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Sexual selection favours traits that confer a competitive advantage in access to mates and to their gametes. This results in males evolving a wide array of adaptations that may be conflictual with female’s interests and even to collateral negative effects on female’s lifespan or reproductive success. Harmful male adaptations are diverse and can be extreme. For example, males of various species evolved adaptations that incur physical damage to the female during copulation, referred to as traumatic mating. Most of these adaptations provide males with a competitive fertilization advantage due to the injection of sperm or non-sperm compounds through the wound. In the spider taxonomical literature, alterations of external genital structures have been reported in females and may result from male inflicted damage during copulation. Contrarily to other cases of traumatic mating, the transfer of sperm or non-sperm compounds does not seem to be the target of selection for external female genital mutilation (EFGM) to evolve. Therefore, investigating EFGM may provide valuable information to extend our understanding of the evolution of harmful male adaptations. In this thesis, I explore this newly discovered phenomenon and combine empirical and theoretical approaches to investigate the causes and consequences of EFGM evolution from male and female perspectives. My findings suggest that EFGM is a natural phenomenon and is potentially widespread throughout spider taxa. I demonstrate the proximal mechanism by which the male copulatory organ mutilates the external female genitalia during genital coupling and show that the mutilation results in full monopolization of the female as mutilated females are unable to remate. Using a theoretical approach, I investigated the conditions for the evolution of EFGM. The model developed suggests that EFGM evolution is favoured for last male sperm precedence and for costs to females that can be relatively high as the male-male competition increases. I present the results of physiological measurements that suggest there is no physiological cost of genital mutilation resulting from healing and immune responses for the female. Finally, I report the results of a behavioural experiment that suggest that females have control over the mutilation and selectively allow or avoid mutilation. These findings suggest that EFGM benefits males by securing paternity, that males and females may have evolved to reduce the costs incurred by the female and that female choice may also play a role in EFGM evolution.
The rapid anthropogenic climate change that is projected for the 21st century is predicted to have severe impacts on ecosystems and on the provision of ecosystem services. With respect to the longevity of trees, forestry in particular has to adapt now to future climate change. This requires profound multidisciplinary knowledge on the direct and indirect climate sensitivity of forest ecosystems on various spatial scales. Predictions on growth declines due to increasing drought exposition during climate change are widely recognized for European beech (Fagus sylvatica L.), which is the major forest tree in European temperate deciduous forests. However, research from other continents or other biomes has shown that winter climate change may also affect forest growth dynamics due to declining snow cover and increased soil cooling. So far, this winter cold sensitivity is largely unexplored in Europe. Thus, particularly focussing on forest growth dynamics and winter cold sensitivity, the goal of this PhD-project was to explore how climate sensitivity of forest ecosystems differs regionally. By doing so, the project aimed to deliver insights about possibilities and limits of upscaling regional knowledge to a global understanding of climate sensitivity. To achieve these goals, this PhD-project integrated five studies (Manuscripts 1–5) that investigated the climate sensitivity of biogeochemical cycles, plant species composition in forests, and forest growth dynamics across spatial scales. In particular, a large-scale gradient-design field experiment simulated the influence of winter climate change on forest ecosystems by snow cover and soil temperature manipulations (Manuscript 1). This study indicated that soil cooling and decreased root nutrient uptake may indirectly reduce growth of adult forest trees. Moreover, this study indicated uniform ecological sensitivity to soil temperature changes across sites along a large winter temperature gradient (ΔT = 4 K across 500 km), irrespective of the site-specific history of snow cover conditions, which motivates upscaling from local winter climate change studies to the regional scale. Although regional climate drives growth of adult forest trees, local factors, such as site-specific edaphic conditions, might control plants in the forest understory. This assumption was tested by mapping the forest understory composition along the same winter temperature gradient as introduced above (Manuscript 2). Across sites, this study found that edaphic conditions explained the spatial turnover in the forest understory composition more than climate, which might moderate direct climate change impacts on the forest understory composition. However, edaphic conditions, forest structure, and climate are linked by triangular interactions. Thus, climate change might still indirectly affect the forest vegetation dynamics. Moreover, a dendroecological study focussed on the same winter temperature gradient from central to cold-marginal beech populations as above in order to identify gradual changes in summer drought and winter cold sensitivity in tree growth (Manuscript 3). Towards the cold distribution margin, the influence of drought on tree growth gradually decreased, while growth reductions were increasingly related to winter cold due to harsher winter climate. By a large-scale dendroecological network study assessed the relationship of growth dynamics to climate and reproductive effort in beech forests across Europe (Manuscript 4). Indeed, this study found the general pattern across the distribution range of beech that high temperature controlled growth indirectly via resource allocation to reproduction. However, the strong, direct drought signal that could be generally detected from dry-marginal to central populations vanished towards the cold-marginal populations, where the more focussed study of Manuscript 3 identified a stronger relationship of tree growth to winter cold. Further extending the scope of this PhD-thesis to global scales, litter decomposition rates were assessed across biomes (Manuscript 5). This study found a robust relationship between climate and decomposition rates, but it also demonstrated large within-biome variability on a local scale. These local scale differences might depend on habitat conditions that, in turn, could be modulated by climate change, which calls for a better exploration of indirect climate sensitivity. In conclusion, this PhD-thesis highlighted that multidisciplinary research can advance the understanding of ecological interactions in forest ecosystems under changing climate scenarios. In this PhD-project, a winter climate change experiment, where site-representative target trees were selected by means of dendroecology, contributed to a mechanistic understanding of winter cold sensitivity in forest growth dynamics. Dendroecological investigations then put the findings in a broader temporal and spatial context by describing local climate sensitivity of tree growth on different spatial scales. This thesis further shows that global generalizations about the relationship of climate and ecological processes in ecosystem models have to be critically reviewed for the need of local and regional adjustment because these processes might experience considerable regional- or local-scale variation. However, this thesis reports uniform sensitivity of ecological processes to altered winter soil temperature regimes across a large winter temperature gradient. Thus, upscaling from insights of previous winter climate change experiments to regional scales is encouraged.
Chemosymbiosis in marine bivalves – unravelling host-symbiont interactions and symbiotic adaptions
(2018)
Symbiosis essentially forms the cornerstone of complex life on earth. Spearheading
symbiosis research in the last few decades include the exploration of diverse mutualistic
animal-bacterial associations from marine habitats. Yet, many facets of symbiotic
associations remain under-examined. Here we investigated marine bivalves of the genera
Bathymodiolus and Codakia, inhabiting hydrothermal vents and shallow water
ecosystems, respectively, and their bacterial symbionts. The symbionts reside
intracellularly within gill epithelia and supply their host with chemoautotrophically fixed
carbon. They oxidize reduced substrates like sulfide (thiotrophic symbionts) and methane
(methanotrophic symbionts) from surrounding fluids for energy generation. The nature of
interactions between host and symbiont at the metabolic and physical level, as well as
between the holobiont and its environment remain poorly understood. In vitro cultivations
of both symbiont and host are difficult till date, hampering the feasibility of targeted
molecular investigations.
We bypassed culture-based experiments by proteogenomically investigating physically
separated fractions of host and symbiont cell components for the bivalves Bathymodiolus
azoricus, Bathymodiolus thermophilus and Codakia orbicularis. Using these
enrichments, we sequenced the symbionts’ genomes and established semi-quantitative
host-symbiont (meta-) proteomic profiles. This combined approach enabled us to resolve
symbiosis-relevant metabolic pathways and adaptations, detect molecular factors
mediating physical interactions amongst partners and to understand the association of
symbiotic traits with the environmental factors prevailing within habitats of the respective
bivalve.
Our results revealed intricate metabolic interdependence between the symbiotic partners.
In Bathymodiolus, these metabolic interactions included (1) the concentration of essential
substrates like CO2 and thiosulfate by the host for the thiotrophic symbiont, and (2) the
host’s replenishment of essential TCA cycle intermediates for the thiotroph that lacks
biosynthetic enzymes for these metabolites. In exchange (3), the thiotroph compensates
the host’s putative deficiency in amino acid and cofactor biosynthesis by cycling aminoacids
derived from imported precursors back to the host. In case of Codakia orbicularis,
the symbionts may metabolically supplement their host with N-compounds derived from
fixation of molecular nitrogen, a trait that was hitherto unknown in chemosynthetic
thiotrophic symbionts.
Individual proteogenomic investigations of the bivalves Bathymodiolus azoricus and
Bathymodiolus thermophilus showed that their symbionts are able to exploit a multitude
of energy sources like sulfide, thiosulfate, methane and hydrogen to fuel chemosynthesis.
