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A novel method for time-resolved tuned diode laser absorption spectroscopy has been developed. In this paper, we describe in detail developed electronic module that controls time-resolution of laser absorption spectroscopy system. The TTL signal triggering plasma pulse is used for generation of two signals: the first one triggers the fine tuning of laser wavelength and second one controls time-defined signal sampling from absorption detector. The described method and electronic system enable us to investigate temporal evolution of sputtered particles in technological low-temperature plasma systems. The pulsed DC planar magnetron sputtering system has been used to verify this method. The 2" in diameter titanium target was sputtered in pure argon atmosphere. The working pressure was held at 2 Pa. All the experiments were carried out for pulse ON time fixed at 100 (is. When changing OFF time the discharge has operated between High Power Impulse Magnetron Sputtering regime and pulsed DC magnetron regime. The effect of duty cycle variation results in decrease of titanium atom density during ON time while length of OFF time elongates. We believe that observed effect is connected with higher degree of ionization of sputtered particles. As previously reported by Bohlmark et al., the measured optical emission spectra in HiPIMS systems were dominated by emission from titanium ions [1].
The region surrounding the excitonic insulator phase is a three-component plasma composed of electrons, holes, and excitons. Due to the extended nature of the excitons, their presence influences the surrounding electrons and holes. We analyze this correlation. To this end, we calculate the density of bound electrons, the density of electrons in the correlated state, the momentum-resolved exciton density, and the momentum-resolved density of electron-hole pairs that are correlated but unbound. We find qualitative differences in the electron-hole correlations between the weak-coupling and the strong-coupling regime.
Abstract
Experimental studies on dusty plasmas containing systems of (super-)paramagnetic dust particles are presented. In our experiments, external (homogeneous as well as inhomogeneous) magnetic fields in the mT range are applied to study the effect on single particles or few-particle systems that are trapped inside the sheath region. The behavior of the paramagnetic dust particles is considerably different than that of dielectric plastic particles, which are widely used in dusty plasmas. It is revealed that especially non-magnetic contributions play an important role in the interaction between superparamagnetic particles.
Abstract
The presented experimental system is a barrier discharge system with plane parallel electrodes. The lateral surface charge distribution being deposited on the dielectric layer during each breakdown is observed optically using the well known electro-optic effect (Pockels effect). The temporal resolution of the surface charge measurement has been increased to 200 ns, and so for the first time it is possible to resolve the charge transfer to the dielectric surface in a single breakdown. In the present measurements, a patterned glow-like barrier discharge is investigated. It is found that the charge reversal in a single discharge spot (microdischarge) starts in the centre and then grows outwards. These experimental findings verify previously unconfirmed predictions from earlier numerical calculations and thereby contribute to a better understanding of the interaction between the plasma and the electrical charge on the electrodes.
During pregnancy, the maternal immune system faces a double dilemma: tolerate the growing semi-allogeneic fetus and at the same time protect the mother and the progeny against pathogens. This requires a fine and extremely regulated equilibrium between immune activation and tolerance. As professional antigen presenting cells, B cells and in particular B-1a B cells, can activate or tolerize T cells and thus participate in the generation or regulation of the immune response. B-1a B cells were involved in the humoral immune response leading to pre-eclampsia, one of the main medical complications during pregnancy. Here we demonstrated that B-1a B cells are additionally involved in cellular immune mechanisms associated with pregnancy complications. Using a mouse model of pregnancy disturbances, we showed that B-1a B cells from animals suffering pregnancy disturbances but not from those developing normal pregnancies induce the differentiation of naïve T cells into Th17 and Th1 cells. This differential role of B-1a B cells during pregnancy seems to be associated with the co-stimulatory molecule CD86 as normal pregnant mice showed lower percentages of CD86 expressing B-1a B cells as compared to pregnant mice developing pregnancy disturbances or to non-pregnant animals. Our data bring to light a new and not explored role of B-1a B cells in the context of pregnancy.
People smile in various emotional contexts, for example, when they are amused or angry or simply being polite. We investigated whether younger and older adults differ in how well they are able to identify the emotional experiences accompanying smile expressions, and whether the age of the smiling person plays a role in this respect. With this aim, we produced 80 video episodes of three types of smile expressions: positive-affect smiles had been spontaneously displayed by target persons as they were watching amusing film clips and cartoons. Negative-affect smiles had been displayed spontaneously by target persons during an interaction in which they were being unfairly accused. Affectively neutral smiles were posed upon request. Differences in the accompanying emotional experiences were validated by target persons' self-reports. These smile videos served as experimental stimuli in two studies with younger and older adult participants. In Study 1, older participants were less likely to attribute positive emotions to smiles, and more likely to assume that a smile was posed. Furthermore, younger participants were more accurate than older adults at identifying emotional experiences accompanying smiles. In Study 2, both younger and older participants attributed positive emotions more frequently to smiles shown by older as compared to younger target persons, but older participants did so less frequently than younger participants. Again, younger participants were more accurate than older participants in identifying emotional experiences accompanying smiles, but this effect was attenuated for older target persons. Older participants could better identify the emotional state accompanying smiles shown by older than by younger target persons. Taken together, these findings indicate that there is an age-related decline in the ability to decipher the emotional meaning of smiles presented without context, which, however, is attenuated when the smiling person is also an older adult.
Inflammation is part of the body's immune response in order to remove harmful stimuli—like pathogens, irritants or damaged cells—and start the healing process. Recurrent or chronic inflammation on the other side seems a predisposing factor for carcinogenesis and has been found associated with cancer development. In chronic pancreatitis mutations of the cationic trypsinogen (PRSS1) gene have been identified as risk factors of the disease. Hereditary pancreatitis (HP) is a rare cause of chronic pancreatic inflammation with an early onset, mostly during childhood. HP often starts with recurrent episodes of acute pancreatitis and the clinical phenotype is not very much different from other etiologies of the disease. The long-lasting inflammation however generates a tumor promoting environment and represents a major risk factor for tumor development This review will reflect our knowledge concerning the specific risk of HP patients to develop pancreatic cancer.
Because of its antimicrobial properties, nonthermal plasma could serve as an alternative to chemical antisepsis in wound treatment. Therefore, this study investigated the inactivation of biofilm-embedded Pseudomonas aeruginosa SG81 by a surface barrier-discharged (SBD) plasma for 30, 60, 150 and 300 s. In order to optimize the efficacy of the plasma, different carrier gases (argon, argon admixed with 1% oxygen, and argon with increased humidity up to approx. 80%) were tested and compared against 0.1% chlorhexidine digluconate (CHG) exposure for 600 s. The antimicrobial efficacy was determined by calculating the difference between the numbers of colony-forming units (CFU) of treated and untreated biofilms. Living bacteria were distinguished from dead by fluorescent staining and confocal laser scanning microscopy. Both SBD plasmas and CHG showed significant antimicrobial effects compared to the untreated control. However, plasma treatment led to a higher antimicrobial reduction (argon plasma 4.9 log<sub>10</sub> CFU/cm<sup>2</sup>, argon with admixed oxygen 3 log<sub>10</sub> CFU/cm<sup>2</sup>, and with increased gas humidity 2.7 log<sub>10</sub> CFU/cm<sup>2</sup> after 300 s) compared to CHG. In conclusion, SBD plasma is suitable as an alternative to CHG for inactivation of Pseudomonas aeruginosa embedded in biofilm. Further development of SBD plasma sources and research on the role of carrier gases and humidity may allow their clinical application for wound management in the future.
Purines of exogenous and endogenous sources are degraded to uric acid in human beings. Concentrations >6.8 mg uric acid/dl serum cause hyperuricemia and its symptoms. Pharmaceuticals and the reduction of the intake of purine-rich food are used to control uric acid levels. A novel approach to the latter proposition is the enzymatic reduction of the purine content of food by purine-degrading enzymes. Here we describe the production of recombinant guanine deaminase by the yeast Arxula adeninivorans LS3 and its application in food. In media supplemented with nitrogen sources hypoxanthine or adenine, guanine deaminase (AGDA) gene expression is induced and intracellular accumulation of guanine deaminase (Agdap) protein occurs. The characteristics of the guanine deaminase isolated from wild-type strain LS3 and a transgenic strain expressing the AGDA gene under control of the strong constitutive TEF1 promoter were determined and compared. Both enzymes were dimeric and had temperature optima of 55°C with high substrate specificity for guanine and localisation in both the cytoplasm and vacuole of yeast. The enzyme was demonstrated to reduce levels of guanine in food. A mixture of guanine deaminase and other purine degradation enzymes will allow the reduction of purines in purine-rich foods.
SummaryBackground: According to the literature, ductoscopy is gaining increasing importance in the diagnosis of intraductal anomalies in cases of pathologic nipple discharge. In a multicenter study, the impact of this method was assessed in comparison with that of standard diagnostics. Patients and Methods: Between 09/2006 and 05/2009, a total of 214 patients from 7 German breast centers were included. All patients underwent elective ductoscopy and subsequent ductal excision because of pathologic nipple discharge. Ductoscopy was compared with the following standard diagnostics: breast sonography, mammography, magnetic resonance imaging (MRI), galactography, cytologic nipple swab, and ductal lavage cytology. The histological and imaging results were compared and contrasted to the results obtained from the nipple swab and cytologic assessment. Results: Sonography had the highest (82.9%) sensitivity, followed by MRI (82.5%), galactography (81.3%), ductoscopy (71.2%), lavage cytology (57.8%), mammography (57.1%), and nipple swab (22.8%). Nipple swabs had the highest (85.5%) specificity, followed by lavage cytology (85.2%), ductoscopy (49.4%), galactography (44.4%), mammography (33.3%), sonography (17.9%), and MRI (11.8%). Conclusion: Currently, ductoscopy provides a direct intraoperative visualization of intraductal lesions. Sensitivity and specificity are similar to those of standard diagnostics. The technique supports selective duct excision, in contrast to the unselective technique according to Urban. Therefore, ductoscopy extends the interventional/diagnostic armamentarium.
Neural characteristics of verbal creativity as assessed by word generation tasks have been recently identified, but differences in resting-state functional connectivity (rFC) between experts and non-experts in creative writing have not been reported yet. Previous electroencephalography (EEG) coherence measures during rest demonstrated a decreased cooperation between brain areas in association with creative thinking ability. Here, we used resting-state functional magnetic resonance imaging to compare 20 experts in creative writing and 23 age-matched non-experts with respect to rFC strengths within a brain network previously found to be associated with creative writing. Decreased rFC for experts was found between areas 44 of both hemispheres. Increased rFC for experts was observed between right hemispheric caudate and intraparietal sulcus. Correlation analysis of verbal creativity indices (VCIs) with rFC values in the expert group revealed predominantly negative associations, particularly of rFC between left area 44 and left temporal pole. Overall, our data support previous findings of reduced connectivity between interhemispheric areas and increased right-hemispheric connectivity during rest in highly verbally creative individuals.
Background: Abdominal surgery is frequently followed by immune dysfunction usually lasting for several days. This is especially important in cases with tumour diseases as an intact immune function is essential in this situation. Therefore, we analysed the outcome of tumour-bearing mice in a mouse model of surgically induced immune dysfunction (SID). Methods: In male C57BL/6 mice, a pancreatic tumour was implanted orthotopically. Following tumour implantation, the model of SID was applied. The control groups were either laparotomised or underwent no surgical procedure. The survival rate was determined by observation for >60 days. The tumour growth progress was imaged by a 7-tesla small animal MRI. Results: On day 60 after tumour implantation, the survival rate in SID mice was reduced to 41%. In the laparotomised group, 81% of mice survived, while the control group had a survival rate of 75%. These differences were significant (SID vs. control: p < 0.02, and SID vs. laparotomy: p < 0.002). The tumour volume was not influenced by the degree of surgical trauma. Conclusion: In pancreatic cancer, the SID model is ideally suited to investigate the influence of SID on this tumour entity.
Background: Alcohol dependence is among the most severely stigmatized mental disorders. We examine whether negative stereotypes and illness beliefs related to alcohol dependence have changed between 1990 and 2011. Methods: We used data from two population surveys with identical methodology that were conducted among German citizens aged ≥18 years, living in the ‘old' German states. They were conducted in 1990 and 2011, respectively. In random subsamples (1990: n = 1,022, and 2011: n = 1,167), identical questions elicited agreement with statements regarding alcohol dependence, particularly with regard to the illness definition of alcohol dependence and blame. Results: Overall, agreement with negative stereotypes did not change in the course of 2 decades. About 55% of the respondents agreed that alcohol dependence is an illness like any other, >40% stated that it was a weakness of character and 30% endorsed that those affected are themselves to blame for their problems. Conclusions: It is apparent that promoting an illness concept of alcohol dependence has not been an easy solution to the problem of stigma. We discuss how the normative functions of alcohol dependence stigma might have prevented a reduction of negative stereotypes.
