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Streptococcus pneumoniae (the pneumococcus) is an opportunistic human pathogen that causes life-threatening diseases including pneumonia, sepsis, meningitis but also non-invasive local infections such as otitis media. Pneumococci have evolved versatile strategies to colonize the upper respiratory tract (URT) of humans. Binding to epithelial surfaces is thereby mediated through direct interactions with host cell receptors or indirectly via binding to components of the extracellular matrix (ECM). However, successful colonization and subsequent infection require S. pneumoniae to cross tissue barriers protected by the immune system of the host. Pneumococci have therefore evolved a wide range of mechanisms to circumvent the antibacterial activity of the immune system such as the acquisition or expression of serine protease activity. Serine protease enzymes have emerged during evolution as one of the most abundant and functionally diverse groups of proteins in eukaryotic and prokaryotic organisms. However, the epithelial barriers, integrins, and other cell surface receptors are often initially inaccessible for pneumococci colonizing the nasopharyngeal cavity. Therefore, pneumococci recruit host-derived extracellular serine proteases such as plasmin(ogen) for extracellular matrix and mucus degradation, which results in enhanced binding to epithelial and endothelial cells. S. pneumoniae expresses four surface-anchored or surface-associated serine proteases depending on the serotype: HtrA, SFP, PrtA, and CbpG. These enzymes belong to the category of trypsin-like or subtilisin-like family proteins, which are characterized by the presence of three-conserved amino acid residues, Ser-His-Asp. The catalytic triads are critical for the cleavage of peptide bonds. Studies focusing on the deletion of single pneumococcal serine proteases are difficult to interpret due to the compensatory effects of the other serine proteases.
Initially, a comprehensive in silico analysis of the distribution and genes organization of pneumococcal serine proteases was carried out in this study. Interestingly, the genes encoding PrtA, HtrA, and CbpG were highly conserved among the 11 analyzed strains. Surprisingly, the gene encoding the subtilisin-like protein SFP was not present in some of the strains and seems to be strain-dependent. Therefore, pneumococci have at least three serine proteases as shown e.g., for serotype 19F_EF3030 strain. Computer-assisted analyses of the structure of pneumococcal serine proteases showed high similarities in the catalytic domains between HtrA and CbpG or between PrtA and SFP in 3D structural models.
The focus of this study lies on the impact of single extracellular pneumococcal serine proteases on pneumococcal pathogenesis during adherence, colonization, virulence and biofilm formation. Therefore, double and triple deletion mutants were generated in the colonizing S. pneumoniae serotype 19F strain EF3030 and the more invasive serotype 4 strain TIGR4, respectively. In adherence studies with human Detroit-562 epithelial cells, we demonstrated that both TIGR4Δcps and 19F_EF3030 mutants without serine proteases or expressing only CbpG, HtrA, or PrtA have a reduced ability to adhere to Detroit-562 cells. In a mouse colonization model, the inactivation of serine proteases in strain 19F_EF3030 strongly reduced nasopharyngeal colonization in CD-1 mice. The bacterial load in the nasopharynx was thereby monitored for a period of 14 days. Mutant strains showed significantly lower bacterial numbers in the nasopharynx on days 2, 3, 7, and 14 post-inoculations.
Following up on pneumococcal pathogenesis, an in vivo acute pneumonia mouse infection model and in vitro phagocytosis was used to analyze the impact of single serine proteases during infection and phagocytosis. Mice were intranasally infected with the bioluminescent TIGR4lux wild-type or isogenic triple mutants expressing only CbpG, HtrA, PrtA, or SFP. The acute lung infection was monitored in real-time by using an IVIS®-Spectrum in vivo imaging system. The TIGR4lux mutant expressing only PrtA showed a significant attenuation and was less virulent in the acute pneumonia model. Phagocytosis assays were conducted using murine J77A.1 macrophages. The number of triple serine protease mutants internalized by macrophages were significantly reduced in comparison to the isogenic wild-type.
