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The electron and negative ion densities in an asymmetric capacitively coupled low-pressure RF plasma in oxygen were systematically studied and compared to the electropositive argon RF plasma during continuous and pulsed power input. This work presents the careful design and realization of a non-invasive 160.28 GHz Gaussian beam microwave interferometry (MWI) as an innovative diagnostic tool. MWI directly provides the line integrated electron density without any model assumption. The high microwave frequency enables one to accurately describe the microwave free space propagation by means of Gaussian beam theory. The microwave interferometer is simultaneously coupled with laser photodetachment to experimentally determine the negative ion density in the CCRF oxygen discharge. This is the first time that both diagnostics were combined in low-pressure capacitively coupled RF oxygen plasmas. This thesis first presents comprehensive measurements of the steady state line integrated electron density in dependence on RF power and pressure for an argon and oxygen plasma. For both gases the electron density increases with RF power. However, the line integrated electron density in oxygen is about a factor 3 to 10 smaller than in argon. The reduced electron density is accompanied by a high number of negative ions, which exceeded the electron density and resulted in a high electronegative mode. With increasing RF power, the plasma switches into a low electronegative mode. Consequently, the discharge operates in two different modes, which are distinguished by their degree of electronegativity. The transition between the high and low electronegative modes is step-like and it was concluded that one can here directly see the discharge switches from the &alpha-mode to the &gamma-mode. The &gamma-mode (low electronegative mode, high RF power) is characterized by a strong increase of the electron density and a simultaneous decrease of the negative ion density. The increase may be connected to the production of secondary electrons by collision detachment of negative ions within the RF sheath (“pseudo-secondary electron”), in addition to the classical &gamma process due to positive ion bombardment of the powered electrode. In comparison to the &gamma-mode the &alpha-mode (high electronegative mode, low RF power) reveals more negative ions than electrons. Furthermore, a simple 0d attachment-detachment model was applied to calculate the effective rate coefficients for dissociative electron attachment and collisional detachment from the experimentally determined values of steady state electron and negative ion density, as well as the detachment decay time constant. Hence, the attachment rate coefficient of the molecular ground and the excited metastable state in dependence on RF power were determined. Moreover, the density of metastable molecular oxygen was estimated to 10% of the molecular ground state oxygen. The influence of each electronegative mode to the entire temporal behavior of the oxygen discharge was intensively investigated by pulsing the discharge. Here it was shown that for the low electronegative mode the afterglow behavior is similar to that of an electropositive argon plasma. In the high electronegative mode an electron density peak in the early afterglow was observed. It was concluded that the electron production originates from the collisional detachment of negative ions. The negative ion loss and the electron production in the early afterglow were modeled numerically with a 0d rate equation system. The model accurately describes the afterglow behavior of both electronegative modes and the additional electron density peak in the early of the high electronegative mode. For the high electronegative mode the molecular oxygen plays an important role as a detachment partner for the production of electrons in the early afterglow. Furthermore, the presence of the negative ions causes fluctuations of plasma parameters. 2d spatial and temporal fluctuations of the ion saturation current are measured during the instability. The temporal and phase resolved optical emission spectroscopy shows a strong change in emission pattern during the instability, which becomes more obvious for one RF cycle at characteristic instability phases. Here, the excitation patterns reveal significant changes in the electron heating mechanisms.
