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Chaetognaths are a fascinating taxon with unique features and a great impact on marine food webs as primary predators of zooplankton. Their phylogenetic position has been subject to many speculations ever since their discovery and even contemporary phylogenomic methods have not yet been able to suggest a stable hypothesis on their phylogenetic position within the Bilateria. Neuroanatomical studies may contribute new aspects to this discussion. This study aims to provide new insights into the chaetognath nervous system using a fresh set of methods to determine characters for a phylogenetic discussion. The method of choice in this case was immunohistochemistry combined with confocal microscopy. Experiments were conducted with a host of antibodies. The most effective target antigenes were RFamides (a family of neuropeptides), synapsins (synaptic proteins), tyrosinated tubulin (a cytoskeletal element, especially in neurites) and BrdU (bromodeoxyuridin, a proliferation marker). Each of those markers was of great use in highlighting certain aspects of the nervous system. A fresh look at the development of juvenile chaetognaths shortly after hatching revealed that the ventral nerve center (VNC) is developing earlier than the brain and that the production of neurotransmitters has already started at hatching. Specifically, some neurons exhibit RFmide-like immunoreactivity (ir). Neurogenesis continues for about five days after hatching and the mode of division in the neuronal stemcells is asymmetrical. In adult chaetognaths, the brain is divided into a stomatogastric anterior and a sensory posterior neuropil domain. It contains a set of individually identifiable neurons that exhibit RFamide-like ir. The study highlights the interspecific variation of brain architecture between representatives of spadellids and sagittids. The VNC consists of two lateral bands of somata that flank a central neuropil. Within the VNC exists a serial arrangement of neurons with RFamide-like ir. A variety of other neurotransmitters and related substances are also present in both, the brain and the VNC. More interspecific differences and similarities were explored in another part of the study, comparing even more different chaetognath species and focusing on the VNC and its internal structure. The two species of Krohnitta have an unusual distribution of nuclei that is not clearly separated into two lateral bands like in other species. Many of the sagittid species exhibit a striation pattern of the neuropil that is mostly absent in other groups and some of their nerve nets show varying degrees of order as opposed to the rather disorganized nerve net in other groups. In addition, immunohistochemical methods were applied to several specimens of Gnathostomula sp. in order to test one of the many hypotheses about the chaetognaths phylogenetic position, a sister-group relationship to gnathostomulids. A comparison between the two taxa, taking into account also other gnathifera and platyhelminthes, makes a sistergroup relationship between chaetognaths and gnathostomulids very unlikely. In conclusion, chaetognaths remain in an enigmatic phylogenetic position and likely branched off close to the deuterostome/protostome split.
The biological decontamination and sterilization is a crucial processing step in producing and reprocessing of medical devices. Since polymer-based materials are increasingly used for the production of medical devices, the application of conventional sterilization processes are restricted to a certain extent. Conventional sterilization techniques on the basis of high temperatures, toxic gases, or ionizing radiation can be detrimental to the functionality and performance of polymeric materials. For this reason, alternative, gentle, and efficient decontamination processes are required. One possible approach is the use of non-thermal physical plasmas. Especially atmospheric pressure plasma is receiving great interest due to the absence of vacuum systems which is highly attractive for the practical applicability. Its mechanisms of action enable the efficient killing and inactivation of micro-organisms which are attributed to the interaction of plasma-generated reactive oxygen and nitrogen species (ROS, RNS) as well as plasma-emitted (V)UV radiation. Owing to the moderate gas temperatures (near or at room temperature) so-called cold plasmas are well-suitable for the treatment of heat-sensitive materials, such as polymers, without affecting their bulk properties. The present work focuses on the investigation of atmospheric pressure plasma processes for the biological decontamination of polymers. The objective is to help elucidate on the one hand the impact of varied plasma process parameters on the inactivation of micro-organisms and on the other hand the influence of plasma on the surface properties of the substrate. The investigations were performed by means of a high-frequency driven plasma jet (from the product line kINPen) operated with argon and argon-oxygen mixtures. Three main aspects were analyzed: 1. The effect of plasma on the viability of micro-organisms dependent on working gas, treatment time, and the sample distance (distance between the jet nozzle and the substrate). 2. The plasma-based removal of microbial biofilms. 3. The effects of the plasma treatment on the surface properties of selected polymers. Additionally to the capability of the applied plasma jet in killing microbes the efficacy of this plasma jet for the removal of complex biological systems (e.g. biofilms) is shown. To model cell constituents of bacteria different synthetic polymers were chosen to gain insight into the decomposition process responsible for biofilm degradation. By investigating the impact of atmospheric pressure plasma on physico-chemical surface properties of various synthetic aliphatic and aromatic polymers the interaction mechanisms between plasma and plasma-exposed material are discussed. These studies are accompanied by applying different optical plasma diagnostic techniques (optical emission spectroscopy and two-photon absorption laser induced fluorescence spectroscopy) to obtain information on the plasma gas phase which contributes to the elucidation of the reaction mechanisms occurring during plasma exposure. Moreover, it is presented to which extent the plasma treatment influences the surface properties of polymers during the plasma-based bio-decontamination process and further, the benefits of surface-functionalized polymers for biomedical application is discussed.
Chronic infections, including periodontal infections, may reduce lung function. To date, there are hardly any population-based studies evaluating the association between periodontitis and lung function. However, there are some studies that used variables associated with obstructive pulmonary diseases (FEV1, FEV1/FVC). Thus, we aimed to assess the potential association of periodontal diseases with lung volumes and airflow limitation in the population-based Study of Health in Pomerania (SHIP). Of 3300 participants aged 25-85 years of the 5-year follow-up (SHIP-1), 1809 subjects participated in lung function examinations. 1465 subjects were included in the analyses. Lung function was measured using spirometry, body plethysmography, helium dilution, and diffusing capacity for carbon monoxide. Periodontal status was assessed by clinical attachment loss, probing depth, and number of missing teeth. Linear regression models using fractional polynomials were used to assess linear and non-linear associations between periodontal disease and lung function adjusting for confounders. Adjusting for age, sex, waist circumference, physical activity, diabetes, asthma, and time between core and pulmonary examination, mean attachment loss was significantly associated with variables of dynamic and static lung volumes, airflow limitation and hyperinflation. Total lung capacity and diffusing capacity for carbon monoxide were not associated with mean attachment loss. Adjustment for smoking and height considerably changed coefficients indicating profound confounding. Including fibrinogen and high sensitive CRP into fully adjusted models did not change coefficients of mean attachment loss. Restricted to never smokers, mean attachment loss was significantly associated with FEV1, FVC, and RV/TLC. Relations with lung function were confirmed for mean probing depth, extent measures of attachment loss/probing depth, and number of missing teeth. Periodontal disease was significantly associated with decreased lung function. Systemic inflammation did not provide a mechanism linking both diseases. However, cohort studies evaluating lung function in the current manner are needed to confirm results from this study and to assess a causal relationship. Furthermore, it needs to be investigated with the help of randomized clinical trials whether prevention or treatment of periodontitis might have a beneficial impact on lung function.
In the framework of the current work has been the plasma initiated and surface catalysed species conversion studied in low pressure and atmospheric plasmas. The aim of the work is to improve the understanding of the internal processes in order to increase the energy efficiency as well as the selectivity of the reaction products of future plasma devices. Beside many technical applications of plasmas, air purification shows great potential. Over the last decades, plasma based pollution control has proofed its ability to remove harmful contaminants or annoying odours from an air stream. However, the energy efficiency and the selectivity of the products are a remaining challenge.
Motivated by these issues, a multi stage packed-bed reactor has been used to remove admixed ethylene and toluene from an air stream. It has been found that the maximum toluene destruction has been 60%, whereas ethylene has been nearly completely removed. The specific energy β has been between 120 and 1600 JL-1. Fourier Transform Infrared spectroscopy, FTIR spectroscopy, has been used to identify and quantify the species H2O, CO2, CO, O3, HNO3, HCN, CH2O, CH2O2, N2O and NO2. However, none of these experiments led to the detection of NO.
The embedment of packing material into a plasma volume leads to increased surface effects. In order to study them, the inner side of a tube reactor, made of Pyrex, served as the surface under study and has been exposed to a rf plasma for 1h. The surface effects of the plasma treatment have been investigated indirectly by studying the oxidation of NO into NO2. After the plasma exposure, the reactor has been evacuated and filled with a gas mixture of 1% NO in N2 / Ar. Both species have been measured using quantum cascade laser absorption spectroscopy, QCLAS. It has been found that, using oxygen containing plasmas, the NO concentration decreased whereas the NO2 concentration increased. Therefore, oxygen containing plasmas are able to deposit oxygen on the surface. The filling with NO leads to the oxidation via the Eley-Rideal mechanism. A simplified model calculation supports these assumptions.