Congenital hyperinsulinism (CHI) causes hypoglycemia due to irregular insulin secretion. In infants, a rapid diagnosis and appropriate management to avoid severe hypoglycemia is mandatory. CHI is a heterogeneous condition at the clinical and genetic level, and disease-causing genes have been identified in about half of the patients. The majority of mutations have been identified in the ABCC8 and KCNJ11 genes encoding subunits of the K<sub>ATP</sub> channel responsible for two distinct histological forms. The diffuse form is caused by autosomal recessive or dominant inherited mutations, whereas the focal form is caused by a paternally transmitted recessive mutation and a second somatic event. We report on an unselected cohort of 136 unrelated patients from the German CHI registry. Mutations in either the ABCC8 or KCNJ11 gene were identified in 61 of these patients (45%). In total, 64 different mutations including 38 novel ones were detected in this cohort. We observed biparental (recessive) inheritance in 34% of mutation-positive patients, dominant inheritance in 11% and paternal transmission of a mutation associated with a focal CHI type in 38%. In addition, we observed inheritance patterns that do not exactly follow the classical recessive or dominant mode, further adding to the genetic complexity of this disease.
Objective: Epithelioid sarcoma (ES) presents unique clinical features in comparison to other sarcoma subtypes. Data regarding the benefits of chemotherapy are very limited. Combination regimens using gemcitabine and docetaxel (Gem/Doce) have proven to be effective, especially in uterine and nonuterine leiomyosarcoma. Yet, there is no available data on the efficacy of Gem/Doce in ES. Methods: A retrospective analysis of the three participating institutions was performed. Twenty-eight patients with an ES diagnosis presented at one of the participating institutions between 1989 and 2012. Of this group, 17 patients received chemotherapy. Results: Patients' median overall survival (OS) after the beginning of palliative chemotherapy was 21 months, and the 1-year OS was 87%. Twelve patients received Gem/Doce with a clinical benefit rate of 83%. The median progression-free survival (PFS) was 8 months for all patients receiving Gem/Doce. The best response was complete remission in 1 patient and partial remission in 6 patients. All 6 patients receiving Gem/Doce as a first-line treatment showed measurable responses with a median PFS of 9 months. Conclusions: In this retrospective study, Gem/Doce was an effective chemotherapeutic regimen for ES. Prospective studies are needed to better assess the effects of this combination drug therapy.
Background: Animal studies and data from a single-center study suggest that tobacco smoke exposure may be a risk factor for precapillary pulmonary hypertension (PH). Objective: We aimed to survey tobacco smoke exposure in a large PH collective and to compare it with epidemiological data from healthy subjects. Methods: This is an international, multicenter, case-control study including patients with pulmonary arterial and chronic thromboembolic PH. All patients were asked specific questions about tobacco smoke exposure. Healthy controls were retrieved from the Swiss Health Survey (n = 18,747). Results: Overall (n = 472), 49% of PH patients were smokers and there was a clear sex difference (women 37%, men 71%). Significantly more PH men were smokers compared with healthy controls, whereas less PH women were ever active smokers. However, 50% of the non-smoking PH women were exposed to secondhand smoke, leading to a significantly higher number of tobacco smoke-exposed individuals compared to healthy controls. PH smokers were significantly younger compared to those not exposed. Conclusion: Active and environmental tobacco smoke exposure is common in PH. The higher prevalence of male PH smokers, the higher exposure to environmental tobacco smoke in PH women compared to healthy controls and the lower age at PH diagnosis in smokers may indicate a pathogenic role of tobacco smoke exposure in PH.
Staphylococcus aureus is a human pathogen that can cause a wide range of diseases. Although formerly regarded as extracellular pathogen, it has been shown that S. aureus can also be internalized by host cells and persist within these cells. In the present study, we comparatively analyzed survival and physiological adaptation of S. aureus HG001 after internalization by two human lung epithelial cell lines (S9 and A549), and human embryonic kidney cells (HEK 293). Combining enrichment of bacteria from host-pathogen assays by cell sorting and quantitation of the pathogen's proteome by mass spectrometry we characterized S. aureus adaptation during the initial phase between 2.5 h and 6.5 h post-infection. Starting with about 2 × 106 bacteria, roughly 1450 S. aureus proteins, including virulence factors and metabolic enzymes were identified by spectral comparison and classical database searches. Most of the bacterial adaptation reactions, such as decreased levels of ribosomal proteins and metabolic enzymes or increased amounts of proteins involved in arginine and lysine biosynthesis, enzymes coding for terminal oxidases and stress responsive proteins or activation of the sigma factor SigB were observed after internalization into any of the three cell lines studied. However, differences were noted in central carbon metabolism including regulation of fermentation and threonine degradation. Since these differences coincided with different intracellular growth behavior, complementary profiling of the metabolome of the different non-infected host cell types was performed. This revealed similar levels of intracellular glucose but host cell specific differences in the amounts of amino acids such as glycine, threonine or glutamate. With this comparative study we provide an impression of the common and specific features of the adaptation of S. aureus HG001 to specific host cell environments as a starting point for follow-up studies with different strain isolates and regulatory mutants.
The Role of Pregnancy-Associated Hormones in the Development and Function of Regulatory B Cells
(2014)
During mammalian pregnancy, highly specialized mechanisms of immune tolerance are triggered in order to allow the semi-allogeneic fetus to grow within the maternal uterus in harmony with the maternal immune system. Among other mechanisms, changes in the endocrine status have been proposed to be at least part of the machinery responsible for the induction of immune tolerance during pregnancy. Indeed, pregnancy-associated hormones, estradiol, progesterone, and human chorionic gonadotropin are known to confer immune suppressive capacity to innate as well as adaptive immune cells. Regulatory B cells, a subpopulation of B lymphocytes with strong immunosuppressive functions, were shown to expand during pregnancy. Furthermore, it is well-known that some women suffering from multiple sclerosis, significantly improve their symptoms during pregnancy and this was attributed to the effect of female sex hormones. Accordingly, estradiol protects mice from developing experimental autoimmune encephalomyelitis by triggering the expansion and activation of regulatory B cells. In this review, we discuss different mechanisms associated with the development, activation, and function of regulatory B cells with a special focus on those involving pregnancy-associated hormones.
Many ethicists consider the rule of nonmaleficence – Do no harm! – to be the most fundamental ethical rule and key to ethics. This rule is taken as the foundation of the present work. I argue that any entity, that can be harmed, ought to be morally considered. Only those entities can be harmed that are inherently goal-directed or striving – in other words, that possess a telos. The reason is that by constantly acting in ways to preserve their being and to prevent their own not-being, goal-directed entities express that they value their own good. To harm such a goal-directed entity therefore means to act against the values and the good of it. The argument so far supports ethical biocentrism, that is, the view that all living, goal-directed beings are harmable, possess interests, and are, thus, morally considerable, while non-living beings are not. Yet, I digress from classical biocentrism since I conclude, based on analysis of evolutionary and biological findings, that the locus of goal-directedness and potential harm is also, if not foremost, situated in genes. Within many species, individual organisms sacrifice themselves for the betterment of their descendants like in praying mantises where males sacrifice themselves and are eaten by the female during copulation. This shows that it is not necessarily the organism as an individual which follows its own interests and goals. Individual organisms are – to a high degree – “directed” by their genes. Even in highly developed animals, genes play a significant role in the goal-directedness of the individuals. An adult human organism, for example, consists of trillions of individual cells. However, all these cells are derived from a single cell – the fertilized egg. Each of our lives begins with a single cell that contains almost all information to finally form our functioning body. Where do all the instructions, the goal-directedness come from to finally form an adult organism if not from the genes contained in this first cell, the zygote? It is the genes of each zygote that contain a set of information for making the appropriate adult. Organisms are largely programmed to do everything necessary to stay in existence, to survive, and finally to pass on their genes successfully – either by reproducing or by helping close relatives that carry a similar set of genes. The main interests of genes lie in their continued existence. This necessitates reproduction since the gene-carrying organisms will inevitably die. Single genes, though, are difficult to morally consider directly since they perform entirely in and through individual organisms. Without the individual organisms, genes cannot survive. The good news for ethics is that the interests of genes and organism usually converge: individual organisms try to survive – as do their genes. In practice, it thus makes much more sense to give moral attention to entire organisms instead of single genes. An advantage of the gene-centric ethical theory proposed here is that the moral relevance of future generations and species can be “directly” justified: Since genes have an interest in their continued existence (in the form of identical copies), they would be harmed if future generations were doomed to inexistence. Within a species with many individuals, each gene is likely to be represented in many organisms. The smaller the gene pool of a species gets, the less likely is the existence of the same gene and, therefore, the less likely is the fulfillment of its fundamental interests. Hence, saving one of the last individuals of an endangered species would be ethically preferable to saving an individual of a populous species. Unfortunately, moral conflicts are abundant – not only concerning biodiversity conservation. We often have to choose between harming either entity A or entity B – for example in the daily questions of food and eating. In such cases, a strictly egalitarian theory (especially an egalitarian biocentric one) would be no real help and without any guiding power. Therefore, on a second level of morality, we have to include additional criteria that help to minimize the overall harm. For these criteria to be objective, universalizable, and thus moral ones, I apply a number of widely accepted ethical principles like the principle of proportionality, impartiality, self-defense, and universalizability. By recurring to these principles, I identify a set of morally relevant criteria for a fair resolution of moral conflict situations which help to minimize the overall harm done. The identified criteria are: (phylogenetic) nearness, endangerment, r- or K-selected species, evolutionary distinctiveness, ability to regrow and to regenerate, pain-susceptibility, and ecosystematic role. In sum, my gene-centric environmental ethical theory provides numerous reasons and arguments for biodiversity conservation – for protecting genes, organisms, species, and ecosystems alike – without neglecting the needs of humans.
The globally threatened Aquatic Warbler (Acrocephalus paludicola) is the rarest migratory songbird in Europe. Before the population declined dramatically after 1960, the Aquatic Warbler was a common species in European mires and river flood¬plains. Today, the global population is estimated to count 27 600 individuals, of which approx. 90 % are concentrated in only three countries during the breeding season: Belarus, Poland and Ukraine. Despite numerous conservation efforts mainly under¬taken in European countries, the population decline has not been stopped. Although the Aquatic Warbler is considered a “European” bird species because of the location of its breeding grounds, it spends up to six months on migration and on the wintering grounds on the African continent. A comprehensive species conservation strategy must therefore include the preservation of African resting and wintering grounds. This study analyses the ecol¬ogy of Aquatic Warbler in its wintering grounds using the example of the Djoudj National Park area in north-western Senegal. The study aims, first, to close knowledge gaps regarding the behaviour and the habitat requirements of Aquatic Warblers during their stay on the wintering grounds to provide a scientific base for long-term species conservation management; second, to assess the importance of the wintering site in the Djoudj area is in a global perspec¬tive; and third, to identify threats to the Djoudj area as a suitable Aquatic Warbler habitat. In a fourth step, science-based management recommendations are formu¬lated to support the ongoing practical conservation work of the Djoudj National Park administration with regard to the Aquatic Warbler. The main outcomes of the study are the following: (I) We confirmed the presence of Aquatic Warblers in the Djoudj area between mid-December and the end of March. (II) The connection between the wintering ground “Djoudj National Park area” and the breeding ground “Biebrza valley” (eastern Poland) was confirmed by the resighting of a ringed Aquatic Warbler individual. (III) The remiges moult of the species was observed under natural conditions for the first time. We confirmed that the Aquatic Warbler undergoes a complete moult on its wintering grounds, following the typical sequence of passerine moult. (IV) Aquatic Warblers occur in shallowly inundated vegetation with dominant stands of Oryza longistaminata, Eleocharis mutata, Scirpus maritimus, Scirpus litto¬ralis and Sporobulus robustus interspersed with small (1–2 m²) areas of open water. The afore mentioned herbaceous species form a homogenous wetland vegetation of approximately 0.6–1.5 m height, with a coverage of 80 % to 100 %. Wild rice (Oryza longistaminata) may provide the most suitable habitat conditions as suggested by the very high density of Aquatic Warblers at sites dominated by this species. Preferential habitat may include a few solitary trees, but open woodland or scrublands are unsuit-able for Aquatic Warbler. Pure stands of cattail (Typha australis) are avoided. The water level in the habitat areas varies between 0 (humid soil) and 40 cm above the ground. Constant inundation seems to be essential, as Aquatic Warblers were never encountered in dry parts of the study area. All known Aquatic Warbler habitats in the study area are influenced by brackish or salty water. (V) During winter Aquatic Warblers use a home range of 3.9 ha (± 1.9) in aver¬age, which is shared with other individuals and species. No territorial behaviour was observed in the winter quarters. (VI) The vegetation and land cover map prepared distinguishes six classes of her¬baceous vegetation and five general land cover classes. (VII) There are 4 729 ha of potential Aquatic Warbler habitat within the study area. (VIII) We estimate the density of the Aquatic Warbler population in the study area to range between 0 and 2.26 individuals per hectare with a total population size of 776 individuals, or 260–4 057 individuals in a 95 % credibility interval. Hence we conclude that 1.1–3.8 % (0.37–19.8 % within the 95 % credibility interval) of the global Aquatic Warbler wintering population are found in the Djoudj area. (VIII) The Aquatic Warbler habitats in the Djoudj area are affected by the inun¬dation regime, water circulation, changes in salinity, grazing, the spread of cattail (Typha australis), the encrustation of vegetation, the protection status of passerine migrator habitats and the expansion of rice cultivation a. Our management proposals for the preservation of existing and the development of new Aquatic Warbler habitats were formulated and incorporated into the Management Plan of the Djoudj National Park 2014–2018.
