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As the animal-to-human interface becomes increasingly narrow, transmission events of zoonotic pathogens between animals and humans become more and more probable. While SARS-CoV-2 already accomplished a spillover infection to humans and is responsible for the current pandemic, the bat H9N2 IAV with so far unknown zoonotic potential was only recently discovered. In order to identify I) the role and potential of a newly discovered, potentially pre-pandemic virus, such as the bat H9N2, or II) possible future prevailing virus mutant variants of an already known pandemic virus, such as SARS-CoV-2, it is important to characterize these emerging viruses in vivo as soon and as good as possible.
The first objective in this dissertation (Publications I and II) therefore deals with the characterization of bat H9N2 and the estimation of its zoonotic or even pandemic potential.
In Publication I, a general susceptibility of directly inoculated Egyptian fruit bats to bat H9N2 was confirmed by successful seroconversion, although exhibiting only moderate viral shedding. All three contact animals remained seronegative, though one contact bat showed slight lesions in the histopathological analysis.
Publication II further addressed the question of the zoonotic potential of this virus. Inoculation of day-old turkey hatchlings demonstrated moderate susceptibility to bat H9N2 infection with a measurable seroconversion, while day-old chicken hatchlings were not susceptible to bat H9N2. Ferrets proved to be highly susceptible to bat H9N2 with high viral shedding, a transmission efficiency rate of 100% to direct contact animals at 2 days post contact, but with only minimal clinical signs. Importantly, the virus demonstrated the ability to evade the MxA-restriction factor and to replicate efficiently in human lung tissue explants. Furthermore, seasonal IAV- and standard IAV-vaccines showed no cross reactivity against the bat-N2 protein in humans. Therefore, further research on such viruses is urgently needed in order to prevent a renewed pandemic situation in the future as caused by SARS-CoV-2.
The second objective in this dissertation dealt with the identification and characterization of emerging SARS-CoV-2 Variants of Concern (VOCs).
Therefore, in Publication III, competitive infection experiments were performed using the Syrian golden hamster, the ferret, and transgenic mouse models (K18-hACE2 and hACE2-KI). These studies revealed replicative and transmissive predominance of Alpha VOC over Beta VOC, but not over SARS-CoV-2 WT in the hamster model, although Beta VOC substantially replicated in the lungs of donor animals. In contrast, the Alpha VOC had an unambiguous replication and transmission advantage over WT SARS-CoV-2 in the ferret and both mouse models. A recombinant SARS-CoV-2 WT-SAlpha virus helped to assign the fitness advantage of this variant particularly to the spike protein-associated mutations.
In Publication IV, in vitro results inferred an early replicative fitness advantage of Omicron BA.1 over Delta VOC, although the opposite was observed in competitively inoculated hamsters, ferrets and naive hACE2-KI mice. In addition, Publication IV demonstrated a disadvantage in transmission for the VOC Omicron BA.1 over the Delta VOC and a lack of susceptibility of ferrets after a single infection with the VOC Omicron BA.1. An mRNA vaccination of K18-hACE2 mice caused a drastic reduction of infectious virus particles in organ material following an infection with a recombinant SARS-CoV-2 WT-SDelta, but not when challenged with the SARS-CoV-2 SOmicron BA.1 clone.
This dissertation includes numerous, comprehensive experimental studies that are generally important for the characterization of emerging, potentially pre-pandemic viruses and may provide crucial information about the future dominance of certain virus variants in an ongoing pandemic. Here, the need for the use of a variety of animal models becomes apparent. By characterizing and classifying potentially zoonotic strains, these methods will help to better prepare for potentially upcoming pandemics and, in the case of a zoonotic or even pandemic event, to better detect and understand the circulating strains and their evolution.
Foraging behavior, neuroanatomy and neuroplasticity in cursorial and stationary hunting spiders
(2023)
The central nervous system (CNS) is the integration center for the coordination and regulation of
all body activities of animals and the source of behavioral patterns, behavioral plasticity and
personality. Understanding the anatomy and the potential for plastic changes of the CNS not only
widens the knowledge on the biology of the respective species, but also enables a more
fundamental understanding of behavioral and ecological patterns. The CNS of species with
different sensory ecologies for example, will show specific differences in the wiring of their CNS,
related to their lifestyle. Spiders are a group of mesopredators that include stationary hunting
species that build webs for prey capture, and cursorial hunting species that do not build capture
webs. These distinct lifestyles are associated with major differences in their sensory equipment,
such as size of the different eyes.