For a more comfortable application of the QCLAS, a compact multi channel spectrometer has been developed, TRIPLE Q. It combines the high time resolution with the possibility to measure the concentration of at least three infrared active species simultaneously. Due to the high time resolution, a huge number of spectra have to be analysed. In order to calculate absolute number densities, an algorithm has been developed which automatically treats typical phenomena like pulse jitter, rapid passage effect or variations of the intensity of the laser pulses.
The gas temperature is an important parameter in plasma physics. Using the TRIPLE Q system, the gas temperature has been determined for pulsed dc plasmas. For this case, NO has been used as a probe gas. From the spectra, the temperature has been calculated using the line ratio method. The relative intensity of the absorption structures of NO at 1900.5cm-1 and 1900.08cm-1 depend on the temperature. Therefore, the ratio has been used to calculate the gas temperature with a time resolution in the μs range.
Vibrationally excited nitrogen can be an energy reservoir that plays an important role in plasma chemistry. In N2 / N2O plasmas, vibrationally excited N2 can undergo relaxation via a resonant vibration vibration coupling between vibrationally excited N2 and N2O. Due to such an efficient energy transfer, the method allows one to study the relaxation of vibrationally excited N2. Using this method, molecules, which are not infrared active, can be monitored. This approach has extended the field of scientific and commercial applications of the QCLAS.
Thiol or sulfhydryl groups are highly reactive functional groups in cellular systems. Molecules carrying thiol groups are mostly derivatives of the amino acid cysteine and are grouped as low molecular weight (LMW)-thiols: coenzyme A (CoA), glutathione (GSH) or bacillithiol (BSH). LMW-thiols can help in the maintenance of the reduced cellular environment as so called redox-buffers. Additionally, they act as co-factors in enzyme reactions or help in the detoxification of reactive oxygen or nitrogen species, electrophilic compounds or thiophilic metalloids (arsenite, tellurite). In proteins from different organisms cysteine is underrepresented compared to other amino acids, but still overtakes diverse roles. It is an important determinant in the tertiary and quaternary structure of proteins. The nucleophilic character of the thiol or thiolate group, respectively, makes cysteine the catalytically active amino acids of different enzymes. As a precursor cysteine participates in the formation of Fe-S clusters and coordinates different co-factors like heme, iron or zinc. The main goal of this study was the investigation of the different cellular thiol pools, now defined as the thiolome. The thiolome is the entity of the cellular thiol pools, i.e. LMW-thiols and protein thiols, and the dynamics between these pools. In Bacillus subtilis and Staphylococcus aureus mixed disulfides between protein thiols and free LMW-thiols, so called S-thiolations, were identified in different proteins in response to the thiol specific reagent diamide. Some of these S-thiolations were located at catalytically active cysteine residues. Subsequent analysis of metabolites supports this: the S-thiolation of the cobalamine-independent methionine-synthase MetE led to a decrease of the cellular methionine content. Additionally, the conversion of threonine to different branched-chain amino acids (BCAAs) was disrupted by the S-thiolation of the branched-chain amino acid aminotransferase YwaA, thereby probably inducing the synthesis of ppGpp, the alarmon of the stringent response. In addition to the identification of S-thiolations a technique was established which allowed the discrimination between intra- and intermolecular disulfides. The non-reducing/ reducing diagonal gel electrophoresis was applied to B. subtilis and S. aureus and confirmed known existing disulfide bonds, e.g. in alkyl hydroperoxide reductase AhpC or the thiol peroxidase Tpx. In response to diamide an increase of specific disulfide bonds in different proteins was observed. The analysis of the LMW-thiol content by an HPLC-approach allowed the observation of the dynamics of the thiolome. In response to diamide the reduced LMW-thiol content decreased by 75%, reduced protein thiols by 60%. Collaborations with other working groups allowed the identification of BSH in this approach. Additionally, an unknown thiol was found that is likely a derivative of BSH. Screening of the LMW-thiol content of different S. aureus-strains under various growth conditions revealed that strains 8325-4 and SH1000 lack BSH. The lack of BSH was attributed to an 8 bp-duplication in the bshC-gene that encodes the last enzyme of the BSH-synthesis. BSH-production was restored by transducing plasmid-borne functional BshC from strain Newman into strains 8325-4 and SH1000. The reconstitution of the BSH-synthesis aided in the resistance to the antibiotic fosfomycin but did not increase the resistance to different oxidants (diamide, sodium hypochlorite, hydrogen peroxide). The production of BSH had also positive effects on the survival of S. aureus inside human bronchial epithelial cells and murine macrophages in phagocytosis assays. Additionally, a GSH-uptake was observed into S. aureus which has before been known as a GSH-free bacterium. Taken together, this thesis provides the first insights into both, the LMW-thiol- and protein thiol pool of low GC, Gram-positive bacteria under different conditions. A plethora of different methodologies was used to describe the thiolome. The bacterial thiolome is a sophisticated system which is tightly regulated, but also flexible enough to not rely on determined molecules like BSH. The influences of the thiolome are not restricted to its own system and regulation, but also affect different branches of cellular physiology like the metabolism of BCAAs.
In aged humans, stroke is a major cause of disability for which no neuroprotective measures are available. In animal studies of focal ischemia, short-term hypothermia often reduces infarct size. Nevertheless, efficient neuroprotection requires long-term, regulated lowering of whole-body temperature. Previously, it is reported that post-stroke exposure to hydrogen sulfide (H2S) effectively lowers whole-body temperature and confers neuroprotection in aged animals. Here we report for the first time that the animals exposed to H2S the normal sleep–wake oscillations are replaced by a low-amplitude EEG dominated by a 4-Hz rhythmicactivity, reminiscent of EEG recordings in hibernating animals. In the present study using magnetic resonance imaging, reverse transcriptase polymerase chain reaction, western blotting and immunofluorescence, we characterized the central nervous system response to H2S -induced hypothermia and report, that annexin A1, a major constituent of peripheral leukocytes that is upregulated after stroke, was consistently downregulated in polymorphonuclear cells in the peri-lesional cortex of post-ischemic, aged rat brain after 48 hours of hypothermia induced by exposure to H2S. This might be due to the reduced kinetics of recruitment, adherence and infiltration of PMN cells by H2S -induced hypothermia. Our findings further suggest that, in contrast to monotherapies that have thus far uniformly failed in clinical practice, prolonged hypothermia has pleiotropic effects on brain physiology that may be necessary for effective protection of the brain after stroke.
The goal of this doctoral thesis is to create and to implement methods for fully automatic segmentation applications in magnetic resonance images and datasets. The work introduces into technical and physical backgrounds of magnetic resonance imaging (MRI) and summarizes essential segmentation challenges in MRI data including technical malfunctions and ill-posedness of inverse segmentation problems. Theoretical background knowledge of all the used methods that are adapted and extended to combine them for problem-specific segmentation applications are explained in more detail. The first application for the implemented solutions in this work deals with two-dimensional tissue segmentation of atherosclerotic plaques in cardiological MRI data. The main part of segmentation solutions is designed for fully automatic liver and kidney parenchyma segmentation in three-dimensional MRI datasets to ensure computer-assisted organ volumetry in epidemiological studies. The results for every application are listed, described and discussed before important conclusions are drawn. Among several applied methods, the level set method is the main focus of this work and is used as central segmentation concept in the most applications. Thus, its possibilities and limitations for MRI data segmentation are analyzed. The level set method is extended by several new ideas to overcome possible limitations and it is combined as important part of modularized frameworks. Additionally, a new approach for probability map generation is presented in this thesis, which reduces data dimensionality of multiple MR-weightings and incorporates organ position probabilities in a probabilistic framework. It is shown, that essential organ features (i.e. MR-intensity distributions, locations) can be well represented in the calculated probability maps. Since MRI data are produced by using multiple MR- weightings, the used dimensionality reduction technique is very helpful to generate a single probability map, which can be used for further segmentation steps in a modularized framework.
