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Background: Depression and obesity are widespread and closely linked. Brain-derived neurotrophic factor (BDNF) and vitamin D are both assumed to be associated with depression and obesity. Little is known about the interplay between vitamin D and BDNF. We explored the putative associations and interactions between serum BDNF and vitamin D levels with depressive symptoms and abdominal obesity in a large population-based cohort. Methods: Data were obtained from the population-based Study of Health in Pomerania (SHIP)-Trend (n = 3,926). The associations of serum BDNF and vitamin D levels with depressive symptoms (measured using the Patient Health Questionnaire) were assessed with binary and multinomial logistic regression models. The associations of serum BDNF and vitamin D levels with obesity (measured by the waist-to-hip ratio [WHR]) were assessed with binary logistic and linear regression models with restricted cubic splines. Results: Logistic regression models revealed inverse associations of vitamin D with depression (OR = 0.966; 95% CI 0.951–0.981) and obesity (OR = 0.976; 95% CI 0.967–0.985). No linear association of serum BDNF with depression or obesity was found. However, linear regression models revealed a U-shaped association of BDNF with WHR (p < 0.001). Conclusion: Vitamin D was inversely associated with depression and obesity. BDNF was associated with abdominal obesity, but not with depression. At the population level, our results support the relevant roles of vitamin D and BDNF in mental and physical health-related outcomes.
Background: Iodine deficiency disorders (IDD) represent a global health threat to individuals and societies. IDD prevention programmes have been introduced in many parts of the world. However, challenges remain, particularly in Europe due to fragmentation and diversity of approaches that are not harmonized. Objectives: This review is dedicated to the public-health impact of IDD prevention programmes. It sums up experiences collected by the EUthyroid consortium so far and provides information on stakeholders that should be involved in actions directed to improve the impact of IDD prevention. Methods: A joint European database for combining registry-based outcome and monitoring data as well as tools for harmonizing study methods were established. Methods for analyzing thyroglobulin from a dried blood spot are available for assessing the iodine status in the general population and at-risk groups. Mother-child cohorts are used for in-depth analysis of the potential impact of mild-to-moderate iodine deficiency on the neurocognitive development of the offspring. A decision-analytic model has been developed to evaluate the long-term effectiveness and cost effectiveness of IDD prevention programmes. Results: EUthyroid has produced tools and infrastructure to improve the quality of IDD monitoring and follows a dissemination strategy targeting policymakers and the general public. There are tight connections to major stakeholders in the field of IDD monitoring and prevention. Conclusions: EUthyroid has taken steps towards achieving a euthyroid Europe. Our challenge is to inspire a greater sense of urgency in both policymakers and the wider public to address this remediable deficit caused by IDD.
Background: Levels or fluctuations in the partial pressure of CO<sub>2</sub> (PCO<sub>2</sub>) may affect outcomes for extremely low birth weight infants. Objectives: In an exploratory analysis of a randomized trial, we hypothesized that the PCO<sub>2</sub> values achieved could be related to significant outcomes. Methods: On each treatment day, infants were divided into 4 groups: relative hypocapnia, normocapnia, hypercapnia, or fluctuating PCO<sub>2</sub>. Ultimate assignment to a group for the purpose of this analysis was made according to the group in which an infant spent the most days. Statistical analyses were performed with analysis of variance (ANOVA), the Kruskal-Wallis test, the χ<sup>2</sup> test, and the Fisher exact test as well as by multiple logistic regression. Results: Of the 359 infants, 57 were classified as hypocapnic, 230 as normocapnic, 70 as hypercapnic, and 2 as fluctuating PCO<sub>2</sub>. Hypercapnic infants had a higher average product of mean airway pressure and fraction of inspired oxygen (MAP × FiO<sub>2</sub>). For this group, mortality was higher, as was the likelihood of having moderate/severe bronchopulmonary dysplasia (BPD), necrotizing enterocolitis (NEC), and poorer neurodevelopment. Multiple logistic regression analyses showed an increased risk for BPD or death associated with birth weight (p < 0.001) and MAP × FiO<sub>2</sub> (p < 0.01). The incidence of adverse neurodevelopment was associated with birth weight (p < 0.001) and intraventricular hemorrhage (IVH; p < 0.01). Conclusions: Birth weight and respiratory morbidity, as measured by MAP × FiO<sub>2</sub>, were the most predictive of death or BPD and NEC, whereas poor neurodevelopmental outcome was associated with low birth weight and IVH. Univariate models also identified PCO<sub>2</sub>. Thus, hypercapnia seems to reflect greater disease severity, a likely contributor to differences in outcomes.
Based on the latest gnomAD dataset, the prevalence of symptomatic hereditary cerebral cavernous malformations (CCMs) prone to cause epileptic seizures and stroke-like symptoms was re-evaluated in this review and calculated to be 1:5,400-1:6,200. Furthermore, state-of-the-art molecular genetic analyses of the known CCM loci are described which reach an almost 100% mutation detection rate for familial CCMs if whole genome sequencing is performed for seemingly mutation-negative families. An update on the spectrum of CCM1, CCM2, and CCM3 mutations demonstrates that deep-intronic mutations and submicroscopic copy-number neutral genomic rearrangements are rare. Finally, this review points to current guidelines on genetic counselling, neuroimaging, medical as well as neurosurgical treatment and highlights the formation of active patient organizations in various countries.
The glioblastoma multiforme (GBM) not only presents the most common tumor of the central nervous system in adults, it is also the most aggressive brain tumor. Although patients suffering from GBM standardly receive a combination of multiple treatments including surgery, radiotherapy and chemotherapy, its prognosis is still poor with a median survival time of only 12-15 months. Therefore, new and effective treatment methods are urgently needed.
A signaling molecule which is both involved in proliferation, migration and invasion of a broad range of healthy and malignant cells is the lipid mediator sphingosine-1-phosphate (S1P). Previous studies have confirmed that sphingosine-1-phosphate (S1P) receptor 1 (S1PR1) is involved in the regulation of proliferation, invasion, metastasis, vascular maturation and angiogenesis of GBM cells, and is closely related to the occurrence and development of tumors. Thus, ACT-209905 (provided by Actelion Pharmaceuticals) as a selective S1PR1 modulator was applied to gain insights into the molecular processes activated by S1PR1 in GBM cells using two human (LN18, U87MG) and one murine (GL261) GBM cell line.
In our in vitro cell viability analyses, we found that ACT-209905 significantly reduced viability of LN18 cells in a concentration dependent manner. A combined administration of ACT-209905 with S1PR2 inhibitors (Compound 16, Compound 16ME – both provided by ONO Pharmaceuticals, and JTE-013 – commercially available) showed a stronger effect than the single administration demonstrating that both S1PR1 and S1PR2 are involved in growth of GBM cells and may interact with each other. Our results also demonstrated that ACT-209905 can induce apoptosis in GBM cells since caspase 3 activity was induced by the S1PR1 modulator which might therefore play an important role in inhibiting the proliferation of GBM cells. Further, we found a significant inhibitory effect of ACT-209905 on the migration and invasion of LN18 and U87MG GBM cells arguing for a participation of S1PR1 signaling in migration and invasion of GBM cells, too. Stimulation of S1P receptors results in the activation of several kinases such as AKT1 and ERK1/2, correspondingly our immunoblot analyses showed a strong activation of both kinases by S1P which was reduced by ACT-209905 in LN18 cells but not in GL261 cells suggesting that different pathways are activated by S1P in these GBM cell lines. Further studies have to be performed to clarify the role of AKT1 and ERK1/2 in the inhibitory effects of ACT-209905 on GBM proliferation, migration and invasion.
Currently, GBM stem cells are discussed as a reason for resistance against the radiochemotherapy and the recurrence of the tumor. Our immunoblot analyses showed that Nestin and CD133, two marker proteins for GBM stem cells, were higher expressed in GBM cells treated with ACT-209905 compared to control or S1P treated LN18 cells. Further investigations in the future might contribute to the elucidation of an involvement of the S1P receptors in the stem cell behavior of GBM cells. Paradoxically to the up-regulation of CD133 and Nestin by ACT-209905, treatment of LN18 stem-like neurospheres with ACT-209905 showed a significant cytotoxic effect of the compound which was even more pronounced in the stem-like neurosphere cells compared to the adherent parental LN18 cells.
Overall, the studies of this work improve our understanding of the complex mechanisms of S1P signaling in GBM cells and might drive the development of its pharmacological modulation as a new therapeutic principle in GBM. Furthermore, an extended knowledge about the molecular effects of ACT-209905 on GBM cells will broaden the understanding for possible future applications and clinical indications.
African swine fever virus (ASFV) is one of the most threatening animal viruses which has dramatically expanded its distribution range within the last years. ASFV was first described and is endemic in sub-Saharan Africa where it is transmitted in a sylvatic cycle between indigenous suids and Ornithodoros soft ticks. Therefore, ASFV is the only known DNA-arbovirus and, in addition to that, the only member of the genus Asfivirus within the family Asfarviridae. Being highly infectious to domestic pigs and wild boar, the virus was introduced into Georgia in 2007 and has subsequently spread throughout eastern Europe reaching the European Union in 2014. Despite almost 100 years of intensive research and the occurrence of African swine fever (ASF) on four continents including Europe, many aspects of its epidemiology, vector dynamics and virus evolution are unknown. In our study, first evidence is presented on endogenous ASFV-like (EASFL)- elements which are integrated into the genome of ASFV natural vectors, O. moubata soft ticks. Through a series of experiments including next-generation sequencing, infection experiments, phylogenetic and BEAST analyses as well as PCR-screening, evidence is provided that these elements belong to an ancestral ASFV strain that might have existed 50,000 to 30,000 years BCE. Further results suggest that the EASFL-elements are involved in protecting ticks against ASFV infection and might belong to a generalised tick defence mechanism. In order to evaluate factors influencing ASFV epidemiology in eastern Europe, experiments were conducted on possible indigenous vector species and circulating virus isolates. In the absence of the natural tick vector, blow fly larvae were considered as possible mechanical vectors involved in ASFV transmission and persistence. Results are presented that even after feeding on highly infectious wild boar tissue, fly larvae and pupae showed no contamination with infectious virus. On the contrary, the maggots appeared to have inactivated the virus in the organ tissue through their salivary secretions. Further experiments conducted on an ASFV-strain isolated from northeastern Estonia resulted in the first report of an ASFV-strain with attenuated phenotype isolated in Eastern Europe. Results from NGS-analyses provided evidence for a major genome reorganisation in that strain that included a large deletion and a duplication of multiple ASFV genes.
Taken together, this study provides novel insights into the epidemiology of ASF and evolution of ASFV one of the major threats to animal health worldwide and therefore does not only contribute significantly to basic research but possibly also to specific knowledge necessary for future disease management.
In the current era of anthropogenic climate change is the long-term survival of all organisms dependent on their ability to respond to changing environmental conditions either by (1) phenotypic plasticity, which allows species to tolerate novel conditions, (2) genetic adaptation, or (3) dispersal to more suitable habitats. The third option, dispersal, allows individuals to escape unfavorable conditions, the colonization of new areas (resulting in range shifts), and affects patterns of local adaptation. It is a complex process serving different functions and involving a variety of underlying mechanisms, but its multi-causality though has been fully appreciated in recent years only. Thus, the aim of this doctoral thesis was to disentangle the relative importance of the multiple factors relevant to dispersal in the copper butterfly Lycaena tityrus, including the individual condition (e.g. morphology, physiology, behavior) and the environmental context (e.g. habitat quality, weather). L. tityrus is a currently northward expanding species, which makes it particularly interesting to investigate traits underlying dispersal. In the first experiment, the influence of weather and sex on movement patterns under natural conditions was investigated. Using the Metatron, a unique experimental platform consisting of interconnected habitat patches, the second experiment aimed to examine the influence of environmental factors (resources, sun) on emigration propensity in experimental metapopulations. Human-induced global change (e.g. climate change, agricultural intensification) poses a substantial challenge to many herbivores due to a reduced availability or quality of feeding resources. Therefore, in the third experiment, the impact of larval and adult food stress on traits related to dispersal ability was investigated. Additionally, the effect of different ambient temperatures was tested. In the fourth experiment, core (Germany) and recently established edge (Estonia) populations were compared in order to explore variation in dispersal ability and life history traits indicative of local adaptation. Dispersal is often related to flight performance, and morphological and physiological traits, which was investigated in experiments 2-4. Butterflies were additionally subjected to behavioral experiments testing for the individual’s exploratory behavior (experiments 3 and 4).
Males and females differed substantially in morphology, with males showing traits typically associated with a better flight performance, which most likely result from selection on males for an increased flight ability to succeed in aerial combats with rivalling males and competition for females. This pattern could be verified by mobility measures under natural conditions and flight performance tests. Interestingly, although females showed traits associated with diminished flight performance, they had a higher emigration propensity than males (though in a context dependent manner). Reasons might be the capability of single mated females to found new populations, to spread their eggs over a wide range or to escape male harassment. Conditions indicative of poor habitat quality such as shade and a lack of resources promoted emigration propensity. The environmental context also affected condition and flight performance. The presence of resources increased the butterflies’ condition and flight performance. Larval and adult food stress in turn diminished flight performance, despite some reallocation of somatic resources in favor of dispersal-related traits. These detrimental effects seem to be mainly caused by reductions in body mass and storage reserves. A similar pattern was found for exploratory behavior. Furthermore, higher temperatures increased flight performance and mobility in the field, demonstrating the strong dependence of flight, and thus likely dispersal, on environmental conditions. Flight performance and exploratory behavior were positively correlated, probably indicating the existence of a dispersal syndrome. The population comparison revealed several differences between edge and core populations indicative of local adaptation and an enhanced dispersal ability in edge populations. For instance, edge populations were characterized by shorter development times, smaller size, and a higher sensitivity to high temperatures, which seem to reflect adaptations to the cooler Estonian climate and a shorter vegetation period. Moreover, Estonian individuals had an enhanced exploratory behavior, which can be advantageous in all steps of the dispersal process and may have facilitated the current range expansion.
In summary, these findings may have important implications for dispersal in natural environments, which should be considered when trying to forecast future species distributions. First, dispersal in this butterfly seems to be a highly plastic, context-dependent trait triggered largely by habitat quality rather than by individual condition. This suggests that dispersal in L. tityrus is not random, but an active process. Second, fast development and an enhanced exploratory behavior seem to facilitate the current range expansion. But third, while deteriorating habitat conditions are expected to promote dispersal, they may at the same time impair flight ability (as well as exploratory
behavior) and thereby likely dispersal rates. For a complete understanding of a complex process such as dispersal, further research is required.
What shapes the prospect for democracy in the aftermath of civil conflicts? Some authors claim a successful transition from violence to elections mainly depends on the ability of political institutions, such as power-sharing arrangements, to mitigate the security dilemma among former battlefield adversaries. Drawing on a broader literature, others point to potential effects of foreign aid on democratic development.
This predominant focus on elections and the security dilemma, however, limits our understanding in a number of ways. We do not know how the choice of post-conflict elites to hold elections is strategically intertwined with their willingness to reform other state institutions. We also have only begun to understand how post-conflict power-sharing governments function as revenue source for elites. Knowing how this economic function drives or obstructs post-conflict democratic development is particularly helpful if we shift our attention to a major source of income for post-conflict elites: foreign aid, and the democratic conditions donors attach to it.
Addressing these gaps, I argue that both the economic utility from office as well as political conditionalities give rise to a rent-seeking/democracy dilemma for post-conflict elites: they can either hold elections and face uncertainty over their access to power, but secure economic rents from aid. Or they refuse to democratize, secure their hold on power, but risk losing revenues when donors withdraw aid. In this situation, their optimal strategy is to agree to democratic reforms in the area on which donors place most value, elections. But to maximize their chances of electoral victory and continued access to rents from office, elites simultaneously restrain an independent rule of law and narrowly distribute private goods to their supporters.
This rent-seeking/democracy dilemma is particularly prevalent in one of the most popular forms of post-conflict institutions: power-sharing governments. Including rebel groups in post-conflict cabinets increases the number of constituencies that need to be sustained from the government budget. In addition, the interim nature of transitional power-sharing cabinets leads elites to steeply discount the future and increase rent-seeking in the short term. My main hypothesis is therefore that large aid flows to extensive power-sharing governments should be associated with improved elections, but limits in the rule of law and more provision of private instead of public goods.
To test this prediction quantitatively, I combine data on aid flows and rebel participation in post-conflict cabinets between 1990 and 2010 with indicators for democratic development, election quality, rule of law, and public goods provision. Results from a wide range of regression models provide empirical support for my argument. Individually, extensive power-sharing governments and large aid flows do not seem to have strong effects. Models that introduce an interaction term between aid and power-sharing, however, yield strong evidence of a rent-seeking/democracy dilemma: Power-sharing and foreign aid jointly predict a positive, but small change in democracy scores as well as cleaner elections. At the same time, they are jointly associated with a limited rule of law and stronger distribution of private goods. For each indicator, I document evidence for mechanisms and changes in the effect over time.