In this thesis, I aimed to answer if a cursorial mesopredator would change its behavior due to
different levels of perceived predation risk, and if this behavior would be influenced by individual
differences (chapter 1); how the visual pathways in the brain of the cursorial hunting jumping
spider Marpissa muscosa differs from that of the nocturnal cursorial hunting wandering spider
Cupiennius salei (chapter 2); to what degree the visual systems of stationary and cursorial hunting
spiders differ and whether CNS areas that process vibratory information show similar differences
(chapter 3); and finally if the CNS in stationary and cursorial hunting spiders shows different
patterns of neuroplasticity in response to sensory input and deprivation during development
(chapter 4).
In chapter 1, I found that jumping spiders adjust their foraging behavior to the perceived level of
risk. By favoring a dark over a light substrate, they displayed a background-matching strategy.
Short pulses of acute risk, produced by simulated bird overflights, had only small effects on the
behavior. Instead, a large degree of variation in behavior was due to among-individual differences
in foraging intensity. These covaried with consistent among-individual differences in activity,
forming a behavioral syndrome. Our findings highlight the importance of consistent amongindividual
differences in the behavior of animals that forage under risk. Future studies should
address the mechanisms underlying these stable differences, as well as potential fitness
consequences that may influence food-web dynamics.
In chapter 2, I found that the visual pathways in the brain of the jumping spider M. muscosa differ
from that in the wandering spider C. salei. While the pathway of the principal eyes, which are
responsible for object discrimination, is the same in both species, considerable differences occur
in the pathway of the secondary eyes, which detect movement. Notably, M. muscosa possesses
an additional second-order visual neuropil, which is integrating information from two different
secondary eyes, and may enable faster movement decisions. I also showed that the tiny posterior
median eye is connected to a first-order visual neuropil which in turn connects to the arcuate body
(a higher-order neuropil), and is thus not vestigial as suggested before. Subsequent studies should
focus on exploring the function of the posterior median eyes in different jumping spider species,
Foraging behavior, neuroanatomy, and neuroplasticity in cursorial and stationary hunting spiders
as they show considerable inter-specific size differences that may be correlated with a differing
connectivity in the brain.
In chapter 3, I described all neuropils and major tracts in the CNS of two stationary (Argiope
bruennichi and Parasteatoda tepidariorum) and two cursorial hunting spiders (Pardosa amentata
and M. muscosa). I found major differences in the visual systems of the secondary eyes between
cursorial and stationary hunting spiders, but also within the groups. A. bruennichi has specialized
retinula cells in two of the secondary eyes, which connect to different higher-order neuropils. P.
tepidariorum has only a single visual neuropil connected to all secondary eyes, and lacks
recognizable mushroom bodies. The neuroanatomy of CNS areas that process mechanosensory
information on the other hand, is remarkably similar between cursorial and stationary hunting
species. This suggests that the same major circuits are used for the processing of mechanosensory
information in both cursorial and stationary hunting spiders. Future studies on functional aspects
of sensory processing in spiders can build on the findings of our study.
In chapter 4, I found that developmental neuroplasticity in response to sensory input differs
between a cursorial (M. muscosa) and a stationary hunting spider (P. tepidariorum). While
deprivation of sensory input leads to a volume increase in several visual and mechanosensory
neuropils M. muscosa, neither sensory deprivation nor sensory enrichment had an effect on the
volume of neuropils in P. tepidariorum. However, exposure to mechanical cues during
development had an effect on the allometric scaling slope of the leg neuropils in both M. muscosa
and P. tepidariorum. Future studies should focus on the genetic and cellular basis of
developmental neuroplasticity in response to sensory input in order to explain the observed
patterns.
Autoclaved aerated concrete (AAC) is a building material that combines heat insulation
properties with sufficient mechanical strength for masonry construction. Compared to
ordinary concrete, the matrix is highly porous (>50%) and hardened by a hydrothermal curing
process at 150°C - 200°C. During this process, quartz sand and portlandite react to form first
calcium silicate hydrates (C-(A)-S-H) with Ca/Si ratios <1.3 and then tobermorite. Especially
tobermorite, which has a much larger crystallite size than C-(A)-S-H, provides improved
mechanical strength. This reaction sequence is influenced by many parameters and
additives of which calcium sulfate is probably the most important. Despite several attempts to
investigate these hydrothermal reactions, the actual reaction mechanism involved when
adding sulfate ions is not fully understood. It has been suggested that the addition of ca.