The investigated bacterial strain 64G3 was isolated from an offshore oil reservoir in Vung Tau, Vietnam. By means of 16S rDNA sequence alignment and DNA-DNA hybridization with Petrotoga mexicana DSM 14811, the isolate was identified as Petrotoga mexicana species. Morphologically, the 64G3 cells were rod-shaped and cell sizes varied widely from 1.0 µm up to 60 µm in length and from 0.6 to 1.2 µm in width. The cells appeared single, pairwise or in chains within a sheath-like structure (a typical characteristic of the order Thermotogales) that ballooned over the cell ends. Cells were immobile and no flagella were observed. Strain 64G3 grew anaerobically at temperatures ranging from 30 to 65°C and within the pH range of 5.0 to 8.5 with optimum growth at 55°C and the pH 7.0. Elemental sulfur and thiosulfate served as alternative electron acceptors whereas sulfate did not. Cellular extract of strain 64G3 grown in a basal medium containing soluble starch displayed hydrolytic activity towards soluble starch. The amylase system includes at least two individual enzymes. Amylase activity of the cell extract was detected in a wide temperature range (30-80°C), with optimal enzyme activity at 75°C. By using degenerate primer for PCR amplification of GH13 enzyme coding regions in combination with other molecular methods, a full amylase coding gene containing four conserved regions of α-amylase was obtained. The deduced sequence showed low identities (up to 40%) to other known amylases. This 1992 bp coding gene was heterologously expressed in E. coli and its product (amylase) was characterized. Under common expression conditions, the 77 kDa amylase (rAmyA) was predominantly produced as inclusion bodies (insoluble protein). The minor amount of soluble active amylase was used for purification and characterization of the enzyme. rAmyA was active on starch at temperatures between 30-55°C, with an optimum at 45oC. It is not thermostable because it was completely inactive after incubation at 65°C for 15 min. The enzyme was active over a pH range from 4.5-8.0, with an optimum at pH 6.5. Beside starch, rAmyA also hydrolysed glycogen, amylose, amylopectin and other oligosaccharides. Pullulan and cyclodextrins were not the substrates for this amylase. The enzyme hydrolyzed starch in an endo-acting manner, releasing maltose and maltotriose as major products and a lesser amount of glucose. On the basis of the primary structure, the substrate specificities and the hydrolysis pattern, rAmyA was classified as an endo-acting α-amylase (EC. 3.2.1.1). The cpn10/60 operon from psychrophilic O. antarctica was cloned and expressed in B. subtilis using a multi-copy plasmid. The amounts of soluble 60 kDa Cpn60 and 10 kDa Cpn10 produced at temperature ranging from 10 - 30°C were high and stable during cell growth. To investigate the impact of psychrophilic chaperonin on cold adaptation, cells with (cpn+) and without (cpn-) cpn10/60 operon were grown at 10 and 15°C. Growth comparison between two strains revealed that psychrophilic chaperonin did not support cold adaptation of B. subtilis at 10 and 15°C as it did in E. coli. A single copy of O. antarctica cpn10/60 operon was integrated into the amyE locus of the B. subtilis chromosome. The yeast α-glucosidase, a theoretic protein substrate for this chaperonin, was heterologously produced in B. subtilis at temperatures ranging from 15-30°C. Within this temperature range, the major amount of this protein appeared as inclusion bodies. Co-expression of O. antarctica cpn10/60 operon at 15°C, however, did not result in a higher activity of glucosidase. Moreover, SDS-PAGE analysis of cellular insoluble fractions revealed that the amount of insoluble enzyme produced in cpn+ cells did not decrease in comparison with that produced in cpn- cells, indicating that the recombinant chaperonin had no impact on recovery of active α-glucosidase from the inclusion bodies.