Finally, two different experimental biofilm models were used to study the influence of serine proteases on biofilm formation grown on an abiotic surface (glass) and a biological surface. Biofilm development on living epithelial cells was stronger after 48 and 72h than on the glass surface. On epithelial substratum, the serine protease mutant with only CbpG+ showed higher and denser biofilm development after 48h and 72h of incubation compared to the parental strains and other serine protease mutants. Moreover, the bacterial dispersal from biofilms was significantly more in the mutant strains lacking serine proteases than in the wild type.
In conclusion, nasopharyngeal colonization is a prerequisite for invasive diseases and transmission. Pneumococcal serine proteases are indispensable for nasopharyngeal colonization and facilitate access to eukaryotic cell-surface receptors by the cleavage of ECM proteins. Thus, serine proteases could be promising candidates for developing antimicrobials to reduce pneumococcal colonization and transmission.
Background:
Microvascular decompression (MVD) success rates exceed 90% in hemifacial spasm (HFS).
However, postoperative recovery patterns and durations are variable.
Objective:
We aim to study factors that might influence the postoperative patterns and duration needed until
final recovery.
Method:
Only patients following de-novo MVD with a minimum follow-up of 6 months were included.
Overall trend of recovery was modeled. Patients were grouped according to recognizable clinical
recovery patterns. Uni- and multivariable analyses were used to identify the factors affecting
allocation to the identified patterns and time needed to final recovery.
Results:
323(92.6%) patients had >90% symptom improvement and 269(77.1%) patients had complete
resolution at the last follow–up. The overall trend of recovery showed steep remission within the
first 6 months, followed by relapse peaking around 8 months with a second remission ~16
months. Five main recovery patterns were identified.
Patterns analysis showed that evident proximal indentation of the facial nerve at REZ, males and
facial palsy are associated with earlier recovery at multivariable and univariable levels. AICA,
AICA/VA compressions and shorter disease durations are related to immediate resolution of the
symptoms only on the univariable level. Time analysis showed that proximal indentation (vs.
distal indentation), males and facial palsy witnessed significantly earlier recoveries.
Conclusion:
Our main finding is that in contrast to peripheral indentation, proximal indentation of the facial
nerve at REZ is associated with earlier recovery. Postoperative facial palsy and AICA
compressions are associated with earlier recoveries. We recommend a minimum of 1 year before
evaluating the final outcome of MVD for HFS.
Discovering Latent Structure in High-Dimensional Healthcare Data: Toward Improved Interpretability
(2022)
This cumulative thesis describes contributions to the field of interpretable machine learning in the healthcare domain. Three research articles are presented that lie at the intersection of biomedical and machine learning research. They illustrate how incorporating latent structure can provide a valuable compression of the information hidden in complex healthcare data.
Methodologically, this thesis gives an overview of interpretable machine learning and the discovery of latent structure, including clusters, latent factors, graph structure, and hierarchical structure. Different workflows are developed and applied to two main types of complex healthcare data (cohort study data and time-resolved molecular data). The core result builds on Bayesian networks, a type of probabilistic graphical model. On the application side, we provide accurate predictive or discriminative models focusing on relevant medical conditions, related biomarkers, and their interactions.
Background: A large body of research indicates that the cognitions individuals have
about their own age and aging, so called self-perceptions of aging (SPA), predict health and
wellbeing in later life. However, much less is known about associations of SPA with
developmental correlates such as personality. Some initial studies have found cross-sectional
and longitudinal associations of the Big Five traits (openness to experience,
conscientiousness, extraversion, agreeableness, and neuroticism) with SPA. Building on these
findings, this thesis aimed at advancing knowledge on associations of personality with SPA.
To this end, cross-sectional associations of the meta-traits of agency, i.e., a focus on the self,
and communion, i.e., a focus on others, with SPA were examined in study 1, and longitudinal
associations of agentic and communal personal values with SPA were examined in study 2.
Study 3 aimed at expanding findings of previous studies on associations of SPA with selfreported
physical function to an objective indicator of physical function, namely, gait pattern.
In all studies, SPA were treated as a multidimensional construct comprising gains and losses.
