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The geometric arena here is a smooth manifold of dimension n equipped with a Riemannian or pseudo-Riemannian metric and an affine connection. Field theories following from a variational principle are considered on this basis. In this context, all invariants which are quadratic in the curvature are determined. The work derives several manifestly covariant formulas for the Euler-Lagrange derivatives or the field equations. Some of these field theories can be interpreted as gravitational theories alternatively to Einstein´s general relativity theory. The work also touches the difficult problem to define and to calculate energy and momentum of a gravitational field.
Streptococcus pneumoniae (pneumococci) are lancet-shaped, Gram-positive, alpha-hemolytic, facultative anaerobic human specific commensals of the upper and lower respiratory tract. Pneumococci may convert to pathogenic bacteria and spread to the lungs and blood. In different population groups, such as children, the elderly and immunocompromised individuals, pneumococci can cause local infections such as bronchitis, rhinitis, acute sinusitis, and otitis media as well as life-threatening invasive diseases such as community-acquired pneumonia, sepsis and meningitis. Pneumococci are surrounded by a rigid and complex exoskeleton, the peptidoglycan, also referred to as murein sacculus. The peptidoglycan (PNG) protects the cells from rupture by osmotic pressure and maintains their characteristic shape. The PNG is a heteropolymer made up of glycan strands that are cross-linked by short peptides and during growth the existing murein is continuously hydrolyzed by specific lytic enzymes to enable the insertion of new peptidoglycan. Bacterial cell-wall hydrolases are essential for peptidoglycan turnover and crucial to preserve cell shape. The D,D-carboxypeptidase DacA and L,D-carboxypeptidase DacB of Streptococcus pneumoniae function in a sequential manner. This study determined the crystal structure of the surface-exposed lipoprotein DacB, which differs considerably from the DacA structure. DacB contains a Zn2+ ion in its catalytic center located in the middle of a fully exposed, large groove. Two different conformations with differently arranged active site topology were identified. In addition the critical residues for catalysis and substrate specificity were identified. Deficiency in DacA or DacB resulted in a modified peptidoglycan peptide composition and led to an altered cell shape of the dac-mutants. In contrast, lgt-mutant lacking lipoprotein diacylglyceryl transferase activity required for proper lipoprotein maturation retained L,D-carboxypeptidase activity and showed an intact murein sacculus. Furthermore, this study demonstrated the pathophysiological effects of disordered DacA or DacB activities. Real-time bioimaging of intranasally infected mice indicated a substantially attenuated virulence of dacB- and dacAdacB-mutants pneumococci, while loss of function of DacA had no significant effect. In addition, uptake of these mutants by professional phagocytes was enhanced, while their adherence to lung epithelial cells was decreased. The second part of this study focused on the functional and structure determination of the soluble dimeric pneumococcal lipoprotein PccL. Because of its calycin fold and structural homology with the lipocalin YxeF from Bacillus subtilis, PccL was introduced as the first member of the lipocalin protein family in pneumococci and named “PccL” (Pneumococcal calycin fold containing Lipoprotein). Similar to other lipocalins, the distinct beta-barrel, which is open at one end, is significantly conserved in PccL. Moreover, the application of the in vivo acute pneumonia mouse infection model and the in vitro phagocytosis as well as adherence invasion studies revealed considerable differences in colonization and invasive infection between the wild-type D39 and the pccL-mutant. In conclusion, this study characterized the crucial role of pneumococcal carboxypeptidases DacA and DacB for PGN architecture, bacterial shape and pathogenesis. By applying in vivo and in vitro approaches, a close relationship between PGN metabolism and pathophysiological effects was discovered. In addition, the high resolution structure of DacB has been solved and analyzed and a structure model with a resolution of 2.0 Å is provided. Furthermore, analysis of the PGN composition was applied to indicate the impact of an impaired lipoprotein biogenesis pathway on localization and activity of DacB. The major impact of carboxypeptidases on cell shape and virulence proposes DacB as a promising target for the development of novel drugs or due to its surface exposition also as a promising vaccine candidate. PccL is the first pneumococcal lipocalin-like protein and this study indicated its contribution to pneumococcal virulence. However, the mechanism and the mode of action of PccL are still unknown and have to be deciphered in further studies.
Humans are exposed to a plethora of microorganisms that reside on outer and inner body surfaces. These are collectively referred to as the human microbiome. The evolutionary relationship between humans and their microbiome is very complex. It is now widely accepted that these microorganisms are not just passive spectators but play an important role in health. The presence or absence of certain microbes is also linked to various diseases, including inflammatory bowel disease, cardiovascular disease, obesity, cancer, and allergies.
Allergies are several conditions caused by a misguided immune response to foreign antigens that are typically harmless. Common allergic diseases include atopic dermatitis (AD), allergic asthma, hay fever, and anaphylaxis. The incidences of allergic diseases are continuously rising, with up to 40% of the human population thought to be sensitised to environmental antigens. This increased incidence is not simply the result of societies becoming more aware and better at diagnosing these diseases. It is believed that the increases in allergies and sensitisation have environmental causes and are related to Western lifestyles. It is known that the rate of allergies is less frequent in developing countries. They are also more likely to occur in urban than rural areas. The prevailing view of the involvement of bacteria in allergies is described by the hygiene hypothesis. The hypothesis claims that decreased exposure to diverse microbial communities early in life increases the risk of developing allergic diseases. There are numerous examples to support this claim. For example, children born and raised in close contact to farm animals or in the presence of pets, and who are thus in direct and constant contact with a complex microbial environment, are protected from allergic diseases. On the other hand, colonisation or infection with certain bacteria increases allergic disease risks. This seems to contradict the hygiene hypothesis.
It appears that the members of the microbiome have different effects on allergy, and the hygiene hypothesis may not apply to every player in the complex microbial diversity that humans are in contact with. Therefore, a better understanding of the host bacterial interaction is required on the level of bacterial species.
This work studies the interplay between bacteria and the immune system to identify and characterise bacterial components with allergenic properties. In this quest, Staphylococcus aureus (S. aureus) and Staphylococcus epidermidis (S. epidermidis) were investigated for their allergenic properties and involvement in different allergic diseases. In the case of S. aureus, evidence is presented on allergic implications for two different components; serine protease-like proteins (Spls) and superantigens (SAg). Furthermore, experimental support is provided on the allergenic properties of the extracellular serine protease (Esp) from S. epidermidis. We argue that stimulating allergic reactions by staphylococci is an immune evasion mechanism that increases the survival chances of the bacteria within the host.
In chapter 1, an introduction is given to both S. aureus and S. epidermidis and their interactions with the immune system. Also, the bacterial components with allergenic properties and allergic diseases with known bacterial involvement are presented. Finally, the question of why bacteria cause allergy is discussed.
Chapter 2 describes allergic reactions to the Spls of S. aureus in a cohort of cystic fibrosis patients. Chapter 3 focuses on the SAgs of S. aureus. SAgs were discovered more than 30 years ago, but their physiological function is still under discussion. In this chapter, the allergenic properties of SAgs and their possible immunological mechanisms are reviewed, and a possible link between SAgs and allergic diseases is discussed. In chapter 4, the focus shifts to S. epidermidis and its involvement in AD. The human immune response to the Esp from S. epidermidis is characterised in healthy and AD individuals. The allergenic properties of Esp imply a detrimental role of S. epidermidis in AD. Finally, chapter 5 summarises and discusses the results of this thesis. In this section, the pieces are put together, and attention is brought back to the question of why bacteria cause allergies.
Oral administration of drugs is the most common, convenient, safest and economical route of drug administration. There is lack of established tools to study the function of transporters in the intestinal absorption of drugs. Because of its favorable physico-chemical, pharmacokinetic and pharmacodynamic characteristics, trospium could be potentially used as a probe substrate to study the function of drug transporters. Therefore, this study was conducted to examine the suitability of trospium chloride as a probe drug to study the function of multidrug transporters in the human body. To this end, two randomized, controlled, four-period, cross-over pharmacokinetic drug interaction studies of oral and intravenous trospium with co-medication of oral clarithromycin or ranitidine were performed in 24 healthy subjects to mechanistically characterize the role of P-gp, OATP1A2, OCT1, OCT2, MATE1 and MATE2-K in the absorption and disposition of trospium. The contribution of the drug transporters in the absorption and disposition of trospium were examined in isolated systems using in vitro uptake and inhibition assays in transporter transfected human cell lines.
OCT1 (Vmax = 0.8 ± 0.1 nmol/min × mg) is a high capacity transporter of trospium compared to OCT2 (Vmax = 0.04 ± 0.01 nmol/min × mg). But the OCT2 (Km = 0.5 ± 0.1 µM) transporter demonstrated a high affinity in the transport of trospium compared to OCT1 (Km = 17.4 ± 2.1 µM). OCT1 genetic alleles *2, *3, *4 and *7 resulted in significant loss of activity and the alleles *5 and *6 caused complete loss of uptake of trospium. The common OCT2 genetic allele Ser270 caused slight but significant increase in activity of OCT2.
Ranitidine inhibits OCT1 (IC50 = 186 ± 25 µM), MATE1 (IC50 = 134 ± 37 µM) and MATE2-K (IC50 = 35 ± 11 µM)-mediated uptake of trospium in vitro. But it is a weak inhibitor of OCT2 transporter (IC50 = 482 ± 105 µM). Using FDA and EMA in vitro to in vivo extrapolation models, ranitidine was predicted to have a potential inhibition effect on intestinal OCT1 ([I]2/IC50 ~40), renal MATE1 ([I]1/IC50 ~0.02) and MATE2-K ([I]1/IC50 ~0.1) transporters in vivo. Clarithromycin was predicted to cause DDI by inhibiting P-gp-mediated efflux of trospium at the intestine ([I]2/IC50 of ~310) and hepatocytes ([I]3/IC50 ~1). Therefore, co-medication of oral clarithromycin was expected to result in an increase in oral absorption and hepatic clearance of trospium but not changes in distribution volume.
In healthy subjects, oral trospium is slowly (MAT ~10 h) and poorly (F ~10 %) absorbed from the jejunum and cecum/ascending colon, widely distributed into the body (Vss = 5 - 6 l/kg) and slowly eliminated (t1/2 = 9 - 10 h) majorly via renal glomerular filtration and tubular secretion (CLR ~500 ml/min). After co-medication of clarithromycin (inhibitor of P-gp), on the contrary to our IVIVE prediction, we found a non-expected but significant expansion of the shallow and deep distribution spaces for trospium by ~27 %. A single dose administration of trospium with co-medication of ranitidine (inhibitor of OCT1) resulted in no effect on the intestinal absorption of trospium. But the renal clearance of trospium decreased slightly (15 %) but significantly.
Intravenously administered trospium (2 mg TC) might be a suitable probe drug to evaluate the effects of a P-gp inhibitor on distribution of a drug. Oral trospium chloride can be selected for DDI studies with new chemical entities (NCE) with predicted inhibitory potential on OCT1 and P-gp and which are available after oral absorption along the small intestine and in the cecum/ascending colon. Another kind of application of trospium chloride might be pharmacogenomics studies in subjects with functionally relevant polymorphisms of P-gp and OCT1 or in patients with suspected transport failure due to intestinal diseases. The function of the efflux transporters MATE1 and MATE2-K in the PTC of the kidneys can be well assessed with the probe drug trospium by measuring its renal clearance.
Introduction: Antiseptics are used for the prophylaxis of infections of acute wounds and for the treatment of critically colonized chronic wounds as well as localized infections of acute and chronic wounds. If an antiseptic with too much tissue toxicity and/or too little efficacy is used, the wound healing can be delayed.
Objective: The aim was to compare the irritation potency of frequently used wound antiseptics by using the hen's egg test on the chorioallantoic membrane (HET-CAM). Additionally, the influence of antiphlogistic active additives which might increase the tolerability was examined. To allow a more extensive comparison, antiseptics classified as obsolete such as hydrogen peroxide, creams on PVP- iodine base, silver sulfadiazine, chlorhexidine and nitrofural as well as the non-antiseptic wound treatment agents dexpanthenol and hemoglobin spray were also examined.
Method: The HET-CAM was used as a semi-in-vivo method to test the tolerability of wound antiseptics to tissues by observing the reactions that occur in the blood vessels of the highly vascularized CAM such as hemorrhage, lysis and coagulation. The irritation score (IS) was calculated and differentiated in 4 ranges according to Spielmann (1991).
Results: The vascular injuries of the CAM were considered as an indirect indicator of the tolerability. It is accepted that agents with no or low irritation potential on the CAM are to be preferred in the clinical practice if they are clinically effective.
Severe CAM reaction was observed after short-term application of octenidine based wound gel (active ingredient octenidine 0.05%) (IS: 10.3) and chlorhexidine digluconate 0.5% solution (IS: 9.5). Moderate reaction was observed for the combination of octenidine 0.05% in aqueous solution with panthenol 1.34% and allantoin 0.2% (IS: 8.7), hydrogen peroxide 1.5% in aqueous solution (IS: 6.1) and hydrogen peroxide 0.5% solution (IS: 5.5). Slight reaction was observed for hydrogen peroxide 1.5% solution in combination with sodium thiocyanate 0.698% (IS: 2.6), sodium thiocyanate 0.698% solution (IS: 2.1) and Dermacyn® (active ingredient NaOCl/HOCl each 0.004) (IS: 1.2). Polihexanide 0.04% in Ringer solution (IS: 0.9), Polihexanide 0.05% in Lipofundin, Granulox® (active agent hemoglobin 10%) (IS: 0) and dexpanthenol 5% solution (IS: 0) showed no reaction. In the long-term observation (24 hours after application), Dermacyn® showed the best results (59% of irritation remained alive after 24 hours). The addition of dexpanthenol and allantoin reduced the irritability only slightly, whereas the decrease of IS of hydrogen peroxide by addition of sodium thiocyanate was almost significant (p 0.0596).
Conclusion: It is suggested that agents with no or low irritation potential on the CAM are to be preferred in the clinical practice if they are clinically effective. It is suggested that further in vivo and in vitro studies are to be undertaken with these agents.
Solely regarding local tolerability, polihexanide and hypochlorite are the antiseptic agents of choice of the tested preparations. The wound oxygenizer hemoglobin spray is tolerated without irritation as well as the negative control 0.9% NaCl solution. Because of their other disadvantages in conjunction with their irritability, the outdated cream formulations on basis of silver sulfadiazine, PVP- iodine, chlorhexidine and nitrofural cannot be recommended for wound antisepsis.
Global change is one of the major challenges our society faces in recent times and is becoming increasingly noticeable in all aspects of our lives. In the last ten years, reports about droughts in Europe increased, contrary to expected natural climate variations and are attributed as indicators of climate change. Droughts resulted in a severe decrease in water levels of lakes, rivers and reservoirs, posing socio-economic and environmental challenges. Climate scenarios by the Intergovernmental Panel on Climate Change (IPCC) project increasing temperatures, more frequent, longer and/or more intense heat waves and warm spells, and an increase in aridity with short-term droughts in the upcoming decades for Western and Central Europe. Some areas – such as Northeast Germany – are already affected by negative water balances and the lowering of lake and groundwater levels. Additionally to possible challenges in water availability, excess nutrients and heavy metals from industrial emissions, agricultural fertilisers and land use changes lead to declining water quality. In the past century, extensive eutrophication and environmental pollution have become major water quality issues in many freshwater bodies.
Nonetheless, water and its availability in a sufficient quantity and quality are prerequisites for life and must be prioritised in future development. The European Union aims for a good status in all surface and groundwater bodies by 2027 regarding their ecological, chemical and quantitative status. However, a profound understanding of eutrophication, pollution sources, and water bodies' reference conditions – referring to pre-anthropogenic conditions – should be available for each system to apply integrated restoration strategies. Moreover, an in-depth understanding of long-term climate variability and its dynamics is indispensable to approach these climate change challenges and reliably predict water availability.
During the past decades, numerous paleoenvironmental studies have been carried out on Northern German sediment archives, using mainly lacustrine sediments to reconstruct hydroclimatic variability, often inferring lake-level variations as key indicators. However, most studies were carried out in areas affected by more maritime or continental climate. Studies from the transition zone are rare. Only few existing studies offer high-resolution records and/or robust chronologies, which limits the understanding of past environmental changes significantly. Besides, the Northern German lowlands have been anthropogenically affected since at least the Neolithic (~5.6 ka cal BP) and, in particular, forest composition and density have recently been shown to have at least partially an impact on lake-level variations. However, a reliable distinction between climatic impacts and anthropogenic interferences is widely missing, which is a problem because many studies were conducted on rather small lacustrine systems in which expected anthropogenic signals are higher, and single events may overprint the climatic signals. These biases lead to an incoherent picture of the past hydroclimatic variability in Northern Germany during the Holocene. To overcome this situation, it is inevitable to identify a suitable sedimentary archive from the transition zone – preferably a large lacustrine system in which natural (supra-)regional paleoenvironmental signals are expected to be not overprinted by single events. Moreover, it is necessary to establish robust chronologies and apply high-resolution methods to infer past environmental changes in a high temporal resolution. Taken together, this could contribute to an enhanced understanding of past environmental and climatic changes in Northern Germany.
This thesis consolidates the evidence for Schweriner See to act as a suitable sedimentary archive in Northern Germany for (supra-)regional climate reconstructions. Schweriner See is a large lowland lake in Northern Germany located within the transition zone from maritime to continental climate. In the first step, (paleo)lacustrine landforms, i.e. beach ridges, subaerial nearshore bar, and a silting-up sequence, are investigated along the north-eastern shoreline using a combined approach of sedimentology (e.g. grain size variations) and the relatively novel method of luminescence profiling offering relative age determinations to understand depositional processes and their chronological framework. Absolute age information is mainly inferred by OSL dating. Secondly, an important prerequisite to interpreting information obtained from lacustrine sediment archives is a thorough understanding of processes controlling sedimentation. Schweriner See is characterized by a complex morphometry, which influences in-lake processes, i.e. i) in-lake productivity, ii) carbonate precipitation and iii) wind- and wave-induced processes, resulting in a distinct spatial heterogeneity. This thesis shows that it is crucial first to understand sedimentary depositional processes and controlling mechanisms to i) select suitable coring location(s) and ii) reconstruct paleoenvironmental and hydroclimatic variations reliably.
Based on bathymetric considerations and inferred in-lake processes, two main coring locations were identified to infer i) the anthropogenic impacts and ii) hydroclimatic variations. Short sediment records from the shallow water areas (< 15 m water depth) cover the most recent environmental history of Schweriner See. A well-dated sedimentary record (210Pb/137Cs and 14C dating) links distinct sedimentary and geochemical changes with historical events. Schweriner See was extensively affected by lake-wide eutrophication and contamination, closely related to sewage and population dynamics within the catchment. The water quality only improved after the German Reunification in 1990 CE when sewage was precluded from Schweriner See. Contamination trends at Schweriner See showed similar trends to different archives along the southern Baltic Sea, implying a common regional driving mechanism, e.g. environmental legalisation.
A well-dated sediment record from the profundal zone (52 m water depth) allowed the reconstruction of large-scale atmospheric conditions during the past 3 ka cal BP by inferring winter temperature variability, the moisture source region and/or evaporative lake water enrichment, which resemble variations in the North Atlantic Oscillation (NAO). The NAO greatly influences the Central European climate, affecting, for example, surface air temperature, precipitation or storm tracks. During 3-2.8 ka and 2.1-0.8 ka cal BP, predominantly positive NAO conditions are reconstructed, which are characterized by warmer winter temperatures, moisture conditions bringing isotopically enriched precipitation from the southern/central North Atlantic to Northern Central Europe and/or warmer temperatures that may result in a higher evaporative isotopic lake water enrichment as a result of northwards displaced westerlies. Conversely, during 2.8-2.1 ka and 0.8-0.1 ka cal BP, results correspond to predominantly negative NAO phases influenced by southwards displaced westerlies. Frequent atmospheric blocking allows for the intrusion of northerly or easterly winds, resulting in colder winter temperatures, isotopically depleted precipitation from the Northern Atlantic and Arctic region and/or a lower evaporative lake water enrichment. In addition to these long-term changes in atmospheric conditions, short-term hydroclimatic variations have been reconstructed, mainly reflecting lake-level variations in conjunction with precipitation variability, with the proxy signal being additionally amplified by wind speed and wave motion. Comparisons with other archives support these results.
So far, the paleoenvironmental reconstruction is limited to the Late Holocene, but initial dating results imply possible interferences until the Late Pleistocene. Therefore, future studies should focus on extending the profundal record from Schweriner See further back in time, providing a high-resolution record covering both the Holocene and possibly the Late Pleistocene.
Many intrastate conflicts see more than one mediation effort. As the sequencing of mediation efforts in intrastate conflicts is neglected in existing research, this project addresses the question how and why previous mediation outcomes have an impact on subsequent mediation onset and subsequent mediation success. Drawing on bargaining theory, it is argued that governments and rebel groups engaged in intrastate conflicts account for previous mediation outcomes in their cost-benefit calculations on subsequent mediation onset, and, should subsequent talks set on, their behaviour during subsequent mediation efforts, which influences subsequent mediation success.
If mediation did not produce an agreement, the persistence of the private information problem is noted by the conflict parties. Yet, no new costs of mediation are uncovered, and hence the conflict parties will agree to subsequent mediation onset. Being aware of the necessity to overcome the private information and the commitment problem, the mediator will seek to account for the concerns of the conflict parties, and thereby work towards subsequent mediation success. If mediation produced a partial agreement, the benefits of mediation are underlined. The private information and the commitment problem seem solved with the assistance of the mediator. Subsequent mediation onset and eventually subsequent mediation success are observed. If a mediated agreement was reneged on by the rebel group, the government will refrain from further talks, pointing out the rebel group’s illegitimacy. If the government reneged on the agreement itself, it will also decide against subsequent mediation, as the previous mediation effort produced an agreement which did not mirror the power distribution in the dyad. Costs of mediation, which outweigh the benefits of it, were highlighted. Rebel groups will opt for mediation regardless which side reneged on an agreement. As both governments and rebel groups have to agree to subsequent mediation for talks to set on, subsequent mediation onset is unlikely if a mediated agreement was reneged on. Given the onset of subsequent mediation after a mediated agreement was reneged on, subsequent mediation success is unlikely to be observed, due to the previously underlined hazards of sharing private information and the persistence of the commitment problem.
The theoretical argument is tested with a mixed-methods approach. The quantitative analysis accounts for mediation efforts in African intrastate conflicts between 1993 and 2007. The qualitative analysis scrutinises the mediation efforts between the Government of Uganda and the Lord’s Resistance Army. The results of both parts of analysis largely go hand-in-hand, and show that partial mediation success and mediation which did not produce an agreement have a positive impact on subsequent mediation onset in particular, but also on subsequent mediation success. Reneged on mediated agreements have a severe negative impact on subsequent mediation onset and subsequent mediation success though.
By addressing the question which impact previous mediation outcomes have on subsequent mediation efforts, this research shows that mediation which does not produce an agreement is not the mediation outcome which needs to be feared by the international community. Instead, the deteriorating impact of short-lived agreements, a mediation outcome which is unaccounted for in existing research as an explanatory variable, becomes apparent. This research has important policy implications, especially for mediators, as it suggests that accepting mediation efforts to end without an agreement is more conducive for subsequent mediation efforts. Moreover, this research points towards the necessity of including reneged on agreements in mediation research as an explanatory variable more extensively, thereby shedding more light onto the dynamics at play in consecutive mediation efforts.
Molybdenum dependent enzymes are involved in essential metabolic transformations in bacteria, plants, and human beings. The extreme instability of the molybdenum cofactor (Moco) prevents its use as an effective treatment for patients with a Moco deficiency. Therefore, the design, develop and execute the artificial molybdenum cofactor models are essential.
In the present thesis, the asymmetric molybdopterin (mpt) model precursors with oxygen functionality and various electronic structures and their Moco model complexes mimicking the natural cofactor have been synthesized and comprehensively investigated through multi-nuclear NMR, MS, IR, resonance Raman, X-ray crystallography, UV-Vis, and electrochemical methods. Notably, the asymmetrically substituted dithiolenes in this thesis are confirmed through a significant push-pull effect, which is tuning its electronic structure. The redox behavior of Moco model complexes was investigated by temperature-dependent cyclic voltammetry. Electronic and vibrational spectral studies were investigated in detail to understand substituents effect on the electronic structure of model complexes and to elucidate roles of mpt in catalysis. Since the model complexes can be considered as structural models for the Moco dependent oxidoreductases, catalytic oxygen atom transfer (OAT) reactions in DMSO/PPh3 were investigated.
The main focus of the present thesis was achieved through the development of various synthetic routes that address phosphonate bearing dithiolene ligands, inspiring the natural mpt. Simultaneously the Minisci protocol was applied for the synthesis of new pterin ketophosphonates, taking into consideration the essential aspects of the natural molybdopterin, including the phosphate anchor group. Even though some aspects of this protocol require further optimizations, but the mentioned synthetic route has exceptional potential and flexibility.
A large portion of the earth's surface is covered with various vegetation classes (i.e. grassland, wetland and agricultural area, forest) of many diverse species and canopy configurations. The ability to assess and to monitor canopy parameters, such as biomass, leaf area index, and vegetation water content, is of vital importance to the study of different agronomic processes. Remote sensing techniques provide a unique capability towards probing different vegetation types and canopy by operating at different bands, observation angle etc. Over the past decades, significant progress has been made in remote sensing techniques of land processes specially vegetation characteristics through development of advanced ground-based, airborne and space-borne microwave sensors, methods and approaches such as theoretical, semi-empirical and empirical models, needed for analyzing the data. These activities have sharply increased in recent years since the launch of different active and passive satellites and sensors. Remote Sensing (RS) science and techniques combined with ground truth data can provide new tools for advanced agricultural crop applications. It has been demonstrated that RS has the ability to estimate biophysical parameters of agricultural crops over time at local, regional, and global scales. In this study, RS images in visible/near infrared (VIS/NIR) domain as well as microwave domain combined with ground truth data were used to assess biophysical parameters of agricultural crop during their whole growing season at Durable Environmental Multidisciplinary Monitoring Information Network (DEMMIN) test site in North East Germany. Ground truth studies were carried out for 31 weeks during 17th April – 13th November 2013 over three crop lands including winter wheat, barley and canola. Landsat 8 OLI, Landsat 7 ETM+ were used for the VIS/NIR studies and TerraSAR-X synthetic aperture radar (SAR) images were used to study biophysical parameters of agricultural crops in microwave part of electromagnetic spectrum. The analysis was conducted by calculating different vegetation indices (VIs) to estimate the biomass (fresh and dry), LAI, and vegetation water content (VWC) of three crops using Landsat 8 OLI and Landsat 7 ETM+ combined with ground truth data. A new concept of Soil Line retrieval from Landsat 8 image was also developed to estimate plant biophysical parameters using soil line related vegetation indices in optical domain of electromagnetic spectrum. Different approaches including univariate, multivariate stepwise regression and semi-empirical water cloud model was also used to estimate the biophysical parameters of agricultural crop using TerraSAR-X data in microwave domain of electromagnetic spectrum. Perhaps the most important conclusion of this study is that the RS approach can provide useful information about estimating agricultural crop parameters over time and local scale, which can therefore provide valuable information to aid the agronomy community.
Until today, more than 100 years after its first description in Italy, the highly pathogenic avian influenza virus (HPAIV) has not lost its fearsome character for wild birds, poultry and humans. On the contrary, the number of outbreaks with high casualty rates in wild birds and poultry has multiplied in recent years and cases of zoonotic infections are also increasingly reported from HPAI endemic areas. The epidemiology of these infections is complex and also involves surface water and possibly sediments of shallow standing waters, which could play a role as a vector medium and/or virus reservoir. The goal of this project was to expand current knowledge of the influence of water on the spread of AIV. As part of this project, we were able to ...
1. ...improve AIV detection methods using real time RT-PCR in terms of sensitivity and breadth of viruses detected. In addition, we succeeded in economizing the procedure so that fewer resources are required and results are obtained faster (publication I: [173]).
2. ...develop an ultrafiltration-based enrichment method for AIV from surface water and evaluate it with field samples from HPAI outbreak areas in wild bird habitats (Wadden Sea coast of Schleswig-Holstein) and previously unaffected regions (Antarctic Weddell Sea) (publication II: [174]). Furthermore, protocols for testing different environmental sample matrices for AIV screening were tested and compared to results of passive monitoring by dabbing diseased or dead wild birds. AIV was detected in more than half (61%) of 44 water samples. We received additional sediment samples from 36 of the 44 water samples. In 18 of 36 of the sediments tested, as well as in 4.16% of 1705 fecal samples tested AIV was detected. However, the studies of the environmental samples mostly yielded only generic AIV detections, with viral loads in the range of the detection limit. This massively hampered further investigations for sub- and pathotyping. In contrast, 79.41% of 68 samples from passive monitoring showed high to very high HPAIV viral loads which also allowed sub- and pathotyping.
3. ...demonstrate in animal experiments that even very low titers (0.1 TCID50 ml-1) of HPAI viral infectivity in water can induce productive infection in susceptible but clinically largely resistant mallard ducks (publication III: [175]). Furthermore, we were able to develop evidence that there is a difference in virus spread that depends on the type of (contaminated) water source. This means that infections on poultry farms with inverted or nipple drinkers may follow a different course than infections in the wild, which are mediated via larger surface waters.
Overall, the results of this project highlight the important role of surface and drinking water, as well as aquatic sediments, in the spread of AIV. The methods developed here for AIV detection extend the possibilities for surveillance of AIV infections; however, passive remains superior to active surveillance of HPAIV infections in several aspects. Examination of various environmental samples did not yield a significant advantage in terms of an early warning system that would indicate the presence or spread of HPAIV in wild bird habitats prior to the occurrence of lethal infections in wild birds.
The aim of the study was to develop and evaluate the reliability and agreement of new computer planimetric method for measurement and assessment of plaque on all types of removable dental prostheses RPDs. The instrument (new method) was tested by evaluating the efficacy of the rotating needles device in cleaning specific parts of RPD. From a database containing 780 images, which were taken in a standardized method for 65 RDPs for 49 participants, 55 images were selected randomly for image analysis. Adobe Photoshop software was used according to a standard operating procedure (SOP) by a main examiner two times in different sessions, and 1 time by 3 other examiners. In order to estimate the intra- and inter-examiner reliability, intraclass correlation coefficients ICC(2,1) was used. Three parameters were used to estimate agreement: standard error of measurement (SEM), smallest detectable change at 95% confidence level (SDC95%), and limits of agreement (LoA) according to Bland¨CAltman method. In the database, only 34 subjects were found with double crown retained removable denture and veneer over the secondary crown. 49x2 (before x after) images for 34 RDPs went under image analyses to calculate POP before and after cleaning the RDPs with the rotating needle device. Data were analysed using Wilcoxon signed-rank test. In all steps of image analysis, both intra-examiner and inter- examiner reliability were excellent with ICC(2,1) values > 0.85 at 95% confidence level. Intra- and inter-examiner values for both, SEM and SDC95% were ¡Ü 6% and ¡Ü17% respectively. The Bland¨CAltman analysis revealed a satisfactory level of agreement. POP is significantly more on the veneer than on the base(B-O), P <0.05. The rotating needles device is effective in cleaning the veneer and base(B-O), P <0.05 with absolute effect size 0.62. No statistical significance was detected in the effectiveness of the rotating needles device between base(B-O) and veneer. This study showed an excellent inter- and intra-examiner reproducibility, satisfactory level of examiners agreement, and acceptable measurement error of the new computer planimetric method . Furthermore, the method can be used with all types of RDPs. The rotating needles device can significantly reduce plaque on the double crown retained removable denture. The Computerized Planimetric Method (CPM) is more suitable for clinical researches because of its objectivity, reliability, high level of standardization, and the ability to detect and quantify small changes in plaque. Extra attention should be given to the veneer over the secondary crown as they are a potential part for RDP plaque accumulation.
Background: COVID-19 lead to the adoption of containment measures including temporary closure of dental clinics. Despite the risk of infection transmission, dental emergencies have not ceased during this pandemic and had to be managed also in the lockdown period.
Aim: To analyze the profiles and offered management options of pediatric patients presenting with dental emergencies during a COVID-19 lockdown.
Design: Retrospective analysis of patient records of children seeking emergency dental treatment during a 7-week lockdown period in 2020 in a university pedodontics clinic in Germany, compared to a similar cohort from 2019. Data on patient level, tooth level, and session level were collected. An analysis of the digital records after 6 months follow-up was performed for the patients who received Non-Aerosol Generating Procedures (NAGP) as management for dental emergency in the lockdown period in 2020.