Urban Green Areas – their functions under a changing lifestyle of local people, the example of Hanoi
(2013)
Hanoi is a rapidly developing city - in terms of area, population and economy. It also has to face social and environmental problems that often accompany the fast development of a city. Increasing environmental pollution leads to a decrease in living conditions, such as clean water, housing, social services, etc., for most of the city’s inhabitants. Other well-known social problems in cities worldwide also occur in Hanoi nowadays, for example inequality, food supply, and unemployment. In addition, the society is altering; lifestyle- change is a permanent process. Today, it seems that the changing process in Asian countries is rather leap-frogging than continuously. Although many research projects concerning to urban green areas in Hanoi have been completed recently, less is known about utilization of parks&gardens in a practical and systematic way. This study aims at contributing to fulfills the gaps with up-to-date facts and figures of parks’ utilization in the inner city of Hanoi. Based on “grounded theory”, triangular methodology was applied to collect empirical data in four main parks in the inner city of Hanoi namely: Thong Nhat, Bach Thao, Hoan Kiem, and Lenin. Scientific observations, visitor countings were done in 2010-2011; including 2143 face-to-face interviews to park users covering the course of the year and a small online-poll of 113 responses. Thirteen interviews with experts have been done in several phases and taken into account for discussing and testing hypotheses. Empirical results have shown that utilization of the parks is in abundance in terms of the use - numbers as well as activities. A comparison between the courses of the day for parks in Berlin and Hanoi shown that the time of using parks in Hanoi is earlier in the day. In details, there is 25% and 1.4% of total daily visitors went to parks in Hanoi and Berlin,, respectively. However, the biggest peak in park-visiting time for both cities is in the afternoon. The findings also clarified that students and retirees are the major users even though there is some different in structures of park user among the four parks. The length of stay depends on how large and interesting a park is. In this aspect, Hanoi parks are very poor in facilities showing by a long list of missing facilities in the parks. However, as there is no alternative, parks in Hanoi still attract a high number of visitors. In general, results from this study have shown a close relationship among socio-economic and political situations in Vietnam with UGAs and its utilization. Influencing factors on parks’ utilization were also indentified, which are social changes, lifestyle changes, economic situation, conflicts in land usage, and maintaining cost for UGAs. Three given hypotheses were confirmed: i) the demand of public UGAs in inner Hanoi will grow mid-term and increase strongly long-term; ii) Hanoi’s residents will claim strongly for more parks in the future; ii) The number of conflicts inside the area of UGAs, among the visitors will occur very soon and require a specific master plan for the development and the management of UGAs. Finally, based on the weaknesses of UGAs in Hanoi recently, two groups of recommendations were also suggested to improve UGAs. Firstly, in terms of quality – quantity: • Retain each square meter of green space as UGA – do not unblock any green space for construction; • The existing UGA have to be well maintained. Secondly, in terms of management – planning: • Elaborate a UGA-masterplan for (inner) Hanoi; • Keep UGA management in the responsibility of public bodies; • Implement participation of affected population defector in the process of planning and management (as it has already been written in planning guidelines); • Be aware of potential conflicts among park user groups; • Establish an UGA monitoring system – involving regular (or even permanent) countings based on up-to-date technology; Realize horizontal partnering structures.
In this work, various aspects of fundamental physics and chemistry of molecular gas discharges are presented with emphasis on the interaction between species, activated by low-pressure plasmas, and surfaces. As already known, synergistic effects of multiple plasma-generated species are responsible for surface modification. However, due to the large number of internal parameters of a discharge and the complex plasma processes the identification of correlations between plasma characteristics and their effects on surfaces are complicated. Therefore, the aim of this thesis is to improve the understanding of several phenomena associated with plasma–surface interactions by measuring or calculating fundamental kinetic, transport or spectroscopic data needed to interpret measurements and hereby, to support some future applications of plasmas.
Musicians use different kinds of imagery. This review focuses on kinesthetic imagery, which has been shown to be an effective complement to actively playing an instrument. However, experience in actual movement performance seems to be a requirement for a recruitment of those brain areas representing movement ideation during imagery. An internal model of movement performance might be more differentiated when training has been more intense or simply performed more often. Therefore, with respect to kinesthetic imagery, these strategies are predominantly found in professional musicians. There are a few possible reasons as to why kinesthetic imagery is used in addition to active training; one example is the need for mental rehearsal of the technically most difficult passages. Another reason for mental practice is that mental rehearsal of the piece helps to improve performance if the instrument is not available for actual training as is the case for professional musicians when they are traveling to various appearances. Overall, mental imagery in musicians is not necessarily specific to motor, somatosensory, auditory, or visual aspects of imagery, but integrates them all. In particular, the audiomotor loop is highly important, since auditory aspects are crucial for guiding motor performance. All these aspects result in a distinctive representation map for the mental imagery of musical performance. This review summarizes behavioral data, and findings from functional brain imaging studies of mental imagery of musical performance.
