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Genomics is the field of modern biology that studies the genome as the sum of all genes of a given organism. Genomics includes the analysis of genomic variations in order to identify genetic susceptibility loci for various human diseases. Besides genomics, there are related fields summarized by the term "Omics" such as transcriptomics and proteomics, studying the sum of all transcripts and proteins in a defined biological system, respectively. Genetic variants, namely single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) are used to identify genomic loci associated with human traits and diseases. Genome-wide association studies (GWASs) based on SNP data have been performed for a wide range of human traits and diseases. In the population-based Study of Health in Pomerania (SHIP) and the independent SHIP-TREND study, whole-genome genotyping data were available for 4081 and 986 individuals, respectively. In contrast to the widely used GWAS based on SNPs, association studies using CNV data are difficult to implement and thus less common. Therefore, one aim of this work was to detect CNVs using the whole-genome genotyping data available for 4081 individuals from SHIP. Another aim was to develop an efficient workflow for the analysis of these CNVs. As most common genetic variants exhibit only relatively small effects on phenotypic variability, large sample sizes are needed to maximize the statistical power to detect such effects. Therefore, the integration of data from multiple collaborating studies is indispensable. In this context, several CNV studies with the SHIP data have been performed and published, for example on body mass index (BMI) phenotypes where the SHIP cohort was used as a population-based control. Trait-associated genetic markers identified through GWASs are often intergenic or synonymous coding, and those loci identified through whole-genome CNV analyses often contain multiple genes, making it difficult to identify the causal variants. In this context, the functional analysis of identified loci aids in determining causal variant(s). One possibility to conduct functional analysis is the expression quantitative trait loci (eQTL) analysis, defined as the association of genome-wide genotyping data with genome-wide gene expression data based on measured transcriptomes. This allows the identification of genetic variants influencing the expression levels of defined genes. A further example are transcriptome-wide association analysis (TWAS), defined as the association of phenotype data with whole-genome expression data. Thus, another aim of this work was to establish an analysis pipeline for processing such expression data, which were available for about 1000 individuals from the SHIP-TREND study. Here, array-based gene expression data were generated using RNA prepared from whole-blood. Interpretation of TWAS results is often difficult, because of possible reverse causation on gene expression data. Furthermore, technical errors of measurement may bias the results. In a comprehensive work, biological and technical factors influencing measured gene expression data have been identified and were subsequently taken into account to improve the association analyses. To further elucidate the molecular mechanisms underlying the relationship of gene expression levels with human traits or diseases, pathway analyses using the Ingenuity Pathway Analysis (IPA) tool have been performed in connection with the TWAS. As for GWASs, the associations identified in TWAS usually exhibit only small effect sizes, highlighting the need for larger studies or meta-analysis to identify all susceptibility variants. In this context several eQTL- and TWAS meta-analyses using the SHIP-TREND data have been performed, for example on the phenotypes age, sex, BMI, smoking status and serum lipid traits. The results of these analyses are in preparation for publication and the most advanced example, the correlation of expression data with BMI, is presented here. The integration of whole-genome genotyping and expression data provides new functional information of the underlying biological mechanisms of complex human traits and diseases. Within the frame of this work, this could be demonstrated for the example of susceptibility to Helicobacter pylori infection.