The theory and empirical results presented in this dissertation have a number of implications for future research. They highlight the importance of moving away from a singular focus on post-conflict elections and looking also at other institutional dimensions of post-conflict politics. My political economy model of power-sharing also demonstrates the utility of explicitly including economic functions of post-conflict institutions into power-sharing and broader peacebuilding research. And I introduce novel evidence into research and practice of aid delivery; this helps not only to clarify academic debates under which conditions aid can be effective, but also informs practitioners who help conflict-affected countries in their transition from war to democracy.
Glacitectonic deformation in the Quaternary caused the tectonic framework of large-scale folds and displaced thrust sheets of Maastrichtian (Upper Cretaceous) chalk and Pleistocene glacial deposits in the southwestern Baltic Sea area.
A wide spectrum of methods has been compiled to unravel the structural evolution of the Jasmund Glacitectonic Complex. The analyses of digital elevation models (DEM) suggest a division into two structural sub-complexes – a northern part with morphological ridges striking NW–SE and a southern part with SW–NE trending ridges. Geological cross sections from the eastern coast (southern sub-complex) were constructed and restored using the software Move™ and the complementary module 2D Kinematic Modelling™.
The final geometric model of the southern sub-complex shows a small-scale fold-and-thrust belt. It includes three different orders of architectural surfaces (see PEDERSEN, 2014): erosional surfaces and the décollement (1st order), thrust faults (2nd order), and beds outlining hanging-wall anticlines as well as footwall synclines (3rd order). Thrust faults of the southern structural sub-complex are mainly inclined towards south, which indicates a local glacier push from the S/SE.
The glacitectonic structures have a surface expression in form of sub-parallel ridges and elongated valleys in between. Geomorphological mapping and detailed landform analyses together with the structural investigations provide an insight into the chronology of sub-complexes formation. The northern part of the glacitectonic complex is suggested to have been formed before the southern one, considering the partly truncated northerly ridges and their superimposition by the southern sub-complex.
Although there is a high number of scientific publications on the glacitectonic evolution of Jasmund, these presented models often lack a consistent theory for the development integrating all parts of the 100 km2 large complex. Therefore, the combination of all results leads to a more self-consistent genetic model for the entire Jasmund Glacitectonic Complex.
Self-affine tiles and fractals are known as examples in analysis and topology, as models of quasicrystals and biological growth, as unit intervals of generalized number systems, and as attractors of dynamical systems. The author has implemented a software which can find new examples and handle big databases of self-affine fractals. This thesis establishes the algebraic foundation of the algorithms of the IFStile package. Lifting and projection of algebraic and rational iterated function systems and many properties of the resulting attractors are discussed.
The Flavivirus genus (Flaviviridae family) comprises the most important arboviruses in the world such as dengue virus, West Nile virus (WNV), Zika virus (ZIKV), Japanese encephalitis virus and yellow fever virus (YFV). Every year, several outbreaks caused by flaviviruses are reported worldwide (i.e.: ZIKV and YFV outbreaks in South America) with a huge impact on economy and public health. In the last few decades, many aspects of the flavivirus biology and the interaction of flaviviruses with host cells have been elucidated. However, many underlying mechanisms concerning receptor usage, entry process and viral interaction with host cell factors are still not completely understood. Integrins, the major class of cell adhesion molecules have been implicated in the infectious cycle of different viruses including flaviviruses. A previous report proposed that a particular integrin, the αVβ3 integrin, might act as a cellular receptor for WNV. However, this hypothesis was not confirmed by other groups. In the present study, murine cell lines lacking the expression of one or more integrin subunits were used to evaluate the involvement of different integrins in the flavivirus infection cycle. Mouse fibroblasts lacking the expression of β1 integrin (MKF-β1-/-) or β3 integrin (MEF-β3-/-) subunits or αVβ3 integrin (MEF-αVβ3-/-) as well as their corresponding wild-type cells were utilized. A second model using Chinese hamster ovary cells (CHO-K1), a cell line that has been described to be refractory to some flaviviruses, were modified to express either αV (CHO-αV+/+) or β3 (CHO-β3+/+) integrin subunits. All cell lines were first characterized by confocal laser microscopy, flow cytometry and functional assays prior to infection to assess their integrin expression. The cell lines were then inoculated with different flaviviruses of public health relevance: WNV, YFV-17D, Usutu virus (USUV), Langat virus (LGTV) and ZIKV. Infection assays were designed in order to evaluate whether integrins influence i) cell susceptibility; ii) binding; iii) internalization and iv) replication of the investigated flaviviruses. Our findings clearly demonstrate that β1, β3 and αVβ3 integrins do not act as flavivirus cellular receptor or attachment factor since their ablation does not completely abrogate flavivirus infection in the investigated cell lines. Flavivirus binding to the cell surface of MEFs, MKFs and CHO cells was not disturbed by the genomic deletion of the above-mentioned integrins. The deletion of β1 and β3 integrin subunit did not affect internalization of any of the flaviviruses tested. In contrast to that, loss of αVβ3 integrin in the MEF-αVβ3-/- cells showed a statistically significant decrease in WNV and USUV internalization while ZIKV, YFV-17D and LGTV internalization remained unaffected suggesting that αVβ3 integrin might be involved in the internalization process of at least some flaviviruses. On the other hand, flavivirus replication was substantially impaired in the integrin-deficient cell lines in comparison to their corresponding wild-type cells. Both, MEF-β3-/- and MKF-β1-/- cells showed a statistically significant reduction on viral load for all flaviviruses tested in comparison to their respective wild-type cells. The MEF-αVβ3-/- cells in particular, showed a strong inhibition of flavivirus replication with a reduction of up to 99% on viral loads for all flaviviruses tested. Levels of flavivirus negative-strand RNA were substantially decreased in MEF-αVβ3-/- cells indicating that integrins might influence flavivirus RNA replication. The ectopic expression of either αV or β3 integrin subunits in CHO cells slightly increased the replication of all flaviviruses tested. Taken together, this is the first report highlighting the involvement of integrins in ZIKV, USUV, LGTV and YFV infection. The results strongly indicate that the investigated integrins play an important role in flavivirus infection and might represent a novel host cell factor that enhances flavivirus replication. Although the exact mechanism of interaction between integrins and flaviviruses is currently unknown, the results provided in this study deepen our insight into flavivirus - host cell interactions and open doors for further investigations.
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.
Functional characterization of a novel protease isolated from a mouse-adapted S. aureus strain
(2018)
Background: The high incidence of methicillin-resistant Staphylococcus aureus
(MRSA) strengthens the need for new effective antibiotics and a protective vaccine. Up till now, mainly human-adapted Staphylococcus aureus strains were used to study S. aureus pathogenicity in mouse models. However, it is known that S. aureus is highly host-specific. Recently, a mouse-adapted S. aureus strain, JSNZ, was identified. This strain could be a promising tool in developing more appropriate infection models. JSNZ produces high amounts of a putative extracellular protease, named JSNZ extracellular protease (Jep). Since the jep gene was only detected in S. aureus isolates from laboratory mice and wild small rodents and shrews, we hypothesize that Jep is important for colonization and infection in mice. The jep deletion mutant previously created by our collaborators from the University of Auckland, New Zealand, intriguingly showed a reduced survival and growth fitness in murine serum and whole blood as compared to the JSNZ wild type (WT) strain.
Objective: To elucidate the role of Jep in the interaction between S. aureus and its
host by comparing the impact of JSNZ WT with a mutant and a complement strain on the murine immune system. In addition, the elucidation of possible genetic factors behind host-adaptation of S. aureus strains isolated from wild rodents and shrews.
Methods: A jep complemented strain was generated by chromosomal replacement.
JSNZ WT, the jep mutant and the complement strain were subjected to functional
assays (whole blood survival assay, coagulation assay). In addition, the genetic
background that might confer host specificity was tested by staph array genotyping.
Results: The mutant strain JSNZDjep was successfully complemented with the jep
gene using a chromosomal integration approach. The WT strain and the
complemented strain produced the Jep protein in comparable amounts.
Unexpectedly, the complemented strains did not behave like the WT strain but rather like the mutant in a series of in vitro assays. Firstly, the growth of both the deletion mutant and the complemented strains was slightly reduced in TSB as compared to the WT strain. Secondly, the jep knockout strain showed a strongly reduced survival in murine whole blood compared to its wild type counterpart, but so did the complemented strain. Finally, the coagulation of murine plasma was less pronounced for the jep deletion mutant and the complemented strain as compared to the JSNZ WT. To exclude a defect in jep gene expression, we compared the amount of Jep expressed during growth in TSB medium for the three strains. The complemented strain produced Jep in a manner similar to the WT strain in a growth-phase dependent manner, suggesting that Jep expression was not affected during the creation of the complemented strain.
The array data showed some differences in the genetic makeup between animal
isolated strains and matched human strains. For example, while all animal isolates of the CC88 lacked the resistance mecA gene it was found in some human isolates of the same strain.
Conclusion: In conclusion, our unidentified mutation created during the generation
of the jep knock-out strain rather than the jep gene itself manipulated the murine
immune response. The responsible gene and the underlying mechanisms remain to
be clarified. Genetic profiling of S. aureus strains allowed us to obtain some valuable information including data about CC49, the most frequently isolated lineage in wild rodents and shrews where compared to the human isolates the murine strains showed clear signs of host adaptation. However, the analysis had several limitations including the small sample size.
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.
Iodine deficiency disorders (IDD) result from insufficient iodine intake, and may lead to many adverse effects on growth, development and thyroid diseases in humans.
Pakistan is a country with history of iodine deficiency.
Before reunification both parts of Germany were iodine deficient. In the Eastern part, however, due to mandatory iodine prophylaxis adaptation in 1983, the iodine status of the population improved from moderate to mild iodine deficiency. After the reunification of Germany in 1989 “voluntary principle” was adopted leading again to a decrease in iodine intake. Germany and Pakistan present different socioeconomics, cultural values and adaptations to the IDD eradication but have resemblance in history of iodine deficiency. In the recent years Germany has improved in IDD eradication more than Pakistan. The purpose of this research was to study the regional influence on iodine nutritional status of pregnant women in Pakistan and to monitor the effectiveness of the iodine fortification programme in the North-East German population.
Pregnant women data was obtained from randomly selected (public and private) prenatal clinics in five districts of the KPK province of Pakistan. Women visited there for their routine checkup between March and September 2012. Data were obtained from almost 250 pregnant women from each district reaching to a total of 1260 in all five districts.
The SHIP project consists of two population-based cohorts, for which only individuals with German citizenship and main residency in the study area were recruited. In the first SHIP cohort; SHIP-0, individuals aged 20-79 years were selected from population registries by a two-stage cluster sampling method. The net sample (without migrated or deceased persons) comprised 6265 eligible subjects, of which 4308 (response 68.8%) participated between 1997 and 2001. A separate stratified random sample of 8826 adults aged 20-79 years was drawn for SHIP-Trend, of which 4420 subjects participated between 2008 and 2012 (response 50.1%) in SHIP-Trend-0.
All the pregnant women were asked to complete a short interview questionnaire containing the information related to sources and reasons for intake and non-intake of iodized salt. The questionnaire also comprised questions related to knowledge of iodized salt nutrition. Information on the number of previous pregnancies and/or abortions (fetal loss due to various reasons, not including voluntary termination of pregnancy) was also obtained. The gestational age of the pregnant women was determined from the first day of the last regular menstrual period with gestational ages of ≤14.9, 28.9, and ≥29 weeks comprising the first, second, and third trimesters of pregnancy, respectively. For goiter assessment in pregnant women the WHO/UNICEF/IGN recommended palpation method was used. UIC was measured using a modification of the Sandell-Kolthoff reaction with spectrophotometric detection. Evaluation of group iodine status was based on median UIC categories defined by the WHO/IGN. These are: recommended – median 150-249 μg/L; mild iodine deficiency – median <150 μg/L.
For the analysis of monitoring trends of thyroid diseases in SHIP, diagnosed thyroid disorders were assessed by computer-assisted personal interviews. Medication data were obtained online using the IDOM program (online drug-database leaded medication assessment) and classified according to the Anatomical-Therapeutic-Chemical (ATC) classification system.In SHIP population goiter assessment was based on thyroid volume determined with ultrasonography. Goiter was defined as a thyroid volume exceeding 18 mL in women and 25 mL in men. Urinary iodine concentrations were measured from spot urine samples by a photometric procedure. Urinary creatinine concentrations were determined with the Jaffé method. Evaluation of group iodine status was based on median UIC categories defined by the WHO/IGN. The iodine/creatinine ratio was calculated by dividing urinary iodine by urinary creatinine concentrations. Serum TSH, fT3, fT4 levels in SHIP study were measured by an immunochemiluminescent procedure. A method comparison between the two TSH laboratory methods showed only negligible differences. High and low serum TSH levels were based on the reference range established from data for SHIP-0 (0.25 mIU/L - 2.12 mIU/L) and SHIP-TREND-0 (0.49 mIU/L - 3.29 mIU/L) respectively (21,22). Anti-TPO Abs were measured by an enzyme immunoassay in the whole SHIP study. The anti-TPO Abs status was defined as follows: normal < 60 IU/ml in men and < 100 IU/ml in women; increased > 60 IU/ml in men and > 100 IU/ml in women; positive: > 200 IU/ml in both sexes.
Thyroid ultrasonography was performed in SHIP-0 using an ultrasound VST-Gateway with a 5 MHz linear array transducer. In SHIP-Trend-0 ultrasonography was performed with a portable device using a 13-MHz linear array transducer. In both studies intra- and inter-observer reliabilities were assessed before the start of the study and semi-annually during the study. For thyroid volume all inter-observer and inter-device variabilities showed mean differences (±2 SD)of < 5% (<25%). Thyroid volume was calculated as length x width x depth x 0.479 (ml) for each lobe (26). The normal thyroid echo pattern was classified as homogeneous. A homogeneous echo pattern with reduced echogenicity was defined as hypoechogenic. Nodular changes exceeding 10 mm in diameter were defined as thyroid nodules.
Multivariable logistic regression analysis adjusting for age was used to regress the outcome measures (knowledge about IDD, iodized salt intake, UIC <150mIU/L and goiter prevalence) on regional influences (as exposure) in each specific district. These results are presented as odd ratios and their 95% confidence interval.
For the analysis in SHIP, all analyses were standardized by base-weights to account for different sampling probabilities. In SHIP-Trend-0, additionally, inverse probability weights for study participation were calculated, which were multiplied with the base-weights. Differences in median levels between SHIP-0 and SHIP-Trend-0 were tested by median regression models; prevalence differences between SHIP-0 and SHIP-Trend-0 were tested by Poisson regression models.
The majority of pregnant women (88.0%) had no knowledge about IDD. A very high (79%) percentage of pregnant women were not taking iodized salt, out of which 36.6% reported that iodized salt would negatively affect reproduction and for 17.0%, it was too expensive. Iodized salt intake in pregnant women was high in the big cities (Peshawar, Nowshehra) and in the urban areas (27.0%)
In 41.3% of the pregnant women, we observed a UIC of >150mIU/L. The median UIC level for the pregnant women was 131µg/L. The total goiter prevalence in pregnant women was 25.5%. The prevalence of UIC <150mIU/L in pregnant women did not differ between rural and urban areas. The results based on logistic regression analysis shows that the prevalence on knowledge about IDD, iodized salt intake, UIC <150mIU/L, and goiter did not differ in pregnant women between urban and rural areas. In district Lakki Marwat except, the pregnant women from urban residence had higher odds of having knowledge on IDD and iodized salt intake than their rural counterparts.
The prevalence of diagnosed thyroid disorders increased from 7.6% [CI 6.9-8.5] in SHIP-0 to 18.9% [CI 17.6-20.1] in SHIP-Trend-0. Likewise, the prevalence of thyroid medication intake increased from 6.2% [CI 5.5-7.0] to 11.1% [CI 10.1-12.2]. The median urinary iodine excretion levels decreased significantly, which was more pronounced in females than in males. The median iodine-to-creatinine ratio declined in all sex- and age-groups with stronger decrease in females than in males. The prevalence of median urinary iodine excretion levels <100µg/L increased between SHIP-0 and SHIP-Trend-0. Median serum TSH levels increased significantly between SHIP-0 and SHIP-Trend-0, resulting in a right shift of the serum TSH level distribution. The prevalence of high serum TSH levels remained almost stable between SHIP-0 and SHIP-Trend-0. Likewise, the prevalence of low TSH remained almost stable between SHIP-0 and SHIP-Trend-0. The prevalence of increased anti-TPO Abs and positive anti-TPO Abs decreased from SHIP-0 to SHIP-Trend-0 in the whole study population. The prevalence of hypoechogenic thyroid pattern decreased from SHIP-0 to SHIP-Trend-0. The median thyroid volume remained similar between SHIP-0 and SHIP-Trend-0 in the whole study population. Goiter prevalence decreased significantly; more pronounced in males than in females, while the prevalence of thyroid nodules increased between SHIP-0 and SHIP-Trend-0.