The LINC (Linker of Nucleo- and Cytoskeleton) complex is an evolutionarily conserved complex of nuclear envelope (NE) proteins that forms a direct connection between the nucleoskeleton and cytoskeleton. Primarily, members of two protein families form the complex: SUN and giant nesprin isoforms that reside in the inner and outer nuclear membrane, respectively, thus forming a “bridge” across the NE. Lamin A/C and emerin are additional LINC complex components. Mutations in the genes encoding the LINC complex components have been associated with at least a dozen diseases, the majority of them muscular diseases. Emery-Dreifuss muscular dystrophy (EDMD), an inherited neuromuscular disorder with variable clinical presentation, is one of these diseases. But only around 46% of all EDMD patients are linked to a disease allele. Except of SUN1 and SUN2 all known LINC complex components had been associated with EDMD. Following a functional candidate gene approach the SUN1 and SUN2 genes were sequenced in a cohort of pseudoanonymized 175 EDMD patients without a known mutation and 70 patients with known causative mutations in other LINC components. Based on these results the pathomechanism causing the phenotype in patients with SUN1 or SUN2 mutations was investigated. Autosomal recessive inheritance was observed in one patient with compound heterozygous SUN1 mutations. Patient myoblasts showed defective protein interactions within the LINC complex, altered mRNA expression levels of some LINC components, an enhanced differentiation rate and defects in myonuclear organization. This provides first insights into a new pathomechanism based on weakening of the LINC complex and resulting in disruption of myonuclear alignment. In six patients with known EMD or LMNA mutations additional heterozygous SUN1 or SUN2 mutations modifying the disease have been identified, causing a significantly more severe course. Thus the modifying effect of SUN mutations found in the present study helps to explain the clinical intra- and interfamilial variability observed in EDMD. Further evidence for the influence of mutations in LINC complex components on the molecular pathology of muscular dystrophies comes from a study on primary fibroblasts of a patient suffering Duchenne muscular dystrophy (DMD) and of a patient showing signs of EDMD and Charcot-Marie-Tooth syndrome (CMT). The DMD patient had apart from a mutation in the DMD gene two variants in genes encoding the LINC components nesprin 1α2 and SUN1. The EDMD/CMT patient carried two variants in nesprin 1α1 and SUN2. Fibroblasts of both patients showed changes in cell adhesion, cell migration, senescence and stress response as well as characteristics typical for laminopathies like changes in nuclear shape and NE composition. Mutations in genes encoding LINC complex proteins are also associated with a number of other diseases. Pleiotropic LMNA mutations have also been linked with progeroid syndromes – genetic diseases that mimic clinical and molecular features of aging including Hutchinson Gilford progeria syndrome (HGPS), mandibuloacral dysplasia (MAD), restrictive dermopathy (RD) and atypical Werner’s syndrome (aWS) as well as a couple of overlapping phenotypes. MAD and RD can also be caused by mutations in ZMPSTE24, a gene encoding the ZMPSTE24 metalloproteinase necessary for the processing of prelamin A to mature lamin A. It is expected that insights into the pathomechanism of this group of diseases might provide clues to normal aging process. Analyzing RD and MAD patients for mutations in the ZMPSTE24 gene, some novel mutations have been identified. Based on this results and a review of the literature regarding ZMPSTE24 mutations could be shown that all mutations involved in RD are null mutations, whereas all patients with MAD are compound heterozygotes carrying one loss-of-function mutation and one missense mutation. This shows a clear genotype-phenotype correlation. A further part of this work is the description of the molecular genetics and functional background of a rare, unclassified progeroid syndrome. The clinical course of the affected patient appeared as an accelerated HGPS finally ending up in a delayed RD with overlapping clinical features of MAD. Mutational analysis revealed a homozygous LMNA mutation caused by a partial uniparental disomy of chromosome 1. Immunohistological analyses of tissue samples taken at the beginning and the end of the disease course showed a decreasing amount of lamin A and increasing amounts of DNA double strand breaks. Functional analysis in transfected human normal fibroblasts showed an impaired ability of the mutant lamin A to recruit 53BP1, a component of the DNA repair pathway, to damaged DNA sites. This case provides the first evidence of human lamin A direct involvement in DNA repair and that increased DNA damage is a major pathophysiological factor in progeroid laminopathies.