Results: The 2020 cohort consisted of 83 patients, while the 2019 cohort included 46 patients showing 45% higher necessity for emergency treatment in 2020. Most common chief complaint was oral mucosal conditions in 2020 (26.4%), and irreversible pulpitis in 2019 (25.5%). Dental caries (without spontaneous pain) was the second most chief complaint in both cohorts (20.7% and 23.4% respectively). Most interventions in 2020 were Minimally Invasive Treatments such as the hall technique and silver diammine fluoride (20.3%), which were in 2019 not considered, followed by pharmacological treatment (16.9%), which were in 2019 also highly used (35.9%). The 6 months follow up for the NAGP revealed benefit in management of the acute dental problem, by either direct treatment or by postponing the treatment need to a later time period.
Conclusion: The COVID-19 pandemic led to increase in emergency pediatric dental visits and shifted treatment options towards less invasive procedures.
In challenging situations, where aerosols increase the risk of infection transmission, NAPD are a viable option in the management of dental emergencies, especially in pediatric dentistry.
Abstract
Background: Behavior management techniques (BMT) are essential in order to
achieve a successful dental treatment with a minimum amount of stress in paediatric
dentistry, but parents are not equally accepting different advanced BMT.
Purpose: To investigate the differences in parental acceptance of advanced
behavior management techniques between University of Greifswald/Germany and
Jordan University/Jordan.
Methods: Parents of the children treated in the pedodontic departments at the
University of Greifswald/Germany and Jordan University/Jordan rated their
acceptance level of four advanced behavior management techniques (passive
restraint, active restraint, nitrous oxide sedation and general anesthesia) for normal
treatment, and for urgent treatment using a five points Likert scale. 200 parents (100
in each university) completed the questionnaire forms for analysis.
Results: Nitrous oxide sedation was rated the most accepted technique in
Greifswald and Jordan (mean 3.78±1.34; 3.22±1.50, respectively). The least
acceptable technique in Greifswald was passive restraint (2.05±1.18) and in Jordan
general anesthesia (2.11±1.30). The parents in Greifswald are significantly more
accepting nitrous oxide sedation than parents in Jordan (p=0.010), while parents in
Jordan are significantly more willing to accept passive restraint (p=0.001). The
acceptance of all advanced behavior management techniques increased significantly
in both groups when the treatment is urgent (p≤0.05),
Conclusions: Parental culture and the urgency of the treatment affect the
acceptance to different behavior management techniques. Moreover, the parental
attitude to the pharmacological technique has changed, as nitrous oxide sedation
generally appears to be the most preferred advanced technique in both groups.
National oral health survey on refugees in Germany 2016/2017: caries and subsequent complications
(2020)
Objectives To assess oral health, caries prevalence, and subsequent complications among recently arrived refugees in Germany and to ompare these findings with the German resident population. Methods This multicenter cross-sectional study recruited 544 refugees aged 3–75+ years; they were examined at ten registration institutions in four federal states in Germany by two calibrated dentists. The refugees were screened for caries (dmft/DMFT) and its complications pufa/PUFA); this data was compared to the resident population via the presentative national oral health surveys). Results The deciduous dentition of the 3-year-old refugees had a mean dmft value of 2.62 ± 3.6 compared with 0.48 dmft in the German resident population, and caries increased to 5.22 ± 3.4 for 6–7-year-olds (Germany: 1.73 dmft). Few refugee children had naturally healthy teeth (7% in 6–7-year-olds, Germany: 56%). In the permanent dentition, the gap in caries prevalence between refugees and the German population decreased with age (35–44-year-olds: 10.55 ± 7.1 DMFT; Germany: 11.2), but refugees exhibited more caries defects (35–44-year-olds DT = 3.13 ± 3.0; Germany: 0.5). German residents had more restorations (35–44-year-olds FT = 4.21 ± 4.6). Regarding complications, the 6–7-year-olds exhibited the highest pufa index (0.86 ± 1.4) which decreased in adolescence (13–17-year-olds, 0.18 ± 0.6) and increased in adults (45–64-year-olds, 0.45 ± 0.8). Conclusion The refugees had high caries experience, often untreated caries teeth and more complications compared with the German resident population, especially in children. Closing this gap by extending preventive systems to the refugees would decrease future treatment needs. Clinical relevance European countries should be prepared for the higher dental treatment needs in recent refugees, especially in
children.
Sealing ability of ProRoot MTA when placed as an apical barrier using three different techniques
(2013)
A one-visit apexification protocol with Mineral Trioxide Aggregate (MTA) can be seen as an alternative to the traditional treatment practices with calcium hydroxide. The aim of this study was to investigate the sealing ability of ProRoot MTA when placed as an apical barrier using three different techniques. Sixty freshly extracted single-rooted human teeth were decoronated and standardized to a root length of 15mm. The root segments were prepared with Gates Glidden burs (size 1-6) to simulate the clinical situation of an open apex and randomly assigned into 3 experimental groups of 20 samples each. 5mm MTA was placed by pluggers (Group 1) paper points (Group 2) or ultrasonic tips (Group 3). Radiographs were taken to verify the placement of the apical barriers. After obturation of all samples with warm gutta-percha (Obtura) and AH26 sealer, the coronal portion of all samples was sealed with Cavit. The root segments were then double coated with nail varnish except for the open apex and were exposed to methylene blue dye for 48 hours at room temperature. Afterwards, the samples were sectioned longitudinally and the extent of dye penetration was measured with a stereomicroscope. The mean depth of dye leakage for Group 1 was 1.34mm (±0.5 SD) Group 2 1.25mm (±0.4 SD) and Group 3 1.14mm (± 0.4 SD). Statistical analysis showed that there were no significant differences among the 3 experimental groups (0.178<p<0.552). In conclusion, ProRoot MTA has a similar sealing ability when placed as an apical barrier with pluggers, paper points or ultrasonic tips.
Background: Restorative treatment for children’s teeth is still an important aspect of dentistry. In the light of an only moderate caries decline in the primary dentition and a persistently low care index in Germany during the past years [DAJ 2010], there is still a demand for further work on recent patterns and outcomes of restorative treatments in primary teeth placed in everyday practices under the Germany National Health System. Objectives: The present study aimed firstly to describe the prevalence of caries and restorations in the primary teeth in Berlin and Germany from the representative Germany surveys [DAJ 2010], secondly, to describe the frequency and distribution of restorative treatment in primary teeth performed in everyday dental practice in Berlin including children age groups from 1- to 13-years of age, thirdly, to evaluate the outcomes of restorative treatment performed in everyday dental practices in these children and finally to compare results of the present study with data from the German National Health System [KZBV 2011] and randomized community data on the longevity of restorations in primary teeth in Denmark [Qvist et al. 2010a]. Material and Methodology: In the first part of present study data from representative German surveys [DAJ 2010] were interpreted to describe and compare the prevalence of caries and restorations in the primary teeth in Berlin and Germany. For the second and third parts data generated from German National Health System in Berlin (KZV-Berlin) on fillings done in everyday practices in primary teeth of 1- to 13-year-olds during 2010/2011 were collected. This data included: distribution of children with dental treatment regardless of the type of intervention provided, of children who received restorative treatments in primary teeth during dental care visits including total number of fillings per child, the number of filled tooth surfaces, retreatment with another filling, stainless steel crowns, pulp involvement and extractions after prior filling therapy. Information on the age of the original fillings at the time of retreatment was also included. The collected data then were entered into a data base for descriptive and analytical analysis. The results were compared with equivalent data from the German National Health System [KZBV 2011] and randomized community data from Denmark [Qvist et al. 2010a]. Results: Result showed a high similarity in patterns of caries and restorative treatment in primary teeth in Berlin and all of Germany as reported in the representative German surveys [DAJ 2010]. About of 84% of 1-13-year-olds insured in the German National Health System in Berlin received dental care during 2010/2011, with considerably lower rates in very young children. Fillings in primary teeth were performed in 31.17% of all children attending the dentist. Most restorations were placed in 5-8-year-olds. In 1-13-year-olds mostly just one filling was placed, more than five fillings were per child were recorded on average for very young age groups (1-4-year-olds). 55.60% of all fillings in primary teeth were two-surface restorations, whereas more than three-surface restorations comprised 6.17% of all fillings and they were performed most frequently in young children of 1-4-years of age. Retreatment to fillings in primary teeth was 7.66% of fillings placed in 1-13-year-olds. Most retreatments took place from 5 to 9 years of age with a peak in 6-year-olds. In 1-3-year-old children fillings showed shorter mean age at the time of retreatment compared to 7-year-olds and above. Retreatment of fillings in primary teeth by stainless steel crowns was very limited with only 5.16% of all retreatments and it was preferred in children from 3 to 7 years of age. The retreatment with pulp involvement was 11.27% of all retreatments. Extractions were almost as often as retreatment as another filling (ratio 4:5), but they were preferred in older children due to the course of exfoliation. Conclusions: Under the conditions of this retrospective study, the restorative treatment with fillings performed within the National Health System in primary teeth in Berlin was very successful with low rates of retreatment and the fillings shows comparable results to data on the longevity of restorations in primary teeth in Denmark. The study highlighted the need to a structured program for prevention in primary teeth, especially for very young children with high caries activity and possibly also different treatment structures with specialized dentists in this field who can perform oral rehabilitations with pulpotomies and stainless steel crowns.
Wadi Wurayah area is located in the north of Fujairah Emirates between the towns of Khor Bidiyah Fakkan and Oman on the Gulf Coast Line in Fujairah Emirates, United Arab Emirates. It lies within a priority World Wide Fund for Nature ( WWF) Global 200 Ecoregions ( ecoregion 127, Arabian Highland Woodlands and Shrublands ), a rich diversity of sheltering rare and endangered mountainous and freshwater habitats and species , and providing opportunities for the revival and sustenance of local livelihoods. However, as most of the United Arab Emirates and the region , the area is undergoing dramatic changes linked to economic diversification and promotion of tourism. The United Arab Emirates in 1999 approved the programmed of work from the UN convention of Biological Diversity ( CBD). This momentum must be used wants it or disappear. In a first move , the United Arab Emirates established the federal Environment Agency ( FEA) that produced the Environmental Law of 1999 with the role to encourage each to Emirates assess its land and coastal / marine resources, formulate plans for establishing protected areas , upgrade those that may already exist , and help implement the environment law. In early 2006, UAE created its first Ministry of Environment and Water ( MEW ), which was before the Ministry of Agriculture and Fisheries. Environmental issues and a greater role of the civil society are now higher on the agenda of the United Arab Emirates government , partner of the Emirates Wildlife Society ( EWS ), the World Wide Fund for Nature ( WWF) - UAE Project Office is the only international conservation NGOs operating in the UAE that plays a pioneering role in partnering with local- governmental institutions to establish win- win solutions. The United Arab Emirates is making tremendous efforts in diversification is the development of tourism. Too often tourism mass , With all of its negative environmental consequences is privileged. However, the more traditional Emirates are seeking alternatives that would preserve their environment and respect the traditional lifestyles of the local communities. This study aims to help a sustainable biosphere reserve integrating oneself local traditional and lifestyle with the conservation of biodiversity and habitat inimitable by providing a model of economical incentives unique to the region . In order to further the implementation of the Wadi Wurayah Biosphere Reserve, this study will: • Implement a set of carefully - targeted actions in Wadi Wurayah and its hinterland and therefore Fujairah Emirates. • Work to demonstrate the feasibility and viability of combining environmental protection in a sensitive area with the preservation of traditional activities. • Support the capacity building of key national and local authorities and selected partners in the Emirates of Fujairah and the UAE So that they have the awareness and skills to fully realize the aims of the study . To set out and develop options for sustainable natural resource management in the proposed Wurayah Biosphere Reserve , one of the UAE as examples of marginal dry lands , building on environmental information system was the best choice using Geographic information systems (GIS ) as a tool. This has been classified to there steps of work: Field Survey and Analysis Lab Office work. As a first step, this study used to survey this area in the light of the work done by the EWSWWF and the Fujairah Municipality, to evaluate the potential and the feasibility of the creation of a Biosphere Reserve. The traditional field survey has been carried out in three batches between January 2007 and January , 2009 for sample collection using specially tailored database forms that suit the properties and nature of the variables measured, and the database . Design The information obtained from field survey included the Landscape and their local classification and distribution , local habitats , water catchments areas , local rangeland systems and indigenous agro -ecological zones. This information in addition to the laboratory analysis has then be transformed into GIS format, and overlaid with the base maps of the study area in order to produce a georeferenced maps. Various types of maps required according the selected works related to area of study have been used as an input data for the GIS system An integrated management methodology / approach has been proposed associated with the plan of work throughout the forthcoming years. The plan of work is designed to be as consistent as possible with that of the concept of the UNESCO 's Man and Biosphere Program.
Streptococcus pneumoniae (the pneumococcus) is an opportunistic human pathogen that causes life-threatening diseases including pneumonia, sepsis, meningitis but also non-invasive local infections such as otitis media. Pneumococci have evolved versatile strategies to colonize the upper respiratory tract (URT) of humans. Binding to epithelial surfaces is thereby mediated through direct interactions with host cell receptors or indirectly via binding to components of the extracellular matrix (ECM). However, successful colonization and subsequent infection require S. pneumoniae to cross tissue barriers protected by the immune system of the host. Pneumococci have therefore evolved a wide range of mechanisms to circumvent the antibacterial activity of the immune system such as the acquisition or expression of serine protease activity. Serine protease enzymes have emerged during evolution as one of the most abundant and functionally diverse groups of proteins in eukaryotic and prokaryotic organisms. However, the epithelial barriers, integrins, and other cell surface receptors are often initially inaccessible for pneumococci colonizing the nasopharyngeal cavity. Therefore, pneumococci recruit host-derived extracellular serine proteases such as plasmin(ogen) for extracellular matrix and mucus degradation, which results in enhanced binding to epithelial and endothelial cells. S. pneumoniae expresses four surface-anchored or surface-associated serine proteases depending on the serotype: HtrA, SFP, PrtA, and CbpG. These enzymes belong to the category of trypsin-like or subtilisin-like family proteins, which are characterized by the presence of three-conserved amino acid residues, Ser-His-Asp. The catalytic triads are critical for the cleavage of peptide bonds. Studies focusing on the deletion of single pneumococcal serine proteases are difficult to interpret due to the compensatory effects of the other serine proteases.
Initially, a comprehensive in silico analysis of the distribution and genes organization of pneumococcal serine proteases was carried out in this study. Interestingly, the genes encoding PrtA, HtrA, and CbpG were highly conserved among the 11 analyzed strains. Surprisingly, the gene encoding the subtilisin-like protein SFP was not present in some of the strains and seems to be strain-dependent. Therefore, pneumococci have at least three serine proteases as shown e.g., for serotype 19F_EF3030 strain. Computer-assisted analyses of the structure of pneumococcal serine proteases showed high similarities in the catalytic domains between HtrA and CbpG or between PrtA and SFP in 3D structural models.
The focus of this study lies on the impact of single extracellular pneumococcal serine proteases on pneumococcal pathogenesis during adherence, colonization, virulence and biofilm formation. Therefore, double and triple deletion mutants were generated in the colonizing S. pneumoniae serotype 19F strain EF3030 and the more invasive serotype 4 strain TIGR4, respectively. In adherence studies with human Detroit-562 epithelial cells, we demonstrated that both TIGR4Δcps and 19F_EF3030 mutants without serine proteases or expressing only CbpG, HtrA, or PrtA have a reduced ability to adhere to Detroit-562 cells. In a mouse colonization model, the inactivation of serine proteases in strain 19F_EF3030 strongly reduced nasopharyngeal colonization in CD-1 mice. The bacterial load in the nasopharynx was thereby monitored for a period of 14 days. Mutant strains showed significantly lower bacterial numbers in the nasopharynx on days 2, 3, 7, and 14 post-inoculations.
Following up on pneumococcal pathogenesis, an in vivo acute pneumonia mouse infection model and in vitro phagocytosis was used to analyze the impact of single serine proteases during infection and phagocytosis. Mice were intranasally infected with the bioluminescent TIGR4lux wild-type or isogenic triple mutants expressing only CbpG, HtrA, PrtA, or SFP. The acute lung infection was monitored in real-time by using an IVIS®-Spectrum in vivo imaging system. The TIGR4lux mutant expressing only PrtA showed a significant attenuation and was less virulent in the acute pneumonia model. Phagocytosis assays were conducted using murine J77A.1 macrophages. The number of triple serine protease mutants internalized by macrophages were significantly reduced in comparison to the isogenic wild-type.
Finally, two different experimental biofilm models were used to study the influence of serine proteases on biofilm formation grown on an abiotic surface (glass) and a biological surface. Biofilm development on living epithelial cells was stronger after 48 and 72h than on the glass surface. On epithelial substratum, the serine protease mutant with only CbpG+ showed higher and denser biofilm development after 48h and 72h of incubation compared to the parental strains and other serine protease mutants. Moreover, the bacterial dispersal from biofilms was significantly more in the mutant strains lacking serine proteases than in the wild type.
In conclusion, nasopharyngeal colonization is a prerequisite for invasive diseases and transmission. Pneumococcal serine proteases are indispensable for nasopharyngeal colonization and facilitate access to eukaryotic cell-surface receptors by the cleavage of ECM proteins. Thus, serine proteases could be promising candidates for developing antimicrobials to reduce pneumococcal colonization and transmission.
Interoceptive sensations, that means, perceptions of the physiological body state, play an important role in the generation and expression of emotion. The focus of the research presented here is on respiratory sensations as specific interoceptive signals. Such respiratory sensations (like the feeling of dyspnea) play an important role in symptom perception in somatic (e.g., asthma) as well as in mental disorders (e.g., anxiety disorders). There are several different ways to manipulate respiratory sensations in an experimental environment, but many of them did not equal sensations in daily life. Here, stimuli (inspiratory resistive loads, caffeine) were used that trigger nearly naturally occurring interoceptive sensations. Taking into account that the elicited interoceptive experience also induces an unpleasant feeling state it is most likely that individuals show defensive physiological responding to such cues and try to avoid them. According to a bidirectional motivational system defensive behaviors are regulated by a defensive motivational system that is activated by threatening cues. From research with exteroceptive stimuli it is known that defensive responding is typically characterized by heightened autonomic arousal, increased respiration, and a potentiated startle eyeblink response. In contrast, only a few studies using interoceptive stimuli have incorporated the measurement of physiological data in their experimental designs. If included, studies show also heightened autonomic responding, whilst a heterogeneous respiratory as well as startle eyeblink responding is observed. Thus, the studies presented here were designed to clarify the factors that mediate defensive responding to interoceptive sensations. Study 1 investigated the influence of anxiety on the subjective, respiratory, and autonomic response to an individually determined inspiratory resistive load, while study 2 focuses on the effect of attentional modulation of the startle eyeblink response to a mild respiratory threat. In study 3 the modulation of subjective, respiratory and autonomic reactions by arousal expectations was examined. Therefore, caffeine, a respiratory stimulant, or a placebo were administered without the participants’ knowledge. The fourth study examined the influence of the process of worrying, a strategy to deal with unpleasant body symptoms, on defensive responding. Depending on the study design subjective, respiratory and autonomic (skin conductance level, heart rate) parameters were assessed as marker for defensive mobilization. In study 2 and 4 the startle eyeblink response was measured as further index of defensive activation. Besides that in study 2 also the P3 component of the event-related potential, as an index for attentional allocation, was recorded. The main findings of the presented dissertation are the following: Study 1 revealed that 1) only high anxiety sensitive individuals reporting also high suffocation fear respond to lower stimulus intensities with stronger defensive responding, and 2) that this group demonstrated a maladaptive compensatory breathing pattern. Additionally, study 2 exhibited that 1) the startle eyeblink response is relatively inhibited during a mild interoceptive threat, and 2) this inhibition corresponds to an attention allocation towards breathing as indicated by a reduced P3 amplitude to the startle noise as well as subjective report. Furthermore, highly anxiety sensitive individuals showed a more pronounced defensive responding if the interoceptive sensations were unexpected (study 3). Recently, study 4 demonstrated that worry led to an increased defensive response mobilization. All studies are discussed in the context of the theoretical background of the defensive response modulation to exteroceptive and interoceptive sensations with respect to mediating factors. Showing exaggerated defensive responding and maladaptive adaptation processes in high anxious individuals the results point towards the important role of interoceptive sensations in the etiology, maintenance and therapy of mental disorders, especially the anxiety disorders.
Therapeutic Sealing of Proximal Tooth Surfaces: Two-Year Clinical and Radiographic Evaluation
(2009)
The diagnosis, prevention and treatment of proximal carious lesions comprise a constant problem in clinical dentistry. The purpose of this investigation was to test the safety and clinical effect of a new treatment for proximal caries. In 50 patients with two proximal initial lesions (D1-3 without cavitation, bitewing X-ray), orthodontic rubber rings were applied to gain access to the interproximal space. One of the lesions was sealed with a thin polyurethane-dimethacrylate foil using a bonding agent (Heliobond®, Vivadent, Schaan/Liechtenstein); the other lesion received oral home-care with dental floss and fluoridated toothpaste and was left as control. In clinical follow-ups after 6 and 12 months and X-ray evaluation after two years, clinical retention of proximal tape and the underlying sealant, marginal adaptation, discoloration, tooth vitality, proximal plaque and gingivitis were checked. In addition, caries was assessed clinically and radiographically. The sealants showed good retention, marginal adaptation and colour. After two years, vitality of all teeth was still positive and no relevant differences in plaque accumulation or gingival status were found between sealed and control teeth. Two sealed surface had to be filled due to caries progression (D3 with cavitation). 9 sealed lesions showed caries regression. In contrast, only 4 control lesions regressed and also two showed progression. The loss of tape had no significant influence on the lesion progression indicating the effect of the underlying bond. All other sealants and control lesions were stable indicating an arrest of the lesion. In conclusion, sealing initial proximal lesions showed no clinical problems and mostly arrest of initial carious lesions on bitewing X-rays.
In fixed orthodontic treatments debonding of brackets during treatment is an unpleasant occurrence for the clinician and the patients and resultes in an increase in treatment costs and duration. For Damon Q brackets recycling would considered as an economic saving option which could be done with using of in office methods such as the sandblasting.
A sample of sixty sound bovine first upper central incisers, were collected, cleaned, and mounted in acrylic blocks for shear bond strength testing.
The total sample was equally divided into two main groups. Each group had 30 teeth and 30 brackets.
The first group had 30 teeth bonded with metal Damon Q brackets, the second group had 30 teeth bonded with metal Mini-Mono® brackets.The study included bonding and rebonding experiments. Therefore the same brackets with their same teeth were used in bonding and in the rebonding experiments. The bonding and the rebonding procedures were done with using 3M Unitek etching, Grengloo adhasive, and Ortho solo bonding. In addition the rebonding procedure was done after cleaning the teeth and recycling their brackets with sandblasting. All specimens were recycled 5000 times for the bonding and rebonding experiments.
The first and second debonding forces were done in Newton using a Zwick Roell machine.
After that SBS and SRS were computed in MPa. Furthermore all the teeth, after each debonding, were examined under a digital scanning microscope VHX-5000, 50X magnifying, to performe the ARA and ARI.
The collected data was statistically analyzed for descriptive statistics as well as significance of differences among the different bracket types, and their ARI scores, in the bonding and rebonding experiments.
The results showed that SRS was significantly higher than SBS of both types of the brackets, and Damon Q brackets had higher SBS, and SRS than Mini-Mono® brackets, and there was no correlation between SBS, SRS and their ARI, ARA.
Background:
Microvascular decompression (MVD) success rates exceed 90% in hemifacial spasm (HFS).
However, postoperative recovery patterns and durations are variable.
Objective:
We aim to study factors that might influence the postoperative patterns and duration needed until
final recovery.
Method:
Only patients following de-novo MVD with a minimum follow-up of 6 months were included.
Overall trend of recovery was modeled. Patients were grouped according to recognizable clinical
recovery patterns. Uni- and multivariable analyses were used to identify the factors affecting
allocation to the identified patterns and time needed to final recovery.
Results:
323(92.6%) patients had >90% symptom improvement and 269(77.1%) patients had complete
resolution at the last follow–up. The overall trend of recovery showed steep remission within the
first 6 months, followed by relapse peaking around 8 months with a second remission ~16
months. Five main recovery patterns were identified.
Patterns analysis showed that evident proximal indentation of the facial nerve at REZ, males and
facial palsy are associated with earlier recovery at multivariable and univariable levels. AICA,
AICA/VA compressions and shorter disease durations are related to immediate resolution of the
symptoms only on the univariable level. Time analysis showed that proximal indentation (vs.
distal indentation), males and facial palsy witnessed significantly earlier recoveries.
Conclusion:
Our main finding is that in contrast to peripheral indentation, proximal indentation of the facial
nerve at REZ is associated with earlier recovery. Postoperative facial palsy and AICA
compressions are associated with earlier recoveries. We recommend a minimum of 1 year before
evaluating the final outcome of MVD for HFS.
The aim of the present dissertation was to investigate the biological and chemical potential of two European mushroom species: Fomitopsis betulina and Calvatia gigantea. For this purpose, different extracts of both fungi were tested for: antimicrobial, antifungal, cytotoxic, in vitro wound healing, and anti-adhesive properties. Bioassay-guided fractionation led to the isolation of bioactive compounds, altogether 20 compounds were isolated and identified. The compounds were obtained from the ethyl acetate extracts, they included triterpenes, sterols and aromatic compounds. The separated substances from both fungi were proved for biological activities, some of them showed antimicrobial and cytotoxic activities.
Eight hundred and fifty two students with an age range 9-13 years (mean 10.34, SD±0.56, 48% females) were recruited from the fifth grade students of different 19 primary schools in Greifswald and East Pomerania. In conjunction with the compulsory dental community examination, additional data were collected with two questionnaires for the children and their parents. Newly generated items were taken from the children’s questionnaire to form short scales for oral health-related knowledge, behaviour, attitudes. Parents’ questionnaire contains questions on socio-economic status (SES) and child’s health. The response rate was 93.2%; 78.8% for children; parents, respectively. Results: The distribution of DMFT values was highly polarized with most of the children (71%) exhibiting no carious defects, fillings or missing teeth in the permanent dentition with a mean of 0.6 ±1.2. There was a significant correlation between DMFT and social class levels (rs=-0.19, p=0.001) with mean DMFT values of 0.9 ± 1.3, 0.6 ±1.1 and 0.4 ± 0.9 for the low, medium and higher social strata, respectively. There was a clear correlation between the dental attitude and dental behaviour (rs=0.32, p=0.003). However, correlations between knowledge vs. attitude and knowledge vs. behaviour were loose. A statistically significant correlation between DMFT and dental behaviour was found (rs=-0.15, p=0.003). It should be noted that children with higher self-esteem were found to have significantly higher dental awareness scores (rs=0.19, p=0.001). General health was a significant predictor for caries incidence (rs=0.08, p=0.01). The frequency of drinking lemonade or ice tea and eating salty snacks (chips, nuts) showed clear correlations with the DMFT (rs=0.17 and 0.13, p<0.01). Prolonged daily TV watching was associated directly with DMFT values (rs=0.13, p=0.001). A significant correlation was found between caries and smoking, even after adjusting for age (rs=0.1, p=0.002). Smoking children had a significantly higher DMFT rate than children who were not smokers with a mean DMFT of 0.9 ±1.5 vs 0.6 ±1.2 (p=0.004). Interestingly, each of prolonged TV watching, more lemonade drinking and smoking were correlated directly with the low socioeconomic status (Spearman correlation coefficient of 0.13, 0.2 and 0.17, respectively, p<0.05). Regarding malocclusion, 64% the subjects had at least one type of anomaly. Crowding and maxillary overjet represented the major proportion 28% and 23%, respectively. Males exhibited significantly higher increased overbite scores than females p=0.04. Whereas the prevalence of crowding was more common in females than males (p=0.05). Amazingly, more malocclusion was registered in children with caries-free primary teeth when compared to children with carious primary teeth (p=0.05). No significant differences in the mean of dmft or DMFT value were found between normal and non normal occlusion (p>0.05). Undergoing to orthodontic treatment was associated with significantly higher dental awareness scores (p=0.003). No correlation between socio-economic status and malocclusion was registered. Conclusion: This thesis confirms the decline and polarisation of dental caries. Dental behaviour was mostly independent of dental knowledge, but depended on dental attitude. Higher scores in dental behaviour resulted in lower DMFT scores; possibly, oral health promotion should strengthen attitude and actual behaviour instead of knowledge. Higher scores in self-esteem and general health connected with lower caries incidence and higher score in dental awareness. Social inequalities was strongly linked with health inequalities with more prevalence of caries, smoking, prolonged TV watching, wrong diet habits and less sealants application among children of low SES. Hence, oral health-related interventions in children sample should be directed at the social structures with more incorporating of oral health promotion programs into other general health promotion programs. This thesis suggests that; the establishment of healthy behaviours such as a regular teeth brushing at school could be one of the most successful ways to involve all children especially children of low SES in dental care. Malocclusion traits were very common in this sample. This underlines the need for more orthodontic preventive programs among children, in order to reducing the risk factors of malocclusion. The association between prevalence of malocclusion and socio economic status could not be established. No generalised conclusion could be drawn about the relationship between caries and malocclusion.
Until now proximal caries is still a significant problem in the clinical dentistry in spite of the caries decline recently. As resin infiltration offers a new micro-invasive treatment to arrest the progression of proximal initial carious lesions, this study aimed to evaluate its clinical applicability, safety and effect. In the study population of 50 children, adolescents and young adults (mean age 17.9 years ± 6.8), ten dentists at University of Greifswald applied the infiltration material ICON® (DMG, Germany) on non-cavitated proximal lesions in permanent and primary teeth as described in the manual instructions from the producer. The results showed good patient satisfaction with the procedure. The time for the infiltration (24.3 min ± 7.4), which included rubber dam application (7.7 min ± 4), and the effort were perceived as comparable to a composite filling by the dentist or as even easier. In three patients (6%), it was not possible to gain sufficient proximal space for the application of an infiltration. The location of the infiltrated tooth, separation problems as well as the routine of the dentists with the infiltration technique had an effect on the duration of the infiltration. A clear learning curve with a reduction of treatment time for subsequent treatments was observed (P < 0.001). Within the follow-up interval of 12 months, vitality of all infiltrated teeth was still positive and no relevant differences in plaque accumulation or gingival status were recorded. In addition, the infiltrated surfaces showed smooth margins and considerable decrease in the discoloration. In the radiographic evaluation after one year, only two lesions (4.7%) have progressed. Thus, caries infiltration is an applicable method for the treatment of initial non-cavitated proximal lesions without prior temporary tooth separation. Even without special training it can be applied easily by dentist and they experience a clear learning curve within the first 5-10 applications. In addition, the infiltration technique shows a high acceptance by the patients. Furthermore, caries infiltration lead to very good results regarding safety and preventing the lesion progression of non-cavitated proximal caries lesions located in the enamel or in the outer third of dentin.
The aim of this retrospective observational study is to describe and discuss various complications that can arise after insertion of alloplastic materials in the field of urogynecology that require further surgical interventions in order to manage them or to at least improve the quality of life in those women. We were able to collect data on 77 patients who fulfilled the criteria. Medical history, data of clinical findings, and outcomes were collected and analyzed. The most common complication seen as an indication for resecting slings or meshes was de novo overactive bladder syndrome (40%). Other indications seen were lower urinary tract obstruction or obstructive voiding symptoms (21%), chronic pain (21%), and de novo dyspareunia (13%). 36% of the patients had recurrent symptoms (failure) after insertion of alloplastic materials in the form of urinary incontinence or prolapse, 32% presented with vaginal erosions, 2 women had severe signs of infection with abscess formation, another 3 women had urogenital fistulae. Other rare complications after mesh or sling insertion are perforations of the urinary bladder or urethra. Proper case selection is the key factor. The use of meshes and slings seems justified only in patients with known connective tissue weakness and recurrences after native tissue repair. Otherwise, patients will be exposed to unnecessary risk without any expectable improvement to their quality of life. Most of the complications are mainly caused by wrong and inadequate surgical techniques, wrong indications, or missed diagnosis of the underlying problem. In addition, lack of long-term follow-up is usually the cause behind the negligence towards many complications. Therefore, only experienced physicians should be allowed to perform such procedures, and long-term postoperative follow-up is strongly recommended. As slings and meshes are used for procedures of choice as means to improve quality of life, and not for life threatening situations, there is a need for intensive informed consent. All possible alternatives have to be discussed, as do the pros and cons of selected procedures, even the rare complications. Mesh or sling resection is considered to be an effective solution for the management of such complications. It has shown a high success rate in comparison to conservative treatment, and the majority of patients were satisfied and experienced a big improvement in their quality of life. The most common complication after resection is the recurrence of primary symptoms, either urinary incontinence or prolapse. Major or serious intra- or postoperative complications are very rare. All complications were classified and given a code according to the classification system of the international urogynecological association and the international continence society (IUGA/ICS) on 2011. The applicability and practicability of this code were evaluated, looking for ways to possibly improve it or to identify missing parameters. Many patients had more than one code, a problem that entirely torpedoed the idea of “simple” classification. Some complications are not covered individually in the classification, such as failure and recurrence or overactive bladder syndrome. These complications should be included. Many cases began with the same code, despite having different complications. Further sub-classifications should be considered to enable the reader to easily recognize the complication at hand. Patients who came with complications more than one year after mesh or sling insertion were categorized as (T4), regardless of whether the complication arose after 1 year of after 10. Therefore, sub-classifications in the (T4) category are recommended. The “site” category was not applicable in many cases. Furthermore, it is necessary that the severity of a complication is discernible, and should be mentioned in the code. We did not find any correlation between the code given and patient satisfaction. After re-modification and completion, the IUGA/ICS code could be more practical for clinical use, which would allow for the comparison of complications and make the assessment of adverse effects easier for research purposes.