In pregnant women in Pakistan due to insufficient awareness campaigns and low literacy ratio in rural areas urinary iodine excretion levels indicate a stable iodine supply, which is still not sufficient. Our results show that rural/urban disparity is affecting the IDD prevention program in rural districts, but not in general. The SHIP data indicate that the improved iodine supply over the past two decades in Germany is paralleled by a reduction in prevalence of IDDs, while no increase was observed in markers of autoimmune thyroid disorders arguing for an optimal iodine supply of the general adult population in Northeast Germany. The increase in prevalence of diagnosed thyroid disorders and the intake of thyroid medication might be because of inappropriate therapeutical decisions which should be made with caution, based on regional TSH reference ranges, its prognostic value, and compliance with treatment.
The fear of somatic sensations is highly relevant in the etiology and maintenance of various disorders. Nevertheless, little is known about this fear of body symptoms and many questions are yet unanswered. Especially physiological studies on interoceptive threat are rare. Therefore, the present thesis investigated defensive mobilization, autonomic arousal, and brain activation during the anticipation of, exposure to, and recovery from unpleasant body sensations. Symptoms were provoked using a standardized hyperventilation procedure in a sample of high (and as controls: low) anxiety sensitive individuals - a population high at risk for developing a panic disorder and high in fear of internal body symptoms.
In study one, anxious apprehension was investigated during anticipation of interoceptive threat (somatic sensations evoked by hyperventilation) and exteroceptive threat (electric shock). Symptom reports, autonomic arousal, and defensive mobilization assessed by the startle eyeblink response were analyzed. Extending the knowledge on anticipation of interoceptive threat, study two investigated the neural networks activated during anxious apprehension of unpleasant body sensations. Symptom reports and startle response data were collected during a learning session after which participants high and low in fear of somatic symptoms attended a fMRI session anticipating threat (hyperventilation – learned to provoke unpleasant symptoms) or safety (normal breathing). Study three examined the actual exposure to internal body symptoms, investigating symptoms reports, autonomic arousal, and the startle eyeblink response during guided breathing (hyperventilation and, as a non-provocative comparison condition, normoventilation) and during recovery. And finally, study four addressed changes in the defensive mobilization during repeated interoceptive exposure via a hyperventilation procedure. High and low anxiety sensitive persons went through two guided hyperventilation and normoventilation procedures that were spaced one week apart while symptom reports, breathing parameters, and startle response magnitudes were measured.
In study one it was demonstrated that the anticipation of exteroceptive threat led to a defensive and autonomic mobilization in high and low anxiety sensitive individuals, while during interoceptive threat only high anxiety sensitive participants were characterized by a potentiated startle response and autonomic activation. Imaging data of study two revealed that 1) during anticipation of hyperventilation all participants were characterized by an increased activation of a fear network consisting of anterior insula/ orbitofrontal cortex and rostral parts of the dorsal anterior cingulate cortex/ dorsomedial prefrontal cortex, 2) high fear individuals showed higher anxious apprehension than low fear controls during the entire context (safe and threat conditions), indexed by an overall stronger activation of the described network, and 3) while low fear controls learned that (undisclosed to all participants) in the fMRI scanner the threat cue was not followed by an unpleasant hyperventilation task, high fear participants continued to show stronger fear network activation to this cue. In study three it was demonstrated, that the hyperventilation procedure led to a marked increase in somatic symptoms and to autonomic arousal. While high and low anxiety sensitive groups did not differ during hyperventilation, in the early recovery only high anxiety sensitive individuals showed defensive mobilization, indicated by potentiated startle response magnitudes, and increased autonomic arousal after hyperventilation as compared to after normoventilation. Substantiating these findings, in study four all participants reported more symptoms during hyperventilation than during normoventilation, in both sessions. Nevertheless, only high anxiety sensitive participants displayed a potentiation of startle response magnitudes after the first hyper- vs. normoventilation. One week later, when the exercise was repeated this potentiation was no longer present and thus both groups no longer differed in their defensive mobilization. Even more, the number of reported baseline symptoms decreased from session one to session two in the high-AS group. While high anxiety sensitive persons reported increased baseline anxiety symptoms in session one, groups did not anymore differ in session two.
These data indicate that the standardized hyperventilation procedure is a valid paradigm to induce somatic symptoms. Moreover, it induces anxious apprehension especially in persons highly fearful of internal body symptoms. The repetition of interoceptive exposure, however, reduces associated fear in highly fearful individuals. Thus, this paradigm might provide an innovative method to study anxious apprehension and also treatment effects in patients with panic disorder. The present findings are integrated and discussed in the light of the current literature.
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.
Dendrochronology, the science of tree-rings is a tool which has been widely used for many years for understanding changes in the environment, as trees react to environmental changes over time. In the contemporary situation, where climate warming in the Arctic is unequivocal and its effects on the Alpine and tundra ecosystems are seen pronouncedly in the past decade, the role of dendro-studies and the use of trees and shrubs alike as proxies of change has become critical. Studies clearly indicate that warming in the Arctic and Alpine tundra has resulted in increased vegetation in recent years. Shrubs, in these sensitive ecosystems, have proven to be highly instrumental as they likely benefit from this warming and hence are good indicators and auditees of this change. Therefore, in this study, we investigate the potential of shrubs in the evolving field of dendro-ecology/climatology.
Studies from classical dendrochronology used annual rings from trees. Further, because of shrub sensitivity to contemporary change, shrub-based dendrochronological research has increased at a notable scale in the last decade and will likely continue. This is because shrubs grow even beyond the tree line and promise environmental records from areas where tree growth is very limited or absent. However, a common limitation noted by most shrub studies is the very hard cross-dating due to asynchronous growth patterns. This limitation poses a major hurdle in shrub-based dendrochronological studies, as it renders weak detection of common signals in growth patterns in population stands. This common signal is traced by using a ‘site-chronology’.
In this dissertation, I studied shrub growth through various resolutions, starting from understanding radial growth within individuals along the length of the stem, to comparison of radial growth responses among male and female shrubs, to comparing growth responses among trees and shrubs to investigation of biome-wide functional trait responses to current warming. Apart from Chapter 4 and Chapter 6, I largely used Juniperus communis sp. for investigations as it is the most widely distributed woody dioecious species often used in dendro-ecological investigations in the Northern Hemisphere.
Primarily, we investigated radial growth patterns within shrubs to better understand growth within individuals by comparing different stem-disks from different stem heights within individuals. We found significant differences in radial growth from different stem-disks with respect to stem heights from same individuals. Furthermore, we found that these differences depending on the choice of the stem-disk affect the resulting site-chronology and hence climate-sensitivity to a substantial extent and that the choice of a stem-disk is a crucial precursor which affects climate-growth relationships.
Secondly, we investigated if gender difference – often reported causing differential radial growth in dioecious trees – is an influential factor for heterogeneous growth. We found that at least in case of Juniperus communis. L and Juniperus communis ssp nana. WILLD there is no substantial gender biased difference in radial growth which might affect the site-chronology. We did find moderate differences between sexes in an overall analysis and attribute this to reproductive effort in females.
In our study to test the potential of shrubs for reconstruction, we used a test case of Alnus viridis ssp crispa. We found a strong correlation between ring-width indices and summer temperature. Initially, the model failed the stability tests when we tested the stability of this relation using a response function model. However, using wood-anatomical analysis we discovered that this was because of abnormal cell-wall formation resulting in very thin rings in the year 2004. Pointer year analysis revealed that the thin rings were caused because of a moth larval outbreak and when corrected for these rings the model passed all stability tests.
Furthermore, to see if trees and shrubs growing in same biomes react to environmental changes similarly, a network analysis with sites ranging from the Mediterranean biome to the Ural Mountains in Russia was carried out. We found that shrubs react better to the current climate warming and have a decoupled divergent temperature response as compared to coexisting trees. This outcome reiterated the importance of shrub studies in relation to contemporary climate change. Even though trees and shrubs are woody forms producing annual rings, they have very different growth patterns and need different methods for analysis and data treatment.
Finally, in a domain-wide network analysis from plant-community vegetation survey, we investigated functional relationships between plant traits (leaf area, plant height, leaf nitrogen content, specific leaf area (SLA), and leaf dry matter content (LDMC)) and abiotic factors viz. temperature and soil moisture. We found a strong relation between summer temperature and community height, SLA and LDMC on a spatial scale. Contrarily, the temporal-analysis revealed SLA and LDMC lagged and did not respond to temperature over the last decade. We realized that there are complex interactions between intra-specific and inter-specific plant traits which differ spatially and temporally impacting Arctic ecosystems in terms of carbon turn over, surface albedo, water balance and heat-energy fluxes. We found that ecosystem functions in the Arctic are closely linked with plant height and will be indicative of warming in the short term future becoming key factors in modelling ecosystem projections.
Individual white spruce (Picea glauca (Moench) Voss) growth limitations at treelines in Alaska
(2018)
White spruce (Picea glauca (Moench) Voss) is one of the most common conifers in Alaska and various treelines mark the species distribution range. Because treelines positions are driven by climate and because climate change is estimated to be strongest in northern latitudes, treeline shifts appear likely. However, species range shifts depend on various species parameters, probably most importantly on phenotypic plasticity, genetic adaptation
and dispersal. Due to their long generation cycles and their immobility, trees evolved to endure a wide variety of climatic conditions. In most locations, interannual climate variability is larger than the expected climate change until 2100. Thus treeline position is typically thought of as the integrated effect of multiple years and to lag behind gradual climate change by several decades. Past dendrochronological studies revealed that growth of white spruce in Alaska can be limited by several climatic variables, in particular water stress and low temperatures. Depending on how the intensity of climate warming, this could result in a leading range edge at treelines limited by low temperatures and trailing treelines where soil moisture is or becomes most limiting. Climate-growth correlations are the dendrochronological version of reaction norms and describe the relationship between an environmental variable and traits like tree-ring parameters (e.g. ring width, wood density, wood anatomy). These correlations can be used to explore potential effects of climate change on a target species. However, it is known that individuals differ with respect to multiple variables like size, age, microsite conditions, competition status or their genome. Such individual differences could be important because they can modulate climate-growth relationships and consequently also range shifts and growth trends. Removing individual differences by averaging tree-ring parameters of many individuals into site chronologies could be an oversimplification that might bias estimates of future white spruce performance. Population dynamics that emerge from the interactions of individuals (e.g. competition) and the range of reactions to the same environmental drivers can only be studied via individual tree analyses. Consequently, this thesis focuses on factors that might alter individual white spruce’ climate sensitivity and methods to assess such effects. In particular, the research articles included explore three topics:
1. First, clones were identified via microsatellites and high-frequency climate signals of clones were compared to that of non-clonal individuals. Clonal and non-clonal individuals showed similar high-frequency climate signals which allows to use clonal and non-clonal individuals to construct mean site chronologies. However, clones were more frequently found under the harsher environmental conditions at the treelines which could be of interest for the species survival strategy at alpine treelines and is further explored in the associated RESPONSE project A5 by David Würth.
2. In the second article, methods for the exploration and visualization of individual-tree differences in climate sensitivity are described. These methods represent a toolbox to explore causes for the variety of different climate sensitivities found in individual
trees at the same site. Though, overlaying gradients of multiple factors like temperature, tree density and/or tree height can make it difficult to attribute a single cause to the range of reaction norms (climate growth correlations).
3. Lastly, the third article attempts to disentangle the effect of age and size on climate-growth correlations. Multiple past studies found that trees of different Ages responded differently to climatic drivers. In contrast, other studies found that trees do not age like many other organisms. Age and size of a trees are roughly correlated, though there are large differences in the growth rate of trees, which can lead to smaller trees that are older than taller trees. Consequently, age is an imperfect Proxy for size and in contrast to age, size has been shown to affect wood anatomy and thus tree physiology. The article compares two tree-age methods and one tree-size method based on cumulative ring width. In line with previous research on aging and Wood anatomy, tree size appeared to be the best predictor to explain ontogenetic changes in white spruce’ climate sensitivity. In particular, tallest trees exhibited strongest correlations with water stress in previous year July. In conclusion, this thesis is about factors that can alter climate-growth relationships (reaction norms) of white spruce. The results emphasize that interactions between climate variables and other factors like tree size or competition status are important for estimates of future tree growth and potential treeline shifts. In line with previous studies on white spruce in Alaska, the results of this thesis underline the importance of water stress for white spruce.
Individuals that are taller and that have more competitors for water appear to be most susceptible to the potentially drier future climate in Alaska. While tree ring based growth trends estimates of white spruce are difficult to derive due to multiple overlaying low frequency (>10 years) signals, all investigated treeline sites showed highest growth at the treeline edge. This could indicate expanding range edges. However, a potential bottleneck for treeline advances and retreats could be seedling establishment, which should be explored in more detail in the future.
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).
Unstable environments and habitats changing due to climate change force individuals to either respond by genetic adaptation, phenotypic plasticity or by dispersal to suitable environments. Theodoxus fluviatilis (Linneaus, 1758) is a good study organisms when researching phenotypic plasticity and genetic adaptation as it naturally appears in freshwater (FW) as well as brackish water (BW) and thus inhabits a wide range of environmental salinities (0-18‰). It is a euryhaline snail that can be found in shallow waters with stony ground or on Fucus spp. and has formed regional subgroups. The brackish water and the freshwater subgroups are spatially separated and the species cannot be found in areas inbetween, e.g. estuaries.
The species shows great variability in shell patterning and shell size and there is still debate whether the subgroups are distinguishable by these traits or not. The mitochdrial RNA marker cytochrome c subunit I did not show differences between the subgroups indicating that they must be closely related, but salinity tolerance has been observed to be higher in BW snails. This might be caused by the different protein expression patterns and osmolyte accumulation (measured as ninhydrin-positive substances) observed in this species in previous studies. The exact mechanisms regulating protein expression and osmolyte accumulation, however, are not fully understood yet.
Data collected for this thesis shows differences in shell size and suggests a less strict grouping of FW and BW individuals as shell sizes of one FW site are more similar to BW individuals than the other FW ones. A better salinity tolerance towards high salinities and a higher physiological salinity limit of BW snails was confirmed and extended by demonstrating an expanded tolerance range through slow acclimation to challenging salinities in snails from both subgroups. This was achieved by a shift in the slope of their reaction norms that was much more pronounced in BW snails than FW ones. S3 individuals showed a shift similar to that of BW individuals. The data for the salinity tolerance indicates that the underlying mechanism for these tolerances are a combination of phenotypic plasticity and genetic adaptation. Despite an acclimation and shift in the slope of the reaction norms and therefore an increased tolerance towards high salinities (plasticity) FW individuals from two collection sites were not able to cope with salinities as high as BW individuals (local adaptation). The general ability to mobilise free amino acids (FAA) as organic osmolytes was not the reason for this tolerance difference. Individuals from BW and FW sites were capable of accumulating quantities of FAAs equally well. Proline, alanine and urea were the most important components of the accumulated cocktail of organic osmolytes. Even though the total amount of FAAs accumulated under hyperosmotic conditions was the same in both subgroups, there were differences in the metabolic pathways involved in osmolyte accumulation in the foot muscle. The data indicates that the hydrolysis of storage proteins and the synthesis of proline and alanine are the main processes to avoid detrimental body volume shrinkage in T. fluviatilis. While FW individuals seemed to rely on the degradation of proteins and synthesis of alanine, BW individuals depended on newly synthesising proline and alanine and accumulating urea as a side product of transamination. The accumulation of urea is a new finding in aquatic living snails and has not been reported as a mechanism to avoid cell volume shrinkage in these animals.
Differing protein expression patterns were observed under control conditions across all collection sites. 9 spots showed volume changes in BW snails opposite to those of FW snails from collection sites S1 and S2. For 6 of those spots, S3 individuals showed patterns similar to those of BW individuals and for the remaining 3 they showed patterns similar to those of FW animals. The patterns observed when exposing snails to hypo- or hyperosmotic stress were not conclusive in relation to pinpointing individual spots that show the same pattern in all collection sites, but revealed the heterogeneity of protein expression in snails from the different collection sites and in the process of osmoregulation. It also showed the general tendency of protein reduction when snails where under osmotic stress of either kind (hypo- or hyperosmotic), which supports the hypothesis of storage protein degradation.
The investigation of an ANP-receptor showed two variations of the encoding sequence expressed in T. fluviatilis. S3 individuals as well as BW individuals were found to express one type, while FW individuals, with the exception of one sample expressed the other type. This showed that the FW subgroup of T. fluviatilis seems to be more heterogeneous than the BW subgroup, but also raises the question of the dispersal history of this species. The collected data indicates that T. fluviatilis individuals are firstly capable of surviving the acidity of a duck's gizzard and secondly can tolerate acute salinity changes to 16‰ when introduced into a new environment. Hence, if snails from the FW were to be transported to waters with a salinity of up to 16‰ by man, bird, drifting plants or some other means of transport, they would most likely survive and possibly be able to thrive and spread.
