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Zinc is an essential trace element for all living organisms. In mammals, including humans and mice, it is required for normal growth, development, hematopoiesis and immune defense. This thesis investigates the influence of zinc on the development of megakaryocytes (MKs), the cells responsible for bone marrow-derived platelet production. Furthermore, a detailed analysis of the expression of zinc import and export transporters (Slc39a/Slc30a genes) is carried out, firstly over the course of MK differentiation and secondly dependent on extracellular zinc.
In the thesis at hand, several sequences of number theoretic interest will be studied in the context of uniform distribution modulo one. <br>
<br>
In the first part we deduce for positive and real \(z\not=1\) a discrepancy estimate for the sequence \( \left((2\pi )^{-1}(\log z)\gamma_a\right) \),
where \(\gamma_a\) runs through the positive imaginary parts of the nontrivial \(a\)-points of the Riemann zeta-function. If the considered imaginary
parts are bounded by \(T\), the discrepancy of the sequence \( \left((2\pi )^{-1}(\log z)\gamma_a\right) \) tends to zero like
\( (\log\log\log T)^{-1} \) as \(T\rightarrow \infty\). The proof is related to the proof of Hlawka, who determined a discrepancy estimate for the
sequence containing the positive imaginary parts of the nontrivial zeros of the Riemann zeta-function. <br>
<br>
The second part of this thesis is about a sequence whose asymptotic behaviour is motivated by the sequence of primes. If \( \alpha\not=0\) is real
and \(f\) is a function of logarithmic growth, we specify several conditions such that the sequence \( (\alpha f(q_n)) \) is uniformly distributed
modulo one. The corresponding discrepancy estimates will be stated. The sequence \( (q_n)\) of real numbers is strictly increasing and the conditions
on its counting function \( Q(x)=\#\lbrace q_n \leq x \rbrace \) are satisfied by primes and primes in arithmetic progessions. As an application we
obtain that the sequence \( \left( (\log q_n)^K\right)\) is uniformly distributed modulo one for arbitrary \(K>1\), if the \(q_n\) are primes or primes
in arithmetic progessions. The special case that \(q_n\) equals the \(\textit{n}\)th prime number \(p_n\) was studied by Too, Goto and Kano. <br>
<br>
In the last part of this thesis we study for irrational \(\alpha\) the sequence \( (\alpha p_n)\) of irrational multiples of primes in the context of
weighted uniform distribution modulo one. A result of Vinogradov concerning exponential sums states that this sequence is uniformly distributed modulo one.
An alternative proof due to Vaaler uses L-functions. We extend this approach in the context of the Selberg class with polynomial Euler product. By doing so, we obtain
two weighted versions of Vinogradov's result: The sequence \( (\alpha p_n)\) is \( (1+\chi_{D}(p_n))\log p_n\)-uniformly distributed modulo one, where
\( \chi_D\) denotes the Legendre-Kronecker character. In the proof we use the Dedekind zeta-function of the quadratic number field \( \Bbb Q (\sqrt{D})\).
As an application we obtain in case of \(D=-1\), that \( (\alpha p_n)\) is uniformly distributed modulo one, if the considered primes are congruent to
one modulo four. Assuming additional conditions on the functions from the Selberg class we prove that the sequence \( (\alpha p_n) \) is also
\( (\sum_{j=1}^{\nu_F}{\alpha_j(p_n)})\log p_n\)-uniformly distributed modulo one, where the weights are related to the Euler product of the function.
The starting point of the thesis is the {\it universality} property of the Riemann Zeta-function $\zeta(s)$
which was proved by Voronin in 1975:
{\it Given a positive number $\varepsilon>0$ and an analytic non-vanishing function $f$ defined on a compact subset $\mathcal{K}$ of the strip $\left\{s\in\mathbb{C}:1/2 < \Re s< 1\right\}$ with connected complement, there exists a real number $\tau$ such that
\begin{align}\label{continuous}
\max\limits_{s\in \mathcal{K}}|\zeta(s+i\tau)-f(s)|<\varepsilon.
\end{align}
}
In 1980, Reich proved a discrete analogue of Voronin’s theorem, also known as {\it discrete universality theorem} for $\zeta(s)$:
{\it If $\mathcal{K}$, $f$ and $\varepsilon$ are as before, then
\begin{align}\label{discretee}
\liminf\limits_{N\to\infty}\dfrac{1}{N}\sharp\left\{1\leq n\leq N:\max\limits_{s\in \mathcal{K}}|\zeta(s+i\Delta n)-f(s)|<\varepsilon\right\}>0,
\end{align}
where $\Delta$ is an arbitrary but fixed positive number.
}
We aim at developing a theory which can be applied to prove the majority of all so far existing discrete universality theorems in the case of Dirichlet $L$-functions $L(s,\chi)$ and Hurwitz zeta-functions $\zeta(s;\alpha)$,
where $\chi$ is a Dirichlet character and $\alpha\in(0,1]$, respectively.
Both of the aforementioned classes of functions are generalizations of $\zeta(s)$, since $\zeta(s)=L(s,\chi_0)=\zeta(s;1)$, where $\chi_0$ is the principal Dirichlet character mod 1.
Amongst others, we prove statement (2) where instead of $\zeta(s)$ we have $L(s,\chi)$ for some Dirichlet character $\chi$ or $\zeta(s;\alpha)$ for some transcendental or rational number $\alpha\in(0,1]$, and instead of $(\Delta n)_{n\in\mathbb{N}}$ we can have:
\begin{enumerate}
\item \textit{Beatty sequences,}
\item \textit{sequences of ordinates of $c$-points of zeta-functions from the Selberg class,}
\item \textit{sequences which are generated by polynomials.}
\end{enumerate}
In all the preceding cases, the notion of {\it uniformly distributed sequences} plays an important role and we draw attention to it wherever we can.
Moreover, for the case of polynomials, we employ more advanced techniques from Analytic Number Theory such as bounds of exponential sums and zero-density estimates for Dirichlet $L$-functions.
This will allow us to prove the existence of discrete second moments of $L(s,\chi)$ and $\zeta(s;\alpha)$ on the left of the vertical line $1+i\mathbb{R}$, with respect to polynomials.
In the case of the Hurwitz Zeta-function $\zeta(s;\alpha)$, where $\alpha$ is transcendental or rational but not equal to $1/2$ or 1, the target function $f$ in (1) or (2), where $\zeta(\cdot)$ is replaced by $\zeta(\cdot;\alpha)$, is also allowed to have zeros.
Until recently there was no result regarding the universality of $\zeta(s;\alpha)$ in the literature whenever $\alpha$ is an algebraic irrational.
In the second half of the thesis, we prove that a weak version of statement \eqref{continuous} for $\zeta(s;\alpha)$ holds for all but finitely many algebraic irrational $\alpha$ in $[A,1]$, where $A\in(0,1]$ is an arbitrary but fixed real number.
Lastly, we prove that the ordinary Dirichlet series
$\zeta(s;f)=\sum_{n\geq1}f(n)n^{-s}$ and $\zeta_\alpha(s)=\sum_{n\geq1}\lfloor P(\alpha n+\beta)\rfloor^{-s}$
are hypertranscendental, where $f:\mathbb{N}\to\mathbb{C}$ is a {\it Besicovitch almost periodic arithmetical function}, $\alpha,\beta>0$ are such that $\lfloor\alpha+\beta\rfloor>1$ and $P\in\mathbb{Z}[X]$ is such that $P(\mathbb{N})\subseteq\mathbb{N}$.
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.
In the framework of the presented doctoral thesis, the plant ubiquitous, non-selective vacuolar cation channel TPC1/SV was electrophysiologically studied in Arabidopsis thaliana mesophyll vacuoles to further enlighten its physiological role in plant stress responses. For this, the hyperactive channel version fou2 (D454N), gaining a non-functional vacuolar calcium sensor, strong retarded growth phenotype and upregulated JA signalling pathway, and eight fou2 reverting WT-like ouf mutants were used. Except of ouf4, all other seven ouf mutants carried a 2nd mutation in the TPC1 gene. Therefore, the TPC1 electrical features of all ouf mutants were electrophysiologically characterized with the patch clamp method and compared with fou2 and WT.
Due to a missense mutation, ouf1 and ouf7 mutants harboured a truncated TPC1 channel protein, resulting in an impaired protein integrity and in turn loss of TPC1 channel activity. Accordingly, ouf1 and ouf7 mimicked the tpc1-2 null mutant with a WT- rather fou2-like phenotype. The ouf2 (G583D D454N) mutant exhibited inactive TPC1 channels, probably because the G583D mutation located in luminal part of the S11 helix caused (i) a shift of the activation threshold to much more positive voltages (i.e. to more than +110 mV) (ii) or channel blockage. As a result of the TPC1 channel inactivity, the ouf2 mutant also imitates the WT-like phenotype of the tpc1-2 null mutant. In the ouf6 mutant (A669V D454N) the 2nd reverting mutation selectively influenced fou2-like SV channel features. Both, the fast activation kinetics and reduced luminal calcium sensitivity were similar in ouf6 and fou2. However, deviations in both, the relative and absolute open channel probability, resulted in strongly reduced (80 %) current density at 0 mM and channel inactivity in the voltage range between -30 mV to +40 mV compared to fou2 and WT. Furthermore, the TPC1 channels in ouf6 exhibited a higher susceptibility to inhibitory luminal Ca2+ than fou2. As a result of these different effects, the TPC1 channel activity almost vanished at high luminal Ca2+ loads, what is very likely the reason that ouf6 lost the fou2-like phenotype. The ouf4 mutation did not change the fou2 TPC1-channel features like fast channel activation, single channel conductance and voltage-dependent gating behaviour. Nevertheless, the TPC1 current density was 80% less in ouf4 than in fou2. Since the TPC1 gene was not the target of the 2nd mutation, it can be assumed that it is modulated via external, yet unknown factor. In the ouf8 mutant the TPC1 channels additionally possess M629I mutation within the selectivity filter II resulting in a 50% decrease in the TPC1 unitary conductance. However, the slightly increased relative open channel probability of the TPC1 channels in ouf8 compared to fou2 appeared to be sufficient to compensate the reduced transport capacity of individual TPC1 channels. As a result, a similar macroscopic outward current density of ouf8 and fou2 was detected in the absence of vacuolar Ca2+. Furthermore, ouf8 mutation did not drastically change the typical fou2 TPC1 channel features such as fast activation, vacuolar calcium insensitivity and voltage dependency. However, a reversible block of the cytosol-directed potassium efflux at increased vacuolar calcium concentration in ouf8 mutant was found. Further inspection of transiently expressed TPC1 channel variants (M629I, M629T) on the single channel level suggest that Met629 of AtTPC1 in the channel pore region is crucial for the unitary channel conductance.
Taken together, current membrane recordings from ouf mutants revealed one common feature: All of them lacked or showed a strongly impaired ability for TPC1-mediated potassium release from the vacuole into the cytosol. Additionally, considering the detected dependence of the vacuolar membrane voltage on TPC1 activity, it thus seems that the TPC1-triggered vacuolar membrane depolarization caused by vacuolar K+ release plays a key role in generation of the fou2-like phenotype. Accordingly, one can conclude that TPC1-dependent vacuolar membrane depolarization and initiation of jasmonate production are likely linked. This statement is supported also by the complete restoration of WT-like plant phenotype and JA signalling in the ouf mutants. Finally, as a control element of the vacuolar membrane voltage TPC1 is probably upstream located in JA signalling pathway and therefore a perfect junction for linking multiple physiological stimuli and response to them.
Im Rahmen der vorgelegten Doktorarbeit wurde der in Pflanzen ubiquitär exprimierte, nicht-selektive vakuoläre Kationenkanal TPC1/SV elektrophysiologisch in Arabidopsis thaliana Mesophyllvakuolen untersucht, um seine physiologische Rolle in der pflanzlichen Stressantwort weiter aufzuklären. Hierfür wurde die hyperaktive Kanalvariante fou2 (D454N), die einen nicht-funktionalen vakuolären Calciumsensor, ein stark verzögertes Pflanzenwachstum und einen hochregulierten Jasmonsäure-Signalweg aufweist, sowie acht ouf Mutanten mit fou2-umkehrenden Phänotyp benutzt. Mit Ausnahme von ouf4 enthalten alle anderen ouf Mutanten eine weitere Mutation im TPC1-Gen. Daher wurden die elektrischen Eigenschaften von TPC1 in allen ouf Mutanten elektrophysiologisch mittels der Patch clamp Technik charakterisiert und mit fou2 und dem Wildtyp verglichen.