The main objective of this research was to enhance the understanding of the inte¬ractions of bentonite with iron in the near field of a HLW-repository. One target was to investigate natural Fe-rich bentonites as a possible analogue. Another topic was to recognize the mineralogical interaction of bentonite with iron powder simulating the contact of bentonite with steel containers (thermodynamic approach). An additional objective was to explore the idea that bentonites have a specific dissolution potential (kinetic approach). In order to take the thermodynamic approach, compacted MX80 bentonite and Friedland clay were used as starting materials for clay/iron interaction experiments in per¬colation systems (Clay/Iron-ratio = 0.1). The natural processes were studied by examining a tropical wea¬thering profile of serpentiniz¬ed diabase from the Thanh Hoa province of Vietnam. The kinetic approach was taken by investigating a series of well characterized bentonites, 9 from API-standard series, 12 from the BGR-collection and 4 others, all of them saturated with deionized water (liquid/solid-ratio = 10/1) and NaCl 1N solution (liquid/solid-ratio = 4/1) for 30 days, followed by exposing the soft gels to mechanical agitation by overhead shaking corresponding to two energy levels (20 rpm and 60 rpm). XRD and TEM – EDX measurement were the major analytical techniques applied in this research, with FT-IR and XRF analyses as additional tools to characterizing the structure and composition of the smectites. Thermodynamic Approach MX80 bentonite and Friedland Clay clearly show that chemical and mineralogical changes have occured in the reaction products. They are exemplified by the neoformation of serpentine and chlorite in certain mixed layer phases. The smectite in the reaction products had also undergone changes especially in the constitution of the octahedral and tetrahedral sheets as well as in the interlayer space. These alterations were evident by the difference in key peak positions and ratios of XRD-patterns, and by TEM-investigations, as well as by different positions and intensities of FT-IR-bands of octahedral and tetrahedral features. The alteration was also seen in the bulk chemical composition data (XRF). MX80 bentonite and Friedland clay show various types and stages of alteration under different experimental conditions. The alteration can be described as “illitization” in open reaction systems and “smectitization” in closed reaction systems. The degree of alteration was controlled by the degree of chemical activities (ion strength, Fe- & Si-activity, con-centration). Higher reactivities give higher degrees of dissolution and release of Si from clay minerals. The oxidation of native iron (Fe0 → Fe2+) was recognized as the main driving force for dissolution, but also the oxidation of Fe2+ (Fe2+ → Fe3+) appeared to reverse an open to a closed reaction system by increased Si-pre¬cipitation. The thermodynamic modelling of C/I-experiments by Mingliang Xie (GRS mbH) verified identified mineralogical alterations in the reaction products. Generally, the contact with metallic iron caused a strong increase in dissolution potential. The reason for this is the reducing potential of oxidation of iron which raised pH to become alkaline and increase dissolution of Si from clay particles. The mineralogical transformations recognized in the experiments, such as the neoformation of serpentine and chlorite phases, were also observed in the tropical weathering profile of serpentinized diabase. The wellknown fast development of Fe-rich montmorillonite in alteration of ultramafic rocks (e.g., Schnellmann, 1964) was also identified by mineralogical investigation of the weather¬ing profile. This confirms that smectitization is linked with higher Fe-activities also in nature. Fe2+ was present in this system and during oxidation acted as driving force for alteration. The reduction potential of Fe-oxidation caused an increase of pH into alkaline conditions. Kinetic Approach The hypothesis that smectite clays have a specific dissolution potential emanated from the study. This would mean that high amounts of Fe and Mg in the octahedral sheet can accelerate alteration in agreement to what was early proposed by Cicel & Novak (1976). The larger ion diameter of Fe and Mg in comparison with Al may well be responsible for a higher sheet stress, which would facilitate dissolution of smectites. The idea proposed Kaufhold & Dohrmann (2008) concerning a mechanism that makes Ca- and Mg-cations in the interlayer space stabilize quasicrystals is also supported by the present study. The performed investigation indicate which mechanisms that serve to protect smectites from undergoing alteration and which promote alteration. Stable smectites, i.e. those with a low specific dissolution potential, were called here “Sleepers”, while fast reacting bentonites, which have a high specific dissolution potential, were termed “Sprinters”. Smectites react with different rates of reaction in laboratory experiments. As said, each smectite sample has its specific potential for dissolution and this potential is controlled by the composition of both the octahedral sheets and the interlayer space. Increasing amounts of octahedral Fe and Mg compared to octahedral Al increase the specific dissolution potential. This potential is also affected by the ion radius, implying that the larger ion radius of Fe and Mg compared to Al increases the mechanical sheet stresses in the octahedral sheet. In summary, this means that, the investigations have confirmed the initial hypothesis concerning the impact of the composition of the octahedral sheet. It results primarily from the pH during the formation of the smectite clay and therefore serves as a geological fingerprint. The Al-Fe ratio in the octahedral sheet influences the stability of the interlayer: A) Aloct > 1.4 and Feoct > 0.2 (per (OH)2 O10) favour delamination of quasicrystals. The swelling pressure increases by a co-volume process between the delaminated layers wiht higher numbers of quasicrystals for Na-dominant population of the interlayer space (Laird, 2006). The microstructural components including both small and large particles and parts of them have a very small ability to move and undergo free rotation. Such Na-montmorillonites are consider as stable phases and have only a low specific dissolution potential. They are „Sleepers“. B) Aloct > 1.4 and Feoct < 0.2 or Aloct < 1.4 and Feoct > 0.2 (per (OH)2 O10) promote demixing of monovalent and divalent interlayer cations (Laird, 2006). In the case of Ca and Mg-dominant interlayers, quasicrystal can break Na-bearing interlayers and help to maintain the quasicrystal structure. Such Ca and Mg-mont¬morillonites can be also be taken as „Sleepers“ because of their low specific dissolution potential. Depending on the octahedral composition, certain cations in the inter¬layer can stabilize bentonites against mineralogical changes. Montmorillonites stabilized by high concentration of Na-cations were classified as belonging to category A, while montmorillonites stabilized by high Ca, Mg-cations in the interlayer sheet were grouped in category B. The classification of a smec¬tite into the categories A or B defined above can be best achieved by IR analyses that yield useful chemical information concerning the composition of the octahedral sheets. Smectites with Na as stabilizing interlayer cation (group A) have shown δAlAlOH-bands with increasing wavenumbers for increasing octahedral Al in FT-IR spectra. The other reaction type of smectite, with Ca, Mg-cations in the interlayers (group B), is characterized by a decreasing octahedral Al-amount for increasing wavenumbers of δAlAlOH-bands in such spectra. Also the FT-IR δAlFeOH-bands are different in the two reaction types of smectite. Increasing octahedral Fe-amounts were mirrored by decreasing wavenumbers of δAlFeOH-bands. However, smectites of group B do contain higher Fe-amounts for the same wavenumber than smectites of group A. Expected alteration of bentonite close and far from a steel canister In the early interaction of smectite-rich clay – the “buffer” - and steel, the system behaves as being chemically closed. Within the clay barrier, Si will be dissolved from clay mineral particles in accordance with its specific dis¬solution potential. The dissolved Si can stay by contributing neoformation of mont¬morillonite layers in mixed layer phases. The interlayer charge decreases by substitution of Mg by Al, which leads to an increase in the swelling pressure. Also minor Si-precipitation may occur if not all the dissolved Si is used up by the neoformed montmorillonite layers. Such precipitation of Si will cause cementation of some quasicrystals and lead to a reduction in porosity. Enhanced temperature and additional Fe-activity, representing an increased reduction potential, increases notably the amount of dissolved Si at the interface between bentonite and steel canister, and as a consequence there will be significant precipitation of Si. The resulting cementation of quasicrystals is ac¬com¬panied also by their collapse which induces broadening of pores. This caused the channel-like migration of infiltrating solutions and switches the system into an open one. Thermodynamic predictions indicate that “illite” will be generated close to the steel canister (via “illitization”) and kaolinite or pyrophyllite to be formed farther away (via smectitization). The “illitization” process results in higher interlayer charges and lower swelling pressures. In contrast, the formation of smectite reduces interlayer charges and promotes higher swelling pressures. At the end of the thermodynamic evolution, the swelling pressure will drop also far from the canister because kaolinite and pyrophyllite are non-swelling minerals. In both cases, the applications of so-called “Sleeper”-bentonites are required to slow the reaction progress. For designers of the engineered barriers in a repository, i.e. the canister and the “buffer” clay, some basic rules are recommend on the basis of the present study. Thus, the presence of native Fe or Fe2+-cations in the clay or in accessory minerals in it, or emanating from the canisters, will speed up the reaction process and make it extensive. Likewise, use of Fe-poor “buffer” clay, representing “Sleepers”-type are suitable for slowing down the reaction. Copper as canister material, and very dense Na-rich montmorillonite of group A as “buffer” seem to be ideal rather than steel/iron and less dense Ca-saturated clay.