The bivalves and their thiotrophic symbionts, however, are particularly adapted to
thiosulfate-utilization, as indicated by mitochondrial production and concentration of
thiosulfate by host and dominant expression of thiosulfate oxidation enzymes in the
symbiont. This may be advantageous, because thiosulfate is less toxic to the host than
sulfide. The central metabolic pathways for energy generation, carbon and nitrogen
assimilation and amino acid biosynthesis in thiotrophic symbionts of both Bathymodiolus
host species are highly conserved. Expression levels of these pathways do, however, vary
between symbionts of both species, indicating differential regulation of enzyme synthesis,
possibly to accommodate differences in host morphology and environmental factors.
Systematic comparison of symbiont-containing and symbiont-free sample types within
and between B. azoricus and B. thermophilus revealed the presence of ‘symbiosisspecific’
features allowing direct host-symbiont physical interactions. Host proteins
engaged in symbiosis-specific functions include 1) a large repertoire of host digestive
enzymes predominant in the gill, possibly facilitating symbiont population control and
carbon acquisition via direct enzymatic digestion of symbiont cells and 2) a set of host
pattern-recognition receptors, which may enable the host to selectively recognize
pathogens or even symbionts “ripe” for consumption. Symbiont proteins engaged in
symbiosis-specific interactions included 3) an enormous set of adhesins and toxins,
putatively involved in symbiont colonization, persistence and host-feeding.
Bathymodiolus symbionts also possess repertoires of CRISPR-Cas and restrictionmodification
genes for phage defense that are unusually large for intracellular symbionts.
Genomic and proteomic comparisons of thiotrophic symbionts of distinct Bathymodiolus
host species from different vent sites revealed a conserved core genome but divergent
accessory genomes. The B. thermophilus thiotroph’s accessory genome was notably more
enriched in genes encoding adhesins, toxins and phage defense proteins than that of other
Bathymodiolus symbionts. Phylogenetic analyses suggest that this enrichment possibly
resulted from horizontal gene acquisition followed by multiple internal gene duplication
events. In others symbionts, these gene functions may be substituted by alternate
mechanisms or may not be required at all: The methanotrophic symbionts of B. azoricus,
for example, has the genetic potential to supplement phage defense functions. Thus, the
accessory genomes of Bathymodiolus symbionts are species- or habitat-associated,
possibly facilitating adaptation of the bivalves to their respective micro- and macroenvironments.
In support of this, we show that symbiont biomass in B. thermophilus,
which hosts only one thiotrophic symbiont phylotype, is considerably higher than in B.
azoricus that hosts thiotrophic and methanotrophic symbionts. This suggests that different
symbiont compositions in each species produce distinct microenvironments within the
holobiont.
Our study presents an exhaustive assessment of the genes and proteins involved in this
bivalve-microbe interaction, hinting at intimate host-symbiont interdependencies and
symbiotic crosstalk between partners. The findings open novel prospects for
microbiologists with regard to mechanisms of host-symbiont interplay within highly
specialized niches, origin and distribution of prokaryote-eukaryote interaction factors
across both mutualistic and pathogenic associations.
This dissertation focusses on the numerical modelling of resonant destabilization of Alfvén eigenmodes by fast ions in fusion plasmas. It especially addresses non-linear simulations of stellarator plasmas in which particle collisions are retained. It is shown that collisions are required for a realistic description of Alfvén waves in plasmas relevant to nuclear fusion.
We start by carefully verifying the implementation of the collision operators into the electromagnetic version of the gyro-kinetic delta-f particle-in-cell code EUTERPE. After these initial benchmarks are completed successfully, the code is in a position to be applied to realistic tokamak and stellarator scenarios.
Since every collision operator needs to fulfil conservation laws, a momentum-conserving version of the pitch-angle scattering operator is implemented. This is in particular important for neoclassical transport simulations aimed at computing flux-surface variations of the electrostatic potential in stellarators.
Using the simplified CKA-EUTERPE model (employing a fixed-mode-structure approximation), we perform non-linear simulations in tokamaks and stellarators. We show that the non-linear dynamics of fast-ion-driven Alfvén eigenmodes is significantly influenced by collisions. They have the potential to enhance the saturation level and to affect the frequency chirping of the modes.
It is thus concluded that collisions play an essential role in determining Alfvén-eigenmode-induced fast-ion transport - an important issue for future fusion devices. In order to address this issue the CKA-EUTERPE model is extended to evolve multiple modes at the same time. First results of this multi-mode version (which enhances the level of realism of the simulations) are shown in the Appendix of the thesis.
Cerebral palsy (CP) remains one of the most common debilitating diseases in the world.
Factors such as neuromuscular incoordination, use of soft diet and delayed oral
clearance of food make maintenance of optimum oral hygiene a challenging task in
these children. The compromised oral hygiene in turn make these children highly
vulnerable to dental disease. Maintaining optimal oral/dental health in CP children is of
utmost importance as these children usually suffer from several associated general
health problems in addition to their primary condition. Poor dental health further
compromises their general health. Nevertheless, CP children often suffer from dental
diseases including dental caries more than healthy children. This underscores the need
for improvement in oral health of the CP children. The CP children are dependent on
those around them for their oral hygiene maintenance and dietary intake. CP children
spend most of their time with health care workers in special centers for them or with
their parents/care takers at home. Therefore, the attitude of special health care workers
and parents towards their dental health is of prime importance. The purpose of this
project included to determine the attitude of special health care workers towards their
dental health and oral health comprehension by parents of CP children. In addition, a
study on caries experience of CP children and associated risk factors was also completed.
The final objective was to identify various potential areas of improvement with ultimate
goal of improving dental health of the CP children.
The study involving special health care workers in a Disabled Children’s Center revealed
that oral health knowledge and practices among the workers could generally be labeled
as satisfactory, however some weak areas (such as trend towards symptom-oriented
utilization of oral health care and lack of knowledge about fluoridated water) were
identified. There is a need to enhance the workers’ knowledge in these areas.
The study involving parents of the CP children showed mixed results. Some areas of
strong oral health comprehension (such as importance of good dental health, harmful
effects of sweetened foods), others satisfactory (such as need for routine dental visits,
use of fluoride) and some weak areas (use of flavored fizzy drinks, bottled/canned juices
and sweetened/flavored milks, seeking early treatment) were identified among parents
of CP children. The results strongly indicated a need for enhanced efforts towards
improvement of oral health comprehension in the parents of the CP children.
The study about caries experience and risk factors in CP children has provided useful
information in an area where literature has been scarce. Almost all the studied children
had clinical dental caries, and most of the caries were untreated. Very few children in
the present study had optimal oral hygiene. This study confirmed the strong correlation
between high dental caries experience and poor oral hygiene. Routine dental check-up
visits and topical fluoride application clearly resulted in lower caries experience. Bottled
juices and crispy potato chips were the two predictors for high caries experience.
As stated before, the goal of the project was to identify various potential areas of
improvement in oral health attitude of special health care workers, oral health
comprehension of the parents of CP children and risk factors for dental caries in CP
children. It is contemplated that by addressing the identified weak areas, an
improvement in dental health and care of the CP children is expected. It is also expected
that the collected information will help in improvement of clinical preventive as well as
restorative services for the CP children. CP children and their parents lead a challenging
life. This project was an effort to assist these children and their parents/care takers with
ultimate goal of improving their oral health and in turn their overall quality of life.
There is an increasingly urgent need to understand and predict how organisms will cope with the environmental consequences of global climate change. Adaptation in any form can be mediated by genetic adaptation and/or by phenotypic plasticity. Disentangling these two adaptive processes is critical in understanding and predicting adaptive responses to environmental change. Usually, disentangling genetic adaptation from phenotypic plasticity requires common garden experiments conducted under controlled laboratory conditions. While these experiments are powerful, it is often difficult to translate the results into natural populations and extrapolate to naturally occurring phenotypic variation. One solution to this problem is provided by the many examples of invasive species that exhibit wide phenotypic variation and that reproduce asexually. Besides selecting the appropriate in situ model, one must carefully choose a relevant trait to investigate. Ecomorphology has been a central theme in evolutionary biology because it reflects how organisms can adapt to their environment through their morphology. Intraspecific ecomorphological studies are especially well suited to identify adaptive pressures and provide insights into the microevolutionary mechanisms leading to the phenotypic differentiation.
One excellent candidate for an intraspecific ecomorphological study aiming to understand adaptation through genetic adaptation and phenotypic plasticity is the invasive New Zealand mudsnail Potamopyrgus antipodarum Gray (1853). This ovoviviparous snail features high variability in shell morphology and has successfully invaded a wide range of fresh- and brackish water habitats around the world. The evolutionary and ecological situations in this species’ native and invasive ranges is drastically different. In New Zealand, P. antipodarum’s native range, sexual and asexual individuals coexist and experience selective pressure by sterilizing endoparasites. By contrast, only a few asexual lineages have been established in invaded regions around the globe, where parasite infection is extremely rare. Here, we took advantage of the low genetic diversity among asexually reproducing European individuals in an attempt to characterize the relative contribution of genetic variation and phenotypic plasticity to the wide variation in shell morphology of this snail.
