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The aim of this thesis was the application of the functional prepolymer NCO-sP(EO-stat-PO) for the development of new biomaterials. First, the influence of the star-shaped polymers on the mechanical properties of biocements and bone adhesives was investigated. 3-armed star-shaped macromers were used as an additive for a mineral bone cement, and the influence on the mechanical properties was studied. Additionally, a previously developed bone adhesive was examined regarding cytocompatibility. The second topic was the examination of novel functionalization steps which were performed on the surface of electrospun fibers modified with NCO-sP(EO-stat-PO). This established method of functionalizing electrospun meshes was advanced regarding the modification with proteins which was then demonstrated in a biological application. Two different kinds of antibodies were immobilized on the fiber surface in a consecutive manner and the influence of these proteins on the cell behavior was investigated. The final topic involved the quantification of surface-bound peptide sequences. By functionalization of the peptides with the UV-reactive molecule 2-mercaptopyridine it was possible to quantify this compound via UV measurements by cleavage of disulfide bridges and indirectly draw conclusions about the number of immobilized peptides.
In the field of mineral biocements and bone adhesives, NCO-sP(EO-stat-PO) was able to influence the setting behavior and mechanical performance of mineral bone cements based on calcium phosphate chemistry. The addition of NCO-sP(EO-stat-PO) resulted in a pseudo-ductile fracture behavior due to the formation of a hydrogel network in the cement, which was then mineralized by nanosized hydroxyapatite crystals following cement setting. Accordingly, a commercially available aluminum silicate cement from civil engineering could be modified.
In addition, it could be shown that the use of NCO-sP(EO-stat-PO) is beneficial for adjusting specific material properties of bone adhesives. Here, the crosslinking behavior of the prepolymer in an aqueous medium was exploited to form an interpenetrating network (IPN) together with a photochemically curing poly(ethylene glycol) dimethacrylate (PEGDMA) matrix. This could be used for the development of a bone adhesive with an improved adhesion to bone in a wet environment. The developed bone adhesive was further investigated in terms of possible influences of the initiator systems. In addition, the material system was tested for cytocompatibility by using different cell lines.
Moreover, the preparation of electrospun fiber meshes via solution electrospinning consisting of poly(lactide-co-glycolide) (PLGA) as a backbone polymer and NCO-sP(EO-stat-PO) as functional additive is an established method for the application of the meshes as a replacement of the native extracellular matrix (ECM). In general, these fibers reveal diameters in the nanometer range, are protein and cell repellent due to the hydrophilic properties of the prepolymer and show a specific biofunctionalization by immobilization of peptide sequences. Here, the isocyanate groups presented on the fiber surface after electrospinning were used to carry out various functionalization steps, while retaining the properties of protein and cell repellency. The modification of the electrospun fibers involved the immobilization of analogs or antagonists of tumor necrosis factor (TNF) and the indirect detection of these by interaction with a light-producing enzyme. Here, a multimodal modification of the fiber surface with RGD to mediate cell adhesion and two different antibodies could be achieved. After culturing the cell line HT1080, the pro- or anti-inflammatory response of cells could be detected by IL-8 specific ELISA measurements.
Furthermore, the quantification of molecules on the surface of electrospun fibers was investigated. It was tested whether the detection by means of super-resolution microscopy would be possible. Therefore, experiments were performed with short amino acid sequences such as RGD for quantification by fluorescence microscopy. Based on earlier results, in which a UV-spectrometrically active molecule was used to detect the quantification of RGD, it was shown that short peptides can also be quantified in a small scale on flat functional substrates (2D) such as NCO-sP(EO-stat-PO) hydrogel coatings, and modified electrospun fibers produced from PLGA and NCO-sP(EO-stat-PO) (3D). In addition, a collagen sequence was used to prove that a successful quantification can be carried out as well for longer peptide chains.
These studies have revealed that NCO-sP(EO-stat-PO) can serve as a functional additive for many applications and should be considered for further studies on the development of novel biomaterials. The rapid crosslinking reaction, the resulting hydrogel formation and the biocompatibility are to be mentioned as positive properties, which makes the prepolymer interesting for future applications.
The first part of this thesis deals with the approximability of the traveling salesman problem. This problem is defined on a complete graph with edge weights, and the task is to find a Hamiltonian cycle of minimum weight that visits each vertex exactly once. We study the most important multiobjective variants of this problem. In the multiobjective case, the edge weights are vectors of natural numbers with one component for each objective, and since weight vectors are typically incomparable, the optimal Hamiltonian cycle does not exist. Instead we consider the Pareto set, which consists of those Hamiltonian cycles that are not dominated by some other, strictly better Hamiltonian cycles. The central goal in multiobjective optimization and in the first part of this thesis in particular is the approximation of such Pareto sets.
We first develop improved approximation algorithms for the two-objective metric traveling salesman problem on multigraphs and for related Hamiltonian path problems that are inspired by the single-objective Christofides' heuristic. We further show arguments indicating that our algorithms are difficult to improve. Furthermore we consider multiobjective maximization versions of the traveling salesman problem, where the task is to find Hamiltonian cycles with high weight in each objective. We generalize single-objective techniques to the multiobjective case, where we first compute a cycle cover with high weight and then remove an edge with low weight in each cycle. Since weight vectors are often incomparable, the choice of the edges of low weight is non-trivial. We develop a general lemma that solves this problem and enables us to generalize the single-objective maximization algorithms to the multiobjective case. We obtain improved, randomized approximation algorithms for the multiobjective maximization variants of the traveling salesman problem. We conclude the first part by developing deterministic algorithms for these problems.
The second part of this thesis deals with redundancy properties of complete sets. We call a set autoreducible if for every input instance x we can efficiently compute some y that is different from x but that has the same membership to the set. If the set can be split into two equivalent parts, then it is called weakly mitotic, and if the splitting is obtained by an efficiently decidable separator set, then it is called mitotic. For different reducibility notions and complexity classes, we analyze how redundant its complete sets are.
Previous research in this field concentrates on polynomial-time computable reducibility notions. The main contribution of this part of the thesis is a systematic study of the redundancy properties of complete sets for typical complexity classes and reducibility notions that are computable in logarithmic space. We use different techniques to show autoreducibility and mitoticity that depend on the size of the complexity class and the strength of the reducibility notion considered. For small complexity classes such as NL and P we use self-reducible, complete sets to show that all complete sets are autoreducible. For large complexity classes such as PSPACE and EXP we apply diagonalization methods to show that all complete sets are even mitotic. For intermediate complexity classes such as NP and the remaining levels of the polynomial-time hierarchy we establish autoreducibility of complete sets by locally checking computational transcripts. In many cases we can show autoreducibility of complete sets, while mitoticity is not known to hold. We conclude the second part by showing that in some cases, autoreducibility of complete sets at least implies weak mitoticity.
Adipose tissue defects and related pathologies still represent major challenges in reconstructive surgery. Based on to the paradigm ‘replace with alike’, adipose tissue is considered the ideal substitute material for damaged soft tissue [1-3]. Yet the transfer of autologous fat, particularly larger volumes, is confined by deficient and unpredictable long term results, as well as considerable operative morbidity at the donor and recipient site [4-6], calling for innovative treatment options to improve patient care.
With the aim to achieve complete regeneration of soft tissue defects, adipose tissue engineering holds great promise to provide functional, biologically active adipose tissue equivalents. Here, especially long-term maintenance of volume and shape, as well as sufficient vascularization of engineered adipose tissue represent critical and unresolved challenges [7-9]. For adipose tissue engineering approaches to be successful, it is thus essential to generate constructs that retain their initial volume in vivo, as well as to ensure their rapid vascularization to support cell survival and differentiation for full tissue regeneration [9,10]. Therefore, it was the ultimate goal of this thesis to develop volume-stable 3D adipose tissue constructs and to identify applicable strategies for sufficient vascularization of engineered constructs. The feasibility of the investigated approaches was verified by translation from in vitro to in vivo as a critical step for the advancement of potential regenerative therapies.
For the development of volume-stable constructs, the combination of two biomaterials with complementary properties was successfully implemented. In contrast to previous approaches in the field using mainly non-degradable solid structures for mechanical protection of developing adipose tissue [11-13], the combination of a cell-instructive hydrogel component with a biodegradable porous support structure of adequate texture was shown advantageous for the generation of volume-stable adipose tissue. Specifically, stable fibrin hydrogels previously developed in our group [14] served as cell carrier and supported the adipogenic development of adipose-derived stem cells (ASCs) as reflected by lipid accumulation and leptin secretion. Stable fibrin gels were thereby shown to be equally supportive of adipogenesis compared to commercial TissuCol hydrogels in vitro. Using ASCs as a safe source of autologous cells [15,16] added substantial practicability to the approach. To enhance the mechanical strength of the engineered constructs, porous biodegradable poly(ε caprolactone)-based polyurethane (PU) scaffolds were introduced as support structures and shown to exhibit adequately sized pores to host adipocytes as well as interconnectivity to allow coherent tissue formation and vascularization. Low wettability and impaired cell attachment indicated that PU scaffolds alone were insufficient in retaining cells within the pores, yet cytocompatibility and differentiation of ASCs were adequately demonstrated, rendering the PU scaffolds suitable as support structures for the generation of stable fibrin/PU composite constructs (Chapter 3).
Volume-stable adipose tissue constructs were generated by seeding the pre-established stable fibrin/PU composites with ASCs. Investigation of size and weight in vitro revealed that composite constructs featured enhanced stability relative to stable fibrin gels alone. Comparing stable fibrin gels and TissuCol as hydrogel components, it was found that TissuCol gels were less resilient to degradation and contraction. Composite constructs were fully characterized, showing good cell viability of ASCs and strong adipogenic development as indicated by functional analysis via histological Oil Red O staining of lipid vacuoles, qRT-PCR analysis of prominent adipogenic markers (PPARγ, C/EBPα, GLUT4, aP2) and quantification of leptin secretion. In a pilot study in vivo, investigating the suitability of the constructs for transplantation, stable fibrin/PU composites provided with a vascular pedicle gave rise to areas of well-vascularized adipose tissue, contrasted by insufficient capillary formation and adipogenesis in constructs implanted without pedicle. The biomaterial combination of stable fibrin gels and porous biodegradable PU scaffolds was thereby shown highly suitable for the generation of volume-stable adipose tissue constructs in vivo, and in addition, the effectiveness of immediate vascularization upon implantation to support adipose tissue formation was demonstrated (Chapter 4).
Further pursuing the objective to investigate adequate vascularization strategies for engineered adipose tissue, hypoxic preconditioning was conducted as a possible approach for in vitro prevascularization. In 2D culture experiments, analysis on the cellular level illustrated that the adipogenic potential of ASCs was reduced under hypoxic conditions when applied in the differentiation phase, irrespective of the oxygen tension encountered by the cells during expansion. Hypoxic treatment of ASCs in 3D constructs prepared from stable fibrin gels similarly resulted in reduced adipogenesis, whereas endothelial CD31 expression as well as enhanced leptin and vascular endothelial growth factor (VEGF) secretion indicated that hypoxic treatment indeed resulted in a pro-angiogenic response of ASCs. Especially the observed profound regulation of leptin production by hypoxia and the dual role of leptin as adipokine and angiogenic modulator were considered an interesting connection advocating further study. Having confirmed the hypothesis that hypoxia may generate a pro-angiogenic milieu inside ASC-seeded constructs, faster vessel ingrowth and improved vascularization as well as an enhanced tolerance of hypoxia-treated ASCs towards ischemic conditions upon implanatation may be expected, but remain to be verified in rodent models in vivo (Chapter 5).
Having previously been utilized for bone and cartilage engineering [17-19], as well as for revascularization and wound healing applications [20-22], stromal-vascular fraction (SVF) cells were investigated as a novel cell source for adipose tissue engineering. Providing cells with adipogenic differentiation as well as vascularization potential, the SVF was applied with the specific aim to promote adipogenesis and vascularization in engineered constructs in vivo. With only basic in vitro investigations by Lin et al. addressing the SVF for adipose repair to date [23], the present work thoroughly investigated SVF cells for adipose tissue construct generation in vitro, and in particular, pioneered the application of these cells for adipose tissue engineering in vivo.
Initial in vitro experiments compared SVF- and ASC-seeded stable fibrin constructs in different medium compositions employing preadipocyte (PGM-2) and endothelial cell culture medium (EGM-2). It was found that a 1:1 mixture of PGM-2 and EGM-2, as previously established for co-culture models of adipogenesis [24], efficiently maintained cells with adipogenic and endothelial potential in SVF-seeded constructs in short and long-term culture setups. Observations on the cellular level were supported by analysis of mRNA expression of characteristic adipogenic and endothelial markers. In preparation of the evaluation of SVF-seeded constructs under in vivo conditions, a whole mount staining (WMS) method, facilitating the 3D visualization of adipocytes and blood vessels, was successfully established and optimized using native adipose tissue as template (Chapter 6).
In a subcutaneous nude mouse model, SVF cells were, for the first time in vivo, elucidated for their potential to support the functional assembly of vascularized adipose tissue. Investigating the effect of adipogenic precultivation of SVF-seeded stable fibrin constructs in vitro prior to implantation on the in vivo outcome, hormonal induction was shown beneficial in terms of adipocyte development, whereas a strong vascularization potential was observed when no adipogenic inducers were added. Via histological analysis, it was proven that the developed structures were of human origin and derived from the implanted cells. Applying SVF cells without precultivation in vitro but comparing two different fibrin carriers, namely stable fibrin and TissuCol gels, revealed that TissuCol profoundly supported adipose formation by SVF cells in vivo. This was contrasted by only minor SVF cell development and a strong reduction of cell numbers in stable fibrin gels implanted without precultivation. Histomorphometric analysis of adipocytes and capillary structures was conducted to verify the qualitative results, concluding that particularly SVF cells in TissuCol were highly suited for adipose regeneration in vivo. Employing the established WMS technique, the close interaction of mature adipocytes and blood vessels in TissuCol constructs was impressively shown and via species-specific human vimentin staining, the expected strong involvement of implanted SVF cells in the formation of coherent adipose tissue was confirmed (Chapter 7).
With the development of biodegradable volume-stable adipose tissue constructs, the application of ASCs and SVF cells as two promising cell sources for functional adipose regeneration, as well as the thorough evaluation of strategies for construct vascularization in vitro and in vivo, this thesis provides valuable solutions to current challenges in adipose tissue engineering. The presented findings further open up new perspectives for innovative treatments to cure soft tissue defects and serve as a basis for directed approaches towards the generation of clinically applicable soft tissue substitutes.
As a cradle of ancient Chinese civilization, the Yellow River Basin has a very long human-environment interrelationship, where early anthropogenic activities re- sulted in large scale landscape modifications. Today, the impact of this relationship
has intensified further as the basin plays a vital role for China’s continued economic
development. It is one of the most densely-populated, fastest growing, and most dynamic
regions of China with abundant natural and environmental resources providing a livelihood for almost 190 million people. Triggered by fundamental economic reforms, the
basin has witnessed a spectacular economic boom during the last decades and can be
considered as an exemplary blueprint region for contemporary dynamic Global Change
processes occurring throughout the country, which is currently transitioning from an
agrarian-dominated economy into a modern urbanized society. However, this resourcesdemanding growth has led to profound land use changes with adverse effects on the Yellow
River social-ecological systems, where complex challenges arise threatening a long-term
sustainable development.
Consistent and continuous remote sensing-based monitoring of recent and past land
cover and land use change is a fundamental requirement to mitigate the adverse impacts
of Global Change processes. Nowadays, technical advancement and the multitude of
available satellite sensors, in combination with the opening of data archives, allow the
creation of new research perspectives in regional land cover applications over heterogeneous landscapes at large spatial scales. Despite the urgent need to better understand the
prevailing dynamics and underlying factors influencing the current processes, detailed
regional specific land cover data and change information are surprisingly absent for this
region.
In view of the noted research gaps and contemporary developments, three major objectives are defined in this thesis. First (i), the current and most pressing social-ecological
challenges are elaborated and policy and management instruments towards more sustainability are discussed. Second (ii), this thesis provides new and improved insights on
the current land cover state and dynamics of the entire Yellow River Basin. Finally (iii),
the most dominant processes related to mining, agriculture, forest, and urban dynamics
are determined on finer spatial and temporal scales.
The complex and manifold problems and challenges that result from long-term abuse
of the water and land resources in the basin have been underpinned by policy choices,
cultural attitude, and institutions that have evolved over centuries in China. The tremendous economic growth that has been mainly achieved by extracting water and exploiting
land resources in a rigorous, but unsustainable manner, might not only offset the economic benefits, but could also foster social unrest. Since the early emergence of the first Chinese dynasties, flooding was considered historically as a primary issue in river management and major achievements have been made to tame the wild nature of the Yellow
River. Whereas flooding is therefore largely now under control, new environmental and
social problems have evolved, including soil and water pollution, ecological degradation,
biodiversity decline, and food security, all being further aggravated by anthropogenic
climate change. To resolve the contemporary and complex challenges, many individual
environmental laws and regulations have been enacted by various Chinese ministries.
However, these policies often pursue different, often contradictory goals, are too general
to tackle specific problems and are usually implemented by a strong top-down approach.
Recently, more flexible economic and market-based incentives (pricing, tradable permits,
investments) have been successfully adopted, which are specifically tailored to the respective needs, shifting now away from the pure command and regulating instruments.
One way towards a more holistic and integrated river basin management could be the
establishment of a common platform (e.g. a Geographical Information System) for data
handling and sharing, possibly operated by the Yellow River Basin Conservancy Commission (YRCC), where available spatial data, statistical information and in-situ measures
are coalesced, on which sustainable decision-making could be based. So far, the collected
data is hardly accessible, fragmented, inconsistent, or outdated.
The first step to address the absence and lack of consistent and spatially up-to-date
information for the entire basin capturing the heterogeneous landscape conditions was
taken up in this thesis. Land cover characteristics and dynamics were derived from
the last decade for the years 2003 and 2013, based on optical medium-resolution hightemporal MODIS Normalized Differenced Vegetation Index (NDVI) time series at 250 m.
To minimize the inherent influence of atmospheric and geometric interferences found in
raw high temporal data, the applied adaptive Savitzky-Golay filter successfully smoothed
the time series and substantially reduced noise. Based on the smoothed time series
data, a large variety of intra-annual phenology metrics as well as spectral and multispectral annual statistics were derived, which served as input variables for random
forest (RF) classifiers. High quality reference data sets were derived from very high
resolution imagery for each year independently of which 70 % trained the RF models. The
accuracy assessments for all regionally specific defined thematic classes were based on the
remaining 30 % reference data split and yielded overall accuracies of 87 % and 84 % for
2003 and 2013, respectively. The first regional adapted Yellow River Land Cover Products
(YRB LC) depict the detail spatial extent and distribution of the current land cover status
and dynamics. The novel products overall differentiate overall 18 land cover and use
classes, including classes of natural vegetation (terrestrial and aquatic), cultivated classes,
mosaic classes, non-vegetated, and artificial classes, which are not presented in previous
land cover studies so far.
Building on this, an extended multi-faceted land cover analysis on the most prominent
land cover change types at finer spatial and temporal scales provides a better and more
detailed picture of the Yellow River Basin dynamics. Precise spatio-temporal products
about mining, agriculture, forest, and urban areas were examined from long-trem Landsat
satellite time series monitored at annual scales to capture the rapid rate of change in four
selected focus regions. All archived Landsat images between 2000 and 2015 were used to
derive spatially continuous spectral-temporal, multi-spectral, and textural metrics. For
each thematic region and year RF models were built, trained and tested based on a stablepixels reference data set. The automated adaptive signature (AASG) algorithm identifies those pixels that did not change between the investigated time periods to generate a
mono-temporal reference stable-pixels data set to keep manual sampling requirements
to a minimum level. Derived results gained high accuracies ranging from 88 % to 98 %.
Throughout the basin, afforestation on the Central Loess Plateau and urban sprawl are
identified as most prominent drivers of land cover change, whereas agricultural land
remained stable, only showing local small-scale dynamics. Mining operations started in
2004 on the Qinghai-Tibet Plateau, which resulted in a substantial loss of pristine alpine
meadows and wetlands.
In this thesis, a novel and unique regional specific view of current and past land cover
characteristics in a complex and heterogeneous landscape was presented by using a
multi-source remote sensing approach. The delineated products hold great potential for
various model and management applications. They could serve as valuable components
for effective and sustainable land and water management to adapt and mitigate the
predicted consequences of Global Change processes.
Analysis of Drug Impurities by Means of Chromatographic Methods: Targeted and Untargeted Approaches
(2022)
The presented works aimed on the analysis of new impurities in APIs and medicinal products. Different subtypes of LC were coupled to suitable detection methods, i.e. UV and various MS techniques, depending on the chemical natures of the analytes and the analytical task.
Unexpected impurities in medicinal products and APIs caused several scandals in the past, concomitant with fatalities or severe side effects in human and veterinary patients. The detection of nitrosamines in sartans led to the discovery of nitrosamines in various other drugs, of which the antibiotic rifampicin was analyzed in this work. An examination of the synthesis of rifampicin revealed a high potential for the formation of 4-methyl-1-nitrosopiperazine (MeNP). An LC-MS/HRMS method suitable for the quantification of MeNP was applied in the analysis of drugs collected from Brazil, Comoros, India, Nepal, and Tanzania, where a single dose of rifampicin is used in the post-exposure prophylaxis of leprosy. All batches were contaminated with MeNP, ranging from 0.7-5.1 ppm. However, application of rifampicin containing up to 5 ppm MeNP was recommended by the regulatory authorities for the post-exposure prophylaxis of leprosy.
In the 1990s the aminoglycoside antibiotic gentamicin attracted attention after causing fatalities in the USA, but the causative agent was never identified unequivocally. The related substance sisomicin was recognized as a lead impurity by the Holzgrabe lab at the University of Würzburg: sisomicin was accompanied by a variety of other impurities and batches containing sisomicin had caused the fatalities. In 2016, anaphylactic reactions were reported after application of gentamicin. A contamination of the medicinal products with histamine, an impurity of the raw material fish peptone used upon the production, could be identified as the cause of the adverse effects. Batches of gentamicin sulfate, which had been stored at the University of Würzburg since the earlier investigations, were analyzed regarding their contamination with histamine to determine whether the biogenic amine was responsible for the 1990s fatalities as well. Furthermore, a correlation with the lead impurity sisomicin was checked. Histamine could be detected in all analyzed batches, but at a lower level than in the batches responsible for the anaphylactic reactions. Moreover, there is no correlation of histamine with the lead impurity sisomicin. Hence, the causative agent for the 1990s fatalities was not histamine and remains unknown.
Another source of impurities is the reaction of APIs with excipients, e.g. the esterification of naproxen with PEG 600 in soft gel capsules. The influence of the formulation’s composition on this reaction was investigated by means of LC-UV. Therefore, the impurity naproxen-PEG-ester (NPEG) was synthesized and used for the development of a method suitable for the analysis of soft gel capsule formulations. Different formulations were stressed for 7 d at 60 °C and the relative amount of NPEG was determined. The formation of NPEG was influenced by the concentrations of water and lactic acid, the pH, and the drug load of the formulation, which can easily be explained by the chemistry behind esterification reactions.
Keeping in mind the huge variety of sources of impurities, it might be impossible to predict all potential impurities of a drug substance/product. Targeted and untargeted approaches were combined in the impurity profiling of bisoprolol fumarate. Eight versions of an LC-HRMS method were developed to enable the detection of a maximum number of impurities: an acidic and a basic buffered LC was coupled to MS detection applying ESI and APCI, both in positive in negative mode. MS and MS/MS data were acquired simultaneously by information dependent acquisition. In the targeted approach, potential impurities were derived from a reaction matrix based on the synthesis route of the API, while the untargeted part was based on general unknown comparative screening to identify additional signals. 18 and 17 impurities were detected in the targeted and the untargeted approach, respectively. The molecular formulae were assessed based on the exact mass and the isotope pattern. Theoretical fragment spectra generated by in silico fragmentation were matched with experimental data to estimate the plausibility of proposed/elucidated structures. Moreover, the detected impurities were quantified with respect to an internal standard.
The field of genetics faces a lot of challenges and opportunities in both research and diagnostics due to the rise of next generation sequencing (NGS), a technology that allows to sequence DNA increasingly fast and cheap.
NGS is not only used to analyze DNA, but also RNA, which is a very similar molecule also present in the cell, in both cases producing large amounts of data.
The big amount of data raises both infrastructure and usability problems, as powerful computing infrastructures are required and there are many manual steps in the data analysis which are complicated to execute.
Both of those problems limit the use of NGS in the clinic and research, by producing a bottleneck both computationally and in terms of manpower, as for many analyses geneticists lack the required computing skills.
Over the course of this thesis we investigated how computer science can help to improve this situation to reduce the complexity of this type of analysis.
We looked at how to make the analysis more accessible to increase the number of people that can perform OMICS data analysis (OMICS groups various genomics data-sources).
To approach this problem, we developed a graphical NGS data analysis pipeline aimed at a diagnostics environment while still being useful in research in close collaboration with the Human Genetics Department at the University of Würzburg.
The pipeline has been used in various research papers on covering subjects, including works with direct author participation in genomics, transcriptomics as well as epigenomics.
To further validate the graphical pipeline, a user survey was carried out which confirmed that it lowers the complexity of OMICS data analysis.
We also studied how the data analysis can be improved in terms of computing infrastructure by improving the performance of certain analysis steps.
We did this both in terms of speed improvements on a single computer (with notably variant calling being faster by up to 18 times), as well as with distributed computing to better use an existing infrastructure.
The improvements were integrated into the previously described graphical pipeline, which itself also was focused on low resource usage.
As a major contribution and to help with future development of parallel and distributed applications, for the usage in genetics or otherwise, we also looked at how to make it easier to develop such applications.
Based on the parallel object programming model (POP), we created a Java language extension called POP-Java, which allows for easy and transparent distribution of objects.
Through this development, we brought the POP model to the cloud, Hadoop clusters and present a new collaborative distributed computing model called FriendComputing.
The advances made in the different domains of this thesis have been published in various works specified in this document.
The extracellular matrix within connective tissues represents a structural scaffold as well as a barrier for motile cells, such as invading tumor cells or passenger leukocytes. It remains unclear how different cell types utilize matrix-degrading enzymes for proteolytic migration strategies and, on the other hand, non-proteolytic strategies to overcome 3D fibrillar matrix networks. To monitor cell migration, a 3D collagen model in vitro or the mouse dermis in vivo were used, in combination with time-lapse video-, confocal- or intravital multiphoton-microscopy, and computer-assisted cell tracking. Expression of proteases, including several MMPs, ADAMs, serine proteases and cathepsins, was shown by flow cytometry, Western blot, zymography, and RT-PCR. Protease activity by migrating HT-1080 fibrosarcoma cells resulting in collagenolysis in situ and generation of tube-like matrix defects was detected by three newly developed techniques:(i) quantitative FITC-release from FITC-labelled collagen, (ii) structural alteration of the pyhsical matrix structure (macroscopically and microscopically), and (iii) the visualization of focal in situ cleavage of individual collagen fibers. The results show that highly invasive ollagenolytic cells utilized a spindle-shaped "mesenchymal" migration strategy, which involved beta1 integrindependent interaction with fibers, coclustering of beta1 integrins and matrix metalloproteinases (MMPs) at fiber bundling sites, and the proteolytic generation of a tube-like matrix-defect by MMPs and additional proteases. In contrast to tumor cells, activated T cells migrated through the collagen fiber network by flexible "amoeboid" crawling including a roundish, elliptoid shape and morphological adaptation along collagen fibers, which was independent of collagenase function and fiber degradation. Abrogation of collagenolysis in tumor cells was achieved by a cocktail of broad-spectrum protease inhibitors at non-toxic conditions blocking collagenolysis by up to 95%. While in T cells protease inhibition induced neither morphodynamic changes nor reduced migration rates, in tumor cells a time-dependent conversion was obtained from proteolytic mesenchymal to non-proteolytic amoeboid migration in collagen lattices in vitro as well as the mouse dermis in vivo monitored by intravital microscopy. Tumor cells vigorously squeezed through matrix gaps and formed constriction rings in regions of narrow space, while the matrix structure remained intact. MMPs were excluded from fiber binding sites and beta1 integrin distribution was non-clustered linear. Besides for fibrosarcoma cells, this mesenchymal-toameboid transition (MAT) was confirmed for epithelial MDA-MB-231 breast carcinoma cells. In conclusion, cells of different origin exhibit significant diversity as well as plasticity of protease function in migration. In tumor cells, MAT could respresent a functionally important cellular and molecular escape pathway in tumor invasion and migration.
The classification of isoparametric hypersurfaces in spheres with a homogeneous focal manifold is a project that has been started by Linus Kramer. It extends results by E. Cartan and Hsiang and Lawson. Kramer does most part of this classification in his Habilitationsschrift. In particular he obtains a classification for the cases where the homogeneous focal manifold is at least 2-connected. Results of E. Cartan, Dorfmeister and Neher, and Takagi also solve parts of the classification problem. This thesis completes the classification. We classify all closed isoparametric hypersurfaces in spheres with g>2 distinct principal curvatures one of whose multiplicities is 2 such that the lower dimensional focal manifold is homogeneous. The methods are essentially the same as in Kramer's 'Habilitationsschrift'. The cohomology of the focal manifolds in question is known. This leads to two topological classification problems, which are also solved in this thesis. We classify simply connected homogeneous spaces of compact Lie groups with the same integral cohomology ring as a product of spheres S^2 x S^m and m odd on the one hand and a truncated polynomial ring Q[a]/(a^m) with one generator of even degree and m > 1 as its rational cohomology ring on the other hand.
A theory of managed floating
(2003)
After the experience with the currency crises of the 1990s, a broad consensus has emerged among economists that such shocks can only be avoided if countries that decided to maintain unrestricted capital mobility adopt either independently floating exchange rates or very hard pegs (currency boards, dollarisation). As a consequence of this view which has been enshrined in the so-called impossible trinity all intermediate currency regimes are regarded as inherently unstable. As far as the economic theory is concerned, this view has the attractive feature that it not only fits with the logic of traditional open economy macro models, but also that for both corner solutions (independently floating exchange rates with a domestically oriented interest rate policy; hard pegs with a completely exchange rate oriented monetary policy) solid theoretical frameworks have been developed. Above all the IMF statistics seem to confirm that intermediate regimes are indeed less and less fashionable by both industrial countries and emerging market economies. However, in the last few years an anomaly has been detected which seriously challenges this paradigm on exchange rate regimes. In their influential cross-country study, Calvo and Reinhart (2000) have shown that many of those countries which had declared themselves as ‘independent floaters’ in the IMF statistics were charaterised by a pronounced ‘fear of floating’ and were actually heavily reacting to exchange rate movements, either in the form of an interest rate response, or by intervening in foreign exchange markets. The present analysis can be understood as an approach to develop a theoretical framework for this managed floating behaviour that – even though it is widely used in practice – has not attracted very much attention in monetary economics. In particular we would like to fill the gap that has recently been criticised by one of the few ‘middle-ground’ economists, John Williamson, who argued that “managed floating is not a regime with well-defined rules” (Williamson, 2000, p. 47). Our approach is based on a standard open economy macro model typically employed for the analysis of monetary policy strategies. The consequences of independently floating and market determined exchange rates are evaluated in terms of a social welfare function, or, to be more precise, in terms of an intertemporal loss function containing a central bank’s final targets output and inflation. We explicitly model the source of the observable fear of floating by questioning the basic assumption underlying most open economy macro models that the foreign exchange market is an efficient asset market with rational agents. We will show that both policy reactions to the fear of floating (an interest rate response to exchange rate movements which we call indirect managed floating, and sterilised interventions in the foreign exchange markets which we call direct managed floating) can be rationalised if we allow for deviations from the assumption of perfectly functioning foreign exchange markets and if we assume a central bank that takes these deviations into account and behaves so as to reach its final targets. In such a scenario with a high degree of uncertainty about the true model determining the exchange rate, the rationale for indirect managed floating is the monetary policy maker’s quest for a robust interest rate policy rule that performs comparatively well across a range of alternative exchange rate models. We will show, however, that the strategy of indirect managed floating still bears the risk that the central bank’s final targets might be negatively affected by the unpredictability of the true exchange rate behaviour. This is where the second policy measure comes into play. The use of sterilised foreign exchange market interventions to counter movements of market determined exchange rates can be rationalised by a central bank’s effort to lower the risk of missing its final targets if it only has a single instrument at its disposal. We provide a theoretical model-based foundation of a strategy of direct managed floating in which the central bank targets, in addition to a short-term interest rate, the nominal exchange rate. In particular, we develop a rule for the instrument of intervening in the foreign exchange market that is based on the failure of foreign exchange market to guarantee a reliable relationship between the exchange rate and other fundamental variables.
The control of quantum mechanical processes, especially the selective manipulation of photochemical reactions by shaped fs laser pulses was successfully demonstrated in many experiments in the fields of physics, chemistry and biology. In this work, attention is directed to the control of two systems that mark a bridge to real synthetic chemistry. In a liquid phase environment the outcome of the photo-induced Wolff rearrangement of an industrially relevant diazonaphthoquinone compound, normally used in photoresists (e.g. Novolak) was optimized using shaped fs laser pulses. In the second series of experiments chemical reactions on a catalyst metal surface which comprise laser induced molecular bond formation channels were selectively manipulated for the first time. The control of liquid phase reactions necessitates adequate spectroscopic signals that are characteristic for the formed product species. Therefore, a pump-probe setup for transient absorption spectroscopy in the mid-infrared for the purpose of investigating ultrafast structural changes of molecules during photoreactions was constructed. This versatile setup enables to monitor structural changes of molecules in the liquid phase and to find appropriate feedback signals for the control of these processes. Prior to quantum control experiments, the photoinduced Wolff-rearrangement reaction of 2-diazo-1-naphthoquinone (DNQ) dissolved in water and methanol was thoroughly investigated. Steady state absorption measurements in the mid-infrared in combination with quantum chemical density functional theory (DFT) calculations revealed the characteristic vibrational bands of DNQ and of possible products. A mid-infrared transient absorption study was performed, to illuminate the structural dynamics of the ultrafast rearrangement reaction of DNQ. The experimental observations indicate, that the Wolff rearrangement reaction of DNQ proceeds within 300 fs. A model for the relaxation dynamics of the ketene photoproduct and DNQ after photoexcitation can be deduced that fits the measured data very well. The object of the quantum control experiments on DNQ was the improvement of the ketene yield. It was shown that the ketene formation after Wolff rearrangement of DNQ is very sensitive to the shape of the applied excitation laser pulses. The variation of single parameters, like the linear chirp as well as the pulse separation of colored double pulses lead to the conclusion that the well known intrapulse dumping mechanism is responsible for the impact of the frequency ordering within the excitation pulse on the photoproduct yield. Adaptive optimizations using a closed learning loop basically lead to the same result. Adaptive fs quantum control was also applied to surface reactions on a catalyst metal surface for the first time. Therefore, the laser-induced catalytic reactions of carbon monoxide (CO) and hydrogen (H2) on a Pd(100) single crystal surface were studied. This photochemical reaction initiated with fs laser pulses has not been observed before. Several product molecules could be synthesized, among them also species (e.g. CH^3+) for whose formation three particles are involved. The systematic variation of different parameters showed that the reactions are sensitive to the catalyst surface, the composition of the adsorbate and to the laser properties. A pump-probe study revealed that they occur on an ultrafast time scale. These catalytic surface reactions were then investigated and improved with phaseshaped fs laser pulses. By applying a feedback optimal control scheme, the reaction outcome could be successfully manipulated and the ratio of different reaction channels could be selectively controlled. Evidence has been found that the underlying control mechanism is nontrivial and sensitive to the specific conditions on the surface. The experiments shown here represent the first successful experiment on adaptive fs quantum control of a chemical reaction between adsorbate molecules on a surface. In contrast to previous quantum control experiments, reaction channels comprising the formation of new molecular bonds rather than the cleavage of already existing bonds are controlled. This work successfully showed that quantum control can be extended to systems closer to situations encountered in synthetic chemistry as was demonstrated in the two examples of the optimization of a complicated rearrangement reaction and the selective formation of chemical bonds with shaped fs laser pulses.