Methods: Study 1 was based on data of 154 adults aged 75 and older that were
recruited in hospital. Data was collected one month after recruitment. In regression analyses,
associations of agentic and communal traits with SPA beyond health were examined. Study 2
was based on data of 6,089 adults aged 40 and older enrolled in the German Ageing Survey
(DEAS). Multiple regression analyses were used to test whether personal value priority
predicted change in SPA over three years beyond age stereotypes. For study 3, latent profile
analysis was employed to detect gait patterns based on data of 150 adults aged 70 and older
collected via an automated walkway at participants’ regular speed and individual maximum
speed. In a next step, associations of SPA with gait patterns beyond personality traits were
investigated in binary logistic regressions.
Results: Agentic and communal personality traits were associated with gain-, but not
loss-related SPA when controlling for health (study 1). In study 2, the value priority of
openness to change (self-direction, stimulation) predicted more gain-related SPA three years
later, while the value priority of conservation (tradition, security) was negatively associated
with gain-related SPA. The value priority of self-enhancement (achievement, power) was
associated with more loss-related SPA three years later. Finally, the value priority of selftranscendence
(universalism, benevolence), i.e. a concern for the well-being of others, was
associated with more gain- and less loss-related SPA at follow-up. In study 3, latent profile
analyses distinguished two groups with different gait patterns in both gait speed conditions.
One group exhibited a slower and less well-coordinated gait pattern, which reflected
functional limitations. The other group exhibited a faster and well-coordinated gait pattern,
which reflected better physical function. More loss-, but not gain-related SPA were associated
with higher likelihood to exhibit a functionally limited gait pattern at regular speed.
Conversely, gain- but not loss-related SPA were associated with higher likelihood to exhibit a
fit gait pattern at individual maximum speed.
Conclusion: Results of this thesis have three main implications for research on SPA.
First, agency and communion may constitute useful dimensions for further investigating SPA
domains, as both were associated with SPA in study 1. Second, findings of study 2 point to
the role of motivation for SPA that needs to be further explored. Third, findings of study 3
indicate that SPA are not only associated with self-reported, but also objectively measured
physical function, which stresses the importance of SPA for health in later life. As a practical
implication, the findings presented here suggest that interventions on SPA should consider
participants’ personality, both on the level of traits and values.
Introduction:
The amniotic fluid – as the medium surrounding the fetus, it is holding a crucial role in the maintenance and development of a successful pregnancy. While providing mechanical protection to the fetus, it also offers considerable immunological defense. In fact, it is known that the amniotic fluid plays a significant role in the innate immune system, as many of its corresponding substances show substantial antimicrobial function. Also, components of the adaptive immune system, including B cells, have been described within the amniotic fluid. An increase of immune cells in the amniotic fluid in cases of intra-amniotic infection indicates their involvement in inflammation-related pathologies of pregnancy. However, especially B cells in the amniotic fluid have not yet been thoroughly investigated.
The aim of this work is a deeper examination of the B-lymphocytes within the amniotic fluid. Based on the analysis of surface molecules this includes their phenotype, origin and func-tion. In the long term this could substantiate our understanding of intraamniotic inflammation and or infection, which are casually linked with preterm birth, fetal inflammatory response syndrome and fetal morbidity.
This, in turn, could pave the way for potential diagnostic methods and treatments.
Methods:
For all experiments 8-12-weeks-old pregnant mice were sacrificed at day 14 of pregnancy. The amniotic fluid was collected and specific cell subsets were isolated using MACS cell separation. Cells were then co-cultured with a bone marrow stromal cell line and stimulated in vitro.
The analysis of the population distribution and cytokine production was performed by flow cytometry. To analyze IgM-levels in the supernatant of the co culture, ELISA was used. Statistical analysis was performed using GraphPad Prism software.
Results:
The amniotic fluid contains different developmental stages of B cells, which most likely are of fetal origin. This is supported by the expression of paternal surface markers. An extensive proliferation and switch towards a more mature phenotype upon co-culture shows that the immature subsets of amniotic fluid B cells are able to expand and mature in vitro. Amniotic
fluid B cells spontaneously produce IgM and show functional adaption upon in vitro stimula-tion as evidenced by the increase of cell activation markers.