Magnetic reconnection is a ubiquitous phenomenon observed in a wide range of magnetized plasmas from magnetic confinement fusion devices to space plasmas in the magnetotail. The process enables the release of accumulated magnetic energy by rapid changes in magnetic topology, heating the plasma in the vicinity of the reconnection site, generating fast particles and allowing a wealth of instabilities to grow. This thesis reports on the results from a newly constructed linear, cylindrical and modular guide field reconnection experiment with highly reproducible events, VINETA.II. A detailed analysis of the reconnecting current sheet properties on a macroscopic and microscopic scale in time and space is presented. In the experiment, four parallel axial wires create a figure-eight in-plane magnetic field with an X-line along the central axis, as well as an axial inductive field that drives magnetic reconnection. Particle-in-cell simulations show that the axial current is limited by sheaths at the boundaries and that electrostatic fields along the device axis always set up in response to the induced electric field. Current sheet formation requires an additional electron current source, realized as a plasma gun, which discharges into a homogeneous background plasma created by a rf antenna. The evolution of the plasma current is found to be dominantly set by its electrical circuit. The current response to the applied electric field is mainly inductive, which in turn strongly influences the reconnection rate. The three-dimensional distribution of the current sheet is determined by the magnetic mapping of the plasma gun along the sheared magnetic field lines, as well as by radial cross-field expansion. This expansion is due to a lack of equilibrium in the in-plane force balance. Resistive diffusion of the magnetic field by E=η j is found to be by far insufficient to account for the high reconnection rate E=-dΨ/dt at the X-line, indicating the presence of large electrostatic fields which do not contribute to dissipative reconnection. High-frequency magnetic fluctuations are observed throughout the current sheet which are compared to qualitatively similar observations in the Magnetic Reconnection Experiment (MRX, Princeton). The turbulent fluctuation spectra in both experiments display a spectral kink near the lower hybrid frequency, indicating the presence of lower hybrid type instabilities. In contrast to the expected perpendicular propagation of mainly electrostatic waves, an electromagnetic wave is found in VINETA.II that propagates along the guide field and matches the whistler wave dispersion. Good correlation is observed between the local axial current density and the fluctuation amplitude across the azimuthal plane. Instabilities driven by parallel drifts can be excluded due to the large required drift velocities or low resulting phase velocities that are not observed. It is instead suggested that a perpendicular, electrostatic lower hybrid mode indeed exists that resonantly excites a parallel, electromagnetic whistler wave through linear mode conversion. The resulting fluctuations are found to be intrinsic to the localized current sheet and are independent of the slower reconnection dynamics. Their amplitude is small compared to the in-plane fields, and have a negligible contribution to anomalous resistivity through momentum transport in the present parameter regime.
Non-healing wounds pose a major burden to patients and health care systems alike. These wounds are chronically stuck in the inflammatory phase of the healing process without transitioning to the proliferative phase. They are also characterized by the excessive presence of leukocytes which are assumed to provoke the persistent inflammation observed in pathological wound healing. Recent studies suggested a beneficial role of cold physical plasma in the treatment of chronic wounds. Hence, it was the central question, whether exposure to cold physical plasma would affect the viability and/or function of human leukocytes. Cold plasma displays various properties of which the generation of reactive molecules, such as reactive oxygen and nitrogen species (ROS/RNS), where found to be central in mediating redox changes in leukocytes. Oxidative stress was present especially in lymphocytes that readily underwent apoptosis after exposure to plasma. This was largely a direct consequence of plasma-generated hydrogen peroxide but not superoxide or RNS. Amount of apoptosis was comparable among several lymphocyte subpopulations, with the wound healing-relevant γδ T cells being least affected. Lymphocyte apoptosis was accompanied by mitochondrial membrane depolarization, caspase 3 activation, DNA fragmentation, and phosphatidylserine exposure. These results are in line with previous characterizations of the intrinsic apoptotic pathway in redox biology, and suggest that plasma-induced apoptosis was not mediated by alternative molecular mechanisms. An important immune response mechanism, the proliferation of lymphocytes, was not interrupted in plasma-treated but non-apoptotic cells. In wounds, a central role of leukocytes is to orchestrate the healing response via the release of small communication molecules called cytokines. Non-healing wounds are associated with elevated amounts of pro-inflammatory IL-1β, IL-6, and TNFα, and plasma-treatment of leukocytes strongly decreased their concentrations. At the same time, the expression of anti inflammatory cytokines (IL-10, TGFβ) was markedly increased. The pro inflammatory chemokine IL-8 was the only molecule to be significantly increased in supernatants of plasma-treated cells. IL-8 is the major chemo-attractant for neutrophil granulocytes. Neutrophils are frequently associated with non-healing wounds. These professional phagocytes are the first to migrate to the site of injury where they inactivate invading pathogens by various mechanisms. Importantly, highly relevant effector functions remained mostly unaffected by plasma treatment: the phagocytosis of bacteria, the oxidative burst, and the intracellular killing of microbes. Of note, plasma induced a strong induction of neutrophil extracellular traps (NETs). Decorated with antimicrobial proteins, NETs are web-like chromatin extrusions that entrap pathogens. These results have several implications for wound healing. Plasma-treated neutrophils were still capable of eradicating bacteria, which are frequently associated with non-healing wounds. In addition, plasma-induced NETs could aid in wound healing by providing an antibacterial scaffold to safeguard against further dissemination of microorganisms. Chronic wounds display a state of sustained inflammation and plasma induced apoptosis but not necrosis in lymphocytes. This was an important finding as necrosis, the involuntary cell death, is associated with the release of intracellular content, enhancing inflammation. By contrast, apoptosis dampens it as dead cells are cleared by macrophages inducing anti inflammatory responses. Further, the cytokine signature of plasma-treated leukocytes was largely non inflammatory, which could further decrease inflammation in wounds. Altogether, this work provided first insight with regard to effects and mechanisms of cold physical plasma treatment of wound-relevant leukocytes. Generally, these cells were affected by a plasma mediated modulation of their redox state. Future studies should include the possibility of redox modulation into their experimental approach to further elucidate the role of ROS/RNS in inflammation and possibly to improve existing wound healing therapies.
In the PhD-thesis a conditional random field approach and its implementation is presented to predict the interaction sites of protein homo- and heterodimers using the spatial structure of one protein partner from a complex. The method includes a substantially simple edge feature model. A novel node feature class is introduced that is called -change in free energy-. The Online Large-Margin algorithm is adapted in order to train the model parameters given a classified reference set of proteins. A significantly higher prediction accuracy is achieved by combining our new node feature class with the standard node feature class relative accessible surface area. The quality of the predictions is measured by computing the area under the receiver operating characteristic.
The present thesis deals with dynamic structures that form during the expansion of plasma into an environment of much lower plasma density. The electron expansion, driven by their pressure, occurs on a much faster time scale than the ion expansion, owed to their mobility. The high inertia of the ions causes the generation of an ambipolar electric field that decelerates the escaping electrons while accelerating the ions. The ambipolar boundary propagates outwards and forms a plasma density front. For a small density differences, the propagation of the front can be described with the linear ansatz for ion acoustic waves. For a large density differences, experiments have shown that the propagation velocity of such a front is still related to the ion sound velocity. However, the reported proportionality factors are scattered over a wide range of values, depending on the considered initial and boundary conditions. In this thesis, the dynamics during plasma expansion are studied with the use of experiments and a versatile particle-in-cell simulation. The experimental investigations are performed in the linear helicon device Piglet. The experiment features a fast valve, which is used to shape the neutral gas density profile. During the pulsed rf-discharges, plasma is generated in the source region and expands collisionless into the expansion chamber. The computer simulation is tailored very close to the experiment and provides a deeper insight in the particle kinetics. The experimental results show the existence of a propagating ion front. Its velocity is typically supersonic and depends on the density ratio of the two plasmas. The ion front features a strong electric field. The front can have similar properties to a double layer is not necessarily a double layer by definition. The computer simulation reveals that the propagating electric field repels the downstream ambient ions. These ions form a stream with velocities up to twice as high as the front velocity. The observed ion density peak is due to the accumulation of the repelled ions and is located at their turning point. The ion front formation depends strongly on the initial ion density profile and is part of a wave-breaking phenomenon. The observed front is followed by a plateau of little plasma density variation. This could be confirmed for the expansion experiment by a comparison with virtual diagnostics in the computer simulation. The plateau has a plasma density determined by the ratio between the high and low plasma density. It consists of streaming ions that have been accelerated in the edge of the main plasma. The presented results confirm and extend findings obtained by independent numerical models and simulations.
The central aim of this thesis was the investigation of protein/polyanion interaction using circular dichroism (CD) spectroscopy, enzyme immune assay (EIA), isothermal titration calorimetry (ITC) and flow cytometry (FC). A further aim was to understand why an endogenous protein becomes immuno-genic when forming a complex. The focus was on the protein platelet factor (PF4), which gained wide interest in the clinical field, due to its role in the life-threatening, immune-driven, adverse drug effect heparin-induced thrombocytopenia (HIT). PF4 is a small homotetrameric chemokine with several basic amino acids on its surface, forming a positively charged ring. The antibodies that are formed during HIT recognize an epitope exposed on PF4, when it is in a complex with heparin at a certain molar ratio at which, PF4 tetramers are aligned on the heparin and forced into close approximation. The main results and conclusions of the thesis are summarized below: 5.1 Evolutionary Conservation of PF4 (Paper I – PF4/Evolution) By carrying out an amino acid sequence survey we found that the positively charged amino acids contributing to the heparin binding site on the surface of PF4 and related proteins are highly conserved in all vertebrates, including fish species. PF4 interacts with the phospholipid lipid A, the innermost part of the lipopolysaccharide (LPS) of Gram negative bacteria. We showed that the shorter the sugar chain of the O antigen, outer and inner core of the LPS were the more PF4 was binding. The interaction of PF4 with lipid A is inhibited by heparin, suggesting that the amino acids known to contribute to heparin binding are also involved in binding to lipid A. 5.2 PF4 Interaction with Polyanions (PA) of varying Length and Degree of Sulfation (Paper II – PF4/PA) CD spectroscopy was found to be a powerful technique to monitor structural changes of PF4 caused by binding to various clinically relevant polyanions. Therefore PF4 was titrated with different PA to investigate the dependencies: i. impact of the PF4:PA molar ratio, ii. degree of polymerization of the PA and iii. degree of sulfation of the PA. In all cases, exposure of HIT-relevant epitope(s) was only observed for PA that also induced changes in secondary structure of PF4. A comparison of results of an immune ¬assay with CD spectroscopic data showed that the extent of complex anti¬genicity correlates well with the magnitude of changes in PF4 secondary structure, and that the structural changes of PF4 have to exceed a certain threshold to achieve PF4/PA complex antigenicity. These findings allowed us to calculate expectation intervals for complex antigenicity solely using CD spectroscopic data. To our knowledge, this was the first demonstration that the capability of drugs to induce antigenicity of PF4 can be assessed without the necessity of in vivo studies or the use of antibodies obtained from immunized patients specific for the antigens. The antigenicity of PF4 in complex is not restricted to negative charges originating from sulfate groups, PA with phosphate groups are also capable (binding to phospholipids). We investigated inorganic polyphosphates (polyP) with a chain length of 75 Pi and showed that the induced secondary structural changes are even higher compared to the changes induced by the different heparins and that the PF4/P75 complexes are antigenic as well. 5.3 PF4 Interaction with defined oligomeric Heparins (Paper III – PF4/defined Heparins) We tested highly purified, monodisperse heparins. In contrast to the clinically relevant but relatively undefined (high polydispersity index) glycosamino glycans reported in paper II (PF4/PA). The defined heparins induced higher secondary structural changes. Here we showed for the first time that strong conformational changes during PF4/PA complex formation are necessary but not sufficient for to the expression of the anti-PF4/heparin antibody binding site. Also, the size of the complexes is not the only prerequisite for anti-PF4/heparin antibody binding (tested by atomic force microscopy). By ITC we found that antigenicity is only induced if the PF4/PA complex has a high binding enthalpy and the complex formation leads to a negative change in entropy. 5.4 PF4/Polyphosphates (polyP) Complex Antigenicity and Interaction with Escherichia coli (E. coli, Paper IV – PF4/polyP) PolyP with chain lengths of 45 Pi and 75 Pi induced remarkable secondary structural changes in the PF4 molecule, thereby exposing the epitope recognized by anti-PF4/heparin antibodies. The induced conformational changes were similar to the changes induced by the defined heparins. Again a high binding enthalpy was observed but here in connection with a positive change in entropy. Further we showed that polyP (≥45 Pi) enhance PF4 binding to the surface of Gram negative E. coli at intermediate concentration and disrupt the binding at elevated polyP concentrations. The increased amounts of PF4 on the bacterial surface also improved the binding of anti-PF4/heparin antibodies and thereby the phagocytosis of the bacteria by poly¬morpho¬nuclear leucocytes. 5.5 Nucleic acid based Aptamers induce structural Changes in the PF4 Molecule (Paper V – PF4/Aptamer) Nucleic acids are another class of molecules containing phosphate groups. Especially after cell damage their extra¬cellular concentration can be locally quite high (>2 mg/ml). We found that certain aptamers form complexes with PF4 and thereby inducing anti-PF4/aptamer antibodies which cross-react with PF4/heparin complexes. Moreover by CD spectroscopy we showed that the protein C-aptamer caused similar secondary structural changes of PF4 like heparin, but already at much lower concentration. The maximally induced changes by the protein-C aptamer were even higher and persisted over a broader concentration range. 5.6 Protamine Interaction with Heparin (Paper VI – PS/Heparin) After the intensive investigation of the complex formation between PF4 and many different classes of PA we assessed another protein for structural changes upon complex formation with heparin. Protamine (PS) a protein in routinely used in post-cardiac surgery to reverse the anticoagulant effects of heparin was found to unfold but not to refold with increasing concentration of PA in solution. 5.7 Conclusion and Outlook When starting this thesis, it was believed that repetitive structures formed by PF4 on a heparin chain mold the epitope recognized by antibodies inducing HIT. These repetitive structures might exhibit similarities with viral capsids and are therefore recognized by the immune system of some patients. We found that induced by the close approximation PF4 changes its conformation, thereby exposing a neoepitope. The conserved positively charged amino acids of the heparin binding site and the involvement of these amino acids in the binding to lipid A confirm our hypothesis of PF4 as part of an ancient immune-mediated host defense mechanism. As possible consequence of the “primitive mechanism of defense” the highly variable O-antigens of LPS might have significantly contributed to an efficient escape mechanism by hiding the structures that made the bacteria vulnerable. In turn polyP might be an adaption of the host improve pathogen recognition by PF4 and further by antibodies inducing phagocytosis of the PF4-marked objects. Although shown only for PF4 and PS, our findings might be applicable to other proteins that also express epitopes upon changes in their secondary structure. Our physicochemical methods may further be applied: i. to drug development for the prediction of antigenicity induced by polyanionic drugs, ii. to guide the development of synthetic heparins and other polyanion based drugs, e.g. aptamers, that do not lead to HIT and iii. to provide relevant aspects for other biological functions of heparins.
