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Institute
- Theodor-Boveri-Institut für Biowissenschaften (115)
- Graduate School of Life Sciences (67)
- Medizinische Klinik und Poliklinik II (45)
- Institut für Anorganische Chemie (44)
- Neurologische Klinik und Poliklinik (36)
- Institut für Organische Chemie (34)
- Institut für Psychologie (34)
- Institut für Informatik (28)
- Institut für Geographie und Geologie (26)
- Klinik und Poliklinik für Anästhesiologie (ab 2004) (25)
Sonstige beteiligte Institutionen
- Siemens AG (2)
- Agricultural Center, BASF SE, 67117 Limburgerhof, Germany (1)
- Center of Excellence for Science and Technology - Integration of Mediterranean region (STIM), Faculty of Science, University of Split, Poljička cesta 35, 2100 Split, Croatia (1)
- Core Unit Systemmedizin (1)
- DFG Forschungsgruppe 2757 / Lokale Selbstregelungen im Kontext schwacher Staatlichkeit in Antike und Moderne (LoSAM) (1)
- Departamento de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain (1)
- Department of Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany (1)
- Deutsches Archäologisches Institut (1)
- Deutsches Zentrum für Luft- und Raumfahrt (DLR), Institut für Raumfahrtsysteme (1)
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck, CMBI, Leopold-Franzens University Innsbruck, Austria (1)
The subject of this thesis is the fabrication and characterization of magnetic topological
insulator layers of (V,Bi,Sb)\(_2\)Te\(_3\) exhibiting the quantum anomalous Hall
effect. A major task was the experimental realization of the quantum anomalous
Hall effect, which is only observed in layers with very specific structural,
electronic and magnetic properties. These properties and their influence on the
quantum anomalous Hall effect are analyzed in detail.
First, the optimal conditions for the growth of pure Bi\(_2\)Te\(_3\) and Sb\(_2\)Te\(_3\) crystal
layers and the resulting structural quality are studied. The crystalline quality of
Bi\(_2\)Te\(_3\) improves significantly at higher growth temperatures resulting in a small
mosaicity-tilt and reduced twinning defects. The optimal growth temperature is
determined as 260\(^{\circ}\)C, low enough to avoid desorption while maintaining a high
crystalline quality.
The crystalline quality of Sb\(_2\)Te\(_3\) is less dependent on the growth temperature.
Temperatures below 230\(^{\circ}\)C are necessary to avoid significant material desorption,
though. Especially for the nucleation on Si(111)-H, a low sticking coefficient is
observed preventing the coalescence of islands into a homogeneous layer.
The influence of the substrate type, miscut and annealing sequence on the growth
of Bi\(_2\)Te\(_3\) layers is investigated. The alignment of the layer changes depending on
the miscut angle and annealing sequence: Typically, layer planes align parallel to
the Si(111) planes. This can enhance the twin suppression due to transfer of the
stacking order from the substrate to the layer at step edges, but results in a step
bunched layer morphology. For specific substrate preparations, however, the layer
planes are observed to align parallel to the surface plane. This alignment avoids
displacement at the step edges, which would cause anti-phase domains. This results
in narrow Bragg peaks in XRD rocking curve scans due to long-range order in
the absence of anti-phase domains. Furthermore, the use of rough Fe:InP(111):B
substrates leads to a strong reduction of twinning defects and a significantly reduced
mosaicity-twist due to the smaller lattice mismatch.
Next, the magnetically doped mixed compound V\(_z\)(Bi\(_{1−x}\)Sb\(_x\))\(_{2−z}\)Te\(_3\) is studied in
order to realize the quantum anomalous Hall effect. The addition of V and Bi to
Sb\(_2\)Te\(_3\) leads to efficient nucleation on the Si(111)-H surface and a closed, homogeneous
layer. Magneto-transport measurements of layers reveal a finite anomalous
Hall resistivity significantly below the von Klitzing constant. The observation of
the quantum anomalous Hall effect requires the complete suppression of parasitic
bulklike conduction due to defect induced carriers. This can be achieved by optimizing
the thickness, composition and growth conditions of the layers.
The growth temperature is observed to strongly influence the structural quality.
Elevated temperatures result in bigger islands, improved crystallographic orientation
and reduced twinning. On the other hand, desorption of primarily Sb is
observed, affecting the thickness, composition and reproducibility of the layers.
At 190\(^{\circ}\)C, desorption is avoided enabling precise control of layer thickness and
composition of the quaternary compound while maintaining a high structural
quality.
It is especially important to optimize the Bi/Sb ratio in the (V,Bi,Sb)\(_2\)Te\(_3\) layers,
since by alloying n-type Bi\(_2\)Te\(_3\) and p-type Sb\(_2\)Te\(_3\) charge neutrality is achieved at
a specific mixing ratio. This is necessary to shift the Fermi level into the magnetic
exchange gap and fully suppress the bulk conduction. The Sb content x furthermore
influences the in-plane lattice constant a significantly. This is utilized to
accurately determine x even for thin films below 10 nm thickness required for the
quantum anomalous Hall effect. Furthermore, x strongly influences the surface
morphology: with increasing x the island size decreases and the RMS roughness
increases by up to a factor of 4 between x = 0 and x = 1.
A series of samples with x varied between 0.56-0.95 is grown, while carefully
maintaining a constant thickness of 9 nm and a doping concentration of 2 at.% V.
Magneto-transport measurements reveal the charge neutral point around x = 0.86
at 4.2 K. The maximum of the anomalous Hall resistivity of 0.44 h/e\(^2\) is observed
at x = 0.77 close to charge neutrality. Reducing the measurement temperature
to 50 mK significantly increases the anomalous Hall resistivity. Several samples
in a narrow range of x between 0.76-0.79 show the quantum anomalous Hall effect
with the Hall resistivity reaching the von Klitzing constant and a vanishing
longitudinal resistivity. Having realized the quantum anomalous Hall effect as the
first group in Europe, this breakthrough enabled us to study the electronic and
magnetic properties of the samples in close collaborations with other groups.
In collaboration with the Physikalisch-Technische Bundesanstalt high-precision
measurements were conducted with detailed error analysis yielding a relative de-
viation from the von Klitzing constant of (0.17 \(\pm\) 0.25) * 10\(^{−6}\). This is published
as the smallest, most precise value at that time, proving the high quality of the
provided samples. This result paves the way for the application of magnetic topological
insulators as zero-field resistance standards.
Non-local magneto-transport measurements were conducted at 15 mK in close
collaboration with the transport group in EP3. The results prove that transport
happens through chiral edge channels. The detailed analysis of small anomalies in
transport measurements reveals instabilities in the magnetic phase even at 15 mK.
Their time dependent nature indicates the presence of superparamagnetic contributions
in the nominally ferromagnetic phase.
Next, the influence of the capping layer and the substrate type on structural properties
and the impact on the quantum anomalous Hall effect is investigated. To
this end, a layer was grown on a semi-insulating Fe:InP(111)B substrate using the
previously optimized growth conditions. The crystalline quality is improved significantly
with the mosaicity twist reduced from 5.4\(^{\circ}\) to 1.0\(^{\circ}\). Furthermore, a layer
without protective capping layer was grown on Si and studied after providing sufficient
time for degradation. The uncapped layer on Si shows perfect quantization,
while the layer on InP deviates by about 5%. This may be caused by the higher
crystalline quality, but variations in e.g. Sb content cannot be ruled out as the
cause. Overall, the quantum anomalous Hall effect seems robust against changes
in substrate and capping layer with only little deviations.
Furthermore, the dependence of the quantum anomalous Hall effect on the thickness
of the layers is investigated. Between 5-8 nm thickness the material typically
transitions from a 2D topological insulator with hybridized top and bottom surface
states to a 3D topological insulator. A set of samples with 6 nm, 8 nm, and
9 nm thickness exhibits the quantum anomalous Hall effect, while 5 nm and 15 nm
thick layers show significant bulk contributions. The analysis of the longitudinal
and Hall conductivity during the reversal of magnetization reveals distinct differences
between different thicknesses. The 6 nm thick layer shows scaling consistent
with the integer quantum Hall effect, while the 9 nm thick layer shows scaling expected
for the topological surface states of a 3D topological insulator. The unique
scaling of the 9 nm thick layer is of particular interest as it may be a result of
axion electrodynamics in a 3D topological insulator.
Subsequently, the influence of V doping on the structural and magnetic properties
of the host material is studied systematically. Similarly to Bi alloying, increased
V doping seems to flatten the layer surface significantly. With increasing V content,
Te bonding partners are observed to increase simultaneously in a 2:3 ratio
as expected for V incorporation on group-V sites. The linear contraction of the
in-plane and out-of-plane lattice constants with increasing V doping is quantitatively
consistent with the incorporation of V\(^{3+}\) ions, possibly mixed with V\(^{4+}\)
ions, at the group-V sites. This is consistent with SQUID measurements showing
a magnetization of 1.3 \(\mu_B\) per V ion.
Finally, magnetically doped topological insulator heterostructures are fabricated
and studied in magneto-transport. Trilayer heterostructures with a non-magnetic
(Bi,Sb)\(_2\)Te\(_3\) layer sandwiched between two magnetically doped layers are predicted
to host the axion insulator state if the two magnetic layers are decoupled and in
antiparallel configuration. Magneto-transport measurements of such a trilayer heterostructure
with 7 nm undoped (Bi,Sb)\(_2\)Te\(_3\) between 2 nm thick layers doped with
1.5 at.% V exhibit a zero Hall plateau representing an insulating state. Similar results
in the literature were interpreted as axion insulator state, but in the absence
of a measurement showing the antiparallel magnetic orientation other explanations
for the insulating state cannot be ruled out.
Furthermore, heterostructures including a 2 nm thin, highly V doped layer region
show an anomalous Hall effect of opposite sign compared to previous samples. A
dependency on the thickness and position of the doped layer region is observed,
which indicates that scattering at the interfaces causes contributions to the anomalous
Hall effect of opposite sign compared to bulk scattering effects.
Many interesting phenomena in quantum anomalous Hall insulators as well as axion
insulators are still not unambiguously observed. This includes Majorana bound
states in quantum anomalous Hall insulator/superconductor hybrid systems and
the topological magneto-electric effect in axion insulators. The limited observation
temperature of the quantum anomalous Hall effect of below 1 K could be increased
in 3D topological insulator/magnetic insulator heterostructures which utilize the
magnetic proximity effect.
The main achievement of this thesis is the reproducible growth and characterization
of (V,Bi,Sb)2Te3 layers exhibiting the quantum anomalous Hall effect. The
detailed study of the structural requirements of the quantum anomalous Hall effect
and the observation of the unique axionic scaling behavior in 3D magnetic
topological insulator layers leads to a better understanding of the nature of this
new quantum state. The high-precision measurements of the quantum anomalous
Hall effect reporting the smallest deviation from the von Klitzing constant
are an important step towards the realization of a zero-field quantum resistance
standard.
The pathophysiological mechanisms of pain in small fiber neuropathy (SFN) are unclear. Based on experimental and clinical studies, sensitized nociceptors in the skin are reported to be involved in pain development. These nociceptors may be sensitized by cutaneous and systemic pain mediators e.g. pro- and anti-inflammatory cytokines. The aim of our study was, to measure the systemic and local gene expression of pro- and anti-inflammatory cytokines in white blood cells (WBC) as well as in primary fibroblasts and keratinocytes obtained from human skin of patients with SFN. Furthermore, gene expression levels of axon guidance molecules and their receptors, as potential regulators of the intraepidermal nerve fiber density (IENFD), were investigated. 55 patients and 31 healthy controls were prospectively recruited. Participants underwent extensive clinical phenotyping and blood sampling, 6-mm skin punch biopsies were taken from the right lateral calf and the upper thigh. Systemic relative gene expression levels (ΔG) of the interleukin (IL)-1β, IL-2, IL-6, IL-8, and tumor necrosis factor (TNF) was measured in WBC. Skin punch biopsies were taken to determine the IENFD and to obtain primary fibroblast and keratinocyte cell cultures. Skin cells were then used for investigation of ΔG in axon guidance molecules netrin 1 (NTN1) and ephrin A4 (EPHA4) as well as their receptors Unc5b receptor, and ephrin A4 (EFNA4) as well as cytokines IL-1β, IL-4, IL-6, IL-8, IL-10, TNF, and transforming growth factor (TGF). Systemically, gene expression of IL-2, IL-8, and TNF was higher in SFN patients compared to healthy controls. In keratinocytes, higher expression levels of NTN1 and TGF were found when comparing the SFN patients to the controls. In fibroblasts higher gene expression was shown in NTN1, Unc5b, IL-6, and IL-8 when comparing patients to healthy controls. The systemically and local elevated levels of pro-inflammatory, algesic cytokines in SFN patients compared to healthy controls, confirms a potential pathophysiological role in the development of neuropathic pain. Data also indicate fibroblasts and keratinocytes to influence subepidermal and intraepidermal nerve fiber growth through the expression of NTN1 and Unc5b. Thus, skin cells may contribute to the development of neuropathic pain through local denervation.
Autologous bone still represents today’s gold standard for the treatment of critical size bone defects and fracture non-unions despite associated disadvantages regarding limitations in availability, donor site morbidity, costs and efficacy. Bone tissue engineered constructs would present a promising alternative to currently available treatments. However, research on preclinical animal studies still fails to provide clinical applicable results able to allow the replacement of currently applied methods. It seems that the idea of bone tissue engineering, which has now been integral part of academic studies for over 30 years, got somehow stuck at an intermediate level, in between intense preclinical research and striven stages of initial clinical trial phases. A clear discrepancy exists between the number of studies with preclinical animal models for bone tissue engineering and the number of clinically approved bone tissue engineered constructs available to patients.
The aim of this thesis was hence to evaluate preclinical animal models for bone tissue engineering as well as the perception of scientists and clinicians towards these models. Moreover, the general role of bone tissue engineering and its clinical need assessed by scientists and surgeons was investigated. A survey was conducted questioning both scientific and clinical opinions on currently available study designs and researchers’ satisfaction with preclinical animal models. Additionally, a literature research was conducted, resulting in 167 papers from the last 10 years that report current designs of preclinical orthotopic animal studies in bone tissue engineering. Thereby, the focus lied on the description of the models regarding animal species, strain, age, gender and defect design. The outcome of the literature search was evaluated and compared to the outcome obtained from the survey.
The survey data revealed that both scientists and surgeons generally remain positive about the future role of bone tissue engineering and its step to clinical translation, at least in the distant future, where it then might replace the current gold standard, autologous bone. Moreover, most of the participants considered preclinical animal models as relevant and well developed but the results as not yet realizable in the clinics. Surgeons thereby demonstrated a slightly more optimistic perception of currently conducted research with animal models compared to scientists. However, a rather inconsistent description of present preclinical study designs could be discerned when evaluating the reported study designs in the survey and the papers of the literature search.
Indeed, defining an appropriate animal species, strain, age, gender, observation time, observation method and surgical design often depends on different indications and research questions and represents a highly challenging task for the establishment of a preclinical animal model. The existing lack of valid guidelines for preclinical testing of bone tissue engineering leads hence to a lack of well standardized preclinical animal models. Moreover, still existing knowledge gaps regarding aspects that affect the process of fracture healing, such as vascularization or immunological aspects, were found to hinder clinical translation of bone tissue engineered constructs.