Aufgrund einer Missense-Mutation beinhalten die Mutanten ouf1 und ouf7 ein verkürztes TPC1 Protein, woraus eine gestörte Proteinintegrität resultiert und daraus wiederum ein Fehlen der TCP1-Kanalaktivität. Dementsprechend ähneln ouf1 und ouf7 der tpc1-2 Nullmutante mit einem WT- oder eher fou2-artigen Phänotyp. Wahrscheinlich weist die ouf2 (G583D D454N) Mutante einen inaktiven TPC1-Kanal auf, weil die G583D Mutation, die in einem luminalen Teil der S11 Helix sitzt, eine Verschiebung der Aktivierungsschwelle hin zu einer höheren Spannung (z. B. mehr als +110 mV) oder einen Kanalblock verursacht. Als Folge der TPC1 Kanal Inaktivität, ahmt die ouf2 Mutante auch den WT-ähnlichen Phänotyp der tpc1-2 Nullmutante nach. In der ouf6 Mutante (A669V D454N) beeinflusst die zweite Mutation selektiv die fou2-ähnlichen SV-Kanaleigenschaften. Sowohl die schnelle Aktivierungskinetik als auch die verringerte luminale Calciumsensitivität waren denen von ouf6 und fou2 ähnlich. Die Abweichungen in der relativen sowie der absoluten Offenwahrscheinlichkeit resultierten jedoch in einer stark reduzierten (80 %) Stromdichte bei 0 mM luminalem Calcium verglichen mit fou2 und dem WT, sowie einer Kanalinaktivität bei Spannungen zwischen -30 mV und +40 mV. Darüber hinaus zeigten die TPC1 Kanäle in ouf6 eine höhere Anfälligkeit für inhibitorisches, luminales Calcium als die in fou2. Das Ergebnis der beiden unterschiedlichen Effekte ist, dass die TPC1 Kanalaktivität bei einer hohen luminalen Calciumkonzentration fast verschwindet, woraus zu schließen ist, dass ouf6 den fou2-ähnlichen Phänotyp verlor. Die ouf4 Mutation veränderte nicht die fou2 TPC1 Kanaleigenschaften, wie die schnelle Kanalaktivierung, die Einzelkanalleitfähigkeit und das spannungsabhängige Verhalten. Nichtsdestotrotz war die TCP1 Stromdichte in ouf4 um 80 % geringer als in fou2. Da das TPC1 Gen nicht das Ziel der zweiten Mutation war, kann angenommen werden, dass es durch äußere, bisher noch unbekannte Faktoren, reguliert wird. In der ouf8 Mutante haben die TPC1 Kanäle zusätzlich eine M629I Mutation innerhalb des zweiten Selektivitätsfilters, welche in einem 50 % Rückgang der TCP1 Einzelkanalleitfähigkeit resultiert. Jedoch scheint die leicht erhöhte Offenwahrscheinlichkeit der TCP1 Kanäle in ouf8, verglichen mit fou2, ausreichend zu sein, um die reduzierte Transportkapazität der individuellen TPC1 Kanäle zu kompensieren. Schlussfolgernd wurde eine ähnliche makroskopische auswärts gerichtete Stromdichte des ouf8 und des fou2 in Abwesenheit vakuolären Calciums entdeckt. Des Weiteren änderte eine ouf8 Mutation die fou2 TPC1 Kanaleigenschaften wie eine schnelle Aktivierung, vakuoläre Calciuminsensitivität und die Spannungsabhängigkeit nicht drastisch. Jedoch wurde ein reversibler Block des Zytosol-gerichteten Kalium Ausstroms bei erhöhten vakuolären Calcium Konzentrationen in ouf8 gefunden. Eine weitere Betrachtung transient exprimierter TPC1 Kanalvarianten (M629I, M629T) auf Einzelkanalebene weist darauf hin, dass das Met629 des AtTPC1 in der Kanalporenregion entscheidend ist für die Einzelkanalleitfähigkeit.
Zusammengefasst zeigt der über die Membran von ouf Mutanten gemessene Strom eine Gemeinsamkeit: Alle zeigten keinen oder einen stark beeinträchtigten TPC1-vermittelten Kaliumausstrom aus der Vakuole ins Zytosol. Unter Berücksichtigung der beobachteten Abhängigkeit der vakuolären Membranspannung von der TPC1 Aktivität, scheint es, als ob die durch TPC1 angeregte Depolarisation der Vakuolenmembran, welche durch die vakuoläre Kaliumfreisetzung bedingt wird, in der Ausbildung des fou2 Phänotyps eine Rolle spielt. Daraus lässt sich ableiten, dass die TPC1-abhängige Depolarisation der Vakuolenmembran und die Jasmonat Bildung vermutlich verbunden sind. Diese Behauptung wird auch gestützt durch die komplette Wiederherstellung des WT-ähnlichen Pflanzenphänotyps und des Jasmonsäure Signalwegs in den ouf Mutanten. Letztendlich ist TPC1 als kontrollierendes Element der vakuolären Membranspannung wahrscheinlich dem Jasmonsäure Signalweg vorgeschaltet und deswegen ein perfekter Knotenpunkt, der verschiedene physiologische Stimuli und ihre Antworten verbindet.
Nowadays, computational-aided investigations become an essential part in the chemical, biochemical or pharmaceutical research. With increasing computing power, the calculation of larger biological systems becomes feasible. In this work molecular mechanical (MM) and quantum mechanical approaches (QM) and the combination of both (QM/MM) have been applied to study several questions which arose from different working groups. Thus, this work comprises eight different subjects which deals with chemical reactions or proton transfer in enzymes, conformational changes of ligands or proteins and verification of experimental data.
This work firstly deals with reaction mechanisms of aromatic inhibitors of cysteine proteases which can be found in many organisms. These enzymes are responsible for various cancer or diseases as for example Human African Trypanosomiasis (HAT) or the Chagas disease. Aromatic SNAr-type electrophiles might offer a new possibility to covalently modify these proteases. Quantum mechanical calculations have been performed to gain insights into the energetics and possible mechanisms.
The next chapter also deals with Trypanosomiasis but the focus was set on a different enzyme. The particularity of Trypanosomiasis is the thiol metabolism which can also be modified by covalent inhibitors. In this context, the wild type and point mutations of the enzyme tryparedoxin have been investigated via molecular dynamic (MD) simulations to examine the influence of specific amino acids in regard to the inhibitor. Experimental data showed that a dimerization of the enzyme occurs if the inhibitor is present. Simulations revealed that the stability of the dimer decreases in absence of the inhibitor and thus confirms these experiments.
Further investigations concerning cysteine proteases such as cruzain and rhodesain have been conducted with respect to experimental kinetic data of covalent vinylsulfone inhibitors. Several approaches such as QM or QM/MM calculations and docking, MD or MMPBSA/MMGBSA simulations have been applied to reproduce these data. The utilization of force field approaches resulted in a qualitatively accurate prediction.
The kinase AKT is involved in a range of diseases and plays an important role in the formation of cancer. Novel covalent-allosteric inhibitors have been developed and crystallized in complex with AKT. It was shown that depending on the inhibitor a different cysteine residue is modified. To investigate these differences in covalent modification computational simulations have been applied.
Enoyl-(acyl carrier) (ENR) proteins are essential in the last step of the fatty acid biosynthesis II (FAS) and represent a good target for inhibition. The diphenylether inhibitor SKTS1 which was originally designed to target the ENR’s of Staphylococcus aureus was also crystallized in InhA, the ENR of Mycobacterium tuberculosis (TB). Crystal structures indicate a change of the inhibitor's tautomeric form. This subject was investigated via MD simulations. Results of these simulations confirmed the tautomerization of the inhibitor.
This work also deals with the development of a covalent inhibitor originating from a non-covalent ligand. The target FadA5 is an essential enzyme for the degradation of steroids in TB and is responsible for chronic tuberculosis. This enzyme was crystallized in complex with a non-covalent ligand which served as starting point for this study. Computations on QM or QM/MM level and docking and MD simulations have been applied to evaluate potential candidates.
The next chapter focuses on the modification of the product spectrum of Bacillus megaterium levansucrase, a polymerase which catalyzes the biosynthesis of fructans. The covalent modification of the wild type or mutants of the enzyme lead to an accumulation of oligosaccharides but also to polymers with higher polymerization degree. To understand these changes in product spectra MD simulations have been performed.
Finally, the proton transfer in catalytic cysteine histidine dyads was investigated. The focus was set on the influence of the relaxation of the protein environment to the reaction. Calculations of the enzymes FadA5 and rhodesain revealed that the preferred protonation state of the dyade depends on the protein environment and has an impact on the reaction barrier. Furthermore, the adaptation of the environment to a fixed protonation state was analyzed via MD simulations.
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.
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.
The Role of Attentional Control and Fear Acquisition and Generalization in Social Anxiety Disorder
(2020)
Although Social Anxiety Disorder (SAD) is one of the most prevalent mental disorders, still little is known about its development and maintenance. Cognitive models assume that deviations in attentional as well as associative learning processes play a role in the etiology of SAD. Amongst others, deficits in inhibitory attentional control as well as aberrations during fear generalization, which have already been observed in other anxiety disorders, are two candidate mechanisms that might contribute to the onset and retention of SAD. However, a review of the literature shows that there is a lack of research relating to these topics. Thus, the aim of the present thesis was to examine in which way individuals with SAD differ from healthy controls regarding attentional control and generalization of acquired fear during the processing of social stimuli.
Study 1 tested whether impairment in the inhibitory control of attention is a feature of SAD, and how it might be influenced by emotional expression and gaze direction of an interactional partner. For this purpose, individuals with SAD and healthy controls (HC) participated in an antisaccade task with faces displaying different emotional expressions (angry, neutral and happy) and gaze directions (direct and averted) serving as target stimuli. While the participants performed either pro- or antisaccades in response to the peripherally presented faces, their gaze behavior was recorded via eye-tracking, and ratings of valence and arousal were obtained. Results revealed that both groups showed prolonged latencies and increased error rates in trials with correct anti- compared to prosaccades. However, there were no differences between groups with regard to response latency or error rates, indicating that SAD patients did not exhibit impairment on inhibitory attentional control in comparison to HC during eye-tracking. Possible explanations for this finding could be that reduced inhibitory attentional control in SAD only occurs under certain circumstances, for example, when these individuals currently run the risk of being negatively evaluated by others and not in the mere presence of phobic stimuli, or when the cognitive load of a task is so high that it cannot be unwound by compensatory strategies, such as putting more effort into a task.
As not only deviations in attentional, but also associative learning processes might be pathogenic markers of SAD, these mechanisms were further addressed in the following experiments. Study 2 is the first that attempted to investigate the generalization of conditioned fear in patients with SAD. To this end, patients with SAD and HC were conditioned to two neutral female faces serving as conditioned stimuli (CS+: reinforced; CS-: non-reinforced) and a fearful face paired with a loud scream serving as unconditioned stimulus (US). Fear generalization was tested by presenting morphs of the two faces (GS: generalization stimuli), which varied in their similarity to the original faces. During the whole experiment, self-report ratings, heart rate (HR) and skin conductance responses (SCR) were recorded. Results demonstrated that SAD patients rated all stimuli as less pleasant and more arousing, and overestimated the occurrence of the US compared to HC, indicating a general hyperarousal in individuals with SAD. In addition, ratings and SCR indicated that both groups generalized their acquired fear from the CS+ to intermediate GSs as a function of their similarity to the CS+. However, except for the HR data, which indicated that only SAD patients but not HC displayed a generalization response in this measure, most of the results did not support the hypothesis that SAD is characterized by overgeneralization. A plausible reason for this finding could be that overgeneralization is just a key characteristic of some anxiety disorders and SAD is not one of them. Still, other factors, such as comorbidities in the individuals with SAD, could also have had an influence on the results, which is why overgeneralization was further examined in study 3.
The aim of study 3 was to investigate fear generalization on a neuronal level. Hence, high (HSA) and low socially anxious participants (LSA) underwent a conditioning paradigm, which was an adaption of the experimental design used study 2 for EEG. During the experiment, steady-state visually evoked potentials (ssVEPs) and ratings of valence and arousal were recorded. Analyses revealed significant generalization gradients in all ratings with highest fear responses to the CS+ and a progressive decline of these reactions with increasing similarity to the CS-. In contrast, the generalization gradient on a neuronal level showed highest amplitudes for the CS+ and a reduction in amplitude to the most proximal, but not distal GSs in the ssVEP signal, which might be interpreted as lateral inhibition in the visual cortex. The observed dissociation among explicit and implicit measures points to different functions of behavioral and sensory cortical processes during fear generalization: While the ratings might reflect an individual’s consciously increased readiness to react to threat, the lateral inhibition pattern in the occipital cortex might serve to maximize the contrast among stimuli with and without affective value and thereby improve adaptive behavior. As no group differences could be observed, the finding of study 2 that overgeneralization does not seem to be a marker of SAD is further consolidated.
In sum, the conducted experiments suggest that individuals with SAD are characterized by a general hyperarousal during the exposition to disorder-relevant stimuli as indicated by enhanced arousal and reduced valence ratings of the stimuli compared to HC. However, the hypotheses that reduced inhibitory attentional control and overgeneralization of conditioned fear are markers of SAD were mostly not confirmed. Further research is required to elucidate whether they only occur under certain circumstances, such as high cognitive load (e.g. handling two tasks simultaneously) or social stress (e.g. before giving a speech), or whether they are not characteristics of SAD at all. With the help of these findings, new interventions for the treatment of SAD can be developed, such as attentional bias modification or discrimination learning.