Metabolomics is the scientific study of metabolites of an organism, cell, or tissue. Metabolomics makes use of different analytical approaches. In this thesis, an analytical platform consisting of proton nuclear magnetic resonance spectroscopy (1H-NMR), gas chromatography-mass spectrometry (GC-MS, EI/quadrupol) and liquid chromatography-mass spectrometry (LC-MS, ESI/TOF) was used for metabolite analysis. Due to the high physicochemical diversity of metabolites, the usage of different analytics is profitable. Focusing on metabolome analysis of microorganisms, the development of viable protocols was prerequisite. To ensure metabolome samples of best possible quality, particularly the sampling procedure has to be optimized for each microorganism to be analyzed individually. In microbial metabolomics, the energy charge value is a commonly used parameter to assure high sample quality (Atkinson 1968). The pathogenic bacterium Staphylococcus aureus and the biotechnical relevant bacterium Bacillus subtilis were main target of research. The sampling protocol development “A protocol for the investigation of the intracellular Staphylococcus aureus metabolome” (Meyer et al. 2010) and “Methodological approaches to help unravel the intracellular metabolome of Bacillus subtilis”s (Meyer et al. 2013) confirmed the need for development and verification of viable protocols. It was observed, that minor differences in the sampling procedure can cause major differences in sample quality. Using the validated analytical platform and the optimized protocols, we were able to investigate the metabolome of S. aureus and B. subtilis under different conditions. Investigations of the pathogenic bacterium S. aureus are of major interest due to its increasing resistance to antibiotics. Methicillin (multi)-resistant S. aureus (MRSA) strains are responsible for several difficult-to-treat infections. The cell wall of bacteria is the target of an array of antibiotics, like the beta-lactam antibiotics. Our study “A metabolomic view of Staphylococcus aureus and Its Ser/Thr kinase and phosphatase deletion mutants: Involvement in cell wall biosynthesis” (Liebeke et al. 2010) revealed the influence of the serine-threonine kinase on cell wall biosynthesis of S. aureus. LC-MS based metabolome data uncovered prevalent wall teichoic acid precursors in the serine-threonine kinase deletion mutant (ΔpknB), and predominantly peptidoglycan precursors in the phosphatase deletion mutant (Δstp), compared to the S. aureus wild type strain 8325. This uncovered a so far undescribed importance of the serine-threonine kinase on the cell wall metabolism and provides new insights into its regulation. The nasopharynx and the human skin are often the ecological niche of S. aureus. Furthermore, S. aureus exists outside its host, for example on catheters. Depending on its niche, S. aureus is exposed to several stress factors and limitation conditions, such as carbon source limitation and starvation. To cope with the latter, a number of regulatory cellular processes take place. In “Life and death of proteins: a case study of glucose-starved Staphylococcus aureus” (Michalik et al. 2012) protein degradation during glucose starvation was monitored. An intriguing observation was that proteins involved in branch chain amino acid biosynthesis and purine nucleotide biosynthesis were distinctly down-regulated in the clpP mutant. This lead to the assumption of a stronger repression of CodY-dependent genes in the clpP mutant. Intracellular metabolome data revealed higher GTP concentrations in the clpP mutant. This may explain the higher CodY activity and thereby stronger repression of CodY-dependent genes in the clpP mutant. Since different S. aureus strains are known to colonize different niches, global carbon source (glucose, glucose 6-phosphate, glycerol, lactate, lactose and a mixture of all) and carbon source limitation dependent exo-metabolome analyses were performed using three different S. aureus strains (HG001: laboratory strain, EN493: human endocarditis isolate and RF122: bovine mastitis strain). The most apparent observation was that RF122 can utilize lactose best, while EN493 and HG001 are better at utilizing glucose-6-phosphate compared to the bovine RF122 strain. Bacillus subtilis is an extensively studied Gram-positive and non-pathogenic bacterium. In the functional genomics approach “System-wide temporal proteomics profiling in glucose-starved Bacillus subtilis” (Otto et al. 2010) growth phase dependent changes in the proteome, transcriptome and extracellular metabolome were monitored. By mass spectrometric analysis of five different cellular subfractions, ~ 52% of the predicted proteins could be identified. To confirm and complete the proteomic data transcriptome and extracellular metabolome analyses were performed. The extracellular metabolome data ensured that cells were glucose-starved and revealed growth phase dependent metabolic footprints. In “A time resolved metabolomics study: The influence of different carbon sources during growth and starvation of Bacillus subtilis” ((Meyer et al. 2013) submitted) four different compounded cultivation media were investigated as only glucose, glucose and malate, glucose and fumarate and glucose and citrate as carbon source. It could be shown, that B. subtilis