The focus of the first two articles was the engineering and application of enzymes for the conversion of the bio-based resources glycerol and its oxidation product glyceraldehyde for the production of the value added product glyceric acid. Article III focuses on the cloning, exploration and engineering of a polyol dehydrogenase, which later on was used as cofactor recycling system in order to produce ε-caprolactone from cyclohexanol as presented in arti-cle IV. The following paragraphs will give a short outline of each article. ARTICLE I: ASYMMETRIC SYNTHESIS OF D-GLYCERIC ACID BY AN ALDITOL OXIDASE AND DIRECTED EVOLUTION FOR ENHANCED OXIDATIVE ACTIVITY TOWARDS GLYCEROL. GERSTENBRUCH, S., WULF, H., MUßMANN, N., O’CONNELL, T., MAURER, K.-H. & BORNSCHEUER, U. T. (2012). Appl. Microbiol. Biotechnol. 96, 1243-1252. The alditol oxidase of Streptomyces coelicolor A3(2) (AldO) was used to catalyze the oxida-tion of glycerol to glyceraldehyde and glyceric acid. The enantioselectivity for the FAD-de-pendent glycerol oxidation was elucidated and different strategies were used to enhance the substrate specificity towards glycerol. Directed evolution by error-prone PCR led to an AldO double mutant with 1.5-fold improved activity for glycerol. Further improvement of activity was achieved by combination of mutations, leading to a quadruple mutant with 2.4-fold higher specific activity towards glycerol compared to the wild-type enzyme. In small-scale biotransformation concentrations up to 2.0 g•l-1 D-glyceric acid could be reached using whole cells. Investi¬gation of the effects of the introduced mutations led to a further identification of es¬sential amino acids with respect to enzyme functionality and structural stability. ARTICLE II: KINETIC RESOLUTION OF GLYCERALDEHYDE USING AN ALDEHYDE DEHYDROGENASE FROM DEINOCOCCUS GEOTHERMALIS DSM 11300 COMBINED WITH ELECTROCHEMICAL COFACTOR RECYCLING. WULF, H., PERZBORN, M., SIEVERS, G., SCHOLZ, F. & BORNSCHEUER, U. T. (2012). J. Mol. Catal. B Enzym. 74, 144-150. Two aldehyde dehydrogenases (ALDH) from Escherichia coli BL21 and Deinococcus geother-malis were cloned, characterized and evaluated according to their applicability for a bio-catalysis setup with electrolytic cofactor recycling. Both ALDHs turned out to have a sim¬ilar substrate scope and favor short to medium chain aldehydes and both oxidize glyceralde¬hyde to D-glyceric acid. The ALDH variant of D. geothermalis shows higher specific activity towards glyceraldehyde and has an elevated optimum temperature compared to the BL21 enzyme. Due to the higher specific activity of the ALDH of D. geothermalis, this enzyme was used to conduct a kinetic resolution of glyceraldehyde with electrolytic NAD+ recycling at a glassy carbon foam electrode with ABTS as redox mediator yielding in 1.8 g•l-1 glyceric acid. ARTICLE III: PROTEIN ENGINEERING OF A THERMOSTABLE POLYOL DEHYDROGENASE. WULF, H.*, MALLIN, H.*, BORNSCHEUER U.T. (2012). Enzyme Microb. Technol. 51, 217-224 (*equally contributed). The new enzyme polyol dehydrogenase PDH-11300 from D. geothermalis was extensively characterized regarding its temperature optimum and thermostability. A peptide stretch responsible for substrate recognition from the PDH-11300 was substituted by this particular stretch of a homolog enzyme, the galactitol dehydrogenase from Rhodobacter sphaeroides (PDH-158), resulting in a chimeric enzyme (PDH-loop). The substrate scopes were deter-mined and basically the chimeric enzyme represented the average of both wild-type en-zymes. A rather unexpected finding was the notably increased T5060, by 7°C to 55.3°C, and an increased specific activity against cyclohexanol. Finally, the cofactor specificity was suc¬cess-fully altered from NADH to NADPH by an Asp55Asn mutation, which is located at the NAD+ binding cleft, without influencing the catalytic properties of the dehydrogenase. ARTICLE IV: A SELF-SUFFICIENT BAEYER-VILLIGER BIOCATALYSIS SYSTEM FOR THE SYNTHESIS OF Ɛ-CAPROLACTONE FROM CYCLOHEXANOL. MALLIN, H. *, WULF, H. *, BORNSCHEUER U.T. (2013). Enzyme Microb. Technol., online, DOI: 10.1016/j.enzmictec.2013.01.007 (*equally contributed). The application of the engineered PDH-loopN mutant [1] (Article III) for the production of ε-caprolactone from cyclohexanol was investigated in a co-immobilization approach with the cyclohexanone monooxygenase from Acinetobacter calcoaceticus. Biotransformation with solubilized enzymes led to an isolated yield of 55% pure ε-caprolactone with no residual cy-clohexanol to be detected. During the immobilization experiments a higher enzyme ratio in favor of the CHMO led to higher reaction velocities. Similarly, the addition of soluble fresh CHMO during reuse of co-immobilization batches significantly increased the activity identi-fying the CHMO as the bottleneck in this reaction setup.