The highly oncogenic alphaherpesvirus Marek’s disease virus (MDV) causes immense economic losses in the poultry industry. The main targets of in vivo MDV infection are primary B and T lymphocytes. The cytolytic infection of B cells leads to depletion of lymphoid cells results in severe immunosuppression. Infected B cells recruit and activate T cells. The close interaction between B cells and T cells enables efficient intercellular transfer of MDV. During infection of T cells, the virus enters a latent state. Infection of T cells can lead to transformation of these cells and formation of lymphoma, which manifest in various visceral organs. This study aimed at the characterization of the proteomes of MDV-infected lymphocytes during the lytic and latent phases of infection.
Previous in vitro studies concerning the MDV pathogenesis and host-virus interactions have been mainly conducted with primary fibroblasts or kidney cells, due to the short lifespan of primary lymphocytes in cell culture. Recently, a cultivation system has been established that extents the lifespan of primary lymphocytes through the addition of cytokines to the growth medium. This allowed the infection of B cells in vitro and to conduct quantitative proteomic analysis of primary lymphocytes. Infection with GFP labelled virus recombinants allowed the isolation of infected cells by FACS for the proteome analysis of MDV infected B lymphocytes. An efficient quantitative proteomic workflow was developed, which consisted of a filter-aided (FASP) digest of the extracted proteins, followed by differential dimethyl chemical labeling of the peptides for quantitative evaluation prior to LC-MALDI TOF/TOF mass spectrometry. Only few alterations of the protein and transcript expression profiles were observed after infection of primary B cells with the very virulent RB-1B and the live-attenuated vaccine strain CVI988/Rispens. Relevant changes in relative protein levels were found for only twelve and six interesting host proteins after RB1B and CVI988 infection, respectively. However, the regulations were confirmed by inspection of the spectra from all experiments. The identified candidates play a role in immune response, translation and inflammatory response.
To confirm the potential infection markers, RNA-seq analysis of three biological replicates of each RB-1B -, CVI988- and mock-infected B cells was performed. Eighty expressed MDV transcripts could be identified, which were associated with lytic infection. The same MDV proteins were identified after infection with RB-1B or CVI988. However, transcriptome and proteome analysis of MDV-infected primary B cells showed only poor correlation. This indicates that the changes in protein expression profiles are mostly due to posttranscriptional events. Infection marker candidates were identified by the RNA-seq analysis, for which the gene expression was altered by MDV infection. Although almost 12,000 transcripts were identified, only few transcript levels changed markedly after MDV infection. The biological processes immune response, apoptotic process, signal transduction, cell migration and response to virus were enriched after MDV infection. The RNA-seq results confirm the observation that alterations of protein levels early after MDV infection are rare.
Most notably, MDV induces transformation of lymphocytes leading to malignant T-cell lymphomas in visceral organs with mortalities of up to 100 %. While several factors involved in MDV tumorigenesis have been identified, the transformation process is not fully understood. Therefore, we set out to fill this knowledge gap using proteome analysis of transformed T-cells ex vivo. In addition, the role of the viral telomerase RNA during transformation was assessed by comparison of tumors that had formed after infection with WT-virus or a telomerase RNA negative mutant. A major obstacle for tumor proteome analyses is the preparation of sufficient amounts of homogenous tumor tissue, as tumors appear with a dispersed morphology in the affected organs. The quantitation of cell types within the tumors indicated varying portions of hepatocytes, connective tissue, and CD3+ lymphocytes even with the same virus strain in different animals. However, the ∆vTR-induced tumors contained lower levels of hepatocytes and higher levels of CD3+ lymphocytes compared to WT tumors in all tested tumor samples. Thus, ∆vTR tumors were chosen for determination of differences in protein expression profiles of tumors and naïve T cells for their lower content of liver cells. We developed a workflow for the proteome analysis of T cell tumors from livers of MDV-infected chickens. Samples included laser capture micro-dissected tissue cuts from tumors and surrounding healthy liver tissue as well as naïve T-cells prepared from thymus. To enable quantitative proteome analysis, samples were digested using the FASP protocol and peptides were isotope-coded by differential dimethyl labeling. To improve proteome analysis peptides were fractionated by preparative isoelectric focusing prior to nano-HPLC MALDI/TOF-TOF mass- spectrometric analysis.
Proteomic analyses of LCM dissected ΔvTR tumor compared to naïve T cells, the main targets of transformation, identified nineteen potential transformation markers but again only minor changes in relative levels were observed. Several of the identified markers could also be verified by RT-qPCR on transcript level. The identified transformation candidates were associated with nucleosome assembly, regulation of transcription, inflammatory response, immune response and oxidation-reduction process.
However, further functional analyses are necessary to fully elucidate the role of the identified markers during MDV infection and transformation.
Background: Depression and obesity are widespread and closely linked. Brain-derived neurotrophic factor (BDNF) and vitamin D are both assumed to be associated with depression and obesity. Little is known about the interplay between vitamin D and BDNF. We explored the putative associations and interactions between serum BDNF and vitamin D levels with depressive symptoms and abdominal obesity in a large population-based cohort. Methods: Data were obtained from the population-based Study of Health in Pomerania (SHIP)-Trend (n = 3,926). The associations of serum BDNF and vitamin D levels with depressive symptoms (measured using the Patient Health Questionnaire) were assessed with binary and multinomial logistic regression models. The associations of serum BDNF and vitamin D levels with obesity (measured by the waist-to-hip ratio [WHR]) were assessed with binary logistic and linear regression models with restricted cubic splines. Results: Logistic regression models revealed inverse associations of vitamin D with depression (OR = 0.966; 95% CI 0.951–0.981) and obesity (OR = 0.976; 95% CI 0.967–0.985). No linear association of serum BDNF with depression or obesity was found. However, linear regression models revealed a U-shaped association of BDNF with WHR (p < 0.001). Conclusion: Vitamin D was inversely associated with depression and obesity. BDNF was associated with abdominal obesity, but not with depression. At the population level, our results support the relevant roles of vitamin D and BDNF in mental and physical health-related outcomes.
Background: Magnetic resonance imaging (MRI) techniques are rarely used in the context of abdominal sepsis and in sepsis research. This study investigates the impact of MRI for monitoring septic peritonitis in an animal model (colon ascendens stent-induced peritonitis, CASP). The CASP model closely mimics that of human disease and is highly standardized. The most frequently employed readout parameter in mouse CASP studies is prolonged or decreased rate of survival. Monitoring the progression of peritonitis via MRI could provide a helpful tool in the evaluation of severity. The use of alternative readout systems could very well reduce the number of research animals. Perspectively, clinical improvement after certain treatment could be classified. Methods: This study describes for the first time MRI findings following the induction of septic peritonitis in mice using the CASP model. Two sublethal groups of mice with septic peritonitis were investigated. Each had received one of two differing stent diameters in order to control the leakage of feces into the abdominal cavity. Each mouse served as its own control. Imaging and analyses were performed blinded. Gut diameters, stomach volume, abdominal organ wall diameters, and volume of the adrenal glands were measured. Serum corticosterone levels were detected using ELISA. Serum IL-6, TNF-α, IL-1β, and IL-10 levels were screened by cytometric bead array. Statistical analysis was performed using the Mann-Whitney U test for nonparametric probes and the Kruskal-Wallis and t tests. Results: Using a 7-tesla MRI scanner 24 and 48 h after induction of septic peritonitis, interenteric fluid, organ swelling of spleen and adrenal glands, as well as dilatation of the stomach were compared to nonseptic conditions. Swelling of adrenal glands resulted in an increased serum corticosterone level. In addition, the wall of the intestine bowel was thickened. Based upon these findings, an MRI score (MRI sepsis score, MSS) for abdominal sepsis in mice was established. Reduced stent sizes led to reduced severity of the abdominal sepsis, which could be reproduced in the MSS, which is described here for the first time. Conclusions: Intraabdominal variations during septic peritonitis are detectable by MRI techniques. MRI methods should become a more important tool for the evaluation of abdominal peritonitis. MSS could provide an interesting tool for the evaluation of therapeutic strategies.
Background: Magnetic resonance imaging (MRI) techniques are rarely used in the context of abdominal sepsis and in sepsis research. This study investigates the impact of MRI for monitoring septic peritonitis in an animal model (colon ascendens stent-induced peritonitis, CASP). The CASP model closely mimics that of human disease and is highly standardized. The most frequently employed readout parameter in mouse CASP studies is prolonged or decreased rate of survival. Monitoring the progression of peritonitis via MRI could provide a helpful tool in the evaluation of severity. The use of alternative readout systems could very well reduce the number of research animals. Perspectively, clinical improvement after certain treatment could be classified. Methods: This study describes for the first time MRI findings following the induction of septic peritonitis in mice using the CASP model. Two sublethal groups of mice with septic peritonitis were investigated. Each had received one of two differing stent diameters in order to control the leakage of feces into the abdominal cavity. Each mouse served as its own control. Imaging and analyses were performed blinded. Gut diameters, stomach volume, abdominal organ wall diameters, and volume of the adrenal glands were measured. Serum corticosterone levels were detected using ELISA. Serum IL-6, TNF-α, IL-1β, and IL-10 levels were screened by cytometric bead array. Statistical analysis was performed using the Mann-Whitney U test for nonparametric probes and the Kruskal-Wallis and t tests. Results: Using a 7-tesla MRI scanner 24 and 48 h after induction of septic peritonitis, interenteric fluid, organ swelling of spleen and adrenal glands, as well as dilatation of the stomach were compared to nonseptic conditions. Swelling of adrenal glands resulted in an increased serum corticosterone level. In addition, the wall of the intestine bowel was thickened. Based upon these findings, an MRI score (MRI sepsis score, MSS) for abdominal sepsis in mice was established. Reduced stent sizes led to reduced severity of the abdominal sepsis, which could be reproduced in the MSS, which is described here for the first time. Conclusions: Intraabdominal variations during septic peritonitis are detectable by MRI techniques. MRI methods should become a more important tool for the evaluation of abdominal peritonitis. MSS could provide an interesting tool for the evaluation of therapeutic strategies.
With improvements in breast imaging, mammography, ultrasound and minimally invasive interventions, the detection of early breast cancer, non-invasive cancers, lesions of uncertain malignant potential, and benign lesions has increased. However, with the improved diagnostic capabilities comes a substantial risk of false-positive benign lesions and vice versa false-negative malignant lesions. A statement is provided on the manifestation, imaging, and diagnostic verification of isolated benign breast tumours that have a frequent manifestation, in addition to general therapy management recommendations. Histological evaluation of benign breast tumours is the most reliable diagnostic method. According to the S3 guideline and information gained from analysis of the literature, preference is to be given to core biopsy for each type of tumour as the preferred diagnostic method. An indication for open biopsy is also to be established should the tumour increase in size in the follow-up interval, after recurring discrepancies in the vacuum biopsy results, or at the request of the patient. As an alternative, minimally invasive procedures such as therapeutic vacuum biopsy, cryoablation or high-intensity focused ultrasound are also becoming possible alternatives in definitive surgical management. The newer minimally invasive methods show an adequate degree of accuracy and hardly any restrictions in terms of post-interventional cosmetics so that current requirements of extensive breast imaging can be thoroughly met.
Abstract
Background: Behavior management techniques (BMT) are essential in order to
achieve a successful dental treatment with a minimum amount of stress in paediatric
dentistry, but parents are not equally accepting different advanced BMT.
Purpose: To investigate the differences in parental acceptance of advanced
behavior management techniques between University of Greifswald/Germany and
Jordan University/Jordan.
Methods: Parents of the children treated in the pedodontic departments at the
University of Greifswald/Germany and Jordan University/Jordan rated their
acceptance level of four advanced behavior management techniques (passive
restraint, active restraint, nitrous oxide sedation and general anesthesia) for normal
treatment, and for urgent treatment using a five points Likert scale. 200 parents (100
in each university) completed the questionnaire forms for analysis.
Results: Nitrous oxide sedation was rated the most accepted technique in
Greifswald and Jordan (mean 3.78±1.34; 3.22±1.50, respectively). The least
acceptable technique in Greifswald was passive restraint (2.05±1.18) and in Jordan
general anesthesia (2.11±1.30). The parents in Greifswald are significantly more
accepting nitrous oxide sedation than parents in Jordan (p=0.010), while parents in
Jordan are significantly more willing to accept passive restraint (p=0.001). The
acceptance of all advanced behavior management techniques increased significantly
in both groups when the treatment is urgent (p≤0.05),
Conclusions: Parental culture and the urgency of the treatment affect the
acceptance to different behavior management techniques. Moreover, the parental
attitude to the pharmacological technique has changed, as nitrous oxide sedation
generally appears to be the most preferred advanced technique in both groups.
Class I and class II glutaredoxins (Grxs) are glutathione (GSH)-dependent proteins, that function as oxidoreductases (class I) or mediate cellular iron trafficking (class II). Some members of class I Grxs like human Grx2 are able to complex a [2Fe-2S] cluster and form a dimeric holo complex, which renders them catalytically inactive and is the basis for their function as redox sensors. Class II Grxs like human Grx5 also complex [2Fe-2S] clusters, however these proteins transfer the clusters to other proteins. Both functionally distinct classes share a similar thioredoxin fold and conserved interaction sites for the non-covalently binding of GSH, which is required to complex the [2Fe-2S] cluster. Furthermore, the proteins from both classes contain a highly nucleophilic active site cysteine that would allow both classes to catalyze GSH-dependent oxidoreduction reactions. Despite of these similar features, only class I Grxs are able to form a mixed disulfide with GSH and to reversibly transfer it to protein thiols (de-/glutathionylation). Interestingly, neither class I Grxs nor class II Grxs can effectively compensate the loss of an essential member of the other class. Even though some structural differences were described earlier, the basis for their different functions remained unknown. In particular, the lack of catalytic activity of class II Grxs as oxidoreductases could not be explained. Here, we demonstrate that the different conformations of a conserved lysyl side chain are the molecular determinant of the oxidoreductase or Fe-S transfer activity of class I and II Grxs, respectively. A specific loop structure that is conserved in all class II Grxs determines one lysyl conformation that prevents the formation of a mixed disulfide of the active site cysteinyl thiol with GSH. Using engineered mutants of hGrx2 and hGrx5, we demonstrated that the exchange of the distinct loop between the classes results in a loss of oxidoreductase function of class I hGrx2 and the gain of oxidoreductase activity of class II hGrx5. The altered GSH binding mode also profoundly changes the [2Fe-2S] cluster binding of the engineered mutants and thereby also influences stability of the holo complexes, a pre-determinant for [Fe-S] cluster transfer activity. With the minor shift of 2 Å in a conserved lysyl side chain orientation we were not only able to modify the catalytic activity of two small human mitochondrial proteins, but on a much larger scale also provided evidence for the previously unknown structural basis that determines the function of all class I and class II Grxs.
The oxidoreductase activity of hGrx2 was also analyzed in vivo in a model of doxorubicin cell toxicity. Applying a mass spectrometrical approach, we identified various mitochondrial proteins as targets for redox regulation. Furthermore, our results gave reason to reconsider some common assumptions regarding doxorubicin-induced apoptosis and the protective function of mitochondrial Grx2.
Currently, plastic materials are an integral part of our lives, but their production mostly bases on fossil fuels or derivatives, which resources are decreasing. Extraction and processing of non-renewable resources have also negative impact on environment. One of the most promising and environmentally friendly approaches is use of microorganism. This PhD dissertation presents the non-conventional yeast Arxula adeninivorans as a host for production of bio-based and biodegradable poly(hydroxyalkanoates) plastics poly(hydroxybutyrate) and co-polymer poly(hydroxybutyrate-co-hydroxyvalerate). Additionally, the constructed yeast strain was able to secrete enantiomerically pure (R)-3-hydroxybutyric acid.
The production of PHAs requires three enzymes: β-ketothiolase, acetoacetyl-CoA reductase and PHA synthase. The strategy followed in this project was divided into two parts. While all three enzymes are responsible for intracellular production of PHA polymer, first two only lead to secretion of (R)-3-HB into culture media, which was used in a first stage of work to establish and optimize polymer production. Both, different bacterial strains and yeast A. adeninivorans were taken into account in screening of the genes encoding aforementioned enzymes. Bacterial genes were chemically synthesized using codon optimization pattern and endogenous genes were obtained using PCR and genomic DNA template from A. adeninivorans LS3 wild-type strain. Each gene was cloned into Xplor2 vector between TEF1 constitutive promoter and PHO5 terminator. Vector containing both thiolase and reductase genes was used for A. adeninivorans transformation.
The best combination of heterologous genes was overexpression of β-ketothiolase gene from Clostridium acetobutylicum and acetoacetyl-CoA reductase gene from Cupriavidus necator which led to secretion of 4.84 g L−1 (R)-3-HB, at a rate of 0.023 g L−1 h−1 over 214 h in shaking flask cultivation. Further optimization by fed-batch culturing with glucose as a carbon source did not improve (R)-3-HB secretion, but the rate of production was doubled to 0.043 g L−1 h−1 [3.78 g L−1 of (R)-3-HB at 89 h].