is able to maintain an intracellular metabolite homeostasis independent of the available carbon source. On the other hand, in the exo-metabolome, carbon source as well as growth phase dependent differences were detected. Furthermore, in this study the influence of ATP and GTP on the activation of the alternative RNA polymerase sigma factor B (σB) was discussed. The concentration of ATP and GTP decreased for all conditions, as cells entered the stationary growth phase. While cell growth on solely glucose and during growth on glucose and additional malate, the ATP and GTP concentrations increased slightly when the consumption of the second carbon source was initiated. Only under these conditions, a considerable σB activity increase during the transition from exponential to stationary growth phase was observed. Furthermore, the developed sampling protocol for metabolome analysis of B. subtilis enabled us to be part of a “multi omics” system biological approach to study the physiological adjustment of B. subtilis to cope with osmotic stress under chemostat conditions.
The objective of the present investigation was to examine the residual antimicrobial activity after a topical exposure of reconstructed human epidermis (RHE) to equimolar solutions of either chlorhexidine digluconate (CHG, 0.144% w/v) or octenidine dihydrochloride (OCT, 0.1% w/v) for 15 min. RHE-associated antiseptic agents were more effective on Staphylococcus aureus than on Pseudomonas aeruginosa. S. aureus was not detected after 24 h of contact, which demonstrated a microbicidal efficacy of greater than 5-log<sub>10</sub> reduction. In contrast, P. aeruginosa was reduced by approximately 2 log<sub>10</sub> at the same incubation time, which parallels the growth of the initial inoculum. This result could be interpreted either as a microbiostatic effect or as an adherence of P. aeruginosa to a low positively charged surface. Small amounts of CHG and OCT can penetrate the stratum corneum. Using these antiseptic agents, the viability of keratinocytes was reduced to 65-75% of that of the untreated RHE control following 24 h incubation in the presence of test microorganisms. With consideration of antimicrobial activity and cytotoxic effect, OCT corresponds better to a biocompatible antiseptic agent than CHG.
The soil living, Gram-positive bacterium Bacillus subtilis is frequently exposed to a wide variety of stress and starvation conditions in its natural environment. In order to survive under these environmental and energy stresses, the bacterium acquired a general stress response mechanism mediated by the alternative sigma factor, SigB. A wide-variety of stress conditions such as environmental stress conditions like ethanol stress, heat stress, oxidative stress, osmotic stress or limitation of glucose, oxygen, phosphate etc.; and low temperature growth induce this SigB-dependent general stress response. Though much is known about the mechanisms of activation of this general stress response, the conditions that induce the SigB regulon and its general functions, the definition of the structure of the SigB regulon is not completely clear. The SigB-dependent general stress regulon has previously been characterized by proteomic approaches as well as DNA-array based expression studies. Genome-wide expression studies performed by Price, Petersohn and Helmann defined the SigB regulon containing well above 100 target genes, however the overlapping list of target genes contains only 67 members. The differences between these studies probably result from the different strains, growth conditions, array platforms and experimental setups used in these studies. The first part of this work presents a targeted microarray analysis, which was performed to gain a better understanding of the structure of the general stress regulon. This is the first study analyzing the gene expression of a wild type strain and its isogenic sigB mutant strain for almost all known SigB inducing conditions, using the same array platform. Furthermore, the kinetics of the gene expression of 252 putative SigB-dependent genes and 36 appropriate control genes were recorded. The data were analyzed using Random Forest, a machine-learning algorithm, by incorporating the knowledge of previous studies. Two Random Forest models were designed in this study. The “expression RF” model was designed to identify genes showing expression differences between wild type and sigB mutant and the “kinetic RF” model to identify genes having a SigB-dependent expression kinetic, but is subject to secondary regulators next to SigB influencing their expression in the sigB mutant. The random forest classification using the “expression RF” model identified 166 genes as SigB regulon members based on the expression differences between the wild type and the sigB mutant strain. A variable importance plot showing the impact during the classification process within the “expression RF” could assign a hierarchy to the stress conditions investigated in this study. This hierarchy suggested all the RsbU-dependent environmental stresses to have higher impact on SigB-dependent gene expression compared to the RsbP-dependent energy stresses. The “kinetic RF” model identified 30 additional genes, having additional regulators next to SigB. The SigB dependency of the 