consolidated actions from local to national and international level is proposed that could help to sustainably bridge existing information gaps and close them on the long run. In the end, progress reporting on the effectiveness of protected areas, and other indicators, can only improve if different governance levels “mind the information gaps” in cooperation, until continued information gathering and sharing hopefully closes these gaps one day.
Degradation of branched chain aliphatic and aromatic petroleum hydrocarbons by microorganisms
(2008)
The overall aim of the work was to investigate the ability of several Gram-positive bacteria including Mycocbacterium neoaurum SBUG 109, Nocardia cyriacigeorgica SBUG 1472 and Rhodococcus ruber SBUG 82 and the yeast Trichosporon mucoides SBUG-Y 801 to degrade and transform branched chain hydrocarbons which occur in petroleum and its fraction products such as gasoline or gas oil and which are known as important and recalcitrant environmental pollutants. Pristane, iso-pentylbenzene and sec-octylbenzene were used in this work as model compounds. These compounds represent significant groups of petroleum constituents (branched chain alkanes and aromatic hydrocarbons). Three bacteria and the yeast T. mucoides SBUG-Y 801 were selected in a screen of 16 hydrocarbon-utilizing strains in the SBUG collection and from 21 isolated hydrocarbon-utilizing strains from oil-contaminated habitats of Saudi Arabian Desert and of Vietnam. The bacteria were identified in cooperation with DSZM (Deutsche Sammlung von Mikroorganismen und Zellkulturen) as M. neoaurum SBUG 109, N. cyriacigeorgica SBUG 1472, R. ruber SBUG 82. These bacterial and yeast strains were shown to possess high potential for degrading and transforming pristane, iso-pentylbenzene and sec-octylbenzene. The intermediates produced by these bacteria during incubation with pristane were analyzed by GC and GC/MS. The products 4-methyl pentanoic acid; methyl butanedioic acid; 2-methyl pentadioic acid; methyl propanedioic acid; 4-methyl heptanedioic acid and 2,6,10,14–tetramethyl-pentadecan–3–one were detected in M. neoaurum cultures. In R. ruber, methyl butanedioic acid; 2-methyl pentadioic acid; 4,8-dimethylnonanoic acid, 4-methyl heptanedioic acid; 2,6,10–trimethylundecanoic acid; 3,7-dimethyl decanedioic acid and 2,6,10,14–tetramethyl–pentadecan–3-one were identified. In N. cyriacigeorgica, 2-methylpentanedioic acid; 4,8-dimethylnonanedioic acid; 2,6-dimethylheptanedioic acid and pristanic acid were found. The detection of 11 intermediates during pristane degradation by the three Gram-positive bacteria provided sufficient information to elucidate in detail three degradative pathways of pristane involving mono-, di- and sub-terminal oxidations. The sub-terminal oxidation by M. neoaurum and R. ruber was demonstrated for the first time. This occurence of a sub-terminal oxidation in these strains was strengthened by further results of aromatic compounds transformation (see below). During this pathway, ketone mono-oxygenation reactions seem to be involved. Because of this it will be of interest to look more closely at the catalytic processes involved and their possible extension to the bio-degradation of other branched chain hydrocarbons. Since in the present study 59 %, 51 % and 84 % of pristane were degraded in 3 weeks by M. neoaurum, R. ruber and N. cyriacigeorgica, this illustrated that the degradation rates of this isoprenoid alkane were high. The bacteria we studied were not only effective degraders of multiple branched chain alkane but also useful transformers of aromatic hydrocarbons. The intermediates produced were analyzed by comparing the retention times and UV/Vis spectra of the HPLC elution profile as well as the retention times and mass spectra of the GC/MS with those of available standards. Using iso-pentylbenzene as a substrate, 8 metabolites were generated by M. neoaurum transformation including product A (phenylacetic acid), B (acetophenone), D (iso-valerophenone), E (succinic acid), F (benzoic acid), G [(2-hydroxy-phenyl)-acetic acid] and H (2-methyl-4-phenyl-butyric acid). We additionally identified an alkyl hydroxylated iso-pentylbenzene derivative as 2-methyl-4-phenyl-butan-2-ol or 2-methyl-4-phenyl-butan-1-ol. Two metabolites (C and D) were detected by N. cyriacigeorgica transformation and three metabolites (A, D and F) were identified by R. ruber transformation which led to the complete biotransformation of this substance. iso-Pentylbenzene transformation by M. neoaurum was initiated by attack on the alkyl side chain followed by ring cleavage. The appearance of iso-valeorophenone confirmed the occurrence of a sub-terminal oxidation mechanism in M. neoaurum and R. ruber. In addition to products A, C, D and G, the identification X-(3–methyl–butyl)-phenol (X means that position of the hydroxy group on the aromatic ring system, such as 2, 3 or 4 remained unclear) in T. mucoides cultivation demonstrated for the first time the capacity of alkyl side chain attack by this organism which was hitherto known only for its ability of ring cleavage. The detection of 15 degradation products of sec-octylbenzene (including 2-phenylpropionic acid, 3-phenylbutyric acid, ß-methylcinnamic acid, 5-phenylhexanoic acid, acetophenone, 2-hydroxy-acetophenone, 2,3-dihydroxy-benzoic acid, succinic acid, 7-phenyloctan-2-one, benzoic acid, phenylacetic acid, 7-phenyl-octan-2-ol, hydroxy-phenylacetic acid and 2-hydroxybenzoic acid), in the studied bacteria pointed to an effective sec-octylbenzene degradation pathway in which dehydrogenation of 3-phenylbutyric acid to form ß-methylcinnamic acid is a newly described option. The identification of 2-phenylpropionic acid and 3-phenylbutyric acid in sec-octylbenzene transformation experiments by T. mucoides confirmed the possibility of alkyl side chain attack by this yeast. Summarizing the results, we describe for the first time in detail the biotransformation of sec-octylbenzene by M. neoaurum, N. cyriacigeorgica, R. ruber and T. mucoides. Our results suggest that these microorganisms may be useful as potential strains for hydrocarbon degradation and it may be of interest to investigate their suitability to solve specific environmental pollutant problems associated with branched chain aliphatic and alkyl-branched compounds which contribute to the persistence of hydrocarbon fractions in the environment.
Understanding of the regulatory mechanisms controlling stress gene expression of S.aureus in response to environmental stress is very essential in studying its fitness and virulence. In this work, the changes in protein expression profiles as well as the gene transcription of S.aureus after heat exposure, osmotic stress and in response to the antibiotic puromycin were studied in order to provide detailed insights into the response of S.aureus to various kinds of environmental stress under in vitro conditions, namely: (1) to investigate the global response of S.aureus to heat stress conditions using transcriptomic and proteomic analyses. (2) to study the transcriptome and proteome of S.aureus in response to antibiotic substance puromycin. (3) to define the proteome signatures of S.aureus under NaCl stress condition. (4) to complete the proteome map of cytoplasmic proteins of S.aureus by identifying proteins exclusively synthesized during the exposure to stress. Firstly, the high resolution 2-D protein gel electrophoresis technique combined with MALDI-TOF-MS and a DNA array approach were used to investigate the cellular response of S.aureus to heat stress. A switch from normal growth temperature to high temperature condition revealed complex changes in the protein expression pattern as well as the genes expression profile. The effect of puromycin stress on S.aureus cells was analyzed, using a gel-based proteomic approach and transcriptomic analyses with DNA microarrays. We compared the protein synthesis pattern as well as the transcription data of S.aureus in response to puromycin stress with that in response to heat shock. The results demonstrated that both stress conditions induced specific, overlapping and general responses. Finally, the protein expression profile of S.aureus in response to NaCl stress was analyzed with 2D gel based proteomic approach. Our proteome analyses revealed the repression of the synthesis of many enzymes belong to different metabolism pathways . In summary, the signatures for stress or starvation stimuli can be used as diagnostic tools for the prediction of the mode of action of new antibiotics or for studying the physiological state of cells grown. Expression of the respective genes under in vivo conditions could provide some ideas on the environmental signals that specifically influence the survival of S.aureus within and outside the host.
The New Zealand coal covering the complete maturity range from peat to high volatile bituminous, thus from early diagenetic to catagenesis coalification levels, has been studied in order to bring out new insights into molecular alterations, macromolecular structural evolution, elemental-compositional changes as function of maturation and to propose which processes cause these changes. As particular note from the previous observations that many immature coals from around the world often have rather high extraction yields. It is uncertain whether or not bitumen affecting on petroleum potential and structural evolution of coals. My purposes were therefore to find out the possible interaction between kerogen and bitumen during pyrolysis, and to elucidate the role of bitumen in defining petroleum potential and structural evolution of coals. Furthermore, it is assumed that low rank coals appear to be well suited for feeding the deep subsurface microbes. The products are released as either CO2 or CO that could be substrates for microbial activity. Thus, in this dissertation, I have calculated the loss of CO2 during diagenesis to give the quantitative feeding potential link to deep biosphere, using a mass balance model. To achieve these purposes, at the primary step, the facies variability as well as the molecular compositional changes within the coal band sequence in regard to distinguish the influences of organofacies and maturity need to be clear. Hence, the first aim was to gather information about depositional environment and insights into the plant communities that have contributed to New Zealand coals. Numerous organic-geochemical techniques were used to analyse the free lipids and macromolecular organic matter. Total organic carbon determination (TOC), bulk δ13Corg isotope analysis, the Rock-Eval pyrolysis, pyrolysis- gas chromatography and infrared spectrometry were performed on the original samples and the residue after solvent extraction. The crude lipid extract was separated into fractions that were then analysed by gas chromatography and gas chromatography-mass spectrometry. The obtained data shows that organic matter of New Zealand coals contains mainly terrestrial higher plant material, with a more or less constant background supply of bacterial biomass, deposited in oxidising environment. Angiosperms contributed as the main proportion of the organic matters. Gymnosperms, particularly the Podocarpaceae, Cupressaceae, Taxodiaceae, Pinanceae and Araucariaceae conifer species, still dominated during the Cretaceous. New Zealand coal is classified as mixed gas- and oil-prone. Hydrogen index values increase from 120 to 280 (mg/g TOC) with increasing maturity, which has been explained by the loss of oxygen during diagenesis. A Transformation Ratio of CO2 (TRCO2) has been formulated here in order to quantify the loss of CO2 for any given coal type. It obviously shows CO2 generation is one of the major features of diagenesis that might feed the deep biosphere. In case of study, about 10 to 105 mg CO2 per gram of total organic carbon have been released during maturation from peat to high volatile bituminous. This is equivalent to 0.23 to 2.4 millimoles CO2 per g TOC. For methanogenesis via CO2 reduction, between 0.92 and 9.6 millimoles hydrogen would be required for complete CO2 reduction during diagenesis. Future work must determine if this is feasible or not. The important role of bitumen in defining the petroleum generation potential was elucidated. The presence of hydrogen transfer agents in bitumen helps to stabilize free radicals hence prevents recombination/ repolymerization processes thus preserving the petroleum generating potential in original coals. Specially, second-order reactions between kerogen and bitumen occurred during pyrolysis that reduce the primary gas yield, but increase the potential secondary gas as well as oil yields. Therefore, it is proposed that pre-extraction of source rocks before pyrolysis, especially coals where extraction yields are particularly high, is not recommended. The comparative investigation with previously studied higher rank Carboniferous German coals showed an excellent fit for both pyrolysis and infrared spectrometry data, suggesting that the New Zealand coals can be considered as natural precursors of the German coals. The structural evolution of coals during maturation is firstly characterized by the enrichment of the aliphatic structures in low rank, peat to high volatile bituminous, then decreases with further maturation. This enrichment of aliphatic carbon content in low rank is accompanied by an increase in the average aliphatic chain length. A slightly enrichment of CH3 group is observed in maturity range 0.9- 2.1% vitrinite reflectance. Secondly, during coalification the content of protonated aromatic carbons increases until R0 ~ 1.6%, then decreases with further maturation.