1.5 wt% significantly improves the mechanical properties due to the enhanced formation and
arrangement of tobermorite in the porous matrix. Since the sulfate content in AAC waste is
exceeding regulatory threshold for low-quality reuse in some countries, the aim of this study
was to investigate in detail the reaction mechanisms involving sulfate addition. Such
knowledge may open up the possibility to improve AAC production and to avoid the need for
sulfate addition. To achieve this goal, this research work focused on investigating the
hydrothermal curing process to determine the sequence of hydrothermal reactions and the
spatial distribution of the phases formed. For this purpose, a new setup for in situ X-ray
diffraction was specifically designed to study hydrothermal reactions and to conduct time
intensive experiments on a normal laboratory diffractometer. In order to quantitatively
evaluate the in situ measurements by Rietveld analysis using TOPAS, it was also necessary
to develop atomistic structure models for C-(A)-S-H phases. This was made possible by
adopting a supercell approach that was previously used to describe turbostratically stacked
clay minerals. The structure models, derived from tobermorite, are placed in an otherwise
empty supercell to simulate the C-(A)-S-H nanostructure. Adopting these methodological
advances, it was possible to obtain absolute phase quantities from in situ data and to track
the reaction kinetics of the hydrothermal curing process. These results were then combined
with ex situ X-ray diffraction and scanning electron microscopy. Confirming previous studies,
the major effect of sulfate ions was the formation and decomposition of hydroxylellestadite. It
was further revealed that C-(A)-S-H formation was delayed during hydroxylellestadite
formation, which is supposed to support the silicate ion diffusion and hence the tobermorite
formation at a stage critical for improved hardening of AAC. This can be linked to the
formation of lower amounts of capillary pores in the range of 1-5 µm, as observed by
scanning electron microscopy, and therefore a lower concentration of inherent defects that
resulted in the improved mechanical properties. This research work highlights how important the spatial distribution of crystallites is for the properties of a building material and how this
distribution can be influenced by small alterations in reaction chemistry.
This dissertation explores and tries to unravel the fundamental basis of G-quadruplex end-folding as well as G-quadruplex interactions with small molecules by thermodynamic and structural approaches. Selective targeting of G-quadruplexes with ligands remains elusive, either because the ligand has
considerable binding affinity for other DNA structures or because it fails to discriminate between different G-quadruplex topologies. Unique structural motifs on the G-quadruplex may enhance or inhibit ligand binding to the G-quadruplex. For such aspects, it is necessary to understand the effect of G-quadruplex motifs or elements on the end-folding in order to better tune certain G-quadruplex topologies as model systems. Importantly for targeting G-quadruplex with ligands, motifs called Quadruplex-duplex (QD) junctions and interfaces are shown to be a binding hotspot
for various G-quadruplex ligands containing an intercalator motif. Binding affinity and selectivity of the ligands are discussed with the support of the NMR structures.
Ion traps such as Paul traps and MR-ToF (multi-reflection time-of-flight) devices are indispensable tools at radioactive ion beam facilities for the preparation of high-quality radioactive ion beams for subsequent experiments or for precise measurements of the properties of radioactive ions, such as nuclear binding energies or nuclear charge radii.
Within the work of this thesis, Doppler- and sympathetic cooling is implemented in a linear Paul-trap cooler-buncher enabling a reduction of the longitudinal emittance of radioactive ion beams resulting in a significant improvement of the ion beam quality. Moreover, a next-generation MR-ToF device is conceptualized in order to achieve isobaric pure beams with a higher ion intensity than state-of-the-art MR-ToF devices can provide. Once fully constructed and commissioned, it will operate at an unprecedented ion beam energy of 30 keV. Both of these advances are expected to become important for a wide range of experimental programs pursued at low-energy branches of RIB facilities ranging from fundamental symmetry studies, nuclear structure, rare isotope studies with antimatter, searches of physics beyond the standard model to material science and the production of medical isotopes.
The next-generation MR-ToF mass separator is based on MIRACLS’ 30-keV MR-ToF device for highly sensitive and high-resolution collinear laser spectroscopy. By storing the ions in the Multi Ion Reflection Apparatus for Collinear Laser Spectroscopy (MIRACLS), the same ion bunch is probed by a spectroscopic laser for thousands of times compared to a single passage in traditional collinear laser spectroscopy (CLS). Dedicated simulation studies show that the accuracy and resolution will be close to traditional single-passage CLS while the sensitivity is significantly enhanced. Hence, measurements of nuclear properties via fluorescence-based CLS of very rare radionuclides as well as highly sensitive and high-precision measurements of electron affinities via laser-photodetachment-threshold spectroscopy of negatively-charged (radioactive) ions will become possible.