The constructions of Lévy processes from convolution semigroups and of product systems from subproduct systems respectively, are formally quite similar. Since there are many more comparable situations in quantum stochastics, we formulate a general categorial concept (comonoidal systems), construct corresponding inductive systems and show under suitable assumptions general properties of the corresponding inductive limits. Comonoidal systems in different tensor categories play a role in all chapters of the thesis. Additive deformations are certain comonoidal systems of algebras. These are obtained by deformation of the algebra structure of a bialgebra. If the bialgebra is even a Hopf algebra, then compatibility with the antipode automatically follows. This remains true also in the case of braided Hopf algebras. Subproduct systems are comonoidal systems of Hilbert spaces. In the thesis we deal with the question, what are the possible dimensions of finite-dimensional subproduct systems. In discrete time, this can be reduced to the combinatorial problem of determining the complexities of factorial languages. We also discuss the rational and continuous time case. A further source for comonoidal systems are universal products, which are used in quantum probability to model independence. For the (r,s)-products, which were recently introduced by S. Lachs, we determine the corresponding product of representations by use of a generalized GNS-construction.
The dentate gyrus (DG) of the hippocampus is one of the stem cell housing niches in the adult mammalian brain. Canonical Wingless-type (Wnt) signals provided by the microenvironment are one of the major niche factors that regulate the differentiation of adult neural stem cells (aNSCs) towards the neuronal lineage. Wnts are part of a complex and diverse set of signaling pathways with a wide range of possible interactions. It remains unknown whether different canonical and non-canonical Wnt signals act in a stage-specific manner to regulate distinctive steps of adult hippocampal neurogenesis. Using in vitro assays on adult hippocampal NSCs, we identified an attenuation of canonical Wnt/ß-Catenin signaling responsiveness in the course of neuronal differentiation, while non-canonical Wnt/Planar Cell Polarity (PCP) signaling events progressively increased. Single-cell genetic manipulations were performed by using retroviral vectors to target dividing progenitor cells in the murine hippocampus. Retrovirus-mediated knockdown of ATP6AP2, a recently discovered core protein involved in both Wnt signaling pathways, revealed that the dual role of this adaptor protein is dependent on the signaling context that is present. We were able to confirm its dual role in neurogenic Wnt signaling in cultured adult hippocampal progenitors (AHPs) for both canonical Wnt signaling in proliferating AHPs and non-canonical Wnt signaling in differentiating AHPs. Specific knockdown of ATP6AP2 in neural progenitor cells in vivo resulted in a decreased induction of neuronal cell fate and severe morphological defects of newborn neurons, likely via altering both canonical and non-canonical Wnt signaling. Furthermore, in vivo knockdown of PCP core proteins CELSR1-3 and FZD3 mimicked the maturational defects of ATP6AP2-deficient neuroblasts but did not affect granule cell fate. In summary, the data presented here characterize a transition of Wnt signaling responsiveness from Wnt/ß-Catenin signaling to non-canonical Wnt/PCP signaling in the course of granule cell fate that was confirmed in a human pluripotent stem cell (hPSC)-based model of dentate granule neurogenesis. Our findings suggest that these pathways show stage-dependent activities and regulate distinct steps of adult dentate granule cell neurogenesis. Conclusively, we provide evidence for a stage-specific regulation of fate determination through the Wnt/ß-Catenin pathway and granule cell morphogenesis through the Wnt/PCP signaling pathway, including the FZD3-CELSR1-3 system. Additionally, the Wnt adaptor protein ATP6AP2 is involved in earlier and later stages of adult neurogenesis and its knockdown in vivo resembles all phenotypic features of both canonical and Wnt/PCP signaling mutants.
Late Quaternary evolution and carbon cycling of tropical peatlands in equatorial Southeast Asia
(2014)
Peatlands are an important component in the global carbon cycle as they act as both long-term sinks for carbon dioxide and significant sources for methane. Over the Holocene period (the past 11,700 years) continuous CO2 uptake by peat accumulation exceeded methane emissions in northern peatlands and resulted in a net-radiative cooling effect on the global climate.Although 11% of the global peatland area is located in the tropics, the role of tropical peatlands in the global carbon cycle and in influencing the Earth’s radiative budget has not been resolved. Climate-carbon cycle models have thus far not included tropical peatlands because reliable data on their past rates of carbon uptake and release are not available. In this thesis this problem has been approached by reconstructing peatland expansion and rates of carbon storage and release over the Late Quaternary (Latest Pleistocene and Holocene) for the largest tropical peatland area, which is located in equatorial SoutheastAsia (i.e. Sumatra, Borneo, Peninsular Malaysia). Peat accumulation in the tropics remains an enigmatic phenomenon, because the constantly high temperatures of 26-27°C should theoretically drive rapid soil carbon turnover and thus not enable the accumulation of peat. Therefore this thesis also explores the mechanisms that cause peat formation in the SoutheastAsian tropics as well as the drivers behind changing rates of carbon accumulation. Carbon dynamics were analyzed at the regional scale (103–105 km2) of SoutheastAsia over millennial timescales (paper, I, II) and at the local scale (101–102 m2) of a peatland site on annual to centennial timescales (paper III, IV). Paper I presents the first systematic classification of the nearly 160,000 km2 SoutheastAsian lowland peatlands (below 70 m a.s.l.) into geographic peatland types. The peatlands were divided into 1) coastal peatlands of PeninsularMalaysia, Sumatra, and Borneo (~130,000 km2) and into inland peatlands (~30,000 km2) of 2) Central Kalimantan (southern Borneo), 3) the Kutai basin (eastern Borneo), and 4) the Upper Kapuas basin (western Borneo). Coastal peatlands formed by primary mire formation directly on freshly exposed marine or mangrove soils with the lowering of the sea level during the Late Holocene. In contrast, inland peatlands formed via paludification on either terrestrial sand soils (Central Kalimantan) or by both paludification and terrestrialization (Kutai basin, Upper Kapuas basin). The sequence of peatland initiation was established by applying the common cumulative basal date frequency approach (paper I). This method revealed clear differences in the timing of peatland initiation: 1) the Upper Kapuas peatlands are the oldest postglacial peat formations and date from 20,000-13,000 cal BP (calendar years before present), 2) inland Central Kalimantan peatlands date from 14,500-9000 cal BP, 3) the Kutai peatlands date from 8300-4900 cal BP, and 4) and the coastal peatlands date from 7700-200 cal BP. Coastal peatlands have a Holocene average carbon accumulation rate of 77 g C m-2 yr-1, being recognized as the globally most effective terrestrial ecosystems in terms of long-term carbon sequestration. Except for the Kutai peatlands, the Holocene average carbon accumulation rates of inland peatlands are significantly lower (20-30 g C m-2 yr-1) and very similar to the average long-term rates of northern peatlands. Fluctuations in past rates of carbon accumulation of SoutheastAsian peatlands could for the first time be linked to paleoclimatic changes, primarily variations in moisture availability (paper I, II). Hydroclimatic influences on carbon accumulation rates were related to shifts in the mean position of the Intertropical Convergence Zone, changes in the intensity of theAustral-Asian monsoon system, and variations in the frequency of the El Niño- Southern Oscillation. In contrast, peatland initiation and expansion was driven by sea-level change (paper I, II). The deglacial rise in sea-level is identified as the primary driver for inland peatland formation in Borneo, because the rising sea-level 1) lowered the hydrological gradients in the SoutheastAsian island archipelago inducing rising ground and surface water levels on these islands, and 2) led to higher atmospheric moisture availability due to the associated expansion of marine water masses on the shelf floor. Paper II shows that inland peatland initiation and expansion was most extensive during deglacial meltwater pulses, when the rate of sea-level rise exceeded 10 mm yr-1. Only when the rate of sea-level rise had slowed down to a threshold of 2.4 mm yr-1 by ~7000 cal BP could peat accumulation along the coasts keep up with the sea-level rise and coastal peatlands could form. Hydro-isostatic adjustment of the Sunda Shelf led to a sea-level lowering by ca. 5 m over the past 4500 years. Falling sea levels exposed extensive marine areas that were rapidly colonized by peat swamp forests.Anewly 140 developed method for the reconstruction of past peatland area based on transfer functions (paper II) reveals that 70%of the peatlands of Sumatra and Kalimantan only formed during the past 4000 years.Moreover, this new transfer function approach shows that the common basal dates approach overestimated the extent of peatlands in the past. This method, in general, leads to higher rates of reconstructed cumulative peat carbon uptake for the past. By combining reconstructed peatland areas and mean rates of carbon accumulation over millennial timescales from each peatland type the carbon uptake of all peatlands from Sumatra and Kalimantan could be quantified for the past 15,000 years (paper II). Carbon uptake remained below 1 Teragram (Tg) C yr-1 from 15,000-5000 cal BP because the total area of peatlands was less than 30,000 km2. Rapid peatland expansion driven by the lowering of sea-level over the past 5000 years increased carbon uptake on Sumatra and Kalimantan to over 7 Tg C yr-1 and resulted in an exponential growth of the regional peat-carbon reservoir to a size of over 20 Pg C. SoutheastAsian peatlands therefore had no significant role in the Late Pleistocene and Early Holocene global carbon cycle. However, because of their rapid expansion after 5000 cal BP by over 100,000 km2 the peatlands of SoutheastAsia became a globally important carbon sink during the Late Holocene and likely caused an atmospheric CO2 drawdown of 1-2 ppm (paper II). This previously unrecognized biospheric carbon sink partly compensated for contemporaneous terrestrial carbon losses associated with the desertification of Northern Africa. The mechanisms that enable high rates of carbon accumulation of coastal peatlands were explored in a peat core study presented in paper III. Here the use of a new coring technique for the tropics and the application of noninvasive geophysical measurements were employed to derive a high-resolution record of carbon accumulation rates. This study provides the first description of peatland pools for SoutheastAsia, which form as tip-up pools from falling trees such as Shorea albida. Based on a pollen and macrofossil record a fossil tip-up pool could be identified in the core and an associated carbon accumulation rate of 100 to over 900 g C m-2 yr-1 determined. Thus tip-up pools function as local hot spots for carbon accumulation, fundamentally different from northern hemisphere peatland pools, which act as net-carbon sources. From a time-series of aerial photographs the rate of tree fall and thus pool formation was determined at 0.4 tree ha-1 yr-1 (paper III).Asimulation model indicates that up to 60%of the peat deposited in peat domes of Borneo is derived from filled up fossil pools – changing the paradigm that Southeast Asian peatlands mainly form from belowground biomass and providing an explanation for the rapid carbon accumulation of these ecosystems. The climate impact of peatlands is, however, not only related to their capacity to rapidly store carbon, because peatlands also release the strong greenhouse gas methane – a by-product of anaerobic decomposition.Ametaanalysis of methane emission data from SoutheastAsian peatlands (paper IV) shows that their average annual methane release of 3 g CH4 m-2 yr-1 is lower than the average annual release of ~9 g CH4 m-2 yr-1 from northern peatlands, although the higher tropical soil temperatures should lead to significantly higher emissions. The limited degree of anaerobic decay is explained by the recalcitrance of the deposited biomass, which contains high amounts of lignin and tannin, providing another explanation for rapid carbon accumulation. Low anaerobic decomposition together with high rates of carbon accumulation imply that limits to vertical peat bog growth in SoutheastAsia are not set by cumulative anaerobic decay as in northern raised bogs. Instead peat bog growth is limited by aerobic decomposition related to water-table lowering as shown by a derived linear relationship between the amount of released CO2 from aerobic peat decomposition and the mean annual depth of the peatland water-table (paper IV). The climatic effect of Southeast Asian peatlands was determined by the global warming potential (GWP) method, which compares carbon uptake with methane emissions in terms of CO2-equivalents. The low methane emissions and high carbon accumulation rates of coastal peatlands result in a net annual uptake of 1340 kg CO2- equiv. ha-1 yr-1 over a 100 year GWP time-horizon. Under natural conditions coastal Southeast peatlands exert a significant net cooling effect on the global climate in contrast to northern peatlands, which have a warming effect or act climatic neutral on this time frame. It can be concluded that the tropical peatlands of SoutheastAsia are the strongest carbon sinks among all peatlands globally with a notable influence on the Earth’s radiative budget. However, today an estimated 90,000 km2 of peatlands in SoutheastAsia is drained for agriculture (e.g. oil palm plantations) and deforestation. These drained peatlands release annually over 140 Tg C yr-1 from aerobic peat 141 decomposition. Drainage also facilitates the regular spread of peat fires in this region, which on average release around 75 Tg C yr-1. Ongoing total carbon losses (~220 Tg C yr-1) exceed the natural carbon uptake by a factor of 25 and demonstrate that the entire SoutheastAsian peatland region has recently switched from a globally important carbon sink to a globally significant source of atmospheric CO2 (paper II, IV).