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.
This thesis aims at improving the current representation of adaptation in economic frameworks of climate change by a) accounting for the time-dependent evolution of the adaptive capacities of countries and b) quantifying unwelcome feedbacks of the adaptation process. In this context, it is proposed that economic assessments of climate change incorporate adaptation as a cyclic and phase-dependent process while devising their cost methodologies. A phase-dependent process acknowledges the existence of adaptation barriers while a cyclic process accounts for potential unwanted feedbacks of adaptation. By analyzing economic assessments against this framework, it is shown that dependencies between phases of adaptation and phases altogether are often disregarded. Furthermore, potential negative consequences associated with adaptation are rarely considered and adaptation is generally assumed to be unconstrained. The assumption of unconstrained adaptation is only acceptable in the context of high adaptive capacity. This concept was further investigated through a review of vulnerability assessments regarding their operation of the adaptive capacity component. It was found that adaptive capacity is mostly equated to proxies that reflect the knowledge, financial and livelihood capacities of the system under analysis. With this theoretical considerations in mind, a dynamic representation of adaptive capacity was elaborated at a country-level. The Human Development Index (HDI) was used as a proxy of the adaptive capacity of countries and its evolution in time extrapolated. The time required for countries to achieve developed world standards of human development was then estimated. The results indicate that between 2005 and 2020, half of the world population will live in countries with low adaptive capacity. This percentage is then progressively reduced to 15% in the year 2050, with marked regional differences. The time required for a country to achieve an appropriate level of development sets a clear constraint on when, and to what extent, the country can engage on climate change adaptation. This does not imply that adaptation will not take place before development occurs. Rather, it calls for adaptation options to be tailored in order to t the current and future adaptive capacities of countries. Obtaining higher levels of adaptive capacity is likely to be associated with negative consequences for the climatic system. The statistical relation between HDI and per-capita emissions of countries was established and future projections made. Between 2010 and 2050 approx. 300 Gt of CO2 are estimated to be associated with the increase of adaptive capacities of current developing countries. This value represents about 30% of the allowed CO2-budgets to restrict global temperatures to an increase of 2 degrees by 2100 compared to pre-industrial times - conditional to a 25% risk of failing to meet the target. For the case of sea-level rise, the modelling framework DIVA (Dynamic Interactive Vulnerability Assessment) was used in order to illustrate the drawbacks of a simplistic representation of adaptation. The results show that adaptation via the construction of protective infrastructure might be economically feasible for particular countries. For others, modeled results fail to provide a clear choice between adaptation or inaction. The assumption of unconstrained adaptation resulted in the valuation of costly protection options whose financial and knowledge requirements can be at odds with the capacities of some coastal countries - namely developing countries. Further, infrastructural protection as adaptive measure to prevent coastal damages can have the counter-productive effect of raising the amount and value of assets at risk. This is a direct result of DIVA disregarding the potential unwelcome feedbacks of adaptation itself. In conclusion, the full potential of economic assessments of climate adaptation is likely to remain unlocked as long as adaptation continues to be misrepresented. The methodologies discussed in this work provide a way forward to alleviate this deficiency in forthcoming assessments. For the case of sea-level rise, the modeling framework DIVA (Dynamic Interactive Vulnerability Assessment) was used in order to illustrate the drawbacks of a simplistic representation of adaptation. The results show that adaptation via the construction of protective infrastructure might be economically feasible for particular countries. For others, modeled results fail to provide a clear choice between adaptation or inaction. The assumption of unconstrained adaptation resulted in the valuation of costly protection options whose financial and knowledge requirements can be at odds with the capacities of some coastal countries - namely developing countries. Further, infrastructural protection as adaptive measure to prevent coastal damages can have the counter-productive effect of raising the amount and value of assets at risk. This is a direct result of DIVA disregarding the potential unwelcome feedbacks of adaptation itself. In conclusion, the full potential of economic assessments of climate adaptation is likely to remain unlocked as long as adaptation continues to be misrepresented. The methodologies discussed in this work provide a way forward to alleviate this deficiency in forthcoming assessments.