XPD is a 5‘-3‘ helicase of the superfamily 2. As part of the transcription factor IIH it functions in transcription initiation and nucleotide excision repair. This work focus on the role of XPD in nucleotide excision repair. NER is a DNA repair pathway unique for its broad substrate range. In placental mammals NER is the only repair mechanism able to remove lesions induced by UV-light. NER can be divided into four different steps that are conserved between pro- and eukaryotes. Step 1 consists of the initial damage recognition, during step 2 the putative damage is verified, in step 3 the verified damage is excised and in the 4th and final step the resulting gap in the DNA is refilled. XPD was shown to be involved in the damage verification step. It was possible to solve the first apo XPD structure by a MAD approach using only the endogenous iron from the iron sulfur cluster. Based on the apo XPD structure several questions arise: where is DNA bound? Where is DNA separated? How is damage verification achieved? What is the role of the FeS cluster? These questions were addressed in this work. Hypothesis driven structure based functional mutagenesis was employed and combined with detailed biochemical characterization of the variants. The variants were analyzed by thermal unfolding studies to exclude the possibility that the overall stability could be affected by the point mutation. DNA binding assays, ATPase assays and helicase assays were performed to delineate amino acid residues important for DNA binding, helicase activity and damage recognition. A structure of XPD containing a four base pair DNA fragment was solved by molecular replacement. This structure displays the polarity of the translocated strand with respect to the helicase framework. Moreover the properties of the FeS cluster were studied by electron paramagnetic resonance to get insights into the role of the FeS cluster. Furthermore XPD from Ferroplasma acidarmanus was investigated since it was shown that it is stalled at CPD containing lesions. The data provide the first detailed insight into the translocation mechanism of a SF2B helicase and reveal how polarity is achieved. This provides a basis for further anlayses understanding the combined action of the helicase and the 4Fe4S cluster to accomplish damage verification within the NER cascade.
The recently discovered human DREAM complex (for DP, RB-like, E2F and MuvB complex) is a chromatin-associated pocket protein complex involved in cell cycle- dependent gene expression. DREAM consists of five core subunits and forms a complex either with the pocket protein p130 and the transcription factor E2F4 to repress gene expression or with the transcription factors B-MYB and FOXM1 to promote gene expression.
Gas2l3 was recently identified by our group as a novel DREAM target gene. Subsequent characterization in human cell lines revealed that GAS2L3 is a microtubule and F-actin cross-linking protein, expressed in G2/M, plays a role in cytokinesis, and is important for chromosomal stability.
The aim of the first part of the study was to analyze how expression of GAS2L3 is regulated by DREAM and to provide a better understanding of the function of GAS2L3 in mitosis and cytokinesis.
ChIP assays revealed that the repressive and the activating form of DREAM bind to the GAS2L3 promoter. RNA interference (RNAi) mediated GAS2L3 depletion demonstrated the requirement of GAS2L3 for proper cleavage furrow ingression in cytokinesis. Immunofluorescence-based localization studies showed a localization of GAS2L3 at the mitotic spindle in mitosis and at the midbody in cytokinesis. Additional experiments demonstrated that the GAS2L3 GAR domain, a putative microtubule- binding domain, is responsible for GAS2L3 localization to the constriction zones in cytokinesis suggesting a function for GAS2L3 in the abscission process.
DREAM is known to promote G2/M gene expression. DREAM target genes include several mitotic kinesins and mitotic microtubule-associated proteins (mitotic MAPs). However, it is not clear to what extent DREAM regulates mitotic kinesins and MAPs, so far. Furthermore, a comprehensive study of mitotic kinesin expression in cancer cell lines is still missing.
Therefore, the second major aim of the thesis was to characterize the regulation of mitotic kinesins and MAPs by DREAM, to investigate the expression of mitotic kinesins in cancer cell line panels and to evaluate them as possible anti-cancer targets.
ChIP assays together with RNAi mediated DREAM subunit depletion experiments demonstrated that DREAM is a master regulator of mitotic kinesins. Furthermore, expression analyses in a panel of breast and lung cancer cell lines revealed that mitotic kinesins are up-regulated in the majority of cancer cell lines in contrast to non-transformed controls. Finally, an inducible lentiviral-based shRNA system was developed to effectively deplete mitotic kinesins. Depletion of selected mitotic kinesins resulted in cytokinesis failures and strong anti-proliferative effects in several human cancer cell lines.
Thus, this system will provide a robust tool for future investigation of mitotic kinesin function in cancer cells.
Localization microscopy is a class of super-resolution fluorescence microscopy techniques. Localization microscopy methods are characterized by stochastic temporal isolation of fluorophore emission, i.e., making the fluorophores blink so rapidly that no two are
likely to be photoactive at the same time close to each other. Well-known localization microscopy methods include dSTORM}, STORM, PALM, FPALM, or GSDIM. The biological community has taken great interest in localization microscopy, since it can enhance the resolution of common fluorescence microscopy by an order of magnitude at little experimental cost.
However, localization microscopy has considerable computational cost since millions of individual stochastic emissions must be located with nanometer precision. The computational cost of this evaluation, and the organizational cost of implementing the complex algorithms, has impeded adoption of super-resolution microscopy for a long time.
In this work, I describe my algorithmic framework for evaluating localization microscopy data.
I demonstrate how my novel open-source software achieves real-time data evaluation, i.e., can evaluate data faster than the common experimental setups can capture them.
I show how this speed is attained on standard consumer-grade CPUs, removing the need for computing on expensive clusters or deploying graphics processing units.
The evaluation is performed with the widely accepted Gaussian PSF model and a Poissonian maximum-likelihood noise model.
I extend the computational model to show how robust, optimal two-color evaluation is realized, allowing correlative microscopy between multiple proteins or structures. By employing cubic B-splines, I show how the evaluation of three-dimensional samples can be made simple and robust, taking an important step towards precise imaging of micrometer-thick samples.
I uncover the behavior and limits of localization algorithms in the face of increasing emission densities.
Finally, I show up algorithms to extend localization microscopy to common biological problems.
I investigate cellular movement and motility by considering the in vitro movement of myosin-actin filaments. I show how SNAP-tag fusion proteins enable imaging with bright and stable organic fluorophores in live cells. By analyzing the internal structure of protein clusters, I show how localization microscopy can provide new quantitative approaches beyond pure imaging.
Implications of Advanced Glycation Endproducts in Oxidative Stress and Neurodegenerative Disorders
(2001)
The reactions of reducing sugars with primary amino groups are the most common nonenzymatic modifications of proteins. Subsequent rearrangements, oxidations, and dehydrations yield a heterogeneous group of mostly colored and fluorescent compounds, termed "Maillard products" or advanced glycation end products (AGEs). AGE formation has been observed on long-lived proteins such as collagen, eye lens crystalline, and in pathological protein deposits in Alzheimer's (AD) and Parkinson's disease (PD) and dialysis-related amyloidosis. AGE-modified proteins are also involved in the complications of diabetes. AGEs accumulate in the the ß-amyloid plaques and neurofibrillary tangles (NFT) associated with AD and in the Lewy bodies characteristic of PD. Increasing evidence supports a role for oxidative stress in neurodegenerative disorders such as AD and PD. AGEs have been shown to contribute towards oxidative damage and chronic inflammation, whereby activated microglia secrete cytokines and free radicals, including nitric oxide (NO). Roles proposed for NO in the pathophysiology of the central nervous system are increasingly diverse and range from intercellular signaling, through necrosis of cells and invading pathogens, to the involvement of NO in apoptosis. Using in vitro experiments, it was shown that AGE-modified bovine serum albumin (BSA-AGE) and AGE-modified ß-amyloid, but not their unmodified proteins, induce NO production in N-11 murine microglia cells. This was mediated by the receptor for AGEs (RAGE) and upregulation of the inducible nitric oxide synthase (iNOS). AGE-induced enzyme activation and NO production could be blocked by intracellular-acting antioxidants: Ginkgo biloba special extract EGb 761, the estrogen derivative, 17ß-estradiol, R-(+)-thioctic acid, and a nitrone-based free radical trap, N-tert.-butyl-*-phenylnitrone (PBN). Methylglyoxal (MG) and 3-deoxyglucosone (3-DG), common precursors in the Maillard reaction, were also tested for their ability to induce the production of NO in N-11 microglia. However, no significant changes in nitrite levels were detected in the cell culture medium. The significance of these findings was supported by in vivo immunostaining of AD brains. Single and double immunostaining of cryostat sections of normal aged and AD brains was performed with polyclonal antibodies to AGEs and iNOS and monoclonal antibodies to Aß and PHF-1 (marker for NFT) and reactive microglia. In aged normal individuals as well as early stage AD brains (i.e. no pathological findings in isocortical areas), a few astrocytes showed co-localisation of AGE and iNOS in the upper neuronal layers of the temporal (Area 22) and entorhinal (Area 28, 34) cortices compared with no astrocytes detected in young controls. In late AD brains, there was a much denser accumulation of astrocytes co-localised with AGE and iNOS in the deeper and particularly upper neuronal layers. Also, numerous neurons with diffuse AGE but not iNOS reactivity and some AGE and iNOS-positive microglia were demonstrated, compared with only a few AGE-reactive neurons and no microglia in controls. Finally, astrocytes co-localised with AGE and iNOS as well as AGE and ß-amyloid were found surrounding mature but not diffuse ß-amyloid plaques in the AD brain. Parts of NFT were AGE-immunoreactive. Immunohistochemical staining of cryostat sections of normal aged and PD brains was performed with polyclonal antibodies to AGEs. The sections were counterstained with monoclonal antibodies to neurofilament components and a-synuclein. AGEs and a-synuclein were colocalized in very early Lewy bodies in the substantia nigra of cases with incidental Lewy body disease. These results support an AGE-induced oxidative damage due to the action of free radicals, such as NO, occurring in the AD and PD brains. Furthermore, the involvement of astrocytes and microglia in this pathological process was confirmed immunohistochemically in the AD brain. It is suggested that oxidative stress and AGEs participate in the very early steps of Lewy body formation and resulting cell death in PD. Since the iNOS gene can be regulated by redox-sensitive transcription factors, the use of membrane permeable antioxidants could be a promising strategy for the treatment and prevention of chronic inflammation in neurodegenerative disorders.
The investigation of interacting multi-agent models is a new field of mathematical research with application to the study of behavior in groups of animals or community of people. One interesting feature of multi-agent systems is collective behavior. From the mathematical point of view, one of the challenging issues considering with these dynamical models is development of control mechanisms that are able to influence the time evolution of these systems.
In this thesis, we focus on the study of controllability, stabilization and optimal control problems for multi-agent systems considering three models as follows: The first one is the Hegselmann Krause opinion formation (HK) model. The HK dynamics describes how individuals' opinions are changed by the interaction with others taking place in a bounded domain of confidence. The study of this model focuses on determining feedback controls in order to drive the agents' opinions to reach a desired agreement. The second model is the Heider social balance (HB) model. The HB dynamics explains the evolution of relationships in a social network. One purpose of studying this system is the construction of control function in oder to steer the relationship to reach a friendship state. The third model that we discuss is a flocking model describing collective motion observed in biological systems. The flocking model under consideration includes self-propelling, friction, attraction, repulsion, and alignment features. We investigate a control for steering the flocking system to track a desired trajectory. Common to all these systems is our strategy to add a leader agent that interacts with all other members of the system and includes the control mechanism.
Our control through leadership approach is developed using classical theoretical control methods and a model predictive control (MPC) scheme. To apply the former method, for each model the stability of the corresponding linearized system near consensus is investigated. Further, local controllability is examined. However, only in the
Hegselmann-Krause opinion formation model, the feedback control is determined in order to steer agents' opinions to globally converge to a desired agreement. The MPC approach is an optimal control strategy based on numerical optimization. To apply the MPC scheme, optimal control problems for each model are formulated where the objective functions are different depending on the desired objective of the problem. The first-oder necessary optimality conditions for each problem are presented. Moreover for the numerical treatment, a sequence of open-loop discrete optimality systems is solved by accurate Runge-Kutta schemes, and in the optimization procedure, a nonlinear conjugate gradient solver is implemented. Finally, numerical experiments are performed to investigate the properties of the multi-agent models and demonstrate the ability of the proposed control strategies to drive multi-agent systems to attain a desired consensus and to track a given trajectory.
Aim of this thesis was to study the contribution of the hosts immune system during tumor regression. A wild-type rejection model was studied in which tumor regression is mediated through an adaptive, T cell host response (Research article 1). Additionally, the relationship between VACV infection and cancer rejection was assessed by applying organism-specific microarray platforms to infected and non-infected xenografts. It could be shown that tumor rejection in this nude mouse model was orchestrated solely by the hosts innate immune system without help of the adaptive immunity. In a third study the inflammatory baseline status of 75 human cancer cell lines was tested in vitro which was correlated with the susceptibility to VACV and Adenovirus 5 (Ad5) replication of the respective cell line (Manuscript for Research article 3). Although xenografts by themselves lack the ability to signal danger and do not provide sufficient proinflammatory signals to induce acute inflammation, the presence of viral replication in the oncolytic xenograft model provides the "tissue-specific trigger" that activates the immune response and in concordance with the hypothesis, the ICR is activated when chronic inflammation is switched into an acute one. Thus, in conditions in which a switch from a chronic to an acute inflammatory process can be induced by other factors like the immune-stimulation induced by the presence of a virus in the target tissue, adaptive immune responses may not be necessary and immune-mediated rejection can occur without the assistance of T or B cells. However, in the regression study using neu expressing MMC in absence of a stimulus such as a virus and infected cancer cells thereafter, adaptive immunity is needed to provoke the switch into an acute inflammation and initiate tissue rejection. Taken together, this work is supportive of the hypothesis that the mechanisms prompting TSD differ among immune pathologies but the effect phase converges and central molecules can be detected over and over every time TSD occurs. It could be shown that in presence of a trigger such as infection with VACV and functional danger signaling pathways of the infected tumor cells, innate immunity is sufficient to orchestrate rejection of manifested tumors.
Insulin-like growth factor-I (IGF-I) is a 70-amino acid polypeptide with a molecular weight of approximately 7.6 kDa acting as an anabolic effector. It is essential for tissue growth and remodeling. Clinically, it is used for the treatment of growth disorders and has been proposed for various other applications including musculoskeletal diseases. Unlike insulin, IGF-I is complexed to at least six high-affinity binding proteins (IGFBPs) exerting homeostatic effects by modulating IGF-I availability to its receptor (IGF-IR) on most cells in the body as well as changing the distribution of the growth factor within the organism.1-3 Short half-lived IGF-I have been the driving forces for the design of localized IGF-I depot systems or protein modification with enhanced pharmacokinetic properties. In this thesis, we endeavor to present a versatile biologic into which galenical properties were engineered through chemical synthesis, e.g., by site-specific coupling of biomaterials or complex composites to IGF-I. For that, we redesigned the therapeutic via genetic codon expansion resulting in an alkyne introduced IGF-I, thereby becoming a substrate for biorthogonal click chemistries yielding a site-specific decoration.
In this approach, an orthogonal pyrrolysine tRNA synthetase (PylRS)/tRNAPyl CUA pair was employed to direct the co-translational incorporation of an unnatural amino acid—¬propargyl-L-lysine (plk)—bearing a clickable alkyne functional handle into IGF-I in response to the amber stop codon (UAG) introduced into the defined position in the gene of interest. We summarized the systematic optimization of upstream and downstream process alike with the ultimate goal to increase the yield of plk modified IGF-I therapeutic, from the construction of gene fusions resulting in (i) Trx-plk-IGF-I fusion variants, (ii) naturally occurring pro-IGF-I protein (IGF-I + Ea peptide) (plk-IGF-I Ea), over the subsequent bacterial cultivation and protein extraction to the final chromatographic purification. The opportunities and hurdles of all of the above strategies were discussed. Evidence was provided that the wild-type IGF-I yields were pure by exploiting the advantages of the pHisTrx expression vector system in concert with a thrombin enzyme with its highly specific proteolytic digestion site and multiple-chromatography steps. The alkyne functionality was successfully introduced into IGF-I by amber codon suppression. The proper folding of plk-IGF-I Ea was assessed by WST-1 proliferation assay and the detection of phosphorylated AKT in MG-63 cell lysate. The purity of plk-IGF-I Ea was monitored with RP-HPLC and SDS-PAGE analysis. This work also showed site-specific coupling an alkyne in plk-IGF-I Ea by copper (I)-catalyzed azide-alkyne cycloaddition (CuAAC) with potent activities in vitro. The site-specific immobilization of plk-IGF-I Ea to the model carrier (i.e., agarose beads) resulted in enhanced cell proliferation and adhesion surrounding the IGF-I-presenting particles. Cell proliferation and differentiation were enhanced in the accessibility of IGF-I decorated beads, reflecting the multivalence on cellular performance.
Next, we aimed at effectively showing the disease environment by co-delivery of fibroblast growth factor 2 (FGF2) and IGF-I, deploying localized matrix metalloproteinases (MMPs) upregulation as a surrogate marker driving the response of the drug delivery system. For this purpose, we genetically engineered FGF2 variant containing an (S)-2-amino-6-(((2-azidoethoxy)carbonyl)amino)hexanoic acid incorporated at its N-terminus, followed by an MMPs-cleavable linker (PCL) and FGF2 sequence, thereby allowing site-directed, specific decoration of the resultant azide-PCL-FGF2 with the previously mentioned plk-IGF-I Ea to generate defined protein-protein conjugates with a PCL in between. The click reaction between plk-IGF-I Ea and azide-PCL-FGF2 was systematically optimized to increase the yield of IGF-FGF conjugates, including reaction temperature, incubation duration, the addition of anionic detergent, and different ratios of the participating biopharmaceutics. The challenge here was that CuAAC reaction components or conditions might oxidize free cysteines of azide-PCL-FGF2 and future work needs to present the extent of activity retention after conjugation. Furthermore, our study provides potential options for dual-labeling of IGF-I either by the introduction of unnatural amino acids within two distinct positions of the protein of interest for parallel “double-click” labeling of the resultant plk-IGF-I Ea-plk or by using a combination of enzymatic-catalyzed and CuAAC bioorthogonal coupling strategies for sequentially dual-labeling of plk-IGF-I Ea.
In conclusion, genetic code expansion in combination with click-chemistry provides the fundament for novel IGF-I analogs allowing unprecedented site specificity for decoration. Considerable progress towards IGF-I based therapies with enhanced pharmacological properties was made by demonstrating the feasibility of the expression of plk incorporated IGF-I using E. coli and retained activity of unconjugated and conjugated IGF-I variant. Dual-labeling of IGF-I provides further insights into the functional requirements of IGF-I. Still, further investigation warrants to develop precise IGF-I therapy through unmatched temporal and spatial regulation of the pleiotropic IGF-I.
Background: Nicotine addiction is the most prevalent type of drug addiction that has been described as a cycle of spiraling dysregulation of the brain reward systems. Imaging studies have shown that nicotine addiction is associated with abnormal function in prefrontal brain regions that are important for cognitive emotion regulation. It was assumed that addicts may perform less well than healthy nonsmokers in cognitive emotion regulation tasks. The primary aims of this thesis were to investigate emotional responses to natural rewards among smokers and nonsmokers and to determine whether smokers differ from nonsmokers in cognitive regulation of positive and negative emotions. To address these aims, two forms of appraisal paradigms (i.e., appraisal frame and reappraisal) were applied to compare changes in emotional responses of smokers with that of nonsmokers as a function of appraisal strategies. Experiment 1: The aim of the first experiment was to evaluate whether and how appraisal frames preceding positive and negative picture stimuli affect emotional experience and facial expression of individuals. Twenty participants were exposed to 125 pairs of auditory appraisal frames (either neutral or emotional) followed by picture stimuli reflecting five conditions: unpleasant-negative, unpleasant-neutral, pleasant-positive, pleasant-neutral and neutral-neutral. Ratings of valence and arousal as well as facial EMG activity over the corrugator supercilii and the zygomaticus major were measured simultaneously. The results indicated that appraisal frames could alter both subjective emotional experience and facial expressions, irrespective of the valence of the pictorial stimuli. These results suggest and support that appraisal frame is an efficient paradigm in regulation of multi-level emotional responses. 8 Experiment 2: The second experiment applied the appraisal frame paradigm to investigate how smokers differ from nonsmokers on cognitive emotion regulation. Sixty participants (22 nonsmokers, 19 nondeprived smokers and 19 12-h deprived smokers) completed emotion regulation tasks as described in Experiment 1 while emotional responses were concurrently recorded as reflected by self-ratings and psychophysiological measures (i.e., facial EMG and EEG). The results indicated that there was no group difference on emotional responses to natural rewards. Moreover, nondeprived smokers and deprived smokers performed as well as nonsmokers on the emotion regulation task. The lack of group differences in multiple emotional responses (i.e., self-reports, facial EMG activity and brain EEG activity) suggests that nicotine addicts have no deficit in cognitive emotion regulation of natural rewards via appraisal frames. Experiment 3: The third experiment aimed to further evaluate smokers’ emotion regulation ability by comparing performances of smokers and nonsmokers in a more challenging cognitive task (i.e., reappraisal task). Sixty-five participants (23 nonsmokers, 22 nondeprived smokers and 20 12-h deprived smokers) were instructed to regulate emotions by imagining that the depicted negative or positive scenario would become less negative or less positive over time, respectively. The results showed that nondeprived smokers and deprived smokers responded similarly to emotional pictures and performed as well as nonsmokers in down-regulating positive and negative emotions via the reappraisal strategy. These results indicated that nicotine addicts do not have deficit in emotion regulation using cognitive appraisal strategies. In sum, the three studies consistently revealed that addicted smokers were capable to regulate emotions via appraisal strategies. This thesis establishes the groundwork for therapeutic use of appraisal instructions to cope with potential self-regulation failures in nicotine addicts.
The massive remodeling of the heart tissue, as observed in response to pressure overload or myocardial infarction, is considered to play a causative role in the development of heart failure. Alterations in the heart architecture clearly affect the mechanical properties of the heart muscle, but they are rooted in changes at the cellular level including modulation of gene expression. Together with integrins, the transmembrane receptors linking the extracellular environment to the cytoskeleton, extracellular matrix (ECM) proteins and matricellular proteins are key components of the remodeling process in the heart. Therefore, this thesis was aimed at analysing the role of integrins in the regulation of gene expression and heart muscle performance during cardiac wound repair induced by pressure overload or myocardial infarction (MI). To investigate the contribution of integrin Beta 1, we characterised the response of mice with a conditional, cardiac-specific deletion of the integrin Beta 1 gene in an experimental model of pressure overload by aortic banding (AB). In particular, we measured physiological alterations and gene expression events in the stressed heart in the presence or absence of integrin Beta 1. Interestingly, mice containing a knock-out allele and the ventricular myocyte-specific conditional allele of the integrin Beta 1 gene were born and grew up to adulthood. Though these animals still exhibited minor amounts of integrin Beta1 in the heart (expressed by non-myocytes), these mice displayed abnormal cardiac function and were highly sensitive to AB. Whereas a compensatory hypertrophic response to pressure overload was observed in wildtype mice, the integrin Beta 1-deficient mice were not able to undergo heart tissue remodeling. Furthermore, ECM gene expression was altered and, in particular, the increased expression of the matricellular protein SPARC after AB was abolished in integrin Beta 1–deficient mice. Interestingly, we also found a transient upregulation of SPARC mRNA during heart remodeling after MI using cDNA macroarrays. Indeed, increased SPARC protein levels were observed starting at day 2 (2.55±0.21fold, p<0.01), day 7 (3.72±0.28 fold, p<0.01) and 1 month (1.9±0.16 fold, p<0.01) after MI, which could be abolished by using an integrin alpha v inhibitor in vivo. Immunofluorescence analysis of heart tissue demonstrated that the increased SPARC expression was confined to the infarcted area and occurred together with the influx of fibroblasts into the heart. In vitro, either TGF-Beta 1 or PDGF-BB stimulated SPARC expression by fibroblasts. Inhibition of integrin alpha v did not interfere with TGF-Beta1 or PDGF induced SPARC secretion as determined by ELISA assays or Western blot. However, secretion of TGF-Beta1 and PDGF-BB by cardiomyocytes was induced by vitronectin, a ligand of integrin alpha v, and this response was blocked by the integrin alpga v inhibitor. Functionally, SPARC modulated the migratory response of fibroblasts towards ECM proteins suggesting that the local deposition of SPARC following MI contributes to scar formation. Taken together, our combined in vivo and in vitro data demonstrate that several integrin subunits play critical roles during tissue remodeling in the injured heart. Integrin-dependent gene expression events such as the upregulation of SPARC following MI are critical to orchestrate the healing response. These processes appear to involve complex cross-talk between different cell types such as cardiomyocytes and fibroblasts to allow for locally confined scar formation. The elucidation of the sophisticated interplay between integrins, matricellular proteins such as SPARC, and growth factors will undoubtedly provide us with a better and clinically useful understanding of the molecular mechanisms governing heart remodeling.
Integrins are transmembrane receptors transmitting mechanical signals from the extracellular matrix (ECM) to the cytoskeleton (outside-in-signaling). Many molecular defects in the link between cytoskeleton and ECM are known to induce cardiomyopathies. alpha v integrin appears to play a major role in several processes relevant to remodeling, such as binding and activation of matrix metalloproteinases as well as regulation of cell proliferation, migration, and differentiation. We hypothesized that alpha v integrin-mediated signaling is required for the compensatory hypertrophy after aortic banding (AB) and associated with the modulation of ECM protein expression. Mice were treated in vivo with a specific integrin alpha v inhibitor or vehicle via osmotic minipumps starting 1 day prior to aortic banding (AB). At day 2 and day 7 following AB or sham-operation, the mice were examined by echocardiography and hemodynamic analyses were performed. Treatment of alpha v Integrin inhibitor led to a dilated cardiomyopathy and congestive heart failure in AB mice (dilated left ventricle, depressed LV function, and pulmonary congestion), but not to hypertrophy as observed in mice without inhibitor treatment. Investigation of downstream signaling revealed significant activation of the p38 Mitogen-Activated Protein Kinase (MAPK), the Extracellular signal-Regulated Kinases 1 and 2 (Erk 1/2), Focal Adhesion Kinase (FAK) and tyrosine-phosphorylation of c-Src in mice 7 days after AB. This response was blunted in mice treated with integrin alpha v inhibitor. Microarrays probing for a total of 96 cell adhesion and ECM genes identified various genomic targets of integrin alpha v mediated signalling. 7 days after AB 18 ECM genes were up-regulated more than 2-fold (n=6), e.g. collagen (8.11 ± 2.2), fibronectin (2.32 ± 0.94), secreted protein, acidic and rich in cysteine (SPARC, 3.78 ± 0.12), A disintegrin-like and metalloprotease (reprolysin type) with trombospondin type 1 (Adamts-1, 3.51 ± 0.81) and Tissue inhibitor of metalloproteinase 2 (TIMP2, 2.23 ± 0.98), whereas this up-regulation was abolished in mice that were treatd by integrin alpha v inhibitor via mini pumps. We conclude that signaling downstream of integrin alpha v is mediated by the MAPK, FAK and c-Src pathways leading to an up-regulation of extracelluar matrix components necessary for the compensatory response of the heart under a condition of pressure overload.
Persistent room temperature phosphorescent (RTP) luminophores have gained remarkable interest recently for a number of applications in security printing, OLEDs, optical storage, time-gated biological imaging and oxygen sensors. We report the first persistent RTP with lifetimes up to 0.5 s from simple triarylboranes which have no lone pairs. We also have prepared 3 isomeric (o, m, p-bromophenyl)-bis(2,6-dimethylphenyl)boranes. Among the 3 isomers (o-, m- and p-BrTAB) synthesized, the ortho-one is the only one which shows dual phosphorescence, with a short lifetime of 0.8 ms and a long lifetime of 234 ms in the crystalline state at room temperature. At last, we checked the RTP properties from the boric acid. We found that the pure boric acid does not show RTP in the solid state.
This thesis deals with the hp-finite element method (FEM) for linear quadratic optimal control problems. Here, a tracking type functional with control costs as regularization shall be minimized subject to an elliptic partial differential equation. In the presence of control constraints, the first order necessary conditions, which are typically used to find optimal solutions numerically, can be formulated as a semi-smooth projection formula. Consequently, optimal solutions may be non-smooth as well. The hp-discretization technique considers this fact and approximates rough functions on fine meshes while using higher order finite elements on domains where the solution is smooth.
The first main achievement of this thesis is the successful application of hp-FEM to two related problem classes: Neumann boundary and interface control problems. They are solved with an a-priori refinement strategy called boundary concentrated (bc) FEM and interface concentrated (ic) FEM, respectively. These strategies generate grids that are heavily refined towards the boundary or interface. We construct an elementwise interpolant that allows to prove algebraic decay of the approximation error for both techniques. Additionally, a detailed analysis of global and local regularity of solutions, which is critical for the speed of convergence, is included. Since the bc- and ic-FEM retain small polynomial degrees for elements touching the boundary and interface, respectively, we are able to deduce novel error estimates in the L2- and L∞-norm. The latter allows an a-priori strategy for updating the regularization parameter in the objective functional to solve bang-bang problems.
Furthermore, we apply the traditional idea of the hp-FEM, i.e., grading the mesh geometrically towards vertices of the domain, for solving optimal control problems (vc-FEM). In doing so, we obtain exponential convergence with respect to the number of unknowns. This is proved with a regularity result in countably normed spaces for the variables of the coupled optimality system.
The second main achievement of this thesis is the development of a fully adaptive hp-interior point method that can solve problems with distributed or Neumann control. The underlying barrier problem yields a non-linear optimality system, which poses a numerical challenge: the numerically stable evaluation of integrals over possibly singular functions in higher order elements. We successfully overcome this difficulty by monitoring the control variable at the integration points and enforcing feasibility in an additional smoothing step. In this work, we prove convergence of an interior point method with smoothing step and derive a-posteriori error estimators. The adaptive mesh refinement is based on the expansion of the solution in a Legendre series. The decay of the coefficients serves as an indicator for smoothness that guides between h- and p-refinement.
Single molecule localization microscopy has seen a remarkable growth since its first
experimental implementations about a decade ago. Despite its technical challenges,
it is already widely used in medicine and biology and is valued as a unique tool
to gain molecular information with high specificity. However, common illumination techniques do not allow the use of single molecule sensitive super-resolution
microscopy techniques such as direct stochastic optical reconstruction microscopy
(dSTORM) for whole cell imaging. In addition, they can potentially alter the
quantitative information.
In this thesis, I combine dSTORM imaging in three dimensions with lattice lightsheet illumination to gain quantitative molecular information from cells unperturbed by the illumination and cover slip effects. Lattice light-sheet illumination
uses optical lattices for beam shaping to restrict the illumination to the detectable
volume. I describe the theoretical background needed for both techniques and detail
the experimental realization of the system as well as the software that I developed
to efficiently evaluate the data.
Eventually, I will present key datasets that demonstrate the capabilities of the
developed microscope system with and without dSTORM. My main goal here was
to use these techniques for imaging the neural cell adhesion molecule (NCAM, also
known as CD56) in whole cells. NCAM is a plasma membrane receptor known to
play a key role in biological processes such as memory and learning. Combining
dSTORM and lattice light-sheet illumination enables the collection of quantitative
data of the distribution of molecules across the whole plasma membrane, and shows
an accumulation of NCAM at cell-cell interfaces. The low phototoxicity of lattice
light-sheet illumination further allows for tracking individual NCAM dimers in living cells, showing a significant dependence of its mobility on the actin skeleton of
the cell.
Anionic Adducts
Sp2-sp3 tetraalkoxy diboron compounds have gained attention due to the development of new, synthetically useful catalytic reactions either with or without transition-metals. Lewis-base adducts of the diboron(4) compounds were suggested as possible intermediates in Cu catalyzed borylation reactions some time ago. However, intermolecular adducts of tetraalkoxy diboron compounds have not been studied yet in great detail. In preliminary studies, we have synthesized a series of anionic sp2-sp3 adducts of B2pin2 with alkoxy-groups (L = [OMe]–, [OtBu]–), a phenoxy-group (L = [4-tBuC6H4O]–) and fluoride (L = [F]–, with [nBu4N]+ as the counter ion) as Lewis-bases.
Neutral Adducts
Since their isolation and characterization, applications of N-heterocyclic carbenes (NHCs) and related molecules, e.g., cyclic alkylaminocarbenes (CAACs) and acyclic diaminocarbenes (aDCs), have grown rapidly. Their use as ligands in homogeneous catalysis and directly in organocatalysis, including recently developed borylation reactions, is now well established. Recently, several examples of ring expansion reactions (RER) involving NHCs were reported to take place at elevated temperatures, involving Be, B, and Si.
Furthermore, preliminary studies in the group of Marder et al. showed the presence of neutral sp2-sp3 diboron compounds with B2pin2 and the NHC Cy2Im. In this work, we focused on the synthesis and characterization of further neutral sp2-sp3 as well as sp3-sp3 diboron adducts with B2cat2 and B2neop2 and different NHCs. Whereas the mono-NHC adduct is stable for several hours at temperatures up to 60 °C, the bis-NHC adducts undergo thermally induced rearrangement to form the ring expanded products compound 26 and 27. B2neop2 is much more reactive than B2cat2 giving ring expanded product 29 at room temperature in quantitative yields, demonstrating that NHC ring expansion and B–B bond cleavage can be very facile processes.
Whereas the mono-NHC adduct is stable for several hours at temperatures up to 60 °C, the bis-NHC adducts undergo thermally induced rearrangement to form the ring expanded products compound 26 and 27. B2neop2 is much more reactive than B2cat2 giving ring expanded product 29 at room temperature in quantitative yields, demonstrating that NHC ring expansion and B–B bond cleavage can be very facile processes.
