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Nano-size silver and copper clusters were produced with a DC magnetron-based gas aggregation source. The typical mass of the studied clusters was in the range of 10000 atoms for copper clusters, and in the range of 1000 atoms for silver clusters. The processes of cluster formation, cluster charging and cluster flow were investigated. Technique for measurement of cluster ion velocity distribution functions was developed and applied. Influence of the magnetron target erosion on the mass spectra was systematically investigated and quantitatively characterized. Results of the present work include an experimental and theoretical investigation of the effects, which are of great importance for the production of cluster beams with the desired properties.
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.
Background: Primary angiitis of the central nervous system (PACNS) is a rare but serious condition. A fraction of patients suffering from PACNS concurrently exhibit pronounced cerebral amyloid angiopathy (CAA) which is characterized by deposits of amyloid-β (Aβ) in and around the walls of small and medium-sized arteries of the brain. PACNS with CAA has been identified as a distinct disease entity, termed Aβ-related angiitis (ABRA). Evidence points to an immune reaction to vessel wall Aβ as the trigger of vasculitis. Objective: To investigate whether the inflammatory response to Aβ has (1) any effect on the status of immune activation in the brain parenchyma and (2) leads to clearance of Aβ from brain parenchyma. Methods: We studied immune activation and Aβ load by quantitative immunohistochemical analysis in brain parenchyma adjacent to affected vessels in 11 ABRA patients and 10 matched CAA controls. Results: ABRA patients showed significantly increased immune activation and decreased Aβ loads in the brain parenchyma adjacent to affected vessels. Conclusion: Our results are in line with the hypothesis of ABRA being the result of an excessive immune response to Aβ and show that this can lead to enhanced clearance of Aβ from the brain parenchyma by immune-mediated mechanisms.
There is a growing interest in the application of non-thermal atmospheric pressure plasma for the treatment of wounds. Due to the generation of various ROS and RNS, UV radiation and electric fields plasma is a very promising tool which can stimulate skin and immune cells. However, not much is known about the mammalian cell responses after plasma treatments on a molecular level. The present work focusses on the impact of plasma on cell signaling in the human keratinocyte cell line HaCaT by using the methods DNA microarray, qPCR, ELISA and flow cytometry. Here, cell signaling mediators such as cytokines and growth factors which could promote wound healing by enhancing angiogenesis, reepithelization, migration and proliferation were of major interest. Additionally, the crosstalk between keratinocytes and monocytes was studied using a co-culture. For the first time extensive investigations on the impact of plasma on cell signaling in human keratinocytes were conducted. The most prominent cytokines and growth factors which were regulated by plasma at gene and protein level were VEGF-A, GM-CSF, HB-EGF, IL-8, and IL-6. The latter was not activated due to the JAK/STAT-pathway but probably by a combined activation of MAPK- and PI3K/Akt-pathways. By the use of conditioned medium it was found out that ROS and RNS generated directly after plasma treatment induced larger effects on cell signaling in keratinocytes than the subsequently secreted growth factors and cytokines. Furthermore, monocytes and keratinocytes hardly altered their secretion profiles in co-culture. From these results it is deduced that the plasma generated reactive species are the main actors during cell signaling. In order to differentiate the impact of ROS and RNS on the cellular response the ambience of the plasma effluent was controlled, varying the ambient gas composition from pure nitrogen to pure oxygen. Thereby a first step towards the attribution of the cellular response to specific plasma generated reactive species was achieved. While IL-6 expression correlated with ROS generated by the plasma source, the cell signaling mediators VEGF-A, GM-CSF and HB-EGF were significantly changed by RONS. Above all hydrogen peroxide was found to play a dominant role for observed cell responses. In summary, plasma activates wound healing related cell signaling mediators as cytokines and growth factors in keratinocytes. It was also shown that the generated reactive species mainly induced cell signaling. For the first time cell responses can be correlated to ROS and RONS in plasma treated cells. These results underline the potential of non-thermal atmospheric pressure plasma sources for their applications in wound treatment.