Using literature review and survey, this thesis points out critical issues that need to be addressed to allow clinical translation of bone tissue engineered constructs. It can be concluded that currently existing study designs with preclinical animal models cannot live up to the claim of providing suitable results for clinical implementation. The here presented comprehensive summary of currently used preclinical animal models for bone tissue engineering reveals a missing consensus on the usage of models such as an apparent lack of reporting and standardization regarding the study designs described in both papers from the literature review and the survey. It thereby indicates a crucial need to improve preclinical animal models in order to allow clinical translation. Despite the fact that participants of the survey generally revealed a positive perception towards the use of bone tissue engineered constructs and affirmed the clinical need for such novel designs, the missing standardization constitutes a main weak point for the provision of reliable study outcome and the translational success of the models. The optimization of reproducibility and reliability, as well as the further understanding of ongoing mechanisms in bone healing in order to develop effective tissue engineered constructs, need to form the basis of all study designs. The study outcomes might then fulfill the requirements of maybe today's and hopefully tomorrow's aging population.
Excitation energy transport in DNA modelled by multi-chromophoric field-induced surface hopping
(2020)
Absorption of ultraviolet light is known as a major source of carcinogenic mutations of DNA. The underlying processes of excitation energy dissipation are yet not fully understood. In this work we provide a new and generally applicable route for studying the excitation energy transport in multi-chromophoric complexes at an atomistic level. The surface-hopping approach in the frame of the extended Frenkel exciton model combined with QM/MM techniques allowed us to simulate the photodynamics of the alternating (dAdT)10 : (dAdT)10 double-stranded DNA. In accordance with recent experiments, we find that the excited state decay is multiexponential, involving a long and a short component which are due to two distinct mechanisms: formation of long-lived delocalized excitonic and charge transfer states vs. ultrafast decaying localized states resembling those of the bare nucleobases. Our simulations explain all stages of the ultrafast photodynamics including initial photoexcitation, dynamical evolution out of the Franck-Condon region, excimer formation and nonradiative relaxation to the ground state.
Chlamydia infect millions worldwide and cause infertility and blinding trachoma. Chlamydia trachomatis (C. trachomatis) is an obligate intracellular gram-negative pathogen with a significantly reduced genome. This bacterium shares a unique biphasic lifecycle in which it alternates between the infectious, metabolically inert elementary bodies (EB) and the non-infections, metabolically active replicative reticular bodies (RB).
One of the challenges of working with Chlamydia is its difficult genetic accessibility. In the present work, the high-throughput method TagRNA-seq was used to differentially label transcriptional start sites (TSS) and processing sites (PSS) to gain new insights into the transcriptional landscape of C. trachomatis in a coverage that has never been achieved before. Altogether, 679 TSSs and 1067 PSSs were detected indicating its high transcriptional activity and the need for transcriptional regulation. Furthermore, the analysis of the data revealed potentially new non-coding ribonucleic acids (ncRNA) and a map of transcriptional processing events. Using the upstream sequences, the previously identified σ66 binding motif was detected.
In addition, Grad-seq for C. trachomatis was established to obtain a global interactome of the RNAs and proteins of this intracellular organism. The Grad-Seq data suggest that many of the newly annotated RNAs from the TagRNA-seq approach are present in complexes. Although Chlamydia lack the known RNA-binding proteins (RBPs), e.g. Hfq and ProQ, observations in this work reveal the presence of a previously unknown RBP.
Interestingly, in the gradient analysis it was found that the σ66 factor forms a complex with the RNA polymerase (RNAP). On the other hand, the σ28 factor is unbound. This is in line with results from previous studies showing that most of the genes are under control of σ66. The ncRNA IhtA is known to function via direct base pairing to its target RNA of HctB, and by doing so is influencing the chromatin condensation in Chlamydia. This study confirmed that lhtA is in no complex. On the other hand, the ncRNA ctrR0332 was found to interact with the SNF2 protein ctl0077, a putative helicase. Both molecules co-sedimented in the gradient and were intact after an aptamer-based RNA pull-down. The SWI2/SNF2 class of proteins are nucleosome remodeling complexes. The prokaryotic RapA from E. coli functions as transcription regulator by stimulating the RNAP recycling. This view might imply that the small ncRNA (sRNA) ctrR0332 is part of the global regulation network in C. trachomatis controlling the transition between EBs and RBs via interaction with the SNF2 protein ctl0077.
The present work is the first study describing a global interactome of RNAs and proteins in C. trachomatis providing the basis for future interaction studies in the field of this pathogen.
For the rational design of new fluorophores, reliable predictions of fluorescence quantum yields from first principles would be of great help. However, efficient computational approaches for predicting transition rates usually assume that the vibrational structure is harmonic. While the harmonic approximation has been used successfully to predict vibrationally resolved spectra and radiative rates, its reliability for non-radiative rates is much more questionable. Since non-adiabatic transitions convert large amounts of electronic energy into vibrational energy, the highly excited final vibrational states deviate greatly from harmonic oscillator eigenfunctions. We employ a time-dependent formalism to compute radiative and non-radiative rates for transitions and study the dependence on model parameters. For several coumarin dyes we compare different adiabatic and vertical harmonic models (AS, ASF, AH, VG, VGF, VH), in order to dissect the
importance of displacements, frequency changes and Duschinsky rotations. In addition we analyze the effect of different broadening functions (Gaussian, Lorentzian or Voigt). Moreover, to assess the qualitative influence of anharmonicity on the internal conversion rate, we develop a simplified anharmonic model. We adress the reliability of these models considering the potential errors introduced by the harmonic approximation and the phenomenological width of the broadening function.
G protein coupled receptor kinases (GRK) phosphorylate and thereby desensitize G protein coupled receptors (GPCR) including β-adrenergic receptors (βAR), which are critical regulators of cardiac function. We identified the Raf kinase inhibitor protein (RKIP) as an endogenous inhibitor of GRK2 that leads to increased cardiac contractility via βAR activation. RKIP binds to the N-terminus (aa1-185) of GRK2, which is important for the GRK2/receptor interaction. Thereby it interferes with the GRK2/receptor interaction without interference with cytosolic GRK2 target activation. In this project, the RKIP/GRK interface was investigated to develop strategies that simulate the effects of RKIP on βAR.
RKIP binding to different isoforms of GRK expressed in the heart was analyzed by protein interaction assays using full-length and N-termini of GRK2, GRK3 and GRK5: 1-53, 54-185 and 1-185. Co-immunoprecipitation (Co-IPs) and pull-down assays revealed that RKIP binds to the peptides of GRK2 and GRK3 but not to the ones of GRK5, which suggests the existence of several binding sites of RKIP within the N-termini of GRK2 and GRK3. To analyze whether the peptides of GRK2 and GRK3 are able to simulate the RKIP mediated interference of the GRK2/receptor interaction, we analyzed the β2-AR phosphorylation in the absence and presence of the peptides. Interestingly, N-termini (aa1-185) of GRK2 and GRK3 reduced β2AR phosphorylation to a comparable extent as RKIP. In line with reduced receptor phosphorylation, the peptides also reduced isoproterenol-stimulated receptor internalization as shown by [3H] CGP-12177 radioligand binding assay and fluorescence microscopy compared to control cells. Subsequently, these peptides increased downstream signaling of β2AR, i.e. the phosphorylation of the PKA substrate phosducin. In an attempt to elucidate the mechanism behind the observed effects, Co-IPs were performed in order to investigate whether the peptides bind directly to the β2-AR and block its phosphorylation by GRK2. Indeed, GRK2 1-185 and GRK3 1-185 could bind the receptor, suggesting that this way GRK2 is prevented from inhibiting the receptor. To investigate the physiological effect of GRK2 1-185, GRK3 1-185 and GRK5 1-185, their effect on neonatal mouse cardiomyocyte contractility and hypertrophy was analyzed. After long-term isoproterenol stimulation, in the presence of GRK2 1 185 and GRK3 1-185 the cross-sectional area of the cardiomyocytes showed no significant increase in comparison to the unstimulated control cells. In addition, upon isoproterenol stimulation, GRK2 1-185 and GRK3 1-185 increased the beat rate in cardiomyocytes, mimicking RKIP while the base impedance, an indicator of viability, remained stable.
The N-termini (1-185) of GRK2 and GRK3 simulated RKIP’s function and had a significant influence on β2AR phosphorylation, on its downstream signaling and internalization, could bind β2-AR, increased beat rate and did not significantly induce hypertrophy, suggesting that they may serve as a model for the generation of new and more specific targeting strategies for GRK mediated receptor regulation.
Over the last decade life sciences have made an enormous leap forward. The development of complex analytical instruments, in particular in fluorescence microscopy, has played a decisive role in this. Scientist can now rely on a wide range of imaging techniques that offer different advantages in terms of optical resolution, recording speed or living cell compatibility. With the help of these modern microscopy techniques, multi-protein complexes can be resolved, membrane receptors can be counted, cellular pathways analysed or the internalisation of receptors can be tracked. However, there is currently no universal technique for comprehensive experiment execution that includes dynamic process capture and super resolution imaging on the same target object. In this work, I built a microscope that combines two complementary imaging techniques and enables correlative experiments in living and fixed cells. With an image scanning based laser spot confocal microscope, fast dynamics in several colors with low photodamage of the cells can be recorded. This novel system also has an improved resolution of 170 nm and was thoroughly characterized in this work. The complementary technique is based on single molecule localization microscopy, which can achieve a structural resolution down to 20-30 nm. Furthermore I implemented a microfluidic pump that allows direct interaction with the sample placed on the microscope. Numerous processes such as living cell staining, living cell fixation, immunostaining and buffer exchange can be observed and performed directly on the same cell. Thus, dynamic processes of a cell can be frozen and the structures of interest can be stained and analysed with high-resolution microscopy. Furthermore, I have equipped the detection path of the single molecule technique with an adaptive optical element. With the help of a deformable mirror, imaging functions can be shaped and information on the 3D position of the individual molecules can be extracted.
Neisseria meningitidis, a commensal β-proteobacterium residing exclusively in the human nasopharynx, is a leading cause of sepsis and epidemic meningitis worldwide. While comparative genome analysis was able to define hyperinvasive lineages that are responsible for most of the cases of invasive meningococcal disease (IMD), the genetic basis of their virulence remains unclear. Recent studies demonstrate that the type II C CRISPR/Cas system of meningococci is associated with carriage and less invasive lineages. CRISPR/Cas, an adaptive defence system against foreign DNA, was shown to be involved in gene regulation in Francisella novicida. This study shows that knockout strains of N. meningitidis lacking the Cas9 protein are impaired in the adhesion to human nasopharyngeal cells in a strain-dependant manner, which constitutes a central step in the pathogenesis of IMD. Consequently, this study indicates that the meningococcal CRISPR/Cas system fulfils functions beyond the defence of foreign DNA and is involved in the regulation of meningococcal virulence.
The effect of late parenthood on the offspring´s physical and mental health status has recently become an increasingly important topic of discussion. Studies on neurodevelopmental disorders in children of older parents (Naserbakht et al., 2011) outline the negative consequences of aging fathers as unpredictable compared to the better-understood unfavorable maternal influences (Cedars et al. 2015). This may be due to the fact that lifelong production of male gametes becomes more susceptible to error, not only for somatic mutations. Non-genomic mechanisms such as epigenetic methylation also alter DNA dynamically throughout life (Jones et al., 2015) and influence the aging human sperm DNA (Jenkins et al., 2014). These methylation changes may be transmitted to the next generation via epigenetic inheritance mechanisms (Milekic et al., 2015), which may negatively impact the sensitive epigenetic regulation of cell differentiation in the embryonic period (Curley et al., 2011; Spiers et al., 2015). Accordingly, Nardone et al. (2014) reported several hypomethylated regions in autistic patients, illustrating potential epigenetic influences on the multifactorial pathogenesis of neuropsychiatric disorders. In the present study, the methylation status of five gene regions in the sperm DNA of males of different ages was analyzed by two techniques - pyrosequencing and deep bisulfite sequencing. Two gene regions, FOXK1 and DMPK, showed a highly significant age-related methylation loss and FOXK1 a reduced methylation variation at the level of single alleles. In addition, the examined gene region of FOXK1 showed significant methylation changes in the fetal cord blood DNA of the respective offspring of the sperm donor. This fact suggests a transfer of age-related methylation loss to the next generation. Interestingly, a methylation analysis at the level of single alleles showed that the methylation loss was inherited exclusively by the father. FOXK1 is a transcription factor that plays an important role in the epigenetic regulation of the cell cycle during embryonic neuronal development (Huang et al., 2004; Wijchers et al., 2006). For this reason, the methylation status of FOXK1 in the blood of autistic patients and an age- and sex-matched control group was investigated. While both groups showed age-associated FOXK1 methylation loss, a faster dynamics of methylation change was observed in the autistic group. Although further studies are needed to uncover inheritance mechanisms of epigenetic information, the present results show an evident influence of age-related methylation changes on offspring. When advising future fathers, it is important to consider how the paternal epigenome is altered by aging and can have a negative impact on the developing embryo.
Comparison of moving and fixed basis sets for nonadiabatic quantum dynamics at conical intersections
(2020)
We assess the performance of two different types of basis sets for nonadiabatic quantum dynamics at conical intersections. The basis sets of both types are generated using Ehrenfest trajectories of nuclear coherent states. These trajectories can either serve as a moving (time-dependent) basis or be employed to sample a fixed (time-independent) basis. We demonstrate on the example of two-state two-dimensional and three-state five-dimensional models that both basis set types can yield highly accurate results for population transfer at intersections, as compared with reference quantum dynamics. The details of wave packet evolutions are discussed for the case of the two-dimensional model. The fixed basis is found to be superior to the moving one in reproducing nonlocal spreading and maintaining correct shape of the wave packet upon time evolution. Moreover, for the models considered, the fixed basis set outperforms the moving one in terms of computational efficiency.
Objectives
Embedded in the Collaborative Research Center “Fear, Anxiety, Anxiety Disorders” (CRC‐TRR58), this bicentric clinical study aims at identifying biobehavioral markers of treatment (non‐)response by applying machine learning methodology with an external cross‐validation protocol. We hypothesize that a priori prediction of treatment (non‐)response is possible in a second, independent sample based on multimodal markers.
Methods
One‐session virtual reality exposure treatment (VRET) with patients with spider phobia was conducted on two sites. Clinical, neuroimaging, and genetic data were assessed at baseline, post‐treatment and after 6 months. The primary and secondary outcomes defining treatment response are as follows: 30% reduction regarding the individual score in the Spider Phobia Questionnaire and 50% reduction regarding the individual distance in the behavioral avoidance test.
Results
N = 204 patients have been included (n = 100 in Würzburg, n = 104 in Münster). Sample characteristics for both sites are comparable.
Discussion
This study will offer cross‐validated theranostic markers for predicting the individual success of exposure‐based therapy. Findings will support clinical decision‐making on personalized therapy, bridge the gap between basic and clinical research, and bring stratified therapy into reach. The study is registered at ClinicalTrials.gov (ID: NCT03208400).