Ecophysiological adaptations of the cuticular water permeability within the Solanaceae family
(2024)
The cuticle, a complex lipidic layer synthesized by epidermal cells, covers and protects primary organs of all land plants. Its main function is to avoid plant desiccation by limiting non-stomatal water loss. The cuticular properties vary widely among plant species. So far, most of the cuticle-related studies have focused on a limited number of species, and studies addressing phylogenetically related plant species are rare. Moreover, comparative studies among organs from the same plant species are still scarce.
Thus, this study focus on organ-specificities of the cuticle within and between plant species of the Solanaceae family. Twenty-seven plant species of ten genera, including cultivated and non- cultivated species, were investigated to identify potential cuticular similarities. Structural, chemical and functional traits of fully expanded leaves, inflated fruiting calyces, and ripe fruits were analyzed.
The surface morphology was investigated by scanning electron microscopy. Leaves were mainly amphistomatic and covered by an epicuticular wax film. The diversity and distribution of trichomes varied among species. Only the leaves of S. grandiflora were glabrous. Plant species of the Leptostemonum subgenus had numerous prickles and non-glandular stellate trichomes. Fruits were stomata-free, except for S. muricatum, and a wax film covered their surface. Last, lenticel- like structures and remaining scars of broken trichomes were found on the surface of some Solanum fruits.
Cuticular water permeability was used as indicators of the cuticular transpiration barrier efficiency. The water permeability differed among plant species, organs and fruit types with values ranging up to one hundred-fold. The minimum leaf conductance ranged from 0.35 × 10-5 m s-1 in S. grandiflora to 31.54 × 10-5 m s-1 in S. muricatum. Cuticular permeability of fruits ranged from 0.64 × 10-5 m s-1 in S. dulcamara (fleshy berry) to 34.98 × 10-5 m s-1 in N. tabacum (capsule). Generally, the cuticular water loss of dry fruits was about to 5-fold higher than that of fleshy fruits.
Interestingly, comparisons between cultivated and non-cultivated species showed that wild species have the most efficient cuticular transpiration barrier in leaves and fruits. The average permeability of leaves and fruits of wild plant species was up to three-fold lower in comparison to the cultivated ones. Moreover, ripe fruits of P. ixocarpa and P. peruviana showed two-times lower cuticular transpiration when enclosed by the inflated fruiting calyx.
The cuticular chemical composition was examined using gas chromatography. Very-long-chain aliphatic compounds primarily composed the cuticular waxes, being mostly dominated by n- alkanes (up to 80% of the total wax load). Primary alkanols, alkanoic acids, alkyl esters and branched iso- and anteiso-alkanes were also frequently found. Although in minor amounts, sterols, pentacyclic triterpenoids, phenylmethyl esters, coumaric acid esters, and tocopherols were identified in the cuticular waxes. Cuticular wax coverages highly varied in solanaceous (62- fold variation). The cuticular wax load of fruits ranged from 0.55 μg cm−2 (Nicandra physalodes) to 33.99 μg cm−2 (S. pennellii), whereas the wax amount of leaves varied from 0.90 μg cm−2 (N. physalodes) to 28.42 μg cm−2 (S. burchellii). Finally, the wax load of inflated fruiting calyces ranged from 0.56 μg cm−2 in P. peruviana to 2.00 μg cm−2 in N. physalodes.
For the first time, a comparative study on the efficiency of the cuticular transpiration barrier in different plant organs of closely related plant species was conducted. Altogether, the cuticular chemical variability found in solanaceous species highlight species-, and organ-specific wax biosynthesis. These chemical variabilities might relate to the waterproofing properties of the plant cuticle, thereby influencing leaf and fruit performances. Additionally, the high cuticular water permeabilities of cultivated plant species suggest a potential existence of a trade-off between fruit organoleptic properties and the efficiency of the cuticular transpiration barrier. Last, the high cuticular water loss of the solanaceous dry fruits might be a physiological adaptation favouring seed dispersion.
Neisseria gonorrhoeae is a human-specific pathogen that causes gonorrhea. It is defined as a super bacterium by the WHO due to the emergence of gonococci that are resistant to a variety of antibiotics and a rapidly increasing infection incidence. Genome-wide investigation of neisserial gene essentiality and novel virulence factors is urgently required in order to identify new targets for anti-neisserial therapeutics. To identify essential genes and new virulence factors, a high-density mutant library in N. gonorrhoeae MS11 was generated by in vitro transposon mutagenesis. The transposon library harbors more than 100,000 individual mutants, a density that is unprecedented in gonococcal research. Essential genes in N. gonorrhoeae were determined by enumerating frequencies of transposon insertion sites (TIS) with Illumina deep sequencing (Tn-seq). Tn-seq indicated an average distance between adjacent TIS of 25 bp. Statistical analysis unequivocally demonstrated 781 genes that were significantly depleted in TIS and thus are essential for Neisseria survival. A subset of the genes was experimentally verified to comprise essential genes and thus support the outcome of the study. The hereby identified candidate essential genes thus may constitute excellent targets for the development of new antibiotics or vaccines.
In a second study, the transposon mutant library was applied in a genome-scale “negative-selection strategy” to identify genes that are involved in low phosphate-dependent invasion (LPDI). LPDI is dependent on the Neisseria porin subtype PorBIA which acts as an epithelial cell invasin in absence of phosphate and is associated with severe pathogenicity in disseminated gonococcal infections (DGI). Tn-seq demonstrated 98 genes, which were involved in adherence to host cells and 43 genes involved in host cell invasion. E.g. the hypothetical protein NGFG_00506, an ABC transporter ATP-binding protein NGFG_01643, as well as NGFG_04218 encoding a homolog of mafI in N. gonorrhoeae FA1090 were experimentally verified as new invasive factors in LPDI. NGFG_01605, a predicted protease, was identified to be a common factor involved in PorBIA, Opa50 and Opa57-mediated neisserial engulfment by the epithelial cells. Thus, this first systematic Tn-seq application in N. gonorrhoeae identified a set of previously unknown N. gonorrhoeae invasive factors which demonstrate molecular mechanisms of DGI.
The RAF family of protein kinases consists of three members, A-RAF, B-RAF and C-RAF. Unlike the other isotypes, B-RAF has been found to have an important function for normal development of the central nervous system (CNS), because newly generated embryonic neurons lacking B-RAF cannot respond to survival factors and undergo cell death in vitro. A second cell lineage affected by the absence of B-RAF are endothelial cells and their death leads to internal bleedings and lethality of B-RAF-/- mice between embryonic day 10.5 (E10.5) and E12.5 precluding an opportunity to further analyze neural B-RAF function at a later stage. In contrast to B-RAF-/- mice, B-RAFKIN/KIN mice, which are B-RAF deficient but express a chimeric protein consisting of the unique N terminus of B-RAF and all the domains of A-RAF in the B-RAF gene locus, survive after midgestation because their endothelial cells are protected from apoptosis. More importantly, overall prevention of abnormal neural apoptosis in the forebrain allows us to study proliferation- or differentiation-oriented function of B-RAF other than its survival effects in CNS development. The detailed investigation of B-RAFKIN/KIN animals was concentrated on cortical development. There were apparent cortical defects in B-RAFKIN/KIN forebrain: Loss of B-RAF led to severe reduction of Brn-2 expressing pyramidal projection neurons accompanied by a disruption of dendrite formation in the upper layers. In further analysis, BrdU labelling experiments showed that from E14.5 to E16.5 cell proliferation in the ventricular zone of the mutant mice was reduced and that the late-born cortical neurons failed to migrate properly. While the proliferation defect of cortical progenitors was associated with reduced ERK activation, the mechanism causing impaired neuronal migration remains to be determined. Our hypothesis is that the subcellular localization of phospho-ERK may be altered in migrating cortical neurons in B-RAFKIN/KIN mice. To confirm in vivo function of B-RAF and further study unknown roles in embryonic neurogenesis as well as other morphogenesis, conditional B-RAF knockouts would be the ideal models, which can efficiently avoid embryonic lethality, prevent unwanted pleiotropic side effects and exclude accumulative compensatory developmental changes from the earliest developmental stage on, through the deletion of genetic material/gene function in selected cells at a specific time. The use of site-specific recombinases such as Cre and the successful development of the reversible tetracycline-based switch have provided powerful venues for creating conditional loss-of-function mouse models. Generation of tetracycline-regulated B-RAF and floxed B-RAF mouse embryonic stem (ES) cell lines was performed. Up to now, high-grade chimeric mice were obtained after blastocyst injection of the modified ES cell clones. The germline transmission from these chimeric mice is currently under investigation. When either of conditional mouse lines is ready, detailed examination in their CNS development would be done to reveal how B-RAF plays a real role for normal development of the nervous system.
SUMOylation, as a post-translational modification, plays a crucial role in several biological processes. Small ubiquitin-like modifier (SUMO) proteins can be reversibly linked to the lysine residues located within specific motifs on numerous target proteins, leading to the change of stability, localization, activity of target proteins, mostly by promoting or interfering with the interaction with other molecules. Consequently, it can regulate gene transcription, migration, cell cycle progression, cellular responses to stress, and tumorigenesis.
NFATc1 belongs to the Nuclear Factor of Activated T-cells (NFAT) transcription factor family, which is dephosphorylated and translocates to the nucleus upon cell stimulation, which provokes Ca2+ signalling. NFAT plays a crucial role in the development and function of the immune system. NFATc1 has three SUMOylation sites at the position of aa 349, 702, and 914. In our previous study, we demonstrated that point mutations performed on the SUMOylation sites on all three or only at the lysine residues K702 and K914 lead to enhanced expression of IL-2 in vitro. To evaluate the function of SUMOylation of NFATc1 on T cell-mediated immunity in vivo, we not only generated a transgenic mouse strain (NFATc1/ΔS+ mouse) by point mutations from Lysine to Arginine on the two SUMOylation sites within exon 10 of Nfatc1 to prevent their SUMOylation, but in combination created another mouse strain (NFATc1/ΔBC+ mouse) that is completely Nfatc1 exon 10-ablated by using the LoxP/Cre system. In NFATc1/ΔS+ T cells, we observed enhanced IL-2 production and less IL-17A and IFN-γ expression. In line with exon 10 bearing the relevant SUMO sites, NFATc1/ΔBC+ CD4+ T cells behaved similarly as NFATc1/ΔS+ ones. The mechanism is that elevated IL-2 secretion can counteract the expression of IL-17A and IFN-γ via STAT5 and Blimp-1 induction. Afterwards, Blimp-1 suppressed IL-2 itself as well as Bcl2A1. Next, we performed two disease models with our NFATc1/ΔS+ mice. In a major mismatch model for acute graft-versus-host disease, we found that the mice transplanted with NFATc1/ΔS+ CD3+ T cells developed less severe disease, and T cells proliferated less due to increased Tregs. Moreover, when transferring 2D2.NFATc1/ΔS+ Th1 plus Th17 cells to Rag1-/- mice to induce experimental autoimmune encephalitis, we also observed ameliorated disease compared to animals with transferred WT T cells as well as increased Tregs.
Taking all data together, the deficiency in SUMOylation of NFATc1 leads to an elevated IL-2 secretion in T cells and subsequent activation of STAT5, which competes with STAT3 to inhibit IL-17A production and promotes Treg expansion, as well as to an enforcement of Blimp-1 expression, which suppresses IFN-γ and IL-2 expression. Consequently and despite a short phase of enhanced IL-2 secretion, the deficiency of SUMOylation on NFATc1 can protect from autoreactive and alloreactive diseases.
Moreover, to further understand the function of SUMOylation of NFATc1 in humans, we started by establishing an in vitro 3D culture system for tonsil organoids, which was successful in the presence of feeder cells, along with IL-4 and IL-7 cytokines. To confirm that our 3D tonsil organoids can respond to real antigens, we used CMV peptides and peptides of spike proteins from Covid-19 as real antigens, and co-cultured with tonsil organoids, which indeed can generate memory cells and plasmablasts. In the end, we also compared 3D to 2D cultures. Although the total numbers of all B cell subsets were much less in 3D culture than that in 2D culture, still, it indicates that this in-vitro culture system has its limitation, while being usable to produce the similar results as 2D did. Therefore, this 3D culture system can be used as a platform to investigate NFATc1/ΔS+ or NFATc1/ΔBC+ TFH and TFR cells in the dynamic of human GC responses.
The transcriptional repressor-Blimp-1 terminates differentiation of B lymphocytes as well as myeloid cells. Our data show that Blimp-1 is highly expressed in freshly isolated murine primary T lymphocytes, particularly its minor splice variant. Ectopic expression of Blimp-1 by retroviral transduction neither dramatically altered secretion of IFN-ã or IL-4 nor did it induce the ability to suppress as regulatory T cells. However, induction of Blimp-1 resulted in not only a significant reduction in the production of IL-2 but also an inability to proliferate as well as in the reduced viability. These results demonstrate that Blimp-1 might mark end stages of lineage differentiation in T cells.
In contrast to c-Myc, a deregulated expression of the MYCN gene is restricted to human neuroendocrine tumours. In most cases, the excessive activity of N-Myc results from a MYCN amplification. In neuroblastoma, amplification of MYCN is a predictor of poor prognosis and resistance to therapy. The inability to target the N-Myc protein directly necessitates the search for alternative targets. This project aimed at identifying genes specifically required for growth and survival of cells that express high levels of N-Myc using high-throughput shRNA screening combined with next generation sequencing. The identification and analysis of these genes will shed light on functional interaction partners of N-Myc.
We screened a shRNA library containing 18,327 shRNAs and identified 148 shRNAs, which were selectively depleted in the presence of active N-Myc. In addition, shRNAs targeting genes that are involved in p53 and ARF turnover and apoptosis were depleted in the cell population during the screen. These processes are known to affect N-Myc-mediated apoptosis. Consequently, these results biologically validated the screen. The 148 shRNAs that showed a significant synthetic lethal interaction with high levels of N-Myc expression were further analysed using the bioinformatics program DAVID. We found an enrichment of shRNAs that target genes involved in specific biological processes. For example, we validated synthetic lethal interactions for genes such as, THOC1, NUP153 and LARP7, which play an important role in the process of RNA polymerase II-mediated transcription elongation. We also validated genes that are involved in the neddylation pathway.
In the screen we identified Cullin 3, which is a component of the BTB-CUL3-Rbx1 ubiquitin ligase that is involved in the turnover of Cyclin E. Depletion of cullin 3 and activation of N-Myc was found to synergistically increase Cyclin E expression to supraphysiological levels, inducing S-phase arrest and a strong DNA damage response.
Together with results from a proteomics analysis of N-Myc associated proteins, our results lead us to the following hypothesis: In a neuroblastoma cell, the high levels of N-Myc result in a conflict between RNA polymerase II and the replication machinery during S-phase. The newly identified interaction partners of N- Myc are required to solve this conflict. Consequently, loss of the interaction leads to a massive DNA damage and the induction of apoptosis. In addition, inhibition or depletion of the essential components of the neddylation pathway also results in an unresolvable problem during S-phase.
DNA damage occurs frequently during normal cellular progresses or by environmental factors. To preserve the genome integrity, DNA damage response (DDR) has evolved to repair DNA and the non-properly repaired DNA induces human diseases like immune deficiency and cancer. Since a large number of proteins involved in DDR are enzymes of ubiquitin system, it is critical to investigate how the ubiquitin system regulates cellular response to DNA damage. Hereby, we reveal a novel mechanism for DDR regulation via activation of SCF ubiquitin ligase upon DNA damage.
As an essential step for DNA damage-induced inhibition of DNA replication, Cdc25A degradation by the E3 ligase β-TrCP upon DNA damage requires the deubiquitinase Usp28. Usp28 deubiquitinates β-TrCP in response to DNA damage, thereby promotes its dimerization, which is required for its activity in substrate ubiquitination and degradation. Particularly, ubiquitination at a specific lysine on β-TrCP suppresses dimerization.
The key mediator protein of DDR, 53BP1, forms oligomers and associates with β-TrCP to inhibit its activity in unstressed cells. Upon DNA damage, 53BP1 is degraded in the nucleoplasm, which requires oligomerization and is promoted by Usp28 in a β-TrCP-dependent manner. Consequently, 53BP1 destruction releases and activates β-TrCP during DNA damage response.
Moreover, 53BP1 deletion and DNA damage promote β-TrCP dimerization and recruitment to chromatin sites that locate in the vicinity of putative replication origins. Subsequently, the chromatin-associated Cdc25A is degraded by β-TrCP at the origins. The stimulation of β-TrCP binding to the origins upon DNA damage is accompanied by unloading of Cdc45, a crucial component of pre-initiation complexes for replication. Loading of Cdc45 to origins is a key Cdk2-dependent step for DNA replication initiation, indicating that localized Cdc25A degradation by β-TrCP at origins inactivates Cdk2, thereby inhibits the initiation of DNA replication.
Collectively, this study suggests a novel mechanism for the regulation of DNA replication upon DNA damage, which involves 53BP1- and Usp28-dependent activation of the SCF(β-TrCP) ligase in Cdc25A degradation.
This dissertation presents controller design methodologies for a formation of cooperative mobile robots to perform trajectory tracking and convoy protection tasks. Two major problems related to multi-agent formation control are addressed, namely the time-delay and optimality problems. For the task of trajectory tracking, a leader-follower based system structure is adopted for the controller design, where the selection criteria for controller parameters are derived through analyses of characteristic polynomials. The resulting parameters ensure the stability of the system and overcome the steady-state error as well as the oscillation behavior under time-delay effect. In the convoy protection scenario, a decentralized coordination strategy for balanced deployment of mobile robots is first proposed. Based on this coordination scheme, optimal controller parameters are generated in both centralized and decentralized fashion to achieve dynamic convoy protection in a unified framework, where distributed optimization technique is applied in the decentralized strategy. This unified framework takes into account the motion of the target to be protected, and the desired system performance, for instance, minimal energy to spend, equal inter-vehicle distance to keep, etc.
Both trajectory tracking and convoy protection tasks are demonstrated through simulations and real-world hardware experiments based on the robotic equipment at Department of Computer Science VII, University of Würzburg.
Amyotrophic lateral sclerosis and spinal muscular atrophy are the two most common motoneuron diseases. Both are characterized by destabilization of axon terminals, axon degeneration and alterations in neuronal cytoskeleton. Accumulation of neurofilaments has been observed in several neurodegenerative diseases but the mechanisms how elevated neurofilament levels destabilize axons are unknown so far. Here, I show that increased neurofilament expression in motor nerves of pmn mutant mice causes disturbed microtubule dynamics. Depletion of neurofilament by Nefl knockout increases the number and regrowth of microtubules in pmn mutant motoneurons and restores axon elongation. This effect is mediated by interaction of neurofilament with the stathmin complex. Depletion of neurofilament increases stathmin-Stat3 interaction and stabilizes the microtubules. Consequently, the axonal maintenance is improved and the pmn mutant mice survive longer. We propose that this mechanism could also be relevant for other neurodegenerative diseases in which neurofilament accumulation is a prominent feature.
Next, using Smn-/-;SMN2 mouse as a model, the molecular mechanism behind synapse loss in SMA is studied. SMA is characterized by degeneration of lower α-motoneurons in spinal cord; however, how reduction of ubiquitously expressed SMN leads to MN-specific degeneration remains unclear. SMN is involved in pre-mRNA splicing (Pellizzoni, Kataoka et al. 1998) and its deficiency in SMA affects the splicing machinery. Neuromuscular junction denervation precedes neurodegeneration in SMA. However, there is no evidence of a link between aberrant splicing of transcripts downstream of Smn and reduced presynaptic axon excitability observed in SMA. In this study, we observed that expression and splicing of Nrxn2, that encodes a presynaptic protein is affected in the SMA mouse and that Nrxn2 could be a candidate that relates aberrant splicing to synaptic motoneuron defects in SMA.
Chlamydia trachomatis (Ct) is an obligate intracellular human pathogen. It causes blinding trachoma and sexually transmitted disease such as chlamydia, pelvic inflammatory disease and lymphogranuloma venereum. Ct has a unique biphasic development cycle and replicates in an intracellular vacuole called inclusion. Normally it has two forms: the infectious form, elementary body (EB); and the non-infectious form, reticulate body (RB). Ct is not easily amenable to genetic manipulation. Hence, to understand the infection process, it is crucial to study how the metabolic activity of Ct exactly evolves in the host cell and what roles of EB and RB play differentially in Ct metabolism during infection. In addition, Ct was found regularly coinfected with other pathogens in patients who got sexually transmitted diseases (STDs). A lack of powerful methods to culture Ct outside of the host cell makes the detailed molecular mechanisms of coinfection difficult to study.
In this work, a genome-scale metabolic model with 321 metabolites and 277 reactions was first reconstructed by me to study Ct metabolic adaptation in the host cell during infection. This model was calculated to yield 84 extreme pathways, and metabolic flux strength was then modelled regarding 20hpi, 40hpi and later based on a published proteomics dataset. Activities of key enzymes involved in target pathways were further validated by RT-qPCR in both HeLa229 and HUVEC cell lines. This study suggests that Ct's major active pathways involve glycolysis, gluconeogenesis, glycerolphospholipid biosynthesis and pentose phosphate pathway, while Ct's incomplete tricarboxylic acid cycle and fatty acid biosynthesis are less active. EB is more activated in almost all these carbohydrate pathways than RB. Result suggests the survival of Ct generally requires a lot of acetyl-CoA from the host. Besides, both EB and RB can utilize folate biosynthesis to generate NAD(P)H but may use different pathways depending on the demands of ATP. When more ATP is available from both host cell and Ct itself, RB is more activated by utilizing energy providing chemicals generated by enzymes associated in the nucleic acid metabolism. The forming of folate also suggests large glutamate consumption, which is supposed to be converted from glutamine by the glutamine-fructose-6-phosphate transaminase (glmS) and CTP synthase (pyrG).
Then, RNA sequencing (RNA-seq) data analysis was performed by me in a coinfection study. Metatranscriptome from patient RNA-seq data provides a realistic overview. Thirteen patient samples were collected and sequenced by our collaborators. Six male samples were obtained by urethral swab, and seven female samples were collected by cervicovaginal lavage. All the samples were Neisseria gonorrhoeae (GC) positive, and half of them had coinfection with Ct. HISAT2 and Stringtie were used for transcriptomic mapping and assembly respectively, and differential expression analysis by DESeq2, Ballgown and Cuffdiff2 are parallelly processed for comparison. Although the measured transcripts were not sufficient to assemble Ct's transcriptome, the differential expression of genes in both the host and GC were analyzed by comparing Ct positive group (Ct+) against Ct-uninfected group. The results show that in the Ct+ group, the host MHC class II immune response was highly induced. Ct infection is associated with the regulation of DNA methylation, DNA double-strand damage and ubiquitination. The analysis also shows Ct infection enhances host fatty acid beta oxidation, thereby inducing mROS, and the host responds to reduce ceramide production and glycolysis. The coinfection upregulates GC's own ion transporters and amino acid uptake, while it downregulates GC's restriction and modification systems. Meanwhile, GC has the nitrosative and oxidative stress response and also increases the ability for ferric uptake especially in the Ct+ group compared to Ct-uninfected group.
In conclusion, methods in bioinformatics were used here in analyzing the metabolism of Ct itself, and the responses of the host and GC respectively in a coinfection study with and without Ct. These methods provide metabolic and metatranscriptomic details to study Ct metabolism during infection and Ct associated coinfection in the human microbiota.
Motivated by the perceived great potential of chiral polymers, the presented work aimed at the investigation of synthesis, solubility and optical activity of chiral poly(2,4-disubstituted-2-oxazoline)s. A novel polymeric carrier based on ABA-type triblock copolymers poly(2-oxazoline)s with chiral and racemic hydrophobic blocks was developed for the formulation of chiral and achiral drugs (Fig. 5.1). Poly(2-methyl-2-oxazoline) (pMeOx) was used as hydrophilic A block, and poly(2-ethyl-4-ethyl-2-oxazoline) (pEtEtOx) and poly(2-propyl-4-methyl-2-oxazoline) (pPrMeOx) were used as hydrophobic B blocks. Curcumin (CUR), paclitaxel (PTX) and chiral/racemic ibuprofen (R/S/RS-IBU) were applied as model drugs. Nanoformulations were prepared consisting of these triblock copolymers and model drugs. ...
Optogenetics became successful in neuroscience with Channelrhodopsin-2 (ChR2), a light-gated cation channel from the green alga Chlamydomonas reinhardtii, as an easy applicable tool. The success of ChR2 inspired the development of various photosensory proteins as powerful actuators for optogenetic manipulation of biological activity. However, the current optogenetic toolbox is still not perfect and further improvements are desirable. In my thesis, I engineered and characterized several different optogenetic tools with new features.
(i) Although ChR2 is the most often used optogenetic actuator, its single-channel conductance and its Ca2+ permeability are relatively low. ChR2 variants with increased Ca2+ conductance were described recently but a further increase seemed possible. In addition, the H+ conductance of ChR2 may lead to cellular acidification and unintended pH-related side effects upon prolonged illumination. Through rational design, I developed several improved ChR2 variants with larger photocurrent, higher cation selectivity, and lower H+ conductance.
(ii) The light-activated inward chloride pump NpHR is a widely used optogenetic tool for neural silencing. However, pronounced inactivation upon long time illumination constrains its application for long-lasting neural inhibition. I found that the deprotonation of the Schiff base underlies the inactivation of NpHR. Through systematically exploring optimized illumination schemes, I found illumination with blue light alone could profoundly increase the temporal stability of the NpHR-mediated photocurrent. A combination of green and violet light eliminates the inactivation effect, similar to blue light, but leading to a higher photocurrent and therefore better light-induced inhibition.
(iii) Photoactivated adenylyl cyclases (PACs) were shown to be useful for light-manipulation of cellular cAMP levels. I developed a convenient in-vitro assay for soluble PACs that allows their reliable characterization. Comparison of different PACs revealed that bPAC from Beggiatoa is the best optogenetic tool for cAMP manipulation, due to its high efficiency and small size. However, a residual activity of bPAC in the dark is unwanted and the cytosolic localization prevents subcellular precise cAMP manipulation. I therefore introduced point mutations into bPAC to reduce its dark activity. Interestingly, I found that membrane targeting of bPAC with different linkers can remarkably alter its activity, in addition to its localization. Taken together, a set of PACs with different activity and subcellular localization were engineered for selection based on the intended usage. The membrane-bound PM-bPAC 2.0 with reduced dark activity is well-tolerated by hippocampal neurons and reliably evokes a transient photocurrent, when co-expression with a CNG channel.
(iv) Bidirectional manipulation of cell activity with light of different wavelengths is of great importance in dissecting neural networks in the brain. Selection of optimal tool pairs is the first and most important step for dual-color optogenetics. Through N- and C-terminal modifications, an improved ChR variant (i.e. vf-Chrimson 2.0) was engineered and selected as the red light-controlled actuator for excitation. Detailed comparison of three two-component potassium channels, composed of bPAC and the cAMP-activated potassium channel SthK, revealed the superior properties of SthK-bP. Combining vf-Chrimson 2.0 and improved SthK-bP “SthK(TV418)-bP” could reliably induce depolarization by red light and hyperpolarization by blue light. A residual tiny crosstalk between vf-Chrimson 2.0 and SthK(TV418)-bP, when applying blue light, can be minimized to a negligible level by applying light pulses or simply lowering the blue
light intensity.
In this thesis we have investigated the effect of NFAT (Nuclear Factor of Activated T Cell) transcription factors on the expression of Rag-(Recombination Activating Genes) genes in murine thymus. The protein products of Rag genes, RAG1 and RAG2, are critical for the recombination and generation of the TCR (T Cell Receptor) repertoire during thymocyte development, and their expression can be suppressed by the activity of NFAT factors. In thymus, the expression of Rag1 and Rag2 genes is induced at the double-negative (DN, CD4-8-) 3 stage, down-regulated at the DN4 stage, re-induced at the double-positive (DP, CD4+8+) stage, and suppressed again at the single-positive (SP, CD4+8- or CD4-8+) stage. Although it is known that TCR signaling suppresses the expression of Rag1 and Rag2 at the SP stage, the signals that mediate the Rag gene down-reulation remain elusive. Here we report that both the calcineurin-NFAT-signaling and MAPKinase signaling pathways, which are activated by TCR signaling during positive selection, mediate the Rag gene down-regulation in DP thymocytes. The calcineurin-NFAT pathway suppresses both the Rag1 and the Rag2 gene expression. This pathway has a stronger suppressive effect on the Rag1 than the Rag2 gene. A synergistic activity between the two NFAT factors NFATc2 and NFATc3 is essential for calcineurin-NFAT signaling to efficiently suppress the Rag gene expression in DP thymocytes. It is likely that the calcineurin-NFAT signaling down-regulates Rag gene expression by suppressing both the Rag anti-silencer element (ASE) activity and the Rag promoter activity. Similarly, MEK-ERK signaling of MAPK signaling pathway mediates the Rag gene suppression in DP thymocytes although the mechanism through which MEK-ERK mediates the Rag gene down-regulation has to be elucidated. In DN thymocytes, it appears that neither the calcineurin-NFAT signaling nor MAPK signaling is involved in the Rag gene down-regulation. However, a role for these two signaling pathways in the Rag gene up-regulation in DN thymocytes is not excluded. In DN thymocytes, pre-TCR signaling stimulates the expression both Nfatc1 and Nfatc2 genes but has no effect on Nfatc3 gene expression. In DN thymocytes, pre-TCR signaling activates Nfatc1α expression but not Nfatc1ß expression, i.e. the two promoters controling Nfatc1 gene xpression are differently controled by pre-TCR signals. Nfatc1α gene expression in DN thymocytes is mainly regulated by the MAPK signaling pathway because activation of Nfatc1α is mediated by MEK-ERK signaling but opposed by JNK signaling. Calcineuirn-NFAT and p38 signaling pathways are not involved in Nfatc1α promoter regulation in DN thymocytes. In DP thymocytes, TCR signaling up-regulates Nfatc1 and Nfatc2 expression but down-regulates Nfatc3 expression. In DP thymocytes, TCR signaling activates Nfatc1α expression. The activation of Nfatc1α in DP thymocytes is mediated by NFATc1, but not or to a less degree by NFATc2 and NFATc3. MEK-ERK, JNK, and p38 signaling pathways are involved in Nfatc1α gene activation in DP thymocytes, probably by activating NFAT trans-activation activity. All these findings illustrate that in thymocytes the expression of NFAT transcription factors – which are essential for thymic development - is controled at multiple levels.
Neisseria gonorrhoeae (GC) is a human specific pathogenic bacterium. Currently, N. gonorrhoeae developed resistance to virtually all the available antibiotics used for treatment. N. gonorrhoeae starts infection by colonizing the cell surface, followed by invasion of the host cell, intracellular persistence, transcytosis and exit into the subepithelial space. Subepithelial bacteria can reach the bloodstream and disseminate to other tissues causing systemic infections, which leads to serious conditions such as arthritis and pneumonia. A number of studies have well established the host-pathogen interactions during the initial adherence and invasion steps. However, the mechanism of intracellular survival and traversal is poorly understood so far. Hence, identification of novel bacterial virulence factors and host factors involved in the host-pathogen interaction is a crucial step in understanding disease development and uncovering novel therapeutic approaches. Besides, most of the previous studies about N. gonorrhoeae were performed in the conventional cell culture. Although they have provided insights into host-pathogen interactions, much information about the native infection microenvironment, such as cell polarization and barrier function, is still missing.
This work focused on determining the function of novel bacterial virulence factor NGFG_01605 and host factor (FLCN) in gonococcal infection. NGFG_01605 was identified by Tn5 transposon library screening. It is a putative U32 protease. Unlike other proteins in this family, it is not secreted and has no ex vivo protease activity. NGFG_01605 knockout decreases gonococcal survival in the epithelial cell. 3D models based on T84 cell was developed for the bacterial transmigration assay. NGFG_01605 knockout does not affect gonococcal transmigration.
The novel host factor FLCN was identified by shRNA library screening in search for factors that affected gonococcal adherence and/or internalization. We discovered that FLCN did not affect N. gonorrhoeae adherence and invasion but was essential for bacterial survival. Since programmed cell death is a host defence mechanism against intracellular pathogens, we further explored apoptosis and autophagy upon gonococcal infection and determined that FLCN did not affect apoptosis but inhibited autophagy. Moreover, we found that FLCN inhibited the expression of E-cadherin. Knockdown of E- cadherin decreased the autophagy flux and supported N. gonorrhoeae survival. Both non-polarized and polarized cells are present in the cervix, and additionally, E-cadherin represents different polarization properties on these different cells. Therefore, we established 3-D models to better understand the functions of FLCN. We discovered that FLCN was critical for N. gonorrhoeae survival in the 3-D environment as well, but not through inhibiting autophagy. Furthermore, FLCN inhibits the E-cadherin expression and disturbs its polarization in the 3-D models. Since N. gonorrhoeae can cross the epithelial cell barriers through both cell-cell junctions and transcellular migration, we further explored the roles FLCN and E-cadherin played in transmigration. FLCN delayed N. gonorrhoeae transmigration, whereas the knockdown of E-cadherin increased N. gonorrhoeae transmigration.
In summary, we revealed roles of the NGFG_01605 and FLCN-E-cadherin axis play in N. gonorrhoeae infection, particularly in relation to intracellular survival and transmigration. This is also the first study that connects FLCN and human-specific pathogen infection.
The universal two-child policy was introduced by the central government of China in 2016 to respond to the country’s deteriorating population problems, but it was soon replaced by a three-child policy in 2021 given that it failed to continuously boost fertility in Chinese society. This dissertation empirically investigates the implementation of universal two-child policy in three Chinese major cities. Based on the data collected through semi-structured interviews with leaders of local family planning agencies, it finds that local officials are primarily devoted to coping with the discontent of the bereaved single-child parents (shidu families), which is an unexpected consequence of the historical one-child policy, rather than working on the tasks regarding birth encouragement. The dissertation suggests understanding the implementation of China’s population policy within the framework of both historical and rational choice institutionalism. The target responsibility system as an effective tool of the central authority drives local agents to fix their attention at tasks that have larger impact on their career. The shifted focus in the implementation of the universal two-child policy is a result of local officials’ emphasis on the task of maintaining social stability. Shidu families are deemed as a salient threat to social order because their discontent with the state support has incurred continuous petitions at both the national and local level, which would severely undermine local officials’ career advancement. However, in the meantime, stability maintenance is found to have become alienated as reflected by the rising costs and that it replaced birth support to be the focus of local family planning agents in the universal two-child policy era. Since the conflict between the shidu group and the state is unlikely to be resolved, the future population policy design and enforcement will continue to be constrained by the shidu problem.
The learned helplessness phenomenon is a specific animal behavior induced by prior exposure to uncontrollable aversive stimuli. It was first found by Seligman and Maier (1967) in dogs and then has been reported in many other species, e.g. in rats (Vollmayr and Henn, 2001), in goldfishes (Padilla, 1970), in cockroaches (Brown, 1988) and also in fruit flies (Brown, 1996; Bertolucci, 2008). However, the learned helplessness effect in fruit flies (Drosophila melanogaster) has not been studied in detail. Thus, in this doctoral study, we investigated systematically learned helplessness behavior of Drosophila for the first time.
