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Taphonomy and palaeoecology of Laetoli as well as Makuyuni, Arusha region in northern Tanzania
(2004)
This thesis is the result of the Hominid Corridor research Project in Tanzania since 1993 to 1995 that include Pliocene and Pleistocene localities. The localities under study include Laetoli and Manyara area in Arusha Region, northern Tanzania. The thesis has the following specific objectives: firstly, to identify taxa recovered from the studied assemblages; secondly, to underpin taphonomic history of the assemblages under study; thirdly, to elucidate further palaeoecological reconstruction of the assemblages; and finally, to examine surface fossil fauna modifications including agents of modifications either hominids or carnivores.
The Upper Laetolil Beds are dated at 3.5 million years ago (Ma) and the Ndolanya Beds are bracketed in age between 3.5 and 2.41 Ma. The Naibadad Beds, also from Laetoli area, are date to be between 2.2 to 2.1 Ma. The Naibadad Beds are correlated with the base of Bed I at Olduvai Gorge. There are so far no absolute dates for Manyara assemblages. Based on biostratigraphic correlation, the younger overlying unit, the Upper Manyara Beds are estimated to belong to Later Pleistocene and the Lower Manyara Beds are estimated to belong to Early Pleistocene. The Upper Manyara Beds are correlated to the age of Bed III at Olduvai Gorge, while the Lower Manyara Beds are interpreted to span the same contemporaneity with the upper part of Bed II at Olduvai Gorge.
At Laetoli localities, terrestrial mammals while localities from Manyara besides terrestrial mammals dominate fauna; they include aquatic species such as fish, crocodiles and hippopotamus. The main families recovered from Upper Laetolil Beds complement those already recovered from former research works by other workers. This is also true for the younger overlying stratigraphic horizon, the Upper Ndolanya Beds. Thus, mammalian families recovered from Upper Laetolil Beds include Bovidae, Carnivora, Elephantidae, Equidae, Lagomorpha, Suidae, Rodentia, Hominoidea and Rhenocerotidae. Remains of an invertebrate, Gastropoda were also recovered. For Upper Ndolanya Beds include almost the same families recovered from Upper Laetolil Beds, but based on former recovery of fossil fauna, these Beds outnumber greatly the Upper Laetolil Beds in bovid composition by 20 per cent. Such a change in species composition is noticed also from South African localities and East African localities such as the East Turkana. This is interpreted to be due to climatic change drier environments that included species adapted to such palaeoclimates.
For the first time, our team has been able to retrieve specimens identifiable to taxa, a pattern that not possible from previous workers who claimed to have recovered too sparse specimens to be identifiable to any taxon.
The Upper Manyara Beds as well as Lower Manyara taxonomic composition include aquatic species besides the large terrestrial mammalian fauna retrieved from there. In due regard, the former horizon is attributed to have affinity with Olduvai Bed III components and the latter, older horizon, is attributed to have affinity with upper parts of Bed II times at Olduvai Gorge. The Lower Manyara Beds can be said to have, in relative terms, affinity to species recovered from site RC 11 of the Chiwondo Beds, Malema region in northern Malawi, although the former site may be equable to the terminal age of the latter locality.
Fossil hominid remains; attributable to genus Homo and possibly species Homo erectus have been recovered from two localities, Mk 2 and Mk, along Lower Manyara Beds. On the other hand, stone tools, identified to belong to the Acheulian industrial technocomplex, were recovered from site Mk 4.
All of fossil fauna from Laetoli sites were mostly exfoliated and there shows to be little effect in terms of hydrodynamic sorting of the fossil bones. However, intense carnivore activity is witnessed due to the almost one to one ratio of proximal to distal ends. This is also true for the Lower Manyara Beds locality. Through examination of surface modifications of the fossil fauna, it has been established that there was carnivore consumption of ungulates. There is no evidence of hominid involvement that has to be testified by stone tools.
Nitric oxide (NO) is a potent mediator with pleiotropic functions such as inhibition of platelet aggregation, smooth muscle relaxation and regulation of neuronal transmission. These effects are mostly mediated by intracellular NO-sensitive guanylyl cyclases (GCs) which convert GTP into the second messenger, cGMP. This messenger in turn activates multiple downstream effectors such as cGMP-dependent protein kinases, cGMP-regulated ion channels and cGMPdependent phosphodiesterases. Mammalian NO-sensitive GCs are obligate heterodimers of an α and β subunit each. Given that these enzymes play a key role in cGMP-mediated pathways, one may anticipate that mechanisms other than allosteric activation via NO may exist to regulate the production and turnover of cGMP. In this thesis, novel aspects of the regulation of the most abundantly expressed GC heterodimer α1β1 are presented.
A possible mechanism of regulation that was tested here, is tyrosine phosphorylation. Using anti-phosphotyrosine antibodies, the phosphorylation of the β1 subunit was detected after incubation of β1-overexpressing COS-1 cells with protein tyrosine phosphatase (PTP) inhibitors such as pervanadate and bpV(phen). β1 phosphorylation on tyrosines was also observed in PC-12 cells which endogenously express GC and in rat aorta after inhibition of PTPs. Furthermore, hydrogen peroxide was found to be a physiological stimulus for the induction of reversible β1 tyrosine phosphorylation in intact cells. Using phenylalanine mutants of different tyrosines, residue 192 (Y192) of β1 was identified as the major phosphorylation site. Consistent with this finding, sequence analyses showed that Y192 forms part of a motif that resembles a preferential target site for Src-like kinases. When tyrosine-phosphorylated, this motif exposes a typical SH2 docking site for members of the Src kinase family.
Experiments with inhibitors of Src kinases, PP1 and PP2, clearly showed that phosphorylation of Y192 is Src-dependent. Preincubation of β1-expressing cells with these inhibitors significantly reduced the level of phosphorylated β1 after bpV(phen) treatment. Furthermore, co-expression of β1 with Src led to a strong phosphorylation of this subunit. Co-precipitation experiments showed that Src interacts with GC. Interestingly, kinases of the Src family are recruited to β1 via the SH2 domain upon phosphorylation of Y192. Together, these results indicate that Src kinases phosphorylate tyrosine 192 thereby creating a docking site for their own SH2 domains. Kinase bound to GC may then catalyze phosphorylation of GC or other downstream effectors. Inhibition of PTPs altered GC activity in two ways: it increased both the basal activity and the YC-1- and BAY 41-2272-stimulated activity two-fold, and it reduced the sensitivity of the enzyme towards NO. The detailed mechanism of action is still unknown, but experiments using the mutant β1[Y192F] demonstrated that residue 192 is not responsible for these effects.
Another major focus of this thesis was the identification of novel GC binding proteins. Using the yeast two-hybrid approach, the carboxy-terminal portion of a protein named AGAP1 (amino acid (aa) 399-804) was found to interact with the catalytic domain of α1 (aa 466-690) and with the regulatory domain of β1 (aa 1-348). Human AGAP1 is a multidomain protein of 804 amino acids with a calculated molecular mass of 89,1 kDa comprising an Arf-GAP (GAP:GTPase activating protein), a putative GTPase domain, two Ankyrin repeats and a PHdomain. Co-precipitation experiments using lysates from mammalian cells overexpressing both binding partners confirmed the interaction of AGAP1 with the GC subunits. Immunofluorescence analyses demonstrated that AGAP1 co-localizes with GC in the cytoplasm of COS-1 cells.
In Northern blots, AGAP1 mRNA was detected in various human and murine tissues showing a comparable expression pattern described for the mRNA of α1 and β1. Using an AGAP1-specific antibody, endogenous protein was precipitated from lysates of HEK-293 cells derived from human embryonic kidney. The same antibody efficiently cross-reacted with the rat homologue (rAGAP1) and immunoprecipitated endogenous rAGAP1 from lysates of PC-12 cells, aorta and heart. The molecular mass of rAGAP1 is larger than that of the human protein, possibly due to an additional exon present in the rat genome. Like β1, AGAP1 is a substrate for tyrosine kinases. Phosphorylation of AGAP1 was detected after inhibition of PTPs or by coexpression of Src. Furthermore, the kinase inhibitor PP2 strongly impaired phosphorylation of AGAP1 after pervanadate treatment suggesting that tyrosine kinases of the Src family are involved. Measurements of cGMP production showed that AGAP1 has no influence on the activity of NO-sensitive GC. Interestingly, inhibition of PTPs potently increased the complex formation between AGAP1 and GC indicating that the interaction between these two proteins is modulated by reversible tyrosine phosphorylation. Whether this effect is due to the phosphorylation of AGAP1 or GC is still unknown. AGAP1 associates with endosomes and exposes Arf-GAP activity towards Arf1 and Arf5 which are involved in vesicular transport. Thus, one may hypothesize that binding of α1β1 to AGAP1 targets GC to distinct subcellular compartments in close proximity to cGMP-dependent effectors, thereby optimizing cGMP generation and fostering cGMP-driven actions.
Taken together, these results demonstrate that beside the modulation of GC by NO the enzyme is regulated by tyrosine phosphorylation and interaction with AGAP1.
Aim of the present study was the characterization of the RORa receptor (Retinoidrelated Orphan Receptor a). RORa is a member of the nuclear receptor family and is involved into the differentiation of Purkinje cells, inflammation, arteriosclerosis, and bone mineralization. Nuclear receptors are transcription factors and mediate biological responses within target cells to outer signals such as lipophilic hormones. They are involved in development, growth, differentiation, proliferation, apoptosis, and maintenance of homeostasis. Ligand binding, posttranslational modifications, and cofactor recruitment control their activity. Nearly all nuclear receptors share a common modular structure with an Nterminal A/B region, a DNA-binding domain (DBD) that is composed of two zinc finger motifs, a hinge region, and a C-terminal ligand-binding domain (LBD). The RORs comprise the subtypes RORa, RORb, and RORg, which are encoded by different genes. All isoforms of the respective subtypes only differ in their A/B domain. This study focused mainly on the exploration of the gene structure, expression, and subcellular distribution of RORa...
Metastatic rhabdomyosarcoma (RMS) is one of the most challenging tumor entities in pediatric oncology caused by treatment resistances and immune escape. Novel chimeric antigen receptor (CAR) immunotherapies as specific, effective and safe treatment provide antitumor cytotoxicity by soluble factors and ligands/receptor signals. Besides its intrinsic potential as innate immune cell the ErbB2-sprecific CAR-engineered natural killer (NK)-92 cell line NK-92/5.28.z also provides CAR-mediated cytotoxicity, resulting in a high lytic capacity against 2D and 3D RMS cell structures in vitro. Also in a xenograft model using immune deficient NOD/Scid/IL2Rγ-/- (NSG) mice inhibited NK-92/5.28.z the tumor growth as long as the cells were administered and therefore prolonged the survival of the animals. The NK-92/5.28.z were distributed by the blood circulation and subsequently infiltrated the tumor tissue. Due to the malignant origin of the NK-92 cell line the cells must be irradiated prior to the use in patients. While the irradiation hampered the proliferation of NK-92/5.28.z cells, the cytotoxicity against RMS cells in vitro is retained for at least 24 hours. In the xenograft model irradiated NK-92/5.28.z cells inhibited the tumor growth but to a lower extent than untreated cells, as irradiated cells have only a limited life span in vivo no durable persistence and remission was achieved. Therefore, combinatorial approaches were focused and while blocking of the PD-1/PD-L1 axis did not resulted in a significantly enhanced tumor cell lysis, the combinatorial treatment with proteasome inhibitor bortezomib exhibited a significant enhanced cytotoxicity against RMS cells at least in vitro. Bortezomib itself induces caspase mediated apoptosis and also the upregulates the expression of TRAIL receptor DR5. The corresponding ligand TRAIL is expressed on the surface of the NK-92/5.28.z and pursuing experiments with purified TRAIL and bortezomib revealed a synergism. NK-92/5.28.z as an off-the-shelf product is therefore feasible for the therapy of metastatic RMS, but it might be necessary to support the cytotoxicity by additive agents like proteasome inhibitor bortezomib to archive durable remission.
Another cell population suitable for RMS CAR-immunotherapy are cytokine induced killer (CIK) cells, a heterogenous cell population generated from autologous PBMCs consisting of T, NK and T-NK cells. Lentivirally transduced ErbB2-specific CAR-CIK cells were previously shown to inhibit the tumor engraftment in a RMS xenograft model. However, lentiviral transduced adoptive immunotherapies bear risks for the transfer in patients, therefore the Sleeping Beauty Transposon System (SBTS) as a non-viral method, which integrates the CAR coding DNA by a cut-and-paste mechanism from a minicircle (MC) into the CIK cells genome is more feasible for the generation of CAR-CIK cells. The Sleeping beauty transposase mRNA and the MC were transferred in the cell by nucleofection, different factors influence the transfection efficiency and viability of the CIK cells in this harsh procedure. In preliminary experiments with MC Venus, a MC encoding eGFP, the highest transfection efficiency with the best proliferative capacity was achieved with cells on day 3 of CIK culture and without the addition of autologous monocytes as feeder cells. For the CAR construct the protocol was further improved by adjusting crucial factors, for this construct the best results were achieved on day 0, without irradiated PBMCs as feeder cells and cultivation in X-Vivo10 medium supplemented with human fresh frozen plasma. The X-Vivo10 medium enhanced the percentage of NK- and T-NK cells significantly compared to CAR-CIK cells cultured in RPMI. Since the gene transfer by SBTS resulted in CAR-CIK cells stably expressing a CAR in all subpopulations, resulting in a significantly enhanced cytotoxicity against RMS cells in vitro, these cells were compared to lentiviral transduced CAR-CIK cells in vitro and in vivo. While the SBTS CAR-CIK cells were superior to viral CAR-CIK cells in 2D short-term assays, the viral cells showed higher lytic capacity in 3D spheroid long-term assays. In a RMS xenograft model lentiviral CAR-CIK cells significantly prolonged the survival of mice and persisted, whereas SBTS CAR-CIKs did not favor the overall survival compared to untreated controls and also did not persist. Phenotypic analysis revealed a highly cytotoxic CD8+ and late effector memory dominant phenotype for SBTS CAR-CIK cells supporting short-term cytotoxicity but also more prone for exhaustion, while viral CAR-CIK cells showed a more balanced phenotype for memory and cytotoxicity. Therefore, the SBTS is feasible for the ErbB2-CAR gene transfer in CAR-CIK resulting in a stable CAR-expression with high short-term cytotoxicity, but these cells are also more prone to exhaustion and the protocol might be adapted further to prevent this limitation for in vivo application.
This work underlines the hard-to-treat characteristics of metastatic RMS, but also shows some approaches for further evaluation like the combination of NK-92/5.28.z cells with bortezomib and the feasibility of the generation of CAR-CIK cells via SBTS.
In narratology, a widely recognized method involves exploring the connection between implied authors and implied readers. It entails correlating abstract narrative components within a text to understand the conveyed message and the multitude of interpretations it can offer. The present study adopts an implied reader-oriented approach to analyze three selected novels from the twentieth and twenty-first centuries—one Nigerian, one Caribbean, and one Kurdish. The aim is to explore the potential readings within these texts, considering the hermeneutic process of critical reading. The selected texts include Chinua Achebe’s Things Fall Apart, (1958), Same Selvon’s The Lonely Londoners, (1956), and Karwan Kakesur’s The Channels of the Armed Monkeys, (2011). This approach closely examines the communication between the author and reader of the text, with a special focus on the varying levels of communication between the components of the narration, including fictional and implied fictional communication.
The implied fictional communication occurs between a narrative agent known as ‘the implied author’ and its fictional counterpart ‘the implied reader’ rather than between the real, flesh and blood authors and readers. I argue that this level of communication is coded, and the act of decoding it is part of the reading process performed by the reader. Certain texts can propose different and sometimes opposing readings which are initially and purposefully designed by the implied author and addressed to different implied readers. These readings are not necessarily the results of different real readers but rather incorporated ones predetermined by the implied author only to be acknowledged and uncovered by the readers. In other words, the latent meaning is and always was an integral part of the text and is not something created by the imaginative reader or critic. The core interest of my thesis lies in identifying prompts and suggestions within the narrative of the selected texts and ultimately understanding the readerships prestructured in them. Identifying the different readers within those texts will provide new reinterpretations that can add undetected values to the reading process and sometimes suggests opposing readings to how those texts have so far been read. Additionally, it is the objective of this thesis to propose new ways that readers can interact with reading literature that would result in a more aesthetic and entertaining reading experience besides providing ways to be more informed and aware of the cues certain narrative texts contain.
There have been numerous critical studies on both narratology and postcolonial or minority literatures; however, there has been little scholarly work that attempts to utilize narratology as a theoretical foundation for understanding postcolonial and minority fiction.