In terms of climate change and climate change mitigation, the quantitative knowledge of global carbon pools is important information. On the one hand, knowledge on the amount of carbon cycling among – and stored in – global pools (i.e. Atmosphere, Biosphere, Cryosphere, Hydrosphere, and Lithosphere) may improve the reliability of models predicting atmospheric CO2 concentrations in terms of fossil fuel combustion. On the other hand, the carbon sequestration potential of specific ecosystems allows for estimating their feasibility regarding carbon trade mechanisms such as the Clean Development Mechanism or the Reducing Emissions from Deforestation and Degradation Program (REDD+). However, up to date, the majority of terrestrial carbon assessments have focused on forests and peatlands, leaving a data gap open regarding the remaining ecosystems. This data gap is likely to be explained by the relatively high carbon densities and/or productivities of forests and peatlands. Nevertheless, to get a precise as possible global picture, information on carbon pools and sequestration of other ecosystems is needed. Although desert ecosystems generally express low carbon densities, they may absolutely store a remarkable amount of carbon due to their large areal extent. In this context, Central Asian Deserts (in particular within the Turanian Deserts, i.e. Karakum, Kysylkum, Muyunkum) likely inhibit comparably high carbon pools as they express a sparse vegetation cover due to an exceptionally high annual precipitation if compared to the World’s deserts. In this dissertation, three important woody plant species – Populus euphratica and Haloxylon aphyllum and Haloxylon persicum – of Central Asian Deserts were investigated for their carbon pools and carbon sequestration potential. These species were chosen as they I) locally express high carbon densities, II) are dominant species, III) have a rather large spatial distribution, and IV) have experienced a strong degradation throughout the 20th century. Thus, they likely show a remarkable potential for carbon re-sequestration through restoration and thus for an application of carbon trade mechanisms (CHAPTER I). P. euphratica was investigated in the nature reserve Kabakly at the Amu Darya, Turkmenistan and in Iminqak at the Tarim He, Xinjiang, China. The assessment of Haloxylon species was restricted to the Turanian deserts west of the Tain Shan. To achieve a first scientific basis for large scale estimates, different methodologies, ranging from allometric formulas, over dendrochronology to remote sensing were combined (CHAPTERS II-V). In CHAPTER II allometric formulas were successfully developed for Haloxylon aphyllum and Haloxylon persicum and applied to six study sites distributed over the Turanian Deserts to represent the allometric variability of Haloxylon species in Central Asia. CHAPTER III derives another allometric formula (only based on canopy area) for H. aphyllum and combines it with a remote sensing analysis from the nature reserve Repetek. Thereby, a first large scale estimate covering the Northeastern Karakum Desert of carbon pools related to mono specific H. aphyllum stands is achieved. CHAPTER IV describes the wood structure of Populus euphratica forests in the nature reserve Kabakly (Turkmenistan) and in Iminqak (Xinjiang, China). In CHAPTER V a dendrochronological approach derives models for predicting the Net Primary Productivity (NPP) and the age of P. euphratica in the nature reserve Kabakly. Thereby, a first feasibility assessment regarding remote sensing analyses and the upscaling of the obtained NPP results is carried out. First estimates based on these local studies (CHAPTER VI), reveal carbon densities ranging from 0.1 – 26.3 t C ha 1 for the three investigated species. Highest maximum and median carbon densities were found for P. euphratica, but Haloxylon aphyllum expressed remarkable maximum carbon densities (13.1 t C ha-1), too. The total carbon pools were estimated at 6480 kt C for P. euphratica, 520 kt C for H. aphyllum stands and 6900 kt C for Haloxylon persicum shrubland. Accounting for the extent of degraded areas, the total re-sequestration potentials of the respective species were estimated at 4320 kt C, 1620 kt C and 21900 kt C, this highlighting the remarkable absolute re-sequestration potential of H. persicum shrubland despite its low average carbon densities. In the end, the main results were put into a broader context (CHAPTER VI), discussing the general feasibility of reforestations both in ecological terms as well as in terms of carbon trade mechanisms. A short example highlights the strong connection between the feasibility of reforestations and the global carbon market. Finally, open research questions are brought forth revealing the yet large research potential of Central Asian Desert ecosystems in general and in terms of carbon sequestration.