This work describes the recent scientific and technical achievements obtained at the high-precision Penning trap mass spectrometer SHIPTRAP. The scientific focus of the SHIPTRAP experiment are mass measurements of short-lived nuclides with proton number larger than 100. The masses of these isotopes are usually determined via extrapolations, systematic trends, predictions based on theoretical models or alpha-decay spectroscopy. In several experiments the masses of the isotopes 252-255No and 255,256Lr have been measured directly. With the obtained results the region of enhanced nuclear stability at the deformed shell closure at the neutron number 152 was investigated. Furthermore, the masses have been used to benchmark theoretical mass models. The measured masses were compared selected mass models which revealed differences between few keV/c² up to several MeV/c² depending on the investigated nuclide and model. In order to perform mass measurements on superheavy nuclei with lower production rates, the efficiency of the SHIPTRAP setup needs to be increased. Currently, the efficiency is 2% and mainly limited by the stopping- and extraction efficiency of the buffer gas cell. The stopping and extraction efficiency of the current buffer gas cell is 12%. To this end, a modified version of the buffer gas cell was developed and characterized with 223Ra ion source. Besides a larger stopping volume and a coaxial injection the new buffer gas cell is operated at a temperature of 40K. The operation at cryogenic temperatures increases the cleanliness of the buffer gas. From extraction measurements and simulations an overall efficiency of 62(3)% was determined which results in an increase by a factor of 5 in comparison to the current buffer gas cell. Aside from high-precision mass measurements of heavy radionuclides the mass differences of metastable isobars was measured to identify candidates for the neutrinoless double-electron capture. Neutrinoless double-electron capture can only occur if the neutrino is its own antiparticle and a physics beyond the standard model exists since the neutrinoless double-electron capture violates the conservation of the lepton number. Due to its expected long half-life this decay has not yet been observed. However, the decay rate is resonantly enhanced if mother and daughter nuclide are degenerate in energy. Suitable candidates for the search of the neutrinoless double-electron capture have been identified with mass difference measurements uncertainties of about 100eV/c². In this work the results of the mass difference measurements of 12 possible candidates are presented.
The impact of inbreeding under different environmental conditions and of artificial selection on cold tolerance was investigated in laboratory populations of the tropical butterfly Bicyclus anynana. The investigation focused on (1) the effects of inbreeding on several fitness-related traits and whether inbred individuals are more susceptible to stress, (2) interactions between inbreeding, genetic adaptation to cold stress and environmental conditions, (3) the effects of artificial selection and inbreeding in the adult stage in other developmental stages, and (4) the effect of inbreeding depression on the heat shock response. Environmental conditions are not constant over time; consequently organisms have to deal with environmental changes. Besides naturally fluctuating conditions, human-induced climate change may increase temperature changes as well as the severity of heat or cold waves. Temperature-stress resistance describes an organism’s ability to cope with stressful temperatures. Enhanced resistance to temperature stress can be reached by phenotypic plasticity or genetic adaptation. Plastic organisms are able to react fast to changing environmental conditions, whereas genetic adaptation is more important for long-term adaptation. Natural habitats may also be affected by human impact, causing habitat loss or fragmentation and changes in population structure. A decrease in the population size may result in inbreeding and inbreeding depression (ID). Consequences of inbreeding are well documented, and inbred individuals are predicted to be more sensitive to environmental stress than outbred individuals. The long term persistence of species and populations depends on their ability to adapt to novel conditions which in turn depends on genetic diversity. Therefore, studies of temperature resistance and its evolution in relation to inbreeding are very important. First a higher susceptibility of inbred individuals to environmental stress was determined in different populations of B. anynana. Inbreeding depression was revealed for several fitness-related traits, but not for immunity traits or heat tolerance. Temperature affected most traits, revealing the importance of temperature on ectotherms; just two hours of thermal stress affected important reproductive, life-history and immunity traits already. Importantly though, no evidence were found that inbred individuals are more susceptible to stressful temperatures than outbred individuals. Genetic adaptation and phenotypic plasticity can interact with one another, resulting in genotype-environmental interactions (G x E). The hypotheses tested here were that some genotypes are more plastic than others and that lines with increased cold stress resistance are less plastic with regard to cold resistance than control lines. To induce plastic responses the exposed lines differed in cold tolerance and inbreeding to different temperatures as well as different feeding regimes and measured fitness-related traits. Several interactions were detected in which a selection regime was involved, but these interactions did not show a clear overall pattern. In summary though, findings were that marginal impacts of directional selection and inbreeding on plastic responses and suggest that, at least for my study organism, the genetic architecture of fitness-related traits is not connected with the architecture of plastic responses. The next investigation concerned with the manifestation of genetic adaptation to produce one specific phenotype across development stages and possible trade-offs. The assumption tested was that there is a genetic link between different developmental stages to produce one definite phenotype by imposing selection in the adult stage only. Lines selected for increased cold resistance in the adult stage were used and increased cold resistance throughout all developmental stages was expected. However, higher cold resistance was found only in the adult stage and not in developmental stages. This could be either the result of a resource allocation trade-off between different stages or that there is no cold resistance phenotype. Thus, if selection takes place in the adult stage it does not affect the others. In the last experiment investigation was directed to determine whether there are negative inbreeding effects on the heat shock protein (HSP) response. Under stressful conditions, organisms produce the HSPs and they act as chaperons required for refolding and repairing of stress degraded proteins. Testing was oriented to find if inbreeding as a genetic stressor´ provokes a higher HSP expression and if there is evidence for higher temperature stress susceptibility on inbred individuals. Findings indeed showed a stronger HSP up-regulation in control compared to inbred lines with a negative inbreeding impact occurrence, which may causally underlie inbreeding depression.
Staphylococcus aureus is a commensal that colonizes the skin and mucosa of 20-30% of the human population without leading to symptoms of diseases. However, it is also the most important cause of nosocomial infections. Those range from minor skin infections to life-threatening diseases such as pneumonia, endocarditis or septicaemia. Development of strains with resistance against many antibiotics complicates the situation further. The variety of strains with their various properties is one reason why no successful vaccine has been introduced to the market, yet. Therefore, efficient strategies for prevention and therapy of these dangerous infections are urgently needed. To accomplish these goals, the understanding of molecular interactions between host and pathogen is indispensable. Within this dissertation, several internalization experiments were performed aiming to investigate the interaction of S. aureus HG001 and human cell lines upon infection on the protein level. In order to obtain sufficient amounts of proteins for comprehensive physiological interpretations, it is necessary to enrich bacteria, secreted bacterial proteins or infected host cells upon internalization. In the framework of this thesis, bacteria which continuously produce green fluorescent protein (GFP) were employed. With that it was possible to sort bacteria from lysed host cells by flow cytometry or to separate host cells carrying bacteria after contact from those which did not. Subsequently, the proteins were proteolytically digested and peptides were analyzed by mass spectrometry in a gel-free proteomics approach. To allow such analyses also for staphylococci which do not produce GFP, such as clinical isolates, an additional protocol was developed. Prior to the infection, bacteria were labeled with fluorescent or para-magnetic nanoparticles. Afterwards bacteria could be separated from host cell debris by fluorescence-based cell sorting or with the help of a strong magnet. In order to cover also important secreted virulence factors of S. aureus HG001, phagosomes and engulfed bacteria and secreted proteins were isolated from infected host cells. Further steps of protocol optimization included improved bacterial cell counting by fluorescence-based flow cytometry, enhanced data analysis by combination of different search algorithms, and comprehensive functional annotation of proteins of the applied strain by sequence comparison with other strains and organisms. First, the proteome adaptation of internalized S. aureus HG001 and the infected A549 host cells was investigated during the first hours of infection. It became clear, that the bacteria replicate inside the host during the first 6.5 h. After internalization the levels of bacterial enzymes involved in protein biosynthesis decreased. Furthermore, bacteria adapted their proteome to the harsh intracellular conditions such as oxygen limitation, cell wall stress, host defense in terms of oxidative stress, and nutrient limitation. After contact to S. aureus HG001, A549 cells produced increased amounts of cytokines (e.g. IL-8, IFN-γ) in comparison to non-treated A549 cells. In addition, activation of the immunoproteasome and hints of early apoptosis activity were observed. Afterwards, the response of S. aureus HG001 to internalization by A549, S9 or HEK 293 cells was compared on the proteome level. It was obvious, that the adaptation to stress and the reduced protein synthesis are conserved mechanisms. Host dependent differences were detected especially in the energy metabolism and the synthesis of some amino acids. Additionally, bacteria showed different intracellular replication patterns depending on the host cell line. A higher percentage of extracellular bacterial proteins was found in isolated phagosomes compared to the sorted samples. Selected low abundant virulence factors could be quantified at two points in time after infection with the help of the sensitive single reaction monitoring (SRM) method. Further, a heterogeneous mixture of several phagosomal maturation steps was present during the first 6.5 h after infection. Finally, the gel-free proteome analyses could be applied to investigate Bordetella pertussis, the cause of whooping cough, during iron limitation and after internalization, and the results were compared to the S. aureus HG001 data.
The Atomic Force Microscope (AFM) has become an important tool for probing the mechanical properties of cells and microparticles by force-indentation experiments. In this thesis optimized AFM approaches for these experiments are developed and applied to three types of living human cells in order to answer biologically relevant questions about their mechanics. These microscopic investigations are then interpreted with respect to nanoscopic and macroscopic biologic parameters, such as the function of cell surface receptors or the size of human heart ventricles. This thesis comprises two physical/technical chapters and three medical/biological chapters. The physical/technical chapters discuss the measurement process itself, aiming for its improvement with respect to a proper data analysis and contact model (for spherical cells). The medical/biological chapters investigate the elasticity of cells by the use of optimized AFM approaches, with respect to the used data analysis.