In this study we investigated the synergistic antimicrobial effect of a dual protocol combining cold atmospheric pressure plasma (CAP) and antimicrobial photodynamic therapy (aPDT) against different planktonic bacterial and yeast species including methicillin-sensitive and methicillin-resistant Staphylococcus aureus, Escherichia coli, extended-spectrum β-lactamase-positive Escherichia coli and Candida albicans. A DBD plasma device was used for CAP treatment while for aPDT, toluidine blue O (TBO) was the photosensitizer (PS) of choice and a radiator emitting visible and water-filtered-Infrared A light (VIS-wIRA) was used as irradiation source.
Microbial suspensions were either exposed to CAP treatment alone, aPDT treatment alone or aPDT followed by CAP exposure in a dual treatment protocol. Aliquots from each suspension were plated on agar plates and the number of colonies surviving after each treatment was counted. Under the experimental conditions conducted in this study, combining sub-lethal exposure doses of CAP and aPDT treatment showed significantly higher antimicrobial efficacy (P<0.0001) compared to single treatments against all tested microorganisms suggesting a synergistic effect which yielded at least 3.3 log microbial reduction corresponding to 99.6 % microbial death. In the dual CAP-aPDT approach, aPDT did not interfere with CAP-induced acidification of solution, a crucial feature for CAP antimicrobial efficiency, which further confirms the promising clinical potential of this combination regime.
We believe that the CAP-aPDT dual approach described in this study holds great potential as a successful novel antimicrobial and healing-supporting strategy especially when directed for the management of acute and chronic wounds and possibly other skin and soft tissue infections. The use of a VIS-wIRA light source in treating skin infections is preferential, due to the additional therapeutic effects of wIRA in wound healing. Furthermore, the enhanced antimicrobial effects of aPDT when combined with CAP as shown in this study may grant for a reduction in treatment times and costs as well as improving patient compliance.
Objectives:
This study investigates the effectiveness of the Cold AP on the alteration of the enamel surface
without using acid etchant by using Conventional photo-activated resin bond to bond the
orthodontic brackets.
Materials and Methods:
One hundred and twenty-five Enamel specimens are prepared from disinfected bovine
mandibular incisors are divided into five groups. Group I: brackets are attached on the enamel
surface with the standard adhesive technique (etch + primer +bond). Group II: the brackets are
attached with the Standard Orthodontic adhesive technique without etching. Group III: the
enamel surface is conditioned with pure Argon Cold atmospheric plasma before the application
of the primer without using an acid etchant. Group IV: the enamel surface is conditioned with
the admixture of Argon Cold atmospheric plasma with 0.5 % Oxygen before the application of
the primer without using acid etchant Group V: after the application of Argon Cold atmospheric
plasma with 0.5 % Oxygen the surface is rewetted by deionized water before the application
of the primer and adhesive. After that, the samples are exposed to thermal cycling. The shear
bond strength of the samples is tested by the universal testing machine which measured the
maximum force at which the brackets are deboned from the tooth surface at a speed of
1mm/minute is measured.
Results:
Significant intergroup differences were found. Group V showed the highest shear bond
strength followed by Group I, VI, III, II respectively. There isn’t a statistical difference in the
values of The Shear bond strength values between Group III and IV.
Conclusions:
this study implies that Cold Atmospheric Plasma is a safe method to change the chemical
surface characteristics of the enamel surface.in addition to the significant importance of plasma
treatment followed by water rewetting, which could enhance adhesion between the orthodontic
attachments and the enamel layer
Infections with Helicobacter pylori are a global challenge that affects both developed and developing countries. This infection is currently treated using multiple antimicrobials that are mostly absorbed after oral administration and subsequently secreted into the gastric lumen. The eradication rates from the different therapeutic regimens, however, are declining nowadays, primarily due to high antibiotic resistance and possibly the mode of drug delivery. H. pylori is commonly found adhering to epithelial cells, and therefore, intragastric drug delivery may be a more direct treatment option. In this work, we developed a new strategy for the local eradication of H. pylori within the stomach.
Initial in vitro experiments revealed that penicillin G shows promising antibiotic activity against resistant strains of H. pylori with MIC values of 0.125 µg/mL. To provide luminal concentrations above the MIC for an extended time, we decided to follow two different formulation strategies: effervescent granules and HPMC-based hydrogel matrix tablets. Among the granule formulations, only one batch was stable and demonstrated excellent performance with respect to drug content, effervescent action, and drug release. It was therefore selected for further in vitro studies. All matrix tablets showed the desired tablet quality requirements and drug release was scalable in vitro by the HPMC concentration.
In order to quantify PGS in various formulations and media, an HPLC method was developed and validated. Due to the stability concerns, the degradation behavior of PGS was studied at different pH. PGS was found to be unstable at acidic pH values, but its stability was higher at more neutral pH values. Sufficient stability was exhibited at pH values above pH 4.5. Due to the instability of PGS in acidic media, alkalizers were added to the matrix tablets to prevent the degradation of the drug within the tablet. Among the alkalizers tested, NaHCO3 showed the most promising results as it significantly enhanced the stability within the matrix and also the concentration of PGS in the dissolution media. The stabilizing effect was caused mainly by the modulation of the microenvironmental pH rather than a pH change in the dissolution media. As a result, these matrix tablets were selected for further in vitro characterization.
In order to guide formulation development, a flow-through model (FTM), which was able to simulate various physiological conditions of the gastric environment, was developed and applied. In contrast to compendial dissolution methods, the FTM allowed studying the effect of gastric secretion, mixing and emptying on the gastric concentration of the drug in vitro. It could be shown that the granules generated a high initial concentration, which decreased over time. On the contrary, the matrix tablets did not provide such a profile due to the absence of pressure events in the model. Further investigations of the matrix tablets in a dissolution stress test device revealed faster drug release if pressure events of physiological relevance are simulated.
In the last part of this thesis, the two formulation concepts were compared in vivo by using the salivary tracer technique. For this purpose, caffeine was used as a model drug. The in vivo investigations suggested that granules administered in a fed state demonstrated longer gastric retention than in a fasted state. In a fed state, effervescent granules provided longer gastric retention of caffeine in comparison to the matrix tablets. Interestingly, the administration of the granules together with 240 mL of tap water provided an even better gastric retention of caffeine than the smaller volume (20 mL). Additional MRI investigations after 4 h of tablets’ intake revealed that the matrix tablets were already disintegrated in vivo.
In conclusion, effervescent granules dosed after food are expected to better maintain intragastric drug concentration over an extended period compared to matrix tablets. Moreover, the carbon dioxide generated after disintegration supports the mixing of the drug with the chyme and thus, provides a uniform distribution of the drug. By this, bacterial sanctuary sites within the stomach can be avoided. The major challenge could be the stability of PGS in acidic media. This problem could be addressed via concomitant administration of PPIs. H2 blockers could also be recommended to address nocturnal acid-breakthrough during the mid-night. In combination with an acid-reducing agent, PGS granule formulations alone or part of the treatment regimens could enable the local eradication of H. pylori directly within the stomach.
Microbial cell factories have been largely exploited for the controlled production of recombinant proteins, including industrial enzymes and biopharmaceuticals. The advent of high-throughput ‘-omics’ techniques have boosted the design of these production systems due to their valuable contribution to the field of systems metabolic engineering, a discipline integrating metabolic engineering with systems and synthetic biology. In order to thrive, the field of systems metabolic engineering needs absolute proteomics data to be generated, as proteins are the central players in the complex metabolic and adaptational networks. Due to advent of mass spectrometry-based proteomics, a substantial amount of absolute proteomic data became available in the past decade. However, membrane proteins remained inaccessible to these efforts.
Nonetheless, comparative studies targeting the membrane proteome have been quite successful in characterizing physiological processes. Hence, label-free proteomics was used in a study (Quesada-Ganuza et al, 2019 – Article I) to identify and optimize PrsA in Bacillus subtilis, for improved yield of amylase. Amylase is one of the most relevant enzymes in the biotechnological sector. By employing a label-free mass spectrometry approach targeting the membrane proteome of this bacterium, relative changes in heterologous and native levels of PrsA could be quantified. The results of this study evidenced that each PrsA shows different relative abundancies, but with no relevant impact in the yield of amylase.
Even though relative protein quantification can already provide a good visualization of the physiological changes occurring between different conditions, they are not sufficient to understand how resources are allocated in the cell under certain physiological conditions. Therefore, a global method for absolute membrane protein quantification remains the biggest requirement for systems metabolic engineering.
Hence, with this work, we successfully developed a mass spectrometry-based approach enabling the absolute quantification of membrane proteins (Antelo-Varela et al, 2019 – Article II). This study was also performed in the Gram-positive model organism Bacillus subtilis, regarded as a prolific microbial cell factory. The method developed in this work combines the comprehensiveness of shotgun proteomics with the sensitivity and accuracy of targeted mass spectrometry. Fundamental to the method is that it relies on the application of a correction and an enrichment factor to calibrate absolute membrane protein abundances derived from shotgun mass spectrometry. This has permitted, for the first time reported, the calculation of absolute membrane protein abundances in a living organism.
The newly developed approach enabled to accurately quantify ~40% of the predicted proteome of this bacterium, offering a clear visualization of the physiological rearrangements occurring upon the onset of osmotic stress. In addition, this work also provides evidence for new membrane protein stoichiometries.
Overall, this study enabled the development of a straightforward methodology long-needed in the scientific and biotechnological community and, for the first time reported, providing absolute abundances of one of the most puzzling fractions of the cell – the membrane proteome.
The next step of the work summarized here was to implement the afore described method to a biotechnological relevant strain, as absolute membrane protein abundances are essential to understand the fundamental principles of protein secretion and production stress. Hence, this work was applied in a genome-reduced B. subtilis strain, ‘midiBacillus’, expressing the major staphylococcal antigen IsaA (Antelo-Varela et al, submitted – Article III). The employed absolute membrane protein quantification methodology enabled the analysis of physiological rearrangements occurring upon the induction of heterologous protein production. This work showed that, even though IsaA was successfully secreted into the growth medium, one of the main requirements for the biotechnological sector, it was still partly accumulated in the cell membrane of this bacterium. This led to an exacerbated physiological response where membrane proteins involved in the management of secretion stress were activated. In addition, this study also showed that a rearrangement of the cell’s translocation machinery occurs upon induction of production, where a ‘game’ of in- and decrease of transporters takes place.
Anticipating the impact of genetic and environmental insults, such as the ones caused by production stress, is essential for the field of systems metabolic engineering. Thus, the highly accurate and comprehensive dataset generated during this work can be implemented in predictive mathematical models, thereby contributing in the rational design of next-generation secretion systems.
Analysis and Reduction of Cellular Heterogeneity in Strain Optimization of Bacillus licheniformis
(2021)
Bacillus species invest substantial resources in inherent cellular processes for pre-adaptation to environmental changes, many of which are dispensable in the controlled environment of industrial bioprocesses. The underlying physiological mechanisms are well characterized in B. subtilis, but only little is known about these processes in the closely related B. licheniformis. Moreover, experimental conditions in previous studies differ from industrial settings in most parameters, foremost in batch cultures or plate-based analysis over fed-batch processes. In this thesis, cellular heterogeneity was analyzed in B. licheniformis in optimized, nutrient-rich media in batch and fed-batch cultivations. Systematic inactivation of genes involved in biofilm formation and synthesis of the flagellar apparatus or global regulators thereof resulted in higher protein production and provided new insights into biofilm formation and cellular heterogeneity in this strain.
In agricultural grasslands, management practice highly determines reproductive success for ground-nesting bird species. The most effective conservation measure is the delay of first mowing dates until broods fledge or bird friendly mowing. Late mowing often implies economical losses for farmers and may increase land use abandonment, which will, in turn, cause habitat deterioration. Thus, grassland bird conservation involves the challenge to protect broods against land use and to promote an appropriate management to sustain habitat quality at the same time. Because of their late and extended breeding season Corncrakes Crex crex are in particular vulnerable to frequent mowing which increases nest destruction, chick mortality and habitat loss.
This thesis aims to gain knowledge on favourable habitat characteristics and brood protection in relation with grassland management to derive implications for the conservation of Corncrake breeding sites in floodplain meadows. Study area is the Lower Oder Valley National Park in northeastern Germany that holds a Corncrake population of 50 to 250 calling males. The study covered two study periods, before (1998-2000) and after (2012-2015) the implementation of new Corncrake conservation measures allowing inferences on the effects of different timing and intensity of mowing for brood protection and habitat conservation.
Breeding was only confirmed on meadows with high forb cover, low sedge cover, low litter heights and a close location to ditches. Radio-tracked females preferred areas with high cover of forbs (> 30%) and a distinct relief heterogeneity, which was associated with increased vegetation diversity. Vegetation characteristics on sites with day calling activity of males showed more similarity with breeding sites than with sites only used for nocturnal calling, supporting the assumption that diurnal calling indicates the occurrence of females. Favoured vegetation structure was best provided by mowing in the preceding year. Low-intensity grazing was less effective in reducing litter and sedge cover, especially when conducted late in the season. In the absence of management, meadows rapidly overgrow and dense litter accumulates from dead plant material in eutrophic floodplains, which increases walking resistance for Corncrakes and may impede prey accessibility. Plant species richness and forb cover declined after land use cessation. Male Corncrakes abandoned calling sites on meadows unmanaged for longer periods.
Besides the availability of suitable nesting sites, food supply and nest predation risk are also related to vegetation structure and may indirectly influence the habitat quality. Faecal samples of Corncrakes consisted mainly of beetles and their larvae, followed by snails, spiders and earthworms. Invertebrate biomass, sampled with pitfall-traps, was twice as high, the numbers of large ground beetles even five times higher on previously unmanaged than on managed meadows. Invertebrate abundance was highest in the first and second years after land use abandonment, but strongly decreased afterwards to a similar level like under annual management. Therefore, unmown refuge strips for Corncrake protection and alternating mowing also enhance invertebrate prey resources in floodplain meadows.
Mammals caused the majority of all observed artificial ground nest predations. Nest predation risk was higher on previously unmanaged than on managed sites. Unmanaged meadows probably attract mammalian predators, because they provide a more favourable vegetation structure for foraging and harbour high numbers of small rodents, increasing also the risk of incidental nest predations. These findings suggest that an annual removal of vegetation, if conducted late in the season to protect grassland birds may reduce predation risk of ground nests in the subsequent year.
Whereas during 1998-2000 half of the study area was managed by the end of July, land use was delayed on meadows occupied by Corncrakes until at least 15 July or 15 August during 2012-2015. On meadows mown between 15 July and 15 August refuge strips were applied. The majority of Corncrake broods were started in the second half of May and mowing postponement until 15 August allows 80% of chicks to fledge without disturbance in the study area. In 65% of broods chicks reach independence (> 14 days old) until 15 July and can be protected by Corncrake friendly mowing because then they are large enough to successfully escape during mowing. Both adults and chicks survived in 10 m wide refuge strips. Because most birds tried to leave the unmown block for the first time when it was up to 30 m wide and only 15 to 30 m wide strips served as temporary habitat for unfledged chicks from mowing to departure, 10 m should be considered as the absolute minimum width for refuge strips.
The strong reduction of land use especially during July should have allowed more chicks to survive until fledging in 2012-2015 than 1998-2000. Besides the protection of nests and higher chick survival, the decline of mowing intensity increased the extent of habitat available for second breeding attempts. In 2012-2015, broods were initiated until late July in the study area. Male Corncrakes showed continuous arrival and departure during the breeding season. Similar departure rates were estimated by a multi-state occupancy model and for radio-tracked males in the same study area and periods, which both left their home ranges spontaneous and due to the impact of mowing. Compared to 1998-2000, total departure of males during June and July was reduced by 50% in 2012-2015, when more calling sites were protected from mowing. Although male Corncrakes show high intra-seasonal dispersal due to their sequential polygamous breeding system, postponed land use should have increased mating opportunities and re-nesting at first breeding sites.
Therefore, future directions of Corncrake conservation in eutrophic floodplains should address the increase of annual late mowing to protect broods and maintain favourable habitat conditions by creating a more flexible mowing regime adjusted to actual occurrence of Corncrakes. This requires expert advice to farmers based on an intense monitoring of calling Corncrakes. Repeated nocturnal surveys during May and June are highly recommended because low detection probability in combination with constant departure substantially underestimated the number of males present. Additionally, diurnal calling activity could improve the identification of breeding sites and timing could be used to estimate chick age in July to select sites for Corncrake friendly mowing. Because currently late mowing dates are unattractive for farmers conservation actions should along with financial compensations for mowing after 15 August promote the utilization of late-cut grass with poor nutrient quality for combustion. Energy production could provide an alternative income for farmers operating in conservation areas with delayed land use dates and will increase their acceptance of Corncrake protection measures.
Transcriptional repression of regulated structural genes in eukaryotes often depends on pleiotropic corepressor complexes. A well-known corepressor conserved from yeast to mammalian systems is Sin3. In addition to Sin3, yeast Cyc8/Tup1 corepressor complex also regulates a diverse set of genes. Both corepressors can be recruited to target genes via interaction with specific DNA-binding proteins, leading to down-regulation of a large number of unrelated structural genes by associated histone deacetylases (HDACs). In vitro interaction studies performed in this work by GST pull-down assays showed that various repressor proteins (such as Whi5, Stb1, Gal80, Rfx1, Ure2, Rdr1, Xbp1, Yhp1, Rox1, Yox1, Dal80 and Mot3) are indeed able to bind pleiotropic corepressors Sin3 and/or Cyc8/Tup1. All repressors interacting with Sin3 contact its paired amphipathic helix domains PAH1 and/or PAH2. Mapping experiments allowed the characterization of minimum repressor domains and to derive a sequence pattern which may be important for repressor interaction with Cyc8 or Sin3. Interactions for some pathway-specific repressors such as Cti6 and Fkh1 have been studied comprehensively; minimal domains of Cti6 and Fkh1 required for interaction with Sin3 have been mapped and subsequently investigated by mutational analysis. In vitro interaction studies could show that amino acids 350-506 of Cti6 bind PAH2 of Sin3. To analyze this Cti6-Sin3 interaction domain (CSID) in more detail, selected amino acids within CSID were replaced by alanine. It turned out that hydrophobic amino acids V467, L481 and L491 L492 L493 are important for Cti6-Sin3 binding. The results of this work also suggest that repression is not executed entirely via Sin3, but rather CSID is also important for contacting pleiotropic corepressor Cyc8. In addition to PAH2 of Sin3, CSID also binds to tetratricopeptide repeats (TPR) of Cyc8. Furthermore, in vitro mapping studies revealed that Fkh1 also binds PAH2 of corepressor Sin3 via its N-terminal domain (aa 51-125). Binding studies with mutagenized Fkh1-Sin3 interaction domain (FSID) showed that Fkh151-125 variants L74A and I78A were unable to bind PAH2 of Sin3. Confirming in vitro studies, Cti6350-506 and Fkh151-125 also displayed in vivo interaction with PAH2 of Sin3 by using the “yeast two -hybrid” system. Chromatin immunoprecipitation (ChIP) analyses have demonstrated Cti6 recruitment to promoters of genes such as RNR3 and SMF3 containing iron responsive elements (IRE). Importantly, Sin3 was also recruited to these promoters but only in the presence of functional Cti6. Similarly, recruitment of Fkh1 and Sin3 to promoters of cell-cycle regulated genes CLB2 and SWI5 was shown. Recruitment of Sin3 was completely Fkh1-dependent. Additional findings of this work shed light on the fact that not only repressor proteins may contact Sin3 but also activator proteins not yet considered for interaction, e. g. specific activators such as Pho4 and Ino2. These findings indicate that Sin3 may fulfill functions beyond acting as a corepressor. In vitro studies on Sin3-Pho4 interaction showed that aa 156-208 of Pho4 are able to bind both PAH1 and PAH2 of Sin3, while an internal region of Ino2 comprising amino acids 119-212 binds to both Sin3 and Cyc8.
The Syilx Okanagan environmental ethic is a philosophy expressed in the practice of Indigeneity as a social (cultural) paradigm and is identified by an inter-reliant experience in the land, as demonstrated in land-use practice which is shaped by the land’s realities as observed, learned and communicated to succeeding generations. Syilx Okanagan Indigeneity reflects an epistemology that optimum human wellbeing cannot be achieved through a human centered ethic but must focus on the optimum ability for the environment to regenerate itself. Syilx Okanagan stories convey the social experience and act as a records system to preserve, maintain and transfer the knowledge of the land. On one level, captikwl contain essential specific environmental knowledge as an oral documentation method, while on another level, as literature, captikwl reconstructs the ethos of interdependency specific to the ecology of the Syilx Okanagan territory through reenactment of nature’s interactions. captikwl in the Nsyilxcen language mimics the dynamic aspects of nature’s required regenerative principles to each succeeding generation, and acts as a feed-back loop reconstructing the social paradigm as an environmental ethic. captikwl might be seen as a distinctly Indigenous human adaptive response scheme within a natural system as it constructs the Syilx Okanagan world and results in behavior with sustainable outcome in the environment. captikwl is a distinct oral artistry that must be read through a literary framework cognizant of oral memory device, structure and Syilx Okanagan context. Okanagan author Morning Dove’s collection of Okanagan stories, as well as, the Mattina and DeSautel bilingual collections and other original version captikwl were consulted. Captikwl demonstrates the concept of tmixw which better translates as a life-force. The word for land is tmxwulaxw, which translates better as a life-force-place, rather than land as location or ecology type. Syilx society demonstrates an “ecological conscience” as the common text through captikwl which is enacted in their social institutions in the manner theorized by respected American conservationist Aldo Leopold, as desirable to achieve within society. The Syilx environmental ethic, rather than a sustainable human ethic of utility, is a willingness to live within a strict imperative to continuously sustain a unity of existence through societal knowledge and reverent practice of respect toward all life-forms. The Syilx environmental ethic diverges from ecocentrism, as articulated by Callicott, in recognizing a fundamental distinction between non-life forms and life forms, in their ability for self-regeneration through inter-reliance, as the focus for delineating moral considerability. The Syilx environmental ethic differs from biocentrism, as articulated by Taylor, in recognizing moral considerability as resting with the on-going life form which is capable of regeneration within its ecology, rather than the singular biological unit. The Syilx environmental ethic also differs from the concept of the ethics of place, as articulated by Berthold-Bond and characterized as an ethical bioregional human utility of a location. Tmixw is the life-force which makes up the tmxwulaxw or life-force-place and the humans are only “placed” as a life-force themselves through Indigeneity as a social paradigm within a criteria of full reciprocity in the regeneration of all life forms of a place. The Syilx environmental ethic also differs from the ethic of sustainability proposed by Daly as a steady state economic model of human utilitarianism, in the positioning of nature treated as capital, to be prudently developed in a way that off-sets depletions of renewable and non-renewable resources in meeting human requirements. The Syilx Okanagan view of economy, while structurally a sustainability model, does not construct value based on human utility as a defining line in decision-making as to which life forms are to be devalued and displaced. Syilx Indigeneity is guided through a societal dialogue practice of Enowkinwixw, a process of decision-making structured to include living within the requirements of the land to fully regenerate. Syilx Okanagan Indigeneity frames an environmental ethic from a tmixwcentric position and offers a model proposing an ethic of re-indigenization as a path to sustainability. The thesis proposes a common text for human society in the form of such literatures, since literature is widely accessible, which demonstrate, imbed and advocate a regenerative land ethic towards the re-indigenization of place.
In this thesis, it was the subject to build a setup to study the interaction of clusters with intense laser light. A magnetron sputter cluster ion source was built to create metal clusters for the planned investigations. Furthermore, a linear Paul trap setup was built in order to allow the investigation of the mentioned interaction at one specific cluster size. The whole apparatus was characterized and first experiments were performed.
Recent experimental campaigns in the Wendelstein 7-X stellarator, a
plasma-confining device designed to investigate the Magnetic Confinement Fusion
(MCF) approach to generating electrical power, have shown that the injection of
fuelling pellets had an unexpected and considerable impact on the performance of
the plasma. Rather than simply refuelling the device and `diluting' the plasma
energy, pellet injection is followed by a significant increase in the ratio of
the ion temperature to the electron temperature. It has been suggested that this
is not merely due to the improved confinement following the reduction of
turbulent transport after the pellet material has homogenised with the bulk
plasma, but also due to a direct transfer of energy from electrons to ions. The
proposed mechanism for this energy transfer is the ambipolar expansion of the
pellet plasmoid, the localised plasma structure produced by the
ionisation of ablated pellet material, along magnetic field lines.
Early work on pellet plasmoid expansion predicted that half the heating power
deposited in plasmoid electrons by collisions with hot ambient electrons is
transferred to plasmoid ions in the form of flow velocity as the plasmoid
expands. The complicated nature of the system of the pellet plasmoid embedded in
the ambient plasma, particularly the behaviour of electrons, which experience
many collisional and collisionless phenomena on multiple disparate timescales,
means that early models of the expansion were not wholly self-consistent, but
rather made use of strong approximations that apply in some regions of the
plasmoid but not in others. For example, only electrons and ions associated with
the plasmoid were rigorously treated, meaning that the framework was one of
`expansion into vacuum'. Combined with the assumption of Maxwellian electrons,
this led to an electric potential that was unbounded at infinity. Naturally, the
validity of the conclusions of such a model are called into question because the
approximations lose their validity far from the plasmoid and as time advances,
yet predictions about the final state of the plasma are desired. A deeper
investigation is required: careful consideration of the phenomena in question
and the timescales (and lengthscales) on which they act must be made in order to
rigorously construct a model that is valid throughout the entire expansion.
The first two papers presented in this thesis iterate on the model established
in the paper that first predicted the electron-to-ion energy transfer; their aim
was to find out how the character of the expansion changes with a more
sophisticated and accurate description of various phenomena, while remaining
within the existing framework of expansion into vacuum. Ultimately, we find that
the qualitative character is unchanged, and that approximately half the heating
power deposited in plasmoid electrons is transferred to ions.
Two other papers in this thesis address the limitations of the original model.
This is achieved by properly considering the electron kinetic problem in a
plasmoid. One paper considers the electron kinetic problem when electrons are
highly isotropised. In this case the kinetic equation can be integrated to
remove all but two independent variables, which is the maximum possible
reduction considering it is a time-dependent problem. The full nonlinear
integro-differential Landau self-collision operator is integrated exactly and
few approximations are made, leading to a rather general kinetic equation.
However, for fuelling pellets some anisotropy in the electron distribution is
expected. Another paper considers the electron kinetic problem (and the entire
plasmoid expansion) allowing for electron anisotropy. Careful consideration of
the ordering of timescales of electron phenomena in a pellet plasmoid leads to a
steady-state kinetic problem that we call collisional quasi-equilibrium (QE). QE
appears in many ways similar to the collisional steady-state characterising a
true thermal equilibrium. It was found that the time-dependent kinetic problem
of the earlier paper, with isotropic electrons, produces the QE distribution
function, corroborating the existence of the QE state. We then take moments of
the electron kinetic equation that is valid on the expansion timescale, assuming
that the electron distribution is that given as the solution to the QE kinetic
problem. This is completely analogous to what is done to obtain the Braginskii
equations or any Chapman-Enskog theory. The result is a set of equations for the
long-term evolution of the macroscopic quantities that describe the distribution
function existing in a quasi-steady-state at each point in time. It is from this
point that one may feasibly describe the plasmoid expansion with an accurate
picture of the electron kinetics and finally obtain the electron-to-ion energy
transfer so desired in a rigorous model of the expansion.
From a broader point of view, the two frameworks provided by these rigorous
investigations of the electron kinetic problem serve as a basis for the future
study of plasmoids. Such a `first-principles' approach to plasmoid dynamics is
novel and interesting in its own right, but it will be demonstrated that such an
approach is essential for pellet plasmoids owing to the fact that they are
poorly described by the `standard tools' of plasma physics.
Using the QE framework it was found that, once more, about half the heating
power experienced by plasmoid electrons is transferred to plasmoid ions. The
incredible robustness of the prediction of such an energy transfer is, in the
author's opinion, the result of the self-similar nature of the expansion found
as a solution to the original model. As a rule, the profiles of self-similar
solutions tend to be attractors for the `real', more complicated, system, and
the qualitative predictions involving no parameters, of which the
electron-to-ion energy transfer is one, tend to be very sturdy.
Aside from fuelling pellets, composed of hydrogen or deuterium, one paper in
this thesis investigates the physics of high-Z pellets that are designed to
terminate the plasma safely in the event of a `disruption', where much of the
magnetic field energy is channelled into a runaway electron beam with
potentially disastrous consequences if the beam encounters a plasma-facing
component. The paper draws on the work carried out in the paper concerning the
kinetic problem of isotropised electrons in a plasmoid.
This thesis is `cumulative'; the vast majority of the work carried out is
described within a set of Papers, labelled A-E, placed at the back of the text.
There is a preceding `wrapper text' (given in numbered Sections) tasked with
introducing the reader to the topic, guiding the reader through the papers, and
expounding some of their main results. Some amount of material not present in
the papers is also provided in the wrapper text. Naturally, the wrapper text
mainly focusses on the results of the papers which are under my first
authorship. In the course of publishing papers over an extended period of time
the nomenclature is bound to vary. Although it is mostly consistent between the
papers, a few difference do arise, and the section `Common symbols and
subscripts' is provided in the frontmatter to alleviate confusion. Particular
care should be taken with the symbols x and z; both can refer to the
coordinate parallel to the magnetic field line, but in papers where z is used
for this purpose x tends to have another definition. In the wrapper text the
choice of symbols is generally chosen to reflect those in the corresponding
paper.
Haloalkanes are serious environmental pollutants commonly employed as pesticides, herbicides, and chemical warfare agents. Although haloalkane production is performed mostly in the chemical industry, it also occurs naturally, mostly enzymatically (halide methyltransferases and haloperoxidases). Elimination of toxic haloalkanes is very important and using haloalkane dehalogenases is a promising and environmentally friendly way to achieve this.[53] Therefore, assays are needed for detecting dehalogenase activity either to find new enzymes or to generate laboratory-evolved variants. In this thesis, a new assay for dehalogenase activity was developed based on halide detection. In this assay halides, as dehalogenase products, are oxidized under mild conditions using the vanadium-dependent chloroperoxidase from Curvularia inaequalis, forming hypohalous acids that are detected using aminophenyl fluorescein.[53] This new halide oxidation assay is much more sensitive than previously known assays, with detection limits of 20 nM for bromide and 1 μM for chloride and iodide. Validation of the assay was done by comparison to a well-established GC-MS method in terms of determining the specific activities of two dehalogenases towards five common substrates (Figure 5).
The HOX assay was modified for iodide-specific detection by using two other dyes, o-phenylenediamine (OPD) and 3,3′,5,5′-tetramethylbenzidine (TBM), instead of APF. Also, selective bromide detection in the presence of the common contaminant chloride was achieved by using a bromoperoxidase. Since the assay relies on halide detection, it is possible to use it for other halide-producing enzymes (Section 8.1). For example, the TMB-modified version was used for screening of halide methyltransferase libraries towards various alkyl iodides.[166] Furthermore, the HOX assay was used to identify promiscuous dehalogenase activity of the epoxide hydrolase CorEH from Corynebacterium sp. C12.[105]
Moreover, studies showed that the HOX assay could be used with in-vitro synthesized protein. Selected dehalogenases, DhlA, DhaA, and DmmA, were synthesized in vitro and used in the assay; the product formation was also validated using GC-MS. In conclusion, the HOX assay can be used with purified protein, whole cells, or in vitro synthesized proteins.