Three groups of flies were tested in heatbox. Control group was in the chambers experiencing constant, mild temperature. Second group, master flies were punished in their chambers by being heated if they stopped walking for 0.9s. The heat pulses ended as soon as they resumed walking again. A third group, the yoked fly, was in their chambers at the same time. However, their behavior didn’t affect anything: yoked flies were heated whenever master flies did, with same timing and durations. After certain amount of heating events, yoked flies associated their own behavior with the uncontrollability of the environment. They suppressed their innate responses such as reducing their walking time and walking speed; making longer escape latencies and less turning around behavior under heat pulses. Even after the conditioning phase, yoked flies showed lower activity level than master and control flies. Interestingly, we have also observed sex dimorphisms in flies. Male flies expressed learned helplessness not like female flies. Differences between master and yoked flies were smaller in male than in female flies. Another interesting finding was that prolonged or even repetition of training phases didn’t enhance learned helplessness effect in flies.
Furthermore, we investigated serotonergic and dopaminergic nervous systems in learned helplessness. Using genetic and pharmacological manipulations, we altered the levels of serotonin and dopamine in flies’ central nervous system. Female flies with reduced serotonin concentration didn’t show helpless behavior, while the learned helplessness effect in male flies seems not to be affected by a reduction of serotonin. Flies with lower dopamine level do not display the learned helplessness effect in the test phase, suggesting that with low dopamine the motivational change in learned helplessness in Drosophila may decline faster than with a normal dopamine level.
Past experience contributes to behavioural organization mainly via learning: Animals learn otherwise ordinary cues as predictors for biologically significant events. This thesis studies such predictive, associative learning, using the fruit fly Drosophila melanogaster. I ask two main questions, which complement each other: One deals with the processing of those cues that are to be learned as predictors for an important event; the other one deals with the processing of the important event itself, which is to be predicted. Do fruit flies learn about combinations of olfactory and visual cues? I probe larval as well as adult fruit flies for the learning about combinations of olfactory and visual cues, using a so called ‘biconditional discrimination’ task: During training, one odour is paired with reinforcement only in light, but not in darkness; the other odour in turn is reinforced only in darkness, but not in light. Thus, neither the odours nor the visual conditions alone predict reinforcement, only combinations of both do. I find no evidence that either larval or adult fruit flies were to solve such task, speaking against a cross-talk between olfactory and visual modalities. Previous studies however suggest such cross-talk. To reconcile these results, I suggest classifying different kinds of interaction between sensory modalities, according to their site along the sensory-motor continuum: I consider an interaction ‘truly’ cross-modal, if it is between the specific features of the stimuli. I consider an interaction ’amodal’ if it instead engages the behavioural tendencies or ‘values’ elicited by each stimulus. Such reasoning brings me to conclude that different behavioural tasks require different kinds of interaction between sensory modalities; whether a given kind of interaction will be found depends on the neuronal infrastructure, which is a function of the species and the developmental stage. Predictive learning of pain-relief in fruit flies Fruit flies build two opposing kinds of memory, based on an experience with electric shock: Those odours that precede shock during training are learned as predictors for punishment and are subsequently avoided; those odours that follow shock during training on the other hand are learned as signals for relief and are subsequently approached. I focus on such relief learning. I start with a detailed parametric analysis of relief learning, testing for reproducibility as well as effects of gender, repetition of training, odour identity, odour concentration and shock intensity. I also characterize how relief memories, once formed, decay. In addition, concerning the psychological mechanisms of relief learning, first, I show that relief learning establishes genuinely associative conditioned approach behaviour and second, I report that it is most likely not mediated by context associations. These results enable the following neurobiological analysis of relief learning; further, they will form in the future the basis for a mathematical model; finally, they will guide the researchers aiming at uncovering relief learning in other experimental systems. Next, I embark upon neurogenetic analysis of relief learning. First, I report that fruit flies mutant for the so called white gene build overall more ‘negative’ memories about an experience with electric shock. That is, in the white mutants, learning about the painful onset of shock is enhanced, whereas learning about the relieving offset of shock is diminished. As they are coherently affected, these two kinds of learning should be in a balance. The molecular mechanism of the effect of white on this balance remains unresolved. Finally, as a first step towards a neuronal circuit analysis of relief learning, I compare it to reward learning and punishment learning. I find that relief learning is distinct from both in terms of the requirement for biogenic amine signaling: Reward and punishment are respectively signalled by octopamine and dopamine, for relief learning, either of these seem dispensible. Further, I find no evidence for roles for two other biogenic amines, tyramine and serotonin in relief learning. Based on these findings I give directions for further research.
The importance of enterprise systems is increasingly growing and they are in the center of attention and consideration by organizations in various types of business and industries from extra-large public or private organizations to small and medium-sized service sector business. These systems are continuously advancing functionally and technologically and are inevitable and ineluctable for the enterprises to maximize their productivity and integration in current competitive national and global business environments.
Also, since local software solutions could not meet the requirements of especially large enterprises functionally and technically, and as giant global enterprise software producers like SAP, Oracle and Microsoft are improving their solutions rapidly and since they are expanding their market to more corners of the globe, demand for these globally branded low-defect software solutions is daily ascending. The agreements for international ERP implementation project consultancy are, therefore, exponentially increasing, while the research on the influencing factors and know-hows is scattered and rare, and thus, a timely urgency for this field of research is being felt.
The final developed five-in-five framework of this study, for the first time, collects all mentioned-in-the-history critical success factors and project activities, while sequencing them in five phases and categorizing them in five focus areas for international ERP implementation projects. This framework provides a bird’s-eye view and draws a comprehensive roadmap or instruction for such projects.
The role of DNA supercoiling in the coordinated regulation of gene expression in Helicobacter pylori
(2004)
Summary Mechanisms of global gene regulation in bacteria are not well characterized yet. Changes in global or local supercoiling of chromosomal DNA are thought to play a role in global gene silencing and gene activation. In Helicobacter pylori, a bacterium with few dedicated transcriptional regulators, the structure of some promoters indicates a dependency on DNA topology. For example, the promoter of the major flagellar subunit gene flaA (ó28-dependent) has a shorter spacing of 13 nucleotides (nt) in comparison to the consensus promoter (15 nt). Supercoiling changes might be a mechanism of gene-specific and global transcriptional regulation in this bacterium. The aim of this study was to elucidate, if changes in global supercoiling have an influence on global gene regulation in H. pylori, and on the temporal regulation of the flagellar biosynthesis pathway in this organism. In the present work, global DNA supercoiling in H. pylori was visualized for the first time, by determining the supercoiling state of plasmids under different growth conditions. Using this method, we showed that cellular supercoiling was clearly growth phase-dependent in H. pylori. Coinciding with increased supercoiling during the growth phases, transcription of the flaA gene was increased, while the transcription of a second ó28-dependent gene with regular promoter spacing (HP0472) was reduced, supporting the hypothesis that growth phase-dependency of promoters might be mediated by changes of DNA topology. Supercoiling in H. pylori could be influenced in a reproducible fashion by inhibition of gyrase using novobiocin, which led to DNA relaxation and to a concomitant decrease of flaA transcript levels. Promoter spacer mutagenesis of the flaA promoter was performed. With flaA promoters of increased or reduced length, transcription of flaA was reduced, less susceptible to supercoiling changes, and, under specific conditions, inverted as compared to the wild type promoter. Transcriptional interdependence between the coupled topA-flaB genes and flaA was found by analysis of the flaA promoter mutants. Chromosomally linked gyrA-flgR, and topA-flaB genes were all dependent on supercoiling and coregulated with each other. Comprehensive transcript profiling (DNA microarrays) of wildtype H. pylori with and without novobiocin treatment identified a number of genes (10% of total genes), including flagellin, virulence and housekeeping genes, which were strongly dependent on and appeared to be synchronized by supercoiling changes (transcriptional up- or downregulation). These findings indicate a tightly coupled temporal regulation of flagellar biogenesis and metabolism in H. pylori, dependent on global supercoiling. A specific group of genes was also regulated in H. pylori by overexpression of Topoisomerase I, as detected by genome-wide analysis (DNA microarray). The DNA-bending protein HU is thought to be responsible for influencing the negative supercoiling of DNA, through its ability to wrap DNA. HU is encoded by the hup single gene in H. pylori, and constitutively expressed during the whole growth curve. An H. pylori hup mutant was constructed. H. pylori cells lacking HU protein were viable, but exhibited a severe growth defect. Our data indicate that the lack of HU dramatically changes global DNA supercoiling, indicating an important function of HU in chromosome structuring in H. pylori. Transcriptome analyses were performed and demonstrated that a total of 66 genes were differentially transcribed upon hup deletion, which include virulence genes and many other cell functions. The data indicate that HU might act as further important global regulator in H. pylori. Increased gene expression of heat shock proteins and a decreased transcription of the urease gene cluster may indicate a co-ordinated response of H. pylori to changes of environmental conditions in its specific ecological niche, mediated by HU. After the whole genomic sequences of H. pylori strains 26695 and J99 were published, two ORFs (HP0116 and HP0440) were presumptively annotated as topoisomerase I orthologs. HP0116 is the functional H. pylori topoisomerase I (TopA). HP0440 (topA2) was found in only few (5 of 43) strains. Western blot analysis indicated that TopA2 is antigenically different from TopA. TopA2 is transcribed in H. pylori, but the protein must be functionally different from TopA, since it is lacking one functionally essential zinc finger motif, and was not able to functionally complement a TopA-deficient E. coli. Like topA, topA2 was also transcribed in a growth phase-dependent manner. We did not find a function of TopA2 in DNA structuring or topology, but, in the present study, we were able for the first time to establish a unique function for TopA2 in global gene regulation, by comprehensive transcriptome analysis (DNA microarray). Transcriptome analysis showed that a total of 46 genes were differentially regulated upon topA2 deletion, which included flagellar genes and urease genes. These results suggest that TopA2 might act as a novel important regulator of both flagellar biosynthesis and urease in H. pylori.
RNA is one of the most abundant macromolecules and plays essential roles in numerous biological processes. This doctoral thesis consists of two projects focusing on RNA structure and RNA-RNA interactions in viral genome packaging. In the first project I developed a method called Functional Analysis of RNA Structure (FARS-seq) to investigate structural features regulating genome dimerization within the HIV-1 5’UTR. Genome dimerization is a conserved feature of retroviral replication and is thought to be a prerequisite for binding to the viral structural protein Pr55Gag during genome packaging. It also plays a role in genome integrity and evolution through recombination, and is linked to a structural switch that may regulate genome packaging and translation within cells. Despite its importance for HIV-1 replication, the RNA signals regulating genome dimerization, and the molecular mechanism leading to the selection of the genome dimer over the monomer for packaging are incompletely understood. The FARS-seq method combines RNA structural information obtained by chemical probing with single nucleotide resolution profiles of RNA function obtained by mutational interference. In this way, we found nucleotides that were critical for dimerization, especially within the well-characterized dimerization motif within stem-loop 1 (SL1). We also found stretches of nucleotides that enhanced genome dimerization upon mutation, suggesting their role in negatively regulating dimerization. A structural analysis identified distinct structural signatures within monomeric and dimeric RNA. The dimeric conformation displayed the canonical transactivation response (TAR), PolyA, primer binding site (PBS), and SL1-SL3 stem-loops, and contained a long range U5-AUG interaction. Unexpectedly, in monomeric RNA, SL1 was reconfigured into long- and short-range base-pairings with PolyA and PBS, respectively. Intriguingly, these base pairings concealed the palindromic sequence needed for dimerization and disrupted the internal loop in SL1 previously shown to contain the major packaging motif for Pr55Gag. We therefore rationally introduced mutations into PolyA and PBS, and showed how these regions regulate genome dimerization, and the binding of Pr55Gag in vitro, as well as genome packaging into virions. These findings give insights into late stages of the HIV-1 life cycle and a mechanistic explanation for the link between RNA dimerization and packaging.
In the second project, I developed a proximity ligation and high-throughput sequencing-based method, RNA-RNA seq, which can measure direct (RNA-RNA) and indirect (protein-mediated) interactions. In contrast to existing methods, RNA-RNA seq is not limited by specific protein or RNA baits, nor to a particular crosslinking reagent. The genome of influenza A virus contains eight segments, which assemble into a “7+1” supramolecular complex. However, the molecular details of genome assembly are poorly understood. Our goal is to use RNA-RNA seq to identify the sites of interaction between the eight genomic RNAs of influenza, and to use this information to define the quaternary RNA architecture of the genome. We showed that RNA-RNA seq worked on model substrates, like the HIV-1 Dimerization Initiation Site (DIS) RNA and purified ribosome, as well as influenza A virus infected cells.
Interleukin 2 (IL-2) was the first cytokine applied for cancer treatment in human history. It has been approved as monotherapy for renal cell carcinoma and melanoma by the FDA and does mediate the regression of the tumors in patients. One of the possible mechanisms is that the administration of IL-2 led to T lymphocytes expansion, including CD4+ and CD8+ T cells. In addition, a recent study demonstrated that antigen-specific T cells could also be expanded through the induction of IL-2, which plays a crucial role in mediating tumor regression. However, despite the long-term and extensive use of IL-2 in the clinic, the ratio of patients who get a complete response was still low, and only about one-fifth of patients showed objective tumor regression. Therefore, the function of IL-2 in cancer treatment should continue to be optimized and investigated. A study by Franz O. Smith et al. has shown that the combination treatment of IL-2 and tumor-associated antigen vaccine has a strong trend to increased objective responses compared to patients with melanoma receiving IL-2 alone. Peptide vaccines are anti-cancer vaccines able to induce a powerful tumor antigenspecific immune response capable of eradicating the tumors. According to the type of antigens, peptide vaccines can be classified into two distinct categories: Tumor-associated antigens (TAA) vaccine and tumor-specific neoantigens (TSA) vaccine. Currently, Peptide vaccines are mainly investigated in phase I and phase II clinical trials of human cancer patients with various advanced cancers such as lung cancer, gastrointestinal tumors, and breast cancers. Vaccinia virus (VACV) is one of the safest viral vectors, which has been wildly used in cancer treatment and pathogen prevention. As an oncolytic vector, VACV can carry multiple large foreign genes, which enable the virus to introduce diagnostic and therapeutic agents without dramatically reducing the viral replication. Meanwhile, the recombinant vaccinia virus (rVACV) can be easily generated by homologous recombination. Here, we used the vaccinia virus as the therapeutic cancer vector, expressing mouse Interleukin 2 (IL-2) and tumor-associated antigens simultaneously to investigate the combined effect of anti-tumor immune response in the 4T1 mouse tumor model. As expected, the VACV driven mIL-2 expression remarkably increased both CD4+ and CD8+ populations in vivo, and the virus-expressed tumor-associated peptides successfully elicited theantigen-specific T cell response to inhibit the growth of tumors. Furthermore, the experiments with tumor-bearing animals showed that the mIL-2 plus tumor antigens expressing VACV vector gave a better anti-cancer response than the mIL-2 alone expressing vector. The combinations did significantly more inhibit tumor growth than mIL-2 treatment alone. Moreover, the results confirmed our previous unpublished data that the mIL-2 expression driven by synthetic early/late promoter in the Lister strain VACV could enhance the tumor regression in the 4T1 mouse model.
Synthesis and Investigation of Borylene Complexes: from Borylene Transfer to Borylene Catenation
(2012)
Within the scope of this thesis, the area of borylene transfer has been broadened by including transition-metal alkynyl complexes and metal-carbon double bonds as borylene acceptors. In addition to double salt elimination, halide abstraction and dehydrogenation processes, a novel high-yield synthetic procedure for terminal borylene complexes was established, i.e. salt elimination and subsequent silylhalogenide liberation. Accordingly, it was possible to prepare [(OC)3(Me3P)Fe=BDur] as a rare example of a neutral arylborylene species. Moreover, this compound has been demonstrated to possess great potential for metathesis reactions and the functionalization of polycyclic aromatic hydrocarbons such as naphthalene. Moreover, it could undergo a phosphine-borylene exchange reaction, yielding the iron bis(borylene) complex [(OC)3Fe(BDur){BN(SiMe3)2}], which has turned out to be applicable for preparation of 1,4-diboracyclohexadiene and unprecedented 1,4-dibora-1,3-butadiene complexes, thus establishing a new type of borylene transfer. Most interestingly, upon transfer of further borylene moieties into the coordination sphere of iron, borylene-catenation was accomplished in a highly controlled manner.
Myocardial infarction (MI) is a leading cause of death worldwide. Timely restoration of coronary blood flow to ischemic myocardium significantly reduces acute infarct mortality and attenuates ventricular remodeling. However, surviving MI patients frequently develop heart failure, which is associated with reduced quality of life, high mortality rate (10% annually), as well as high healthcare expenditures. The main processes involved in the evolution of heart failure post-MI are the great loss of contractile cardiomyocytes during ischemia-reperfusion and the subsequent complex structural and functional alterations, which are rooted in modifications at molecular and cellular levels in both the infarcted and non-infarcted myocardium. However, we still lack efficient treatments to prevent the development and progression of left ventricular remodeling. The improved survival rate of acute MI patients combined with the lack of effective therapy for post-MI remodeling contributes to the high prevalence of heart failure. Cardiac Magnetic Resonance Imaging (MRI) is an important tool for diagnosis and assessment of MI. With the advancement of this technology, the frontier of MRI has been extended to probing molecular and cellular events in vivo and non-invasively. In combination with assessment of morphology and function, the visualization of essential molecular and cellular markers in vivo could provide comprehensive, multifaceted views of the healing process in infarcted hearts, which might give new insight for the treatment of acute MI. In this thesis, molecular and cellular cardiac MRI methods were established to visualize and investigate inflammation and calcium flux in the healing process of acute MI in vivo, in a clinically relevant rat model.
Neurodegeneration plays an essential role in Parkinson’s disease (PD). Several crucial neuronal pro-and antidegeneration markers were described to be altered in disease models accompanied by neurodegeneration. In the AAV1/2-A53T-aSyn PD rat model progressive time-dependent motor impairment and neurodegeneration in the nigrostriatal tract starting from 2 weeks after PD model induction could be found. Downregulation of Nrf2 in SN and nigrostriatal axon localization, a trend of Tau downregulation in SN and upregulation in axon localization in the AAV1/2-A53T-aSyn PD rat model were observed, indicating potential therapeutic value of these two molecular targets in PD. No alterations of SARM1 and NMNAT2 could be detected, indicating little relevance of these two molecules with our AAV1/2-A53T-aSyn rat model.
Thermoplastic polymers have a history of decades of safe and effective use in the clinic as implantable medical devices. In recent years additive manufacturing (AM) saw increased clinical interest for the fabrication of customizable and implantable medical devices and training models using the patients’ own radiological data. However, approval from the various regulatory bodies remains a significant hurdle. A possible solution is to fabricate the AM scaffolds using materials and techniques with a clinical safety record, e.g. melt processing of polymers. Melt Electrowriting (MEW) is a novel, high resolution AM technique which uses thermoplastic polymers. MEW produces scaffolds with microscale fibers and precise fiber placement, allowing the control of the scaffold microarchitecture. Additionally, MEW can process medical-grade thermoplastic polymers, without the use of solvents paving the way for the production of medical devices for clinical applications. This pathway is investigated in this thesis, where the layout is designed to resemble the journey of a medical device produced via MEW from conception to early in vivo experiments. To do so, first, a brief history of the development of medical implants and the regenerative capability of the human body is given in Chapter 1. In Chapter 2, a review of the use of thermoplastic polymers in medicine, with a focus on poly(ε-caprolactone) (PCL), is illustrated, as this is the polymer used in the rest of the thesis. This review is followed by a comparison of the state of the art, regarding in vivo and clinical experiments, of three polymer melt AM technologies: melt-extrusion, selective laser sintering and MEW. The first two techniques already saw successful translation to the bedside, producing patient-specific, regulatory-approved AM implants. To follow in the footsteps of these two technologies, the MEW device parameters need to be optimized. The MEW process parameters and their interplay are further discussed in Chapter 3 focusing on the importance of a steady mass flow rate of the polymer during printing. MEW reaches a balance between polymer flow, the stabilizing electric field and moving collector to produce reproducible, high-resolution scaffolds. An imbalance creates phenomena like fiber pulsing or arcing which result in defective scaffolds and potential printer damage. Chapter 4 shows the use of X-ray microtomography (µCT) as a non-destructive method to characterize the pore-related features: total porosity and the pore size distribution. MEW scaffolds are three-dimensional (3D) constructs but have long been treated in the literature as two-dimensional (2D) ones and characterized mainly by microscopy, including stereo- and scanning electron microscopy, where pore size was simply reported as the distance between the fibers in a single layer. These methods, together with the trend of producing scaffolds with symmetrical pores in the 0/90° and 0/60/120° laydown patterns, disregarded the lateral connections between pores and the potential of MEW to be used for more complex 3D structures, mimicking the extracellular matrix. Here we characterized scaffolds in the aforementioned symmetrical laydown patterns, along with the more complex 0/45/90/135° and 0/30/60/90/120/150° ones. A 2D pore size estimation was done first using stereomicroscopy, followed by and compared to µCT scanning. The scaffolds with symmetrical laydown patterns resulted in the predominance of one pore size, while those with more complex patterns had a broader distribution, which could be better shown by µCT scans. Moreover, in the symmetrical scaffolds, the size of 3D pores was not able to reach the value of the fiber spacing due to a flattening effect of the scaffold, where the thickness of the scaffold was less than the fiber spacing, further restricting the pore size distribution in such scaffolds. This method could be used for quality assurance of fabricated scaffolds prior to use in in vitro or in vivo experiments and would be important for a clinical translation. Chapter 5 illustrates a proof of principle subcutaneous implantation in vivo experiment. MEW scaffolds were already featured in small animal in vivo experiments, but to date, no analysis of the foreign body reaction (FBR) to such implants was performed. FBR is an immune reaction to implanted foreign materials, including medical devices, aimed at protecting the host from potential adverse effects and can interfere with the function of some medical implants. Medical-grade PCL was used to melt electrowrite scaffolds with 50 and 60 µm fiber spacing for the 0/90° and 0/60/120° laydown patterns, respectively. These implants were implanted subcutaneously in immunocompetent, outbred mice, with appropriate controls, and explanted after 2, 4, 7 and 14 days. A thorough characterization of the scaffolds before implantation was done, followed by a full histopathological analysis of the FBR to the implants after excision. The scaffolds, irrespective of their pore geometry, induced an extensive FBR in the form of accumulation of foreign body giant cells around the fiber walls, in a manner that almost occluded available pore spaces with little to no neovascularization. This reaction was not induced by the material itself, as the same reaction failed to develop in the PCL solid film controls. A discussion of the results was given with special regard to the literature available on flat surgical meshes, as well as other hydrogel-based porous scaffolds with similar pore sizes. Finally, a general summary of the thesis in Chapter 6 recapitulates the most important points with a focus on future directions for MEW.
Development and application of computational tools for RNA-Seq based transcriptome annotations
(2019)
In order to understand the regulation of gene expression in organisms, precise genome annotation is essential. In recent years, RNA-Seq has become a potent method for generating and improving genome annotations. However, this Approach is time consuming and often inconsistently performed when done manually. In particular, the discovery of non-coding RNAs benefits strongly from the application of RNA-Seq data but requires significant amounts of expert knowledge and is labor-intensive. As a part of my doctoral study, I developed a modular tool called ANNOgesic that can detect numerous transcribed genomic features, including non-coding RNAs, based on RNA-Seq data in a precise and automatic fashion with a focus on bacterial and achaeal species. The software performs numerous analyses and generates several visualizations. It can generate annotations of high-Resolution that are hard to produce using traditional annotation tools that are based only on genome sequences. ANNOgesic can detect numerous novel genomic Features like UTR-derived small non-coding RNAs for which no other tool has been developed before. ANNOgesic is available under an open source license (ISCL) at https://github.com/Sung-Huan/ANNOgesic.
My doctoral work not only includes the development of ANNOgesic but also its application to annotate the transcriptome of Staphylococcus aureus HG003 - a strain which has been a insightful model in infection biology. Despite its potential as a model, a complete genome sequence and annotations have been lacking for HG003. In order to fill this gap, the annotations of this strain, including sRNAs and their functions, were generated using ANNOgesic by analyzing differential RNA-Seq data from 14 different samples (two media conditions with seven time points), as well as RNA-Seq data generated after transcript fragmentation. ANNOgesic was
also applied to annotate several bacterial and archaeal genomes, and as part of this its high performance was demonstrated. In summary, ANNOgesic is a powerful computational tool for RNA-Seq based annotations and has been successfully applied to several species.
Among the defense strategies developed in microbes over millions of years, the innate adaptive CRISPR-Cas immune systems have spread across most of bacteria and archaea. The flexibility, simplicity, and specificity of CRISPR-Cas systems have laid the foundation for CRISPR-based genetic tools. Yet, the efficient administration of CRISPR-based tools demands rational designs to maximize the on-target efficiency and off-target specificity. Specifically, the selection of guide RNAs (gRNAs), which play a crucial role in the target recognition of CRISPR-Cas systems, is non-trivial. Despite the fact that the emerging machine learning techniques provide a solution to aid in gRNA design with prediction algorithms, design rules for many CRISPR-Cas systems are ill-defined, hindering their broader applications.
CRISPR interference (CRISPRi), an alternative gene silencing technique using a catalytically dead Cas protein to interfere with transcription, is a leading technique in bacteria for functional interrogation, pathway manipulation, and genome-wide screens. Although the application is promising, it also is hindered by under-investigated design rules. Therefore, in this work, I develop a state-of-art predictive machine learning model for guide silencing efficiency in bacteria leveraging the advantages of feature engineering, data integration, interpretable AI, and automated machine learning. I first systematically investigate the influential factors that attribute to the extent of depletion in multiple CRISPRi genome-wide essentiality screens in Escherichia coli and demonstrate the surprising dominant contribution of gene-specific effects, such as gene expression level. These observations allowed me to segregate the confounding gene-specific effects using a mixed-effect random forest (MERF) model to provide a better estimate of guide efficiency, together with the improvement led by integrating multiple screens. The MERF model outperformed existing tools in an independent high-throughput saturating screen. I next interpret the predictive model to extract the design rules for robust gene silencing, such as the preference for cytosine and disfavoring for guanine and thymine within and around the protospacer adjacent motif (PAM) sequence. I further incorporated the MERF model in a web-based tool that is freely accessible at www.ciao.helmholtz-hiri.de.
When comparing the MERF model with existing tools, the performance of the alternative gRNA design tool optimized for CRISPRi in eukaryotes when applied to bacteria was far from satisfying, questioning the robustness of prediction algorithms across organisms. In addition, the CRISPR-Cas systems exhibit diverse mechanisms albeit with some similarities. The captured predictive patterns from one dataset thereby are at risk of poor generalization when applied across organisms and CRISPR-Cas techniques. To fill the gap, the machine learning approach I present here for CRISPRi could serve as a blueprint for the effective development of prediction algorithms for specific organisms or CRISPR-Cas systems of interest. The explicit workflow includes three principle steps: 1) accommodating the feature set for the CRISPR-Cas system or technique; 2) optimizing a machine learning model using automated machine learning; 3) explaining the model using interpretable AI. To illustrate the applicability of the workflow and diversity of results when applied across different bacteria and CRISPR-Cas systems, I have applied this workflow to analyze three distinct CRISPR-Cas genome-wide screens. From the CRISPR base editor essentiality screen in E. coli, I have determined the PAM preference and sequence context in the editing window for efficient editing, such as A at the 2nd position of PAM, A/TT/TG downstream of PAM, and TC at the 4th to 5th position of gRNAs. From the CRISPR-Cas13a screen in E. coli, in addition to the strong correlation with the guide depletion, the target expression level is the strongest predictor in the model, supporting it as a main determinant of the activation of Cas13-induced immunity and better characterizing the CRISPR-Cas13 system. From the CRISPR-Cas12a screen in Klebsiella pneumoniae, I have extracted the design rules for robust antimicrobial activity across K. pneumoniae strains and provided a predictive algorithm for gRNA design, facilitating CRISPR-Cas12a as an alternative technique to tackle antibiotic resistance.
Overall, this thesis presents an accurate prediction algorithm for CRISPRi guide efficiency in bacteria, providing insights into the determinants of efficient silencing and guide designs. The systematic exploration has led to a robust machine learning approach for effective model development in other bacteria and CRISPR-Cas systems. Applying the approach in the analysis of independent CRISPR-Cas screens not only sheds light on the design rules but also the mechanisms of the CRISPR-Cas systems. Together, I demonstrate that applied machine learning paves the way to a deeper understanding and a broader application of CRISPR-Cas systems.
Regulation of effector T cells is an important mechanism to control organ-specific inflammation. Thereby regulatory T cells (Treg cells) are essential for maintaining peripheral immune tolerance and for establishing parenchyma immune homeostasis. A novel population of natural human Treg characterized by the constitutive expression of the immune-tolerogenic human HLA-G molecule has been identified. In the first part of the study, we elucidated the mechanism(s) by which CD4+ HLA-Gpos Treg modulates their cellular targets namely autologous HLA-G negative responder T cells (HLAGneg Tresp). Using a suppression system free of antigen-presenting cells (APC), we demonstrate a T-T cell interaction resulting in suppression of HLA-Gneg Tresp. We could also show that this suppression was independent of cell-cell contact. Importantly, stimulus of T cell receptor (TCR) on HLA-Gpos Treg facilitated their suppressive capacity. We also observed that removal of HLA-Gpos Treg from the established co-cultures could restore the ability of HLA-Gneg Tresp to proliferate upon TCR re-stimulation, indicating that the suppression was reversible. Further, HLA-Gpos Treg–mediated suppression was critically depending on the secretion of IL-10 but not TGF-β. Taken together, this part of the work provides an in-depth characterization of the mechanisms of how HLA-Gpos Treg suppresses T responder cells in direct T-T interactions. Understanding the suppressive mechanism used by HLA-Gpos Treg may help to develop therapeutic strategies to modulate regulatory arms of T-cell suppression. In the second part of this study, the potential role of HLA-Gpos Treg in the pathophysiological process of Multiple Sclerosis (MS), a prototypic autoimmune inflammatory central nervous system (CNS), has been investigated. We found that HLA-Gpos Treg are enriched in the cerebrospinal fluid (CSF) from MS patients, but not in non-inflammatory controls. CSFderived HLA-Gpos Treg showed predominance of central memory (CD45RA-CD27+) phenotype, exhibited markers of activation (ICOS), and had significantly higher expression of the inflammatory chemokine receptor CCR5. Importantly, these cells demonstrated as potent suppressors to autologous CD4+ T-cell proliferation. Using an in vitro model of human blood brain barrier, we showed that HLA-Gpos Treg have a strong propensity to migrate, which could be facilitated by MIP1α and RANTES (ligands of CCR5) but not MIP3β (a ligand of CCR7). The HLA-Gpos Treg migration triggered by chemokines was also associated with a gain of suppressive capacity upon cellular transmigration. In contrast to CD4+CD25+ naturally occurring FoxP3-expressing Treg, HLA-Gpos Treg from patients with MS did not exhibit impaired function, suggesting that HLA-Gpos Treg are selectively recruited to the sites of CNS inflammation in an effort to combat destructive inflammation during MS. Our results contribute to the understanding of the role and function of HLA-Gpos Treg and provide an important example of “beneficial” T-cell inflammation in CNS autoimmunity- interesting both from a patho/-physiological and a therapeutically point of view.
The light-gated cation channel Channelrhodopsin-2 was discovered and characterized in 2003. Already in 2005/2006 five independent groups demonstrated that heterologous expression of Channelrhodopsin-2 is a highly useful and simply applicable method for depolarizing and thereby activating nerve cells. The application of Channelrhodopsin-2 revolutionized neuroscience research and the method was then called optogenetics. In recent years more and more light-sensitive proteins were successfully introduced as “optogenetic tools”, not only in neuroscience. Optogenetic tools for neuronal excitation are well developed with many different cation-conducting wildtype and mutated channelrhodopsins, whereas for inhibition of neurons in the beginning (2007) only hyperpolarizing ion pumps were available. The later discovered light-activated anion channels (anion channelrhodopsins) can be useful hyperpolarizers, but only at low cytoplasmic anion concentration. For this thesis, I optimized CsR, a proton-pumping rhodopsin from Coccomyxa subellipsoidea, which naturally shows a robust expression in Xenopus laevis oocytes and plant leaves. I improved the expression and therefore the photocurrent of CsR about two-fold by N-terminal modification to the improved version CsR2.0, without altering the proton pump function and the action spectrum. A light pulse hyperpolarised the mesophyll cells of CsR2.0-expressing transgenic tobacco plants (N. tabacum) by up to 20 mV from the resting membrane potential of -150 to -200 mV. The robust heterologous expression makes CsR2.0 a promising optogenetic tool for hyperpolarization in other organisms as well. A single R83H point-mutation converted CsR2.0 into a light-activated (passive) proton channel with a reversal potential close to the Nernst potential for intra-/extra-cellular H+ concentration. This light-gated proton channel is expected to become a further useful optogenetic tool, e.g. for analysis of pH-regulation in cells or the intercellular space. Ion pumps as optogenetic tools require high expression levels and high light intensity for efficient pump currents, whereas long-term illumination may cause unwanted heating effects. Although anion channelrhodopsins are effective hyperpolarizing tools in some cases, their effect on neuronal activity is dependent on the cytoplasmic chloride concentration which can vary among neurons. In nerve cells, increased conductance for potassium terminates the action potential and K+ conductance underlies the resting membrane potential in excitable cells. Therefore, several groups attempted to synthesize artificial light-gated potassium channels but 2 all of these published innovations showed serious drawbacks, ranging from poor expression over lacking reversibility to poor temporal precision. A highly potassium selective light-sensitive silencer of action potentials is needed. To achieve this, I engineered a light-activated potassium channel by the genetic fusion of a photoactivated adenylyl cyclase, bPAC, and a cAMP-gated potassium channel, SthK. Illumination activates bPAC to produce cAMP and the elevated cAMP level opens SthK. The slow diffusion and degradation of cAMP makes this construct a very light-sensitive, long-lasting inhibitor. I have successfully developed four variants with EC50 to cAMP ranging from 7 over 10, 21, to 29 μM. Together with the original fusion construct (EC50 to cAMP is 3 μm), there are five different light- (or cAMP-) sensitive potassium channels for researchersto choose, depending on their cell type and light intensity needs.
Aging is known to be a risk factor for structural abnormalities and functional decline in the nervous system. Characterizing age-related changes is important to identify putative pathways to overcome deleterious effects and improve life quality for the elderly. In this study, the peripheral nervous system of 24-month-old aged C57BL/6 mice has been investigated and compared to 12-month-old adult mice. Aged mice showed pathological alterations in their peripheral nerves similar to nerve biopsies from elderly human individuals, with nerve fibers showing demyelination and axonal damage. Such changes were lacking in nerves of adult 12-month-old mice and adult, non-aged humans. Moreover, neuromuscular junctions of 24-month-old mice showed increased denervation compared to adult mice. These alterations were accompanied by elevated numbers of macrophages in the peripheral nerves of aged mice. The neuroinflammatory conditions were associated with impaired myelin integrity and with a decline of nerve conduction properties and muscle strength in aged mice.