Deterioration of gait and alterations of physiological gait initiation contribute significantly to the burden of disease in Parkinson's disease. This paper systematically investigates disease-specific alterations during the postural phases of gait initiation and demonstrates the influence of dopaminergic networks by assessing levodopa mediated improvements in motor performance and correlation of motor behavior with loss of striatal and cortical dopaminergic neurons. Particular attention is given to known confounders such as initial stance and anthropometrics.
Myeloid-derived suppressor cells (MDSCs) constitute of monocytic (M-MDSCs) and granulocytic cell subsets (G-MDSCs)and were initially described as suppressors of T-cell function in tumor microenvironments. Recent studies have shown the involvement of MDSCs in a number of infectious diseases including Mycobacterium tuberculosis (Mtb) infection. MDSCs are tremendously accumulated in patients with Mtb infection and exert a suppressive effect on T cell responses against mycobacteria. Mycobacterium bovis BCG, the only available vaccine against Mtb fails to protect against the adult pulmonary tuberculosis (TB). Understanding the mechanisms of MDSC suppression for immunity against mycobacterial infection will provide a rational basis to improve anti- TB vaccination and host-directed therapies against TB. In this study, we investigated the role of three lipid-rich components of the plasma membrane, Caveolin-1(Cav-1), Acid Sphingomyelinase (ASM) and asialo-GM1 on BCG-activated MDSCs.
Cav-1 is one of the vital components of caveolae (plasma membrane invaginations) which regulates apoptosis and lipid metabolism. In this work, we found that MDSCs upregulated Cav-1, TLR4 and TLR2 expression after BCG infection on the cell surface. However, Cav-1 deficiency resulted in a selective defect in the intracellular TLR2 accumulation in the M-MDSC, but not G-MDSC subset. Further analysis indicated no difference in the phagocytosis of BCG by M-MDSCs from WT and Cav1-/- mice but a reduced capacity to up-regulate surface markers, to secrete various cytokines, induce iNOS and NO production. These defects correlated with deficits of Cav1-/- MDSCs in the suppression of T cell proliferation. Among the signaling pathways that were affected by Cav-1 deficiency, we found lower phosphorylation of NF-kB and p38 mitogen-activated protein kinase (MAPK) in BCG - activated MDSCs.
ASM is an enzyme present in lysosomes and is translocated to the cell surface where it hydrolyzes sphingomyelin into ceramide. Flow cytometric studies revealed that MDSCs phagocytosed BCG independent of inhibiting ASMase using pharmacological inhibitors (amitryptiline or desipramine) or MDSCs from WT and ASM-/-. Suppression of ASMase or using ASM-/- MDSCs resulted in reduced NO production and decreased cytokine secretion by MDSCs in response to BCG. Furthermore, MDSCs inhibited by amitryptiline had impaired AKT phosphorylation upon BCG infection.
Asialo-GM1 is a ganglioside expressed on the cell surface of MDSCs reported to cooperate with TLR2 for activating ERK signaling. Here, in this study, we found that asialo-GM1 expression was upregulated specifically upon mycobacterial infection and not upon any other stimulus. We noted that the soluble form of asialo-GM1 bound to BCG. Flow cytometric studies revealed that blocking
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asialo-GM1 did not affect the phagocytosis of BCG into MDSCs. Furthermore, blocking of asialo- GM1 had no effect on the cytokine and NO secretion or AKT signaling.
Collectively, the data presented in this work implicated that Cav-1, ASM, asialo-GM1 are dispensable for the internalization of BCG. Rather, Cav-1 and ASM are required for the functional activation of MDSCs. Although asialo-GM1 binds to BCG, we did not find any difference in the functional activation of MDSCs after blocking asialo-GM1. This study provides insights into the role of lipid raft components of the MDSC cell membrane during mycobacterial infection.
In dynamic CE MR perfusion imaging the passage of an intravenously injected CA bolus through tissue is monitored to assess the myocardial pefusion state.
To enable this, knowledge of the shape of CA wash-in through upstream epicardial vessels is required, the so-called AIF.
For technical reasons this cannot be quantified directly in the supplying vessels and is thus measured in the left ventricle, which introduces the risk of systematic errors in quantification of MBF due to bolus dispersion in coronary vessels.
This means occuring CA dispersion must be accounted in the quantification process in order to produce reliable and reproducible results.
In order to do this, CFD simulations are performed to analyze and approximate these errors and deepen insights and knowledge gained from previous CFD analyses on both idealized as well as realistic and pathologically altered 3D geometries.
In a first step, several different procedures and approaches are undertaken in order to accelerate the performed workflow, however, maintaining a sufficient degree of numerical accuracy.
In the end, the implementation of these steps makes the analysis of the cardiovascular 3D model of unprecedented detail including vessels at pre-arteriolar level feasible at all.
The findings of the Navier-Stokes simulations are thus validated with regard to different aspects of cardiac blood flow.
These include the distribution of VBF into the different myocardial regions, the areals, which can be associated to the large coronary arteries as well as the fragmentation of VBF into vessels of different diameters.
The subsequently performed CA transport simulations yield results on the one hand confirming previous studies.
On the other hand, interesting additional knowledge about the behavior of CA dispersion in coronary arteries is obtained both regarding travelled distance as well as vessel diameters.
The relative dispersion of the so-called vascular transport function, a characterizing feature of vascular networks, shows a linear decrease with vessel diameter.
This results in asymptotically decreased additional dispersion of the CA time curve towards smaller and more distal vessels.
Nonetheless, perfusion quantification errors are subject to strong regional variability and reach an average value of $(-28\pm16)$ \% at rest across the whole myocardium.
Depending on the distance from the inlet and the considered coronary tree, MBF errors up to 62 \% are observed.
Background
- Brain-Computer Interfaces (BCI) enable their users to interact and communicate with the environment without requiring intact muscle control. To this end, brain activity is directly measured, digitized and interpreted by the computer. Thus, BCIs may be a valuable tool to assist severely or even completely paralysed patients. Many BCIs, however, rely on neurophysiological potentials evoked by visual stimulation, which can result in usability issues among patients with impaired vision or gaze control. Because of this, several non-visual BCI paradigms have been developed. Most notably, a recent study revealed promising results from a tactile BCI for wheelchair control. In this multi-session approach, healthy participants used the BCI to navigate a simulated wheelchair through a virtual apartment, which revealed not only that the BCI could be operated highly efficiently, but also that it could be trained over five sessions. The present thesis continues the research on this paradigm in order to - confirm its previously reported high performance levels and trainability - reveal the underlying factors responsible for observed performance increases - establish its feasibility among potential impaired end-users
Methods
- To approach these goals, three studies were conducted with both healthy participants and patients with amyotrophic lateral sclerosis (ALS). Brain activity during BCI operation was recorded via electroencephalography (EEG) and interpreted using a machine learning-based linear classifier. Wheelchair navigation was executed according to the classification results and visualized on a monitor. For offline statistical analysis, neurophysiological features were extracted from EEG data. Subjective data on usability were collected from all participants. Two specialized experiments were conducted to identify factors for training.
Results and Discussion
- Healthy participants: Results revealed positive effects of training on BCI performances and their underlying neurophysiological potentials. The paradigm was confirmed to be feasible and (for a non-visual BCI) highly efficient for most participants. However, some had to be excluded from analysis of the training effects because they could not achieve meaningful BCI control. Increased somatosensory sensitivity was identified as a possible mediator for training-related performance improvements. Participants with ALS: Out of seven patients with various stages of ALS, five could operate the BCI with accuracies significantly above chance level. Another ALS patient in a state of near-complete paralysis trained with the BCI for several months. Although no effects of training were observed, he was consistently able to operate the system above chance level. Subjective data regarding workload, satisfaction and other parameters were reported.
Significance
- The tactile BCI was evaluated on the example of wheelchair control. In the future, it could help impaired patients to regain some lost mobility and self-sufficiency. Further, it has the potential to be adapted to other purposes, including communication. Once visual BCIs and other assistive technologies fail for patients with (progressive) motor impairments, vision-independent paradigms such as the tactile BCI may be among the last remaining alternatives to interact with the environment. The present thesis has strongly confirmed the general feasibility of the tactile paradigm for healthy participants and provides first clues about the underlying factors of training. More importantly, the BCI was established among potential end-users with ALS, providing essential external validity.
This paper deals with the taxonomical position and the nomenclature of two taxa belonging to the genus Sedum (Crassulaceae), today treated as Phedimus, namely Sedum middendorffianum Maxim var. diffusum Praeger and Sedum oppositifolium Sims. The correct taxonomical application of names is based on the nomenclatural types designated here.
The ability to differentiate into mesenchymal lineages, as well as immunomodulatory, anti-inflammatory, anti-apoptotic, and angiogenic properties give ASCs great therapeutic potential. Through their culture as multicellular, three-dimensional spheroids this potential can even be enhanced. Accordingly, 3D spheroids are not only promising candidates for the application in regenerative medicine and inflammatory disease therapy, but also for the use as building blocks in tissue engineering approaches. Due to the resemblance to physiological cell-cell and cell-matrix interactions, 3D spheroids gain higher similarity to real tissues, what makes them a valuable tool in the development of bioactive constructs equivalent to native tissues in terms of its cellular and extracellular structure. Especially, to overcome the still tremendous clinical need for adequate implants to repair soft tissue defects, 3D spheroids consisting of ASCs are a promising approach in adipose tissue engineering. Nevertheless, studies on the use of ASC-based spheroids as building blocks for fat tissue reconstruction have so far been very rare. In order to optimally exploit their therapeutic potential to further their use in regenerative medicine, including adipose tissue engineering approaches, a 3D spheroid model consisting of ASCs was characterized extensively in this work. This included not only the elucidation of the structural features, but also the differentiation capacity, gene expression, and secretory properties. In addition, the elucidation of underlying mechanisms contributing to the improved therapeutic efficiency was addressed.
Merkel cell carcinoma (MCC) is a deadly skin cancer, and about 80% of its cases have been shown to harbor integrated Merkel polyomavirus in the tumor cell genome. Viral oncoproteins expressed in the tumor cells are considered as the oncogenic factors of these virus-positive Merkel cell carcinoma (VP-MCC). In contrast, the molecular pathogenesis of virus-negative MCC (VN-MCC) is less well understood. Using gene expression analysis of MCC cell lines, we found histone methyltransferase PRDM8 to be elevated in VN-MCC. This finding was confirmed by immunohistochemical analysis of MCC tumors, revealing that increased PRDM8 expression in VN-MCC is also associated with increased H3K9 methylation. CRISPR-mediated silencing of PRDM8 in MCC cells further supported the histone methylating role of this protein in VN-MCC. We also identified miR-20a-5p as a negative regulator of PRDM8. Taken together, our findings provide insights into the role of PRDM8 as a histone methyltransferase in VN-MCC tumorigenesis.
Liquid chromatography has become the gold standard for modern quality control and purity analytics since its establishment in the 1930s. However, some analytical questions remain very challenging even today. Several molecules and impurities do not possess a suitable chromophore for the application of UV detection or cannot be retained well on regular RP columns. Possible solutions are found in derivatization procedures, but they are time consuming and can be prone to errors. In order to detect non chromophore molecules underivatized, the concept of aerosol based universal detection was established with the introduction of the evaporative light scattering detector (ELSD) in the 1970s and the charged aerosol detector (CAD) followed in 2002. These two challenging fields – polar and non chromophore molecules – are tackled in this thesis.
An overview of applications of the CAD in the literature and a comparison to its aerosol based competitors and MS is presented, emphasizing on its high sensitivity and robustness. Parameters and techniques to overcome the drawbacks of CAD, such as the use of gradient compensation or adjusted evaporation temperatures are discussed. A consideration of aspects and drawbacks of data transformation such as the integrated power function value (PFV) in the GMP environment is performed.
A method for the fatty acid analysis in polysorbate 80 that was developed on HPLC CAD was transferred to UHPLC CAD. Time and eluent savings of over 75% and 40%, respectively, as well as ways to determine the optimal CAD parameters resulted from this investigation. The evaporation temperature was determined as the most crucial setting, which has to be adjusted with care. Optimal signal to noise ratios are found at a compromise between maintaining analyte signal and reducing background noise. The incorporation of semi volatile short chain fatty acids enabled the observation of differences based on volatility of the analyte. E.g. for semi volatiles, an improved linearity by means of adjusting the PFV is achieved at values below 1.0 instead of at elevated PFVs.
Using sugars and sugar related antibiotics, a proof-of-concept was given that artificial neural networks can describe correlations between the structure and physicochemical properties of molecules and their response in CAD. Quantitative structure property relationships obtained by design of experiment approaches were able to predict the response of unseen substances and yielded insights on the response generation of the detector, which heavily relies on the formed surface area of the dried particle. Further work can substantiate upon these findings, eventually building a library of diverse eluent compositions, analytes and settings.
In order to cope with a chromatographically challenging substances, the application of ion pairing reversed phase chromatography coupled to low wavelength UV detection has been shown as a possible approach for the amino acid L asparagine. A method capable of compendial purity analysis in one single HPLC approach, thus making the utilization of the semi quantitative TLC-ninhydrin analysis obsolete, resulted from this. One cyclic dipeptide impurity (diketoasparagine) that was formerly not assessed, could be identified in several batches and added to the monograph of the Ph.Eur.
Studying ibandronate sodium with CAD and ELSD, it was found that randomly occurring spike peaks represent a major flaw of the ELSD when high sample load is present. The research with this non chromophore bisphosphonate drug furthermore shed light on possible drawbacks of mixed mode chromatography methods and ways to overcome these issues. Due to strong adsorption of the analyte onto the column, over ten injections of the highly concentrated test solution were found to be necessary to ensure reproducible peak areas. Preconditioning steps should thus be evaluated for mixed mode approaches during method development and validation.
Last, using a ternary mixed mode stationary phase coupled to CAD, a method for the impurity profiling of pamidronate disodium, also applicable to the assessment of phosphate and phosphite in four other bisphosphonate drugs, has been developed. This represents a major advantage over the Ph.Eur. impurity profiling of pamidronate, which requires two different methods, one of which is only a semi quantitative TLC approach.
Worldwide, cold regions are undergoing significant alterations due to climate change. Snow, the most widely distributed cold region component, is highly sensitive to climate change. At the same time, snow itself profoundly impacts the Earth’s energy budget, biodiversity, and natural hazards, as well as hydropower management, freshwater management, and winter tourism/sports. Large parts of the cold regions in Europe are mountain areas, which are densely populated because of the various ecosystem services and socioeconomic well-being in mountains. At present, severe consequences caused by climate change have been observed in European mountains and their surrounding areas. Yet, large knowledge gaps hinder the development of effective regional and local adaptation strategies. Long-term and evidence-based regional studies are urgently needed to enhance the comprehension of regional responses to climate change.
Earth Observation (EO) provides long-term consistent records of the Earth’s surface. It is a great alternative and/or supplement to conventional in-situ measurements which are usually time-consuming, cost-intensive and logistically demanding, particularly for the poor accessibility of cold regions. With the assistance of EO, land surface dynamics in cold regions can be observed in an objective, repeated, synoptic and consistent way. Thanks to free and open data policies, long-term archives such as Landsat Archive and Sentinel Archive can be accessed free-of-charge. The high- to medium-resolution remote sensing imagery from these freely accessible archives gives EO-based time series datasets the capability to depict snow dynamics in European mountains from the 1980s to the present. In order to compile such a dataset, it is necessary to investigate the spatiotemporal availability of EO data, and develop a spatiotemporally transferable framework from which one can investigate snow dynamics.
