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Die vorliegende Arbeit beschäftigt sich mit der geochemischen und isotopischen Analyse detritischer Zirkonminerale aus rezenten Sedimenten des weit verzweigten Orange- und Vaal River Flusssystems in Südafrika. Zirkone kristallisieren überwiegend aus krustalen Schmelzen und sind äußerst resistent gegenüber jeglicher Zerstörung und damit ein idealer Kandidat zur Rekonstruktion früherer Krustenbildungsprozesse der geologischen Erdgeschichte. Der kombinierte Ansatz der U-Pb Altersdatierung, der Hf Isotopie und der Spurenelementgeochemie mittels Laserablation und des Einsatzes induktiv-gekoppelter Sektorfeld- und Multikollektormassenspektrometer ermöglicht es die krustale Wachstums- und Entwicklungsgeschichte des südafrikanischen Kratons zu erfassen. Die mehr als 1200 U-Pb Analysen der Zirkone weisen 4 tektonische Hauptphasen des südafrikanischen Kontinents nach: 1. die Panafrikanische Orogenese (0.5-0.7 Ga), 2. das Namaqua-Natal Faltengürtelorogen (1.0-1.3 Ga), 3. die Kheis Orogenese (1.8-2.0 Ga) und 4. die westliche Kaapvaal-Kratonisierung (2.9-3.2 Ga). Allerdings zeigt sich, dass die 13 Probenlokationen überwiegend lokale bzw. regionale U-Pb Altersdaten ihrer umgebenden Herkunftsgebiete liefern. Die Hf Isotopie der Zirkone der verschiedenen tektonischen Hauptphasen Südafrikas stellen ihre differenzierte Akkretions- und Aufschmelzungsgeschichte dar. Die panafrikanischen Zirkone zeigen eine ausgeprägte Durchmischung von juvenilem und recyceltem Material. Die mesoproterozoischen (Namaquan) Zirkone entstanden aus juvenilem Magma während eines Inselbogen-Kontinent-Kollisionsereignisses. Die paläoproterozoischen und archaischen Zirkone sind Produkte von aufgeschmolzener prä-existierender kontinentaler Kruste oder vom Mantel abstammende Schmelzen, die durch kontinentale Kruste kontaminiert wurden. Die berechneten Hf Modellalter, so genannte „Mantelextraktionsalter" ergeben zwei Maxima, die zwei Stadien juvenilem Krustenwachstums einschließen, einmal vor 1.4 und 3.2 Ga. Dieses krustale Wachstum zeigt eine Übereinstimmung mit den progressiv episodischen Modellen von Nagler & Kramers (1998) sowie Condie (2000) mit Höhepunkten zwischen 3.0 und 2.0 Ga sowie den Studien von Wang et al. (2008) mit krustalen Wachstumsperioden von 1.6 bis 2.2 und 2.9 bis 3.4 Ga auf dem Nordamerikanischen Kontinent und auf dem Gondwana-Kontinent (Australien) von Hawkesworth & Kemp 2006) und implizieren wohl ein globales kontinentales Krustenwachstum. Die Abgrenzung und Wiedererkennung der Zirkone anhand der chemischen Zusammensetzung zu möglichen Muttergesteinen zeigen noch keine viel versprechenden Ergebnisse. Generell weisen die Zirkone eine magmatische granitoide Zusammensetzung kontinentalen Ursprungs auf. Eine Auffälligkeit stellen die erhöhten Spuren- und leichten Seltenenerdelemente in Zirkonen jeglicher Altersklassen dar. Nachfolgende Arbeiten müssen zeigen, wie und ob diese Anreicherungen Einfluss auf die chemische Zusammensetzung, die U-Pb Datierung und vor allem die Hf-Isotopie der Zirkone haben.