This study examines fictional texts from Nigerian, Caribbean, and Kurdish literature, employing the narratological concept known as ‘Multiple Implied Readers’. By incorporating concepts from Brian Richardson’s ‘Singular Text, Multiple Implied Readers’, and Peter J. Rabinowitz’s ‘authorial audiences’, I explore the various readerships that the texts could encompass. This exploitation may lead to the discovery of new readings, interpretations, and meanings that would otherwise remain undetected. These structures introduce provocative indeterminacies that challenge the reader’s synthesis of information into coherent configurations of meaning. Consequently, this approach not only enhances the reading experience but also opens doors to new interpretations of the text. In some cases, these interpretations could even dismantle prior understandings and propose entirely new readings.
The concepts of the implied author and implied reader have been studied before in relation to various disciplines of narratology. However, by applying them in conjunction with the relatively less researched subject of multiple implied readers, I aim to shed light on important aspects of these readings. This exploration could prove beneficial for literature students as well as critical readers of literary texts, revealing the potential of these texts to accommodate more than one implied reader within their narratives.
While high-quality climate reconstructions of some past warm periods in the Cenozoic era now exist, the geological processes responsible for driving the observed longterm changes in atmospheric CO2 are not sufficiently well understood. The long-term change in atmospheric CO2 across the Cenozoic has been proposed to be driven by processes such as terrestrial weathering, organic carbon production and burial, reverse weathering, and volcanic degassing. One way of constraining the relative importance of the various driving forces proposed so far is to better understand the degree to which ocean chemistry has changed because the chemistry of seawater responds to geologic processes that drive atmospheric CO2. In addition, knowledge of the concentration of the major elements in seawater is crucial for accurately applying proxies such as those based on the boron isotopic composition and Mg/Ca of marine carbonates (a proxy for palaeo pH/CO2 and palaeotemperature, respectively). Previously reported records of seawater composition are primarily derived from fluid inclusions in marine evaporites; however, the results are sparse due to the limited availability of such deposits. In this thesis, changes in the Eocene seawater chemistry were reconstructed using trace element (elements/Ca) and isotopic (δ26Mg) proxies in a Larger Benthic Foraminifera (LBFs), i.e., Nummulites sp., to constrain the driving processes of long-term changes in seawater chemistry.
To achieve the objective of this thesis, first, a measurement protocol was established using LA-ICPMS to measure the K/Ca ratio simultaneously with other element/calcium ratios, which is challenging due to the interference of ArH+ on K+. Utilising this newly established measurement protocol, laboratory-cultured Operculina ammonoides grown at different seawater calcium concentrations ([Ca2+]), repeated at different temperatures, as well as modern O. ammonoides collected from different regions exhibiting a range of seawater parameters, were investigated. A significant correlation was observed between K/Casw and K/CaLBF, allowing K/CaLBF to potentially be used as a proxy for seawater major ion reconstructions. In addition, modern O. ammonoides demonstrated no significant influence of most seawater parameters (temperature, salinity, pH, or [CO32-]) on K/CaLBF. Modern O.
ammonoides were also assessed for their Mg isotopic composition (δ26Mg), revealing no significant effect of temperature or salinity on δ26MgLBF. Furthermore, the Mg isotopic fractionation in O. ammonoides was found to be close to that of inorganic calcite, indicating minimal vital effects in these large benthic foraminifera.
Operculina ammonoides is the nearest living relative of the abundant Eocene genus Nummulites, enabling the reconstruction of seawater chemistry using the calibration based on O. ammonoides. The trace elemental/calcium proxies, including Na/Ca, K/Ca, and Mg/Ca, as well as the δ26Mg proxy, were investigated in Eocene Nummulites. The result showed that during the Eocene, [Ca2+]sw was 1.6-2 times higher, while [K+]sw was ~2 times lower than the modern seawater composition. Furthermore, [Mg2+]sw decreased from the early Eocene (54.3− +9 7..69 mmol kg-1 at ~55 Ma) to Late Eocene (37.8− +4 4..3 4 mmol kg-1 at ~31 Ma), followed by
an increase toward modern seawater [Mg]. In contrast, the variability in δ26Mgsw values remained within a narrow range of ~0.3 ‰ throughout the Cenozoic. The reconstructed [Ca2+]sw agrees with the suggestion that Cenozoic seawater chemistry changes can be explained via a change in the seafloor spreading rate. When combined with existing records, the observed minimal change in δ26Mgsw with an increase in [Mg2+]sw suggests an additional possible role of a decrease in the formation of authigenic clay minerals coincident with the Cenozoic decline in deep ocean temperature, which is also supported by the increase in the [K+]sw reconstructed here for the first time. This finding highlights that the reduction in seafloor-spreading rate and decline in reverse weathering during the Cenozoic era has played a significant role in the evolution of seawater chemistry, emphasizing the importance of these processes in driving long-term changes in the carbon cycle.
The core of this work is represented by the investigation of the chiral phase transition, using Monte Carlo simulations and unimproved staggered fermions, both in the weak and strong coupling regimes of Quantum Chromodynamics. Based on recent results from Monte Carlo simulations, both using unimproved staggered fermions and Wilson fermions, the chiral phase transition in the continuum and chiral limit shows compatibility with a second-order phase transition for Nf (number of flavours) in range [2:7], at zero baryon chemical potential. This achievement relies on the analytic continuation of Nf to non-integer values on the lattice, which allows to make use of extrapolation techniques to the chiral limit, where simulations are not possible. Furthermore, these results provide a resolution to the ambiguous scenario for Nf = 2 in the chiral limt. The first part of this thesis is devoted to the investigation of the chiral phase transition when a non-zero imaginary baryon chemical potential is involved, whose value corresponds to the 81% of the Roberge-Weiss one. Using the same extrapolation techniques aforementioned, the order of the chiral phase transition in the continuum and chiral limit shows compatibility with a second-order phase transition for Nf in range [2:6], highlighting a lack of dependence of the order of the chiral phase transition on the imaginary baryon chemical potential value. The second part of this thesis is about the study of the extension of the first-order chiral region in the strong coupling regime, at zero baryon chemical potential. Using Monte Carlo techniques, this can be done by investigating the Z2 boundary on a coarse lattice, whose temporal extent reads Nt = 2, and simulations are realised for Nf = 4, 8. The results in the weak coupling regime show, for $Nt = 8, 6, 4 and fixed Nf value, an inflating first-order chiral region. As in the strong coupling limit a second-order chiral phase transition is expected, the first-order chiral region has to shrink as the strong coupling regime is approached, resulting in a non-monotonic behaviour of the Z2 boundary. For Nf = 8, a critical mass on the Z2 boundary has been obtained, confirming the expected non-monotonic behaviour. For Nf = 4 the results do not provide a unique conclusion: Either a Z2 boundary at extremely low bare quark mass or a second-order chiral phase transition in the O(2) universality class in the chiral limit can take place. In addition to the two main topics, the performances of the second-order minimum norm integrator (2MN) and the fourth-order minimum norm integrator (4MN) have been compared, after implementing the 4MN one in the CL2QCD code used to realise our simulations. The 2MN integrator had already been implemented in the code since the first version was released. The two integrators belong to the class of symplectic integrators and represent an essential component of the RHMC algorithm, involved in our investigation. This step is extremely important, in order to guarantee the best quality when collecting data from simulations, and the results of the comparison suggested to favor the 2MN integrator, for both the topics.
Abdominal aortic aneurysm (AAA) is the most common type of aortic aneurysm, which is defined as a dilation of the abdominal aorta over 3.0 cm or more. Surgical repair is the golden standard for the treatment of AAA, in which open surgical repair (OSR) and endovascular aneurysm repair (EVAR) are the main approaches. Technically speaking, the lesion segment of aueurysm is completely replaced by a graft during OSR, while in EVAR, the lesion is insulated by a stentgraft. EVAR is a less invasive treatment than OSR and shows a lower early mortality rate, although the long-term advantages of EVAR over OSR remain inconclusive.
Endoleak, especially the type II endoleak (T2EL), is a common complication after EVAR. According to research, 16-28% of the patients develop a T2EL after EVAR, and it accounts for nearly three in four of all types of endoleaks. Around 30-50% of the T2EL resolved spontaneously during the follow-up, however, it still causes a secondary intervention in many patients. Therefore, it is critical to monitor endoleaks after repair.
Patent aortic branches in the stent-overlapped area and vasa vasorum have been identified as potential sources of blood flow in T2EL. However, the mechanisms of biological changes or remodeling of the aneurysm sac after the repair are still not clear, but they have been considered to play an important role in the development of endoleaks. Unfortunately, it is impossible to obtain a tissue sample of the aortic wall in patients who underwent EVAR.
MicroRNAs (miRNAs) are a class of small single-stranded non-coding RNAs that inhibit the expression of target message RNA (mRNA). miR-29b/29c, miR-155, and miR-15a are miRNAs associated with regulating extracellular matrix (ECM) components, inflammation, and proliferation, respectively. All four miRNAs have been identified as biomarkers of AAA, not only in aneurysm tissue but also extracellular as circulating miRNAs. However, it is still unknown whether they can reflect the biological changes after AAA repair. Thus, we conducted a prospective study to investigate the changes in expression of circulating miR-29b, miR-29c, miR-155, and miR-15a before (T0), 3 days (T1), and 3 months (T2) after AAA repair.
A total of 39 patients were recruited for this study, 17 of whom were repaired by OSR and 22 of whom were repaired by EVAR. Four patients failed the T2 follow-up due to the Covid-19 pandemic. No significant changes were found in the expression of miR-29b, miR-29c, miR-155, and miR-15a. There were also no obvious differences between OSR and EVAR. However, the T1 expression of miR-15a was significantly lower in patients without endoleak after EVAR than in those who developed endoleak after EVAR and those who were repaired by OSR. Unfortunately, these differences did not persist to the T2 follow-up, and no other differences were found among these patients.
In summary, miR-15a is a miRNA that significantly changes in AAA patients. This study demonstrates that the expression of circulating miR-15a is lower in patients without endoleak three days after EVAR, compared to those who had endoleak after EVAR and those who underwent OSR. The results suggest that miR-15a might be involved in the early aortic remodeling after EVAR as an indicator of endoleak.
A powerful technique to distinguish the enantiomers of a chiral molecule is the Coulomb Explosion Imaging (CEI). This technique allows us to determine the handedness of a single molecule. In CEI, the molecule becomes charged by losing many electrons in a very short period of time by interacting with the light. The repulsion forces between the positive charged particles of the molecule leads the molecule to break into parts-fragments. By measuring the three vector momentum of (at least) four fragments, the handedness observable can be determined. In this thesis, CEI is induced by absorption of a single high energy photon, which creates an inner-shell hole (K shell) of the molecule. The subsequent cascade of Auger decays lead to fragmentation. We decided to work with the formic acid molecule in this thesis. Two different experiments were conducted. The first experiment focused on exciting electrons to different energy states, while the second experiment focused on extracting directly a photoelectron to the continuum and measure the angular distribution of the photoelectron in the molecular frame. The primary goal was to search for chiral signal in a pure achiral planar molecule under the previous electron processes. The results of these findings were further implemented to two more molecules.
In the framework of the LHC Injectors Upgrade Project (LIU), the CERN Proton Synchrotron Booster (PSB) went through major upgrades resulting in new effects to study, challenges to overcome and new parameter regimes to explore. To assess the achievable beam brightness limit of the machine, a series of experimental and computational studies in the transverse planes were performed. In particular, the new injection scheme induces optics perturbations that are strongly enhanced near the half-integer resonance. In this thesis, methods for dynamically measuring and correcting these perturbations and their impact on the beam performance will be presented. Additionally, the quality of the transverse beam distributions and strategies for improvement will be addressed. Finally, the space charge effects when dynamically crossing the half-integer resonance will be characterized. The results of these studies and their broader significance beyond the PSB will be discussed.
Methods using environmental DNA to explore and analyze biodiversity from previously unexplored habitats and ecosystems have become increasingly popular in recent years. This is particularly due to the potential reduction in necessary taxonomic expertise, the opportunity to assess microorganismal communities, and decreased time investments required to cover large spatial extents. In forests, the surface of tree bark is an important habitat for epiphytic diversity. Because of the large surface area rich in micro-niches, the seasonal stability of the substrate, and the longevity of trees, tree bark surfaces provide an ideal habitat for many species. Yet, we lack a comprehensive understanding of their communities and the environmental drivers behind the community assembly. These missing links hinder the exploration of the forest microbiome as a whole and limits our understanding of functions of a large forest habitat and its connections to other forest microbiomes. With a holistic eDNA metabarcoding approach, encompassing samples of three major taxonomic groups (e.g. bacteria, fungi, and green algae), as well as simultaneous collections from multiple forest habitats we can contribute to closing these gaps and increase our knowledge of the forest microbiome.
My dissertation is set within the framework of the Biodiversity Exploratories and was conducted in four parts: I. the establishment of an eDNA metabarcoding workflow to reveal the local diversity of the bark surface microbiome; II. the upscaling of the method to large geographic and environmental gradients to uncover the drivers of the microbiome; III. the integration of soil and bark samples to investigate compositional differences in two important forest habitats; IV. the evaluation of eDNA metabarcoding as a tool for biodiversity assessments of lichen diversity in forests.
In the first part, I developed a simple, cost-effective and fast sampling strategy to acquire eDNA samples from the bark of trees in forest ecosystems. Using readily available medical-specimen-collection swabs I sampled bark surfaces of individual trees in Central German forests and used metabarcoding to amplify marker genes of green algae, fungi and bacteria. From the sequencing reads I calculated the first diversity estimates of the major organismal groups of bark surface microbiomes from Central European forests. Overall the methodology produced reliable results, allowing for an expanded sampling in the second part.
In the second part of the dissertation, I expanded the sampling based on the results of part one. I collected bark surface samples from the three regions of the Biodiversity Exploratories covering large spatial and environmental gradients representative for Central European forests. The collection included composite samples from 150 plots and over 750 trees. Utilizing measurements of climatic and forest structure variables provided by the Biodiversity Exploratories, as well as my own community data, I identified the biotic and abiotic drivers behind alpha and beta diversity of the bark surface microbiome.
In the third part, I studied the differences between the bark surface as an unexplored and the soil as an example of a well characterized forest microbiome. Using only the fungal part of the large sampling campaign and soil samples obtained from the same plots at the same time, I assessed the commonalities and differences of the micro-communities of these distinct forest niches. Furthermore, I included two coniferous and one deciduous tree species to examine, if the effect of tree species, previously shown for soil microbiomes, also holds true for the bark surface.
In the last part of my dissertation, I used eDNA in a more applied way as a tool in biodiversity assessments of lichenized fungi. I compared the results from eDNA metabarcoding to an expert floristic mapping conducted in the same plots in 2007/2008. I assigned functional guilds to the fungal taxa obtained in the large sampling campaign and used a subset that was assigned as lichenized fungi.
In conclusion, I showed that eDNA metabarcoding is a valuable tool to reveal the unknown diversity of microorganisms in forest ecosystems. In particular, my results advance our understanding of the bark surface microbiome, an underexplored habitat within forests. The tightly linked interactions of the three major microbial groups underline that studies need to take holistic approaches across multiple taxonomic groups to deepen our understanding of processes governing the assembly of microbiomes. Results from my dissertation may serve as a foundation to inform hypotheses addressing the functions of forest microbiomes. The massive diversity data collected may also contribute to closing the gap in our understanding of macro-organisms and micro-organisms with respect to diversity distributions and patterns of richness, and serve as a baseline for predictions of biodiversity responses under future anthropogenic change.
Biotechnological processes offer better production conditions for a wide variety of goods of industrial interest. The production of aromatic compounds, for example, involves molecules of great value for cosmetic, plastic, agrochemical and pharmaceutic industries. However, the yield of such processes frequently prevents a proper implementtation that would allow the replacement of traditional production processes.
Numerous rational engineering approaches have been attempted to enhance metabolic pathways associated with desired products. Unfortunately, genetic modifications and heterologous pathway expression often lead to a higher metabolic burden on the producing organisms, ultimately leading to reduced production levels and fitness.
This project utilised adaptive laboratory evolution to better understand the development of synthetic cooperative consortia, using S. cerevisiae as a model organism. Specifically, a synthetic cooperative consortium was developed around the exchange of lysine and tyrosine, which was subjected to adaptive laboratory evolution aiming to induce mutations that would improve the system’s fitness either by enhanced production or upgraded stress resistance. Consequently, the mutant strains isolated after the evolution rounds were sequenced to identify relevant variations that could be related to the growth and production phenotypes observed.
