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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.
Allocation planning describes the process of allocating scarce supply to individual customers in order to prioritize demands from more important customers, i.e. because they request a higher service-level target. A common assumption across publications is that allocation planning is performed by a single planner with the ability to decide on the allocations to all customers simultaneously. In many companies, however, there does not exist such a central planner and, instead, allocation planning is a decentral and iterative process aligned with the company's multi-level hierarchical sales organization.
This thesis provides a rigorous analytical and numerical analysis of allocation planning in such hierarchical settings. It studies allocation methods currently used in practice and shows that these approaches typically lead to suboptimal allocations associated with significant performance losses. Therefore, this thesis provides multiple new allocation approaches which show a much higher performance, but still are simple enough to lend themselves to practical application. The findings in this thesis can guide decision makers when to choose which allocation approach and what factors are decisive for their performance. In general, our research suggests that with a suitable hierarchical allocation approach, decision makers can expect a similar performance as under centralized planning.
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.
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.
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.
The human body is colonized by trillions of microbes from all three domains of life – eukaryotes, bacteria and archaea. The lower gastrointestinal tract is the most densely colonized part of the body, harbouring a diverse and dynamic community of microbes. While the importance of bacteria in this so-called microbiota is well acknowledged, the role of commensal fungi remains underexplored. The most prominent fungus of the human gastrointestinal microbiota is Candida albicans. This fungus occasionally causes life-threatening disseminated infections in individuals with debilitated immune defences. It is this “pathogenic” facet that has received the most attention from researchers in the past, leaving many aspects of its “commensal” lifestyle understudied. Using gnotobiotic mice as a model system to explore the biology of C. albicans in the mammalian gut, in this dissertation I establish the global response of the host to C. albicans monocolonization as well as the spatial distribution of the fungus in the intestine in the context of co-colonization with single gut bacterial species. The fungus elicited transcriptome changes in murine intestinal tissue, which included the activation of a reactive oxygen species-related defence mechanism and the induction of regulators of the circadian clock circuitry. Both responses have previously been described in the context of a complete bacterial microbiota. Imaging the intestine of animals monocolonized with the fungus or co-colonized with C. albicans and the gut bacteria Bacteroides thetaiotaomicron or Lactobacillus reuteri revealed that the fungus was embedded in a B. thetaiotaomicron-promoted outer mucus layer in the murine colon. The gel-like outer mucus constitutes a unique microhabitat, distinct in microbial composition from the adjacent intestinal lumen. This finding indicates that bacteria can shape the specific microhabitat occupied by the fungus in the intestine. Overall, the results described in this dissertation suggest that gnotobiotic mice constitute a valuable tool to dissect multiple aspects of the interactions among host, commensal fungi and cohabiting bacteria.
ADMM-Type Methods for Optimization and Generalized Nash Equilibrium Problems in Hilbert Spaces
(2020)
This thesis is concerned with a certain class of algorithms for the solution of constrained optimization problems and generalized Nash equilibrium problems in Hilbert spaces. This class of algorithms is inspired by the alternating direction method of multipliers (ADMM) and eliminates the constraints using an augmented Lagrangian approach. The alternating direction method consists of splitting the augmented Lagrangian subproblem into smaller and more easily manageable parts.
Before the algorithms are discussed, a substantial amount of background material, including the theory of Banach and Hilbert spaces, fixed-point iterations as well as convex and monotone set-valued analysis, is presented. Thereafter, certain optimization problems and generalized Nash equilibrium problems are reformulated and analyzed using variational inequalities and set-valued mappings. The analysis of the algorithms developed in the course of this thesis is rooted in these reformulations as variational inequalities and set-valued mappings.
The first algorithms discussed and analyzed are one weakly and one strongly convergent ADMM-type algorithm for convex, linearly constrained optimization. By equipping the associated Hilbert space with the correct weighted scalar product, the analysis of these two methods is accomplished using the proximal point method and the Halpern method.
The rest of the thesis is concerned with the development and analysis of ADMM-type algorithms for generalized Nash equilibrium problems that jointly share a linear equality constraint. The first class of these algorithms is completely parallelizable and uses a forward-backward idea for the analysis, whereas the second class of algorithms can be interpreted as a direct extension of the classical ADMM-method to generalized Nash equilibrium problems.
At the end of this thesis, the numerical behavior of the discussed algorithms is demonstrated on a collection of examples.
Fluorinated compounds are an important motif, particularly in pharmaceuticals, as one-third of the top performing drugs have fluorine in their structures. Fluorinated biaryls also have numerous applications in areas such as material science, agriculture, crystal engineering, supramolecular chemistry, etc. Thus, the development of new synthetic routes to fluorinated chemical compounds is an important area of current research. One promising method is the borylation of suitable precursors to generate fluorinated aryl boronates as versatile building blocks for organic synthesis.
Chapter 1
In this chapter, the latest developments in the synthesis, stability issues, and applications of fluorinated aryl boronates in organic synthesis are reviewed. The catalytic synthesis of fluorinated aryl boronates using different methods, such as C–H, C–F, and C–X (X = Cl, Br, I, OTf) borylations are discussed. Further studies covering instability issues of the fluorinated boronate derivatives, which are accelerated by ortho-fluorine, have been reported, and the applications of these substrates, therefore, need special treatment.
Numerous groups have reported methods to employ highly fluorinated aryl boronates that anticipate the protodeboronation issue; thus, polyfluorinated aryl boronates, especially those containing ortho-fluorine substituents, can be converted into chloride, bromide, iodide, phenol, carboxylic acid, nitro, cyano, methyl esters, and aldehyde analogues. These substrates can be applied in many cross-coupling reactions, such as the Suzuki-Miyaura reaction with aryl halides, the Chan-Evans-Lam C–N reaction with aryl amines or nitrosoarenes, C–C(O) reactions with N-(aryl-carbonyloxy)phthalamides or thiol esters (Liebskind-Srogl cross-coupling), and oxidative coupling reactions with terminal alkynes. Furthermore, the difficult reductive elimination from the highly stable complex [PdL2(2,6-C6F2+nH3-n)2] was the next challenge to be targeted in the homocoupling of 2,6-di-fluoro aryl pinacol boronates, and it has been solved by conducting the reaction in arene solvents that reduce the energy barrier in this step as long as no coordinating solvent or ancillary ligand is employed.
Chapter 2
In this chapter, phenanthroline-ligated copper complexes proved to be efficient catalysts for the Suzuki-Miyaura cross-coupling of highly fluorinated aryl boronate esters (ArF–Bpin) with aryl iodides or bromides. This newly developed method is an attractive alternative to the traditional methods as copper is an Earth-abundant metal, less toxic, and cheaper compared to the traditional methods which commonly required palladium catalysts, and silver oxide that is also often required in stoichiometric amounts. A combination of 10 mol% copper iodide and 10 mol% phenanthroline, with CsF as a base, in DMF, at 130 ˚C, for 18 hours is efficient to cross-couple fluorinated aryl pinacol boronates with aryl iodides to generate cross-coupled products in good to excellent yields. This method is also viable for polyfluorophenyl borate salts such as pentafluorophenyl-BF3K. Notably, employing aryl bromides instead of aryl iodides for the coupling with fluorinated aryl–Bpin compounds is also possible; however, increased amounts of CuI/phenanthroline catalyst is necessary, in a mixture of DMF and toluene (1:1).
A diverse range of π···π stacking interactions is observed in the cross-coupling products partly perfluorinated biaryl crystals. They range from arene–perfluoroarene interactions (2-(perfluorophenyl)naphthalene and 2,3,4-trifluorobiphenyl) to arene–arene (9-perfluorophenyl)anthracene) and perfluoroarene–perfluoroarene (2,3,4,5,6-pentafluoro-2’methylbiphenyl) interactions.
Chapter 3
In this chapter, the efficient Pd-catalyzed homocoupling reaction of aryl pinacol pinacol boronates (ArF–Bpin) that contain two ortho-fluorines is presented. The reaction must be conducted in a “noncoordinating” solvent such as toluene, benzene, or m-xylene and, notably, stronger coordinating solvents or ancillary ligands have to be avoided. Thus, the Pd center becomes more electron deficient and the reductive elimination becomes more favorable. The Pd-catalyzed homocoupling reaction of di-ortho-fluorinated aryl boronate derivatives is difficult in strongly coordinating solvents or in the presence of strong ancillary ligands, as the reaction stops at the [PdL2(2,6-C6F2+nH3-n)2] stage after the transmetalations without the reductive elimination taking place. It is known that the rate of reductive elimination of Ar–Ar from [ML2(Ar)(Ar)] complexes containing group-10 metals decreases in the order Arrich–Arpoor > Arrich–Arrich > Arpoor–Arpoor. Furthermore, reductive elimination of the most electron-poor diaryls, such as C6F5–C6F5, from [PdL2(C6F5)2] complexes is difficult and has been a challenge for 50 years, due to their high stability as the Pd–Caryl bond is strong. Thus, the Pd-catalyzed homocoupling of perfluoro phenyl boronates is found to be rather difficult.
Further investigation showed that stoichiometric reactions of C6F5Bpin, 2,4,6-trifluorophenyl–Bpin, or 2,6-difluorophenyl–Bpin with palladium acetate in MeCN stops at the double transmetalation step, as demonstrated by the isolation of cis-[Pd(MeCN)2(C6F5)2], cis-[Pd(MeCN)2(2,4,6-C6F3H2)2], and cis-[Pd(MeCN)2(2,6-C6F2H3)2] in quantitative yields. Thus, it can be concluded that the reductive elimination from diaryl-palladium complexes containing two ortho-fluorines in both aryl rings, is difficult even in a weakly coordinating solvent such as MeCN. Therefore, even less coordinating solvents are needed to make the Pd center more electron deficient. Reactions using “noncoordinating” arene solvents such as toluene, benzene, or m-xylene were conducted and found to be effective for the catalytic homocoupling of 2,6-C6F2+nH3-nBpin. The scope of the reactions was expanded. Using toluene as the solvent, the palladium-catalyzed homocoupling of ArF–Bpin derivatives containing one, two or no ortho-fluorines gave the coupled products in excellent yields without any difficulties.
DFT calculations at the B3LYP-D3/def2-TZVP/6-311+g(2d,p)/IEFPCM // B3LYP-D3/SDD/6-31g**/IEFPCM level of theory predicted an exergonic process and lower barrier (< 21 kcal/mol) for the reductive elimination of Pd(C6F5)2 complexes bearing arene ligands, compared to stronger coordinating solvents (acetonitrile, THF, SMe2, and PMe3), which have high barriers ( > 33.7 kcal/mol). Reductive elimination from [Pd(ηn-Ar)(C6F5)2] complexes have low barriers due to: (i) ring slippage of the arene ligand as a hapticity change from η6 in the reactant to ηn (n ≤ 3) in the transition state and the product, which led to less σ-repulsion; and (ii) more favorable π-back-bonding from Pd(ArF)2 to the arene fragment in the transition state.