30 genes identified by the “kinetic RF” model was validated by screening for SigB promoter motifs within the upstream region of these genes. The hierarchical clustering of the obtained motifs scores with the expression ratios of the SigB regulon members predicted in the current work revealed that only a subset of genes displayed correlation of gene expression values and sequence motifs. As this observation is not true for all sets of genes, it cannot be generalized that gene expression is only correlated with the corresponding motif scores. In total 196 SigB regulon members could be classified by this targeted oligo nucleotide microarray study. The majority of these regulon members were preceded by a putative SigB promoter motif either identified previously or predicted in the current work. The inclusion of the broad range of stress conditions, from environmental stresses to energy limiting conditions enabled a more detailed characterization of the structure of the general stress regulon of B. subtilis. The implementation of machine learning algorithms allowed the prediction with a minimum number of false-positives. In the second part of this work a high resolution tiling array analysis for the majority of growth conditions, stresses and changes in carbon sources supply was exploited for the screening for new SigB targets within already annotated or newly annotated RNA features. Thereby 133 previously un-annotated RNA features, which were completely new, were assigned to the SigB regulon. 50 of these 133 new features encode antisense RNAs which can have potential influence on the transcription / translation of their sense RNAs targets. A set of 282 annotated genes were indentified to be SigB regulon members, comparison with the targeted oligo nucleotide study, 90 genes were newly identified and not known to be SigB-dependent before. The analysis of the expression levels of these genes by k-means clustering revealed a cluster of 32 genes having low induction levels in all SigB-inducing conditions, although the majority of these genes possess a well-conserved SigB promoter motif. However, all these genes are probably subject to the control of regulators other than SigB, which might mask the typical strong SigB-dependent induction in the analyzed stress conditions. The analysis of the expression levels of the SigB regulon under a variety of conditions, revealed the SigB-dependent expression in conditions such as growth on plates, in swarming cells, biofilm formation and growth on glycerol as a carbon source. The possible reason for the induction of the SigB regulon during growth on plates and in swarming cells was supposed to be due to scarcity of the nutrients on plates, e.g. glucose limitation. SigB-dependent genes were likely induced during growth on glycerol due to the oxygen limitation that arose during the growth. However, induction of the SigB regulon during biofilm formation is assumed to be due to the phosphate limitation. The description of these new SigB activating stimuli gains support from the fact that the majority of the SigB-dependent genes were induced under these growth conditions. In addition to the general stress response, B. subtilis cells have stress specific adaptive mechanisms such as osmotic response, which was addressed in the third part of this dissertation. The frequent flooding and drying of the soil triggered osmotic stress, one of the most common stress conditions encountered by soil bacteria. Bacterial cells are equipped with osmo-specific adaptation responses in which specific regulation of a set of genes is used to maintain proper cellular function. It was known from previous studies that a large set of genes were influenced in expression by salt shock as well as growth at high osmolarity. Detailed analysis of the tiling array data revealed 467 differentially regulated newly annotated features during salt shock and 251 newly annotated features that were expressed at a different level during continuous growth at high versus low osmolarity. A comparison of the studies that used the sigB knockout mutant with the tiling array study also provided support for the sigma factor competition in control of the expression of osmo-adaptive genes. The level of induction of specific osmo-adaptive genes was much higher in the sigB mutant strain compared to the wild type strain. Furthermore, the tiling array data revealed a SigB-dependent antisense RNA S1290 upstream of the opuB operon that transports choline to the cell. The presence of this antisense RNA had a potential impact on the transcription of the opuB operon, during salt shock. In agreement with the previous studies, the tiling array data assigned the osmotically regulated proHJ operon to the SigE regulon, with a SigE promoter upstream. In addition, the significantly higher percentage of proline among spore coat proteins also supports the assumption that osmotic synthesis of proline might play a role during the generation of spores. In conclusion, the tiling array data revealed newly annotated RNA features that are regulated during the general stress response as well as the osmotic response of the cell. The current work identifies new conditions that induce the majority of SigB-dependent genes as well as the new features that regulate the osmotically induced genes.