T cells play an essential role in the immune system. Engaging the T cell receptor (TCR) initiates a cascade of signaling events that activates the T cells. Neutral sphingomyelinase (NSM) is a member of a superfamily of enzymes responsible for the hydrolysis of sphingomyelin into phosphocholine and ceramide. Sphingolipids are essential mediators in signaling cascades involved in apoptosis, proliferation, stress responses, necrosis, inflammation, autophagy, senescence, and differentiation.
Upon specific ablation of NSM2, T cells proved to be hyper-responsive to CD3/CD28 co-stimulation, indicating that the enzyme acts to dampen early overshooting activation of these cells. It remained unclear whether a deregulated metabolic activity supports the hyper-reactivity of NSM2 deficient T cells. This work demonstrates that the ablation of NSM2 activity affects the metabolism of the quiescent CD4+ T cells. These accumulate ATP in mitochondria and increase basal glycolytic activity by increasing the basal glucose uptake and GLUT1 receptor expression, which, altogether, raises intracellular ATP levels and boosts cellular respiration. The increased basal metabolic activity is associated with rapid phosphorylation of S6, a mTORC1 target, as well as enhanced elevation total ATP levels within the first hour after CD3/CD28 costimulation. Increased metabolic activity in resting NSM2 deficient T cells does, however, not support sustained stimulated responses. While elevated under steady-state conditions and elevated early after co-stimulation in NSM2 deficient CD4+ T cells, the mTORC1 pathway regulating mitochondria size, oxidative phosphorylation, and ATP production is impaired after 24 hours of stimulation. Taken together, the absence of NSM2 promotes a hyperactive metabolic state in unstimulated CD4+ T cells yet fails to support sustained T cell responses upon antigenic stimulation without affecting T cell survival.
The present dissertation aims to shed light on different mechanisms of socio-emotional feedback in social decision-making situations. The objective is to evaluate emotional facial expressions as feedback stimuli, i.e., responses of interaction partners to certain social decisions. In addition to human faces, artificial emojis are also examined due to their relevance for modern digital communication. Previous research on the influence of emotional feedback suggests that a person's behavior can be effectively reinforced by rewarding stimuli. In the context of this dissertation, the differences in the feedback processing of human photographs and emojis, but also the evaluation of socially expected versus socially unexpected feedback were examined in detail in four studies. In addition to behavioral data, we used the electroencephalogram (EEG) in all studies to investigate neural correlates of social decision-making and emotional feedback.
As the central paradigm, all studies were based on a modified ultimatum game. The game is structured as follows: there is a so-called proposer who holds a specific amount of money (e.g., 10 cents) and offers the responder a certain amount (e.g., 3 cents). The responder then decides whether to accept or reject the offer. In the version of the ultimatum game presented here, different types of proposers are introduced. After the participants have accepted or rejected in the role of the responder, the different proposers react to the participant’s decision with specific emotional facial expressions. Different feedback patterns are used for the individual experiments conducted in the course of this dissertation.
In the first study, we investigated the influence of emotional feedback on decision-making in the modified version of the ultimatum game. We were able to show that a proposer who responds to the acceptance of an offer with a smiling face achieves more accepted offers overall than a control proposer who responds to both accepted and rejected offers with a neutral facial expression. Consequently, the smile served as a positive reinforcement. Similarly, a sad expression in response to a rejected offer also resulted in higher acceptance rates as compared to the control identity, which could be considered an expression of compassion for that proposer. On a neuronal level, we could show that there are differences between simply looking at negative emotional stimuli (i.e., sad and angry faces) and their appearance as feedback stimuli after rejected offers in the modified ultimatum game. The so-called feedback-related negativity was reduced (i.e., more positive) when negative emotions appeared as feedback from the proposers. We argued that these findings might show that the participants wanted to punish the proposers by rejecting an offer for its unfairness and therefore the negative feedback met their expectations. The altered processing of negative emotional facial expressions in the ultimatum game could therefore indicate that the punishment is interpreted as successful. This includes the expectation that the interaction partner will change his behavior in the future and eventually make fairer offers.
In the second study we wanted to show that smiling and sad emojis as feedback stimuli in the modified ultimatum game can also lead to increased acceptance rates. Contrary to our assumptions, this effect could not be observed. At the neural level as well, the findings did not correspond to our assumptions and differed strongly from those of the first study. One finding, however, was that the neural P3 component showed how the use of emojis as feedback stimuli particularly characterizes certain types of proposers. This is supported by the fact that the P3 is increased for the proposer who rewards an acceptance with a smile as well as for the proposer who reacts to rejection with a sad emoji compared to the neutral control proposer.
The third study examined the discrepancy between the findings of the first and second study. Accordingly, both humans and emojis representing the different proposers were presented in the ultimatum game. In addition, emojis were selected that showed a higher similarity to known emojis from common messenger services compared to the second study. We were able to replicate that the proposers in the ultimatum game, who reward an acceptance of the offer with a smile, led to an increased acceptance rate compared to the neutral control proposers. This difference is independent of whether the proposers are represented by emojis or human faces. With regard to the neural correlates, we were able to demonstrate that emojis and human faces differ strongly in their neural processing. Emojis showed stronger activation than human faces in the face-processing N170 component, the feedback-related negativity and the P3 component. We concluded that the results of the N170 and feedback-related negativity could indicate a signal for missing social information of emojis compared to faces. The increased P3 amplitude for emojis might imply that emojis appear unexpectedly as reward stimuli in a social decision task compared to human faces.
The last study of this project dealt with socially unexpected feedback. In comparison to the first three studies, new proposer identities were implemented. In particular, the focus was on a proposer who reacted to the rejection of an offer unexpectedly with a smile and to the acceptance with a neutral facial expression. According to the results, participants approach this unexpected smile through increased rejection, although it is accompanied by financial loss. In addition, as reported in studies one and three, we were able to show that proposers who respond to the acceptance of an offer with a smiling face and thus meet the expectations of the participants have higher offer acceptance rates than the control proposer. At the neuronal level, especially the feedback from the socially unexpected proposer led to an increased P3 amplitude, which indicates that smiling after rejection is attributed a special subjective importance.
The experiments provide new insights into the social influence through emotional feedback and the processing of relevant social cues. Due to the conceptual similarity of the studies, it was possible to differentiate between stable findings and potentially stimulus-dependent deviations, thus creating a well-founded contribution to the current research. Therefore, the novel paradigm presented here, and the knowledge gained from it could also play an important role in the future for clinical questions dealing with limited social competencies.
Periglacial environments are facing dramatic changes. Warming air temperatures and strong snow cover variations fundamentally affect landforming processes in this hotspot region of Climate Change. But before we can assess the response of landform development to a changing climate, we need to enhance our understanding of the internal structure of those landforms. Within this study, a broad scope of landform types from alpine and subarctic regions is investigated: rock glaciers, solifluction lobes, palsas and patterned ground. By using the geophysical methods 2-D and 3-D ERI, as well as GPR surveying, structural differences and similarities between landform units of different or the same landform types are highlighted. This enables a reconstruction of their past and a projection of their future development.
Neisseria meningitidis (N. meningitidis) is a human commensal that occasionally causes life-threatening infections such as bacterial meningitis and septicemia. Despite experi-mental evidence that the expression of small non-coding RNAs (sRNAs) as well as the RNA chaperone Hfq affect meningococcal physiology, the impact of RNA-based regula-tion (riboregulation) on fitness and virulence in N. meningitidis is only poorly understood. Therefore, this study addressed these issues using a combination of high-throughput tech-nologies.
A differential RNA-sequencing (dRNA-seq) approach was applied to produce a single-nucleotide resolution map of the primary transcriptome of N. meningitidis strain 8013. The dRNA-seq analysis predicted 1,625 transcriptional start sites including 65 putative sRNAs, of which 20 were further validated by northern blot analysis. By Hfq RNA im-munopreci-pitation sequencing a large Hfq-centered post-transcriptional regulatory net-work comprising 23 sRNAs and 401 potential mRNA targets was identified. Rifampicin stability assays demonstrated that Hfq binding confers enhanced stability on its associat-ed sRNAs. Based on these data, the interactions of two paralogous sRNAs and their cog-nate target mRNA prpB were validated in vivo as well as in vitro. Both sRNAs directly repress prpB encoding a methylisocitrate lyse which was previously shown to be involved in meningococcal colonization of the human nasopharynx.
Besides the well-described RNA chaperone Hfq, FinO-domain proteins have recently been recognized as a widespread family of RNA-binding proteins (RBPs) with regulatory roles in diverse bacteria. They display an intriguing bandwidth of target sites, ranging from a single RNA pair as recognized by plasmid-encoded FinO to the global RNA regu-lons of enterobacterial ProQ proteins. To better understand the intrinsic targeting mode of this RBP family, in vivo targets of the minimal ProQ protein of N. meningitidis were de-termined. In vivo UV crosslinking with RNA deep sequencing (UV-CLIP) identified as-sociations of ProQ with 16 sRNAs and 166 mRNAs encoding a variety of biological functions and thus revealed ProQ as another global RBP in meningococci. It could be shown that meningococcal ProQ predominantly binds to highly structured RNA regions including DNA uptake sequences (DUS) and rho-independent transcription terminators and stabilizes many of its RNA targets as proved by rifampicin stability experiments. As expected from the large suite of ProQ-bound RNAs, proQ deletion globally affects both gene and protein expression in N. meningitidis, changing the expression levels of at least 244 mRNAs and 80 proteins. Phenotypic analyses suggested that ProQ promotes oxida-tive stress tolerance and UV damage repair capacity, both of which are required for full virulence of N. meningitidis.
Together, this work uncovers the co-existence of two major post-transcriptional regulons, one governed by ProQ, the other by Hfq, in N. meningitidis. It further highlights the role of these distinct RBPs and its associated sRNAs to bacterial virulence and indicates that riboregulation is likely to contribute to the way how meningococci adapt to different host niches.
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.
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.
We are living in a system that underlies permanent environmental changes due to the rotation of our planet. These changes are rhythmic with the most prominent one having a period of about 24 hours, but also shorter and longer rhythms characterize our environment. To cope with the ever-changing environmental conditions, it is thought to be beneficial if an organism can track and anticipate these changes. The so called endogenous clocks enable this and might provide a fitness advantage. To investigate and unravel the mechanism of endogenous clocks Chronobiologists have used different model organisms. In this thesis Drosophila melanogaster was used as model organism with its about 150 clock neurons representing the main endogenous clock of the fly in the central brain.
The molecular mechanisms and the interlocked feedback loops with the main circadian key players like period, timeless, clock or cycle are under investigation since the 1970s and are characterized quite well so far. But the impact of a functional endogenous clock in combination with diverse factors and the resulting fitness advantages were analysed in only a few studies and remains for the most part unknown. Therefore the aim of this thesis was to unravel the impact of Drosophila melanogaster`s endogenous clock on the fitness of the fly. To achieve this goal different factors – like day length, humidity and food composition – were analyzed in wild type CS and three different period mutants, namely perL, perS and per01, that carry a point mutation altering or abolishing the free-running period of the fruit fly as well as a second arrhythmic strain, clkAR.
In competition assay experiments wild type and clock mutant flies competed for up to 63 generations under a normal 24 hour rhythm with 12 hours light/day and 12 hours darkness/night (LD12:12) or T-cycles with 19 or 29 hours, according to the mutants free-running period, or constant light (LL) in case of the arrhythmic mutant as well as under natural-like outdoor conditions in two consecutive years. Overall the wild type CS strain was outcompeting the clock mutant strains independent of the environmental conditions. As the perL fly strain elongated their free-running period, the competition experiments were repeated with naturally cantonized new fly strains. With these experiments it could be shown that the genetic background of the fly strains – which are kept for decades in the lab, with backcrosses every few years – is very important and influences the fitness of flies. But also the day length impacts the fitness of the flies, enabling them to persist in higher percentage in a population under competition. Further factors that might influence the survival in a competing population were investigated, like e.g. mating preferences and locomotor activity of homo- and heterozygous females or sperm number of males transferred per mating. But these factors can still not explain the results in total and play no or only minor roles and show the complexity of the whole system with still unknown characteristics.
Furthermore populations of flies were recorded to see if the flies exhibit a common locomotor activity pattern or not and indeed a population activity pattern could be recorded for the first time and social contact as a Zeitgeber could be verified for Drosophila melanogaster.
In addition humidity and its impact on the flies´ fitness as well as a potential Zeitgeber was examined in this thesis. The flies experienced different relative humidities for eclosion and wing expansion and humidity cycle phase shifting experiments were performed to address these two different questions of fitness impact and potential Zeitgeber. The fruit fly usually ecloses in the morning hours when the relative humidity is quite high and the general assumption was that they do so to prevent desiccation. The results of this thesis were quite clear and demonstrate that the relative humidity has no great effect on the fitness of the flies according to successful eclosion or wing expansion and that temperature might be the more important factor. In the humidity cycle phase shifting experiments it could be revealed that relative humidity cannot act as a Zeitgeber for Drosophila melanogaster, but it influences and therefore masks the activity of flies by allowing or surpressing activity at specific relative humidity values.