Conclusion:
For the first time a deep investigation of B-cells within the amniotic fluid was performed, covering phenotype and cell functionality. This work shows that there is a B cell compartment within the amniotic fluid, which, to a certain extent, is able to mature and gain functionality when exposed to external stimuli. This supports the hypothesis of the amniotic fluid as crucial immunological line of defense against inflammatory and infectious challenges during pregnancy.
Coding constraints imposed by the very small genome sizes of negative-strand RNA viruses (NSVs) have led to the development of numerous strategies that increase viral protein diversity, enabling the virus to both establish a productive viral replication cycle and effectively control the host antiviral response. Arenaviruses are no exception to this, and previous findings have demonstrated that the nucleoprotein (NP) of the highly pathogenic Junín virus (JUNV) exists as three additional N-terminally truncated isoforms of 53 kD (NP53kD), 47 kD (NP47kD), and 40 kD (NP40kD). The two smaller isoforms (i.e. NP47kD and NP40kD) have been characterized as products of caspase cleavage, which appears to serve a decoy function to inhibit apoptosis induction. However, whether they have additional functions in the viral replication cycle remains unknown. Further, the origin and function of NP53kD has not yet been described.
In order to first identify the mechanism responsible for production of the NP53kD variant, a possible role of additional caspase cleavage sites was first excluded using a site mutagenesis approach. Subsequently, alanine mutagenesis was then used to identify a region responsible for NP53kD production. As a result, three methionine residues were identified within the characterized sequence segment of NP, linking the production of NP53kD to an alternative in-frame translation initiation. Further site-directed mutagenesis of the previously identified putative in-frame methionine codons (i.e. M78, M80 and M100) finally led to the identification of translation initiation at M80 as being predominantly responsible for the production of NP53kD. Once the identity of all three NP isoforms was known, it was then of further interest to more deeply characterize their functional roles. Consistent with the N-terminal domain containing RNA binding and homotrimerization motifs that are relevant for the viral RNA synthesis process, it could be demonstrated that all three truncated NP isoforms lost the ability to support viral RNA synthesis in a minigenome assay. However, they also did not interfere with viral RNA synthesis by full-length NP, nor did they affect the ability of the matrix protein Z to inhibit viral RNA synthesis. Moreover, it was observed that loss of the oligomerization motifs in the N-terminus also affected the subcellular localization of all three NP isoforms, which were no longer localized in discrete perinuclear inclusion bodies, but rather showed a diffuse distribution throughout the cytoplasm, with the smallest isoform NP40kD also being able to enter the nucleus. Surprisingly, the 3'-5' exonuclease function of NP, which is associated with the C-terminal domain and plays a role in inhibiting interferon induction by digestion of double-stranded RNAs, was found to be retained only by the NP40kD isoform, despite that all three isoforms retained the associated domain. Finally, previous studies using transfected NP and chemical induction of apoptosis have suggested that cleavage of NP at the caspase motifs responsible for generating NP47kD and NP40kD plays a role in controlling activation of the apoptosis pathway. Therefore, to further characterize the connection between the generation of NP isoforms and the regulation of apoptosis in a viral context, recombinant JUNVs deficient in the respective isoforms were generated. Unlike infections with wild-type JUNV, mutations of the caspase cleavage sites resulted in the induction of caspases activation. Surprisingly, however, this was also the case for mutation of the alternate start codon responsible for NP53kD generation.
Taken together, the data from this study suggest a model whereby JUNV generates a pool of smaller NP isoforms with a predominantly cytoplasmic distribution. As a result of this altered localization, NP53kD appears to be able to serve as the substrate for further generation of NP47kD and NP40kD by caspase cleavage. Not only does this cleavage inhibit apoptosis induction during JUNV infection, it also results in a cytoplasmic isoform of NP that retains strong 3'-5' exonuclease activity (i.e. NP40kD) and thus may play an important role in preventing viral double-stranded RNA accumulation in the cytoplasm, where it can lead to activation of IFN signaling. Overall, such results emphasize the relevance of alternative protein isoforms in virus biology, and particularly in regulation of the host response to infection.