Objective: The purpose of this study was to determine the accuracy and reliability of Frankfort horizontal plane identification using displays of multi-planar reconstructed MRI images, and propose it as a sufficiently stable and standardized reference plane for craniofacial structures Materials and Methods: MRI images of 43 adolescent randomly selected subjects were obtained from the longitudinal population based cohort study SHIP-2 using a T1-weighted 3D sequence. Five examiners independently identified the three landmarks that form FH plane. Intra-examiner reproducibility and inter-examiner reliability, correlation coefficients (ICC), coefficient of variability and Bland-Altman plots were obtained for all landmarks coordinates to assess reproducibility. Intra-examiner reproducibility and inter-examiner reliability in terms of location and plane angulation were also assessed. Results: Intra- and inter-examiner reliabilities for X, Y and Z coordinates of all three landmarks were excellent with ICC values ranging from 0.914 to 0.998. Differences among examiners were more in X and Z than in Y dimensions. The Bland–Altman analysis demonstrated excellent intra- as well as inter-examiner agreement between examiners in all coordinates for all landmarks. Intra-examiner reproducibility and inter-examiner reliability of the three landmarks in terms of distance showed mean differences between 1.3 to 2.9 mm, Mean differences in plane angulation were between 1.0° to 1.5° among examiners. Conclusion: This study revealed excellent intra-examiner and inter-examiner reproducibility of Frankfort Horizontal plane through 3D landmark identification in MRI. Sufficiently stable landmark-based reference plane could be used for different treatments and studies.
Aim: To evaluate the association of Insulin-like Growth Factor (IGF) I related variables with periodontitis in the population-based Study of Health in Pomerania (SHIP). Material and Methods: From the cross-sectional SHIP, 2293 subjects with clinical attachment loss (CAL) data and 2398 subjects with tooth count data aged 20-59 years were analysed. Serum IGF-I and IGF binding protein (BP)-3 levels were determined by chemiluminescence immunoassays. Linear and logistic regressions with fractional polynomials were used to study associations between IGF-related variables and mean CAL or high tooth loss. For non-linear relations between IGFBP-3 and mean CAL, graphical presentations of fractional polynomials were used to deduce knots for linear splines. Results: In fully adjusted models, for serum IGFBP-3 values ≤1200 ng/mL, mean CAL increased significantly for decreasing serum IGFBP-3 levels (B=-0.027 (95% CI, -0.049; -0.005), p=0.02). The odds for high tooth loss decreased significantly for high serum IGFBP-3 values (OR=0.97 (0.95; 0.99), p=0.02). Serum IGF-I levels and the IGF-I/IGFBP-3 ratio were not related to mean CAL or tooth loss after full adjustment. Conclusions: Low serum IGFBP-3 levels might be associated with higher levels of periodontal disease. Neither serum IGF-I nor IGF-I/IGFBP-3 ratios were associated with periodontitis.
Until now proximal caries is still a significant problem in the clinical dentistry in spite of the caries decline recently. As resin infiltration offers a new micro-invasive treatment to arrest the progression of proximal initial carious lesions, this study aimed to evaluate its clinical applicability, safety and effect. In the study population of 50 children, adolescents and young adults (mean age 17.9 years ± 6.8), ten dentists at University of Greifswald applied the infiltration material ICON® (DMG, Germany) on non-cavitated proximal lesions in permanent and primary teeth as described in the manual instructions from the producer. The results showed good patient satisfaction with the procedure. The time for the infiltration (24.3 min ± 7.4), which included rubber dam application (7.7 min ± 4), and the effort were perceived as comparable to a composite filling by the dentist or as even easier. In three patients (6%), it was not possible to gain sufficient proximal space for the application of an infiltration. The location of the infiltrated tooth, separation problems as well as the routine of the dentists with the infiltration technique had an effect on the duration of the infiltration. A clear learning curve with a reduction of treatment time for subsequent treatments was observed (P < 0.001). Within the follow-up interval of 12 months, vitality of all infiltrated teeth was still positive and no relevant differences in plaque accumulation or gingival status were recorded. In addition, the infiltrated surfaces showed smooth margins and considerable decrease in the discoloration. In the radiographic evaluation after one year, only two lesions (4.7%) have progressed. Thus, caries infiltration is an applicable method for the treatment of initial non-cavitated proximal lesions without prior temporary tooth separation. Even without special training it can be applied easily by dentist and they experience a clear learning curve within the first 5-10 applications. In addition, the infiltration technique shows a high acceptance by the patients. Furthermore, caries infiltration lead to very good results regarding safety and preventing the lesion progression of non-cavitated proximal caries lesions located in the enamel or in the outer third of dentin.