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.
Lung dendritic cells facilitate extrapulmonary bacterial dissemination during pneumococcal pneumonia
(2013)
Streptococcus pneumoniae is a leading cause of bacterial pneumonia worldwide. Given the critical role of dendritic cells (DCs) in regulating and modulating the immune response to pathogens, we investigated here the role of DCs in S. pneumoniae lung infections. Using a well-established transgenic mouse line which allows the conditional transient depletion of DCs, we showed that ablation of DCs resulted in enhanced resistance to intranasal challenge with S. pneumoniae. DCs-depleted mice exhibited delayed bacterial systemic dissemination, significantly reduced bacterial loads in the infected organs and lower levels of serum inflammatory mediators than non-depleted animals. The increased resistance of DCs-depleted mice to S. pneumoniae was associated with a better capacity to restrict pneumococci extrapulmonary dissemination. Furthermore, we demonstrated that S. pneumoniae disseminated from the lungs into the regional lymph nodes in a cell-independent manner and that this direct way of dissemination was much more efficient in the presence of DCs. We also provide evidence that S. pneumoniae induces expression and activation of matrix metalloproteinase-9 (MMP-9) in cultured bone marrow-derived DCs. MMP-9 is a protease involved in the breakdown of extracellular matrix proteins and is critical for DC trafficking across extracellular matrix and basement membranes during the migration from the periphery to the lymph nodes. MMP-9 was also significantly up-regulated in the lungs of mice after intranasal infection with S. pneumoniae. Notably, the expression levels of MMP-9 in the infected lungs were significantly decreased after depletion of DCs suggesting the involvement of DCs in MMP-9 production during pneumococcal pneumonia. Thus, we propose that S. pneumoniae can exploit the DC-derived proteolysis to open tissue barriers thereby facilitating its own dissemination from the local site of infection.
Rich knowledge about global nutrient cycles and functional interactions can be gained from the perspective of complex microbial proteomes. In this thesis, the application of environmental proteomics allowed for a direct in situ analysis of habitat-specific proteomes expressed by respective microbial communities from two different marine ecosystems. In the first part of this thesis, unculturable symbiont populations from tubeworms that colonize hydrothermal vents of the Pacific deep sea became accessible by use of community proteomics. This branch of environmental proteomics is generally employed to ascertain simple microbial assemblages derived from in situ samples. The proteome study was aimed at analyzing adaptations of seemingly monospecific symbionts to different hosts, the tubeworms Tevnia jerichonana und Riftia pachyptila. A comparison of the newly sequenced genomes of symbiont populations from both hosts confirmed that both symbioses involve the same bacterial species. Also the proteome analysis by 2D-PAGE showed a high physiological homogeneity for symbionts from both worm species, although the hosts are exposed to different geochemical conditions. Thus, the hosts provide their symbionts with a relatively stable internal environment by attenuation of external influences. Only minor variations in the symbionts proteomes reflected the differential environmental conditions outside the worms. Hence, the symbionts were able to fine-tune major metabolic pathways and oxidative stress in response to only minor chemical changes within their hosts. Moreover, new components of important physiological processes of the bacterial symbionts, like the sulfide oxidation and carbon fixation, were identified by in-depth proteomics of the Riftia symbiosis model system. The in situ protein samples showed as well that, in contrast to an earlier hypothesis, nitrate is used as an alternative electron acceptor. In the second part of this thesis, another branch of environmental proteomics called metaproteomics was applied to investigate the response of a bacterioplankton community to a spring phytoplankton bloom in the North Sea. Recurrent plankton blooms are a common phenomen of coastal areas, which however has only been investigated with limited resolution in biodiversity. Based on large-scale proteomic data sets it was found that specialized populations of Bacteroidetes, Gammaproteobacteria and Alphaproteobacteria exhibited differential protein expression patterns. These involved oligomer transporters, glycoside hydrolases and phosphate acquisition proteins. A successive utilization of algal organic matter by microbes indicated a series of ecological niches occupied by the heterotrophic picoplankton. Key proteins, identified by metaproteomics, were