The HOX assay application in microfluidic droplets was investigated since an ultra-high-throughput assay for haloalkane dehalogenases is needed. This investigation showed no leakage of reaction components and products in the short term (~24 h), based on tests done on water-in-oil droplets generated by microfluidic chips. Even though 20 μM droplets were not working, 70 μM droplets were successful for assay implementation. Since the Damborsky group in Brno (CZ) and the deMello group in Zürich (CH), have large dehalogenase libraries and more experience in microfluidics, respectively, we collaborated with these groups to finalize implementation of the assay in an ultrahigh-throughput format. Since the studies are ongoing, final results could not yet be shown in this thesis. However, it can be noted that the issue with 20 μm droplets has been sorted out since our collaborators in Brno noticed that the low fluorescence of the droplets is actually caused by excessive accumulation of fluorescein, which is self-quenching, resulting in low fluorescence once the concentration exceeds 1 μM. By lowering the APF concentration they could optimize the maximum amount of fluorescein formed, and a mutant library has now been successfully screened by our collaborators at the ETH. The last topic of the thesis was an investigation of converting an epoxide hydrolase into a haloalkane dehalogenase. These studies focused on increasing the minor dehalogenase activity of two previously identified epoxide hydrolase (Cif) variants. These Cif variants hardly led to soluble proteins, the PROSS algorithm was used to increase soluble expression. New variants of Cif were generated using a 3DM analysis and the PROSS[164] design. The activities of these variants were determined with the newly developed HOX assay in a whole-cell format. Cif23 E153N-H269D and the PROSS D7 E153N-H269D variant, were found being active against 1,2-dibromoethane. Since the determination of enzyme concentration was hard to measure due to the expression/purification problem, specific activities could not be determined. To solve this problem, a HiBiT-tag was added to the selected variants for determining soluble expression. However, the planned studies could not be completed because of a lack of time and will form the basis for a future study.
Streptococcus pneumoniae (pneumococci) are Gram-positive cocci and commensals of the human upper respiratory tract. Pneumococcal pathogenesis requires adherence to host cells and dissemination through cellular barriers and to evade host defense mechanisms. The Pneumococcal surface protein C (PspC) is an important virulence factor which has a crucial role in pneumococcal adhesion to host cells and immune evasion by manipulating the host complement system. To elucidate the pneumococcal adherence and uptake mechanism via factor H glycosaminoglycans (dermatan sulfate and heparin) were employed as competitive inhibitors in infection experiments with epithelial cells or human polymorphonuclear leukocytes (PMNs). Glycosaminoglycans significantly inhibited the FH mediated pneumococcal adherence and subsequent invasion to host epithelial cells. Furthermore, the short consensus repeats of FH which promotes the adhesion of pneumococci to host cells were identified by blocking experiments with domain mapped antibodies for specific regions of FH. Moreover, this study indicates that FH acts as adhesion molecule via cellular receptors recognized as integrin CR3 on human PMNs. Binding of Factor H loaded pneumococci to integrins CR3 was assessed by flow cytometry. Pneumococci coated with Factor H showed a significantly increased association with PMNs. This interaction was blocked by anti-CR3 antibodies and Pra1. This project further aims to study mechanisms of pneumococcal endocytosis by host cells, their intracellular fate, and the pathogen induced host cell signal transduction cascades including the calcium signaling upon pneumococcal infection of host cells via the PspC-hpIgR interaction. To assess now the role of protein tyrosine kinases (PTKs) during pneumococcal infection via PspC, cell culture infections were performed in presence of pharmacological inhibitors of PTKs and MAPKs or by employing genetic interference techniques. Blocking the function of Src or ER1/2 and JNK and genetic-knock down of Src and FAK reduced significantly internalization of pneumococci. These data indicated the importance of a coordinated signaling between Src PTKs, ERK1/2, and JNK during PspC-pIgR-mediated uptake of pneumococci by host epithelial cells. The impact of host cells intracellular calcium concentrations on pneumococcal PspC-hpIgR mediated internalization was studied. Intracellular calcium measurement of epithelial cells performed in the presence of pneumococci suggested a calcium influx in host epithelial cells and importantly this calcium influx was PspC- hpIgR specific as pspC-deficient pneumococci were unable to mediate calcium mobilization in host cells. The increase in intracellular calcium [Ca2+]i was dependent on phospholipase C as pretreatment of cells with a phospholipase C-specific inhibitor abolished the increase in [Ca2+]i. Furthermore, role of host intracellular calcium concentrations during pneumococcal internalization was demonstrated by employing specific pharmacological inhibitors and calcium chelators in epithelial cell culture infection assays. The results revealed that elevated host cells calcium concentrations diminished pneumococcal internalization while lower calcium concentration in host epithelial cells promoted pneumococcal uptake. This study further demonstrates that dynamin, clathrin and caveolin play a key role during pneumococcal endocytosis into host cells via PspC-hpIgR. The use of specific pharmacological inhibitors or genetic interference approaches against dynamin, clathrin and caveolin in epithelial cell culture infection assays significantly blocked pneumococcal uptake. Furthermore, confocal microscopy revealed that pneumococci co-localize with clathrin. At later stages of the infection the pathogen is sorted to early, late and recycling endosomes as indicated by co-localization of pneumococci with endosomal markers such as Rab5, Rab4, Rab 7, and Lamp1. In order to get further insights into PspC-hpIgR mediated uptake mechanisms, a chimeric PspC was constructed and expressed heterologously on the surface of Lactococcus lactis. Immunofluorescence staining, immunoblot and flow cytometric analysis of L. lactis confirmed the expression of PspC on the bacterial surface. Moreover the ability of recombinant lactococci expressing PspC to adhere to and to invade pIgR-expressing epithelial cells confirmed the functional activity of PspC when exposed on the lactococcal surface. PspC expressing lactococci confirmed the specificity of PspC-hpIgR mediated endocytosis in host epithelial cells as PspC deficient lactococci were not taken up by these host cells. Confocal microscopic analysis demonstrated that only PspC expressing lactococci were sorted to early, late and recycling endosomes, similar to the intracellular fate of S. pneumoniae.
Synthesis and evaluation of pseudosaccharin amine derivatives as potential elastase inhibitions
(2006)
Elastase is a serine protease which by definition is able to solubilize elastin by hydrolytic cleavage.Human Leukocyte Elastase, HLE (EC 3.4.21.37), is involved in deseases such as adult respiatory distress syndrome, pulmonary emphysema, smoking related chronic bronchitits, ischemic-reperfusion injury and rheumatoid arthritis. Hence, the elastase inhibitors have clinical utility in these diseases. Heterocyclic compounds are one of the most important classes of the elastase inhibitiors. In the present work different pseudosaccharin amine derivatives were synthesized and tested against the elastase. The synthesis of pseudosaccharin amine dervatives was carried out from the amines and(1,1-dioxobenzo[d]isothiazol-3-ylsulfanyl)acetonitrile in different solvents. Futhermore, the pseudosaccharin amines were obtained by refluxing the thiosaccarinates in absolute acetic acid. The reaction of 3-ethoxybenzo[d]isothiazole 1,1-dioxide with different amines in dioxane under reflux resulted into the desired pseudosaccharin amine derivatives in higher yields. Pseudosaccharin chloride was also used in the synthesis of these derivatives.A detail study of the synthesis of pseudosaccharin amine dervatives from the above differnt routes is described. Peptides were also synthesized by using the mixed anhydride method. The ester, acid, amide and peptide derivatives were tested against the Porcine Pancreatic Elastase (PPE) and Human Leukocyte Elastase (HLE). The esters were found to be the reversible inhibitors of HLE. The process of the PPE inhibion by cyanomethyl(2S)-2-(1,1-dioxobenzo[d]isothiazol-3-ylamino)-3-methylbutanoate was studied. Michaelis-Menten curve and Lineweaver-Burk double reciprocal plot were constructed in order to study the kinetic of this reaction. The compounds showing high inhibition of HLE were further stuied for determination of their inhibitory constant(Ki). The esters were found to be the higly active compounds against HLE. The cyanomethyl(2S)-2-(1,1-dioxobenzo[d]isothiazol-3-ylamino)-3-methylbutanoate and cyanomethyl(2S,3S)-2-(1,1-dioxobenzo[d]isothiazol-3-ylamino)-3-methylpentanoate showed the competitive reversible inhibition of HLE.The cyanomethyl(2S,3S)-2-(1,1-dioxobenzo[d]isothiazol-3-ylamino)-3-methylpentanoate is highly potent inhibitor of HLE. The possible mechanism of inhibition of elastase by these compounds is discussed. Molecular modelling of some of the ester derivatives is also discussed.
Studies of stroke in experimental animals have demonstrated the neuroprotective efficacy of a variety of interventions; however, most such strategies have failed to show clinical benefits in aged humans. One possible explanation for this discrepancy between animal and clinical studies may be the role that age plays in the recovery of the brain following insult. For example, the poor functional recovery of aged rats after stroke may be caused by a decline in brain plasticity. Although the incidence of ischemic stroke increases dramatically with advancing age, relatively few studies have been conducted on aged animals, which would mimic most closely the context in which stroke occurs in humans. We have shown that, at one week following stroke, there was vigorous expression of MAP1B and its mRNA, as well as MAP2 protein, in the border zone adjacent to the infarct of 3 month- and 20 month-old male Sprague Dawley rats. Hypothesis: The decline in brain plasticity is caused by an age-related decline in the upregulation of factors promoting brain plasticity (MAP1B, ßAPP) and an age-related increase in astroglial scaring and in the expression of neurotoxins such as beta amyloid. Methods: Focal cerebral ischemia was produced by reversible occlusion of the right middle cerebral artery in 3- and 20-month-old male Sprague Dawley rats. The functional outcome was assessed in neurobehavioral tests at 3, 7, 14, and 28 days post-stroke. At these time points, brains were removed and analyzed for markers of (i) brain plasticity (microtubule-associated protein 1B, MAP1B, secreted forms of fi-amyloid precursor protein); (ii) neurogenesis (BrdU-positive cells, doublecortin, nestin); (iii) neurotoxicity (B-amyloid aggregates); (iv) inflammation (microglia, astrocytes, oligodendrocytes, endothelial cells). Results: (1) There was a non-significant tendency for blood pressure to be higher in old than in young rats. By post-stroke day 3 the infarct volume covered about 15% of the cortical neurons in young and 28% in aged rats. By day 7, infarct volumes were roughly equal in the two age groups. (2) Cell counting showed increases in the number of BrdU-positive cells in the infarcted area of old rats at day 3 post-stroke. This increase became even more dramatic at day 7 post-stroke in aged rats. There was no significant contribution of apoptosis to cell death. (3) Behaviorally, young rats recovered gradually and reached a maximum of 90% of baseline performance at day 14, post-stroke while the aged rats recovered only to a maximum of 70% of pre-surgery performance by week 2 post-stroke, and remained at that level. (4) The temporal pattern of recovery correlated well with the expression of growth-associated phenotype of ßAPP as well as with MAP1B accumulation in varicosities along axons (an indicator of growth) in cortical areas affected by stroke and was at maximum between days 14 to 28 in young rats. In contrast, aged rats showed delayed (day 28) and reduced axonal remodelling as well as a delayed (day 28) expression of growth-associated ßAPP. Instead, the neurotoxic carboxy-terminal form of ßAPP steadily accumulated over time and reached a maximum at day 14 in aged rats as compared to 28d for the young rats. Nestin, a marker for immature neurons, overlapped with BrdU-labelled cells at day 7 post-stroke in corpus callosum and at the infarct border in both young and aged rats, suggesting increased stroke-induced neurogenesis. (5) In young rats there was a gradual activation of both microglia and astrocytes that peaked by days 14 to 28 with the formation of a glial scar. In contrast, aged rats showed an accelerated astrocytic and microglial reaction that peaked in week 1 post-stroke. We also noted a strong activation of oligodendrocytes at early stages of infarct development in all rats that persisted in aged rats. Evolution of astrocytic and microglial reactivity closely paralled the time course of scar formation in both young and aged rats and coincided with the stagnation in the recovery rate of aged rats. Conclusions: The time course of functional recovery in young rats correlated well with the expression of plasticity proteins such as MAP1B and ßAPP while an early and persistent expression of the neuro toxic fragment AB in conjunction with a delayed expression of MAP1B and ßAPP may impede functional recovery in aged rats. The results also suggest that a temporally anomalous glial reaction to cerebral ischemia in aged rats leads to the premature formation of scar tissue that impedes functional recovery to stroke.
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.
In this work, the regioselectivity of different Baeyer-Villiger monooxygenases (BVMOs) for the conversion of selected substrates was reversed or improved by protein engineering. These studies highlight the importance of substrate positioning for the regioselectivity and that the position of the substrate can be efficiently influenced by introducing proper mutations. It was shown that the beneficial mutations for all BVMOs were partly in corresponding positions. Additionally, the sulfoxidation activity and the stability of BVMOs were targeted and improved by applying protein engineering.
Pharmaceutical residues are found in increasing concentrations in the environment and in potable water where they have verifiable effects on aquatic life. Conventional methods for water treatment are not able to sufficiently abate these generally stable compounds. It was found that physical plasma generated directly in water can degrade several of these recalcitrant organic pollutants. Studies on the basic plasma chemical processes for the model system of phenol showed that the degradation is primarily caused by hydroxyl radicals. This was confirmed by reaction chemistry and spin trap enhanced electron paramagnetic resonance spectroscopy (EPR). The degradation of diclofenac and its by-products were investigated in detail to perform a first risk-assessment of the new technology. Findings are not limited to the application of plasma but applicable to other advanced oxidation processes (AOP) that are based on the generation of hydroxyl radicals as well. Additionally, pulsed corona plasma and pulsed electric fields were assessed for their capacity to kill Legionella pneumophila in water. Whereas it was possible to kill L. Pneumophila with both methods, plasma treatment resulted in an enhanced bacterial killing. Therefore, advanced oxidation processes (AOP) and plasma treatment in particular are some of the few feasible approaches to decompose recalcitrant compounds in water.
In modern-day organic synthesis, transitional metal catalysis has become an essential tool-kit to access the biologically significant complex organic scaffolds. The activation profile of these sophisticated catalytic systems in cross-coupling chemistry and ring-closing processes has been well appreciated and frequently employed by the scientific community.
The present thesis is describing the results of interdisciplinary research involving medicinal chemistry and transitional metal homogeneous catalysis. A molybdenum mediated process was employed to access 32 unprecedented heterocyclic fused poly sulfur ring containing pentathiepins in moderate to good yields as a part of medicinal chemistry. Biologically significant, such as quinoxaline, pyrazine, pyridine, nicotinamide, quinoline, imdazo-pyrazine, pyrrolo-pyrazine, purine, and pyridine sulfonamide scaffolds were functionalized with pentathiepin unit via multi-step organic synthesis. Essentially, the Sonogashira cross-coupling and(Et4N)2[MoO(S4)2] mediated ring-closing steps were commonly employed in all pentathiepin syntheses. The analytically pure samples were characterized by 1H, 13C, 19F-NMR, FTIR, ESI-MS, CHNS, and X-ray single-crystal diffraction analysis. Notably, all pentathiepins exhibited an ABX3 multiplet pattern between δ: 4.2-4.5 ppm with the integration of 2H for the ethoxy functional group's methylene protons substituted on the five-membered ring of pentathiepin, which was later considered as a fingerprint for pentathiepin formation. The mechanistic investigations via control experiments suggest that the tetra sulfur ring Mo(IV) precursor (Et4N)2[MoO(S4)2] is vital along with elemental sulfur for the pentathiepin formation, and the Mo(IV) complex regenerates in the reaction. Furthermore, For the first time, the GPx1 enzyme inhibitor properties of novel fused heterocyclic pentathiepins were established, where these probes exhibited 9-12 folds higher potency than mercaptosuccinic acid. Notably, <1 µM concentration of quinoxaline, pyrazine, and quinoline fused pentathiepins were potent enough to inhibit 50% of GPx1 enzyme activity. Additionally, cytotoxicity, antimicrobial and antifungal studies were conducted for all pentathiepins. In anticancer investigations, the IC50 concentrations for all pentathiepins were ranging between 0.22 to 4.7 µM.
The second half of the thesis introduces a novel water-soluble Pd/PTABS as a potent catalyst for C-X (X = N, O, and S) cross-coupling chloroheteroarenes and halonucleosides. The novel, mild and efficient Pd/PTABS catalytic system was successfully employed at low catalytic loadings (1 mol%) for the amination (C−N), etherification (C−O), and thioetherification (C−S) of chloroheteroarenes at ambient to moderate temperatures. The Pd/PTABS catalyst is well-tolerating various heterocyclic scaffolds, and under the optimized catalytic conditions, various secondary amines, electron-rich or electron-poor phenols, thiophenols, and alkylthiols, were efficiently employed as nucleophilic coupling partners. Notably, the catalyst offered tremendous regio and chemoselectivity with excellent temperature control. Besides, novel sulfones and sulfoximines were prepared from the thioethers obtained via Pd/PTABS. The catalyst was employed efficiently for synthesizing biologically significant known drugs or drug candidates such as alogliptin (anti-diabetic agent), XRK 469 (antitumor agent), and Imuran-Azathioprine (immunosuppressive) in competitive yields. Preliminary DFT investigations were performed, and based on the DFT analysis, the electropositive character of the phosphorous atom in quaternary ammonium salts of PTABS supports the heteroatom directed C−Cl activation hypothesis.
This thesis presents the production of polyanionic clusters within two ion storage devices:
Considering a Penning trap, the accessible range of polyanionic aluminium clusters has been expanded up to the 10th charge state. In particular, abundance curves for clusters with 5 to 9 excess electrons have been measured for the first time and analysed with respect to their lifetime-dependent appearance sizes. These sizes reveal a nearly quadratic dependency on the charge state for experimentally accessible lifetimes.
Additionally, the production of polyanionic clusters has been enabled in a radiofrequency ion trap. Therefore, the transition from a harmonic to a digital 2- and 3-state guiding signal has been investigated with respect to the ion storage. The passing of electrons through the trap during field-free periods of the guiding signal led to the first production of polyanionic clusters within a radiofrequency ion trap.
The intracellular life cycle of the human immunodeficiency virus (HIV) is modelled using ordinary differential equations (ODEs). Model parameters are obtained from the literature or fitted to experimental data using parameter estimation procedures. Key steps in the life cycle are inhibited singly and in combination to show the effects on viral replication. The results validate the success of highly active antiretroviral therapy (HAART), and in addition DNA nuclear import is identified as a novel influential therapeutic target.
Purpose: To assess the comparative efficacy and the long-term cost-utility of alternative minimally invasive glaucoma surgeries (MIGSs) when combined with cataract surgery in patients with primary open-angle glaucoma (POAG).
Methods: Treatment effects, as measured by the 1-year reduction in intraocular pressure (IOP), were estimated with an adjusted indirect treatment comparison. Evidence from randomized clinical trials was identified for four different MIGS methods. A disease-transition model was developed by capturing clinically relevant POAG stages and the expected natural disease evolution. Outcomes of the disease-transition model were the comparative utility [quality-adjusted life years (QALYs)], cost and cost-utility of included strategies in a lifetime horizon.
Results: Estimated 1-year IOP reductions were: cataract surgery - 2.05 mmHg (95% CI - 3.38; - 0.72), one trabecular micro-bypass stent - 3.15 mmHg (95% CI - 5.66; - 0.64), two trabecular micro-bypass stents - 4.85 mmHg (95% CI - 7.71; - 1.99) and intracanalicular scaffold - 2.25 mmHg (95% CI - 4.87; 0.37). Discounted outcomes from the disease-transition model appraised the strategy of two trabecular micro-bypass stents with cataract surgery in the moderate POAG stage as the one providing the greatest added value, with 10,955€ per additional QALY. Improved outcomes were seen when assessing MIGS in the moderate POAG stage.
Conclusions: When indirectly comparing alternative MIGS methods combined with cataract surgery, the option of two trabecular micro-bypass stents showed both a superior efficacy and long-term cost-utility from a German perspective. Moreover, outcomes of the disease-transition model suggest POAG patients to beneficiate the most from an earlier intervention in the moderate stage contrary to waiting until an advanced disease is present.
There is a growing interest in the application of non-thermal atmospheric pressure plasma for the treatment of wounds. Due to the generation of various ROS and RNS, UV radiation and electric fields plasma is a very promising tool which can stimulate skin and immune cells. However, not much is known about the mammalian cell responses after plasma treatments on a molecular level. The present work focusses on the impact of plasma on cell signaling in the human keratinocyte cell line HaCaT by using the methods DNA microarray, qPCR, ELISA and flow cytometry. Here, cell signaling mediators such as cytokines and growth factors which could promote wound healing by enhancing angiogenesis, reepithelization, migration and proliferation were of major interest. Additionally, the crosstalk between keratinocytes and monocytes was studied using a co-culture. For the first time extensive investigations on the impact of plasma on cell signaling in human keratinocytes were conducted. The most prominent cytokines and growth factors which were regulated by plasma at gene and protein level were VEGF-A, GM-CSF, HB-EGF, IL-8, and IL-6. The latter was not activated due to the JAK/STAT-pathway but probably by a combined activation of MAPK- and PI3K/Akt-pathways. By the use of conditioned medium it was found out that ROS and RNS generated directly after plasma treatment induced larger effects on cell signaling in keratinocytes than the subsequently secreted growth factors and cytokines. Furthermore, monocytes and keratinocytes hardly altered their secretion profiles in co-culture. From these results it is deduced that the plasma generated reactive species are the main actors during cell signaling. In order to differentiate the impact of ROS and RNS on the cellular response the ambience of the plasma effluent was controlled, varying the ambient gas composition from pure nitrogen to pure oxygen. Thereby a first step towards the attribution of the cellular response to specific plasma generated reactive species was achieved. While IL-6 expression correlated with ROS generated by the plasma source, the cell signaling mediators VEGF-A, GM-CSF and HB-EGF were significantly changed by RONS. Above all hydrogen peroxide was found to play a dominant role for observed cell responses. In summary, plasma activates wound healing related cell signaling mediators as cytokines and growth factors in keratinocytes. It was also shown that the generated reactive species mainly induced cell signaling. For the first time cell responses can be correlated to ROS and RONS in plasma treated cells. These results underline the potential of non-thermal atmospheric pressure plasma sources for their applications in wound treatment.
The rapid neutron-capture or the r-process is responsible for the origin of about half of the neutron-rich atomic nuclei in the universe heavier than iron. For the calculation of the abundances of those nuclei, atomic masses are required as one of the input parameters with very high precision. In the present work, the masses of the neutron-rich Zn isotopes (A=71 to 81) lying in the r-process path have been measured in the ISOLTRAP experiment at ISOLDE/CERN. The mass of 81Zn has been measured directly for the first time. The half-lives of the nuclides ranged from 46.5 h (72Zn) down to 290 ms (81Zn). In case of all the nuclides, the relative mass uncertainty (∆m/m) achieved was in the order of 1E-8 corresponding to a 100-fold improvement in precision over previous measurements.
1. "Sole or Whole" – Quilting the Racialized Subject Calgary feminist and scholar Aruna Srivastava tackles the complex question of what it means to be "mixed-race/mixedblood/halfbreed/mestizo/hybrid/hyphenated?" in her editorial to Hyphe Nation (1996). In response to her question, this study of contemporary African-Canadian literature suggests that mixed-race Canadians are often constructed as the Other in Canadian society. In consequence, constructions of "racial hybridity" in African-Canadian literature usually aim at carving out a space that doesnt marginalize "racial" mixing but eviscerates restrictive Manichean constructions of identity in order to promulgate concepts of wholeness and self-definition. In consequence, African-Canadian mixed-race writers create hybrid identities that are infinite, multilayered, fragmented and yet whole. They reflect the processes of shifting, overlapping and re-creation in the process of creating identity and can hence be read as representations of complex, de-central, non-hierarchical identities. They are quilting multidimensional racialized subjects. 2. Signifying the In-Between: "Race", "Racial Hybridity" and Questions of Belonging "Race" is not a biological category. Rather it represents a social construction predicated upon the interpretation of difference. It was designed to establish, justify or perpetuate hegemonic social structures and is adherent to the principle of white supremacy. Contemporary "race" theory often neglects the experiences of racially mixed individuals because it fails to offer flexible models of identity in which bi- and multiracial people find themselves represented. This thesis argues in favor of a poetics of difference that accepts and recognizes the heterogeneity of subjectivities while taking into consideration the various dimensions of class, gender, sexuality and ethnicity. Accordingly, constructions of racial hybridity in contemporary African-Canadian literature demonstrate that racism must be acknowledged as an ideology in which people believe and upon which people act. Thus identities often bear the stamp of various histories of resistance and domination, while tackling the question of belonging and re-defining Canadianness. 3. African-Canadian Borderlands References to interracial contacts and the existence of bi- and multiracial people have been omitted from the official founding narratives of the Canadian nation. African-Canadian writers have therefore been successful chroniclers of the past and filled blanks in Canadian historiography in order to shed light on hitherto repressed or erased knowledge. Part of this process is also the inscription of the mixed-race experience into Canadas past. Along this line, bi- and multiracial Canadians often criticize that the state-proclaimed policy of multiculturalism fails to take their manifold racial and ethnic subjectivities into account. 4. "From Sole to Whole" – African-Canadian Mixed-Race Poetics Mixed-race characters in US-American literature often appear in the literary motif of the "tragic mulatto" and it is often implicitly suggested that the bi- or multiracial protagonist is categorized as black. In contrast, African-Canadian constructions of racial hybridity less frequently adhere to the stereotype of the "tragic mulatto" and leave more space for employing alternative modes of racial and ethnic identification. Canadian writers of mixed descent have created a mixed-race poetics that calls attention to contexts, relationships, intersections and wholes. They encourage sites of inclusiveness, incessant shifting and discontinuity in the process of constructing identities. Nevertheless, modes of identification among racially hybrid writers in Canada vary, ranging from detesting whiteness to claiming a Black Nationalist stance. In general, however, they support the idea of fluid and flexible identities. The answer to the initial question of Srivastava is hence given by a vast variety of African-Canadian subject positions. An essentially "black" or "racially mixed" Canadian subject does not exist. Instead, constructions of racial hybridity in African-Canadian literature offer a holistic view of identity and aim at re-conceptualizing the various senses of self and community in Canada. This strategy provides a significant means of self-empowerment and self-reclamation – making racially mixed African-Canadians "whole" instead of "sole".
Novel heterocyclic alpha-phosphinoamino acids, by structural relationship named 3-phosphaprolines, were obtained by cyclocondensation of 2-phenylphosphinoethylamines with glyoxylic, pyruvic or phenylglyoxylic acid at room temperature in diethylether. The reactions proceed via primary attack of the P-lone electron pair, as shown by the synthesis of phosphonium glycolates from tertiary phosphines and glyoxylic acid, and addition of PH at the carbonyl group. The ring closure proceeds by replacement of the hydroxy by the amino group and is kinetically controlled. NMR monitoring of the phosphaprolines in CD3OD over several days indicates changes of the diastereoisomer ratios leading to higher contents of the more stable trans-diastereoisomers. The zwitterionic compounds are soluble in part in CD3OD, DMF or DMSO, are somewhat sensitive to air in solution and may undergo hydrolysis with larger amounts of water. The structures are proved by multinuclear NMR spectra and two crystal structure analyses. Suitable phosphaprolines as well phosphonium glycolates and Ni(COD)2 allow to generate precatalysts, activated by NaH for the oligomerisation of ethylene to mainly linear products with methyl and vinyl end groups. Some additional investigations with phosphinophenolates, another type of P-C-C-O- ligands, were performed for comparison. Precatalysts prepared from 2-phosphinophenolesters and Ni(COD)2 at room temperature were characterized by multinuclear NMR but decomposed on heating to stable nickel cis-bis(P,O-chelate) complexes. Heating precatalysts generated from a phosphinophenolester or phosphinophenols and Ni(COD)2 in the presence of ethylene under pressure led to linear ethylene oligomers. These reactions are much faster than the above mentioned conversions with NaH activated P,O-Ni-catalysts. In the presence of 9-decenol with unprotected remote hydroxyl group incorporation of a small amount of isolated hydroxyoctyl side groups takes place, detected by 13C NMR spectroscopy. Finally it is stated that the development of a facile synthesis and the characterization of the properties of the phosphaprolines pave the way for derivatisation and further studies with these novel types of amino acids.
This study validates a newly-developed scale of consumer culture at individual-level in purchase-consumption context. Following unipolar approach in measurement, the applicable-reliable scale for consumer culture analyzes plausible effects of the seven cultural dimensions on three selected consumer-behaviors; anticipated regret, and two further purchase behaviors of variety-seeking and Quality-consciousness, comparing both Hedonic and Utilitarian aspect of consumer decisions. The interaction among the three behavioral variables are also studied. Feeling the necessity of cultural investigations in rather-unknown countries, Iran and Germany are focused.Iran is among the culturally undiscovered markets with an ever increasing demand; also German consumers have several unknown aspects in their purchase behaviors. Finally, the role of contextual elements — nationality, demographic profile and task— in consumer purchase behaviors are separately analyzed.
Background: Common to most theory-based intervention approaches is the idea of supporting intentions to increase the probability of behavior change. This principle works only if (a) intentions can be explained by the hypothesized socio-cognitive constructs, and (b) people actually do what they intend to do. The overall aim of this thesis was to test these premises using two health behavior theories applied to reducing at-risk alcohol use. Method: The three papers underlying this thesis were based on data of the randomized controlled “Trial Of Proactive Alcohol interventions among job-Seekers” (TOPAS). A total of 1243 job-seekers with at-risk alcohol use were randomized to stage tailored intervention (ST), non-stage tailored intervention (NST), or control group. The ST participants (n = 426) were analyzed in paper 1. Paper 2 was based on the baseline and 3-month data provided by the NST participants (n = 433). Paper 3 was based on baseline, 3-, 6-, and 15-month data provided by the control and ST group not intending to change alcohol use (n = 629). Latent variable modeling was used to investigate the associations of social-cognitive constructs and intentional stages (paper 1), the extent to which intentions were translated into alcohol use (paper 2), and the different trajectories of alcohol use among people not intending to change as well as the ST effect on the trajectories (paper 3). Results: Persons in different intentional stages differed in the processes of change in which they engaged, in the importance placed by them on the pros and cons of alcohol use, and in the perceived ability to quit (ps < 0.01). The association between intentions and alcohol use was weak. The magnitude of this intention-behavior gap depended on the extent to which normative expectations have changed over time (p < 0.01) and was reduced when controlling for the mediating effect of temporal stability of intentions. The gap was also present among people not intending to change: Even without intervention, 35% of the persons reduced the amount of alcohol use after 15 months (p < 0.05) and 2% achieved abstinence. Persons with heavier drinking (33%) and persons with low but frequent use (30%) did not change. Persons with frequent alcohol use seem to benefit less from ST than those with occasional use, although differences were not statistically significant. Conclusions: Intentions can be quite well explained by the hypothesized socio-cognitive constructs. In a sample of persons who were, as a whole, little motivated to change, the precision of how well intentions predict subsequent alcohol use was modest though. Time and socio-contextual influences should be considered.
This thesis focuses on the establishment of biocatalytic cascade reactions for the production and detection of industrially relevant flavor and fragrance compounds for food and cosmetic products. To meet the consumer’s demand for those products to be natural, environmentally friendly biocatalytic manufacturing processes that operate GMO-free must be established. Thus, this thesis presents such pathways for the production of an industrially relevant long-chain hydroxy fatty acid and the important flavor and aroma compound raspberry ketone. Furthermore, a biosensor for aldehyde detection was implemented to facilitate screening for suitable biocatalysts that produce industrially relevant aldehydes that are widely applied in the flavor and fragrance industry.
Discovering Latent Structure in High-Dimensional Healthcare Data: Toward Improved Interpretability
(2022)
This cumulative thesis describes contributions to the field of interpretable machine learning in the healthcare domain. Three research articles are presented that lie at the intersection of biomedical and machine learning research. They illustrate how incorporating latent structure can provide a valuable compression of the information hidden in complex healthcare data.