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.
Gout was described by Hippocrates in the 5th century BC as a disease of rich people and linked with excess food and alcohol. It is caused by long-lasting hyperuricemia, which is a result of an imbalance between excretion and production of uric acid. The surplus of uric acid leads to deposition of monosodium urate crystals in the joints, which can initiate a painful inflammation called a gout attack. Despite various pharmacological treatments for this disease, a low purine diet remains the basis of all gout therapies. Since food is rich in purines, the aim of this project was to develop a novel enzyme system to decrease the purine content of food, what should result in reduced serum urate concentration in patients with hyperuricemia. The system consists of five degrading enzymes (adenine deaminase, guanine deaminase, xanthine oxidoreductase, urate oxidase and purine nucleoside phosphorylase) that combined in one product are able to hydrolyse all purines to a highly soluble allantoin, which can be easily removed from the body. This approach provides the patients a possibility to reduce the symptoms and frequency of gout attacks or even doses of prescribed drugs. In order to obtain necessary system components, yeast Arxula adeninivorans LS3 was screened for enzyme activities. A. adeninivorans is known to utilise various purines and this ability is a result of activity of desired enzymes, two of which, adenine deaminase and xanthine oxidoreductase, are in focus of this thesis. The analysis of growth of A. adeninivorans on various carbon and nitrogen sources gave the first insight into the cells’ nutrient preferences indicating the presence of purine degrading enzymes, such as adenine deaminase and xanthine oxidoreductase. Purines, such as adenine and hypoxanthine, could be utilised by this yeast as sole carbon and nitrogen sources and were shown to trigger the gene expression of the purine degradation pathway. Enzyme activity tests and quantitative real-time PCR method allowed for identification of the best inducers for adenine deaminase and xanthine oxidoreductase, as well as their concentration and time of induction. The adenine deaminase (AADA) and the xanthine oxidoreductase (AXOR) genes were isolated and subjected to homologous expression in A. adeninivorans cells using Xplor®2 transformation/expression platform. The selected transgenic strains accumulated the recombinant adenine deaminase in very high concentrations. The expression of AXOR gene posed difficulties and remained a challenge. Additional expression of both proteins in alternative E. coli system was undertaken but failed for AXOR gene. The recombinant adenine deaminase and wild-type xanthine oxidoreductase were purified and characterized biochemically. The characterization included determination of optimal pH and temperature, stability in different buffers and temperatures, molecular weight, substrate spectrum, enzyme activators and inhibitors, kinetics and intracellular localisation. The determination of these parameters was necessary to ensure optimal conditions for application of these enzymes in the industry. At the final stage, the enzymes were combined in one mix with provided guanine deaminase and urate oxidase and used to degrade purines in selected food constituents. The application was successful and demonstrated the potential of this approach for the production of food with lower purine concentration.