further investigated by studying a model bacterium to define their specificities regarding the utilization of algal glycans. By isotope labeling of proteins, quantitative proteomics of the North Sea isolate Gramella forsetii KT0803, a Bacteroidetes representative could be conducted. The adaptation to the algal polysaccharides alginate and laminarin in comparison with glucose was analyzed. G. forsetii proved to be a specialist for the chosen algal polymers, in particular for glucans like laminarin. Primarily comprehensive clusters, the so-called polysaccharide utilization loci (PULs) were activated. The results of this model study complemented the basic concepts obtained by the metaproteomic approach about carbon cycling in coastal systems. The accessibility of numerous unculturable marine microbes by environmental proteomics allows to improve our understanding of interactions that drive symbioses or complex communities. Adaptations to environmental parameters, such as the abundance of substrates, can be analyzed and associated with respective populations. Thus statements can be made for functional groups of microorganisms, their ability for the creation of niches and their flexibility to respond to varying environmental impacts. The increasing number of marine model bacteria enables targeted analysis of specificities and adaptations and hence to support the environmental proteomics approach.
Inflammation is an adaptive response that is triggered by noxious stimuli and conditions, such as infection and tissue injury. Neutrophils, eosinophils, monocytes, tissue macrophages and dendritic cells can all ingest bacteria, tissues debris and apoptotic cells after injury or infection. These cells derived from bone marrow progenitors, circulate in the blood and migrate to peripheral tissues. Macrophages produce and secrete a cascade of pro-inflammatory and anti-inflammatory cytokines, such as interleukin-6 (IL-6), IL-10, and IL-12 that are trafficked and secreted by constitutive exocytosis. IL-10 and IL-6 are known to be rapidly induced during infection and / or injury, which make them possible mediators of early phagocyte recruitment. This thesis work aimed at detailed investigation of role of these cytokines in peritoneal inflammation. Under normal physiological conditions peritoneal cavity of normal BALB/c mice contains mainly CD45+ lymphocytes and CD11b+ myeloid cells with typical macrophage phenotype. The resident peritoneal cells play an important role in organismal homeostasis by taking part in innate and adaptive immunity. To explore this in detail, the physiological properties of peritoneal resident macrophage populations were studied under steady state and during inflammation conditions. Upon rapid induction of sterile inflammation by thioglycollate or lipopolysaccharide, the resident peritoneal cells could no longer be recovered in a peritoneal wash 6h after treatment. During ceacal content (CC) peritonitis, these cells were lost even more rapidly. Neutrophils, monocytes and lymphocytes replace the resident peritoneal phagocyte populations. During sepsis the absence of peritoneal macrophages decreases neutrophils recruitment to the inflammatory site and subsequently increases sepsis. Upon peritoneal wash cell transfer, total peritoneal cells could be recovered from the peritoneum of non infected mice, whereas these cells disappeared after CC infection in mice. The fate of resident peritoneal cells and their migration into lymphoid organs such as omentum and parathymic lymph nodes was further studied following induction of peritoneal infection. The CC infection induced lost cells from peritoneum were emigrated into omentum and parathymic lymph nodes but not in mesenteric lymph nodes. R1 cells were mostly observed in parathymic lymph nodes after 72h of infection but not after 1h, whereas, R2 cells were selectively observed in omentum just 1h after infection and 72h as well. These results were further confirmed by adoptive transfer showing emigration of R2 cells into omentum 1h after infection. Additionally, analysis of cytokine production after CC peritonitis showed early production of IL-10 and IL-6, which is in agreement with earlier findings and further supports the importance of these cytokines in phagocyte recruitment. The role of IL-10, IL-6 and other cytokines as possible mediators of early inflammation and in the recruitment of monocytes, neutrophils or eosinophils to the peritoneum during inflammation was determined by cytokine application. The intraperitoneal application of IL-10 recruited monocytes, neutrophils, T cells, B cells and eosinophils to the peritoneum. However, IL-10 knockout mice showed even increased recruitment of leucocytes to the peritoneal cavity in CC infection suggesting their IL-10 independent recruitment with the exception of eosinophils. Even though