The present work is the first work dealing with turbulence in the WEGA stellarator. The main object of this work is to provide a detailed characterisation of electrostatic turbulence in WEGA and to identify the underlying instability mechanism driving turbulence. The spatio-temporal structure of turbulence is studied using multiple Langmuir probes providing a sufficiently high spatial and temporal resolution. Turbulence in WEGA is dominated by drift wave dynamics. Evidence for this finding is given by several individual indicators which are typical features of drift waves. The phase shift between density and potential fluctuations is close to zero, fluctuations are mainly driven by the density gradient, and the phase velocity of turbulent structures points in the direction of the electron diamagnetic drift. The structure of turbulence is studied mainly in the plasma edge region inside the last closed flux surface. WEGA can be operated in two regimes differing in the magnetic field strength by almost one order of magnitude (57mT and 500mT, respectively). The two regimes turned out to show a strong difference in the turbulence dynamics. At 57mT large structures with a poloidal extent comparable to the machine dimensions are observed, whereas at 500mT turbulent structures are much smaller. The poloidal structure size scales nearly linearly with the inverse magnetic field strength. This scaling may be argued to be related to the drift wave dispersion scale. However, the structure size remains unchanged when the ion mass is changed by using different discharge gases. Inside the last closed flux surface the poloidal ExB drift in WEGA is negligible. The observed phase velocity is in good agreement with the electron diamagnetic drift velocity. The energy in the wavenumber-frequency spectrum is distributed in the vicinity of the drift wave dispersion relation. The three-dimensional structure is studied in detail using probes which are toroidally separated but aligned along connecting magnetic field lines. As expected for drift waves a small but finite parallel wavenumber is found. The ratio between the average parallel and perpendicular wavenumber is in the order of 10^-2. The parallel phase velocity of turbulent structures is in-between the ion sound velocity and the Alfvènvelocity. In the parallel dynamics a fundamental difference between the two operational regimes at different magnetic field strength is found. At 500mT turbulent structures can be described as an interaction of wave contributions with parallel wavefronts. At 57mT the energy in the parallel wavenumber spectrum is distributed among wavenumber components pointing both parallel and antiparallel to the magnetic field vector. In both cases turbulent structures arise preferable on the low field side of the torus. Some results on a novel field in plasma turbulence are given, i.e. the study of turbulence as a function of resonant magnetic field perturbations leading to the formation of magnetic islands. Magnetic islands in WEGA can be manipulated by external perturbation coils. A significant influence of field perturbations on the turbulence dynamics is found. A distinct local increase of the fluctuation amplitude and the associated turbulent particle flux is found in the region of magnetic islands.
Genetic heterogeneity and molecular genetic diagnostics in primary and secondary laminopathies
(2008)
Laminopathies are a group of rare genetic disorders caused by mutations in genes encoding proteins of the nuclear lamina. One can distinguish between primary and secondary laminopathies. Primary laminopathies representing at least fourteen disease phenotypes arise through pleiotropic mutations in LMNA - the gene that codes for the A-type lamins A and C, mutations in LMNB1 encoding lamin B1 and mutations in LMNB2 encoding lamin B2. Secondary laminopathies including disease phenotypes also observed in primary laminopathies are caused by genes encoding proteins related to the nuclear lamina like ZMPSTE24 (FACE1), LAP2, LBR and thus reflecting genetic heterogeneity in laminopathies. The goal of the present investigation was to study pleiotropy and genetic heterogeneity in primary and secondary laminopathies by analysis of genotype/phenotype correlations. Emery-Dreifuss muscular dystrophy (EDMD), dilated cardiomyopathy with conduction disturbances (CMD1A), familial partial lipodystrophy (FPLD), mandibuloacral dysplasia (MAD), progeroid syndrome, atypical Werner syndrome (aWRN), restrictive dermopathy (RD) and Hallermann-Streiff syndrome (HSS) were included as disease phenotypes to look for their association with LMNA (primary laminopathies) and ZMPSTE24 (secondary laminopathies). Additionally, EDMD patients without STA or LMNA mutations were tested for ZMPSTE24 mutations. A functional candidate gene approach was applied using NARF and SREBF1 in patients suffering secondary laminopathies including FPLD, MAD, HGPS and RD, who were excluded from having LMNA and ZMPSTE24 mutations. Finally, practical consequences of the present study have been considered in genetic counseling and prevention of primary and secondary laminopathies. Screening for mutations in LMNA, ZMPSTE24 (FACE1), NARF and SREBF1 was carried out by PCR using intronic primers flanking each of the exons of the genes tested. The PCR products were tested for changes by heteroduplex analysis and directly sequenced by a cycle-sequencing procedure. Each DNA variation found was checked for its frequency in 386 chromosomes of an ethnically matched control population. For primary laminolathies, 249 unrelated individuals suffering EDMD, CMD1A (DCM), FPLD, MAD, HGPS, aWRN, RD, Hallermann-Streiff syndrome or only partially showing clinical features of the afore mentioned disease phenotypes were tested for LMNA mutations. Eighteen independent LMNA mutations were found in 249 unrelated patients resulting in a general detection rate of 7.2% Summary Dissertation 83 Among the 79 unrelated Caucasian patients and seven families suffering EDMD or EDMD-like disease phenotypes, 14 were found with LMNA mutations, including p.E33G, p.R249Q, p.L263P, p.R377H, p.M348I, p.R249W, p.R453W, p.R527P, p.L530R and p.R644C have been found, resulting in a detection rate of 17.7%. Of the ten different mutations, the three mutations p.L263P, p.M348I and p.L530R are novel. The other seven mutations have been reported before to be pathogenic. There is strong evidence that indicates the pathogenicity of the three novel mutations, p.L263P, p.M348I and p.L530R. Firstly, the mutations exchanged evolutionary highly conserved amino acids as shown by orthologous gene comparisons. Secondly, they were not found in 386 alleles of a reference population. Moreover, the mutations are located in the α- helical rod or globular domains of lamins A and C that might lead to the disruption of their nuclear function causing in skeletal and cardiac muscular malfunction. The LMNA p.M348I mutation was found in a Belgian male patient (G-13730) who also carried a STA c.1A>G, p.0 mutation. The STA mutation leading to a loss of emerin has previously shown to be causative for X-linked recessive EDMD and would explain the lack of emerin and a pathogenic effect found in the affected male by itself. But co-segregation of LMNA p.M348I with cardiac conduction disturbances in female family members showed an additional cardiac effect of this mutation to the pathology. This observation is one of the very rare pieces of evidence for digenic (oligo-allelic) pathogenesis in a neuromuscular disease phenotype of laminopathies. It points to related pathogenic mechanisms in EDMD and CMD1A that are not associated with STA and LMNA but with other so far unknown genes functionally related to the nuclear envelope. The known mutation p.R453W of the LMNA gene represents a mutational hot spot. So, it was not unexpectedly found in four unrelated EDMD patients of this study. Other recurrent mutations p.R249Q and p.R377H were found in two patients each. Variable phenotypic expression of the LMNA p.R644C mutation, ranging from no clinical signs to fully expressed EDMD was observed in an Austrian family in the present study. This mutation has reportedly been associated with strikingly diverse phenotypes in unrelated patients including left ventricular hypertrophy, limb girdle muscle weakness, CMD1A, FPLD or atypical lipodystrophy, neuropathy and atypical progeria. But the mechanism of pathogenesis is unknown. The apparent non-penetrance in relatives raises questions about the clinical significance of this missense mutation. However, the observations Summary Dissertation 84 in the present family and in those previously published provide evidence that the risk to express a laminopathy in close relatives is likely to be low but reasonable. Of the 49 unrelated Caucasian patients suffering CMD1A four mutations, p.E161K, c.- 3_+12del, p.Y259C and p.R377H, were found resulting in a detection rate of 8.2%, which did not significantly differ from the 2.5% found in 197 dilated cardiomyopathy patients of an earlier study. This overall low detection rate reflects the wide genetic and environmental heterogeneity of the pathogenesis in dilated cardiomyopathy. Otherwise, LMNA mutations may cause dilated cardiomyopathy in about 5% of the cases. The wide overlapping phenotypic and genetic similarities between Hallermann-Streiff syndrome (HSS) and HGPS, made HSS a good candidate disease for a primary laminopathy caused by LMNA mutations. But there was no co-segregating disease causing mutation identified. Thus, this study excluded HSS for the first time to be associated to LMNA and adds to the molecular genetic differentiation by excluding HSS from primary laminopathies. Among 32 individuals of 12 families suffering restrictive dermopathy, 22 individuals have been found to carry the ZMPSTE24 mutations c.50delA, c.209_210delAT, c.1085 - 1086insT or c.1385T>G. The mutation c.1085 -1086insT is a recurrent mutation that occurred in the present sample with a frequency of 68% in all RD patients with a ZMPSTE24 mutation. Three mutations, c.50delA, c.209_210delAT and c.1385T>G, are novel mutations. Like the c.1085 -1086insT mutation, c.209_210delAT and c.50delA lead to a frame shift, which putatively results in a non-functional truncated peptide. As an additional indication for a pathogenic effect, the novel mutations c.50delA and c.209_210delAT were not found in 386 alleles of a normal reference population. The first ZMPSTE24 missense mutation c.1385T>G (p.L462R) changing a highly conserved amino acid was found in patient from Guinea suffering from a clinically unequivocal case of restrictive dermopathy. The mutation was heterozygous in the patient but also in the healthy mother. A second pathogenic mutation should be expected. This hypothesis could not be proven, as there was no sufficient test material available from the patient and other family members. Moreover, there was no appropriate African (Guinea) reference population available, which could have been used to estimate the frequency of p.L462R. Thus, it cannot be excluded that p.L462R might be a polymorphism or rare non-pathogenic variant in the ethnic group the patient belongs to. Genetic instability in ZMPSTE24 has interfered with the molecular genetic diagnosis of restrictive dermopathy leading to the inability to distinguish between homozygotes and heterozygotes for the ZMPSTE24 mutation c.1085-1086insT. The reason is a repeated Summary Dissertation 85 thymine (T)9 c.1076-1085 in ZMPSTE24 that can cause a slippage of DNA polymerases. By sequencing cDNAs obtained from homozygous wild-type [(T)9], heterozygous [(T)9/(T)10] and homozygous mutant [(T)10] individuals by using regular Taq polymerase (Fermentas) or high fidelity polymerase (Pfu) for the sequencing reaction the genetic instability was quantified. High error rates up to 23% were found if regular Taq polymerase (Fermentas) was used for sequencing while using high fidelity polymerase (Pfu) resulted in error rates of 6.2 % or lower. As a practical consequence, high fidelity polymerase should always be used to distinguish homozygous mutant [(T)10] individuals from heterozygous [(T)9//(T)10] by sequencing. A high percentage of EDMD patients was tested negative for mutations in STA or LMNA (Bonne et al., 2003). Therefore, other genes are supposed to be involved in the molecular pathology of EDMD. ZMPSTE24 was considered as a promising functional candidate gene in this study, as the gene product - the ZMPSTE24 peptide - takes part in the post-translational modification of lamin A. The negative result of the present study points to a rather unlikely association of EDMD with ZMPSTE24. Additionally, NARF can very likely be excluded by this study from being associated with FPLD, MAD, HGPS and RD, while SREBF1 has obviously no association with FPLD. By the present study, diagnostic tools have been established for molecular genetic diagnosis of several very rare primary and secondary laminopathies, which has a direct practical impact on disease management of laminopathies. Now, the molecular definition of the diseases by association with a specific mutation can be used for genotype/phenotype correlation, predictive diagnosis and prenatal diagnosis.
In this work we will analyse the capabilities of several numerical techniques for the description of different physical systems. Thereby, the considered systems range from quantum over semiclassical to classical and from few- to many-particle systems. For each case we address an interesting, partly unsolved question. Despite the different topics we address in the individual chapters, the problems under study are somehow related because we focus on the time evolution of the system. In chapter 1 we investigate the behaviour of a single quantum particle in the presence of an external disordered background (static potentials). Starting from the quantum percolation problem, we address the fundamental question of a disorder induced (Anderson-) transition from extended to localised single-particle eigenstates. Distinguishing isolating from conducting states by applying a local distribution approach for the local density of states (LDOS), we detect the quantum percolation threshold in two- and three-dimensions. Extending the quantum percolation model to a quantum random resistor model, we comment on the possible relevance of our results to the influence of disorder on the conductivity in graphene sheets. Furthermore, we confirm the localisation properties of the 2D percolation model by calculating the full quantum time evolution of a given initial state. For the calculation of the LDOS as well as for the Chebyshev expansion of the time evolution operator, the kernel polynomial method (KPM) is the key numerical technique. In chapter 2 we examine how a single quantum particle is influenced by retarded bosonic fields that are inherent to the system. Within the Holstein model, these bosonic degrees of freedom (phonons) give rise to an infinite dimensional Hilbert space, posing a true many-particle problem. Constituting a minimal model for polaron formation, the Holstein model allows us to study the optical absorption and activated transport in polaronic systems. Using a two-dimensional variant of the KPM, we calculate for the first time quasi-exactly the optical absorption and dc-conductivity as a function of temperature. Concerning the numerical technique, the close relation to the time evolution in the other chapters get clear if we identify temperature with an imaginary time. In chapter 3 we come back to the time evolution of a quantum particle in an external, static potential and investigate the capability of semiclassical approximations to it. Considering various one-dimensional geometries, we address basic quantum effects as tunneling, interference and anharmonicity. The question is, to which extend and at which numerical costs, several semiclassical methods can reproduce the exact result for the quantum dynamics, calculated by Chebyshev expansion. To this end we consider the linearised semiclassical propagator method, the Wigner-Moyal approach and the recently proposed quantum tomography. A conceptually very interesting aspect of the compared semiclassical methods is their relation to different representations of quantum mechanics (wave function/density matrix, Wigner function, quantum tomogram). Finally, in chapter 4 we calculate the dynamics of a classical many-particle system under the influence of external fields. Considering a low-temperature rf-plasma, we investigate the interplay of the plasma dynamics and the motion of dust particles, immersed into the plasma for diagnostic reasons. In addition to the huge number of involved particles, the numerical description of this systems faces the challenge of a large range of involved time and length scales. Exploiting the mass differences of plasma constituents and dust particles allows for separating the PIC description of the plasma from the MD simulation of the dust particles in the effective surrounding plasma.