The insights derived from this project are expected to contribute to further developing synthetic cooperative consortia with utilitarian purposes.
Hyperparasitic fungi on black mildews (Meliolales, Ascomycota) : hidden diversity in the tropics
(2023)
Meliolales (Sordariomycetes, Ascomycota) is a group of obligate plant parasitic microfungi mainly distributed in the tropics and subtropics. Meliolalean fungi are commonly known as “black mildews”, as they form black, superficial hyphae on the surface of vegetative and reproductive organs of vascular plants. They are considered biotrophic parasites, and the infections caused by black mildews can lead to a decrease in the photosynthetic activity of plants, as well as to an increase in the temperature and respiration rate of their leaves.
Meliolales are frequently parasitized by hyperparasitic fungi, i.e., parasitic fungi that have parasitic hosts. These hyperparasites are all Ascomycota and belong mainly to the Dothideomycetes and Sordariomycetes. Although hyperparasites represent a megadiverse group, species were only described by morphology until 1980, and the systematic position of more than 60 % of known species is still unclear. In addition, there are no DNA reference sequences available in public databases for any of the species of hyperparasites of Meliolales, and no ecological studies have been done up to now.
Before this study, no exact number of hyperparasitic fungi growing on colonies of black mildews existed. Here, we present a checklist including 189 species of fungi known to be hyperparasitic on Meliolales, but the number of existing species is likely to be even higher. The elaboration of this species checklist laid the foundations for this investigation, as it helped to understand the present state of knowledge of hyperparasitic fungi on Meliolales worldwide.
For the present study, fresh specimens of leaves infected with colonies of Meliolales and hyperparasites were opportunistically collected at 32 collection sites in Western Panama and Benin, West Africa, in 2020 and 2022, respectively. In total, 100 samples of plant specimens infected with black mildews were collected, of which 58 samples were parasitized by hyperparasitic fungi. 31 species and morphospecies of hyperparasitic fungi were identified. In addition, 35 historical specimens, including 12 type specimens, were examined for the present work.
DNA of hyperparasitic fungi was isolated directly from conidia, synnemata, apothecia, perithecia or pseudothecia of fresh and dried specimens. The main challenges faced by scientists in doing molecular studies of hyperparasitic fungi are related to the fact that the hyperparasitic fungi are intermingled with tissues of the meliolalean hosts and other organisms present in a given sample. This makes the isolation of DNA exclusively from the hyperparasite difficult. Moreover, hyperparasitic fungi on Meliolales are biotrophs and cannot be grown axenically. The hosts themselves are also biotrophic, further complicating DNA isolation from either partner. These factors have contributed to a lack of reference sequences in public databases. After more than 100 attempts, DNA of 20 specimens of hyperparasitic fungi, representing seven species, has been isolated in the context of the present investigation. Three partial nuclear gene regions were amplified and sequenced: nrLSU, nrSSU and nrITS. The datasets were assembled for phylogenetic analyses applying Maximum Likelihood (ML) and Bayesian inference (BI) methods. DNA sequences of hyperparasitic fungi on Meliolales were generated for the first time in the context of the present investigation.
Hyperparasitic fungi on Meliolales do not represent a single systematic group, but a polyphyletic ecological guild of fungi. Because of this huge diversity, only the systematics of species of perithecioid hyperparasites, as well as of the species of the genera Atractilina and Spiropes known to be hyperparasitic on black mildews was discussed in this thesis, as they represented the most common groups of fungi found in Benin and Panama. The results indicated, for example, the systematic position of Dimerosporiella cephalosporii and Paranectriella minuta in the Sordariomycetes and Dothideomycetes, respectively. In addition, the first record of a hyperparasitic fungus of black mildews in the Lecanoromycetes, namely Calloriopsis herpotricha, is reported here. The systematics of Atractilina parasitica and of some species of Spiropes is also discussed here.
In the context of the present investigation, four species new to science were described. They are presented with detailed descriptions, photos and scientific illustrations. Taxonomic studies of this thesis also generated seven new synonyms, nine new records for Benin, seven for Panama, one for Africa and two for mainland America, as well as the confirmation of one anamorph-teleomorph connection by molecular sequence data.
The ecology of hyperparasitic fungi on Meliolales is complex and far from being completely understood. The hypothesis of host specificity between hyperparasitic fungi, their meliolalean hosts and their plant hosts was tested for the first time, through a tritrophic network analysis. Results indicate that hyperparasites of Meliolales are generalists concerning genera of Meliolales, but apparently specialists at the level of order. In addition, hyperparasitic fungi tend to be found alongside their meliolalean hosts, suggesting a pantropical distribution.
Die Zahl der gramnegativen Bakterien auf der WHO-Liste der Antibiotikaresistenzen hat in den letzten Jahrzehnten erheblich zugenommen. Schätzungen zufolge wird die Antibiotikaresistenz bis 2050 tödlicher sein als Krebs. Die äußere Membran gramnegativer Bakterien ist aufgrund ihres wichtigsten Strukturbestandteils, des Lipopolysaccharids (LPS), sehr anpassungsfähig an Umweltveränderungen. Das LPS macht gramnegative Bakterien von Natur aus resistent gegen viele Antibiotika und führt somit zu Antibiotikaresistenz. Der bakterielle ATP-bindende Kassettentransporter (ABC-Transporter) MsbA spielt eine entscheidende Rolle bei der Regulierung der bakteriellen Außenmembran, indem er das Kern-LPS durch ATP-Hydrolyse über die Innenmembran von gramnegativen Bakterien flockt. Darüber hinaus fungiert diese Floppase als Efflux-Pumpe, indem sie Medikamente durch die innere Membran transportiert, was sie zu einem interessanten Ziel für Medikamente macht. Vor kurzem wurden zwei verschiedene Klassen von MsbA-Inhibitoren entdeckt: (1) Tetrahydrobenzothiophene (TBT), die den LPS-Transport aufheben, und (2) Chinolinderivate, die sowohl die ATP-Hydrolyse als auch die LPS-Translokation blockieren. Darüber hinaus hat die Bestimmung der 3D-Struktur von MsbA durch Rontgen- und Kryo-EM mehrere interessante Zustände der Floppase ergeben. Die Kernspinresonanzspektroskopie ist eine hervorragende biophysikalische Methode zur Ergänzung der vorhandenen 3D-Strukturdaten. Insbesondere ermöglicht die Festkörper-NMR die Untersuchung von Membranproteinen in einer nativen Umgebung (z. B. in einer Lipiddoppelschicht). In der Vergangenheit hat unser Labor mithilfe der Festkörper-NMR einige detaillierte Mechanismen von MsbA aufgedeckt. Trotz der zahlreichen Fortschritte bei der Untersuchung der ABC-Transporterprotein-Superfamilie ist der spezifische Prozess der Substrattranslokation von MsbA noch immer unbekannt. Es wird angenommen, dass dieser Translokationsprozess über die Kopplungshelices (CHs) erfolgt, die sich zwischen der Transmembranregion (TMD) und der Nukleotidbindungsdomäne (NBD) befinden. Nukleotid-Bindungsdomäne (NBD). Zu diesem Zweck wird dem Zusammenspiel zwischen der TMD und der NBD über die CHs besondere Aufmerksamkeit gewidmet, mit dem Ziel, den Prozess der Substrattranslokation mithilfe von funktionellen Assays und Festkörper-NMR zu verstehen. Bei letzterem wurden spezifische Reporter in die CHs eingeführt, um Konformationsänderungen in 2D-spektroskopischen Daten zu verfolgen. Darüber hinaus wurde zeitaufgelöste NMR eingesetzt, um die Auswirkungen verschiedener Substrate in der TMD während der ATP-Hydrolyse in der NBD sichtbar zu machen. Die einzigartigen Reporter in den CHs haben Konformationsänderungen in bestimmten katalytischen Zuständen gezeigt. Darüber hinaus scheinen verschiedene Substrate die Kinetik der ATP-Hydrolyse zu beeinflussen. Die Ergebnisse zeigten, dass einige Substrate einen bevorzugten katalytischen Zustand innerhalb des ATP-Hydrolyse Zyklus aufweisen, der möglicherweise einen gekoppelten oder ungekoppelten Kinasemechanismus hat. Diese Ergebnisse könnten verschiedene Einblicke in die molekulare Struktur potenzieller neuer Antibiotika liefern.
This thesis provides a detailed derivation of dissipative spin hydrodynamics from quantum field theory for systems composed of spin-0, spin-1/2, or spin-1 particles.
The Wigner function formalism is introduced for quantum fields in the respective representations of the Poincaré group, and the conserved currents, i.e., the energy-momentum tensor and the total angular momentum tensor, in various so-called pseudogauges are derived. An expansion around the semiclassical limit in powers of the Planck constant is performed.
Subsequently, kinetic equations are obtained for binary elastic scattering, using both the de Groot-van Leeuwen-van Weert and Kadanoff-Baym method, with the latter retaining the effect of quantum statistics. The resulting collision term features both local and nonlocal contributions, with the latter providing a relaxation mechanism for the spin degrees of freedom of the quasiparticles. The local-equilibrium distribution function is derived from the requirement that the local part of the collision term vanishes.
From quantum kinetic theory, dissipative spin hydrodynamics is then constructed via the method of moments, extended to particles with spin. The system of moment equations is closed via the Inverse-Reynolds Dominance (IReD) approach, resulting in a set of equations of motion describing the evolution of both ideal and dissipative degrees of freedom. The application to polarization phenomena relevant to heavy-ion collisions is discussed.
Upper mantle shear zones are complex systems where deformation is commonly closely interacting with metamorphic (solid-solid) and/or melt/fluid-rock reactions. Here, feedback processes between deformation, reactions, grain size reduction and phase mixing result in strain weakening and the localization of deformation. The expression of these interlinked processes is portrayed by the microfabrics of strained peridotites and pyroxenites. The present thesis is focusing on these processes and their impact on the deformation in three upper mantle shear zones situated in the peridotite massifs of Lanzo (Italian Alps), Erro-Tobbio (Italian Alps) and Ronda (Betic Cordillera, Spain). In all three shear zones, the presence of melt led to phase mixing either by interstitial crystallization of pyroxenes from a Si-saturated and partially also highly evolved melt or by melt-rock reactions of pyroxene porphyroclasts with a Si-undersaturated melt. The effect of melt on the localization of strain is twofold and variable. Enhanced deformation by melt-wetted boundaries is assumed for all shear zones. Additionally, phase mixing by crystallization of interstitial pyroxenes or melt-rock reactions reduce or maintain the grain size by the formation of fine grained neoblasts and secondary phase boundary pinning. In this regard, pre- to early syn-kinematic, map-scale percolation of OH-bearing, evolved melts in the NW Ronda peridotite massif and the associated crystallization of interstitial pyroxenes result in the activation of grain size sensitive deformation mechanisms in the entire melt-effected area. In the rocks collected at Erro-Tobbio, syn-kinematic melt-rock reactions of pyroxene porphyroclasts and Si-undersaturated melt led to the formation of ultramylonitic neoblast tails (grain size ~10 μm). Compared to the adjacent coarser-grained olivine-dominated matrix, the activation of diffusion creep led to an increase in the strain rate by an order of magnitude within interconnected ultramylonitic layers. Strain localization and softening in ultramylonitic layers are also documented in the Lanzo samples. Neoblast tails of pyroxene porphyroclasts were likewise identified as their precursor. The phase assemblage of the tails, including ortho- and clinopyroxene, olivine, plagioclase, and spinel (± amphibole), and their geochemical trends suggest, unlike in Erro-Tobbio, a formation by continuous net-transfer reactions enhanced by the spinel lherzolite to plagioclase lherzolite transition.
The new results obtained from the three studied shear zones underscore the importance of reactions for the interlinked processes of grain size reduction, phase mixing, strain localization and strain softening in upper mantle shear zones. Concerning strain localization, the nature of the reaction (solid-solid, melt/fluid-rock) seems to play a subordinate role compared to its timing. Pre- to early syn-kinematic melt-triggered reactions result in strain localization along map-scale shear zones. Late stage syn-kinematic melt-rock or metamorphic reactions under high stress conditions are capable of localizing the deformation along discrete, sub-centimeter thick ultramylonites.
Blockchains in public administration : a RADIUS on blockchain framework for public administration
(2023)
The emergence of blockchain technology has generated a great deal of attention, as reflected in numerous scientific and journalistic articles. However, the implementation of blockchain for public administrations in Germany has encountered a setback owing to unsuccessful initiatives. Initial enthusiasm was followed by disillusionment. Nevertheless, technology continues to evolve. This paper examines whether the use of a blockchain can still optimize the processes of public administrations. Not only the failed projects are analysed, but also more current applications of the technology and their potential relevance for the administration, especially in the state of Hesse.
To answer if blockchains are promising to administrations, a Design Science Research (DSR) research approach is chosen. The DSR method is a research-based approach that aims to create new and innovative solutions to real-world problems through the development and evaluation of artefacts such as models, methods, or prototypes. For this work, the implementation of a framework to realize an Authentication, Authorization, and Accounting (AAA) system on the blockchain was identified as profitable. The framework aims to implement the aforementioned AAA tasks using a blockchain. The Remote Authentication Dial-In User Service (RADIUS) protocol has been identified as a potential protocol of the AAA system. The goal is to create a way to implement the system either entirely on a blockchain or as a hybrid system. Various blockchain technologies will be considered. Suitable for development, the framework AAA-me is named.
The development of AAA-me has shown that the desired framework for implementing RADIUS on the blockchain is possible in various degrees of implementation. Previous work mostly relied on full development. Additionally, it has been shown that AAA-me can be used to perform hybrid integration at different implementation levels. This makes AAA-me stand out from the few hybrid previous approaches. Furthermore, AAA-me was investigated in different laboratory environments. This was to determine the expected resilience against Single Point of Failure (SPOF). The results of the lab investigation indicated that a RADIUS system on top of a blockchain can provide benefits in terms of security and performance. In the lab environment, times were measured within which a series of authorization requests were processed. In addition, it was illustrated how a RADIUS system implemented using blockchain can protect itself against Man-in-the-Middle (MITM) attacks.
Finally, in collaboration with the Hessian Central Office for Data Processing (German: Hessische Zentrale für Datenverarbeitung) (HZD), another test lab demonstrated how a RADIUS system on the blockchain can integrate with the existing IT systems of the German state of Hesse. Based on these findings, this work reevaluated the applicability of blockchain technology for public administration processes.
The work has thus shown that the use of a blockchain can still be purposeful. However, it has also been shown that an implementation can bring many problems with it. The small number of blockchain developers and engineers also poses the risk of finding people to develop and maintain a system. In addition, one faces the problem of determining an architecture now that will be applied to many projects in the future. However, each project can, in turn, have an impact on the choice of architecture. Once one has solved this problem and a blockchain infrastructure is available, it can be established quickly and be more SPOF resistant, for example, for Public Key Infrastructure (PKI) systems.
AAA-me was only applied in lab and test environments. As a result, no real data ran over its own infrastructure. This allowed the necessary flexibility for development. However, system-related properties could appear in real situations that are not detectable here in this way. Furthermore, the initial stage of AAA-me’s development is still in its infancy. Many manual adjustments need to be made in order for this to integrate with an existing RADIUS system. Also, no system security effort in and of itself has been carried out in the lab environments. Thus, vulnerabilities can quickly open up on web servers due to misconfigurations and missing updates. For the above reasons, productive use should be discouraged unless major developments are carried out.
Discrepancies between knockdown and knockout animal model phenotypes have long stood as a perplexing phenomenon. Several mechanisms explaining such observations have been proposed, namely the toxicity or the off-target effects of the knockdown reagents, as well as, in certain cases, genetic robustness – an organism's ability to maintain its phenotype despite genetic perturbations. In addition to these explanations, transcriptional adaptation (TA), a phenomenon defined as an event whereby a mutation in one gene leads to transcriptional upregulation or downregulation of another, adapting, gene or genes expression, has been recently proposed as an alternative explanation for the conflicting knockdown and knockout phenotype paradox.
Since its discovery in 2015, TA's precise mechanism remains a subject of ongoing research. Majority of evidence suggests that mutant mRNA degradation plays a central in TA. Epigenetic remodeling is also thought to play a role, as evidenced by an increase in active histone marks at the transcription start sites of the adapting genes. Whether mRNA degradation is indeed the key player in TA remains debated. Furthermore, it is still unknown how exactly TA develops, what adapting genes it targets, and whether genomic mutations that render mutant mRNA sensitive to degradation are required for TA to occur.