Heparin is an anticoagulant drug. It is important in the treatment of deep vein thrombosis,pulmonary embolism and during surgeries. Heparin-induced thrombocytopenia (HIT) is a severe adverse reaction caused by the formation of ultralarge complexes of platelet factor 4 (PF4) with unfractionated heparin (UFH). It can lead to limb loss or fatal events like stroke, myocardial infarction or pulmonary embolism. HIT has an incidence of about 3% in patients receiving anticoagulative heparin treatment. PF4 is a tetrameric protein, released from the α-granules of platelets upon activation. PF4 is known to form antigenic complexes with UFH accompanied by structural changes of PF4. In this thesis, the size and size distribution of PF4 and PF4/heparin complexes were analyzed using asymmetrical flow field-flow-fractionation (AF4), photon correlation spectroscopy (PCS) and atomic force microscopy (AFM). PF4 tends to form auto-aggregates and to adsorb to different surfaces, including regenerated cellulose, polyethersulfone, quartz and glass. The aggregates are less pronounced in solutions at isotonic NaCl concentration. Arginine and Tween 20 were identified as possible ingredients to hinder the auto-aggregation of PF4. Also, it is shown by combining circular dichroism (CD) spectroscopy, atomic force microscopy (AFM) and isothermal titration calorimetry (ITC) with UFH and defined chain length (16-, 8-, 6-, 5-mer) heparins that structural changes (i.e., increase in β-sheets) alone are not sufficient to induce antigenicity. While UFH, 16-, 8-, and 6-mer heparins all induced an increase in the antiparallel β-sheet content to > 30% (as determined by CD spectroscopy), complex antigenicity as measured by anti-PF4/heparin antibody binding in an enzyme-linked immunosorbent assay (EIA) was only induced by UFH and 16-mer heparin. Fondaparinux (5-mer heparin), which forms in vitro non-antigenic complexes with PF4, did not induce structural changes of PF4. Interestingly, the structural changes induced by antigenic UFH and 16-mer heparin but not by non-antigenic shorter heparins were reversible at higher heparin concentrations. Furthermore, the complexes formed by PF4 with longer heparins were larger than those formed with shorter heparins as shown by atomic force microscopy (AFM). UFH, HO16 and HO08 are able to form ultralarge multimolecular complexes with PF4. ITC data indicated strong electrostatic interactions and energetically unfavorable conformational changes of PF4 with longer heparins, while for the short heparins, favorable conformational changes in the structure of PF4 are induced. This explains the reversibility of the structural changes seen for UFH and HO16 upon addition of an over-saturating amount of heparin. Finally, using differential scanning calorimetry (DSC) the thermal stability of PF4 and PF4/heparin complexes was assessed. Despite its tendency to form auto-aggregates, PF4 is a heat-stable protein. This stability is, length dependently, even increased in complex with heparins. This work shows important differences in the binding between PF4 and heparins of different chain length and might be relevant for the understanding of other biological functions of heparins (e.g., involvement in allergic and inflammatory reactions).
Magnetic reconnection is a fundamental plasma process where a change in field line connectivity occurs in a current sheet at the boundary between regions of opposing magnetic fields. In this process, energy stored in the magnetic field is converted into kinetic and thermal energy, which provides a source of plasma heating and energetic particles. Magnetic reconnection plays a key role in many space and laboratory plasma phenomena, e.g. solar flares, Earth’s magnetopause dynamics and instabilities in tokamaks. A new linear device (VINETAII) has been designed for the study of the fundamental physical processes involved in magnetic reconnection. The plasma parameters are such that magnetic reconnection occurs in a collision-dominated regime. A plasma gun creates a localized current sheet, and magnetic reconnection is driven by modulating the plasma current and the magnetic field structure. The plasma current is shown to flow in response to a combination of an externally induced electric field and electrostatic fields in the plasma, and is highly affected by axial sheath boundary conditions. Further, the current is changed by an additional axial magnetic field (guide field), and the current sheet geometry was demonstrated to be set by a combination of magnetic mapping and cross-field plasma diffusion. With increasing distance from the plasma gun, magnetic mapping results in an increase of the current sheet length and a decrease of the width. The control parameter is the ratio of the guide field to the reconnection magnetic field strength. Cross-field plasma diffusion leads to a radial expansion of the current sheet at low guide fields. Plasma currents are also observed in the azimuthal plane and were found to originate from a combination of the field-aligned current component and the diamagnetic current generated by steep in-plane pressure gradients in combination with the guide field. The reconnection rate, defined via the inductive electric field, is shown to be directly linked to the time-derivative of the plasma current. The reconnection rate decreases with increasing ratio of the guide field to the reconnection magnetic field strength, which is attributed to the plasma current dependency on axial boundary conditions and the plasma gun discharge. The above outlined results offer insights into the complex interaction between magnetic fields, electric fields, and the localized current flows during reconnection.
In summary, the transcriptome data demonstrated that acute RAP for 7h induces significant changes in the expression of several left atrial genes, including those reflecting ANG II-mediated oxidative stress, tissue remodeling, and energy depletion. Furthermore, the results from the dronedarone study demonstrated that this drug is capable of attenuating most of RAP-induced changes in oxidative stress-related gene expression. Accordingly, the haemodynamic parameters also showed that dronedarone reduced RAP-induced microvascular flow abnormalities. This view is supported by the observation that in the used porcine model of acute AF, dronedarone decreased RAP-dependent PKC phosphorylation, NADPH isoform expression, F2-isoprostane release and IκBα phosphorylation. Additionally, the results of the irbesartan study indicate that ET-1 contributes to AF-dependent atrial fibrosis by synergistic activity with ANG-II to stimulate SGK1 expression and enhance phosphorylation of the SGK1 protein which, in turn, induces CTGF. The latter has been consistently associated with tissue fibrosis. In support of this view, in vitro analyses using HL-1 cells verified CTGF induction after short episodes of RAP and additionally in response to exogenous addition of ET-1. Accordingly, irbesartan was shown to attenuate most of the RAP-dependent changes in atrial or ventricular gene expression.
Simulations of Short Model Peptides and Practically Relevant Modeled Titanium Implant Surfaces
(2014)
One of the aims of this work was to generate a non restrained force field model including carbon contamination to make the adsorption simulations more realistic and comparable with experimental data. Another purpose was to find out how the special recognition of small linker proteins on titanium dioxide is working. During this work a fixed and a non restrained rutile (100) model was used and critical properties were observed which are not only related to the surface. The rigid water layers on top of the oxide are very important for the protein and peptide adsorption. Therefore the first discussing object were the properties of the water layers and how they can be influenced. The charge distribution on the surface was found to have a big effect on them. Depending on the charges of the surface atoms or the functional groups, resulting out of the hydroxylation equilibrium, precisely the first water layer gets more rigid or smother. This has a big effect on biomolecule adsorption. The peptides need to penetrate these water layers to generate direct interaction points. The correct description of the surface in molecular dynamic simulations therefore has a high influence on the results. The better the model is the better the findings are comparable with experimental ones. Additionally carbon contamination was mimicked by using a monolayer of pentanol molecules. This fits very good with experimental data (e.g. contact angle) and make the oxide model more hydrophobic. Interaction of proteins and peptides in experiments or in medical use are often observed under normal air conditions, which means that the scaffold is i) hydroxylated by water and ii) carbon contaminated in a short period of time. Therefore investigations were done to find out how the contamination influences the adsorption of a formally know good or bad binding peptide (TiOBP1; TiOBP2). It was found that the TiOBP1 is able to bind the different surface modifications very well which coincides with observations made in experiments. The way of adsorption (direct or indirect) depends on the water layers properties. The first layer on high charged surface models is that rigid, that the peptide is not able to adsorb in a direct way. On the carbon contaminated oxide model the adsorption is possible by reducing the flexibility of the secondary structure motive. In the case of TiOBP2 adsorption on the clean surface model results in only weak binding or even in no interaction. Whereas on the carbon contaminated dioxide the once know bad binder is able to interact with the Pentanol monolayer. No direct adsorption is observed but the hydrophobic side chains have the possibility to orient themselves according to the hydrophobic layer without changing significantly in the secondary structure motive. An additional test peptide (minTBP) adsorbs without being affected by the contamination. This raises the question if the distribution of hydrophobic to hydrophilic amino acids has influence on the adsorption ability according to clean and contaminated surface. For experimental application it could be of interest to generated peptides (GEPI´s) which bind both surface types without changing the secondary structure motives then as we know functionality is based on these structures. In the case of the PHMB polymer adsorption was observed depending on the hydroxylation ratio and therefore on the charge density of the rutile (100) surface. After analysis of the simulations takeaways from experiments could be substantiated. The PHMB interacts with the negative charged surface via the first water layer as a film. So the new force field model describing the rutile (100) titanium dioxide surface with additional carbon contamination model of one monolayer pentanol fits the experimental data very well. The adsorption studied on this surfaces indicates that the contamination as expected makes the surface more hydrophobic and influences the adsorption behavior of the tested peptides especially the secondary structure of TiOBP1. This indeed enhances experimental investigations. Peptides which e.g. link organic and inorganic parts should be good adsorbing on clean and contaminated surfaces by keeping their functionality. Furthermore experimental data can be substantiated by using atomistic simulations like in the case of PHMB adsorption.
The systemic renin-angiotensin system (RAS) is an endocrine system that is mainly known to regulate blood pressure, fluid and electrolyte balance as well as volume homeostasis in the body through different active metabolites, the angiotensin (Ang) peptides. In addition, local renin-angiotensin systems have been discovered in various tissues, including the islet of Langerhans. Starting with angiotensinogen, the precursor of all angiotensin peptides which is cleaved into the decapeptide Ang I by renin, the RAS is divided into three axes. The main classical RAS axis is composed of angiotensin converting enzyme (ACE), angiotensin (Ang) II, and the Ang II type 1 receptor (AT1R), whereas the two alternative RAS axes comprise either ACE2, Ang-(1-7) and the receptor Mas or the aminopeptidase N (APN), Ang IV and the insulin-regulated aminopeptidase (IRAP). The activation of the main ACE/Ang II/AT1R RAS axis has been associated with metabolic syndrome, type 2 diabetes mellitus, and islet dysfunction. The detrimental effects resulting from the pathological activation of this axis have been shown to be attenuated or even abolished by the pharmacological inhibition of components of the main RAS axis. However, the impact of the two alternative ACE2/Ang-(1-7)/Mas and APN/Ang IV/IRAP RAS axes on islet function is less well understood. Previous studies mainly focused on the possible protective actions of Ang-(1-7) via the receptor Mas in insulin-sensitive tissues and on well known risk factors of metabolic syndrome (insulin resistance, hyperglycemia, obesity, hypertension and dyslipidemia). Thus, the impact of this axis on β-cell function and, in particular, insulin production and release was examined in the present study. Glucose and fatty acids have been subjects of diabetic research because they are established pathophysiologically relevant features of the metabolic syndrome and are known to harm β cells, phenomena which are referred to as gluco- or lipotoxicity, respectively. The pathophysiologically relevant factors glucose, saturated fatty acid (FA) palmitic acid (PA), and the methyl ester of the omega-3 fatty acid docosahexaenoic acid (DHA-ME) were used in the present study to characterize the local β-cell RAS as well as β-cell function under pathophysiological conditions. Results of the present work demonstrate the expression of selected components of the RAS in isolated murine islets of Langerhans and the rat insulinoma cell line BRIN-BD11 under basal conditions. The alternative ACE2/Ang-(1-7)/Mas and APN/Ang IV/IRAP RAS axes were activated by high glucose in BRIN-BD11 cells after 24 h. Coincidently with these findings insulin production was found to be increased. In contrast, the expression of components of the main ACE/Ang II/AT1R RAS axis and the Ang II type 2 receptor (AT2R) were not affected under the same conditions (Härdtner et al., 2013). Both FAs, PA and DHA-ME were shown to alter the expression of components of the renin-angiotensin system in BRIN-BD11 cells. PA increased the expression of AT1R, the receptor of the main RAS axis, and of AT2R, whereas that of the receptor of the alternative ACE2/Ang-(1-7)/Mas RAS axis, Mas, appeared to be down-regulated at basal low glucose concentrations (5.5 mM). These effects were accompanied by a dose-dependent reduction of the insulin production and secretion. In contrast, DHA-ME augmented the expression of components of the ACE2/Ang-(1-7)/Mas axis and IRAP at low glucose concentrations, an effect which could be partially enhanced under high glucose conditions (25 mM). At basal glucose concentrations DHA-ME reduced the insulin secretion, whereas it was increased under high glucose conditions. However, the insulin mRNA amount remained unaffected by DHA-ME. Additionally, in contrast to glucose and palmitic acid, DHA-ME significantly increased the production of reactive oxygen species, at least hydrogen peroxide after 30 min. Expression alterations of components of the alternative ACE2/Ang-(1-7)/Mas RAS axis by glucose and PA correlated strongly with the corresponding insulin secretion and production. Therefore, an involvement of the ACE2/Ang-(1-7)/Mas RAS axis in the regulation of insulin secretion and production was hypothesized and validated in primary islets of Langerhans of both Mas-deficient and wild-type mice. Islets were exposed to the preferred natural ligand for Mas, Ang-(1-7), or to its pharmacological agonists or antagonists, respectively....