First measurement campaigns employing MIRACLS’ 1.5-keV MR-ToF device confirm the outstanding boost in signal sensitivity and provide confidence in the application of the MIRACLS technique for the measurement of scarcely produced radioactive ions that have been so far beyond the reach of conventional techniques. Furthermore, the electron affinity of 35Cl was measured, which is in perfect agreement with the literature value. These measurements will serve as important benchmarks for modern atomic and nuclear theory, especially in its description of nuclear charge radii.
In summary, the implementation of Doppler and sympathetic cooling at RIB facilities, the conceptualization of a 30-keV MR-ToF apparatus for highly selective and high-flux mass separation as well as for highly sensitive and high-resolution fluorescence-based laser spectroscopy and the expansion of the MIRACLS technique for the study of negatively-charged ions will enable unprecedented new measurement opportunities at RIB facilities.
Increasing environmental changes primarily due to anthropogenic impacts, are affecting organisms all over the planet. In general, scientists distinguish between three different ways in which organisms can respond to environmental changes in their habitat: extinction, dispersal and adaptation. An example of organisms which are highly adaptable and can easily cope with new and changing environments are invasive species which are able to colonize new habitats with only few individuals. To successfully survive in their new environment, invasive species adapt fast to novel abiotic and biotic parameters, such as different temperature regimes. Phenotypic plasticity which enables organisms to quickly modify their phenotype to new environmental conditions, explains the success in adaptation of invasive species.
While underlying mechanisms of phenotypic plasticity are not fully understood, one possible “motor” of phenotypic plasticity is epigenetics. Especially DNA methylation could explain the fast changes of the organism’s phenotype due to plasticity when experiencing changing environments, as invasive species do. DNA methylation could even contribute to the adaptation of invasive species via phenotypic plasticity, especially with clonally reproducing species. Methods such as common garden experiments with clonally reproducing species are a useful tool to differentiate between phenotypic plasticity and genetic adaptation because the confusing effects of genetic variation are lowered in clonally reproducing species.
Our overall goal was to evaluate the genetic adaptive potential of New Zealand mud snail (Potamopyrgus antipodarum) populations from Europe since they went through an extreme bottleneck after colonizing Europe only 180-360 generations ago. Seemingly, two different clonal lineages colonized Europe because two 16 s rRNA and cytochrome b haplotypes were found across different European countries, haplotypes t and z. The NZMS is a highly successful invasive species that is nowadays nearly globally distributed. The shells of the NZMS show a habitat-dependent high variability and are a fitness-relevant trait. The high variability in shell morphology is due to both genetic variation and phenotypic plasticity. To disentangle genetic from environmental effects on the shell morphology NZMS, we conducted a common garden experiment. We kept asexually reproducing females from eleven European populations in climate cabinets with three different temperatures to produce offspring. We compared shell size and shape across three generations using the geometric morphometrics approach. Furthermore, we estimated reaction norms, maternal effects, broad-sense heritability, the coefficient of genetic variation (CVA) and evolvability (IA) in shell size and shape across different temperature conditions. Additionally, we investigated the reproductive rate of the parental generation.
Results showed that the shell morphology of the parental generation differed across populations. In contrast, the shell morphology of offspring generations became more similar. The reaction norms of the F1 generation were rather variable across the three temperatures. However, we were able to observe a haplotype-dependent pattern across the reaction norms suggesting a restricted genetic differentiation among NZMS in Europe. We detected high heritability values in size indicating a high genetic influence. Heritability values for shape were lower than in size. Generally, heritability varied slightly depending on temperature. Size seemed to have a higher evolvability than shape. However, the values of all our calculations were very low which indicates that the European NZMS populations are genetically diminished. The reproductive rate of the parental generation was rather haplotype than temperature dependent. In summary, we were able to display that the NZMS is capable to plastically adapt its shell morphology to different temperatures showing significant differences between the two haplotypes. Nevertheless, the low evolvability values indicate that little genetic variation has formed since the arrival of the NZMS in Europe and therefore, European NZMS seem to have a reduced ability to react to selection.