The primary objective of this study is to practically apply geostatistical tools that can help to improve an evaluation of groundwater quality for a particular area. The Nam Dinh area, an area of 70 x 70 km2, located in the Southern part of the Red River Delta, was selected as a source for different data sets to be used as case studies. A set of geostatistical tools has thus been applied to the different real data sets which were collected from the coastal Quaternary aquifers in the different campaigns. This gives us a yardstick by which the success of a specific approach can be measured. Throughout the thesis a series of the case studies are, in turn, represented in order to get insight into and an understanding of what various geostatistical tools can do and, more importantly, what their shortcomings are. There are nine different methods of data analyses use in this thesis, which include: (1) Major Ion Comparison, (2) Graphic Plots, (3) Exploratory Statistical Data Analysis, (4) Variogram Analysis, (5) Spatial Estimation Using Kriging, (6) Cluster Analysis, (7) Principle Component Analysis, (8) Multivariate Regionalization Analysis, and (9) Contamination Risk Mapping Using Indicator Kriging. First, major ion comparison and graphic analysis are performed in order to get a general hydrogeochemical view of the collected datasets, before stepping into a further geostatistical approach. By these analyses, various groundwater types are observed and a general hydrochemical trend is visualized using Stiff- and Piper diagrams as well as site maps. The major ion ratios in relation to TDS concentration are compared to investigate the origin of water. Second, a statistical exploratory data analysis is applied to describe the important features of the data by which the character of a specific hydrogeochemical variable might be recognized. Deviations from the Gaussian probability model are detected and appropriate transformations for a formal analysis in geostatistics are selected. Since the Theory of Regionalized Variables (Mathéron 1971; short term: Geostatistics) assumes Gaussian distribution the hydrochemical variables used here are checked for normality. These analyses show that although the data are facing some problems such as outliers and they are very positively skewed at the linear scale, this can effectively be minimized by transforming the data to log-scale. Third, both variogram analyses and Kriging techniques are used to spatially estimate a rectangular 36x36 estimation grid within an area of 70 x 70 km based on the sampled locations (85, 45 and 74 and 38 visited locations for the Pleistocene RS, the Pleistocene DS, the Holocene RS, the Holocene DS, respectively). These estimated values are then used to map the spatiotemporal variability of groundwater quality. In practice, estimation of unknown values and mapping of concentrations of a specific variable can, of course, easily be created by many available software programs. However, error variances are always present in any estimation due to a level of uncertainty, so the reliability of how these estimates could be yielded has also been evaluated in this case study. A critical assessment of all possible variations, tightly related to the seasonal change, directional influence, spatial distribution and prediction error is conducted and concluded. Fourth, Cluster Analysis (CA), Principle Component Analysis (PCA) and Multivariate Regionalization Analysis (RA) are applied to three main datasets of all Quaternary aquifers in the Nam Dinh area to discover the relationships among measured hydrochemical parameters by which we can detect and regionalize major factors which have an impact upon groundwater quality. These approaches are also to overcome the plethora of data that is usually a common problem for any one who has already tackled groundwater data. In this case study both clustering and R mode principal component analyses are thus performed based on the following parameters: The log-transformed concentrations of all measured major ions and of NO3-, NO2-, NH4+, PO42-, i.e. 11 variables from three different datasets of the main aquifers. By cluster analysis three classes of water types, ranging from freshwater to brackish-saltwater types, are typically grouped. Finally, Indicator Kriging (IK) is performed to evaluate the risks of arsenic contamination. The focus of this approach is to assess contamination risk expressed as probability of exceeding threshold- values. The region may thus be subdivided into “safe” and “unsafe” zones on the basis of probability maps which mark contaminated all places where the risk of arsenic contamination exceeds a given threshold for drinking water purpose. By this case study, it is shown that Indicator Kriging is a useful method which has some advantages for many contamination studies. Firstly, it is well known as the non-parametric technique which can be appreciably used when a dataset does not reach normal shape or nearly normal shape as in this situation. Secondly, the outlier problem that often exists in any analysis can be overcome when applying this method. Thirdly, it can be applied in practice to delimit a study area into “safe zone” or “unsafe zone” from which decision-making on the water supply can be decided for the remediation of a contaminated water source or selecting an appreciative source for exploitation. The combined use of spatial (Geostatistics) and multivariate statistical measures have proven to be of major assistance in questions of assessing groundwater quality especially in less sampled regions. A major advantage lies in the possibility of simultaneously creating spatial estimates as well as estimation confidence limits.
Genome-wide responses and regulatory mechanisms to thiol-specific electrophiles in Bacillus subtilis
(2008)
The soil-dwelling bacterium Bacillus subtilis is regarded as model organism for functional genomic research of low GC Gram-positive bacteria. Recently, the group of Haike Antelmann has monitored the expression profile of B. subtilis after exposure to phenolic compounds. Interestingly, proteome and transcriptome analyses showed a strong overlap in the expression profile after exposure to catechol, MHQ that auto-oxidized to quinones and the thiol-reactive electrophile diamide. The response to electrophilic quinones and diamide is governed by a complex network of transcription factors, including Spx, CtsR, PerR, CymR and the novel MarR-type repressors MhqR (YkvE), YodB and YvaP. The regulatory mechanisms of these novel thiol-stress sensors YodB and YvaP are studied as part of this thesis in collaboration with the group of Peter Zuber (Oregon). YodB negatively regulates the expression of the nitroreductase YodC and the azoreductase YocJ (AzoR1) after exposure to electrophilic quinones and diamide. The azoreductase AzoR1 is a paralog of AzoR2 that is under control of MhqR. Both paralogous azoreductases (AzoR1 and AzoR2) have common functions in quinone and azo-compound reduction to protect cells against the thiol reactivity of electrophiles. DNA binding activity of YodB is directly inhibited by thiol-reactive compounds in vitro. Mass spectrometry approaches suggested that YodB is regulated by a thiol-(S)-alkylation mechanism in response to quinones. Mutational analyses revealed that the conserved Cys6 residue of YodB is required for optimal repression in vivo and in vitro. Recent studies further suggest that YodB is redox-regulated by intersubunit disulfide formation in vivo by diamide. In addition to the azoreductases, several thiol-dependent dioxygenases confer resistance to quinones. In collaboration with Kazuo Kobayashi (Nara), the YodB-paralogous MarR/DUF24-family regulator, YvaP was identified as repressor of the catechol-2,3-dioxygenase encoding yfiDE (catDE) operon. DNA binding activity of YvaP was also directly inhibited by quinones and diamide in vitro indicating that also YvaP is regulated via post-translational modifications. Mutational analyses showed that the conserved Cys7 is essential for YvaP regulation in vivo and serves as sensor for thiol-reactive compounds. In addition, also the basic amino acids K19, R20 are essential for YvaP repression in vivo as well as conserved basic arginine and lysine residues located in the DNA binding helix-turn-helix (HTH) motif. Non-reducing PAGE analysis suggests the formation of an intersubunit disulfide bond in a YvaP dimer upon treatment with quinones and diamide in vitro. Besides quinones, also aldehydes are electrophilic compounds which react via the thiol-(S)-alkylation reaction with thiols. Thus, we were also interested in the response of B. subtilis to the toxic electrophiles methylglyoxal (MG) and formaldehyde (FA). We analyzed the changes in the transcriptome and proteome of B. subtilis after exposure to MG and FA. Like quinone compounds, both MG and FA induce the thiol-specific stress response. Metabolomic approaches confirmed that these reactive aldehydes deplete the cellular thiol pool and thus act like quinones as another class of thiol-reactive electrophiles. Additionally, MG and FA also triggered responses to overcome DNA damage. Our studies further revealed the specific induction of two FA detoxification pathways regulated by the MarR/DUF24 family repressor HxlR, and the novel MerR/NmlR-type regulator YraB (AdhR). HxlR positively regulates the hxlAB operon encoding the ribulose monophosphate pathway. AdhR positively regulates an adhA-yraA operon that encodes the thiol-dependent formaldehyde dehydrogenase (AdhA) and the DJ1/PfpI-like cysteine proteinase (YraA), and the yraC gene that encodes a γ-carboxymuconolactone decarboxylase. Thus, the AdhR regulon is involved in the detoxification of FA to formate via the formaldehyde dehydrogenase AdhA which catalyzes the cleavage of S-hydroxymethylcysteine adducts. In addition, the cysteine proteinase YraA could be involved in the degradation of S-hydroxymethylcysteine-modified and damaged protein thiols. In collaboration with the group of John Helmann (Ithaca), it was shown that AdhR binds in vitro to a conserved inverted repeat between the -10 and -35 promoter elements upstream of adhA, yraB and yraC. In addition, we showed that the conserved Cys52 of AdhR is essential for aldehyde sensing and activation of adhA-yraA transcription in vivo. Thus, we speculate that redox regulation of AdhR involves thiol-(S)-alkylation of this Cys52 residue by aldehydes as another novel mechanism of bacterial physiology.
The properties of the ion feature of the Thomson scattering signal are investigated. Firstly, the description of the atomic form factor by hydrogen-like wave functions is reviewed and better screening charges are obtained. Then the ionic structure in systems with several ion species is calculated from the HNC integral equation.
The human antibody response to experimental colonization with Staphylococcus aureus NCTC8325-4
(2008)
The four main work packages and their most important results are briefly described as following. 1. Characterization of the extracellular proteome of S. aureus NCTC8325-4 Reference maps of the extracellular proteins of S. aureus NCTC8325-4 were produced at pH ranges 6-11 and 4-7. In total, 119 (pH 6-11) and 177 (pH 4-7) protein spots were identified, corresponding to 48 and 114 proteins, respectively. Among them were many well-known virulence factors such as alpha-hemolysin (Hla), beta-hemolysin Hlb, gamma-hemolysin subunits (HlgA-C), hyaluronate lyase (HysA) and staphylococcal superantigen-like protein 11 (Ssl11). We also detected various extracellular enzymes, which can cause tissue degradation and are involved in nutrient acquisition, for example, autolysin (Atl), glycerol ester hydrolase (Geh), lipase (Lip), thermonuclease (Nuc), several serine proteases SplA-F (SplA-F), V8 protease (SspA), cysteine protease (SspB), staphopain thiol proteinase (88195808, SspP). Many of these proteins probably also contribute to the virulence of S. aureus. 2. Optimization of a 2-D immunoblot (IB) method for the comprehensive investigation of IgG binding to S. aureus extracellular proteins (strain NCTC8325-4) The immune proteome of S. aureus NCTC8325-4 was revealed by probing 2-D blots of S. aureus extracellular proteins at the two pH ranges 6-11 and 4-7 with a pool of sera from 16 volunteers. IgG binding was detected with high sensitivity using a peroxidase-coupled secondary Ab in combination with an ECL-substrate. With application of the software package Delta2D, we could clearly define 66 immune reactive spots on the immunoblots (IBs) of pH range 6-11 and 38 spots on IBs of pH range 4-7. 72 of these 104 immune reactive spots could be identified by matching the IBs with the protein reference maps. These spots represented 36 identified proteins, many of which are known virulence factors, or they are involved in bacterial cell wall biosynthesis and degradation. Generally, the most abundant proteins were also highly immune reactive, but there was no strict correlation between protein abundance and immune reactivity. Some low abundance proteins, especially basic proteins, showed high immune reactivity on 2-D IBs, for example, Atl, 88195808 (SspP) and iron-regulated surface determinant protein A (IsdA). On the other hand, we observed proteins, which were present in large amounts but did not bind IgG such as peptidoglycan hydrolase (LytM) and a hypothetical protein 88193909 (SAOUHSC_00094). 3. Determination of the anti-staphylococcal Ab profiles of S. aureus carriers and noncarriers Comparing the serum IgG binding patterns of sera from the 16 individual volunteers, we observed pronounced heterogeneity in total IgG binding, spot patterns and spot intensities. Five spots were stronger in carriers than in noncarriers (P< 0.05, Mann-Whitney U test). These spots represent IgG binding to SspA, SspB, IsaA, and two hypothetical proteins. A principal component analysis based on differential IgG binding to these spots showed that the carriers were more closely related to each other than the noncarriers, but that they could not be clearly separated from the noncarriers. 4. Does experimental colonization induce changes of the anti-staphylococcal Ab profiles? Finally, we tested whether symptom-free experimental colonization of the 16 volunteers with S. aureus NCTC8325-4 elicited an IgG response. When we compared sera obtained before colonization with those taken 4 weeks after the inoculation with the laboratory S. aureus strain, we did not observe major changes in the Ab patterns. We conclude that short- term colonization with a strain of low virulence does not suffice to induce an Ab production, which is comparable to that present already before the colonization. Thus, either long term high density colonization is required, or as we consider most likely, the adaptive immune response is primarily triggered by (minor) S. aureus infections. Taken together, in this work we have separated the soluble proteins from complex extracellular S. aureus protein extracts with good reproducibility, large coverage (pH 6-11 and 4-7) and high resolution. With application of an ECL substrate, our 2-D immunoblotting procedure resulted in the highly sensitive detection of IgG binding over a wide range of signal intensities. The most important finding with this technique was the pronounced variability of anti-staphylococcal Ab profiles in healthy adults. This could well explain differences in susceptibility to S. aureus infection and its complications. The Ab responses are presumably triggered by long-term colonization or, more likely, by minor infections with S. aureus, since experimental nasal colonization of healthy volunteers with a bacterial strain of low virulence did not induce impressive changes in the Ab profiles.