This thesis will discuss the different fields of application of the two soft ionization techniques ESI and MALDI in microbial proteomics and their importance for a better understanding of bacteria physiology. The general development in the past 25 years coming from 2D-gel analysis and protein identification by peptide mass fingerprint analysis via MALDI-TOF to genome wide quantitative LC-ESI-MS experiments with fast and sensitive ESI instruments is exemplary shown for the Gram-positive bacterium Bacillus subtilis in article I. Even though 2D-PAGE in conjunction with MALDI-MS is still an important tool in proteomic research, the more recently established global quantitative LC-ESI-MS workflows gain more and more relevance as they overcome 2D-PAGE based protein restrictions and enable the acquisition of higher accurate protein quantities. In article II such a workflow was used to analyze the physiological adaptation of Staphylococcus aureus to vancomycin treatment on a global-scale. Also post-translational modifications of proteins, that are important for regulation of their activity and allow rapid adaption to changed environmental conditions, could be analyzed by LC-ESI-MS workflows using special enrichment strategies (article III and IV). Despite the mentioned discrimination and less accurate quantification of proteins, 2D-PAGE analyses are still advantageous when analyzing large-scale time series experiments. To gain highly time resolved data but also very accurate relative quantities on a global-scale, 2D-PAGE-MALDI-MS and LC-ESI-MS techniques have been combined to investigate dynamic proteome adaptations of B. subtilis during nutrition shift as part of a global systems biology approach (article V). Also absolute quantities of proteins are of high interest for systems biology, but are still challenging to obtain on large-scale as well as with sufficient accuracy. In article VI a method that again combined 2D-PAGE-MALDI-MS and LC-ESI-MS was introduced to gain absolute protein quantities on global-scale. Utilizing the complementarity of 2D-PAGE and LC-ESI-MS this new workflow enabled fast and cost efficient data acquisition on absolute scale. In article VII we described for the first time a global quantitative LC-MALDI-MS workflow. Cross validation with an LTQ Orbitrap proofed that LC-MALDI-MS is able to process complex samples and obtain highly reliable quantities. The comparative analysis of data gained with both instrument types revealed biases for certain biochemical properties of MALDI as well as ESI instruments, resulting in a general complementarity of both ionization techniques. Article I Becher, D., Büttner, K., Moche, M., Hessling, B., Hecker, M., 2011. From the genome sequence to the protein inventory of Bacillus subtilis. Proteomics 11, 2971–2980. Article II Hessling,B., Bonn,F., Herbst,F.-A., Rappen,G.-M., Bernhardt,J., Hecker,M. and Becher,D. Global proteome analysis of vancomycin stress in Staphylococcus aureus. Submitted to Mol. Cell Proteomics. Article III Elsholz, A.K.W., Turgay, K., Michalik, S., Hessling, B., Gronau, K., Oertel, D., Mäder, U., Bernhardt, J., Becher, D., Hecker, M., Gerth, U., 2012. Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis. Proc. Natl. Acad. Sci. U.S.A. 109, 7451–7456. Article IV Chi, B.K., Gronau, K., Mäder, U., Hessling, B., Becher, D., Antelmann, H., 2011. S-bacillithiolation protects against hypochlorite stress in Bacillus subtilis as revealed by transcriptomics and redox proteomics. Mol. Cell Proteomics 10, M111.009506. Article V Buescher,J.M., Liebermeister,W., Jules,M., Uhr,M., Muntel,J., Botella,E., Hessling,B., Kleijn,R.J., Le Chat,L., Lecointe,F., et al. (2012) Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science, 335, 1099–1103. Article VI Maass, S., Sievers, S., Zühlke, D., Kuzinski, J., Sappa, P.K., Muntel, J., Hessling, B., Bernhardt, J., Sietmann, R., Völker, U., Hecker, M., Becher, D., 2011. Efficient, global-scale quantification of absolute protein amounts by integration of targeted mass spectrometry and two-dimensional gel-based proteomics. Anal. Chem. 83, 2677–2684. Article VII Hessling,B., Büttner,K., Hecker,M. and Becher,D. Global relative quantification with LC-MALDI – cross-validation with LTQ-Orbitrap proves reliability and reveals complementary ionization preferences. Submitted to Mol. Cell Proteomics.
I have investigated the role played by reactive oxygen species (ROS) generated by the phagocyte NADPH oxidase system in the innate immune response. I first looked at effector functions by asking whether ROS released from phagocytes might be effective in the killing of extracellular bacteria. Since bacteria can be killed in many other ways – for example by proteases or by cationic peptides – I made use of the recently demonstrated capacity of ROS to remove discontinuities from the surface of gold as the basis of an in vivo assay for extracellular ROS. Unlike bacterial killing, this readout system is not affected by enzymes, cationic peptides or other biological anti-bacterial agents. By this means I was able to use wild type mice and a congenic strain which lacks the gene coding for the gp91 subunit of the phagocyte NADPH oxidase to demonstrate that ROS generated by the NADPH oxidase system are indeed found outside the cells during an inflammation in vivo and that their principle source is neutrophil granulocytes rather than tissue macrophages. Since ROS released by these cells will be non-specific in its action it is to be expected that the releasing cell will itself suffer considerable damage. This fits well to the known short life of activated neutrophils and may explain the established fact that their death is dependent on the NADPH oxidase system. The long lived macrophages, in contrast, restrict their production of extracellular ROS. ROS are increasingly being found to be involved in both intra and intercellular signalling processes I looked for an involvement of NADPH oxidase derived ROS in the recruitment of neutrophils to sites of inflammation in vivo. Since the gene coding for the gp91 subunit of the NADPH oxidase is on the X chromosome I made use of a mosaic expression strategy based on X chromosomal inactivation. The results show that indeed ROS serves as a component of the neutrophil recruitment process in the critical early stages of an infection. Possible mechanisms are explored.
Beams of ions and electrons are a source of free energy which can be transferred to waves via an instability. Beams exist in almost all plasma environments, but their instabilities are particularly important for the dynamics of space plasmas. In the absence of collisions, the instability drives waves to large amplitudes and forms nonlinear structures such as solitary waves. The electric fields in these waves can scatter particles in the background plasma, or disrupt currents. Both of these effects are important for the overall dynamics of the plasma. In this thesis, both electron and ion beam plasma instabilities have been investigated in the linear plasma device VINETA and using a Particle-in-Cell simulation. The electron beam instability has been demonstrated by previous authors to be a useful diagnostic for the plasma density. The spatial resolution of previous results was confirmed at a few millimetres, and a temporal resolution of 1ms was shown for the first time. An ion beam was generated with a double plasma discharge. Compared to space, this environment and indeed most laboratory plasmas have considerably higher collisionality and a limited spatial extent which introduces gradients in the plasma. Gradients perpendicular to the beam propagation direction are linked to a decrease of both the wavelength and amplitude of the instability. It was observed in both experiment and simulation that gradients in sheaths at the boundaries of the plasma not only affect the time averaged plasma parameters, but also excite instabilities. Fluctuations within the sheath spread the beam in velocity space, effectively increasing its temperature. Warmer beams require a higher drift velocity to excite an instability. This was also confirmed by experimental and numerical results. Collisions are shown to be the dominant damping force for the electron beam instability. For ions, collisions play an important role in the simulation, but appear to be overshadowed by Landau damping from impurities in the experiment. When boundary conditions are removed from the simulation, wave amplitudes increase and nonlinear effects become important. Saturation by particle trapping and coalescence of phase space holes is observed, which could eventually lead to the solitary waves as they are observed in space plasmas.
The general stress response comprises approximately 200 genes and is driven by the alternative sigma factor SigB. Besides the process of sporulation with approximately 500 involved gene products under initial control of Spo0A are the two most significant and extensive cellular responses that can be observed in B. subtilis. The general stress response provides vegetative growing as well as non-growing and non-sporulating cells with a comprehensive cross-protective and preventive multiple stress resistance to various hostile environmental conditions. In contrast, the endospore is the most resistant but also dormant cell type produced by B. subtilis. The scope of this study was the identification of regulatory cascades driven by the general stress response sigma factor SigB to further elucidate the structure and function of the general stress regulon itself and to uncover potential intersections between the SigB response and other major developmental programs in the regulatory network of B. subtilis. It could be shown that the general stress regulon member yqgZ encodes a functional paralogue of Spx, the global regulator of the diamide stress regulon in B. subtilis. Global transcriptome and proteome studies led to the characterization of an YqgZ sub-regulon consisting of 53 positively and 18 negatively regulated genes. Due to its stringent SigB-dependent expression as well as its concerted action with SigB in regulation of its target genes YqgZ was renamed to MgsR which stands for “modulator of the general stress response”. Activity control of MgsR is stringently controlled at multiple levels. In addition to induction by SigB these mechanisms include (i) a positive autoregulatory loop of MgsR on the transcription level of its own structural gene, (ii) a post-translational redox-sensitive activation step by the formation of an intramolecular disulfide-bond within a conserved -CXXC-motif and (iii) rapid proteolytic degradation of MgsR by the ClpCP and ClpXP proteases, resul ting in extremely short in vivo half-lifes below 6 minutes. It was demonstrated that the activation of SigB is a prerequisite but not sufficient for a full expression of all general stress genes and that the SigB-dependent expression of MgsR provides the opportunity for additional redox-sensitive signal-reception, -processing and -integration beyond the primary decision of SigB activation. Our results describe a regulatory cascade integrating secondary oxidative stress signals into a SigB mediated regulatory cascade that is aimed at a precise fine tuning of target gene expression whose products are necessary for proper management of oxidative stress. Although primary oxidative stress stimuli do not typically induce SigB, our observation of redox-sensitive control by MgsR and several other reports that pointed at the implication of the general stress proteins in oxidative stress management led to the proposal that secondary oxidative stress may be a common component of multip le severe physical stress stimuli. This assumption could be supported by the results of a comprehensive phenotype screening of 94 mutants in single general stress genes upon treatment with hydrogen peroxide and the superoxide generating agent paraquat. A substantial amount of 62 mutants (66%) displayed significantly decreased survival rates in response to oxidative stress. The information gained by this phenotypic screening analysis provides a valuable basis for more directed assays to elucidate the biochemical functions of many so far uncharacterized general stress proteins and demonstrates that the SigB response and the regulatory fine tuning by MgsR plays a pivotal role in protection from secondary oxidative stress. Furthermore, it has been intensively discussed throughout the literature of the last years that the general stress response and the process of sporulation may represent mutually exclusive survival strategies of a non-growing B. subtilis cell, but the molecular basis for this assumption was missing until recently. By the identification of a functional SigB-type promoter (PsigB) adjacent to the spo0E, this gene was newly assigned to the general stress regulon. The spo0E gene encodes a phosphatase that specifically inactivates the master regulator of sporulation Spo0A~P by dephosphorylation. The SigB dependent induction of spo0E causes a block of sporulation specific transcription and produces a sporulation deficient phenotype. This effect was overcome by a deletion of the spo0E-SigB promoter, thus clearly addresses SigB activity. This regulatory mechanism is the first example for an integration of SigB inducing stimuli into the decision making process of sporulation initiation that provides a link to interconnect these two dominant and very likely mutually exclusive responses in the regulatory network of B. subtilis. The data presented here provide deeper insights into the structure and function of the general stress regulon in stress management.