Methodologically, this thesis gives an overview of interpretable machine learning and the discovery of latent structure, including clusters, latent factors, graph structure, and hierarchical structure. Different workflows are developed and applied to two main types of complex healthcare data (cohort study data and time-resolved molecular data). The core result builds on Bayesian networks, a type of probabilistic graphical model. On the application side, we provide accurate predictive or discriminative models focusing on relevant medical conditions, related biomarkers, and their interactions.
Underground hard coal mining operations irreversibly disrupt the pre-existing mechanical equilibrium of the geological media. The employment of high-recovery methods modifies the stress field of the sedimentary sequence, generating movement and faulting of the rock layers above and below mined seams. These new fracture zones do affect the original conditions of the hydrogeological system by modifying flow pathways and increasing the permeability of the rock sequence. Moreover, the surface area of rock exposed to air and water is increased, conditioning the water-rock interaction. Despite this rather clear conceptualization, flow and reactive transport processes in fractured overburdens are rarely modeled simultaneously. Discrete setups that consider fractures and porous matrix require extensive characterization of both media, which is impractical for regional case studies. As a result, most post-mining models explicitly ignore fracture structures by employing the equivalent porous approach or even both media with lumped parameter models. However, omitting either medium represents a delicate simplification, considering that mining-related fractures control the rate and direction of water flow within moderately permeable but relatively highly porous rock sequences.
In this dissertation, the specific contribution of fractured and matrix continua to the transient discharge and water quality of a post-mining coal zone is quantified and evaluated. For this purpose, dual and multiple interacting continua models are employed to simulate fluid flow and reactive mass transport in fractured and variable water-saturated rock sequences. The effectiveness of the models is evaluated by simulating the origin, generation and transport of acid mine drainage (i.e., water with elevated concentrations of hydrogen, iron, sulfate and chloride) within the shallow overburden of the Ibbenbüren Westfield. Compared to other coal districts in Germany, this area is strongly delimited by the local geology and topography, resulting in a well-defined hydrogeological system to test the models. Petrographic and chemical analyses performed on core samples from the area show the strong influence of mining-derived fractures on the water-rock interaction within the Carboniferous sequence. The presence of oxidized pyrite along with amorphous iron hydroxide phases in weathering fronts on both sides of the fractures demonstrates the exchange of solutes and gases between the fractured and the porous matrix media.
Based on the previous evidence, the TOUGHREACT software is employed to characterize flow and reactive transport processes in the Westfield. However, each of the two processes is simulated at separate stages to have more control in the adjustment of sensitive parameters for which little information is available. For the flow component, a dual continuum model, with Richard’s equations is used to characterize the unsaturated water flow in both fractured and matrix media. Under this approach, the model adequately reproduces the bimodal flow behavior of the discharges measured in the mine drainage for the years 2008 and 2017. Simulation results show how the fractured continuum generates intense discharge events during the winter months while the rock matrix controls smooth discharge limbs in summer, when water is slowly released back to the fractures. With the flow component calibrated, the second part of the study incorporates the geochemical processes into the model based on actual data from the rock samples. Their simulation requires extending the two-continuum setup to a multiple continua model with five nested block strings: one for the fractures and four for the rock matrix. This further subdivision prevents under-representations of kinetic reactions with short equilibrium length scales and numerical instabilities due to lack of chemical and flow gradients. As a result, the new multiple continua model provides good agreement with respect to long- and short-term concentrations and discharge trends measured in the mine drainage. The flow of oxygen and meteoric water through the fractured continuum leads to a high and steady release of hydrogen, iron and sulfate ions derived from pyrite oxidation in the matrix continua closest to the fractures. Moreover, high chloride concentrations result from the mixing and gradual release of relatively immobile solutes in the matrix as they interact with percolating water in the fracture. Both findings are equally congruent with the reactive pyrite oxidation and iron hydroxide precipitation fronts identified in the fractured core samples.
In the end, the multiple continua models, the simulation procedure and the results of the benchmark and sensitivity analysis scenarios developed for the Westfield pave the way for the application of the approach in other mining zones. The first candidate emerges in the Ibbenbüren Eastfield, where a coupled elemental-isotopic approach included in this thesis has confirmed that water-conducting fracture zones are primary elements for solute generation and transport in the first 300 meters of the overburden. In the latter case, calibration and verification of the models can be complemented with measurements of δ34S in sulfates and δ18O, δ2H, and Tritium in water.
In den Weltmeeren findet rund die Hälfte der jährlichen globalen Kohlenstofffixierung statt, davon ein großer Anteil in küstennahen Regionen. Hier kommt es zu wiederkehrenden saisonalen Algenblüten, die durch eine zeitlich begrenzte explosionsartige Vermehrung von Mikroalgen (hauptsächlich Diatomeen und Coccolithophoren) charakterisiert sind. Vor allem Frühjahrsblüten (März-Mai) haben aufgrund ihrer zeitlichen und räumlichen Vorhersagbarkeit einen hohen Stellenwert als Modellsysteme, anhand deren sich der Kohlenstoffkreislauf der Meere untersuchen lässt.
Mikroalgen produzieren eine große Vielfalt an Makromolekülen, die für die mit ihnen vergesellschafteten Bakterien als Nahrungsgrundlage dienen. Besonders im Fokus stehen hier die für den Kohlenstoffkreislauf relevanten Polysaccharide. Im Gegensatz zu anderen natürlichen Makromolekülen wie DNA oder Proteinen können Polysaccharide aus vielen verschiedenen Monomeren mit unterschiedlichsten Bindungen bestehen. Zusätzlich finden sich an diesen Zuckermonomeren viele Modifikationen wie Acetylierungen, Methylierungen oder Sulfatierungen, die die Komplexität weiter erhöhen. Diese Variabilität bedingt eine hohe strukturelle und funktionale Diversität. So können Polysaccharide Speicherstoffe, Zellwandbestandteile oder Teile der extrazellulären Matrix darstellen.
Komplementär hierzu besitzen Polysaccharid-verwertende Bakterien entsprechend komplexe, enzymatische Abbaumechanismen. Besonders hervorzuheben sind hier die Bakterien des Phylums Bacteroidota, die sich in verschiedensten Nischen auf den Abbau von Polysacchariden spezialisiert haben. Sie finden sich in Bodenproben, als Teil der menschlichen Darmflora, oder eben auch als bedeutende Begleiter von Algenblüten.
Bacteroidota (und in marinen Systemen hauptsächlich die zu ihnen gehörenden Flavobakterien) besitzen zum Abbau diverser Polysaccharide sogenannte Polysaccharide utilization loci (PULs), genomische Inseln, die alle notwendigen Proteine zur Aufnahme und Abbau eines bestimmten Polysaccharids codieren. Hierzu gehören hochspezifische Enzyme (Carbohydrate-active enzymes, CAZymes), transkriptionelle Regulatoren sowie Transportersysteme, die initial gespaltene Oligosaccharide über die Membran in das Bakterium transportieren, wo sie von weiteren Enzymen vollständig abgebaut werden. Diese Co-Lokalisation der benötigten Gene und deren gemeinsame Regulation stellt einen enormen Selektionsvorteil der Bacteroidota dar und ist der Grund, warum sie, ähnlich wie Algen, einer jährlich wiederkehrenden Sukzession folgen, die sich gut untersuchen lässt.Die Forschungsartikel, die Teil dieser Doktorarbeit sind, untersuchen das Zusammenspiel von Polysaccharid-produzierenden Algen mit den Bakterien, die sie abbauen, aber auch darauf basierende Beziehungen der Bakterien untereinander. Die erste Publikation beschäftigt sich mit dem weit verbreiteten Speicherpolysaccharid α-Glucan, für das der Großteil der blütenbegleitenden Bakterien einen spezifischen aktiven PUL besitzt. Eine Untersuchung der in der Blüte vorhandenen Algenarten bestätigte, dass die Blüte von β-Glucan-produzierenden Algen dominiert wird. Da Bakterien aber selbst α-Glucane als Speicherpolysaccharide verwenden, konnte gezeigt werden, dass nicht die Algen selbst, sondern die Bakterien Hauptproduzent dieser Polysaccharide während einer Phytoplanktonblüte sind. Bakterielle Proteine, die dem Abbau von Algen-β-Glucan und dem daraus folgenden Aufbau von bakteriellem α-Glucan dienen, waren in Umweltproben und in Laborkulturen unter ähnlichen Bedingungen abundant. Die Untersuchung von extrahiertem bakteriellem Polysaccharid bewies, dass dieses nicht nur α-Glucan enthält, sondern dass dieses Polysaccharid auch in der Lage war, α-Glucan PULs mariner Bakterien zu induzieren. Hier zeigte sich ein innerhalb des marinen Kohlenstoffkreislaufs bisher wenig berücksichtigter Kreislauf, indem Bakterien Polysaccharide anderer Bakterien nutzen, die z.B. durch Viren lysiert wurden.
Die anderen zwei Artikel dieser Arbeit befassen sich mit dem Abbau von Zellwandpolysacchariden durch blütenassoziierte Modellbakterien. In einer der Studien wird detailliert der Abbau eines β-Mannans (ein Polysaccharid das hauptsächlich aus dem Monosaccharid Mannose besteht) durch ein Bakterium des Genus Muricauda beschrieben. Die PUL-Struktur dieses Bakteriums kam in mehreren anderen Phytoplanktonblüten-assoziierten Bakterien vor. Diese Beobachtung wies darauf hin, dass es sich hier um ein Mannan mit zusätzlichen Galactose- und Glucose-Substitutionen handelte. Proteom-Untersuchungen bestätigten, dass das Bakterium derartige Substrate unter Induktion des β-Mannan-PULs nutzen können. β-Mannan konnte durch Antikörpermarkierung in Blütenproben sowie spezifischen Mikroalgenarten (Chaetoceros, Coscinodiscus) nachgewiesen werden. Die in dieser Publikation charakterisieren β-Mannan-PUL-codierten Enzyme waren in der Lage, dieses Signal zu löschen, was bewies, dass Muricauda sp. Mannan-basierte Zellwandpolysaccharide bestimmter Arten von Mikroalgen abbauen kann.
Die dritte Studie geht näher auf den Abbau von Xylanen (bestehend aus Xylose) durch ein blütenassoziiertes Bakterium des Genus Flavimarina ein. In diesem Bakterium wurden anhand der enthaltenen Xylanasen zwei putative Xylan-PULs annotiert. Wachstumsexperimente und Proteom-Untersuchungen zeigten, dass einer dieser PULs hauptsächlich bei Wachstum auf Glucoronoxylan induziert wird, während der andere PUL aufArabinoxylane stärker reagierte. Untersuchung der PUL-CAZymes bestätigte diese Ergebnisse durch Charakterisierung mehrerer Xylanasen sowie Glucoronidasen und Arabinofuranosidasen. Zusätzlich codierten beide PULs für Esterasen, die eine Modifikation der natürlichen Substrate durch Acetylierungen oder Methylierungen nahelegen. Da all diese Merkmale von terrestrischen Xylanen geteilt werden und in Blütenproben aus Küstennahen Regionen Xylane nachgewiesen wurden, ist es möglich, dass Bakterien aus solchen Regionen sowohl Xylane terrestrischen Ursprungs (z.B. durch Flusseinspeisung) sowie marinen Ursprungs abbauen können.
In this work, the discovery, expression and characterization of new eukaryotic Baeyer-Villiger monooxygenases (BVMOs) from yeasts has been shown. A rational design of one of these enzymes led to the identification of key residues to alter the sulfoxidation activity of this group of enzymes. Additionally, in another rational design approach, the cofactor specificity of the BVMO cyclohexanone monooxygenase from Acinetobacter calcoaceticus could be substantially altered to accept the much cheaper and therefore industrially more relevant cofactor NADH.
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.
Body sensations play a crucial role in the etiology and maintenance of diverse anxiety and health problems (e.g., in panic disorder or respiratory diseases) as they may be perceived as threatening and consequently elicit anxious responses. The factors that may affect the perception of bodily sensations as a threat and thus modulate the anxious response to body sensations have so far rarely been studied. Therefore, the present thesis targeted at elucidating the effect of contextual (i.e., the predictability, expectation, and proximity of a threat) and dispositional factors (i.e., tendency to fear arousal sensations or trait fear of suffocation) on the defensive response to body sensations.
In study 1, it was investigated how a personality factor, that is, fear of suffocation, affects the acquisition of fear to body sensations (i.e., mild dyspnea induced by inspiratory resistive loads) and contexts when faced with a predictable and unpredictable respiratory threat (i.e., severe dyspnea). Study 2 aimed at examining the main and interactive effects of the tendency to fear arousal sensations, again a personality trait factor, and current arousal expectations as varied by situational variables on anxious responding to arousal sensations. In this study, expected and unexpected arousal sensations were induced by administering caffeine in coffee or bitter lemon soda, respectively. Moreover, in study 3, it was explored how subjective anxiety, bodily symptoms, and defensive respiratory responses change and might culminate into active defense behavior (i.e., escape/active avoidance) during increasing dyspnea that was evoked by inspiratory resistive loads increasing in intensity. For a detailed analysis of the factors that contribute to the initiation and maintenance of avoidance of or escape from increasing dyspnea, in study 4 changes in subjective, autonomic, somatic reflex and brain responses were analyzed during repeated avoidance of increasing dyspnea.
In study 1, it was demonstrated that only individuals who fear suffocation learned to fear mild dyspnea preceding the onset of severe dyspnea and developed anxiety during a context of unpredictable respiratory threat. Moreover, the data from study 2 indicate that individuals who fear arousal sensations show an increased attention allocation towards unexpected arousal sensations and higher threat appraisal when expecting arousal sensations. Increasing intensity of dyspnea as provoked in study 3 led to increased defensive respiratory responses that were associated with increased symptom reports in individuals with high compared to low fear of suffocation. Moreover, culminating dyspnea elicited repeated avoidance behavior preceded by increases in defensive respiratory mobilization. The analysis of repeated avoidance of increasing dyspnea in study 4 revealed that physiological fear responses might be involved in the initial initiation of this avoidance behavior while no indication of response preparation and physiological arousal was related to persistent avoidance.
Taken together, the present data suggest that the fear of suffocation, as well as the tendency to fear arousal sensations along with the predictability, expectation, or proximity of interoceptive threat, may increase the perceived threat and thus the anxious response to body sensations. Therefore, contextual and dispositional factors may set the stage for the culmination of body sensations into defensive action and might contribute to the development of pathological anxiety and fear of body sensations. The present findings are integrated into the current literature and discussed in relation to the development and maintenance of pathological anxiety and fear of body sensations.
Mind the gap: Information gaps and bridging options in assessing in-situ conservation achievements
(2008)
The biodiversity crisis has gained political attention on a global level. The “2010 Target” of the Convention on Biological Diversity (CBD) aims to significantly reduce the loss of biodiversity by 2010. In order to achieve this, a network of representative and effectively managed protected areas is to be established. The effectiveness of protected areas thus represents one indicator for progress towards the CBD’s 2010 Target. However, indicators require information. The present study, in a first step, reviews the availability of open access long-term ecological data for assessing protected area effectiveness. This review shows two parallel – though contradictory – phenomena: data overkill and data scarcity. While the number of online databases providing open access data on biodiversity has grown tremendously, no long-term ecological data for a larger set of protected areas can be openly accessed. Reasons for this data scarcity are discussed. Based on this lack of information, in a second step, a method to bridge information gaps through social science research is aspired. An innovative Conservation Success Framework is developed, which defines and relates conservation needs, conservation capacity and conservation actions, its three main components. The basic assumption is that conservation can only be successful where the conservation capacity exists that is required to implement the conservation actions determined by the conservation needs. The framework was used to develop open and closed questionnaires for application in two Mexican biosphere reserves, the Sierra Gorda and the Sierra de Manantlán. As "conservation success" is often immeasurable in protected areas in practice due to unspecific conservation objectives the term is for the case studies substituted by “conservation achievements”, i.e. clearly noticeable effects from conservation actions. Overall, almost 60 interviews were conducted with different stakeholder groups. The gained information is validated through social science research techniques, such as triangulation of perspectives and active and passive observation. Based on this, conservation needs are identified and conservation capacities summarised and discussed for both case study sites. Implemented conservation actions addressing identified conservation needs and conservation capacity constraints are then analysed. In addition, noticeable effects from conservation actions on the state of biodiversity at case study sites, i.e. the conservation achievements, are described. Where locally available, non-open access data (as opposing open access data) are used to verify the findings from the social science research. Identified conservation achievements at both case study sites are evident both from quantitative information (for example forest cover increase according to non-open access data) and qualitative information (for example perceived change in the occurrence of illegal activities according to interviews). In addition, rather “intangible” indicators that can only be revealed through qualitative surveys are identified for both sites. This study thus highlights the crucial importance of integrating different types of data, ecological and socio-economic, as well as quantitative and qualitative ones. The present study concludes with a series of recommendations 1) to local practitioners at the two case study sites, and 2) to the international conservation community. Local practitioners may benefit from the present study because its results provide for each site a) an overview of existing conservation needs and implemented conservation actions; b) an easy way to identify action gaps; c) a baseline to identify progress indicators; and d) an overview of diverse perspectives on the current effectiveness of the biosphere reserves. These benefits are considered of particular importance as they can be influential in the revision of the site’s management plans, which both are now approximately ten years old and will soon be revised. The international conservation community will not be able to make a clear statement in the year 2010 about the effectiveness of protected areas on a global level due to a lack of information and transparency. However, the year 2010 should not be considered an end point for measuring progress in in-situ conservation; instead protected area quality standards must be created, effectiveness evaluations institutionalised and efforts to foster regular reporting must continue. Consequently, a scheme of consolidated actions from local to national and international level is proposed that could help to sustainably bridge existing information gaps and close them on the long run. In the end, progress reporting on the effectiveness of protected areas, and other indicators, can only improve if different governance levels “mind the information gaps” in cooperation, until continued information gathering and sharing hopefully closes these gaps one day.
Dilated cardiomyopathy (DCM) is a myocardial disorder characterised by ventricular dilation with reduced left ventricular ejection fraction (LVEF). Immunoadsorption (IA) followed by immunoglobulin (IgG) substitution (IA/IgG) has been shown to be a promising therapeutic intervention to recover myocardial functions in DCM patients. The beneficial effects of IA/IgG therapy are associated with increased LVEF, decreased left ventricular inner diameter at diastole (LVIDd) and reduced myocardial inflammation. Despite knowing the cardiac benefits of IA/IgG, the precise molecular mechanism induced by therapy is still elusive. Additionally, only ≈60 % DCM patients treated with IA/IgG demonstrated improved heart function. Moreover, the reasons for this differential outcome among DCM patients after treatment have not been clearly understood. In this study, efforts were made to uncover the therapy induced proteomic changes in the heart of responders (relative change in LVEF ≤ 20%, LVEF < 5% absolute value) and non-responders using a global proteomic approach. Apart from it, proteomic profiling of endomyocardial biopsies and plasma was performed to find protein biomarker candidates which might be useful to distinguish responder and non-responder DCM patients before immunoadsorption therapy and support a selective and individualized treatment. To reveal therapy induced myocardial proteomic changes, endomyocardial biopsies of DCM patients before and after therapy were compared. LVEF increased (32 ± 8 to 45±7, p<0.002) and LVIDd decreased (66 ± 6 to 60±6, p<0.040) after therapy in responders, whereas non-responders did not show any significant changes in these clinical parameters. To address the changes in the myocardial proteome induced by therapy, a label-free proteomic approach was applied. The most prominent proteomic differences between both subgroups were observed in cytoskeletal, fibrosis, and extracellular matrix proteins. Therapy linked benefit in responders seems to be highly associated with the lower abundance of fibrotic and extracellular matrix proteins which seems to reflect a lower activity of transforming growth factor-β signaling. To elucidate proteomic differences between responders and non-responders at baseline, endomyocardial biopsies and plasma proteome profiling were performed. Responder and non-responder DCM patients did not show any significant differences in the clinical parameters (LVEF, LVIDd, age, inflammation, etc.) before IA/IgG therapy except for disease duration that was in tendency higher among non-responders. Proteomics profiling of endomyocardial biopsies revealed 54 differentially abundant proteins between responders and non-responders. Among those proteins, Protein S100-A8 and kininogen-1 was found higher whereas perilipin-4 was found lower abundant in responders. Plasma profiling of these subgroups revealed five proteins (S100-A8, S100-A9, C-Reactive protein, lipopolysaccharide-binding protein, and cysteine-rich secretory protein) displaying strong discriminative power between responders and non-responders. Higher abundance of Protein S100-A8 was observed in myocardium as well as in plasma among responders. Protein S100-A8 might be a potential candidate to distinguish responders and non-responders at baseline, and its potential utility at clinical levels must be evaluated. The last objective of the thesis was to establish a workflow for the relative quantitation of phosphopeptides for samples generally obtained in small amounts like myocardial biopsies. To address this question, optimization was performed with HL-1 cardiomyocytes using a PolyMAC phosphopeptide enrichment kit and the effect of TGF-β1 on the phosphoproteome was evaluated as a proof-of-principle study. Using only 200µg protein of each sample up to 2000 phosphopeptides with an efficiency of >90 percent could be covered. In total, upon TGF-β1 incubation alterations of 214, 92, and 53 phosphopeptides were observed after 1, 6 and 24 hours, respectively. Differentially altered phosphopeptides belonged to many signaling pathways including the ubiquitin-proteasome pathway, cytoskeletal regulation by Rho GTPase, calcium signaling, and TGF-β signaling. Thus, in this study a workflow for relative quantitation of phosphopeptides was established that may be later applied to precious biopsy samples. Along with this, TGF- β1 induced phosphoproteome was analysed in HL-1 cardiomyocytes.
Currently, plastic materials are an integral part of our lives, but their production mostly bases on fossil fuels or derivatives, which resources are decreasing. Extraction and processing of non-renewable resources have also negative impact on environment. One of the most promising and environmentally friendly approaches is use of microorganism. This PhD dissertation presents the non-conventional yeast Arxula adeninivorans as a host for production of bio-based and biodegradable poly(hydroxyalkanoates) plastics poly(hydroxybutyrate) and co-polymer poly(hydroxybutyrate-co-hydroxyvalerate). Additionally, the constructed yeast strain was able to secrete enantiomerically pure (R)-3-hydroxybutyric acid.
The production of PHAs requires three enzymes: β-ketothiolase, acetoacetyl-CoA reductase and PHA synthase. The strategy followed in this project was divided into two parts. While all three enzymes are responsible for intracellular production of PHA polymer, first two only lead to secretion of (R)-3-HB into culture media, which was used in a first stage of work to establish and optimize polymer production. Both, different bacterial strains and yeast A. adeninivorans were taken into account in screening of the genes encoding aforementioned enzymes. Bacterial genes were chemically synthesized using codon optimization pattern and endogenous genes were obtained using PCR and genomic DNA template from A. adeninivorans LS3 wild-type strain. Each gene was cloned into Xplor2 vector between TEF1 constitutive promoter and PHO5 terminator. Vector containing both thiolase and reductase genes was used for A. adeninivorans transformation.
The best combination of heterologous genes was overexpression of β-ketothiolase gene from Clostridium acetobutylicum and acetoacetyl-CoA reductase gene from Cupriavidus necator which led to secretion of 4.84 g L−1 (R)-3-HB, at a rate of 0.023 g L−1 h−1 over 214 h in shaking flask cultivation. Further optimization by fed-batch culturing with glucose as a carbon source did not improve (R)-3-HB secretion, but the rate of production was doubled to 0.043 g L−1 h−1 [3.78 g L−1 of (R)-3-HB at 89 h].
The product of acetoacetyl-CoA reductase is (R)-3-HB-CoA and further removing of CoA moiety is needed for acid secretion into culture media. A. adeninivorans is able to conduct this process without any additional modification but the conversion rate is unknown. Two thioesterases, cytosolic TesBp encoded by TesB gene from E. coli and mitochondrial ATes1p encoded by ATES1 gene from A. adeninivorans, were analysed to enhance secretion process. Additionally, a cytosolic version of ATES1 gene (ATES1cyt) was tested. All three genes were expressed in A. adeninivorans cells under TEF1 constitutive promoter together with thiolase and reductase genes. Despite detected enzymatic activity the yield of (R)-3-HB synthesis and secretion was not increased. Moreover, overexpressed thioesterases negatively influenced cell growth, indicating that they act on other metabolic components. The results provided two sets of information, first, the endogenous secretion system is sufficient for (R)-3-HB production; second, further screening of suitable genes needs to be performed.
Based on optimization of (R)-3-HB synthesis, thiolase gene (thl) from C. acetobutylicum and reductase gene (phaB) from C. necator were chosen to combine with PHA synthase gene (phaC) for creating the PHB-V producing strain. The PHA synthase expression module, containing TEF1 promoter and PHO5 terminator, was cloned into Xplor2 vector together with thiolase and reductase expression modules and used for A. adeninivorans transformation. The engineered strain accumulated up to 7.47% PHB of dcw. During the set of cells passaging A. adeninivorans lost the ability to accumulate polymer with maximal 23.1 % of primary accumulation level. Additionally, use of a vector including hygromycin B antibiotic resistance marker (instead of auxotrophic marker in Xplor2) did not improve polymer accumulation and stability.
To counteract the effect of loss of accumulation stability, phasin gene (phaP1), originated from C. necator, was introduce together with PHA pathway genes. First screening cultivations resulted in stabilizing of polymer production reaching 9.58 % PHB of dcw and only 12.0 % loss of production ability. Further experiments increased PHB content with 19.9% PHB of dcw (3.85 g L-1) after 180 h of cultivation using rich medium. Use of another thiolase gene, the second thiolase from C. necator (bktB), which theoretically should induce production of PHBV copolymer, led to accumulation only 11.4% PHB of dcw after 139 h and no PHV fraction was detected.
Variation of the ratio between flask volume and amount of media influences the level of aeration. Importantly, decrease of aeration level significantly increased polymer synthesis. Additionally, PHB-V copolymer accumulation has been induced by use of different carbon source co-substrates. Use of rich media supplemented with ethanol allow the strain with thl thiolase to accumulate up to 42.9 % PHB of dcw without PHV fraction and with bktB thiolase to 30.5 % PHB of dcw. Nevertheless, despite of lower total amount of polymer, supplementation with 1-propanol allow both strains to accumulate PHB-V copolymer with 7.30 %mol and 22.5 %mol of PHV for thl and bktB strains, respectively.
Optimization based on genetic engineering further enhanced polymer production yield led to exceeding of 50 % PHB-V of dcw. For doubling the gene dosage, PHA synthesizing strains of A. adeninivorans were again transformed with Xplor2 vector containing PHA pathway genes. Resulting strains exhibited twice the level of enzymatic activities of thiolase and reductase compared with strains transformed once with expression vector. In a shaking flask experiment the strain transformed twice with vector containing bktB thiolase reached after 240 h 52.1% PHB-V of dcw (10.8 g L-1) with 12.3 %mol of PHV fraction which is the highest level found in yeast. As another genetic approach, a fusion strain has been created. Two different strains have been established and merged using protoplast fusion technique. Doubling of genetic material resulted in similar level of copolymer produced by Arxula as in former experiments (50.2% of dcw, 10.7 g L-1).
Culture conditions were optimized in controllable cultivation using fed-batch mode. Although optimal oxygen and pH level and continuous carbon source and nitrogen feeding were maintained, final polymer level in % of dry mass was around three times lower than for shaking flask experiment. Nevertheless, efficient growth of Arxula in fed-batch mode led to increase of total copolymer level in g L-1 (16.5 g L-1 compare to 10.8 g L-1 for shaking flasks) showing the feasibility of using Arxula strain for up-scaling production of copolymer.
Acetyl-CoA is a main precursor in synthesis of PHB-V copolymer and change of its pool was investigated. ATP citrate lyase is a cytosolic enzyme converting citrate into oxaloacetate and acetyl-CoA, supporting the biosynthesis of fatty acids. Two genes encoding Acl subunits from Aspergillus nidulans (AnAcl1 and AnAcl2) were again cloned into Xplor2 vector and transformed into A. adeninivorans PHA producing strain. Despite of higher enzymatic activity of AnAclp, accumulation of polymer was around three times higher for control without expression of lyase genes. Expectedly, the strain expressing AnAcl1/2 genes accumulated larger amount of each stearic, palmitic and oleic acid in both standard and fatty acid inducing conditions (lower nitrogen level). Thus, overexpression of AnAcl1/2 genes in A. adeninevorans cells may improve biosynthesis of fatty acids but is ineffective for PHB polymer accumulation.
The aim of the project was use of starch-based media, manufactured as by-products, for polymer production. Genetically engineered Arxula strains were cultivated using these media instead of glucose-based media. Although yeast cells were both able to secrete (R)-3-HB and to accumulate PHB, the yield was lower than for previous media. Additionally, only trace of PHV was found at the end of cultivation time when 1-propanol was supplemented. Obtained results showed that use of cheaper media is a promising approach to decrease production costs but further optimization needs to be performed especially for extended scale of production.
Determination of produced copolymer has been done based on microscopic analysis and studies of physical and chemical properties. Results revealed that Arxula accumulated PHA polymer in cytosolic granules with a similar size range compared to the ones produced by bacteria. The physicochemical study showed that produced polymer exhibited slightly different properties in comparison to bacterial polymer with similar content of PHV, i.e. very-low molecular mass, higher melting and glass transition temperature.
All above results showed that A. adeninivorans is a promising host for PHB-V production. Expression of phasin greatly increased production and stability of polymer, which led to an accumulation level never found before in yeast. Further optimization in higher production scale using cheap starch-based media may establish Arxula strain as a valuable tool for industrial production of PHB-V copolymer.
Orthohantaviruses are rodent-borne pathogens distributed all over the world, which do not cause visible disease in their reservoir host. Puumala orthohantavirus (PUUV) causes most human hantavirus disease cases in Europe and is transmitted by the bank vole (Clethrionomys glareolus). Hantaviruses have a tri-segmented genome consisting of the large (L) segment, coding for the RNA-dependent RNA polymerase (RdRP), the medium (M) segment, encoding the glycoproteins, and the small (S) segment. The S-segment contains two major overlapping open reading frames (ORF) coding for the nucleocapsid (N) protein and a non-structural (NSs) protein, a putative type I interferon (IFN-I) antagonist. To date, pathogenesis and reservoir host adaptation of hantaviruses are poorly understood due to missing adequate cell culture and animal models.
In contrast to previous studies, in this work, data from spring and summer 2019 indicated a high vole abundance, a high PUUV prevalence in voles and high human incidence for some endemic regions in Germany, but elsewhere values were low to moderate. Regional and local human health institutions need to be aware about the heterogeneous distribution of human PUUV infection risk.
For a better understanding of virus-host associations, two novel cell lines from bank voles and common voles each were generated and their susceptibility and replication capacities for a variety of zoonotic and non-zoonotic viruses were analyzed. The PUUV strain Vranica/Hällnäs showed efficient replication in a new bank vole kidney cell line, but not in four other cell lines of bank and common voles. Vice versa, Tula orthohantavirus (TULV) replicated in the kidney cell line of common voles, but was hampered in its replication in other cell lines. Several viruses, such as Cowpox virus, Vaccinia virus, Rift Valley fever virus, and Encephalomyocarditis virus 1 replicated in all four cell lines. West Nile virus, Usutu virus, Sindbis virus and Tick-borne encephalitis virus replicated only in a part of the cell lines. These results indicate a tissue or species specific tropism for many of the tested viruses and the potential value of vole cell lines to address such questions in detail.
Using one of these new cell lines, the first German PUUV strains were isolated from bank voles caught in the highly endemic region around Osnabrück. Complete genomes were determined by target-enrichment-mediated high-throughput sequencing from original lung tissue, after isolation and after additional passaging in VeroE6 cells and a bank vole-derived kidney cell line. Different single amino acid substitutions were observed in the RdRP of the two stable PUUV isolates. The PUUV strain isolated on VeroE6 cells showed a lower titer when propagated on bank vole cells compared to VeroE6 cells. Additionally, glycoprotein precursor (GPC)-derived virus-like particles of a German PUUV strain from the same region allowed the generation of monoclonal antibodies that reacted with the isolated PUUV strains.