Modern cavity QED and cavity optomechanical systems realize the interaction of light with mesoscopic devices, which exhibit discrete (atom-like) energy spectra or perform micromechanical motion. In this thesis we have studied the crossover from the quantum regime to the classical limit of two prototypical models, the Dicke model and the generic optomechanical model. The physical problems considered in this approach range from a ground state phase transition, its dynamical response to general nonequilibrium dynamics including Hamiltonian and driven dissipative chaotic motion. The classical limit of these models follows from the classical limit of at least one of its subsystems. The classical equations of motion result from the respective quantum equations through the application of the semiclassical approximation, i.e., the neglect of quantum correlations. The approach of the results from quantum mechanics to the prediction of the classical equations can be obtained by subsequently decreasing the respective scaling parameter. In order to obtain exact results we have utilized advanced numerical methods, e.g., the Lanczos diagonalization method for ground state calculations, the Kernel Polynomial Method for dynamical response functions, Chebyshev recursion for time propagation, and quantum state diffusion for open system dynamics. We have studied the quantum phase transition of the Dicke model in the classical oscillator limit. Our work shows that in this limit the transition occurs already for finite spin length but with the same critical behavior as in the classical spin limit. We have derived an effective model for the oscillator degrees of freedom and have discussed the differences of both classical limits with respect to quantum fluctuations around the mean-field ground state and spin-oscillator entanglement. In this thesis we have proposed a variational ansatz for the Dicke model which extends the mean-field description through the inclusion of spin-oscillator correlations. The ansatz becomes correct in the limit of large oscillator frequency and in the limit of a large spin. For the latter it captures the leading quantum corrections to the classical limit exactly including the spin-oscillator entanglement entropy. We have studied the dynamics of spin and oscillator coherent states in the nonresonant Dicke model at weak coupling. In this regime periodic collapses and revivals of Rabi oscillations occur, which are accompanied by the buildup and decay of atom-field entanglement. The spin-oscillator wave function evolves into a superposition of multiple field coherent states that are correlated with the spin configuration. In our work we provide a description of the underlying dynamical mechanism based on perturbation theory. Our analysis shows that collapse and revival at nonresonance is distinguished from the resonant case treated within the rotating wave approximation by the appearance of two time scales instead of one. We have extended our study of the Dicke dynamics to the case of increasing spin length, as the system approaches the classical spin limit. We described the emergence of collective excitations above the ground state that converge to the coupled spin-oscillator oscillations observed in the classical limit. With increased spin length the corresponding Green functions thus reveal quantum dynamical signatures of the quantum phase transition. For the dynamics at larger coupling and energy, classical phase space drift and quantum diffusion hinders the direct comparison of quantum and classical observables. As we show in our work, signatures of classical quasiperiodic orbits can be identified in the Husimi phase-space functions of the propagated wave function and individual eigenstates with energies close to that of the quasiperiodic orbits. The analysis of the generic optomechanical system complements our study of cavity QED systems by a quantum dissipative system. In this thesis we have shown for the first time, how the route to chaos in the classical optomechanical system takes place, given as a sequence of consecutive period doubling bifurcations of self-induced cantilever oscillations. In addition to the semiclassical dynamics we have analyzed the possibility of chaotic motion in the quantum regime. Our results showed that quantum mechanics protects the optomechanical system against irregular dynamics. In sufficient distance to the semiclassical limit simple periodic orbits reappear and replace the classically chaotic motion. In this way direct observation of the dynamical properties of an optomechanical system makes it possible to pin down the crossover from quantum to classical mechanics.
The laser-matter interaction is a topic of current research. In this context, the interaction of intensive laser radiation with atomic clusters is of special interest. Du to the small cluster size, the laser field can penetrate the whole cluster volume, which leads to a high absorption of energy in the cluster. As a result, plasmas with high density and high temperature are produced. In the early phase of the laser-cluster interaction, free electrons are initially created in the cluster due to tunnel ionization or photoionization. Via collisions of these electrons with the cluster atoms, the ionization is increased and thus a dense nanoplasma is produced, which is heated by the laser. If free electrons leave the cluster during the laser-cluster interaction (outer ionization), a positive charge buildup is created. The associated charge repulsion finally can lead to the fragmentation of the cluster due to Coulomb explosion. Experimentally, interesting phenomena emerging from laser-excited clusters are observed, e.g., the creation of fast electrons, the production of highly charged ions, and X-ray emission. In this dissertation, the interaction of Gaussian laser pulses in the infrared regime with argon and xenon clusters is simulated by means of a nanoplasma model. Considering laser intensities in the non-relativistic regime, the relevant processes such as ionization, heating and expansion are theoretically described in this model with a set of coupled rate equations and hydrodynamic equations. One focus of the thesis is on the heating of the nanoplasma via inverse bremsstrahlung (IB), which is due to the absorption of laser photons in electron-ion collisions. In particular, the important question is investigated whether the consideration of the ionic structure – that means, the nuclear charge and the bound electrons – modifies the electron-ion collisions and thus the IB heating rate. Starting from a quantum statistical description, effective electron-ion potentials are used which account for both the screening due to the dense plasma and the inner ionic structure. Within the quantum mechanical first Born approximation, the consideration of the ionic structure leads to a drastic increase of the IB heating rate, in particular for high nuclear charges and low ionic charge states. However, for the parameters relevant in experiments, the applicability of the first Born approximation is questionable. Therefore, quantum mechanical calculations going beyond the first-order perturbation theory are performed. In addition, the IB heating rate is investigated with different classical methods. These are based either on transport cross sections for elastic electron-ion scattering or on classical simulations of inelastic scattering processes. Also within the classical approaches, the consideration of the ionic structure leads to an increase of the heating rate. However, this increase is shown to be only moderate. In a further part, the thesis focuses on the question how the dynamics of the laser-cluster interaction is influenced by the consideration of excited states. This is explored exemplarily for argon clusters excited by single or double laser pulses. The consideration of excitation processes in the nanoplasma leads to a decrease of the electron temperature and to an increase of the density of free electrons. Moreover, it is shown that the consideration of excitation processes results in an essential acceleration of the ionization dynamics. As a consequence, the mean ionic charge state in the plasma as well as the number of highly charged ions is significantly increased. For the population of ground states and excited states within an ionic charge state Z, collisional deexcitation processes play an important role. By means of an analytical relation between excitation and deexcitation cross sections, the rates for the respective processes in the presence of the laser field are calculated. The role of deexcitation processes is studied in detail, showing that the inclusion of these processes is essential for the correct theoretical description of the photon emission from laser-excited clusters. Based on these results, the photon yield is calculated for selected radiative transitions resulting from highly charged argon ions in the UV and X-ray regime.
Prostate volume estimation in MR images for epidemiological and clinical studies – new methods
(2014)
Benign prostatic hyperplasia (BPH) is one of the most widespread diseases among men older than 50 years. The literature provides various cut-off values for pathological enlargement of the prostate. Prostate volume (PV) measurement in large population-based studies would allow deriving more objective reference values and a more valid early BPH diagnosis. A fully automated method is therefore required. In the clinical context, the measurement of the PV is important for treatment response monitoring in the clinical applications for BPH management research, and an accurate method for PV is essential. Magnetic Resonance Imaging was used for PV estimation. Two methods based on the Support Vector Machines (SVM) were developed: the binary Support Vector Machines (C SVM)-based method for epidemiological studies and the single-class Support Vector Machines (S SVM)-based method for clinical studies. The second method was additionally compared to the ellipsoid formula for PV estimation, which is widespread in the clinic. The comparison between volume measurement of the C SVM-based method and manual delineation of observers A and B yielded a strong correlation (Spearmans rank correlation coefficients ñ of 0.936 [p < 0.001] and 0.859 [p < 0.001], respectively). Comparing the C SVM-based method and the two manual delineations by observers A and B shows an agreement with a mean difference of 3.0 ml (95% confidence interval of -3.1 to +9.2 ml) and 1.9 ml (95% confidence interval of −7.1 to +10.8 ml), respectively. The S SVM-based method and the reference PV (manual delineation of observer A) show excellent correlation (Spearmans rank correlation coefficient ñ = 0.965, p < 0.001), while the ellipsoid formula is less well correlated with the reference PV (Spearmans rank correlation coefficient ñ = 0.873, p < 0.001). The mean difference between S SVM and the reference PV was −0.05 ml (95% confidence interval of −3.8 to +3.7 ml); on the other hand, the mean difference between the ellipsoid formula and the reference PV was much greater, with 8.6 ml (95% confidence interval of +1 to +16.2 ml). The C SVM-based method has considerable potential for integration in epidemiological studies. The prostate volumes obtained by the S SVM-based method agreed excellently with the reference and would be clinically useful for urologists in prostate volumetric analysis.
Energetic ions are made to collide with atmospheric molecules. Positively charged ions of argon (Ar^+), helium (He^+), hydrogen (H_2^+ ), and protons (H^+) with energies of 50 keV to 350 keV are used as the bombarding ion. The ion beam of desired energy is produced using a linear ion accelerator at the University of Greifswald. The mass and energy distribution of sputtered particles were analysed using an Electrostatic Quadrupole SIMS (EQS) analyser. The target gases used are oxygen (O_2), sulfur hexafluoride (SF_6), and nitrogen (N_2). The ionized and fragmented particles due to collisions have been investigated. We have discovered a new process for negative ion formation in energetic ion collision with O_2 and SF_6 molecules. The process is a two body reaction between the projectile and the molecule without the need for a third particle (such as an external electron). It requires a direct charge transfer from the projectile to the molecule leaving it intact as O_2^- or SF_6^- . The process is experimentally confirmed by using a proton as projectile which does not have an electron to transfer. In comparison with positive ion fractions (O_2^+ , SF_5^+ ), the negative ions fraction is smaller by 2 orders of magnitude. This shows that the two body charge exchange process is weak due to the larger energy transfer required compared to the positive ion forming mechanisms. The two body charge exchange mechanism is not observed for ion collisions with N_2 molecule. No stable negative ion exist for N_2 molecule. The collision cross section for the ion formation during energetic ion – O_2 collision has been determined within the investigated impact energy. For SF_6 molecule the partial ion fraction of the secondary ions are determined for different projectiles involved. This kind of investigation is of great importance mainly in atmospheric physics. Energetic ions are constantly emitted from mass of the energy sources in the universe (e.g. sun). They interact with planetary objects or atmosphere on their way. A deep knowledge about the interaction processes is necessary to understand the ionospheric physics and space exploration. As second part of my thesis, a GaAs(100) surface is bombarded with 150 keV Ar^+ ion beam. From etching the surface to thin film coating, ion bombardment on solid surface found great role in the fabrication process of modern electronic and optical devices. In order to increase the knowledge on sputtering materials and because of profound importance in modern electronics, we choose GaAs(100) as our target. Among the sputtered atoms and ions, small sized cluster ions having more than 6 atoms have been identified. GaAs is a heteroatomic semiconductor containing gallium and arsenic in equal ratio. A preferential phenomenon of ’abundant sputtering’ of gallium compared to little arsenic (GaAs) has been investigated from their mass intensity. The experimental ion counts are compared with theoretically predicted relative abundance. This phenomenon of preferential sputtering is known for atomic species of sputtered GaAs but not for the sputtered cluster ions. The main reasons for this abundant sputtering of one element is attributed to the difference in ion formation energies and surface compositional change taking place during the sputtering process. Another notable characteristics is the preference in charge state among the sputtered ions. For instance, among sputtered atomic ions the ion counts of Ga^+ is 3 orders larger than As^+ ion and As^- is 2 orders larger than Ga^- ion. To get a clue for this behavior, we have investigated the energy distribution of both negatively and positively charged clusters. Different ion formation mechanisms were discussed. The energy distribution of atomic ion is partially explained by using a modified theory given by M. W. Thompson.
Within this thesis the protein engineering, immobilization and application of enzymes in organic synthesis were studied in order to enhance the productivity of diverse biotransformations. Article I is a review about Baeyer-Villiger monooxygenases (BVMO) and provides a detailed overview of the most recent advantages in the application of that enzyme class in biocatalysis. Protein engineering of a former uncharacterized polyol-dehydrogenase (PDH) identified in the mesothermophilic bacterium Deinococcus geothermalis 11300 is described in Article II. Article III covers the combination of one PDH mutant with a BVMO in a closed-loop cascade reaction, thus enabling direct oxidation of cyclohexanol to ε-caprolactone with an internal cofactor recycling of NADP(H). Article IV and Article V report a process optimization for transamination reactions due to a newly developed immobilization protocol for five (S)- and (R)-selective aminotransferases (ATA) on chitosan support. Furthermore, the immobilized ATAs were applied in asymmetric amine synthesis. In Article VI, an ATA immobilized on chitosan, an encapsulated BVMO whole cell catalyst and a commercially available immobilized lipase were applied in a traditional fixed-bed (FBR) or stirred-tank reactor (STR), and were compared to a novel reactor design (SpinChem, SCR) for heterogeneous biocatalysis.