To determine the pathological impact of macrophages in the aging mice, macrophage depletion was performed in mice by oral administration of CSF-1R specific kinase (c-FMS) inhibitor PLX5622 (300 mg/kg body weight), which reduced the number of macrophages in the peripheral nerves by 70%. The treated mice showed attenuated demyelination, less muscle denervation and preserved muscle strength. This indicates that macrophage-driven inflammation in the peripheral nerves is partially responsible for the age-related neuropathy in mice.
Based on previous observations that systemic inflammation can accelerate disease progression in mouse models of neurodegenerative diseases, it was hypothesized that systemic inflammation can exacerbate the peripheral neuropathy found in aged mice. To investigate this hypothesis, aged C57BL/6 mice were intraperitoneally injected with a single dose of lipopolysaccharide (LPS; 500 μg/kg body weight) to induce systemic inflammation by mimicking bacterial infection, mostly via activation of Toll-like receptors (TLRs). Altered endoneurial macrophage activation, highlighted by Trem2 downregulation, was found in LPS injected aged mice one month after injection. This was accompanied by a so far rarely observed form of axonal perturbation, i.e., the occurrence of “dark axons” characterized by a damaged cytoskeleton and an increased overall electron density of the axoplasm. At the same time, however, LPS injection reduced demyelination and muscle denervation in aged mice. Interestingly, TREM2 deficiency in aged mice led to similar changes to LPS injection. This suggests that LPS injection likely mitigates aging-related demyelination and muscle denervation via Trem2 downregulation.
Taken together, this study reveals the role of macrophage-driven inflammation as a pathogenic mediator in age-related peripheral neuropathy, and that targeting macrophages might be an option to mitigate peripheral neuropathies in aging individuals. Furthermore, this study shows that systemic inflammation may be an ambivalent modifier of age-related nerve damage, leading to a distinct type of axonal perturbation, but in addition to functionally counteracting, dampened demyelination and muscle denervation. Translationally, it is plausible to assume that tipping the balance of macrophage polarization to one direction or the other may determine the functional outcome in the aging peripheral nervous system of the elderly.
In order to test the effects of environmental factors on different characteristics of plant leaf waxes, barley plants (Hordeum vulgare) were abiotically stress treated (exposure to darkness, heavy metal, high salt concentrations and drought), and biotically stressed by the infection with powdery mildew (Blumeria graminis f.sp. hordei; Bgh). Different wax parameters like amount, chemical composition, and micromorphology of epicuticular wax crystals, were investigated. Etiolated leaves of barley showed distinctly reduced wax amounts and modifications in their relative composition. The alterations of these wax parameters might be a result of a developmental delay, which could have been caused by a decreased availability of energy for cellular processes, due to lack of light. Cadmium exposure led to a 1.5-fold increase of wax amount, while chemical composition was unaffected. In drought- and salt-stressed plants, all investigated leaf wax parameters remained unaltered. In each of the abiotic treatments, the microstructure of epicuticular wax crystals, formed as typical platelets, was not modified. Even after 6d infection with powdery mildew (Bgh), neither locally nor systemically enforced modifications of wax features were revealed.
The analyzed leave surfaces, resulting from these four abiotic and the biotic treatment (phenotypic approach), were compared to altered leaf surfaces’ characteristics of 18 analyzed eceriferum (cer-) wax mutants (genotypic approach). Within the screening, 5 mutants were selected which distinctly differed from the wild-type in wax amount, portions of epi- and intracuticular wax fraction, relative chemical composition, crystal morphology, and surface wettability (hydrophobicity).
Apart from quantitative and qualitative effects on the leaf waxes, environmentally enforced modifications in cuticular waxes might be reflected in molecular processes of wax biogenesis. Therefore, a barley wax-microarray was established. 254 genes were selected, which are putatively involved in processes of de novo fatty acid biosynthesis, fatty acid elongation, and modification, and which are supposed to take part in lipid-trafficking between cell compartments, and transport of wax components to the outer cell surface. The regulations within the expression pattern evoked by the respective treatments were correlated with the corresponding analytical wax data, and the observed molecular effects of a 3d powdery mildew infection were compared with succeeding fungal morphogenesis. Etiolation and cadmium exposition pointed to transcriptional modifications in the de novo fatty acid synthesis, and in the screened, transport-related mechanisms, which correlate with respective alterations in surface wax characteristics. Moderate changes in the gene expression pattern, evoked by drought- and salinity-stress, might give hints for evolved adaptations in barley to such common habitat stresses. Theinvasion of powdery mildew into the epidermal host cells was reflected in the regulation of several genes. Beside other functions, these genes take part in pathogen defense, and intracellular component transport, or they encode transcription factors. The different modifications within the molecular responses evoked by the investigated abiotic treatments, and the effects of powdery mildew infection representing a biotic stressor, were compared between the different treatments.
In order to test the potential impact of different wax parameters on Bgh, conidia germination and differentiation was comparably investigated on leaf surfaces of abiotically stressed wild-type and cer-mutants, isolated cuticles, and further artificial surfaces. The rates of conidial development were similar on each of the leaf surfaces resulting from the abiotic treatments, while a significant reduction of the germination and differentiation success was revealed for the wax mutant cer-yp.949. Compared to the wild-type, developmental rates on isolated cuticles and extracted leaf waxes of the mutant cer-yp.949 indicated a modified embedding of cuticular waxes, and a possibly changed three-dimensional structure of the cer-yp.949 cuticle, which might explain the reduced conidial developmental rates on leaf surfaces of this particular mutant.
Experiments with Bgh conidia on mechanically de-waxed leaf surfaces (selective mechanical removal of the epicuticular leaf waxes with glue-like gum arabic, followed by an extraction of the intracuticular wax portion with chloroform) demonstrated the importance of the wax coverage for the germination and differentiation of the fungal conidia. On all dewaxed leaf surfaces, except those of cer-yp.949, the differentiation success of the germlings was significantly reduced, by about 20% (“wax-effect”). This result was verified through an artificial system with increased conidia developmental rates on glass slides covered with extracted leaf waxes. Further comparative tests with the major components of barley leaf wax, hexacosanol and hexacosanal, showed that the germination and differentiation of powdery mildew conidia not only depends on the different chemistry, but is also influenced by the respective surface hydrophobicity. Compared to hexacosanol, on hexacosanal coated glass surfaces, higher germination and differentiation rates were achieved, which correlated with increased levels of surface hydrophobicity. Developmental rates of conidia on hydrophobic foils demonstrated that hydrophobicity, as a sole surface factor, may stimulate the conidial germination and differentiation processes. Moreover, the survival of conidia on artificial surfaces is determined by additional surface derived factors, e.g. the availability of water, and a pervadable matrix.
During infection, bacteria need to adapt to a changing environment and have to endure various stress conditions. Small non-coding RNAs are considered as important regulators of bacterial gene expression and so allow quick adaptations by altering expression of specific target genes. Regulation of gene expression in the human-restricted pathogen Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhoea, is only poorly understood. The present study aims a better understanding of gene regulation in N. gonorrhoeae by studying small non-coding RNAs.
The discovery of antisense RNAs for all opa genes led to the hypothesis of asRNA-mediated degradation of out-of-frame opa transcripts. Analysis of asRNA expression revealed a very low abundance of the transcripts and inclusion of another phase-variable gene in the study indicates that the asRNAs are not involved in degradation of out-of-frame transcripts.
This doctoral thesis focuses on the analysis of trans-acting sRNAs. The sibling sRNAs NgncR_162 and NgncR_163 were discovered as post-transcriptional regulators altering expression of genes involved in metabolic processes, amino acid uptake and transcriptional regulation. A more detailed analysis by in silico and transcriptomic approaches showed that the sRNAs regulate a broad variety of genes coding for proteins of central metabolism, amino acid biosynthesis and degradation and several transport processes. Expression levels of the sibling sRNAs depend on the growth phase of the bacteria and on the growth medium. This indicates that NgncR_162 and NgncR_163 are involved in the adaptation of the gonococcal metabolism to specific growth conditions.
This work further initiates characterisation of the sRNA NgncR_237. An in silico analysis showed details on sequence conservation and a possible secondary structure. A combination of in silico target prediction and differential RNA sequencing resulted in the identification of several target genes involved in type IV pilus biogenesis and DNA recombination. However, it was not successful to find induction conditions for sRNA expression. Interestingly, a possible sibling sRNA could be identified that shares the target interaction sequence with NgncR_237 and could therefore target the same mRNAs.
In conclusion, this thesis provides further insights in gene regulation by non-coding RNAs in N. gonorrhoeae by analysing two pairs of sibling sRNAs modulating bacterial metabolism or possibly type IV pilus biogenesis.
The present study concerned mainly on the source, facies, and sedimentary environments of the Middle to Upper Jurassic strata in the Kerman and Tabas areas, east-central Iran. The composition of sandstones, and heavy mineral analysis point to pre-existing sedimentary, low, middle to upper rank metamorphic, and plutonic rocks of the Kalmard, Posht-e-Badam, Bayazeh, and Zarand-Kerman areas as the source rocks. According to the diagram of WELTJE et al. (1998), most samples from the Middle-Upper Jurassic rocks suggest a moderate to high elevation of the source area, and indicate a semi-arid and mediterranean to sub-humid climate. In the Qt-F-L ternary diagrams of DICKINSON et al. (1983), most point counting data from the Lower Siliciclastic Member and the top of the Hojedk Formation plot in the recycled orogen (Quartzose recycled) area of the diagram. The sandstones in this area can be interpreted as being derived from the Mid-Cimmerian Movements. Sixteen different types of siliciclastic-carbonate, and evaporatic sedimentary environments have been recognized. Thirty-nine macroinvertebrate taxa have been identified. Ten ichnotaxa have been taxonomically described from the Middle to Upper Jurassic rocks. Quite likely, before rotation of CEIM which were associated with counterclockwise block-rotation, equivalent rocks of the Bidou Formation occurred along the tectonic zone between the Yazd and the Tabas blocks (probably during the Middle Jurassic to Lower Cretaceous). However, from the Cretaceous onwards, most of the Bidou Formation has been removed by a combination of strike-slip and reverse movements of the Kashmar-Kerman tectonic zone. Roughly, these block-rotation movements occurred after the Cretaceous. During the Middle to Upper Jurassic, the tectonic activities were vertical movements producing the sedimentary pattern in the CEIM.
1. Since the early nineteenth century describing (and understanding) patterns of distribution of biodiversity across the Earth has represented one of the most significant intellectual challenges to ecologists and biogeographers. Among the most striking patterns of species richness are: the latitudinal and elevational gradients, with peaks in number of species at low latitudes and somewhere at mid altitudes, although other patterns, e.g. declines with increasing elevation, are often observed. Even in highly diverse tropical regions, species richness is not evenly distributed but there are “hotspots” of biodiversity where an exceptional number of species, especially endemics, are concentrated. Unfortunately, such areas are also experiencing dramatic loss of habitat. Among vertebrate taxa, amphibians are facing the most alarming number of extinctions. Habitat destruction, pollution and emergence of infectious diseases such as chytridiomycosis, are causing worldwide population declines. Responses to these drivers can be multidirectional and subtle, i.e. they may not be captured at the species but at the genetic level. Moreover, present patterns of diversity can result from the influence of past geological, climatic and environmental changes.
In this study, I used a multidisciplinary and multilevel approach to understand how and to which extent the landscape influences amphibian diversity. Mount Kilimanjaro is an exceptional tropical region where the landscape is rapidly evolving due to land use changes; additionally, there is a broad lack of knowledge of its amphibian fauna. During two rainy seasons in 2011, I recorded anurans from the foothills to 3500 m altitude; in addition, I focused on two river frog species and collected tissue samples for genetic analysis and swabs for detection of chytridiomycosis, the deadly disease caused by Batrachochytrium dendrobatidis (Bd).
2. I analyzed how species richness and composition change with increasing elevation and anthropogenic disturbance. In order to disentangle the observed patterns of species diversity and distribution, I incorporated inferences from historical biogeography and compared the assemblage of Mt. Kilimanjaro and Mt. Meru (both recent volcanoes) with those of the older Eastern Arc Mountains. Species richness decreased with elevation and locally increased in presence of water bodies, but I did not detect effects of either anthropogenic disturbance or vegetation structure on species richness and composition. Moreover, I found a surprisingly low number of forest species. Historical events seem to underlie the current pattern of species distribution; the young age of Mt. Kilimanjaro and the complex biogeographic processes which occurred in East Africa during the last 20 million years prevented montane forest frogs from colonizing the volcano.
3. I focused on the genetic level of biodiversity and investigated how the landscape, i.e. elevation, topographic relief and land cover, influence genetic variation, population structure and gene flow of two ecologically similar and closely related river frog species, namely Amietia angolensis and Amietia wittei. I detected greater genetic differentiation among populations in the highland species (A. wittei) and higher genetic variation in the lowland species (A. angolensis), although genetic diversity was not significantly correlated with elevation. Importantly, human settlements seemed to restrict gene flow in A. angolensis, whereas steep slopes were positively correlated with gene flow in A. wittei. This results show that even ecologically similar species can respond differently to landscape processes and that the spatial configuration of topographic features combined with species-specific biological attributes can affect dispersal and gene flow in disparate ways.
4. River frogs of the genus Amietia seem to be particularly susceptible to chytridiomycosis, showing the highest pathogen load in Kenya and other African countries. In the last study, I collected swab samples from larvae of A. angolensis and A. wittei for Bd detection. Both species resulted Bd-positive. The presence of Bd on Mt. Kilimanjaro has serious implication. For instance, Bd can be transported by footwear of hikers from contaminated water and soil. Tourists visiting Mt. Kilimanjaro may translocate Bd zoospores to other areas such as the nearby Eastern Arc Mts. where endemic and vulnerable species may still be naïve to the fungus and thus suffer of population declines.
5. My study significantly contributed to the knowledge of the amphibian fauna of Mt. Kilimanjaro and of East Africa in general, and it represents a valuable tool for future conservation actions and measures. Finally, it highlights the importance of using a multidisciplinary (i.e. community ecology, historical biogeography, landscape genetics, disease ecology) and multilevel (i.e. community, species, population, gene) approach to disentangle patterns of biodiversity.
Growth factor induced signaling cascades are key regulatory elements in tissue development, maintenance and regeneration. Deregulation of the cascades has severe consequences, leading to developmental disorders and neoplastic diseases. As a major function in signal transduction, activating mutations in RAF family kinases are the cause of many human cancers. In the first project described in this thesis we focused on B-RAF V600E that has been identified as the most prevalent B-RAF mutant in human cancer. In order to address the oncogenic function of B-RAF V600E, we have generated transgenic mice expressing the activated oncogene specifically in lung alveolar epithelial type II cells. Constitutive expression of B-RAF V600E caused abnormalities in alveolar epithelium formation that led to airspace enlargements. These lung lesions showed signs of tissue remodeling and were often associated with chronic inflammation and low incidence of lung tumors. Inflammatory cell infiltration did not precede the formation of emphysema-like lesions but was rather accompanied with late tumor development. These data support a model where the continuous regenerative process initiated by oncogenic B-RAF-driven alveolar disruption provides a tumor-promoting environment associated with chronic inflammation. In the second project we focused on wild type B-RAF and its role in an oncogenic-C-RAF driven mouse lung tumor model. Toward this aim we have generated compound mice in which we could conditionally deplete B-RAF in oncogenic-C-RAF driven lung tumors. Conditional elimination of B-RAF did not block lung tumor formation however led to reduced tumor growth. The diminished tumor growth was not caused by increased cell death instead was a consequence of reduced cell proliferation. Moreover, B-RAF ablation caused a reduction in the amplitude of the mitogenic signalling cascade. These data indicate that in vivo B-RAF is dispensable for the oncogenic potential of active C-RAF; however it cooperates with oncogenic C-RAF in the activation of the mitogenic cascade.
N-heterocyclic carbenes (NHC) are utilized for the stabilization of reactive compounds, for the activation of strong bonds, and as ligands in transition metal chemistry. In contrast to neutral NHCs, few examples of anionic or even dianionic NHCs are known. One approach for the synthesis of anionic carbenes is the deprotonation of neutral or anionic precursors, bearing Lewis acids instead of alkyl or aryl substituents. Following this strategy, novel anionic and dianionic NHCs, featuring weakly coordinating fluorinated borane and phosphorane substituents or coordinating tricyanoborane substituents were synthesized within the scope of this thesis. These carbenes possess unprecedented stabilities compared to related species. Furthermore, their electronic and steric properties can be directly adjusted by the type of Lewis acid attached. Their potential as ligands with highly shielding weakly coordinating substituents next to the carbene coordination center was demonstrated by the syntheses of the respective NHC selenium adducts and NHC gold(I) complexes. In contrast anionic NHCs with coordinating tricyanoborane moieties have an outstanding potential as ditopic ligands with coordination being possible at the carbene center and via the cyano groups. Their beneficial ligand properties were demonstrated by the syntheses of the respective NHC selenium adducts and NHC nickeltricarbonyl complexes. The combination of electronic properties, the large buried volume, the negative charge, the possibility to act as ditopic or ligands with weakly coordinating groups, and the ease of accessibility render borane- and phosphorane functionalized NHCs unique novel ligands. A further project of this PhD thesis deals with the steric properties of Lewis acids. Therefore, an easy-to-apply model was designed to quantify the steric demand of Lewis acids. Using the results of this evaluation, a second model was developed which judges the steric repulsion in Lewis acid/base adduct formation for arbitrary sets of acids and bases.
Perovskite oxides are a very versatile material class with a large variety of outstanding physical properties.
A subgroup of these compounds particularly tempting to investigate are oxides involving high-\(Z\) elements, where spin-orbit coupling is expected to give rise to new intriguing phases and potential application-relevant functionalities. This thesis deals with the preparation and characterization of two representatives of high-\(Z\) oxide sample systems based on KTaO\(_3\) and BaBiO\(_3\).
KTaO\(_3\) is a band insulator with an electronic valence configuration of Ta 5\(d\)\(^0\) . It is shown that by pulsed laser deposition of a disordered LaAlO\(_3\) film on the KTaO\(_3\)(001) surface, through the creation of oxygen vacancies, a Ta 5\(d\)\(^{0+\(\delta\)}\) state is obtained in the upmost crystal layers of the substrate. In consequence a quasi two dimensional electron system (q2DES) with large spin-orbit coupling emerges at the heterointerface. Measurements of the Hall effect establish sheet carrier densities in the range of 0.1-1.2 10\(^{14}\) cm\(^2\), which can be controlled by the applied oxygen background pressure during deposition and the LaAlO\(_3\) film thickness. When compared to the prototypical oxide q2DESs based on SrTiO\(_3\) crystals, the investigated system exhibits exceptionally large carrier mobilities of up to 30 cm\(^2\)/Vs (7000 cm\(^2\)/Vs) at room temperature (below 10 K). Through a depth profiling by photoemission spectra of the Ta 4\(f\) core level it is shown that the majority of the Ta 5\(d\)\(^0\) charge carriers, consisting of mobile and localized electrons, is situated within 4 nm from the interface at low temperatures. Furthermore, the momentum-resolved electronic structure of the q2DES \(buried\) underneath the LaAlO\(_3\) film is probed by means of hard X-ray angle-resolved photoelectron spectroscopy. It is inferred that, due to a strong confinement potential of the electrons, the band structure of the system is altered compared to \(n\)-doped bulk KTO. Despite the constraint of the electron movement along one direction, the Fermi surface exhibits a clear three dimensional momentum dependence, which is related to a depth extension of the conduction channels of at least 1 nm.
The second material, BaBiO\(_3\), is a charge-ordered insulator, which has recently been predicted to emerge as a large-gap topological insulator upon \(n\)-doping. This study reports on the thin film growth of pristine BaBiO\(_3\) on Nb:SrTiO\(_3\)(001) substrates by means of pulsed laser deposition. The mechanism is identified that facilitates the development of epitaxial order in the heterostructure despite the presence of an extraordinary large lattice mismatch of 12 %. At the heterointerface, a structurally modified layer of about 1.7 nm thickness is formed that gradually relieves the in-plane strain and serves as the foundation of a relaxed BBO film. The thereupon formed lattice orders laterally in registry with the substrate with the orientation BaBiO\(_3\)(001)||SrTiO\(_3\)(001) by so-called domain matching, where 8 to 9 BaBiO\(_3\) unit cells align with 9 to 10 unit cells of the substrate. Through the optimization of the deposition conditions in regard to the cation stoichiometry and the structural lattice quality, BaBiO\(_3\) thin films with bulk-like electronic properties are obtained, as is inferred from a comparison of valence band spectra with density functional theory calculations. Finally, a spectroscopic survey of BaBiO\(_3\) samples of various thicknesses resolves that a recently discovered film thickness-controlled phase transition in BaBiO\(_3\) thin films can be traced back to the structural and concurrent stoichiometric modifications occuring in the initially formed lattice on top of the SrTiO\(_3\) substrate rather than being purely driven by the smaller spatial extent of the BBO lattice.
More warning Advanced Driver Assistance Systems (ADAS) will be integrated into the European vehicles in the coming years, due to the ongoing progress on the way to automated driving and Euro NCAP requirements. Furthermore, upcoming technologies like Car-2-X will extend the sensory horizon of ADAS and enable the possibility to warn drivers earlier against various hazards than today. Regarding this progress, increasing numbers of different ADAS warnings will be communicated to the driver. In this context, an important question is how multiple ADAS warnings can be integrated into the Human Machine Interface (HMI) of vehicles and which warning elements are needed to ensure warning acceptance, efficiency and understandability seen from the driver’s point of view.
Two driving simulator studies were conducted and the effects of specific warning elements examined to develop a concept for the integration of upcoming warning ADAS, which focuses on early collision warnings. The implemented early warnings were defined with a warning onset of approximately two seconds before the last possible warning onset. Main questions were whether and how drivers profit from warning direction cues and/or warning object cues for their response to a hazard, and how these cues affect the acceptance of an integrated warning ADAS approach. Furthermore, it was analyzed whether a generalized warning can be used for a cluster of different ADAS concerning the group “warning of collisions”. Therefore critical scenarios in rural and urban surroundings were evaluated, including frontal and lateral (intersections) scenarios. Unnecessary warnings and false alarms have also been taken into account.
The results indicate that early warning direction cues have a high potential to assist drivers with an ADAS warning cluster which covers warning of collisions. In contrast, warning object cues seem to be less important for the drivers’ performance and acceptance regarding early collision warnings. According to these findings, this thesis provides recommendations which warning elements should be included into future ADAS warnings in favor of an integrated warning approach.
Asymptomatische Bakteriurie (ABU) stellt eine bakterielle Infektion der Harnblase über einen langen Zeitraum dar, die häufig von Escherichia coli hervorgerufen wird, ohne dass typische Symptome einer Harnwegsinfektion auftreten. Um die Charakteristika von ABU E. coli Isolaten genauer zu untersuchen, wurden die Geno- und Phänotypen von 11 ABU-Isolaten verglichen. Außerdem wurden in mehreren aufeinanderfolgenden in vivo-Reisolaten des Modell-ABU Stammes 83972 die Veränderungen im Transkriptom, Proteom und Genom während einer langfristigen Persistenz in der menschlichen Blase charakterisiert. Schließlich wurde der Effekt des menschlichen Wirtes auf die bakterielle Adaptation durch einen Vergleich von in vitro- mit in vivo-kultivierten Stämmen abgeschätzt. ABU-Isolate stellt eine heterogene Gruppe von Organismen dar. Diese können den vier phylogenetischen Hauptgruppen von E. coli sowie unterschiedlichen klonalen Gruppen zugeordnet werden. Dementsprechend unterscheiden sie sich erheblich bezüglich der Zusammensetzung des Genomes, der Genomgröße und auch der Ausstattung mit UPEC-typischen Virulenz-assoziierten Genen. Multi-Lokus-Sequenz-Typisierung legt nahe, dass bestimmte ABU Stämme sich durch Genomreduktion aus UPEC Stämmen entwickelt haben, die eine Harnwegsinfektion mit charakteristischen Symptomen auslösen konnten. Folglich erlaubt die hohe Genomplastizität von E. coli keine generalisierte Betrachtung einzelner Isolate eines Klons. Genomreduktion über Punktmutationen, Genom-Reorganisation und Deletionen resultierte in der Inaktivierung einiger Gene, die für einige UPEC Virulenz-Faktoren kodieren. Dies stützt die Vorstellung, dass eine verminderte bakterielle Aktivierung der Entzündung der Wirtsschleimhaut den Lebensstil von ABU (bei diesen E. coli-)Isolaten fördert. Genregulation und genetische Diversität sind Strategien, die es Bakterien ermöglichen unter sich fortlaufend ändernden Bedingungen zu leben bzw. zu überleben. Um die anpassungsbedingten Veränderungen bei einem langfristigen Wachstum in der Blase zu untersuchen, wurden aufeinanderfolgende Reisolate, denen eine langfristige in vivo-Kolonisierung im menschlichen Wirt beziehungsweise eine in vitro-Kultivierung vorausgegangen ist, im Hinblick auf Veränderungen Genexpression und Genomorganisation analysiert. In diesem Zusammenhang konnte gezeigt werden, dass E. coli in der Lage ist, seine metabolischen Netzwerke verschiedenen Wachstumsbedingungen anzupassen und individuelle bakterielle Kolonisierungsstrategien entwickeln kann. Transkriptom- und Proteom-Analysen zeigten verschiedene metabolische Strategien zur Nährstoffbeschaffung und Energieproduktion bei untersuchten in vivo-Reisolaten vom Stamm 83972, die es ihnen ermöglichen, den Wirt zu kolonisieren. Das Zurückgreifen auf D-Serin, Deoxy- und Ribonucleoside sowie die bidirektionale Umwandlung zwischen Pentose und Glucuronat waren hoch-regulierte Stoffwechselwege, die die in vivo-Reisolate mit zusätzlicher Energie für ein effizientes Wachstum in der Blase versorgen. Zudem wurden in dieser Studie die Netzwerke für eine Reaktion auf Abwehrmechanismen des Wirtes erforscht: Erstmals wurde hier die Rolle der Klasse-III-Alkoholdehydrogenase AdhC, bekannt durch ihre Bedeutung bei der Entgiftung von Stickstoffmonoxid, bei der Wirtsantwort während einer asymptomatischen Bakteriurie gezeigt. Aufeinanderfolgende in vivo- und in vitro-Reisolate vom Stamm 83972 wurden ebenfalls bezüglich ihrer Genomstruktur analysiert. Einige Veränderungen in der Genomstruktur der aufeinanderfolgenden Reisolate, die von einer humanen Kolonisierungsstudie stammen, implizieren die Bedeutung einer Interaktion der Bakterien mit dem Wirt bei der Mikroevolution der Bakterien. Dagegen war die Genomstruktur von Reisolaten eines langfristigen in vitro-Kultivierungsexperiments, bei dem sich der Stamm 83972 ohne Wirtskontakt vermehrt hat, nicht von Veränderungen betroffen. Das legt nahe, dass die Immunantwort eine Genomplastizität fördert und somit eine treibende Kraft für den ABU Lebensstil und die Evolution im Harnwegstrakt ist.
In this thesis we study various aspects of chaos synchronization of time-delayed coupled chaotic maps. A network of identical nonlinear units interacting by time-delayed couplings can synchronize to a common chaotic trajectory. Even for large delay times the system can completely synchronize without any time shift. In the first part we study chaotic systems with multiple time delays that range over several orders of magnitude. We show that these time scales emerge in the Lyapunov spectrum: Different parts of the spectrum scale with the different delays. We define various types of chaos depending on the scaling of the maximum exponent. The type of chaos determines the synchronization ability of coupled networks. This is, in particular, relevant for the synchronization properties of networks of networks where time delays within a subnetwork are shorter than the corresponding time delays between the different subnetworks. If the maximum Lyapunov exponent scales with the short intra-network delay, only the elements within a subnetwork can synchronize. If, however, the maximum Lyapunov exponent scales with the long inter-network connection, complete synchronization of all elements is possible. The results are illustrated analytically for Bernoulli maps and numerically for tent maps. In the second part the attractor dimension at the transition to complete chaos synchronization is investigated. In particular, we determine the Kaplan-Yorke dimension from the spectrum of Lyapunov exponents for iterated maps. We argue that the Kaplan-Yorke dimension must be discontinuous at the transition and compare it to the correlation dimension. For a system of Bernoulli maps we indeed find a jump in the correlation dimension. The magnitude of the discontinuity in the Kaplan-Yorke dimension is calculated for networks of Bernoulli units as a function of the network size. Furthermore the scaling of the Kaplan-Yorke dimension as well as of the Kolmogorov entropy with system size and time delay is investigated. Finally, we study the change in the attractor dimension for systems with parameter mismatch. In the third and last part the linear response of synchronized chaotic systems to small external perturbations is studied. The distribution of the distances from the synchronization manifold, i.e., the deviations between two synchronized chaotic units due to external perturbations on the transmitted signal, is used as a measure of the linear response. It is calculated numerically and, for some special cases, analytically. Depending on the model parameters this distribution has power law tails in the region of synchronization leading to diverging moments. The linear response is also quantified by means of the bit error rate of a transmitted binary message which perturbs the synchronized system. The bit error rate is given by an integral over the distribution of distances and is studied numerically for Bernoulli, tent and logistic maps. It displays a complex nonmonotonic behavior in the region of synchronization. For special cases the distribution of distances has a fractal structure leading to a devil's staircase for the bit error rate as a function of coupling strength. The response to small harmonic perturbations shows resonances related to coupling and feedback delay times. A bi-directionally coupled chain of three units can completely filter out the perturbation. Thus the second moment and the bit error rate become zero.
Dynamic interactions and their changes are at the forefront of current research in bioinformatics and systems biology. This thesis focusses on two particular dynamic aspects of cellular adaptation: miRNA and metabolites.
miRNAs have an established role in hematopoiesis and megakaryocytopoiesis, and platelet miRNAs have potential as tools for understanding basic mechanisms of platelet function. The thesis highlights the possible role of miRNAs in regulating protein translation in platelet lifespan with relevance to platelet apoptosis and identifying involved pathways and potential key regulatory molecules. Furthermore, corresponding miRNA/target mRNAs in murine platelets are identified. Moreover, key miRNAs involved in aortic aneurysm are predicted by similar techniques. The clinical relevance of miRNAs as biomarkers, targets, resulting later translational therapeutics, and tissue specific restrictors of genes expression in cardiovascular diseases is also discussed.
In a second part of thesis we highlight the importance of scientific software solution development in metabolic modelling and how it can be helpful in bioinformatics tool development along with software feature analysis such as performed on metabolic flux analysis applications. We proposed the “Butterfly” approach to implement efficiently scientific software programming. Using this approach, software applications were developed for quantitative Metabolic Flux Analysis and efficient Mass Isotopomer Distribution Analysis (MIDA) in metabolic modelling as well as for data management. “LS-MIDA” allows easy and efficient MIDA analysis and, with a more powerful algorithm and database, the software “Isotopo” allows efficient analysis of metabolic flows, for instance in pathogenic bacteria (Salmonella, Listeria). All three approaches have been published (see Appendices).
Computer Science approaches (software, database, management systems) are powerful tools to boost research. Here they are applied to metabolic modelling in infections as well as health care management. Starting from a comparative analysis this thesis shows own steps and examples towards improvement in metabolic modelling software and health data management. In section 2, new experimental data on metabolites and enzymes induce high interest in metabolic modelling including metabolic flux calculations. Data analysis of metabolites, calculation of metabolic fluxes, pathways and their condition-specific strengths is now possible by an advantageous combination of specific software. How can available software for metabolic modelling be improved from a computational point of view? A number of available and well established software solutions are first discussed individually. This includes information on software origin, capabilities, development and used methodology. Performance information is obtained for the compared software using provided example data sets. A feature based comparison shows limitations and advantages of the compared software for specific tasks in metabolic modeling. Often found limitations include third party software dependence, no comprehensive database management and no standard format for data input and output. Graphical visualization can be improved for complex data visualization and at the web based graphical interface. Other areas for development are platform independency, product line architecture, data standardization, open source movement and new methodologies. The comparison shows clearly space for further software application development including steps towards an optimal user friendly graphical user interface, platform independence, database management system and third party independence especially in the case of desktop applications. The found limitations are not limited to the software compared and are of course also actively tackled in some of the most recent developments. Other improvements should aim at generality and standard data input formats, improved visualization of not only the input data set but also analyzed results. We hope, with the implementation of these suggestions, metabolic software applications will become more professional, cheap, reliable and attractive for the user. Nevertheless, keeping these inherent limitations in mind, we are confident that the tools compared can be recommended for metabolic modeling for instance to model metabolic fluxes in bacteria or metabolic data analysis and studies in infection biology. ...
This work is composed of three main parts: remote control of mobile systems via Internet, ad-hoc networks of mobile robots, and remote control of mobile robots via 3G telecommunication technologies. The first part gives a detailed state of the art and a discussion of the problems to be solved in order to teleoperate mobile robots via the Internet. The focus of the application to be realized is set on a distributed tele-laboratory with remote experiments on mobile robots which can be accessed world-wide via the Internet. Therefore, analyses of the communication link are used in order to realize a robust system. The developed and implemented architecture of this distributed tele-laboratory allows for a smooth access also with a variable or low link quality. The second part covers the application of ad-hoc networks for mobile robots. The networking of mobile robots via mobile ad-hoc networks is a very promising approach to realize integrated telematic systems without relying on preexisting communication infrastructure. Relevant civilian application scenarios are for example in the area of search and rescue operations where first responders are supported by multi-robot systems. Here, mobile robots, humans, and also existing stationary sensors can be connected very fast and efficient. Therefore, this work investigates and analyses the performance of different ad-hoc routing protocols for IEEE 802.11 based wireless networks in relevant scenarios. The analysis of the different protocols allows for an optimization of the parameter settings in order to use these ad-hoc routing protocols for mobile robot teleoperation. Also guidelines for the realization of such telematics systems are given. Also traffic shaping mechanisms of application layer are presented which allow for a more efficient use of the communication link. An additional application scenario, the integration of a small size helicopter into an IP based ad-hoc network, is presented. The teleoperation of mobile robots via 3G telecommunication technologies is addressed in the third part of this work. The high availability, high mobility, and the high bandwidth provide a very interesting opportunity to realize scenarios for the teleoperation of mobile robots or industrial remote maintenance. This work analyses important parameters of the UMTS communication link and investigates also the characteristics for different data streams. These analyses are used to give guidelines which are necessary for the realization of or industrial remote maintenance or mobile robot teleoperation scenarios. All the results and guidelines for the design of telematic systems in this work were derived from analyses and experiments with real hardware.