Clostridioides difficile is the leading cause of antibiotic-associated diarrhea referring to infections of the gastrointestinal tract in the course of (broad-spectrum)antibiotic therapy. While antibiotic therapy, preferentially with fidaxomicin or vancomycin, often stops the acute infection, recurrence events due to remaining spores and biofilm-associated cells are observed in up to 20% of cases. Therefore, new antibiotics, which spare the intestinal microbiota and eventually clear infections with C. difficile are urgently required. In this light, the presented work aimed at the evaluation and characterization of three natural product classes, namely chlorotonils, myxopyronins and chelocardins, with respect to their antimicrobial activity spectrum under anaerobic conditions and their potential for the therapy of C. difficile infections. Briefly, compounds of all three classes were screened for their activity against a panel of anaerobic bacteria. Subsequently, the systemic effects of selected derivatives of each compound class were analyzed in C. difficile using a proteomics approach. Finally, appropriate downstream experiments were performed to follow up on hypotheses drawn from the proteomics datasets. Thereby, all three compound classes demonstrated significant activity against C. difficile. However, chelocardins similarly inhibited the growth of other anaerobes excluding chelocardins as antibiotic candidates for C. difficile infection therapy. In contrast, chlorotonils demonstrated significantly higher in vitro activity against C. difficile and close relatives compared to a small panel of other anaerobes. In addition, it could be shown that chlorotonils affect intracellular metal homeostasis as demonstrated in a multi-omics approach. The data led to speculate that chlorotonils eventually affect cobalt and selenate availability in particular. Moreover, a metaproteomics approach verified that oral chlorotonil treatment only marginally affected the intestinal microbiota of piglets on taxonomic and functional level. Furthermore, the proteome stress response of C. difficile 630 to myxopyronin B, which similarly showed elevated activity against C. difficile compared to a few other anaerobes, indicated that the antibiotic inhibited early toxin synthesis comparatively to fidaxomicin. Finally, evidence is provided that C. difficile 630 responds to dissipation of its membrane potential by production and accumulation of aromatic metabolites.
This work investigates turbulence in the core plasma of the optimised stellarator
Wendelstein 7-X. It focuses on experimental characterisation and
evaluation of the electrostatic micro-instabilities, which drive turbulent fluctuations,
and the saturation of turbulence by zonal flows. Expectations for
Wendelstein 7-X are formulated by reviewing theoretical work and with
the help of gyrokinetic simulations. The experimental analysis centres on
line-integrated density fluctuation measurements with the phase contrast
imagining diagnostic in electron cyclotron heated hydrogen discharges. An
absolute amplitude calibration was implemented, and a method for reliable
determination of dominant phase velocities in wavenumber-frequency
spectra of density fluctuations has been developed. Line-averaged density
fluctuation levels are observed to vary between magnetic configurations.
The wavenumber spectra exhibit a dual cascade structure, indicating fully
developed turbulence. The dominant instability driving turbulent density
fluctuations on transport relevant scales is identified as ion-temperaturegradient-
driven modes, which are mainly localised in the edge region of the
confined plasma. Despite the line-integrated nature of the measurement, the
localisation of density fluctuations is shown by comparing their dominant
phase velocity with the radial profile of the E × B rotation velocity due to
the ambipolar neoclassical electric field. Nonlinear gyrokinetic simulations
and a simplified plasma rotation model within a synthetic diagnostic confirm
the localisation. Oscillations of the dominant phase velocity indicate
the existence of zonal flows as a saturation mechanism of ion-temperaturegradient-
driven turbulence. A direct effect on turbulent density fluctuation
amplitudes and radial transport is observed.
With an increasing trend towards neoliberal immigration policies, the migration regime provides flexibility with regard to the workforce and the labour market as a whole. And there has been more engagement between research on the labour regime for migrant workers in global production networks (GPN) (Coe and Hess, 2013, Baglioni et al., 2022, Raj-Reichert, 2013). As functional and geographical fragmentation of production poses challenges for collective labour power at the nodes of GPNs (Mosley, 2010), for migrant workers in particular, new needs for research on how the connection between flexibilisation and migration shapes the local labour market arise conceptually and empirically (Baglioni et al., 2022).