Chapter 4
In this chapter, the efficient Pd-catalyzed C–Cl borylation of aryl chlorides containing two ortho-fluorines is presented. The reactions are conducted under base-free conditions to prevent the decomposition of the di-ortho-fluorinated aryl boronates, which are unstable in the presence of base. A combination of Pd(dba)2 (dba = dibenzylideneacetone) with SPhos (2-dicyclohexylphosphino-2′,6′-dimethoxybiphenyl) as a ligand is efficient to catalyze the C–Cl borylation of aryl chlorides containing two ortho-fluorine substituents without base, and the products were isolated in excellent yields. The substrate scope can be expanded to aryl chloride containing one or no ortho-fluorines and the borylated products were isolated in good to very good yield. This method provides a nice alternative to traditional methodologies using lithium or Grignard reagents.
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.
Multiple myeloma (MM) is a disease of terminally differentiated B-cells which accumulate in the bone marrow leading to bone lesions, hematopoietic insufficiency and hypercalcemia. Genetically, MM is characterized by a great heterogeneity. A recent next-generation sequencing approach resulted in the identification of a signaling network with an accumulation of mutations in receptor-tyrosine kinases (RTKs), adhesion molecules and downstream effectors. A deep-sequencing amplicon approach of the coding DNA sequence of the six RTKs EPHA2, EGFR, ERBB3, IGF1R, NTRK1 and NTRK2 was conducted in a patient cohort (75 MM samples and 68 corresponding normal samples) of the “Deutsche Studiengruppe Multiples Myelom (DSMM)” to further elucidate the role of RTKs in MM. As an initial approach the detected mutations were correlated with cytogenetic abnormalities and clinical data in the course of this thesis. RTK mutations were present in 13% of MM patients of the DSMM XI trial and accumulated in the ligand-binding and tyrosine-kinase domain. The newly identified mutations were associated with an adverse patient survival, but not with any cytogenetic abnormality common in MM. Especially rare patient-specific SNPs (single nucleotide polymorphism) had a negative impact on patient survival. For a more comprehensive understanding of the role of rare RTK SNPs in MM, a second amplicon sequencing approach was performed in a patient cohort of the DSMM XII trial that included 75 tumor and 184 normal samples. This approach identified a total of 23 different mutations in the six RTKs EPHA2, EGFR, ERBB3, IGF1R, NTRK1 and NTRK2 affecting 24 patients. These mutations could furthermore be divided into 20 rare SNPs and 3 SNVs (single nucleotide variant). In contrast to the first study, the rare SNPs were significantly associated with the adverse prognostic factor del17p.
IGF1R was among the most commonly mutated RTKs in the first amplicon sequencing approach and is known to play an important role in diverse cellular processes such as cell proliferation and survival. To study the role of IGF1R mutations in the hard-to-transfect MM cells, stable IGF1R-knockdown MM cell lines were established. One of the knockdown cell lines (L363-C/C9) as well as a IGF1R-WT MM cell line (AMO1) were subsequently used for the stable overexpression of WT IGF1R and mutant IGF1R (N1129S, D1146N). Overall, an impact on the MAPK and PI3K/AKT signaling pathways was observed upon the IGF1R knockdown as well as upon WT and mutant IGF1R overexpression. The resulting signaling pattern, however, differed between different MM cell lines used in this thesis as well as in a parallel performed master thesis which further demonstrates the great heterogeneity described in MM.
Taken together, the conducted sequencing and functional studies illustrate the importance of RTKs and especially of IGF1R and its mutants in the pathogenesis of MM. Moreover, the results support the potential role of IGF1R as a therapeutic target for a subset of MM patients with mutated IGF1R and/or IGF1R overexpression.
Chapter two reports the catalytic triboration of terminal alkynes with B2pin2 using readily available Cu(OAc)2 and PnBu3. Various 1,1,2-triborylalkenes, a class of compounds which have been demonstrated to be potential Matrix Metalloproteinase-2 (MMP-2) inhibitors, are obtained directly in moderate to good yields. The process features mild reaction conditions, broad substrate scope, and good functional group tolerance were observed. This Cu-catalyzed reaction can be conducted on a gram scale to produce the corresponding 1,1,2-triborylalkenes in modest yields. The utility of these products is demonstrated by further transformation of the C-B bonds to prepare gem-dihaloborylalkenes (F, Cl, Br), monohalodiborylalkenes (Cl, Br), and trans-diaryldiborylalkenes, which serve as important synthons and have previously been challenging to prepare.
A convenient and efficient one step synthesis of 1,1,1-triborylalkanes was achieved via sequential dehydrogenative borylation and double hydroboration of terminal alkynes with HBpin (HBpin = pinacolborane) catalyzed by inexpensive and readily available Cu(OAc)2. This protocol proceeded under mild conditions, furnishing 1,1,1-tris(boronates) with wide substrate scope, excellent selectivity and good functional group tolerance, and is applicable to gram-scale synthesis without loss of yield. The 1,1,1-triborylalkanes can be used in the preparation of α-vinylboronates and borylated cyclic compounds, which are valuable but previously rare compounds. Different alkyl groups can be introduced stepwise via base-mediated deborylative alkylation to produce racemic tertiary alkyl boronates, which can be readily transformed into useful tertiary alcohols.
Chapter 4 reported a NaOtBu-catalyzed mixed 1,1-diboration of terminal alkynes with an unsymmetrical diboron reagent BpinBdan. This Brønsted base-catalyzed reaction proceeds in a regio- and stereoselective fashion affording 1,1-diborylalkenes with two different boryl moieties in moderate to high yields, and is applicable to gram-scale synthesis without loss of yield or selectivity. Hydrogen bonding between the Bdan group and tBuOH is proposed to be responsible for the observed stereoselectivity. The mixed 1,1-diborylalkenes can be utilized in stereoselective Suzuki-Miyaura cross-coupling reactions.
Divalent cations are important second messengers triggering various signal transduction events in platelets. Whereas calcium channel blockers have an established antithrombotic effect and the regulation of Ca2+ homeostasis has been elucidated in platelets, the molecular regulation of Mg2+ and Zn2+ homeostasis has not been investigated so far.
In the first part of the thesis, the role of -type serine-threonine kinase linked to transient receptor potential cation channel, subfamily M, member 7 (TRPM7) in platelets was investigated. Using Trpm7R/R mice with a point mutation deleting the kinase activity, we showed that the TRPM7 kinase regulates platelet activation via immunoreceptor tyrosine-based activation motif (ITAM), hem(ITAM) and protease-activated receptor (PAR) signaling routes. Furthermore, Trpm7R/R mice were protected from in vivo thrombosis and stroke, thus establishing TRPM7 kinase as a promising anti-thrombotic target.
In the second part of the thesis, the role of TRPM7 channel in a megakaryocyte (MK) and platelet-specific knockout mouse, Trpm7fl/fl-Pf4Cre, was investigated. Here, we observed that depending on the type of stimulation, Trpm7fl/fl-Pf4Cre platelets showed either enhanced or inhibited responses. Although Trpm7fl/fl-Pf4Cre mice were thrombocytopenic, no differences to wildtype mice were observed in models of in vivo thrombosis and stroke. The above two studies highlight that inhibition of TRPM7 kinase but not the channel itself (in MKs and platelets) may be a promising anti-thrombotic strategy.
Besides TRPM7, we investigated the role of magnesium transporter 1 (MAGT1) in platelet Mg2+ homeostasis and found that MAGT1 primarily regulates receptor-operated calcium entry (ROCE) in platelets specifically upon GPVI activation. This physiological crosstalk is triggered by protein kinase C (PKC) isoforms. Platelets from Magt1-/y mice hyper-reacted to GPVI and thromboxane A2 (TXA2) receptor stimulation in vitro. Consequently, Magt1-/y platelets were found to be pro-thrombotic in disease models of thrombosis and stroke.
To compare platelet ITAM-signaling to the immune system, we further investigated the role of MAGT1 in T and B cells. We described the primary role of MAGT1 in mice under pathogen-free conditions. Magt1-/y B cells showed dysregulated Mg2+ and Ca2+ homeostasis upon B-cell receptor activation, thereby altering Syk, LAT, phospholipase C (PLC)2 and PKC phosphorylation. In contrast to human MAGT1-deficient T cells, development and effector functions of mouse Magt1-/y T cells showed no alterations.
Finally, in the last part of the thesis, we described methods to measure intracellular free zinc [Zn2+]i in human and mouse platelets with storage pool disease (SPD). We propose to measure the [Zn2+]i status in SPD platelets as a relatively easy diagnostic to screen platelet granule abnormalities.
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.
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.
Affordable prices for 3D laser range finders and mature software solutions for registering multiple point clouds in a common coordinate system paved the way for new areas of application for 3D point clouds. Nowadays we see 3D laser scanners being used not only by digital surveying experts but also by law enforcement officials, construction workers or archaeologists. Whether the purpose is digitizing factory production lines, preserving historic sites as digital heritage or recording environments for gaming or virtual reality applications -- it is hard to imagine a scenario in which the final point cloud must also contain the points of "moving" objects like factory workers, pedestrians, cars or flocks of birds. For most post-processing tasks, moving objects are undesirable not least because moving objects will appear in scans multiple times or are distorted due to their motion relative to the scanner rotation.
The main contributions of this work are two postprocessing steps for already registered 3D point clouds. The first method is a new change detection approach based on a voxel grid which allows partitioning the input points into static and dynamic points using explicit change detection and subsequently remove the latter for a "cleaned" point cloud. The second method uses this cleaned point cloud as input for detecting collisions between points of the environment point cloud and a point cloud of a model that is moved through the scene.
Our approach on explicit change detection is compared to the state of the art using multiple datasets including the popular KITTI dataset. We show how our solution achieves similar or better F1-scores than an existing solution while at the same time being faster.
To detect collisions we do not produce a mesh but approximate the raw point cloud data by spheres or cylindrical volumes. We show how our data structures allow efficient nearest neighbor queries that make our CPU-only approach comparable to a massively-parallel algorithm running on a GPU. The utilized algorithms and data structures are discussed in detail. All our software is freely available for download under the terms of the GNU General Public license. Most of the datasets used in this thesis are freely available as well. We provide shell scripts that allow one to directly reproduce the quantitative results shown in this thesis for easy verification of our findings.