The basic question which drove our whole work was to find a meaningful noncommutative gauge theory even for the time-like case ($\theta^{0 i} \neq 0$). In order to be able to tackle questions regarding unitarity, it is not sufficient to consider theories which include the noncommutative parameter only up to a finite order. The reason is that in order to investigate tree-level unitarity or the optical theorem in loops one has to know the behavior of the noncommutative theory for center-of-mass energies much greater than the noncommutative scale. Therefore an effective theory, that is by construction only valid up to the noncommutative scale, isn't sufficient for our purpose. Our model is based on two fundamental assumptions. The first assumption is given by the commutation relations \eqref{eq:ncalg}. This led to the Moyal-Weyl star-product \eqref{eq:astproduct2} which replaces all point-like products between two fields. The second assumption is to assume that the model built this way is not only invariant under the noncommutative gauge transformation but also under the commutative one. In order to obtain an action of such a model one has to replace the fields by their appropriate \swms. We chose the gauge fixed action \eqref{eq:actioncgf} as the fundamental action of our model. After having constructed the action of the NCQED including the {\swms} we were confronted with the problem of calculating the {\swms} to all orders in $\tMN$. By means of \cite{bbg} we could calculate the {\swms} order by order in the gauge field, where each order in the gauge field contains all orders in the noncommutative parameter (\cf chapter \ref{chapter:swms}). By comparing the maps with the result we obtained from an alternative ansatz \cite{bcpvz}, we realized that already the simplest {\swm} for the gauge field is not unique. In chapter \ref{chapter:ambiguities} we examined this ambiguity, which we could parametrised by an arbitrary function $\astf$. The next step was to derive the Feynman rules for our NCQED. One finds that the propagators remain unchanged so that the free theory is equal to the commutative QED. The fermion-fermion-photon vertex contains not only a phase factor coming from the Moyal-Weyl star-product but also two additional terms which have their origin in the \swms. Beside the 3-photon vertex which is already present in NCQED without {\swms} and which has also additional terms coming from the \swms, too, one has a contact vertex which couples two fermions with two photons. After having derived all the vertices we calculated the pair annihilation scattering process $e^+ e^- \rightarrow \gamma \gamma$ at Born level. By choosing the parameter $\kggg = 1$ (\cf section \ref{sec:represent}), we found that the amplitude of the pair annihilation process becomes equal to the amplitude of the NCQED without \swms. This means that, at least for this process, the NCQED excluding {\swms} is only a special case of NCQED including \swms. On the basis of the pair annihilation process, we afterwards investigated tree-level unitarity. In order to satisfy the tree-level unitarity we had to constrain the arbitrary function $\astf$. We found that the series expansion of $\astf$ has to start with unity. In addition, the even part of the function must not increase faster than $s^{-1/2} \log(s)$ for $s \rightarrow \infty$, whereas the odd part of the $\astf$-function can't be constrained, at least by the process we considered. By assuming these constrains for the $\astf$-function, we could show that tree-level unitarity is satisfied if one incorporates the uncertainties present in the energy and the momenta of the scattered particles, \ie the uncertainties of the center-of-mass energy and the scattering angles. This uncertainties are not exclusively present due to the finite experimental resolution. A delta-like center-of-mass energy as well as delta-like momenta are in general not possible because the scattered particles are never exact plane waves.
Single-molecule microscopy is one of the decisive methodologies that allows one to clarify cellular signaling in both spatial and temporal dimentions by tracking with nanometer precision the diffusion of individual microscopic particles coupled to relevant biological molecules. Trajectory analysis not only enables determination of the mechanisms that drive and constrain the particles motion but also to reveal crucial information about the molecule interaction, mobility, stoichiometry, all existing subpopulations and unique functions of particular molecules. Efficacy of this technique depends on two problematic issues the usage of the proper fluorophore and the type of biochemical attachment of the fluorophore to a biomolecule. The goal of this study was to evolve a highly specific labeling method suitable for single molecule tracking, internalization and trafficking studies that would attain a calculable 1:1 fluorophore-to-receptor stoichiometry. A covalent attachment of quantum dots to transmembrane receptors was successfully achieved with a techinque that amalgamates acyl carrier protein (ACP) system as a comparatively small linker and coenzyme A (CoA)-functionalized quantum dots. The necessity of optimization of the quantum dot usage for more precise calculation of the membrane protein stoichiometries in larger assemblies led to the further study in which methods maximizing the number of signals and the tracking times of diverse QD types were examined. Next, the optimized techniques were applied to analyze behavior of interleukin-5 β-common chain receptor (IL-5Rβc) receptors that are endogenously expressed at low level on living differentiated eosinophil-like HL-60 cells. Obtained data disclosed that perused receptors form stable and higher order oligomers. Additionally, the mobility analysis based on increased in number (>10%) uninterrupted 1000-step trajectories revealed two patterns of confined motion. Thereupon methods were developed that allow both, determination of stoichiometries of cell surface protein complexes and the acquisition of long trajectories for mobility analysis. Sequentially, the aforementioned methods were used to scrutinize on the mobility, internalization and recycling dynamics characterization of a G protein-coupled receptor (GPCRs), the parathyroid hormone receptor (PTHR1) and several bone morphogenetic proteins (BMPs), a member of the TGF-beta superfamily of receptors. These receptors are two important representatives of two varied membrane receptor classes. BMPs activate SMAD- and non-SMAD pathways and as members of the transforming growth factor β (TGF-β) superfamily are entailed in the regulation of proliferation, differentiation, chemotaxis, and apoptosis. For effective ligand induced and ligand independent signaling, two types of transmembrane serine/threonine kinases, BMP type I and type II receptors (BMPRI and BMPRII, respectively) are engaged. Apparently, the lateral mobility profiles of BMPRI and BMPRII receptors differ markedly, which determinate specificity of the signal. Non-SMAD signaling and subsequent osteoblastic differentiation of precursor cells particularly necessitate the confinement of the BMP type I receptor, resulting in the conclusion that receptor lateral mobility is a dominative mechanism to modulate SMAD versus non-SMAD signaling during differentiation. Confined motion was also predominantly observed in the studies devoted to, entailed in the regulation of calcium homeostasis and in bone remodeling, the parathyroid hormone receptor (PTHR1), in which stimulation with five peptide ligands, specific fragments of PTH: hPTH(1–34), hPTHrP(107–111)NH2; PTH(1–14); PTH(1–28) G1R19, bPTH(3–34), first four belonging to PTH agonist group and the last to the antagonist one, were tested in the wide concentration range on living COS-1 and AD293 cells. Next to the mobility, defining the internalization and recycling rates of the PTHR1 receptor maintained in this investigation one of the crucial questions. Internalization, in general, allows to diminish the magnitude of the receptor-mediated G protein signals (desensitization), receptor resensitization via recycling, degradation (down-regulation), and coupling to other signaling pathways (e.g. MAP kinases). Determinants of the internalization process are one of the most addressed in recent studies as key factors for clearer understanding of the process and linking it with biological responses evoked by the signal transduction. The internalization of the PTH-receptor complex occurs via the clathrin-coated pit pathway involving β-arrestin2 and is initiated through the agonist occupancy of the PTHR1 leading to activation of adenylyl cyclase (via Gs), and phosphatidylinositol-specific phospholipase Cβ (via Gq). Taken together, this work embodies complex study of the interleukin-5 β-common chain receptor (IL-5Rβc) receptors, bone morphogenetic proteins (BMPs) and the parathyroid hormone receptor with the application of single-molecule microscopy with the newly attained ACP-quantum dot labeling method and standard techniques.
This work is concerned with the numerical approximation of solutions to models that are used to describe atmospheric or oceanographic flows. In particular, this work concen- trates on the approximation of the Shallow Water equations with bottom topography and the compressible Euler equations with a gravitational potential. Numerous methods have been developed to approximate solutions of these models. Of specific interest here are the approximations of near equilibrium solutions and, in the case of the Euler equations, the low Mach number flow regime. It is inherent in most of the numerical methods that the quality of the approximation increases with the number of degrees of freedom that are used. Therefore, these schemes are often run in parallel on big computers to achieve the best pos- sible approximation. However, even on those big machines, the desired accuracy can not be achieved by the given maximal number of degrees of freedom that these machines allow. The main focus in this work therefore lies in the development of numerical schemes that give better resolution of the resulting dynamics on the same number of degrees of freedom, compared to classical schemes.
This work is the result of a cooperation of Prof. Klingenberg of the Institute of Mathe- matics in Wu¨rzburg and Prof. R¨opke of the Astrophysical Institute in Wu¨rzburg. The aim of this collaboration is the development of methods to compute stellar atmospheres. Two main challenges are tackled in this work. First, the accurate treatment of source terms in the numerical scheme. This leads to the so called well-balanced schemes. They allow for an accurate approximation of near equilibrium dynamics. The second challenge is the approx- imation of flows in the low Mach number regime. It is known that the compressible Euler equations tend towards the incompressible Euler equations when the Mach number tends to zero. Classical schemes often show excessive diffusion in that flow regime. The here devel- oped scheme falls into the category of an asymptotic preserving scheme, i.e. the numerical scheme reflects the behavior that is computed on the continuous equations. Moreover, it is shown that the diffusion of the numerical scheme is independent of the Mach number.
In chapter 3, an HLL-type approximate Riemann solver is adapted for simulations of the Shallow Water equations with bottom topography to develop a well-balanced scheme. In the literature, most schemes only tackle the equilibria when the fluid is at rest, the so called Lake at rest solutions. Here a scheme is developed to accurately capture all the equilibria of the Shallow Water equations. Moreover, in contrast to other works, a second order extension is proposed, that does not rely on an iterative scheme inside the reconstruction procedure, leading to a more efficient scheme.
In chapter 4, a Suliciu relaxation scheme is adapted for the resolution of hydrostatic equilibria of the Euler equations with a gravitational potential. The hydrostatic relations are underdetermined and therefore the solutions to that equations are not unique. However, the scheme is shown to be well-balanced for a wide class of hydrostatic equilibria. For specific classes, some quadrature rules are computed to ensure the exact well-balanced property. Moreover, the scheme is shown to be robust, i.e. it preserves the positivity of mass and energy, and stable with respect to the entropy. Numerical results are presented in order to investigate the impact of the different quadrature rules on the well-balanced property.
In chapter 5, a Suliciu relaxation scheme is adapted for the simulations of low Mach number flows. The scheme is shown to be asymptotic preserving and not suffering from excessive diffusion in the low Mach number regime. Moreover, it is shown to be robust under certain parameter combinations and to be stable from an Chapman-Enskog analysis.
Numerical results are presented in order to show the advantages of the new approach.
In chapter 6, the schemes developed in the chapters 4 and 5 are combined in order to investigate the performance of the numerical scheme in the low Mach number regime in a gravitational stratified atmosphere. The scheme is shown the be well-balanced, robust and stable with respect to a Chapman-Enskog analysis. Numerical tests are presented to show the advantage of the newly proposed method over the classical scheme.
In chapter 7, some remarks on an alternative way to tackle multidimensional simulations are presented. However no numerical simulations are performed and it is shown why further research on the suggested approach is necessary.
The incidence of cancer cases is rising steadily, while improved early detection and new cancer-specific therapies are reducing the mortality rate. In addition to curing cancer or prolonging life, increasing the quality of life is thus an important goal of oncology, which is why the burdens of cancer and treatment are becoming more important. A common side effect of cancer and its therapy is cancer-related fatigue, a tiredness that manifests itself on physical, emotional and cognitive levels and is not in proportion to previous physical efforts. Since the etiology of fatigue has not yet been fully clarified, symptom-oriented therapy is preferable to cause-specific therapy. In addition to activity management, sleep hygiene, and cognitive behavioral therapy, mind-body interventions such as yoga are recommended for reducing fatigue.
Previous studies with small sample sizes were able to examine the efficacy of yoga regarding fatigue predominantly in patients with breast cancer. Long-term effects of yoga have rarely been studied and there have been no attempts to increase long-term effects through interventions such as reminder e-mails. This dissertation takes a closer look at these mentioned aspects of the study sample and long-term effects. An 8-week randomized controlled yoga intervention was conducted, including patients with different cancer types reporting mild to severe fatigue. Following the 8-week yoga therapy, a randomized group of participants received weekly reminder e-mails for 6 months for regular yoga practice, whereas the control group did not receive reminder e-mails.
The first paper is a protocol article, which addresses the design and planned implementation of the research project this dissertation is based upon. This serves to ensure better replicability and comparability with other yoga studies. Due to a very low consent rate of patients in the pilot phase, it was necessary to deviate from the protocol article in the actual implementation and the planned inclusion criterion of fatigue >5 was reduced to fatigue >1.
The second paper examines the efficacy of the eight-week yoga intervention. Patients in the intervention group who participated in the yoga classes seven times or more showed a significantly greater reduction in general and physical fatigue than those who participated less often. The efficacy of yoga was related to the number of attended yoga sessions. Women with breast cancer who participated in yoga reported greater reductions in fatigue than women with other cancer types. There was also an improvement for depression and quality of life after eight weeks of yoga therapy compared to no yoga therapy. These results imply that yoga is helpful in reducing depression and cancer-related fatigue, especially in terms of physical aspects and improving quality of life.
The third paper focuses on the efficacy of reminder e-mails in terms of fatigue and practice frequency. Patients who received reminder e-mails reported greater reductions in general and emotional fatigue, as well as significant increases in practice frequency, compared to patients who did not receive reminder e-mails. Compared to fatigue scores before yoga, significantly lower fatigue and depression scores and higher quality of life were reported after yoga therapy and at follow-up six months later. Weekly e-mail reminders after yoga therapy may have positive effects on general and emotional fatigue and help cancer patients with fatigue establish a regular yoga practice at home. However, higher practice frequency did not lead to higher improvement in physical fatigue as found in Paper 2. This may indicate other factors that influence the efficacy of yoga practice on physical fatigue, such as mindfulness or side effects of therapy.
This research project provides insight into the efficacy of yoga therapy for oncology patients with fatigue. It is important that such interventions be offered early, while fatigue symptoms are not too severe. Regular guided yoga practice can reduce physical fatigue, but subsequent yoga practice at home does not further reduce physical fatigue. Reminder emails after completed yoga therapy could only reduce patients' emotional fatigue. It may be that physical fatigue was reduced as much as possible by the previous yoga therapy and that there was a floor effect, or it may be that reminder emails are not suitable as an intervention to reduce physical fatigue at all. Further research is needed to examine the mechanisms of the different interventions in more detail and to find appropriate interventions that reduce all levels of fatigue equally.
This thesis is devoted to Bernoulli Stochastics, which was initiated by Jakob Bernoulli more than 300 years ago by his master piece 'Ars conjectandi', which can be translated as 'Science of Prediction'. Thus, Jakob Bernoulli's Stochastics focus on prediction in contrast to the later emerging disciplines probability theory, statistics and mathematical statistics. Only recently Jakob Bernoulli's focus was taken up von Collani, who developed a unified theory of uncertainty aiming at making reliable and accurate predictions. In this thesis, teaching material as well as a virtual classroom are developed for fostering ideas and techniques initiated by Jakob Bernoulli and elaborated by Elart von Collani. The thesis is part of an extensively construed project called 'Stochastikon' aiming at introducing Bernoulli Stochastics as a unified science of prediction and measurement under uncertainty. This ambitious aim shall be reached by the development of an internet-based comprehensive system offering the science of Bernoulli Stochastics on any level of application. So far it is planned that the 'Stochastikon' system (http://www.stochastikon.com/) will consist of five subsystems. Two of them are developed and introduced in this thesis. The first one is the e-learning programme 'Stochastikon Magister' and the second one 'Stochastikon Graphics' that provides the entire Stochastikon system with graphical illustrations. E-learning is the outcome of merging education and internet techniques. E-learning is characterized by the facts that teaching and learning are independent of place and time and of the availability of specially trained teachers. Knowledge offering as well as knowledge transferring are realized by using modern information technologies. Nowadays more and more e-learning environments are based on the internet as the primary tool for communication and presentation. E-learning presentation tools are for instance text-files, pictures, graphics, audio and videos, which can be networked with each other. There could be no limit as to the access to teaching contents. Moreover, the students can adapt the speed of learning to their individual abilities. E-learning is particularly appropriate for newly arising scientific and technical disciplines, which generally cannot be presented by traditional learning methods sufficiently well, because neither trained teachers nor textbooks are available. The first part of this dissertation introduces the state of the art of e-learning in statistics, since statistics and Bernoulli Stochastics are both based on probability theory and exhibit many similar features. Since Stochastikon Magister is the first e-learning programme for Bernoulli Stochastics, the educational statistics systems is selected for the purpose of comparison and evaluation. This makes sense as both disciplines are an attempt to handle uncertainty and use methods that often can be directly compared. The second part of this dissertation is devoted to Bernoulli Stochastics. This part aims at outlining the content of two courses, which have been developed for the anticipated e-learning programme Stochastikon Magister in order to show the difficulties in teaching, understanding and applying Bernoulli Stochastics. The third part discusses the realization of the e-learning programme Stochastikon Magister, its design and implementation, which aims at offering a systematic learning of principles and techniques developed in Bernoulli Stochastics. The resulting e-learning programme differs from the commonly developed e-learning programmes as it is an attempt to provide a virtual classroom that simulates all the functions of real classroom teaching. This is in general not necessary, since most of the e-learning programmes aim at supporting existing classroom teaching. The forth part presents two empirical evaluations of Stochastikon Magister. The evaluations are performed by means of comparisons between traditional classroom learning in statistics and e-learning of Bernoulli Stochastics. The aim is to assess the usability and learnability of Stochastikon Magister. Finally, the fifth part of this dissertation is added as an appendix. It refers to Stochastikon Graphics, the fifth component of the entire Stochastikon system. Stochastikon Graphics provides the other components with graphical representations of concepts, procedures and results obtained or used in the framework of Bernoulli Stochastics. The primary aim of this thesis is the development of an appropriate software for the anticipated e-learning environment meant for Bernoulli Stochastics, while the preparation of the necessary teaching material constitutes only a secondary aim used for demonstrating the functionality of the e-learning platform and the scientific novelty of Bernoulli Stochastics. To this end, a first version of two teaching courses are developed, implemented and offered on-line in order to collect practical experiences. The two courses, which were developed as part of this projects are submitted as a supplement to this dissertation. For the time being the first experience with the e-learning programme Stochastikon Magister has been made. Students of different faculties of the University of Würzburg, as well as researchers and engineers, who are involved in the Stochastikon project have obtained access to Stochastikon Magister via internet. They have registered for Stochastikon Magister and participated in the course programme. This thesis reports on two assessments of these first experiences and the results will lead to further improvements with respect to content and organization of Stochastikon Magister.
Plant-derived natural products and their analogs continue to play an important role in the discovery of new drugs for the treatment of human diseases. Potentially promising representatives of secondary metabolites are the naphthylisoquinoline alkaloids, which show a broad range of activities against protozoan pathogens, such as plasmodia, leishmania, and trypanosoma. Due to the increasing resistance of those pathogens against current therapies, highly potent novel agents are still urgently needed. Thus, it is worthy to discover new naphthylisoquinoline alkaloids hopefully with pronounced bioactivities by isolation from plants or by synthesis. The naphthylisoquinoline alkaloids are biosynthetically related to another class of plant-derived products, the naphthoquinones, some of which have been recently found to display excellent anti-multiple myeloma activities without showing any cytotoxicities on normal blood cells. Multiple myeloma still remains incurable, although remissions may be induced with co-opted therapeutic treatments. Therefore, more potent naphthoquinones are urgently required, and can be obtained by isolation from plants or by synthesis. In detail, the results in this thesis are listed as follows: 1) Isolation and characterization of naphthylisoquinoline alkaloids from the stems of a Chinese Ancistrocladus tectorius species. Nine new naphthylisoquinoline alkaloids, named ancistectorine A1 (60), N-methylancistectorine A1 (61), ancistectorine A2 (62a), 5-epi-ancistectorine A2 (62b), 4'-O-demethylancistectorine A2 (63), ancistectorine A3 (64), ancistectorine B1 (65), ancistectorine C1 (66), and 5-epi-ancistrolikokine D (67) were isolated from the Chinese A. tectorius and fully characterized by chemical, spectroscopic, and chiroptical methods. Furthermore, the in vitro anti-infectious activities of 60-62 and 63-66 have been tested. Three of the metabolites, 61, 62a, and 62b, exhibited strong antiplasmodial activities against the strain K1 of P. falciparum without showing significant cytotoxicities. With IC50 values of 0.08, 0.07, and 0.03 μM, respectively, they were 37 times more active than the standard chloroquine (IC50 = 0.26 μM). Moreover, these three compounds displayed high antiplasmodial selectivity indexes ranging from 100 to 3300. According to the TDR/WHO guidelines, they could be considered as lead compounds. In addition, seven alkaloids, 69-74 (structures not shown here), were isolated from A. tectorius that were known, but new to the plant, together with another fourteen known compounds (of these, only the structures of the three main alkaloids, 5a, 5b, and 78 are shown here), which had been previously found in the plant. The three metabolites ancistrocladine (5a), hamatine (5b), and (+)-ancistrocline (78) were found to show no or moderate activities against the MM cell lines. 2) Isolation and characterization of naphthylisoquinoline alkaloids from the root bark of a new, botanically yet undescribed Congolese Ancistrocladus species. An unprecedented dimeric Dioncophyllaceae-type naphthylisoquinoline alkaloid, jozimine A2 (84), as first recognized by G. Bauckmann from an as yet undescribed Ancistrocladus species, was purified and characterized as part of this thesis. Its full structural assignment was achieved by spectroscopic and chiroptical methods, and further confirmed by an X-ray diffraction analysis, which had never succeeded for any other dimeric naphthylisoquinoline alkaloids before. Structurally, the dimer is composed of two identical 4'-O-demethyldioncophylline A halves, coupled through a sterically hindered central axis at C-3',3'' of the two naphthalene moieties. Pharmacologically, jozimine A2 (84) showed an extraordinary antiplasmodial activity (IC50 = 1.4 nM) against the strain NF54 of P. falciparum. Beside jozimine A2 (85), another new alkaloid, 6-O-demethylancistrobrevine C (84), and four known ones, ancistrocladine (5a), hamatine (5b), ancistrobrevine C (86), and dioncophylline A (6) were isolated from the Ancistrocladus species, the latter in a large quantity (~500 mg), showing that the plant produces Ancistrocladaceae-type, mixed-Ancistrocladaceae/Dioncophyllaceae-type, and Dioncophyllaceae-type naphthyl- isoquinoline alkaloids. Remarkably, it is one of the very few plants, like A. abbreviatus, and A. barteri, that simultaneously contain typical representatives of all the above three classes of alkaloids. 3) Semi-synthesis of jozimine A2 (85), 3'-epi-85, jozimine A3 (93) and other alkaloids from dioncophylline A (6). The dimeric naphthylisoquinoline alkaloids, jozimine A2 (85) and 3'-epi-85, constitute rewarding synthetic targets for a comparative analysis of their antiplasmodial activities and for a further confirmation of the assigned absolute configurations of the isolated natural product of 85. They were semi-synthesized in a four-step reaction sequence from dioncophylline A (6) in cooperation with T. Büttner. The key step was a biomimetic phenol-oxidative dimerization at C-3' of the N,O-dibenzylated derivative of 89 by utilizing Pb(OAc)4. This is the first time that the synthesis of such an extremely sterically hindered (four ortho-substituents) naphthylisoquinoline alkaloid – with three consecutive biaryl axes! – has been successfully achieved. A novel dimeric naphthylisoquinoline, jozimine A3 (93), bearing a 6',6''-central biaryl axis, was semi-synthesized from 5'-O-demethyldioncophylline A (90) by a similar biomimetic phenol-oxidative coupling reaction as a key step, by employing Ag2O. HPLC analysis with synthetic reference material of 3'-epi-85 and 93 for co-elution revealed that these two alkaloids clearly are not present in the crude extract of the Ancistrocladus species from which jozimine A2 (85) was isolated. This evidences that jozimine A2 (85) is very specifically biosynthesized by the plant with a high regio- and stereoslectivity. Remarkably, the two synthetic novel dimeric naphthylisoquinoline alkaloids 3'-epi-85 and 93 were found to display very good antiplasmodial activities, albeit weaker than that of the natural and semi-synthetic product 85. Additionally, the two compounds 3'-epi-85 and 93 possessed high or moderate selectivity indexes, which were much lower than that of 85. However, they can still be considered as new lead structures. Two unprecedented oxidative products of dioncophylline A, the diastereomeric dioncotetralones A (94a) and B (94b), were synthesized from dioncophylline A (6) in a one-step reaction. Remarkably, the aromatic properties in the “naphthalene” and the “isoquinoline” rings of 94a and 94b are partially lost and the “biaryl” axis has become a C,C-double bond, so that the two halves are nearly co-planar to each other, which has never been found among any natural or synthetic naphthylisoquinoline alkaloid. Their full structural characterization was accomplished by spectroscopic methods and quantum-chemical CD calculations (done by Y. Hemberger). The presumed reaction mechanism was proposed in this thesis. In addition, one of the two compounds, 94a, exhibited a highly antiplasmodial activity (IC50 = 0.09 μM) with low cytotoxicity, and thus, can be considered as a new promising lead structure. Its 2'-epi-isomer, 94b, was inactive, evidencing a significant effect of chirality on the bioactivity. Of a number of naphthylisoquinoline alkaloids tested against the multiple-myeloma cell lines, the three compounds, dioncophylline A (6), 4'-O-demethyldioncophylline A (89), and 5'-O-demethyldioncophylline A (90) showed excellent activities, even much stronger than dioncoquinones B (10), C (102), the epoxide 175, or the standard drug melphalan. 4) Isolation and characterization of bioactive naphthoquinones from cell cultures of Triphyophyllum peltatum. Three new naphthoquinones, dioncoquinones C (102), D (103), and E (104), the known 8-hydroxydroserone (105), which is new to this plant, and one new naphthol dimer, triphoquinol A (107), were isolated from cell cultures of T. peltatum in cooperation with A. Irmer. Dioncoquinone C (102) showed an excellent activity against the MM cells, very similar to that of the previously found dioncoquinone B (10), without showing any inhibitory effect on normal cells. The other three naphthoquinones, 103105, were inactive or only weakly active. 5) Establishment of a new strategy for a synthetic access to dioncoquinones B (10) and C (102) on a large scale for in vivo experiments and for the synthesis of their analogs for first SAR studies. Before the synthesis of dioncoquinone B (10) described in this thesis, two synthetic pathways had previously been established in our group. The third approach described here involved the preparation of the joint synthetic intermediate 42 with the previous two routes. The tertiary benzamide 135 was ortho-deprotonated by using s-BuLi/TMEDA, followed by transmetallation with MgBr2▪2Et2O, and reaction with 2-methylallyl bromide (139). It resulted in the formation of ortho-allyl benzamide 140, which was cyclized by using methyl lithium to afford the naphthol 42. This strategy proved to be the best among the established three approaches with regard to its very low number of steps and high yields. By starting with 136, this third strategy yielded the related bioactive natural product, dioncoquinone C (102), which was accessed by total synthesis for the first time. To identify the pharmacophore of the antitumoral naphthoquinones, a library of dioncoquinone B (10) and C (102) analogs were synthesized for in vitro testing. Among the numerous naphthoquinones tested, the synthetic 7-O-demethyldioncoquinone C (or 7-O-hydroxyldioncoquinone B) (145), constitutes another promising basic structure to develop a new anti-MM agent. Furthermore, preliminary SAR results evidence that the three hydroxy functions at C-3, C-5, and C-6 are essential for the biological properties as exemplarily shown through the compounds 10, 102, and 145. All other mixed OH/OMe- or completely OMe-substituted structures were entirely inactive. By a serendipity the expoxide 175 was found to display the best anti-MM activity of all the tested isolated metabolites from T. peltatum, the synthesized naphthoquinones, and their synthetic intermediates. Toxic effects of 175 on normal cells were not observed, in contrast to the high toxicities of all other epoxides. Thus, the anti-MM activity of 175 is of high selectivity. The preliminary SAR studies revealed that the 6-OMe group in 175 is required, thus differed with the above described naphthoquinones (where 6-OH is a requisite in 10, 102, and 145), which evidenced potentially different modes of action for these two classes of compounds. 6) The first attempted total synthesis of the new naturally occurring triphoquinone (187a), which was recently isolated from the root cultures of T. peltatum in our group. A novel naphthoquinone-naphthalene dimer, 187a (structure shown in Chapter 10), was isolated in small quantities from the root cultures of T. peltatum. Thus, its total synthesis was attempted for obtaining sufficient amounts for selected biotestings. The key step was planned to prepare the extremely sterically hindered (four ortho-substituents) binaphthalene 188 by a coupling reaction between the two 2-methylnaphthalene derivatives. Test reactions involving a system of two simplified 2-methylnaphthylboron species and 2-methylnaphthyl bromide proved the Buchwald ligand as most promising. The optimized conditions were then applied to the two true - highly oxygenated - coupling substrates, between the 2-methylnaphthylboron derivatives 210, 211, 213, or 214 and the 2-methylnaphthyl iodides (or bromides) 215 (206), 215 (206), 212 (205), or 212 (205), respectively. Unfortunately, this crucial step failed although various bases and solvent systems were tested. This could be due to the high electron density of the two coupling substrates, both bearing strongly OMOM/OMe-donating function groups. Therefore, a more powerful catalyst system or an alternative synthetic strategy must be explored for the total synthesis of 187a. 7) Phytochemical investigation of the Streptomyces strain RV-15 derived from a marine sponge. Cyclodysidins A-D (216-219), four new cyclic lipopeptides with a- and ß-amino acids, were isolated from the Streptomyces strain RV15 derived from a marine sponge by Dr. U. Abdelmohsen. Their structures were established as cyclo-(ß-AFA-Ser-Gln-Asn-Tyr-Asn-Ser-Thr) by spectroscopic analysis using 2D NMR techniques and CID-MS/MS in the course of this thesis. In conclusion, the present work contributes to the discovery of novel antiplasmodial naphthylisoquinoline alkaloids and antitumoral naphthoquinones, which will pave the way for future studies on these two classes of compounds.
In this study, we developed an innovative nanoparticle formulation to facilitate the delivery of antitumor antibodies to tumor sites. The study commenced with the utilization of 13 bispecific antibody fusion proteins, which targeted the Fn14 receptor, thereby validating the pivotal role of crosslinking in Fn14 receptor activation. Subsequently, gold nanoparticles were activated using COOH-PEG-SH in combination with EDC/NHS, and subsequently conjugated with two Fn14-targeting antibodies, PDL192 and 5B6. Following this, a pH-sensitive shell was generated on the outer layer of the antibody-coupled gold nanoparticles through the application of chemically modified polylysine. The resultant complexes, termed MPL-antibody-AuNP, demonstrated a release profile reminiscent of the tumor microenvironment (TME). Notably, these complexes released antibody-AuNPs only in slightly acidic conditions while remaining intact in neutral or basic environments. Functionality analysis further affirmed the pH-sensitive property of MPL-antibody-AuNPs, demonstrating that the antibodies only initiated potent Fn14 activation in slightly acidic environments. This formulation holds potential for applicability to antibodies or ligands targeting the 80 TNFRSF family, given that gold nanoparticles successfully served as platforms for antibody crosslinking, thereby transforming these antibodies into potent agonists. Moreover, the TME disintegration profile of MPL mitigates the potential cytotoxic effects of antibodies, thereby circumventing associated adverse side effects. This study not only showcases the potential of nanoparticle formulations in targeted therapy, but also provides a solid foundation for further investigations on their clinical application in the context of targeting category II TNFRSF receptors with antibodies or ligands.
This dissertation explores the local gazetteers of West Lake that were compiled by literati of the Ming dynasty. In 1547, the first West Lake gazetteer was published by the local literatus of Hangzhou, Tian Rucheng 田汝成. In the late sixteenth and early seventeenth centuries, accompanying the huge enthusiasm for West Lake and the flourishing of its tourism, the production of West Lake gazetteers reached its peak. This trend, however, was reduced by the turmoils in the last years of the Ming and the dynastic transition, a period when West Lake had also experienced destruction. Nevertheless, the practice was resumed in the first decades of the Qing dynasty by some literati who had survived the disasters. One prominent work of this period was compiled by the Ming loyalist and “remnant subject” Zhang Dai 張岱, who wrote an author’s preface in 1671. This dissertation can be divided into two parts. The first part focuses on the editorial principles of compilers, e.g., which materials are included, how they are organized and presented. It explores various possible intentions of the compilers, such as scholarly and documentary, practical and oriented toward tour-guiding, didactic and educational, and personal and nostalgic ones. The second part focuses on some of the perceptions, attitudes, and values of literati focusing on West Lake. The discourses analyzed in this part include West Lake as a hybrid between metropolitan city and sheer wilderness, as a national symbol and object of nostalgia of the lost dynasty, and as a place of pleasure-seeking and indulgence. While a discourse often had a long tradition and historical development, the emphasis of the study is on the late sixteenth and early seventeenth centuries, i.e., the late Ming.
Virulent Agrobacterium tumefaciens strains transfer and integrate a DNA region of the tumor-inducing (Ti) plasmid, the T-DNA, into the plant genome and thereby cause crown gall disease. The most essential genes required for crown gall development are the T-DNA-encoded oncogenes, IaaH (indole-3-acetamide hydrolase), IaaM (tryptophan monooxygenase) for auxin, and Ipt (isopentenyl transferase) for cytokinin biosynthesis. When these oncogenes are expressed in the host cell, the levels of auxin and cytokinin increase and cause cell proliferation. The aim of this study was to unravel the molecular mechanisms, which regulate expression of the agrobacterial oncogenes in plant cells. Transcripts of the three oncogenes were expressed in Arabidopsis thaliana crown galls induced by A. tumefaciens strain C58 and the intergenic regions (IGRs) between their coding sequences (CDS) were proven to have promoter activity in plant cells. These promoters possess eukaryotic sequence structures and contain cis-regulatory elements for the binding of plant transcription factors. The high-throughput protoplast transactivation (PTA) system was used and identified the Arabidopsis thaliana transcription factors WRKY18, WRKY40, WRKY60 and ARF5 to activate the Ipt oncogene promoter. No transcription factor promoted the activity of the IaaH and IaaM promoters, despite the fact that the sequences contained binding elements for type B ARR transcription factors. Likewise, the treatment of Arabidopsis mesophyll protoplasts with cytokinin (trans-zeatin) and auxin (1-NAA) exerted no positive effect on IaaH and IaaM promoter activity. In contrast, the Ipt promoter strongly responded to a treatment with auxin and only modestly to cytokinin. The three Arabidopsis WRKYs play a role in crown gall development as the wrky mutants developed smaller crown galls than wild-type plants. The WRKY40 and WRKY60 genes responded very quickly to pathogen infection, two and four hours post infection, respectively. Transcription of the WRKY18 gene was induced upon buffer infiltration, which implicates a response to wounding. The three WRKY proteins interacted with ARF5 and with each other in the plant nucleus, but only WRKY40 together with ARF5 increased activation of the Ipt promoter. Moreover, ARF5 activated the Ipt promoter in an auxin-dependent manner. The severe developmental phenotype of the arf5 mutant prevented studies on crown gall development, nevertheless, the reduced crown gall growth on the transport inhibitor response 1 (TIR1) tir1 mutant, lacking the auxin sensor, suggested that auxin signaling is required for optimal crown gall development. In conclusion, A. tumefaciens recruits the pathogen defense related WRKY40 pathway to activate Ipt expression in T-DNA-transformed plant cells. IaaH and IaaM gene expression seems not to be controlled by transcriptional activators, but the increasing auxin levels are signaled via ARF5. The auxin-depended activation of ARF5 boosts expression of the Ipt gene in combination with WRKY40 to increase cytokinin levels and induce crown gall development.