These results implied that phenotypic plasticity is important for the adaptation to different environmental conditions in the NZMS and maybe other molluscan species. Since classical experimental approaches can only describe the resulting phenotypes, we also intended to shed more light on the mechanistic side of environmentally induced phenotypic modifications using DNA methylation analysis. Although molluscs represent one of the most diverse taxa within the metazoan and are found in many different habitats, our knowledge of the DNA methylation in molluscs is scarce. Therefore, we aimed at deepening and summarizing our understanding about DNA methylation in molluscs. Publicly available molluscan genomic and transcriptomic data of all eight mollusc classes was downloaded to search for DNA methyltransferases (DNMTs 1-3) responsible for DNA methylation. Additionally, we estimated the normalized CpG dinucleotide content (CpG o/e) indicating the presence/absence and the frequency of DNA methylation in the genome. The CpG o/e ratio refers to the level of DNA methylation in the genome. Based on the sensitivity of methylated cytosines to mutate into thymine residues, species having a high germline methylation in genomic regions over evolutionary time, also have a lower CpG content, which is called CpG depletion. In contrary, species with a limited germline methylation in genomic regions over evolutionary time, show a higher CpG content and lack CpG depletion. The presence or absence of CpG depletion can be calculated with the CpG o/e ratio. Ultimately, the goal of our analyses was to gain insight into the evolution of methylation in molluscs.
We detected DNMTs in all eight mollusc classes and in most of the species. It is therefore plausible that the last common ancestor of molluscs has already had the enzymatic machinery which is needed for DNA methylation. However, various species did not possess the complete DNMT toolkit indicating evolutionary modification in DNA methylation. In general, we found a wide distribution of the bimodal CpG o/e pattern in six mollusc classes, resulting from CpG depletion. The genes in these groups seem to be divided into genes with a high degree of methylation and genes with a lower degree of methylation. This implies that DNA methylation seems to be rather common in molluscs. Species of Solenogastres and Monoplacophora were not or only sparsely methylated. It seems that those mollusc groups have undergone a reduction in DNA methylation. We hope that our investigations will demonstrate the lacking knowledge in epigenetics of molluscs and encourage scientist to execute and continue genetic studies on molluscs.
Emerging infectious diseases are among the greatest threats to human, animal and plant health as well as to global biodiversity. They often arise following the human-mediated transport of a pathogen beyond its natural geographic range, where host species are typically not well adapted due to a lack of co-evolutionary host-pathogen dynamics. One such pathogen is the fungus Pseudogymnoascus destructans (Pd), which causes White-Nose disease in hibernating bats. While Pd was first observed in North America where it has led to mass-mortalities in some bat species, the pathogen originates from Eurasia where infection is not associated with mortality. Most of the Pd research has focused on the invasive North American range, which likely underestimated the genetic structure of the pathogen and the role it might play in the disease dynamics.
In my work, I therefore evaluated the genetic structure of Pd in its native range with the aim of uncovering cryptic diversity and further use population genetic data to address some key ecological aspects of the disease dynamics. With an extensive reference collection of more than 5,000 isolates from 27 countries I first demonstrated strong differentiation between two monophyletic clades across several genetic measures (multi-locus genotypes, full genome long-read sequencing and Illumina NovaSeq on isolate pools). These findings are consistent with the presence of two cryptic species which are both causative agents of bat White-Nose disease (‘Pd-1’, which corresponds to P. destructans sensu stricto, and ‘Pd-2’). Both species exist in the same geographic range and co-occur in the same hibernacula (i.e., in sympatry), though with specialised host preferences. I further described the fine-scale population structure in Eurasia which revealed that most genotypes are unique to single hibernacula (more than 95% of genotypes). The associated differences in microsatellite allele frequencies among hibernacula allowed the use of assignment methods to assign the North American isolates (exclusively Pd-1) to regions in Eurasia. Hence, a region in Ukraine (Podilia) is the most likely origin of the North American introduction.
To gain further insights into the spatial and temporal dynamics of White-Nose disease on a localised scale, several hibernacula were sampled with high intensity (artificial hibernaculum in Germany and natural karst caves in Bulgaria). Low rates of Pd gene flow were observed even among closely situated hibernacula. This indicates that Pd does not remain viable on bats over summer or it would be frequently exchanged among bats (and hence hibernacula) resulting in a homogenous distribution of genotypes. Instead, bats need to become re-infected each hibernation season to explain the yearly re-occurrence of White-Nose disease. Given the distribution and richness of Pd genotypes on hibrnacula walls and infected bats of the same hibernacula, bats become infected from the hibernacula walls when they return after summer. This means that environmental reservoirs exist within hibernacula (i.e., the walls) on which Pd spores persist during bat absence and which drive the yearly re-occurrence of White-Nose disease. In an experimental setup, I confirmed the long-term viability of Pd spores on abiotic substrate for at least two years and furthermore discovered temporal variations in Pd spores’ ability to germinate. In fact, these variations followed a seasonal pattern consistent with the timing of bats absence (reduced germination) and presence (increased germination) and could indicate adaptations of Pd to the bats’ life-cycle. The infection of bats from environmental reservoirs hence seems to be a central aspect of White-Nose disease dynamics and Pd biology.