The learning theory of panic disorder differs between panic attacks and anxious apprehension as distinct emotional states. Acute panic is accompanied by extreme fear, experience of strong body symptoms reflecting autonomic surge and flight tendencies. In contrast, anxious apprehension is associated with hypervigilance towards bodily sensations and increased distress when subtle somatic symptoms are identified. Following animal models, these clinical entities reflect different stages of defensive reactivity depending upon the imminence of interoceptive or exteroceptive threat cues with lowest distance to threat during panic attacks. We tested this model by investigating the dynamics of defensive reactivity in a large group of patients suffering from panic disorder and agoraphobia (PD/AG) prior to a multicenter controlled clinical trial. Three hundred forty-five patients participated in a standardized behavioral avoidance test (being entrapped in a small, dark chamber for 10 minutes). Defensive reactivity was assessed measuring avoidance and escape behavior, self reports of anxiety and panic symptoms, autonomic arousal (heart rate and skin conductance), and potentiation of the startle reflex before and during the exposure period of the behavioral avoidance test. While 125 patients showed strong anxious apprehension during the task (as indexed by increased reports of anxiety, elevated physiological arousal, and startle potentiation), 72 patients escaped from the test chamber. Active escape was initiated at the peak of the autonomic surge accompanied by an inhibition of the startle response as predicted by the animal model. These physiological responses were observed during 34 reported panic attacks as well. We found evidence that defensive reactivity in PD/AG patients is dynamically organized ranging from anxious apprehension to panic with increasing proximity of interoceptive threat. Importantly, the patients differed quite substantially according defensive reactivity during the behavioral avoidance test despite all patients received the same principal diagnosis. These differences can be explained in part by differences in the disposition according to two genetic variants previously associated with panic disorder. Patients carrying the risk variant of a polymorphism in the neuropeptide S receptor gene showed an overall increased heart rate during the whole behavioral avoidance test reflecting an enhanced sympathomimetic activation and consequently arousal level. During the entrapment situation in which heart rate further increased over an already elevated baseline level, risk variant carriers were prone to experience more panic symptoms. This is in line with the learning perspective of panic disorder, postulating that internal cues of elevated arousal increase the chance of experiencing another panic attack once they have been associated with aversive responses. Furthermore, the risk variant of a polymorphism in the monoamine oxidase A gene was observed to augment the occurrence of panic attacks and escape behavior preparation. In addition, we find evidence that suggest an enhanced resistance to corrective learning experiences as indicated by a lack of a reduction of avoiding and escaping behavior during repeated test chamber exposures in wait-list control patients carrying the risk gene variant. Both effects may strengthen the learning mechanism hypothesized to be involved in the pathogenesis of panic disorder. Exteroceptive and interoceptive cues previously associated with the initial panic attack might trigger subsequent attacks in risk allele carriers more rapidly while simultaneously the opportunity to dissolve once established associations due to contradictory experiences is limited. Now, differential dispositions regarding defensive reactivity in PD/AG patients has to be linked to mechanisms supposed to be involved in exposure based therapy. First outcome evaluations of the clinical trial indicated that a behavioral therapy variant suggested to be linked with higher fear activation during exposure exercises is more effective than another. Further analyses have to proof whether those patients showing a clear specific fear response during the behavioral avoidance test benefit more than others from exposure based therapy.
Primary Pan-CT is associated with improved clinical course and outcome in polytrauma patients
(2012)
The early clinical management of patients with polytrauma remains challenging. Clinical examination is unreliable in identifying the presence and severity of injuries, and diagnostic imaging plays a central role in the evaluation of the injury pattern. In the last decade, whole body multi slice computed tomography (Pan-CT) performed immediately after admission gained recognition in Europe and United States. Its utility and value, given the lack of accuracy data and concerns about unnecessary exposure to radiation, is undefined. The primary objective of this retrospective cohort study was to compare survival of multiple trauma (polytrauma) patients (Injury Severity Score [ISS] ≥ 16) prior to (1999 - 2002) and after (2002 - 2004) the introduction of a Pan-CT-based trauma resuscitation algorithm at a maximum care university medical centre. Secondary objectives were to compare the complication rates and duration of intensive care treatment. The study included 123 patients (mean age 34.6 years [SD 16.8], mean ISS 26.7 [SD 8.7]) in the control and 104 (mean age 39.8 years [SD 20.0], mean ISS 28.6 [SD 10.5]) patients in the intervention period. Die Baseline criteria were well balanced amongst both cohorts except for age (34.6 versus 39.8 years, p = 0.034). Both cohorts had a similar predicted probability of survival using the TRISS method (77.5 versus 77.6%, p = 0.979). Raw mortality decreased markedly but not statistically significantly in Pan-CT cohort (17.9 versus 11.5%, risk ratio (RR) 0.65, 95% confidence interval (CI) 0.34 - 1.24). However, after adjustment for injury severity, by mortality odds ratio of 0.40 (95% CI 0.17 – 0.95, p = 0.038) Pan-CT patients were 2.5 times more likely to survive. The mean difference in the duration of ICU treatment (5.1, 95% CI 1.2 – 9.0 days), days on respirator (5.3, 95% CI 2.0 - 8.6), and number of complications (0.4, 95% CI 0.2 – 0.8) was statistically significant and in favour of the Pan-CT-period.
This thesis describes investigations of metal clusters stored in an ion-cyclotron resonance (ICR) trap, as well as corresponding trap research and development. Charged clusters are produced and investigated in the experimental setup Cluster-Trap, comprising a cluster-ion source, an ICR trap and a time-of-flight (ToF) mass spectrometer. In the framework of its move to the new building of the Institute of Physics, new components have been added to the ClusterTrap setup. A radio-frequency ion trap is now used for cluster ion preparation prior to the performance of cluster experiments in the ICR trap. A quadrupole ion deflector allows an optimized usage of the ICR trap, as well as simultaneous use of several ion sources and detectors. The implementation of a potential lift at the ToF mass spectrometer enables a more flexible operation of the setup with ion energies up to several hundreds of electron volts. The new components have been tested and characterized, and the experimental procedures have been adapted. An important aspect of cluster investigations is the manipulation of trapped ions by application of appropriate excitation fields. For the ICR trap, a vector representation model has been developed for quick analysis of radial excitation fields, applied to the quarter-segmented ring electrode of an ICR trap. Its application has been demonstrated for asymmetric radial quadrupolar excitation of stored cluster ions, confirming the observation of unintended ion ejection from the trap. Investigation of multiply negatively charged metal clusters at ClusterTrap has been continued. By the "electron-bath" technique, i.e. simultaneous storage of cluster mono-anions and electrons in the ICR trap, high charge states are produced up to a limit which arises from restrictions for ion trapping. A modification of the electron bath, which bypasses this limit, has been introduced and demonstrated by the first-time production and detection of aluminum cluster anions carrying five excess electrons (penta-anions). Results of the penta-anion production as a function of the trapping voltage relate to the Coulomb potentials of the cluster anions involved, in agreement with previous findings. The observed poly-anionic clusters are meta-stable and their abundance as a function of the cluster size is determined by their lifetimes. Observed poly-anion abundances are described by a thermionic-emission approach, by means of the Richardson-Dushman formula. The height of the Coulomb potential in the formula is decreased to match experimental data, thus accounting for electron tunneling. Poly-anions are observed only above a minimum cluster size, the appearance size. To determine this limit from experimental results, a new data evaluation method has been introduced, which considers the poly-anion lifetimes and respective abundances of a range of cluster sizes. As a result, the experimental appearance size is larger than the smallest poly-anionic cluster observed, in contrast to previous approaches.