Analysing the ecomorphology of 425 European P. antipodarum in a geometric-morphometric framework, using brood size as proxy for fecundity, and mtDNA and nuclear SNPs to account for relatedness and identify reproductive mode, we hypothesized that 1) shell variation in the invasive range should be adaptive with respect to colonization of novel habitats, and 2) at least some of the variation might be caused by phenotypic plasticity. We then expanded our ecomorphological scope by analysing 996 native specimens, expecting 1) genetic and morphological diversity to be higher in the native range compared to invaded regions; 2) morphological diversity to be higher in sexual compared to asexual individuals according to the frozen niche hypothesis; and 3) shell morphology to be habitat specific, hence adaptative. In a last part, we used computational fluid dynamics simulations to calculate relative drag and lift forces of three shell morphologies (globular, intermediate, and slender). Here, we tested the overall hypothesis that shell morphology in gastropods is an adaptation against dislodgement through lift rather than drag forces, which would explain the counterintuitive presence of wider shells with shorter spires in lotic environments. With a final flow tank experiment, we tested the specific hypothesis that the dislocation velocity of living snails is positively linked to foot size, and that the latter can be predicted by shell morphology, in particular the aperture area as assumed by several authors.
As expected, we found genetic and morphological diversity to be higher in native than in invasive snails, but surprisingly no higher morphological diversity in sexual versus asexual individuals. The relationships between shell morphology, habitat, and fecundity were complex. Shape variation was primarily linked to genetic relatedness, but specific environmental factors including flow rate induced similar shell shapes. By contrast, shell size was largely explained by environmental factors. Fecundity was correlated with size, but showed trade-offs with shape in increasingly extreme conditions. With increasing flow and in smaller habitats such as springs, the trend of shell shape becoming wider was reversed, i.e. snails with slender shells were brooding more embryos. This increase in fitness was explained by our CFD simulations: in lotic habitats, slender shells experience less drag and lift forces compared to globular shells. We found no correlation between foot size and shell shape or aperture area showing that the assumed aperture/foot area correlation should be used with caution and cannot be generalized for all aquatic gastropod species. Finally, shell morphology and foot size were not related to dislodgement speed in our flow tank experiment. We concluded that the relationship of shell morphology and flow velocity is more complex than assumed. Hence, other traits must play a major role in decreasing dislodgement risk in stream gastropods, e.g. specific behaviours or pedal mucus stickiness. Although we did not find that globular shells are adaptations decreasing dislodgement risk, we cannot rule out that they are still flow related adaptations. For instance, globular shells are more crush-resistant and might therefore represent a flow adaptation in terms of diminishing damage caused by tumbling after dislodgement or against lotic specific crush-type predators.
At this point, we can conclude that shell morphology in P. antipodarum varies at least in part as an adaptation to specific environmental factors. This study shows how essential it is to reveal how plastic, genetically as well as phenotypically, adaptive traits in species can be and to identify the causal factors and how these adaptations affect the fitness in order to better predict how organisms will cope with changing environmental conditions.
Many intrastate conflicts see more than one mediation effort. As the sequencing of mediation efforts in intrastate conflicts is neglected in existing research, this project addresses the question how and why previous mediation outcomes have an impact on subsequent mediation onset and subsequent mediation success. Drawing on bargaining theory, it is argued that governments and rebel groups engaged in intrastate conflicts account for previous mediation outcomes in their cost-benefit calculations on subsequent mediation onset, and, should subsequent talks set on, their behaviour during subsequent mediation efforts, which influences subsequent mediation success.
If mediation did not produce an agreement, the persistence of the private information problem is noted by the conflict parties. Yet, no new costs of mediation are uncovered, and hence the conflict parties will agree to subsequent mediation onset. Being aware of the necessity to overcome the private information and the commitment problem, the mediator will seek to account for the concerns of the conflict parties, and thereby work towards subsequent mediation success. If mediation produced a partial agreement, the benefits of mediation are underlined. The private information and the commitment problem seem solved with the assistance of the mediator. Subsequent mediation onset and eventually subsequent mediation success are observed. If a mediated agreement was reneged on by the rebel group, the government will refrain from further talks, pointing out the rebel group’s illegitimacy. If the government reneged on the agreement itself, it will also decide against subsequent mediation, as the previous mediation effort produced an agreement which did not mirror the power distribution in the dyad. Costs of mediation, which outweigh the benefits of it, were highlighted. Rebel groups will opt for mediation regardless which side reneged on an agreement. As both governments and rebel groups have to agree to subsequent mediation for talks to set on, subsequent mediation onset is unlikely if a mediated agreement was reneged on. Given the onset of subsequent mediation after a mediated agreement was reneged on, subsequent mediation success is unlikely to be observed, due to the previously underlined hazards of sharing private information and the persistence of the commitment problem.
The theoretical argument is tested with a mixed-methods approach. The quantitative analysis accounts for mediation efforts in African intrastate conflicts between 1993 and 2007. The qualitative analysis scrutinises the mediation efforts between the Government of Uganda and the Lord’s Resistance Army. The results of both parts of analysis largely go hand-in-hand, and show that partial mediation success and mediation which did not produce an agreement have a positive impact on subsequent mediation onset in particular, but also on subsequent mediation success. Reneged on mediated agreements have a severe negative impact on subsequent mediation onset and subsequent mediation success though.
By addressing the question which impact previous mediation outcomes have on subsequent mediation efforts, this research shows that mediation which does not produce an agreement is not the mediation outcome which needs to be feared by the international community. Instead, the deteriorating impact of short-lived agreements, a mediation outcome which is unaccounted for in existing research as an explanatory variable, becomes apparent. This research has important policy implications, especially for mediators, as it suggests that accepting mediation efforts to end without an agreement is more conducive for subsequent mediation efforts. Moreover, this research points towards the necessity of including reneged on agreements in mediation research as an explanatory variable more extensively, thereby shedding more light onto the dynamics at play in consecutive mediation efforts.
Myxomycetes are protists belonging to the super-group Amoebozoa. The traditional taxonomic system, which is now largely outdated by molecular studies, recognizes five orders: Liceales, Trichiales, Physarales, Stemonitales and Echinosteliales. Molecular phylogenies revealed two basal clades: Physarales and Stemonitales (the so-called dark-spored myxomycetes) are the first; the other above-mentioned orders form the second (the bright-spored myxomycetes). However, except for Echinosteliales none of the traditional orders appears to be monophyletic in the traditionally used delimitation. The dark-spored myxomycetes encompass the majority of the described morphospecies. Due to the high genetic divergence in DNA sequences between the bright- and dark-spored myxomycetes, only the latter are considered in this dissertation. Historically myxomycetes have been described as fungi, due to their macroscopically visible fructifications which, though considerably smaller, resemble those of fungi. These fruit bodies provide enough morphological traits to support a morphological species concept with currently ca. 1000 species described. Therefore diversity studies of myxomycetes have been conducted for over 200 years and a substantial body of data on ecology and distribution of these fructifications exist. From these studies myxomycetes are known to form often distinct communities across terrestrial ecosystems with highly specific habitat requirements, such as snowbanks (nivicolous), herbivore dung (coprophilous) or decaying wood (xylophilous). However knowledge on the myxamoebae – the trophic life stage of the myxomycetes – is very scarce. Only recent advances in molecular techniques such as direct species identification based on DNA sequences from environmental samples (ePCR), have made studies of myxamoebae (and other microbes) possible. From these first molecular based studies myxomycetes are currently estimated to account for between 5 to almost 50% of all soil amoebae, and have been shown to be present in a wide variety of soils. To fully take advantage of these new methods, a molecular DNA marker needs to be established as well as a reference sequence database. The usability of a DNA marker gene depends on its ability to separate species by a distinction between intra- and interspecific divergence between sequences of the same and related species, the so-called ‘barcoding gap’.
The first part of this thesis (article I and II) deals with the subject of establishing such a DNA marker and database, and in doing so touches upon the subject of ‘what is a myxomycetes species?’
A total of 1 200 specimens were compiled into a reference database (the largest database to date of dark-spored myxomycetes). The genetic distance from sequence-to-sequence was used to assess genetic clade structures within morphospecies and putative biospecies (sexually isolated linages) were identified. The result was an estimate of hidden diversity, exceeding that of described morphospecies by 99%. The optimum sequence similarity threshold for OTU-picking (genetic species differentiation, denoted Operational Taxonomic Unit) with the used SSU marker was identified as 99.1% similarity.