Pds ability to remain viable for extended periods outside the host increases its risk of being anthropogenically transported and might have played a role in the emergence of White-Nose disease in North America. The existence of a second species (Pd-2) poses a great additional danger to North American bats considering that its introduction there could lead to deaths and associated population declines in so-far unaffected species given what is known about differing host species preferences in Eurasian bats. Even within the native range of Pd, the movement of Pd between differentiated fungal populations could facilitate genetic exchanges (e.g., through sexual reproduction) between genetically distant genotypes. Such genetic exchanges could lead to phenotypic jumps in pathogenicity or host-species preferences and should hence be prevented.
The native range of a pathogen holds great potential to better understand the genetic and ecological basis of a (wildlife) disease. My work informs about the dangers associated with the accidental transport of Pd (and other pathogens) and highlights the need for ‘prezootic’ biosecurity-oriented strategies to prevent disease outbreaks globally. Once a pathogen has arrived in a new geographic range, and particularly if it has environmentally durable spores (as demonstrated for Pd), it will be difficult/impossible to eradicate. Furthermore, a pathogen’s ability to remain viable outside the host and infect them from environmental reservoirs has been associated with an increased risk of species extinctions and needs to be considered when designing management strategies to mitigate disease impact.
The deep geological underground represents an important georesource for the short-
term storage of renewable energy and the long-term reduction of greenhouse gas emissions. To ensure the economic viability and safety of any subsurface storage project, detailed characterisation of the quality and integrity of the reservoir and its cap rock is required. This characterisation includes the accurate determination of the petrophysical properties, such as porosity and permeability, as well as the potential mineral reactions, such as the dissolution of reactive phases, which may occur during the lifespan of such a project. Clay minerals are common components of many reservoir systems and, depending on their type and structure, can have a significant impact on storage and transport properties. These processes are, however, currently not well understood. In order to address these issues, the main focus of this thesis is on mineralogical analyses using X-ray diffraction (XRD) and microstructural studies using focused ion beam scanning electron microscopy (FIB-SEM) together with micro X-ray computed tomography (µXCT) to gain a better understanding of the influence of clay minerals on reservoir and cap rock properties.
A central part of this thesis focuses on the analysis of clay minerals and pore structures of the Bebertal Sandstone of the Parchim Formation (Early Permian, Upper Rotliegend), which is considered a natural analogue for the tight reservoir sandstones of the North German Basin. Two illite polytypes with a variety of characteristic structures have been identified in the Bebertal sandstone. Disordered 1Md illite forms the majority of the observed structures, which include omnipresent grain coatings, altered permeable feldspar grains and pore-filling meshwork structures. Trans-vacant 1M illite represents the second and youngest generation of authigenic illite and occurs as fibrous to lath-shaped particles that grew into open pore spaces and led to a significant reduction in porosity and permeability during late diagenesis. Based on these results, a model for the formation of illite polytypes in the aeolian layers of the Bebertal sandstone was developed that describes the temporal and spatial evolution of porosity and permeability during diagenesis. Information from this model was then used to improve the prediction of permeability of the Bebertal sandstone based on µXCT pore space models and direct numerical simulations. To achieve this, a micro-scale pore space model was created that allowed the simulation of permeability reduction by clay minerals by including nanoporous illite domains based on a novel morphological algorithm. By performing Navier-Stokes-Brinkman simulations, more accurate predictions of permeabilities with respect to experimentally determined values were obtained compared to conventional Navier-Stokes simulations.
The detailed characterisation of the Bebertal sandstone has shown that natural reservoir rocks are usually complex heterogeneous systems with small-scale variations in texture,
composition, porosity and permeability. Flow-through experiments on the Bebertal sandstone revealed that the coupled geochemical and hydrodynamic processes that occur during the dissolution of calcite could not be predicted by reactive transport models. Therefore, as part of this thesis, a novel approach for developing synthetic sandstones at low temperatures based on geopolymer binder was developed. It is shown that simpler and more homogeneous porous materials can be produced with porosity and permeability values in the range of natural sandstones. These can be used to better understand the dynamic and coupled processes relevant to the storage of renewable energy in reservoir rocks through improved experimental constraints.
