Refine
Year of publication
Document Type
- Doctoral Thesis (5585) (remove)
Language
- German (3549)
- English (2007)
- French (9)
- Latin (5)
- Spanish (5)
- Portuguese (4)
- Italian (3)
- Multiple languages (2)
- mis (1)
Has Fulltext
- yes (5585) (remove)
Is part of the Bibliography
- no (5585)
Keywords
- Deutschland (15)
- Gentherapie (14)
- HIV (13)
- Apoptosis (12)
- Membranproteine (12)
- NMR-Spektroskopie (11)
- RNA (11)
- RNS (10)
- Nanopartikel (9)
- Proteomics (9)
Institute
- Medizin (1465)
- Biowissenschaften (813)
- Biochemie und Chemie (723)
- Physik (581)
- Pharmazie (329)
- Biochemie, Chemie und Pharmazie (285)
- Geowissenschaften (138)
- Neuere Philologien (113)
- Gesellschaftswissenschaften (110)
- Psychologie (97)
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.
Precise tune determination and split beam emittance reconstruction at the CERN PS synchrotron
(2023)
In accelerator physics, the need to improve the performance and better control the operating point of an accelerator has become, year after year, an increasingly important need in order to achieve higher energies and brightness, as well as point-like particle beams. If this involves increasingly advanced technological developments (in terms, for example, of materials for more intense superconducting magnets), it can not take place in the absence of targeted studies of linear and non-linear beam dynamics. In the context of this Ph.D. thesis in physics, linear and non-linear dynamics of charged particles in circular accelerators is the topic that will be discussed and treated in detail. In particular, the presentation and discussion of the results will be divided in two main topics: the need to know the physical properties of a proton beam; and the development of innovative methods to determine and study the accelerator’s working point. With regard to the first topic, an innovative procedure will be presented to determine the transverse size of the PS beam in the beam extraction phase. Among the different ways the extraction occurs at the PS, the analysed one is based on the transverse splitting of the beam by means of non-linear fields. Thus, the knowledge of the transverse beam size is not trivial since resonant linear and non-linear beam structures (namely, core and islands) arise and, for each of them, the beam size has to be quantified. This parameter is crucial for two main reasons: the accelerator that will receive the beam exiting the upstream accelerator may have restrictions (physical or magnetic) that involve a partial or total loss of the incoming beam; and any experiments located downstream of the considered accelerator may need a beam with a transversal size as constant as possible; consequently, its monitoring and control are essential. The second topic concerns the accurate determination of the working point of an accelerator, defined as the number of transverse oscillations the particle beam travels per unit of accelerator circumference, both horizontally and vertically. This quantity is called horizontal and vertical tune, respectively. Their knowledge is also crucial to understand whether the beam will be stable or unstable. In fact, not all tune values are acceptable, as there are particular values that bring the beam into resonance. In this configuration, the amplitude of the transverse oscillations of the particles increases in an uncontrolled manner and leads to the loss of all or part of the beam. Note that, in particular operating conditions, the resonant conditions are sought and desired to model, in a suitable way, the transversal shape of the beam, such as the above mentioned PS extraction scheme. It is even clearer how much the determination of the machine working point is essential to determine the operating conditions of an accelerator. In this context, several methods (also taken from the field of applied mathematics) to calculate the tune will be demonstrated and tested numerically on different types of synthetic signals. At the end of this description, the use of experimental data will allow to obtain the benchmark of a new method for the direct calculation of some characteristic quantities of non-linear beam dynamics (namely, the amplitude detuning, i.e. the variation of tune as a function of intensity of the perturbation provided to the beam.
Caspase-2 is the evolutionary most conserved member of the caspase family and was shown to be involved in genotoxic stress induced apoptosis, control of aneuploidy, and ageing related metabolic changes. However, its role in apoptosis seems redundant due to the observation, that knockout does not inhibit apoptotic signalling exclusively. Instead, knockout of caspase-2 leads to tumor susceptibility in vivo, which led to the assumption, that caspase-2 has non-apoptotic functions and can act as a tumor suppressor. The underlying mechanism of the tumor suppressor activity of caspase-2 has not been clarified so far. Furthermore, caspase-2, has a prominent, and as pro-enzyme exclusive localisation in the nucleus and other subcellular compartments, implicating a distinct and location specific role.