The term atomic cluster relates to compounds of at least two or three atoms. Thereby the physical properties are size dependent and the property transitions between single atoms and bulk material are not always smooth. Ion traps allow it to observe internal cluster properties independent from the influence of external forces. In this work the electron induced decay of singly negatively charged atomic clusters was observed. The dissociation cross section of the clusters is dominated by detachment of the only weakly bound outer electrons. For simple atoms at low electron energies a simple scaling law can be obtained that includes only the binding energies of the valence electrons. Nevertheless for larger sizes theoretical calculations predict so called "giant resonances" as dominant decay process in metal clusters. Due to mass limitations in storage rings exist so far only cross section measurements for simple anions and small negative molecules. In this work the electron detachment cross sections of small negatively charged carbon (Cn- n=2-12), aluminium (Aln- n=2-7) and silver clusters (Agn- n=1-11) were measured in an electrostatic ion beam trap. The classical scaling law, including only the binding energies of the valence electrons, turned out to be not sufficient, especially for larger clusters. In order to improve the correlation between measured and predicted values it was proposed to involve the influence of the cluster volume and the specific polarisability induced by long range coulomb interaction. For silver clusters the best agreement was obtained using a combination of the projected area reduced by the polarisability. The existence of "giant resonances" could not be confirmed. According to theory for clusters with a broad internal energy distribution, a power-law decay close to 1/time is expected. For some clusters the lifetime behaviour would be strongly quenched by photon emission. The thermionic evaporative decay of anionic aluminium and silver clusters in a size range from one to ten constituents was tested but a correlation could be only found incidentally for a few cluster sizes.
Multiply negatively charged aluminium clusters and fullerenes were generated in a Penning trap using the "electron-bath" technique. Aluminium monoanions were generated using a laser vaporisation source. After this, two-, three- and four-times negatively charged aluminium clusters were generated for the first time. This research marks the first observation of tetra-anionic metal clusters in the gas phase. Additionally, doubly-negatively charged fullerenes were generated. The smallest fullerene dianion observed contained 70 atoms.
Interaction of injected dust particles with metastable neon atoms in a radio frequency plasma
(2008)
Spatial density and temperature profiles of neon metastables produced in a radio frequency (rf) discharge were investigated by means of tunable diode laser absorption spectroscopy. The experiments were performed in the PULVA1 reactor, which is designed for the study of complex (dusty) plasmas. The line averaged measured density is about 1.5×1015 m−3 in the bulk and drops almost linearly in the plasma sheath. The gas temperature is in the range of 370–390 K. The flow of metastable atoms in the plasma sheath deduced from the spatial density distribution is dominated by the flow towards the rf electrode. The sheath length is supposed as the effective diffusion length in the plasma sheath region. This approximation was used to investigate the interaction of injected particles with the plasma. The observations and estimation provide evidence for a significant interaction between metastable atoms and powder particles which is important for energy transfer from the plasma to the particles. The power per unit area absorbed by dust particles due to the collision of metastable atoms with the dust particle surface is in the range of a few tens of mW m−2.
A paradigm was developed to experimentally investigate the dysregulation of affective reactivity in clinical depression. The literature so far reported evidence for three directions of dysregulation - negative potentiation, positive attenuation, and emotion context insensitivity. Therefore a paradigm was designed to allow to test all three hypotheses simultaneously. Furthermore, to enable generalization across the specific stimuli used in the experiment, stimuli of two sensory modalities were used - pictures and sounds. Because it was hypothesized, that the specificity of affective reactivity of depressed patients will be especially prominent in long lasting affective situations, a categorically blocked presentation mode was chosen. Regarding the dependent variables, a multimethod approach was conducted. Besides self-report ratings of the feeling state, startle responses, skin conductance responses, heart rate, and the electromyogram of the corrugator and zygomatic muscle were recorded. In a separate session, BOLD-responses during picture viewing were collected by functional magnetic resonance imaging (fMRI). Both sessions were conducted with three samples: a healthy student sample, a depressed outpatient sample, and a healthy age and gender matched control sample. The results of the patient sample support an integration of the emotion context insensitivity and the negative potentiation hypothesis. Patients reported generally to feel more unpleasant and more aroused than healthy controls. Skin conductance and startle responses were modulated by valence to a smaller degree in the patients than in the controls. No group differences were found in the facial muscle activity. BOLD-responses were potentiated during unpleasant compared to neutral pictures in the patient but not in the control group in the amygdala, the insular cortex and the orbito frontal cortex. A model to integrate these results is developed. Its central assumption is, that the inability to respond to affective stimuli is an aversive experience and therefore leads to a negativity bias in attention and cognition. Direction of further research and implications for psychotherapies are discussed.
Solifuges (Solifugae, Arachnida) are an important element of the fauna especially in arid and desert environments. Unfortunately, this animal group has only been extremely poorly studied not only in terms of morphology, but also ecology, physiology, systematics and phylogeny. The present study aimed to provide a detailed overview of their anatomy and ultrastructure. Representatives of these peculiar animals were investigated by means of light and electron microscopy in order to gain new insights in their functional morphology and also to evaluate potential characters for their systematic and future phylogenetic studies. The histology and ultrastructure of the following organ systems have been investigated: tarsal structures, sensory structures and nervous system, coxal glands, alimentary system, respiratory system, circulatory system and reproductive systems. Additionally, a camel spider in Baltic amber was described, representing the second known specimen of fossil Solifugae in Baltic amber. Further on, the entire mitochondrial genome of Nothopuga sp. was sequenced for comparison with other solifuges and chelicerates in order to reveal changes in their gene order.
Infrared laser absorption spectroscopy (IRLAS) employing both tuneable diode and quantum cascade lasers (TDLs, QCLs) has been applied with both high sensitivity and high time resolution to plasma diagnostics and trace gas measurements.
TDLAS combined with a conventional White type multiple pass cell was used to detect up to 13 constituent molecular species in low pressure Ar/H2/N2/O2 and Ar/CH4/N2/O2 microwave discharges, among them the main products such as H2O, NH3, NO and CO, HCN respectively. The hydroxyl radical has been measured in the mid infrared (MIR) spectral range in-situ in both plasmas yielding number densities of between 1011 ... 1012 cm-3. Strong indications of surface dominated formation of either NH3 or N2O and NO were found in the H2-N2-O2 system. In methane containing plasmas a transition between deposition and etching conditions and generally an incomplete oxidation of the precursor were observed.
The application of QCLs for IRLAS under low pressure conditions employing the most common tuning approaches has been investigated in detail. A new method of analysing absorption features quantitatively when the rapid passage effect is present is proposed. If power saturation is negligible, integrating the undisturbed half of the line profile yields accurate number densities without calibrating the system. By means of a time resolved analysis of individual chirped QCL pulses the main reasons for increased effective laser line widths could be identified. Apart from the well-known frequency down chirp non-linear absorption phenomena and bandwidth limitations of the detection system may significantly degrade the performance and accuracy of inter pulse spectrometers. The minimum analogue bandwidth of the entire system should normally not fall below 250 MHz.
QCLAS using pulsed lasers has been used for highly time resolved measurements in reactive plasmas for the first time enabling a time resolution down to about 100 ns to be achieved. A temperature increase of typically less than 50 K has been established for pulsed DC discharges containing Ar/N2 and traces of NO. The main NO production and depletion reactions have been identified from a comparison of model calculations and time resolved measurements in plasma pulses of up to 100 ms. Considerable NO struction is observed after 5 ... 10 ms due to the impact of N atoms.
Finally, thermoelectrically cooled pulsed and continuous wave (cw) QCLs have been employed for high finesse cavity absorption spectroscopy in the MIR. Cavity ring down spectroscopy (CRDS) has been performed with pulsed QCLs and was found to be limited by the intrinsic frequency chirp of the laser suppressing an efficient intensity build-up inside the cavity. Consequently the accuracy and advantage of an absolute internal absorption calibration is not achievable. A room temperature cw QCL was used in a complementary cavity enhanced absorption spectroscopy (CEAS) configuration which was equipped with different cavities of up to ~ 1.3 m length. This spectrometer yielded path lengths of up to 4 km and a noise equivalent absorption down to 4 x 10-8 cm-1Hz-1/2. The corresponding molecular concentration detection limit (e.g. for CH4, N2O and C2H2 at 1303 cm-1/7.66 μm) was generally below 1 x 1010 cm-3 for 1 s integration times and one order of magnitude less for 30 s integration times. The main limiting factor for achieving even higher sensitivity is the residual mode noise of the cavity. Employing a ~ 0.5 m long cavity the achieved sensitivity was good enough for the selective measurement of trace atmospheric constituents at 2.2 mbar.
(A paperback version is published by Logos under ISBN 978-3-8325-2345-9.)
Alcohol-related somatic disorders are highly prevalent among general hospital inpatients. Alcohol problem drinking can be differentiated into alcohol use disorders (alcohol dependence and alcohol abuse) and three subtypes of drinking above recommended levels (at-risk drinking only [AR], heavy episodic drinking only [HE], at-risk and heavy episodic drinking [ARHE]). The aims of this study were threefold. First, proportions of alcohol problem drinking among general hospital inpatients in a region of north-eastern Germany were estimated (study 1). Second, among individuals with alcohol problem drinking the association between beverage preference and alcohol-related diseases was tested (study 2). Third, subtype differences regarding demographics, alcohol-related variables, motivation to change drinking behaviors, and the risk to develop short-term alcohol dependence among the three subtypes of drinking above recommended levels were analyzed (study 3). The data presented in this dissertation are based on the randomized controlled trial “Early Intervention at General Hospitals”, which is part of the Research Collaboration Early Substance Use Intervention (EARLINT). Study 1 includes a sample of consecutively admitted general hospital inpatients between 18 and 64 years old (n = 14,332). The study adopted a two-stage-sampling approach: (a) screening and (b) ascertainment of alcohol problem drinking. Those who were identified with alcohol problem drinking were asked for written consent for further study participation. This included further baseline assessment, the consent to use routine treatment diagnoses and participation in a follow-up interview 12 months after hospitalization. For study 2, routine treatment diagnoses were provided by hospital physicians for a total of 1,011 men with problem drinking. These diagnoses were classified into three categories according to their alcohol-attributable fractions (AAF): diseases totally attributable to alcohol by definition (AAF=1), diseases partially attributable to alcohol (AAF<1) and diseases with no empirical relationship to alcohol or with a possibly protective effect associated with alcohol (AAF=0). Study 3 was restricted to study participants with drinking above recommended levels (n=425). Study 1: Among all general hospital inpatients, 8.9% were identified with current problem drinking in the following descending order: 5.3% exhibited alcohol use disorders and 3.6% drinking above recommended levels. Higher proportions of problem drinking were found at rural sites compared to urban sites (13.7 vs. 7.5%, p<.001). Study 2: Because of the low proportion of women with alcohol problem drinking the following analyses were restricted to males. Multinomial regression analyses revealed different risks for alcohol-related diseases in relation to beverage preference while controlling for alcohol-associated and demographic confounders. Compared to all other groups, spirits only drinkers had the highest risk for having a disease with AAF>0; e.g., beer only drinkers had lower odds of having a disease with AAF<1 (odds ratio, OR=0.50, 95% confidence interval, CI: 0.27-0.92). Study 3: Men with alcohol use disorder were excluded from the following analysis. At baseline, multinomial logistic regression revealed differences between individuals with AR, HE and ARHE while controlling for age. ARHE was associated with higher odds of having a more severe alcohol problem (OR=2.06, CI: 1.23-3.45), using formal help (OR=2.21, CI: 1.02-4.79), and having a disease with AAF=1 (OR=3.43, CI: 1.58-7.43), compared with AR. In addition, individuals with ARHE had higher odds of taking action to change drinking behaviors (i.e., beginning to implement change) than individuals with HE (OR=2.29, CI: 1.21-4.34) or AR (OR=2.11, CI: 1.15-3.86). At follow-up, individuals with ARHE had higher odds of having alcohol dependence according to the DSM-IV (OR=4.73, CI: 1.01–22.20) compared to individuals with AR. In addition to alcohol use disorders, drinking above recommended levels is a common problem among general hospital inpatients. Thus, the implementation of systematic alcohol screening and brief interventions should be considered. These data suggest an association between beverage preference and alcohol-related diseases. Among hospitalized problem drinkers, spirits only drinkers had the greatest risk of having diseases with AAF>0. Of the three subtypes of drinking above recommended levels, ARHE seems to be particularly problematic because there appears to be an indication of a subclinical diagnosis. To provide adequate intervention, clinical practice should distinguish between the three groups of drinking above recommended levels. Brief alcohol intervention should be tailored to the individual’s motivation to change and to the type of alcohol problem drinking. The effectiveness of such a procedure remains to be evaluated in further studies.