As final experiments the lifespan of wild type and clock mutant flies was investigated under different day length and with different food qualities to unravel the impact of these factors on the fitness and therefore survival of the flies on the long run. As expected the flies with nutrient-poor minimum medium died earlier than on the nutrient-rich maximum medium, but a small effect of day length could also be seen with flies living slightly longer when they experience environmental day length conditions resembling their free-running period. The experiments also showed a fitness advantage of the wild type fly strain against the clock mutant strains for long term, but not short term (about the first 2-3 weeks).
As a conclusion it can be said that genetic variation is important to be able to adapt to changing environmental conditions and to optimize fitness and therefore survival. Having a functional endogenous clock with a free-running period of about 24 hours provides fitness advantages for the fruit fly, at least under competition. The whole system is very complex and many factors – known and unknown ones – play a role in this system by interacting on different levels, e.g. physiology, metabolism and/or behavior.
The initial goal was the conversion of Bifidobacterium adolescentis Sucrose Phosphorylase (BaSP) into a polyphenol glucosidase by structure based enzyme engineering. BaSP was chosen because of its ability to utilize sucrose, an economically viable and sustainable donor substrate, and transfer the glucosyl moiety to various acceptor substrates. The introduction of aromatic residues into the active site was considered a viable way to render it more suitable for aromatic acceptor compounds by reducing its polarity and potentially introducing π-π-interactions with the polyphenols. An investigation of the active site revealed Gln345 as a suitable mutagenesis target. As a proof of concept BaSP Q345F was employed in the glycosylation of (+)-catechin, (-)-epicatechin and resveratrol. The variant was selective for the aromatic acceptor substrates and the glucose disaccharide side reaction was only observed after almost quantitative conversion of the aromatic substrates. A crystal structure of BaSP Q345F in complex with glucose was obtained and it displayed an unexpected shift of an entire domain by 3.3 Å. A crystal structure of BaSP D192N-Q345F, an inactive variant in complex with resveratrol-3-α-D-glucosid, the glucosylation product of resveratrol, synthesized by BaSP Q345F was solved. It proved that the domain shift is in fact responsible for the ability of the variant to glycosylate aromatic compounds. Simultaneously a ligand free crystal structure of BaSP Q345F disproved an induced fit effect as the cause of the domain shift. The missing link, a crystal structure of BaSP Q345F in the F-conformation is obtained. This does not feature the domain shift, but is in outstanding agreement with the wildtype structure. The domain shift is therefore not static but rather a step in a dynamic process. It is further conceivable that the domain shifted conformation of BaSP Q345F resembles the open conformation of the wild type and that an adjustment of a conformational equilibrium as a result of the Q345F point mutation is observed. An investigation into the background reaction, the formation of glucose-glucose disaccharides of BaSP Q345F and three further variants that addressed the same region (L341C, D316C-L341C and D316C-N340C) revealed the formation of nigerose by BaSP Q345F.
In the recent years, translational studies comparing imaging data of animals and humans have gained increasing scientific interests with crucial findings stemming from both, human and animal work. In order to harmonize statistical analyses of data from different species and to optimize the transfer of knowledge between them, shared data acquisition protocols and combined statistical approaches have to be identified. Following this idea, methods of data analysis, which have until now mainly been used to model neural responses of electrophysiological recordings from rodent data, were applied on human hemodynamic responses (i.e. Blood-Oxygen-Level-Dependent BOLD signal) as measured via functional magnetic resonance imaging (fMRI).
At the example of two attention and impulsivity networks, timing dynamics and amplitude of the fMRI signal were determined (study 1). Study 2 described the same parameters frequency-specifically, and in study 3, the complexity of neural processing was quantified in terms of fractality. Determined parameters were compared with regard to the subjects’ task performance / impulsivity to validate findings with regard to reports of the current scientific debate.
In a general discussion, overlapping as well as additional information of methodological approaches were discussed with regard to its potential for biomarkers in the context of neuropsychiatric disorders.
This thesis aims for a better understanding of the mechanisms underlying anxiety as well as trauma- and stressor-related disorders and the development of new therapeutic approaches. I was first interested in the associative learning mechanisms involved in the etiology of anxiety disorders. Second, I explored the therapeutic effects of transcutaneous vagus nerve stimulation (tVNS) as a promising new method to accelerate and stabilize extinction learning in humans.
For these purposes, I applied differential anxiety conditioning protocols realized by the implementation of virtual reality (VR). Here, a formerly neutral virtual context (anxiety context, CTX+) is presented whereby the participants unpredictably receive mildly aversive electric stimuli (unconditioned stimulus, US). Another virtual context (safety context, CTX-) is never associated with the US. Moreover, extinction of conditioned anxiety can be modeled by presenting the same contexts without US delivery. When unannounced USs were administered after extinction, i.e. reinstatement, the strength of the “returned” conditioned anxiety can provide information on the stability of the extinction memory.
In Study 1, I disentangled the role of elemental and conjunctive context representations in the acquisition of conditioned anxiety. Sequential screenshots of two virtual offices were presented like a flip-book so that I elicited the impression of walking through the contexts. Some pictures of CTX+ were paired with an US (threat elements), but not some other screenshots of the same context (non-threat elements), nor the screenshots depicting CTX- (safety elements). Higher contingency ratings for threat compared to non-threat elements revealed elemental representation. Electro-cortical responses showed larger P100 and early posterior negativity amplitudes elicited by screenshots depicting CTX+ compared to CTX- and suggested conjunctive representation. These results support the dual context representation in anxiety acquisition in healthy individuals.
Study 2 addressed the effects of tVNS on the stabilization of extinction learning by using a context conditioning paradigm. Potentiated startle responses as well as higher aversive ratings in CTX+ compared to CTX- indicate successful anxiety conditioning. Complete extinction was found in startle responses and valence ratings as no differentiation between CTX+ and CTX- suggested. TVNS did not affect extinction or reinstatement of anxiety which may be related to the inappropriate transferability of successful stimulation parameters from epilepsy patients to healthy participants during anxiety extinction.
Therefore, in Study 3 I wanted to replicate the modulatory effects of tVNS on heart rate and pain perception by the previously used parameters. However, no effects of tVNS were observed on subjective pain ratings, on pain tolerance, or on heart rate. This led to the conclusion that the modification of stimulation parameters is necessary for a successful acceleration of anxiety extinction in humans.
In Study 4, I prolonged the tVNS and, considering previous tVNS studies, I applied a cue conditioning paradigm in VR. Therefore, during acquisition a cue (CS+) presented in CTX+ predicted the US, but not another cue (CS-). Both cues were presented in a second context (CTX-) and never paired with the US. Afterward, participants received either tVNS or sham stimulation and underwent extinction learning. I found context-dependent cue conditioning only in valence ratings, which was indicated by lower valence for CS+ compared to CS- in CTX+, but no differential ratings in CTX-. Successful extinction was indicated by equal responses to CS+ and CS-. Interestingly, I found reinstatement of conditioned fear in a context-dependent manner, meaning startle response was potentiated for CS+ compared to CS- only in the anxiety context. Importantly, even the prolonged tVNS had no effect, neither on extinction nor on reinstatement of context-dependent cue conditioning. However, I found first evidence for accelerated physiological contextual extinction due to less differentiation between startles in CTX+ compared to CTX- in the tVNS than in the sham stimulated group.
In sum, this thesis first confirms the dual representation of a context in an elemental and a conjunctive manner. Second, though anxiety conditioning and context-dependent cue conditioning paradigms worked well, the translation of tVNS accelerated extinction from rats to humans needs to be further developed, especially the stimulation parameters. Nevertheless, tVNS remains a very promising approach of memory enhancement, which can be particularly auspicious in clinical settings.
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.
Recent advances in Natural Language Preprocessing (NLP) allow for a fully automatic extraction of character networks for an incoming text. These networks serve as a compact and easy to grasp representation of literary fiction. They offer an aggregated view of the text, which can be used during distant reading approaches for the analysis of literary hypotheses. In their core, the networks consist of nodes, which represent literary characters, and edges, which represent relations between characters. For an automatic extraction of such a network, the first step is the detection of the references of all fictional entities that are of importance for a text. References to the fictional entities appear in the form of names, noun phrases and pronouns and prior to this work, no components capable of automatic detection of character references were available. Existing tools are only capable of detecting proper nouns, a subset of all character references. When evaluated on the task of detecting proper nouns in the domain of literary fiction, they still underperform at an F1-score of just about 50%. This thesis uses techniques from the field of semi-supervised learning, such as Distant supervision and Generalized Expectations, and improves the results of an existing tool to about 82%, when evaluated on all three categories in literary fiction, but without the need for annotated data in the target domain. However, since this quality is still not sufficient, the decision to annotate DROC, a corpus comprising 90 fragments of German novels was made. This resulted in a new general purpose annotation environment titled as ATHEN, as well as annotated data that spans about 500.000 tokens in total. Using this data, the combination of supervised algorithms and a tailored rule based algorithm, which in combination are able to exploit both - local consistencies as well as global consistencies - yield an algorithm with an F1-score of about 93%. This component is referred to as the Kallimachos tagger.
A character network can not directly display references however, instead they need to be clustered so that all references that belong to a real world or fictional entity are grouped together. This process widely known as coreference resolution is a hard problem in the focus of research for more than half a century. This work experimented with adaptations of classical feature based machine learning, with a dedicated rule based algorithm and with modern techniques of Deep Learning, but no approach can surpass 55% B-Cubed F1, when evaluated on DROC. Due to this barrier, many researchers do not use a fully-fledged coreference resolution when they extract character networks, but only focus on a more forgiving subset- the names. For novels such as Alice's Adventures in Wonderland by Lewis Caroll, this would however only result in a network in which many important characters are missing. In order to integrate important characters into the network that are not named by the author, this work makes use of automatic detection of speaker and addressees for direct speech utterances (all entities involved in a dialog are considered to be of importance). This problem is by itself not an easy task, however the most successful system analysed in this thesis is able to correctly determine the speaker to about 85% of the utterances as well as about 65% of the addressees. This speaker information can not only help to identify the most dominant characters, but also serves as a way to model the relations between entities.
During the span of this work, components have been developed to model relations between characters using speaker attribution, using co-occurrences as well as by the usage of true interactions, for which yet again a dataset was annotated using ATHEN. Furthermore, since relations between characters are usually typed, a component for the extraction of a typed relation was developed. Similar to the experiments for the character reference detection, a combination of a rule based and a Maximum Entropy classifier yielded the best overall results, with the extraction of family relations showing a score of about 80% and the quality of love relations with a score of about 50%. For family relations, a kernel for a Support Vector Machine was developed that even exceeded the scores of the combined approach but is behind on the other labels.
In addition, this work presents new ways to evaluate automatically extracted networks without the need of domain experts, instead it relies on the usage of expert summaries. It also refrains from the uses of social network analysis for the evaluation, but instead presents ranked evaluations using Precision@k and the Spearman Rank correlation coefficient for the evaluation of the nodes and edges of the network. An analysis using these metrics showed, that the central characters of a novel are contained with high probability but the quality drops rather fast if more than five entities are analyzed. The quality of the edges is mainly dominated by the quality of the coreference resolution and the correlation coefficient between gold edges and system edges therefore varies between 30 and 60%.
All developed components are aggregated alongside a large set of other preprocessing modules in the Kallimachos pipeline and can be reused without any restrictions.
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.
This Thesis explores hybrid structures on the basis of quantum spin Hall insulators, and in particular the interplay of their edge states and superconducting and magnetic order. Quantum spin Hall insulators are one example of topological condensed matter systems, where the topology of the bulk bands is the key for the understanding of their physical properties. A remarkable consequence is the appearance of states at the boundary of the system, a phenomenon coined bulk-boundary correspondence. In the case of the two-dimensional quantum spin Hall insulator, this is manifested by so-called helical edge states of counter-propagating electrons with opposite spins. They hold great promise, \emph{e.g.}, for applications in spintronics -- a paradigm for the transmission and manipulation of information based on spin instead of charge -- and as a basis for quantum computers. The beginning of the Thesis consists of an introduction to one-dimensional topological superconductors, which illustrates basic concepts and ideas. In particular, this includes the topological distinction of phases and the accompanying appearance of Majorana modes at their ends. Owing to their topological origin, Majorana modes potentially are essential building-blocks for topological quantum computation, since they can be exploited for protected operations on quantum bits. The helical edge states of quantum spin Hall insulators in conjunction with $s$-wave superconductivity and magnetism are a suitable candidate for the realization of a one-dimensional topological superconductor. Consequently, this Thesis investigates the conditions in which Majorana modes can appear. Typically, this happens between regions subjected to either only superconductivity, or to both superconductivity and magnetism. If more than one superconductor is present, the phase difference is of paramount importance, and can even be used to manipulate and move Majorana modes. Furthermore, the Thesis addresses the effects of the helical edge states on the anomalous correlation functions characterizing proximity-induced superconductivity. It is found that helicity and magnetism profoundly enrich their physical structure and lead to unconventional, exotic pairing amplitudes. Strikingly, the nonlocal correlation functions can be connected to the Majorana bound states within the system. Finally, a possible thermoelectric device on the basis of hybrid systems at the quantum spin Hall edge is discussed. It utilizes the peculiar properties of the proximity-induced superconductivity in order to create spin-polarized Cooper pairs from a temperature bias. Cooper pairs with finite net spin are the cornerstone of superconducting spintronics and offer tremendous potential for efficient information technologies.