To investigate the role of PUUV and other vole-borne hantavirus NSs proteins, the evolution of the NSs and N encoding sequences was investigated by a field study in bank voles and the NSs sequences were characterized in vitro for their inhibitory effect on the human interferon-β promoter. Analysis of blood and lung samples of 851 bank voles trapped during 2010-2014 in Baden-Wuerttemberg and North Rhine-Westphalia resulted in detection of 27.8% PUUV-specific antibody positive bank voles, whereas in 22.3% PUUV-specific RNA was detected. In the hantavirus outbreak years 2010 and 2012 PUUV prevalence in bank voles was higher compared to 2011, 2013 and 2014. Sequences of the S segment of all positive bank voles showed amino acid and nucleotide sequence types of the NSs-ORF with temporal and/or local variation, whereas the N-ORF was highly conserved. One sequence type persisted over the whole observation period in both regions. The NSs coding sequence was highly divergent among regional bank vole populations in the outbreak year 2012.
Transfection experiments resulted in the detection of different products of the NSs-ORF of PUUV, TULV, Prospect Hill and Khabarovsk orthohantaviruses, due to translation initiation at different methionine codons along the coding sequence. Using luciferase reporter assays, the NSs proteins of PUUV, TULV, Prospect Hill and Khabarovsk orthohantaviruses showed inhibition of IFN-I induction of up to 70%, whereas Sin Nombre and Andes orthohantavirus NSs proteins showed a reduced effect compared to the other NSs proteins. The first 20 amino acids of the N-terminal region of PUUV NSs were found to be crucial for IFN-I promoter inhibition.
In conclusion, the newly established cell lines, antibodies, reporter assays and PUUV isolates are highly valuable tools for future hantavirus research. The activity of PUUV NSs protein in human cells contributes to our understanding of virus-host interactions and highlights the importance of corresponding future reservoir host studies. Hantavirus surveillance studies showed the necessity for timely information of the potential human PUUV infection risk to public health institutions in endemic areas to initiate appropriate actions.
Streptococcus pneumoniae (pneumococci) and Staphylococcus aureus (S. aureus) are human-specific commensals of the upper respiratory tract. Every individual is asymptomatically colonized with both bacteria at least once in their life-time. The opportunistic pathogens can affect further organs and invade into deeper tissue. The occupation of normally sterile niches of the human body with the bacteria can lead to local infections such as sinusitis, otitis media and abscesses, or to life-threatening diseases like pneumonia, meningitis or sepsis. A strong interaction between the bacterium and the respiratory epithelial cells is a prerequisite for a successful colonization. This interaction is ensured by bacterial surface proteins, so called adhesins. The binding of the adhesins to the epithelial lineage occurs predominantly indirectly via components of the extracellular matrix (ECM), but also directly to cellular receptors. Pneumococci and S. aureus bind to various ECM glycoproteins, amongst others: fibronectin, fibrinogen, vitronectin, and collagen. Also binding of both pathogens to human thrombospondin-1 has been described. Thrombospondin-1 is mainly stored in the α-granula of thrombocytes (platelets) and released into the circulation upon activation. However, thrombospondin-1 is also produced and secreted by other cell types like endothelial cells, macrophages, and fibroblasts, which gets subsequently incorporated as component into the ECM. So far, no thrombosponin-1-binding adhesins of pneumococci were identified. PspC, Hic, and PavB are important surface-localized virulence factors, which were shown to interact with human ECM and plasma proteins. PspC and Hic bind to vitronectin and factor H, which inhibits the complement cascade of the human immune system. PavB interacts with fibronectin and plasminogen, and a pavB-deficient mutant of S. pneumoniae showed diminished capacity in colonization in a mouse model. Among the surface proteins of S. aureus, only Eap was identified as thrombospondin-1-binding adhesin. Beyond colonization, pneumococci and S. aureus can enter the blood circulation, interact with platelets, and cause their activation. The aggregation of platelets, especially initiated by S. aureus, plays an important role in the clinic, because most of the septic patients develop thrombocytopenia. Surface localized factors of
S. pneumoniae triggering platelet activation are unknown to date. In contrast, few proteins of S. aureus with potential to activate platelets, including Eap, were identified previously.
This study identified the surface proteins PavB, PspC, and Hic of S. pneumoniae as specific ligands of the human thrombospondin-1. Flow cytometric, surface plasmon resonance spectroscopic and immunological analyses revealed interactions between the pneumococcal proteins and soluble as well as immobilized thrombospondin-1. The use of specific pneumococcal deletion mutants verified the importance of the three virulence factors as binding partners of soluble thrombospondin-1. The results suggest that pneumococci are capable of acquiring soluble thrombospondin-1 from blood as well as utilizing immobilized glycoprotein of the ECM as substrate for adhesion. Furthermore, the thrombospondin-1-binding domain within the pneumococcal proteins was analyzed by use of recombinant fragments of PavB, PspC, and Hic. The binding capacity of thrombospondin-1 increased proportionally with the amount of repetitive sequences in PavB and PspC, and the length of the α-helical region within the Hic molecule. The binding behavior of thrombospondin-1 towards PavB and PspC is comparable with that of the ECM proteins vitronectin and fibronectin, but is unique towards Hic.
The localization of the binding domain of the adhesins within the thrompospondin-1 molecule occurred via use of glycosaminoglycans as competitive inhibitors for the interaction. The results suggest that the pneumococcal proteins Hic and PspC target the identical binding region within thrombospondin-1, which differs from the binding domain for PavB. However, all three virulence factors seem to bind in the N-terminal part of thrombospondin-1.
Two-dimensional gel electrophoresis, thrombospondin-1 overlay assay and subsequent mass spectrometric analysis identified AtlA of S. aureus as a surface localized interaction partner of human thrombospondin-1. Moreover, a vitronectin binding activity for AtlA was determined. Immunological and surface plasmon resonance binding studies with recombinant AtlA fragments revealed that interactions with both matrix proteins is mediated via the C-terminal located repeats R1R2 of the AtlA amidase domain. Binding of thrombospondin-1 and vitronectin occurred not simultaneously, due to a competitive inhibition.
The second part of the study focused on the activation of human platelets by recombinant pneumococcal and staphylococcal proteins. In total, 28 proteins of S. pneumoniae and 52 proteins of S. aureus were incubated with human platelets. The activation of the cells was detected by flow cytometry using the activation markers P-selectin and the dimerization of the integrin αIIbβIII. The proteins CbpL, PsaA, PavA, and SP_0899 of S. pneumoniae induced platelet activation, however, the detailed mechanism has to be deciphered in further studies. Furthermore, the secreted proteins CHIPS, FLIPr, and AtlA of S. aureus were discovered as inductors for the activation of platelets. In addition, the domains of AtlA and Eap, crucial for platelet activation, were narrowed down. Interestingly, CHIPS, FLIPr, and Eap were described as inhibitors of neutrophil recruitment. Platelets are recently recognized as immune cells, due to the expression of immune receptors. The data obtained in this study highlight a comprehensive spectrum of effects of the S. aureus proteins towards different type of immune cells. Besides the activation of platelets in suspension buffer and plasma, the aggregation of platelets in whole blood was triggered by the proteins CHIPS, AtlA, and Eap. These results suggest a contribution of the proteins during the S. aureus-induced infectious endocarditis. Secretion of the platelet activating virulence factors, which were identified within this study, might represent a pathogenic strategy during S. aureus infection in which a direct contact between S. aureus and platelets is not required or even avoided.
In conclusion, PavB, PspC, and Hic of S. pneumoniae and AtlA of S. aureus were identified as interaction partners of human thrombospondin-1. Furthermore, CHIPS, FLIPr, AtlA, and Eap were characterized as platelet activators. This study provides candidates for the development of protein-based vaccines, to prevent bacterial colonization and to neutralize secreted pathogenic factors.
LPAIV H9N2 and HPAIV H5N8 clade 2.3.4.4 viruses have been frequently isolated from domestic and wild birds in Germany and they are endemic in poultry worldwide. H9N2 is known to donate gene segments to other AIV with high case fatality rate in humans (e.g. H5N1, H7N9). Similarly, H5N8 devastated poultry worldwide since 2014 and has been recently isolated from humans. Therefore, it is important to understand the genetic predisposition for adaptation of H9N2 and H5N8 AIV in poultry and mammals. In the first publication, we focused on the variable hemagglutinin cleavage site (HACS) of European and Non-European H9N2 viruses, since the HACS is a main virulence determinant of AIV in birds. We found a preferential substitution of non-basic amino acids (G, A, N, S, D, K) in the HACS at position 319 of European H9N2 viruses compared to non-European H9N2 viruses. Recombinant viruses carrying different non-basic amino acids in the HACS modulated replication in vitro. While these non-basic amino acids did not affect virulence or transmission in chickens, they modulated virulence and replication in turkeys. Moreover, H9N2 viruses with non-basic amino acids in the HACS were able to replicate in mammalian brain cells for multiple cycles even without trypsin. In the second publication, we addressed the question whether reassortment between two recent German H9N2 and H5N8 clade 2.3.4.4. B viruses is possible and analysed the impact on virus fitness in mammals and birds. We found that H9N2 PB1 and NP segments were not compatible to generate infectious H5N8 viruses and this incompatibility was due to mutations outside the packaging region. However, H9N2 NS alone or in combination with PB2 and PA significantly increased replication of H5N8 in human cells. Moreover, H9N2 PB2, PA and/or NS segments increased virulence of H5N8 in mice. Interestingly, in chickens, reassortment with H9N2 gene segments, particularly NS, partially or fully impaired chicken-to-chicken transmission. These results indicate that the evolution of H9N2/H5N8 reassortants showing high virulence for mammals is unlikely to occur in chickens. In the third publication, we focused on the NS1 protein of different HPAIV H5N8 clade 2.3.4.4 viruses from 2013 to 2019 and studied the impact of its C-terminus (CTE) variation on virus fitness in chickens and ducks. Our findings revealed a preferential selection for a certain NS1 CTE length in 2.3.4.4. H5N8 clade A (237 aa) and B (217 aa) viruses over the common length of 230 aa. Indeed, the NS1 CTE can affect virus virulence and pathogenesis in a species and virus clade dependent manner. In chickens, although there was no impact on virulence, NS1 CTE of H5N8-A and H5N8-B, regardless of the length, have evolved towards higher efficiency to block the IFN response. In ducks, NS1 CTE contributed to efficient transmission, replication and high virulence of H5N8-B. In the fourth publication, we assessed the impact of variable length of NS1 on H5N8 virus replication in human cells and virulence in mice. We showed that NS1 of H5N8-B virus unlike the vast majority of NS1 of AIV, shared preferences for short NS1 similar to human and zoonotic influenza viruses. This virus (i) was able to efficiently block IFN and apoptosis induction which might be the first steps for efficient adaptation to human cells and (ii) without prior adaptation replicated at higher levels and was more virulent in mice than H5N8-A. The virulence of the latter virus increased after shortening the NS1 similar to H5N8-B virus. Therefore, it is conceivable that truncation in NS1 is a determinant for adaptation of H5N8 in mammals irrespective of its impact on virus fitness in poultry. Findings in this dissertation indicated that HA mutations in the European H9N2 and NS1 variations in H5N8 viruses play a role in virus fitness in poultry and/or mammals. These results improve our current understanding for AIV adaptation and are useful to assess the potential of these viruses to infect mammals.
Background: A large body of research indicates that the cognitions individuals have
about their own age and aging, so called self-perceptions of aging (SPA), predict health and
wellbeing in later life. However, much less is known about associations of SPA with
developmental correlates such as personality. Some initial studies have found cross-sectional
and longitudinal associations of the Big Five traits (openness to experience,
conscientiousness, extraversion, agreeableness, and neuroticism) with SPA. Building on these
findings, this thesis aimed at advancing knowledge on associations of personality with SPA.
To this end, cross-sectional associations of the meta-traits of agency, i.e., a focus on the self,
and communion, i.e., a focus on others, with SPA were examined in study 1, and longitudinal
associations of agentic and communal personal values with SPA were examined in study 2.
Study 3 aimed at expanding findings of previous studies on associations of SPA with selfreported
physical function to an objective indicator of physical function, namely, gait pattern.
In all studies, SPA were treated as a multidimensional construct comprising gains and losses.
Methods: Study 1 was based on data of 154 adults aged 75 and older that were
recruited in hospital. Data was collected one month after recruitment. In regression analyses,
associations of agentic and communal traits with SPA beyond health were examined. Study 2
was based on data of 6,089 adults aged 40 and older enrolled in the German Ageing Survey
(DEAS). Multiple regression analyses were used to test whether personal value priority
predicted change in SPA over three years beyond age stereotypes. For study 3, latent profile
analysis was employed to detect gait patterns based on data of 150 adults aged 70 and older
collected via an automated walkway at participants’ regular speed and individual maximum
speed. In a next step, associations of SPA with gait patterns beyond personality traits were
investigated in binary logistic regressions.
Results: Agentic and communal personality traits were associated with gain-, but not
loss-related SPA when controlling for health (study 1). In study 2, the value priority of
openness to change (self-direction, stimulation) predicted more gain-related SPA three years
later, while the value priority of conservation (tradition, security) was negatively associated
with gain-related SPA. The value priority of self-enhancement (achievement, power) was
associated with more loss-related SPA three years later. Finally, the value priority of selftranscendence
(universalism, benevolence), i.e. a concern for the well-being of others, was
associated with more gain- and less loss-related SPA at follow-up. In study 3, latent profile
analyses distinguished two groups with different gait patterns in both gait speed conditions.
One group exhibited a slower and less well-coordinated gait pattern, which reflected
functional limitations. The other group exhibited a faster and well-coordinated gait pattern,
which reflected better physical function. More loss-, but not gain-related SPA were associated
with higher likelihood to exhibit a functionally limited gait pattern at regular speed.
Conversely, gain- but not loss-related SPA were associated with higher likelihood to exhibit a
fit gait pattern at individual maximum speed.
Conclusion: Results of this thesis have three main implications for research on SPA.
First, agency and communion may constitute useful dimensions for further investigating SPA
domains, as both were associated with SPA in study 1. Second, findings of study 2 point to
the role of motivation for SPA that needs to be further explored. Third, findings of study 3
indicate that SPA are not only associated with self-reported, but also objectively measured
physical function, which stresses the importance of SPA for health in later life. As a practical
implication, the findings presented here suggest that interventions on SPA should consider
participants’ personality, both on the level of traits and values.
A central point of this thesis is the investigation of surface structure and surface forces, which are created by single layers of linear polyelectrolytes (PE). In detail, the properties of cationic poly(allylamine)hydrochloride (PAH) and poly-l-lysine (PLL) and anionic sodium poly(styrene sulfonate) (PSS) are determined, which have been physisorbed onto oppositely charged silica surfaces in presence of a predefined salt concentration IAds. For these investigations, a new averaging method for colloidal probe (CP) force profiles is developed, which leads to an ultimate force resolution of 1 pN after the data processing, (signal to noise ratio of > 1000). Furthermore, a new kind of tapping mode imaging is presented (so called colloidal probe tapping mode, CPTM), which uses a CP instead of a sharp tip and hence which allows to resolve lateral inhomogeneously distributed surface forces. The basics to understand such-like obtained tapping mode images are developed. For adsorption from salt-free solution (IAds = 0) the dominance of an electrostatic double layer repulsion is observed, which is commonly attributed to the adsorption of the PE chains into a rather flat and compact layer and which is in full agreement with theoretical predictions and enormous experimental data available in literature. However, even a small addition of salt to the deposition solution (i.e. IAds > 1 mM NaCl) introduces a new contribution to the surface force, which is attributed to PE chains that are non-flatly physisorbed. Using scaling considerations, it is shown for all investigated PE that this non-flat conformation can be described by brush-like chain adsorption (cf. Section 3.3.5); other conformations like mushroom or pancake are excluded (cf. Section 5.3). Interestingly, these non-flatly physisorbed chains combine properties of neutral and PE brushes: (i) The force is very well described by the theory of Alexander and de Gennes (AdG, cf. Section 5.4). By fitting the AdG force law to the data, it is possible to determine the (brush) thickness L of the PE layer and the average distance s between brush-like physisorbed chains. Although the chains are charged the electrostatic contribution to the surface forces is too small to be noticeable (cf. Section 5.4.2). (ii) The thickness L of this PE layer is much larger compared to the compact layer (observed for salt-free adsorption) and is also subject to a pronounced swelling and shrinking if the bulk salt concentration I is decreased or increased, respectively. Surprisingly, all measurements indicate that L follows a scaling law known for salted end-grafted PE brushes, i.e. L ~ N (I s^2)^(-1/3) (with N denoting the degree of polymerization). Furthermore, the osmotic brush phase is never observed in the experiments, but chain stretching up to 1 / 3 of the contour length is regularly achieved. CPTM imaging applied to PSS shows that the brush-like physisorbed chains are not homogenously distributed over the surface, but form brush domains which coexist with flatly physisorbed chains (cf. sections 5.5 and 5.6). This clearly shows that PSS generally physisorbs in two distinct phases, which differ in conformation (flat vs. brush) and the surface force caused (electrostatic vs. steric repulsion). The force profile of the two phase system is in good approximation simply the superposition of a steric and an electrostatic repulsion, whereby their respective contribution to the composed force profile is given by their area fraction. The quantitative analysis reveals that L and s of the brush phase are independent on IAds. This is remarkable, as a change in IAds is known to induce a continuous transition between a stretched (low IAds) and coiled chain conformation (high IAds) in the deposition solution (cf. [Fleer1993, Yashiro2002]). Hence, one can conclude that the conformation in solution does not necessarily correspond to the conformation after adsorption. It is also shown that the area fraction A of the brush domains strongly depends on N and IAds. For example, for constant N the scaling relation A ~ sqrt(IAds) is determined, which is very similar to the common observation that the surface coverage %Gamma of adsorbed PE layers increases also with %Gamma ~ sqrt(IAds) [Schmitt1996, Cosgrove1986, Ahrens2001, Yim2000, Gopinadhan2007, Cornelson2010]. This suggest that brush-like physisorbed PE chains are responsible for the increase in %Gamma. In fact, Section 5.6 shows that the mass of the brush phase is approx. 0.5 mg/m² which is comparable to the increase in %Gamma reported in literature for IAds = 1 M NaCl [Cosgrove1986, Schmitt1996, Ahrens2001]. As a change in IAds does not affect L and s, but solely the brush area fraction A, it is argued in Section 5.6 that an increase in IAds can be understood as a phase transition from the (disordered) flat phase towards the (ordered and extended) brush phase. Here, further theoretical considerations would be desirable.
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.
Introduction:
The amniotic fluid – as the medium surrounding the fetus, it is holding a crucial role in the maintenance and development of a successful pregnancy. While providing mechanical protection to the fetus, it also offers considerable immunological defense. In fact, it is known that the amniotic fluid plays a significant role in the innate immune system, as many of its corresponding substances show substantial antimicrobial function. Also, components of the adaptive immune system, including B cells, have been described within the amniotic fluid. An increase of immune cells in the amniotic fluid in cases of intra-amniotic infection indicates their involvement in inflammation-related pathologies of pregnancy. However, especially B cells in the amniotic fluid have not yet been thoroughly investigated.
The aim of this work is a deeper examination of the B-lymphocytes within the amniotic fluid. Based on the analysis of surface molecules this includes their phenotype, origin and func-tion. In the long term this could substantiate our understanding of intraamniotic inflammation and or infection, which are casually linked with preterm birth, fetal inflammatory response syndrome and fetal morbidity.
This, in turn, could pave the way for potential diagnostic methods and treatments.
Methods:
For all experiments 8-12-weeks-old pregnant mice were sacrificed at day 14 of pregnancy. The amniotic fluid was collected and specific cell subsets were isolated using MACS cell separation. Cells were then co-cultured with a bone marrow stromal cell line and stimulated in vitro.
The analysis of the population distribution and cytokine production was performed by flow cytometry. To analyze IgM-levels in the supernatant of the co culture, ELISA was used. Statistical analysis was performed using GraphPad Prism software.
Results:
The amniotic fluid contains different developmental stages of B cells, which most likely are of fetal origin. This is supported by the expression of paternal surface markers. An extensive proliferation and switch towards a more mature phenotype upon co-culture shows that the immature subsets of amniotic fluid B cells are able to expand and mature in vitro. Amniotic
fluid B cells spontaneously produce IgM and show functional adaption upon in vitro stimula-tion as evidenced by the increase of cell activation markers.
Conclusion:
For the first time a deep investigation of B-cells within the amniotic fluid was performed, covering phenotype and cell functionality. This work shows that there is a B cell compartment within the amniotic fluid, which, to a certain extent, is able to mature and gain functionality when exposed to external stimuli. This supports the hypothesis of the amniotic fluid as crucial immunological line of defense against inflammatory and infectious challenges during pregnancy.
Myxomycetes are protists belonging to the super-group Amoebozoa. The traditional taxonomic system, which is now largely outdated by molecular studies, recognizes five orders: Liceales, Trichiales, Physarales, Stemonitales and Echinosteliales. Molecular phylogenies revealed two basal clades: Physarales and Stemonitales (the so-called dark-spored myxomycetes) are the first; the other above-mentioned orders form the second (the bright-spored myxomycetes). However, except for Echinosteliales none of the traditional orders appears to be monophyletic in the traditionally used delimitation. The dark-spored myxomycetes encompass the majority of the described morphospecies. Due to the high genetic divergence in DNA sequences between the bright- and dark-spored myxomycetes, only the latter are considered in this dissertation. Historically myxomycetes have been described as fungi, due to their macroscopically visible fructifications which, though considerably smaller, resemble those of fungi. These fruit bodies provide enough morphological traits to support a morphological species concept with currently ca. 1000 species described. Therefore diversity studies of myxomycetes have been conducted for over 200 years and a substantial body of data on ecology and distribution of these fructifications exist. From these studies myxomycetes are known to form often distinct communities across terrestrial ecosystems with highly specific habitat requirements, such as snowbanks (nivicolous), herbivore dung (coprophilous) or decaying wood (xylophilous). However knowledge on the myxamoebae – the trophic life stage of the myxomycetes – is very scarce. Only recent advances in molecular techniques such as direct species identification based on DNA sequences from environmental samples (ePCR), have made studies of myxamoebae (and other microbes) possible. From these first molecular based studies myxomycetes are currently estimated to account for between 5 to almost 50% of all soil amoebae, and have been shown to be present in a wide variety of soils. To fully take advantage of these new methods, a molecular DNA marker needs to be established as well as a reference sequence database. The usability of a DNA marker gene depends on its ability to separate species by a distinction between intra- and interspecific divergence between sequences of the same and related species, the so-called ‘barcoding gap’.
The first part of this thesis (article I and II) deals with the subject of establishing such a DNA marker and database, and in doing so touches upon the subject of ‘what is a myxomycetes species?’
A total of 1 200 specimens were compiled into a reference database (the largest database to date of dark-spored myxomycetes). The genetic distance from sequence-to-sequence was used to assess genetic clade structures within morphospecies and putative biospecies (sexually isolated linages) were identified. The result was an estimate of hidden diversity, exceeding that of described morphospecies by 99%. The optimum sequence similarity threshold for OTU-picking (genetic species differentiation, denoted Operational Taxonomic Unit) with the used SSU marker was identified as 99.1% similarity.
The second part of this thesis (article III and IV) presents ecological studies conducted with NGS (ePCR) in which the established threshold and database are applied and are demonstrated to provide reliable and novel insights into the soil myxamoebae community. It is investigated whether the occurrence of fruit bodies reflects the distribution of soil myxamoebae, and the research questions ‘do myxomycetes show broader realized niches as soil amoebae than as fructifications?’ and ‘are myxamoebae distributions correlated to potential prey organisms (fungi and bacteria)?’ are investigated.
In the ecological study presented in article III parallel metabarcoding of bacteria, fungi and dark-spored myxomycete was used for the first time in a joint approach to analyze the communities from an elevational transect in the northern limestone German Alps (48 soil samples). Illumina sequencing of the soil samples revealed 1.68 Mio sequences of a section of the rRNA gene, which were assigned to 578 operational taxonomic units (OTU) from myxomycetes. These show a high similarity (>98%) to 42 different morphospecies (the respective figures for bacteria and fungi were 2.16/5710/215 and 3.68/6133/260, respectively). Multivariate analyses were carried out to disentangle microbial interplay and to identify the main environmental parameters determining the distribution of myxamoebae and thus setting the boundaries for their ecological niches. Potential interactions between the three target organisms were analysed by integrating community composition and phylogenetic diversity with environmental parameters. We identified niche differentiation for all three communities (bacteria, fungi and myxamoebae) which was strongly driven by the vegetation. Bacteria and fungi displayed similar community responses, driven by symbiont species and plant substrate quality. Myxamoebae showed a more patchy distribution, though still clearly stratified among genera, which seemed to be a response to both structural properties of the habitat and specific bacterial taxa. In addition we find an altitudinal species turn-over for all three communities, most likely explained by adaptation to harsh environmental conditions. Finally a high number of myxomycetes OTUs (associated with the genus Lamproderma) not currently represented in our reference database were found, representing potentially novel species. This study is the first to report niche differentiation between the guild of nivicolous (“snowbank”) myxomycetes and thus fine-scale niche differentiation among a predatory soil protist; identifying both potential food preferences and antagonistic interactions with specific bacterial taxa.
Finally, the second ecological study (article IV) focuses on comparing the distribution of myxamoebae revealed by ePCR of soil samples with fructifications collected from the same area (714 specimens determined to 30 morphospecies, which form 70 unique ribotypes that can be assigned to 45 ribotype clusters using a 99.1% similarity threshold). The study found a strong coherency between the two inventories, though with species specific relative differences in abundance, which can in part be attributed to the visibility of the fructifications. In addition, a year to year comparison of fructification records gives support to the hypothesis that the abundance of fructifications depends strongly on the onset of snowfall in the previous autumn and the soil temperature regime throughout the winter.
Responses of bovine and human neutrophils to members of the Mycobacterium tuberculosis complex
(2023)
PMN are one of the most important cells of the innate immune system and are responsible for fast clearance of invading pathogens in most circumstances. The role of human PMN during mycobacterial infection have been widely studied. Nevertheless, there are contradicting results regarding their role in protection or pathology during TB. Similar studies focusing on bovine PMN and their role in M. bovis infection remain understudied. Also, not much is known about attenuation of M. tb in cattle and responses of PMN to this MTBC member.
The major aims of this study were to i) gain insights into bovine PMN biology and the cellular processes triggered by challenge with virulent mycobacteria and to ii) find out whether interspecies differences result in different outcomes upon in vitro challenge. In the first part of the work, a new isolation method for bovine PMN from whole blood was developed. Human and bovine PMN have different buoyant properties and hence need to be isolated using different procedures. The magnetic isolation method developed within this thesis is robust and results in very good yields of highly pure, viable bovine PMN populations. This is extremely advantageous and indispensable for downstream functional assays that are required to be performed on a single day.
The second goal of this study was to compare and contrast the functional differences between bovine and human PMN upon BCG infection. The findings reveal for the first time that human PMN phagocytose more BCG in comparison to bovine counterparts. Non-opsonized bacteria were internalized via the lectin-like C-domain, require cholesterol and an active cytoskeleton in human PMN, whereas opsonized bacteria entered cells via the CR3 and, in particular, CD11b. It remains unresolved why bovine PMN reacted differently, notably phagocytosis remained unaltered, to various treatments, including blocking monoclonal antibodies to CD11b and chemical inhibitors altering the cell membrane. Nonetheless, the increased uptake of BCG by human PMN correlates to more potent response of these cells in functional assays in comparison to bovine PMN. No PMN intrinsic differences were found in the basal cholesterol content. Comparative assays with the virulent strains would be essential in order to generalize these observations.
The third aim was to investigate the responses of bovine PMN to BCG, M. tb and M. bovis. While there was no difference in uptake between BCG and M. tb, serum opsonized BCG was taken up at a higher amount. This finding suggests differential binding of bacterial epitopes to host cell receptors which modulates mycobacteria uptake. However, between the virulent strains M. tb and M. bovis, the human-adapted bacillus was phagocytosed at a higher rate which hints towards the possibility of rapid recognition and clearance of M. tb in bovine host thereby possibly preventing pathology. The release of selective cytokines by PMN post infection with the virulent strains offers baseline information relevant for processes that probably occur in vivo. This work for the first time provides insights into responses of bovine PMN to mycobacteria in a two-tier approach: by cross-species analysis of PMN responses to selected mycobacterium and by head-to-head analysis of bovine PMN to animal-adapted and human-adapted mycobacteria.
As a prospect for future research in bovine PMN biology in the context of mycobacterial infection, it would be highly advantageous to compare the subcellular localization of M. tb and M. bovis in bovine PMN using confocal and/or electron microscopy. This analysis would confer proof on attachment or internalization of mycobacteria by PMN and identify the features of the mycobacteria-containing compartments. Also, in-depth investigations of additional entry pathways for the pathogen in bovine cells would be informative for unlocking downstream cell signaling events. In addition, PMN viability studies will be meaningful particularly in bovine PMN challenged with M. bovis and M. tb, given the impact of death patterns on tissue pathology. Current results and follow up studies will contribute to the understanding of the roles of PMN in controlling elimination or growth of M. bovis and M. tb in cattle.
Coding constraints imposed by the very small genome sizes of negative-strand RNA viruses (NSVs) have led to the development of numerous strategies that increase viral protein diversity, enabling the virus to both establish a productive viral replication cycle and effectively control the host antiviral response. Arenaviruses are no exception to this, and previous findings have demonstrated that the nucleoprotein (NP) of the highly pathogenic Junín virus (JUNV) exists as three additional N-terminally truncated isoforms of 53 kD (NP53kD), 47 kD (NP47kD), and 40 kD (NP40kD). The two smaller isoforms (i.e. NP47kD and NP40kD) have been characterized as products of caspase cleavage, which appears to serve a decoy function to inhibit apoptosis induction. However, whether they have additional functions in the viral replication cycle remains unknown. Further, the origin and function of NP53kD has not yet been described.
In order to first identify the mechanism responsible for production of the NP53kD variant, a possible role of additional caspase cleavage sites was first excluded using a site mutagenesis approach. Subsequently, alanine mutagenesis was then used to identify a region responsible for NP53kD production. As a result, three methionine residues were identified within the characterized sequence segment of NP, linking the production of NP53kD to an alternative in-frame translation initiation. Further site-directed mutagenesis of the previously identified putative in-frame methionine codons (i.e. M78, M80 and M100) finally led to the identification of translation initiation at M80 as being predominantly responsible for the production of NP53kD. Once the identity of all three NP isoforms was known, it was then of further interest to more deeply characterize their functional roles. Consistent with the N-terminal domain containing RNA binding and homotrimerization motifs that are relevant for the viral RNA synthesis process, it could be demonstrated that all three truncated NP isoforms lost the ability to support viral RNA synthesis in a minigenome assay. However, they also did not interfere with viral RNA synthesis by full-length NP, nor did they affect the ability of the matrix protein Z to inhibit viral RNA synthesis. Moreover, it was observed that loss of the oligomerization motifs in the N-terminus also affected the subcellular localization of all three NP isoforms, which were no longer localized in discrete perinuclear inclusion bodies, but rather showed a diffuse distribution throughout the cytoplasm, with the smallest isoform NP40kD also being able to enter the nucleus. Surprisingly, the 3'-5' exonuclease function of NP, which is associated with the C-terminal domain and plays a role in inhibiting interferon induction by digestion of double-stranded RNAs, was found to be retained only by the NP40kD isoform, despite that all three isoforms retained the associated domain. Finally, previous studies using transfected NP and chemical induction of apoptosis have suggested that cleavage of NP at the caspase motifs responsible for generating NP47kD and NP40kD plays a role in controlling activation of the apoptosis pathway. Therefore, to further characterize the connection between the generation of NP isoforms and the regulation of apoptosis in a viral context, recombinant JUNVs deficient in the respective isoforms were generated. Unlike infections with wild-type JUNV, mutations of the caspase cleavage sites resulted in the induction of caspases activation. Surprisingly, however, this was also the case for mutation of the alternate start codon responsible for NP53kD generation.
Taken together, the data from this study suggest a model whereby JUNV generates a pool of smaller NP isoforms with a predominantly cytoplasmic distribution. As a result of this altered localization, NP53kD appears to be able to serve as the substrate for further generation of NP47kD and NP40kD by caspase cleavage. Not only does this cleavage inhibit apoptosis induction during JUNV infection, it also results in a cytoplasmic isoform of NP that retains strong 3'-5' exonuclease activity (i.e. NP40kD) and thus may play an important role in preventing viral double-stranded RNA accumulation in the cytoplasm, where it can lead to activation of IFN signaling. Overall, such results emphasize the relevance of alternative protein isoforms in virus biology, and particularly in regulation of the host response to infection.