Turbulence is a state of a physical system characterized by a high degree of spatiotemporal disorder. Turbulent processes are driven by instabilities exhibiting complex nonlinear dynamics, which span over several spatial as well as temporal scales. Apart from fluids and gases, turbulence is observed in plasmas. While turbulent mixing of a system is sometimes a desired effect, often turbulence is an undesired state. In hot, magnetically confined plasmas, envisaged for energy generation by thermonuclear fusion, plasma turbulence is clearly a problem, since the magnetic confinement time is drastically deteriorated by turbulent transport. Hence, a control mechanism to influence and to suppress turbulence is of significance for future fusion power devices. An important area of plasma turbulence is drift wave turbulence. Drift waves are characterized by currents parallel to the ambient magnetic field, that are tightly coupled to a coherent mode structure rotating in the perpendicular plane. In the present work, the control of drift waves and drift wave turbulence is experimentally investigated in the linear magnetized helicon experiment VINETA. Two different open-loop control systems - electrostatic and electromagnetic - are used to drive dynamically parallel currents. It is observed that the dynamics of the drift waves can be significantly influenced by both control schemes. If the imposed mode number as well as the rotation direction match those of the drift waves, classical synchronization effects like, e.g., frequency locking, frequency pulling, and Arnold tongues are observed. These confirm the nonlinear interaction between the control signal and the drift wave dynamics. Finally, the broadband drift wave turbulence, and thereby turbulent transport, is considerably reduced if the applied control signal is sufficiently large in amplitude.
The experimental determination of the electron energy distribution of a low pressure glow discharge in neon from emission spectroscopic data has been demonstrated. The method extends an approach by Fischer and Dose [5]. The spectral data were obtained with a simple overview spectrometer and analyzed using a strict probabilistic, Bayesian data analysis. It is this Integrated Data Analysis (IDA) approach, which allows the significant extraction of non-thermal properties of the electron energy distribution function (EEDF). The results bear potential as a non-invasive alternative to probe measurements. This allows the investigation of spatially inhomogeneous plasmas (gradient length smaller than typical probe sheath dimensions) and plasmas with reactive constituents. The diagnostic of reactive plasmas is an important practical application, needed e.g. for the monitoring and control of process plasmas. Moreover, the experimental validation of probe theories for magnetized plasmas as a long-standing topic in plasma diagnostics could be addressed by the spectroscopic method.
Therapeutic Sealing of Proximal Tooth Surfaces: Two-Year Clinical and Radiographic Evaluation
(2009)
The diagnosis, prevention and treatment of proximal carious lesions comprise a constant problem in clinical dentistry. The purpose of this investigation was to test the safety and clinical effect of a new treatment for proximal caries. In 50 patients with two proximal initial lesions (D1-3 without cavitation, bitewing X-ray), orthodontic rubber rings were applied to gain access to the interproximal space. One of the lesions was sealed with a thin polyurethane-dimethacrylate foil using a bonding agent (Heliobond®, Vivadent, Schaan/Liechtenstein); the other lesion received oral home-care with dental floss and fluoridated toothpaste and was left as control. In clinical follow-ups after 6 and 12 months and X-ray evaluation after two years, clinical retention of proximal tape and the underlying sealant, marginal adaptation, discoloration, tooth vitality, proximal plaque and gingivitis were checked. In addition, caries was assessed clinically and radiographically. The sealants showed good retention, marginal adaptation and colour. After two years, vitality of all teeth was still positive and no relevant differences in plaque accumulation or gingival status were found between sealed and control teeth. Two sealed surface had to be filled due to caries progression (D3 with cavitation). 9 sealed lesions showed caries regression. In contrast, only 4 control lesions regressed and also two showed progression. The loss of tape had no significant influence on the lesion progression indicating the effect of the underlying bond. All other sealants and control lesions were stable indicating an arrest of the lesion. In conclusion, sealing initial proximal lesions showed no clinical problems and mostly arrest of initial carious lesions on bitewing X-rays.
Age-related brain injuries including stroke, are a major cause of physical and mental disabilities. Therefore studying the basic mechanism underlying functional recovery after brain stroke in middle aged subjected it is of considerable clinical interest. Data from our lab and elsewhere indicate that, behaviorally, middle aged rats were more severely impaired by stroke than were young rats, and they also showed diminished functional recovery. Infarct volume did not differ significantly in young and middle aged animals, but critical differences were apparent in the cytological response to stroke, most notably an age-related acceleration of the establishment of the glial scar. The early infarct in older rats is associated with a premature accumulation of BrdU-positive microglia and astrocytes, persistence of activated oligodendrocytes, a high incidence of neuronal degeneration, and accelerated apoptosis. In middle aged rats, neuroepithelial-positive cells were rapidly incorporated into the glial scar, but these neuroepithelial-like cells did not make a significant contribution to neurogenesis in the infarcted cortex in young or middle aged animals. Stroke is accompanied by a strong inflammatory reaction in the brain. We hypothesized that a mild systemic inflammatory reaction as caused by periodontal disease prior to stroke onset, may exert a neuroprotective effect in a rat model of focal ischemia. To test this hypothesis, marginal periodontitis was induced in BB/LL Wistar rats for 3 weeks. Two weeks after periodontitis initiation, focal cerebral ischemia was produced by reversible occlusion of the right middle cerebral artery. After a survival time of 7 days after ischemia, rat brains were analyzed. In addition, markers of systemic inflammation were determined in a different group of laboratory animals at 14 days after the onset of periodontitis. We found that rats with a mild systemic inflammation had a significantly reduced infarct volume and a significant reduction in the number of brain macrophages in the infarcted area. Conclusions: The available evidence indicates that the middle aged brain has the capability to mount a cytoproliferative response to injury, but the timing of the cellular and genetic response to cerebral insult is deregulated in middle aged animals, thereby further compromising functional recovery. In addition we found that that mild systemic inflammation elicited prior to stroke onset may have a neuroprotective effect in rats by reducing the infarct volume and tissue destruction by brain macrophages.
The Caribbean is a geologically complex region with several different plate boundary interactions. Geodynamic reconstructions of the northwestern Caribbean region have been particularly controversial in terms of the number of arcs, subduction polarity, and timing of collision. This thesis develops a refined tectonic reconstruction for the northwestern Caribbean based on a review of geological data of Cuba and a regional analysis within the northwestern Caribbean context. With regard to plausibility, significant emphasis was put on the degree and qualitiy of visualization. Three crustal sections across key areas in western, central, and eastern Cuba have been constructed in order to conduct an evolutionary interpretation in three dimensions. Western and central Cuba constitute an orogenic belt resulting from the collision of a mid- to Late Cretaceous volcanic arc - the "Great Caribbean Arc" - with the southern paleomargin of North America. The collision process apparently started in the Campanian, but major north- to northeast-directed thrusting processes at the southern Bahamas margin culminated during the Paleocene. A continous southwest-dipping polarity of the "Great Caribbean Arc", at least from the Aptian-Albian, can be infered from (1) its Late Cretaceous approach towards the North American margin, (2) the magnitude of top to the north directed tectonic transport in the Cuba orogenic belt, and (3) the internal structures of the metamorphic fore-arc assemblages and their evolution on the north side of the arc. An Early Cretaceous southwest-dipping origin of the "Great Caribbean Arc" along the northern fringe of the Chortís Block appears to be in all probability. This concept provides a link between (1) middle Late Cretaceous collision processes along the Matagua suture zone, (2) the Turonian termination of "Great Caribbean Arc"-activity on Jamaica, and (3) the late Campanian onset of collision in the Cuba orogenic belt. The collision of the "Great Caribbean Arc" with the Bahamas margin hampered relative northward motion of the Caribbean Plate from the late Campanian onward. Continued northward push finally resulted in the commencement of north-dipping subduction. Late Cretaceous commencement of north-dipping subduction was accompanied by superposition of oceanic crust and large-scale north-directed gravity sliding on the upper plate, as documented by ophiolitic slide-masses and Maastrichtian olistostromes in eastern Cuba (Nipe - Cristal and Moa Baracoa ophiolite massifs) as well as on Jamaica (ophiolites of the Bath-Dunrobin Complex) and the southern peninsula of Hispaniola. Progress of north-dipping subduction was responsible for the emergence of a Paleocene to Middle Eocene volcanic arc which spanned the northwestern Caribbean along the southern boundary of the Yucatán Basin while the Chortís Block and the Nicaragua Rise were still in a paleoposition to the south of the Maya Block. North-dipping subduction and the associated volcanic arc isolated the Yucatán Basin from its original affiliation to the Caribbean Plate. Relative northward motion of the Caribbean Plate and activity of the Paleogene volcanic arc stopped after the Eocene arrival of thickened oceanic crust of the Caribbean Large Igneous Province at the north-dipping subduction zone. After the late Early Eocene commencement of spreading at the Mid-Cayman Rise, North America - Caribbean relative motion was taken up along the sinistral Oriente Fault with estimated amounts of 800 to 1000 km offset since the Middle Eocene. This transform margin dissmembered the northwestern Caribbean extend of the Paleocene to Middle Eocene volcanic arc. Its eastern bend was uncoupled in the course of this process and may be represented by the Aves Ridge. South-central Hispaniola can be restored to a Middle Eocene position to the south of eastern Cuba, which accounts for an approximate Cenozoic displacement of 200 to 300 km. Therefore, most of the western prolongation of the Oriente Fault must be accommodated at the northern bounding-faults of the southern peninsula of Hispaniola. The proposed synthesis is in clear accordance with the paradigm of plate tectonics, corroborating its capability to incorporate even a complex region like the Caribbean.
In 1992, the international regime 'Agenda 21' was agreed upon. Accordingly, countries worldwide have been undergoing reforms in their water management into Integrated Water Resources Management (IWRM). The implementation is promoted by international actors. The main institutional aspects of IWRM are the river basin approach, clear property rights allocation, and application of economical instruments. In former centrally planned economies, the process of IWRM implementation has been coincided with transformation for the market economy. The implementation of institutional aspects of IWRM in countries under transition is connected with high transaction costs. Against this background, the comparative empirical study was initialised in order to analyse institutional change of water management towards IWRM in Vietnam and in Poland. Two models of river basin organisations were examined. Consequently, pros and cons of decentralised polycentric and hierarchical unicentric river basin organisations have been evaluated. Formal institutions were studied with the use of an in-depth review of legislation in Vietnam and in Poland. The EU Water Frame Directive (EU WFD) and other international policies were also examined. For the empirical study in Vietnam and in Poland, actors were interviewed as experts. The results of the study on both countries were discussed separately, and conclusions were drawn in a comparative manner. Water management reforms towards IWRM in Vietnam and in Poland have been generating multi-level governance processes including international, national and sub-national levels. The implementation of IWRM in Vietnam is supported by international donor agencies. In Poland, the implementation of the EU WFD is coordinated by the European Commission in a hierarchical manner. In comparison to international joint-development projects in Vietnam, the European Commission enforces international IWRM policy more effectively. Since the resumption of ODA in early 1990s, water resources management has been institutionalised in Vietnam by international support. In 1998, a Water Law was established in Vietnam. The intended separation of water resources management from water service provisions caused fragmentation between the Ministry of Natural Resources and Environment, and the Ministry of Agriculture and Rural Development, respectively. This ‘silo-effect’ has been intensified by the competition for international ODA. The power struggles affect even agencies within ministries. Polycentric river basin committees have been established as entities subordinated to the Ministry of Agriculture and Rural Development, as well as the Ministry of Natural Resources and Environment. However, because of weak property rights allocation and the absence of administrative powers, the river basin organisations work ineffectively. The river basin has not yet been established as a sub-national area of political action. Decisions sustained to be made at central level and are affected by the information problem due to largely centralised organisations of Vietnamese water management. The sub-national level is characterised by very low planning and management capacities. In Poland, unicentric river basin organisations were established in 1991. They are aligned with hydrological borders. Water resources planning and management are carried out according to river basins and water regions in order to implement the EU WFD. The river basin has been established as a new area of decision-making. Conflicts between local-governments have been resolved after the reforms. Nevertheless, spatial management planning, environmental protection planning, water service delivery, etc., are further carried out by local self-governments. To integrate water resources planning and management with these services, horizontal coordination is of critical importance. However, this is hampered by problems of ‘spatial fit’. Moreover, a high degree of horizontal cross-border communication increases information problems in hierarchical organisations. Thus, features of polycentric governance models become increasingly important in order to fully implement the EU WFD in Poland.