This thesis investigates the charged moments and the symmetry-resolved
entanglement entropy in the context of the AdS3/CFT2 duality. In the
first part, I focus on the holographic U(1) Chern-Simons-Einstein gravity,
a toy model of AdS3/CFT2 with U(1) Kac-Moody symmetry. I
start with the vacuum background with a single entangling interval. I
show that, apart from a partition function in the grand canonical ensemble,
the charged moments can also be interpreted as the two-point
function of vertex operators on the replica surface. For the holographic
description, I propose a duality between the bulk U(1) Wilson line and
the boundary vertex operators. I verify this duality by deriving the
effective action for the Chern-Simons fields and comparing the result
with the vertex correlator. In the twist field approach, I show that the
charged moments are given by the correlation function of the charged
twist operators and the additional background operators. To solve the
correlation functions involved, I prove the factorization of the U(1) extended
conformal block into a U(1) block and a Virasoro block. The
general expression for the U(1) block is derived by directly summing
over the current descendant states, and the result shows that it takes
an identical form as the vertex correlators. This leads to the conclusion
that the disjoint Wilson lines compute the neutral U(1) block. The final
result for the symmetry-resolved entanglement entropy shows that
it is always charge-independent in this model. In the second part, I
study charged moments in higher spin holography, where the boundary
theory is a CFT with W3 symmetry. I define the notion of the
higher spin charged moments by introducing a spin-3 modular charge
operator. Restricting to the vacuum background with a single entangling
interval, I employ the grand canonical ensemble interpretation
and calculate the charged moments via the known higher spin black
hole solution. On the CFT side, I perform a perturbative expansion for
the higher spin charged moments in terms of the connected correlation
functions of the spin-3 modular charge operators. Using the recursion
relation for the correlation functions of the W3 currents, I evaluate the
charged moments up to the quartic order of the chemical potential. The
final expression matches with the holographic result. My results both
for U(1) Chern-Simons Einstein gravity and W3 higher spin gravity
constitute novel checks of the AdS3/CFT2 correspondence.
PTPN22 encodes the lymphoid tyrosine phosphatase Lyp that can dephosphorylate Lck, ZAP-70 and Fyn to attenuate TCR signaling. A single-nucleotide polymorphism (C1858T) causes a substitution from arginine (R) to tryptophan (W) at 620 residue (R620W). Lyp-620W has been confirmed as a susceptible allele in multiple autoimmune diseases, including type 1 diabetes (T1D). Several independent studies proposed that the disease-associated allele is a gain-of-function variant. However, a recent report found that in human cells and a knockin mouse containing the R620W homolog that Ptpn22 protein degradation is accelerated, indicating Lyp-620W is a loss-of-function variant. Whether Lyp R620W is a gain- or loss-of-function variant remains controversial. To resolve this issue, we generated two lines (P2 and P4) of nonobese diabetic (NOD) mice in which Ptpn22 can be inducibly silenced by RNAi. We found long term silencing of Ptpn22 increased spleen cellularity and regulatory T (Treg) cell numbers, replicating the effect of gene deletion reported in the knockout (KO) B6 mice. Notably, Ptpn22 silencing also increased the reactivity and apoptotic behavior of B lymphocytes, which is consistent with the reduced reactivity and apoptosis of human B cells carrying the alleged gain-of-function PTPN22 allele. Furthermore, loss of Ptpn22 protected P2 KD mice from spontaneous and Cyclophosphamide (CY) induced diabetes. Our data support the notion that Lyp-620W is a gain-of-function variant. Moreover, Lyp may be a valuable target for the treatment of autoimmune diseases.
A large variety of sex determination systems have been described in fish. However, almost no information is available about sex determination in the classical fish models, the zebrafish Danio rerio and the pufferfish Takifugu rubripes. A DNA-binding protein gene called dmrt1bY (or DMY) has been recently described as an outstanding candidate for the primary sex-determining gene in the medaka fish Oryzias latipes. But this gene is not the universal master sex-determining gene in teleost fish, since dmrt1bY is not found in most other fishes. Hence, other fish models need to be examined including the platyfish Xiphophorus maculatus. Xiphophorus maculatus has three types of sex chromosomes (X, Y and W; females are XX, WX or WY; males are XY or YY). Its gonosomes are at an early stage of differentiation. The sex-determining locus on the sex chromosomes is flanked by two receptor tyrosine kinase genes, the Xmrk oncogene and its protooncogenic progenitor gene egfrb, which both delimit a region of about 0.6 centiMorgans. This situation should allow the positional cloning of the sex-determining gene (SD) of the platyfish. For this purpose, Bacterial Artificial Chromosome (BAC) contigs were assembled from a BAC library of XY males constructed in our laboratory, using the oncogene Xmrk, egfrb, as well as a Y-specific pseudogene called ps-criptY as starting points. The ps-criptY sequence was found to be closely linked to the SD gene, since no recombination was observed between SD and ps-criptY in more than 400 individuals tested. Two major BAC contigs for the X chromosome (about 2.5 Mb) and three major BAC contigs for the Y chromosome (about 3.5 Mb) were built up and analyzed by strategic sequencing. These are some of the largest contigs ever assembled for the sex chromosomes of a non-mammalian vertebrate species. The molecular analysis of the ps-criptY contig was the major objective of this work. The Y-specific ps-criptY contig has been extended over 1 Mb in this work with 58 identified molecular markers. Approximatively 700 kb of non-redundant sequences has been obtained from this contig by strategic sequencing. Numerous Y-linked markers from the contig including ps-criptY were also detected on the X chromosome. Nevertheless, major structural differences were observed between the X and Y chromosomes. Particularly, a large region, which is present at one copy on the X chromosome and contains several candidate genes, was found to be duplicated on the Y chromosome. Evidence for an inversion in the sex-determining region and for the Y-specific accumulation of a repeated sequence called XIR was also obtained. Such events might correspond to an initiation of differentiation between both types of gonosomes. Accumulation of transposable elements was also observed in the ps-criptY contig. A DNA transposable element, helitron, was isolated from the sex-determining region of X. maculatus. Three copies of helitron are located on the ps-criptY contig and one copy on the X-linked contig (helitron has roughly 15 copies per haploid genome). No in-frame stop codon, truncation or intron was found in these four copies, which present high nucleotide identities to each other. This suggests that helitron elements might be active or have been recently active in X. maculatus. A consensus open reading frame of helitron was also assembled from medaka (Oryzias latipes) genomic sequences. Two candidate genes from the ps-criptY contig are also located on the W chromosome in the X. maculatus Usumacinta strain (heterogamety). These markers show the relationship between the different types of gonosomes and allow to compare the male and female heterogameties in the platyfish. Several gene candidates were identified in the ps-criptY contig. However, some of them such as msh2, cript, igd and acr probably correspond to pseudogenes. Interestingly, a novel gene, called swimy, is exclusively expressed in spermatogonia of the adult testis. Swimy is a gene encoding a DNA-binding protein with several putative DNA-binding domains. The data suggest that swimy is a very promising candidate for the master SD gene. Another novel gene, which is called fredi and encodes a novel helix-turn-helix protein, is predominately expressed in the adult testis and currently under scrutiny. There is no doubt that the master SD gene of X. maculatus will be identified by positional cloning. Further molecular analysis of the contigs built in this work will shed new light on the molecular mechanism of sex determination and the evolution of sex chromosomes in fish.
The discovery, heterologous expression, and characterization of channelrhodopsin-2 (ChR2) – a light-sensitive cation channel found in the green alga Chlamydomonas reinhardtii – led to the success of optogenetics as a powerful technology, first in neuroscience. ChR2 was employed to induce action potentials by blue light in genetically modified nerve cells. In optogenetics, exogenous photoreceptors are expressed in cells to manipulate cellular activity. These photoreceptors were in the beginning mainly microbial opsins. During nearly two decades, many microbial opsins and their mutants were explored for their application in neuroscience. Until now, however, the application of optogenetics to plant studies is limited to very few reports. Several optogenetic strategies for plant research were demonstrated, in which most attempts are based on non-opsin optogenetic tools. Opsins need retinal (vitamin A) as a cofactor to generate the functional protein, the rhodopsin. As most animals have eyes that contain animal rhodopsins, they also have the enzyme - a 15, 15'-Dioxygenase - for retinal production from food-supplied provitamin A (beta-carotene). However, higher plants lack a similar enzyme, making it difficult to express functional rhodopsins successfully in plants. But plant chloroplasts contain plenty of beta-carotene. I introduced a gene, coding for a 15, 15'-Dioxygenase with a chloroplast target peptide, to tobacco plants. This enzyme converts a molecule of β-carotene into two of all-trans-retinal. After expressing this enzyme in plants, the concentration of all-trans-retinal was increased greatly. The increased retinal concentration led to increased expression of several microbial opsins, tested in model higher plants. Unfortunately, most opsins were observed intracellularly and not in the plasma membrane. To improve their localization in the plasma membrane, some reported signal peptides were fused to the N- or C-terminal end of opsins. Finally, I helped to identify three microbial opsins -- GtACR1 (a light-gated anion channel), ChR2 (a light-gated cation channel), PPR (a light-gated proton pump) which express and work well in the plasma membrane of plants. The transgene plants were grown under red light to prevent activation of the expressed opsins. Upon illumination with blue or green light, the activation of these opsins then induced the expected change of the membrane potential, dramatically changing the phenotype of plants with activated rhodopsins.
This study is the first which shows the potential of microbial opsins for optogenetic research in higher plants, using the ubq10 promoter for ubiquitous expression. I expect this to be just the beginning, as many different opsins and tissue-specific promoters for selective expression now can be tested for their usefulness. It is further to be expected that the here established method will help investigators to exploit more optogenetic tools and explore the secrets, kept in the plant kingdom.
Microbial species (bacteria and archaea) in the gut are important for human health in various ways. Not only does the species composition vary considerably within the human population, but each individual also appears to have its own strains of a given species. While it is known from studies of bacterial pan-genomes, that genetic variation between strains can differ considerably, such as in Escherichia coli, the extent of genetic variation of strains for abundant gut species has not been surveyed in a natural habitat. This is mainly due to the fact that most of these species cannot be cultured in the laboratory. Genetic variation can range from microscale genomic rearrangements such as small nucleotide polymorphism (SNP) to macroscale large genomic rearrangements like structural variations. Metagenomics offers an alternative solution to study genetic variation in prokaryotes, as it involves DNA sequencing of the whole community directly from the environment. However, most metagenomic studies to date only focus on variation in gene abundance and hence are not able to characterize genetic variation (in terms of presence or absence of SNPs and genes) of gut microbial strains of individuals.
The aim of my doctorate studies was therefore to study the extent of genetic variation in the genomic sequence of gut prokaryotic species and its phenotypic effects based on: (1) the impact of SNP variation in gut bacterial species, by focusing on genes under selective pressure and (2) the gene content variation (as a proxy for structural variation) and their effect on microbial species and the phenotypic traits of their human host.
In the first part of my doctorate studies, I was involved in a project in which we created a catalogue of 10.3 million SNPs in gut prokaryotic species, based on metagenomes. I used this to perform the first SNP-based comparative study of prokaryotic species evolution in a natural habitat. Here, I found that strains of gut microbial species in different individuals evolve at more similar rates than the strains within an individual. In addition, I found that gene evolution can be uncoupled from the evolution of its originating species, and that this could be related to selective pressure such as diet, exemplified by galactokinase gene (galK). Despite the individuality (i.e. uniqueness of each individual within the studied metagenomic dataset) in the SNP profile of the gut microbiota that we found, for most cases it is not possible to link SNPs with phenotypic differences. For this reason I also used gene content as a proxy to study structural variation in metagenomes.
In the second part of my doctorate studies, I developed a methodology to characterize the variability of gene content in gut bacterial species, using metagenomes. My approach is based on gene deletions, and was applied to abundant species (demonstrated using a set of 11 species). The method is sufficiently robust as it captures a similar range of gene content variability as has been detected in completely sequenced genomes. Using this procedure I found individuals differ by an average of 13% in their gene content of gut bacterial strains within the same species. Interestingly no two individuals shared the same gene content across bacterial species. However, this variation corresponds to a lower limit, as it is only accounts for gene deletion and not insertions. This large variation in the gene content of gut strain was found to affect important functions, such as polysaccharide utilization loci (PULs) and capsular polysaccharide synthesis (CPS), which are related with digestion of dietary fibers.
In summary, I have shown that metagenomics based approaches can be robust in characterizing genetic variation in gut bacterial species. I also illustrated, using examples both for SNPs and gene content (galK, PULs and CPS), that this genetic variation can be used to predict the phenotypic characteristics of the microbial species, as well as predicting the phenotype of their human host (for example, their capacity to digest different food components). Overall, the results of my thesis highlight the importance of characterizing the strains in the gut microbiome analogous to the emerging variability and importance of human genomics.
Blumeria graminis, the obligate biotrophic grass powdery mildew, is a highly pathogenic fungus capable of inflicting foliar diseases and of causing severe yield losses. There is asexual and sexual propagation in the life cycle of B. graminis. In the epidemiological processes of this pathogen, both types of spores - asexual conidia and sexual ascospores – are crucial.
Conidia of B. graminis are demonstrated to perceive cuticular very-long-chain aldehydes as molecular signal substances notably promoting germination and differentiation of the infection structure (the appressorium) – the prepenetration processes – in a concentration- and chain-length-dependent manner. Conidial germination and appressorium formation are known to be dramatically impeded by the presence of free water on the host surface. However, sexually formed ascospores are reported to easily germinate immersed in water. There are abundant assays on conidial prepenetration processes. However, with respect to the stimulating effects of very-long-chain aldehydes and to the influence of the presence of free water, ascosporic prepenetration processes are still obscure.
In order to study the effects of very-long-chain aldehydes on the ascosporic prepenetration processes of wheat powdery mildew fungus B. graminis f. sp. tritici, Formvar®-based in vitro systems were applied to exclude the secondary host effects (such as host resistance) and to reproducibly provide homogeneous hydrophobic substratum surfaces. By the presence of even-numbered very-long-chain aldehydes (C22 - C30), the appressorium formation of the ascospores was notably triggered in a chain-length dependent manner. N-octacosanal (C28) was the most inducing aldehyde tested. Unlike conidia, ascospores could easily differentiate immersed in water and showed a more variable differentiation pattern even with a single germ tube differentiating an appressorium.
To evaluate the alternative management against barley powdery mildew fungus Blumeria graminis f. sp. hordei, the suppressing effects of UV-C irradiation on the developmental processes of conidia on artificial surfaces (in vitro) and on host leaf surfaces (in vivo) were assayed. In vitro and in vivo, a single dose of 100 J m-2 UV-C was adequate to decrease conidial germination to < 20 % and to reduce appressorium formation to values < 5 %. UV-C irradiation negatively affected colony pustule size and vegetative propagation. Under photoperiodic conditions of 2h light/16h dark, 6h dark/12h light or 6h dark/18h light, UV-C-treated conidia showed photoreactivation (photo-recovery). White light-mediated photoreactivation was most effective immediately after UV-C irradiation, suggesting that a prolonged phase of darkness after UV-C application increased the efficacy of management against B. graminis. UV-C irradiation increased transcript levels of three putative photolyase genes in B. graminis, indicating those were probably involved in photoreactivation processes. However, mere white light or blue light (wavelength peak, 475 nm) could not induce the up-regulation of these genes.
To determine whether visible light directly impacted the prepenetration and penetration processes of this powdery mildew pathogen, conidia of Blumeria graminis f. sp. hordei and Blumeria graminis f. sp. tritici were inoculated onto artificial surfaces and on host leaf surfaces. Samples were analyzed after incubation periods under light conditions (white light intensity and spectral quality). Increasing white light intensities directly impaired conidial prepenetration processes in vitro but not in vivo. Applying an agar layer under the wax membrane compensated for conidial water loss as a consequence of high white light irradiation. Light stimulated in vitro and in vivo the appressorium elongation of B. graminis in a wavelength-dependent manner. Red light was more effective to trigger the elongation of appressorium than blue light or green light assayed.
Taken together, the findings of this study demonstrate that 1) a host surface recognition principle based on cuticular very-long-chain aldehydes is a common feature of B. graminis f. sp. tritici ascospores and conidia; 2) the transcriptional changes of three putative photolyase genes in B. graminis are mediated in a UV-C-dependent manner; 3) light directly affected the (pre)penetration processes of B. graminis.
This dissertation is divided into three studies by addressing the following constitutive research questions in the context of the biotechnology industry: (1) How do different types of inter-firm alliances influence a firm’s R&D activity? (2) How does an increasing number and diversity of alliances in a firm’s alliance portfolio affect its R&D activity? (3) What is the optimal balance between exploration and exploitation? (1) To answer these research questions the first main chapter analyzes the impact of different types of alliances on the R&D activities of successful firms in the biotechnology industry. Following the use of a new approach to measuring changes in research activities, the results show that alliances are used to specialize in a certain research field, rather than to enter a completely new market. This effect becomes smaller when the equity involvement of the partners in the alliance project increases. (2) The second main chapter analyzes the impact on innovation output of having heterogeneous partners in a biotechnology firm’s alliance portfolio. Previous literature has stressed that investment in the heterogeneity of partners in an alliance portfolio is more important than merely engaging in multiple collaborative agreements. The analysis of a unique panel dataset of 20 biotechnology firms and their 8,602 alliances suggests that engaging in many alliances generally has a positive influence on a firm’s innovation output. Furthermore, maintaining diverse alliance portfolios has an inverted U-shaped influence on a firm’s innovation output, as managerial costs and complexity levels become too high. (3) And the third main chapter investigates whether there is an optimal balance to be found between explorative and exploitative innovation strategies. Previous literature states that firms that are ambidextrous (i.e., able to focus on exploration and exploitation simultaneously) tend to be more successful. Using a unique panel dataset of 20 leading biotechnology firms and separating their explorative and exploitative research, the chapter suggests that firms seeking to increase their innovation output should avoid imbalances between their explorative and exploitative innovation strategies. Furthermore, an inverted U-shaped relationship between a firm’s relative research attention on exploration and its innovation output is found. This dissertation concludes with the results of the dissertation, combines the findings, gives managerial implications and proposes areas for potential further research.
For the differentiation of a embryonic stem cells (ESCs) to neuronal cells (NCs) a complex and coordinated gene regulation program is needed. One important control element for neuronal differentiation is the repressor element 1 silencing transcription factor (REST) complex, which represses neuronal gene expression in non-neuronal cells. Crucial effector proteins of the REST complex are small phosphatases such as the CTDSPs (C-terminal domain small phosphatases) that regulate polymerase II activity by dephosphorylating the C-terminal domain of the polymerase, thereby repressing target genes. The stepwise inactivation of REST, including the CTDSPs, leads to the induction of a neuron-specific gene program, which ultimately induces the formation of neurons. The spatio-temporal control of REST and its effector components is therefore a crucial step for neurogenesis.
In zebrafish it was shown that the REST-associated CTDSP2 is negatively regulated by the micro RNA (miR) -26b. Interestingly, the miR-26b is encoded in an intron of the primary transcript of CTDSP2. This gives the fundament of an intrinsic regulatory negative feedback loop, which is essential for the proceeding of neurogenesis. This feedback loop is active during neurogenesis, but inactive in non-neuronal cells. The reason for this is that the maturation of the precursor miR (pre-miR) to the mature miR-26 is arrested in non neuronal cells, but not in neurons. As only mature miRs are actively repressing genes, the regulation of miR-26 processing is an essential step in neurogenesis.
In this study, the molecular basis of miR-26 processing regulation in the context of neurogenesis was addressed. The mature miR is processed from two larger precursors: First the primary transcript is cleaved by the enzyme DROSHA in the nucleus to form the pre-miR. The pre-miR is exported from the nucleus and processed further through the enzyme DICER to yield the mature miR. The mature miR can regulate gene expression in association with the RNA-induced silencing complex (RISC).
Multiple different scenarios in which miR processing was regulated were proposed and experimentally tested. Microinjection studies using Xenopus leavis oocytes showed that slowdown or blockage of the nucleo-cytoplasmic transport are not the reason for delayed pre-miR-26 processing. Moreover, in vitro and in vivo miR-processing assays showed that maturation is most likely regulated through a in trans acting factor, which blocks processing in non neuronal cells.
Through RNA affinity chromatographic assays using zebrafish and murine lysates I was able to isolate and identify proteins that interact specifically with pre-miR-26 and could by this influence its biogenesis. Potential candidates are FMRP/FXR1/2, ZNF346 and Eral1, whose functional characterisation in the context of miR-biogenesis could now be addressed.
The second part of my thesis was executed in close colaboration with the laboratory of Prof. Albrecht Müller. The principal question was addressed how miR-26 influences neuronal gene expression and which genes are primarily affected. This research question could be addressed by using a cell culture model system, which mimics ex vivo the differentiation of ESCs to NCs via neuronal progenitor.
For the functional analysis of miR-26 knock out cell lines were generated by the CRISPR/Cas9 technology. miR-26 deficient ESC keep their pluripotent state and are able to develop NPC, but show major impairment in differentiating to NCs. Through RNA deep sequencing the miR-26 induced transcriptome differences could be analysed.
On the level of mRNAs it could be shown, that the expression of neuronal gene is downregulated in miR-26 deficient NCs. Interestingly, the deletion of miR-26 leads to selectively decreased levels of miRs, which on one hand regulate the REST complex and on the other hand are under transcriptional control by REST themself. This data and the discovery that induction of miR-26 leads to enrichment of other REST regulating miRs indicates that miR-26 initiates neurogenesis through stepwise inactivation of the REST complex.
Anxiety disorders (AD) are common, disabling mental disorders, which constitute the most prevalent mental health condition conveying a high individual and socioeconomic burden. Social anxiety disorder (SAD), i.e. fear in social situations particularly when subjectively scrutinized by others, is the second most common anxiety disorder with a life time prevalence of 10%. Panic disorder (PD) has a life time prevalence of 2-5% and is characterized by recurrent and abrupt surges of intense fear and anticipatory anxiety, i.e. panic attacks, occurring suddenly and unexpected without an apparent cue.
In recent years, psychiatric research increasingly focused on epigenetic mechanisms such as DNA methylation as a possible solution for the problem of the so-called “hidden heritability”, which conceptualizes the fact that the genetic risk variants identified so far only explain a small part of the estimated heritability of mental disorders.
In the first part of this thesis, oxytocin receptor (OXTR) gene methylation was investigated regarding its role in the pathogenesis of social anxiety disorder. In summary, OXTR methylation patterns were implicated in different phenotypes of social anxiety disorder on a categorical, neuropsychological, neuroendocrinological as well as on a neural network level. The results point towards a multilevel role of OXTR gene hypomethylation particularly at one CpG site (CpG3, Chr3: 8 809 437) within the protein coding region of the gene in SAD.
The second part of the thesis investigated monoamine oxidase A (MAOA) gene methylation regarding its role in the pathogenesis of panic disorder as well as – applying a psychotherapy-epigenetic approach – its dynamic regulation during the course of cognitive behavioural therapy (CBT) in PD patients. First, MAOA hypomethylation was shown to be associated with panic disorder as well as with panic disorder severity. Second, in patients responding to treatment MAOA hypomethylation was shown to be reversible up to the level of methylation in healthy controls after the course of CBT. This increase in MAOA methylation along with successful psychotherapeutic treatment was furthermore shown to be associated with symptom improvement regarding agoraphobic avoidance in an independent replication sample of non-medicated patients with PD.
Taken together, in the future the presently identified epigenetic patterns might contribute to establishing targeted preventive interventions and personalized treatment options for social anxiety disorder or panic disorder, respectively.
In this work the synthesis of dendritic macromolecules and small redox cascades was reported and studies of their energy and electron transfer properties discussed.
The chromophores in the dendrimers and the redox cascades are linked via triazoles, which were built up by CuAAC. Thereby, a synthetic concept based on building blocks was implemented, which allowed the exchange of all basic components. Resulting structures include dendrimers composed exclusively of TAAs (G1–G3), dendrimers with an incorporated spirobifluorene core (spiro-G1 and spiro-G2) and the donor-acceptor dendrimer D-A-G1, in which the terminal groups are exchanged by NDIs.
Furthermore, a series of model compounds was synthesised in order to achieve a better understanding of the photophysical processes in the dendrimers.
A modification of the synthetic concept for dendrimers enabled the synthesis of a series of donor-acceptor triads (T-Me, T-Cl and T-CN) consisting of two TAA donors and one NDI acceptor unit. The intermediate TAA chromophore ensured a downhill redox gradient from the NDI to the terminal TAA, which was proved by cyclic voltammetry measurements. The redox potential of the intermediate TAA was adjusted by different redox determining substituents in the “free” p-position of the TAA. Additionally, two dyads (Da and Db) were synthesised which differ in the junction of the triazole to the TAA or the NDI, respectively. In these cascades a nodal-plane along the N-N-axes in the NDI and a large twist angle between the NDI and the N-aryl substituent guaranteed a small electronic coupling.
The photophysical investigations of the dendrimers focused on the homo-energy transfer properties in the TAA dendrimers G1–G3. Steady-state emission spectroscopy revealed that the emission takes place from a charge transfer state. The polar excited state resulted in a strong Stokes shift of the emission, which in turn led to a small spectral overlap integral between the absorption of the acceptor and the emission of the donor in the solvent relaxed state. According to the Förster theory, the overlap integral strongly determines the energy transfer rate. Fluorescence up-conversion measurements showed a strong and rapid initial fluorescence anisotropy decay and a much slower decrease on the longer time scale. The experiment revealed a fast energy transfer in the first 2 ps followed by a much slower energy hopping. Time resolved emission spectra (TRES) of the model compound M indicated a solvent relaxation on the same time scale as the fast energy transfer.
The Förster estimation of energy transfer rates in G1 explains fast energy transfer in the vibrotionally relaxed state before solvent relaxation starts. Thereby, the emission spectrum of G1 in cyclohexane served as the time zero spectrum. Thus, solvent relaxation and fast energy transfer compete in the first two ps after excitation and it is crucial to discriminate between energy transfer in the Franck-Condon and in the solvent relaxed state. Furthermore, this finding demonstrates that fast energy transfer occurs even in charge transfer systems where a large Stokes shift prevents an effective spectral overlap integral if there is a sufficient overlap integral in before solvent relaxation.
Energy transfer upon excitation was also observed in the spiro dendrimers spiro-G1 and spiro-G2 and identified by steady-state emission anisotropy measurements. It was assumed that the energy in spiro-G1 is completely distributed over the entire molecule while the energy in spiro-G2 is probably distributed over only one individual branch. This finding was based on a more polarised emission of spiro-G2 compared to spiro-G1. This issue has to be ascertained by e.g. time resolved emission anisotropy measurements in further energy transfer studies.
Concerning the electron transfer properties of TAA-triazole systems the radical cations of G1–G2, spiro-G1 and spiro-G2 and of the model compound M were investigated by steady-state absorption spectroscopy. Experiments showed that the triazole bridge exhibits small electronic communication between the adjacent chromophores but still possesses sufficient electronic coupling to allow an effective electron transfer from one chromophore to the other.
Due to the high density of chromophores, their D-A-D structure and their superficial centrosymmetry, the presented dendrimers are prospective candidates for two-photon absorption applications.
The dyads, triads and the donor-acceptor dendrimer D-A-G1 were investigated regarding their photoinduced electron transfer properties and the effects that dominate charge separation and charge recombination in these systems.
The steady-state absorption spectra of all cascades elucidated a superposition of the absorption characteristics of the individual subunits and spectra indicated that the chromophores do not interact in the electronic ground state.
Time resolved transient absorption spectroscopy of the cascades was performed in the fs- and ns-time regime in MeCN and toluene as solvent. Measurements revealed that upon with 28200 cm-1 (355) nm and 26300 cm-1 (380 nm), respectively, an electron is transferred from the TAA towards the NDI unit yielding a CS state. In the triads at first a CS1 state is populated, in which the NDI is reduced and the intermediate TAA1 is oxidised. Subsequently, an additional electron transfer from the terminal TAA2 to TAA1 led to the fully CS2 state. Fully CS states of the dyads and triads exhibit lifetimes in the ns-time regime. In contrast for Db in MeCN, a lifetime of 43 ps was observed for the CS state together with the population of a 3NDI state. The signals of the other CS states decay biexponentially, which is a result of the presence of the 1CS and the 3CS states. While magnetic field dependent measurements of Db did not show an effect due to the large singlet-triplet splitting, T-CN exhibited a strong magnetic field dependence which is an evidence for the 1CS/3CS assignment. Further analysis of the singlet-triplet dynamics are required and are currently in progress.
Charge recombination occurred in the Marcus inverted region for compounds solved in toluene and in the Marcus normal region for MeCN as solvent. However, a significant inverted region effect was observed only for Db. Triads are probably characterised by charge recombination rates in the inverted and in the normal region near to the vertex of the Marcus parabola. Hence the inverted region effect is not pronounced and the rate charge recombination rates are all in the same magnitude. However, compared to the charge recombination rate of Db the enlarged spatial distance between the terminal TAA and the NDI in the fully CS2 states in the triads resulted in reduced charge recombination rates by ca. one order of magnitude.
More important than a small charge recombination rate is an overall lifetime of the CS states and this lifetime can significantly be enhanced by the population of the 3CS state. The reported results reveal that a larger singlet-triplet splitting in the dyads led to a CS state lifetime in the us time regime while a lifetime in the ns-time regime was observed in cases of the triads. Moreover, the singlet-triplet splitting was found to be solvent dependent in the triads, which is a promising starting point for further investigations concerning singlet-triplet splitting.
The donor-acceptor dendrimer D-A-G1 showed similar characteristics to the dyads. The generation of a CS state is assumed due to a clear NDI radical anion band in the transient absorption spectrum. Noteworthy, the typical transient absorption band of the TAA radical cation is absent for D A-G1 in toluene. Bixon-Jortner analysis yielded a similar electronic coupling in D-A-G1 compared to the dyads. However, the charge recombination rate is smaller than of Db due to a more energetic CS state, which in the inverted region slows down charge recombination. In combination a singlet-triplet splitting similar to the dyads prolongs the CS state lifetime up to 14 us in diluted solution. Both effects result in an even better performance of D-A-G1 concerning energy conversion. D A-G1 is therefore a promising key structure for further studies on light harvesting applications. In a prospective study a second generation donor-acceptor dendrimer D-A-G2 might be an attractive structure accessible by “click reaction” of 13 and 8. D-A-G2 is expected to exhibit a downhill oriented gradient of CS states as assumed from the CV studies on G1–G3.
Upon approval of a drug, the stability of the API and the FPP has to be studied intensively because it determines the shelf-life. If a drug is found to be stable, the expiry date is arbitrary set to five years at the maximum, if a drug tends to undergo degradation, the expiry date is set shorter. The drug product must comply with predefined specifications in accordance with the ICH guidelines Q6A and Q6B during its entire market life. The content of the active substance is required to be within a specification of 95–105% of its labeled claim until expiry corresponding to the ICH guideline Q1A(R2). However, there is little or scattered literature information addressing the stability of drug products beyond their expiry dates. The objective of this thesis was to study and assess the long-term stability of a collection involving numerous pure drug substances and ampoules manufactured in the 20th century. The content and the impurity profile were examined by means of appropriate analytical methods, mainly using liquid chromatography. The results were compared to data being available in the literature. Assessing the stability regarding the dosage form and the affiliation of the drug class was conducted.
The experimental studies comprise the examination of 50 drug substances manufactured 20–30 years ago and 14 long expired ampoules which were older than 40 years in the time of analysis, exceeding many times the maximum shelf life of five years.
For investigation of the solid drug substances, pharmacopoeial methods were applied as far as possible. Indeed, results of the study showed that 44 tested substances still complied with the specification of the Ph. Eur. with regard to the content and impurity profile, even after more than two decades of storage.
For analysis of the injection solutions, HPLC-UV and HPLC-ESI/MS techniques were applied, commonly based on liquid chromatography methods of the Ph. Eur. for determination of related substances. Each method was further validated for its application to ensure accurate API quantification corresponding to ICH Q2(R1). Quite a few ampoules were identified to show surprisingly high stability. In spite of their age of 53–72 years, APIs such as caffeine, etilefrine, synephrine, metamizole sodium, furosemide, and sodium salicylate complied with the specified content that is valid nowadays, respectively. Nevertheless, typical degradation reaction, e.g. hydrolysis, oxidation, or isomerization, was observed in all remaining ampoules. Various degrees of hydrolysis were revealed for scopolamine, procaine, and adenosine triphosphate, the contents were decreased to 71%, 70%, and 15% of the declared concentrations, respectively. In the epinephrine and dipyridamole ampoules, oxidative degradation has been occurred, finding respective API contents of more or less 70%. For dihydroergotamine, excessive decomposition by epimerization was observed, resulting in an API content of 21% and degradation by isomerization was found in lobeline, still containing 64% of the labeled claim.
In conclusion, supported by the data of the present studies and the literature, defining and authorizing a longer shelf-life may be applicable to numerous pharmaceuticals which should be considered by pharmaceutical manufacturers and regulatory authorities, if justified based on stability studies. A general extension of the shelf-lives of drug products and the abolishment or extension of the maximum shelf-life limit of five years would prevent disposing of still potent medications and save a lot of money to the entire health care system.
Ischemia-reperfusion injury (I/R injury) is a common complication in ischemic stroke (IS) treatment, which is characterized by a paradoxical perpetuation of tissue damage despite the successful re-establishment of vascular perfusion. This phenomenon is known to be facilitated by the detrimental interplay of platelets and inflammatory cells at the vascular interface. However, the spatio-temporal and molecular mechanisms underlying these cellular interactions and their contribution to infarct progression are still incompletely understood. Therefore, this study intended to clarify the temporal mechanisms of infarct growth after cerebral vessel recanalization. The data presented here could show that infarct progression is driven by early blood-brain-barrier perturbation and is independent of secondary thrombus formation. Since previous studies unravelled the secretion of platelet granules as a molecular mechanism of how platelets contribute to I/R injury, special emphasis was placed on the role of platelet granule secretion in the process of barrier dysfunction. By combining an in vitro approach with a murine IS model, it could be shown that platelet α-granules exerted endothelial-damaging properties, whereas their absence (NBEAL2-deficiency) translated into improved microvascular integrity. Hence, targeting platelet α-granules might serve as a novel treatment option to reduce vascular integrity loss and diminish infarct growth despite recanalization.