eosinophils are effector cells which are recruited to the site of inflammation; during homeostasis eosinophils constitute an abundant leukocyte population in the gastrointestinal tract. Therefore, possible role of eosinophils in bacterial infection was further studied using Δdbl GATA mice which lack mature eosinophils. In the absence of eosinophils, the monocyte and neutrophil recruitment was unaffected after CC infection, while there was increased T and B cell recruitment at the same time. The Δdbl GATA mice also showed reduced production of IL-4, 18h after infection. The eosinophils secrete IL 4 which may induce alternative macrophage activation. These results together with cytokine administration and IL-10 ko mouse data suggest a novel and major role of IL-10 in attracting and in recruiting eosinophils after peritoneal infection. Altogether, present thesis work demonstrates a new aspect of IL-10 interaction with eosinophils in mouse peritoneal environment during peritonitis. It gives a new insight for understanding the possible role of eosinophils in modulating the peritoneal environment in resolution of bacterial infection and can be useful in designing new approaches for therapeutic strategies in combating sepsis and peritoneal inflammation.
We introduce a multi-step machine learning approach and use it to classify data from EEG-based brain computer interfaces. This approach works very well for high-dimensional EEG data. First all features are divided into subgroups and linear discriminant analysis is used to obtain a score for each subgroup. Then it is applied to subgroups of the resulting scores. This procedure is iterated until there is only one score remaining and this one is used for classification. In this way we avoid estimation of the high-dimensional covariance matrix of all features. We investigate the classifification performance with special attention to the small sample size case. For the normal model, we study the asymptotic error rate when dimension p and sample size n tend to infinity. This indicates how to defifine the sizes of subgroups at each step. In addition we present a theoretical error bound for the spatio-temporal normal model with separable covariance matrix, which results in a recommendation on how subgroups should be formed for this kind of data. Finally some techniques, for example wavelets and independent component analysis, are used to extract features of some kind of EEG-based brain computer interface data.
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 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.
Background: This study aims to assess the role of ductoscopy for detecting intraductal anomalies in patients with nipple discharge in comparison to conventional tests and to find an effective combination of both approaches. Materials and Methods: Prior to duct excision, ductoscopy was performed in 97 women. Histologic and all other diagnostic results were compared. Sensitivity, specificity, and efficiency were calculated for all methods. These parameters were also calculated for all possible test combinations in 12 patients who had completed all tests. Results: Breast sonography reached the highest sensitivity (64.1%) and efficiency (64%); mammography had the highest specificity (100%). The sensitivity of ductoscopy was 53.2%, its specificity 60%, and its efficiency 55.1%. Among combinations of all methods, the combination ductoscopy + galactography was the most sensitive (80%). Mammography, magnetic resonance imaging, and ductoscopy were each 100% specific. Ductoscopy was the most efficient (75%) single method. Conclusion: Ductoscopy is a valuable test for diagnosing intraductal lesions in patients with nipple discharge. It is more efficient than conventional tests in patients undergoing all tests.
Abstract
We formulate exact generalized nonequilibrium fluctuation relations for the quantum mechanical harmonic oscillator coupled to multiple harmonic baths. Each of the different baths is prepared in its own individual (in general nonthermal) state. Starting from the exact solution for the oscillator dynamics we study fluctuations of the oscillator position as well as of the energy current through the oscillator under general nonequilibrium conditions. In particular, we formulate a fluctuation–dissipation relation for the oscillator position autocorrelation function that generalizes the standard result for the case of a single bath at thermal equilibrium. Moreover, we show that the generating function for the position operator fulfils a generalized Gallavotti–Cohen-like relation. For the energy transfer through the oscillator, we determine the average energy current together with the current fluctuations. Finally, we discuss the generalization of the cumulant generating function for the energy transfer to nonthermal bath preparations.