Type 2 diabetes mellitus is one of the most challenging health problems for the next decades. The impact of type 2 diabetes mellitus on health care systems is largely driven by the increasing prevalence, the management of the disease and subsequent comorbidities, even in people with prediabetes or undiagnosed type 2 diabetes mellitus. An early detection of high risk groups is necessary to identify and modify risk factors such as obesity, physical inactivity or cigarette smoking which showed regional disparities in their distribution within a country. This leads to the assumption that there might be regional disparities regarding the prevalence and incidence of type 2 diabetes mellitus as well. For Germany as for other countries, comparable data on possible regional disparities in the prevalence and incidence of type 2 diabetes mellitus are missing. The aim of the present dissertation is to estimate the prevalence and incidence of type 2 diabetes mellitus on regional level within Germany, and to estimate the smoking prevalence as a modifiable risk factor in individuals with type 2 diabetes mellitus using data from the Diabetes Collaborative Research of Epidemiologic Studies consortium (DIAB CORE) within the Competence Net Diabetes in Germany. Well comparable data of five regional studies and one nationwide reference study are included: the Study of Health in Pomerania (SHIP); the Cardiovascular Disease, Living and Ageing in Halle Study (CARLA); the Dortmund Health Study (DHS); the Heinz Nixdorf Recall Study (HNR); the Cooperative Health Research in the Region of Augsburg Study (KORA); and the German National Health Interview and Examination Survey 1998 (GNHIES 98). First, the prevalence of type 2 diabetes mellitus was estimated. Data from five regional population-based studies and one nationwide study conducted between 1997 and 2006 with participants aged 45 to 74 years were analyzed. Type 2 diabetes mellitus prevalence estimates based on self-reports (standardized to the German population for the regional studies, reference date 2007/12/31) were compared. Of 11,688 participants of the regional studies, 1,008 had a known type 2 diabetes mellitus, corresponding to a prevalence of 8.6% (95% confidence interval [CI] 8.1% 9.1%). The standardized prevalence was highest in the East with 12.0% (95% CI 10.3% 13.7%) and lowest in the South of Germany with 5.8% (95% CI 4.9% 6.7%).Second, the incidence of type 2 diabetes mellitus was estimated. Data from participants (baseline age 45 to 74 years) from five regional population-based studies were included. The incidence rates per 1,000 person-years (95% CI) and the cumulative incidence (95% CI) from regional studies were directly standardized to the German population (reference date 2007/12/31) and weighted by inverse probability weights for losses to follow-up. Of 8,787 participants, 521 (5.9%) developed type 2 diabetes mellitus corresponding to an incidence rate of 11.8 per 1,000 person-years (95% CI 10.8 12.9). The incidence of known type 2 diabetes mellitus showed regional disparities within Germany. The incidence was highest in the East and lowest in the South of Germany with 16.9 (95% CI 13.3 21.8) vs. 9.0 (95% CI 7.4 11.1) per 1,000 person-years, respectively. Third, the smoking prevalence in participants aged 20 to 79 years with type 2 diabetes mellitus in the regional SHIP and the nationwide GNHIES 98 was estimated. Prevalence estimates of cigarette smoking were calculated using weights reflecting the European adult population (reference date 2005/12/31). The overall prevalence of current smoking was lower among participants with type 2 diabetes mellitus than among participants without type 2 diabetes mellitus (17.3% vs. 38.0% in SHIP and 24.7% vs. 32.1% in GNHIES 98). In both studies, the prevalence of current smoking was highest in men aged 20 to 39 years, in particular among men with type 2 diabetes mellitus. To conclude, considerable disparities in prevalence and incidence of type 2 diabetes mellitus indicate the need for interventions on the regional level within Germany. Former smoking was more prevalent among both men and women with type 2 diabetes mellitus in comparison to current and non-smoking. This finding probably reflects behavioural changes secondary to the disease onset and medical counselling. The finding that men aged 20 to 39 years with type 2 diabetes mellitus were more often current smokers than men without type 2 diabetes mellitus underpins the importance of smoking as one of the main modifiable risk factors for type 2 diabetes mellitus.
High-throughput expression data have become the norm in molecular biology research. However, the analysis of expression data is statistically and computationally challenging and has not kept up with their generation. This has resulted in large amounts of unexplored data in public repositories. After pre-processing and quality control, the typical gene expression analysis workflow follows two main steps. First, the complexity of the data is reduced by removing the genes that are redundant or irrelevant for the biological question that motivated the experiment, using a feature selection method. Second, relevant genes are investigated to extract biological information that could aid in the interpretation of the results. Different methods, such as functional annotation, clustering, network analysis, and/or combinations thereof are useful for the latter purpose. Here, I investigated and presented solutions to three problems encountered in the expression data analysis workflow. First, I worked on reducing complexity of high-throughput expression data by selecting relevant genes in the context of the sample classification problem. The sample classification problem aims to assign unknown samples into one of the known classes, such as healthy and diseased. For this purpose, I developed the relative signal-to-noise ratio (rSNR), a novel feature selection method which was shown to perform significantly better than other methods with similar objectives. Second, to better understand complex phenotypes using high-throughput expression data, I developed a pipeline to identify the underlying biological units, as well as their interactions. These biological units were assumed to be represented by groups of genes working in synchronization to perform a given function or participate in common biological processes or pathways. Thus, to identify biological units, those genes that had been identified as relevant to the phenotype under consideration through feature selection methods were clustered based on both their functional annotations and expression profiles. Relationships between the associated biological functions, processes, and/or pathways were investigated by means of a co-expression network. The developed pipeline provides a new perspective to the analysis of high-throughput expression data by investigating interactions between biological units. Finally, I contributed to a project where a network describing pluripotency in mouse was used to infer the corresponding network in human. Biological networks are context-specific. Combining network information with high-throughput expression data can explain the control mechanisms underlying changes and maintenance of complex phenotypes. The human network was constructed on the basis of orthology between mouse and human genes and proteins. It was validated with available data in the literature. The methods and strategies proposed here were mainly trained and tested on microarray expression data. However, they can be easily adapted to next-generation sequencing and proteomics data.
Bats are ancient mammals that evolved more than 50 million years ago. There are 1,240 different species (> 20% of mammalian species) described so far, which represent one of the most abundant, diverse and widely distributed mammalian groups. Bats are the only mammals which actively fly and therefore can migrate to different areas of the world. It has been increasingly recognized that bats are reservoirs for more than 100 virus species, and several are associated with animal and human epidemics. As natural hosts of rabies virus (RABV) and related lyssaviruses, bats have become a focus of research not only in South America and Africa, but also in Europe and North America. Bats are also considered to be unique in their potential to host emerging and re-emerging zoonotic viruses. To evaluate and reduce the potential risk of rabies transmission to humans or carnivore hosts (like fox, raccoon and dog etc.), active and passive surveillance studies of bat have been performed. Using these approaches diverse lyssaviruses have been detected in bats. However, these studies did not explain the rarely discovered epidemics and the underlying resistance or immune mechanisms in bats as natural hosts for lyssaviruses. Probably, bats are more resistant to lyssavirus infections than other animals. This hypothesis is introducing the research questions of the present thesis: (1) How do the innate immune responses protect bats from fatal outcome of lyssavirus infections? Interferon (IFN) responses which can be induced by the recognition of viruses by pattern recognition receptors act as the first line of defense against lyssavirus infections. Therefore, type I and type III IFNs from European bats were cloned and functionally characterized in this thesis (Chapter 2 and 4). (2) How do the lyssaviruses adapt to escape the host defenses by counteracting the IFN-mediated immune responses? And how do the bats control the viral replication via the IFN responses? To explore the complicated interactions and understand how European bats (Eptesicus serotinus, Myotis myotis and Nyctalus noctula) interact with European bat lyssaviruses (EBLV-1 and 2), a natural host related model for investigations of the bat´s immune system and the virus-host interactions has to be established. Since all of 52 identified European bats species are endangered and strictly protected, stable cell lines from different tissues of M. myotis for in vitro studies were developed and used for molecular and functional studies (Chapter 3 and 4). The data obtained from this thesis revealed that: (a) European bat IFNs do have similar but also distinct molecular characteristics compared with other mammalian IFNs (Chapter 2 and 4); (b) Both investigated bat type I IFNs, IFN-Kappa; and IFN-Omega; present potent anti-lyssaviral activities and display a pathogen associated pattern in the tested cell line (Chapter 2); (c) The established immortalized M. myotis cell lines are differently susceptible to lyssaviruses and contain a functional IFN-mediated signaling cascade (Chapter 3); (d) Bat type III IFN-Lambda;s display cell-type specific functions due to the distinct expression of the IFN-Lambda; receptor (Chapter 4); (e) In bat cell lines a possible evasive strategy of lyssavirus is based on the counteraction of IFN production and/or IFN-mediated defensive pathways (Chapter 3); (f) The higher resistance of brain derived cell line MmBr compared to other cell lines to lyssavirus infection indicates the natural ability of bat´s central nervous system to control the growth of neurotropic virus, which might be an essential reason for the nonclinical outcome (Chapter 3). Overall, the present thesis provides first insights into IFN-mediated innate immune responses against RABV and EBLVs infection in their natural reservoir hosts and an useful toolbox for comparative analysis of virus-host interactions.
The metabolomic approach is one part of the "-omics" cascade further comprising genomic, transcriptomic, and proteomic investigations. Since information about the metabolome of the important human pathogenic bacterium Staphylococcus aureus is scarce, the aim of this thesis is the characterization of the exo- and endometabolome of this bacterium on a most global scale. For this, the metabolomic platform consisting of the analytical instruments used for 1H-NMR spectroscopy, HPLC-MS, and GC-MS analysis was applied. First, the requirements for an accurate sampling procedure for the analysis of intracellular metabolites are presented, explaining important pitfalls during the sampling and the subsequent metabolome analysis via HPLC-MS and GC-MS (book chapter I). The challenging task of the metabolite identification is demonstrated, as well as the requirements for absolute quantification of intracellular metabolites. In order to enhance the knowledge about the staphylococcal physiology and the biochemical network, the impact of different stresses and varying cultivation media on the bacterial metabolite pool was investigated in several studies. In article I, a first description of the primary metabolism of growing S. aureus COL cells cultivated aerobically in CDM is provided. This study also monitored the adaptation to glucose starvation on the level of metabolites and proteins. The uptake of all amino acids and the secretion and reuse of overflow metabolites were analyzed in a time-dependent manner. During the switch to a non-growing state, a drastic rearrangement of the amino acid pool in the bacterial cells was detected, and intracellular amounts of glycolytic intermediates were found to decrease in parallel to extracellular glucose exhaustion. During infection processes, S. aureus has to cope with varying levels of oxygen supply, including anaerobic conditions. A global metabolomic approach investigated the adaptation of S. aureus COL to strict anaerobic conditions using CDM as the culture medium. Thereby only linear growth was possible despite the higher uptake rate of glucose compared to aerobically, logarithmically growing cells. In an anoxic environment, S. aureus mainly switched on the less reliable lactic acid fermentation. Only serine and threonine but no alanine were significantly taken up. Subsequent glucose limitation led to energy starvation indicated by a drop in the adenylate energy charge. This was accompanied with an arrest of the fermentative metabolism and declining numbers of colony-forming units without taking advantage of the energy supplying arginine deiminase pathway. Compared to the established CDM, the eukaryotic cell culture medium RPMI 1640 provides more in vivo-like growth conditions. In article II, the growth behavior and the metabolic footprint of the S. aureus strains COL and HG001 were investigated during the aerobic cultivation in RPMI 1640 medium. Both strains are commonly used in laboratory research. The observed uptake and secretion pattern of extracellular metabolites provides important information for infection studies in which this medium is used for the precultivation of S. aureus. The extracellular accumulation of the noncanonical D-amino acid D-isoleucine was an interesting outcome. The strain specific metabolic footprint points to noteworthy differences in the biochemical system of both strains. Moreover, this study demonstrates the impact of the cultivation medium on the metabolic status of bacterial cells. Due to increasing resistance against a large number of antibiotics, community- and hospital- acquired infections with S. aureus are of major concern in medical therapy. Thus, greater knowledge about adaptive mechanisms after antibiotic treatment is required. In article III, the response of S. aureus HG001 to antibiotics with varying target sides, such as ciprofloxacin, erythromycin, fosfomycin, vancomycin, and ampicillin, was investigated on the metabolite level. Thereby, the abundances of 176 intracellular metabolites were observed in a time-dependent manner, thus providing the most comprehensive experimental metabolite dataset so far available for S. aureus. None of the antibiotic compounds led to alterations of single metabolite amounts, but mostly entire metabolic pathways were affected. The intermediates of the cell wall biosynthesis were affected by each antibiotic, confirming this pathway as the most potential target for new antibacterial compounds. The metabolite composition of human nasal secretions and human sweat was analyzed, since such secretions present natural habitats of S. aureus during the colonization of typical host sides. The results confirm that the bacteria has to cope with low concentrations of most of the amino acids but large amounts of urea and lactate during host colonization. Considering the supply of amino acids, the results support the usage of the RPMI 1640 medium as a step to more in vivo-like cultivation experiments. Moreover, essential information for future studies about the adaptation of S. aureus to more in vivo growth conditions is provided. Altogether, the metabolomic approach was proven to be an important tool for helping unravel the complex bacterial metabolism and the environmental factors that also play a role in the virulence of Staphylococcus aureus.