Abstract Atmospheric Pressure Discharges have attracted much interest in recent years. The development of a new processes based on this discharge needs a clear understanding of plasma and discharge physics and chemistry. At the present time much attention is paid to the chemical processes in barrier discharge plasma in various gas mixtures, since the understanding of these processes is necessary for the development of industrial reactors. Besides these, hydrocarbons are being used for the formation of diamond like or amorphous carbon (DLC) films. Specially, hydrogenated amorphous carbon (a-C: H) and plasma polymerization. In this work we have used Dielectric Barrier Discharge (DBD) a plasma device used to investigate simple hydrocarbon reactions in a plasma phase. Our aim of plasma phase chemical reaction studies is to form molecular hydrogen, higher order hydrocarbons CnHm up to n ≥ 12 series and nitrogen - containing organic complexes using simple hydrocarbons. Deposition of thin organic films or DLC films were carried out using the DBD. In this study we have chosen certain combination of gases such as C2Hm/N2 (m = 2, 4, 6) and C2Hm/Ar (m = 2, 4, 6); the purpose of using N2 and Ar gases are to dilute and stabilize the hydrocarbon plasma and to investigate plasma chemical reactions with nitrogen gas. All reactions were carried out under an atmospheric pressure (300 mbar) with gas ratio 1:2; Experiments were performed by applying high voltage with a frequency 5.5 kHz. The plasma phase diagnostics have been investigated using mass spectrometry and FTIR spectroscopy. Formation of molecular hydrogen, N-containing organic complexes and higher order hydrocarbons with C ≥ 12, have been investigated with mass spectrometry. FTIR spectroscopy reveals the formation of substituted alkanes (sp3), alkenes (sp2) and alkynes (sp) and nitrogen containing functional groups from the individual gases which are used in this work. Abundant formation of acetylene occurs with C2H6 and C2H4 as precursor gases. Amorphous hydrogenated carbon nitride (a-CNx:H) films have been deposited on Si (100) and glass substrates using gas mixtures C2Hm/N2 (m = 2, 4, 6). Surface chemical compositions have been derived from Fourier Transform Infrared Reflection Absorption Spectroscopy (FT-IRRAS) and X-ray Photo electron Spectroscopy (XPS). FT-IRRAS and XPS show the presence of sp, sp2 and sp3 bonds of carbon and nitrogen for C2Hm/N2 thin films. Various functional groups such as amines, saturated and unsaturated alkyl groups have been identified. Thin films obtained from C2H2/N2 and C2H4/N2 gas mixture had a larger N/C ratio when compared to the film obtained from C2H6/N2. Thickness, refractive index and extinction co-efficient were investigated by ellipsometry. Rate of deposition have been investigated. Different surface morphology has been derived using Scanning Electron Microscopy. Amorphous hydrogenated carbon (a-C:H) films or diamond like carbon (DLC) films have been deposited on Si (100) and glass substrates using gas mixtures C2Hm/Ar (m = 2, 4, 6). Diagnostics for the deposited films have been done using different spectroscopic techniques. Surface chemical compositions have been derived from Fourier Transform Infrared Reflection Absorption Spectroscopy (FT-IRRAS) and X-ray Photo electron Spectroscopy (XPS). FT-IRRAS show the presence of sp, sp2 and sp3 bonds of carbon and hydrogen for C2Hm/Ar (m = 2, 4, 6) thin films. The characteristic peak for C1s has been observed from XPS. Thickness, refractive index and extinction co-efficient were investigated by ellipsometry. Rate of deposition have been investigated.
Independence is a basic concept of probability theory and statistics. In a lot of fields of sciences, dependency of different variables is gained lots of attention from scientists. A measure, named information dependency, is proposed to express the dependency of a group of random variables. This measure is defined as the Kullback-Leibler divergence of a joint distribution with respect to a product-marginal distribution of these random variables. In the bivariate case, this measure is known as mutual information of two random variables. Thus, the measure information dependency has a strong relationship with the Information Theory. The thesis aims to give a thorough study of the information dependency from both mathematical and practical viewpoints. Concretely, we would like to research three following problems: 1. Proving that the information dependency is a useful tool to express the dependency of a group of random variables by comparing it with other measures of dependency. 2. Studying the methods to estimate the information dependency based on the samples of a group of random variables. 3. Investigating how the Independent Component Analysis problem, an interesting problem in statistics, can be solved using information dependency.
Dilated Cardiomyopathy is a chronic myocardial disease characterized by progressive depression of contractile function and ventricular dilatation. It is the leading cause of heart failure and the most common reason for heart transplantation. Besides genetic causes, viral infection and autoimmune response are considered to play a major role in the etiology of the disease. Among different viruses that cause the disease, Coxsackievirus B3 (CVB3) is predominantly associated with the development and progression of the disease. Moreover, Coxsackievirus induced myocarditis in the mouse mimics human myocarditis and dilated cardiomyopathy. In the murine model, the disease progresses over a period of 90 days from acute myocarditis to chronic myocarditis and further develops into dilated cardiomyopathy and congestive heart failure. Though much is known about the progression of the disease, the molecular events occurring after infection with CVB3 are not completely understood. In the current study, comparative proteomic analysis of A.BY/SnJ mouse hearts 84 days post infection (84 d p.i.) with CVB3 and age-matched non-infected mouse hearts was performed. 2D-DIGE and gel-free LC-MS/MS were used to characterize the changes occurring at the molecular level and Western Blot analysis as well as immunohistochemical staining was carried out for validation of results. A total of 101 distinct proteins were identified as displaying dilated cardiomyopathy-associated changes in A.BY/SnJ mouse hearts 84 d p.i. compared to age matched controls. Comprehensive analysis by both DIGE and gel-free proteomics revealed proteins related to lipid metabolism (18%), carbohydrate metabolism (14%), cell morphogenesis (14%) and respiratory electron transport chain (9%) to display significantly altered levels in diseased mouse hearts. The significant increase in extracellular matrix proteins observed in mouse hearts 84 d p.i. indicated extensive fibrosis. On the other hand, proteins related to energy metabolism were identified at lower levels in infected mouse hearts than in controls. These proteomics data and the decrease in activities measured for complexes I-IV of the respiratory electron transport chain in A.BY/SnJ mouse hearts 84 d p.i compared to age matched controls, indicate a diminished energy supply in the dilated hearts of CVB3 infected mice. Furthermore, proteins associated with muscle contraction were identified at lower levels in mouse hearts 84 d p.i. compared to age matched controls indicating compromised myocardial contractility due to virus induced dilated cardiomyopathy. While extracellular matrix proteins and contractile proteins were identified in the DIGE analysis, proteins of lipid metabolism which are mostly mitochondrial in origin and have a pI > 7 were identified by gel-free proteomics indicating the advantages of both methods. Gel based analysis also aided in the identification of protein isoforms/ species which allows conclusions on post translational modifications and protein processing. Thus, the current study also identified infection related changes in the phosphorylation of selected proteins. Phosphospecific staining of the gels demonstrated increased phosphorylation of myosin regulatory light chain - ventricular isoform, actin - aortic smooth muscle isoform, heat shock protein 90B, and heat shock protein beta-1 in infected mouse hearts. Extensive degradation of proteins was not observed in the dilated heart. As described earlier, virus induced dilated cardiomyopathy develops over a period of 90 days in the murine model during which the mice also grow and undergo aging. Since aging is one of the factors influencing the susceptibility of animals to disease, age dependent changes in the proteome of mouse hearts were also studied by comparing 4 months old (84d) A.BY/SnJ mice with 1 month old mice as controls. Complementary analyses by 2D-DIGE and gel-free LC-MS/MS analysis revealed 96 distinct proteins displaying age associated differences in intensity. These proteins are related to lipid metabolism (19%), protein transport (17%) and electron transport chain (12%). Mitochondrial proteins such as carnitine-o-palmitoyltranferase 1, carnitine-o-palmitoyltranferase 2, and carnitine-O-acetyltransferase involved in lipid metabolism and transport were identified at significantly higher levels indicating higher energy demand in 4 months old mice compared to controls. This conclusion is complemented by observation of decreases in the levels of respiratory electron transport chain proteins especially of subunits of ATP synthase as a member of complex V. Furthermore, an increase in intracellular transport proteins was also observed in 4 months old mouse hearts compared to one month old controls. An increase in the level of vesicular transport proteins likely constitutes a secondary effect leading to endoplasmic reticulum associated protein degradation. In the two studies described above, altered mitochondrial functioning and thereby decreased energy/ATP production was very prominent indicating the role of mitochondria in health and disease. The exchange of ADP/ATP across the mitochondrial membrane is carried out by the carrier protein adenine nucleotide translocase1 (ANT1). To improve understanding of the influence of