Among the available EO image archives, the Landsat Archive has the longest uninterrupted records of the Earth’s land surface. Furthermore, its 30 m spatial resolution fulfils the requirements for snow monitoring in complex terrains. Landsat data can yield a time series of snow dynamics in mountainous areas from 1984 to the present. However, severe Landsat data gaps have occurred across certain regions of Europe. Moreover, the Landsat Level 1 Precision and Terrain (L1TP) data is scarcer (up to 50% less) in high-latitude mountainous areas than in low-latitude mountainous areas. Given the abovementioned facts, the Regional Snowline Elevation (RSE) is selected to characterize the snow dynamics in mountainous areas, as it can handle cloud obstructions in the optical images. In this thesis, I present a five-step framework to derive and densify RSE time series in European mountains, i.e. (1) pre-processing, (2) snow detection, (3) RSE retrieval, (4) time series densification, and (5) Regional Snowline Retreat Curve (RSRC) production.
The results of the intra-annual RSE variations show a uniquely high variation in the beginning of the ablation seasons in the Alpine catchment Tagliamento, mainly toward higher elevation. As for inter-annual variations of RSE, median RSE increases in all selected catchments, with an average speed of around 4.66 m ∙ a−1 (median) and 5.87 m ∙ a−1 (at the beginning of the ablation season). The fastest significant retreat is observed in the catchment Drac (10.66 m ∙ a−1, at the beginning of the ablation season), and the slowest significant retreat is observed in the catchment Uzh (1.74 m ∙ a−1, at the beginning of the ablation season). The increase of RSEs at the beginning of the ablation season is faster than the median RSEs, whose average difference is nearly 1.21 m ∙ a−1, particularly in the catchment Drac (3.72 m ∙ a−1). The results of the RSRCs show a significant rise in RSEs at the beginning of the ablation season, except for the Alpine catchment Alpenrhein and Var, and the Pyrenean catchment Ariege. It indicates that 11.8 and 3.97 degrees Celsius less per year are needed for the regional snowlines to reach the middle point of the RSRC in the Tagliamento and Tysa, respectively. The variation of air temperature is regarded as an example of a potential climate driver in this thesis. The retrieved monthly mean RSEs are highly correlated (mean correlation coefficient "R" ̅ = 0.7) with the monthly temperature anomalies, which are more significant in months with extremely low/high temperature. Another case study that investigates the correlation between river discharges and RSEs is carried out to demonstrate the potential consequences of the derived snowline dynamics. The correlation analysis shows a good correlation between river discharges and RSEs (correlation coefficient, R=0.52).
In this thesis, the developed framework signifies a better understanding of the snow dynamics in mountain areas, as well as their potential triggers and consequences. Nonetheless, an urgent need persists for: (1) validation data to assess long-term snow-related observations based on high-resolution EO data; (2) further studies to reveal interactions between snow and its ambient environment; and (3) regional and local adaptation-strategies coping with climate change. Further studies exploring the above-mentioned research gaps are urgently needed in the future.
The subject of this thesis is the growth of Hg\(_{1-x}\)Cd\(_2\)Te layers via molecular beam epitaxy (MBE).
This material system gives rise to a number of extraordinary physical phenomena related to its electronic band structure and therefore is of fundamental interest in research.
The main results can be divided into three main areas, the implementation of a temperature measurement system based on band edge thermometry (BET), improvements of CdTe virtual substrate growth and the investigation of Hg\(_{1-x}\)Cd\(_2\)Te for different compositions.
The role of the adhesion and degranulation promoting adapter protein (ADAP) in platelet production
(2020)
Bone marrow (BM) megakaryocytes (MKs) produce platelets by extending proplatelets into sinusoidal blood vessels. Although this process is fundamental to maintain normal platelet counts in circulation only little is known about the regulation of directed proplatelet formation.
As revealed in this thesis, ADAP (adhesion and degranulation promoting adapter protein) deficiency (constitutive as well as MK and platelet-specific) resulted in a microthrombocytopenia in mice, recapitulating the clinical hallmark of patients with mutations in the ADAP gene. The thrombocytopenia was caused by a combination of an enhanced removal of platelets from the circulation by macrophages and a platelet production defect. This defect led to an ectopic release of (pro)platelet-like particles into the bone marrow compartment, with a massive accumulation of such fragments around sinusoids. In vitro studies of cultured BM cell-derived MKs revealed a polarization defect of the demarcation membrane system, which is dependent on F-actin dynamics. ADAP-deficient MKs spread on collagen and fibronectin displayed a reduced F-actin content and podosome density in the lowest confocal plane. In addition, ADAP-deficient MKs exhibited a reduced capacity to adhere on Horm collagen and in line with that the activation of beta1-integrins in the lowest confocal plane of spread MKs was diminished. These results point to ADAP as a novel regulator of terminal platelet formation.
Beside ADAP-deficient mice, three other knockout mouse models (deficiency for profilin1 (PFN1), Wiskott-Aldrich-syndrome protein (WASP) and Actin-related protein 2/3 complex subunit 2 (ARPC2)) exist, which display ectopic release of (pro)platelet-like particles. As shown in the final part of the thesis, the pattern of the ectopic release of (pro)platelet-like particles in these genetically modified mice (PFN1 and WASP) was comparable to ADAP-deficient mice. Furthermore, all tested mutant MKs displayed an adhesion defect as well as a reduced podosome density on Horm collagen. These results indicate that similar mechanisms might apply for ectopic release.
Background
The Changsha Communiqué (2008) calls for a greater account to be taken of the ethical aspects of xenotransplantation as well as of public perception. This also applies to the field of hospital chaplaincy. So far, there has been no empirical exploration of the assessment and acceptance of xenotransplantation by pastoral workers in German‐speaking countries. In view of the prospect of clinical trials, in‐depth research is both sensible and necessary, since both xeno‐ and allotransplantation can have far‐reaching consequences for patients, their relatives, and the social environment. In addition to the tasks of health monitoring, questions of the individual handling with and integration of a xenotransplant must also be considered. They can affect one's own identity and self‐image and thus also affect religious dimensions. Hence, they make a comprehensive range of accompaniment necessary.
Methods
This paper presents the first explorative results of a Dialogue Board with Christian, Jewish, and Muslim hospital chaplains. It explores pastoral challenges of xenotransplantation for the German‐speaking countries, in particular (a) self‐image and tasks of hospital pastoral care, (b) religious aspects of transplantation, and (c) religious aspects of xenotransplantation as anticipated by the hospital pastors.
Results
Depending on their religious background, hospital chaplains see different pastoral challenges when xenotransplantation reaches clinical stage. In particular, the effects on the identity and religious self‐image of those affected must be taken into account. Three desiderata or recommendations for action emerged from the Dialogue Board: (a) initial, advanced and further training for hospital pastoral workers, (b) contact points for patients, and (c) interreligious cooperation and a joint statement. All participants of the Dialogue Board emphasized the chances of xenotransplantation and expressed their hope that xenogenic transplants could save patients or improve the quality of their life substantially.
Conclusions
Xenotransplantation can affect the identity work of patients and relatives also in religious terms. In order to provide better pastoral and psychosocial support for these persons within the framework of the hospital, it is important to reflect on such challenges at an early stage and to develop concepts for pastoral further training and pastoral care in xenotransplantation.
Megakaryocyte localization in the bone marrow depending on the knock-out of small Rho GTPases
(2020)
This work focuses on megakaryocyte physiology with a special interest in the description of the localization of megakaryocytes in the bone marrow in mice single-deficient of the small Rho GTPase RhoA or double-deficient for RhoA and Cdc42. RhoA knock-out mice revealed intraluminal presence of megakaryocytes in bone marrow sinusoids. In a next step, potential aggravation, attenuation or preservation of this phenotype was studied in related mouse strains and also in the setting of platelet depletion and blockage of important megakaryocyte and platelet glycoprotein receptors in order to understand underlying singling pathways. A second part of this thesis studied the role of RhoF in filopodia formation and scrutinized RhoF deficient mice with regard to platelet activation and degranulation.
Genome-wide association studies revealed CLEC16A as a candidate gene for Type 1 Diabetes and multiple other autoimmune disorders. The function of CLEC16A remains unknown. However, previous work showed that the CLEC16A ortholog ema and the murine Clec16a were both implicated in autophagy, a process partially required for MHC class II loading and antigen presentation. Furthermore, studies could show that autophagy was required in thymic epithelial cells for antigen presentation during T cell selection, suggesting a possible role of CLEC16A in T cell selection in the thymus. Additionally, it was postulated that CLEC16A may function as an expression quantitative trait locus for its neighboring genes and that Clec16a KD was involved in pancreatic islet function and impaired insulin secretion and glucose homeostasis. Prior to this work, Schuster et al. had created a Clec16a KD NOD mouse, which was protected from spontaneous autoimmune diabetes.
For this work it was hypothesized that CLEC16A variation serves as a Type 1 Diabetes risk gene by affecting autophagy in thymic epithelial cells, which modulates antigen presentation and shapes the T cell repertoire. To expand and complement previous findings by Schuster et al., this thesis aimed to investigate how CLEC16A modifies the function of thymic epithelial cells. For this purpose, CLEC16A KD was induced in human cells via RNA interference and autophagy was studied through immunoblotting. Additionally, inflammation of pancreatic tissue in Clec16a KD NOD mice was scored using H.E. stained pancreatic sections. Thymic transplantation experiments were conducted to test whether the effects of Clec16a KD were T cell intrinsic. Also, intraperitoneal glucose tolerance tests were performed to study glucose homeostasis in Clec16a KD NOD animals. Finally, using qPCR, gene expression levels of neighboring genes such as Dexi and Socs1 were measured to study Clec16a as an expression quantitative trait locus.
In combination with the findings of Schuster et al., this thesis demonstrates that Clec16a KD reduces the severity of insulitis and protects from onset of spontaneous diabetes in the NOD mouse. Disease protection is conveyed by impaired autophagy in TEC, which leads to altered T cell selection and hyporeactive CD4+ T cells. The effects of Clec16a KD in the NOD mouse are thymus intrinsic. Glucose homeostasis remains unchanged in the Clec16a KD NOD mouse and plays no role in disease protection. Clec16a and Dexi presented similar expression levels, but further studies are required to investigate a clear link between these two genes. Finally, impaired autophagy could be replicated in human CLEC16A KD cells, which demonstrates a conserved function of CLEC16A and suggests a possible link between CLEC16A variation and risk of autoimmune disease in human.
The human body is laden with trillions of microorganisms that belong to all three domains of life. Some species of this microbiota subsist as harmless commensals in healthy adults, but under certain circumstances, they can cause mucosal disease or even systemic, life-threatening infections. While the bacterial members of our microbiota are heavily studied today, much less attention is afforded to eukaryotic species that colonize different mucocutaneous surfaces of the human body. This dissertation focuses on identifying regulatory circuits that enable a prominent member of these eukaryotes, C. albicans, to, on the one hand, live on a specific mammalian mucosal surface as a harmless commensal and, on the other hand, proliferate as a pathogen. Since the ultimate source of many fatal Candida infections is the gastrointestinal (GI) tract of the infected individual, this organism is particularly suited to distinguishing traits essential for the gut colonization of commensal fungi and their ability to cause disease. Sequence-specific DNA-binding proteins that regulate transcription are important to most biological processes; I thus used these proteins as starting points to gain insights into 1) how a specific transcription regulator promotes virulence in C. albicans; 2) which traits C. albicans requires to inhabit the GI tract of a specific, well-defined mouse model as a harmless commensal; and 3) how three previously undescribed transcriptional regulators contribute to the commensal colonization of the digestive tract of this mouse model. Altogether, this work advances the knowledge concerning the biology of commensal fungi in the mammalian gut and genetic determinants of fungal commensalism, as well as pathogenicity.
A mouse model for genetic deletion of presynaptic BDNF from adult hippocampal mossy fiber terminals
(2020)
Brain-derived neurotrophic factor (BDNF) is a modulator and mediator of structural and functional plasticity at synapses in the central nervous system. Despite our profound knowledge about the synaptic function of BDNF at synapses, it is still controversially discussed whether synaptic BDNF acts primarily from pre- or postsynaptic sites. In the central nervous system, several studies show that mossy fiber (MF) projections formed by hippocampal granule neurons store the highest amount of BDNF. However, immunofluorescence and RNA labelling studies suggest that MF BDNF is primarily produced by granule neurons. Multiple other studies prefer the view that BDNF is primarily produced by postsynaptic neurons such as CA3 pyramidal neurons. Here, we question whether the BDNF, which is stored in the mossy fiber synapse, is primarily produced by granule neurons or whether by other cells in the MF-CA3 microcircuit. After standardization of immunolabelling of BDNF, confocal imaging confirmed the localization of BDNF in presynaptic MF terminals. This anterograde location of synaptic BDNF was also found in distinct regions of the fear and anxiety circuit, namely in the oval nucleus of the bed nucleus stria terminals (ovBNST) and in the central amygdala. To find out whether the presynaptic BDNF location is due to protein translation in the corresponding presynaptic dentate gyrus (DG) granule neuron, we developed and characterized a mouse model that exhibits BDNF deletion specifically from adult DG granule neurons. In this mouse model, loss of presynaptic BDNF immunoreactivity correlated with the specific Creactivity in granule neurons, thus confirming that MF BDNF is principally released by granule neurons. After BDNF deletion from granule neurons, we observed more immature neurons with widely arborized dendritic trees. This indicated that local BDNF deletion also affects the local adult neurogenesis, albeit Cre-mediated BDNF deletion only occur in adult granule neurons. Since BDNF is a master regulator of structural synaptic plasticity, it was questioned whether it is possible to visualize presynaptic, synapse-specific, structural plasticity in mossy fiber synapses. It was established that a combination of Cre-techniques together with targeting of GFP to membranes with the help of palmitoylation / myristoylation anchors was able to distinctly outline the synaptic structure of the BDNF-containing MF synapse. In summary, the mouse model characterized in here is suited to investigate the synaptic signalling function of presynaptic BDNF at the mossy fiber terminal, a model synapse to investigate microcircuit information processing from molecule to behaviour.
My dissertation comprises three studies: (1) an assessment of honey bee colony losses in the USA between 2014 and 2015, (2) an exploration of the potential of reclaimed sand mines as bee habitat, and (3) an evaluation of native and non-native pollinator friendly plants in regard to their attraction to bees. While the first study focuses on honey bees, the latter two studies primarily take wild bees or entire bee communities in focus.
The study on honey bee colony losses was conducted within the framework of the Bee Informed Partnership (BIP, beeinformed.org) and aligns with the annual colony loss surveys which have been conducted in the USA since the winter of 2006/2007. It was the fourth year for which summer and annual losses were calculated in addition to winter losses. Among participants, backyard beekeepers were the largest group (n = 5690), although sideline (n = 169) and commercial (n = 78) beekeepers managed the majority (91.7 %) of the 414 267 surveyed colonies. Overall, 15.1 % of the estimated 2.74 million managed colonies in the USA were included in the study. Total honey bee colony losses (based on the entirety of included colonies) were higher in summer (25.3 %) than in winter (22.3 %) and amounted to 40.6 % for the entire 2014/2015 beekeeping year. Average colony losses per beekeeper or operation were higher in winter (43.7 %) than in summer (14.7 %) and amounted to 49 % for the entire 2014/2015 beekeeping year. Due to the dominance of backyard beekeepers among participants, average losses per operation (or unweighted loss) stronger reflected this smaller type of beekeeper. Backyard beekeepers mainly named colony management issues (e.g., starvation, weak colony in the fall) as causes for mortality, while sideline and commercial beekeepers stronger emphasized parasites or factors outside their control (e.g., varroa, nosema, queen failure).