The second part of this thesis (article III and IV) presents ecological studies conducted with NGS (ePCR) in which the established threshold and database are applied and are demonstrated to provide reliable and novel insights into the soil myxamoebae community. It is investigated whether the occurrence of fruit bodies reflects the distribution of soil myxamoebae, and the research questions ‘do myxomycetes show broader realized niches as soil amoebae than as fructifications?’ and ‘are myxamoebae distributions correlated to potential prey organisms (fungi and bacteria)?’ are investigated.
In the ecological study presented in article III parallel metabarcoding of bacteria, fungi and dark-spored myxomycete was used for the first time in a joint approach to analyze the communities from an elevational transect in the northern limestone German Alps (48 soil samples). Illumina sequencing of the soil samples revealed 1.68 Mio sequences of a section of the rRNA gene, which were assigned to 578 operational taxonomic units (OTU) from myxomycetes. These show a high similarity (>98%) to 42 different morphospecies (the respective figures for bacteria and fungi were 2.16/5710/215 and 3.68/6133/260, respectively). Multivariate analyses were carried out to disentangle microbial interplay and to identify the main environmental parameters determining the distribution of myxamoebae and thus setting the boundaries for their ecological niches. Potential interactions between the three target organisms were analysed by integrating community composition and phylogenetic diversity with environmental parameters. We identified niche differentiation for all three communities (bacteria, fungi and myxamoebae) which was strongly driven by the vegetation. Bacteria and fungi displayed similar community responses, driven by symbiont species and plant substrate quality. Myxamoebae showed a more patchy distribution, though still clearly stratified among genera, which seemed to be a response to both structural properties of the habitat and specific bacterial taxa. In addition we find an altitudinal species turn-over for all three communities, most likely explained by adaptation to harsh environmental conditions. Finally a high number of myxomycetes OTUs (associated with the genus Lamproderma) not currently represented in our reference database were found, representing potentially novel species. This study is the first to report niche differentiation between the guild of nivicolous (“snowbank”) myxomycetes and thus fine-scale niche differentiation among a predatory soil protist; identifying both potential food preferences and antagonistic interactions with specific bacterial taxa.
Finally, the second ecological study (article IV) focuses on comparing the distribution of myxamoebae revealed by ePCR of soil samples with fructifications collected from the same area (714 specimens determined to 30 morphospecies, which form 70 unique ribotypes that can be assigned to 45 ribotype clusters using a 99.1% similarity threshold). The study found a strong coherency between the two inventories, though with species specific relative differences in abundance, which can in part be attributed to the visibility of the fructifications. In addition, a year to year comparison of fructification records gives support to the hypothesis that the abundance of fructifications depends strongly on the onset of snowfall in the previous autumn and the soil temperature regime throughout the winter.
Bacteria are exposed to oxidative stress as an unavoidable consequence of their aerobic lifestyle. Reactive oxygen species (ROS) are generated in the stepwise one-electron reduction of molecular oxygen during the respiration. Pathogens encounter ROS during the oxidative burst of macrophages as part of the host immune defense. Besides ROS, bacteria also have to cope with reactive chlorine, electrophilic and nitrogen species (RCS, RES, RNS). To cope with these reactive species, bacteria have evolved different defense and repair mechanisms. To maintain the reduced state of the cytoplasm, they utilize low molecular weight (LMW) thiols. LMW thiols are small thiol-containing compounds that can undergo post-translational thiolmodifications with protein thiols, termed as S-thiolations. S-thiolations function as major redox regulatory and thiol-protection mechanism under oxidative stress conditions. In eukaryotes and Gram-negative bacteria, the tripeptide glutathione (GSH) functions as major LMW thiol, which is present in millimolar concentrations. The Actinomycetes, such as Mycobacterium and Corynebacterium species do not produce GSH and utilize instead mycothiol (MSH) as their alternative LMW thiol. In Firmicutes, including Bacillus and Staphylococcus species, bacillithiol (BSH) functions as the major LMW thiol. LMW thiols protect protein thiols against the irreversible overoxidation of cystein residues to sulfinic and sulfonic acids. In addition, LMW thiols contribute to the virulence and survival of pathogens, function in metal homeostasis and serve as enzyme cofactors for detoxification of xenobiotics and antibiotics. In this doctoral thesis, we aimed to investigate the roles of MSH and BSH in redox regulation of main metabolic enzymes under oxidative stress in the pathogens Corynebacterium diphtheriae and Staphylococcus aureus. Previous redox proteomics studies identified the glyceraldehyde-3-phosphate dehydrogenase GapDH and the aldehyde dehydrogenase AldA as S-thiolated in S. aureus and C. diphtheriae. Thus, we aimed to study the redox regulation of the metabolic enzyme GapDH in C. diphtheriae in response to NaOCl and H2O2 stress by S-mycothiolation, which is described in chapter 1. Moreover, we studied the involvement of the mycoredoxin-1 (Mrx1) and thioredoxin (Trx) pathways in reactivation of S-mycothiolated GapDH in vitro. Using shotgun proteomics, 26 S-mycothiolated proteins were identified under NaOCl stress in C. diphtheriae. These are involved in energy metabolism (Ndh, GlpD) and in the biosynthesis of amino acids (ThrA, LeuB), purines (PurA) and cell wall metabolites (GlmS). The glycolytic GapDH was identified as conserved target for S-thiolation across Gram-positive bacteria. GapDH was the most abundant protein, contributing with 0.75 % to the total cystein proteome. Moreover, GapDH is a conserved target for redox regulation and S-glutathionylation in response to oxidative stress in several prokaryotic and eukaryotic organisms. Treatment of GapDH with NaOCl and H2O2 in the absence of MSH resulted in irreversible enzyme inactivation due to overoxidation. Pretreatment of GapDH with MSH prior to H2O2 or NaOCl exposure resulted in reversible inactivation due to S-mycothiolation of the active site Cys153. Since S-mycothiolation is faster compared to overoxidation, S-mycothiolation efficiently protects the GapDH active site against overoxidation. The activity of S-mycothiolated GapDH could be restored by both, the Mrx1 and Trx pathway in vitro. Interestingly, the recovery of Smycothiolated GapDH by Mrx1 was faster compared to its reduction by the Trx pathway. In previous studies, the reactivation of S-mycothiolated Mpx and MrsA by the mycoredoxin pathway occurred also faster compared to the Trx pathway, which is consistent with our results. We were further interested to analyze the redox regulation of the glyceraldehyde-3phosphate dehydrogenase Gap of S. aureus under NaOCl and H2O2 stress, which is described in chapter 2. Using the quantitative redox proteomic approach OxICAT, 58 NaOCl-sensitive cystein residues with >10% thiol oxidation under NaOCl stress were identified. Gap and AldA showed the highest oxidation increase of 29% under NaOCl stress at their active site cystein residues. Using shotgun proteomics, five S-bacillithiolated proteins were identified, including Gap, AldA, GuaB, RpmJ and PpaC. Gap contributed with 4 % as most abundant cystein protein to the total cystein proteome. Our activity assays demonstrated that Gap of S. aureus is highly sensitive to overoxidation by H2O2 and NaOCl in vitro in the absence of BSH. The active site Cys151 of Gap was oxidized to the BSH mixed disulfide under H2O2 and NaOCl stress in the presence of BSH in vitro, which resulted in the reversible Gap inactivation. Moreover, inactivation of Gap by NaOCl and H2O2 due to S-bacillithiolation was faster compared to overoxidation, indicating that S-bacillithiolation protects the Gap active site against overoxidation in vitro. We further showed that the bacilliredoxin Brx catalyzes the reduction of S-bacillithiolated Gap in vitro. Molecular docking of BSH into the Gap active site revealed that S-bacillithiolation does not require major structural changes. Apart from Gap, the aldehyde dehydrogenase AldA was identified as S-bacillithiolated at its active site Cys279 under NaOCl stress in S. aureus previously. Thus, the expression, function, redox regulation and structural changes of AldA were analysed under NaOCl and aldehyde stress in S. aureus as summarized in chapter 3. AldA was S-bacillithiolated in the presence of H2O2 and BSH as demonstrated in BSH-specific Western blots in vitro. The expression of aldA was previously shown to be regulated by the alternative sigma factor SigmaB in S. aureus. Transcription of aldA was strongly increased in a SigmaB-independent manner under formaldehyde, NaOCl and diamide stress in S. aureus. Using an aldA deletion mutant, we demonstrated that aldA is required for growth and survival under NaOCl stress in S. aureus. The purified AldA enzyme was shown to catalyze the oxidation of various aldehyde substrates, including formaldehyde, methylglyoxal, glycolaldehyde and acetaldehyde in vitro. In addition, the function of the conserved Cys279 for AldA activity was investigated in vivo and in vitro. The purified AldAC279S mutant was shown to be inactive for aldehyde oxidation in vitro. Moreover, the aldAC279S mutant was very sensitive under NaOCl stress in vivo, and this phenotype could be reversed using the aldA complemented strain. These experiments demonstrate the function of Cys279 for AldA activity both in vitro and in vivo. AldA activity assays showed that AldA is sensitive to overoxidation and irreversible inactivation by H2O2 alone in vitro. In the presence of BSH, AldA is protected against overoxidation by reversible Sbacillithiolation in vitro. Molecular docking and molecular dynamics simulations revealed that BSH occupies two different positions in the Cys279 active site, which depend on the NAD+ cofactor. In the apoenzyme, BSH forms the disulfide with Cys279 in the “resting” state position, while Cys279 is S-bacillithiolated in the “attacking” state position in the holoenzyme in the presence of the NAD+ cofactor.