The product of acetoacetyl-CoA reductase is (R)-3-HB-CoA and further removing of CoA moiety is needed for acid secretion into culture media. A. adeninivorans is able to conduct this process without any additional modification but the conversion rate is unknown. Two thioesterases, cytosolic TesBp encoded by TesB gene from E. coli and mitochondrial ATes1p encoded by ATES1 gene from A. adeninivorans, were analysed to enhance secretion process. Additionally, a cytosolic version of ATES1 gene (ATES1cyt) was tested. All three genes were expressed in A. adeninivorans cells under TEF1 constitutive promoter together with thiolase and reductase genes. Despite detected enzymatic activity the yield of (R)-3-HB synthesis and secretion was not increased. Moreover, overexpressed thioesterases negatively influenced cell growth, indicating that they act on other metabolic components. The results provided two sets of information, first, the endogenous secretion system is sufficient for (R)-3-HB production; second, further screening of suitable genes needs to be performed.
Based on optimization of (R)-3-HB synthesis, thiolase gene (thl) from C. acetobutylicum and reductase gene (phaB) from C. necator were chosen to combine with PHA synthase gene (phaC) for creating the PHB-V producing strain. The PHA synthase expression module, containing TEF1 promoter and PHO5 terminator, was cloned into Xplor2 vector together with thiolase and reductase expression modules and used for A. adeninivorans transformation. The engineered strain accumulated up to 7.47% PHB of dcw. During the set of cells passaging A. adeninivorans lost the ability to accumulate polymer with maximal 23.1 % of primary accumulation level. Additionally, use of a vector including hygromycin B antibiotic resistance marker (instead of auxotrophic marker in Xplor2) did not improve polymer accumulation and stability.
To counteract the effect of loss of accumulation stability, phasin gene (phaP1), originated from C. necator, was introduce together with PHA pathway genes. First screening cultivations resulted in stabilizing of polymer production reaching 9.58 % PHB of dcw and only 12.0 % loss of production ability. Further experiments increased PHB content with 19.9% PHB of dcw (3.85 g L-1) after 180 h of cultivation using rich medium. Use of another thiolase gene, the second thiolase from C. necator (bktB), which theoretically should induce production of PHBV copolymer, led to accumulation only 11.4% PHB of dcw after 139 h and no PHV fraction was detected.
Variation of the ratio between flask volume and amount of media influences the level of aeration. Importantly, decrease of aeration level significantly increased polymer synthesis. Additionally, PHB-V copolymer accumulation has been induced by use of different carbon source co-substrates. Use of rich media supplemented with ethanol allow the strain with thl thiolase to accumulate up to 42.9 % PHB of dcw without PHV fraction and with bktB thiolase to 30.5 % PHB of dcw. Nevertheless, despite of lower total amount of polymer, supplementation with 1-propanol allow both strains to accumulate PHB-V copolymer with 7.30 %mol and 22.5 %mol of PHV for thl and bktB strains, respectively.
Optimization based on genetic engineering further enhanced polymer production yield led to exceeding of 50 % PHB-V of dcw. For doubling the gene dosage, PHA synthesizing strains of A. adeninivorans were again transformed with Xplor2 vector containing PHA pathway genes. Resulting strains exhibited twice the level of enzymatic activities of thiolase and reductase compared with strains transformed once with expression vector. In a shaking flask experiment the strain transformed twice with vector containing bktB thiolase reached after 240 h 52.1% PHB-V of dcw (10.8 g L-1) with 12.3 %mol of PHV fraction which is the highest level found in yeast. As another genetic approach, a fusion strain has been created. Two different strains have been established and merged using protoplast fusion technique. Doubling of genetic material resulted in similar level of copolymer produced by Arxula as in former experiments (50.2% of dcw, 10.7 g L-1).
Culture conditions were optimized in controllable cultivation using fed-batch mode. Although optimal oxygen and pH level and continuous carbon source and nitrogen feeding were maintained, final polymer level in % of dry mass was around three times lower than for shaking flask experiment. Nevertheless, efficient growth of Arxula in fed-batch mode led to increase of total copolymer level in g L-1 (16.5 g L-1 compare to 10.8 g L-1 for shaking flasks) showing the feasibility of using Arxula strain for up-scaling production of copolymer.
Acetyl-CoA is a main precursor in synthesis of PHB-V copolymer and change of its pool was investigated. ATP citrate lyase is a cytosolic enzyme converting citrate into oxaloacetate and acetyl-CoA, supporting the biosynthesis of fatty acids. Two genes encoding Acl subunits from Aspergillus nidulans (AnAcl1 and AnAcl2) were again cloned into Xplor2 vector and transformed into A. adeninivorans PHA producing strain. Despite of higher enzymatic activity of AnAclp, accumulation of polymer was around three times higher for control without expression of lyase genes. Expectedly, the strain expressing AnAcl1/2 genes accumulated larger amount of each stearic, palmitic and oleic acid in both standard and fatty acid inducing conditions (lower nitrogen level). Thus, overexpression of AnAcl1/2 genes in A. adeninevorans cells may improve biosynthesis of fatty acids but is ineffective for PHB polymer accumulation.
The aim of the project was use of starch-based media, manufactured as by-products, for polymer production. Genetically engineered Arxula strains were cultivated using these media instead of glucose-based media. Although yeast cells were both able to secrete (R)-3-HB and to accumulate PHB, the yield was lower than for previous media. Additionally, only trace of PHV was found at the end of cultivation time when 1-propanol was supplemented. Obtained results showed that use of cheaper media is a promising approach to decrease production costs but further optimization needs to be performed especially for extended scale of production.
Determination of produced copolymer has been done based on microscopic analysis and studies of physical and chemical properties. Results revealed that Arxula accumulated PHA polymer in cytosolic granules with a similar size range compared to the ones produced by bacteria. The physicochemical study showed that produced polymer exhibited slightly different properties in comparison to bacterial polymer with similar content of PHV, i.e. very-low molecular mass, higher melting and glass transition temperature.
All above results showed that A. adeninivorans is a promising host for PHB-V production. Expression of phasin greatly increased production and stability of polymer, which led to an accumulation level never found before in yeast. Further optimization in higher production scale using cheap starch-based media may establish Arxula strain as a valuable tool for industrial production of PHB-V copolymer.
Optomechanical (om) systems are characterized by their nonlinear light-matter interaction. This is responsible for unique dynamic properties and allows the detection of a variety of classical and quantum mechanical phenomena on a microscopic as well as on a macroscopic scale. In this work we have studied the dynamic behavior of two laser-driven om systems, the single om cell ("cavity optomechanics / membrane-in-the-middle setup") and a two-dimensional hexagonal array of these cells ("om graphene"). The first case was motivated by the possibility to detect the transition from quantum mechanics to classical mechanics directly on the basis of the dynamic behavior. For this we focus on multistability effects of the optical and mechanical degrees of freedom, that are modeled by harmonic oscillators. Our description is based on the quantum optical master equation, which takes into account the environmental interaction assuming a vanishing temperature. As a consequence of decoherence, the dynamics occur near the semiclassical limit, i.e. it is characterized by quantum fluctuations. The quantum-to-classical transition is realized formally by rescaling the equations of motion. In the classical limit, quantum fluctuations disappear and the mean field equations were evaluated by analytical and numerical methods. We found that classical multistability is characterized by stationary signatures on the route to chaos, as well as by the coexistence of single-periodic orbits for the mechanical degree of freedom. The latter point was extensively evaluated by means of a self-consistent approach. For the dynamics in the quantum regime quantum fluctuations cannot be neglected. For this purpose, the master equation was solved by means of a numerical implementation of the Quantum State Diffusion (QSD) method. Based on Wigner and autocorrelation functions, we were able to show that quantum multistability is a dynamic effect: chaotic dynamics is suppressed and there is a time-dependent distribution of the phase space volume on classical simple-periodic orbits. The results can be interpreted within a semiclassical picture, which makes use of the single QSD quantum trajectory. Accordingly, the quantum-classical transition is explained as a time-scale effect, which is determined by tunneling probabilities in an effective mean-field potential. The subject of the second part of the work is the transport of low-energy Dirac quasiparticles in om graphene, propagating as light and sound waves. For this purpose, we investigated the scattering of a plane light wave by laser-induced photon-phonon coupling planar and circular barriers. The starting point is the om Dirac equation, which results from the continuum approximation of the Hamiltonian description of the two-dimensional array near the semiclassical limit. This work was motivated by the rich and interesting relativistic transport and tunneling phenomena found for electrons in graphene, which now appear in a new way. The reason is the presence of the new spin degree of freedom, which distinguishes the optical and mechanical excitations. In this spin space, the om interaction can be understood as a potential, which in our analysis consists of a time-independent and a time-dependent sinusoidal part. For the first case of a static barrier, the transport is elastic and is characterized by stationary scattering signatures. After solving the scattering problem via continuity conditions we were able to identify different scattering regimes depending on scattering parameters. In addition to relativistic phenomena such as Klein tunneling, simple parameter variation allows to use the barrier as a resonant light-sound interconverter and angle-dependent emitter. For the oscillating barrier, the transport is inelastic and is characterized by dynamic scattering signatures. To solve the time-periodic scattering problem, we have applied the Floquet theory for an effective two-level system. As a result of the barrier oscillation, photons and phonons can get and give away energy portions in the form of integer multiples of the oscillation frequency. The interference of short (classical) and long-wave (quantum) components leads to mixing of the scattering regimes. This allows to use the barrier as a time-periodic light-sound interconverter with interesting radiation characteristics. In addition, we have argued that the oscillating barrier provides the necessary energetic conditions for detecting zitterbewegung.
Streptococcus pneumoniae (pneumococci) and Staphylococcus aureus (S. aureus) are human-specific commensals of the upper respiratory tract. Every individual is asymptomatically colonized with both bacteria at least once in their life-time. The opportunistic pathogens can affect further organs and invade into deeper tissue. The occupation of normally sterile niches of the human body with the bacteria can lead to local infections such as sinusitis, otitis media and abscesses, or to life-threatening diseases like pneumonia, meningitis or sepsis. A strong interaction between the bacterium and the respiratory epithelial cells is a prerequisite for a successful colonization. This interaction is ensured by bacterial surface proteins, so called adhesins. The binding of the adhesins to the epithelial lineage occurs predominantly indirectly via components of the extracellular matrix (ECM), but also directly to cellular receptors. Pneumococci and S. aureus bind to various ECM glycoproteins, amongst others: fibronectin, fibrinogen, vitronectin, and collagen. Also binding of both pathogens to human thrombospondin-1 has been described. Thrombospondin-1 is mainly stored in the α-granula of thrombocytes (platelets) and released into the circulation upon activation. However, thrombospondin-1 is also produced and secreted by other cell types like endothelial cells, macrophages, and fibroblasts, which gets subsequently incorporated as component into the ECM. So far, no thrombosponin-1-binding adhesins of pneumococci were identified. PspC, Hic, and PavB are important surface-localized virulence factors, which were shown to interact with human ECM and plasma proteins. PspC and Hic bind to vitronectin and factor H, which inhibits the complement cascade of the human immune system. PavB interacts with fibronectin and plasminogen, and a pavB-deficient mutant of S. pneumoniae showed diminished capacity in colonization in a mouse model. Among the surface proteins of S. aureus, only Eap was identified as thrombospondin-1-binding adhesin. Beyond colonization, pneumococci and S. aureus can enter the blood circulation, interact with platelets, and cause their activation. The aggregation of platelets, especially initiated by S. aureus, plays an important role in the clinic, because most of the septic patients develop thrombocytopenia. Surface localized factors of
S. pneumoniae triggering platelet activation are unknown to date. In contrast, few proteins of S. aureus with potential to activate platelets, including Eap, were identified previously.
This study identified the surface proteins PavB, PspC, and Hic of S. pneumoniae as specific ligands of the human thrombospondin-1. Flow cytometric, surface plasmon resonance spectroscopic and immunological analyses revealed interactions between the pneumococcal proteins and soluble as well as immobilized thrombospondin-1. The use of specific pneumococcal deletion mutants verified the importance of the three virulence factors as binding partners of soluble thrombospondin-1. The results suggest that pneumococci are capable of acquiring soluble thrombospondin-1 from blood as well as utilizing immobilized glycoprotein of the ECM as substrate for adhesion. Furthermore, the thrombospondin-1-binding domain within the pneumococcal proteins was analyzed by use of recombinant fragments of PavB, PspC, and Hic. The binding capacity of thrombospondin-1 increased proportionally with the amount of repetitive sequences in PavB and PspC, and the length of the α-helical region within the Hic molecule. The binding behavior of thrombospondin-1 towards PavB and PspC is comparable with that of the ECM proteins vitronectin and fibronectin, but is unique towards Hic.
The localization of the binding domain of the adhesins within the thrompospondin-1 molecule occurred via use of glycosaminoglycans as competitive inhibitors for the interaction. The results suggest that the pneumococcal proteins Hic and PspC target the identical binding region within thrombospondin-1, which differs from the binding domain for PavB. However, all three virulence factors seem to bind in the N-terminal part of thrombospondin-1.
Two-dimensional gel electrophoresis, thrombospondin-1 overlay assay and subsequent mass spectrometric analysis identified AtlA of S. aureus as a surface localized interaction partner of human thrombospondin-1. Moreover, a vitronectin binding activity for AtlA was determined. Immunological and surface plasmon resonance binding studies with recombinant AtlA fragments revealed that interactions with both matrix proteins is mediated via the C-terminal located repeats R1R2 of the AtlA amidase domain. Binding of thrombospondin-1 and vitronectin occurred not simultaneously, due to a competitive inhibition.
The second part of the study focused on the activation of human platelets by recombinant pneumococcal and staphylococcal proteins. In total, 28 proteins of S. pneumoniae and 52 proteins of S. aureus were incubated with human platelets. The activation of the cells was detected by flow cytometry using the activation markers P-selectin and the dimerization of the integrin αIIbβIII. The proteins CbpL, PsaA, PavA, and SP_0899 of S. pneumoniae induced platelet activation, however, the detailed mechanism has to be deciphered in further studies. Furthermore, the secreted proteins CHIPS, FLIPr, and AtlA of S. aureus were discovered as inductors for the activation of platelets. In addition, the domains of AtlA and Eap, crucial for platelet activation, were narrowed down. Interestingly, CHIPS, FLIPr, and Eap were described as inhibitors of neutrophil recruitment. Platelets are recently recognized as immune cells, due to the expression of immune receptors. The data obtained in this study highlight a comprehensive spectrum of effects of the S. aureus proteins towards different type of immune cells. Besides the activation of platelets in suspension buffer and plasma, the aggregation of platelets in whole blood was triggered by the proteins CHIPS, AtlA, and Eap. These results suggest a contribution of the proteins during the S. aureus-induced infectious endocarditis. Secretion of the platelet activating virulence factors, which were identified within this study, might represent a pathogenic strategy during S. aureus infection in which a direct contact between S. aureus and platelets is not required or even avoided.
In conclusion, PavB, PspC, and Hic of S. pneumoniae and AtlA of S. aureus were identified as interaction partners of human thrombospondin-1. Furthermore, CHIPS, FLIPr, AtlA, and Eap were characterized as platelet activators. This study provides candidates for the development of protein-based vaccines, to prevent bacterial colonization and to neutralize secreted pathogenic factors.
Objectives: We aimed to update the 2010 evidence- and consensus-based national clinical guideline on the diagnosis and management of uncomplicated urinary tract infections (UTIs) in adult patients. Materials and Methods: An interdisciplinary group consisting of 17 representatives of 12 medical societies and a patient representative was formed. Systematic literature searches were conducted in MEDLINE, EMBASE, and the Cochrane Library to identify literature published in 2010–2015. Results: We provide 75 recommendations and 68 statements in the updated evidence- and consensus-based national clinical guideline. The diagnostics part covers practical recommendations on cystitis and pyelonephritis for each defined patient group. Clinical examinations, as well as laboratory testing and microbiological pathogen assessment, are addressed. Conclusion: In accordance with the global antibiotic stewardship initiative and considering new insights in scientific research, we updated our German clinical UTI guideline to promote a responsible antibiotic use and to give clear hands-on recommendations for the diagnosis and management of UTIs in adults in Germany for healthcare providers and patients.