Turbulence is a state of a physical system characterized by a high degree of spatiotemporal disorder. Turbulent processes are driven by instabilities exhibiting complex nonlinear dynamics, which span over several spatial as well as temporal scales. Apart from fluids and gases, turbulence is observed in plasmas. While turbulent mixing of a system is sometimes a desired effect, often turbulence is an undesired state. In hot, magnetically confined plasmas, envisaged for energy generation by thermonuclear fusion, plasma turbulence is clearly a problem, since the magnetic confinement time is drastically deteriorated by turbulent transport. Hence, a control mechanism to influence and to suppress turbulence is of significance for future fusion power devices. An important area of plasma turbulence is drift wave turbulence. Drift waves are characterized by currents parallel to the ambient magnetic field, that are tightly coupled to a coherent mode structure rotating in the perpendicular plane. In the present work, the control of drift waves and drift wave turbulence is experimentally investigated in the linear magnetized helicon experiment VINETA. Two different open-loop control systems - electrostatic and electromagnetic - are used to drive dynamically parallel currents. It is observed that the dynamics of the drift waves can be significantly influenced by both control schemes. If the imposed mode number as well as the rotation direction match those of the drift waves, classical synchronization effects like, e.g., frequency locking, frequency pulling, and Arnold tongues are observed. These confirm the nonlinear interaction between the control signal and the drift wave dynamics. Finally, the broadband drift wave turbulence, and thereby turbulent transport, is considerably reduced if the applied control signal is sufficiently large in amplitude.
Ebolaviruses are zoonotic pathogens causing severe hemorrhagic fevers in humans
and non-human primates with high case fatality rates. In recent years, the number and
scope of outbreaks has increased, highlighting the importance of better understanding
the molecular aspects of ebolaviral infection and host cell interactions in order to be able to better control this virus.
To facilitate virus genome replication, transcription and protein expression,
ebolaviruses recruit and interact with specific host factors. These interactions play a key role in viral infection and influence virus survival and disease outcome. Based on a genome-wide siRNA screen, the three host factors CAD, NXF1 and UAP56 were
recently identified to be involved in ebolavirus genome replication and/or transcription
and/or mRNA-translation. However, mechanistical details of how these host factors
affect the ebolavirus lifecycle remained elusive.
In this thesis I analyzed the functional interactions between EBOV and these newly
identified host proteins in order to better understand the virus-host interface. To this
end I used siRNA knockdown as well as overexpression of these host proteins in
combination with different reverse-genetics based lifecycle modelling assays to
investigate the influence of CAD, NXF1 and UAP56 on individual aspects of the EBOV
lifecycle. Using these systems in relation with a host factor knockdown I was able to
show that the provision of pyrimidines by CAD plays an important role for both EBOV
genome replication and transcription, whereas NXF1 is predominantly required for
mRNA transport. I furthermore used immunofluorescence analysis to examine whether
these host factors are recruited by one or more EBOV proteins to inclusion bodies,
which represent physical sites of ebolavirus genome replication. During these
experiments, I was able to show that CAD and NXF1, and possibly also UAP56, are
recruited to EBOV inclusion bodies in order to fulfill their individual function for EBOV RNA synthesis or later steps in protein expression. Additionally, I was able to show that the uptake of NXF1 into NP-induced inclusion bodies is most likely mediated via the C-terminal domain of NP, and that the FG-repeat interaction domains of NXF1 are sufficient for recruitment. Further, my data indicate that RNA interaction of both NXF1 and NP is not required for this process, but rather important for exit of NXF1 from inclusion bodies. I therefore suggest that the viral mRNA is transferred in inclusionbodies from NP to NXF1, which leads to a rapid export of the NXF1 packed viral mRNA into the cytosol for mRNA translation.
The exact mechanism of how these host factors are recruited into inclusion bodies and whether they have similar functions in the lifecycle of other negative-sense RNA viruses still needs to be investigated. Nevertheless, this study increases our understanding of virus-host interaction of ebolaviruses, and thus helps to identify targets for the development of novel therapeutics against these viruses.
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.
Interactive Visualization for the Exploration of Aligned Biological Networks and Their Evolution
(2011)
Network Visualization is a widely used tool in biology. The biological networks, as protein-interaction-networks are important for many aspects in life. Today biologists use the comparison of networks of different species (network alignment) to understand the networks in more detail and to understand the underlying evolution. The goal of this work is to develop a visualization software that is able to visualize network alignments and also their evolution. The presented software is the first software for such visualization tasks. It uses 3D graphics and also animations for the dynamic visualization of evolution. This work consists of a review of the Related Work, a chapter about our Graph-based Approach for Interactive Visualization of Evolving Network Alignments, an explanation of the Graph Layout Algorithm and some hints for the Software System.
Clostridioides difficile is the leading cause of antibiotic-associated diarrhea referring to infections of the gastrointestinal tract in the course of (broad-spectrum)antibiotic therapy. While antibiotic therapy, preferentially with fidaxomicin or vancomycin, often stops the acute infection, recurrence events due to remaining spores and biofilm-associated cells are observed in up to 20% of cases. Therefore, new antibiotics, which spare the intestinal microbiota and eventually clear infections with C. difficile are urgently required. In this light, the presented work aimed at the evaluation and characterization of three natural product classes, namely chlorotonils, myxopyronins and chelocardins, with respect to their antimicrobial activity spectrum under anaerobic conditions and their potential for the therapy of C. difficile infections. Briefly, compounds of all three classes were screened for their activity against a panel of anaerobic bacteria. Subsequently, the systemic effects of selected derivatives of each compound class were analyzed in C. difficile using a proteomics approach. Finally, appropriate downstream experiments were performed to follow up on hypotheses drawn from the proteomics datasets. Thereby, all three compound classes demonstrated significant activity against C. difficile. However, chelocardins similarly inhibited the growth of other anaerobes excluding chelocardins as antibiotic candidates for C. difficile infection therapy. In contrast, chlorotonils demonstrated significantly higher in vitro activity against C. difficile and close relatives compared to a small panel of other anaerobes. In addition, it could be shown that chlorotonils affect intracellular metal homeostasis as demonstrated in a multi-omics approach. The data led to speculate that chlorotonils eventually affect cobalt and selenate availability in particular. Moreover, a metaproteomics approach verified that oral chlorotonil treatment only marginally affected the intestinal microbiota of piglets on taxonomic and functional level. Furthermore, the proteome stress response of C. difficile 630 to myxopyronin B, which similarly showed elevated activity against C. difficile compared to a few other anaerobes, indicated that the antibiotic inhibited early toxin synthesis comparatively to fidaxomicin. Finally, evidence is provided that C. difficile 630 responds to dissipation of its membrane potential by production and accumulation of aromatic metabolites.
Cancer is one of the leading causes of death in industrialized nations. Nowadays, cancer therapy mainly consists of surgery, radiation and chemotherapy. Thanks to intensive research alternative treatment strategies like gene therapy and especially immunotherapies are on the rise. Immunotherapies base on the idea of stimulating and supporting the patients immune system to generate an effective anti-tumor immune response. Dendritic Cells are perfect targets for this purpose, since these potent antigen-presenting immune cells influence the balance of the immune system by defining the route of action. Stimulation of these cells by activation of cellular signaling pathways results in maturation, upregulation of surface molecules and secretion of cytokines. A20 has been identified as a regulator of dendritic cell maturation and attenuator of their immune stimulating properties. Hence, the blockade of that natural inhibitor reveals an elegant way to activate cellular pathways of DCs. A siRNA against A20 obtains a functional blockade via RNA interference if it can be delivered into the cytoplasm of the target cells. CpG oligodeoxynucleotides can be used for this intracellular transport. CpGs contain DNA motifs similar to those found in bacteria. Innate immune cells can detect this DNA via the toll-like receptor 9 getting activated and stimulated. CpG oligodeoxynucleotides are already in clinical use as adjuvants in vaccines and in cancer therapy approaches. Linking A20-specific siRNA to CpG enables A20 regulation and cell stimulation selectively in toll-like receptor 9 expressing cells, like dendritic cells. Aim of this study was to investigate if these constructs trigger immune cell activation and if they are able to break immune-suppression in the tumor environment to enhance anti-tumor immunity. A long-term growth factor dependent bone marrow-derived dendritic cell culture has been established in order to analyze the CpG-siRNA A20 effects on murine dendritic cells. The constructs were internalized shortly after administration (1 hour) and led to cell stimulation/activation. The intraperitoneal treatment with the constructs induced local cellular activation and systemic IL-6, TNF-α cytokine production in healthy mice. Subcutaneous growing B16 melanoma tumors were treated peritumorally to analyse whether the observed immune-stimulation has effects on established tumors. The silencing of A20 enhances CpG-induced activation of NF-κB followed by elevated expression of IL-6, TNF-α and IL-12 in this tumor model. These changes led to enhanced anti-tumor immune responses manifested by increased numbers of tumor-specific cytotoxic T cells, high levels of tumor cell apoptosis and delayed tumor growth. New constructs were designed and tested on dendritic cells isolated from healthy donors in order to test whether the obtained results for the murine system are applicable to the human system. CpG-siRNA A20 constructs induced cell activation and cytokine expression (IL-6, TNF-α) significantly more than CpG alone. Even though responds of the donor DCs were variable, there are promising similarities to the results of the mouse experiments. The significant role of A20 in controlling the immune-stimulatory activity of DCs has been confirmed in this study. The novel CpG-siRNA A20 constructs provide a strategy for simultaneous A20 silencing and CpG-mediated cell stimulation directly in vivo. This therapeutic approach induces potent adaptive and innate immune responses against established tumors in mouse melanoma model leading to prolongation of survival. CpG-targeted A20 blockade is a new immune-stimulatory approach, which could be suitable for supplementation or optimization of clinical tumor treatments.
Impurity ions pose a potentially serious threat to fusion plasma performance by affecting the confinement in various, usually deleterious, ways. Due to the creation of helium ash during fusion reactions and the interaction of the plasma with the wall components, which makes it possible for heavy ions to penetrate into the core plasma, impurities can intrinsically not be avoided. Therefore, it is essential to study their behaviour in the fusion plasma in detail. Within the framework of this thesis, different problems arising in connection with impurities have been investigated. 1. Collisional damping of zonal flows in tokamkas: The effect of impurities on the collisional damping of zonal flows is investigated. Since the Coulomb collision frequency increases with increasing ion charge, heavy, highly charged impurities play an important role in this process. The effect of such impurities on the linear response of the plasma to an external potential perturbation, as caused by zonal flows, is calculated with analytical methods and compared with numerical simulations, resulting in good agreement. 2. Impurity transport driven by microturbulence in tokamaks: Fine scale turbulence driven by microinstabilities is a source of particle and heat transport in a fusion reactor. A semi-analytical model is presented describing the resulting impurity fluxes and the stability boundary of the underlying mode. The results are compared with numerical simulations. Both the impurity flux and the stability boundary are found to depend strongly on the plasma parameters such as the impurity density and the temperature gradient. 3. Pfirsch-Schlüter transport in stellarators: Due to geometry effects, collisional transport plays a much more prominent role in stellarators than in tokamaks. Analytical expressions for the particle and heat fluxes in an impure, collisional plasma are derived from first principles. Contrary to the tokamak case, where collisional transport is exclusively caused directly by friction, in stellarators an additional source of transport exists, namely pressure anisotropy. Since this term is, contrary to the contribution from friction, non-ambipolar, it plays an important role regarding the ambipolar electric field. Furthermore, the behaviour of heavy impurities in the presence of strong radial temperature and density gradients is studied, which lead to a redistribution of the impurities on the flux surfaces. As a consequence, the radial impurity flux is decreased considerably compared with a plasma in which the impurities are evenly distributed on the flux surfaces.
The thesis deals with ions stored in an electrostatic ion beam trap. In the first part of the thesis the so-called self-synchronization effect is discussed. It is demonstrated that the time a bunch of injected ions is conserved by the self-synchronization effect depends on the number of injected ions. In the second part of the thesis the cooling of small anionic cobalt and copper clusters is addressed. Measurements on anionic copper clusters consisting of four to seven atoms are presented and the decay of hot clusters is observed in order to draw conclusions on the internal temperature and the cooling process itself. Afterwards measurements on Co4- are discussed and a measurement scheme based on laser induced delayed electron emission is presented enabling to monitor the internal energy distribution of the clusters over storage time in a temperature-controlled environment. The cooling of initially hot clusters as well as the heating of initially cold clusters were observed.
In the present work, mass determinations of the eleven neutron-deficient nuclides (99-109)Cd, of ten neutron-rich silver nuclides (112-114,121,123)Ag, and seven neutron-rich cadmium nuclides (114,120,122-124,126,128)Cd are reported. Due to the clean production of the neutron-deficient nuclides it was possible to reduce the experimental uncertainties down to 2 keV, whereas the measurements of neutron-rich nuclides were hampered by the presence of contaminations from more stable In and Cs nuclides. In the case of 99Cd and 123Ag the masses were determined for the first time and for the other nuclides the mass uncertainties could be reduced by up to a factor of 50 as in the case of 100Cd. In the case of a potential isomeric mixture as for (115,117,119)Ag and 123Cd, where no assignment to either the ground state or the excited state was possible, the experimental results were adjusted accordingly. Afterwards all results were included in the framework of the atomic-mass evaluation and thus linked and compared with other experimental data. In the case of the neutron-deficient Cd nuclides a conflict between the mass values obtained in the present work and those published by the JYFLTRAP group could be solved by performing an atomic-mass evaluation. These mass measurements are an important step towards an understanding of the physics of the rp process that will enable a more reliable determination of the composition of the produced material at A = 99. It has been shown that the mass of 99Cd strongly affects the A = 99 production in an X-ray burst model, and that uncertainties have been significantly reduced from more than an order of magnitude to about a factor of 3. The dominant source of uncertainty is now the mass of 100In. In principle, other uncertainties will also contribute. These include those of masses of lighter Cd isotopes, where similar rp-process branchpoints occur and which might affect feeding into the 99Cd branchpoint. In addition, nuclear reaction rate uncertainties will also play a role. However, as reaction rates affect branchings in a linear fashion, while mass differences enter exponentially, mass uncertainties will tend to dominate. Also, which reaction rates are important depends largely on nuclear masses. For example, for low Sp(100In) a (p,γ)-(γ,p) equilibrium will be established between 99Cd and 100In and the 100In(p,γ) reaction rate would affect the A = 99 production, while for larger Sp(100In) the 99Cd(p,γ) reaction rate might be more relevant. Therefore, the mass uncertainties should be addressed first. The presented results are relevant for any rp-process scenario with a reaction flow through the 99Cd region. Here, an X-ray burst model has been used to investigate in detail the impact of the present measurements on such an rp process. The νp process in core collapse supernovae might be another possible scenario for an rp process in the 99Cd region. It it is planed to also explore whether in that case mass uncertainties have a similar impact on the final composition. On the neutron-rich side of the valley of stability for the Cd and Ag chains of nuclides, the r process has not yet been reached. Further technical development on suppression of contaminants are required. This includes improvements on the ISOLDE side, e.g., by improving the selectivity of the transfer line or on the ISOLTRAP setup by implementing an electrostatic ion beam trap for a fast and efficient isobaric selection. Nevertheless the obtained results contribute to the knowledge of nuclear structure. The trends in the two-neutron separation-energy S2n and the interaction between the last neutrons and last protons ΔVpn were corrected to more smooth evolutions, as already seen in other regions of the nuclear chart. The strongest corrections have been observed for even-N nuclides, were more new experimental data are available. Thus, new measurements on odd-N nuclides are suggested. This also is underlined by the trends observed in the Garvey-Kelson relations for the neutron-rich Cd nuclides. Furthermore, it has been shown, that the prominent structure of the ΔVpn for an entire chain of nuclides including inflexion points can be reproduced by using simple relations between quantum numbers of the occupied orbits. This approach connects ten values for each nuclide with only one adjusted parameter. This has been investigated for 63 ΔVpn values of even-even nuclides in the vicinity of Z = 50 and 50 ≤ N ≤ 82. The simple model works remarkably well for the elements Cd, Sn, and Te. Small deviation have been observed for the Xe and Pd nuclides which were explained with the limitations of the model to the vicinity of the close shells, where the nuclides have only few valence protons and neutrons.
Background: Intact socio-cognitive abilities, such as theory of mind (ToM), facial emotion recognition (FER), social decision making (SDM) and visual perspective taking (VPT), are essential for human well-being and quality of life. Impairment in social cognition can have major implications for health in affected individuals and society as a whole. Evidence for changes in social cognition in healthy and pathological aging processes, such as subjective cognitive decline (SCD) and mild cognitive impairment (MCI), is currently either sparse or inconclusive. It is important to determine how social cognition changes in healthy and pathological aging and provide grounds for targeted and early assessment and intervention. The aims of this thesis were to investigate social cognition across four domains, in particular, ToM, FER, SDM and VPT, in healthy young and older individuals, as well as in individuals with cognitive deficits, such as SCD and MCI. In the case of a decline, further goals were to investigate the degree of impairment and the domains affected.
Methods: A systematic literature search was conducted in four major academic databases, MEDLINE, Web of Science Core Collection, CENTRAL, and PsycInfo, for studies investigating social cognition in healthy young and old individuals as well as individuals affected by SCD and MCI which met the inclusion criteria. The primary outcome was ToM and secondary outcomes were FER, SDM and VPT. After a systematic review was performed, studies eligible for meta-analysis were divided according to comparison groups and outcomes. Random-effects meta-analyses were conducted using standardized mean differences (SMD). Risk of Bias was assessed using the “Tool to assess risk of bias in cohort studies” modified for the present study design.
Results: After a thorough systematic literature search, 86 studies containing 88 comparisons were included in the systematic review, of which 47 were eligible for quantitative analysis. The meta-analysis revealed a progressive decline in ToM and FER abilities from young adulthood to MCI. Varying effect sizes demonstrated different trajectories of change for specific domains. Due to a lack of research, data investigating SDM and VPT, as well as SCD were insufficient for quantitative analysis.
Conclusion: ToM and FER decline gradually from healthy to pathological aging. Therefore, assessment of social cognition is important and should be incorporated in routine neurocognitive testing, so that targeted interventions can be introduced when needed. With this information in mind, future research should focus on the development of new assessment tools, as well as preventive and treatment strategies. This review also identified research gaps in certain populations (e.g. SCD, middle age, MCI-subtypes) as well as domains (VPT and SDM) that need to be addressed in the future.
This work proposes and experimentally evaluates a new method and the first prototypic design of an apparatus for the objective assessment of peripheral dynamic stereovision. Peripheral dynamic stereovision is understood as the ability to perceive, recognize and observe moving objects in the visual periphery without sacrificing foveal fixation, i.e. shifting the line of sight (e.g. moving the eyes or the head) and loosing attention to the scene of interest. The presence of stereopsis on top further enhances the perceptive quality by adding the third dimension with judgment of depth and estimation of relative spatial positions as central clues for orientation, coordinative interaction and navigation in space. Based on findings that moving stereoscopic contours can induce distinctive optokinetic reactions, a panoramic stimulus pattern was rotated round subjects’ heads. Designed after the Frisby Stereotest, solely the binocular parallax resulting from the plate thickness carries stereoscopic information, excluding all other depth clues. A specially fitted goggle frame assured correct binocular alignment of the subjects adding objectivity. In first experiments, voluntary reactions (pushing a buzzer button) and involuntarily triggered ocular responses have been registered. The Performance Level (PL) and Confidence Ratio (CR) were introduced as benchmarks for voluntary reactions. Despite larger spreads, the PL averaged at 60 % while an elevated CR confirmed a low error rate of 16 % and thus high overall credibility. Poor performance of available recording hard- and software, in many cases, rendered the analysis of involuntary ocular reactions less exhaustive. It was however observable that objects that appear in the periphery of the visual field triggered the onset of nystagmoid search and tracking mechanisms. Finally, mean peripheral locations of subjects’ active reactions have been established at 30 degrees. The outcome of this pilot study in principle confirmed basic feasibility, conceptual validity and practical applicability of this novel method. Prospective fields of application with raised demands on peripheral dynamic stereopsis have been identified and critically assessed. The applicative possibilities and exclusive advantages of this test combining the assessment of stereopsis and dynamic visual field testing have not been matched by solutions published so far. Before however commercialization should be aimed at, design-related issues, including the implementation of electrophysiological ocular measurements, need to be addressed first to lead the post-prototype development to higher diagnostic expressiveness and reliability.
This dissertation focuses on the characterization of novel enzymes and metabolic pathways that fulfill crucial functions during marine carbohydrate degradation by Bacteroidetes and thus contributes to an advanced understanding of the global carbon cycle. Depolymerization and utilization of marine polysaccharides by Bacteroidetes requires a tremendous repertoire of enzymes with a wide range of functions. For instance, during the breakdown of the marine red algal polysaccharide porphyran, an oxidative demethylation of the methoxy sugar 6-O-methyl-D-galactose (G6Me) by cytochrome P450 monooxygenases occurs. This reaction produces huge amounts of cytotoxic formaldehyde, marine bacteria capable of degrading porphyran must therefore possess suitable formaldehyde detoxification pathways. Consequently, Article I focus on the identification of possible formaldehyde detoxification pathways in marine
Flavobacteriia, which led to the discovery of the ribulose monophosphate pathway as specific pathway for the detoxification of formaldehyde in certain Bacteroidetes like Zobellia galactanivorans. Furthermore, it was demonstrated in Article II that alcohol dehydrogenases play an essential role in the microbial utilization of G6Me and therefore possess a function in porphyran degradation. Discovering novel enzymes, entire enzymatic cascades or biotechnologically important microorganisms that can metabolize these marine carbohydrates also contributes to the utilization of marine polysaccharides as feedstock for potential biotechnological applications. A prospective biorefinery process was proposed in Article III by the identification of Bacillus licheniformis as promising utilizer of marine carbohydrate-derived monosaccharides and the creation of a microbial cell factory capable of growing on ulvan, a marine carbohydrate obtainable from algal bloom-dominating green algae, enabling an industrial use of the renewable and abundant algal biomass in future.
Although the Pleistocene deposits exposed in the steep coastal cliffs of Mecklenburg-Vorpommern have been studied for more than a century, the depositional conditions of many lithostratigraphic units remain unclear. There is, in particular, a question whether the individual tills (locally more than 9 successive till units) are mainly subglacial deposits or resedimented (mass flows) in origin (at least in part). The Pleistocene deposits preserve information concerning the former glacial depositional processes. Detailed micromorphological analysis of these deposits can provide key information regarding these processes and thereby aid in the reconstruction of former glacial environments. The island of Rügen is located on the southwestern Baltic Sea coast and was situated in the marginal zone of the Scandinavian Ice Sheet during the last glacial period (Weichselian). Therefore, the region is considered as an ideal area for reconstructing the complex fluctuations in the position of the margin of this ice sheet as it expanded across the Baltic Sea and into northern Germany. Successive glacial advances and retreats of the ice sheet can be reconstructed by specific glacial sedimentation processes and flow-direction criteria derived from a variety of glacial deposits. The investigation area is located near Sassnitz on Rügen, where an imbricated and folded Weichselian succession disconformably overlies Maastrichtian chalk bedrock. The individual till units were sampled for micromorphological analyses to identify the former depositional conditions. Detailed description of the sedimentology and variation in facies, the description of macroscale deformation structures provides the context for the detailed micromorphology study. The three dimensional analysis of the microfabrics is based on the microstructural mapping methodology which enables the identification and interpretation of polyphase deformation within subglacial sediments.
On the aqueous phase chemistry of atmospheric-pressure plasma jets for biomedical applications
(2021)
Cold atmospheric-pressure plasmas are candidate biomedical tools proposed for various applications, such as biological decontamination, cancer regression, and promotion of wound healing. Plasmas, which are in the fourth state of matter, can be generated using inert gases (e.g., argon, helium, ambient air) and different source concepts. Together with the applied parameters, the source design defines the chemical-physical characteristics of the resulting plasma, leading in turn to variable biochemical effects on biological matter. The medical effectiveness of cold plasmas has been proven in vitro and in vivo, also in clinical trials for wound healing in patients using two certified plasmas sources, the kINPen MED and the PlasmaDerm. However, molecular mechanisms leading to those effects are unclear. In the same way, it must be studied if the modulation of plasma properties could improve the specificity of biological effects. These findings are needed to define the concept of plasma dose to be optimized in targeting peculiar pathologic conditions. The present thesis consisting of five peer-reviewed publications has investigated these aspects of plasma research.
In the gaseous phase of cold plasmas, various components with biological activity are produced, such as radiation (e.g., vacuum UV, UV) and reactive species (e.g., •O, 1O2, •OH, •NO, •NO2, O3). As most gaseous species are short-lived, liquid compartments surrounding cells and molecular structures could mediate their transformation and/or the production of other aqueous species. For this reason, plasma-induced aqueous chemistry has been mainly investigated in this thesis. The reaction pathways of reactive oxygen and nitrogen species in liquid were analyzed by monitoring the oxidative modifications induced on tyrosine and cysteine, which are biological structures essential in cellular protein functioning. Liquid chromatography and mass spectrometry-based strategies have been elaborated to elucidate structural changes and characterize the oxidative pattern occurring on the tracers after treatment with plasmas.
As a first result, it could be shown that the oxidative pattern induced on tyrosine or cysteine variated qualitatively and quantitatively with the applied conditions, reflecting the action of differently produced/deposited species in liquid. Biologically relevant structures were identified and in part quantified (e.g., cystine, sulfonic acid, sulfinic acid, S-sulfonate, S-nitrosocysteine, nitrotyrosine, nitrosotyrosine). By using isotopically labeled oxygen or nitrogen in the gas plasma, or labeled oxygen in the target liquid, the incorporation of gaseous or aqueous species in the tracer’s structures was monitored via mass spectrometry. With this strategy, the reaction mechanisms involving gaseous oxygen and nitrogen species at the liquid interface were clarified, as well as the de novo production of reactive species in liquid. Short-lived gaseous oxygen species such as atomic and singlet oxygen (•O, 1O2), predominantly formed in conditions with oxygen in the plasma gas, were able to modify the cysteine structures in highly oxidized derivatives, such as cysteine sulfonic acid. Due to their half-life, however, their activity occurred mainly at the interface. Vacuum UV radiation and •O also led to the formation in liquid of hydroxyl radicals (•OH) and hydrogen peroxide (H2O2), due to water photolysis and homolysis. Water-derived species were responsible for the formation of reversible modifications, such as cysteine S-sulfonate, cystine, and cystine sulfoxides. Nitrosative modifications (e.g., S-nitrosocysteine, nitrosotyrosine, nitrotyrosine) could be observed only in conditions with both nitrogen and oxygen in the plasma gas, and further optimization occurred in presence of water molecules in the gas. In this case, the formation and action of peroxynitrite (ONOO-) in generating nitrotyrosine was proven by using a scavenger molecule for ONOO-.
Finally, the cysteine product pattern was applied as a tool to characterize and compare the overall chemistry generated in liquid by different plasma sources and applied parameters. These findings aim to support and contribute to the definition of plasma dose for plasma medicine, through the standardization, control, tuning, and optimization of plasma parameters and plasma liquid chemistry. These results may be applied in the future to improve the specificity and selectivity of the biological effects generated by the described atmospheric-pressure plasma jets.
The soluble blood protein beta2-glycoprotein I (beta2GPI; 326 aa, MW: 48 kDa, 5 domains) is one of the most abundant proteins in human serum and exhibits two main conformational states: the circular or closed conformation, where the first domain (DI) is bound to the last domain (DV) of the protein, and the linear or open conformation. The defined physiological function of beta2GPI is still unknown, though several roles in pro- and anticoagulation as well as oxidative stress protection were discovered. The open form is considered to play a crucial role in the systemic autoimmune disease antiphospholipid syndrome (APS), which is an acquired thrombophilia characterized by recurring thrombotic events and pregnancy morbidity. Beta2GPI constitutes the main antigen for APS autoantibodies which are supposed to bind a cryptic epitope within DI after a conformational change from closed to open form. However, the pathophysiological mechanism of APS is poorly understood. Therefore, investigating the structural dynamics of this protein in relation to its antigenicity is of high interest.
Post-translational modifications (PTM) of a target protein often show an impact on the formation of neoantigens, for instance in the autoimmune-mediated diseases type 1 diabetes mellitus, rheumatoid arthritis, or multiple sclerosis. Such modified antigens may lead to immune tolerance breakdown as they are unknown to the immune system, which therefore could mistakes self for non-self proteins. In this thesis, two frequently occurring PTM were introduced to beta2GPI and their impact on the protein conformation was studied by biophysical tools (i.e. atomic force microscopy (AFM) imaging, transmission electron microscopy (TEM) imaging, dynamic light scattering (DLS), and circular dichroism (CD) spectroscopy). In order to examine immunopathophysiological relevance of these PTM, additional insights were gained from ELISA which was used to examine binding of anti-DI autoantibodies purified from the blood of APS patients to the modified beta2GPI species.
A characteristic feature of beta2GPI is the high content of lysine residues. Previously, opening of beta2GPI was found to be triggered by a drastic shift in pH and salt concentration (pH 11.5 and 1.15 M NaCl), which results in reversible uncharging of the lysine residues. The aim of this study was to investigate the beta2GPI conformation after lysine acetylation as a model system, to elucidate the role of lysine residues on the conformational dynamics of this protein, and to examine anti-DI autoantibody binding to both the untreated as well as acetylated species.
A strategy to permanently open up the closed form under physiological conditions by chemical acetylation of lysine residues utilizing the sensitive acetylation agent acetic acid N-hydroxysuccinimide ester (NHS-Ac) was established. Complete and specific lysine acetylation was verified by quantification of primary amines exerting a fluoraldehyde o-phthaldialdehyde (OPA) reagent assay, as well as by native PAGE and western blot analysis with an anti-acetylated lysine antibody. Beta2GPI acetylation revealed a partial opening of beta2GPI molecules. Compared to untreated, i.e. native beta2GPI which exhibited 93% of the molecules in closed and 7% in open form, complete lysine residue acetylation generated 39% of beta2GPI in closed and 61% in open conformation as shown by AFM high-resolution imaging. pH 11.5-treated beta2GPI was used as a reference in the applied methods and revealed 38% of the protein in closed and 62% in open conformation. Thus, a significant shift in beta2GPI conformation occurred upon lysine residue acetylation as well as basic pH-treatment. The data indicate that lysine residue acetylation destabilizes the closed form, leading to a facilitated opening of the structure. The closed conformation might be predominantly stabilized by electrostatic interactions of lysine residues, which potentially control the conformational dynamics of this glycoprotein. ELISA confirmed that anti-DI autoantibodies do not bind to untreated (closed) beta2GPI. Although acetylated beta2GPI was shown to have a substantial portion of open proteins, no binding of anti-DI autoantibodies to the acetylated species was found either. Hence, acetylated lysine residues may disrupt the immunorelevant epitope in DI which prevents antibody binding. This finding reveals a new hint for epitope organization. However, further detailed epitope mapping has to be performed.
Beta2GPI carries two structural disulfide bonds per domain, whereas an additional disulfide bond Cys288/Cys326 is located at the C-terminus of DV near the putative contact interface of DI and DV in the closed conformation. It was previously shown that beta2GPI is a substrate of thiol oxidoreductases, including human thioredoxin-1 (Trx-1) generating different redox states of disulfide bond Cys288/Cys326, which might serve as a scavenger in oxidative stress protection in the blood stream. In APS patients, anti-DI antibody titers as well as an enhanced risk for thrombotic events are associated with an increase in the oxidized state of the protein. Hitherto, no structural study has been performed in order to prove a correlation of the redox state and the conformation of beta2GPI. Therefore, investigations of beta2GPI conformation in different redox states of disulfide bond Cys288/Cys326 were carried out. In addition, binding of anti-DI autoantibodies to the untreated (native) as well as reduced protein should be explored.