The final part of this thesis reports on a detailed clay mineral and pore space study of
three shale formations and one mudstone that were identified as potential seals for the Mt. Simon sandstone reservoir in the Illinois Basin. During the Illinois Basin - Decatur Project, this reservoir was used for the sequestration of one megaton of supercritical carbon dioxide. In order to better assess the quality of the sealing units and to better understand the role of the intergranular clay mineral matrix as potential pathway for fluid migration, a multi-scale evaluation was conducted that included thin section analysis, quantitative evaluation of minerals by scanning electron microscopy (QEMSCAN), mercury intrusion capillary pressure (MICP) measurements, quantitative XRD and high-resolution FIB-SEM. The results allow for the classification of the studied formations into primary and secondary seals and emphasise the importance of three-dimensional clay-mineral-related pore structure characterisations in cap rock studies. XRD proved the most reliable method for the identification and quantification of clay minerals in the studied cap rocks and mudstones. In contrast, FIB-SEM and QEMSCAN provided the spacial constraints for reconstructing fluid flow pathways within the clay mineral matrix.
Overall, this thesis highlights the importance of the precise identification of clay minerals in geological reservoirs and their cap rocks. It also illustrates the need for three-dimensional characterisation and modelling of the associated small pore structures for an improved understanding of the rocks diagenetic history as well as the prediction of the transport and storage properties of these crustal reservoir systems.
Underground hard coal mining operations irreversibly disrupt the pre-existing mechanical equilibrium of the geological media. The employment of high-recovery methods modifies the stress field of the sedimentary sequence, generating movement and faulting of the rock layers above and below mined seams. These new fracture zones do affect the original conditions of the hydrogeological system by modifying flow pathways and increasing the permeability of the rock sequence. Moreover, the surface area of rock exposed to air and water is increased, conditioning the water-rock interaction. Despite this rather clear conceptualization, flow and reactive transport processes in fractured overburdens are rarely modeled simultaneously. Discrete setups that consider fractures and porous matrix require extensive characterization of both media, which is impractical for regional case studies. As a result, most post-mining models explicitly ignore fracture structures by employing the equivalent porous approach or even both media with lumped parameter models. However, omitting either medium represents a delicate simplification, considering that mining-related fractures control the rate and direction of water flow within moderately permeable but relatively highly porous rock sequences.
In this dissertation, the specific contribution of fractured and matrix continua to the transient discharge and water quality of a post-mining coal zone is quantified and evaluated. For this purpose, dual and multiple interacting continua models are employed to simulate fluid flow and reactive mass transport in fractured and variable water-saturated rock sequences. The effectiveness of the models is evaluated by simulating the origin, generation and transport of acid mine drainage (i.e., water with elevated concentrations of hydrogen, iron, sulfate and chloride) within the shallow overburden of the Ibbenbüren Westfield. Compared to other coal districts in Germany, this area is strongly delimited by the local geology and topography, resulting in a well-defined hydrogeological system to test the models. Petrographic and chemical analyses performed on core samples from the area show the strong influence of mining-derived fractures on the water-rock interaction within the Carboniferous sequence. The presence of oxidized pyrite along with amorphous iron hydroxide phases in weathering fronts on both sides of the fractures demonstrates the exchange of solutes and gases between the fractured and the porous matrix media.
Based on the previous evidence, the TOUGHREACT software is employed to characterize flow and reactive transport processes in the Westfield. However, each of the two processes is simulated at separate stages to have more control in the adjustment of sensitive parameters for which little information is available. For the flow component, a dual continuum model, with Richard’s equations is used to characterize the unsaturated water flow in both fractured and matrix media. Under this approach, the model adequately reproduces the bimodal flow behavior of the discharges measured in the mine drainage for the years 2008 and 2017. Simulation results show how the fractured continuum generates intense discharge events during the winter months while the rock matrix controls smooth discharge limbs in summer, when water is slowly released back to the fractures. With the flow component calibrated, the second part of the study incorporates the geochemical processes into the model based on actual data from the rock samples. Their simulation requires extending the two-continuum setup to a multiple continua model with five nested block strings: one for the fractures and four for the rock matrix. This further subdivision prevents under-representations of kinetic reactions with short equilibrium length scales and numerical instabilities due to lack of chemical and flow gradients. As a result, the new multiple continua model provides good agreement with respect to long- and short-term concentrations and discharge trends measured in the mine drainage. The flow of oxygen and meteoric water through the fractured continuum leads to a high and steady release of hydrogen, iron and sulfate ions derived from pyrite oxidation in the matrix continua closest to the fractures. Moreover, high chloride concentrations result from the mixing and gradual release of relatively immobile solutes in the matrix as they interact with percolating water in the fracture. Both findings are equally congruent with the reactive pyrite oxidation and iron hydroxide precipitation fronts identified in the fractured core samples.