The Effect of the Patients Nutritional Status on Immune Alterations Induced by Ischemic Stroke
(2018)
Ischemic stroke is one of the leading causes of death and disability throughout the world.
One important aspect of stroke pathophysiology are immunological changes after stroke, especially a combination of post stroke immunodepression, leading to
infectious complications after stroke and an activation of the immune system, leading to cerebral injury. Adipose tissue has several immunological functions and obesity
leads to immunological complications and is accompanied by a chronic immune activation.
To study the effects of body weight and obesity on the immune system and measure weight and fat tissue changes after ischemic stroke we conducted the LIPS Trial and enrolled 50 stroke patients and 16 control subjects between July 2015 and July 2016. On the day of admission and on the days 1, 2, 3, 4, 5, 7, 30, 90 and 180 after admission stroke patients were weighed with an in-bed scale, body composition was measured with BIA, the triceps-skin fold thickness was measured, the NIHSS scale was obtained and blood was drawn. FACS-analysis was performed and triglycerides,cholesterol, CRP and PCT were measured at the central laboratory facility of the Universitätsmedizin Greifswald. Luminex-multiplex analysis for multiple cyto- and chemokines was performed at the Multiplex Facility at the University Leiden. A cerebral MRI and an abdominal MRI were performed shortly after admission and on days 5-7 for most patients and the infarct volume, abdominal fat and hepatic fat percentage were measured. On days 30, 90 and 180 after stroke Bartel Index and mRS were obtained.
After stroke our patients showed the typical immunological changes described previously as stroke induced immune alterations, namely a post stroke immunodepression as well as signs of an activated immune system and an acute
phase response. Our patients lost weight, but only 1.7 ± 0.5 kg. Skinfold thickness did not change during the course of our trial and abdominal fat measurement did not change in stroke patients. Immunological parameters (leukocytes, neutrophils,CRP, PCT, IL-6) did not differ between BMI subgroups (normal weight: BMI < 25,overweight: BMI ≥ 25, < 30, obese: BMI ≥ 30) and in this trial we could not detect a
difference in patients with normal weight, overweight or obesity in the post stroke periode. In an additional analysis we could show that rapid clinical improvement
did result in a rapid improvement of post stroke immune alterations, especially for leukocytes, neutrophils, IL-6 and CRP.
In this thesis, size-sensitive phenomena of three-dimensional dust crystals emerged in a low temperature plasma are presented. Depending on the number of particles in the system phase transitions, collective vortex motions and large-scaled expansions can be observed. To investigate these fascinating effects an advanced experimental setup as well as new evaluation methods have been developed. This thesis will present these new techniques and the gained insights.
Background/Aim: Laparoscopic single-port surgery has emerged as a growing trend in minimally invasive surgery. Single-port access is preferred among women undergoing gynecologic surgery who have cosmetic concerns about scarring. Furthermore, this approach results in comparable clinical outcomes to standard laparoscopic surgery and perioperative morbidity rates have been reported to be low. The hypothesis is that a single-port technique might offer such advantages over the standard multi-port laparoscopy as less postoperative pain and better cosmetic results by decreasing abdominal wall tissue trauma. The potential disadvantages of single-port approaches are the larger umbilical incision and the technical difficulties. There are only a few randomized studies in the literature that investigate the value and safety of single-incision laparoscopic surgery in gynecological surgery. The aim of this study was to compare the safety and quality of life in patients who undergo single-incision laparoscopic assisted vaginal hysterectomy and those who undergo conventional laparoscopic assisted vaginal hysterectomy.
Methods: In a prospective randomized trial, 64 patients from three different centers in Germany were randomized (1:1) to conventional laparoscopic assisted vaginal hysterectomy (n=32) or single-incision laparoscopic assisted vaginal hysterectomy (n=30). Data was collected on 60 patients who fulfilled the criteria.
Results: The baseline characteristics of patients were similar in both groups. The mean operative time was comparable in both groups (68.2 vs 73.6 min., p = 0.409). Within the two groups, no differences were seen regarding estimated blood loss (p = 0.915), intra- and postoperative complications (p = 0.944), and wound infection rates (p = 0.944). Patients within the single-incision laparoscopic surgery group experienced significantly less pain in the first 24 hours postoperatively (p = 0.006), while pain scores at days 3, 5, 7 and 2 months postoperatively were comparable.
Conclusion: This study demonstrates that single-incision laparoscopic assisted vaginal hysterectomy is a reliable and safe setup in gynecologic surgery. Compared to conventional laparoscopic assisted vaginal hysterectomy, Notably, patients undergoing single-incision laparoscopic assisted vaginal hysterectomy experienced less pain postoperatively.
Herpesviruses are a fascinating group of enveloped DNA viruses, which rely on membrane fusion for infectious entry and direct cell-to-cell spread. Compared with many other enveloped viruses, they utilize a remarkably complex fusion machinery. Three conserved virion proteins, the bona fide fusion protein gB, and the presumably gB activating gH/gL heterodimer constitute the conserved core fusion machinery and are believed to drive membrane fusion in a cascade-like fashion. Activation of this cascade in most alphaherpesviruses is proposed to be triggered by binding of gD to specific host cell receptors. The molecular details of this fusion process, however, remain largely elusive. Yet, a detailed mechanistic knowledge of this process would be greatly beneficial for the development of efficient countermeasures against a variety of diseases. In this thesis, the functional relevance of individual components of the essential gH/gL complex of the alphaherpesvirus PrV has been assessed by two different approaches: by reversion analysis (paper II) and site-directed mutagenesis (papers III-V). In contrast to other herpesviruses, gL-deleted PrV is able to perform limited cell-to-cell spread, providing the unique opportunity to passage the entry-deficient virus in cell culture to select for PrV revertants capable of infecting cells gL-independently. This approach already resulted in an infectious gL-negative PrV mutant (PrV-ΔgLPass), in which the function of gL was compensated by formation of a gDgH hybrid protein. Here, the requirements for gL-independent infectivity of a second independent revertant (PrV-ΔgLPassB4.1), were analyzed. Sequencing of the genes encoding for gB, gH and gD, revealed mutations in each of them. By means of a robust infection-free, transfection-based cell-cell fusion assay (paper I), we identified two amino acid substitutions in the gL-binding domain I of gHB4.1 (L70P, W103R) as sufficient to compensate for lack of gL. Two mutations in gB (G672R, ΔK883) were found to enhance fusogenicity, probably by lowering the energy, required for gB refolding from pre- to postfusion conformation. Coexpression of gHB4.1 and gBB4.1 led to an excess fusion, which was completely suppressed by gDB4.1 in the fusion assays. This was surprising since PrV gD is normally not required for in vitro fusion or direct viral cell-to-cell spread, clearly separating this process from fusion during entry, for which PrV gD is essential. The fusion inhibiting effect of gDB4.1 could be attributed to a single point mutation resulting in an amino acid substitution within the ectodomain (A106V). In conclusion, these results indicated that gL is not central to the fusion process, as its function can be compensated for. As found so far, gL-independent infectivity can be realized by compensatory mutations in gH (as in PrV-ΔgLPass) or in gH plus gB (as in PrV-ΔgLPassB4.1). Excessive fusion induced by gHB4.1 and gBB4.1 was counter-regulated by gDB4.1, indicating that the interplay between these proteins is precisely regulated and further implies that gL and gD, despite being not absolutely essential for the fusion process, have important regulatory functions on gH and/or gB.