In this study, a novel caspase-2 specific substrate, termed p54nrb, was identified. P54nrb is harbouring a caspase-2 specific cleavage site at the aspartate residue D422, and cleavage of p54nrb leads apparently to disruption of its putative DNA binding domain at the C-terminus.
P54nrb is a nuclear multifunctional RNA and DNA binding protein, known for roles in transcriptional regulation, DNA unwinding and repair, RNA splicing, and retention of defective RNA. Overexpression of p54nrb has been observed in several human cancers, such as cervix carcinoma, melanoma, and colon carcinoma.
Data from this study revealed, that depletion of p54nrb in tumor cell lines results in a loss of resistance to drug induced cell death and to reduced capability of anchorage independent growth, which is functionally equivalent to a reduced tumorigenic potential. Meanwhile, p54nrb depletion alone is not cytotoxic.
The investigation of p54nrb dependent gene regulations by high resolution quantitative proteomics uncovered an altering expression of multiple tumorigenic genes. For two of these candidates, the tumorigenic protease cathepsin-Z and the anti-apoptotic gelsolin, p54nrb dependent expression was detected universally in all three investigated tumor cell lines, cervix carcinoma, melanoma, and colon carcinoma. Additionally, a direct interaction of p54nrb with the cathepsin Z and gelsolin encoding DNA, but not with their corresponding mRNA, could be demonstrated.
Conjointly, this study unveils a novel mechanistic feature of caspase-2 as a tumor suppressor. The caspase-2—p54nrb axis can orchestrate the levels of several tumorigenic proteins and thereby determine the cell death susceptibility and long-term tumor survival. These findings might be of great value for future therapeutic interventions and for overcoming drug resistance of tumors.
Ziel der Arbeit ist es die Eigenschaften und die Häufigkeit von Rezidiven der primär und sekundär therapierten Basalzellkarzinome der MKPG, insbesondere in Abhängigkeit der Lokalisation und des Resektionsstatus zu evaluieren und mit den Ergebnissen der Literatur zu vergleichen, um ein optimiertes chirurgisches Vorgehen zu sichern.
Precise intensity monitoring at CRYRING@ESR: on designing a Cryogenic Current Comparator for FAIR
(2023)
In the field of today’s beam intensity diagnostic there is a significant gap in the non-interceptive, calibrated measurement of the absolute intensity of continuous (unbunched) dc beams with current amplitudes below 1 μA. At the Facility for Antiproton and Ion Research (FAIR) low-intensity DC beams will occur during slow extraction from the synchrotrons as well as for coasting beams of highly-charged or exotic nuclei in the storage rings. The lack of adequate beam instrumentation limits the experimental program as well as the accuracy of experimental results.
The Cryogenic Current Comparator (CCC) can close the diagnostic gap with a high-precision dc current reading independent of ion-species and of beam parameters. However, the established detector design based on a core with high magnetic permeability and on a radial shield geometry has well-known weaknesses concerning magnetic shielding efficiency and intrinsic current noise. To eliminate these weaknesses, a novel coreless CCC with a co-axial shield was constructed and combined with a high-performance SQUID contributed by the Leibniz-Institute of Photonic Technology (Leibniz-IPHT Jena). The new axial CCC model was compared to a radial CCC with the established design provided by the Friedrich-Schiller-University Jena. According to numerical simulations prepared at TU Darmstadt and test measurements of the detectors in the laboratory, the new design offered a significant improvement of the shielding factor – from 75dB to 207dB at the required dimensions – and eliminated all noise contributions from the core material, promising an improved current resolution. Although the lower inductance of the pickup coil reduced the coupling to the beam significantly, the noise properties of the new CCC type were comparable to the classical version with a high-permeability core. However, the expected decrease of the low-frequency noise and thus an increase of the current resolution could not be observed at this stage of development.