This thesis reports on the applications of a particular N-heterocyclic silylene, Dipp2NHSi (1), as an ambiphilic reagent in main group chemistry and as a ligand in transition metal chemistry. One focus of the work lies in the evaluation of the differences in the reactivity of N-heterocyclic silylenes in main group element and transition metal chemistry in comparison with the in these areas nowadays ubiquitous N-heterocyclic carbenes. The first chapter gives an insight into the reactivity of Dipp2NHSi with respect to different types of main group element compounds. Silylene 1 was reacted with group 13 compounds. Adduct formation was observed with AlI3, Al(C6F5)3 and B(C6F5)3 which led to isolation of Dipp2NHSi·AlI3 (2), Dipp2NHSi·Al(C6F5)3 (3) and Dipp2NHSi·B(C6F5)3 (4). Furthermore, the reactivity of Dipp2NHSi (1) with respect to different elementhalide bonds was investigated. The reaction with elemental bromine and iodine leads to the dihalosilanes Dipp2NHSiBr2 (5) and Dipp2NHSiI2 (6). Utilizing methyl iodide, benzyl chloride and benzyl bromide, the insertion products Dipp2NHSi(I)(Me) (10), Dipp2NHSi(Cl)(benzyl) (11) and Dipp2NHSi(Br)(benzyl) (12) are obtained. Thus, insertion is preferred to reductive coupling with formation of RH2C–CH2R (R = H, Ph) and the corresponding dihalosilane. The reaction of 1 with Me3SnCl leads to the diazabutene {(Me3Sn)N(Dipp)CH}2 (9). The reaction of 1 with Ph2SnCl2 gives exclusively Dipp2NHSiCl2 (8) and cyclic polystannanes (Ph2Sn)n. The reactivity of 1 towards selected 1,3-dipolar compounds was also examined and Dipp2NHSi was reacted with azides of different size. The reaction with adamantyl azide led to the formation of the tetrazoline 13. For the reaction with the sterically less demanding trimethylsilyl azide the azido silane Dipp2NHSi(N(SiMe3)2)(N3) (14) and the degradation product 14* was isolated. The cyclosilamine 15 was formed from the reaction of 1 with 2,6-(diphenyl)phenyl azide. The bonding situation and ligation properties of Dipp2NHSi in transition metal complexes was assessed in the second part of the thesis by means of theoretical calculations and experimental investigations. Calculations on the main electronic features of Me2Im/Me2NHSi and Dipp2NHSi/Dipp2Im revealed significant differences in the frontier orbital region of these compounds, which affect the ligation properties of NHSis in general. It was demonstrated that NHSis show significantly different behaviour concerning their coordination chemistry. In particular, one energetically low lying π-acceptor orbital seems to determine the coordination chemistry of these ligands. To provide experimental support for these calculations, the silylene complexes [M(CO)5(Dipp2NHSi)] (M = Cr 16, Mo 17, W 18) were synthesized from Dipp2NHSi and [M(CO)6] (M = Cr, Mo, W) and the tungsten NHSi complex 18 was compared to the NHC complexes [W(CO)5(iPr2Im)] (19), [W(CO)5(iPr2ImMe)] (20) and [W(CO)5(Me2ImMe)] (21). The bonding of Me2Im and Me2NHSi (= L) to transition metal complexes has been assessed with DFT calculations for the model systems [Ni(L)], [Ni(CO)3(L)], and [W(CO)5(L)]. These studies revealed some common features in the difference between M–NHSi and M–NHC bonding which largely affect the bonding situation in transition metal complexes. NHSis show a propensity for bridging two metal atoms which was demonstrated on three different examples. Dipp2NHSi reacts with [Ni(CO)4] to form the dinuclear silylene-bridged complex [{Ni(CO)2(μ-Dipp2NHSi)}2] (22) upon CO elimination. The reduction of [Ni(η5-C5H5)2] with lithium naphthalenide in the presence of Dipp2NHSi yielded the NHSi-bridged Ni(I) dimer [{(η5 C5H5)Ni(µ-Dipp2NHSi)}2] (23). The dimeric half-sandwich complex [{(η5-C5H5)Fe(CO)2}2] led upon reaction with Dipp2NHSi to the formation of the dinuclear, NHSi-bridged complex [{(η5-C5H5)Fe(CO)}2(µ-CO)(µ-Dipp2NHSi)] (24). The insertion of Dipp2NHSi into metal halide bonds was investigated in a series of manganese complexes [Mn(CO)5(X)] (X = Cl, Br, I). The reaction of Dipp2NHSi with [Mn(CO)5(I)] led to substitution of two carbonyl ligands with Dipp2NHSi (1) to afford the tricarbonyl complex [Mn(CO)3(Dipp2NHSi)2(I)] (25). In 25, the iodide ligand is aligned in the {Mn(CO)3} plane, located between both NHSi silicon atoms. Treatment of [Mn(CO)5(Br)] with two equivalents of Dipp2NHSi afforded the complex [Mn(CO)3(Dipp2NHSi)2(Br)] (26), in which the bromide ligand is distorted towards one of the NHSi ligands. The reaction of the silylene ligand with [Mn(CO)5(Cl)] at room temperature afforded a mixture of two products, [Mn(CO)3(Dipp2NHSi)2(Cl)] (27*) and the insertion product [Mn(CO)4(Dipp2NHSi)(Dipp2NHSi-Cl)] (27). Complete transfer of a halide to the silylene was achieved for the reaction of Dipp2NHSi with [(η5-C5H5)Ni(PPh3)(Cl)] to yield [Ni(PPh3)(η5-C5H5)(Dipp2NHSi-Cl)] (28). Similarly, the reaction with [(η5-C5H5)Fe(CO)2(I)] led to the formation of [(η5 C5H5)Fe(CO)2(Dipp2NHSi-I)] (29).
The contribution of this dissertation is to empirically analyze the link between income distribution, sectoral financial balances, and the current account. Firstly, it examines the relationship between the personal and the functional income distribution which may have rather different implications for aggregate demand and the current account. Secondly, it analyzes the importance of different sectors of the economy for current account balances and tests whether households are able to fully pierce the institutional veils of the corporate and the government sector. Thirdly, it investigates how changes in the personal and the functional income distribution affect the saving and investment decisions of the household and the corporate sector, and hence the current account. Finally, it shows how different growth regimes are linked to different patterns of personal and functional income distribution, and how differences in wage bargaining institutions contribute to explaining these different patterns of income distribution.
Knowing then defeating: The Ubiquitin activating enzyme, a promising target for cancer therapy
(2020)
Ubiquitin is a 76 amino acid long polypeptide, which is present throughout eukaryotes in a highly conserved fashion. Ubiquitin can modify proteins by becoming covalently attached to them. Eukaryotic cells employ ubiquitin to maintain and regulate fundamental cellular processes like protein degradation, the immune response and transcriptional and translational regulation. Transfer of ubiquitin to the substrate is achieved by the catalysis of three classes of enzymes namely E1, E2 and E3. Together these enzymes form a pyramidal hierarchy, where E1 stands at the apex and E3 enzymes form the base of the pathway.
The ubiquitin activating enzyme 1 (UBA1) plays a major role in ubiquitylation being the ubiquitin-dedicated E1 enzyme. In addition, it is the only enzyme in this pathway to use ATP as an energy source to catalyze two important reactions. The products of these reactions, ubiquitin adenylate and ubiquitin thioester, are the essential intermediate states of ubiquitin, for being conjugated to the target protein. With the help of X-ray crystallography and biochemical approaches, snapshots of multiple catalytic states of UBA1, where it is bound to Mg-ATP, ubiquitin and the E2 Ubc13 as substrates could be captured. With the help of these high-resolution crystal structures, deeper insights into the enzymatic mechanism of UBA1 could be attained. The resulting insights into the catalytic cycle were further validated by biochemical assays. It could be shown that ATP acts as a molecular switch to induce the enzyme’s open conformation. Ubiquitin-binding to the enzyme leads to domain rotations, which facilitate the recruitment of a cognate E2 enzyme. The interdomain communication as well as the cross-talk with the substrates and the products fuel the enzymatic cycle of UBA1.
Due to the proven efficacy of proteasome inhibitors for cancer treatment, which block degradation of proteins labeled with ubiquitin, enzymes participating in the ubiquitylation cascade have been targeted by researchers for the development of novel anti-cancer therapeutics. UBA1 inhibition has been shown to preferentially induce cell death in malignant cells, and it can also be used as a strategy to overcome resistance against proteasome inhibitors. MLN7243, an adenosyl sulfamate inhibitor developed by Millenium Pharmaceutical to specifically target UBA1, is currently in Phase-I clinical trials for the treatment of solid tumors. UBA1 could be crystallized in complex with three adenosyl sulfamate inhibitors covalently linked to ubiquitin, which are promising drug candidates for cancer therapy. The inhibitors employed, MLN7243, MLN4924 and ABPA3, show distinct specificities towards different E1 enzymes. With the help of crystal structures the specificity determinants of these inhibitors could be deciphered, which were further confirmed by inhibition assays as well as molecular dynamics simulations. Together these crystal structures provide a starting point for developing E1-specific inhibitors, which, besides their potential for medicinal purposes, are important tools to better understand the function of the ubiquitin system as well as the action of ubiquitin-like proteins.
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.
Potential evolutionary responses to landscape heterogeneity and systematic environmental trends
(2020)
Over the course of the last century, humans have witnessed drastic levels of global environmental change that endangered both, the survival of single species as well as biodiversity itself. This includes climate change, in both environmental means and in variance and subsequently frequent extreme weather events, as well as land use change that species have to cope with.
With increasing urbanization, increasing agricultural area and increasing intensification, natural habitat is not only lost, but also changes its shape and distribution in the landscape. Both aspects can heavily influence an individual's fitness and therefore act as a selective force promoting evolutionary change.
This way climate change influences individuals' niches and dispersal. Local adaptation and dispersal are not independent of each other. Dispersal can have two opposite effects on local adaptation. It can oppose local adaptation, by promoting the immigration of maladapted indi-
viduals or favor local adaptation by introducing better adapted genotypes. Which of those effects of dispersal on local adaptation emerges in a population depends on the dispersal strategies and the spatial structure of the landscape. In principle an adaptive response can include adjustment of the niche optimum as well as habitat tolerance (niche width) or (instead) ecological tracking of adequate conditions by dispersal and range shifting. So
far, there has been no extensive modeling study of the evolution of the environmental niche optimum and tolerance along with dispersal probability in complex landscapes. Either only dispersal or (part of ) the environmental niche can evolve or the landscapes used are not realistic but rather a very abstract representation of spatial structures.
I want to try and disentangle those different effects of both local adaptation and dispersal during global change, as well as their interaction, especially considering the separation between the effects of increasing mean and increasing variance. For this, I implemented an individual based model (IBM), with escalating complexity.
I showed that both on a temporal as well as on a spatial scale, variation can be more influential then mean conditions.
Indeed, the actual spatial configuration of this heterogeneity and the relationship between spatial and temporal heterogeneity affect the evolution of the niche and of dispersal probability more than temporal or spatial mean conditions. I could show that in isolated populations, an increase of an environmental attribute's mean or variance can lead to extinction, under certain conditions. In particular, increasing variance cannot be tracked forever, since increasing tolerance has distinct limits of feasibility. Increasing mean conditions can also occur too fast to be tracked, especially from generalist individuals. When expanding the model to the metapopulation level without a temporal environmental trend, the degree of spatial vs.temporal heterogeneity influenced the evolution of random dispersal heavily. With increasing spatial heterogeneity, individuals from extreme and rare patches
evolve from being philopatric to dispersive, while individuals from average patches switch in the opposite direction.