Significance of Hyperbaric Oxygenation in the Treatment of Fournier’s Gangrene: A Comparative Study
(2018)
Introduction: Hyperbaric oxygenation (HBO), in addition to anti-infective and surgical therapy, seems to be a key treatment point for Fournier’s gangrene. The aim of this study was to investigate the influence of HBO therapy on the outcome and prognosis of Fournier’s gangrene. Patients and Methods: In the present multicenter, retrospective observational study, we evaluated the data of approximately 62 patients diagnosed with Fournier’s gangrene between 2007 and 2017. For comparison, 2 groups were distinguished: patients without HBO therapy (group A, n = 45) and patients with HBO therapy (group B, n = 17). The analysis included sex, age, comorbidities, clinical symptoms, laboratory and microbiological data, debridement frequency, wound dressing, antibiotic use, outcome and prognosis. The statistical analysis was performed with GraphPad Prism 7® (GraphPad Software, Inc., La Jolla, USA). Results: Demographic data showed no significant differences. The laboratory parameters C-reactive protein and urea were significantly higher in group B (group B: 301.7 vs. 140.6 mg/dL; group A: 124.8 vs. 54.7 mg/dL). Sepsis criteria were fulfilled in 77.8 and 100% of the patients in groups A and B respectively. Treatment in the intensive care unit (ICU) was therefore indicated in 69% of the patients in group A and 100% of the patients in group B. The mean ICU stay was 9 and 32 days for patients in groups A and B respectively. The wound debridement frequency and hospitalization stay were significantly greater in group B (13 vs. 5 debridement and 40 vs. 22 days). Initial antibiosis was test validated in 80% of the patients in group A and 76.5% of the patients in group B. Mortality was 0% in group B and 4.4% in the group A. Conclusion: The positive influence of HBO on the treatment of Fournier’s gangrene can be estimated only from the available data. Despite poorer baseline findings with comparable risk factors, mortality was 0% in the HBO group. The analysis of a larger patient cohort is desirable to increase the significance of the results.
Background and Aims: Gastrointestinal stromal tumors (GISTs) are rare malignancies but the most common mesenchymal tumors of the digestive tract. Recent advances in diagnostic imaging and an increasing incidence will confront us more frequently with stromal tumors. This single center study aimed to characterize GIST patients in terms of tumor location, clinical presentation, metastasis formation, as well as associated secondary malignancies. Methods: In a retrospective study, 104 patients with a histologically confirmed diagnosis of GIST, collected between 1993 and 2011, were characterized for several clinical features. Results: The most common GIST location was the stomach (67.6%) followed by the small intestine (16.2%). Gastrointestinal bleeding (55.8%) and abdominal pain (38.5%) were the most frequently reported symptoms whereas about one-third of patients remained clinically asymptomatic (31.6%); 14.4% of patients had either synchronous or metachronous metastases and there was a significant prevalence also in the low risk group. The proportion of secondary malignant associated neoplasms was 31% in our GIST cohort, among which gastrointestinal, genitourinary tumors, and breast cancer were the most prevalent. Conclusion: There was a considerable risk for metastasis formation and the development of secondary neoplasias that should encourage discussion about the appropriate surveillance strategy after surgery for GIST.
Background: We aimed to update the 2010 evidence- and consensus-based national clinical guideline on the diagnosis and management of uncomplicated urinary tract infections (UTIs) in adult patients. Results are published in 2 parts. Part 1 covers methods, the definition of patient groups, and diagnostics. This second publication focuses on treatment of acute episodes of cystitis and pyelonephritis as well as on prophylaxis of recurrent UTIs. Materials and Methods: An interdisciplinary group consisting of 17 representatives of 12 medical societies and a patient representative was formed. Systematic literature searches were conducted in MEDLINE, EMBASE, and the Cochrane Library to identify literature published in 2010–2015. Results: For the treatment of acute uncomplicated cystitis (AUC), fosfomycin-trometamol, nitrofurantoin, nitroxoline, pivmecillinam, and trimethoprim (depending on the local rate of resistance) are all equally recommended. Cotrimoxazole, fluoroquinolones, and cephalosporins are not recommended as antibiotics of first choice, for concern of an unfavorable impact on the microbiome. Mild to moderate uncomplicated pyelonephritis should be treated with oral cefpodoxime, ceftibuten, ciprofloxacin, or levofloxacin. For AUC with mild to moderate symptoms, instead of antibiotics symptomatic treatment alone may be considered depending on patient preference after discussing adverse events and outcomes. Primarily non-antibiotic options are recommended for prophylaxis of recurrent urinary tract infection. Conclusion: In accordance with the global antibiotic stewardship initiative and considering new insights in scientific research, we updated our German clinical UTI guideline to promote a responsible antibiotic use and to give clear hands-on recommendations for the diagnosis and management of UTIs in adults in Germany for healthcare providers and patients.
Significance of Hyperbaric Oxygenation in the Treatment of Fournier’s Gangrene: A Comparative Study
(2018)
Introduction: Hyperbaric oxygenation (HBO), in addition to anti-infective and surgical therapy, seems to be a key treatment point for Fournier’s gangrene. The aim of this study was to investigate the influence of HBO therapy on the outcome and prognosis of Fournier’s gangrene. Patients and Methods: In the present multicenter, retrospective observational study, we evaluated the data of approximately 62 patients diagnosed with Fournier’s gangrene between 2007 and 2017. For comparison, 2 groups were distinguished: patients without HBO therapy (group A, n = 45) and patients with HBO therapy (group B, n = 17). The analysis included sex, age, comorbidities, clinical symptoms, laboratory and microbiological data, debridement frequency, wound dressing, antibiotic use, outcome and prognosis. The statistical analysis was performed with GraphPad Prism 7® (GraphPad Software, Inc., La Jolla, USA). Results: Demographic data showed no significant differences. The laboratory parameters C-reactive protein and urea were significantly higher in group B (group B: 301.7 vs. 140.6 mg/dL; group A: 124.8 vs. 54.7 mg/dL). Sepsis criteria were fulfilled in 77.8 and 100% of the patients in groups A and B respectively. Treatment in the intensive care unit (ICU) was therefore indicated in 69% of the patients in group A and 100% of the patients in group B. The mean ICU stay was 9 and 32 days for patients in groups A and B respectively. The wound debridement frequency and hospitalization stay were significantly greater in group B (13 vs. 5 debridement and 40 vs. 22 days). Initial antibiosis was test validated in 80% of the patients in group A and 76.5% of the patients in group B. Mortality was 0% in group B and 4.4% in the group A. Conclusion: The positive influence of HBO on the treatment of Fournier’s gangrene can be estimated only from the available data. Despite poorer baseline findings with comparable risk factors, mortality was 0% in the HBO group. The analysis of a larger patient cohort is desirable to increase the significance of the results.
Rabies virus (RABV) is an ancient, highly neurotropic rhabdovirus that causes lethal encephalitis. Most RABV pathogenesis determinants have been identified with laboratory-adapted or attenuated RABVs, but details of natural RABV pathogenesis and attenuation mechanisms are still poorly understood. To provide a deeper insight in the cellular mechanism of pathogenies of field RABV, this work was performed to assess virus strain specific differences in intra-neuronal virus transport, to identify cell culture adaptive mutations in recombinant field viruses and to explore shRNA-expressing RABVs as research tools for targeted host manipulation in infected cells.
Comparison of chimeric RABVs with glycoprotein (G) ecto-domains of different lyssaviruses, together with field RABVs from dog and fox in dorsal root ganglion (DRG) neurons revealed no detectable differences in the axonal accumulation of the viruses. This indicates that previously described G-dependent transport of newly formed RABV in axons can occur both in laboratory-adapted and field RABV. Moreover, partial overlap of nucleoprotein (N) and G protein particles in field virus infected DRG axons supported the hypothesis of the “separate model” for anterograde RABV transport.
Serial passages of recombinant dog and fox field clones in different cell lines led to the identification of general (D266N) and cell line specific (K444N) adaptive mutations in the G ecto-domain of both viruses. In BHK cells, synergistic effects of D226N, K444N and A417T on field dog virus G protein surface localization led to the loss of endoplasmic reticulum (ER) retention of G and increased virus titers in the supernatant, indicating that limited virus release by ER retention is a major bottleneck in cell culture adaptation. In addition, selection of mutations within the C-terminus of the RABV phosphoprotein (P) (R293H and R293C in fox and dog viruses, respectively) led to the hypothesis of altered binding affinities to nucleoprotein and RNP complexes. Identification of the above mentioned amino acid substitutions together with alterations in a suboptimal transcription stop signal in the P/M gene border indicated that adaptation to cell culture replication occurs on both levels, RNA transcription/replication and virus release.
To evaluate the possibility of an expression of a functional microRNA-adapted short-hairpin RNAs (miR-shRNA) expressing RABV, recombinant RABVs encoding miR-shRNAs against cellular Dynein Light Chain 1 (DYNLL1) and Acidic Nuclear Phosphoprotein 32 family member B (ANP32B) were generated. In spite of cytoplasmic transcription of the respective mRNAs, downregulation of DYNLL1 and ANP32B mRNA and respective protein levels in infected cells revealed correct processing to functional shRNAs. Specific downregulation of the cellular genes at 2, 3 and 4 days post infection further demonstrated feasibility of the approach in standard cell lines. However, it remained open whether miR-shRNA expressing RABV can be used to study neuro-infection in vivo. Since first attempts in primary rat neuron cultures failed, it has to be clarified in further experiments whether this strategy can be used in mature, non-dividing neurons or whether breakdown of the nucleus in the course of cell division is a requirement for the processing of cytoplasmically expressed miR-RNA by nuclear RNases.
By providing novel insights in axonal RABV transport and cell culture adaptive mutations this work extends the current understanding of RABV pathogenesis in natural and non-natural cell environments. Moreover, it provides a basis for further pathogenicity studies in which the impact of cell culture adaptation through increased virus release on RABV virulence can be investigated. With successful expression of functional miR-shRNAs from RABV vectors, this work also provides a tool for RABV gene targeting in infected cell lines and thus may contribute to the further investigation of RABV-host-cell-interactions.
Streptococcus pneumoniae is a commensal of the human upper respiratory tract and
the etiological agent of several life-threatening diseases. This pathogen is the model bacterium
for natural competence. Furthermore, the pneumococci played an important role in the
identification of DNA as the main molecule involved in bacterial transformation. As a result,
studies on the pneumococcal genome provided an initial overview of the genetic potential of
this pathogen. The pneumococcus is a highly versatile bacterium possessing a high rate of
uptake and recombination of exogenous DNA from neighboring bacteria. As such, a significant
diversity in the genome content among the different pneumococcal strains has been reported.
The capsular polysaccharide, an important pneumococcal virulence factor, is the best example
on the pneumococcal diversity. There are over 98 serotypes characterized to date presenting
differences in their capsule (cps) locus. Additional to the cps locus, the pneumococcus also
presents 13 genomic islets annotated as regions of diversity (RD) encoded in the auxiliary
genome. Remarkably, 8 of the pneumococcal RD studied so far have been associated with
virulence. Furthermore, the ongoing sequencing of over 4000 pneumococcal genomes have
shed light on the conservation level of well-known pneumococcal virulence factors.
Interestingly, important pneumococcal virulence determinants show variations in the gene and
protein sequence among the different strains. Prototypes are for example the pneumococcal
surface protein C (PspC) and pneumococcal adherence and virulence factor B (PavB).
Conversely, gene regulation in S. pneumoniae is carried out by highly conserved and genome-
wide distributed transcriptional factors. Overall, the pneumococci interplays with its
environment with 4 major regulatory systems: quorum sensing (QS), stand-alone
transcriptional regulators, small RNAs (sRNAs) and two-component regulatory systems (TCS).
Some of these systems are multifaceted and share more than one feature. Furthermore, there
is crosstalk among the different systems, requiring the activation of a signaling cascade to
function properly.
A comprehensive analysis of the distribution and conservation of pneumococcal
virulence factors and TCS was obtained in this study. The results are summarized as a
simplified variome in which 25 pneumococcal strains with a complete sequenced genome were
analyzed. Interestingly, the genes encoding the glycolytic protein enolase and the toxin
pneumolysin were the most conserved virulence determinants. Additionally, the high level of
conservation was confirmed for the pneumococcal TCS regulators, especially for WalKR,
CiaRH and TCS08.
The main focus of this study was on the regulatory functions of pneumococcal TCS.
With this in mind, an extensive and detailed systematic review of the 13 pneumococcal TCS
and its orphan RR was undertaken. For this purpose, every pneumococcal TCS was analyzed
for its reported functional and structural information along with its contribution to the main
pathophysiology of the pneumococci. In brief, S. pneumoniae can utilize its TCS for the
regulation of important cellular processes and the sensing of detectable signals in the
environment. Additionally, the role of TCS in pneumococcal processes and signal sensing can
be divided further. In the first place, pneumococcal TCS regulate competence and fratricide,
the production of bacteriocins and host-pathogen interaction processes, while the detectable
signals include cell-wall perturbations, environmental stress, and nutrients. As a conclusion
from this section, it is possible to analyze the pneumococcal TCS in a comprehensive manner.
There is a complex network among the different pneumococcal regulators and the TCS play
an important role. Moreover, these systems are highly conserved and essential for the proper
functioning of the pneumococcus as a pathogen.
Following up on pneumococcal TCS, this study focused especially on the TCS08.
Interestingly, the pneumococcal TCS08 has been previously associated with the regulation of the cellobiose metabolism. Furthermore, this system has also been reported to regulate the
expression of genes encoded in the RD4 (Pilus-1). Remarkably, the pneumococcal TCS08
was shown to be highly homologous to the SaeRS system of Staphylococcus aureus. Initially,
mutant strains lacking a single (Δrr08 or Δhk08) or both components (Δtcs08) of the TCS08
were generated in pneumococcal D39 and TIGR4 strains. Transcriptomics and functional
assays showed a downregulation of the PI-1 in the absence of the complete tcs08, while PavB
presented an upregulation in the Δhk08 knockout. Moreover, an important number of genes
coding for intermediary metabolism proteins were also found to be differentially expressed by
microarray analysis. As such, the TIGR4Δhk08 strain presented a downregulation for the
cellobiose operon (cel). In contrast, an upregulation was reported for the fatty acid biosynthesis
(fab) and arginine catabolism (arc) operons. Conversely, a decrease in gene expression was
seen in the TIGR4Δrr08 strain for the arc operon. Finally, in vivo murine pneumonia and sepsis
models highlighted an involvement of TCS08 in pneumococcal virulence. Remarkably, the
different TCS08 mutants presented a strain dependent effect on their virulence severity. The
TIGR4Δrr08, and all TCS08 mutants in D39 showed a decrease in virulence in the pneumonia
model, with no changes in sepsis. Conversely, the absence of HK08 in TIGR4 presented a
highly virulent phenotype in both pneumonia and sepsis models. To sum up, the pneumococcal
TCS08 influenced the expression of genes involved in fitness and colonization. Specifically,
those coding for the adhesins PavB and PI-1 and fitness proteins from the cel, arc and fab
operons. Remarkably, the highest changes in expression were observed in the strains lacking
the HK08. Additionally, TCS08 has a strain dependent impact on pneumococcal virulence as
showed by murine pneumonia and sepsis models when comparing the effects in D39 and
TIGR4.
Climate Change-Induced Shift of Tree Growth Sensitivity at a Central Himalayan Treeline Ecotone
(2018)
Introduction
We retrospectively evaluated the efficacy and toxicity of gross tumor volume (GTV) mean dose optimized stereotactic body radiation therapy (SBRT) for primary and secondary lung tumors with and without robotic real-time motion compensation.
Materials and methods
Between 2011 and 2017, 208 patients were treated with SBRT for 111 primary lung tumors and 163 lung metastases with a median GTV of 8.2 cc (0.3–174.0 cc). Monte Carlo dose optimization was performed prioritizing GTV mean dose at the potential cost of planning target volume (PTV) coverage reduction while adhering to safe normal tissue constraints. The median GTV mean biological effective dose (BED)10 was 162.0 Gy10 (34.2–253.6 Gy10) and the prescribed PTV BED10 ranged 23.6–151.2 Gy10 (median, 100.8 Gy10). Motion compensation was realized through direct tracking (44.9%), fiducial tracking (4.4%), and internal target volume (ITV) concepts with small (≤5 mm, 33.2%) or large (>5 mm, 17.5%) motion. The local control (LC), progression-free survival (PFS), overall survival (OS), and toxicity were analyzed.
Results
Median follow-up was 14.5 months (1–72 months). The 2-year actuarial LC, PFS, and OS rates were 93.1, 43.2, and 62.4%, and the median PFS and OS were 18.0 and 39.8 months, respectively. In univariate analysis, prior local irradiation (hazard ratio (HR) 0.18, confidence interval (CI) 0.05–0.63, p = 0.01), GTV/PTV (HR 1.01–1.02, CI 1.01–1.04, p < 0.02), and PTV prescription, mean GTV, and maximum plan BED10 (HR 0.97–0.99, CI 0.96–0.99, p < 0.01) were predictive for LC while the tracking method was not (p = 0.97). For PFS and OS, multivariate analysis showed Karnofsky Index (p < 0.01) and tumor stage (p ≤ 0.02) to be significant factors for outcome prediction. Late radiation pneumonitis or chronic rip fractures grade 1–2 were observed in 5.3% of the patients. Grade ≥3 side effects did not occur.