Throughout the experiments described in this Dissertation, I have designed an inducible TA system where TA can be triggered on demand and its effects on the cell’s transcriptome followed through time. I have demonstrated that degradation-prone transgenes, once induced and expressed, can be efficiently degraded, resulting in the protein loss-independent upregulation of adapting genes via TA. Adapting genes with higher degree of sequence similarity become upregulated faster than genes with lower degree of sequence similarity. Further functionality of this approach to study TA is limited by the leakiness of the inducible gene expression system; however, constitutively expressed degradation-prone transgenes were used to demonstrate TA in human cells.
In addition, I have developed an approach to target wild-type cytoplasmic mRNAs without altering the cell’s genome and reported a TA-like phenomenon, which manifested as adapting gene upregulation not relying on mutations in other genes. Cytoplasmic mRNA cleavage with CRISPR-Cas13d triggered a TA-like response in three different gene models: Actg1 knockdown, Ctnna1 knockdown, and Nckap1 knockdown. After comparing two different modes of triggering TA, CRISPR-Cas9 knockout versus CRISPR-Cas13d knockdown, I reported little overlap between the dysregulated genes and suggested that diverse mRNA degradation modes led to distinct TA responses. In addition, the transcriptional increase of Actg2 caused by CRISPR-Cas13d-mediated Actg1 mRNA cleavage did not require chromatin accessibility changes.
Experiments and genetic tools described in this dissertation investigated how TA develops from its earliest onset, how it affects the global transcriptome of the cell, as well as provided compelling evidence for an mRNA degradation-central TA mechanism. I have created tools to study both direct and indirect TA gene targets and unveiled important insights into the temporal dynamics of TA. Genes with higher sequence similarity were found to be upregulated more rapidly than those with lower similarity. Furthermore, it was revealed that the epigenetic properties of TA responses vary depending on the triggering mechanism. Cas13d-mediated degradation of wild-type mRNAs led to immediate transcriptional enhancement independent of epigenetic changes, which stood in contrast to previously measured alterations in chromatin accessibility in CRISPR-Cas9 mutants. This research has thus significantly advanced our knowledge of TA and provided valuable tools and findings that contribute to the broader understanding of gene expression regulation in response to mRNA degradation.
Type 1 diabetes (T1D) is precipitated by the autoimmune destruction of the insulin-producing beta-cells in the pancreatic islets of Langerhans. Chemokines have been identified as major conductors of the islet infiltration by autoaggressive leukocytes, including antigen-presenting cells and islet autoantigen-specific T cells. We have previously generated a roadmap of the gene expression in the islet microenvironment during T1D in a mouse model and found that most of the chemokine axes are chronically upregulated during T1D. We focused our attention on CXCL10/CXCR3, CCL5/CCR5, CXCL16/CCR6, CX3CL1/CX3CR1, and XCL1/XCR1. First, we found that the absence of CCR6 and of CX3CR1 diminished T1D incidence in a mouse model for T1D. Further, the XCL1/XCR1 chemokine axis is of particular interest, since XCR1 is exclusively expressed on convention dendritic cells type 1 (cDC1) that excel by their high capacity for T cell activation. Here we demonstrate that cDC1 expressing XCR1 are present in and around the islets of patients with T1D and of islet-autoantibody positive individuals. Further, in an inducible mouse model for T1D, we show that XCL1 plays an important role in the attraction of highly potent dendritic cells expressing XCR1 to the islets. XCL1-deficient mice display a diminished infiltration of XCR1+ cDC1 and subsequently also a reduced magnitude and activity of islet autoantigen-specific T cells. XCR1-deficient mice display a reduced magnitude and activity of islet autoantigen-specific T cells. A 3D-visualization of the entire pancreas reveals that both XCL1-deficient mice and XCR1-deficient mice indeed maintain most of their functional islets after induction of the disease. Thus, the absence of XCL1 results in a profound decrease in T1D incidence. The XCR1-deficiency also reduces T1D incidence, even if in a less drastic way compared to XCL1-deficiency. An interference with the XCL1/XCR1 chemokine axis might constitute a novel target for the therapy for T1D.
The simultaneous inhibition of HDACs and BET proteins has shown promising anti-proliferative effects against different cancer types, including the difficult to treat pancreatic cancer. In this work, the strategy of concurrently targeting HDACs and BET proteins was pursued by developing different types of dual inhibitors.
By developing a novel scaffold that selectively inhibits HDAC1/2 together with BET proteins in cells, an effective tool for the investigation of pancreatic cancer, and other diseases which are sensitive to epigenetic processes, was created. The compound’s small size further gives the opportunity to further develop the inhibitor towards optimized pharmacokinetic properties, potentially resulting in a drug for cancer treatment.
A second novel approach that was pursued, was the development of a small-molecule degrader, targeting HDACs and BET proteins. Through synthesizing a variety of different molecules, a compound that was capable of lowering BRD4 levels and, at the same time, increasing histone acetylation was developed. While additional mechanistic investigations are needed to verify the degradation, the potent antiproliferative effects in pancreatic cancer cells encourage further studies following this alternative new strategy.
Aim: The cytochrome P450 reductase (POR) along with the cytochrome P450 enzymes (CYP) are responsible for the metabolism of a multitude of metabolites important for the maintenance of tissue function. Defects in this system have been associated with cardiovascular diseases. These enzymes are known to produce vasoactive lipids that modulate vascular tone. The aim of this study was to identify the consequence of a loss in endothelial POR for vascular function.
Methods and Results: To identify the endothelial contribution of the POR/CYP450 system to vascular function, we generated an endothelial-specific, tamoxifen-inducible POR knockout mouse (ecPOR-/-). Under basal condition ecPOR-/- already exhibited endothelial dysfunction in aorta and mesenteric vessels (acetylcholine-dependent relaxation, LogEC50 -7.6M for CTR vs. -7.2M for ecPOR-/- in aorta) and lower nitric oxide levels in the plasma (CTR: 236.8 ±77.4; ecPOR-/- 182.8 ±34.1 nmol/L). This dysfunction was coupled to attenuated eNOS function detected by the heavy arginine assay and decreased eNOS phosphorylation on S1177. Furthermore, insulin-induced phosphorylation of the eNOS activator, AKT, was also attenuated in the aorta from ecPOR-/- mice as compared to control mice. CYP450-dependent EET production was lower in plasma, lung and aorta of ecPOR-/- mice and this was accompanied with increased levels of vasoconstriction prostanoids (lipidomics of aorta, plasma and lung freshly isolated from CTR and ecPOR-/- mice). MACE-RNAseq from these aortas also showed a significant increase in genes annotated to eicosanoid production. In an in vivo angiotensin II model, acute deletion of POR increased the blood pressure as measured by telemetry and tail cuff (137.4 ± 15.9 mmHg in WT; 152.1 ± 7.154 mmHg in ecPOR-/-). In a rescue experiment using the NSAID naproxen, the increase in blood pressure induced by deletion of endothelial POR was abolished.
Conclusion: Collectively, in endothelial cells POR regulates eNOS activity and orchestrates the metabolic fate of arachidonic acid towards the vessel dilating EETs and away from deleterious prostanoids. In the absence of POR this endothelial regulation is compromised leading to vascular dysfunction.
This thesis develops a naturalist theory of phenomenal consciousness. In a first step, it is argued on phenomenological grounds that consciousness is a representational state and that explaining consciousness requires a study of the brain’s representational capacities. In a second step, Bayesian cognitive science and predictive processing are introduced as the most promising attempts to understand mental representation to date. Finally, in a third step, the thesis argues that the so-called “hard problem of consciousness” can be resolved if one adopts a form of metaphysical anti-realism that can be motivated in terms of core principles of Bayesian cognitive science.
In this thesis, the flow coefficients vn of the orders n = 1 − 6 are studied for protons and light nuclei in Au+Au collisions at Ebeam = 1.23 AGeV, equivalent to a center-of-mass energy in the nucleon-nucleon system of √sNN = 2.4 GeV. The detailed multi-differential measurement is performed with the HADES experiment at SIS18/GSI. HADES, with its large acceptance, covering almost full azimuth angle, combined with its high mass-resolution and good particle-identification capability, is well equipped to study the azimuthal flow pattern not only for protons, deuterons, and tritons but also for charged pions, kaons, the φ-mesons, electrons/positrons, as well as light nuclei like helions and alphas. The high statistics of more than seven billion Au-Au collisions recorded in April/May 2012 with HADES enables for the first time the measurement of higher order flow coefficients up to the 6th harmonic. Since the Fourier coefficient of 7th and 8th order are beyond the statistical significance only an upper bound is given. The Au+Au collision system is the largest reaction system with the highest particle multiplicities, which was measured so far with HADES. A dedicated correction method for the flow measurement had to be developed to cope with the reconstruction in-efficiencies due to occupancies of the detector system. The systematical bias of the flow measurement is studied and several sources of uncertainties identified, which mainly arise from the quality selection criteria applied to the analyzed tracks, the correction procedure for reconstruction inefficiencies, the procedures for particle identification (PID) and the effects of an azimuthally non-uniform detector acceptance. The systematic point-to-point uncertainties are determined separately for each particle type (proton, deuteron and triton), the order of the flow harmonics vn, and the centrality class. Further, the validity of the results is inspected in the range of their evaluated systematic uncertainties with several consistency checks. In order to enable meaningful comparisons between experimental observations and predictions of theoretical models, the classification of events should be well defined and in sufficiently narrow intervals of impact parameter. Part of this work included the implementation of the procedure to determine the centrality and orientation of the reaction.
In the conclusion the experimental results are discussed, including various scaling properties of the flow harmonics. It is found that the ratio v4/v2 for protons and light nuclei (deuterons and tritons) at midrapidity for all centrality classes approaches values close to 0.5 at high transverse momenta, which was suggested to be indicative for an ideal hydrodynamic behaviour. A remarkable scaling is observed in the pt dependence of v2 (v4) at mid-rapidity of the three hydrogen isotopes, when dividing by their nuclear mass number A (A^2) and pt by A. This is consistent with naive expectations from nucleon coalescence, butraises the question whether this mass ordering can also be explained by a hydrodynamical-inspired approach, like the blast-wave model. The relation of v2 and v4 to the shape of the initial eccentricity of the collision system is studied. It is found that v2 is independent of centrality for all three particle species after dividing it by the averaged second order participant eccentricity v2/⟨ε2⟩. A similar scaling is shown for v4 after division by ⟨ε2⟩^2.
This thesis contains three theoretical works about certain aspects of the interplay of electronic correlations and topology in the Hubbard model.
In the first part of this thesis, the applicability of elementary band representations (EBRs) to diagnose interacting topological phases, that are protected by spatial symmetries and time-reversal-symmetry, in terms of their single-particle Matsubara Green’s functions is investigated. EBRs for the Matsubara Green’s function in the zero-temperature limit can be defined via the topological Hamiltonian. It is found that the Green’s function EBR classification can only change by (i) a gap closing in the spectral function at zero frequency, (ii) the Green’s function becoming singular i.e. having a zero eigenvalue at zero frequency or (iii) the Green’s function breaking a protecting symmetry. As an example, the use of the EBRs for Matsubara Green’s functions is demonstrated on the Su-Schriefer-Heeger model with exact diagonalization.
In the second part the Two-Particle Self-Consistent approach (TPSC) is extended to include spin-orbit coupling (SOC). Time-reversal symmetry, that is preserved in the presence of SOC, is used to derive new TPSC self-consistency equations including SOC. SOC breaks spin rotation symmetry which leads to a coupling of spin and charge channel. The local and constant TPSC vertex then consists of three spin vertices and one charge vertex. As a test case to study the interplay of Hubbard interaction and SOC, the Kane-Mele-Hubbard model is studied. The antiferromagnetic spin fluctuations are the leading instability which confirms that the Kane-Mele-Hubbard model is an XY antiferromagnet at zero temperature. Mixed spin-charge fluctuations are found to be small. Moreover, it is found that the transversal spin vertices are more strongly renormalized than the longitudinal spin vertex, SOC leads to a decrease of antiferromagnetic spin fluctuations and the self-energy shows dispersion and sharp features in momentum space close to the phase transition.
In the third part TPSC with SOC is used to calculate the spin Hall conductivity in the Kane-Mele-Hubbard model at finite temperature. The spin Hall conductivity is calculated once using the conductivity bubble and once including vertex corrections. Vertex corrections for the spin Hall conductivity within TPSC corresponds to the analogues of the Maki-Thompson contributions which physically correspond to the excitation and reabsorption of a spin, a charge or a mixed spin-charge excitation by an electron. At all temperatures, the vertex corrections show a large contribution in the vicinity of the phase transition to the XY antiferromagnet where antiferromagnetic spin fluctuations are large. It is found that vertex corrections are crucial to recover the quantized value of −2e^2/h in the zero-temperature limit. Further, at non-zero temperature, increasing the Hubbard interaction leads to a decrease of the spin Hall conductivity. The results indicate that scattering of electrons off antiferromagnetic spin fluctuations renormalize the band gap. Decreasing the gap can be interpreted as an effective increase of temperature leading to a decrease of the spin Hall conductivity.
Trait-dependent effects of biotic and abiotic filters on plant regeneration in Southern Ecuador
(2024)
Tropical forests have always fascinated scientists due to their unique biodiversity. However, our understanding of ecological processes shaping the complexity of tropical rainforests is still relatively poor. Plant regeneration is one of the processes that remain understudied in the tropics although this is a key process defining the structure, diversity and assembly of tropical plant communities. In my dissertation, I combine experimental, observational and trait-based approaches to identify processes shaping the assembly of seedling communities and compare associations between environmental conditions and plant traits across plant life stages. By working along a steep environmental gradient in the tropical mountains of Southern Ecuador, I was able to investigate how processes of plant regeneration vary in response to biotic and abiotic factors in tropical montane forests.
My dissertation comprises three complementary chapters, each addressing an individual research question. First, I studied how trait composition in plant communities varies in relation to the broad- and local-scale environmental conditions and across the plant life cycle. I measured key traits reflecting different ecological strategies of plants that correspond to three stages of the plant life cycle (i.e., adult trees, seed rain and recruiting seedlings). I worked on 81 subplots along an elevational gradient covering a large climatic gradient at three different elevations (1000, 2000 and 3000 m a.s.l.). In addition, I measured soil and light conditions at the local spatial scale within each subplot. My findings show that the trait composition of leaves, seeds and seedlings changed similarly across the elevational gradient, but that the different life stages responded differently to the local gradients in soil nutrients and light availability. Consequently, my findings highlight that trait-environment associations in plant communities differ between large and small spatial scales and across plant life stages.
Second, I investigated how seed size affects seedling recruitment in natural forests and in pastures in relation to abiotic and biotic factors. I set up a seed sowing experiment in both habitat types and sowed over 8,000 seeds belonging to seven tree species differing in seed size. I found that large-seeded species had higher proportions of recruitment in the forests compared to small-seeded species. However, small-seeded species tended to recruit better in pastures compared to large-seeded species. I showed that high surface temperature was the main driver of differences in seedling recruitment between habitats, because it limited seedling recruitment of large-seeded species. The results from this experiment show that pasture restoration requires seed addition of large-seeded species and active protection of recruiting seedlings in order to mitigate harmful conditions associated with high temperatures in deforested areas.
Third, I examined the associations between seedling beta-diversity and different abiotic and biotic factors between and within elevations. I applied beta-diversity partitioning to obtain two components of beta-diversity: species turnover and species richness differences. I associated these components of beta-diversity with biotic pressures by herbivores and fungal pathogens and environmental heterogeneity in light and soil conditions. I found that species turnover in seedling communities was positively associated with the dissimilarity in biotic pressures within elevations and with environmental heterogeneity between elevations. Further, I found that species richness differences increased primarily with increasing environmental heterogeneity within elevations. My findings show that the associations between beta-diversity of seedling communities and abiotic and biotic factors are scale-dependent, most likely due to differences in species sorting in response to biotic pressures and species coexistence in response to environmental heterogeneity.
My dissertation reveals that studying processes of community assembly at different plant life stages and spatial scales can yield new insights into patterns and processes of plant regeneration in tropical forests. I investigated how community assembly processes are governed by abiotic and biotic filtering across and within elevations. I also experimentally explored how the process of seedling recruitment depends on seed size-dependent interactions, and verified how these effects are associated with abiotic and biotic filtering. Identifying such processes is crucial to inform predictive models of environmental change on plant regeneration and successful forest restoration. Further exploration of plant functional traits and their associations with local-scale environmental conditions could effectively support local conservation efforts needed to enhance forest cover in the future and halt the accelerating loss of biodiversity.
In this work I investigate two different systems - spin systems and charge-density-waves. The same theoretical method is used to investigate both types of system. My investigations are motivated by experimental investigations and the goal is to describe the experimental results theoretically. For this purpose I formulate kinetic equations starting from the microscopical dynamics of the systems.