With the last expansion to a different set of landscapes with varying degrees of edge density, I could show that edge effects are strong in pseudo-agricultural landscapes, while
in pseudo-natural habitats they were hardly found, regardless of emigration strategy. Sharp edges select against dispersal in the edge patches and could potentially further isolate populations in agricultural landscapes.
The work I present here can also be expanded further and I present several suggestions on what to do next. These expansions could help the realism of the model and eventually shed light on its bearing on ecological global change predictions. For example species distribution models or extinction risk models would be more precise, if they included both spatial and temporal variation. The current modeling practices might not be suffcient to
describe the possible outcomes of global change, because spatio-temporal heterogeneity and its influence on species' niches is too important to be ignored for longer.
Parkinson’s disease (PD) is among the most common neurodegenerative conditions, and it is characterized by the progressive loss of dopaminergic neurons and a great variability in clinical expression. Despite several effective medications, it still causes disability as all patients show treatment-resistant symptoms and complications.
A possible reason for this therapeutic-burden and great clinical variability lies in a probable misconception about its pathophysiology, one that focuses on neurodegeneration, while largely neglecting its functional consequences and the related compensatory changes. In this thesis, I expand on the hypothesis that some PD symptoms have a dysfunctional origin and reflect derangements of neural network dynamics, the means by which brain coordination supports any motor behaviour. In particular, I have investigated resting tremor and freezing of gait, two common symptoms with an enigmatic mechanism and suboptimal management.
In the case of tremor, I predicted a pathological change in response to dopamine loss, which included the activation of noradrenergic (NA) neurons of the locus coeruleus (LC) projecting to the cerebellum. This compensatory LC activation that supports dopaminergic neurons might indeed come at the expense of tremor development. To assess the role of LC-NA in tremor development, I recorded tremor occurrence in the reserpinized rat model of PD, one of very few showing tremor, after selective lesioning (with the neurotoxin DSP-4) of the LC-NA terminal axons. DSP-4 induced a severe reduction of LC-NA terminal axons in the cerebellar cortex and this was associated with a significant reduction in tremor development. Unlike its development, tremor frequency and the akinetic rigid signs did not differ between the groups, thus suggesting a dopaminergic dependency. These findings suggest that the LC-NA innervation of the cerebellum has a critical role for PD tremor, possibly by exerting a network effect, which gates the cerebello-thalamic-cortical circuit into pathological oscillations upon a dopaminergic loss in the basal ganglia.
In contrast, for the study of freezing of gait, I worked with human PD subjects and deep brain stimulation, a therapeutic neuromodulation device that in some prototypes also allows the recording of neural activity in freely-moving subjects. Gait freezing is a disabling PD symptom that suddenly impairs effective stepping, thus causing falls and disability. Also in this study, I hypothesized that the underlying pathophysiology may be represented by dysfunctional neural network dynamics that abruptly impair locomotor control by affecting the communication in the supraspinal locomotor network. To test this hypothesis, I investigated the coupling between the cortex and the subthalamic nucleus, two main nodes of the supraspinal locomotor network, in freely-moving subjects PD patients and also performed molecular brain imaging of striatal dopamine receptor density and kinematic measurements. I found that in PD patients, walking is associated with cortical-subthalamic stable coupling in a low-frequency band (i.e. θ-α rhythms). In contrast, these structures decoupled when gait freezing occurred in the brain hemisphere with less dopaminergic innervation. These findings suggest that freezing of gait is a “circuitopathy”, with dysfunctional cortical-subcortical communication.
Altogether the results of my experiments support the hypothesis that the pathophysiology of PD goes beyond neurodegenerative (loss-of-function) processes and that derangement of neural network dynamics coincides with some disabling PD symptoms, thus suggesting that PD can be interpreted as the combination of multiple circuitopathies.
Nowadays, employees have to work with applications, technical services, and systems every day for hours. Hence, performance degradation of such systems might be perceived negatively by the employees, increase frustration, and might also have a negative effect on their productivity. The assessment of the application's performance in order to provide a smooth operation of the application is part of the application management. Within this process it is not sufficient to assess the system performance solely on technical performance parameters, e.g., response or loading times. These values have to be set into relation to the perceived performance quality on the user's side - the quality of experience (QoE).
This dissertation focuses on the monitoring and estimation of the QoE of enterprise applications. As building models to estimate the QoE requires quality ratings from the users as ground truth, one part of this work addresses methods to collect such ratings. Besides the evaluation of approaches to improve the quality of results of tasks and studies completed on crowdsourcing platforms, a general concept for monitoring and estimating QoE in enterprise environments is presented. Here, relevant design dimension of subjective studies are identified and their impact of the QoE is evaluated and discussed. By considering the findings, a methodology for collecting quality ratings from employees during their regular work is developed. The method is realized by implementing a tool to conduct short surveys and deployed in a cooperating company.
As a foundation for learning QoE estimation models, this work investigates the relationship between user-provided ratings and technical performance parameters. This analysis is based on a data set collected in a user study in a cooperating company during a time span of 1.5 years. Finally, two QoE estimation models are introduced and their performance is evaluated.
Despite the advancement in the treatment from genotoxic drugs to more targeted therapies, multiple myeloma (MM) remains incurable. MM is known for its complex genetic heterogeneity as different genetic lesion accrue over the course of the disease. The current work focuses on the functional analysis of genetic lesions found at the time of diagnosis and relapse and their potential role regarding therapy response and refractory disease. Genetic lesions involving tumor suppressor gene TP53, are found at diagnosis and tend to accrue during disease progression. Different types of mono- and biallelic TP53 alterations were emulated in the AMO1 cell line model, were functionally characterized and tested for their potential role in therapy response. Both types of single hit TP53 alteration (deletion 17p and TP53 point mutations) were found to have similar adverse effects on the functionality of the p53 system and response to genotoxic drugs which were completely abolished in the case of double hit TP53 alterations (no p53 expression, or mutant overexpression in wild type TP53 deletion background). Whereas, sensitivity to proteasome inhibitors remained unaltered. Using the clonal competition assay (CCA), single TP53 hit clones were found to have a fitness advantage over wildtype cells. Proliferative cell fitness was further enhanced in double hit TP53 clones, as they dominated wildtype and single hit TP53 clones in the CCA. Presence of external selection pressure in the form of low dose melphalan expedited the intrinsic fitness advantage. Alterations found in CUL4B, a component of CRL4-CRBN protein complex, a target of immunomodulatory drugs (IMiDs), were also functionally analyzed in the current study. Hotspot mutations and mutations found in IMiDs refractory patients were modelized in L363 cells and their role in IMiDs sensitivity was studied. CUL4B mutations were found not to be involved in providing lenalidomide resistance to the cell, whereas knocking CUL4B out was observed to provide negative fitness to the cells in CCA. In the presence of external selection pressure, these clones showed fitness, which was lost in the case of lenalidomide withdrawal. This shows that some alterations may play a role in refractory patients only in the presence of therapy, and as soon as therapy is discontinued, these altered clones may disappear such as clones with alterations in CUL4B. On the other hand, some alterations provide drug-independent intrinsic positive fitness, however, be further enhanced by drug exposure, such as seen in case of TP53 altered clones. Therefore, close monitoring and functional analysis of evolving clones is desired during disease progression, as it can be helpful in therapeutic guidance to achieve a better outcome for patients.
Background: Integrase strand transfer inhibitors (INSTIs) are the latest addition to the array of antiretroviral compounds used to treat an infection with Human Immunodeficiency Virus (HIV). Due to their high efficacy and increased tolerability, INSTIs have become an integral part of first-line therapy in most high-income countries over the past years. However, little is known about HIV-1’s genetic inter- and intra-subtype diversity on the Integrase (IN)-gene and its impact on the emergence of INSTI-resistance. In the absence of a functional cure, long-term efficacy of first-line compounds remains paramount for reducing virological failure and curbing on-going HIV transmissions. South Africa, harbouring more than 20% of the global HIV burden (7.7 / 37.9 million people), requires international attention in order to globally pursue UNAIDS’ (Joint United Nations Programme on HIV/AIDS) 90-90-90 goals and the road to ending the HIV/AIDS (Acquired immunodeficiency syndrome) pandemic by 2030.
Methods: In this study, the prevalence of INSTI-resistance associated mutations (RAM) was investigated in a cohort of 169 archived drug-naïve blood samples from multiple collection sites around Cape Town, South Africa. Viral RNA was isolated from plasma samples, the integrase fragment amplified by RT-PCR and subsequently sequenced by Sanger-sequencing. Additionally, all publicly available drug-naïve, South African IN sequences, isolated before the availability of the first INSTIs in 2007, were retrieved from the Los Alamos HIV sequence database (n=284). All sequences were analysed for RAMs using the Stanford HIV Drug resistance database. The identification of polymorphism in the South African subtype C IN consensus sequence allowed for comparative analyses with global subtype B, as well as subtype C sequences, from countries other than South Africa.
Results: The IN gene could be amplified and sequenced in 95/169 samples (56%). Phylogenetic inference revealed close homology between three sequence-pairs, warranting the exclusion of 3/95 sequences from further analyses. Of the 92 samples used for mutational analyses, 86/92 (93.5%) belonged to subtype C, 5/92 (5.4%) to subtype B and 1/92 (1.1%) to subtype A. The prevalence of major and accessory INSTI RAMs was 0/92 (0%) and 1/91 (1.1%), respectively, similar to the observed rates of 8/284 (2.8%) and 8/284 (2.8%) in the database sequences (p = 0.2076 and p = 0.6944, Fisher’s exact test). Compared to subtype B IN sequences, 15 polymorphisms were significantly enriched in South African subtype C sequences (corrected p<0.0015. Fisher’s exact test, Bonferroni post-hoc procedure).
Compared to subtype C IN sequences isolated outside South Africa, four polymorphisms were significantly enriched in this study cohort (corrected p<0.0014, Fisher’s exact test, Bonferroni post-hoc procedure). The highest prevalence margin was observed for the polymorphism Met50Ile being present in 60.1% of South African subtype C sequences, compared to 37% in non-South African subtype C sequences.
Conclusions: The low prevalence of major and minor RAMs in all South African Integrase sequences predicts a high susceptibility to INSTIs, however, the presence of natural polymorphisms, in particular Met50Ile, in the majority of sequences warrants further monitoring under therapeutic pressure, as their role in mutational pathways leading to INSTI- resistance is yet to be determined. Additionally, this study revealed the presence of substantial inter- and intra-subtype diversity within the HIV-1 Subtype C IN-gene. These results implicate the need for more research on a regional, potentially patient-specific level, as mutational insights from other diverse backgrounds may not accurately represent the South African context. The implementation of a national pre-treatment INSTI-resistance screening program may provide necessary insights into the development of mutational pathways leading to INSTI-resistance under therapeutic pressure for the South African context and thereby bring South Africa one step closer to achieving UNAIDS 90-90-90 goals and ending the AIDS epidemic by 2030.