This dissertation aims at developing a conceptual framework of migrant labour regime (MLR) with a particular focus on the interplay of the role of the state, the firm and labour market intermediaries (LMI) in global production networks (GPN) and illustrates this by the example of Filipino migrant workers in the Taiwanese semiconductor industry. Furthermore, the study examines working conditions of
migrant workers to expand the conceptualization of social upgrading.
The primary data for this dissertation are collected through semi-structured interviews with key persons in the semiconductor industry and survey of 457 Filipino migrant workers in two clusters of the Taiwanese semiconductor industry: Kaohsiung and Hsinchu. On the one hand, the study demonstrates the different roles of actors and connections within the GPN. For example, firstly, it emphasises the importance of the state and firms in shaping the MLR. Secondly, the coordination between contract manufacturers and lead firms in the GPN leads to a transformation of the workplace, e.g., intensification and increased flexibility. Thirdly, LMIs play a role in facilitating and mediating migrant labour in the transnational labour market. The coupling between the local labour market and the GPN is essential to understand the dynamics resulting from commercial pressure and inter-firm relationships. One the other hand, the study uses social upgrading as an analytical lens to examine the working conditions and further improve the understanding of the migration process in the cross-border labor market.
The exchange of water and dissolved elements between the continents and the oceans occurs via different routes in the hydrological cycle, such as rivers, atmospheric exchange, and submarine groundwater discharge (SGD). In addition, the elemental fluxes in the coastal waters may strongly depend on benthic water-solid-microbe interactions close to the sediment-water interface. It is becoming increasingly recognized that SGD can impact diagenesis and act as a source of water and dissolved substances for coastal ecosystems. The qualitative and quantitative assessment of SGD is still challenging as it requires the identification of suitable geochemical tracers for the complex hydrological and biogeochemical processes in the subterranean estuary. In this study, geochemical analyses were combined with geophysical, hydrological, and biological investigations to gain insights into the mechanisms driving SGD in coastal waters. In addition, onshore ground and surface waters were evaluated to identify the processes controlling the potential end member. The surveys were performed along the Baltic Sea coast: Warnow River and Wismar Bay in Germany, the Gulf of Gdańsk and Puck Bay in Poland, and Hanko Bay in Finland. The results suggest that the analyzed surface water system was strongly impacted by seasonal variations, while SGD displayed a much more stable composition throughout the year. New areas of SGD were also identified along the Baltic Sea. It was also observed that anthropogenic coastal infrastructures could promote SGD affecting the water balance and the benthic fluxes. At other sites, the SGD was associated with natural structures such as pockmarks. The stable isotopic composition of the fresh component of SGD was close to the meteoric water at most sites; however, old groundwaters from distinct aquifers were identified. Combining all sites, SGD showed high variability, ranging from near 0 to up to 300 L m-2 d-1, and the saline SGD was more dominant than the fresh component. The fluxes obtained at one site were even higher than the surface runoff. SGD was higher on sandy sediments, but the elemental fluxes were relatively low. Despite low SGD at muddy sites, interfacial elemental fluxes, enhanced by intense diagenesis in the top sediments, resulted in higher chemical fluxes to the water column. The sediment porewater gradients at the SGD impacted sites suggest that the advective upward flow of groundwater increased the elemental fluxes across the sediment-water interface. Therefore, the dissolved substances of SGD are partly impacted by the processes in the soil zone and aquifer during groundwater development, and partly impacted by the early diagenetic process in the surface sediments. Overall, this study shows the importance of SGD for the biogeochemical cycles of coastal waters. Moreover, 6 it can be concluded that a combination of interdisciplinary approaches can provide a better understanding and assessment of SGD in a specific environment. Although all the studies presented here are local, the methodology and results presented in this thesis can be replicated and thus provide assistance in other coastal areas.