First of all, a method is formulated to derive the kinetic equations diagrammatically. Within this method an expansion in equal-time connected correlation functions is carried out. The generating functional of connected correlations is employed to derive the method.
The first system to be investigated is a thin stripe of the magnetic insulator yttrium-iron-garnet (YIG). Magnons are pumped parametrically with an external microwave field. The motivation of my theoretical investigations is to explain the experimental observations. In a small parameter range close to the confluence field strength where confluence processes of two parametrically pumped magnons with the same wave vector becomes kinematically possible the efficiency of the pumping is reduced or enhanced depending on the pumping field strength. Because it is expected that that confluence and splitting processes of magnons are essential for the experimental observations I go beyond the kinetic theories that are conventionally applied in the context of parametric excitations in YIG and investigate the influence of cubic vertices on the parametric instability of magnons in YIG.
Furthermore, the influence of phonons is investigated. Usually in the literature these are taken into account as heat bath. Here, I want to explain experiments where an accumulation of magnetoelastic bosons - magnon-phonon-quasi-particles - has been observed. I employ the method of kinetic equations to investigate this phenomenon theoretically. The kinetic theory is able to reproduce the experimental observations and it is shown that the accumulation of magnetoelastic bosons is purely incoherent.
Finally, charge-density waves (CDW) in quasi-one-dimensional materials will be investigated. Charge-density waves emerge from a Peierls-instability and are a prime example for spontaneous symmetry breaking in solids. Again, the motivation for my theoretical investigations are an experiment where the spectrum of amplitude and phase phonon modes has been measured. Starting from the Fröhlich-Hamiltonian I derive kinetic equations and from these kinetic equations the equations of motion for the CDW order parameter can be derived. The frequencies and damping rates of amplitude and phase phonon modes will be derived from the linearized equations of motion. I compare my theory with existing methods. Furthermore, I also investigate the influence of Coulomb interaction.
This thesis investigates exotic phases within effective models for strongly interacting matter.
The focus lies on the chiral inhomogeneous phase (IP) that is characterized by a spontaneous breaking of translational symmetry and the moat regime, which is a precursor phenomenon exhibiting a non-trivial mesonic dispersion relation.
These phenomena are expected to occur at non-zero baryon densities, which is a parameter region that is mostly non-accessible to first-principle investigations of Quantum chromodynamics (QCD).
As an alternative approach, we consider the Gross-Neveu (GN) and Nambu-Jona-Lasinio (NJL) model within the mean-field approximation, which can be regarded as effective models for QCD.
We focus on two aspects of the moat regime and the IP in these models.
First, we investigate the influence of the employed regularization scheme in the (3+1)-dimensional NJL model, which is nonrenormalizable, i.e., the regulator cannot be removed.
We find that the moat regime is a robust feature under change of regularization scheme, while the IP is sensitive to the specific choice of scheme.
This suggests that the moat regime is a universal feature of the phase diagram of the NJL model, while the IP might only be an artifact of the employed regulator.
Second, we study the influence of the number of spatial dimensions on the emergence of the IP.
To this end, we investigate the GN model in noninteger spatial dimensions d.
We find that the IP and the moat regime are present for d < 2, while they are absent for d > 2.
This demonstrates the central role of the dimensionality of spacetime and illustrates the connection of previously obtained results in this model in integer number of spatial dimensions.
Moreover, this suggests that the occurrence of these phenomena in three spatial dimensions is solely caused by the finite regulator.
In summary, this thesis contributes to advancing our understanding of the phase structure of QCD, particularly regarding the existence and characteristics of inhomogeneous phases and the moat regime.
Even though the investigations are performed within effective models, they provide valuable insight into the aspects that are crucial for the formation of an inhomogeneous chiral condensate in fermionic theories.
By combining two unique facilities at the Gesellschaft fuer Schwerionenforschung (GSI), the Fragment Separator (FRS) and the Experimental Storage Ring (ESR), the first direct measurement of a proton capture reaction of stored radioactive isotopes was accomplished. The combination of well-defined ion energy, an ultra-thin internal gas target, and the ability to adjust the beam energy in the storage ring enables precise, energy-differentiated measurements of the (p,gamma) cross sections. The new setup provides a sensitive method for measuring (p,gamma) reactions relevant for nucleosynthesis processes in supernovae, which are among the most violent explosions in the universe and are not yet well understood. The cross sections of the 118Te(p,gamma) and 124Xe(p,gamma) reactions were measured
at energies of astrophysical interest. The heavy ions were stored with energies of 6 MeV/nucleon and 7 MeV/nucleon and interacted with a hydrogen gas-jet target.
The produced proton-capture products were detected with a double-sided silicon strip detector. The radiative recombination process of the fully stripped ions and electrons from the hydrogen target was used as a luminosity monitor.
Additionally, post-processing nucleosynthesis simulations within the NuGrid [1] research platform have been performed. The impact of the new experimental results on the p-process nucleosynthesis around 124Xe and 118Te in a core-collapse supernova was investigated. The successful measurement of the proton capture cross sections of radioactive isotopes rises the motivation to proceed with experiments in lower energy regions.
[1] M. Pignatari and F. Herwig, “The nugrid research platform: A comprehensive simulation approach for nuclear astrophysics,” Nuclear Physics News, vol. 22, no. 4, pp. 18–23, 2012.
This dissertation is concerned with the task of map-based self-localization, using images of the ground recorded with a downward-facing camera. In this context, map-based (self-)localization is the task of determining the position and orientation of a query image that is to be localized. The map used for this purpose consists of a set of reference images with known positions and orientations in a common coordinate system. For localization, the considered methods determine correspondences between features of the query image and those of the reference images.
In comparison with localization approaches that use images of the surrounding environment, we expect that using images of the ground has the advantage that, unlike the surrounding, the visual appearance of the ground is often long-term stable. Also, by using active lighting of the ground, localization becomes independent of external lighting conditions.
This dissertation includes content of several published contributions, which present research on the development and testing of methods for feature-based localization of ground images. Our first contribution examines methods for the extraction of image features that have not been designed to be used on ground images. This survey shows that, with appropriate parametrization, several of these methods are well suited for the task.
Based on this insight, we develop and examine methods for various subtasks of map-based localization in the following contributions. We examine global localization, where all reference images have to be considered, as well as local localization, where an approximation of the query image position is already known, which allows for disregarding reference images with a large distance to this position.
In our second contribution, we present the first systematic comparison of state-of-the-art methods for ground texture based localization. Furthermore, we present a method, which is characterized by its usage of our novel feature matching technique. This technique is called identity matching, as it matches only those features with identical descriptors, in contrast to the state-of-the-art that also matches features with similar descriptors. We show that our method is well suited for global and local localization, as it has favorable scaling with the number of reference images considered during the localization process. In another contribution, we develop a variant of our localization method that is significantly faster to compute, as it applies a sampling approach to determine the image positions at which local features are extracted, instead of using classical feature detectors.
Two further contributions are concerned with global localization. The first one introduces a prediction model for the global localization performance, based on an evaluation of the local localization performance. This allows us to quickly evaluate any considered parameter settings of global localization methods. The second contribution introduces a learning-based method that computes compact descriptors of ground images. This descriptor can be used to retrieve the overlapping reference images of a query image from a large set of reference images with little computational effort.
The most recent contribution included in this dissertation presents a new ground image database, which was recorded with a dedicated platform using a downward-facing camera. In addition to the data, we also explain our guidelines for the construction of the platform. In comparison with existing databases, our database contains more images and presents a larger variety of ground textures. Furthermore, this database enables us to perform the first systematic evaluation of how localization performance is affected by the time interval between the point in time at which the reference images are recorded and the point in time at which the query image is recorded. We find out that for outdoor areas all ground texture based localization methods have reliability issues, if the time interval between the recording of the query and reference images is large, and also if there are different weather conditions. These findings point to remaining challenges in ground texture base localization that should be addressed in future work.
Matroids are combinatorial objects that generalize linear independence. A matroid can be represented geometrically by its Bergman fan and we compare the symmetries of these two objects. Sometimes, the Bergman fan has additional automorphisms, which are related to Cremona transformations in projective space. Their existence depends on a combinatorial property of the matroid, as has been shown by Shaw and Werner, and we study the consequences for the structure of such matroids. This allows us to gain a better understanding of the so-called Cremona group of a matroid and we apply our results to root system matroids.
A central concern in genetics is to identify mechanisms of transcriptional regulation. The aim is to unravel the mapping between the DNA sequence and gene expression. However, it turned out that this is extremely complex. Gene regulation is highly cell type-specific and even moderate changes in gene ex- pression can have functional consequences.
Important contributors to gene regulation are transcription factors (TFs), that are able to directly interact with the DNA. Often, a first step in understanding the effect of a TF on the gene’s regulation is to identify the genomic regions a TF binds to. Therefore, one needs to be aware of the TF’s binding preferences, which are commonly summarized in TF binding motifs. Although for many TFs the binding motif is experimentally validated, there is still a large number of TFs where no binding motif is known. There exist many tools that link TF binding motifs to TFs. We developed the method Massif that improves the performance of such tools by incorporating a domain score that uses the DNA binding domain of the studied TF as additional information.
TF binding sites are often enriched in regulatory elements (REMs) such as promoters or enhancers, where the latter can be located megabases away from its target gene. However, to understand the regulation of a gene it is crucial to know where the REMs of a gene are located. We introduced the EpiRegio webserver that holds REMs associated to target genes predicted across many cell types and tissues using STITCHIT, a previously established method. Our publicly available webserver enables to query for REMs associated to genes (gene query) and REMs overlapping genomic regions (region query). We illus- trated the usefulness of EpiRegio by pointing to a TF that occurs enriched in the REMs of differential expressed genes in circPLOD2 depleted pericytes. Further, we highlighted genes, which are affected by CRISPR-Cas induced mutations in non-coding genomic regions using EpiRegio’s region query. Non-coding genetic variants within REMs may alter gene expression by modifying TF binding sites, which can lead to various kinds of traits or diseases. To understand the underlying molecular mechanisms, one aims to evaluate the effect of such genetic variations on TF binding sites. We developed an accurate and fast statistical approach, that can assess whether a single nucleotide polymorphism (SNP) is regulatory. Further, we combined this approach with epigenetic data and additional analyses in our Sneep workflow. For instance, it enables to identify TFs whose binding preferences are affected by the analyzed SNPs, which is illustrated on eQTL datasets for different cell types. Additionally, we used our Sneep workflow to highlight cardiovascular disease genes using regulatory SNPs and REM-gene interactions.
Overall, the described results allow a better understanding of REM-gene interactions and their interplay with TFs on gene regulation.
In this thesis, we present a detailed consideration of both qualitative and quantitative properties of static spherically symmetric solutions of the Einstein equations with self-interacting scalar fields. Our focus is on solutions with naked singularities. We study the qualitative properties of the solutions of the Einstein equations with real static self-interacting $N$ scalar fields, making some assumptions on self-interaction. We provide a rigorous proof that the corresponding solutions will be regular up to $r=0$. Furthermore, we find the rigorous form of asymptotic solutions near the singularity and at spatial infinity. We construct some examples of spherical-like naked singularities at $r=r_s\neq0$ in curvature coordinates.
We analyze the stability of the previously considered solutions against odd-parity gravitational perturbations and also examine the fundamental quasi-normal modes spectra. For the general class of the self-interaction potential, we demonstrate well-posedness of the initial problem and stability for positively defined potentials. As an example, we numerically study the case of the scalar field with power-law self-interaction potential and find the fundamental quasi-normal modes frequencies. We demonstrate that they differ from the standard Schwarzschild black hole case.
We study in detail the motion of particles in the vicinity of previously considered solutions. Mainly, we are interested in considering properties of the distribution of stable circular orbits around the corresponding configurations and images of the accretion disk for a distant observer. For all cases, we find possible types of stable circular orbit distributions and domains of parameters where they are realized.
We also demonstrate that the presence of self-interaction can lead to a new type of circular orbit distributions, which is absent in the linear massless scalar field case. We build Keplerian disk images in the plane of a distant observer and demonstrate the possibility to mimic the shadows of black holes.
This cumulative dissertation contains four self-contained chapters on stochastic games and learning in intertemporal choice.
Chapter 1 presents an experiment on value learning in a setting where actions have both immediate and delayed consequences. Subjects make a series of choices between abstract options, with values that have to be learned by sampling. Each option is associated with two payoff components: One is revealed immediately after the choice, the other with one round delay. Objectively, both payoff components are equally important, but most subjects systematically underreact to the delayed consequences. The resulting behavior appears impatient or myopic. However, there is no inherent reason to discount: All rewards are paid simultaneously, after the experiment. Elicited beliefs on the value of options are in accordance with choice behavior. These results demonstrate that revealed impatience may arise from frictions in learning, and that discounting does not necessarily reflect deep time preferences. In a treatment variation, subjects first learn passively from the evidence generated by others, before then making a series of own choices. Here, the underweighting of delayed consequences is attenuated, in particular for the earliest own decisions. Active decision making thus seems to play an important role in the emergence of the observed bias.
Chapter 2 introduces and proves existence of Markov quantal response equilibrium (QRE), an application of QRE to finite discounted stochastic games. We then study a specific case, logit Markov QRE, which arises when players react to total discounted payoffs using the logit choice rule with precision parameter λ. We show that the set of logit Markov QRE always contains a smooth path that leads from the unique QRE at λ = 0 to a stationary equilibrium of the game as λ goes to infinity. Following this path allows to solve arbitrary finite discounted stochastic games numerically; an implementation of this algorithm is publicly available as part of the package sgamesolver. We further show that all logit Markov QRE are ε-equilibria, with a bound for ε that is independent of the payoff function of the game and decreases hyperbolically in λ. Finally, we establish a link to reinforcement learning, by characterizing logit Markov QRE as the stationary points of a game dynamic that arises when all players follow the well-established reinforcement learning algorithm expected SARSA.
Chapter 3 introduces the logarithmic stochastic tracing procedure, a homotopy method to compute stationary equilibria for finite and discounted stochastic games. We build on the linear stochastic tracing procedure (Herings and Peeters 2004), but introduce logarithmic penalty terms as a regularization device, which brings two major improvements. First, the scope of the method is extended: it now has a convergence guarantee for all games of this class, rather than just generic ones. Second, by ensuring a smooth and interior solution path, computational performance is increased significantly. A ready-to-use implementation is publicly available. As demonstrated here, its speed compares quite favorable to other available algorithms, and it allows to solve games of considerable size in reasonable times. Because the method involves the gradual transformation of a prior into equilibrium strategies, it is possible to search the prior space and uncover potentially multiple equilibria and their respective basins of attraction. This also connects the method to established theory of equilibrium selection.
Chapter 4 introduces sgamesolver, a python package that uses the homotopy method to compute stationary equilibria of finite discounted stochastic games. A short user guide is complemented with discussion of the homotopy method, the two implemented homotopy functions logit Markov QRE and logarithmic tracing, and the predictor-corrector procedure and its implementation in sgamesolver. Basic and advanced use cases are demonstrated using several example games. Finally, we discuss the topic of symmetries in stochastic games.
Thomas Bowrey, who was an employee of the British colonial government, visited the Malay-speaking region at the end of the 17th century and published a dictionary of Malay (1701) which consists of 12,683 headwords. It is one of the oldest and largest collections of data on this language, which was the first language of the people he came into contact with while travelling through the Malay Peninsula, spending most of his time in harbours along its west coast. Malay, which was spoken in the various trading centres of this area (e.g. Penang, Malacca), had long previously begun to develop into a form of lingua franca during Bowrey’s stay there due to the fact that traders, especially those from Arabic countries (beginning in the 12th century), China (from the 15th century onwards), Portugal (since 1511), the Netherlands (since 1641), and less so from England, came into contact with Malays speaking their local dialects in the various trading posts in Malaya and probably began to become acquainted with the trade-language variant. Thus, Bowrey must have observed and recorded elements of both.
The data he collected is not limited to Malay variants spoken in coastal areas, but includes material from dialects which he encountered during his travels throughout the Malay Peninsula, though without, however, describing the locations in which he took notes on the lexicon and clauses. Not all of his material was written into manuscript form during his stay in Southeast Asia. A large part of his notes taken in situ were prepared for publication during his long journey home. His notes, which were used to print his dictionary, are in part kept in British libraries. Most of the material accessible to the public was studied during the preparation of this thesis.