The human body is laden with trillions of microorganisms that belong to all three domains of life. Some species of this microbiota subsist as harmless commensals in healthy adults, but under certain circumstances, they can cause mucosal disease or even systemic, life-threatening infections. While the bacterial members of our microbiota are heavily studied today, much less attention is afforded to eukaryotic species that colonize different mucocutaneous surfaces of the human body. This dissertation focuses on identifying regulatory circuits that enable a prominent member of these eukaryotes, C. albicans, to, on the one hand, live on a specific mammalian mucosal surface as a harmless commensal and, on the other hand, proliferate as a pathogen. Since the ultimate source of many fatal Candida infections is the gastrointestinal (GI) tract of the infected individual, this organism is particularly suited to distinguishing traits essential for the gut colonization of commensal fungi and their ability to cause disease. Sequence-specific DNA-binding proteins that regulate transcription are important to most biological processes; I thus used these proteins as starting points to gain insights into 1) how a specific transcription regulator promotes virulence in C. albicans; 2) which traits C. albicans requires to inhabit the GI tract of a specific, well-defined mouse model as a harmless commensal; and 3) how three previously undescribed transcriptional regulators contribute to the commensal colonization of the digestive tract of this mouse model. Altogether, this work advances the knowledge concerning the biology of commensal fungi in the mammalian gut and genetic determinants of fungal commensalism, as well as pathogenicity.
Cuticular hydrocarbons (CHC) abound on the surface of arthropods. In spite of their simple structure (molecules of carbon and hydrogen atoms), they provide pivotal functions in insects: their hydrophobic properties confer the insects a means to regulate water balance and avoid desiccation, whereas their diversity has enhanced their use as signals and cues in a wide range of communication and recognition processes. Although the study of CHC in insects over the past two decades has provided great insight into the wide range of functions they play, there is still a gap in understanding how they diversify and evolve. In this thesis, I have used members of the family Chrysididae to explore patterns of diversification of CHC. Most of the species of cuckoo wasps in this study are specialized parasitoids or kleptoparasites of mainly solitary hymenopteran hosts. Other hosts of the family include butterflies or stick insects. Cuckoo wasps are a particular interesting model to study the evolution of cuticular hydrocarbons because of their chemical adaptations that allow them to remain unrecognized by their hosts. Chemical insignificance (the reduction of the total amount of CHC on the cuticle) and chemical mimicry (the de novo production of CHC profiles resembling those of their female host) have been described in some representatives of the family and unpublished evidence suggests chemical deception is widespread in Chrysididae (Chapter 2). Nonetheless, to trace the evolution of any trait of interest, a reliable phylogenetic reconstruction of the family is required. Therefore, the first study of this thesis constitutes the largest and to-date most reliable phylogenetic reconstruction of the family Chrysididae, which includes representatives of 186 species of cuckoo wasps. While the results of this phylogenetic reconstruction are consistent with previous ideas on the relationships of subfamilies and tribes, it shows the existence of several non-monophyletic genera (Chapter 3). CHC are involved in intraspecific recognition, often acting as contact sex pheromones. Nevertheless, it is not yet understood to what extent CHC profiles differ between the two sexes and whether some compound classes are more prevalent in one or the other sex. So far, no comparison of CHC profiles of males and females has been done for more than a dozen of related species. In Chapter 4, I describe and compare CHC profiles of females and males of 58 species of cuckoo wasps in order to evaluate whether and to what extent CHC profiles of these species differ between the sexes. I demonstrated that CHC profiles of cuckoo wasps are frequently (more than 90% of the species analyzed) and strongly dimorphic (both sexes of a given species tend to produce very different CHC compounds). Methyl-branched compounds tend to be more prevalent in males (especially dimethyl-branched compounds) and unsaturated compounds prevail in females. Moreover, a sex-specific pattern in the distribution of the double bond position of alkenes was evident: internal double bond positions (> 11) occur predominantly in males, whereas alkenes with the doublé bond at position 9 were more abundant and frequent in females (Chapter4). In Chapter5, I investigated how CHC profiles of cuckoo wasps differ across species. Are CHC profiles of cuckoo wasps species-specific, enabling their use as cues for species recognition? How do CHC profiles resemble phylogenetic relatedness? In Chapter 5, I try to answer these questions by comparing CHC profiles of 59 species of cuckoo wasps. CHC profiles of cuckoo wasps are shown to be species (and sex-) specific. I show that CHC profiles are useful as a complementary tool to help delimiting taxonomically difficult sibling species. Moreover, the evaluation of CHC profiles of five commonly occurring species within a genus, showed little or no geographical variation. However, CHC profiles of closely related species may differ strongly among each other, not being useful to track the evolutionary history of species (Chapter 5). Sexual selection is generally credited for generating striking sexual dimorphism by causing changes in male traits. Most often, sexual selection has a stronger effect on males, who compete for access to and may be selected by females, thus male traits may rapidly evolve. Nevertheless, in cuckoo wasps, it appears that it is the female sex the one evolving faster changes, with females of very closely related species showing extremely divergent profiles. One plausible reason for this disparity is that natural selection acting on female’s CHC profiles may be stronger than sexual selection on males (Chapter 6). Since females of cuckoo wasps are most probably engaged in an evolutionary arms race with their female hosts, CHC profiles of female cuckoo wasps are likely rapidly evolving, thus explaining part of the strong observed sexual dimorphism of CHC (Chapter 6). In fact, Chapter 7 shows evidence of a possible ongoing evolutionary arms race between five cuckoo wasps of the genus Hedychrum and their hosts. Hedychrum species parasitize either Coleoptera-hunting or Hymenoptera-hunting digger wasps. Since the coleopteran prey of the former digger wasps is naturally better protected against fungus infestation, these wasps do not embalm their prey with alkene-enriched secretions as do the Hymenoptera-hunting digger wasps. Thus, Coleoptera-hunting digger wasps can apparently diversify their profiles to escape chemical mimicry. Interestingly, only female cuckoo wasps of these hosts have started producing the same compound classes and even the same CHC compounds as those of their hosts. Male cuckoo wasps, however retain an alkene-enriched CHC profile that reflects the molecular phylogeny of the genus (Chapter 7). Whereas, a larger number of parasite-host comparisons may be needed to further conclude that an arms race between cuckoo wasps and their hosts is capable of generating sexual dimorphism of cuckoo wasps, this thesis constitutes the first effort towards this, providing a starting point for further studies. Finally, I provide some methodological tools that may help in speeding up the sometimes cumbersome process of analyzing and identifying CHC profiles. One of the most time-demanding steps in the processing of CHC data is the alignment of CHC chromatograms. This process is often done manually, because alignment programs are mostly designed for metabolomics or are just recently being developed. I analyzed CHC profiles using a combined approach with two freely available programs. I used AMDIS (Automated Mass Spectral Deconvolution and Identification System, http://chemdata.nist.gov/mass-spc/amdis/) to deconvolute and automatically identify all CHC of interest present in a chromatogram. I then developed a series of R scripts to correct for potential, unavoidable errors while processing CHC chromatograms with AMDIS. Chapter 8 explains this procedure. In the next chapter, I developed a program that helps in the identification of one commonly occurring class of hydrocarbons. The limited number of linear alkanes (only one per carbon atom) and their characteristic diagnostic ion allows a rapid and unambigous identification of these substances. In opposition, unsaturated and methyl-branched compounds are more difficult to identify, as a result of the much larger diversity of existing compounds. To identify unsaturated compounds a derivatization is necessary to determine the position of the double bond. Methyl-branched alkanes, however can be identified from the original chromatogram if their diagnostic ions are known. Nonetheless, polymethyl-branched alkanes (e.g., compounds with two or more methyl groups along the chain) are often difficult to identify, because they may appear in mixes (e.g., 3,7 diMeC27 and 3,9 diMeC27), and tables containing the diagnostic ions are not easily available. Therefore, I developed a program that creates a table with all possiblemethyl-branched compounds containing up to 4 methyl groups, and that provides their diagnostic ions and a calculated retention index. This may allow a much faster identification of the methyl-branched compound a researcher is dealing with, without having to lose time in the tedious calculations by hand. The program is able to correctly identify, or at least, greatly reduce the number of possible options for the identification of an unknown methyl-branched compound. Thus, using this tool, most methyl-branched compounds can be readily identified (Chapter 9). This thesis ends with a general discussion (Chapter 10). Overall, this work provides a comprehensive overview of the diversity of cuticular hydrocarbons of cuckoo wasps. The analyses presented here shed light on the emergence and evolution of interspecific diversity and intraspecific sexual dimorphism of CHC profiles. In addition, two technical methods have been developed that could greatly facilitate the CHC analysis of insects.
Objectives: The aim of this work is to define critical warning brainstem auditory evoked potential (BAEP) signs as a marker for the postoperative hearing outcome.
Study design: Retrospective study
Setting: Tertiary referral center
Patients: 162 patients who underwent resection of acoustic neuroma via a transtemporal approach with intraoperative monitoring (IOM) at the Department of Otorhinolaryngology, Plastic, Esthetic and Reconstructive Head and Neck Surgery, from January 2011 to December 2017.
Interventions: BAEP was performed in all patients; while intraoperative direct recording of the cochlear nerve function was done in 131 patients.
Main Outcome Measure: postoperative hearing thresholds (Pure tone audiometry).
Results: The most significant risk factor is the permanent loss of wave V as it increases the risk of postoperative hearing loss by 18 times; followed by three-steps increment of the stimulus intensity as it increases the risk by 5.75 times; and finally the response thresholds obtained during the intraoperative direct recording of cochlear nerve function. Each unite increment of the threshold increases the risk of postoperative hearing loss by 6.7%.
Conclusions: We believe that the intraoperative BAEP critical signs during IOM detected in this study can be used as a helpful tool to predict postoperative hearing loss in patients with acoustic neuroma.
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.
Serotonin (5-hydroxytryptamine, 5-HT) is a neurotransmitter involved in early
developmental processes such as cell proliferation, migration, and differentiation.
Recent research in humans showed that the brain 5-HT system and CDH13 are
interlinked in the genetics of neurodevelopmental disorders including attention-
deficit/hyperactivity disorder and autism spectrum disorder (Lesch et al., 2008;
Neale et al., 2008; Neale, Medland, Ripke, Anney, et al., 2010; Neale, Medland,
Ripke, Asherson, et al., 2010; Sanders et al., 2011; Sanders et al., 2015; Zhou et
al., 2008). This study introduces Cadherin-13 (CDH13), a cell adhesion protein, as
a contributor to the development and function of the 5-HT system. Our
experiments show that the absence of CDH13 increases the density of 5-HT
neurons in the developing dorsal raphe (DR) and increases the 5-HT innervation
of the prefrontal cortex in mouse embryonic stages. CDH13 is also observed in
radial glial cells, an important progenitor cell type linked to neuronal migration.