Asymmetrical capacitively coupled RF discharges in oxygen, argon and hydrogen have been experimentally investigated with the innovative technique of the phase resolved optical emission spectroscopy. This diagnostic tool allows to measure spatio-temporally resolved emission intensities of electronically excited species with a high resolution. The spatial (axial) resolution was better than 1 mm and a temporal resolution of about 1.5 ns has been achieved. Therefore the plasma induced optical emission within the RF cycle (TRF = 73.75 ns) from the RF sheath region with a typical mean sheath thickness of about 5mm has been studied. Spatio-temporally resolved optical emission patterns of the following optical transitions have been measured for a total gas pressure in the range of 20 to 100 Pa and self-bias voltages between -50 and -550 V: Oxygen plasma Emission at 777.4 nm and 844.6 nm (atomic oxygen) Argon plasma Emission at about 751 nm and 841 nm (argon) Hydrogen plasma Emission at 656.3nm (atomic hydrogen, H alpha-line) These transitions are the most prominent ones of the investigated excited species in these plasmas as could be shown from overview spectra of the plasma induced optical emission in the range from 350 to 850 nm. For the first time such extensive PROES measurements in oxygen CCRF plasmas are presented in this work. The additional investigations of argon and hydrogen plasmas serve as a reference and for a direct comparison with results from the literature. The temporal behavior of the emission intensity is influenced by the effective lifetime of the emitting states which is on the order of the nanosecond time scale of the RF cycle. Therefore, it does not represent the real temporal behavior of the excitation. A simple method has been applied to calculate relative excitation rates from the measured emission intensities to distinguish different excitation mechanisms and their correct relative temporal behavior. In a close collaboration within the framework of the Sonderforschungsbereich Transregio 24 'Fundamentals of Complex Plasmas' a newly 1d3v PIC-MCC code for simulations of capacitive RF discharges in oxygen has been developed by Matyash et al. The very close coupling of experiment and modeling allowed a really detailed and microscopic understanding of the processes and dynamics from the sheath to the bulk plasma in CCRF discharges. The spatio-temporally resolved excitation rate profiles show four different excitation structures (I-IV). Excitation processes due to the following mechanisms in CCPs could be identified and characterized: I Electrons expelled from growing sheath II Electrons detached from negative ions (collisions with neutrals) + secondary electrons from the electrode surface (ion bombardment) III Field-reversal effect, reduced mobility of electrons (electron-neutral collisions) IV Heavy-particle collisions These excitation mechanisms are characterized by different temporal and spatial behaviors of the excitation rate within the RF cycle. Additionally it has been shown that the excitation by electron impact in the investigated oxygen plasmas results mainly from dissociative electron impact excitation (O2 + e -> O + O* + e) and not from direct electron impact excitation (O + e -> O* + e). Actinometry measurements show that the results are not really credible. Thus actinometry is not applicable on the investigated oxygen RF plasma. A challenge in interpretation is the observed excitation pattern IV. Pattern IV has to be caused in connection with heavy particle collisions nearby the electrode surface and could be observed in all the three plasmas oxygen, argon and hydrogen. It is located directly in front of the powered electrode and appears during almost the whole RF cycle. The temporal modulation is nearly sinusoidal and weak in comparison to the first three patterns. This is due to the weak RF modulation of the ion flux towards the electrode surface which has been proven by a PIC simulation. It could be shown that the modulation degree of pattern IV depends on the transition time of the corresponding positive ions through the RF sheath which is influenced by the ion mass. In oxygen as well as in argon CCRF plasmas pattern IV is less modulated than in hydrogen CCRF plasmas due to the heavier ions in oxygen and argon. Additionally the modulation degree increases with increasing pressure due to the more confined plasma at higher pressures which is yielding in a stronger modulated ion current towards the powered electrode.
The introduction of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) enabled the separation and visualization of a substantial fraction of an organism’s entire proteome, and when mass spectrometry entered protein science, these proteins became even amenable to identification on a grand scale. Nevertheless, important classes of proteins elude a separation on classical 2 D gels, as the ones showing extremes in isoelectric point or molecular weight, and foremost very hydrophobic proteins naturally embedded in lipid membranes. This thesis aimed at the establishment and adaptation of alternatives to 2-D PAGE. New techniques allowing for an identification and quantification of critical protein classes were designed and adopted to physiological questions in the Gram-positive bacteria Bacillus subtilis and Staphylococcus aureus. In a comprehensive study on cytoplasmic proteins of S. aureus COL the number of proteins identified by a 2-D gel based approach could be extended by 650 proteins employing gel free technologies. Application of these complementary methods resulted in the establishment of a comprehensive reference map of the cytosolic proteome in growing and non-growing S. aureus cells which can serve as basis for further physiological investigations. Gel free separation of complex protein digests was likewise used in a quantitative study on heat stress in B. subtilis. By implementation of the iTRAQ® technology four different physiological states could be relatively quantified in one experiment. A parallel generation of 2-D gel based data enabled the depiction of strengths and weaknesses of protein quantitation by both, spot intensities on 2-D gels and iTRAQ® signal intensities in MS/MS spectra. Furthermore, new insights into heat sensitivity of pivotal enzymes involved in amino acid biosynthesis could be delivered. The institution of gel free approaches and advancements in 2-D PAGE provide the tools to penetrate into yet unamenable scopes of proteomes. A review on proteome coverage in B. subtilis gives an overview on the strategies which have been explored for most comprehensive protein identification in various sub-proteomes. Although more than one third of B. subtilis’ open reading frames could be demonstrated on protein level, one has to be aware of the fact that it still is a long way to achieve complete coverage of its proteome. Integral membrane proteins make up about one quarter of the entirety of proteins in a cell. Despite their large portion they are clearly understudied due to the intricacy of identification. Their low abundance and non-accessibility of membrane-spanning domains represent major experimental difficulties. The establishment of a protocol efficiently depleting cytosolic proteins by membrane shaving and targeting trans-membrane peptides by novel digestion strategies essentially facilitated identification of highly hydrophobic integral membrane proteins. This protocol was not only successfully applied to the membrane proteome of growing S. aureus cells, but was shown to be applicable in B. subtilis as well. Both studies displayed the novel membrane shaving approach to be highly complementary to a previously established separation of membrane proteins via 1 D PAGE. A combination of the two techniques resulted in identification of about half of the theoretical membrane proteome in both bacteria, and hence layed the foundation for advanced and quantitative analyses. In this regard, 14N/15N metabolically labeled membrane samples of growing and non-growing cells of S. aureus COL were relatively quantified revealing a significant difference in amount for more than one third of the proteins. A corresponding experimental setup was used to compare the membrane proteomes of S. aureus SA113 and its mutant deficient in the lysylphosphatidylglycerol synthetase MprF. Interesting quantitative differences were obtained for proteins most likely involved in the regulation of cellular surface net charge as well as for virulence-associated proteins.
We present classical and hybrid modeling approaches for genetic regulatory networks focusing on promoter analysis for negatively and positively autoregulated networks. The main aim of this thesis is to introduce an alternative mathematical approach to model gene regulatory networks based on piecewise deterministic Markov processes (PDMP). During somitogenesis, a process describing the early segmentation in vertebrates, molecular oscillators play a crucial role as part of a segmentation clock. In mice, these oscillators are called Hes1 and Hes7 and are commonly modeled by a system of two delay differential equations including a Hill function, which describes gene repression by their own gene products. The Hill coefficient, which is a measure of nonlinearity of the binding processes in the promoter, is assumed to be equal to two, based on the fact that Hes1 and Hes7 form dimers.However, by standard arguments applied to binding analysis, we show that a higher Hill coefficient is reasonable. This leads to results different from those in literature which requires a more sophisticated model. For the Hes7 oscillator we present a system of ordinary differential equations including a Michaelis-Menten term describing a nonlinear degradation of the proteins by the ubiquitinpathway. As demonstrated by the Hes1 and Hes7 oscillator, promoter behavior can have strong influence on the dynamical behavior of genetic networks. Since purely deterministic systems cannot reveal phenomenons caused by the inherent random fluctuations, we propose a novel approach based on PDMPs. Such models allow to model binding processes of transcription factors to binding sites in a promoter as random processes, where all other processes like synthesis, degradation or dimerization of the gene products are modeled in deterministic manner. We present and discuss a simulation algorithm for PDMPs and apply it to three types of genetic networks: an unregulated gene, a toggle switch, and a positively autoregulated network. The different regulation characteristics are analyzed and compared by numerical means. Furthermore, we determine analytical solutions of the stationary distributions of one negatively, and three positively autoregulated networks. Based on these results, we analyze attenuation of noise in a negative feedback loop, and the question of graded or binary response in autocatalytic networks.
This thesis constitutes a computational study of charge and ion drag force on micron-sized dust particles immersed in rf discharges. Knowledge of dust parameters like dust charge, floating potential, shielding and ion drag force is very crucial for explaining complex laboratory dusty plasma phenomena, such as void formation in microgravity experiments and wakefield formation in the sheaths. Existing theoretical models assume standard distribution functions for plasma species and are applicable over a limited range of flow velocities and collisionality. Kinetic simulations are suitable tools for studying dust charging and drag force computation. The main aim of this thesis is to perform three dimensional simulations using a Particle-Particle-Particle-Mesh ($P^3M$) model to understand how the dust parameters vary for different positions of dust in rf discharges and how these parameters on a dust evolve in the presence of neighboring dust particles. At first, rf discharges in argon have been modelled using a three-dimensional PIC-MCC code for the discharge conditions relevant to the dusty plasma experiments. All necessary elastic and inelastic collisions have been considered. The plasma background is found collisional, charge-exchange collisions between ions and neutrals being dominant. Electron and ion distributions are non-Maxwellian. The dominant heating mechanism is Ohmic. Then, simulations have been done to compute the dust parameters for various sizes of dust located at different positions in the rf discharges. Dust charge and floating potential in the presheath are slightly larger than the values in the bulk due to the higher electron flux to the dust particle in the presheath. From presheath to the sheath the charge and floating potential values decrease due to the decrease of the electron current to the dust. A linear dependence of dust potential on dust size has been found, which results in a nonlinear dependence of the dust charge with the dust size when the particle is assumed to be a spherical capacitor. This has been verified by independently counting the charges collected by the dust. %where indeed it has been noted that the dust charge %scales nonlinearly with the dust size. The computed dust parameters are also compared with theoretical models. Simulated dust floating potentials are comparable to values obtained from Allen-Boyd-Reynolds (ABR) and Khrapak models, but much smaller than the values obtained from Orbit Motion Limited (OML) model. The dust potential distribution behaves Debye-H\"{u}ckel-like. The shielding lengths are in between ion and electron Debye lengths. % indicating shielding by both ions and electrons. Further, the orbital drag force is typically larger than the collection drag force. The total drag force for the collisional case is larger than for the collisionless case and it scales nonlinearly with the dust size. The collection drag values and size-scaling agrees with Zobnin's model. The charging and drag force computation is then extended to two and multiple static dust particles in the rf discharge to study the influence of neighboring dust particles on the dust parameters. Initially, the dust parameters on two dust particles are computed for various interparticle separation distances and for dust particles placed at different locations in the rf discharge. It is observed that for dust separations larger than the shielding length the dust parameters for the two dust particles match with the single dust particle values. As the dust separation is equal to or less than the shielding length the ion drag force increases due to the buildup of a parallel drag force component. However, the main dust properties like charge, potential, vertical component of ion drag are not affected considerably. This is attributed to the smaller collection impact parameter values compared to the dust separation. %This is because the %collection impact parameter values in the sheath and the presheath are smaller %than the smallest dust separation and in case of the dust in the bulk, the %collection impact parameter is comparable with the dust separation. Then the dust charges on multiple dust particles located at different positions in the discharge and arranged along the discharge axis are also computed. It is found that the charges of the multiple dust particles in the bulk or presheath do not differ much from the single particle values at that location. But the dust charges of multiple dust particles located in the sheath drastically differ from the single dust parameter values. Due to ion focusing from dust particles in the upper layers, the ion current increases to dust particles in the lower layers resulting in smaller charge values. This is as well the case where dust particles are vertically aligned as in the standard experiments of dusty plasmas. In conclusion, this work used a fully kinetic (PIC and MD or $P^3M$) model to study the physics of dust charging in rf plasmas. Our simulations revealed that the dust parameters vary considerably from the bulk to the sheath. The CX collisions increase flux to the dust thereby affecting the dust parameters and their scaling with dust size. Also, a dust particle affects the charging dynamics of its neighbor only when their separation is within the shielding length. In the plasma sheath, ion focussing can cause great reduction in dust charges.