The second study took place at reclaimed sand mines. Sand mines represent anthropogenically impacted habitats found worldwide, which bear potential for bee conservation. Although floral resources can be limited at these habitats, vegetation free patches of open sandy soils and embankments may offer good nesting possibilities for sand restricted and other bees. We compared bee communities as found in three reclaimed sand mines and at adjacent roadside meadows in Maryland, USA, over two years. Both sand mines and roadsides hosted diverse bee communities with 111 and 88 bee species, respectively. Bee abundances as well as richness and Shannon diversity of bee species were higher in sand mines than at roadsides and negatively correlated with the percentage of vegetational ground cover. Species composition also differed significantly between habitats. Sand mines hosted a higher proportion of ground nesters, more uncommon and more ‘sand loving’ bees similar to natural sandy areas of Maryland. Despite the destruction of the original pre-mining habitat, sand mines thus appear to represent a unique habitat for wild bees, particularly when natural vegetation and open sand spots are encouraged. Considering habitat loss, the lack of natural disturbance regimes, and ongoing declines of wild bees, sand mines could add promising opportunities for bee conservation which has hitherto mainly focused on agricultural and urban habitats.
The third study was an experimental field study on pollinator friendly plants. Bees rely on the pollen and nectar of plants as their food source. Therefore, pollinator friendly plantings are often used for habitat enhancements in bee conservation. Non-native pollinator friendly plants may aid in bee conservation efforts, but have not been tested and compared with native pollinator friendly plants in a common garden experiment. In this study, we seeded mixes of 20 native and 20 non-native pollinator friendly plants in two separate plots at three sites in Maryland, USA. For two years, we recorded flower visitors to the plants throughout the blooming period and additionally sampled bees with pan traps. A total of 3744 bees (120 species) were sampled in the study. Of these, 1708 bees (72 species) were hand netted directly from flowers for comparisons between native and non-native plants. Depending on the season, bee abundance and species richness was either similar or lower (early season and for richness also late season) at native plots compared to non-native plots. Additionally, the overall bee community composition differed significantly between native and non-native plots. Furthermore, native plants were associated with more specialized plant-bee visitation networks compared to non-native plants. In general, visitation networks were more specialized in the early season than the later seasons. Four species (Bombus impatiens, Halictus poeyi/ligatus, Lasioglossum pilosum, and Xylocopa virginica) out of the five most abundant bee species (also including Apis mellifera) foraged more specialized on native than non-native plants. Our study showed that non-native plants were well accepted by a diverse bee community and had a similar to higher attraction for bees compared to native plants. However, we also demonstrated alterations in foraging behavior, bee community assemblage, and visitation networks. As long as used with caution, non-native plants can be a useful addition to native pollinator friendly plantings. This study gives a first example of a direct comparison between native and non-native pollinator friendly plants.
Modern agriculture is the basis of human existence, a blessing, but also a curse. It provides nourishment and well-being to the ever-growing human population, yet destroys biodiversity-mediated processes that underpin productivity: ecosystem services such as water filtration, pollination and biological pest control. Ecological intensification is a promising alternative to conventional farming, and aims to sustain yield and ecosystem health by actively managing biodiversity and essential ecosystem services. Here, I investigate opportunities and obstacles for ecological intensification. My research focuses on 1) the relative importance of soil, management and landscape variables for biodiversity and wheat yield (Chapter II); 2) the influence of multi-scale landscape-level crop diversity on biological pest control in wheat (Chapter III) and 3) on overall and functional bird diversity (Chapter IV). I conclude 4) by introducing a guide that helps scientists to increase research impact by acknowledging the role of stakeholder engagement for the successful implementation of ecological intensification (Chapter V).
Ecological intensification relies on the identification of natural pathways that are able to sustain current yields. Here, we crossed an observational field study of arthropod pests and natural enemies in 28 real-life wheat systems with an orthogonal on-field insecticide-fertilizer experiment. Using path analysis, we quantified the effect of 34 factors (soil characteristics, recent and historic crop management, landscape heterogeneity) that directly or indirectly (via predator-prey interactions) contribute to winter wheat yield. Reduced soil preparation and high crop rotation diversity enhanced crop productivity independent of external agrochemical inputs. Concurrently, biological control by arthropod natural enemies could be restored by decreasing average field sizes on the landscape scale, extending crop rotations and reducing soil disturbance. Furthermore, reductions in agrochemical inputs decreased pest abundances, thereby facilitating yield quality.
Landscape-level crop diversity is a promising tool for ecological intensification. However, biodiversity enhancement via diversification measures does not always translate into agricultural benefits due to antagonistic species interactions (intraguild predation). Additionally, positive effects of crop diversity on biological control may be masked by inappropriate study scales or correlations with other landscape variables (e.g. seminatural habitat). Therefore, the multiscale and context-dependent impact of crop diversity on biodiversity and ecosystem services is ambiguous. In 18 winter wheat fields along a crop diversity gradient, insect- and bird-mediated pest control was assessed using a natural enemy exclusion experiment with cereal grain aphids. Although birds did not influence the strength of insect-mediated pest control, crop diversity (rather than seminatural habitat cover) enhanced aphid regulation by up to 33%, particularly on small spatial scales. Crop diversification, an important Greening measure in the European Common Agricultural Policy, can improve biological control, and could lower dependence on insecticides, if the functional identity of crops is taken into account. Simple measures such as ‘effective number of crop types’ help in science communication.
Although avian pest control did not respond to landscape-level crop diversity, birds may still benefit from increased crop resources in the landscape, depending on their functional grouping (feeding guild, conservation status, habitat preference, nesting behaviour). Observational studies of bird functional diversity on 14 wheat study fields showed that non-crop landscape heterogeneity rather than crop diversity played a key role in determining the richness of all birds. Insect-feeding, non-farmland and non-threatened birds increased across multiple spatial scales (up to 3000 m). Only crop-nesting farmland birds declined in heterogeneous landscapes. Thus, crop diversification may be less suitable for conserving avian diversity, but abundant species benefit from overall habitat heterogeneity. Specialist farmland birds may require more targeted management approaches.
Identifying ecological pathways that favour biodiversity and ecosystem services provides opportunities for ecological intensification that increase the likelihood of balancing conservation and productivity goals. However, change towards a more sustainable agriculture will be slow to come if research findings are not implemented on a global scale. During dissemination activities within the EU project Liberation, I gathered information on the advantages and shortcomings of ecological intensification and its implementation. Here, I introduce a guide (‘TREE’) aimed at scientists that want to increase the impact of their research. TREE emphasizes the need to engage with stakeholders throughout the planning and research process, and actively seek and promote science dissemination and knowledge implementation. This idea requires scientists to leave their comfort zone and consider socioeconomic, practical and legal aspects often ignored in classical research.
Ecological intensification is a valuable instrument for sustainable agriculture. Here, I identified new pathways that facilitate ecological intensification. Soil quality, disturbance levels and spatial or temporal crop diversification showed strong positive correlations with natural enemies, biological pest control and yield, thereby lowering the dependence on agrochemical inputs. Differences between functional groups caused opposing, scale-specific responses to landscape variables. Opposed to our predictions, birds did not disturb insect-mediated pest control in our study system, nor did avian richness relate to landscape-level crop diversity. However, dominant functional bird groups increased with non-crop landscape heterogeneity. These findings highlight the value of combining different on-field and landscape approaches to ecological intensification. Concurrently, the success of ecological intensification can be increased by involving stakeholders throughout the research process. This increases the quality of science and reduces the chance of experiencing unscalable obstacles to implementation.
In this thesis, three species were investigated for the conservation of two non-conventional T cell systems, the CD1d/ iNKT cell system and the BTN3/ Vγ9Vδ2 T cell system. Non-conventional T cells are αβ or γδ T cells that do not fit into the classical mode of antigen recognition and adaptive responses. These T cells recognize antigens different from classical peptide antigens and are not restricted to the polymorphic MHC molecules but rather to non-polymorphic antigen-presenting molecules. The iNKT cell subset is restricted by the lipid antigen-presenting molecule CD1d and carries out immunomodulatory functions by rapid cytokine secretion. The molecular basis of this system, the semi-invariant iNKT TCR chains and CD1d were proven to be expressed and compared to homologs in human and rodents. Cotton rats possess multiple members of the AV14 and BV8 family and only one isoform of CD1d which is comparable to findings in the rat.
Moreover, the reactivity of primary cells to glycolipid antigens could be shown, and an iNKT
cell-like population was detected in primary cells using newly developed cotton rat CD1d oligomers. These were also applied to test the capacity of CD1d to present typical glycolipid
antigens to iNKT TCR transductants. In addition, expression of cotton rat iNKT TCR α and β chains in TCR-negative cell lines was used to show successful pairing and detection of glycolipids in the context of CD1d. In summary, the conservation of a functional CD1d/iNKT cell system in the cotton rat could be shown, and tools were developed to study this cell subset in the course of infectious diseases. The Vγ9Vδ2 T cell subset is the major γδ T cell subset in human peripheral blood and has the unique ability to contribute to immune surveillance by detecting pyrophosphorylated metabolites of isoprenoid synthesis that indicate cell stress, transformation or infection. Up to this date, phosphoantigen-reactive γδ T cells have only been shown in primate species. However, evidence for the existence and functional conservation of the genes implied in the BTN3/Vγ9Vδ2 T cell system was found in several placental mammal species,
and two candidate species were chosen for further investigation. The nine-banded armadillo, a valuable model for leprosy research, was shown to possess homologous genes to TRGV9, TRDV2 and BTN3. In this study, the expression of productive rearrangements of TRDV2 gene segments could be shown in peripheral blood samples, but no evidence was found for the expression of a functional TRGV9 rearrangement or BTN3 molecules. Moreover, determinants of phosphoantigen-reactive Vγ9Vδ2 T cells and functional BTN3 molecules were found to still be prevalent in armadillo genes. This makes the armadillo an interesting model to study the structural determinants that allow phosphoantigen recognition by a functional Vγ9Vδ2 T cell subset although this species is merely a witness for a functional system in a placental mammal ancestor. In contrast, alpacas were shown to express functional Vγ9Vδ2 T cells which conserved many features of the human counterpart. Expression of Vγ9Vδ2 pairings could be shown by single-cell PCR and functional phosphoantigenreactive pairings were observed. This phosphoantigen reactivity was also shown in PBMC cultures with a newly developed antibody specific for alpaca Vδ2Jδ4 chains. Moreover, a more detailed study of the alpaca TCR repertoire showed similarities to “γδ high” species like
camelids and cattle which possess an extended family of TRDV genes. The γ and δ loci of alpaca
TCR genes were drafted based on genomic information and cDNA studies and provide an overview for more detailed studies. Conservation of phosphoantigen recognition by the single BTN3 molecule of alpacas was shown in 293T knock out cell lines, and BTN3 detection on PBMCs was investigated with a newly developed alpaca BTN3-specific antibody. These findings prove the existence of a functional BTN3-dependent phosphoantigen-reactive Vγ9Vδ2 T cell subset and provide a basis for the future study of this cell system in a non-primate species. Moreover, as the first non-primate candidate species with the BTN3/Vγ9Vδ2 T cell system the alpaca is an important outgroup for research in this field. The use of a single BTN3 variant in contrast to three human isoforms that work together renders the alpaca a unique and to this date indispensable model for Vγ9Vδ2 T cells.
In conclusion, this study provides an overview of the applicability of new animal models in the
study of the non-conventional T cell subsets iNKT cells and Vγ9Vδ2 T cells and leads the way for a better understanding of structural and functional relationships.
Multiple myeloma (MM) is a disease of terminally differentiated B-cells which accumulate in the bone marrow leading to bone lesions, hematopoietic insufficiency and hypercalcemia. Genetically, MM is characterized by a great heterogeneity. A recent next-generation sequencing approach resulted in the identification of a signaling network with an accumulation of mutations in receptor-tyrosine kinases (RTKs), adhesion molecules and downstream effectors. A deep-sequencing amplicon approach of the coding DNA sequence of the six RTKs EPHA2, EGFR, ERBB3, IGF1R, NTRK1 and NTRK2 was conducted in a patient cohort (75 MM samples and 68 corresponding normal samples) of the “Deutsche Studiengruppe Multiples Myelom (DSMM)” to further elucidate the role of RTKs in MM. As an initial approach the detected mutations were correlated with cytogenetic abnormalities and clinical data in the course of this thesis. RTK mutations were present in 13% of MM patients of the DSMM XI trial and accumulated in the ligand-binding and tyrosine-kinase domain. The newly identified mutations were associated with an adverse patient survival, but not with any cytogenetic abnormality common in MM. Especially rare patient-specific SNPs (single nucleotide polymorphism) had a negative impact on patient survival. For a more comprehensive understanding of the role of rare RTK SNPs in MM, a second amplicon sequencing approach was performed in a patient cohort of the DSMM XII trial that included 75 tumor and 184 normal samples. This approach identified a total of 23 different mutations in the six RTKs EPHA2, EGFR, ERBB3, IGF1R, NTRK1 and NTRK2 affecting 24 patients. These mutations could furthermore be divided into 20 rare SNPs and 3 SNVs (single nucleotide variant). In contrast to the first study, the rare SNPs were significantly associated with the adverse prognostic factor del17p.
IGF1R was among the most commonly mutated RTKs in the first amplicon sequencing approach and is known to play an important role in diverse cellular processes such as cell proliferation and survival. To study the role of IGF1R mutations in the hard-to-transfect MM cells, stable IGF1R-knockdown MM cell lines were established. One of the knockdown cell lines (L363-C/C9) as well as a IGF1R-WT MM cell line (AMO1) were subsequently used for the stable overexpression of WT IGF1R and mutant IGF1R (N1129S, D1146N). Overall, an impact on the MAPK and PI3K/AKT signaling pathways was observed upon the IGF1R knockdown as well as upon WT and mutant IGF1R overexpression. The resulting signaling pattern, however, differed between different MM cell lines used in this thesis as well as in a parallel performed master thesis which further demonstrates the great heterogeneity described in MM.
Taken together, the conducted sequencing and functional studies illustrate the importance of RTKs and especially of IGF1R and its mutants in the pathogenesis of MM. Moreover, the results support the potential role of IGF1R as a therapeutic target for a subset of MM patients with mutated IGF1R and/or IGF1R overexpression.