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.
The thesis describes experimental results based on optical diagnostics of low- pressure discharges. The models, which are necessary for the interpretation of the experimental data, are developed and simulations are done. The contents can be categorized into the following topics: 1) the time-resolved tunable diode laser absorption spectroscopy of excited states of argon in pulsed magnetron discharge and modeling the plasma afterglow; 2) optical emission- and laser absorption spectroscopy of excited states of argon in radio-frequency (rf) discharge and calculation of the escape factor for self-absorption; 3) fast video recording of the oscillatory motion of a dust particle in rf discharge and analysis of the data.
Bacteria are an integral part of modern biotechnology. They are used to make a variety of products, such as foods, drugs, as well as a multitude of chemicals. In order to increase their production rates molecular biotechnology offers many tuning points, starting from the selection of an applicable host, over its geno- and phenotypical characterization, followed by genetic manipulations for an optimized metabolism and stabilisation of production processes. This work comprises the optimization of Bacillus subtilis as an expression system. It describes the steps taken for selection and genomic characterization of the B. subtilis wild type strain ATCC 6051, the subsequent optimizations of the strain in respect to growth and productivity, as well as the characterization of its behaviour in a variety of cultivation conditions. The B. subtilis strain most commonly found in laboratories around the world is the first sequenced Gram-positive organism B. subtilis 168. Zeigler et al. showed that strain 168 is not a real wild type. Instead it was created through random mutagenesis with X-rays and selected for transformability. This strain has been used as the basis for popular B. subtilis strains in heterologous gene expression such as the extracellular protease deficient WB strains. Growth experiments showed the real wild type strain ATCC 6051 to be superior to its mutated ancestor 168, making it a solid basis for the construction of an optimized B. subtilis expression system. In order to gain a full understanding of the genomic and corresponding physiological differences between the two systems, B. subtilis ATCC 6051 was sequenced and compared to the genome of B. Subtilis 168. Several variations on geno- and phenotypic level could be revealed, that resulted in particular from genes involved in natural competency, the metabolism of amino acids and chemotaxis. This genomically well characterized B. subtilis ATCC 6051 was improved in respect to its application as an expression host. Improvements were achieved through the inactivation of both sporulation and reduction of autolysis, leading to a more robust behaviour during the overproduction and secretion of a reporter enzyme. A positive effect on the activity of an acetoin induced promoter by the addition of second copies for its transcription factors SigmaL and AcoR could be observed. Anaerobic zones and areas with excess glucose caused by insufficient mixing are common conditions in large scale bioprocesses and lead to oscillating conditions for the cells. In turn, this oscillation provokes an excretion of so called overflow metabolites, which can negatively affect the bacterial productivity. Detailed scientific characterizations of industrial scale processes under such oscillating conditions are scarce due to the high costs and logistics involved. A B. Subtilis sporulation mutant was thus examined in respect to its extra- and intracellular metabolites in a scale-down, two-compartment reactor giving hints about conditions the host is exposed to and how it reacts. To improve tolerance thresholds and utilization capacity for such metabolites in B. subtilis, the glyoxylate cycle was transferred from its close relative Bacillus licheniformis into the genome of B. subtilis. This feature enabled our B. subtilis ACE mutant to grow on acetate. The improved strain showed higher tolerance towards excess glucose in a fed-batch as well as higher productivity during the expression of a reporter enzyme in comparison to the wild type. The ACE strain and B. licheniformis showed an increased formation of glycolate during growth with the glyoxylate cycle. This with regard to bacteria undescribed metabolite seems to play a role as a by-product of the glyoxylate cycle. Summarizing, this thesis deals with the characterization and optimization of B. subtilis for growth on overflow metabolites, enhancements of the acoA-expression system and the influence of sporulation and lysis mutants on its activity. Complementary, the host was begun to be characterized in respect to its behaviour in industrial scale processes.