In this work, the investigation of dusty plasma by means of tunable diode laser spectroscopy was carried out. Special interest was focused on the interactions of dust particles and metastable atoms. At first, Al density and temperature in dc and pulsed magnetron discharges were measured. Measurements with argon as working gas show an expected behavior of the measured atom density and temperature. Decrease of absorption signal was observed in argon/oxygen and argon/methane mixtures. A small admixture of oxygen leads to a complete disappearance of the absorption signal indicating vanishing Al atom density. The effect is believed to be caused by the oxidation of the magnetron target. This decrease reveals typical hysteresis behavior caused by poisoning of the target. Significant difference between critical oxygen flow value in dc and pulsed modes was registered. Then dust formation and plasma behaviors in hydrocarbon containing plasmas were analysed. The dust growing plasmas (Ar/C2H2, Ar/CH4 and Ar/C3H6 rf plasmas) were characterized by laser transmission and scattering methods, ion energy distribution function and mass spectrum evolution by plasma processing monitor, and the spatial distribution in pristine plasma and the temporal behavior of the metastable atom density in processing plasma using TDLAS. Pristine plasma were then characterized in term of metastable density and temperature. The radial distribution of neon metastable atom density in capacitive coupled rf discharge can be approximated to a Gaussian profile with the width smaller than plasma chamber radius. The diffusion flow of metastable atoms deduced from their spatial density distribution gives the loss of metastable atom in the plasma sheath. Argon metastable density was measured in rf plasma and compared with a simple model for metastable density. The model explains well the trend of metastable density with respect to the change of plasma input power. Metastable density of dusty plasma with injected dust particles was measured and compared to that of pristine plasma. The particle heating by metastable atoms was strongly evidenced. The power absorbed by dust particles due to bombardment of metastable atoms onto a dust particle surface in our experiments is about 0.04 Wm-2 for the low dust density case and lower for higher dust density which is in the same order as the contributions of kinetic energy of ions and electrons and the energy released by their recombination on the grain surface. The influence of dust particle density and size on metastable density was studied. Through measuring metastable density, TDLAS can be used as a tool to study the dust growth process in processing plasma.
Tourette syndrome has been associated with impairments of performance monitoring and alterations of attentional and executive functions. This impairment has been linked to fronto-striatal dysfunctions, which comprise the same braincircuits that are actively engaged in the suppression of tics. We compared behavioral performance and performance monitoring in nineteen boys with Tourette syndrome (TS) (mean age 12.64 years, ± 2.05) and nineteen age-matched controls (mean age 13.16 years, ± 2.29) in a Go/NoGo paradigm. This paradigm was designed to test for problems with inhibition and attention when withholding the response to NoGo targets following repetitive Go targets. The results indicated similar performance accuracy in the TS group and the control group. TS participants showed the expected pattern of Post-Error Slowing, but responded significantly also slower to correct Go trials than the controls. The reaction times (RT) to NoGo targets in commission errors, however, did not differ between the groups. The results suggest that boys with TS develop inhibitory adaptive strategies (overall slower reaction times) to maintain high performance accuracy. These effects may be suspended prior to and during NoGo commission errors.
The Syilx Okanagan environmental ethic is a philosophy expressed in the practice of Indigeneity as a social (cultural) paradigm and is identified by an inter-reliant experience in the land, as demonstrated in land-use practice which is shaped by the land’s realities as observed, learned and communicated to succeeding generations. Syilx Okanagan Indigeneity reflects an epistemology that optimum human wellbeing cannot be achieved through a human centered ethic but must focus on the optimum ability for the environment to regenerate itself. Syilx Okanagan stories convey the social experience and act as a records system to preserve, maintain and transfer the knowledge of the land. On one level, captikwl contain essential specific environmental knowledge as an oral documentation method, while on another level, as literature, captikwl reconstructs the ethos of interdependency specific to the ecology of the Syilx Okanagan territory through reenactment of nature’s interactions. captikwl in the Nsyilxcen language mimics the dynamic aspects of nature’s required regenerative principles to each succeeding generation, and acts as a feed-back loop reconstructing the social paradigm as an environmental ethic. captikwl might be seen as a distinctly Indigenous human adaptive response scheme within a natural system as it constructs the Syilx Okanagan world and results in behavior with sustainable outcome in the environment. captikwl is a distinct oral artistry that must be read through a literary framework cognizant of oral memory device, structure and Syilx Okanagan context. Okanagan author Morning Dove’s collection of Okanagan stories, as well as, the Mattina and DeSautel bilingual collections and other original version captikwl were consulted. Captikwl demonstrates the concept of tmixw which better translates as a life-force. The word for land is tmxwulaxw, which translates better as a life-force-place, rather than land as location or ecology type. Syilx society demonstrates an “ecological conscience” as the common text through captikwl which is enacted in their social institutions in the manner theorized by respected American conservationist Aldo Leopold, as desirable to achieve within society. The Syilx environmental ethic, rather than a sustainable human ethic of utility, is a willingness to live within a strict imperative to continuously sustain a unity of existence through societal knowledge and reverent practice of respect toward all life-forms. The Syilx environmental ethic diverges from ecocentrism, as articulated by Callicott, in recognizing a fundamental distinction between non-life forms and life forms, in their ability for self-regeneration through inter-reliance, as the focus for delineating moral considerability. The Syilx environmental ethic differs from biocentrism, as articulated by Taylor, in recognizing moral considerability as resting with the on-going life form which is capable of regeneration within its ecology, rather than the singular biological unit. The Syilx environmental ethic also differs from the concept of the ethics of place, as articulated by Berthold-Bond and characterized as an ethical bioregional human utility of a location. Tmixw is the life-force which makes up the tmxwulaxw or life-force-place and the humans are only “placed” as a life-force themselves through Indigeneity as a social paradigm within a criteria of full reciprocity in the regeneration of all life forms of a place. The Syilx environmental ethic also differs from the ethic of sustainability proposed by Daly as a steady state economic model of human utilitarianism, in the positioning of nature treated as capital, to be prudently developed in a way that off-sets depletions of renewable and non-renewable resources in meeting human requirements. The Syilx Okanagan view of economy, while structurally a sustainability model, does not construct value based on human utility as a defining line in decision-making as to which life forms are to be devalued and displaced. Syilx Indigeneity is guided through a societal dialogue practice of Enowkinwixw, a process of decision-making structured to include living within the requirements of the land to fully regenerate. Syilx Okanagan Indigeneity frames an environmental ethic from a tmixwcentric position and offers a model proposing an ethic of re-indigenization as a path to sustainability. The thesis proposes a common text for human society in the form of such literatures, since literature is widely accessible, which demonstrate, imbed and advocate a regenerative land ethic towards the re-indigenization of place.
Application of quantum cascade laser absorption spectroscopy to studies of fluorocarbon molecules
(2009)
The recent advent of quantum cascade lasers (QCLs) enables room-temperature mid-infrared spectrometer operation which is particularly favourable for industrial process monitoring and control, i.e. the detection of transient and stable molecular species. Conversely, fluorocarbon containing radio-frequency discharges are of special interest for plasma etching and deposition as well as for fundamental studies on gas phase and plasma surface reactions. The application of QCL absorption spectroscopy to such low pressure plasmas is typically hampered by non-linear effects connected with the pulsed mode of the lasers. Nevertheless, adequate calibration can eliminate such effects, especially in the case of complex spectra where single line parameters are not available. In order to facilitate measurements in fluorocarbon plasmas, studies on complex spectra of CF4 and C3F8 at 7.86 μm (1269 – 1275 cm-1) under low pressure conditions have been performed. The intra-pulse mode, i.e. pulses of up to 300 ns, was applied yielding highly resolved spectral scans of ∼ 1 cm-1 coverage. Effective absorption cross sections were determined and their temperature dependence was studied in the relevant range up to 400 K and found to be non-negligible.
Fluorocarbon containing capacitively coupled radio frequency (cc-rf) plasmas are widely used in technical applications and as model systems for fundamental investigations of complex plasmas. Absorption spectroscopy based on pulsed quantum cascade lasers (QCL) was applied in the mid-IR spectral range of 1269-1275 cm-1. Absolute densities of the precursor molecule CF4 and of the stable product C3F8 were measured with a time resolution of up to 1 ms in pulsed CF4/H2 asymmetrical cc-rf (13.56 MHz) discharges. For this purpose both the non-negligible temperature dependence of the absorption coefficients and the interference of the absorption features of CF4 and C3F8 had to be taken into account in the target spectral range. Therefore, at two different spectral positions composite absorption spectra were acquired under the same plasma conditions in order to discriminate between CF4 and C3F8 contributions. A total consumption of∼ 12 % was observed for CF4 during a 1 s plasma pulse, whereas C3F8 appeared to be produced mainly from amorphous fluorocarbon layers deposited at the reactor walls. A gas temperature increase by ∼ 100 K in the plasma pulse was estimated from the measurements. Additionally, not yet identified unresolved absorption (potentially from the excited CF4 molecule) was found during the àon-phase'.
An interesting aspect in the research of complex (dusty) plasmas is the experimental study of the interaction of micro-particles with the surrounding plasma for diagnostic purposes. Local electric fields can be determined from the behaviour of particles in the plasma, e.g. particles may serve as electrostatic probes. Since in many cases of applications in plasma technology it is of great interest to describe the electric field conditions in front of floating or biased surfaces, the confinement and behaviour of test particles is studied in front of floating walls inserted into a plasma as well as in front of additionally biased surfaces. For the latter case, the behaviour of particles in front of an adaptive electrode, which allows for an efficient confinement and manipulation of the grains, has been experimentally studied in terms of the dependence on the discharge parameters and on different bias conditions of the electrode. The effect of the partially biased surface (dc and rf) on the charged micro-particles has been investigated by particle falling experiments. In addition to the experiments, we also investigate the particle behaviour numerically by molecular dynamics, in combination with a fluid and particle-in-cell description of the plasma.
Tunable diode laser absorption spectroscopy of argon metastable atoms in Ar/C2H2 dusty plasmas
(2009)
The tunable diode laser absorption spectroscopy method was used to measure Ar metastable density in order to study the dust growth process in hydrocarbon-containing plasmas. A simple model was proposed that successfully interprets the experimental results of pristine plasmas. The model is also suitable for explaining the influence of dust particle size on metastable density and for examining the dust growth process. The metastable density responded strictly to the formation of dust particles and their growth in processing plasmas. Using metastable density as an indicator is, therefore, a non-intrusive and effective method for the study of the dust growth process in hydrocarbon-containing plasmas.
Discovery of novel Baeyer-Villiger monooxygenases and their application in organic synthesis.
(2009)
The application of BVMOs in kinetic resolution is a versatile alternative for the synthesis of optically pure esters. Within this thesis BVMOs proved to be highly active against a broad range of linear and aryl aliphatic ketones yielding a variety of enantiopure products. Among the beta-hydroxy ketones several CHMOs and BVMOPsfl showed the best results (E > 100), whereas the application of the latter enzyme also allowed access to the abnormal esters (regioisomeric excess > 40%). Interestingly, some enzymes showed a reduced activity and selectivity with a growing chain length of the ketone, suggesting that middle-chain ketones (C8-C10) might be preferred. Moreover, the production of optically pure 1,2-diols was observed (yields 8-50%), resulting from an in vivo hydrolysis of the 2-hydroxy alkyl acetates. Regarding the N-protected beta-amino ketones, results were different. While the majority of CHMOs catalyzed linear substrates showing high enantioselectivities (for CHMOBrevi1 and CHMOBrachy E > 100, c = 40-50%), BVMOPsfl did not convert nitrogen bearing linear ketones, although this might also be justified with the methylcarbamate protecting group. Interestingly, the number of BVMOs catalyzing oxidation of spatially more demanding linear branched beta-amino ketones was greatly reduced, indicating steric hindrance that was also combined with a decrease in selectivity. Similar to the observation for beta-hydroxy ketones, also the 2 amino alkyl acetates hydrolyzed furnishing 2-amino alcohols (yields 9-52%). Moreover, hydrolysis of the “abnormal“ esters allowed an alternative access to valuable native and non-native β-amino acids. In a two step process, using CDMO from R. ruber and CAL-B, it was possible to generate N-protected (+)-beta-leucine. During kinetic resolutions of aryl aliphatic ketones it was observed that the highest enantio¬selectivities could be achieved utilizing HAPMOJD1, HAPMOACB and PAMO, enzymes typically preferring aromatic substrates. Biotransformation with 3-phenyl-2-butanone revealed an E-value > 100 for HAPMOJD1 (S-selective). Nevertheless, also BVMOPsfl converted this sub¬strate (E = 43), and also CHMOAcineto and CPMO oxidized it, although selectivity was rather low (E < 5). Interestingly, BVMOKT2440 was the only examined enzyme showing R selectivity (E = 13). Additionally, increasing the scale and performing biotransformation in a baffled flask could increase enantioselectivity of BVMOPsfl from E = 43 to 82. The discovery of novel enzymes with diverse properties is still a main goal of the biotechnological industry. Within these studies, two BVMOs (BVMOKT2440 and HAPMOJD1) could be successfully amplified from genomic DNA using different PCR-methods. Then, expression in E. coli was optimized, revealing that the reduction of expression temperature, implementation of E. coli JM109 or RosettaTM (DE3), possessing the pRARE plasmid to facilitate translation of rare codons in the latter case, and/or co-expression of chaperones (pGro7: GroEL/ES-familiy) could increase the amount of soluble and active protein. Both enzymes were subjected to biocatalysis and it was found that BVMOKT2440 preferentially oxidized linear ketones, while HAPMOJD1 dominantly converted aryl aliphatic ketones. The latter enzyme could be purified by anion exchange and affinity chromatography allowing examination of kinetic parameters. Thereby, HAPMOJD1 displayed lowest KM-values for acetophenone derivatives bearing their substituent in para-position (KM < 320 µM). Moreover, also aldehydes and heteroaromatic compounds were oxidized and also sulfoxidation was observed. Interestingly it was found, that both BVMO genes are located in the direct neighborhood of a dehydrogenase and a hydrolase. This led to the suggestion that these enzymes may be metabolically connected in the degradation of their natural substrate.