ANT1 in the heart, comparative proteomic analysis using gel-free LC-MS/MS was performed with hearts of 3 months old rats over-expressing ANT1 using hearts from age-matched wild type animals as controls. A total of four hundred and thirty three proteins were identified with at least two peptides, of which eighty seven proteins displayed small but significant (p<0.05) changes in intensity. Proteins related to integrin linked kinase signalling and myocardial contraction displayed increased levels whereas proteins of the mitochondrial respiratory electron transport chain displayed decreased levels in ANT1 overexpressing hearts compared to wild type animals. Oxyblot analysis performed to study changes in the protein oxidation did not reveal any significant difference in the oxidative state of the proteins between the wild type and transgenic animals. To understand the influence of ANT1 overexpression in virus induced dilated cardiomyopathy, comparative proteomic analyses was performed for the mitochondrial fractions from the hearts of 8 months old rats of the wild type and ANT1 transgenic animals infected with CVB3. Of a total of 370 identified proteins, 83 proteins displayed altered levels in ANT1 overexpressing animals compared to controls. Proteins related to mitochondrial electron transport chain, fatty acid metabolism, contractility and cell structure displayed decreased levels in the infected transgenic animals compared to controls indicating decreased energy metabolism and myocardial contractility besides compromised cell structure. Besides viral causes of dilated cardiomyopathy, autoimmunity also plays a major role in the development of myocarditis and dilated cardiomyopathy. Therefore proteomic analyses of experimental models of autoimmune myocarditis generated by active immunization of rats with peptides of FcγIIa receptor -CEPPWIQVLKEDTVTL (peptide 1) designated as FcR animals and CRCRMEETGISEPI (peptide 2) designated as FcR2 animals- was performed. Of the 303 proteins identified with at least two peptides by gel-free LC-MS/MS analysis. 43 proteins displayed intensities greater than 1.2 fold in FcR rat hearts and 49 proteins displayed intensities greater than 1.2 fold in FcR2 rat hearts compared to animals injected with KLH adjuvant treated as controls. The majority of the alterations (>70%) were observed in both autoimmune models. Thus, immunization leading to an induction of the acute phase response signalling was observed in both experimental setups. Furthermore, the increased amount of proteins such as lumican or procollagen alpha 1, type 1 indicated the presence of fibrosis after immunization independent of the peptide used. In summary, using proteomics the current thesis addresses the changes in protein profiles of two models of dilated cardiomyopathy, namely, virus induced dilated cardiomyopathy and autoimmunity induced dilated cardiomyopathy in mouse and rat models of disease. 2D-DIGE and gel-free LC-MS/MS analysis are complementary techniques which provided a comprehensive view of the changes in the protein profile of hearts of the different animal models. Altered mitochondrial function resulting in decreased energy metabolism and compromised myocardial contractility were prominent in viral models of cardiomyopathy whereas intense acute phase response signalling was observed as a characteristic feature of autoimmune dilated cardiomyopathy. Altered mitochondrial function was also prominent in age associated changes in the heart of A.BY/SnJ mice indicating the role and influence of mitochondria in health and in disease.
The human brain is distinguished by its remarkable size, high energy consumption, and cognitive abilities compared to all other mammals and non-human primates. However, little is known about what has accelerated brain evolution in the human lineage. One possible explanation is that the appearance of advanced communication skills and language has been a driving force of human brain development. The phenotypic adaptations in brain structure and function which occurred on the way to modern humans may be associated with specific molecular signatures in today’s human genome and/or transcriptome. Genes that have been linked to language, reading, and/or autism spectrum disorders are prime candidates when searching for genes for human-specific communication abilities. The database and genome-wide expression analyses we present here revealed a clustering of such communication-associated genes (COAG) on human chromosomes X and 7, in particular chromosome 7q31-q36. Compared to the rest of the genome, we found a high number of COAG to be differentially expressed in the cortices of humans and non-human primates (chimpanzee, baboon, and/or marmoset). The role of X-linked genes for the development of human-specific cognitive abilities is well known. We now propose that chromosome 7q31-q36 also represents a hot spot for the evolution of human-specific communication abilities. Selective pressure on the T cell receptor beta locus on chromosome 7q34, which plays a pivotal role in the immune system, could have led to rapid dissemination of positive gene variants in hitchhiking COAG.
The autism susceptibility locus on human chromosome 7q32 contains the maternally imprinted MEST and the non-imprinted COPG2 and TSGA14 genes. Autism is a disorder of the ‘social brain’ that has been proposed to be due to an overbalance of paternally expressed genes. To study regulation of the 7q32 locus during anthropoid primate evolution, we analyzed the methylation and expression patterns of MEST, COPG2, and TSGA14 in human, chimpanzee, Old World monkey (baboon and rhesus macaque), and New World monkey (marmoset) cortices. In all human and anthropoid primate cortices, the MEST promoter was hemimethylated, as expected for a differentially methylated imprinting control region, whereas the COPG2 and TSGA14 promoters were completely demethylated, typical for transcriptionally active non-imprinted genes. The MEST gene also showed comparable mRNA expression levels in all analyzed species. In contrast, COPG2 expression was downregulated in the human cortex compared to chimpanzee, Old and New World monkeys. TSGA14 either showed no differential regulation in the human brain compared to chimpanzee and marmoset or a slight upregulation compared to baboon. The human-specific downregulation supports a role for COPG2 in the development of a ‘social brain’. Promoter methylation patterns appear to be more stable during evolution than gene expression patterns, suggesting that other mechanisms may be more important for inter-primate differences in gene expression.
Abstract
In the 21st century, most of the world’s glaciers are expected to retreat due to further global warming. The range of this predicted retreat varies widely as a result of uncertainties in climate and glacier models. To calibrate and validate glacier models, past records of glacier mass balance are necessary, which often only span several decades. Long-term reconstructions of glacier mass balance could increase the precision of glacier models by providing the required calibration data. Here we show the possibility of applying shrub growth increments as an on-site proxy for glacier summer mass balance, exemplified by Salix shrubs in Finse, Norway. We further discuss the challenges which this method needs to meet and address the high potential of shrub growth increments for reconstructing glacier summer mass balance in remote areas.
Abstract
We present experiments on the luminescence of excitons confined in a potential trap at milli-Kelvin bath temperatures under continuous-wave (cw) excitation. They reveal several distinct features like a kink in the dependence of the total integrated luminescence intensity on excitation laser power and a bimodal distribution of the spatially resolved luminescence. Furthermore, we discuss the present state of the theoretical description of Bose–Einstein condensation of excitons with respect to signatures of a condensate in the luminescence. The comparison of the experimental data with theoretical results with respect to the spatially resolved as well as the integrated luminescence intensity shows the necessity of taking into account a Bose–Einstein condensed excitonic phase in order to understand the behaviour of the trapped excitons.
ZusammenfassungDer Aufsatz bietet den ersten konsistenten Überblick über den Wandel der politischen Positionen der protestantischen Theologie in der DDR. Mit Hilfe von Anregungen aus der Cambridge School der Ideengeschichte geht der Text der Frage nach, inwieweit die ostdeutsche evangelische Theologie Resistenzpotential gegenüber dem politischen Anpassungsdruck des SED-Regimes aufzubringen vermochte. Dabei widersprechen die Autoren der in der Forschung verbreiteten Auffassung, die Protestanten hätten die Theologie in obrigkeitstreuer Tradition einmal mehr den neuen Verhältnissen angepasst. Vielmehr lässt sich ein deutlicher Bruch nach 1945 erkennen, eine jahrelang anhaltende Kritik an der atheistischen Regierung und ein theologisches Ringen um ein angemessenes Obrigkeitsverständnis. Erst äußere Anlässe brachten die Kirchen dazu, ihre fundamentalkritische Theologie Zug um Zug aufzugeben. Dazu gehört die Zementierung der deutschen Teilung, die den Rückhalt der ostdeutschen Kirchen in der gesamtdeutschen EKD schwächte, oder auch die Ungleichheit in der Verteilung der Machtmittel, die die Kirchen an den Staat auslieferten. Neben diesen strukturellen Gründen benennen die Autoren ideelle Motive wie die Kritik an der Institution EKD, durch die sich die jüngeren Theologen von der älteren Generation ablösen wollten. Einflussreich waren auch internationale ökumenische Diskurse, die seit den siebziger Jahren den Kapitalismus zunehmend kritisch und den Sozialismus entsprechend positiv einordneten. Obwohl die wenigen verbliebenen Christen sich immer wieder unangepasst verhielten, ließ sich die Theologie insgesamt mehr und mehr zur Rechtfertigung des Anpassungsweges einspannen. Nicht sie bestimmte die politische Haltung. Vielmehr gaben äußere Faktoren die theologischen Positionsbestimmungen der Kirche vor.