A three-dimensional reconstruction carried out with super-resolution microscopy,
identifies 5-HT neurons intertwined with radial glial cells, and CDH13 clusters at
contact points between these cells. This indicates a potential contribution of
CDH13 to the migration of DR 5-HT neurons. As CDH13 is strongly expressed in
5-HT neurons, we asked whether the selective deletion of CDH13 from these cells
is sufficient to generate the alterations observed in the Cdh13 constitutive
knockout mouse line.
In 5-HT conditional Cdh13 knockout mice (Cdh13 cKO) an increase in DR 5-HT
neurons in the embryonic and adult brains is observed, as well as 5-HT
hyperinnervation of cortical regions. Therefore, illustrating that the lack of CDH13
from 5-HT neurons alone impacts DR formation and serotonergic innervation.
Behavioral testing conducted on Cdh13 cKO mice showed delayed learning in
visuospatial learning and memory processing, as well as, changes in sociability
parameters. To find out how CDH13 localizes in human 5-HT neurons, CDH13 was
visualized in neurons that derived from human induced pluripotent stem cells
(iPSC). Super-resolution microscopy confirmed CDH13 expression in a subgroup
of induced human neurons positive for typical hallmarks of 5-HT neurons, such as
expression of Tph2, the neuron-specific tryptophan hydroxylase, and synaptic
structures. In summary, the work included in this thesis presents a detailed
analysis of CDH13 expression and localization in the 5-HT system and shows that
deletion of CDH13 from 5-HT neurons affects specific higher-order functions of the
brain.
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.
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.
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.
Humans in our environment are of special importance to us. Even if our minds are
fixated on tasks unrelated to their presence, our attention will likely be drawn
towards other people’s appearances and their actions.
While we might remain unaware of this attentional bias at times, various studies have demonstrated the preferred visual scanning of other humans by recording eye movements in laboratory settings. The present thesis aims to investigate the circumstances under and the mechanisms by which this so-called social attention operates.
The first study demonstrates that social features in complex naturalistic scenes are prioritized in an automatic fashion. After 200 milliseconds of stimulus presentation, which is too brief for top-down processing to intervene, participants targeted image areas depicting humans significantly more often than would be expected from a chance distribution of saccades. Additionally, saccades towards these areas occurred earlier in time than saccades towards non-social image regions. In the second study, we show that human features receive most fixations even when bottom-up information is restricted; that is, even when only the fixated region was visible and the remaining parts of the image masked, participants still fixated on social image regions longer than on regions without social cues. The third study compares the influence of real and artificial faces on gaze patterns during the observation of dynamic naturalistic videos. Here we find that artificial faces, belonging to humanlike statues or machines, significantly predicted gaze allocation but to a lesser extent than real faces. In the fourth study, we employed functional magnetic resonance imaging to investigate the neural correlates of reflexive social attention. Analyses of the evoked blood-oxygenation level dependent responses pointed to an involvement of striate and extrastriate visual cortices in the encoding of social feature space.
Collectively, these studies help to elucidate under which circumstances social
features are prioritized in a laboratory setting and how this prioritization might be achieved on a neuronal level. The final experimental chapter addresses the question whether these laboratory findings can be generalized to the real world. In this study, participants were introduced to a waiting room scenario in which they interacted with a confederate. Eye movement analyses revealed that gaze behavior heavily depended on the social context and were influenced by whether an interaction is currently desired. We further did not find any evidence for altered gaze behavior in socially anxious participants. Alleged gaze avoidance or hypervigilance in social
anxiety might thus represent a laboratory phenomenon that occurs only under very specific real-life conditions. Altogether the experiments described in the present
thesis thus refine our understanding of social attention and simultaneously
challenge the inferences we can draw from laboratory research.
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.
Time-triggered communication is widely used throughout several industry do-
mains, primarily for reliable and real-time capable data transfers. However,
existing time-triggered technologies are designed for terrestrial usage and not
directly applicable to space applications due to the harsh environment. In-
stead, specific hardware must be developed to deal with thermal, mechanical,
and especially radiation effects.
SpaceWire, as an event-triggered communication technology, has been used
for years in a large number of space missions. Its moderate complexity, her-
itage, and transmission rates up to 400 MBits/s are one of the main ad-
vantages and often without alternatives for on-board computing systems of
spacecraft. At present, real-time data transfers are either achieved by prior-
itization inside SpaceWire routers or by applying a simplified time-triggered
approach. These solutions either imply problems if they are used inside dis-
tributed on-board computing systems or in case of networks with more than
a single router are required.
This work provides a solution for the real-time problem by developing
a novel clock synchronization approach. This approach is focused on being
compatible with distributed system structures and allows time-triggered data
transfers. A significant difference to existing technologies is the remote clock
estimation by the use of pulses. They are transferred over the network and
remove the need for latency accumulation, which allows the incorporation of
standardized SpaceWire equipment. Additionally, local clocks are controlled
decentralized and provide different correction capabilities in order to handle
oscillator induced uncertainties. All these functionalities are provided by a developed Network Controller (NC), able to isolate the attached network and
to control accesses.
Structural equation modeling (SEM) has been used and developed for decades across various domains and research fields such as, among others, psychology, sociology, and business research. Although no unique definition exists, SEM is best understood as the entirety of a set of related theories, mathematical models, methods, algorithms, and terminologies related to analyzing the relationships between theoretical entities -- so-called concepts --, their statistical representations -- referred to as constructs --, and observables -- usually called indicators, items or manifest variables.
This thesis is concerned with aspects of a particular strain of research within SEM -- namely, composite-based SEM. Composite-based SEM is defined as SEM involving linear compounds, i.e., linear combinations of observables when estimating parameters of interest.
The content of the thesis is based on a working paper (Chapter 2), a published refereed journal article (Chapter 3), a working paper that is, at the time of submission of this thesis, under review for publication (Chapter 4), and a steadily growing documentation that I am writing for the R package cSEM (Chapter 5). The cSEM package -- written by myself and my former colleague at the University of Wuerzburg, Florian Schuberth -- provides functions to estimate, analyze, assess, and test nonlinear, hierarchical and multigroup structural equation models using composite-based approaches and procedures.
In Chapter 1, I briefly discuss some of the key SEM terminology.
Chapter 2 is based on a working paper to be submitted to the Journal of Business Research titled “Assessing overall model fit of composite models in structural equation modeling”. The article is concerned with the topic of overall model fit assessment of the composite model. Three main contributions to the literature are made. First, we discuss the concept of model fit in SEM in general and composite-based SEM in particular. Second, we review common fit indices and explain if and how they can be applied to assess composite models. Third, we show that, if used for overall model fit assessment, the root mean square outer residual covariance (RMS_theta) is identical to another well-known index called the standardized root mean square residual (SRMR).
Chapter 3 is based on a journal article published in Internet Research called “Measurement error correlation within blocks of indicators in consistent partial least squares: Issues and remedies”. The article enhances consistent partial least squares (PLSc) to yield consistent parameter estimates for population models whose indicator blocks contain a subset of correlated measurement errors. This is achieved by modifying the correction for attenuation as originally applied by PLSc to include a priori assumptions on the structure of the measurement error correlations within blocks of indicators. To assess the efficacy of the modification, a Monte Carlo simulation is conducted. The paper is joint work with Florian Schuberth and Theo Dijkstra.
Chapter 4 is based on a journal article under review for publication in Industrial Management & Data Systems called “Estimating and testing second-order constructs using PLS-PM: the case of composites of composites”. The purpose of this article is threefold: (i) evaluate and compare common approaches to estimate models containing second-order constructs modeled as composites of composites, (ii) provide and statistically assess a two-step testing procedure to test the overall model fit of such models, and (iii) formulate recommendation for practitioners based on our findings. Moreover, a Monte Carlo simulation to compare the approaches in terms of Fisher consistency, estimated bias, and RMSE is conducted. The paper is joint work with Florian Schuberth and Jörg Henseler.
Although the contribution to the Isotropic Gamma-Ray Background (IGRB) from unresolved extragalactic objects has been studied for many years, its exact composition and origin are as of yet unknown. It is suspected that diffuse processes such as dark matter annihilation contribute to the total IGRB, as well as unresolved gamma-ray emission from Active Galactic Nuclei (AGN), including radio galaxies. Radio galaxies are a source class that emit strongly at radio wavelengths, some of which have also been detected at gamma-ray wavelengths by the Fermi Large Area Telescope (Fermi-LAT), and by very high energy gamma-ray Cherenkov telescopes. It is thought that due to the orientation of their jets, radio galaxies are detected less numerously at gamma-ray energies than blazars. Furthermore, only a small number of radio galaxies have been detected at gamma-ray energies though it is considered that others do as well. It is for these reasons that gamma-ray emitting radio galaxies, an interesting and elusive class of objects, are selected for investigation in this work.
In order to reach the goal of better understanding diffuse processes, it is necessary to model the radio galaxy spectral energy distributions (SEDs). As AGN emission is variable with respect to time, it is critical to use simultaneously collected observations. Calculation of the SED based on simultaneous, multiwavelength data across the electromagnetic spectrum produces a reasonably accurate representation of the state of an object in a given time range. The gamma-ray emitting radio galaxies M 87, NGC 1275, Pictor A, and Centaurus A are selected here based on having been detected in very high energy gamma-rays by Cherenkov telescopes, as well as in other wavelengths. A uniquely consistent analysis approach is applied, in which each radio galaxy is analyzed the same way using simultaneously collected data. This approach sets it apart from other studies.
Fermi-LAT raw data for each source in the sample is analyzed in time ranges which directly overlap the very high energy gamma-ray Cherenkov observations, as well as several other wavelength ranges. A synchrotron self-Compton (SSC) model is applied, which provides accurate treatment of synchrotron and inverse-Compton processes occurring in the jets of AGN, while estimating physical characteristics of the source. It is found that the spectra of M 87, NGC 1275, Pictor A, and Centaurus A can be well described by the same SSC model, producing values for the physical characteristics such as the doppler factor and magnetic field, which are relatively consistent with each other.
In order to characterize the diffuse emission from dark matter self-annihilation, the radio galaxy SEDs are also fit with a dark matter model, resulting in an estimated dark matter particle mass of around 4.7 TeV which lies within predicted ranges.
The highly dense regions near the black holes of AGN provide the optimal conditions for detecting these signatures. It is also found here that discrepancies between the expected emission and the observed emission in the spectra of some radio galaxies can be explained using the combined SSC and dark matter model. As emission from dark matter annihilation is expected to remain steady with respect to time, a key feature of this work is the novelty of the combined SSC and dark matter model, and the finding that dark matter characteristics may be revealed through similar multiwavelength analyses during future low emission states of the AGN.