Conclusion
Robotic SBRT is a safe and effective treatment for lung tumors. Reducing the PTV prescription and keeping high GTV mean doses allowed the reduction of toxicity while maintaining high local tumor control. The use of real-time motion compensation is strongly advised, however, well-performed ITV motion compensation may be used alternatively when direct tracking is not feasible.
Ductal Mucus Obstruction and Reduced Fluid Secretion Are Early Defects in Chronic Pancreatitis
(2018)
Objective: Defective mucus production in the pancreas may be an important factor in the initiation and progression of chronic pancreatitis (CP), therefore we aimed to (i) investigate the qualitative and quantitative changes of mucus both in human CP and in an experimental pancreatitis model and (ii) to correlate the mucus phenotype with epithelial ion transport function.
Design: Utilizing human tissue samples and a murine model of cerulein induced CP we measured pancreatic ductal mucus content by morphometric analysis and the relative expression of different mucins in health and disease. Pancreatic fluid secretion in CP model was measured in vivo by magnetic resonance cholangiopancreatography (MRCP) and in vitro on cultured pancreatic ducts. Time-changes of ductal secretory function were correlated to those of the mucin production.
Results: We demonstrate increased mucus content in the small pancreatic ducts in CP. Secretory mucins MUC6 and MUC5B were upregulated in human, Muc6 in mouse CP. In vivo and in vitro fluid secretion was decreased in cerulein-induced CP. Analysis of time-course changes showed that impaired ductal ion transport is paralleled by increased Muc6 expression.
Conclusion: Mucus accumulation in the small ducts is a combined effect of mucus hypersecretion and epithelial fluid secretion defect, which may lead to ductal obstruction. These results suggest that imbalance of mucus homeostasis may have an important role in the early-phase development of CP, which may have novel diagnostic and therapeutic implications.
Background
The role of platelets for mediating closure of the ductus arteriosus in human preterm infants is controversial. Especially, the effect of low platelet counts on pharmacological treatment failure is still unclear.
Methods
In this retrospective study of 471 preterm infants [<1,500 g birth weight (BW)], who were treated for a patent ductus arteriosus (PDA) with indomethacin or ibuprofen, we investigated whether platelet counts before or during pharmacological treatment had an impact on the successful closure of a hemodynamically significant PDA. The effects of other factors, such as sepsis, preeclampsia, gestational age, BW, and gender, were also evaluated.
Results
Platelet counts before initiation of pharmacological PDA treatment did not differ between infants with later treatment success or failure. However, we found significant associations between low platelet counts during pharmacological PDA therapy and treatment failure (p < 0.05). Receiver operating characteristic (ROC) curve analysis showed that platelet counts after the first, and before and after the second cyclooxygenase inhibitor (COXI) cycle were significantly associated with treatment failure (area under the curve of >0.6). However, ROC curve analysis did not reveal a specific platelet cutoff-value that could predict PDA treatment failure. Multivariate logistic regression analysis showed that lower platelet counts, a lower BW, and preeclampsia were independently associated with COXI treatment failure.
Conclusion
We provide further evidence for an association between low platelet counts during pharmacological therapy for symptomatic PDA and treatment failure, while platelet counts before initiation of therapy did not affect treatment outcome.
Intranasal Vaccination With Lipoproteins Confers Protection Against Pneumococcal Colonisation
(2018)
Streptococcus pneumoniae is endowed with a variety of surface-exposed proteins representing putative vaccine candidates. Lipoproteins are covalently anchored to the cell membrane and highly conserved among pneumococcal serotypes. Here, we evaluated these lipoproteins for their immunogenicity and protective potential against pneumococcal colonisation. A multiplex-based immunoproteomics approach revealed the immunogenicity of selected lipoproteins. High antibody titres were measured in sera from mice immunised with the lipoproteins MetQ, PnrA, PsaA, and DacB. An analysis of convalescent patient sera confirmed the immunogenicity of these lipoproteins. Examining the surface localisation and accessibility of the lipoproteins using flow cytometry indicated that PnrA and DacB were highly abundant on the surface of the bacteria. Mice were immunised intranasally with PnrA, DacB, and MetQ using cholera toxin subunit B (CTB) as an adjuvant, followed by an intranasal challenge with S. pneumoniae D39. PnrA protected the mice from pneumococcal colonisation. For the immunisation with DacB and MetQ, a trend in reducing the bacterial load could be observed, although this effect was not statistically significant. The reduction in bacterial colonisation was correlated with the increased production of antigen-specific IL-17A in the nasal cavity. Immunisation induced high systemic IgG levels with a predominance for the IgG1 isotype, except for DacB, where IgG levels were substantially lower compared to MetQ and PnrA. Our results indicate that lipoproteins are interesting targets for future vaccine strategies as they are highly conserved, abundant, and immunogenic.
Tuberculosis (TB) has tremendous public health relevance. It most frequently affects the lung and is characterized by the development of unique tissue lesions, termed granulomas. These lesions encompass various immune populations, with macrophages being most extensively investigated. Myeloid derived suppressor cells (MDSCs) have been recently identified in TB patients, both in the circulation and at the site of infection, however their interactions with Mycobacterium tuberculosis (Mtb) and their impact on granulomas remain undefined. We generated human monocytic MDSCs and observed that their suppressive capacities are retained upon Mtb infection. We employed an in vitro granuloma model, which mimics human TB lesions to some extent, with the aim of analyzing the roles of MDSCs within granulomas. MDSCs altered the structure of and affected bacterial containment within granuloma-like structures. These effects were partly controlled through highly abundant secreted IL-10. Compared to macrophages, MDSCs activated primarily the NF-κB and MAPK pathways and the latter largely contributed to the release of IL-10 and replication of bacteria within in vitro generated granulomas. Moreover, MDSCs upregulated PD-L1 and suppressed proliferation of lymphocytes, albeit with negligible effects on Mtb replication. Further comprehensive characterization of MDSCs in TB will contribute to a better understanding of disease pathogenesis and facilitate the design of novel immune-based interventions for this deadly infection.
Platelets transfusion is a safe process, but during or after the process, the recipient may experience an adverse reaction and occasionally a serious adverse reaction (SAR). In this review, we focus on the inflammatory potential of platelet components (PCs) and their involvement in SARs. Recent evidence has highlighted a central role for platelets in the host inflammatory and immune responses. Blood platelets are involved in inflammation and various other aspects of innate immunity through the release of a plethora of immunomodulatory cytokines, chemokines, and associated molecules, collectively termed biological response modifiers that behave like ligands for endothelial and leukocyte receptors and for platelets themselves. The involvement of PCs in SARs—particularly on a critically ill patient’s context—could be related, at least in part, to the inflammatory functions of platelets, acquired during storage lesions. Moreover, we focus on causal link between platelet activation and immune-mediated disorders (transfusion-associated immunomodulation, platelets, polyanions, and bacterial defense and alloimmunization). This is linked to the platelets’ propensity to be activated even in the absence of deliberate stimuli and to the occurrence of time-dependent storage lesions.
Medical education research has focused almost entirely on the education of future physicians. In comparison, findings on other health-related occupations, such as medical assistants, are scarce. With the current study, we wanted to examine the knowledge-is-power hypothesis in a real life educational setting and add to the sparse literature on medical assistants. Acquisition of vocational knowledge in vocational education and training (VET) was examined for medical assistant students (n = 448). Differences in domain-specific vocational knowledge were predicted by crystallized and fluid intelligence in the course of VET. A multiple matrix design with 3 year-specific booklets was used for the vocational knowledge tests of the medical assistants. The unique and joint contributions of the predictors were investigated with structural equation modeling. Crystallized intelligence emerged as the strongest predictor of vocational knowledge at every stage of VET, while fluid intelligence only showed weak effects. The present results support the knowledge-is-power hypothesis, even in a broad and more naturalistic setting. This emphasizes the relevance of general knowledge for occupations, such as medical assistants, which are more focused on learning hands-on skills than the acquisition of academic knowledge.
Do We Need to Rethink the Epidemiology and Healthcare Utilization of Parkinson's Disease in Germany?
(2018)
Epidemiological aspects of Parkinson's disease (PD), co-occurring diseases and medical healthcare utilization of PD patients are still largely elusive. Based on claims data of 3.7 million statutory insurance members in Germany in 2015 the prevalence and incidence of PD was determined. PD cases had at least one main hospital discharge diagnosis of PD, or one physician diagnosis confirmed by a subsequent or independent diagnosis or by PD medication in 2015. Prevalence of (co-)occurring diseases, mortality, and healthcare measures in PD cases and matched controls were compared. In 2015, 21,714 prevalent PD cases (standardized prevalence: 511.4/100,000 persons) and 3,541 incident PD cases (standardized incidence: 84.1/100,000 persons) were identified. Prevalence of several (co-)occurring diseases/complications, e.g., dementia (PD/controls: 39/13%), depression (45/22%), bladder dysfunction (46/22%), and diabetes (35/31%), as well as mortality (10.7/5.8%) differed between PD cases and controls. The annual healthcare utilization was increased in PD cases compared to controls, e.g., regarding mean ± SD physician contacts (15.2 ± 7.6/12.2 ± 7.3), hospitalizations (1.3 ± 1.8/0.7 ± 1.4), drug prescriptions (overall: 37.7 ± 24.2/21.7 ± 19.6; anti-PD medication: 7.4 ± 7.4/0.1 ± 0.7), assistive/therapeutic devices (47/30%), and therapeutic remedies (57/16%). The standardized prevalence and incidence of PD in Germany as well as mortality in PD may be substantially higher than reported previously. While frequently diagnosed with co-occurring diseases/complications, such as dementia, depression, bladder dysfunction and diabetes, the degree of healthcare utilization shows large variability between PD patients. These findings encourage a rethinking of the epidemiology and healthcare utilization in PD, at least in Germany. Longitudinal studies of insurance claims data should further investigate the individual and epidemiological progression and healthcare demands in PD.
Planning Modes for Major Transportation Infrastructure Projects (MTIPs): Comparing China and Germany
(2018)
Arm Ability Training (AAT) has been specifically designed to promote manual dexterity recovery for stroke patients who have mild to moderate arm paresis. The motor control problems that these patients suffer from relate to a lack of efficiency in terms of the sensorimotor integration needed for dexterity. Various sensorimotor arm and hand abilities such as speed of selective movements, the capacity to make precise goal-directed arm movements, coordinated visually guided movements, steadiness, and finger dexterity all contribute to our “dexterity” in daily life. All these abilities are deficient in stroke patients who have mild to moderate paresis causing focal disability. The AAT explicitly and repetitively trains all these sensorimotor abilities at the individual's performance limit with eight different tasks; it further implements various task difficulty levels and integrates augmented feedback in the form of intermittent knowledge of results. The evidence from two randomized controlled trials indicates the clinical effectiveness of the AAT with regard to the promotion of “dexterity” recovery and the reduction of focal disability in stroke patients with mild to moderate arm paresis. In addition, the effects have been shown to be superior to time-equivalent “best conventional therapy.” Further, studies in healthy subjects showed that the AAT induced substantial sensorimotor learning. The observed learning dynamics indicate that different underlying sensorimotor arm and hand abilities are trained. Capacities strengthened by the training can, in part, be used by both arms. Non-invasive brain stimulation experiments and functional magnetic resonance imaging data documented that at an early stage in the training cortical sensorimotor network areas are involved in learning induced by the AAT, yet differentially for the tasks trained. With prolonged training over 2 to 3 weeks, subcortical structures seem to take over. While behavioral similarities in training responses have been observed in healthy volunteers and patients, training-induced functional re-organization in survivors of a subcortical stroke uniquely involved the ipsilesional premotor cortex as an adaptive recruitment of this secondary motor area. Thus, training-induced plasticity in healthy and brain-damaged subjects are not necessarily the same.
Objective: To evaluate the efficacy and tolerability of brivaracetam (BRV) in a severely drug refractory cohort of patients with epileptic encephalopathies (EE).
Method: A multicenter, retrospective cohort study recruiting all patients treated with EE who began treatment with BRV in an enrolling epilepsy center between 2016 and 2017.
Results: Forty-four patients (27 male [61%], mean age 29 years, range 6 to 62) were treated with BRV. The retention rate was 65% at 3 months, 52% at 6 months and 41% at 12 months. A mean retention time of 5 months resulted in a cumulative exposure to BRV of 310 months. Three patients were seizure free during the baseline. At 3 months, 20 (45%, 20/44 as per intention-to-treat analysis considering all patients that started BRV including three who were seizure free during baseline) were either seizure free (n = 4; 9%, three of them already seizure-free at baseline) or reported at least 25% (n = 4; 9%) or 50% (n = 12; 27%) reduction in seizures. An increase in seizure frequency was reported in two (5%) patients, while there was no change in the seizure frequency of the other patients. A 50% long-term responder rate was apparent in 19 patients (43%), with two (5%) free from seizures for more than six months and in nine patients (20%, with one [2 %] free from seizures) for more than 12 months. Treatment-emergent adverse events were predominantly of psychobehavioural nature and were observed in 16%.
Significance: In this retrospective analysis the rate of patients with a 50% seizure reduction under BRV proofed to be similar to those seen in regulatory trials for focal epilepsies. BRV appears to be safe and relatively well tolerated in EE and might be considered in patients with psychobehavioral adverse events while on levetiracetam.
Background: Biomarkers for gains of evidence based interventions for upper limb motor training in the subacute stage following stroke have rarely been described. Information about these parameters might help to identify patients who benefit from specific interventions and to determine individually expected behavioral gains for a certain period of therapy.
Objective: To evaluate predictors for hand motor outcome after arm ability training in the subacute stage after stroke selected from known potentially relevant parameters (initial motor strength, structural integrity of the pyramidal tract and functional motor cortex integrity).
Methods: We applied the arm ability training (AAT) over 3 weeks to a subpopulation of stroke patients with mild arm paresis, i.e., in 14 patients on average 4 weeks after stroke. The following biomarkers were measured before therapy onset: grip strength on the affected hand, transcranial magnetic stimulation recruitment curve steepness over the primary motor hand area [slope ratio between the ipsilesional hemisphere (IH) and contralesional hemisphere (CH)], and diffusion weighted MRI fractional anisotropy (FA) in the posterior limb of the internal capsule (PLIC; determined as a lateralization index between IH and CH). Outcome was assessed as the AATgain (percentage improvement over training). The “Test d'Evaluation des Membres Supérieurs de Personnes Âgées” (TEMPA) was assessed before and after training to test for possible associations of AAT with activity of daily living.
Results: A stepwise linear regression identified the lateralization index of PLIC FA as the only significant predictor for AAT-gain (R2 = 0.519; P = 0.029). AAT-gain was positively associated (r = 0.59; P = 0.028) with improvement in arm function during daily activities (TEMPA).
Conclusions: While all mildly affected patients achieved a clinically relevant therapeutic effect, pyramidal tract integrity nevertheless had a modifying role for clinical benefit.
Together with endothelial cells and the glomerular basement membrane, podocytes form the size-specific filtration barrier of the glomerulus with their interdigitating foot processes. Since glomerulopathies are associated with so-called foot process effacement—a severe change of well-formed foot processes into flat and broadened processes—visualization of the three-dimensional podocyte morphology is a crucial part for diagnosis of nephrotic diseases. However, interdigitating podocyte foot processes are too narrow to be resolved by classic light microscopy due to Ernst Abbe's law making electron microscopy necessary. Although three dimensional electron microscopy approaches like serial block face and focused ion beam scanning electron microscopy and electron tomography allow volumetric reconstruction of podocytes, these techniques are very time-consuming and too specialized for routine use or screening purposes. During the last few years, different super-resolution microscopic techniques were developed to overcome the optical resolution limit enabling new insights into podocyte morphology. Super-resolution microscopy approaches like three dimensional structured illumination microscopy (3D-SIM), stimulated emission depletion microscopy (STED) and localization microscopy [stochastic optical reconstruction microscopy (STORM), photoactivated localization microscopy (PALM)] reach resolutions down to 80–20 nm and can be used to image and further quantify podocyte foot process morphology. Furthermore, in vivo imaging of podocytes is essential to study the behavior of these cells in situ. Therefore, multiphoton laser microscopy was a breakthrough for in vivo studies of podocytes in transgenic animal models like rodents and zebrafish larvae because it allows imaging structures up to several hundred micrometer in depth within the tissue. Additionally, along with multiphoton microscopy, lightsheet microscopy is currently used to visualize larger tissue volumes and therefore image complete glomeruli in their native tissue context. Alongside plain visualization of cellular structures, atomic force microscopy has been used to study the change of mechanical properties of podocytes in diseased states which has been shown to be a culprit in podocyte maintenance. This review discusses recent advances in the field of microscopic imaging and demonstrates their currently used and other possible applications for podocyte research.