The widespread use of natural and synthetic estrogens or chemicals with estrogenic activities is causing an increasing accumulation of estrogenic compounds in the environment. Already at very low concentrations these estrogenics can severely affect the wildlife, particularly in an aquatic environment. For these reasons measuring devices for detecting estrogen contaminations are in great demand. The majority of the analytical methods and bioassays on the market so far, lack semi-online adaptability, and usually cannot be used for automatic and continuous determination. Therefore, we have embarked on the development of new systems, which are able to fulfil those demands. The EstraMonitor combines recombinant A. adeninivorans G1212/YRC102-hERa-phyK yeast cells as the microbial component with an amperometric detection method to analyze estrogenic contaminations. A. adeninivorans G1212/YRC102-hERa-phyK was constructed by Kaiser et al. (2010). These cells were engineered to co-express the human estrogen receptor (hERa) gene and the inducible phytase (phyK, derived from Klebsiella sp. ASR1) reporter gene under control of a promoter with estrogen response elements (EREs). In the presence of estrogenic substances, such as 17ß -estradiol (E2), the phyK gene is expressed and recombinant phytase is secreted into the media. The level of phytase is quantified by amperometric detection using substrate p-aminophenyl phosphate (p-APP). Phytase dephosphorylates p-aminophenyl phosphate (p-APP) into an intermediate product p-aminophenol (p-AP). p-AP is electroactive and oxidized at the electrode. This generates electrons and produces a current which is proportional to the level of phytase activity. Since phytase activity is directly correlated to the E2 concentration, the estrogenic activity can thus be calculated from the current measured. The microbial component of the EstraMonitor, the non-immobilized A. adeninivorans G1212/YRC102-hERa-phyK, works well with the amperometric method in a quantitative manner. The optimal applied potential determined for amperometric measurements was 150 mV and provided a low background signal for the amperometric detection. The half maximal effective concentration (EC50) and limit of detection (LoD) values for E2 obtained from amperometric measurements with the EstraMonitor were 69.9 ng L-1 and 44.5 ng L-1, respectively. The measuring procedure of the EstraMonitor system including incubation of A. adeninivorans G1212/YRC102-hERa-phyK cells with E2, subsequently incubation with electrochemical substrate (p-APP), and signal recordation is completed within only 4 h and 10 min. Out of this total time, amperometric detection including substrate incubation and signals recordation takes only 10 min out of total time. The use of immobilized cells for a microbial biosensor is an essential advantage of the EstraMonitor system because it allows easy-handiness next to long-term stability and reusability. Immobilized A. adeninivorans G1212/YRC102-hERa-phyK cells revealed excellent properties which make them very suitable for semi-online, automatic and continuous monitoring. They were stable up to 30 days when stored at 4 °C. Furthermore, they could be reused up to 15 times. The EC50 and LoD values achieved for E2 using immobilized cells in combination with amperometric detection were 20.9 and 8.3 ng L-1, respectively. Furthermore, this application also removes the need to separate cells by centrifugation, to sterilize the samples as well as to cultivate repeatly. Additionally, both immobilized and non-immobilized A. adeninivorans G1212/YRC102-hERa-phyK cells remain fully functional in a wide range of untreated wastewater samples and in environments containing up to 5% NaCl. To enhance the sensitivity and reduce the time for estrogenic determination, an alternative A. adeninivorans G1214/YRC103-hERa-phyK strain was developed. This strain can produce a detectable amount of phytase within 2 h after induction with E2. It offers an improved microbial component in terms of sensitivity and time-effectiveness. In addition, to reduce the cost for estrogenic detection an alternative substrate, ascorbic acid 2-phosphate (AA2P), was tested. AA2P, which is both cheap and widely available, performed better than p-APP. The EC50 and LoD values for E2 obtained with AA2P were 15.69 and 0.92 ng L-1 versus 20.09 and 8.3 ng L-1 when examined with p-APP, respectively. Taken together, the EstraMonitor is an automated system with respect to sample cycling, sample measuring and calibration supplemented with an alarm function. This system makes it possible to control estrogenic activity semi-online, automatically and continuously. These are advantages of the EstraMonitor compared to other estrogenic detection systems. It can thus be concluded that, the EstraMonitor is a powerful and feasible semi-online device for monitoring estrogenic activity especially adapted for the use in sewage treatment plants.
In this thesis, all three BVMOs from Pseudomonas putida NCIMB10007, that were known to be responsible for the ability of this strain to degrade camphor since the 1950s were successfully made available as recombinant biocatalysts. While the genomic sequence of 2,5-DKCMO was available from the database, the genes encoding 3,6-DKCMO and OTEMO had to be identified using certain PCR-techniques first. All three enzymes were cloned into standard plasmids enabling convenient expression in E. coli facilitating the application of the enzymes in organic chemistry. Their synthetic potential was already reported during the 1990s, but at that time their efficient application was limited due to difficulties with respect to low production levels and insufficient purity and separation of enzyme fractions. These drawbacks are now overcome. Furthermore, biochemical characterization of the camphor-degrading BVMOs was performed including the substrate spectra of these enzymes. Thereby OTEMO turned out not only to have a broad substrate scope accepting mono- and bicyclic aliphatic and arylaliphatic ketones, but also to efficiently convert alpha/beta-unsaturated cycloalkanones due to the similarity of these compounds to OTEMOs natural substrate. Finally, the major limitation in the synthetic application of Type II BVMOs was addressed by searching a flavin-reductase suitable for coupling to these two-component oxygenases. Putative candidates from the respective P. putida strain were identified by the use of amino acid motifs conserved in other representatives of two-component systems. While these enzymes failed, flavin-reductase Fre from E. coli - that also contained the motifs - was shown to enhance the activity of the DKCMOs when applied as crude cell extract as well as pure enzyme. This finding represents a key step for future application of Type II BVMOs.
Indoloquinoline derivatives are very interesting compounds for pharmaceutical applications because of their broad spectrum of biological activity. However, phenyl-substituted indoloquinolines suffer from solubility problems in aqueous solution and require the synthesis of better soluble derivatives for their effective application. Therefore, the indoloquinoline derivatives were covalently attached to two different types of cationic aminoalkyl linkers. After having successfully established the synthesis and subsequent purification of the novel derivatives that could be isolated in excellent yields, these ligands were characterized in this thesis with regard to their spectral properties in different environments and their sequence specific binding to different types of nucleic acids with a variety of spectroscopic methods.
In order to identify possible experimental signatures of the superfluid to Mott-insulator quantum phase transition we calculate the charge structure factor S(k, ω) for the one-dimensional Bose-Hubbard model using the dynamical density-matrix renormalisation group (DDMRG) technique. Particularly we analyse the behaviour of S(k, ω) by varying – at zero temperature–the Coulomb interaction strength within the first Mott lobe. For strong interactions, in the Mott-insulator phase, we demonstrate that the DDMRG results are well reproduced by a strong-coupling expansion, just as the quasi-particle dispersion. In the super-fluid phase we determine the linear excitation spectrum near k = 0. In one dimension, the amplitude mode is absent which mean-field theory suggests for higher dimensions.
Patients with atrial fibrillation (AF) often present with typical angina pectoris and mildly elevated levels of cardiac troponin (non-ST-segment elevation myocardial infarction) during an acute episode of AF. However, in a large proportion of these patients, significant coronary artery disease is excluded by coronary angiography, which suggests that AF itself influences myocardial blood flow. The present review summarizes the effect of AF on the occurrence of ventricular oxidative stress, redox-sensitive signaling pathways and gene expression, and microcirculatory flow abnormalities in the left ventricle.
Ribozymes for Aminoacylation
(2012)
Aminoacyl-tRNA synthetases (aaRS) are at the heart of modern translation, catalyzing the accurate biosynthesis of aminoacyl-tRNAs. According to the RNA world hypothesis, the early translation system should have aminoacylation ribozymes for RNA aminoacylation. For this, an aaRS ribozyme system, consisting of the KK13 ribozyme and the C3a ribozyme was successfully designed, which can perform both amino acid activation and aminoacyl transfer reaction. Generation of such aminoacylation ribozyme system would fill up the gap between the RNA world and the modern biological world. In addition, two types of diversified aminoacylation ribozymes, symmetrical ribozymes and self-assembling ribozymes were successfully developed, which may have great meaning in the origin of life.