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.
Platelet activation and aggregation at sites of vascular injury involves massive cytoskeletal re-organization, which is required for proper platelet function. Moreover, the cytoskeleton plays central roles in megakaryo- and thrombopoiesis. Thus, cytoskeletal protein aberrations can be the underlying reason for many pathological phenotypes. Although intensive research is carried out to identify the key players involved in cytoskeletal reorganization, the signaling cascades orchestrating these complex processes are still poorly understood. This thesis investigates the role of three actin-binding proteins, Coactosin-like (Cotl) 1, Profilin (Pfn) 1 and Thymosin (T) β4, in platelet formation and function using genetically modified mice.
ADF-H-containing proteins such as Twinfilin or Cofilin are well characterized as regulators of thrombopoesis and cytoskeletal reorganization. Although Cotl1 belongs to the ADF-H protein family, lack of Cotl1 did not affect platelet count or cytoskeletal dynamics. However, Cotl1-deficiency resulted in significant protection from arterial thrombus formation and ischemic stroke in vivo. Defective GPIb-vWF interactions and altered second wave mediator release present potential reasons for the beneficial effect of Cotl1-deficiency. These results reveal an unexpected function of Cotl1 as a regulator of thrombosis and hemostasis, establishing it as a potential target for a safe therapeutic therapy to prevent arterial thrombosis or ischemic stroke.
Recent studies showed that the organization of the circumferential actin cytoskeleton modulates calpain-mediated αIIbβ3 integrin closure, thereby also controlling αIIbβ3 integrin localization. The second part of this thesis identified the actin-sequestering protein Pfn1 as a central regulator of platelet integrin function as Pfn1-deficient platelets displayed almost abolished αIIbβ3 integrin signaling. This translated into a profound protection from arterial thrombus formation and prolonged tail bleeding times in vivo which was caused by enhanced calpain-dependent integrin closure. These findings further emphasize the importance of a functional actin cytoskeleton for intact platelet function in vitro and in vivo.
Tβ4 is a moonlighting protein, acting as one of the major actin-sequestering proteins in cells of higher eukaryotes and exerting various paracrine functions including anti-inflammatory, immunomodulatory and pro-angiogenic effects. Although excessively studied, its role for cytoskeletal dynamics, the distinction between endo- and exogenous protein function and its uptake and release mechanisms are still poorly understood. Constitutive Tβ4-deficiency resulted in thrombocytopenia accompanied by a largely diminished G-actin pool in platelets and divergent effects on platelet reactivity. Pre-incubation of platelets with recombinant Tβ4 will help to understand the function of endo- and exogenous protein, which is under current investigation.
Maintenance of tumor vasculature integrity is indispensable for tumor growth and thus affects tumor progression. Previous studies have identified platelets as major regulators of tumor vascular integrity, as their depletion selectively renders tumor vessels highly permeable, causing massive intratumoral hemorrhage. While these results establish platelets as potential targets for anti-tumor therapy, depletion is not a treatment option due to the essential role of platelets for hemostasis. This thesis demonstrates for the first time that functional inhibition of glycoprotein (GP) VI on the platelet surface rapidly induces tumor hemorrhage and diminishes tumor growth similar to complete platelet depletion but without inducing systemic bleeding complications. Both, the intratumoral bleeding and tumor growth arrest could be reverted by depletion of Ly6G+ cells confirming them to be responsible for the induction of bleeding and necrosis within the tumor. In addition, GPVI inhibition increased intra-tumoral accumulation of co-administered chemotherapeutic agents, thereby resulting in a profound anti-tumor effect. In summary, this thesis manifests platelet GPVI as a key regulator of vascular integrity specifically in growing tumors, serving as a potential basis for the development of anti-tumor strategies.
In the second part of this thesis, light is shed on the modulating role of bridging integrator 2 (BIN2) in platelet Ca2+ signaling. Stromal interaction molecule 1 (STIM1) mediated store-operated calcium entry (SOCE) is the major route of Ca2+ influx in platelets, triggered by inositol trisphosphate receptor (IP3R)-dependent Ca2+ store release. In this thesis, the BAR domain superfamily member BIN2 was identified as the first Ca2+ signaling modulator, interacting with both, STIM1 and IP3R in platelets. Deletion of BIN2 resulted in reduced Ca2+ store release and Ca2+ influx in response to all tested platelet agonists. These defects were a consequence of impaired IP3R function in combination with defective STIM1-mediated SOC channel activation, while Ca2+ store content and agonist-induced IP3 production were unaltered. These results establish BIN2 as a central regulator of platelet Ca2+ signaling.
The third part of this thesis focuses on the effect of the soluble neuronal guidance protein Sema7A on platelet function. Rosenberger et al. discovered that Sema7A cleavage from red blood cells increases the formation of platelet-neutrophil complexes, thereby reinforcing thrombo-inflammation in myocardial ischemia-reperfusion injury (MIRI). This thesis establishes soluble Sema7A as a stimulator of platelet thrombus formation via its interaction with platelet GPIbα, thereby reinforcing PNC formation. Thus, interfering with the GPIb-Sema7A interaction during MIRI represents a potential strategy to reduce cardiac damage and improve clinical outcome following MI.
Chapter 1
N-Heterocyclic olefins (NHOs), relatives of N-heterocyclic carbenes (NHCs), exhibit high nucleophilicity and soft Lewis basic character. To investigate their π-electron donating ability, NHOs were attached to triarylborane π-acceptors (A) giving donor(D)-π-A compounds 1-3. In addition, an enamine π-donor analogue (4) was synthesized for comparison.
UV-visible absorption studies show a larger red shift for the NHO-containing boranes than for the enamine analogue, a relative of a CAAC. The red shifted absorption of NHO-containing boranes indicate smaller energy gaps of NHO-containing boranes than CAAC-containing boranes. Solvent-dependent emission studies indicate that 1-4 have moderate intramolecular charge transfer (ICT) behavior.
Electrochemical investigations reveal that the NHO-containing boranes have extremely low reversible oxidation potentials (e.g., for 3, E1/2ox = –0.40 V vs. Fc/Fc+ in THF) which indicate the electron rich property of NHOs.
Furthermore, TD-DFT calculations were carried out on these four D-π-A boranes. The results show that the LUMOs of 1-4 only show a small difference, but the HOMOs of 1-3 are much more destabilized than that of the enamine-containing 4, which is in agreement with the electrochemical investigations and confirms the stronger donating ability of NHOs.
Chapter 2
Since the beginning of this century, the chemistry of (hetero)arene-fused boroles has attracted increasing interest. (Hetero)arene-fused boroles exhibit strong Lewis acidity, distinct fluorescence properties, strong electron accepting abilities, etc. However, their chemistry been only very briefly reviewed either as part of reviews on “free” boroles or on boron-doped polycyclic aromatic hydrocarbons (PAHs). In this chapter, we addressed the chemistry of (hetero)arene-fused boroles from fundamentals to their widely varying applications. It includes:
1) Synthetic methodology Both historical and recently developed strategies for the synthesis of fused boroles.
2) Stabilities A comparison of different kinetic protection strategies.
3) 9-Borafluorenes with a fluorinated backbone Application as Lewis acids, forming ion pairs with Cp2Zr(CH3)2 and applied as activators for polymerization, activators of H2, and other related applications.
4) Donor-acceptor 9-borafluorenes Applications as F– “turn on” sensors, potential applications as electron accepting units for organic (opto)electronics, bipolar transporting materials, TADF materials, and different functionalization strategies.
5) Heteroarene-fused boroles Enhanced antiaromaticity, unique coordination mode and their interesting properties.
6) Intramolecular dative bonding in 9-borafluorenes Bond-cleavage-induced intramolecular charge transfer (BICT), BICT-induced large Stoke shifts and dual emissions, application as a ratiometric sensor.
7) 9-Borafluorene-based main chain polymers Application in polymer chemistry and their distinct properties, e.g., as a sensor for gaseous NH3.
8) Electrochemistry A comparison of electron-accepting ability of different functionalized fused boroles through electrochemical studies.
9) Chemical reduction of fused boroles Stable radical anions and dianions of fused boroles and their properties.
10) Three-coordinate borafluorenium cations Cationic 9-borafluorenes and their interesting properties, e.g., in THF, reversible thermal colour switching properties.
Finally, a conclusion and outlook regarding the chemistry, properties and applications, and suggestions for areas which require further study was provided.
Chapter 3
Interested in fusing electron-poor arene onto boroles, two electron-poor phenylpyridyl-fused boroles, [TipPBB1]4 and TipPBB2 were prepared. [TipPBB1]4 is a white solid adopting a unique coordination mode, which forming a tetramer with a cavity in both the solid state and solution (1H DOSY). The boron center of TipPBB2 is 4-coordinate in the solid state, evidenced by a solid-state 11B{1H} RSHE/MAS NMR study, but the system dissociates in solution, leading to 3-coordinate borole species.
[TipPBB1]4 exhibits two reduction processes which are attributed to the phenylpyridyl cores. TipPBB2 also exhibits two reduction processes with the first half-reduction potential of E1/2red = –1.94 V. The electron accepting ability of TipPBB2 is largely enhanced and comparable to that of FMesBf. This enhanced electron accepting ability is attributed to the electron withdrawing property of the pyridyl group.
TipPBB2 exhibits concentration- and temperature-dependent dual fluorescence in solution. With the temperature is lowered, the emission intensity decreases (Figure 6.4, left). We suggested that the dual fluorescence is caused by an equilibrium between 3-coordinate TipPBB2 and a weak intermolecular adduct of TipPBB2 via a B–N bond. This hypothesis was further supported by lifetime measurements at different concentrations, low temperature excitation spectra low temperature 1H NMR spectra and lifetime measurements upon addition of DMAP to a solution of TipPBB2 to simulate the 4-coordiante TipPBB2 species. Interestingly, the ratio of the relative percentages of the two lifetimes shows a linear relationship with temperature; thus, TipPBB2 could serve as a fluorescent thermometer.
Furthermore, theoretical studies were carried out on TipPBB2, and two models, ((BMe3)TipPBB1(NMe3) and (BMe3)TipPBB2(NMe3)), which utilize a BMe3 group as the Lewis acid coordinated to pyridine and an NMe3 group as the Lewis base coordinated to the boron center of the borole, were used to simulate the [TipPBB1]4 and intermolecular 4-coordinate TipPBB2, respectively. Theoretical studies indicate that the HOMO of TipPBB2 is located at the Tip group, which is in contrast to its borafluorene derivatives for which the HOMOs are located on the borafluorene cores.
Chapter 4
Two derivatives of phenylpyridyl-fused boroles were prepared via functionalization of the pyridyl groups in two different directions, namely an electron-rich dihydropyridine moiety (compound 10) and an electron-deficient N-methylpyridinium cation (compound 11). Both compounds were fully characterized. The 11B NMR signal of compound 10 was observed at 58.8 ppm in CDCl3, which suggests strong conjugation between the boron atom and dihydropyridine moiety. Compound 11 shows a reversible coordination to THF which was confirmed by NMR studies. Compared to other 2,4,6-triisopropylphenyl protected 9-borafluorenes which only coordinate to CH3CN or DMF, the coordination of the weaker and bulkier THF to compound 11 indicates an extremely electron-deficient boron center in compound 11.
The electron-rich property of the dihydropyridine moiety of compound 10 was confirmed by its oxidation potential (Epc = +0.37 V). Due to the strong conjugation of the dihydropyridine moiety with the boron atom, the reduction potential of compound 10 shifts cathodically and is more negative than –2.5 V. Compound 11 exhibits three reduction processes with the first reversible reduction potential at Ered1/2 = –1.23 V, which is significantly anodically shifted compared to that of its precursor (TipPBB2) or its framework 1-methyl-2-phenylpyridin-1-ium triflate (12). This significantly anodically shifted reduction potential confirms an extremely electron-deficient property of compound 11.
Photophysical studies indicate that the lowest energy transition of compound 10 is more likely a locally-excited (LE) transition and compound 11 exhibits a polarized ground state.
Furthermore, we performed theoretical studies for both compounds. The electron cloud distribution of the HOMO of compound 10 supports the strong conjugation between the boron atom and the dihydropyridine moiety in the ground state. An extremely low LUMO energy was determined by theoretical studies which confirmed the extremely electron-deficient property of compound 11.
Chapter 5
Inspired by the enhancement of electron accepting ability with increasing numbers of electron withdrawing groups at boron, we tried to study the properties of a bis(pyridyl)arylboranes. In our attempt to synthesize a bis(pyridyl)arylborane, we obtained a bis(2-pyridyl)methoxyborate Li+ complex which is as a dimer both in solution and the solid state.
In the solid state, compound [16]2 is a dimer containing two bis(2-pyridyl)methoxyborate which are linked by two lithium cations. Each lithium cation coordinates to one methoxy group and two pyridyl groups, one from each of the two bis(2-pyridyl)methoxyborate anions. The parameters of [16]2 were compared with other bis(2-pyridyl)methoxyborate stabilized Pt(IV) complex, bis(2-pyridyl)hydroxylborate stabilized Ru(II) complex and the dimer of EtAl(OMe)(2-pyridyl)2Li.