Earlier works on this dictionary are quite limited in scope. They deal with very specific aspects such as the meanings of headwords found between the letters A and C (Rahim Aman, 1997 & 1998), and the work of Nor Azizah, who deals with the lexical change found in Bowrey’s dictionary between D and F, and syntactic and sociolinguistic aspects (Mashudi Kader, 2009), and collective nouns by Tarmizi Hasrah (2010). This study will discuss Bowrey’s dictionary as a whole in order to describe its contribution to our knowledge of linguistic and non-linguistic facts in 17th century Malaya. Besides analysing Malay synchronically, this thesis also deals with historical-comparative questions and asks whether Bowrey contributes to our knowledge of the changes to the Malay language between the 17th and 21st centuries.
In order to answer the research questions, this study not only relies on the dictionary in its entirety, but also on the notes found in British libraries as well as other material on early Malay, such as the Pigafetta list (1523), Houtman (1598–1603), and the Wilkinson dictionary (1901) as a complement to Bowrey’s dictionary; at the same time, the Malay Concordance Project (online), the SEAlang Project (online), Kamus Besar Bahasa Indonesia (online), and Kamus Dewan Edisi Keempat (2007) will represent modern Malay. It should be borne in mind that in contrast to the Thomas Bowrey dictionary (TBD), Kamus Dewan Edisi Keempat (KDE4) does not hold information on colloquial forms of Malay, many of which reflect features of lingua franca Malay. This study is divided into two different branches, namely the consideration of synchronic aspects and historical comparative aspects.
Finally, this study concludes that the Malay language in Thomas Bowrey’s dictionary is heavily influenced by both external and internal factors prevalent to the 17th century. The Malay language recorded in the Thomas Bowrey dictionary is very similar to modern Malay. The similarities between the Malay language of the 17th century and the Malay language of today are considerable, even though there are, of course, still some notable variances.
The role of USP22 in nucleic acid sensing pathways and interferon-induced necroptotic cell death
(2023)
Every day, living organisms are challenged by internal and external factors that threaten to bring imbalance to their tightly regulated systems and disrupt homeostasis, leading to degeneration, and ultimately death. More than ever, we face the challenge of combating diseases such as COVID-19 caused by infection with the SARS-CoV-2 coronavirus. It is therefore crucial to identify host factors that control antiviral defense mechanisms. In addition, in the fight against cancer, it is becoming increasingly important to identify markers that could be used for targeted therapy to influence cellular processes and determine cell fate.
As a deubiquitylating enzyme, ubiquitin specific peptidase 22 (USP22) mediates the removal of the small molecule ubiquitin, which is post-translationally added to target proteins, thereby regulating several important processes such as protein degradation, activation or localization. Through its deubiquitylating function, USP22 controls several biological processes such as cell cycle regulation, proliferation and cancer immunoresistance by modulating key proteins involved in these pathways. Lately, USP22 was reported to positively regulate TNFα-mediated necroptosis, an inflammatory type of programmed cell death, in various human tumor cell lines by affecting RIPK3 phosphorylation. In addition, USP22 as a part of the Spt-Ada-Gcn5 acetyltransferase (SAGA) transcription complex is known to regulate gene expression by removing ubiquitin from histones H2A and H2B. However, little is known about the role of USP22 in global gene expression.
In this study, we performed a genome-wide screen in the human colon carcinoma cell line HT-29 and identified USP22 as a key negative regulator of basal interferon (IFN) expression. We further demonstrated that the absence of USP22 results in increased STING activity and ubiquitylation, both basally and in response to stimulation with the STING agonist 2'3'-cGAMP, thereby affecting IFNλ1 expression and basal expression of antiviral ISGs. In addition, we were able to establish USP22 as a critical host factor in controlling SARS-CoV-2 infection by regulating infection, replication, and the generation of infectious virus particles, which we attribute in part to its role in regulating STING signaling.
In the second part of the study, we connected the findings of USP22-dependent regulation of IFN signaling and TNFα-induced necroptosis and investigated the role of USP22 during necroptosis induced by the synergistic action of IFN and the Smac mimetic BV6 in caspase-deficient settings. We identified USP22 as a negative regulator of IFN-induced necroptosis, which does not depend on STING expression, but relies on a yet unknown mechanism.
In summary, we identify USP22 as an important regulator of IFN signaling with important implications for the defense against viral infections and regulation of the necroptotic pathway that could be exploited for devising targeted therapeutic strategies against viral infections and related diseases like COVID-19, and advancing precision medicine in cancer treatment.
Molecular oxygen (O2) is essential for numerous metabolic processes. Not surprisingly, hypoxia and the resulting adaptations play a pivotal role in pathophysiology, e.g., in cancer or in inflammatory diseases. Of note, myeloid cells are known to accumulate in hypoxic regions such as tumor cores or rheumatoid arthritis joints and may contribute to disease progression. While most studies so far concentrated on transcriptional adaptation by the hypoxia-inducible factors (HIF) 1 and 2 under short term hypoxia, prolonged oxygen deprivation and alternative post-transcriptional regulation are rather poorly investigated.
Consequently, the aim of the study was to generate a comprehensive overview of mRNA de novo synthesis and degradation and its contribution to total mRNA changes in monocytic cells in the course of hypoxia.
To this end, I used thiol-linked alkylation for the metabolic sequencing of RNA (SLAM-Seq) to characterize RNA dynamics under hypoxia. Specifically, I labeled monocytic THP-1 cells under normoxia (N), acute hypoxia (AH; 8 h 1% O2), or chronic hypoxia (CH; 72 h 1% O2) with 4-thiouridine (4sU), which allows for transcriptome-wide identification of de novo synthesized mRNAs and estimation of their half-lives. Total mRNA expression analyses revealed that most changes occurred under CH. Considering that HIF accumulation and resulting transcriptional regulation was shown to decline again under CH, I further analyzed the impact of RNA stability on gene expression. I observed a global reduction in RNA half-lives under hypoxia, indicative for the attenuation of energy-consuming protein synthesis upon oxygen deprivation. Moreover, I observed a subgroup of hypoxic destabilized transcripts with resulting decreased mRNA expression under CH, which consisted of 59 nuclear-encoded mitochondrial mRNAs. This might prevent futile production of new mitochondria under conditions, where mitochondria are even actively degraded to prevent production of detrimental reactive oxygen species.
While stability-regulated transcripts were mainly destabilized under hypoxia, the vast majority of differentially de novo synthesized transcripts were upregulated.
Functional analyses revealed not only hypoxia, but also cholesterol homeostasis and inflammatory response as top enriched terms, corroborating findings on total mRNA level. Focusing on hypoxia-altered cholesterol metabolism, I observed an 9 accumulation of early and a decrease in late cholesterol precursors, which are separated by several oxygen-dependent enzymatic steps. Although total cholesterol levels were only slightly reduced, my data indicate locally lowered endoplasmic reticulum (ER) cholesterol levels under hypoxia, which cause feedback activation of the ER cholesterol-sensing transcription factor sterol regulatory element-binding protein 2 (SREBP2) and induction of cholesterol biosynthesis enzymes. Interestingly, a broad range of interferon-stimulated genes (ISGs), mainly known for their antiviral function, was also induced under hypoxia with similar kinetics as SREBP2 targets, suggesting an immunometabolic crosstalk. While the availability of certain cholesterol biosynthesis intermediates as well as a direct involvement of SREBP2 seemed rather unlikely to cause hypoxic ISG induction, changes in intracellular cholesterol distribution appeared crucial for the hypoxic induction of chemokine-ISGs. Mechanistically, I found that MyD88-dependent toll-like receptor 4 (TLR4) signaling contributes to enhanced hypoxic ISG induction, likely sensitized by changes in cholesterol dynamics. Importantly, hypoxia amplified induction of chemokine-ISGs in monocytes upon treatment with severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) spike protein via TLR4 similarly as after addition of infectious virus, which might contribute to systemic inflammation in hypoxemic patients with severe coronavirus disease-2019 (COVID-19).
Taken together, I comprehensively analyzed RNA dynamics in hypoxic monocytes. Specifically, I identified RNA stability as a modulating mechanism to limit production of mitochondria under oxygen-restricted conditions. Moreover, I characterized the immunometabolic crosstalk between disturbed cholesterol homeostasis and spontaneous induction of interferon (IFN)-signaling in hypoxic monocytes, which might contribute to systemic inflammation in severe cases of COVID-19.
In this thesis, the early time dynamics in a heavy ion collision of Pb-Nuclei at LHC center-of-mass energies of 5 TeV is studied. Right after the collision the system is out-of-equilibrium and essentially gluon dominated, with their density saturating at a specific momentum scale Q_s. Based on a separation of scales for the soft and hard gluonic degrees of freedom, the initial state is given from an effective model, known as the Color Glass Condensate. Within this model, the soft gluons behave classical to leading order, making it possible to study their dynamics in gauge invariant fashion on a three dimensional lattice, solving Hamiltonian field equations of motion, keeping real time. Quark-Antiquark pairs are produced in the gluonic medium, known as the Glasma and manifest themselves as a source of quantum fluctuations.
They enter the dynamics of the gluons as a current, making the system semi-classical. In lattice simulations, the non-equilibrium system is tested for pressure isotropization, which is a necessary ingredient to reach a local thermal equilibrium (LTE), making a hydrodynamical description at a later stage possible. In addition, the occupation of energy modes is studied with its implications on thermalization and classicality.
The role of Apelin signaling and endocardial protrusions during cardiac development in zebrafish
(2023)
During cardiac development, cardiomyocytes (CMs) are delaminated from the compact muscle wall to increase the muscle mass of the heart. This process is also known as cardiac trabeculation. It has been shown that growth factors produced by endocardial cells (EdCs) are required for myocardial morphogenesis and growth. In particular, Neuregulin produced by EdCs promotes myocardial trabeculation. The deficiency of Neuregulin signaling leads to hypotrabeculation. Endocardial protrusions project from the endocardium to the myocardium are also essential for the trabeculae onset. Yet current studies only introduce the function of endocardial sprouts descriptively. This article first reports the mechanisms of endocardial sprouting during myocardial trabeculation. By living imaging, we first demonstrate that EdCs interact with CMs through membrane protrusions in zebrafish embryos. More interestingly, these protrusions stay in close contact with their target CMs in spite of the cardiac contraction. We utilize loss-of-function strategies to report the importance of myocardial apelin, which induces endocardial protrusion formation. Zebrafish lacking Apelin signaling exhibit defects in endocardial protrusion formation as well as excessive deposition of cardiac jelly and hypotrabeculation. Notably, we also present data that blocking protrusion formation in endocardial cells phenocopies the trabeculation defects in apelin mutants. Mechanistically, endocardial-derived Neuregulin requires Apelin signaling mediated endocardial protrusions, and Neuregulin dependent pERK expression is attenuated in the condition of reduced endocardial protrusion formation. Together, our data suggest that endocardial-myocardial communication through endocardial protrusions acts as an underlying principle allowing myocardial growth.
Understanding the brain's proactive nature and its ability to anticipate the future has been a longstanding pursuit in philosophy and scientific research. The predictive processing framework explains how the brain generates predictions based on environmental regularities and adapts to both predicted and unpredicted events. Prediction errors (PE) occur when sensory evidence deviates from predictions, triggering cognitive and neural processes that enhance learning and subsequent memory. However, the effects of PE on episodic memory have not been clearly explained. This dissertation aims to address three key questions to advance our understanding of PE and episodic memory. First, how does the degree of PE influence episodic memory, and how do expected and unexpected events interact in this process? Second, what insights can be gained from studying the electrophysiological activity associated with prediction violations, and what role does PE play in subsequent memory benefits? Lastly, how do memory processes change across the lifespan, and how does this impact the brain's ability to remember events? By answering these questions, this dissertation contributes to advancing our understanding of the cognitive and neural mechanisms underlying the relationship PE and episodic memory.
Das Experiment ALICE (A Large Ion Collider Experiment) am CERN (Conseil Européen pour la Recherche Nucléaire) LHC (Large Hadron Collider) fokussiert sich auf die Untersuchung stark wechselwirkender Materie unter extremen Bedingungen. Solche Bedingungen existierten wenige Mikrosekunden nach dem Urknall, als die Temperaturen so hoch waren, dass Partonen (Quarks und Gluonen) nicht zu farbneutralen Hadronen gebunden waren. In solch einem Quark-Gluon-Plasma können sich die Partonen frei bewegen, wobei sie allerdings mit anderen Partonen aus dem Medium stark wechselwirken. Am LHC werden Bleikerne auf ultra-relativistische Energien von bis zu 2.68 TeV beschleunigt und zur Kollision gebracht, wobei für weniger als 10 fm/c ein QGP entsteht, das schnell expandiert. Die Partonen hadronisieren, wenn das QGP sich auf Temperaturen von weniger als der Phasenübergangstemperatur von ≈155MeV abkühlt. Die finalen Teilchen- und Impulsverteilungen werden werden vom ALICE Detektor gemessen und geben Aufschluss auf elementare Prozesse im QGP.
Die TPC (Time Projection Chamber ) ist eines der wichtigsten Detektorsysteme von ALICE. Sie trägt maßgeblich zur Rekonstruktion von Teilchenspuren und zur Identifikation der Teilchensorten bei mittleren Rapiditäten bei. Die TPC ist eine große zylindrische Spurendriftkammer und besteht aus einem 88mˆ3 großen Gasvolumen, das von der zentralen Hochspannungselektrode in zwei Seiten geteilt wird. Durchquert ein Teilchen das Gasvolumen, ionisiert es entlang seiner Spur eine spezifische Menge von Gasatomen. Die Ionisationselektronen driften entlang des extrem homogenen elektrischen Feldes zu den Auslesekammern an den Endkappen auf beiden Seiten der TPC. Die Messung der Position und der Menge der Ionisationselektronen erlaubt die Rekonstruktion der Teilchenspur sowie, in Kombination mit der Impulsmessungen über die Krümmung der Teilchenspur im Magnetfeld, die Bestimmung der Teilchensorte über den spezifischen Energieverlust pro Wegstrecke im Gas. Das Gasvolumen der TPC war in LHC Run 1 (2010–2013) mit Ne-CO_2 (90-10) gefüllt. Die Gasmischung wurde zu Ar-CO_2 (88-12) für Run 2 (2015–2018) geändert. Als Auslesekammern wurden Vieldrahtproportionalkammern verwendet, die aus einer segmentierten Ausleseebene, einer Anodendrahtebene, einer Kathodendrahtebene und einem Gating-Grid (GG) bestehen. Das GG is eine zusätzliche Drahtebene, die durch zwei verschiedene Spannungseinstellungen transparent oder undurchlässig für Elektronen und positive Ionen geschaltet werden kann.
In den ersten Daten von Run 2 bei hohen Interaktionsraten wurden große Verzerrungen der gemessenen Spurpunkte beobachtet, die auf Grund von Verzerrungen des Driftfeldes auftreten und nicht von Daten aus Run 1 bekannt waren. Diese Verzerrungen treten nur sehr lokal an den Grenzen von manchen der inneren Auslesekammern (IROCs) auf. Zudem wurden auch große Verzerrungen in einer (C06) der äußeren Auslesekammern (OROCs) festgestellt, die sich bei einem bestimmten Radius über die ganze Breite der Kammer erstrecken. Die Ergebnisse dieser Arbeit befassen sich mit der Untersuchung jener Verzerrungen und ihrer Ursache, sowie mit der Entwicklung von Strategien um die Verzerrungen zu minimieren.