Neurosteroids, comprising pregnane, androstane, and sulfated steroids can alter neuronal excitability through interaction with ligand-gated ion channels and other receptors and have therefore a therapeutic potential in several brain disorders. They can be formed in brain cells or are synthesized by an endocrine gland and reach the brain by penetrating the blood–brain barrier (BBB). Especially sulfated steroids such as pregnenolone sulfate (PregS) and dehydroepiandrosterone sulfate (DHEAS) depend on transporter proteins to cross membranes. In this review, we discuss the involvement of ATP-binding cassette (ABC)- and solute carrier (SLC)-type membrane proteins in the transport of these compounds at the BBB and in the choroid plexus (CP), but also in the secretion from neurons and glial cells. Among the ABC transporters, especially BCRP (ABCG2) and several MRP/ABCC subfamily members (MRP1, MRP4, MRP8) are expressed in the brain and known to efflux conjugated steroids. Furthermore, several SLC transporters have been shown to mediate cellular uptake of steroid sulfates. These include members of the OATP/SLCO subfamily, namely OATP1A2 and OATP2B1, as well as OAT3 (SLC22A3), which have been reported to be expressed at the BBB, in the CP and in part in neurons. Furthermore, a role of the organic solute transporter OSTα-OSTβ (SLC51A/B) in brain DHEAS/PregS homeostasis has been proposed. This transporter was reported to be localized especially in steroidogenic cells of the cerebellum and hippocampus. To date, the impact of transporters on neurosteroid homeostasis is still poorly understood. Further insights are desirable also with regard to the therapeutic potential of these compounds.
Action comprehension that is related to language or gestural integration has been shown to engage the motor system in the brain, thus providing preliminary evidence for the gestural-verbal embodiment concept. Based on the involvement of the sensorimotor cortex (M1) in language processing, we aimed to further explore its role in the cognitive embodiment necessary for gestural-verbal integration. As such, we applied anodal (excitatory) and sham transcranial direct current stimulation (tDCS) over the left M1 (with reference electrode over the contralateral supraorbital region) during a gestural-verbal integration task where subjects had to make a decision about the semantic congruency of the gesture (prime) and the word (target). We used a cross-over within-subject design in young subjects. Attentional load and simple reaction time (RT) tasks served as control conditions, applied during stimulation (order of three tasks was counterbalanced). Our results showed that anodal (atDCS) compared to sham tDCS (stDCS) reduced RTs in the gestural-verbal integration task, specifically for incongruent pairs of gestures and verbal expressions, with no effect on control task performance. Our findings provide evidence for the involvement of the sensorimotor system in gestural-verbal integration performance. Further, our results suggest that functional modulation induced by sensorimotor tDCS may be specific to gestural-verbal integration. Future studies should now evaluate the modulatory effect of tDCS on semantic congruency by using tDCS over additional brain regions and include assessments of neural connectivity.
The present study seeks to determine potential associations between viral infections and neuropsychiatric diseases. To address this issue, we investigated the peptide commonalities between viruses that have been related to psychiatric and neurological disorders—such as rubella, human immunodeficiency virus, and herpesviruses—and human distal-less homeobox (DLX) proteins expressed in developing brain—namely, DLX1, DLX2, DLX5, and DLX6. Peptide matching analyses revealed a high degree of pentapeptide sharing. From an immunological perspective, this overlap is relevant because pentapeptides are endowed with immunogenicity and antigenicity—that is, they are immune determinants. Moreover, infection-induced immune cross-reactions might have functional, spatial, and temporal implications related to the functions and expression patterns of DLX1 and DLX5 in the fetal and adult human brain. In sum, our data support the hypothesis that viral infections may be linked to neuropsychiatric diseases through autoimmune cross-reactions caused by molecular mimicry between viral proteins and brain-specific DLX self-antigens.
In classical models of tumorigenesis, the accumulation of tumor promoting chromosomal aberrations is described as a gradual process. Next-generation sequencing-based methods have recently revealed complex patterns of chromosomal aberrations, which are beyond explanation by these classical models of karyotypic evolution of tumor genomes. Thus, the term chromothripsis has been introduced to describe a phenomenon, where temporarily and spatially confined genomic instability results in dramatic chromosomal rearrangements limited to segments of one or a few chromosomes. Simultaneously arising and misrepaired DNA double-strand breaks are also the cause of another phenomenon called chromoplexy, which is characterized by the presence of chained translocations and interlinking deletion bridges involving several chromosomes. In this study, we demonstrate the genome-wide identification of chromosomal translocations based on the analysis of translocation-associated changes in spatial proximities of chromosome territories on the example of the cutaneous T-cell lymphoma cell line Se-Ax. We have used alterations of intra- and interchromosomal interaction probabilities as detected by genome-wide chromosome conformation capture (Hi-C) to infer the presence of translocations and to fine-map their breakpoints. The outcome of this analysis was subsequently compared to datasets on DNA copy number alterations and gene expression. The presence of chained translocations within the Se-Ax genome, partly connected by intervening deletion bridges, indicates a role of chromoplexy in the etiology of this cutaneous T-cell lymphoma. Notably, translocation breakpoints were significantly overrepresented in genes, which highlight gene-associated biological processes like transcription or other gene characteristics as a possible cause of the observed complex rearrangements. Given the relevance of chromosomal aberrations for basic and translational research, genome-wide high-resolution analysis of structural chromosomal aberrations will gain increasing importance.
Two decades of research indicate that visual processing is typically enhanced for items that are in the space near the hands (near-hand space). Enhanced attention and cognitive control have been thought to be responsible for the observed effects, amongst others. As accumulating experimental evidence and recent theories of dual-tasking suggest an involvement of cognitive control and attentional processes during dual tasking, dual-task performance may be modulated in the near-hand space. Therefore, we performed a series of three experiments that aimed to test if the near-hand space affects the shift between task-component processing in two visual-manual tasks. We applied a Psychological Refractory Period Paradigm (PRP) with varying stimulus-onset asynchrony (SOA) and manipulated stimulus-hand proximity by placing hands either on the side of a computer screen (near-hand condition) or on the lap (far-hand condition). In Experiment 1, Task 1 was a number categorization task (odd vs. even) and Task 2 was a letter categorization task (vowel vs. consonant). Stimulus presentation was spatially segregated with Stimulus 1 presented on the right side of the screen, appearing first and then Stimulus 2, presented on the left side of the screen, appearing second. In Experiment 2, we replaced Task 2 with a color categorization task (orange vs. blue). In Experiment 3, Stimulus 1 and Stimulus 2 were centrally presented as a single bivalent stimulus. The classic PRP effect was shown in all three experiments, with Task 2 performance declining at short SOA while Task 1 performance being relatively unaffected by task-overlap. In none of the three experiments did stimulus-hand proximity affect the size of the PRP effect. Our results indicate that the switching operation between two tasks in the PRP paradigm is neither optimized nor disturbed by being processed in near-hand space.
Three-year-olds and 4-year-olds have severe difficulties solving standard mental rotation tasks. Only 5-year-olds solve such tasks above chance reliably. In contrast studies relying on simplified mental rotation tasks indicate that infants discriminate between an object and its mirror image. Furthermore in another simplified mental rotation task with 3-year-olds, a linear relation between angular disparity and reaction time typical for mental rotation was revealed. Therefore it was assumed that 3-year-olds’ capabilities are underestimated. In the current study, 3-year-olds were trained in two isolated sessions to solve standard mental rotation tasks and were tested in a third session. Three-year-olds solved this test above chance as a group – a substantial number of them doing so on an individual level. However, a linear relation between angular disparity and reaction time, that would indicate an analog mental transformation, was not discernable. Nevertheless, these findings are in accordance with a continuous line describing mental rotation in infants and older children. And, these also indicate that children’s mental rotation capabilities might be underestimated.
Production-Integrated Compensation in Environmental Offsets—A Review of a German Offset Practice
(2018)
Biocidal Agents Used for Disinfection Can Enhance Antibiotic Resistance in Gram-Negative Species
(2018)
Recent research suggests that the P3b may be closely related to the activation of the locus coeruleus-norepinephrine (LC-NE) system. To further study the potential association, we applied a novel technique, the non-invasive transcutaneous vagus nerve stimulation (tVNS), which is speculated to increase noradrenaline levels. Using a within-subject cross-over design, 20 healthy participants received continuous tVNS and sham stimulation on two consecutive days (stimulation counterbalanced across participants) while performing a visual oddball task. During stimulation, oval non-targets (standard), normal-head (easy) and rotated-head (difficult) targets, as well as novel stimuli (scenes) were presented. As an indirect marker of noradrenergic activation we also collected salivary alpha-amylase (sAA) before and after stimulation. Results showed larger P3b amplitudes for target, relative to standard stimuli, irrespective of stimulation condition. Exploratory post hoc analyses, however, revealed that, in comparison to standard stimuli, easy (but not difficult) targets produced larger P3b (but not P3a) amplitudes during active tVNS, compared to sham stimulation. For sAA levels, although main analyses did not show differential effects of stimulation, direct testing revealed that tVNS (but not sham stimulation) increased sAA levels after stimulation. Additionally, larger differences between tVNS and sham stimulation in P3b magnitudes for easy targets were associated with larger increase in sAA levels after tVNS, but not after sham stimulation. Despite preliminary evidence for a modulatory influence of tVNS on the P3b, which may be partly mediated by activation of the noradrenergic system, additional research in this field is clearly warranted. Future studies need to clarify whether tVNS also facilitates other processes, such as learning and memory, and whether tVNS can be used as therapeutic tool.
Submerged macrophytes play a key role in north temperate shallow lakes by stabilizing clear-water conditions. Eutrophication has resulted in macrophyte loss and shifts to turbid conditions in many lakes. Considerable efforts have been devoted to shallow lake restoration in many countries, but long-term success depends on a stable recovery of submerged macrophytes. However, recovery patterns vary widely and remain to be fully understood. We hypothesize that reduced external nutrient loading leads to an intermediate recovery state with clear spring and turbid summer conditions similar to the pattern described for eutrophication. In contrast, lake internal restoration measures can result in transient clear-water conditions both in spring and summer and reversals to turbid conditions. Furthermore, we hypothesize that these contrasting restoration measures result in different macrophyte species composition, with added implications for seasonal dynamics due to differences in plant traits. To test these hypotheses, we analyzed data on water quality and submerged macrophytes from 49 north temperate shallow lakes that were in a turbid state and subjected to restoration measures. To study the dynamics of macrophytes during nutrient load reduction, we adapted the ecosystem model PCLake. Our survey and model simulations revealed the existence of an intermediate recovery state upon reduced external nutrient loading, characterized by spring clear-water phases and turbid summers, whereas internal lake restoration measures often resulted in clear-water conditions in spring and summer with returns to turbid conditions after some years. External and internal lake restoration measures resulted in different macrophyte communities. The intermediate recovery state following reduced nutrient loading is characterized by a few macrophyte species (mainly pondweeds) that can resist wave action allowing survival in shallow areas, germinate early in spring, have energy-rich vegetative propagules facilitating rapid initial growth and that can complete their life cycle by early summer. Later in the growing season these plants are, according to our simulations, outcompeted by periphyton, leading to late-summer phytoplankton blooms. Internal lake restoration measures often coincide with a rapid but transient colonization by hornworts, waterweeds or charophytes. Stable clear-water conditions and a diverse macrophyte flora only occurred decades after external nutrient load reduction or when measures were combined.
The obligate anaerobe, spore forming bacterium Clostridioides difficile (formerly Clostridium difficile) causes nosocomial and community acquired diarrhea often associated with antibiotic therapy. Major virulence factors of the bacterium are the two large clostridial toxins TcdA and TcdB. The production of both toxins was found strongly connected to the metabolism and the nutritional status of the growth environment. Here, we systematically investigated the changes of the gene regulatory, proteomic and metabolic networks of C. difficile 630Δerm underlying the adaptation to the non-growing state in the stationary phase. Integrated data from time-resolved transcriptome, proteome and metabolome investigations performed under defined growth conditions uncovered multiple adaptation strategies. Overall changes in the cellular processes included the downregulation of ribosome production, lipid metabolism, cold shock proteins, spermine biosynthesis, and glycolysis and in the later stages of riboflavin and coenzyme A (CoA) biosynthesis. In contrast, different chaperones, several fermentation pathways, and cysteine, serine, and pantothenate biosynthesis were found upregulated. Focusing on the Stickland amino acid fermentation and the central carbon metabolism, we discovered the ability of C. difficile to replenish its favored amino acid cysteine by a pathway starting from the glycolytic 3-phosphoglycerate via L-serine as intermediate. Following the growth course, the reductive equivalent pathways used were sequentially shifted from proline via leucine/phenylalanine to the central carbon metabolism first to butanoate fermentation and then further to lactate fermentation. The toxin production was found correlated mainly to fluxes of the central carbon metabolism. Toxin formation in the supernatant was detected when the flux changed from butanoate to lactate synthesis in the late stationary phase. The holistic view derived from the combination of transcriptome, proteome and metabolome data allowed us to uncover the major metabolic strategies that are used by the clostridial cells to maintain its cellular homeostasis and ensure survival under starvation conditions.
Aquaporins (AQPs) facilitate the transepithelial water flow involved in epithelial fluid secretion in numerous tissues; however, their function in the pancreas is less characterized. Acute pancreatitis (AP) is a serious disorder in which specific treatment is still not possible. Accumulating evidence indicate that decreased pancreatic ductal fluid secretion plays an essential role in AP; therefore, the aim of this study was to investigate the physiological and pathophysiological role of AQPs in the pancreas. Expression and localization of AQPs were investigated by real-time PCR and immunocytochemistry, whereas osmotic transmembrane water permeability was estimated by the dye dilution technique, in Capan-1 cells. The presence of AQP1 and CFTR in the mice and human pancreas were investigated by immunohistochemistry. Pancreatic ductal HCO3- and fluid secretion were studied on pancreatic ducts isolated from wild-type (WT) and AQP1 knock out (KO) mice using microfluorometry and videomicroscopy, respectively. In vivo pancreatic fluid secretion was estimated by magnetic resonance imaging. AP was induced by intraperitoneal injection of cerulein and disease severity was assessed by measuring biochemical and histological parameters. In the mice, the presence of AQP1 was detected throughout the whole plasma membrane of the ductal cells and its expression highly depends on the presence of CFTR Cl- channel. In contrast, the expression of AQP1 is mainly localized to the apical membrane of ductal cells in the human pancreas. Bile acid treatment dose- and time-dependently decreased mRNA and protein expression of AQP1 and reduced expression of this channel was also demonstrated in patients suffering from acute and chronic pancreatitis. HCO3- and fluid secretion significantly decreased in AQP1 KO versus WT mice and the absence of AQP1 also worsened the severity of pancreatitis. Our results suggest that AQP1 plays an essential role in pancreatic ductal fluid and HCO3- secretion and decreased expression of the channel alters fluid secretion which probably contribute to increased susceptibility of the pancreas to inflammation.
Tree growth at northern boreal treelines is generally limited by summer temperature, hence tree rings serve as natural archives of past climatic conditions. However, there is increasing evidence that a changing summer climate as well as certain micro-site conditions can lead to a weakening or loss of the summer temperature signal in trees growing in treeline environments. This phenomenon poses a challenge to all applications relying on stable temperature-growth relationships such as temperature reconstructions and dynamic vegetation models. We tested the effect of differing ecological and climatological conditions on the summer temperature signal of Scots pine at its northern distribution limits by analyzing twelve sites distributed along a 2200 km gradient from Finland to Western Siberia (Russia). Two frequently used proxies in dendroclimatology, ring width and maximum latewood density, were correlated with summer temperature for the period 1901–2013 separately for (i) dry vs. wet micro-sites and (ii) years with dry/warm vs. wet/cold climate regimes prevailing during the growing season. Differing climate regimes significantly affected the temperature signal of Scots pine at about half of our sites: While correlations were stronger in wet/cold than in dry/warm years at most sites located in Russia, differing climate regimes had only little effect at Finnish sites. Both tree-ring proxies were affected in a similar way. Interestingly, micro-site differences significantly affected absolute tree growth, but had only minor effects on the climatic signal at our sites. We conclude that, despite the treeline-proximal location, growth-limiting conditions seem to be exceeded in dry/warm years at most Russian sites, leading to a weakening or loss of the summer temperature signal in Scots pine here. With projected temperature increase, unstable summer temperature signals in Scots pine tree rings might become more frequent, possibly affecting dendroclimatological applications and related fields.
Mendelian randomization (MR) is a framework for assessing causal inference using cross-sectional data in combination with genetic information. This paper summarizes statistical methods commonly applied and strait forward to use for conducting MR analyses including those taking advantage of the rich dataset of SNP-trait associations that were revealed in the last decade through large-scale genome-wide association studies. Using these data, powerful MR studies are possible. However, the causal estimate may be biased in case the assumptions of MR are violated. The source and the type of this bias are described while providing a summary of the mathematical formulas that should help estimating the magnitude and direction of the potential bias depending on the specific research setting. Finally, methods for relaxing the assumptions and for conducting sensitivity analyses are discussed. Future researches in the field of MR include the assessment of non-linear causal effects, and automatic detection of invalid instruments.