A continuous arms race between the development of novel antibiotics and the evolution of corresponding resistance mechanisms in bacteria has been observed, since antibiotic agents like arsphenamines (e.g. Salvarsan, developed by Paul Ehrlich [1]), sulphonamides (e.g. Prontosil, Gerhard Domagk [2]) and penicillin (Alexander Fleming [3]) were first applied to effectively cure bacterial infections in the early 20th century. The rapid emergence of resistances in contrast to the currently lagging discovery of antibiotics displays a severe threat to human health. Some serious infectious diseases, such as tuberculosis or melioidosis, which were either thought to be an issue only in Third-World countries in case of tuberculosis, or regionally restricted with respect to melioidosis, are now on the rise to expand to other areas. In contrast, methicillin-resistant Staphylococcus aureus (MRSA) is already present in clinical setups all over the world and causes severe infections in immunocompromised patients. Thus, there is an urgent need for new and effective antimicrobial agents, which impair vital functions of the pathogen’s metabolism.
One central metabolic pathway is represented by the bacterial fatty-acid synthesis pathway (FAS II), which is essential for the synthesis of long and branched-chain fatty acids, as well as mycolic acids. These substances play a major role as modulating components of the properties of the most important protective barrier – the cell envelope. The integrity of the bacterial cell wall and the associated membrane(s) is crucial for cell growth and for protection against physical strain, intrusion of antibiotic agents and regulation of uptake of ions and other small molecules. Thus, this central pathway represents a promising target for antibiotic action against pathogens to combat infectious diseases. The last and rate-limiting step is catalysed by the trans-2-enoyl-ACP reductase (ENR) FabI or InhA (in mycobacteria), which has been demonstrated to be a valuable target for drug design and can be addressed, amongst others, by diphenyl ether (DPE) compounds, derived from triclosan (TCL) – the first one of this class which was discovered to bind to ENR enzymes [4, 5].
Based on this scaffold, inhibitors containing different combinations of substituents at crucial positions, as well as a novel type of substituent at position five were investigated regarding their binding behaviour towards the Burkholderia pseudomallei and Mycobacterium tuberculosis ENR enzymes bpFabI and InhA, respectively, by structural, kinetic and in-vivo experiments. Generally, substitution patterns modulate the association and dissociation velocities of the different ENR inhibitors in the context of the two-step slow-onset binding mechanism, which is observed for both enzymes. These alterations in the rapidity of complex formation and decomposition have a crucial impact on the residence time of a compound and hence, on the pharmacokinetic properties of potential drug candidates. For example, the substituents at the 2’-position of the DPE scaffold influence the ground- and transition state stability during the binding process to bpFabI, whereas 4’-substituents primarily alter the transition state [6]. The novel triazole group attached to the 5-position of the scaffold, targeting the hydrophobic part of the substrate-binding pocket in InhA, significantly enhances the energy barrier of the transition state of inhibitor binding [7] and decelerates the association- as well as the dissociation processes. Combinations with different substituents at the 2’-position can enhance or diminish this effect, e.g. by ground-state stabilisation, which will result in an increased residence time of the respective inhibitor on InhA.
Further structural investigations carried out in this work, confirm the proposed binding mode of a customised saFabI inhibitor [8], carrying a pyridone moiety on the DPE scaffold to expand interactions with the protein environment. Structural and preliminary kinetic data confirm the binding of the same inhibitor to InhA in a related fashion. Comparisons with structures of the ENR inhibitor AFN-1252 [9] bound to ENR enzymes from other organisms, addressing a similar region as the pyridone-moiety of the DPE inhibitor, suggest that also the DPE inhibitor bears the potential to display binding to homologues of saFabI and InhA and may be optimised accordingly.
Both of the newly investigated substituents, the pyridone moiety at the 4’-position as well as the 5-triazole substituent, provide a good starting point to modify the DPE scaffold also towards improved kinetic properties against ENR enzymes other than the herein studied and combining both groups on the DPE scaffold may have beneficial effects. The understanding of the underlying binding mechanism is a crucial factor to promote the dedicated design of inhibitors with superior pharmacokinetic characteristics.
A second target for a structure-based drug-design approach is the interaction surface between ENR enzymes and the acyl-carrier protein (ACP), which delivers the growing acyl chain to each distinct enzyme of the dissociated FAS-II system and presumably recognises its respective interaction partner via electrostatic contacts. The interface between saACP and saFabI was investigated using different approaches including crosslinking experiments and the design of fusion constructs connecting the ACP and the FabI subunits via a flexible linker region of varying lengths and compositions. The crosslinking studies confirmed a set of residues to be part of the contact interface of a previously proposed complex model [10] and displayed high crosslinking efficiency of saACP to saFabI when mutated to cysteine residues. However, crystals of the complex obtained from either the single components, or of the fusion constructs usually displayed weak diffraction, which supports the assumption that complex formation is highly transient. To obtain ordered crystals for structural characterisation of the complex it is necessary to trap the complex in a fixed state, e.g. by a high-affinity substrate attached to ACP [11], which abolishes rapid complex dissociation. For this purpose, acyl-coupled long-residence time inhibitors might be a valuable tool to elucidate the detailed architecture of the ACP-FabI interface. This may provide a novel basis for the development of inhibitors that specifically target the FAS-II biosynthesis pathway.
The molecular chaperone Hsp90 facilitates the folding and activation of a wide array of structurally and functionally diverse client proteins. Hsp90 presents a central node of protein homeostasis and is frequently involved in the development of many human diseases. Although Hsp90 is a promising target for disease treatment, the mechanism by which Hsp90 facilitates client recognition and maturation is poorly understood.
The shape of the homodimeric protein resembles a molecular clamp that opens and closes in response to binding and hydrolysis of ATP. Structural studies reveal a network of distinct local conformational rearrangements that coordinate the slow transition into the hydrolysis-active, closed state configuration (time order of minutes). However, the kinetics of local conformational changes remain elusive because spectroscopic tools that can detect them have been missing so far.
Fluorescence quenching of extrinsic fluorophores by the natural amino acid Tryptophan is based on a photoinduced electron transfer (PET) reaction, which requires sub-nanometer contact between fluorophore and Tryptophan. This quenching mechanism has been developed into a 1-nm spectroscopic tool for the detection of rapid protein folding dynamics. Within the scope of this doctoral thesis, PET-reporter systems were designed to investigate the kinetics of local conformational motions that are part of the mechanistic core of the Hsp90 chaperone cycle. ATP-triggered kinetics of closure of the ATP-lid as well as swapping of the N-terminal ß-strand across subunits and association of the N-terminal and middle-domain were estimated in solution. Bulk experiments revealed that local motions occur on similar timescales and are in good agreement with the ATP-hydrolysis rate. Functional mutations demonstrated that local motions act cooperatively. Furthermore, the lid was shown to close via a two-step process consisting of a rapid lid-reconfiguration in direct response to ATP-binding, followed by slow closure of the lid. The co-chaperone Aha1 seems to act early in the chaperone cycle by remodelling of the lid and by stabilization of apo Hsp90 in a NM-domain pre-associated conformation.
A two-colour single-molecule PET microscopy method was developed to observe local motions at remote positions simultaneously and in real-time. Thus, directionality within the network of local conformational changes could be revealed. In a first attempt, the feasibility of detecting PET-complexes on the single-molecule surface was tested on Hsp90 constructs that report on only one motion (one-colour single-molecule PET microscopy). PET-quenched complexes could be distinguished from photobleached fluorophores through oxidation by molecular oxygen, resulting in fluorescence recovery. In two-colour experiments, a dimmed state was identified for PET-quenched complexes, but not for all of the used PET-reporter systems. Results suggest that local motions occur simultaneously within the time-resolution of the experiment (0.3 sec). Furthermore, bi-exponential kinetics of transition into the closed clamp configuration indicate a more complex mechanism of clamp-closure than of clamp-opening, which could be well described by a mono-exponential function.
In this thesis we discuss the potential of nanodevices based on topological insulators. This novel class of matter is characterized by an insulating bulk with simultaneously conducting boundaries. To lowest order, the states that are evoking the conducting behavior in TIs are typically described by a Dirac theory. In the two-dimensional case, together with time- reversal symmetry, this implies a helical nature of respective states. Then, interesting physics appears when two such helical edge state pairs are brought close together in a two-dimensional topological insulator quantum constriction. This has several advantages. Inside the constriction, the system obeys essentially the same number of fermionic fields as a conventional quantum wire, however, it possesses more symmetries. Moreover, such a constriction can be naturally contacted by helical probes, which eventually allows spin- resolved transport measurements.
We use these intriguing properties of such devices to predict the formation and detection of several profound physical effects. We demonstrate that narrow trenches in quantum spin Hall materials – a structure we coin anti-wire – are able to show a topological super- conducting phase, hosting isolated non-Abelian Majorana modes. They can be detected by means of a simple conductance experiment using a weak coupling to passing by helical edge states. The presence of Majorana modes implies the formation of unconventional odd-frequency superconductivity. Interestingly, however, we find that regardless of the presence or absence of Majoranas, related (superconducting) devices possess an uncon- ventional odd-frequency superconducting pairing component, which can be associated to a particular transport channel. Eventually, this enables us to prove the existence of odd- frequency pairing in superconducting quantum spin Hall quantum constrictions. The symmetries that are present in quantum spin Hall quantum constrictions play an essen- tial role for many physical effects. As distinguished from quantum wires, quantum spin Hall quantum constrictions additionally possess an inbuilt charge-conjugation symmetry. This can be used to form a non-equilibrium Floquet topological phase in the presence of a time-periodic electro-magnetic field. This non-equilibrium phase is accompanied by topological bound states that are detectable in transport characteristics of the system. Despite single-particle effects, symmetries are particularly important when electronic in- teractions are considered. As such, charge-conjugation symmetry implies the presence of a Dirac point, which in turn enables the formation of interaction induced gaps. Unlike single-particle gaps, interaction induced gaps can lead to large ground state manifolds. In combination with ordinary superconductivity, this eventually evokes exotic non-Abelian anyons beyond the Majorana. In the present case, these interactions gaps can even form in the weakly interacting regime (which is rather untypical), so that the coexistence with superconductivity is no longer contradictory. Eventually this leads to the simultaneous presence of a Z4 parafermion and a Majorana mode bound at interfaces between quantum constrictions and superconducting regions.
Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes
(2020)
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression–regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule – glucosamine-6-phosphate – to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
The eukaryotic parasite Trypanosoma brucei has evolved sophisticated strategies to persist within its mammalian host. Trypanosomes evade the hosts' immune system by antigenic variation of their surface coat, consisting of variant surface glycoproteins (VSGs). Out of a repertoire of thousands of VSG genes, only one is expressed at any given time from one of the 15 telomeric expression sites (ES). The VSG is stochastically exchanged either by a transcriptional switch of the active ES (in situ switch) or by a recombinational exchange of the VSG within the active ES. However, for infections to persist, the parasite burden has to be limited. The slender (sl) bloodstream form secretes the stumpy induction factor (SIF), which accumulates with rising parasitemia. SIF induces the irreversible developmental transition from the proliferative sl to the cell cycle-arrested but fly-infective stumpy (st) stage once a concentration threshold is reached. Thus, antigenic variation and st development ensure persistent infections and transmissibility. A previous study in monomorphic cells indicated that the attenuation of the active ES could be relevant for the development of trypanosomes. The present thesis investigated this hypothesis using the inducible overexpression of an ectopic VSG in pleomorphic trypanosomes, which possess full developmental competence. These studies revealed a surprising phenotypic plasticity: while the endogenous VSG was always down-regulated upon induction, the ESactivity determined whether the VSG overexpressors arrested in growth or kept proliferating. Full ES-attenuation induced the differentiation of bona fide st parasites independent of the cell density and thus represents the sole natural SIF-independent differentiation trigger to date. A milder decrease of the ES-activity did not induce phenotypic changes, but appeared to prime the parasites for SIF-induced differentiation. These results demonstrate that antigenic variation and development are linked and indicated that the ES and the VSG are independently regulated. Therefore, I investigated in the second part of my thesis how ES-attenuation and VSG-silencing can be mediated. Integration of reporters with a functional or defective VSG 3'UTR into different genomic loci showed that the maintenance of the active state of the ES depends on a conserved motif within the VSG 3'UTR. In situ switching was only triggered when the telomere-proximal motif was partially deleted, suggesting that it serves as a DNA-binding motif for a telomere-associated protein. The VSG levels seem to be additionally regulated in trans based on the VSG 3'UTR independent of the genomic context, which was reinforced by the regulation of a constitutively expressed reporter with VSG 3' UTR upon ectopic VSG overexpression.
Downregulation of miR-221-3p expression in prostate cancer (PCa) predicted overall and cancer-specific survival of high-risk PCa patients. Apart from PCa, miR-221-3p expression levels predicted a response to tyrosine kinase inhibitors (TKI) in clear cell renal cell carcinoma (ccRCC) patients. Since this role of miR-221-3p was explained with a specific targeting of VEGFR2, we examined whether miR-221-3p regulated VEGFR2 in PCa. First, we confirmed VEGFR2/KDR as a target gene of miR-221-3p in PCa cells by applying Luciferase reporter assays and Western blotting experiments. Although VEGFR2 was mainly downregulated in the PCa cohort of the TCGA (The Cancer Genome Atlas) database, VEGFR2 was upregulated in our high-risk PCa cohort (n = 142) and predicted clinical progression. In vitro miR-221-3p acted as an escape mechanism from TKI in PC3 cells, as displayed by proliferation and apoptosis assays. Moreover, we confirmed that Sunitinib induced an interferon-related gene signature in PC3 cells by analyzing external microarray data and by demonstrating a significant upregulation of miR-221-3p/miR-222-3p after Sunitinib exposure. Our findings bear a clinical perspective for high-risk PCa patients with low miR-221-3p levels since this could predict a favorable TKI response. Apart from this therapeutic niche, we identified a partially oncogenic function of miR-221-3p as an escape mechanism from VEGFR2 inhibition.
How genomic and ecological traits shape island biodiversity - insights from individual-based models
(2020)
Life on oceanic islands provides a playground and comparably easy\-/studied basis
for the understanding of biodiversity in general. Island biota feature many
fascinating patterns: endemic species, species radiations and species with
peculiar trait syndromes. However, classic and current island biogeography
theory does not yet consider all the factors necessary to explain many of these
patterns. In response to this, there is currently a shift in island biogeography
research to systematically consider species traits and thus gain a more
functional perspective. Despite this recent development, a set of species
characteristics remains largely ignored in island biogeography, namely genomic
traits. Evidence suggests that genomic factors could explain many of the
speciation and adaptation patterns found in nature and thus may be highly
informative to explain the fascinating and iconic phenomena known for oceanic
islands, including species radiations and susceptibility to biotic invasions.
Unfortunately, the current lack of comprehensive meaningful data makes studying
these factors challenging. Even with paleontological data and space-for-time
rationales, data is bound to be incomplete due to the very environmental
processes taking place on oceanic islands, such as land slides and volcanism,
and lacks causal information due to the focus on correlative approaches. As
promising alternative, integrative mechanistic models can explicitly consider
essential underlying eco\-/evolutionary mechanisms. In fact, these models have
shown to be applicable to a variety of different systems and study questions.
In this thesis, I therefore examined present mechanistic island models to
identify how they might be used to address some of the current open questions in
island biodiversity research. Since none of the models simultaneously considered
speciation and adaptation at a genomic level, I developed a new genome- and
niche-explicit, individual-based model. I used this model to address three
different phenomena of island biodiversity: environmental variation, insular
species radiations and species invasions.