Consequently, the classical CCC based on the radial shielding and high-permeability core had to be installed in CRYRING@ESR to provide best possible intensity measurements for the upcoming experimental campaign. In CRYRING the CCC was operated with beam currents between 1nA and 20μA and with different ion species (H, Ne, O, Pb, U). It was shown that the CCC provides a noise-limited current resolution of better than 3.2 nArms at a bandwidth of 200 kHz as well as a noise level below 40 pA/√Hz above 1 kHz. During the operation, the main noise sources of the accelerator environment had to be identified and suitable mitigation strategies were developed. Temperature and pressure fluctuations were suppressed with a newly-designed cryogenic support system based on a 70 l helium bath cryostat, developed and built in collaboration with the Institut für Luft- und Kältetechnik Dresden, in combination with a helium re-liquefier. The cryogenic operating time was restricted to around 7 days, which must be expanded significantly in the future. Digital filters were developed to remove the perturbations of the helium liquefier and of the neighboring dipole magnets. Given the promising results the CCC system can be considered as a prototype for future CCCs at FAIR.
Structure-function relationships in substrate binding protein dependent secondary transporters
(2023)
This work provides new insights into the relevance of SBP dependent secondary transport systems, especially in the thus far under-researched subgroup of TAXI transporters. Importantly, we identified and characterized the TAXI transport system TAXIPm-PQM from Proteus mirabilis. We demonstrated that, in contrast to previously characterized SBP dependent secondary transport systems, TAXIPm-PQM is a proton coupled system and transports the C5-dicarboxylate α- ketoglutarate. Since initially the transport of α-ketoglutarate could only be demonstrated in vivo but not in vitro using established protocols (Mulligan et al. 2009), we investigated in detail the differences between the in vivo and in vitro assay. This resulted in a bioinformatic analysis of TRAP and TAXI signal peptides, which strongly implied that TAXIPm-P requires a transmembrane anchor to allow for transport. We then provided TAXIPm-P surface tethered to the membrane in in vitro transport assays and confirmed the prediction of our bioinformatic analysis that TAXIPm-PQM deploys a membrane-anchored instead of a soluble SBP. Furthermore, the TAXI transport system TAXIMh-PQM from Marinobacter hydrocarbonoclasticus transports fumarate only if both membrane domains Q and M are present. For further characterization, Michaelis-Menten kinetics and affinities were determined for both TAXI transport systems TAXIPm-PQM from Proteus mirabilis and TAXIMh-PQM from Marinobacter hydrocarbonoclasticus. In addition, nanobodies were selected for the membrane domain TAXIPm-QM from Proteus mirabilis to stabilize different conformations which can serve in subsequent structural elucidation studies. Furthermore, the TRAP SBP TRAPHi-SiaP from Haemophilus influenzae was shown to interact not only with its corresponding membrane domain TRAPHi-SiaQM but with at least one additional transporter. It was thereby excluded that TRAPHi- SiaP transfers N-acetylneuraminic acid to the only native E. coli TRAP transporter TRAPEc-YiaMNO and suggested to rather interact with a SBP dependent ABC transport system as this protein family represents the largest SBP dependent protein group in E. coli (Moussatova et al. 2008).
This research attempts to provide for an overview of the state of co-operation between the United Nations and regional organizations like the CoE, OSCE, EU and NATO during the last Yugoslav wars, considering the 1991-2008 period. In this case, the "reconstruction" of what the organisations did in each of the countries involved in the conflicts, the country-by-country approach used in writing the research and the consideration of both headquarters and field level should facilitate the understanding of the state of things at that time. The research further includes an analysis of the co-operative trends developed by the considered international organisations since the beginning of the 1990s and is concluded by a reflection on the normative relevance of the issue of "international cooperation". In this case, the intention of the author was to go beyond the general policy level approach used for the description of UN-regional organizations interaction and propose a re-consideration of the concept of "international co-operation" as a possible normative tool in guiding the so far nebulous division of tasks of international actors in conflict-related scenarios. In this case, the concise description of the general framework for co-operation under Chapter VIII of the UN Charter, already matter of wide debate by academics and practitioners, sets the frame for a more elaborate, and hopefully innovative, consideration of the notion of "international cooperation". This, of course, is to be contextualized to the lessons learned extrapolated from the case study.