The radio galaxy sample is then extended to include all gamma-ray emitting radio galaxies detected by the Fermi-LAT, and a calculation of the core radio, total radio, and gamma-ray luminosities is followed through. A future step in extending this work would be to estimate the gamma-ray luminosity function of radio galaxies and their percent contribution to the total IGRB, based on the widely agreed upon assumption that a reasonable estimate of the gamma-ray luminosity function of a population can be attained by appropriately scaling its radio luminosity function, as gamma-ray luminosities and radio luminosities are strongly linearly correlated. This work has also provided the basis for such a calculation by outlining the theory and initial steps.
It is the hope that the vast scope of the gathered data, its simultaneity, and the use of consistent analysis methods across the sample, will provide an improved foundation for a future calculation of the contribution of this population to the IGRB, as well as encourage stricter requirements for multiwavelength studies.
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.
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.
Deterioration of gait and alterations of physiological gait initiation contribute significantly to the burden of disease in Parkinson's disease. This paper systematically investigates disease-specific alterations during the postural phases of gait initiation and demonstrates the influence of dopaminergic networks by assessing levodopa mediated improvements in motor performance and correlation of motor behavior with loss of striatal and cortical dopaminergic neurons. Particular attention is given to known confounders such as initial stance and anthropometrics.
Modern agriculture is the basis of human existence, a blessing, but also a curse. It provides nourishment and well-being to the ever-growing human population, yet destroys biodiversity-mediated processes that underpin productivity: ecosystem services such as water filtration, pollination and biological pest control. Ecological intensification is a promising alternative to conventional farming, and aims to sustain yield and ecosystem health by actively managing biodiversity and essential ecosystem services. Here, I investigate opportunities and obstacles for ecological intensification. My research focuses on 1) the relative importance of soil, management and landscape variables for biodiversity and wheat yield (Chapter II); 2) the influence of multi-scale landscape-level crop diversity on biological pest control in wheat (Chapter III) and 3) on overall and functional bird diversity (Chapter IV). I conclude 4) by introducing a guide that helps scientists to increase research impact by acknowledging the role of stakeholder engagement for the successful implementation of ecological intensification (Chapter V).
Ecological intensification relies on the identification of natural pathways that are able to sustain current yields. Here, we crossed an observational field study of arthropod pests and natural enemies in 28 real-life wheat systems with an orthogonal on-field insecticide-fertilizer experiment. Using path analysis, we quantified the effect of 34 factors (soil characteristics, recent and historic crop management, landscape heterogeneity) that directly or indirectly (via predator-prey interactions) contribute to winter wheat yield. Reduced soil preparation and high crop rotation diversity enhanced crop productivity independent of external agrochemical inputs. Concurrently, biological control by arthropod natural enemies could be restored by decreasing average field sizes on the landscape scale, extending crop rotations and reducing soil disturbance. Furthermore, reductions in agrochemical inputs decreased pest abundances, thereby facilitating yield quality.
Landscape-level crop diversity is a promising tool for ecological intensification. However, biodiversity enhancement via diversification measures does not always translate into agricultural benefits due to antagonistic species interactions (intraguild predation). Additionally, positive effects of crop diversity on biological control may be masked by inappropriate study scales or correlations with other landscape variables (e.g. seminatural habitat). Therefore, the multiscale and context-dependent impact of crop diversity on biodiversity and ecosystem services is ambiguous. In 18 winter wheat fields along a crop diversity gradient, insect- and bird-mediated pest control was assessed using a natural enemy exclusion experiment with cereal grain aphids. Although birds did not influence the strength of insect-mediated pest control, crop diversity (rather than seminatural habitat cover) enhanced aphid regulation by up to 33%, particularly on small spatial scales. Crop diversification, an important Greening measure in the European Common Agricultural Policy, can improve biological control, and could lower dependence on insecticides, if the functional identity of crops is taken into account. Simple measures such as ‘effective number of crop types’ help in science communication.
Although avian pest control did not respond to landscape-level crop diversity, birds may still benefit from increased crop resources in the landscape, depending on their functional grouping (feeding guild, conservation status, habitat preference, nesting behaviour). Observational studies of bird functional diversity on 14 wheat study fields showed that non-crop landscape heterogeneity rather than crop diversity played a key role in determining the richness of all birds. Insect-feeding, non-farmland and non-threatened birds increased across multiple spatial scales (up to 3000 m). Only crop-nesting farmland birds declined in heterogeneous landscapes. Thus, crop diversification may be less suitable for conserving avian diversity, but abundant species benefit from overall habitat heterogeneity. Specialist farmland birds may require more targeted management approaches.
Identifying ecological pathways that favour biodiversity and ecosystem services provides opportunities for ecological intensification that increase the likelihood of balancing conservation and productivity goals. However, change towards a more sustainable agriculture will be slow to come if research findings are not implemented on a global scale. During dissemination activities within the EU project Liberation, I gathered information on the advantages and shortcomings of ecological intensification and its implementation. Here, I introduce a guide (‘TREE’) aimed at scientists that want to increase the impact of their research. TREE emphasizes the need to engage with stakeholders throughout the planning and research process, and actively seek and promote science dissemination and knowledge implementation. This idea requires scientists to leave their comfort zone and consider socioeconomic, practical and legal aspects often ignored in classical research.
Ecological intensification is a valuable instrument for sustainable agriculture. Here, I identified new pathways that facilitate ecological intensification. Soil quality, disturbance levels and spatial or temporal crop diversification showed strong positive correlations with natural enemies, biological pest control and yield, thereby lowering the dependence on agrochemical inputs. Differences between functional groups caused opposing, scale-specific responses to landscape variables. Opposed to our predictions, birds did not disturb insect-mediated pest control in our study system, nor did avian richness relate to landscape-level crop diversity. However, dominant functional bird groups increased with non-crop landscape heterogeneity. These findings highlight the value of combining different on-field and landscape approaches to ecological intensification. Concurrently, the success of ecological intensification can be increased by involving stakeholders throughout the research process. This increases the quality of science and reduces the chance of experiencing unscalable obstacles to implementation.
Deubiquitinases are regulators of the ubiquitin proteasome system that counteract the ubiquitination cascade by removing ubiquitin from substrates and cleaving ubiquitin chains. Due to their involvment in various important pathways, they are associated with several diseases and may thus present promising drug targets. The two related ubiquitin specific proteases USP25 and USP28 share a highly conserved amino acid sequence but perform distinct biological functions. USP28 plays roles in cell cycle regulation and was also linked to several types of cancer. It adopts oncogenic functions by rescuing the oncoproteins MYC and JUN from proteasomal degradation, which is induced by the E3-ligase SCF (FBW7). Opposingly, USP28 also regulates the stability of the tumor suppressor FBW7 itself. USP25 contributes to a balanced innate immune system by stabilizing TRAF3 and TRAF6 and lately was found to promote Wnt-signaling by deubiquitinating TNKS.
Due to the high level of identity of both proteases, a recent attempt to inhibit USP28 led to cross reactivity against USP25. In our study, we characterized both USP25 and USP28 structurally and functionally using x-ray crystallography, biochemical as well as biophysical approaches to determine similarities and differences that can be exploited for the development of specific inhibitors.
The crystal structure of the USP28 catalytic domain revealed a cherry-couple like dimer that mediates self-association by an inserted helical subdomain, the USP25/28 catalytic domain inserted domain (UCID). In USP25, the UCID leads to formation of a tetramer composed of two interlinked USP28-like dimers. Structural and functional analysis revealed that the dimeric USP28 is active, whereas the tetrameric USP25 is auto inhibited. Disruption of the tetramer by a cancer-associated mutation or a deletion-variant activates USP25 through dimer formation in in vitro assays and leads to an increased stability of TNKS in cell studies. Furthermore, in vitro data showed that neither ubiquitin nor substrate binding led to the activation of the USP25 tetramer construct. With the structure of the C-terminal domain of USP25, we determined the last unknown region in the enzyme as a separately folded domain that mediates substrate interactions.
Combined the structures of the USP25 and USP28 catalytic domains and the functional characterization of both enzymes provide novel insights into the regulation of USPs by oligomerization. Furthermore, we identified individual features of each protease that might be explored for the development of specific small molecule inhibitors.
Gastrointestinal infections account for high morbidity and mortality in humans every year across the globe. The increasing emergence of antibiotic resistance among the gastrointestinal pathogens and the induction of virulence factors by antibiotics makes it highly risky to only depend on antibiotic therapy for intestinal infections. Most of these infections are associated with an imbalance in the gut microbial population whereas the restoration of the balance with probiotic supplements can result in an improvement of the health condition. Probiotics are therefore considered as successful support in the treatment of gastrointestinal infections.
E. coli Nissle 1917 (EcN) is the active component of the probiotic medication Mutaflor® and has been used in the treatment of various gastrointestinal disorders for more than 100 years. Several studies have reported antagonistic effects of EcN against enterohemorrhagic E. coli (EHEC) in vitro and in vivo. However, detailed investigations on the probiotic mechanisms and safety aspects of EcN are a pre-requisite, for administering EcN to treat EHEC infected patients or to use EcN as a prophylactic for the patient’s close contacts.
In this regard, the first part of the study aimed to understand the nature and behaviour of EcN in the presence of pathogenic or non-pathogenic E. coli strains. Transcriptomic analysis was deployed to this end. We investigated the changes in EcN’s transcriptome after different time points of coculture with the EHEC strain EDL933 or the K-12 strain MG1655. The transcriptome data reported a strain-specific response in EcN at all the investigated time points (3 h, 5 h, 7 h and 8 h) of coincubation. The alterations in gene regulation of EcN were highly pronounced in initial timepoints (3 h and 5 h) of coincubation with EDL933, which gradually decreased over time. In the presence of MG1655, the alterations were strongly differentially regulated only at later time points (7 h and 8 h). The unique transcriptional response of EcN towards two different E. coli strains, that are genetically more than 98 % identical, was startling.
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More importantly, this can be considered as a beneficial trait of EcN over a chemical-pharmaceutical preparation like an antibiotic that might act identically on all target cells.
Bacteriophages are one of the most abundant members of gut microbiota. On the one hand, the infection of a probiotic strain by a lysogenic phage could transfer genetic material coding for pathogenic factors or antibiotic resistance into an otherwise beneficial probiotic bacterium and thereby converting it into a virulent pathogenic bacterium. On the other hand, infection by a lytic phage could result in bacterial lysis and prevent the bacterium from exerting its probiotic effect. Thus, in order to successfully establish and colonise the gut, it is crucial for any probiotic to be resistant against phage infections. To address this, in the second part of the study, we investigated the phage resistance of EcN towards the lysogenic lambda and the lytic T4 phage.
EcN showed complete resistance against tested phages and was also able to inactivate these phages upon coincubation. In the case of lambda phages, the resistance was attributed to the presence of a lambdoid prophage (prophage 3) in the genome of EcN. In addition, the overexpression of one of the early genes of EcN’s prophage 3 (i.e. phage repressor gene pr) in the phage sensitive MG1655 conferred partial protection against lambda phage infection. Moreover, the inactivation was mediated by binding of lambda phages to its receptor LamB. Experiments with lytic T4 phages revealed that the EcN’s K5 polysaccharide capsule was crucial for its T4 phage resistance, while its lipopolysaccharide (LPS) inactivated the T4 phages. Apart from protecting itself, EcN displayed even a protective role for the tested K-12 strains, by interfering with the lysogeny and lysis by these phages.