Using only a single model I could show that small-bodied species with flexible
genomes are successful under environmental variation, that a complex combination
of dispersal abilities, reproductive strategies and genomic traits affect the
occurrence of species radiations and that invasions are primarily driven by the
intensity of introductions and the trait characteristics of invasive
species. This highlights how the consideration of functional traits can promote
the understanding of some of the understudied phenomena in island biodiversity.
The results presented in this thesis exemplify the generality of integrative
models which are built on first principles. Thus, by applying such models to
various complex study questions, they are able to unveil multiple biodiversity
dynamics and patterns. The combination of several models such as the one I
developed to an eco\-/evolutionary model ensemble could further help to identify
fundamental eco\-/evolutionary principles. I conclude the thesis with an outlook
on how to use and extend my developed model to investigate geomorphological
dynamics in archipelagos and to allow dynamic genomes, which would further
increase the model's generality.
The nucleus of statehood is situated at the local level: in the village, the neighborhood, the city district. This is where a community, beyond the level of the family, first develops collective rules that are intended to ensure its continued existence. But usually this is not the only level of governance at play. Above it, there are supralocal formations of power, varying in scope from regional networks to empires, which supplement the local orders or compete with them. The premise of this Research Unit is that local forms of self-governance are especially heterogeneous and prominent, wherever supralocal statehood exists in the mode of weak permeation. The central question of our approach is how local forms of self-governance work in this context. We will examine the relations to the state level as well as to other local groups as they develop over time; the scope and spatial contingency of forms of self-governance; their legitimization and the interdependency with the organization and collective identity of those groups which carry them out; finally, we will turn our attention to the significance of self-governance for the configuration of weak statehood. The empirical focus will be at the local level, which has so far been largely neglected in the research on governance beyond the state. In order to achieve this, we will work with case studies that are structured by categories and situated in geographical areas and time periods that lie outside of modern Europe with its particular development of statehood since the Late Middle Ages: in Antiquity, and in the Global South of the present. By incorporating these different time frames, we hope to contribute to overcoming the dichotomy between the modern and pre-modern era, which is often given canonical status. Our goal is to create a comparative analysis of different configurations of order as well as the development of a typology of patterns of local governance. The structure of the empirical comparison itself promises methodological insights, since it will entail recognizing, dealing with, and overcoming disciplinary limitations. Starting with the identification of typical patterns and processes, we hope to gain a better grasp of the mechanisms by which local configurations of order succeed, while at the same time advancing the theoretical debate. This will allow us to make an interdisciplinary contribution to the understanding of fundamental elements of statehood and local governance that are of central importance, especially in the context of weak statehood. The insights we hope to gain by adopting this historical perspective will contribute to understanding a present that is not based exclusively on its own, seemingly completely new preconditions, and will thus significantly sharpen the political analysis of various forms of governance.
Humans tend to believe in what they can see with their own eyes. Hence, visualization methods like microscopy have always been extremely popular since their invention in the 17th century. With the advent of super-resolution microscopy, the diffraction limit of ~200 - 250 nm could be overcome to enable more detailed insights into biological samples. Especially the single molecule localization microscopy method dSTORM offers the possibility of quantitative bioimaging. Hereby, the repetitive photoswitching of organic dyes in the presence of thiols is exploited to enable a lateral resolution of 20 nm. Another, recently introduced super-resolution method is expansion microscopy (ExM) which physically expands the sample to increase the resolution by the expansion factor from four to even twenty. To enable this, the sample is embedded into a hydrogel, homogenized using an unspecific proteinase and expanded in distilled water. Within this thesis, both methods were used to shed light on plasma membrane receptor distributions and different bacterial and fungal pathogens. In the first part of this thesis dSTORM was used to elucidate the “Receptome”, the entirety of all membrane receptors, of the cell line Jurkat T-cells and primary T-cells. Within this project we could successfully visualize and quantify the distribution of the plasma membrane receptors CD2, CD3, CD4, CD5, CD7, CD11a, CD20, CD28, CD45, CD69 and CD105 with receptor densities ranging from 0.8 cluster/µm² in case of CD20 and 81.4 cluster/µm² for the highly abundant CD45 in activated primary T-cells at the basal membrane. Hereby, we could also demonstrate a homogeneous distribution of most receptors, while only few were clustered. In the case of CD3-clusters were detected in Jurkat T-cells and in primary activated T-cells, but not in naïve ones, demonstrating the activation of this receptor. This was followed by the application of dSTORM to three different clinical projects involving the receptors CD38, BCMA and CD20 which are immunotherapeutic targets by monoclonal antibodies and CAR T-cells. In the first two projects dSTORM was applied to determine the receptor upregulation upon exposure of various drugs to MM1.S cells or primary multiple myeloma patient cells. This increase in membrane receptor expression can subsequently enhance the efficacy of therapies directed against these receptors. Within the CD20-project, the superior sensitivity of dSTORM compared to flow cytometry could be demonstrated. Hereby, a substantially higher fraction of CD20-positive patient cells was detected by dSTORM than by flow cytometry. In addition, we could show that by dSTORM CD20-positive evaluated cells were eradicated by immunotherapeutic CAR T-cell treatment. These studies were followed by whole cell super-resolution imaging using both LLS-3D dSTORM and 10x ExM to exclude any artifacts caused by interactions with the glass surface. In 10x ExM signal amplification via biotinylated primary antibodies and streptavidin ATTO 643 was essential to detect even single antibodies directed against the heterodimer CD11a with standard confocal microscopes. Albeit probably not quantitative due to the process of gelation, digestion and expansion during the ExM protocol, even some putative dimers of the receptor CD2 could be visualized using 10x ExM-SIM, similar to dSTORM experiments. Within the second part of this thesis, expansion microscopy was established in bacterial and fungal pathogens. ExM enabled not only an isotropic fourfold expansion of Chlamydia trachomatis, but also allowed the discrimination between the two developmental forms by the chlamydial size after expansion into reticulate and elementary bodies. Hereafter, a new α-NH2-ω-N3-C6-ceramide was introduced enabling an efficient fixation and for the first time the use of lipids in both, 4x and 10x ExM, termed sphingolipid ExM. This compound was used to investigate the ceramide uptake and incorporation into the cell membrane of Chlamydia trachomatis and Simkania negevensis. For Chlamydia trachomatis the combined resolution power of 10x ExM and SIM even allowed the visualization of both bacterial membranes within a distance of ~30 nm. Finally, ExM was applied to the three different fungi Ustilago maydis, Fusarium oxysporum and Aspergillus fumigatus after enzymatic removal of the fungal cell wall. In case of Ustilago maydis sporidia this digestion could be applied to both, living cells resulting in protoplasts and to fixed cells, preserving the fungal morphology. This new protocol could be demonstrated for immunostainings and fluorescent proteins of the three different fungi.
The CXC chemokine receptor 4 (CXCR4) and the atypical chemokine receptor 3 (ACKR3) are seven transmembrane receptors that are involved in numerous pathologies, including several types of cancers. Both receptors bind the same chemokine, CXCL12, leading to significantly different outcomes. While CXCR4 activation generally leads to canonical GPCR signaling, involving Gi proteins and β‐arrestins, ACKR3, which is predominantly found in intracellular vesicles, has been shown to signal via β‐arrestin‐dependent signaling pathways. Understanding the dynamics and kinetics of their activation in response to their ligands is of importance to understand how signaling proceeds via these two receptors.
In this thesis, different Förster resonance energy transfer (FRET)‐based approaches have been combined to individually investigate the early events of their signaling cascades. In order to investigate receptor activation, intramolecular FRET sensors for CXCR4 and ACKR3 were developed by using the pair of fluorophores cyan fluorescence protein and fluorescence arsenical hairpin binder. The sensors, which exhibited similar functional properties to their wild‐type counterparts, allowed to monitor their ligand-induced conformational changes and represent the first RET‐based receptor sensors in the field of chemokine receptors. Additional FRET‐based settings were also established to investigate the coupling of receptors with G proteins, rearrangements within dimers, as well as G protein activation. On one hand, CXCR4 showed a complex activation mechanism in response to CXCL12 that involved rearrangements in the transmembrane domain of the receptor followed by rearrangements between the receptor and the G protein as well as rearrangements between CXCR4 protomers, suggesting a role of homodimers in the activation course of this receptor. This was followed by a prolonged activation of Gi proteins, but not Gq activation, via the axis CXCL12/CXCR4. In contrast, the structural rearrangements at each step of the signaling cascade in response to macrophage migration inhibitory factor (MIF) were dynamically and kinetically different and no Gi protein activation via this axis was detected. These findings suggest distinct mechanisms of action of CXCL12 and MIF on CXCR4 and provide evidence for a new type of sequential signaling events of a GPCR. Importantly, evidence in this work revealed that CXCR4 exhibits some degree of constitutive activity, a potentially important feature for drug development. On the other hand, by cotransfecting the ACKR3 sensor with K44A dynamin, it was possible to increase its presence in the plasma membrane and measure the ligand‐induced activation of this receptor. Different kinetics of ACKR3 activation were observed in response to CXCL12 and three other agonists by means of using the receptor sensor developed in this thesis, showing that it is a valuable tool to study the activation of this atypical receptor and pharmacologically characterize ligands. No CXCL12‐induced G protein activation via ACKR3 was observed even when the receptor was re-localized to the plasma membrane by means of using the mutant dynamin. Altogether, this thesis work provides the temporal resolution of signaling patterns of two chemokine receptors for the first time as well as valuable tools that can be applied to characterize their activation in response to pharmacologically relevant ligands.
Induced pluripotent stem cells (iPSCs) have been recognised as a virtually unlimited source of stem cells that can be generated in a patient-specific manner. Due to these cells’ potential to give rise to all differentiated cell types of the human body, they have been widely used to derive differentiated cells for drug screening and disease modelling purposes. iPSCs also garner much interest as they can potentially serve as a source for cell replacement therapy. Towards the realisation of these biomedical applications, this thesis aims to address challenges that are associated with scale-up, safety and biofabrication.
Firstly, the manufacture of a high number of human iPSCs (hiPSCs) will require standardised procedures for scale-up and the development of a flexible bioprocessing method, since standard adherent hiPSC culture exhibits limited scalability and is labour-intensive. While the quantity of cells that are required for cell therapy depends largely on the tissue and defect that these replacing cells are meant to correct, an estimate of 1 × 10^9 has been suggested to be sufficient for several indications, including myocardial infarction and islet replacement for diabetes. Here, the development of an integrated, microcarrier-free workflow to transition standard adherent hiPSC culture (6-well plates) to scalable stirred suspension culture in bioreactors (1 L working volume, 2.4 L maximum working volume) is presented. The two-phase bioprocess lasts 14 days and generates hiPSC aggregates measuring 198 ± 58 μm in diameter on the harvesting day, yielding close to 2 × 10^9 cells. hiPSCs can be maintained in stirred suspension for at least 7 weeks with weekly passaging, while exhibiting pluripotency-associated markers TRA-1-60, TRA-1-81, SSEA-4, OCT4, and SOX2. These cells retain their ability to differentiate into cells of all the three germ layers in vitro, exemplified by cells positive for AFP, SMA, or TUBB3. Additionally, they maintain a stable karyotype and continue to respond to specification cues, demonstrated by directed differentiation into beating cardiomyocyte-like cells. Therefore, the aim of manufacturing high hiPSC quantities was met using a state-of-the-art scalable suspension bioreactor platform.
Secondly, multipotent stem cells such as induced neural stem cells (iNSCs) may represent a safer source of renewable cells compared to pluripotent stem cells. However, pre-conditioning of stem cells prior to transplantation is a delicate issue to ensure not only proper function in the host but also safety. Here, iNSCs which are normally maintained in the presence of factors such as hLIF, CHIR99021, and SB431542 were cultured in basal medium for distinct periods of time. This wash-out procedure results in lower proliferation while maintaining key neural stem cell marker PAX6, suggesting a transient pre-differentiated state. Such pre-treatment may aid transplantation studies to suppress tumourigenesis through transplanted cells, an approach that is being evaluated using a mouse model of experimental focal demyelination and autoimmune encephalomyelitis.
Thirdly, biomedical applications of stem cells can benefit from recent advancements in biofabrication, where cells can be arranged in customisable topographical layouts. Employing a 3DDiscovery bioprinter, a bioink consisting of hiPSCs in gelatin-alginate was extruded into disc-shaped moulds or printed in a cross-hatch infill pattern and cross-linked with calcium ions. In both discs and printed patterns, hiPSCs recovered from these bioprints showed viability of around 70% even after 4 days of culture when loaded into gelatin-alginate solution in aggregate form. They maintained pluripotency-associated markers TRA-1-60 and SSEA-4 and continued to proliferate after re-plating. As further proof-of-principle, printed hiPSC 3D constructs were subjected to targeted neuronal differentiation, developing typical neurite outgrowth and resulting in a widespread network of cells throughout and within the topology of the printed matrix. Staining against TUBB3 confirmed neuronal identity of the differentiated cellular progeny. In conclusion, these data demonstrate that hiPSCs not only survive the 3D-printing process but were able to differentiate along the printed topology in cellular networks.
Deubiquitinases are regulators of the ubiquitin proteasome system that counteract the ubiquitination cascade by removing ubiquitin from substrates and cleaving ubiquitin chains. Due to their involvment in various important pathways, they are associated with several diseases and may thus present promising drug targets. The two related ubiquitin specific proteases USP25 and USP28 share a highly conserved amino acid sequence but perform distinct biological functions. USP28 plays roles in cell cycle regulation and was also linked to several types of cancer. It adopts oncogenic functions by rescuing the oncoproteins MYC and JUN from proteasomal degradation, which is induced by the E3-ligase SCF (FBW7). Opposingly, USP28 also regulates the stability of the tumor suppressor FBW7 itself. USP25 contributes to a balanced innate immune system by stabilizing TRAF3 and TRAF6 and lately was found to promote Wnt-signaling by deubiquitinating TNKS.
Due to the high level of identity of both proteases, a recent attempt to inhibit USP28 led to cross reactivity against USP25. In our study, we characterized both USP25 and USP28 structurally and functionally using x-ray crystallography, biochemical as well as biophysical approaches to determine similarities and differences that can be exploited for the development of specific inhibitors.
The crystal structure of the USP28 catalytic domain revealed a cherry-couple like dimer that mediates self-association by an inserted helical subdomain, the USP25/28 catalytic domain inserted domain (UCID). In USP25, the UCID leads to formation of a tetramer composed of two interlinked USP28-like dimers. Structural and functional analysis revealed that the dimeric USP28 is active, whereas the tetrameric USP25 is auto inhibited. Disruption of the tetramer by a cancer-associated mutation or a deletion-variant activates USP25 through dimer formation in in vitro assays and leads to an increased stability of TNKS in cell studies. Furthermore, in vitro data showed that neither ubiquitin nor substrate binding led to the activation of the USP25 tetramer construct. With the structure of the C-terminal domain of USP25, we determined the last unknown region in the enzyme as a separately folded domain that mediates substrate interactions.
Combined the structures of the USP25 and USP28 catalytic domains and the functional characterization of both enzymes provide novel insights into the regulation of USPs by oligomerization. Furthermore, we identified individual features of each protease that might be explored for the development of specific small molecule inhibitors.