RNA research is very important since RNA molecules are involved in various gene regulatory mechanisms as well as pathways of cell physiology and disease development.1 RNAs have evolved from being considered as carriers of genetic information from DNA to proteins, with the three major types of RNA involved in protein synthesis, including messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).2 In addition to the RNAs involved in protein synthesis numerous regulatory non-coding RNAs (ncRNAs) have been discovered in the transcriptome. The regulatory ncRNAs are classified into small ncRNAs (sncRNAs) with transcripts less than 200 nucleotides (nt) and long non-coding RNAs (lncRNAs) with more than 200 nt.3
LncRNAs represent the most diverse and versatile class of ncRNAs that can regulate cellular functions of chromatin modification, transcription, and post-transcription through multiple mechanisms.4 They are involved in the formation of RNA:protein, RNA:RNA and RNA:DNA complexes as part of their gene regulatory mechanism.4,5 The RNA:DNA interactions can be divided into RNA:DNA heteroduplex formation, also called R-loops, and RNA:DNA:DNA triplex formation. In triplex formation, RNA binds to the major groove of double-stranded DNA through Hoogsteen or reverse Hoogsteen hydrogen bonding, resulting in parallel or anti-parallel triplexes, respectively. In vitro studies have confirmed the formation of RNA:DNA:DNA triplexes.6 However, the extent to which these interactions occur in cells and their effects on cellular function are still not understood, which is why these structures are so exciting to study (Chapter I RNA:DNA:DNA Triplexes).
This cumulative thesis investigates several functional and regulatory important RNAs. The first project involves the improved biochemical and biophysical characterization of RNA:DNA:DNA triplex formation between lncRNAs of interest and their target genes. Triplex formation was confirmed by a series of experiments including electromobility shift assays (EMSA), thermal melting assays, circular dichroism (CD), and liquid state nuclear magnetic resonance (NMR) spectroscopy. The following is a summary of the main findings of these publications.
In research article 5.1, the oxygen-sensitive HIF1α-AS1 was identified as a functionally important triplex-forming lncRNA in human endothelial cells using a combination of bioinformatics techniques, RNA/DNA pulldown, and biophysical experiments. Through RNA:DNA:DNA triplex formation, endogenous HIF1α-AS1 decreases the expression of several genes, including EPH receptor A2 (EPHA2) and adrenomedullin (ADM), by acting as an adaptor for the repressive human silencing hub (HUSH) complex, which has been studied by our collaborators in the groups of Leisegang and Brandes.
2) Triplex formation between HIF1α-AS1 and the target genes EPHA2 and ADM was investigated in biochemical and biophysical studies. The EMSA results indicated that HIF1α-AS1 forms a low mobility RNA:DNA:DNA triplex complex with the EPHA2 DNA target sequence. The CD spectrum of the triplex showed distinct features compared to the EPHA2 DNA duplex and the RNA:DNA heteroduplex. Melting curve analysis revealed a biphasic melting transition for triplexes, with a first melting point corresponding to the dissociation of the RNA strand with melting of the Hoogsteen hydrogen bonds. The second, higher melting temperature corresponds to the melting of stronger Watson-Crick base pairing. Stabilized triplexes were formed using an intramolecular EPHA2 DNA duplex hairpin construct in which both DNA strands were attached to a 5 nucleotide (nt) thymidine linker. This approach allowed improved triplex formation with lower RNA equivalents and higher melting temperatures. By NMR spectroscopy, the triplex characteristic signals were observed in the 1H NMR spectrum, the imino signals in a spectral region between 9 and 12 ppm resulting from the Hoogsteen base pairing. To elucidate the structural and sequence specific Hoogsteen base pairs 2D 1H,1H-NOESY measurements of the EPHA2 DNA duplex and the HIF1α-AS1:EPHA2 triplex were performed. The 1H,1H-NOESY spectrum of the HIF1α-AS1:EPHA2 triplex with a 10-fold excess of RNA was semi-quantitatively analyzed for changes in the DNA duplex spectrum. We discovered, strong and moderate attenuation of cross peak intensities in the imino region of the NOESY spectrum. This attenuation was proposed to result from weakening of Watson-Crick base pairing by Hoogsteen hydrogen bonding induced by RNA binding. The Hoogsteen interactions can be mapped based on the analysis of the cross peak attenuation in the NOESY spectra, which we used to generate a structural model of the RNA:DNA:DNA triplex. These biophysical results support the physiological function of HIF1α as a triplex-forming lncRNA that recruits the HUSH-epigenetic silencing complex to specific target genes such as EPHA2 and ADM, thereby silencing their gene expression through RNA:DNA:DNA triplex formation.