In summary, this work highlights two novel positive traits of the probiotic strain EcN: i) the strain-specific response that was evident from the global transcriptome analysis of EcN when incubated with other E. coli strains, and ii) lytic and lysogenic phage resistance. Both these traits are additional safety aspects for a well-characterised probiotic strain and encourage its application in therapeutics.
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.
Dispersal is a life-history trait affecting dynamics and persistence of populations; it evolves under various known selective pressures. Theoretical studies on dispersal typically assume 'natal dispersal', where individuals emigrate right after birth. But emigration may also occur during a later moment within a reproductive season ('breeding dispersal'). For example, some female butterflies first deposit eggs in their natal patch before migrating to other site(s) to continue egg-laying there. How breeding compared to natal dispersal influences the evolution of dispersal has not been explored. To close this gap we used an individual-based simulation approach to analyze (i) the evolution of timing of breeding dispersal in annual organisms, (ii) its influence on dispersal (compared to natal dispersal). Furthermore, we tested (iii) its performance in direct evolutionary contest with individuals following a natal dispersal strategy. Our results show that evolution should typically result in lower dispersal under breeding dispersal, especially when costs of dispersal are low and population size is small. By distributing offspring evenly across two patches, breeding dispersal allows reducing direct sibling competition in the next generation whereas natal dispersal can only reduce trans-generational kin competition by producing highly dispersive offspring in each generation. The added benefit of breeding dispersal is most prominent in patches with small population sizes. Finally, the evolutionary contests show that a breeding dispersal strategy would universally out-compete natal dispersal.
Endophytes live in partial symbiosis inside a plant and have been detected in all tested plants. They belong to the group of fungi or bacteria and their ecological function is mostly unknown. The fungal endophytes of the genus Epichloë belong to a special group of endophytes. Epichloë endophytes live symbiotically inside cool season grass species and some of them are able to produce alkaloids toxic to vertebrates and insects. Their symbiosis is seen as mutualistic for the following reasons: the fungus provides the plant herbivore resistance by producing alkaloids, and it increases the plant’s drought tolerance as well as its biomass production. In return, the grass provides the fungus shelter, nutrients and dispersal. Epichloë endophytes are host specific and the ability to produce alkaloids differs between species. In order to estimate intoxication risks in grasslands, it is necessary to detect infection rates of different grass species with Epichloë endophytes, and to determine the genotypes and chemotypes of the Epichloë species as well as the produced alkaloid concentrations. Factors like land-use intensity or season may have an influence on infection rates and alkaloid concentrations. Also, different methodological approaches may lead to different results. In this doctoral thesis my general aim was to evaluate intoxication risks in German grasslands caused by Epichloë endophytes. For that I investigated infection rates of different grass species and the genotypes and chemotypes of their Epichloë endophytes in German grasslands (Chapter II). Furthermore, I compared alkaloid concentrations detected with dry and fresh plant weight and different analytical methods. I also detected possible changes on the influence of season or land-use intensity (Chapter III). Additionally, I examined infections with Epichloë endophytes and alkaloid concentrations in commercially available grass seed mixtures and determined how that influences the intoxication risk of grazing animals in Europe (Chapter IV).
It is of agricultural interest to estimate intoxication risks for grazing livestock on German grasslands due to Epichloë infected grass species. Therefore, it is important to investigate which grasses are infected with the Epichloë endophyte, if the endophytes have the ability to produce vertebrate and invertebrate toxic alkaloids and if the alkaloids are indeed produced. I showed that Epichloë festucae var. lolii infecting agriculturally important Lolium perenne lacked the starting gene for ergovaline biosynthesis. Hence, vertebrate toxic ergovaline was not detected in the majority of the collected L. perenne plants. The detection of alkaloid concentrations is an important tool to estimate intoxication risk for vertebrates, but also invertebrates. My studies showed that the usage of dry plant material is crucial to quantify the correct alkaloid concentrations, and that alkaloid concentrations can vary depending on the detection method. Hence, the usage of validated, similar detection methods is important to be able to compare alkaloid concentrations from different studies. Nevertheless, the trends of seasonal changes and the influence of land-use intensity stayed the same, regardless if dry or fresh plant weight was used. Also, alkaloid concentrations were below toxicity thresholds on population level, regardless of the method used. Two commercially available forage grass and two commercially available turf grass seed mixtures were infected with Epichloë endopyhtes and alkaloids were detected. This might contribute to the spreading of Epichloë endopyhtes in Germany, therefore seed mixtures should be tested for Epichloë infections. My results indicate that the intoxication risk is generally low in Germany at the moment, although that might change due to climate change, an increase of monocultural land-use, or the seeding of Epichloë infected grass seeds.
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 recent years, great progress has been made in the area of Artificial Intelligence (AI) due to the possibilities of Deep Learning which steadily yielded new state-of-the-art results especially in many image recognition tasks.
Currently, in some areas, human performance is achieved or already exceeded.
This great development already had an impact on the area of Optical Music Recognition (OMR) as several novel methods relying on Deep Learning succeeded in specific tasks.
Musicologists are interested in large-scale musical analysis and in publishing digital transcriptions in a collection enabling to develop tools for searching and data retrieving.
The application of OMR promises to simplify and thus speed-up the transcription process by either providing fully-automatic or semi-automatic approaches.
This thesis focuses on the automatic transcription of Medieval music with a focus on square notation which poses a challenging task due to complex layouts, highly varying handwritten notations, and degradation.
However, since handwritten music notations are quite complex to read, even for an experienced musicologist, it is to be expected that even with new techniques of OMR manual corrections are required to obtain the transcriptions.
This thesis presents several new approaches and open source software solutions for layout analysis and Automatic Text Recognition (ATR) for early documents and for OMR of Medieval manuscripts providing state-of-the-art technology.
Fully Convolutional Networks (FCN) are applied for the segmentation of historical manuscripts and early printed books, to detect staff lines, and to recognize neume notations.
The ATR engine Calamari is presented which allows for ATR of early prints and also the recognition of lyrics.
Configurable CNN/LSTM-network architectures which are trained with the segmentation-free CTC-loss are applied to the sequential recognition of text but also monophonic music.
Finally, a syllable-to-neume assignment algorithm is presented which represents the final step to obtain a complete transcription of the music.
The evaluations show that the performances of any algorithm is highly depending on the material at hand and the number of training instances.
The presented staff line detection correctly identifies staff lines and staves with an $F_1$-score of above $99.5\%$.
The symbol recognition yields a diplomatic Symbol Accuracy Rate (dSAR) of above $90\%$ by counting the number of correct predictions in the symbols sequence normalized by its length.
The ATR of lyrics achieved a Character Error Rate (CAR) (equivalently the number of correct predictions normalized by the sentence length) of above $93\%$ trained on 771 lyric lines of Medieval manuscripts and of 99.89\% when training on around 3.5 million lines of contemporary printed fonts.
The assignment of syllables and their corresponding neumes reached $F_1$-scores of up to $99.2\%$.
A direct comparison to previously published performances is difficult due to different materials and metrics.
However, estimations show that the reported values of this thesis exceed the state-of-the-art in the area of square notation.
A further goal of this thesis is to enable musicologists without technical background to apply the developed algorithms in a complete workflow by providing a user-friendly and comfortable Graphical User Interface (GUI) encapsulating the technical details.
For this purpose, this thesis presents the web-application OMMR4all.
Its fully-functional workflow includes the proposed state-of-the-art machine-learning algorithms and optionally allows for a manual intervention at any stage to correct the output preventing error propagation.
To simplify the manual (post-) correction, OMMR4all provides an overlay-editor that superimposes the annotations with a scan of the original manuscripts so that errors can easily be spotted.
The workflow is designed to be iteratively improvable by training better models as soon as new Ground Truth (GT) is available.
This thesis is concerned with the solution of control and state constrained optimal control problems, which are governed by elliptic partial differential equations. Problems of this type are challenging since they suffer from the low regularity of the multiplier corresponding to the state constraint. Applying an augmented Lagrangian method we overcome these difficulties by working with multiplier approximations in $L^2(\Omega)$. For each problem class, we introduce the solution algorithm, carry out a thoroughly convergence analysis and illustrate our theoretical findings with numerical examples.
The thesis is divided into two parts. The first part focuses on classical PDE constrained optimal control problems. We start by studying linear-quadratic objective functionals, which include the standard tracking type term and an additional regularization term as well as the case, where the regularization term is replaced by an $L^1(\Omega)$-norm term, which makes the problem ill-posed. We deepen our study of the augmented Lagrangian algorithm by examining the more complicated class of optimal control problems that are governed by a semilinear partial differential equation.
The second part investigates the broader class of multi-player control problems. While the examination of jointly convex generalized Nash equilibrium problems (GNEP) is a simple extension of the linear elliptic optimal control case, the complexity is increased significantly for pure GNEPs. The existence of solutions of jointly convex GNEPs is well-studied. However, solution algorithms may suffer from non-uniqueness of solutions. Therefore, the last part of this thesis is devoted to the analysis of the uniqueness of normalized equilibria.
Plants have evolved many mechanisms to defend against herbivores and pathogens. In many cases, these mechanisms took other duties. One example of such a neofunction- alisation would be carnivory. Carnivory evolved from the defence against herbivores. Instead of repelling the predator with a bitter taste, the plant kills it and absorbs its nutrients. A second example can be found in the pollination process. Many of the genes involved here were originally part of defence mechanisms against pathogens. In this thesis, I study these two examples on a genomic and transcriptomic level. The first project, Genomics of carnivorous Droseraceae, aims at obtaining annotated genome sequences of three carnivorous plants. I assembled the genome of Aldrovanda vesiculosa, annotated those of A. vesiculosa, Drosera spatulata and Dionaea muscipula and com- pared their genomic contents. Because of the high repetitiveness of the D. muscipula genome, I also developed reper, an assembly free method for detection, classification and quantification of repeats. With that method, we were able to study the repeats without the need of incorporating them into a genome assembly. The second large project investigates the role of DEFL (defensin-like) genes in pollen tube guidance in tobacco flowers. We sequenced the transcriptome of the SR1 strain in different stages of the pollination process. I assembled and annotated the transcriptome and searched for differentially expressed genes. We also used a method based on Hidden- Markov-Models (HMM) to find DEFLs, which I then analysed regarding their expression during the different stages of fertilisation. In total, this thesis results in annotated genome assemblies of three carnivorous Droser- aceae, which are used as a foundation for various analyses investigating the roots of car- nivory, insights into the role of DEFLs on a transcriptomic level in tobacco pollination and a new method for repeat identification in complex genomes.