Medulloblastoma is one of the most common malignant childhood brain tumors. Although advances in multimodal treatment have significantly improved the survival rate, the outcome of children is still very poor. Therefore, there is an urgent need to develop novel approaches that can increase survival and reduce long term side effects of patients. Histone deacetylase inhibitors (HDIs) have emerged as a promising new class of antineoplastic agents in cancer therapy. Among them, suberoylanilide hydroxamic acid (SAHA, vorinostat, Zolinza®) is a highly potential HDI which has been approved for treatment of cutaneous T-cell lymphoma and is currently used for treatment of various tumor cell types both in vivo and in vitro. However, only little information has been reported on the effects of SAHA on primary central nervous system (CNS) tumors including medulloblastoma. The DAOY cell line represents the most widely used model cell line for investigation of medulloblastoma. In a recent study, it was reported that SAHA induces apoptosis and cell cycle arrest of DAOY cells (Sonnemann et al., 2006). However, the molecular mechanisms underlying this antitumor activity are still not clear. Therefore, in this study, effects of SAHA on DAOY cells were analysed at the protein level by using both gel-based and gel-free proteomic approaches. A 2D proteome reference map of DAOY cells in pH range of 4-7 was created from control and 10 µM SAHA treated cells via a combined analysis using 2D electrophoresis and MALDI-TOF/TOF-MS. This reference map covers 1196 identified protein spots of more than 770 distinct proteins. This is the first report of a 2D proteome map of SAHA treated DAOY cells. Moreover, the number of covered proteins was increased with the aid of a 1D-RP-LC-ESI-MS/MS analysis. Both methods together gave rise to a total of over 1200 distinct protein species, which is the largest catalogue of proteins identified in DAOY cells so far. In SAHA treated cells, a series of proteins were found to be subjected to protein degradation after treatment with the drug, including mainly cytoskeleton proteins (e.g. beta-tubulin, beta/gamma-actin, vimentin, filamin interacting protein 1), heat shock protein HS90B and a component of the FACT chromosomal remodelling complex (SSRP1). Most of those proteins are known substrates for caspases. Interestingly, several of these protein degradations are reported as typical apoptotic events in brain cells such as fragmentations of lamin A/C, alpha-spectrin, myosin-9 and SSRP1. The 2D reference map was then used as an annotated database for further investigation of changes in protein expression and protein modification profiles of DAOY cells following SAHA treatment. By using the 2D-DIGE technique, SAHA was found to induce significant changes in protein levels of DAOY cells, especially at the concentration of 10 µM while considerably fewer changes in the protein pattern were observed after treatment with the lower dose of 2 µM. Quantitative analysis of total protein extracts using the 2D-DIGE technique (employing pH range of 4-7) and spectral counting (employing a 1D-RP-LC separation) resulted in the identification of 213 differentially expressed proteins after treatment with 10 µM SAHA. Most of the targeted proteins belong to the groups of cytoskeleton proteins (e.g. lamin B1, calreticulin, dynexin), heat shock proteins (e.g. HSP71, HSP7C, CH60, GRP78) and brain signal transductors (e.g. 14-3-3E, 14-3-3T, CRK, MARCS). Other proteins that changed in levels after SAHA treatment include proteins involved in chromatin remodelling (e.g. RUBV1, RUBV2), transcription regulation (e.g. YBOX, CBX5), redox regulation (e.g. TXND4, TXND5, BIEA), metabolism (e.g. G6PI, K6PP, LDHB) and RNA processing (HNRP K). In addition, cathepsin D, one of autophagic executors, was increased by SAHA treatment while different subunits of the 26S proteasome complex were decreased in levels after addition of SAHA. Interestingly, we found alterations of mitochondrial proteins indicating the perturbation of mitochondrial function. VDACs are pore forming proteins located on the outer mitochondrial membrane which is known to play an important role in the release of apoptogenic proteins such as cytochrome-c from mitochondria to cytoplasm and induction of apoptosis. In this study, VDAC1 and VDAC3 were found to be overexpressed after incubation with SAHA, which might lead to an extensive release of apoptogenic proteins. This result is consistent with the study of Sonnemann and co-workers showing that SAHA induced the mitochondrial apoptotic pathway of DAOY cells (Sonnemann et al., 2006). Furthermore, these results are also in agreement with the previously known antitumor activities of SAHA reported for other cancer cell lines, e.g. the up-regulation of heat shock proteins, prostaglandin synthase 3, ubiquinol cytochrome c reductase or the down-regulation of MARCS proteins. …………………
ZfSl 54 (2009) 2, 224-240 Ulrike Jekutsch Zur Schau gestellte Fiktion: Die Erfindung polnischer Frühgeschichte in Słowackis Tragödien „Balladyna“ und „Lilla Weneda“SummaryJuliusz Słowacki’s tragedies “Balladyna” (1834, publ. 1839) and “Lilla Weneda” (1840) are set in legendary pre-historical times. Reflecting the Polish nation-building process, they outline invented episodes und char-acters in the beginnings of the first Polish state. With these plays, Słowacki wanted to give his people poeti-cally created legends, which would enrich their scanty stock of stories from pre-historical times and fill out the gaps in their national historical knowledge. Słowacki’s foreword to “Balladyna” serves as an introduc-tion to a projected cycle of plays about Polish pre-history. Here, the playwright openly exposes the fictional-ity of both characters and plot, and he draws attention to the many historical inconsistencies and anachro-nisms in the text. At the same time, he claims that the intrinsic truth of poetry ranks higher than mere factual accuracy, and that his plays, despite their historical inaccuracy, may become Polish-pre-history. His inven-tion of new episodes of Polish pre-history is aimed polemically against contemporary historiography – espe-cially against two issues, i. e. first, romantic historiography’s pretension to play the role of universal art (Universalwissenschaft), and secondly, the traditional Polish idealization of known figures of pre-history. The article discusses these two aspects of Słowacki’s plays, focussing on his polemics against contemporary Polish historiography and especially against Joachim Lelewel.
Effect of surgical intervention on the activation status of circulating monocytes and T-cells
(2009)
Major surgery causes alterations in immune function which results in immune suppression in post surgical patients. Deactivation of monocytes in these patients is characterised by the reduced ability of these cells to produce pro-inflammatory cytokines on stimulation with LPS in vitro and by markedly reduced HLA-DR expression. Immune suppression in patients with systemic inflammation has also been associated with a high level of apoptosis in both the circulating T and B cell populations. In addition post surgical T cells have a reduced capacity to proliferate ex vivo in response to co-ligation of the T cell receptor and CD-28. Considering these impairments of immune system, this study aimed to define the extent of immune modulation in both innate and adaptive system in a cohort of surgical patients. Measurment of the level of HLA-DR expression of monocytes in these patients showed a considerable change in monocyte phenotype in the immediate post operative period. In line with previous work, all patients showed a considerable reduction in monocytic surface HLA-DR expression which persisted for many hours and those who had post surgical septic complications showed the most severe reduction. Importantly, patients with minor surgical intervention also exhibited decreased HLA-DR expression. Gene expression analysis of monocyte in these patients showed the up-regulated transcripts of genes involved in extravasation and realignment of the cytoskeleton. Analysis of periperal T cell demonstrated a significant reduction in their number in the circulation and a sharp raise in the number of apoptotic T –cells in the immediate post surgical period. Microarray analysis of T cells from patients who developed sepsis and patients with an uneventful recovery within the post-operative period (3 days) showed a substantial reduction in the transcriptional activity of many genes in both groups. However, this down regulation of T cell transcriptional activity appears to be a rather broad and non specific effect since it is not restricted to particular functional pathways. Real time PCR analysis of both the CD4+ and CD8+ populations using selected down-regulated genes showed that the change in transcriptional profile is equally evident both in CD4+ and CD8+ T-cells. The cause of this transient immune depression following surgery remains to be established and it may represent an important enabling factor which contributes to the development of post surgical infections and inflammatory complications.
In the present work, mass determinations of the eleven neutron-deficient nuclides (99-109)Cd, of ten neutron-rich silver nuclides (112-114,121,123)Ag, and seven neutron-rich cadmium nuclides (114,120,122-124,126,128)Cd are reported. Due to the clean production of the neutron-deficient nuclides it was possible to reduce the experimental uncertainties down to 2 keV, whereas the measurements of neutron-rich nuclides were hampered by the presence of contaminations from more stable In and Cs nuclides. In the case of 99Cd and 123Ag the masses were determined for the first time and for the other nuclides the mass uncertainties could be reduced by up to a factor of 50 as in the case of 100Cd. In the case of a potential isomeric mixture as for (115,117,119)Ag and 123Cd, where no assignment to either the ground state or the excited state was possible, the experimental results were adjusted accordingly. Afterwards all results were included in the framework of the atomic-mass evaluation and thus linked and compared with other experimental data. In the case of the neutron-deficient Cd nuclides a conflict between the mass values obtained in the present work and those published by the JYFLTRAP group could be solved by performing an atomic-mass evaluation. These mass measurements are an important step towards an understanding of the physics of the rp process that will enable a more reliable determination of the composition of the produced material at A = 99. It has been shown that the mass of 99Cd strongly affects the A = 99 production in an X-ray burst model, and that uncertainties have been significantly reduced from more than an order of magnitude to about a factor of 3. The dominant source of uncertainty is now the mass of 100In. In principle, other uncertainties will also contribute. These include those of masses of lighter Cd isotopes, where similar rp-process branchpoints occur and which might affect feeding into the 99Cd branchpoint. In addition, nuclear reaction rate uncertainties will also play a role. However, as reaction rates affect branchings in a linear fashion, while mass differences enter exponentially, mass uncertainties will tend to dominate. Also, which reaction rates are important depends largely on nuclear masses. For example, for low Sp(100In) a (p,γ)-(γ,p) equilibrium will be established between 99Cd and 100In and the 100In(p,γ) reaction rate would affect the A = 99 production, while for larger Sp(100In) the 99Cd(p,γ) reaction rate might be more relevant. Therefore, the mass uncertainties should be addressed first. The presented results are relevant for any rp-process scenario with a reaction flow through the 99Cd region. Here, an X-ray burst model has been used to investigate in detail the impact of the present measurements on such an rp process. The νp process in core collapse supernovae might be another possible scenario for an rp process in the 99Cd region. It it is planed to also explore whether in that case mass uncertainties have a similar impact on the final composition. On the neutron-rich side of the valley of stability for the Cd and Ag chains of nuclides, the r process has not yet been reached. Further technical development on suppression of contaminants are required. This includes improvements on the ISOLDE side, e.g., by improving the selectivity of the transfer line or on the ISOLTRAP setup by implementing an electrostatic ion beam trap for a fast and efficient isobaric selection. Nevertheless the obtained results contribute to the knowledge of nuclear structure. The trends in the two-neutron separation-energy S2n and the interaction between the last neutrons and last protons ΔVpn were corrected to more smooth evolutions, as already seen in other regions of the nuclear chart. The strongest corrections have been observed for even-N nuclides, were more new experimental data are available. Thus, new measurements on odd-N nuclides are suggested. This also is underlined by the trends observed in the Garvey-Kelson relations for the neutron-rich Cd nuclides. Furthermore, it has been shown, that the prominent structure of the ΔVpn for an entire chain of nuclides including inflexion points can be reproduced by using simple relations between quantum numbers of the occupied orbits. This approach connects ten values for each nuclide with only one adjusted parameter. This has been investigated for 63 ΔVpn values of even-even nuclides in the vicinity of Z = 50 and 50 ≤ N ≤ 82. The simple model works remarkably well for the elements Cd, Sn, and Te. Small deviation have been observed for the Xe and Pd nuclides which were explained with the limitations of the model to the vicinity of the close shells, where the nuclides have only few valence protons and neutrons.
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.
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.
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.