Both PrV-ΔgLPass mutants had acquired compensatory mutations in gH affecting the predicted gL-binding domain I in gH. By construction of an artificial gH32/98, which lacked the predicted gL-binding domain and was similar to the recently crystallized gH-core fragment present in the gDgH hybrid protein, we identified the N-terminal part of PrV gH as essential for gH function during fusion (paper III). gH32/98 was unable to promote fusion of wild-type gB in fusion assays and led to a total loss of function in the viral context. These results indicated that the gD moiety, present in gDgH, is critical for proper function of the gH-core fragment. We hypothesize that the gD moiety may adopt a stabilizing or modulating influence on the gH structure, which is normally executed by gL and important for interaction of gH with wild-type gB. Remarkably, substitution of wild-type gB by gBB4.1 rescued function of gH32/98 in the cellular and viral contexts. These findings suggest that gBB4.1 has been selected for interaction with “gL-less” gH. In conclusion, these results demonstrated that gL and the gL-binding domain are not strictly required for membrane fusion during virus entry and spread but that compensatory mutations must be present in gB to restore a fully functional fusion machinery. These results strongly support the notion of a functional gH-gB interaction as a prerequisite for membrane fusion.
In addition to the N-terminal domain, we identified the transmembrane domain of PrV gH as an essential component of the fusion machinery, while the cytoplasmic domain was demonstrated to play a modulatory but nonessential role (paper IV). Whereas truncation or substitution of the PrV gH TMD by a gpi-anchor or the analogous sequence from PrV gD rendered gH non-functional, the HSV-1 gH TMD was found to functionally substitute for the PrV gH TMD in cell-cell fusion and complementation assays. Since residues in the TMD which are conserved between HSV and PrV gH but absent in PrV gD, are placed on one face of an α-helical wheel plot, we hypothesize that the gH TMD has an intrinsic property to interact with membrane components such as lipids or other molecules as a requirement for promoting membrane fusion.
In a final study focusing on the function of gH, we identified the N-glycosylation sites utilized by PrV gH, and determined their individual role in viral infection (paper V). PrV gH was found to be modified by N-glycans at five potential glycosylation sites. N-glycans at PrV specific N77 and the highly conserved site N627 were found to be critical for efficient membrane fusion in the fusion assays, and during viral entry and cell-to-cell spread. N627 was further shown to be crucial for proper gH transport and maturation. In contrast, inactivation of N604, conserved in the Varicellovirus genus, enhanced in vitro fusion activity and viral cell-to-cell spread. These findings demonstrated a role of the N-glycans in proper localization and function of PrV gH.
Because Moringa is rich in secondary metabolites and phenolics, we faced a challenge in extracting a pure DNA required for AFLP (the first proposed genotyping method). Later, different DNA isolation methods were tested to overcome the obstacles caused by phenolics and sugars, an AFLP protocol that worked well with the cultivated seedlings at the botanical garden in Greifswald. The markers for the Internal Transcribed Spacer (ITS) were as well tested that showed a monomorphic structure between all samples. Finally, SSR (microsatellite) markers were established. To optimize DNA extraction, the method of Doyle and Doyle was modified and optimized. This is an ideal method for obtaining a non-fragmented DNA that could be used for AFLP. In addition, two other DNA extraction methods; (KingFisher Flex robot using Omega M1130 extraction Kits, and spin columns and 96-plates using Stratec kits). Although we achieved similar results for both Robot kits (Omega) and Stratec kits, the amplification for most of the samples extracted with Robot did not work, therefore the Stratec kit was the method of choice as it has also a lower cost, combined with a high quality of DNA. For ITS, no polymorphism was found for 28 samples of M. peregrina from Sinai (sequences submitted to GenBank). However, since microsatellite markers of M. peregrina were not known, it was a challenge to try a cross amplification from other species with well-known microsatellite primers. Cross-amplification of 16 primers known from the related species M. oleifera was tested, and three multiplex PCR reactions were established after testing different annealing temperatures and different primers concentrations. This included 13 primers out of the 16 investigated markers which gave a reliable band. All methods used for genetic assessments for the different Moringa species are compiled in a comparative review to look for connections between the different Moringa species. For Moringaceae, M. oleifera and M. peregrina are closely related to each other. Both species have slender trunks, with thick, tough bark and tough roots and bilaterally symmetrical flowers with a short hypanthium. All but one SSR markers used in this study are highly informative However, the degree of polymorphy varied considerably within the 13 markers used. The Probability of Identity (PI) for all loci was 2.6 x 10-9 with high resolution. The percentage of polymorphic loci for all populations was 88.5±2.2; figures for single populations were 92.3%, 84.6%, 84.6%, and 92.3% for the wadis WM, WA, WF, and WZ, respectively. The genotype accumulation curve as well demonstrated that 7–8 markers were necessary to discriminate between 100% of the multilocus genotypes. Significant departures from HWE were detected for eight loci (P < 0.001), probably due a high degree of inbreeding within population. The observed (HO) and expected (HE) heterozygosities ranged from 0 to 0.86 and from 0 to 0.81, respectively. However, for the pooled population, excluding the monomorphic locus MO41, HO and HE ranged from 0.069 to 0.742 and from 0.126 to 0.73 with averages of 0.423 and 0.469, respectively. The mean of FST was 0.133, indicating that, due to the long generation time of M. peregrina, there is still relatively little differentiation between the four remaining populations. An analysis of molecular variance (AMOVA) revealed that the old populations of M. peregrina are still genetically diverse where 75% of variance was recorded within individuals and 83% within populations. An analysis with STRUCTURE, varying the parameter K between 1 and 7, revealed the most pronounced genetic structure for K=3, thus uniting the populations from two neighboured wadis (W. Agala and W. Feiran). The three groups seem to be now genetically isolated. (They may be remainders of a formerly contiguous population, especially when considering the change towards a drier climate in Northern Africa within the last 6000 years). Six clones of each two individuals collected from the same wadi were found, pointing to vegetative dispersal via broken twigs, which may have rooted after flash floods. It may be an alternative mode of reproduction under harsh conditions. Our data reveal a low gene flow between three of the four wadis, suggesting that the trees are relictual populations. In general, conservation of populations from the three genetically most diverse wadis and cross-breeding of trees within a reforestation program is recommended as an effective strategy to ensure the survival of M. peregrina at Sinai, Egypt.
As the tree of life is populated with sequenced genomes ever more densely, the new challenge is the accurate and consistent annotation of entire clades of genomes. In my dissertation, I address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or—if not—where the exon gains and losses are plausible given the species tree. The multi-species gene finding problem is formulated as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach.
I tested the novel approach on whole-genome alignments of 12 vertebrate and 12 Drosophila species. The accuracy was evaluated for human, mouse and Drosophila melanogaster and compared to competing methods. Results suggest that the new method is well-suited for annotation of a large number of genomes of closely related species within a clade, in particular, when RNA-Seq data are available for many of the genomes. The transfer of existing annotations from one genome to another via the genome alignment is more accurate than previous approaches that are based on protein-spliced alignments, when the genomes are at close to medium distances. The method is implemented in C++ as part of the gene finder AUGUSTUS.
Analysis of partial migration strategies of Central European raptors based on ring re-encounter data
(2018)
The phenomenon of partial migration in birds in
which some individuals of a population are migratory while others stay in the breeding area is of increasing scientific interest. The strategies of partial migratory raptors from Central Europe are, however, unclear for most species. We analysed ring re-encounter data of Common Kestrels Falco tinnunculus, Eurasian Sparrowhawks Accipter nisus and Common Buzzards Buteo buteo ringed in Germany in terms of distances and directions between ringing and re-encounter sites. We investigated possible differences between sexes and age classes, as well as effects of ringing region, seasonal weather (in the form of North Atlantic Oscillation indices) and long-term temporal changes (including climate change) on migratory strategies by means of generalized linear models. We found that migration is mostly conducted by juveniles, although migratory adults were also found. In general, males tend to migrate less than females and juveniles less than adults.
Kestrels showed differences between age classes and sexes and they responded to weather in summer and autumn. The migration activities of Kestrels decreased over years. Sparrowhawks from different regions showed no differences in migration activity and no responses to long-term temporal changes. They did not respond to seasonal weather either. Buzzards showed strong responses to winter weather (‘winter escapes’) predominantly in highland regions, and a reduction of migratory intensity probably due to global warming.