The absolute density of the metastable N2(A,v=0) molecule was extensively studied in nitrogen barrier discharges at 500 mbar. For the detection of the metastables laser-induced fluorescence spectroscopy (LIF) was used, at which for the calibration of the absoute metastables density a comparison with Rayleigh scattering was performed. To get the ratio of the LIF signal to the Rayleigh signal it is shown that the LIF signal is the convolution of the Rayleigh signal with an exponential decay. Besides, the different cross sections are calculated and the ratio of the detection sensitivities at the laser and fluorescence wavelength is determined. As a first step on the way to atmospheric pressure barrier discharges, the laser-induced fluorescence spectroscopy was implemented in low pressure capacitively coupled radio-frequency discharges. The determined metastables density in the capacitively coupled radio-frequency discharge is somewhat below 10^12 cm^(-3) at 40 Pa and somewhat below 10^13 cm^(-3) at 1000 Pa. The axial density profiles show a nearly symmetric shape due to the long lifetime of the metastable state. At a pressure of 500 mbar the two discharge modes of the barrier discharge, the filamentary and the diffuse mode, were analysed. The filamentary mode was mainly investigated in an asymmetric discharge configuration. Typical densities in the detection volume are in the range of 10^13 cm^(-3), resulting in maximal densities of up to 10^15 cm^(-3) in the microdischarge channel. Such large densities are in agreement with the fast decay by the pooling reaction after the maximum of the metastables density in the afterglow of the discharge pulse. The time dependent measurements in the afterglow of single microdischarges offer a delay of the metastables production with respect to the discharge current. This delay indicates that the metastables production takes place mostly by cascades from higher triplet states, which are in turn excited by electron impact. The axial density profiles show a maximum in metastables density in front of the anode in agreement with optical emission spectroscopy, but which cannot be clearly identified because of the asymmetric discharge configuration. The measurements for the diffuse discharge mode were performed in a symmetric discharge configuration. The metastables density is in the range of 10^13 cm^(-3). It increases during the current pulse of the discharge and decays afterwards. The maximum of the metastables density is delayed with respect to the maximum of the discharge current. The depletion of metastables in the early discharge afterglow is dominated by the pooling reaction, afterwards quenching by nitrogen atoms becomes important assuming a nitrogen atom density in the order of 10^14 cm^(-3). As for the filamentary mode, the losses by diffusion are negligible for the measurement positions. The measured axial density profiles show an accumulation of metastables in front of the anode, whereas the density in front of the cathode is below the detection limit. To calculate the metastables current density to the dielectrics after the discharge pulse a simulation is developed including the dominant volume processes for the depletion of metastables and the axial diffusion. Starting point for the simulation is the axial metastables density distribution at the end of the discharge pulse. The calculated metastables current density at the dielectrics is in the range of 10^14 cm^(-2)s^(-1). With the use of recently calculated secondary electron emission coefficients a comparison of the secondary electron emission by metastables with the discharge current is done. It is figured out that the secondary electron emission current is large enough to be important during the discharge ignition. To expand the simulation to the whole voltage cycle, the excitation of metastables is assumed to be proportional to the discharge current and electron density. Using this model, the measured time dependences of the metastables density are well reproduced for the investigated parameter variations. This is not the case for the axial profiles, where a metastables loss process is missed to explain the formation of a density plateau in front of the anode during the discharge pulse. The intended calculation of the metastables current density shows that the delay of the metastables production with respect to the discharge current might be responsible for the ignition of microdischarges at the beginning of the discharge pulse.