Identification of new natural products from nematode-associated bacteria using mass spectrometry
(2023)
This work aims to find unknown natural products produced by bacteria, that live in close association with nematodes and to elucidate their structure by using mass spectrometry.
The first chapter of this work is dedicated to the detection of hitherto unknown natural products by using a metabolomics approach and subsequent structure elucidation of said compounds. This chapter includes metabolomics analysis of Xenorhabdus szentirmaii wild type and knockout mutants, overproduction of the target compound, identification of derivatives from other strains and MS based structure elucidation.
The second and third chapters are about natural products that protect C. elegans from B. thuringiensis infections.
The second chapter deals with natural products that protect the nematode host without killing the pathogen. I deployed molecular biology methods to generate deletion and overproduction strains of a target compound, identified it via LC-MS/MS analysis and used LC-MS/MS and lipidomics to analyse the chemical properties of the active compound.
The third chapter aims at finding natural products, which are produced by Pseudomonas strains MYb11 and MYb12, respectively. These natural products display the ability to protect C. elegans by killing B. thuringiensis. I identified said compounds via fractionation and subsequent bioactivity testing. After identification, I generated production strains of the target compounds and elucidated the structure of the bioactive derivative.
The last chapter deals with the structure elucidation of peptides produced by an unusual GameXPeptide synthetase in Xenorhabdus miraniensis. I analysed producer strains of GameXPeptides using LC-MS and elucidated the structural differences between the known GameXPeptides, produced by P. luminescens TT01, and the unusual ones produced by X. miraniensis.
Nok Eisen : zentralnigerianische Eisenverhüttung in der Mitte des ersten Jahrtausends vor Christus
(2023)
Based on excavations, excavation documentation and archaeometallurgical analyses, this thesis aims to characterise Nok iron production in central Nigeria through a contextually based investigation.
In 2010, 2011, 2013 and 2016, the Nok research project at Goethe University Frankfurt/Main in collaboration with the National Commission for Museums and Monuments, Nigeria excavated 27 iron-smelting furnaces from 8 sites 60 kilometres north of Abuja. All furnaces date around the middle of the first millennium BCE. Absolute dates, relative pottery chronology and terracotta figurine finds in furnace contexts suggest their affiliation to the Nok context. In comparison, all 27 furnaces resemble each other closely regarding their design and spacial arrangement. The numbers of furnaces per site, furnace width, furnace wall angle and thickness as well as pits beneath the furnaces are just some features with similar qualities. The similarities of the smelting sites also extend into their finds: the structure of tuyères and their position in situ as well as macroscopic slag morphology and distribution. Find morphology and distribution as well as furnace structure suggest a highly standardized way of Nok iron production. However, archaeometallurgical analyses show heterogeneous use of raw materials between sites and/or furnaces. In similarly structured furnaces different kinds of iron ore were smelted leaving a high iron content in the respective slags. This hints at an early stage of iron production in which the smelting process was limited to one operative set-up.