Recent evidence revealed that pathomechanisms underlying I/R injury are already instrumental during large vessel occlusion. This indicates that penumbral tissue loss under occlusion and I/R injury during reperfusion share an intertwined relationship. In accordance with this notion, human observational data disclosed the presence of a neutrophil dominated immune response and local platelet activation and secretion, by the detection of the main components of platelet α-granules, within the secluded vasculature of IS patients. These initial observations of immune cells and platelets could be further expanded within this thesis by flow cytometric analysis of local ischemic blood samples. Phenotyping of immune cells disclosed a yet unknown shift in the lymphocyte population towards CD4+ T cells and additionally corroborated the concept of an immediate intravascular immune response that is dominated by granulocytes. Furthermore, this thesis provides first-time evidence for the increased appearance of platelet-leukocyte-aggregates within the secluded human vasculature. Thus, interfering with immune cells and/or platelets already under occlusion might serve as a potential strategy to diminish infarct expansion and ameliorate clinical outcome after IS.
The eukaryotic parasite Trypanosoma brucei has evolved sophisticated strategies to persist within its mammalian host. Trypanosomes evade the hosts' immune system by antigenic variation of their surface coat, consisting of variant surface glycoproteins (VSGs). Out of a repertoire of thousands of VSG genes, only one is expressed at any given time from one of the 15 telomeric expression sites (ES). The VSG is stochastically exchanged either by a transcriptional switch of the active ES (in situ switch) or by a recombinational exchange of the VSG within the active ES. However, for infections to persist, the parasite burden has to be limited. The slender (sl) bloodstream form secretes the stumpy induction factor (SIF), which accumulates with rising parasitemia. SIF induces the irreversible developmental transition from the proliferative sl to the cell cycle-arrested but fly-infective stumpy (st) stage once a concentration threshold is reached. Thus, antigenic variation and st development ensure persistent infections and transmissibility. A previous study in monomorphic cells indicated that the attenuation of the active ES could be relevant for the development of trypanosomes. The present thesis investigated this hypothesis using the inducible overexpression of an ectopic VSG in pleomorphic trypanosomes, which possess full developmental competence. These studies revealed a surprising phenotypic plasticity: while the endogenous VSG was always down-regulated upon induction, the ESactivity determined whether the VSG overexpressors arrested in growth or kept proliferating. Full ES-attenuation induced the differentiation of bona fide st parasites independent of the cell density and thus represents the sole natural SIF-independent differentiation trigger to date. A milder decrease of the ES-activity did not induce phenotypic changes, but appeared to prime the parasites for SIF-induced differentiation. These results demonstrate that antigenic variation and development are linked and indicated that the ES and the VSG are independently regulated. Therefore, I investigated in the second part of my thesis how ES-attenuation and VSG-silencing can be mediated. Integration of reporters with a functional or defective VSG 3'UTR into different genomic loci showed that the maintenance of the active state of the ES depends on a conserved motif within the VSG 3'UTR. In situ switching was only triggered when the telomere-proximal motif was partially deleted, suggesting that it serves as a DNA-binding motif for a telomere-associated protein. The VSG levels seem to be additionally regulated in trans based on the VSG 3'UTR independent of the genomic context, which was reinforced by the regulation of a constitutively expressed reporter with VSG 3' UTR upon ectopic VSG overexpression.
The aim of the present work was to improve drug monitoring in patients with various diseases in the context of precision medicine. This was pursued through the development and validation of mass spectrometric methods for determining the drug concentrations of kinase inhibitors and their clinical application. Besides conventional approaches to determine plasma level concentrations, the focus was also on alternative sampling techniques using volumetric absorptive microsampling (VAMS).
A conventional LC-MS/MS method was developed for the determination of cabozantinib in human EDTA plasma and validated according to the guidelines of the European and United States drug authorities (EMA, FDA). The method met the required criteria for linearity, accuracy and precision, selectivity, sensitivity, and stability of the analyte. Validation was also performed for dilution integrity, matrix effect, recovery, and carry-over, with results also in accordance with the requirements. The importance of monitoring the exposure of cabozantinib was demonstrated by a clinical case report of a 34-year-old female patient with advanced adrenocortical carcinoma who also required hemodialysis due to chronic kidney failure. Expected cabozantinib plasma concentrations were simulated for this off-label use based on a population pharmacokinetic model. It was shown that the steady state trough levels were much lower than expected but could not be explained by hemodialysis. Considering the critical condition and potential drug-drug interaction with metyrapone, a substance the patient had taken among several others during the observation period, individual pharmacokinetics could consequently not be estimated without drug monitoring.
In addition, a VAMS method for simultaneous determination of ten kinase inhibitors from capillary blood was developed. This microsampling technique was mainly characterized by the collection of a defined volume of blood, which could be dried and subsequently analyzed. The guidelines for bioanalytical method validation of the EMA and FDA were also used for this evaluation. As the nature of dried blood samples differs from liquid matrices, further parameters were investigated. These include the investigation of the hematocrit effect, process efficiency, and various stability conditions, for example at increased storage temperatures. The validation showed that the developed method is suitable to analyze dried matrix samples accurate, precise, and selective for all analytes. Apart from the stability tests, all acceptance criteria were met. The decreased stability of two analytes was probably due to the reproducible but reduced recovery. In vitro studies provided results on the VAMS-to-plasma correlation to predict the analyte distribution between both matrices, at least in an exploratory manner. It revealed a heterogeneous picture of analytes with different VAMS-to-plasma distributions. Furthermore, the analysis of 24 patient samples indicated the applicability of at-home VAMS. Both should be confirmed later as part of the clinical validation.
The clinical investigation of the VAMS method pursued two objectives. On the one hand, the simultaneous collection of VAMS and serum samples should enable a conversion of the determined concentrations and, on the other hand, the feasibility of autonomous microsampling at home should be examined more closely. For the former, it could be shown that different conversion methods are suitable for converting VAMS concentrations into serum levels. The type of conversion was secondary for the prediction. However, the previously defined criteria could not be fulfilled for all five kinase inhibitors investigated. The framework conditions of the study led to increased variability, especially for analytes with short half-life. A low and varying hematocrit, caused by the underlying disease, also made prediction difficult for a specific patient collective. For the second objective, investigating the feasibility of VAMS, different aspects were considered. It could be shown that the majority of patients support home-based microsampling. The acceptance is likely to increase even further when microsampling is no longer part of a non-interventional study, but participation is accompanied by targeted monitoring and subsequent adjustment of the therapy. The fact that additional training increases understanding of the correct sampling procedure is also a source of confidence. Demonstrated stability during storage under real-life conditions underlines the practicality of this sampling technique.
Taken together, mass spectrometric methods for both plasma and VAMS could be developed and validated, and their clinical application could be successfully demonstrated. The availability of simple bioanalytical methods to determine kinase inhibitor exposure could improve access to prospective studies and thus facilitate the implementation of routine therapeutic drug monitoring.
Graphs provide a key means to model relationships between entities.
They consist of vertices representing the entities,
and edges representing relationships between pairs of entities.
To make people conceive the structure of a graph,
it is almost inevitable to visualize the graph.
We call such a visualization a graph drawing.
Moreover, we have a straight-line graph drawing
if each vertex is represented as a point
(or a small geometric object, e.g., a rectangle)
and each edge is represented as a line segment between its two vertices.
A polyline is a very simple straight-line graph drawing,
where the vertices form a sequence according to which the vertices are connected by edges.
An example of a polyline in practice is a GPS trajectory.
The underlying road network, in turn, can be modeled as a graph.
This book addresses problems that arise
when working with straight-line graph drawings and polylines.
In particular, we study algorithms
for recognizing certain graphs representable with line segments,
for generating straight-line graph drawings,
and for abstracting polylines.
In the first part, we first examine,
how and in which time we can decide
whether a given graph is a stick graph,
that is, whether its vertices can be represented as
vertical and horizontal line segments on a diagonal line,
which intersect if and only if there is an edge between them.
We then consider the visual complexity of graphs.
Specifically, we investigate, for certain classes of graphs,
how many line segments are necessary for any straight-line graph drawing,
and whether three (or more) different slopes of the line segments
are sufficient to draw all edges.
Last, we study the question,
how to assign (ordered) colors to the vertices of a graph
with both directed and undirected edges
such that no neighboring vertices get the same color
and colors are ascending along directed edges.
Here, the special property of the considered graph is
that the vertices can be represented as intervals
that overlap if and only if there is an edge between them.
The latter problem is motivated by an application
in automated drawing of cable plans with vertical and horizontal line segments,
which we cover in the second part.
We describe an algorithm that
gets the abstract description of a cable plan as input,
and generates a drawing that takes into account
the special properties of these cable plans,
like plugs and groups of wires.
We then experimentally evaluate the quality of the resulting drawings.
In the third part, we study the problem of abstracting (or simplifying)
a single polyline and a bundle of polylines.
In this problem, the objective is to remove as many vertices as possible from the given polyline(s)
while keeping each resulting polyline sufficiently similar to its original course
(according to a given similarity measure).
Internet applications are becoming more and more flexible to support diverge user demands and network conditions. This is reflected by technical concepts, which provide new adaptation mechanisms to allow fine grained adjustment of the application quality and the corresponding bandwidth requirements. For the case of video streaming, the scalable video codec H.264/SVC allows the flexible adaptation of frame rate, video resolution and image quality with respect to the available network resources. In order to guarantee a good user-perceived quality (Quality of Experience, QoE) it is necessary to adjust and optimize the video quality accurately. But not only have the applications of the current Internet changed. Within network and transport, new technologies evolved during the last years providing a more flexible and efficient usage of data transport and network resources. One of the most promising technologies is Network Virtualization (NV) which is seen as an enabler to overcome the ossification of the Internet stack. It provides means to simultaneously operate multiple logical networks which allow for example application-specific addressing, naming and routing, or their individual resource management. New transport mechanisms like multipath transmission on the network and transport layer aim at an efficient usage of available transport resources. However, the simultaneous transmission of data via heterogeneous transport paths and communication technologies inevitably introduces packet reordering. Additional mechanisms and buffers are required to restore the correct packet order and thus to prevent a disturbance of the data transport. A proper buffer dimensioning as well as the classification of the impact of varying path characteristics like bandwidth and delay require appropriate evaluation methods. Additionally, for a path selection mechanism real time evaluation mechanisms are needed. A better application-network interaction and the corresponding exchange of information enable an efficient adaptation of the application to the network conditions and vice versa. This PhD thesis analyzes a video streaming architecture utilizing multipath transmission and scalable video coding and develops the following optimization possibilities and results: Analysis and dimensioning methods for multipath transmission, quantification of the adaptation possibilities to the current network conditions with respect to the QoE for H.264/SVC, and evaluation and optimization of a future video streaming architecture, which allows a better interaction of application and network.
Although the field of fungal infections advanced tremendously, diagnosis of invasive pulmonary aspergillosis (IPA) in immunocompromised patients continues to be a challenge. Since IPA is a multifactorial disease, investigation from different aspects may provide new insights, helpful for improving IPA diagnosis. This work aimed to characterize the human immune response to Aspergillus fumigatus in a multilevel manner to identify characteristic molecular candidates and risk factors indicating IPA, which may in the future support already established diagnostic assays. We combined in vitro studies using myeloid cells infected with A. fumigatus and longitudinal case-control studies investigating patients post allogeneic stem cell transplantation (alloSCT) suffering from IPA and their match controls.
Characteristic miRNA and mRNA signatures indicating A. fumigatus-infected monocyte-derived dendritic cells (moDCs) demonstrated the potential to differentiate between A. fumigatus and Escherichia coli infection. Transcriptome and protein profiling of alloSCT patients suffering from IPA and their matched controls revealed a distinctive IPA signature consisting of MMP1 induction and LGAL2 repression in combination with elevated IL-8 and caspase-3 levels. Both, in vitro and case-control studies, suggested cytokines, matrix-metallopeptidases and galectins are important in the immune response to A. fumigatus. Identified IPA characteristic molecular candidates are involved in numerous processes, thus a combination of these in a distinctive signature may increase the specificity. Finally, low monocyte counts, severe GvHD of the gut (grade ≥ 2) and etanercept administration were significantly associated with IPA diagnosis post alloSCT. Etanercept in monocyte-derived macrophages (MDM) infected with A. fumigatus downregulates genes involved in the NF-κB and TNF-α pathway and affects the secretion of CXCL10.
Taken together, identified characteristic molecular signatures and risk factors indicating IPA may in the future in combination with established fungal biomarkers overcome current diagnostic challenges and help to establish tailored antifungal therapy. Therefore, further multicentre studies are encouraged to evaluate reported findings.
Extreme value theory is concerned with the stochastic modeling of rare and extreme events. While fundamental theories of classical stochastics - such as the laws of small numbers or the central limit theorem - are used to investigate the asymptotic behavior of the sum of random variables, extreme value theory focuses on the maximum or minimum of a set of observations. The limit distribution of the normalized sample maximum among a sequence of independent and identically distributed random variables can be characterized by means of so-called max-stable distributions.
This dissertation concerns with different aspects of the theory of max-stable random vectors and stochastic processes. In particular, the concept of 'differentiability in distribution' of a max-stable process is introduced and investigated. Moreover, 'generalized max-linear models' are introduced in order to interpolate a known max-stable random vector by a max-stable process. Further, the connection between extreme value theory and multivariate records is established. In particular, so-called 'complete' and 'simple' records are introduced as well as it is examined their asymptotic behavior.
Neuronal representation and processing of chemosensory communication signals in the ant brain
(2008)
Ants heavily rely on olfaction for communication and orientation and ant societies are characterized by caste- and sex-specific division of labor. Olfaction plays a key role in mediating caste-specific behaviours. I investigated whether caste- and sex-specific differences in odor driven behavior are reflected in specific differences and/or adaptations in the ant olfactory system. In particular, I asked the question whether in the carpenter ant, Camponotus floridanus, the olfactory pathway exhibits structural and/or functional adaptations to processing of pheromonal and general odors. To analyze neuroanatomical specializations, the central olfactory pathway in the brain of large (major) workers, small (minor) workers, virgin queens, and males of the carpenter ant C. floridanus was investigated using fluorescent tracing, immunocytochemistry, confocal microscopy and 3D-analyzes. For physiological analyzes of processing of pheromonal and non-pheromonal odors in the first odor processing neuropil , the antennal lobe (AL), calcium imaging of olfactory projection neurons (PNs) was applied. Although different in total glomerular volumes, the numbers of olfactory glomeruli in the ALs were similar across the female worker caste and in virgin queens. Here the AL contains up to ~460 olfactory glomeruli organized in 7 distinct clusters innervated via 7 antennal sensory tracts. The AL is divided into two hemispheres regarding innervations of glomeruli by PNs with axons leaving via a dual output pathway. This pathway consists of the medial (m) and lateral (l) antenno-cerebral tract (ACT) and connects the AL with the higher integration areas in the mushroom bodies (MB) and the lateral horn (LH). M- and l-ACT PNs differ in their target areas in the MB calyx and the LH. Three additional ACTs (mediolateral - ml) project to the lateral protocerebrum only. Males had ~45% fewer glomeruli compared to females and one of the seven sensory tracts was absent. Despite a substantially smaller number of glomeruli, males possess a dual PN output pathway to the MBs. In contrast to females, however, only a small number of glomeruli were innervated by projection neurons of the m-ACT. Whereas all glomeruli in males were densely innervated by serotonergic processes, glomeruli innervated by sensory tract six lacked serotonergic innervations in the female castes. It appears that differences in general glomerular organization are subtle among the female castes, but sex-specific differences in the number, connectivity and neuromodulatory innervations of glomeruli are substantial and likely to promote differences in olfactory behavior. Calcium imaging experiments to monitor pheromonal and non-pheromonal processing in the ant AL revealed that odor responses were reproducible and comparable across individuals. Calcium responses to both odor groups were very sensitive (10-11 dilution), and patterns from both groups were partly overlapping indicating that processing of both odor classes is not spatially segregated within the AL. Intensity response patterns to the pheromone components tested (trail pheromone: nerolic acid; alarm pheromone: n-undecane), in most cases, remained invariant over a wide range of intensities (7-8 log units), whereas patterns in response to general odors (heptanal, octanol) varied across intensities. Durations of calcium responses to stimulation with the trail pheromone component nerolic acid increased with increasing odor concentration indicating that odor quality is maintained by a stable pattern (concentration invariance) and intensity is mainly encoded in the response durations of calcium activities. For n-undecane and both general odors increasing response dynamics were only monitored in very few cases. In summary, this is the first detailed structure-function analyses within the ant’s central olfactory system. The results contribute to a better understanding of important aspects of odor processing and olfactory adaptations in an insect’s central olfactory system. Furthermore, this study serves as an excellent basis for future anatomical and/or physiological experiments.
Bacterial mastitis is caused by invasion of the udder, bacterial multiplication and induction of
inflammatory responses in the bovine mammary gland. Disease severity and the cause of disease are
influenced by environmental factors, the cow’s immune response as well as bacterial traits. Escherichia coli (E. coli) is one of the main causes of acute bovine mastitis, but although pathogenic E. coli strains can be classified into different pathotypes, E. coli causing mastitis cannot unambiguously be distinguished from commensal E. coli nor has a common set of virulence factors
been described for mastitis isolates. This project focussed on the characterization of virulence-
associated traits of E. coli mastitis isolates in comprehensive analyses under conditions either
mimicking initial pathogenesis or conditions that E. coli mastitis isolates should encounter while entering the udder. Virulence-associated traits as well as fitness traits of selected bovine mastitis or faecal E. coli strains were identified and analyzed in comparative phenotypic assays. Raw milk whey was introduced to
test bacterial fitness in native mammary secretion known to confer antimicrobial effects.
Accordingly, E. coli isolates from bovine faeces represented a heterogeneous group of which some
isolates showed reduced ability to survive in milk whey whereas others phenotypically resembled
mastitis isolates that represented a homogeneous group in that they showed similar survival and
growth characteristics in milk whey. In contrast, mastitis isolates did not exhibit such a uniform phenotype when challenged with iron shortage, lactose as sole carbon source and lingual
antimicrobial peptide (LAP) as a main defensin of milk. Reduced bacterial fitness could be related to LAP suggesting that bacterial adaptation to an intramammary lifestyle requires resistance to host
defensins present in mammary secretions, at least LAP.
E. coli strain 1303 and ECC-1470 lack particular virulence genes associated to mastitis isolates. To find out whether differences in gene expression may contribute to the ability of E. coli variants to cause mastitis, the transcriptome of E. coli model mastitis isolates 1303 and ECC-1470 were analyzed to
identify candidate genes involved in bacterium-host interaction, fitness or even pathogenicity during bovine mastitis.
DNA microarray analysis was employed to assess the transcriptional response of E. coli 1303 and
ECC-1470 upon cocultivation with MAC-T immortalized bovine mammary gland epithelial cells to
identify candidate genes involved in bacterium-host interaction. Additionally, the cell adhesion and invasion ability of E. coli strain 1303 and ECC-1470 was investigated. The transcriptonal response to the presence of host cells rather suggested competition for nutrients and oxygen between E. coli and MAC-T cells than marked signs of adhesion and invasion. Accordingly, mostly fitness traits that may also contribute to efficient colonization of the E. coli primary habitat, the gut, have been utilized by the mastitis isolates under these conditions. In this study, RNA-Seq was employed to assess the bacterial transcriptional response to milk whey.
According to our transcriptome data, the lack of positively deregulated and also of true virulence-associated determinants in both of the mastitis isolates indicated that E. coli might have adapted by other means to the udder (or at least mammary secretion) as an inflammatory site. We identified traits that promote bacterial growth and survival in milk whey. The ability to utilize citrate promotes fitness and survival of E. coli that are thriving in mammary secretions. According to our results, lactoferrin has only weak impact on E. coli in mammary secretions. At the same time bacterial determinants involved in iron assimilation were negatively regulated, suggesting that, at least during the first hours, iron assimilation is not a challenge to E. coli colonizing the mammary gland. It has been hypothesized that cellular iron stores cause temporary independency to extracellular accessible iron. According to our transcriptome data, this hypothesis was supported and places iron uptake
systems beyond the speculative importance that has been suggested before, at least during early
phases of infection. It has also been shown that the ability to resist extracytoplasmic stress, by oxidative conditions as well as host defensins, is of substantial importance for bacterial survival in mammary secretions.
In summary, the presented thesis addresses important aspects of host-pathogen interaction and
bacterial conversion to hostile conditions during colonization of the mastitis inflammatory site, the mammary gland.
Organic solar cells have great potential to become a low-cost and clean alternative to conventional photovoltaic technologies based on the inorganic bulk material silicon. As a highly promising concept in the field of organic photovoltaics, bulk heterojunction (BHJ) solar cells consist of a mixture of an electron donating and an electron withdrawing component. Their degree of intermixing crucially affects the generation of photocurrent. In this work, the effect of an altered blend morphology on polaron pair dissociation, charge carrier transport, and nongeminate recombination is analyzed by the charge extraction techniques time delayed collection field (TDCF) and open circuit corrected transient charge extraction (OTRACE). Different comparative studies cover a broad range of material systems, including polymer and small-molecule donors in combination with different fullerene acceptors. The field dependence of polaron pair dissociation is analyzed in blends based on the polymer pBTTT-C16, allowing a systematic tuning of the blend morphology by varying the acceptor type and fraction. The effect of both excess photon energy and intercalated phases are minor compared to the influence of excess fullerene, which reduces the field dependence of photogeneration. The study demonstrates that the presence of neat fullerene domains is the major driving force for efficient polaron pair dissociation that is linked to the delocalization of charge carriers. Furthermore, the influence of the processing additive diiodooctane (DIO) is analyzed using the photovoltaic blends PBDTTT-C:PC71BM and PTB7:PC71BM. The study reveals amulti-tiered alteration of the blend morphology of PBDTTT-C based blends upon a systematic increase of the amount of DIO. Domains on the hundred nanometers length scale in the DIO-free blend are identified as neat fullerene agglomerates embedded in an intermixed matrix. With the addition of the additive, 0.6% and 1% DIO already substantially reduces the size of these domains until reaching the optimum 3% DIO mixture, where a 7.1% power conversion efficiency is obtained. It is brought into connection with the formation of interpenetrating polymer and fullerene phases. Similar to PBDTTT-C, the morphology of DIO-free PTB7:PC71BM blends is characterized by large fullerene domains being decreased in size upon the addition of 3% DIO. OTRACE measurements reveal a reduced Langevin-type, super-second order recombination in both blends. It is demonstrated that the deviation from bimolecular recombination kinetics cannot be fully attributed to the carrier density dependence of the mobility but is rather related to trapping in segregated PC71BM domains. Finally, with regard to small-molecule donors, a higher yield of photogeneration and balanced transport properties are identified as the dominant factors enhancing the efficiency of vacuum deposited MD376:C60 relative to its solution processed counterpart MD376:PC61BM. The finding is explained by a higher degree of dimerization of the merocyanine dye MD376 and a stronger donor-acceptor interaction at the interface in the case of the vacuum deposited blend.
Fluorescence microscopy is a form of light microscopy that has developed during the 20th century and is nowadays a standard tool in Molecular and Cell biology for studying the structure and function of biological molecules. High-resolution fluorescence microscopy techniques, such as dSTORM (direct Stochastic Optical Reconstruction Microscopy) allow the visualization of cellular structures at the nanometre scale (10−9 m). This has already made it possible to decipher the composition and function of various biopolymers, such as proteins, lipids and nucleic acids, up to the three-dimensional (3D) structure of entire organelles. In practice, however, it has been shown that these imaging methods and their further developments still face great challenges in order to achieve an effective resolution below ∼ 10 nm. This is mainly due to the nature of labelling biomolecules. For the detection of molecular structures, immunostaining is often performed as a standard method. Antibodies to which fluorescent molecules are coupled, recognize and bind specifcally and with high affnity to the molecular section of the target structure, also called epitope or antigen. The fluorescent molecules serve as reporter molecules which are imaged with the use of a fluorescence microscope. However, the size of these labels with a length of about 10-15 nm in the case of immunoglobulin G (IgG) antibodies, cause a detection of the fluorescent molecules shifted to the real position of the studied antigen. In dense regions where epitopes are located close to each other, steric hindrance between antibodies can also occur and leads to an insuffcient label density. Together with the shifted detection of fluorescent molecules, these factors can limit the achievable resolution of a microscopy technique. Expansion microscopy (ExM) is a recently developed technique that achieves a resolution improvement by physical expansion of an investigated object. Therefore, biological samples such as cultured cells, tissue sections, whole organs or isolated organelles are chemically anchored into a swellable polymer. By absorbing water, this so-called superabsorber increases its own volume and pulls the covalently bound biomolecules isotropically apart. Routinely, this method achieves a magnifcation of the sample by about four times its volume. But protocol variants have already been developed that result in higher expansion factors of up to 50-fold. Since the ExM technique includes in the frst instance only the sample treatment for anchoring and magnifcation of the sample, it can be combined with various standard methods of fluorescence microscopy. In theory, the resolution of the used imaging technique improves linearly with the expansion factor of the ExM treated sample. However, an insuffcient label density and the size of the antibodies can here again impair the effective achievable resolution. The combination of ExM with high-resolution fluorescence microscopy methods represents a promising strategy to increase the resolution of light microscopy. In this thesis, I will present several ExM variants I developed which show the combination of ExM with confocal microscopy, SIM (Structured Illumination Microscopy), STED (STimulated Emission Depletion) and dSTORM. I optimized existing ExM protocols and developed different expansion strategies, which allow the combination with the respective imaging technique. Thereby, I gained new structural insights of isolated centrioles from the green algae Chlamydomonas reinhardtii by combining ExM with STED and confocal microscopy. In another project, I combined 3D-SIM imaging with ExM and investigated the molecular structure of the so-called synaptonemal complex. This structure is formed during meiosis in eukaryotic cells and contributes to the exchange of genetic material between homologous chromosomes. Especially in combination with dSTORM, the ExM method showed its high potential to overcome the limitations of modern fluorescence microscopy techniques. In this project, I expanded microtubules in mammalian cells, a polymer of the cytoskeleton as well as isolated centrioles from C. reinhardtii. By labelling after expansion of the samples, I was able to signifcantly reduce the linkage error of the label and achieve an improved label density. In future, these advantages together with the single molecule sensitivity and high resolution obtained by the dSTORM method could pave the way for achieving molecular resolution in fluorescence microscopy
The importance of proactive and timely prediction of critical events is steadily increasing, whether in the manufacturing industry or in private life. In the past, machines in the manufacturing industry were often maintained based on a regular schedule or threshold violations, which is no longer competitive as it causes unnecessary costs and downtime. In contrast, the predictions of critical events in everyday life are often much more concealed and hardly noticeable to the private individual, unless the critical event occurs. For instance, our electricity provider has to ensure that we, as end users, are always supplied with sufficient electricity, or our favorite streaming service has to guarantee that we can watch our favorite series without interruptions. For this purpose, they have to constantly analyze what the current situation is, how it will develop in the near future, and how they have to react in order to cope with future conditions without causing power outages or video stalling.
In order to analyze the performance of a system, monitoring mechanisms are often integrated to observe characteristics that describe the workload and the state of the system and its environment. Reactive systems typically employ thresholds, utility functions, or models to determine the current state of the system. However, such reactive systems cannot proactively estimate future events, but only as they occur. In the case of critical events, reactive determination of the current system state is futile, whereas a proactive system could have predicted this event in advance and enabled timely countermeasures. To achieve proactivity, the system requires estimates of future system states. Given the gap between design time and runtime, it is typically not possible to use expert knowledge to a priori model all situations a system might encounter at runtime. Therefore, prediction methods must be integrated into the system. Depending on the available monitoring data and the complexity of the prediction task, either time series forecasting in combination with thresholding or more sophisticated machine and deep learning models have to be trained.
Although numerous forecasting methods have been proposed in the literature, these methods have their advantages and disadvantages depending on the characteristics of the time series under consideration. Therefore, expert knowledge is required to decide which forecasting method to choose. However, since the time series observed at runtime cannot be known at design time, such expert knowledge cannot be implemented in the system. In addition to selecting an appropriate forecasting method, several time series preprocessing steps are required to achieve satisfactory forecasting accuracy. In the literature, this preprocessing is often done manually, which is not practical for autonomous computing systems, such as Self-Aware Computing Systems. Several approaches have also been presented in the literature for predicting critical events based on multivariate monitoring data using machine and deep learning. However, these approaches are typically highly domain-specific, such as financial failures, bearing failures, or product failures. Therefore, they require in-depth expert knowledge. For this reason, these approaches cannot be fully automated and are not transferable to other use cases. Thus, the literature lacks generalizable end-to-end workflows for modeling, detecting, and predicting failures that require only little expert knowledge.
To overcome these shortcomings, this thesis presents a system model for meta-self-aware prediction of critical events based on the LRA-M loop of Self-Aware Computing Systems. Building upon this system model, this thesis provides six further contributions to critical event prediction. While the first two contributions address critical event prediction based on univariate data via time series forecasting, the three subsequent contributions address critical event prediction for multivariate monitoring data using machine and deep learning algorithms. Finally, the last contribution addresses the update procedure of the system model. Specifically, the seven main contributions of this thesis can be summarized as follows:
First, we present a system model for meta self-aware prediction of critical events. To handle both univariate and multivariate monitoring data, it offers univariate time series forecasting for use cases where a single observed variable is representative of the state of the system, and machine learning algorithms combined with various preprocessing techniques for use cases where a large number of variables are observed to characterize the system’s state. However, the two different modeling alternatives are not disjoint, as univariate time series forecasts can also be included to estimate future monitoring data as additional input to the machine learning models. Finally, a feedback loop is incorporated to monitor the achieved prediction quality and trigger model updates.
We propose a novel hybrid time series forecasting method for univariate, seasonal time series, called Telescope. To this end, Telescope automatically preprocesses the time series, performs a kind of divide-and-conquer technique to split the time series into multiple components, and derives additional categorical information. It then forecasts the components and categorical information separately using a specific state-of-the-art method for each component. Finally, Telescope recombines the individual predictions. As Telescope performs both preprocessing and forecasting automatically, it represents a complete end-to-end approach to univariate seasonal time series forecasting. Experimental results show that Telescope achieves enhanced forecast accuracy, more reliable forecasts, and a substantial speedup. Furthermore, we apply Telescope to the scenario of predicting critical events for virtual machine auto-scaling. Here, results show that Telescope considerably reduces the average response time and significantly reduces the number of service level objective violations.
For the automatic selection of a suitable forecasting method, we introduce two frameworks for recommending forecasting methods. The first framework extracts various time series characteristics to learn the relationship between them and forecast accuracy. In contrast, the other framework divides the historical observations into internal training and validation parts to estimate the most appropriate forecasting method. Moreover, this framework also includes time series preprocessing steps. Comparisons between the proposed forecasting method recommendation frameworks and the individual state-of-the-art forecasting methods and the state-of-the-art forecasting method recommendation approach show that the proposed frameworks considerably improve the forecast accuracy.
With regard to multivariate monitoring data, we first present an end-to-end workflow to detect critical events in technical systems in the form of anomalous machine states. The end-to-end design includes raw data processing, phase segmentation, data resampling, feature extraction, and machine tool anomaly detection. In addition, the workflow does not rely on profound domain knowledge or specific monitoring variables, but merely assumes standard machine monitoring data. We evaluate the end-to-end workflow using data from a real CNC machine. The results indicate that conventional frequency analysis does not detect the critical machine conditions well, while our workflow detects the critical events very well with an F1-score of almost 91%.
To predict critical events rather than merely detecting them, we compare different modeling alternatives for critical event prediction in the use case of time-to-failure prediction of hard disk drives. Given that failure records are typically significantly less frequent than instances representing the normal state, we employ different oversampling strategies. Next, we compare the prediction quality of binary class modeling with downscaled multi-class modeling. Furthermore, we integrate univariate time series forecasting into the feature generation process to estimate future monitoring data. Finally, we model the time-to-failure using not only classification models but also regression models. The results suggest that multi-class modeling provides the overall best prediction quality with respect to practical requirements. In addition, we prove that forecasting the features of the prediction model significantly improves the critical event prediction quality.
We propose an end-to-end workflow for predicting critical events of industrial machines. Again, this approach does not rely on expert knowledge except for the definition of monitoring data, and therefore represents a generalizable workflow for predicting critical events of industrial machines. The workflow includes feature extraction, feature handling, target class mapping, and model learning with integrated hyperparameter tuning via a grid-search technique. Drawing on the result of the previous contribution, the workflow models the time-to-failure prediction in terms of multiple classes, where we compare different labeling strategies for multi-class classification. The evaluation using real-world production data of an industrial press demonstrates that the workflow is capable of predicting six different time-to-failure windows with a macro F1-score of 90%. When scaling the time-to-failure classes down to a binary prediction of critical events, the F1-score increases to above 98%.
Finally, we present four update triggers to assess when critical event prediction models should be re-trained during on-line application. Such re-training is required, for instance, due to concept drift. The update triggers introduced in this thesis take into account the elapsed time since the last update, the prediction quality achieved on the current test data, and the prediction quality achieved on the preceding test data. We compare the different update strategies with each other and with the static baseline model. The results demonstrate the necessity of model updates during on-line application and suggest that the update triggers that consider both the prediction quality of the current and preceding test data achieve the best trade-off between prediction quality and number of updates required.
We are convinced that the contributions of this thesis constitute significant impulses for the academic research community as well as for practitioners. First of all, to the best of our knowledge, we are the first to propose a fully automated, end-to-end, hybrid, component-based forecasting method for seasonal time series that also includes time series preprocessing. Due to the combination of reliably high forecast accuracy and reliably low time-to-result, it offers many new opportunities in applications requiring accurate forecasts within a fixed time period in order to take timely countermeasures. In addition, the promising results of the forecasting method recommendation systems provide new opportunities to enhance forecasting performance for all types of time series, not just seasonal ones. Furthermore, we are the first to expose the deficiencies of the prior state-of-the-art forecasting method recommendation system.
Concerning the contributions to critical event prediction based on multivariate monitoring data, we have already collaborated closely with industrial partners, which supports the practical relevance of the contributions of this thesis. The automated end-to-end design of the proposed workflows that do not demand profound domain or expert knowledge represents a milestone in bridging the gap between academic theory and industrial application. Finally, the workflow for predicting critical events in industrial machines is currently being operationalized in a real production system, underscoring the practical impact of this thesis.
Utility is perhaps the most central concept in modern economic theorizing. However, the behaviorist reduction to Revealed Preference not only removed the psychological content of utility but experimental investigations also exposed numerous anomalies in this theory.
This program of research focused on the psychological processes by which utility judgments are generated. For this purpose, the standard assumption of a homogeneous concept is substituted by the Utilitarian Duality Hypothesis.
In particular, judgments concerning categorical utility (uCat) infer an object's category based on its attributes which may subsequently allow the transfer of evaluative information like feelings or attitudes. In contrast, comparative utility (uCom) depends on the distance to a reference value on a specific dimension of comparison. Importantly, dimensions of comparison are manifold and context dependent.
In a series of experiments, we show that the resulting Dual Utility Model is able to explain several known anomalies in a parsimonious fashion. Moreover, we identify central factors determining the relative weight assigned to both utility components.
Finally, we discuss the implications of the Utilitarian Duality for both, the experimental practice in economics as well as the consequences for economic theorizing. In sum, we propose that the Dual Utility Model can serve as an integrative framework for both the rational model and its anomalies.