The explanatory power of ringing data, however, is limited by low re-encounter rates and temporal and spatial heterogeneity in re-encounter probability. Spatial heterogeneity mainly depends on the distribution of observers as well as on their willingness to report a re-encountered ring to the corresponding ringing scheme. We analyzed a data set of ringing and re-encounter data of Kestrels, Buzzards and Sparrowhawks provided by the EURING Data Bank. We calculated monthly re-encounter rates across Europe and, for different time periods, we predicted re-encounters for individuals of these species ringed in Germany, on the assumption that re-encounter probabilities are evenly distributed at the highest value observed within the respective home ranges. Subsequently, we tested for correlation between re-encounter rates and human population density. The number of predicted re-encounters exceed the observed by 50-300 %. We found differences between monthly re-encounter rates and between different prediction periods. Distances (between ringing and re-encounter sites) differ significantly between observations and predicted re-encounters, with higher distances in predictions. Correlation between re-encounter rates and human population density is significant, but correlation coefficients are low (ρ = 0.291-0.511). Correcting for observer heterogeneity can help to analyze ring re-encounter data e.g. in terms of dispersal and migration. However, a comprehensive data collection and a digitalization of possible prior data records by the respective ringing schemes may allow advances in this method even further.
Manipulating and utilizing plasmas becomes a more and more important task in various research fields of physics and in industrial developments. Especially in nowadays spacerelevant applications there are different ideas to modify plasmas concerning particular tasks.
One major point of interest is the ability to influence plasmas using magnetic fields. To study the underlying physical effects that were achieved by these magnetic fields for both scenarios Particle-in-Cell simulations were done. Two examples are discussed in this thesis.
The first example originates from an experiment performed by the European Space Agency ESA in collaboration with the German Space Agency DLR. To verify the possibility of heat-flux reduction by magnetic fields onto the thermal protection system of a space vehicle a simplified experiment on earth was developed. Most of the heat that is created during re-entry comes from compression of the air ahead of the hypersonic vehicle, as a result of the basic thermodynamic relation between temperature and pressure. The shock front, which builds up in front of the vehicle deflects most of the heat and prohibits the surface of the space vehicle from direct contact with the maximum flux. State of the art spacecrafts use highly developed materials like ceramics to handle the enormous heat. An attractive approach to reduce costs is to use magnetic fields for heat-flux reduction. This would allow the use of cheaper materials and thus reduce costs for the whole space mission. A partially-ionized Argon beam was used to create a certain heat-flux onto a target. The main finding of the experimental campaign was a large mitigation of heat-flux by applying a dipole-like magnetic field. The Particle-in-Cell method was able to reproduce experimental observations like the heat-flux reduction. An additionally implemented optical diagnostics module allowed to confirm the results of the spectroscopy done during the experiment. The underlying effect that is responsible for the heat-flux reduction was identified as a coupling between the modified plasma and the dominating neutral flux component. The plasma, that is guided towards the target, act as a shield in front of the target surface for arriving neutrals. These neutrals are slowed down by charge-exchange collisions. Furthermore the magnetic field induces an increased turbulent transport that is also needed to reach a reduction in heat-ux. The turbulent transport was also obtained by three-dimensional Direct Simulation Monte Carlo simulations. Unfortunately, such source driven turbulence can not be expected in space, so that a heat flux reduction in real space applications is questionable. Nevertheless, other effects like the induced turbulence by the rotating vehicle can compensate the missing source driven effect.
The second scenario in which a magnetic field is used to modify the heat flux of a plasma is the operation of the pulsed cathodic arc thruster. The same Particle-in-Cell code was used to simulate a typical pulse of this newly developed thruster of Neumann Space Pty Ltd. The typical behavior of the thruster could be reproduced numerically. The thrust is mainly produced by fast electrons. These electrons are accelerated by electric fields as a result of a plasma-beam instability. This plasma-beam instability was verified by a phase space diagnostics for the electrons. To demonstrate the influence of the magnetic field a simulation of the cathodic arc thruster without magnetic field and one with magnetic field were compared. It was shown that the use of a magnetic field leads to a ten times larger thrust by directing the heat ux. The resulting narrow plume is an additional Advantage of the particle guiding magnetic field. This narrowness of the plume reduces the danger of interaction with other components of the space vehicle.
Both scenarios demonstrate the different capabilities for electromagnetic fields to manipulate plasmas and especially the corresponding heat-flux with respect to certain tasks. The possibilities range from reducing the heat-flux onto a target to maximizing the thrust by directing the heat-ux. This thesis demonstrates that simulations are a great tool to support experiments and to deliver an improved physics understanding. They help to identify the basic physics principles in the different systems, because they can deliver information not accessible to experiments.
In particular, a better understanding of the influence of electromagnetic fields on the heat-flux distribution in space-relevant applications was obtained. This can be the basis for further simulation-guided optimization, e.g. for the design of more effective cathodic arc thrusters. Here, the goal is to minimize costs for prototypes by replacing the hardware by virtual prototypes in the simulations. This allows to test basic design ideas in advance and get more highly-optimized designs at a fraction of time and costs.
Ion thrusters are Electric Propulsion systems used for satellites and space missions. Within
this work, the High Efficient Multistage Plasma Thruster (HEMP-T), patented by the
THALES group, is investigated. It relies on plasma production by magnetised electrons.
Since the confined plasma in the thruster channel is non-Maxwellian, the near-field plume
plasma is as well. Therefore, the Particle-In-Cell method combined with a Monte-Carlo
Collision model (PIC-MCC) is used to model both regions. In order to increase the sim-
ulated near-field plume region, a non-equidistant grid is utilised, motivated by the lower
plasma density in the plume. To minimise artificial self-forces at grid points bordered by
cells of different size a modified method for the electric field calculation was developed in
this thesis. In order to investigate the outer plume region, where electric field and collisions
are negligible, a ray-tracing Monte-Carlo model is used. With these simulation methods,
two main questions are addressed in this work.
What are the basic mechanisms for plasma confinement, plasma-wall-interaction
and thrust generation?
For the HEMP-T the plasma is confined by magnetic fields in the thruster channel, generated
by cylindrical permanent magnets with opposite polarity. Due to different Hall parameters,
electrons are magnetised, while ions are not. Therefore, the dominating electron transport
is parallel to the magnetic field lines. In the narrow cusp regions, the magnetic mirror effect
reduces the electron flux towards the wall and confines the electrons like in a magnetic
bottle. At the anode, propellant gas streams into the thruster channel, which gets ionised
by the electrons creating the plasma. As a result of the electron oscillation between the two
cusp regions, ionisation of the propellant gas is efficient.
The magnetic field configuration of the HEMP-T also influences the plasma potential inside
the thruster channel. Close to the symmetry axis, the mainly axial magnetic field results in
a flat potential. At the inner wall, the field configuration reduces the plasma wall interaction
to only the narrow cusp regions. Here, the floating potential of the dielectric channel wall
and its plasma sheath result in a rather low radial potential drop compared to the applied
anode potential. As a result, the electric potential is rather flat and impinging ions at the
thruster channel wall have energies below the sputter threshold energy of the wall material.
Therefore, no sputtering appears at the dielectric wall. At the thruster exit the confinement
by the magnetic field is weakened and the potential drops with nearly the full anode voltage.
The resulting electric field accelerates the generated ions into the plume and generate the
thrust, but they are also able to sputter surfaces. During terrestrial testing, sputteringat vacuum vessel walls leads to the production of impurities. The amount of back-flux
towards the channel exit is determined by the sputter yield of the vacuum chamber wall. A
large distance between thruster exit and vessel wall reduces the back-flux and smooths the
pattern of deposition inside the thruster channel. Dependent on their material, the evolving
deposited layers can get conductive, modify by this the potential distribution and reduce
the thrust.
For the HEMP-T, ions are mainly generated at high potential close to the applied anode
potential. Therefore, the accelerated ions producing the thrust gain the maximum energy
as observed in experiment. Ions emitted from the thruster into different angles in the
plume contribute mainly to the ion current at angles between 30 ◦ and 90 ◦ . They mainly
originate from ionisation at the thruster exit. The resulting angular distribution of the
ejected ion current is close to the one of the experiment, slightly shifted by about ten
degrees to higher emission angles. In front of the thruster exit, electrons are trapped by
electrostatics forces. This enhanced density allows ionisation and an additional electron
density structure establishes.
What are possible physics based ideas for optimisation of an ion thruster?
An optimised thruster should have a high ionisation rate inside the thruster channel, low
erosion and an ion angular distribution with small contributions at high angles for min-
imised thruster satellite interactions. In experiments, the HEMP-T satisfies already quite
nicely these requests. In the simulations, low erosion inside the thruster channel and angular
ion distributions close to the experimental data are demonstrated. However, the ionisation
efficiency is lower and radial ion losses are larger than in experiment. A possible explanation
of these differences is an underestimated transport perpendicular to the magnetic field lines,
well known for magnetised plasmas.
A successful example for an optimisation using numerical simulations is the reduction of
back-flux of sputtered impurities during terrestrial experiments by an improved set-up of
the vacuum vessel. The implementation of baffles reduces the back-flux towards the thruster
exit and therefore deposition inside the channel. These improvements were successfully im-
plemented in the experiment and showed a reduction of artefacts during long time measure-
ments. This leads to a stable performance, as it is expected in space.