To confirm the coordination mode in solution, 1H DOSY spectroscopy was carried out in CD2Cl2. The van der Waals radius obtained by 1H DOSY nicely matches with the result from the solid state and thus proves the dimer of 16 is persistent in solution.
Finally, different Lewis acids (e.g., TMSCl, BF3•Et2O, AlCl3, HCl) were used to attempt to detach the methoxy group of [16]2. However, we observed either decomposition or selective cleavage of the Tip group, or no reaction at all, rather than cleavage of the methoxy group from boron.
Structure-property relationships in poly(2-oxazoline)/poly(2-oxazine) based drug formulations
(2020)
According to estimates, more than 40% of all new chemical entities developed in pharmaceutical industry are practically insoluble in water. Naturally, the demand for excipients which increase the water solubility and thus, the bioavailability of such hydrophobic drugs is enormous. Poly(2-oxazoline)s (POx) are currently intensively discussed as highly versatile class of biomaterials. Although selected POx based micellar drug formulations exhibit extraordinarily high drug loadings > 50 wt.% enabling high anti-tumor efficacies in vivo, the formulation of other hydrophobic compounds has failed. This casts doubt on the general understanding in which a hydrophobic active pharmaceutical ingredient is dissolved rather unspecifically in the hydrophobic core of the micelles following the fundamental concept of “like dissolves like”. Therefore, a closer look at the interactions between all components within a formulation becomes increasingly important. To do so, a large vehicle platform was synthesized, loaded with various hydrophobic drugs of different structure, and the formulations subsequently characterized with conventional and less conventional techniques. The obtained in-depth insights helped to develop a more thorough understanding about the interaction of polymer and incorporated API finally revealing morphologies deviating from a classical core/shell structure. During these studies, the scarcely investigated polymer class of poly(2-oxazine)s (POzi) was found as promising drug-delivery vehicle for hydrophobic drugs. Apart from this fundamental research, the anti-tumor efficacy of the two APIs curcumin and atorvastatin has been studied in more detail. To increase the scope of POx and POzi based formulations designed for intravenous administration, a curcumin loaded hydrogel was developed as injectable drug-depot.
In this study, we examined the regional grey matter density in 35 spider phobic patients and 33 age, gender and education matched healthy controls. We used a method called Voxel-Based Morphometry, which allowed us to conduct a voxel- by-voxel analysis of the entire brain. We also tried to determine if there was any relationship between the severity of fear (expressed in BAT and SPQ score) and grey matter density. Based on previous findings, we expected to find structural changes in the following brain regions:
- prefrontal cortex;
- orbitofrontal cortex;
- anterior cingulate cortex;
- insula;
- visual and associative cortices.
Between-group comparison of spider phobic patients and healthy controls yielded no significant results. Additionally, and as expected, we did not find a between- group difference in TIV. Surprisingly, however, we found several brain regions whose GMD was significantly correlated with severity of spider phobia.
The score that correlated with several regions GMD and yielded the largest cluster was the SPQ. SPQ was positively correlated with dorsal anterior cingulate, right insula and left inferior parietal lobule. Final distance in centimetres was correlated with left superior frontal gyrus and right paracentral lobule densities. All correlations were observed at a cluster level and no significant results at peak level were found. Interestingly, out of all BAT fear values, only BAT when the spider was taken away had a positive correlation with GMD (vermis). There were no indications of reduced GMD in spider phobic patients.
Overall, our regions of significance were in line of those of other structural and functional neuroimaging studies in the field of specific phobia. As expected, we found GMD changes in the prefrontal cortex, ACC, insula and the associative
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cortices. The functions of these regions such as processing of disgust, attention, autonomous responses, consolidation of memory and regulation of affect support the possible involvement of these structures in SP.
We did, however, also yield some unexpected results (vermis, right paracentral lobule). Interestingly and in contrast to other studies, our results were only limited to the phobic group itself- we found no regions of significance in the SP-HC between-group analysis.
In the future, more VBM studies with larger size of spider phobic subjects should be conducted, further investigating both the between-group differences and the correlation between spider phobia severity and GMD. Additionally, studies should investigate the relationship between structural changes and activation patterns observed in fMRI, find out whether brain changes precede the clinical symptoms or vice versa and see, if structural changes normalize in response to CBT the same way functional changes do.
Structural and functional elucidation of the Type VIIb secretion system from Staphylococcus aureus
(2020)
The Type VII secretion system (T7SS) is linked to virulence and long-term pathogenesis in a broad range of Gram-positive bacteria, including the human commensal and pathogen Staphylococcus aureus. The Type VIIb secretion system (T7SSb) is responsible for the export of small toxic proteins, which induce antibacterial immune responses and mediate bacterial persistence in the host. In addition, it is also involved in bacterial competition. The T7SSb requires several proteins to build up the secretion machinery. This work focuses on the structural and functional investigation of the motor ATPase EssC and the putative pore forming, multi-pass membrane component EsaA. Both proteins are indispensable for substrate secretion.
EssC belongs to the FtsK/SpoIIIE ATPase family and is conserved among the T7SSs. It contains three C-terminal, cytosolic ATPase domains, designated as EssC- D1, -D2 and -D3, whereby EssC-D3 is the most distal one. In this thesis, I am presenting the crystal structure of the EssC-D3 at 1.7 Å resolution. As the deletion of EssC-D3 abrogates substrate export, I have demonstrated that this domain comprises a hydrophobic, surface-exposed pocket, which is required for substrate secretion. More specifically, I have identified two amino acids involved in the secretion process. In addition, my results indicate that not only EssC-D3 is important for substrate interaction but also EssC-D2 and/or EssC-D1. Unlike in the related Yuk T7SSb of Bacillus subtilis, the ATPase activity of D3 domain contributes to substrate secretion. Mutation of the modified Walker B motif in EssC-D3 diminishes substrate secretion completely.
The membrane protein EsaA encompasses an extracellular segment spanning through the cell wall of S. aureus. I was able to reveal that this part folds into a stable domain, which was crystallized and diffracted up to 4 Å. The first attempts to dissolve the structure failed due to a lack of homologues structures. Therefore, crystals for single-wavelength anomalous dispersion, containing selenomethionyl-substitutes, were produced and the structure solution is still in progress. Preliminary experiments addressing the function of the extracellular domain indicate an important role in substrate secretion and bacterial competition.
Gene expression and transfer of the genetic information to the next generation forms the basis of cellular life. These processes crucially rely on DNA, thus the preservation, transcription and translation of DNA is of fundamental importance for any living being. The general transcription factor TFIIH is a ten subunit protein complex, which consists of two subcomplexes: XPB, p62, p52, p44, p34, and p8 constitute the TFIIH core, CDK7, CyclinH, and MAT1 constitute the CAK. These two subcomplexes are connected via XPD. TFIIH is a crucial factor involved in both, DNA repair and transcription. The central role of TFIIH is underlined by three severe disorders linked to failure of TFIIH in these processes: xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy. Only limited structural and functional data of TFIIH are available so far. Here, the model organism Chaetomium thermophilum was utilized with the aim to structurally and functionally characterize TFIIH. By combining the expression and purification of single TFIIH subunits with the co-expression and co-purification of dual complexes, a unique and powerful modular system of the TFIIH core subunits could be established, encompassing all proteins in high quality and fully functional. This system permits the step-wise assembly of TFIIH core, thereby making it possible to assess the influence of the intricate interaction network within TFIIH core on the overall enzymatic activities of TFIIH, which has not been possible so far. Utilizing the single subunits and dual complexes, a detailed interaction network of TFIIH core was established, revealing the crucial role of the p34 subunit as a central scaffold of TFIIH by linking the two proteins p44 and p52. Our studies also suggest that p62 constitutes the central interface of TFIIH to the environment rather than acting as a scaffold. TFIIH core complexes were assembled and investigated via electron microscopy. Preliminary data indicate that TFIIH adopts different conformational states, which are important to fulfill its functions in transcription and DNA repair. Additionally, a shortened construct of p62 was used to develop an easy-to-use, low cost strategy to overcome the crystallographic phase problem via cesium derivatization.
The work in this thesis contains three main topics. These are the passage from discrete to continuous models by means of $\Gamma$-convergence, random as well as periodic homogenization and fracture enabled by non-convex Lennard-Jones type interaction potentials. Each of them is discussed in the following.
We consider a discrete model given by a one-dimensional chain of particles with randomly distributed interaction potentials. Our interest lies in the continuum limit, which yields the effective behaviour of the system. This limit is achieved as the number of atoms tends to infinity, which corresponds to a vanishing distance between the particles. The starting point of our analysis is an energy functional in a discrete system; its continuum limit is obtained by variational $\Gamma$-convergence.
The $\Gamma$-convergence methods are combined with a homogenization process in the framework of ergodic theory, which allows to focus on heterogeneous systems. On the one hand, composite materials or materials with impurities are modelled by a stochastic or periodic distribution of particles or interaction potentials. On the other hand, systems of one species of particles can be considered as random in cases when the orientation of particles matters. Nanomaterials, like chains of atoms, molecules or polymers, are an application of the heterogeneous chains in experimental sciences.
A special interest is in fracture in such heterogeneous systems. We consider interaction potentials of Lennard-Jones type. The non-standard growth conditions and the convex-concave structure of the Lennard-Jones type interactions yield mathematical difficulties, but allow for fracture. The interaction potentials are long-range in the sense that their modulus decays slower than exponential. Further, we allow for interactions beyond nearest neighbours, which is also referred to as long-range.
The main mathematical issue is to bring together the Lennard-Jones type interactions with ergodic theorems in the limiting process as the number of particles tends to infinity. The blow up at zero of the potentials prevents from using standard extensions of the Akcoglu-Krengel subadditive ergodic theorem. We overcome this difficulty by an approximation of the interaction potentials which shows suitable Lipschitz and Hölder regularity. Beyond that, allowing for continuous probability distributions instead of only finitely many different potentials leads to a further challenge.
The limiting integral functional of the energy by means of $\Gamma$-convergence involves a homogenized energy density and allows for fracture, but without a fracture contribution in the energy. In order to refine this result, we rescale our model and consider its $\Gamma$-limit, which is of Griffith's type consisting of an elastic part and a jump contribution.
In a further approach we study fracture at the level of the discrete energies. With an appropriate definition of fracture in the discrete setting, we define a fracture threshold separating the region of elasticity from that of fracture and consider the pointwise convergence of this threshold. This limit turns out to coincide with the one obtained in the variational $\Gamma$-convergence approach.
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.
Prediction intervals are needed in many industrial applications. Frequently in mass production, small subgroups of unknown size with a lifetime behavior differing from the remainder of the population exist. A risk assessment for such a subgroup consists of two steps: i) the estimation of the subgroup size, and ii) the estimation of the lifetime behavior of this subgroup. This thesis covers both steps. An efficient practical method to estimate the size of a subgroup is presented and benchmarked against other methods. A prediction interval procedure which includes prior information in form of a Beta distribution is provided. This scheme is applied to the prediction of binomial and negative binomial counts. The effect of the population size on the prediction of the future number of failures is considered for a Weibull lifetime distribution, whose parameters are estimated from censored field data. Methods to obtain a prediction interval for the future number of failures with unknown sample size are presented. In many applications, failures are reported with a delay. The effects of such a reporting delay on the coverage properties of prediction intervals for the future number of failures are studied. The total failure probability of the two steps can be decomposed as a product probability. One-sided confidence intervals for such a product probability are presented.
The stability of Trp in pure solutions and in parenteral AA formulations was evaluated with regard to typically used manufacturing processes, storage conditions and primary packaging. Therefore, thorough stability studies on Trp solutions were conducted beforehand. The applied stressing method, i.e. steam sterilization by autoclave, are chemically seen relatively mild but showed to be efficient to induce Trp degradation in the presence of oxygen. Subsequent identification, separation and characterization were challenging due to similar substance properties, numerous stereoisomers and pairs of diastereomers found amongst them. However, the identified o-aminoacetophenone compounds, Kyn and NFK, are associated with photo reactivity and have photo-oxidizing properties. Thus, best possible protection from UV-light, together with strict oxygen expulsion, are the most important criteria to impede Trp degradation after autoclaving.
The identification of Trp degradation products was assisted by the compilation of a substance library, which included manifold reported and chemically plausible Trp degradation substances. The substances were classified for priority and their early or late-stage occurrence. The large number of possible substances and stereoisomers was narrowed down with the information retrieved from LC-UV/MS experiments. However, final identification was achieved by the synthesis of proposed substances as references. The following eight substances were characterized as Trp degradation substances: Kyn, NFK and three pairs of diastereomers R,R/R,S DiOia, R,R/R,S Oia and cis/trans PIC. Fig. 33 shows the proposed degradation pathway and demonstrates the close chemical relationship, which may be an explanation for the conversion of some substances into each other during the storage period. The proposed pathway brings together the results of different Trp stability and stressing studies, respectively [89, 94, 97, 98, 103, 133]. To our knowledge, the simultaneous formation of the identified degradation substances has not been reported before and especially not under the stressing conditions applied.