Amplification of N-MYC is a poor prognostic and survival marker of neuroblastoma. To broaden the scope of knowledge in N-MYC cancer biology, interactors of N-MYC should be investigated. TFIIIC complex was identified as a new protein interacting partner of N-MYC. TFIIIC is a core component of RNAPIII transcription machinery which is important for the synthesis of tRNA genes. TFIIIC recognizes and binds to B-box located internal of tRNA genes which subsequently initiate the RNAPIII transcription process. Apart from the role in RNAPIII transcription machinery, TFIIIC is an architectural protein. TFIIIC binds to thousands of sites across the genome without RNAPIII and TFIIIB. These binding loci are known as Extra TFIIIC (ETC) sites at which TFIIIC perform its role in genome organization. However, knowledge of TFIIIC is mostly restricted to studies conducted in yeasts, the exact function of TFIIIC and how it regulates N-MYC remains to be elucidated. To obtain a better overview about TFIIIC functions, two TFIIIC subunits (TFIIIC5 and TFIIIC2) which represent sub-complexes A and B were chosen for investigation. ChIP-seq experiment of RNAPIII transcription machinery was performed. It showed that both TFIIIC subunits functioned together as a complex. Next, joint binding sites of two TFIIIC subunits and N-MYC were identified. The data revealed that co-occupancies between N-MYC and TFIIIC subunits had different preference on genomic distribution. Furthermore, TFIIIC5 exhibited strong binding association with architectural proteins RAD21 and CTCF whereas TFIIIC2 was only modestly enriched with these two proteins. Both TFIIIC subunits showed equal but weak enrichment with accessory protein CAPH2. Despite the weak association with other architectural proteins, TFIIIC2 binds preferentially to repetitive elements SINE. In order to understand how TFIIIC5 affects other architectural proteins in chromatin binding, cells were depleted of TFIIIC protein upon doxycycline induction of shRNA. N-MYC binding was not affected. Yet, 50% reduction of RAD21 binding to joint N-MYC/TFIIIC sites was noticed. CAPH2 binding was increased at some joint sites while some did not respond. Lastly, CTCF did not show changes in binding under the effect of TFIIIC5 knockdown. In summary, the data indicated TFIIIC subunits from different sub-complexes diverge in functions other than tRNA synthesis. The association of TFIIIC5 with architectural proteins and TFIIIC2 with SINE elements were suggested to be distinct mechanisms to regulate N-Myc directly or indirectly.
In reconstructive and plastic surgery, there exists a growing demand of adequate tissue implants, since currently available strategies for autologous transplantation are limited by complications including transplant failure and donor site morbidity. By developing in vitro and in vivo autologous substitutes for defective tissue sites, adipose tissue engineering can address these challenges, although there are several obstacles to overcome. One of the major limitations is the sufficient vascularization of in vitro engineered large constructs that remains crucial and demanding for functional tissues. Decellularized jejunal segments may represent a suitable scaffolding system with preexisting capillary structures that can be repopulated with human microvascular endothelial cells (hMVECs), and a luminal matrix applicable for the adipogenic differentiation of human adipose-derived stem cells (hASCs). Hence, co-culture of these cells in jejunal segments, utilizing a custom-made bioreactor system, was characterized in terms of vascularization and adipose tissue development. Substantial adipogenesis of hASCs was demonstrated within the jejunal lumen in contrast to non-induced controls, and the increase of key adipogenic markers was verified over time upon induction. The development of major extracellular matrix components of mature adipose tissue, such as laminin and collagen IV, was shown within the scaffold in induced samples. Successful reseeding of the vascular network with hMVECs was demonstrated in long-term culture and co-localization of vascular structures and adipogenically differentiated hASCs was observed. Therefore, these results represent a novel approach for in vitro engineering of vascularized adipose tissue constructs that warrants further investigations in preclinical studies.
Another still existing obstacle in adipose tissue engineering is the insufficient knowledge about the applied cells, for instance the understanding of how cells can be optimally expanded and differentiated for successful engineering of tissue transplants. Even though hASCs can be easily isolated from liposuction of abdominal fat depots, yielding low donor site morbidity, huge numbers of cells are required to entirely seed complex and large 3D matrices or scaffolds. Thus, cells need to be large-scale expanded in vitro on the premise of not losing their differentiation capacity caused by replicative aging. Accordingly, an improved differentiation of hASCs in adipose tissue engineering approaches remains still desirable since most engineered constructs exhibit an inhomogeneous differentiation pattern. For mesenchymal stem cells (MSCs), it has been shown that growth factor application can lead to a significant improvement of both proliferation and differentiation capacity. Especially basic fibroblast growth factor (bFGF) represents a potent mitogen for MSCs, while maintaining or even promoting their osteogenic, chondrogenic and adipogenic differentiation potential. As there are currently different contradictory information present in literature about the applied bFGF concentration and the explicit effect of bFGF on ASC differentiation, here, the effect of bFGF on hASC proliferation and differentiation capacity was investigated at different concentrations and time points in 2D culture. Preculture of hASCs with bFGF prior to adipogenic induction showed a remarkable effect, whereas administration of bFGF during culture did not improve adipogenic differentiation capacity. Furthermore, the observations indicated as mode of action an impact of this preculture on cell proliferation capacity, resulting in increased cellular density at the time of adipogenic induction. The difference in cell density at this time point appeared to be pivotal for increased adipogenic capacity of the cells, which was confirmed in a further experiment employing different seeding densities. Interestingly, furthermore, the obtained results suggested a cell-cell contact-mediated mechanism positively influencing adipogenic differentiation. As a consequence, subsequently, studies were conducted focusing on intercellular communication of these cells, which has hardly been investigated to date.
Despite the multitude of literature on the differentiation capacity of ASCs, little is reported about the physiological properties contributing to and controlling the process of lineage differentiation. Direct intercellular communication between adjacent cells via gap junctions has been shown to modulate differentiation processes in other cell types, with connexin 43 (Cx43) being the most abundant isoform of the gap junction-forming connexins. Thus, in the present study we focused on the expression of Cx43 and gap junctional intercellular communication (GJIC) in hASCs, and its significance for adipogenic differentiation of these cells. Cx43 expression in hASCs was demonstrated histologically and on the gene and protein expression level and was shown to be greatly positively influenced by cell seeding density. Functionality of gap junctions was proven by dye transfer analysis in growth medium. Adipogenic differentiation of hASCs was shown to be also distinctly elevated at higher cell seeding densities. Inhibition of GJIC by 18α-glycyrrhetinic acid significantly compromised adipogenic differentiation, as demonstrated by histology, triglyceride quantification, and adipogenic marker gene expression. Flow cytometry analysis showed a lower proportion of cells undergoing adipogenesis when GJIC was inhibited, further indicating the importance of GJIC in the differentiation process. Altogether, these results demonstrate the impact of direct cell-cell communication via gap junctions on the adipogenic differentiation process of hASCs and may contribute to further integrate direct intercellular crosstalk in rationales for tissue engineering approaches.
Antigenic variation of surface proteins is a commonly used strategy among pathogens to evade the host immune response [63]. The mechanism underlying antigenic variation relies on monoallelic exclusion of a single gene from a hypervariable multigene family combined with repeated, systematic changes in antigen expression. In many systems, these gene families are arranged in subtelomeric contingency loci that are subject to both transcriptional repression and enhanced mutagenesis and recombination [16].
Eviction of a selected gene from a repressed antigen repertoire can be achieved e.g. by recombination into a dedicated, transcriptionally permissive site or by local epigenetic alterations in chromatin composition of the selected gene.
Both processes are ultimately affected by genome architecture. Architectural proteins controlling antigenic variation have, however, remained elusive in any pathogen.
The unicellular protozoan parasite Trypanosoma brucei evades the host immune response by periodically changing expression of a single variant surface glycoprotein (VSG) from a repertoire of ~3000 VSG genes – the largest mutually exclusively expressed gene family described today. To activate a selected VSG gene, it needs to be located in a dedicated expression site that becomes subject to relocation into a distinct, transcriptionally active subnuclear compartment, the expression site body (ESB). Whereas this emphasizes the importance of nuclear architecture in regulating antigen expression in T. brucei, the mechanisms underlying spatial positioning of DNA in T. brucei are not well understood.
In this study I applied genome-wide chromosome conformation capture (Hi-C) to obtain a comprehensive picture of the T. brucei genome in three dimensions, both in procyclic and bloodstream form parasites. Hi-C revealed a highly structured nucleus with megabase chromosomes occupying distinct chromosome territories. Further, specific trans interactions between chromosomes, among which are clusters of centromeres, rRNA genes and procyclins became apparent. With respect to antigenic variation, Hi-C revealed a striking compaction of the subtelomeric VSG gene repertoire and a strong clustering of transcriptionally repressed VSG-containing expression sites. Further, Hi-C analyses confirmed the spatial separation of the actively transcribed from the silenced expression sites in three dimensions.
I further sought to characterize architectural proteins mediating nuclear architecture in T. brucei. Whereas CTCF is absent in non-metazoans, we found cohesin to be expressed throughout the cell cycle, emphasizing a function beyond sister chromatid cohesion in S-phase.
By Chromatin-Immunoprecipitation with sequencing (ChIPseq), I found cohesin enrichment to coincide with the presence of histone H3 vari- ant (H3.V) and H4 variant (H4.V). Most importantly, cohesin and the histone variants were enriched towards the VSG gene at silent and active expression sites.
While the deletion of H3.V led to increased clustering of expression sites in three dimensions and increased chromatin accessibility at expression site promoters, the additional deletion of H4.V increased chromatin accessibility at expression sits even further.
RNAseq showed that mutually exclusive VSG expression was lost in H3.V and H4.V single and double deletion mutants. Immunofluorescence imaging of surface VSGs, flow cytometry and single-cell RNAseq revealed a progressive loss of VSG-2 expression, indicative of an increase in VSG switching rate in the H3.V/H4.V double deletion mutants. Using long-read sequencing technology, we found that VSG switching occurred via recombination and concluded, that the concomitant increase in spatial proximity and accessibility among expression sites facilitated the recombination event.
I therefore identified the histone variants H3.V and H4.V to act at the interface of global nuclear architecture and chromatin accessibility and to represent a link between genome architecture and antigenic variation.
Plants have evolved many mechanisms to defend against herbivores and pathogens. In many cases, these mechanisms took other duties. One example of such a neofunction- alisation would be carnivory. Carnivory evolved from the defence against herbivores. Instead of repelling the predator with a bitter taste, the plant kills it and absorbs its nutrients. A second example can be found in the pollination process. Many of the genes involved here were originally part of defence mechanisms against pathogens. In this thesis, I study these two examples on a genomic and transcriptomic level. The first project, Genomics of carnivorous Droseraceae, aims at obtaining annotated genome sequences of three carnivorous plants. I assembled the genome of Aldrovanda vesiculosa, annotated those of A. vesiculosa, Drosera spatulata and Dionaea muscipula and com- pared their genomic contents. Because of the high repetitiveness of the D. muscipula genome, I also developed reper, an assembly free method for detection, classification and quantification of repeats. With that method, we were able to study the repeats without the need of incorporating them into a genome assembly. The second large project investigates the role of DEFL (defensin-like) genes in pollen tube guidance in tobacco flowers. We sequenced the transcriptome of the SR1 strain in different stages of the pollination process. I assembled and annotated the transcriptome and searched for differentially expressed genes. We also used a method based on Hidden- Markov-Models (HMM) to find DEFLs, which I then analysed regarding their expression during the different stages of fertilisation. In total, this thesis results in annotated genome assemblies of three carnivorous Droser- aceae, which are used as a foundation for various analyses investigating the roots of car- nivory, insights into the role of DEFLs on a transcriptomic level in tobacco pollination and a new method for repeat identification in complex genomes.
Divalent cations are important second messengers triggering various signal transduction events in platelets. Whereas calcium channel blockers have an established antithrombotic effect and the regulation of Ca2+ homeostasis has been elucidated in platelets, the molecular regulation of Mg2+ and Zn2+ homeostasis has not been investigated so far.
In the first part of the thesis, the role of -type serine-threonine kinase linked to transient receptor potential cation channel, subfamily M, member 7 (TRPM7) in platelets was investigated. Using Trpm7R/R mice with a point mutation deleting the kinase activity, we showed that the TRPM7 kinase regulates platelet activation via immunoreceptor tyrosine-based activation motif (ITAM), hem(ITAM) and protease-activated receptor (PAR) signaling routes. Furthermore, Trpm7R/R mice were protected from in vivo thrombosis and stroke, thus establishing TRPM7 kinase as a promising anti-thrombotic target.
In the second part of the thesis, the role of TRPM7 channel in a megakaryocyte (MK) and platelet-specific knockout mouse, Trpm7fl/fl-Pf4Cre, was investigated. Here, we observed that depending on the type of stimulation, Trpm7fl/fl-Pf4Cre platelets showed either enhanced or inhibited responses. Although Trpm7fl/fl-Pf4Cre mice were thrombocytopenic, no differences to wildtype mice were observed in models of in vivo thrombosis and stroke. The above two studies highlight that inhibition of TRPM7 kinase but not the channel itself (in MKs and platelets) may be a promising anti-thrombotic strategy.
Besides TRPM7, we investigated the role of magnesium transporter 1 (MAGT1) in platelet Mg2+ homeostasis and found that MAGT1 primarily regulates receptor-operated calcium entry (ROCE) in platelets specifically upon GPVI activation. This physiological crosstalk is triggered by protein kinase C (PKC) isoforms. Platelets from Magt1-/y mice hyper-reacted to GPVI and thromboxane A2 (TXA2) receptor stimulation in vitro. Consequently, Magt1-/y platelets were found to be pro-thrombotic in disease models of thrombosis and stroke.
To compare platelet ITAM-signaling to the immune system, we further investigated the role of MAGT1 in T and B cells. We described the primary role of MAGT1 in mice under pathogen-free conditions. Magt1-/y B cells showed dysregulated Mg2+ and Ca2+ homeostasis upon B-cell receptor activation, thereby altering Syk, LAT, phospholipase C (PLC)2 and PKC phosphorylation. In contrast to human MAGT1-deficient T cells, development and effector functions of mouse Magt1-/y T cells showed no alterations.
Finally, in the last part of the thesis, we described methods to measure intracellular free zinc [Zn2+]i in human and mouse platelets with storage pool disease (SPD). We propose to measure the [Zn2+]i status in SPD platelets as a relatively easy diagnostic to screen platelet granule abnormalities.
Efficient quadrupolar chromophores (A–pi–A) with triarylborane moieties as acceptors have been studied by the Marder group regarding their non‐linear optical properties and two‐photon absorption ability for many years. Within the present work, this class of dyes found applications in live‐cell imaging. Therefore, the dyes need to be water‐soluble and water‐stable in diluted aqueous solutions, which was examined in Chapter 2. Furthermore, the influence of the pi‐bridge on absorption and emission maxima, fluorescence quantum yields and especially the two-photon absorption properties of the chromophores was investigated in Chapter 3. In Chapter 4, a different strategy for the design of efficient two‐photon excited fluorescence imaging dyes was explored using dipoles (D–A) and octupoles (DA3). Finding the optimum balance between water‐stability and pi‐conjugation and, therefore, red‐shifted absorption and emission and high fluorescence quantum yields, was investigated in Chapter 5