Purpose: The cyclin-dependent kinase (Cdk) inhibitor p27Kip1 may be involved in regulating re-entry of residual hepatocytes into the cell cycle upon loss of liver tissue by partial hepatectomy (PH). As yet, changes in Kip1 expression during the initial period following PH are not well-characterized. We investigated immediate changes in Kip1 mRNA and protein levels as well as changes in Kip1 phosphorylation in liver tissue within the relevant time window between surgery and the onset of DNA synthesis at 10–12 h.
Methods: We used real-time PCR, quantitative Western blotting, and immune histochemistry on tissue samples of adult rats obtained during or between 2 and 10 h after surgical removal of two thirds of the liver to analyze Kip1 mRNA or protein levels, respectively, or to quantify nuclear expression of Kip1.
Results: Kip1 mRNA was down-regulated within 4 h after PH by 60% and remained unchanged thereafter up to 10 h. With a lag phase of 2–3 h, Kip1-protein was down-regulated to a level of 40% of the control. The level of Thr187-phosphorylated Kip1 started to increase at 4 h and reached a maximum level at 8–10 h after PH. Kip1 immunoreactivity was observed in 30% of the hepatocytes before PH. Within 6–8 h after PH, more than half of the hepatocytes lost nuclear Kip1 signals. Kip1-specific micro-RNAs (miRNA221, miRNA222) were not changed upon PH.
Conclusions: A portion of hepatocytes in adult rats constitutively express Kip1 and down-regulate Kip1 immediately upon PH. This response involves transcriptional processes (loss of Kip1 mRNA) as well as accelerated degradation of existing protein (increase in pThr187-phosphorylation mediating polyubiquitinylation and proteasomal degradation of Kip1). Kip1 down-regulation occurs precisely within the intervall between surgery and onset of DNA synthesis which supports the hypothesis that it mediates activation of G0/0S-phase Cdk/cyclin-complexes and re-entry of hepatocytes into the cell cycle.
Abstract
The surface charge distribution deposited by the effluent of a dielectric barrier discharge driven atmospheric pressure plasma jet on a dielectric surface has been studied. For the first time, the deposition of charge was observed phase resolved. It takes place in either one or two events in each half cycle of the driving voltage. The charge transfer could also be detected in the electrode current of the jet. The periodic change of surface charge polarity has been found to correspond well with the appearance of ionized channels left behind by guided streamers (bullets) that have been identified in similar experimental situations. The distribution of negative surface charge turned out to be significantly broader than for positive charge. With increasing distance of the jet nozzle from the target surface, the charge transfer decreases until finally the effluent loses contact and the charge transfer stops.
The development of innovative coatings with multifunctional properties is an ambitious task in modification of material surfaces. A novel approach is a hybrid method combining the non-thermal plasma processing with nanotechnology for the development of multifunctional surface coatings. The conception of the hybrid coating process is based on three steps: the preparation of a suspension consisting of an organic liquid and functional nanoparticles, the deposition of the suspension as a thin liquid film on the material surface, and the plasma modification of the liquid organic film to achieve a thin solid composite film with embedded nanoparticles demonstrating multifunctional properties and good adherence on the substrate material. In this work the liquid polydimethylsiloxane (PDMS) was applied as a model system, and the experimental investigations were focused on the PDMS plasma modification. In particular, the specific role of the different plasma components and the influence of the plasma and processing parameters on the PDMS modification were studied. The applied capacitively coupled radio frequency (CCRF) plasma was analyzed by electric probe measurements and optical emission spectroscopy, whereas the molecular changes in PDMS due to plasma-induced chemical reactions were studied by the Fourier transform infrared reflection absorption spectroscopy. Additionally, the photocatalytic activity of thin composite films consisting of plasma cross-linked PDMS with embedded TiO2 nanoparticles was demonstrated. During the investigation it was found that the CCRF discharge modifies efficiently thin liquid PDMS films to solid coatings. The samples were positioned in the plasma bulk at floating potential. The