Background: Hepatitis E virus (HEV) is the etiological agent of an acute self-limiting hepatitis in humans worldwide. The main route of infection is by ingestion of food or water contaminated with the virus. In Germany, several hundred human cases are reported each year, while preliminary studies suggest a high infestation rate of herds of domestic pig (Sus scrofa domesticus) and sounders of wild boar (Sus scrofa). Autochthonous cases are originating mainly from zoonotic transmission from domestic pig and wild boar, but other animals may also be involved. Recently, a novel strain of HEV (ratHEV) had been found in Norway rats (Rattus norvegicus) in Germany, that could contribute to human epidemiology. Therefore, the aim of this study was to assess the seroprevalence of both HEV and the novel ratHEV in human, domestic pig and rat. For each of the three mammal species, an indirect immunoglobulin G (IgG) enzyme-linked immunosorbent assay (ELISA) was established, that based on an Escherichia coli-expressed carboxy-terminal segment (GT3-Ctr, amino acid (aa) 326–608) of the capsid protein of the autochthonous genotype 3 (GT3), derived from a wild boar from Germany. In parallel, a segment from ratHEV homologous to GT3-Ctr was also expressed in E. coli (ratHEV-Ctr, aa315–599) and was used in the ELISA. Hence, the established tests detect antibodies directed against HEV GT3 when using GT3-Ctr as antigen and ratHEV when using ratHEV-Ctr. Results: The GT3-based in-house human IgG test was validated using a commercial assay and showed high specificity and sensitivity. The average human population (represented by a panel of blood donors from Berlin and Brandenburg) reached a seroprevalence of 12.3% (37/301) with the in-house ELISA. A panel of forestry workers from Brandenburg had an even higher seroprevalence of 21.4% (119/555). Furthermore, ratHEV-specific antibodies could be detected in several sera of forestry workers. The novel ratHEV-based rat IgG ELISA could not be compared to similar tests, however, parallel testing with GT3-Ctr and statistical inference allowed conclusion of a seroprevalence. Rats trapped from several sites in Germany had an overall seroprevalence of 24.5% (36/147). The sera were reactive exclusively with ratHEV-Ctr. As with the in-house ELISA for human sera, the porcine IgG test was validated using a commercial assay, yielding high specificity and sensitivity. A panel of domestic pigs from ten federal states of Germany showed a seroprevalence of 42.7% (383/898) when tested with the in-house ELISA. Reactivity with ratHEV was present, but seemed to be caused mostly by cross-reactivity to GT3-Ctr. Conclusion: The HEV seroprevalence observed for human sera of the average population of Germany is among the highest in Europe and has been confirmed recently by other authors. The high seroprevalence found in forestry workers suggests that they should be counted as a risk group for HEV infection. Populations of rats have been shown to be infested heavily with ratHEV, as rats from all trapping sites situated within cities had a high prevalence for ratHEV exclusively and no serum reacted exclusively with GT3-Ctr. Seroprevalence in domestic pigs was demonstrated to be distributed evenly across federal states and districts. However, a vast difference of infestation could be detected in different herds, suggesting either differences in husbandry conditions, or an external source of infection that acts locally only. The rare but exclusive reactivity of human sera with ratHEV as well as the high cross-reactivity of swine sera with ratHEV suggests that viral strains other than the ones already known may contribute to cases of hepatitis E.
The pollen record is a powerful proxy to reconstruct past terrestrial vegetation, but quantifying plant abundances is strongly limited because plants produce pollen in different amounts and pollen is dispersed differently. Further complications arise from the use of percentage data. Finally, a pollen grain deposited at a site may have arrived from proximate or distant sources, which implies that a single pollen sample may reflect very different vegetation scenarios. Present thesis suggests improving quantitative reconstructions of past vegetation by refined calibration of the pollen-vegetation relationship (paper I) and application of the downscaling approach (papers II-IV). Paper I primarily addresses the questions of pollen production and dispersal by calibrating the pollen-vegetation relationship. Data analysis employs the common extended R-value (ERV) approach and a new data-model comparison method, which appears more suitable than the ERV approach. For the first time PPEs have been calculated using three contrasting pollen dispersal options, including a Lagrangian stochastic (LS) model. The study proves that the underlying pollen dispersal model is a crucial parameter in PPE calculations and that the calculations with the LS model produce more reliable and realistic PPEs. Papers II to IV address quantitative reconstructions of past vegetation. Using the newly developed downscaling approach, the three studies explore fine scaled vegetation patterns in NE Germany during the Late Glacial and early Holocene. The main assumption of the downscaling approach is that the present day pattern of abiotic site conditions (e.g. the pattern of soil substrates) existed, at least to a large extend, also during the study periods. The basic principle of the approach is to test, whether pollen deposition in sites across a landscape is correlated to that site pattern. The first application of the approach (paper II) has shown a close correlation between