In the end, the multiple continua models, the simulation procedure and the results of the benchmark and sensitivity analysis scenarios developed for the Westfield pave the way for the application of the approach in other mining zones. The first candidate emerges in the Ibbenbüren Eastfield, where a coupled elemental-isotopic approach included in this thesis has confirmed that water-conducting fracture zones are primary elements for solute generation and transport in the first 300 meters of the overburden. In the latter case, calibration and verification of the models can be complemented with measurements of δ34S in sulfates and δ18O, δ2H, and Tritium in water.
Introduction
The concept of thermal ablation has proven a minimally invasive alternative or accompaniment to conventional tumour therapy. Patients with hepatic primary tumours or metastases are able to profit from it. Several modalities of thermal ablation exist, including radiofrequency ablation, microwave ablation and laser ablation. They differ in regards to their indications and their physical backgrounds, yet they all share the same aim: the hyperthermic ablation of tumorous target tissue.
At this point in time the maximum ablation diameter attained in a singular session using a singular applicator is about 30 mm. The maximum attainable volume is about 23 cm3. However, the mean and median of hepatic lesions exceed that number with about 50 mm. Most hepatic tumours therefore cannot be easily ablated in toto.
One of the main limitations of thermal ablation is the periprocedural transformation of vital tissue into a boundary layer. This boundary layer prevents efficient energy transmission into peripheral tissue and thus limits the potential of thermal ablation. The boundary layer is usually located centrally around the ablation applicator. In laser ablation the formation of this boundary layer is called carbonisation.
A technically simple, yet potentially effective approach to delay or prevent the formation of this boundary layer is the usage of a spacer. This perfused spacer cools the central zone surrounding the applicator. Therefore central temperatures remain beyond the point of carbonisation.
Methods
The development of two spacer prototypes took place in cooperation with the AG “Experimentelle Radiologie” of the University Clinic Charité. The first fully closed prototype featured an internal circulation of cooling fluid without tissue perfusion. The second open prototype perfused into tissue through an opened tip.
The conduct of this study included ex vivo experiments on bovine livers (n = 15) by means of laser ablation. Ablation diameter and ablation volume were recorded through MR-guided volumetry and manual displacement volumetry. The mean values of diameter and volume that were recorded when the stand-alone applicator system was used were then compared to the mean values recorded when using the closed spacer-supported applicator system and the open spacer-supported applicator system. The difference in values between the three applicator types were then examined for statistical significance using SPSS.
To exclude covariates a preliminary experiment was conducted which aimed to maximise power input of the laser and time interval while minimising the chance of carbonisation. For that, one of the variables was increased in intervals and the ablation diameter of all three applicator types was measured until carbonisation occurred.
Results
In the preliminary experiment it was found that following the increase of the pre-set power input of the laser a proportional increase of ablation diameter followed. However when increasing power input above 25 Watt almost instantaneous carbonisation of the central tissue occurred. This was the same for all three applicator types.
When increasing the time interval > 10 minutes the stand-alone applicator system showed central carbonisation, which was not the case when using the closed spacer-supported applicator system or the open spacer-supported applicator system. The two spacer prototypes only experienced carbonisation when a time interval of > 25 minutes was set. Thus the comparison of all three applicator types was conducted at 25 Watt and 10 minutes, whereas the comparison between the closed spacer-supported applicator system and the open spacer-supported applicator system was conducted at 25 Watt and 25 minutes.
During the first experiment the stand-alone applicator system achieved mean values of 37.50 mm ablation diameter and 23.61 cm3 ablation volume. This was a statistically significant (p < 0.001) increase to the values either spacer was able to attain: the closed spacer-supported applicator system recorded a mean value of 28.67 mm ablation diameter and 18.12 cm3 ablation volume, whereas the open spacer-supported applicator system recorded a mean value of 31.00 mm ablation diameter and 18.49 cm3 ablation volume. However, setting a longer time interval was not possible when the stand-alone applicator system was used for ablation. Due to this, a second experiment comparing mean ablation diameter and volume between the two spacer prototypes followed.
During the second experiment with a time interval of 25 minutes the closed spacer-supported applicator system attained a mean value of 52.07 mm ablation diameter and 75.25 cm3 ablation volume. These values showed a statistically significant (p < 0.001) difference in comparison to the open spacer-supported applicator system with mean values of 47.60 mm ablation diameter und 72.20 cm3 ablation volume.
Discussion
Within the framework of this study it was proven that the presence of a spacer between laser applicator and hepatic tissue was able to achieve a significant increase in ablation diameter and ablation volume. By using a closed spacer an increase in volume by a 3.19 factor of change was possible. The open spacer obtained an increase in volume by a 3.06 factor of change. The concept of using a spacer in thermal ablation as a proof of concept study is therefore valid and suitable for further pre-clinical studies.