penetration depth of particles like neutrals, ions, electrons and radicals in the film is strongly limited. The heating of samples in the CCRF discharge is weak to modify PDMS by itself and only the plasma radiation is able to transform the liquid bulk to solid one. It is known that the absorption onset of PDMS lies in the VUV region (below 200 nm). The energetic VUV radiation penetrates into the PDMS film on a thickness from several hundred nanometers to few micrometers and initiates photochemical reactions there. Thus, different gases like Ar, Xe, O2, H2O, air and H2 were tested to provide the strongest VUV emission intensity of the CCRF discharge. Discharge pressure and power were varied for all these gases and it was found that at all conditions the H2 plasma demonstrates drastically stronger emission. Thus, H2 gas was selected for the plasma treatment of liquid PDMS films. The IRRAS analysis revealed the transformation process of PDMS with the degradation of CH3 groups, the formation of new groups like SiOH, CH2 and SiH, the formation of the SiOx material and crosslinking. It was found that the modification effect is not uniform across the film thickness. The top region with an initial thickness up to 100 nm loses all CH3 groups, in the underlying region the CH3 concentration increases gradually from zero to the value for PDMS, if the film was thick enough. The methyl-free SiOx top layer contains also SiOH and SiH groups. Furthermore, the SiH groups are concentrated only in a very thin layer with a thickness below 10 nm. The presence of the unscreened polar SiOSi and SiOH groups on the surface causes the adsorption of H2O from the atmosphere, which was also observed by IRRAS. By means of the spectroscopic ellipsometry it was found out that all above described regions experience a shrinking. The reason is the crosslinking and loss of material. The most shrunken layer is the top SiOx layer with the shrinking ratio (final thickness/initial thickness) of 0.55 - 0.60. Further, this ratio gradually rise up to the value of 0.95 in the deeper region, which has the concentration of CH3 groups of about that for PDMS. After the analysis of all results the depth of effective modification was estimated at 300 400 nm for the most optimal conditions. The optimization of the plasma VUV intensity was realized by variation of discharge pressure and power. The strongest plasma emission at studied conditions provided the irradiance of the sample of ca. 13 mW/cm2. However, such strong radiation causes very strong production rate of the gases. These products leave the modifying film slower as they are produced, what causes their accumulation in there. Their pressure grows up leading to formation of bubbles, which later explode. Finally, the film becomes heavily damaged. To avoid this effect the pressure and the RF power were changed to reduce the irradiance to 6 - 7 mW/cm2. This resulted in the absence of any damages.
Prediction of high caries increment in adults – a 5-year longitudinal study from North-East Germany
(2013)
The aim of this study is to develop an easily applicable prediction model for high coronal caries increment in adults (20-79 years) from a representative sample (N=2,565) to identify a high risk-group for specific caries prevention. The data from SHIP-0 (1997-2001) and the 5-year follow-up SHIP-1 (2002-2006) is used for analyses. The oral health examination was conducted according to WHO criteria [1997]. The drop-out analysis reveals that drop-outs are significantly older, have a lower school education, are more frequently current smokers, but have a better self-perception of their teeth. The majority of the study-population (76%) has caries incidence in this 5-year period. Caries increment shows a polarized distribution, as the high caries increment group (≥9 surfaces in half-mouth, 11.4% of the sample) comprise 40% of the total increment. The variables male gender, age ≥40 years, lower school education or lower income, current smoking, pain-associated dental visit, baseline caries experience and a non-satisfying self-perception of teeth show a statistically significant influence on high caries increment. The prediction model allows a fair to good prediction on an epidemiological level for men (AUC=0.75). The factors smoking, school education and pain-associated visit only have a significant impact on the prediction of high caries increment in men. Due to very high caries prevalence and increment a population-based prevention in adults should be optimized first, before risk-group specific preventive programmes might be implemented.