The application of a traditional RP-HPLC method was compared to two developed IP-HPLC methods and a RP-HPLC methods using a modified perfluorinated column. Orthogonal analyses methods and especially the combination of UV and MS detection are necessary in order to indicate potentially undetected degradation substances. Main evaluation criteria were the separation performance, analyses time, reproducibility and feasibility. The best results upon assessment of all Trp degradation products, in both; pure Trp solutions and pharmaceutical formulations, were obtained by a traditional RP-HPLC. The optimized method was validated according to ICH guidelines Q2(R1) and meets the criteria of a stability-indicating HPLC-UV method. The validated method has a sufficient separation performance with an adequate selectivity indicating the Trp degradation substances next to each other and next to other AAs in finished pharmaceutical formulations.
The detailed knowledge of Trp degradation and the method presented may be transferred practically to the pharmaceutical industry processing Trp-containing products. In general, the findings might contribute to the quality management of such pharmaceutical products during
manufacturing and storage. Additionally, the study results provide basic information for the establishment of an impurity consideration following the ICH guidelines Q3B (R2) (impurities in new drug products) for products containing Trp. However, further development of the method applying more sophisticated detectors or more potent HPLC techniques like e.g. UHPLC and the implication of more sensitive (MS) detectors like ToF-MS would be advantageous with regard to economic and practical aspects.
Nanoelectronics is an essential technology for down-scaling beyond the limit of silicon-based electronics. Single-Wall Carbon Nanotubes (SWNT) are semiconducting components that exhibit a large variety of properties that make them usable for sensing, telecommunication, or computational tasks. Due to their high surface to volume ratio, carbon nanotubes are strongly affected by molecular adsorptions, and almost all properties depend on surface adsorption. SWNT with smaller diameters (0.7-0.9nm) show a stronger sensitivity to surface effects. An optimized synthesis route was developed to produce these nanotubes directly. They were produced with a clean surface, high quality, and large lengths of 2 μ m. The results complement previous studies on larger diameters (0.9-1.4nm). They allow performing statistically significant assumptions for a perfect nanotube, which is selected from a subset of nanotubes with good emission intensity, and high mechanical durability. The adsorption of molecules on the surface of carbon nanotubes influences the motion and binding strength of chargeseparated states in this system. To gain insight into the adsorption processes on the surface with a minimum of concurrent overlapping effects, a microscopic setup, and a measurement technique were developed. The system was estimated to exhibit excellent properties like long exciton diffusion lengths (>350nm), and big exciton sizes (8.5(5)nm), which was substantiated by a simulation. We studied the adsorption processes at the surface of Single-Wall Carbon Nanotubes for molecules in the gas phase, solvent molecules, and surfactant molecules. The experiments were all carried out on suspended individualized carbon nanotubes on a silicon wafer substrate. The experiments in the gas-phase showed that the excitonic emission energy and intensity experiences a rapid blue shift during observation. This shift was associated with the spontaneous desorption of large clusters of gaseous molecules caused by laser heat up. The measurement of this desorption was essential for creating a reference to an initially clean surface and allows us to perform a comparison with previous measurements on this topic. Furthermore, the adsorption of hydrogen on the nanotube surface at high temperatures was investigated. It was found that a new emission mode arises slightly red-shifted to the excitonic emission in these systems. The new signal is almost equally strong as the main excitonic peak and was associated with the brightening of dark excitons at sp3-defects through a K-phonon assisted pathway. The finding is useful for the direct synthesis of spintronic devices as these systems are known to act as single-photon emitters. The suspended nanotubes were further studied to estimate the effect of solvent adsorption on the excitonic states during nanotube dispersion for each nanotube individually. A significant quantum yield loss is observable for hexane and acetonitrile, while the emission intensity was found to be the strongest in toluene. The reference to a clean surface allowed us to estimate the exact influence of the dielectric environment of adsorbing solvents on the excitonic emission energy. Solvent adsorption was found to lead to an energy shift that is almost twice as high as suggested in previous studies. The amount of this energy shift, however, was comparably similar for all solvents, which suggests that the influence of the distinct dielectric constant in the outer environment less significantly influences the energy shift than previously thought. An interesting phenomenon was found when using acetonitrile as a solvent, which leads to greatly enhanced emission properties. The emission is more than twice as high as in the same air-suspended nanotubes, which suggests a process that depends on the laser intensity. In this study, it was reasonably explained how an energy down-conversion is possible through the coupling of the excitonic states with solvent vibrations. The strength of this coupling, however, also suggests adsorptions to the inside of the tubular nanotube structure leading to a coupled vibration of linear acetonitrile molecules that are adsorbed to the inner surface. The findings are important for the field of nanofluidics and provide an excellent system for efficient energy down-conversion in the transmission window of biological tissue. Having separated the pure effect of solvent adsorption allowed us to study the undisturbed molecular adsorption of polymers in these systems. The addition of polyfluorene polymer leads to a slow but stepwise intensity increase. The intensity increase is overlapping with a concurrent process that leads to an intensity decrease. Unfortunately, observing the stepwise process has a low spacial resolution of only 100-250nm, which is in the range of the exciton diffusion length in these systems and hinders detailed analysis. The two competing and overlapping processes processes are considered to originate from slow π-stacking and fast side-chain binding. Insights into this process are essential for selecting suitably formed polymers. However, the findings also emphasize the importance of solvent selection during nanotube dispersion since solvent effects were proven to be far more critical on the quantum yield in these systems. These measurements can shed light on the ongoing debate on polymers adsorption during nanotube individualization and allow us to direct the discussion more towards the selection of suitable solvents. This work provides fundamental insights into the adsorption of various molecules on the surface of individually observed suspended Single-Wall Carbon Nanotubes. It allows observing the adsorption of individual molecules below the optical limit in the solid, liquid, and gas phases. Nanotubes are able to act as sensing material for detecting changes in their direct surrounding. These fundamental findings are also crucial for increasing the quantum yield of solvent-dispersed nanotubes. They can provide better light-harvesting systems for microscopy in biological tissue and set the base for a more efficient telecommunication infrastructure with nano-scale spintronics devices and lasing components. The newly discovered solvent alignment in the nanotube surrounding can potentially also be used for supercapacitors that are needed for caching the calculation results in computational devices that use polymer wrapped nanotubes as transistors. Although fundamental, these studies develop a strategy to enlighten this room that is barely only visible at the bottom of the nano-scale.
This cumulative dissertation is organized as follows:
After the introduction, the second chapter, based on “Asymptotic independence of bivariate order statistics” (2017) by Falk and Wisheckel, is an investigation of the asymptotic dependence behavior of the components of bivariate order statistics. We find that the two components of the order statistics become asymptotically independent for certain combinations of (sequences of) indices that are selected, and it turns out that no further assumptions on the dependence of the two components in the underlying sample are necessary. To establish this, an explicit representation of the conditional distribution of bivariate order statistics is derived.
Chapter 3 is from “Conditional tail independence in archimedean copula models” (2019) by Falk, Padoan and Wisheckel and deals with the conditional distribution of an Archimedean copula, conditioned on one of its components. We show that its tails are independent under minor conditions on the generator function, even if the unconditional tails were dependent. The theoretical findings are underlined by a simulation study and can be generalized to Archimax copulas.
“Generalized pareto copulas: A key to multivariate extremes” (2019) by Falk, Padoan and Wisheckel lead to Chapter 4 where we introduce a nonparametric approach to estimate the probability that a random vector exceeds a fixed threshold if it follows a Generalized Pareto copula. To this end, some theory underlying the concept of Generalized Pareto distributions is presented first, the estimation procedure is tested using a simulation and finally applied to a dataset of air pollution parameters in Milan, Italy, from 2002 until 2017.
The fifth chapter collects some additional results on derivatives of D-norms, in particular a condition for the existence of directional derivatives, and multivariate spacings, specifically an explicit formula for the second-to-last bivariate spacing.
Traditional fashion retailers are increasingly hard-pressed to keep up with their digital competitors. In this context, the re-invention of brick-and-mortar stores as smart retail environments is being touted as a crucial step towards regaining a competitive edge. This thesis describes a design-oriented research project that deals with automated product tracking on the sales floor and presents three smart fashion store applications that are tied to such localization information: (i) an electronic article surveillance (EAS) system that distinguishes between theft and non-theft events, (ii) an automated checkout system that detects customers’ purchases when they are leaving the store and associates them with individual shopping baskets to automatically initiate payment processes, and (iii) a smart fitting room that detects the items customers bring into individual cabins and identifies the items they are currently most interested in to offer additional customer services (e.g., product recommendations or omnichannel services). The implementation of such cyberphysical systems in established retail environments is challenging, as architectural constraints, well-established customer processes, and customer expectations regarding privacy and convenience pose challenges to system design. To overcome these challenges, this thesis leverages Radio Frequency Identification (RFID) technology and machine learning techniques to address the different detection tasks. To optimally configure the systems and draw robust conclusions regarding their economic value contribution, beyond technological performance criteria, this thesis furthermore introduces a service operations model that allows mapping the systems’ technical detection characteristics to business relevant metrics such as service quality and profitability. This analytical model reveals that the same system component for the detection of object transitions is well suited for the EAS application but does not have the necessary high detection accuracy to be used as a component of an automated checkout system.
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.
The aim of the thesis was to develop water soluble poly(2-oxazoline) (POx) copolymers with new side group functionalities, which can be used for the formation of hydrogels in biomedical applications and for the development of peptide-polymer conjugates.
First, random copolymers of the monomer MeOx or EtOx with ButEnOx and EtOx with DecEnOx were synthesized and characterized. The vinyl functionality brought into the copolymer by the monomers ButEnOx and DecEnOx would later serve for post-polymerization functionalization. The synthesized copolymers were further functionalized with thiols via post-polymerization functionalization using a newly developed synthesis protocol or with a protected catechol molecule for hydrogel formation. For the formation of peptide-polymer conjugates, a cyclic thioester, namely thiolactone acrylamide and an azlactone precursor, whose synthesis was newly developed, were attached to the side chain of P(EtOx-co-ButEnOx) copolymers.
The application of the functionalized thiol copolymers as hydrogels using thiol-ene chemistry for cross-linking was demonstrated. The swelling behavior and mechanical properties were characterized. The hydrophilicity of the network as well as the cross-linking density strongly influenced the swelling behavior and the mechanical strength of the hydrogels. All hydrogels showed good cell viability results.
The hydrogel networks based on MeOx and EtOx were loaded with two dyes, fluorescein and methylene blue. It was observed that the uptake of the more hydrophilic dye fluorescein depended more on the ability of the hydrogel to swell. In contrast, the uptake of the more hydrophobic dye methylene blue was less dependent on the swelling degree, but much more on the hydrophilicity of the network.
For the potential application as cartilage glue, (biohybrid) hydrogels were synthesized based on the catechol-functionalized copolymers, with and without additional fibrinogen, using sodium periodate as the oxidizing agent. The system allowed for degradation due to the incorporated ester linkages at the cross-linking points. The swelling behavior as well as the mechanical properties were characterized. As expected, hydrogels with higher degrees of cross-linking showed less swelling and higher elastic modulus. The addition of fibrinogen however increased the elasticity of the network, which can be favorable for the intended application as a cartilage glue. Biological evaluation clearly demonstrated the advantage of degradable ester links in the hydrogel network, where chondrocytes were able to bridge the artificial gap in contrast to hydrogels without any ester motifs.
Lastly, different ways to form peptide-polymer conjugates were presented. Peptides were attached with the thiol of the terminal cysteine group to the vinyl side chain of P(EtOx-co-ButEnOx) copolymers by radical thiol-ene chemistry. Another approach was to use a cyclic thioester, thiolactone, or an azlactone functionality to bind a model peptide via native chemical ligation. The two latter named strategies to bind peptides to POx side chains are especially interesting as one and in the case of thiolactone two free thiols are still present at the binding site after the reaction, which can, for example, be used for further thiol-ene cross-linking to form POx hydrogels.
In summary, side functional poly(oxazoline) copolymers show great potential for numerous biomedical applications. The various side chain functionalities can be introduced by an appropriate monomer or by post-polymerization functionalization, as demonstrated. By their multi-functionality, hydrogel characteristics, such as cross-linking degree and mechanical strength, can be fine-tuned and adjusted depending on the application in the human body. In addition, the presented chemoselective and orthogonal reaction strategies can be used in the future to synthesize polymer conjugates, which can, for example, be used in drug delivery or in tissue regeneration.
Sharpening super-resolution by single molecule localization microscopy in front of a tuned mirror
(2020)
The „Resolution Revolution" in fluorescence microscopy over the last decade has given rise to a variety of techniques that allow imaging beyond the diffraction limit with a resolution power down into the nanometer range. With this, the field of so-called super-resolution microscopy was born. It allows to visualize cellular architecture at a molecular level and thereby achieve a resolution level that had been previously only accessible by electron microscopy approaches.