At first, cysteine residues of untreated, i.e. native beta2GPI were confirmed to be completely in oxidized state using Ellman’s reagent assay and the absence of binding of a thiol-specific agent. Statistical analyses of AFM images revealed that untreated beta2GPI was mainly in closed conformation (80% in closed and 20% in open conformation) in the respective system. In this study, an optimized protocol for enzymatic reduction of disulfide bond Cys288/Cys326 was established. The agent TCEP was used to reduce human Trx-1, which in turn enzymatically reduced beta2GPI. To block reoxidation of free thiols and to facilitate product analysis, cysteine residues of reduced beta2GPI were subsequently labeled with the sensitive and thiol-specific reagent 3-(N-maleimidopropionyl) biocytin (MPB), which carries a biotin function. During protocol establishment, complete and specific reduction of disulfide bond Cys288/Cys326 was confirmed utilizing SDS-PAGE, streptavidin western blot, mass spectrometry (MS) analyses, and a biotin quantification assay. Protocol improvements constituted a homogenous system with remarkable decrease of unspecifically reduced beta2GPI. Upon beta2GPI reduction, AFM imaging revealed no significant shift in protein conformation (75% in closed and 25% in open conformation). These results were qualitatively confirmed by TEM imaging. Therefore, reduction of beta2GPI disulfide bond Cys288/Cys326 did not result in a major conformational change of the protein. Upon in vitro reduction, the closed form is still the main conformation and a direct correlation of beta2GPI redox state and conformation must be refused. Furthermore, beta2GPI reduction led to a strong and statistically highly significant increase in anti-DI autoantibody binding compared to untreated beta2GPI. Thus, the reduced form might be the antigenic form of the protein. In contrast to previous knowledge, these findings suggest that anti-DI autoantibodies may also bind to the closed conformation under certain conditions. Hypothetically, reduction of beta2GPI could induce a minor structural change in DV that might facilitate the binding of APS autoantibodies.
Overall, this study reveals that PTM of beta2GPI may lead to a critical level of destabilization of the closed conformation (as in the case of acetylated beta2GPI) or significantly increase the binding of APS autoantibodies (as in the case of reduced beta2GPI), both of which could have a large impact on APS disease. However, further investigations are necessary to put these new findings in the context of APS immunopathophysiology.
Transition metal complexes play a crucial role in antitumor therapy. Complexes of platinum, ruthenium as well as lanthanum and gallium have been investigated in preclinical as well as in clinical studies. The best known platinum(II) agents approved worldwide, cisplatin or carboplatin, are used in nearly 50% of all cancer therapies. This work focused on the development of new metal-based drugs that could act against human cancer cells. It was motivated in part by previous work with Cu(II) complexes, reporting new coordination compounds of SOD mimicking and cytotoxic activities. On the basis of this work we chose several commercially available heterocyclic ligands to synthesize new metal ion complexes in search of their interesting biological activity. New as well as previously reported Cu(II), Co(II), Pt(II) and Zn(II) complexes were synthesized using various ligands (1-6). Almost all chelating 2:1 ligand-metal complexes were obtained generally in water at room temperature in the reaction of metal(II) chloride with corresponding aromatic nitrogen ligands bearing an O-carboxylate group ligand. The synthesized chelating complexes were characterized by the use of spectroscopic methods, elemental analyses and HPLC chromatography and some by X-ray crystallography. Such coordination compounds are easily formed by transition metals with free orbitals d that can accept the donor electron pairs. The coordination is through the heterocyclic nitrogen and carboxylate oxygen donor atoms, which was shown by analysis of the characteristic functional groups in the IR spectra. The d-d transitions and absorption of visible light in Cu(II) and Co(II) complexes make them highly colored, blue, green or green-blue, respectively. The configuration of the coordination center was established in some cases by X-ray crystallography. Most of the already published structures possess the trans configuration. This led to the assumption that other uncrystallized complexes were also trans configured. However, X-ray data of the Cu(II) complex of 5 showed quite unexpectedly the cis configuration. On the other hand, the LC/MS experiments with the Pt(II) complex of 5 indicated that this complex exists in two isomeric forms, i.e., cis and trans at the Pt(II) center. Through the use of density functional calculations we optimized the structures and calculated the energies and dipole moments. The differences in energy for all complexes were about 6 to 15-fold lower when compared to cis and transplatin. The DFT calculations confirmed that the trans-isomers are more stable than their cis-isomers. UV-Vis stability studies with most of the synthesized complexes as well as some other Cu(II) complexes were performed to study the spectral changes over 24 h in addition of glutathione, a tripeptide present in the cancer cells and ascorbate that were added to the incubations. The results indicated time-dependent changes and instability of the complexes in the cells and their possible decomposition to lose the ligand and release the metal ion. In the case of Cu(II) complexes, reduction of Cu(II) to Cu(I) may take place. New species such as GSSG could arise and the complexes may decarboxylate, but these structures were not elucidated. The synthesized coordination metal(II) complexes were tested for their potential antiproliferative activities by using the crystal violet staining method in a panel of human cancer cell lines. Out of all complexes, three Pt(II) complexes of 2, 5 and 6 showed satisfactory activity and for these complexes the IC50 values were additionally determined in new RT-4, DAN-G and MCF-7 cancer cell lines. Interestingly, the active complexes were the chelating trans complexes which is quite unexpected, based on the difference in activities between cis and transplatin. All of the complexes were tested for their potential antimicrobial activities in comparison to the standard antibiotics on such bacterial strains as Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa and yeast Candida maltosa. Co(II) complexes have been especially known to act against bacterial strains. The activity of the Co(II) complexes was indeed the highest of all metal(II) complexes. The ligand 2 (a nicotinic acid isomer) was also found active. This fact could explain why some antibacterial activity was found in the MIC assay. In addition to the complexes synthesized in this work, several novel heterocyclic metal(II) complexes of copper, ruthenium, platinum, gallium, osmium and lanthanum from other research groups were screened for their antiproliferative activity, some of which exhibited very potent activity in the cancer cell lines. In conclusion, Pt(II) complexes with bis-chelating heterocyclic carboxylate ligands represent a particularly interesting new class of compounds from the view point of their structural and biological properties.
Reactive oxygen species (ROS) can damage all cellular macromolecules and also produce secondary reactive intermediates, like reactive electrophilic species (RES) that include quinones or aldehydes. Low molecular weight (LMW) thiols are small thiol-containing compounds that play essential roles in the defense against ROS and RES in all organisms. The best studied LMW thiol is the tripeptide glutathione (GSH). Firmicutes bacteria including Bacillus und Staphylococcus species have been recently discovered to utilize the redox buffer bacillithiol (BSH). LMW thiols function as redox buffers to maintain the reduced state of the cytoplasm. Under conditions of oxidative stress, LMW thiols also react with protein thiols to form mixed LMW thiol – protein disulfides, termed S-thiolations, as major protection mechanism. Investigating the role of BSH in oxidative stress response and ROS-induced S-thiolations in Firmicutes bacteria was one subject of this PhD thesis. Specifically, the regulatory mechanisms and post-translational thiol-modifications in response to NaOCl stress were studied in the model bacterium for low-GC Gram-positive bacteria Bacillus subtilis. The transcriptome profile after NaOCl stress was indicative of disulfide stress and overlapped strongly with the response to diamide. NaOCl stress caused induction of the thiol- and oxidative stress-specific Spx, CtsR, PerR and OhrR regulons. Thiol redox proteomics identified only few NaOCl-sensitive proteins with reversible thiol-oxidations. Using mass spectrometry, eleven proteins were identified that were oxidized to mixed BSH protein disulfides (S-bacillithiolated) in B. subtilis cells after NaOCl-exposure. Methionine synthase MetE is the most abundant S-bacillithiolated protein in B. subtilis and other Bacillus species after NaOCl exposure. S-bacillithiolation of OhrR repressor leads to upregulation of the OhrA peroxiredoxin that confers together with BSH specific protection against NaOCl. S-bacillithiolation of MetE, YxjG, PpaC, and SerA causes hypochlorite-induced methionine starvation as supported by the induction of the S-box regulon. To further assess the conservation of targets for S-bacillithiolations in other Firmicutes bacteria, we studied the S-bacillithiolomes of Bacillus megaterium, Bacillus pumilus, Bacillus amyloliquefaciens, and Staphylococcus carnosus under NaOCl stress conditions. In total, 54 S-bacillithiolated proteins were identified, including 29 unique proteins and 8 conserved proteins involved in amino acid and cofactor biosynthesis, nucleotide metabolism, translation, protein quality control, redox and antioxidant functions. Together our data support a major role of BSH redox buffer in redox control and thiol protection of conserved and essential proteins against irreversible oxidation by S-bacillithiolations in Firmicutes bacteria. In response to ROS and RES, bacteria also activate the expression of antioxidant and detoxification enzymes, such as catalases, peroxidases, thiol-dependent peroxiredoxins and other specific oxidoreductases to detoxify ROS and RES. These defense mechanisms are often controlled by redox-sensitive transcription factors. B. subtilis encodes redox-sensing MarR-type regulators belonging to the OhrR and DUF24-families that are conserved among bacteria. Hence, we were further interested in this PhD thesis to study at the molecular and structural level the redox-sensing mechanisms of novel redox-sensing MarR/DUF24-type regulators in B. subtilis. We have characterized the regulatory mechanisms of HypR, YodB and CatR that sense and respond to hypochlorite, diamide and quinones stress. HypR is the first DUF24-family regulator whose crystal structure was resolved. HypR senses specifically disulfide stress and controls positively expression of the flavin oxidoreductase HypO after NaOCl and diamide stress. HypR resembles a 2-Cys-type regulator with a reactive nucleophilic N-terminal Cys14 and a second C-terminal Cys49. Besides HypR, B. subtilis encodes further MarR/DUF24-family members including the paralogous YodB and CatR repressors that sense quinones and diamide. YodB controls the azoreductase AzoR1, the nitroreductase YodC, and the Spx regulator. YodB resembles a 2-Cys-type MarR/DUF24-family regulator with three Cys residues (Cys6, Cys101, and Cys108) that form intermolecular disulfides in vivo under oxidative stress. YodB and its paralog CatR were further identified as repressors of the catDE operon encoding a catechol-2,3-dioxygenase that also contributes to quinone resistance. Although CatR is a 1-Cys-type regulator, our data showed that CatR also forms intermolecular disulfide in response to diamide and quinones in vitro. Thus, HypR, YodB and CatR are controlled by 2-Cys-type thiol-disulfide redox switches to sense disulfide and RES stress conditions, and to control specific RES detoxification enzymes.
In the search for new antifungal agents, this study dealt with the antimicrobial screening, extraction, isolation, structural elucidation as well as selective biological investigations of the isolated compounds. In addition, the impact of the culture conditions on growth and on biosynthesis of bioactive compounds was also studied. Besides, selective cyanobacteria were axenized and the taxonomy as well as the genetic relationship of axenic cyanobacteria that produced bioactive compounds with some other cyanobacteria was identified basing on the 16S rRNA gene sequences. 22 Vietnamese and 6 German cyanobacterial strains were screened for their antifungal activity using the agar diffusion assay. Among them, the MeOH/water extract from the biomass obtained from a laboratory culture of strain Bio 33, isolated from the Baltic Sea near Rügen Island, exhibited a specific antifungal activity against Candida maltosa and others human pathogenous fungi such as Candida albicans, Candida krusei, Aspergillus fumigatus, Microsporum gypseum, Trichophyton rubrum and Mucor sp. Besides, it was very impressed that extracts of strain Bio 33 showed no antibacterial activity against Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus aureus. The taxonomy basing on 16S rRNA gene sequence of the axenic Bio 33 identified this strain as Anabaena cylindrica species. As a result of the bioassay-guided fractionation of the crude MeOH/water extract, four new lipopeptides, named balticidins A – D, were isolated. These lipopeptides represent a new structural type with the co-occurrence of a glycosylated cyclic peptide, a fatty acid containing chlorine and a disaccharide moiety. The main active fraction isolated from the MeOH/water extract of the biomass of Bio 33 which contains the four lipopeptides exhibited only marginal cytotoxic activity against the human bladder carcinoma cell line 5637 (IC50 = 93 μg/ml). The weak cytotoxic activity and the absence of antibacterial effects in the used in vitro test systems opens a promising future for further investigations to clarify the antifungal mechanism and for in vivo applications of the new lipopeptides. Different media, temperature, light intensity and period of irradiance, the depletion of nitrate and the trace element cobalt were investigated to figure out conditions at which Bio 33 produces maximum of balticidins under laboratory conditions. Temperature was the most apparent factor influencing the growth of Bio 33 and the production of balticidins. Bio 33 grew best in BG 11 medium plus 0.5% NaCl at 26°C, under white fluorescent continuous light and a light intensity of 20 μmol photons m-2 s-1. Nevertheless, under the same conditions, 22.5°C was the best temperature for the production of balticidins. Besides, harvesting of Bio 33 during the logarithmic growth phase, particularly at 20th day, should supply approximately maximum quantity of balticidins. At 22.5°C and 20 μmol photons m-2 s-1 under 24 h continuous irradiance, the depletion of nitrate had no negative effect on the growth and concentration of balticidin A but increased balticidin B and decreased balticidin C; the absence of cobalt slightly decreased the growth but had no clear effect on the production of balticidins. On the other hand, extracts of the culture medium of the Vietnamese cyanobacterium TVN40, exhibited antifungal activity against Candida maltosa and weak antibacterial activity. Extraction of the culture medium with XAD-16 and elution of the XAD-bounded compounds by different solvents resulted in five fractions (water, 80% MeOH, 100% MeOH, acetone, dichloromethan). Four compounds have been isolated from the 80% MeOH fraction and one was identified as a dioxindole derivative. Structural elucidation of the other three compounds is still in progress. TVN40 was formerly identified as an Anabaena sp. according to the morphological properties, but the 16S rRNA gene sequence confirms that the strain belongs to the genus Nostoc. Microscopic examination of TVN40 revealed that the filamentous strain was not a unialgal but a mixed culture with strange round cells (SRCs) - a unicellular cyanobacterium belonging to the order Chroococcales. Laboratory cultures of the pure filamentous strain TVN40, the isolated SRCs and the mixed culture of both strains were established. Both TVN40 and SRC culture media were responsible for the antibacterial activity against B. subtilis, S. aureus and E. coli. However, only the extract of the culture medium of TVN40 was active against C. maltosa. The supplement of cobalt enhanced the antimicrobial activity of the culture medium. Pure strains showed higher activity in comparison to the mixed culture of TVN40 and SRC.
Non-thermal atmospheric pressure plasma has drawn more and more attention to the field of wound healing research during the last two decades. It is characterized by a unique composition, which includes amongst others free radicals, ions and electrons. Furthermore, non-thermal plasma exhibits temperatures that are below those inducing thermal cell damage. Next to its well-established anti-bacterial properties, plasma can have lethal as well as stimulating effects on mammalian cells. Therefore, the medical application of non-thermal plasma on chronic wounds seems to be a promising tool to enable healing processes. However, less is known about the plasma-mediated induction of intracellular signaling pathways in human immune cells, which play a leading part in the process of wound recovery and removal of pathogens. Therefore, this thesis examined the cellular effects of a non-thermal atmospheric pressure plasma treatment on human immune cells using the argon plasma jet kinpen 09. Here, the CD4+ T helper cell line Jurkat, the monocyte cell line THP-1 as well as the corresponding primary cells were investigated. First, cell survival and apoptosis induction was assessed in response to non-thermal plasma treatment by growth curves and flow cytometric assays. On the one hand it could be shown that primary cells are more susceptible to plasma treatment than the respective cell lines. On the other hand, monocytes responded less sensitive to plasma exposure than lymphocytes. Furthermore, this thesis outlined the impact of non-thermal plasma treatment on the gene expression level of immune cells. Therefore, DNA microarray analysis was performed with the cell lines Jurkat and THP-1. It became obvious that plasma exposure modulated the expression of several genes in both cell types. Differential expression of distinct target genes was further validated by quantitative PCR in the immune cell lines. Here, elevated gene expression levels of JUN and FOS in Jurkat cells and increased transcription of JUND in THP-1 cells in response to plasma treatment were made visible. JUN, FOS and JUND are components of the transcription factor AP-1, which is involved amongst others in gene expression of IL-8 and HMOX-1. Consequently, transcriptional induction of the inflammatory cytokine IL-8 as well as the enzymes HMOX-1 and GSR was detected in plasma-treated THP-1 cells. In addition, alterations in the protein activation levels were analyzed in plasma-treated Jurkat, THP-1 cells and primary monocytes. Since some of the identified target genes are known to be associated with the MAPK pathways, the regulation of these cascades was further investigated by western blot analysis. In all investigated cell types the pro-proliferative signaling molecules ERK 1/2 and MEK 1/2 as well as the pro-apoptotic signaling proteins p38 MAPK and JNK 1/2 were activated in a plasma treatment time dependent manner. In contrast to Jurkat and primary monocytes, the anti-apoptotic HSP27 was only induced in THP-1 cells in response to plasma exposure. Moreover, modulation of cytokine production and secretion was examined in the different immune cell types and co-cultured THP-1 and HaCaT keratinocytes by ELISA or flow cytometry. While Jurkat cells showed no plasma-mediated regulation of cytokine expression, THP-1 cells revealed an increased IL-8 secretion after long plasma time duration (360 s). Additionally, the intracellular expression levels of IL-6 and IL-8 were modulated in primary monocytes by plasma exposure. While short plasma treatment caused no alteration of the number of cells expressing IL-8 an up-regulation of the intracellular IL-6 level occurred after 30 s of plasma treatment. Long plasma treatment times resulted in a significant decrease of the intracellular IL-8 and IL-6 production levels. Furthermore, co-cultured THP-1 and HaCaT cells as well as mono-cultured THP-1 and HaCaT cells were examined regarding their cytokine secretion profile. Here, cells treated with plasma (180 s) as well as LPS and plasma (180 s and LPS) were compared with untreated cells. IL-6, IL-8 and GM-CSF secretion was induced by both plasma and plasma combined with LPS treatment in mono-cultivated HaCaT cells and co-cultured cells. Though, the highest cytokine secretion levels were reached in the plasma and LPS exposed co-culture. In contrast, mono-cultivated THP-1 cells only showed an increased secretion of IL-6, IL-8 and TNFa after incubation with plasma together with LPS exposed medium. In conclusion, this study revealed for the first time the non-thermal plasma-modulated expression of numerous genes and cytokines and the activation state of various signaling cascades in human immune cells. Thus, it contributes to gain a better understanding of the immune-modulatory impacts of plasma that might promote the wound healing process.
Coastal and marginal seas – like the Baltic Sea – serve as natural reaction sites for the turnover and accumulation of land-derived inputs. The main location for the modification and deposition of the introduced material is, in most cases, not the water mass, but the sediment. Its key function as central reactor in the interaction between land and sea has so far been insufficiently studied and assessed. This study was part of the interdisciplinary SECOS project that aimed to identify and evaluate the service functions of sediments in German coastal seas in the context of human use with a focus on the Baltic Sea. One of its goals was to assess sediment functions related to the intermediate storage or final sink of imported material like nutrients and contaminants, and quantify their inventory as well as their mass accumulation rates on multi-decadal to multi-centennial time scales. For that, a detailed examination of the natural and anthropogenic processes that interfere with sediment accumulation in the south-western Baltic Sea basins is essential.
In terms of climate change and climate change mitigation, the quantitative knowledge of global carbon pools is important information. On the one hand, knowledge on the amount of carbon cycling among – and stored in – global pools (i.e. Atmosphere, Biosphere, Cryosphere, Hydrosphere, and Lithosphere) may improve the reliability of models predicting atmospheric CO2 concentrations in terms of fossil fuel combustion. On the other hand, the carbon sequestration potential of specific ecosystems allows for estimating their feasibility regarding carbon trade mechanisms such as the Clean Development Mechanism or the Reducing Emissions from Deforestation and Degradation Program (REDD+). However, up to date, the majority of terrestrial carbon assessments have focused on forests and peatlands, leaving a data gap open regarding the remaining ecosystems. This data gap is likely to be explained by the relatively high carbon densities and/or productivities of forests and peatlands. Nevertheless, to get a precise as possible global picture, information on carbon pools and sequestration of other ecosystems is needed. Although desert ecosystems generally express low carbon densities, they may absolutely store a remarkable amount of carbon due to their large areal extent. In this context, Central Asian Deserts (in particular within the Turanian Deserts, i.e. Karakum, Kysylkum, Muyunkum) likely inhibit comparably high carbon pools as they express a sparse vegetation cover due to an exceptionally high annual precipitation if compared to the World’s deserts. In this dissertation, three important woody plant species – Populus euphratica and Haloxylon aphyllum and Haloxylon persicum – of Central Asian Deserts were investigated for their carbon pools and carbon sequestration potential. These species were chosen as they I) locally express high carbon densities, II) are dominant species, III) have a rather large spatial distribution, and IV) have experienced a strong degradation throughout the 20th century. Thus, they likely show a remarkable potential for carbon re-sequestration through restoration and thus for an application of carbon trade mechanisms (CHAPTER I). P. euphratica was investigated in the nature reserve Kabakly at the Amu Darya, Turkmenistan and in Iminqak at the Tarim He, Xinjiang, China. The assessment of Haloxylon species was restricted to the Turanian deserts west of the Tain Shan. To achieve a first scientific basis for large scale estimates, different methodologies, ranging from allometric formulas, over dendrochronology to remote sensing were combined (CHAPTERS II-V). In CHAPTER II allometric formulas were successfully developed for Haloxylon aphyllum and Haloxylon persicum and applied to six study sites distributed over the Turanian Deserts to represent the allometric variability of Haloxylon species in Central Asia. CHAPTER III derives another allometric formula (only based on canopy area) for H. aphyllum and combines it with a remote sensing analysis from the nature reserve Repetek. Thereby, a first large scale estimate covering the Northeastern Karakum Desert of carbon pools related to mono specific H. aphyllum stands is achieved. CHAPTER IV describes the wood structure of Populus euphratica forests in the nature reserve Kabakly (Turkmenistan) and in Iminqak (Xinjiang, China). In CHAPTER V a dendrochronological approach derives models for predicting the Net Primary Productivity (NPP) and the age of P. euphratica in the nature reserve Kabakly. Thereby, a first feasibility assessment regarding remote sensing analyses and the upscaling of the obtained NPP results is carried out. First estimates based on these local studies (CHAPTER VI), reveal carbon densities ranging from 0.1 – 26.3 t C ha 1 for the three investigated species. Highest maximum and median carbon densities were found for P. euphratica, but Haloxylon aphyllum expressed remarkable maximum carbon densities (13.1 t C ha-1), too. The total carbon pools were estimated at 6480 kt C for P. euphratica, 520 kt C for H. aphyllum stands and 6900 kt C for Haloxylon persicum shrubland. Accounting for the extent of degraded areas, the total re-sequestration potentials of the respective species were estimated at 4320 kt C, 1620 kt C and 21900 kt C, this highlighting the remarkable absolute re-sequestration potential of H. persicum shrubland despite its low average carbon densities. In the end, the main results were put into a broader context (CHAPTER VI), discussing the general feasibility of reforestations both in ecological terms as well as in terms of carbon trade mechanisms. A short example highlights the strong connection between the feasibility of reforestations and the global carbon market. Finally, open research questions are brought forth revealing the yet large research potential of Central Asian Desert ecosystems in general and in terms of carbon sequestration.
In this thesis, a stereoscopic camera system is presented that is designed for the use on parabolic flights for the investigation of dusty plasmas under microgravity conditions. This camera system consists of three synchronously triggered high-speed cameras observing a common volume of approximately (15 × 15 × 15) mm³ size. In this volume, the three-dimensional trajectories of a large number of particles surrounded by a dense dust cloud were reconstructed. For this task an intricate set of reconstruction algorithms has been developed, including a four-frame linking algorithm and a complex combined 2D/3D tracking algorithm for a reliable tracking of 3D particles. Furthermore, these algorithms effectively suppress so-called ghost particles in the evaluation process which are reconstructed from falsely identified 2D particle correspondences. Dusty plasmas under microgravity conditions are of special interest due to their complex structure and the variety of observable dynamic phenomena. Under typical discharge conditions, a central dust-free void is formed, surrounded by a dense particle cloud. Since the void is inherently dust-free, particles shot into the void can be uniquely identified and used to probe plasma properties inside this region. In the dust cloud itself, processes like self-excited dust-density waves can be observed under suitable experimental conditions. Using the presented camera setup and reconstruction algorithms, two parts of a dusty plasma under microgravity on parabolic flights are investigated. Initially, the force field creating and sustaining the central void is deduced and characterized. The combination of ion drag and electric field force is measured and compared to current models of the ion drag, showing a good agreement with these models. While previous investigations on the forces were limited to two-dimensional slices through the void, our measurements represent the first three-dimensional quantitative analysis of a large fraction of the void region. From this analysis the structure of the force field is determined and separated into a radial and a non-radial (or orthogonal) contribution. It is shown that the radial contribution dominates in the central void, while non-radial forces increase in magnitude close to the void edge. The radial domination is also observed in the velocity distribution of the probe particles which is significantly shifted to radially outward directed velocities for particles leaving the void. Assuming a strictly radial force profile in the horizontal mid-plane of the void, the friction coefficient determining the interaction of the probe particles with the neutral gas background is experimentally determined and shown to match the theoretical expectation. Subsequently, particles at the outer surface of the dust cloud are reconstructed. There, the particles are found to oscillate due to dust-density waves propagating through the high-density dust cloud. For the investigation of the correlation between waves and oscillating particles, the instantaneous wave and oscillation properties are determined and the instantaneous phase difference is obtained. Modeling the probe particles as driven, damped harmonic oscillators, these phase differences between waves and particles are interpreted with respect to the resonance frequency of the oscillating particles. Spatial variations of the phase difference are observed that may be attributed to different frequencies of the dust-density waves, or to changes of the resonance frequency induced by changing local plasma parameters. From a few measurements of particles oscillating at their resonance frequency, information about the surrounding plasma or properties of the particles themselves can be deduced. However, a larger number of reconstructed trajectories is necessary in order to interpret the phase differences on a reliable data basis. The presented camera setup in combination with the evaluation algorithms is a flexible system for the investigation of three-dimensional dusty plasmas. Its robust construction allows the operation of the system in challenging environments such as on parabolic flights, where spatial limitations and vibrations produced by the aircraft make special demands on such a diagnostic tool. This versatility makes our stereoscopic camera setup and the reconstruction process a suitable standard diagnostic for the application with dusty plasmas; this system will therefore be used in future research amongst other things for the investigation of boundary layers in extended three-dimensional dust clouds under microgravity.
The thesis investigates the occurrence of the Early Modern European witch-hunt within the distinctively diverse society of the Grand Duchy of Lithuania. Positioned at the intersection of Latin and post-Byzantine cultures, along with Western and Eastern Christianity, this region lay on the frontlines of the Reformation and Counter-Reformation. The research aims to analyze the specific characteristics of the witch-hunt in this area, considering it a case study of social and cultural interaction within a borderland. It focuses particularly on identifying the distinctive aspects of the Lithuanian witch-hunt, examining the social and cultural roots of the witch trials, and exploring their relationship to the broader social and cultural developments of the period.
Central to this study is a detailed examination of the witch trials and an analysis of court materials. The thesis posits a socio-cultural interpretation of witch persecutions, arguing that they were culturally influenced manifestations of social tensions, enacted through legal mechanisms. The emergence of new Early Modern challenges, such as the social consequences of agrarian reform, the expansion of manorialism, and serfdom, led to novel tensions, conflicts, and responses, including accusations of witchcraft. The importation of authoritative foreign ideas about witchcraft reinvigorated, facilitated, and shaped pre-existing moderate indigenous beliefs, a process facilitated by religious struggles and Catholic post-Tridentine confessionalization. The Lithuanian legal system provided an environment conducive to an intensive witch-hunt, with witchcraft being a secular grave felony tried in highly decentralized and poorly supervised courts. However, this potential was largely unrealized. The study argues that the cultural diversity of the society played a major role in inhibiting the spread of Western witchcraft discourse, thereby limiting the extent of the witch-hunt in the Grand Duchy of Lithuania.
This work investigates turbulence in the core plasma of the optimised stellarator
Wendelstein 7-X. It focuses on experimental characterisation and
evaluation of the electrostatic micro-instabilities, which drive turbulent fluctuations,
and the saturation of turbulence by zonal flows. Expectations for
Wendelstein 7-X are formulated by reviewing theoretical work and with
the help of gyrokinetic simulations. The experimental analysis centres on
line-integrated density fluctuation measurements with the phase contrast
imagining diagnostic in electron cyclotron heated hydrogen discharges. An
absolute amplitude calibration was implemented, and a method for reliable
determination of dominant phase velocities in wavenumber-frequency
spectra of density fluctuations has been developed. Line-averaged density
fluctuation levels are observed to vary between magnetic configurations.
The wavenumber spectra exhibit a dual cascade structure, indicating fully
developed turbulence. The dominant instability driving turbulent density
fluctuations on transport relevant scales is identified as ion-temperaturegradient-
driven modes, which are mainly localised in the edge region of the
confined plasma. Despite the line-integrated nature of the measurement, the
localisation of density fluctuations is shown by comparing their dominant
phase velocity with the radial profile of the E × B rotation velocity due to
the ambipolar neoclassical electric field. Nonlinear gyrokinetic simulations
and a simplified plasma rotation model within a synthetic diagnostic confirm
the localisation. Oscillations of the dominant phase velocity indicate
the existence of zonal flows as a saturation mechanism of ion-temperaturegradient-
driven turbulence. A direct effect on turbulent density fluctuation
amplitudes and radial transport is observed.
In contrast to its terrestrial counterpart, the metabolic degradation of marine polysaccharides is underexplored. This work aimed to functionally characterize ulvan- and xylan-degrading enzymes from marine Bacteroidetes in order to clarify the metabolic degradation pathway. For the provision of a broad polysaccharide substrate spectrum, ulvan from several different algal sources was extracted to be used in further characterization experiments. The structural differences of these ulvans could be demonstrated by enzymatic degradation with ulvan-active enzymes. In order to clarify the synergistic catalytic effects of polysaccharide sulfatases with GHs in the degradation process of ulvan, several putative sulfatases from F. agariphila were produced recombinantly in E. coli. For that, a coexpression with an FGE encoding gene was required. It could be demonstrated that several glycoside hydrolases are inhibited, if their
substrate is sulfated at the cleavage position and that a previous desulfation using one of the sulfatases enabled the further degradation. Some of the sulfatases showed an endolytic or exolytic cleavage behavior like reported for several GHs. With the combined catalytic activities, it was possible to successfully elucidate the complex ulvan degradation mechanism for the first time, which enables the use of ulvan as a biotechnological source for the production of fine chemicals and pharmaceuticals. This degradation mechanism was shown to be complemented by an alternative pathway that helps with the degradation of uronic acid-containing oligosaccharides. Here, the synergistic effects of a multimodular enzyme containing a sulfatase and rhamnosidase domain were demonstrated. Furthermore, the first dehydratase participating in the degradation of oligosaccharides was revealed. The functional characterization of putative xylan-targeting PULs from two Flavobacteriia revealed the existence of marine endolytic and exolytic xylanases. The enzymes of these PULs were produced recombinantly in E. coli and were used in biocatalysis reactions on xylan from beechwood, xylan from P. palmata or commercial xylooligosaccharide standards. Further side chain-active GHs were found to exclusively be active on either standards or xylan. The great variation of genetic equipment was demonstrated by comparing the enzyme activities of these PUL structures assuming different ecological adaptations of these organisms especially, because these PULs do not code for any putative sulfatases, which is uncommon for PULs targeting xylan. A different degradation behavior of the investigated enzymes suggested a preferred conversion of β-1,4-linked xylan, potentially present in some microalgae. The acquired insight of the metabolic ulvan and xylan utilization greatly expands the scientific knowledge about the ecologic interplays in marine environments concerning the polysaccharide utilization. It indicates the necessity of backup mechanisms for metabolic processes in order to get access to complex marine carbon sources in nature. Several small degradation cascades complement each other to break down substrate compounds to monomeric level for the use of structurally diverse polysaccharides. This expands the insights into the metabolic processes in the degradation of marine polysaccharides, which are an important part of the understanding of the ecological interactions in aquatic habitats and the ocean’s carbon cycle.
The characterization of ulvan- and xylan-active enzymes and the clarification of their substrate scopes allow to use these enzymes in future production of carbohydrate-derived chemical products for many industrial applications, making it possible to use algal waste for recycling to high value materials with even beneficial effect for the environment.
With this thesis, studies which form the bedrock for the long term goal of first wall heat load control and optimization for the advanced stellarator Wendelstein 7-X are developed, described and put into context. It is laid out how reconstruction of features of the edge magnetic field from plasma facing component heat loads is an important first step and can successfully be achieved by artificial neural networks. A detailed study of plasma facing component heat load distribution, potential overloads and overload mitigation possibilities is made in first order approximation of the impact of the main plasma dynamic effects.
This work focuses the glycoprotein H of PrV which was analysed by structure-based functional analyses by targeted site-directed mutagenesis. Disulfid bridges were introduced at specific sites and the effects on the fusion mechanism investigated. A revertant was obtained and characterised during the studies, as well as chimeric glycoprotein H proteins were constructed, combining the different domains of the glycoproteins Hs of PrV and HSV1.