PINUS pollen percentages and the distance weighted abundance of sandy soils and between BETULA pollen percentages and the distance weighted abundance of morainic till during the Allerød period, indicating that pine and birch formed rather separate stands on either substrate type. The cooling of the Younger Dryas induced significant changes in the vegetation of NE Germany. By combining pollen percentage and pollen accumulation rate data paper III identified a sharp vegetation boundary between the Mecklenburg and Brandenburg area at about 53 °N. The downscaling approach, here used with pollen accumulation rate data, suggests that in the North small tree stands could only exist in sheltered positions. The sharp vegetation boundary is possibly related to a climatic gradient and the southern permafrost limit, which itself may result from the formation of sea ice on the North Atlantic north of 53°N during winter. The warming of the Holocene again allowed the expansion of forests in the study area. Paper IV uses high resolution pollen (accumulation rate) data to study the successive forest formation, including the immigration of hazel, and explores vegetation patterns and composition during these successive stages using the extended downscaling approach. This approach addresses the problems related to differential pollen production, dispersal and the use of percentage data by applying simulations. It reveals that initially pine and birch established, as during the Allerød period, in largely separate stands with pine dominating on sandy soils and birch dominating on fine grained soils. Also open rich vegetation persisted, possibly due to seasonal drought, mainly on fine grained soils. Hazel later mainly spread on sites that received additional wetness from ground or surface water; it did not enter pine dominated forests on well drained sandy soils. Overall, the early Holocene vegetation of the study area was sharply differentiated by soil humidity and fertility. To conclude, present thesis has revealed vegetation patterns and species site preferences in NE Germany during three periods of the Lateglacial and early Holocene. The results improve our understanding of vegetation history in northern Central Europe, specifically for periods of rapid climate change. The approaches applied are flexible with respect to the type and quality of pollen data used and may be implemented using standard software packages.
This thesis describes the implementation and first on-line application of a multi-reflection time-of-flight (MR-ToF) mass analyzer for high-resolution mass separation at the ISOLTRAP mass spectrometer at ISOLDE/CERN. On the one hand, the major objective was to improve ISOLTRAPs mass-measurement capabilities with respect to the ratio of delivered contaminating ions to ions of interest. On the other hand, the time necessary to purify wanted from unwanted species should be reduced as much as possible to enable access to even more exotic nuclei. The device has been set up, optimized and tested at the University of Greifswald before its move to ISOLTRAP. The achieved performance comprises mass resolving powers of up to 200000 reached at observation times of 30ms and a contamination suppression of about four orders of magnitude by use of a Bradbury-Nielsen gate. With the characteristics, it outperforms clearly the so far state-of-the-art purification method of a gas-filled Penning trap. To improve the utilization of the MR-ToF mass analyzer, the in-trap lift method has been developed. It simplifies the application and optimization of the device, which is a crucial time factor in an on-line experiment. The device was the first of its kind successfully applied to radioactive ion beams for a mass analysis, for a mass separation (in combination with the Bradbury-Nielsen gate) as a preparatory step for a subsequent Penning-trap mass measurement and as a high-precision mass spectrometer of its own. The later was recently used for the first mass measurement of the neutron-rich calcium isotopes 53Ca and 54Ca. The so-far achieved mass-resolving power of 200000 belongs to the highest reported for time-of-flight mass analyzers at all. The first successful application of the MR-ToF system as the only mass separator at ISOLTRAP resulted in the mass measurement of 82Zn. The new mass value has been compared to mass extrapolations of the most recent Hartree-Fock-Bogoliubov (HFB) mass models, HFB-19 to HFB-21, of the BRUSLIB collaboration. The mass of the nuclide is of high interest for the compositions and depth profile of the outer crust of neutron stars. In the classical model of the outer crust of a cold, non-accrediting and non-rotating neutron star, the sequence of nuclides found within this parts is determined mainly by the binding energy of exotic nuclides. The crustal compositions determined with the three HFB mass models differed with respect to the appearance of a layer of 82Zn, originating from different mass extrapolations of this mass. With the new experimental data, the extrapolations could be evaluated. It was found that the HFB-21 mass value differs less from the experimental data than the ones from HFB-19 and 20. Therefore, in the classical model, 82Zn does not appear anymore in the outer crust. Due to its high resolution and very fast measurement time, the MR-ToF mass analyzer will be an important instruments for future activities at ISOLTRAP, at the ISOLDE facility in general, and at other radioactive ion-beam facilities.
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.
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.
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.