One of these promising techniques is single molecule localization microscopy (SMLM) in its most varied forms such as direct stochastic optical reconstruction microscopy (dSTORM) which are based on the temporal separation of the emission of individual fluorophores. Localization analysis of the subsequently taken images of single emitters eventually allows to reconstruct an image containing super-resolution information down to typically 20 nm in a cellular setting. The key point here is the localization precision, which mainly depends on the image contrast generated the by the individual fluorophore’s emission. Thus, measures to enhance the signal intensity or reduce the signal background allow to increase the image resolution achieved by dSTORM. In my thesis, this is achieved by simply adding a reflective metal-dielectric nano-coating to the microscopy coverslip that serves as a tunable nano-mirror.
I have demonstrated that such metal-dielectric coatings provide higher photon yield at lower background and thus substantially improve SMLM performance by a significantly increased localization precision, and thus ultimately higher image resolution. The strength of this approach is that ─ except for the coated cover glass ─ no specialized setup is required. The biocompatible metal-dielectric nano-coatings are fabricated directly on microscopy coverslips and have a simple three-ply design permitting straightforward implementation into a conventional fluorescence microscope. The introduced improved lateral resolution with such mirror-enhanced STORM (meSTORM) not only allows to exceed Widefield and Total Internal Reflection Fluorescence (TIRF) dSTORM performance, but also offers the possibility to measure in a simplified setup as it does not require a special TIRF objective lens.
The resolution improvement achieved with meSTORM is both spectrally and spatially tunable and thus allows for dual-color approaches on the one hand, and selectively highlighting region above the cover glass on the other hand, as demonstrated here.
Beyond lateral resolution enhancement, the clear-cut profile of the highlighted region provides additional access to the axial dimension. As shown in my thesis, this allows for example to assess the three-dimensional architecture of the intracellular microtubule network by translating the local localization uncertainty to a relative axial position. Even beyond meSTORM, a wide range of membrane or surface imaging applications may benefit from the selective highlighting and fluorescence enhancing provided by the metal-dielectric nano-coatings. This includes for example, among others, live-cell Fluorescence Correlation Spectroscopy and Fluorescence Resonance Energy Transfer studies as recently demonstrated.
Honest actions predominate human behavior. From time to time, this general preference must yield to dishonest actions, which require an effortful process of overcoming initial honest response activation. This thesis presents three experimental series to elucidate this tug-of-war between honest and dishonest response tendencies in overtly committed instances of lies, thereby joining recent efforts to move from a sheer phenomenological perspective on dishonest responding as being more difficult than honest responding to a precise description of the underlying cognitive processes. The consideration of cognitive theories, empirical evidence, and paradigms from different research fields – dishonesty, cognitive control and sensorimotor stage models of information processing – lay the groundwork for the research questions and methodological approach of this thesis.
The experiments pinpoint the underlying conflict of dishonest responding in the central, capacity-limited stage of information processing (Experiments 1 to 4), but they also demonstrate that cognitive control processes (Experiments 5 to 7) and the internalization of false alibis (Experiments 8 to 11) can reduce or even completely eliminate this conflict. The data reveals great flexibility at the cognitive basis of dishonest responding: On the one hand, dishonest responding appears to rely heavily on capacity-limited processes of response selection to overcome honest response tendencies alongside up- and downstream consequences of response activation and monitoring. On the other hand, agents have powerful tools to mitigate these effortful processes through control adaptation and false alibis. These results support and expand current theorizing of the cognitive underpinnings of dishonest responding. Furthermore, they are alerting from an applied perspective on the detection of lies, especially when considering the flexibility of even basic cognitive processes in the face of false alibis. A promising way to move forward from here would be a fine-grained discrimination of response activation, passive decay and active inhibition of honest representations in dishonest responding and the assessment of the adaptiveness of these processes.
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.
L-type calcium channels (LTCCs) control crucial physiological processes in cardiomyocytes such as the duration and amplitude of action potentials, excitation-contraction coupling and gene expression, by regulating the entry of Ca2+ into the cells. Cardiac LTCCs consist of one pore-forming α1 subunit and the accessory subunits Cavβ, Cavα2δ and Cavγ. Of these auxiliary subunits, Cavβ is the most important regulator of the channel activity; however, it can also have LTCC-independent cellular regulatory functions. Therefore, changes in the expression of Cavβ can lead not only to a dysregulation of LTCC activity, but also to changes in other cellular functions. Cardiac hypertrophy is one of the most relevant risk factors for congestive heart failure and depends on the activation of calcium-dependent prohypertrophic signaling pathways. However, the role of LTCCs and especially Cavβ in this pathology is controversial and needs to be further elucidated.
Of the four Cavβ isoforms, Cavβ2 is the predominant one in cardiomyocytes. Moreover, there are five different splice variants of Cavβ2 (Cavβ2a-e), differing only in the N-terminal region. We reported that Cavβ2b is the predominant variant expressed in the heart. We also revealed that a pool of Cavβ2 is targeted to the nucleus in cardiomyocytes. The expression of the nuclear Cavβ2 decreases during in vitro and in vivo induction of cardiomyocyte hypertrophy and overexpression of a nucleus-targeted Cavβ2 completely abolishes the in vitro induced hypertrophy. Additionally, we demonstrated by shRNA-mediated protein knockdown that downregulation of Cavβ2 enhances the hypertrophy induced by the α1-adrenergic agonist phenylephrine (PE) without involvement of LTCC activity. These results suggest that Cavβ2 can regulate cardiac hypertrophy through LTCC-independent pathways. To further validate the role of the nuclear Cavβ2, we performed quantitative proteome analyses of Cavβ2-deficient neonatal rat cardiomyocytes (NRCs). The results show that downregulation of Cavβ2 influences the expression of various proteins, including a decrease of calpastatin, an inhibitor of the calcium-dependent cysteine protease calpain. Moreover, downregulation of Cavβ2 during cardiomyocyte hypertrophy drastically increases calpain activity as compared to controls after treatment with PE. Finally, the inhibition of calpain by calpeptin abolishes the increase in PE-induced hypertrophy in Cavβ2-deficient cells. These results suggest that nuclear Cavβ2 has Ca2+- and LTCC-independent functions during the development of hypertrophy. Overall, our results indicate a new role for Cavβ2 in antihypertrophic signaling in cardiac hypertrophy.
Nicotinamide N-methyltransferase (NNMT) is a new regulator of energy homeostasis. Its expression is increased in models of obesity and diabetes. An enhanced NNMT level is also caused by an adipose tissue-specific knockout of glucose transporter type 4 (GLUT4) in mice, whereas the overexpression of this glucose transporter reduced the NNMT expression. Furthermore, the knockdown of the enzyme prevents mice from diet-induced obesity (DIO) and the recently developed small molecule inhibitors for NNMT reverses the DIO. These previous findings demonstrated the exclusive role of NNMT in adipose tissue and further make it to a promising target in obesity treatment. However, the regulation mechanism of this methyltransferase is not yet clarified.
The first part of the thesis focus on the investigation whether pro-inflammatory signals are responsible for the enhanced NNMT expression in obese adipose tissue because a hallmark of this tissue is a low-level chronic inflammation. Indeed, the NNMT mRNA in our study was elevated in obese patients compared with the control group, whereas the GLUT4 mRNA expression does not differ between lean and obese humans. To analyze whether pro inflammatory signals, like interleukin (IL 6) and tumor necrosis factor α (TNF-α), regulate NNMT expression 3T3-L1 adipocytes were treated with these cytokines. However, IL 6, TNF α, and leptin, which is an alternative activator of the JAK/STAT pathway, did not affect the NNMT protein or mRNA level in differentiated 3T3-L1 adipocytes. The mRNA and protein levels were measured by quantitative polymerase chain reaction (qPCR) and western blotting.
In the second part of this study, 3T3-L1 adipocytes were cultivated with varying glucose concentrations to show whether NNMT expression depends on glucose availability. Further studies with activators and inhibitors of AMP-activated protein kinase (AMPK) and mechanistic target of rapamycin (mTOR) signaling pathways were used to elucidate the regulation mechanism of the enzyme.
The glucose deprivation of differentiated 3T3-L1 adipocytes led to a 2-fold increase in NNMT expression. This effect was confirmed by the inhibition of the glucose transports with phloretin as well as the inhibition of glycolysis with 2-deoxyglucose (2-DG). AMPK serves as an intracellular energy sensor and the pharmacological activation of it enhanced the NNMT expression. This increase was also caused by the inhibition of mTOR. Conversely, the activation of mTOR using MHY1485 prevented the effect of glucose deprivation on NNMT. Furthermore, the NNMT up-regulation was also blocked by the different autophagy inhibitors.
Taken together, NNMT plays a critical role in autophagy in adipocytes, because an inhibition of this process prevented the augmented NNMT expression during glucose starvation. Moreover, the effect on NNMT protein and mRNA level depends on AMPK and mTOR. However, pro-inflammatory signals did not affect the expression. Further in vivo studies have to clarify whether AMPK activation and mTOR inhibition as well as autophagy are responsible for the increased NNMT levels in obese adipose tissue. In future this methyltransferase emerges as an awesome therapeutic target for obesity.
In the last two decades, coherent multidimensional femtosecond spectroscopy has become a powerful and versatile tool to investigate chemical dynamics of a broad variety of quantum systems. The combination of transient information, equivalent to pumpprobe spectroscopy, with information about coupling between energetic states and the system environment allows an extensive insight into atomic and molecular properties. Many experimental 2D setups employ the coherence-detected approach, where nonlinear system responses are emitted as coherent electric _elds which are detected after spatial separation from the excitation pulses. As an alternative to this experimentally demanding approach, population-based 2D spectroscopy has been established. Here, the coherent information is encoded in the phases of a collinear excitation-pulse train and extracted from incoherent signals like uorescence via phase cycling. In principle, the use of uorescence as observable can boost the sensitivity down to the single-molecule level. The aim of this work was the realization of a pulse-shaper assisted fully collinear uorescence-detected 2D setup and the conducting of proof-of-principle experiments in the liquid phase. This inherently phase-stable and compact setup has been presented in chapter 3, with the utilized pulse shaper granting amplitude and phase modulation on a shot-to-shot basis. Two di_erent types of white-light sources have been applied and evaluated with regard to their respective advantages for 2D uorescence spectroscopy. A variety of artifact sources that can occur with the present setup have been discussed, and correction schemes and instructions for avoiding these artifacts have been provided. In chapter 4, the setup has been demonstrated by employing a four-pulse sequence on cresyl violet in ethanol. A detailed data-acquisition and data-analysis procedure has been presented, where phase cycling is used for extraction of the nonlinear contributions. Depending on the phase-cycling scheme, it is possible to recover all nonlinear contributions in a single measurement. Well-known quantum-beating behavior of cresyl violet during the population time could be reproduced. Due to measuring in a rotating-frame environment and 1 kHz shot-to-shot pulse incrementation, it was possible to obtain a 2D spectrum for one population time in 6 s. Via error evaluation it has been shown that 10_ averaging (1 min) is su_cient to obtain a root-mean-square error of < 0:05 compared to 400_ averaging, proving that the utilized acquisition scheme is well suited. The realization of the _rst experimental uorescence-detected 2Q 2D experiment and the _rst experimental access to the theoretically predicted 1Q-2Q contribution
Availability of water and desiccation of important water reservoirs is a vital challenge in semi-arid to arid climates with growing economy and population. Low quantities of precipitation and high evaporation rates leave the water supply vulnerable to human activity and climatic variations. Endorheic basins of Northern Iran were hydrologically landlocked within geological timescales and thus bear evidence of past variations of water resources in generations of water related landforms, like abandoned lake level shorelines, alluvial fans and stream terraces. Understanding the development of these landforms reveals crucial information about past water reservoirs and landscape history.
This study offers a comprehensive approach on understanding the geomorphological development of the landscape throughout Late Pleistocene and Holocene times. It integrates remote sensing and geographic information system analysis, with geomorphological and stratigraphical mapping fieldwork and detailed sedimentological investigations.
The work shows the importance of analytical geomorphological mapping for delineating stratigraphic units of the Iranian Quaternary. Thus, several phases of drying and lake level retreat were identified in parallel geoarchives and could be dated to a time span from today to Late Pleistocene. The findings link the fate of the citizens of the ancient city of "Tepe Hissar" to their access to water and to the power of geomorphological processes, which started changing their environment.
Quantitative genetics is the study of continuously distributed traits and their ge-
netic components. Recent developments in DNA sequencing technologies and
computational systems allow researchers to conduct large scale in silico studies.
However, going from raw DNA reads to genomic prediction of quantitative traits
with the help of neural networks is a long and error-prone process. In the course
of this thesis, many steps involved in this process will be assessed in depth. Chap-
ter 2 will feature a study that compares the landscape of chloroplast genome as-
sembly tools. Chapter 3 will present a software to perform genome-wide associa-
tion studies using modern tools, which allow GWAS-Flow to outperform current
state of the art software packages. Chapter 4 will give an in depth introduc-
tion to machine learning and the nature of quantitative traits and will combine
those to genomic prediction with artificial neural networks and compares the re-
sults to those of algorithms based on linear mixed models. Finally, in Chapter 5
the results from the previous chapters are summarized and used to elucidate the
complex nature of studies concerning quantitative genetics.