Messungen der Verzerrungen in den IROCs und Vergleiche mit Simulationen lassen darauf schließen, dass die Verzerrungen von positiver Raumladung hervorgerufen werden, die durch Gasverstärkung an sehr begrenzten Regionen der Auslesekammern entsteht und sich durch das Driftvolumen bewegt. Es werden charakteristische Abhängigkeiten von der Interaktionsrate sowie systematische Veränderungen bei Umkehrung der Orientierung des Magnetfeldes gemessen. Eine erneute Analyse von Run 1 Daten mit den Methoden aus Run 2 zeigt, dass die Verzerrungen bereits in Run 1 auftraten, jedoch durch die Ne-Gasmischung und niedrigere Interaktionsraten um eine Größenordnung kleiner waren. Neue Daten aus Run 2, für die die Gasmischung zeitweise wieder von Ar-CO_2 zu Ne-CO_2- N_2 geändert wurde, bestätigen die Ergebnisse der Run 1 Datenanalyse. Der Ursprung der Raumladung wird systematisch eingegrenzt. Es werden einzelne IROCs identifiziert, an deren Anodendrähten die Raumladung entsteht. Physikalische Modelle ermöglichen es, die Entstehung der Raumladung auf das Volumen zurückzuführen, das sich zwischen zwei IROCs befindet. Damit besteht die Vermutung, dass einzelne Spitzen von Anodendrähten am äußeren Rand dieser IROCs in das Gasvolumen hineinragen und somit hohe elektrische Felder erzeugen, an denen Gasverstärkung stattfindet. Die positiven Ionen können dann ungehindert in das Driftvolumen gelangen. Um diesen Effekt zu unterdrücken, wird das Potential der Cover-Elektroden angepasst, die sich auf den Befestigungsvorrichtungen der Drahtebenen an den Kammerrändern befinden. Dadurch kann die Menge von Ionisationselektronen, die in das Volumen zwischen zwei IROCs hineindriftet und vervielfacht wird, eingeschränkt werden. Über elektro-statische Simulationen und Messungen wird eine Einstellung für das Cover-Elektroden-Potential gefunden, mit der die Verzerrungen auf 30 % reduziert werden können. Die Verzerrungen in OROC C06 entstehen durch positive Ionen, die aus der Verstärkungsregion in das Driftvolumen gelangen, da an dieser bestimmten Stelle zwei aufeinanderfolgende GG-Drähte den Kontakt verloren haben. Die Verzerrungen werden um mehr als einen Faktor 3 reduziert, indem die Hochspannung der Anodendrähte um 50 V und somit der Gasverstärkungsfaktor um einen Faktor 2 verringert wird und indem das Potential der noch funktionierenden GG-Drähte erhöht wird.
Zusammenfassend konnten die lokalen Raumladungsverzerrungen für die letzte Pb−Pb Strahlzeit von Run 2 auf weniger als 1cm bei den höchsten Interaktionsraten verringert werden. Zudem wurde der Anteil des von Raumladungsverzerrungen betroffenen Volumens der TPC signifikant verringert, sodass die ursprüngliche Auflösung der Spurrekonstruktion wieder erreicht werden konnte.
Necroptosis is an immunogenic form of programmed cell death characterized by plasma membrane accumulation of activated mixed lineage kinase domain-like (MLKL) that eventually leads to membrane disruption and release of danger-associated molecular patterns (DAMPs). Necroptotic cell death is tightly controlled by checkpoints, including compartmentalization as well as post-translational modifications (PTMs), like phosphorylation and ubiquitination of receptor-interacting protein kinase (RIPK) 1, RIPK3 and MLKL. Removal of plasma membrane-located activated MLKL via endocytosis or exocytosis can counteract necroptosis, but up till now, the exact mechanisms by which necroptosis is regulated downstream of MLKL activation and oligomerization are not fully understood.
Ubiquitination is a key post-translational modification that regulates various cellular processes including cell survival and cell death signaling via ubiquitination of RIPK1, RIPK3 and MLKL. M1-linked (linear) poly-ubiquitination is mediated exclusively by the linear ubiquitin chain assembly complex (LUBAC) which critically regulates cell fate and immune signaling via death receptors such as TNF receptor 1 (TNFR1).
In this study, we demonstrate that M1 poly-Ubiquitin (poly-Ub) increases during necroptosis which can be blocked by inhibition of LUBAC activity with the small-molecule HOIL-1-interacting protein (HOIP) inhibitor HOIPIN-8 or by loss of LUBAC catalytic subunit HOIP. Intriguingly, HOIPIN-8, as well as the HOIP inhibitor gliotoxin, and HOIP knockdown effectively prevent TNFα/smac mimetic/zVAD.fmk-induced necroptotic cell death in cells of human origin, without affecting necroptotic RIPK1 and RIPK3 phosphorylation, necrosome formation and oligomerization of phosphorylated MLKL. We demonstrate that HOIPIN-8 treatment inhibits MLKL translocation to intracellular membranes and accumulation in plasma membrane hotspots as well as MLKL exocytosis. We further confirm that HOIPIN-8 treatment suppresses necroptotic cell death in primary human pancreatic organoids (hPOs). Using time-lapse imaging and live/dead staining, we demonstrate loss of organoid structure and hPO cell death induced by smac mimetics and caspase inhibitors, thus providing a novel platform to investigate necroptosis in near physiological settings. Inhibition of LUBAC activity with HOIPIN-8 prevents hPO collapse and extends cell viability. Of note, loss of the M1 Ub-targeting deubiquitinating enzymes (DUBs) OTU DUB with linear linkage specificity (OTULIN) and cylindromatosis (CYLD) in human cell lines does not affect necroptosis induction and HOIPIN-8-mediated rescue of necroptosis. Intriguingly, inhibition of LUBAC activity with HOIPIN-8 does not block necroptotic cell death in murine cell lines.
Using massive analyses of cDNA ends (MACE)-seq-based global transcriptome analysis we confirm that necroptosis induces a pro-inflammatory cytokine profile which is dependent on LUBAC function and necroptotic signaling. Loss of LUBAC activity prevents the MLKL-dependent production and release of pro-inflammatory cytokines and chemokines.
Finally, we identify Flotillin-1 and -2 (FLOT1/2) as putative targets of necroptosis-induced M1 poly-Ub. Ubiquitin-binding in ABIN and NEMO (UBAN)-based pulldowns of M1 poly-ubiquitinated proteins revealed enrichment of FLOTs after necroptosis induction which is dependent on LUBAC activity and can be blocked with necroptosis inhibitors Nec-1s, GSK’872 and NSA, targeting RIPK1, RIPK3 and MLKL, respectively. Of note, loss of FLOT1/2 potentiates necroptosis suppression induced by LUBAC inhibition with HOIPIN-8.
Together, these findings identify LUBAC-mediated M1 poly-Ub as an important mediator of necroptosis and identify FLOTs as novel putative targets of LUBAC-mediated M1 poly-Ub during necroptosis. In addition, by modeling necroptosis in primary human organoids, we further expand the spectrum of experimental models to study necroptosis in human cellular settings.
Influenza is a contagious respiratory disease caused by influenza A and influenza B viruses. The World Health Organisation (WHO) reports that annual influenza epidemics result in approximately 1 billion infections, 3 to 5 million severe cases, and 300 to 650 thousand deaths. Understanding hidden mechanisms that lead to optimal vaccine efficacy and improvement antiviral treatment strategies remain continuous and central tasks. First, regarding the immune response to vaccines and natural infections, the antibody response echoes the dynamics of diverse immune elements such as B-cells, and plasma cells. Also, responses reflect the processes for B-cells to gain and adapt affinity for the virus. Antibodies (Abs) that respond to the virus surface proteins, particularly to the hemagglutinin (HA), have been identified to protect against infection. The Abs responses binding to HA can be broadly protective as this protein is considerably accessible on the virion. When following sequential infections with similar influenza strains, i.e. two infections with different strains of a subtype, an enhanced breadth and magnitude of Abs response is developed, mainly after the second infection. The effect of being effective to new strains is called Abs cross-reaction.
On the other hand, as for antiviral treatment, the WHO currently approves the use of neuraminidase inhibitors (NIs) such as zanamivir and oseltamivir. Diverse research areas such as system biology, learning-based methods, control theory, and systems pharmacology have guided the development of modern treatment schemes. To do so, mathematical models are used to describe a wide range of phenomena such as viral pathogenesis, immune responses, and the drug's dynamics in the body. Drug dynamics are usually expressed in two phases, pharmacokinetics (PK) and pharmacodynamics (PD) - the PK/PD approach. These schemes leverage pre-clinical and clinical data through modeling and simulation of infection and drug effects at diverse levels. Under such a framework, control-based scheduling systems seek to tailor optimal antiviral treatment for infectious diseases. Thus, influenza treatment can be theoretically studied as a control-based optimization duty (about systems stability, bounded inputs, and optimality). Finally, towards real-world implementation, learning-based methods such as neural networks (NNs) can guide solving issues on the control-based performance. Using NNs as identifiers provide a setting to deal with infrequent measures and uncertain parameters for the control systems.
This thesis theoretically explores central mechanisms in influenza infection via modeling and control approaches. In the first project, we explore how and to what extent antibody-antigen affinity flexibility could guide the Abs cross-reaction in two sequential infections using a hypothetical family of antigens. The set of antigens generally represent strains of influenza, such as those of a subtype. Each antigen is composed of a variable and a conserved area, generically representing the structures of the HA, head, and stalk, respectively. We test diverse scenarios of affinity thresholds in the conserved and variable areas of the antigens. The Abs response reaches a high magnitude when using equivalent affinity thresholds in the conserved and variable areas during the first infection. However, improved cross-reaction is developed when slightly increasing the affinity threshold of the variable area for the second infection. Key mutations via affinity maturation is a feature that, together with affinity flexibility between infections, guides Abs cross-reaction in the model outcome. These results could correlate with studies pointing out that broad responses might be dependent on reaching specific mutations for getting affinity to a newly presented antigen while broadly reaching related antigens. The general platform may serve as a proof-of-concept for exploring fundamental mechanisms that favor the Abs cross-reaction.
In a second project, theoretical schemes are developed to combine impulsive and inverse optimal control strategies to address antiviral treatment scheduling. We present results regarding stability, passivity, bounded inputs, and optimality using impulsive action. The study is founded on mathematical models of the influenza virus (target-cell limited model) adjusted to data from clinical trials. In these studies, participants were experimentally infected with influenza H1N1 and treated with NIs. Results show that control-based strategies could tailor dosage and reduce the amount of medication by up to 44%. Also, control-based treatment reaches the efficacy (98%) of the current treatment recommendations by the WHO. Monte Carlo simulations (MCS) disclose the robustness of the proposed control-based techniques. Using MCS, we also explore the applicability to the individualized treatment of infectious diseases through virtual clinical trials. Furthermore, bounded control strategies are applied directly in drug dose estimation accounting for overdose prevention. Finally, due to the limitations of the available technology intended for clinical practice, we emphasize the necessity of developing system identifiers and observers for real-world applications.
In the third project, the problem of data scarcity and infrequent measures in the real world is handled by means of learning-based methods. System identification is derived using a Recurrent High Order Neural Network (RHONN) trained with the Extended Kalman filter (EKF). Lessons learned from impulsive control frameworks are taken to develop a neural inverse optimal impulsive control --neurocontrol. The treatment efficacy is tested for early (one day post-infection) and late (2 to 3 days post-infection) treatment initiation. The neurocontrol reaches an efficacy of up to 95% while saving almost 40% of the total drug in the early treatment. Robustness is tested via virtual clinical trials using MCS.
Lastly, taking all together, the schemes developed in this thesis for modeling the Abs cross-reaction and control-based treatment tailoring can be extended and adapted to explore similar phenomena in different respiratory pathogens, such as SARS-CoV-2.
Get3 in Arabidopsis
(2021)
Der guided entry of tail-anchored proteins (GET) Biogenese-Weg vermittelt den Transport und die Insertion von tail-anchor (TA) Proteinen in die Doppellipidschicht des Endoplasmatischen Retikulums (ER). TA Proteine sind dadurch gekennzeichnet, dass sie eine Transmembran Domäne (TMD) in den letzten 50 Aminosäuren ihrer Sequenz beherbergen. Diese TMD enthält die notwendigen Informationen, mit denen die Proteine an ihren jeweiligen subzellulären Zielort transportiert werden können. TA Proteine erfüllen eine Vielzahl von essentiellen biologischen Prozessen, sie fungieren zum Beispiel als Rezeptoren, sind maßgeblich an der Fusion von Vesikeln beteiligt sowie an der Initiation von Apoptose. Durch ihren modularen Aufbau können TA Proteine nicht mit dem Signalerkennungspartikel interagieren und müssen deshalb posttranslational zum ER geleitet werden. Im Modellorganismus Bäckerhefe (Saccharomyces cerevisiae) ist der GET Biogenese-Weg am besten beschrieben und läuft wie folgt ab: Nach der Termination der Translation bindet das Protein SgtA das TA Protein und händigt es über den Adapter-Komplex, bestehend aus Get4 und Get5, an die zytosolische ATPase Get3 aus. Get3 ist der zentrale Zielsteuerungsfaktor des GET Biogenese-Weges. Sobald sich ein Komplex aus Zeilsteuerungsfaktor und TA Protein gebildet hat, wird dieses zur Membran des ERs überführt. Dort wird das TA Protein an den Rezeptorkomplex bestehend aus Get1 und Get2 übergeben, welcher anschließend die Insertion des TA Proteins in die Doppellipidschicht des ERs initiiert.
Get3 hat im zellulären Kontext noch eine weitere Funktion. Unter oxidativem Stress oder Energie depletierenden Bedingungen wird Get3 zu spezifischen Foci rekrutiert, an denen sich noch weitere durch Stress -induzierbare Proteine, wie z.B. die der Familie der Hitze Stress Proteine (HSPs) versammeln. Analysen haben gezeigt, dass Get3 unter den oben genannten Bedingungen, Konformationsänderungen durchläuft und dann als ATP unabhängige Holdase fungiert. Diese kann die exponierten, hydrophoben Anteile von Proteinen binden, um dadurch die Proteostasis aufrechtzuhalten.
Durch die Bedeutsamkeit der TA Proteinen ist die zentrale ATPase Get3 in allen Domänen des Lebens hochgradig konserviert. Phylogenetische Analysen ergaben, dass sich Get3 im Allgemeinen in eine „A“ Gruppe sowie eine „BC“ Gruppe aufspaltet. Im Modellorganismus Arabidopsis thaliana (Ackerschmalwand) wurden drei Orthologe zu Get3 identifiziert. Eins davon gehört zu der „A“ Gruppe und befindet sich im Zytoplasma. Die anderen zwei Orthologe befinden sich in den Organellen endo-symbiotischen Ursprungs und gehören der „BC“ Gruppe an. Untersuchungen an verschiedenen Deletionsmutanten in A. thaliana haben gezeigt, dass die Mutationen einzelner GET Komponenten zu einer signifikanten Verkürzung der Haarwurzeln führen, obwohl der restliche Habitus der Pflanze unverändert bleibt. Diesbezüglich wurde SYP123 als einziges TA Proteine identifiziert, dessen Abundanz durch die Deletion von GET Komponenten beeinflusst werden kann. Von den anderen beiden Orthologen organellären Ursprungs ist, abgesehen von ihrer Lokalisation nichts weiter bekannt
Vier Orthologe Gruppen in Pflanzen
Da bislang nicht mehr als zehn Pflanzenarten für phylogenetische Analysen herangezogen wurden, wurden in dieser Arbeit die taxonomischen Beziehungen von Get3 zu einander in 50 Spezies der Viridiplantae auf Basis der Orthologie sowie Homologie untersucht. Dies führte zur Identifizierung einer zytolischen (AtGet3a), einer plastidären (AtGet3b), einer mitochondriellen (AtGet3c) sowie einer Monokotyledone spezifischen Gruppe (SBGet3). Die Lokalisation der ersten drei Gruppen wurde in selektierten Pflanzen, sowohl homolog als auch heterolog, der unterschiedlichen Spezies mittels saGFP untersucht, und es konnte gezeigt werden, dass mehrere Get3 Orthologe mit unterschiedlichen subzellulären Lokalisationen eine unter Pflanze häufig auftretende Eigenschaft ist. Das Weitern konnte gezeigt werden, dass manche Komponenten des Präzielsteuerungskomplexes (SgtA und Get4) sowie des Rezeptorkomplexes (Get1) in fast allen der 50 untersuchten Pflanzenarten vorhanden sind. Dies weist auf eine Konservierung des gesamten GET Biogenese-Weges in Pflanzen hin.
Get3a in Arabidopsis thaliana
Da die molekulare Zusammensetzung des Präzielsteuerungskomplexes für AtGet3a in A. thaliana nicht bekannt ist, habe ich Co-Immunpräzipitationen mit Zellextrakten aus weißer Zellkultur und einen von mir selbst aufgereinigten Antikörper gegen AtGet3a durchgeführt. Nach anschließender Gelelektrophorese und einer Anfärbung mit Coomassie Brilliant Blue ließ sich ein reproduzierbares Muster aus Proteinbanden erkennen, welche ausgeschnitten und mittels LC-MS/MS analysiert wurden. Dadurch wurde ein putativer Kandidat für Get5 identifiziert sowie eine Assoziation mit Chaperonen und proteasomalen Untereinheiten.
Um die Zielsteuerungseffizienz und Topologie von ER-Membranproteinen zu analysieren habe ich (i) die rekombinante Synthese eines Modell-TA Proteins mit glykosylierbarem opsin bovine glycosylation Tag (OPG) etabliert sowie (ii) eine Methode etabliert um in isolierten Protoplasten die Richtigkeit der Insertion zu überprüfen. Mit Hilfe dieser Methoden können nun verschiedene Mutanten auf ihre Insertions-Wirksamkeit untersucht werden. Desweitern können durch Mutationsanalysen die notwendigen physikochemischen Eigenschaften für die Erkennung des Substrates ermittelt werden.
