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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 Psychologie (35)
- Institut für Organische Chemie (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.