Most animals live solitarily, but for some species the benefits of group living outweigh the costs and social communities have evolved. Truly social societies are characterized by cooperation in tasks like foraging, predator defense and brood care. In the most extreme cases, non-reproducing individuals act as helpers and provision offspring of reproducing individuals at the cost of their own reproductive success. This alloparental care is attributed to kin selection that provides the helpers with inclusive fitness benefits. However, how reproductive role is determined and in which ways virgin helpers in a group benefit the community is not always well understood.
Spiders are known to be generalist hunters, which in many cases do not shy away from cannibalism. Thus, most spiders live solitarily. However, in a few species a permanently social lifestyle has evolved in which individuals live together throughout their life, providing an intriguing case of social evolution. These spider communities are characterized by lack of premating dispersal leading to extreme inbreeding, by reproductive skew, in which only a proportion of females reproduce and by cooperative breeding of the reproducing females. It has been assumed that the large proportion of virgin females act as helpers not only in foraging and web maintenance but also during brood care. In the social spider Stegodyphus dumicola brood care involves the intensive task of regurgitation feeding, at which mothers regurgitate their own liquefied body tissue. At the end of brood care, the offspring sucks the mothers dry during matriphagy, leading to the death of brood caring females and a semelparous lifestyle. In the closely related solitarily breeding Stegodyphus lineatus virgin females do not provide brood care. The ability of virgin females in S. dumicola to care for offspring would thus depict an adaptation to sociality and cooperative breeding. I therefore aimed to clarify the role and significance of virgin females in colonies of social spiders and furthermore investigated a possible mechanism of how reproductive role within a colony is determined.
I investigated whether there is differential task participation in a non-reproductive task and the task of brood care among reproducing mothers and virgin females (helpers) in Stegodyphus dumicola. The study provides explicit evidence that brood care – including egg sac care, regurgitation feeding and matriphagy – is performed by mothers as well as by virgin helpers. Virgin females in a colony can thus rightfully be termed allomothers. However, the task participation differed between the reproductive states. While mothers engaged more often in brood care, virgin females were more active in foraging. However, the active provisioning of offspring by the virgin females decreases the motherly workload as is suggested by the extended brood care period in comparison to solitary breeders. The observations on virgin allomaternal care are supported by histological studies on the midgut tissue of brood caring females, which revealed that mothers and virgin helpers undergo comparable morphological changes in preparation of regurgitation feeding. The changes in virgin females correlate to ovarian development that might depict an internal maturation process which sets virgin females in the right state to provide care. The morphological changes in mothers and virgin helpers of S. dumicola are less comprehensive than in the solitarily breeding S. lineatus mothers. This indicates that cooperatively caring females are able to save on their resources, provision offspring for longer and thus are probably able to increase survival of the brood by an extended care period. A surprising consequence of cooperative brood care is the ability of mothers to produce a second viable egg sac, even when the first brood is successful. Mothers of the cooperative breeding S. dumicola can thus depart from the strictly semelparous lifestyle and instead invest part of their resources in a second clutch. This finding identified a new way of how cooperative breeding enhances breeding success of reproducers and thus inclusive fitness for helpers as well, thus adding to the benefits of allomaternal care.
Virgin females did not store significantly lower amounts of lipids in their midgut tissue than mothers, raising the question of how much reproductive role of females is determined by competition for resources during growth, as often assumed. Another possible determinant of female reproductive skew is the characteristic male scarcity in spider colonies, with only about 12 percent of spiders being male. Males are assumed to mature early within a few days and die early, thus leaving late maturing females unmated due to lack of mating partners. However, my studies provided evidence that male maturation is more skewed than expected and males might survive several months. Subadult females did not accelerate molting when an adult male was present, which could further indicate, that male presence is not a limiting factor on reproduction in males. Furthermore, males are able copulate with up to 16 females and did not show e preference for large females during mating trials. Males are thus able to fertilize all females, provided all females mature in time. I therefore suggest, that male scarcity is not major determinant of reproductive skew in females, especially in small and middle-sized colonies in which female maturation might only be moderately skewed.
My studies were able to demonstrate the meaning of the large proportion of unmated females in a colony of the social spider S. dumicola. Virgin helpers support mothers during brood care and thus do not only enhance the brood care period but facilitate mothers to produce multiple clutches. Virgin females are able to care as they undergo similar morphological changes as mothers’ do. This seems to be facilitated by an internal maturation process, indicated by ovarian development and oviposition by virgin females, both of which has never been observed in virgins of the subsocial species. How reproductive role is determined remains unclear, but I was able to exclude male scarcity as a major factor influencing reproductive skew.
This work study a monolayer of branched poly(ethyleneimine (PEI) adsorbed onto oppositely charged surfaces with iron chelates or iron ions in the absorption solution. The conformation of adsorbed PEI is explored in the dependence of the composition of the adsorption solution by measuring the surface forces using atomic force microscopy (AFM) with the colloidal probe (CP) at different ionic strengths (INaCl) in surrounding aqueous solution. The surface coverage of these layers is investigated using X-ray reflectivity.
PEI solutions show different pH values with iron chelates (pH = 3), iron ions (pH = 4.67) or pure water (pH = 9.3) at room temperature. Low surface coverage of PEI at pH = 3 adjusted by monovalent ions was also observed. However, adsorbing PEI with iron ions or iron chelates and washing with pure water shifts the pH, leading to an adsorbed PEI layer with high coverage. In our observation, the influence of iron ions and iron chelates on the surface coverage of PEI film is stronger than the pH effect. PEI adsorbed from a pure water solution shows flat conformation. Surface force measurements with CP show that PEI adsorbed from solutions containing iron chelates or iron ions cause almost identical steric forces. The thickness of the brush L is determined as a function of the ionic INaCl in the measuring solution. It scales as a polyelectrolyte brush.
The maximum number density of gold nanoparticles (AuNPs) adsorbed onto the PEI brushes was identical and larger than on flatly adsorbed PEI. On the PEI layer with the larger surface coverage, the AuNPs aggregate; on the PEI layer with the lower surface coverage they do not aggregate. Taken together, these results contribute to understanding the mechanisms determining surface coverage and conformation of PEI and demonstrate the possibility of controlling surface properties, which is highly desirable for potential future applications.
In this thesis, we also investigate the top layer (PSS and PDADMA) of polyelectrolyte multilayer (PEM) films. PEM films were prepared by sequential adsorption of oppositely charged PEs on solid substrates. PEM films consist of polydiallyldimethylammonium (PDADMA) as polycation and the polystyrene sulfonate (PSS) as polyanion. PDADMA has a smaller linear charge density than PSS. For this system, two different growth regimes are known: parabolic and linear. I studied the top layer (PSS and PDADMA) conformation of PEM films and how the structure of this top layer is affected by increasing the number of PDADMA/PSS layer pairs N and the addition of salt to the surrounding solution.
The INaCl was changed during the force-distance measurements. PSS terminated films always show electrostatic forces at INaCl < 0.1 M and flat conformation. The surface charge density is always negative at INaCl < 0.1 M. The surface charge of the PSS top layer starts to turn from negative to positive at N ≥ 14. At N between 13 and 15, adsorbed PSS cannot compensate all the excess PDADMA charge. This leads to an accumulation of the positive extrinsic sites within the PSS terminated film beyond a specific N. At INaCl ≈ 0.1 M, an exponential decaying force was measured. This is an indication of unusual long-ranged hydration force (decay length λ-1 ≈ 0.2-0.5 nm), and PSS terminated film shows zwitterionic or neutral surface. At INaCl > 0.1 M, a non-electrostatic action occurs and the PSS terminated film reswells in solution.
PDADMA terminated surface consisting of few layers show a flat conformation and the electrostatic forces were measured. For N ≥ 9 and INaCl ≤ 0.1 M, steric forces were measured. The force-distance profiles are well-explained by Alexander and de Gennes theory. PDADMA chains show a maximum L that is around 40-45 % of the contour length. For INaCl ≈ 0.1 M, and N > 9, a flat, neutral or zwitterionic surface is found (λ-1 ≈ 0.3-0.9 nm). For N = 9 and INaCl > 0.1 M, a strong screening of electrostatic interaction and attractive forces are observed. For N > 9 and INaCl > 0.1 M, the ion adsorption into the PE chains leads to an increase in the monomer size and as a result, the L increases and PDADMA brushes reswell again into the solution.
These data show that by varying N and INaCl, different surface forces can be obtained: Electrostatic forces (flat chains) both positive and negative, steric forces (brush), hydration force (flat, neutral or zwitterionic surface), and effects not yet explained (reswelling brush).