Eine weit verbreitete Methode im GET Feld ist die tail-anchor translocation (TAT). Bei dieser Methode werden isolierte mikrosomale Fraktionen des rauen ERs mit rekombinanten Komplexen bestehend aus Zielsteuerungsfaktor und TA Protein inkubiert. Durch einen rekombinanten OPG, der im Lumen des ERs post-translational modifiziert werden kann, ist die Beobachtung einer zeitabhängigen Kinetik der Glykosylierung möglich. Dieses System wurde bislang nur für Komponenten aus Säugern oder Hefen benutzt, aber noch nie mit einem System auf pflanzlicher Basis. Um dies zu verwirklichen, habe ich die rekombinante Proteinexpression soweit optimiert, dass der Großteil des synthetisierten Proteins sich im löslichen Anteil des Lysats statt in den Inclusion Bodies befand. Mittels dieser Optimierung konnte ich die Ko-Expression von Zielsteuerungsfaktor mit TA Protein als löslichen Komplex etablieren. Ergänzend zu den löslichen Komplexen habe ich eine geeignete Methode etabliert um mittels Saccharosegradienten mikrosomale Fraktionen aufzutrennen in denen AtGet3a angereichert ist. Leider müssen noch die Parameter der Reaktion optimiert werden, aber die Akquirierung alle nötigen Bestandteile ist etabliert.
Tinnitus is a symptom experienced by most people at least once in their lifetime. In most documented cases, a new onset of chronic tinnitus can be chronologically correlated with hearing loss. However, tinnitus can also occur in people with (apparently) normal hearing and remains without a traceable preceding cause. Despite the frequency of occurrence of tinnitus, the pathophysiological mechanisms are still not fully understood. A currently proposed hypothesis focuses on a "hidden" hearing loss called synaptopathy as a pathomechanism of tinnitus in normal hearing subjects. In the present study, the objective was to test whether finestructure audiometry or measurement of otoacoustic emissions can reveal possibly overlooked hearing impairment in presumed normalhearing individuals with chronic tinnitus. Thus, a hearing loss not audiologically detectable by the usual methods would supplement or replace the presumed synaptopathic pathomechanism. Another objective was to attempt to replicate the existing findings of another research group on synaptopathy as cause for tinnitus in normal hearing people. Schaette and McAlpine (2011) were able to demonstrate a significant difference in wave I amplitudes between groups of normal hearing subjects with and without chronic tinnitus by deriving clickevoked auditory brainstem potentials, thus supporting the hypothesis of synaptopathy18.
For the present study, a cohort of normal-hearing subjects consisting of a group of tinnitus subjects (N = 15) and a control group (N = 14) was tested. Manual puretone audiometry with 11 test frequencies was conducted to determine hearing performance. Inclusion criteria were defined as air conducted hearing thresholds of 10 dB HL or lower. A deviation at a test frequency of 15 dB HL or less was tolerated. Data of tinnitus characteristics, such as pitch and intensity, were collected by presentation and matching of comparative tones, quality and subjective disturbance by questionnaire. Furthermore, data was obtained from both test groups by Békésy gliding frequency audiometry (794 test frequencies), as well as DPOAE measurement (36 test frequencies) and auditory brainstem response (ABR) audiometry (derivation of early auditory evoked potentials). The results showed a correlation of the determined tinnitus comparison pitch with the frequency location of the largest deviation (impairment) from the normal hearing curve in the Békésy gliding frequency audiometry (p = 0.032). All further analyses of the finestructure hearing curve (steepness of hearing loss, slope, number of hearing loss dips) showed no statistically significant relationship between the morphology of the fine-structure hearing curve and tinnitus characteristics. Finestructure measurement revealed areas of hearing loss that were not mapped in manual puretone audiometry. These "undetected" hearing losses would have led to the exclusion of 12 of 29 subjects (41.4 %) if the finestructure hearing curve had been used as an inclusion criterion. A direct comparison of the mean finestructure hearing curves of both test groups showed a statistically significant better mean hearing performance of the tinnitus group (p < 0.05) in 3 different test frequency ranges (1.5 kHz, 3 kHz, 7 kHz) with a maximum of 4 dB HL. Analy-sis of the mean amplitudes of wave I of the ABRs showed, contrary to expectation, a weak trend toward higher amplitudes in the tinnitus group (p = 0.06). According to Schaette and McAlpine (2011), synaptopathy pathogenesis should have resulted in an opposite trend, i.e., a decrease in wave I amplitude in the tinnitus group. As a secondary finding, a weak trend between wave I amplitude and subjectively perceived disturbance of tinnitus was demonstrated (p = 0.06). Statistical analysis of the parameters determined from the DPOAE measurements did not reveal any significant differences between the tinnitus group and control group. Direct comparison of the DPOAE and finestructure hearing curves, revealed a significant difference in the differences of the frequencyspecific measurements around 2.4 kHz (p = 0.007).
The results of the study suggest that in previous studies with supposedly normal hearing tinnitus subjects there were unrecognized hearing losses that either went unrecognized by the screening by manual puretone audiometry, or subjects with previously aboveaverage hearing experienced a subtle spontaneous decrease in their hearing as tinnitus pathogenesis. This assumption is also supported by the fact that there is a significant correlation between the frequency range of the greatest hearing loss in the finestructure hearing curves and the tinnitus frequency.
The suspected pathomechanism of synaptopathy in "normal hearing" subjects with tinnitus could not be confirmed. The correlation between wave I amplitudes and subjectively perceived disturbance by tinnitus, indicated by the data of this study, should be investigated in more detail in future studies. Further research with more accurate measurement methods and larger subject groups is needed to clarify the hypothesis "Genesis of chronic subjective tinnitus without hearing loss".
The impact of the Covid-19 pandemic called for rapid responses in face of unprecedented challenges. In this context, earning more about the causative agent SARS-CoV-2 becomes imperative. Therefore, clinical virus isolates were studied with focus on infectivity, replication kinetic, and caspase activity.
Firstly, clinical specimens collected from patients were tested for infectivity in cell culture. Combined with polymerase chain reaction results, a formula predicting infectivity in cell culture based on abundance of viral RNA was developed. Additionally, analysis of different specimen types, sources, and material, elucidate the question of infectivity. Here, infectivity was demonstrated in specimens derived from different parts of the respiratory tract, including specimens collected from deceased persons. A protocol for virus isolation on human airway epithelium in air-liquid interface culture was established.
Secondly, replication kinetics of 20 clinical isolates were compared, including a subset of seven sequenced isolates. All isolates replicated in the colon epithelial cell culture model. Within the subset, differences between isolates carrying the D614G amino acid exchange and with original spike protein were observed.
Lastly, elevated caspase activity was demonstrated in two cell culture models including human airway epithelium in air-liquid interface culture.
Subsequently, caspase inhibition by small-molecule compound Emricasan and its effects on the cytopathic effect observed in cell culture were studied. Here, increased cell survival in a colon epithelial cell line was shown with unimpaired virus replication. Elevated caspase activity was identified as early marker of infection and validated by testing across 20 clinical virus isolates.
This study offers information on infectivity that can help shape the understanding of transmission risk. As such, parts of the data collected here were used for validation of rapid antigen tests. The insights gained by studying caspase activity contributed in part to the development of a drug screening method by Bojkova et al.,41 thus aiding routine laboratory workflow. It was demonstrated that Emricasan exhibits no antiviral effect, while the finding of increased cell survival in cell culture could give rise to further research on prevention of tissue damage.
Um sich an ändernde Umwelteinflüsse und metabolische Bedürfnisse anpassen zu können, ist es für Zellen essenziell, dass Boten-RNA (engl. messenger RNA, mRNA) stetig und schnell nach der Translation abgebaut wird. In Prokaryoten ist dafür der Proteinkomplex Degradosom verantwortlich, in dem Endo- und Exoribonukleasen RNase E und PNPase das RNA-Transkript in kleinere Fragmente und schließlich einzelne Nukleotide spalten. Die DEAD-Box Helikase RhlB im Komplex dient zusätzlich dazu, mögliche Sekundärstrukturen in der RNA zu entfalten, welche sonst die weitere Degradation behindern würden. Es konnte gezeigt werden, dass RhlB’s sehr geringe katalytische Aktivität – gemessen durch ATP-Verbrauch und Rate an entwundener RNA – signifikant durch die allosterische Bindung an Komplexpartner RNase E erhöht wird. Gleichzeitig deuten andere Studien darauf hin, dass RhlB eine mögliche Selektivität für doppelsträngige RNA-Substrate mit 5‘-Einzelstrang-Überhängen aufweist.
Diese Arbeit liefert neue Erkenntnisse in Bezug auf die Kommunikation zwischen den Degradosom-Komponenten RhlB und RNase E aus E. coli, indem das potenzielle Wechselspiel zwischen RhlBs RNA-Selektivität und der allosterischen Aktivierung durch RNase E untersucht wurde. Der vielseitige Einsatz NMR-spektroskopischer Techniken sowie die Verwendung kurzer RNA-Substrate mit spezifischen Strang-Eigenschaften ermöglicht es, mit einen ungewöhnlichen, RNA-zentrierten Ansatz an diese unzureichend verstandene Protein-Interaktion heranzugehen.
Zunächst wurden hierzu eine Reihe kurzer doppelsträngiger RNA-Konstrukte hergestellt, die sich nicht nur in ihren Einzelstrang-Merkmalen unterscheiden, sondern auch die thermodynamischen Anforderungen eines DEAD-Box Helikase Substrats erfüllen, und gleichzeitig eine ausreichende NMR-spektroskopische Signal-Zuordnung erlauben. Die thermale Stabilität, das Faltungsverhalten sowie die 1H Imino-protonen- und 13C HSQC-Zuordnungen aller geeigneten Konstrukte wurden erfolgreich bestimmt.
Um den Einfluss spezifischer RNA-Substrate sowie die Bindung zweier verschiedener RNase E Fragmente auf RhlBs ATP-Umsatzrate zu untersuchen, wurde sich zunächst eines photometrischen Phosphat-Assays bedient. Damit konnte deutlich gezeigt werden, dass RhlB in Abwesenheit des Komplex-Partners nicht in der Lage ist, signifikante Mengen an ATP umzusetzen, unabhängig davon, welches RNA-Konstrukt eingesetzt wird. Die Bindung der RNase E Fragmente erhöhte signifikant die ATP-Hydrolyse-Rate der Helikase, wobei die größte Aktivierung für den RNA-Duplex mit 5‘-Einzelstrang sowie ein einzelsträngiges Substrat zu beobachten ist. Da diese Ergebnisse deutlich eine RNA-Abhängigkeit beim ATP-Umsatz der Helikase zeigen, wurde untersucht, ob diese Unterschiede ihren Ursprung bereits in der Bindung der spezifischen RNA-Substrate haben. Mittels einer Mischapparatur, die es erlaubt die enzymatische Reaktion direkt im Spektrometer zu initiieren sowie zeitaufgelöster 31P NMR-Experimente konnte die allosterische Aktivierung der ATP-Hydrolyse-Rate von RhlB auch unter NMR-spektroskopischen Messbedingungen nachgewiesen werden.
Da die Ergebnisse des ATPase Assays deutlich eine RNA-Abhängigkeit bei der ATP-Umsatz-Rate der Helikase zeigen, wurde zusätzlich untersucht, ob diese Unterschiede ihren Ursprung in den Affinitäten für die verschiedenen RNA-Substrate haben und ob diese durch die Bindung von RNase E and RhlB beeinflusst werden. Um im gleichen Zuge zu überprüfen, ob die Bindung der RNA an RhlB die RNA-Konformation oder Basenpaarung ändert, werden 1H NMR-Titrationsexperimente durchgeführt. Es konnte erstmals gezeigt werden, dass RhlB eine inhärente Präferenz für Duplexe mit 5‘-Überhang gegenüber Konstrukten mit 3‘-Überhang oder stumpfen Enden besitzt, was sich in einer erhöhten Affinität zeigt. Zusätzlich offenbaren die Messungen, dass RNase Es allosterische Bindung selektiv die Affinität gegenüber Konstrukten mit Einzelstrang-Überhang erhöht, während die Affinität zu RNA Duplexen ohne Überhang sogar verringert wird. Diese Ergebnisse liefern erstmals einen Nachweis, dass RNase E aktiv Einfluss auf RhlBs RNA-Bindung nimmt. Weder die Bindung der RNA and RhlB noch an den RhlB/RNase E Komplex scheint die Basenpaarung oder Konformation der RNA-Substrate zu beeinflussen, da lediglich eine homogene Peak-Verbreitung aller Imino-Protonen-Signale im 1H NMR-Spektrum beobachtet werden konnte.
Chapter I of this work addressed the piggyBac (PB) transposon system, a non-viral genome engineering tool that is capable of efficiently performing stable integration of DNA sequences into a target cells genome and has already been used in clinical trials. However, the PB transposase has the problematic property of preferentially integrating transposons near transcriptional start sites (TSSs). This increases the likelihood of causing genotoxic effects, limiting its potential use as a tool in clinical applications. It has been shown in the past that the PB transposase shows physical interactions with BET proteins (e.g. BRD4) through Co-IP experiments. Representatives of these proteins are part of the transcriptional activation complex and are abundant at TSSs. Accordingly, it was previously proposed that this interaction is the underlying cause for the biased integration preference. For the first chapter of this thesis, the goal was to disrupt this interaction potentially modifying said integration preference. A secondary structure hypothesized to be mainly responsible for said interaction was extensively mutated resulting in several PB variants that were analyzed for their interaction capacity through a series of Co-IP experiments with BRD4. In total, seven substitutions were identified (E380F, V390K, T392Y, M394R, K407C, K407Q, and K407V) which exhibited reduced interaction capacity with BRD4. Each of the aforementioned mutants were used to generate integration libraries and, through NGS, it was determined if the integration preferences of the respective mutants had changed. In the immediate range 200 base pairs up- and downstream from known TSSs all mutants used exhibited a reduced integration bias. At a wider observation window 3 kbp up- and downstream from TSSs, further mutants with the substitutions M394R, T392Y and V390K showed a reduction in integration frequency of 17.3%, 1.5% and 5.4%, respectively, compared to the wildtype. Of particular note was the M394R mutant, which showed a reduction in all window sizes analyzed with a maximum of 65% less integration preference in the immediate vicinity of TSSs, theoretically generating a safety advantage over the wildtype transposase.
Chapter II was dedicated to the overall safety improvement for transposon-based gene modification and addresses the time point after the transgene has already been integrated and serious side effects may not be preventable. With this in mind, the aim was to develop a novel suicide-switch that can be stably introduced into cells via transposition, and reliably leads to cell death of the modified cells once activated. A system based on CRISPR/Cas9 was developed, where single guide RNAs were used to guide the Cas9 nuclease to Alu elements. These are short, repetitive sequences, which are distributed over the human genome in more than one million copies. Inducing double strand breaks within these elements would lead to genomic fragmentation and cell death. To be inducible, a transcriptional as well as post- translational control mechanism was added. Transcription of the Cas9 nuclease was regulated using a tet-on system, making expression dependent on doxycycline (DOX) supplementation. Furthermore, a version of the Cas9 nuclease called arC9 was used that allows double strand break generation only in the presence of 4-Hydroxytamoxifen (4-HT). Together with an expression cassette for the Alu-specific guide RNA and an expression cassette for the reverse tetracycline controlled transactivator all components were arranged between transposase-specific recognition sequences on a plasmid to allow transposon-system based gene transfer. The system was tested in HeLa cells. First, conditional expression of the arC9 nuclease was confirmed by addition of 1 μg/ml DOX. Second, the suicide-switch was further induced by adding 200 nM 4-HT and protein extracts were assayed for the KAP1 phosphorylation. Only upon induction with DOX and 4-HT phosphorylated KAP1 was detected, indicating DNA damage. Further, extensive growth and survival experiments were conducted to determine the effect of suicide-switch induction on cell proliferation and survival. Between 24 and 48 hours after induction, a halt in cell division was detected, after which extensive cell death was observed. Within 5 days post induction, >99% of all cells were eliminated. In the absence of both inducers, no significant differences in survival were observed compared to control cells line lacking Alu-specific guide RNAs. Microscopic examinations of the <1% surviving cell fraction revealed a senescence-associated phenotype and showed no signs of resumption of the cell division process. Accordingly, the second chapter of this thesis also achieved its goal in developing a functional suicide-switch that can be inserted into human cells via transposition, is highly dependent on the necessary induction signals, and exhibits excellent elimination capabilities in the context tested.