The stress-dependent dynamics of Saccharomyces cerevisiae tRNA and rRNA modification profiles
(2021)
RNAs are key players in the cell, and to fulfil their functions, they are enzymatically modified. These modifications have been found to be dynamic and dependent on internal and external factors, such as stress. In this study we used nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS) to address the question of which mechanisms allow the dynamic adaptation of RNA modifications during stress in the model organism S. cerevisiae. We found that both tRNA and rRNA transcription is stalled in yeast exposed to stressors such as H2O2, NaAsO2 or methyl methanesulfonate (MMS). From the absence of new transcripts, we concluded that most RNA modification profile changes observed to date are linked to changes happening on the pre-existing RNAs. We confirmed these changes, and we followed the fate of the pre-existing tRNAs and rRNAs during stress recovery. For MMS, we found previously described damage products in tRNA, and in addition, we found evidence for direct base methylation damage of 2′O-ribose methylated nucleosides in rRNA. While we found no evidence for increased RNA degradation after MMS exposure, we observed rapid loss of all methylation damages in all studied RNAs. With NAIL-MS we further established the modification speed in new tRNA and 18S and 25S rRNA from unstressed S. cerevisiae. During stress exposure, the placement of modifications was delayed overall. Only the tRNA modifications 1-methyladenosine and pseudouridine were incorporated as fast in stressed cells as in control cells. Similarly, 2′-O-methyladenosine in both 18S and 25S rRNA was unaffected by the stressor, but all other rRNA modifications were incorporated after a delay. In summary, we present mechanistic insights into stress-dependent RNA modification profiling in S. cerevisiae tRNA and rRNA.
In this report, we perform structure validation of recently reported RNA phosphorothioate (PT) modifications, a new set of epitranscriptome marks found in bacteria and eukaryotes including humans. By comparing synthetic PT-containing diribonucleotides with native species in RNA hydrolysates by high-resolution mass spectrometry (MS), metabolic stable isotope labeling, and PT-specific iodine-desulfurization, we disprove the existence of PTs in RNA from E. coli, S. cerevisiae, human cell lines, and mouse brain. Furthermore, we discuss how an MS artifact led to the initial misidentification of 2′-O-methylated diribonucleotides as RNA phosphorothioates. To aid structure validation of new nucleic acid modifications, we present a detailed guideline for MS analysis of RNA hydrolysates, emphasizing how the chosen RNA hydrolysis protocol can be a decisive factor in discovering and quantifying RNA modifications in biological samples.
The present work was devised to address the systematic analysis of samples from a range of Roman non-ferrous metal artefacts from different archaeological contexts and sites in the Roman provinces of Germania Superior. One of the focal points of this study is the provenancing of different lead objects from five important Roman settlements between 15 BC and the beginning of fourth century AD. For this purpose, measurements were made on lead and copper ore samples from the Siegerland, Eifel, Hunsrück and Lahn-Dill area in Germany and supplemented with data from the literature to create a data bank of lead isotope ratios of European deposits. Compositional analysis of lead objects by Electron Microprobe analysis showed that Romans were able to purify lead from ore up to 99%. Multi-Collector Inductively Coupled Plasma Mass-Spectrometry was used to determine the source of lead, which played an important role in nearly all aspects of Roman life. Lead isotope ratios were measured for ore samples from German deposits from the eastern side of the Rhine (Siegerland, Lahn-Dill, Ems) and the western side of the Rhine (Eifel, Hunsrück), which contained enough ore reserves to answer the increasing local demand and are believed to have been mined during the Roman period. This data together with those from Mediterranean ore deposits from the literature was used to establish a data bank. The Mediterranean ore deposits range from Cambrian (high 207Pb/206Pb) to tertiary (lower 207Pb/206Pb) values. In particular, the Cypriot deposits are younger, while the Spanish deposits fall either with the younger Sardic ores or close to the older Cypriot ores. The lead isotope ratios of most German ore deposits fall in between the 208Pb/206Pb vs. 207Pb/206Pb ratios of Sardinia and Cyprus, where the lead isotope signature of ore deposits from France and Britain are also found. Over 240 lead objects were measured from Wallendorf (second century BC to first century AD) Dangstetten (15-8 BC), Waldgirmes (AD 1-10), Mainz (AD 1-300), Martberg (first to fourth centuries AD) & Trier (third to fourth centuries AD). Comparing the lead isotope ratios of lead objects and those from German ores shows that the source of over 85 percent of objects are Eifel ore deposits, but the Roman’s had also imported lead from the Southern Massif Central and from Great Britain. A further topic of this work was the systematic study of the variation of copper isotope ratios in different copper minerals and the mechanisms, which controls copper isotope fractionation in ores deposits. For this purpose, copper isotope analyses were made by Multi-Collector Inductively Coupled Plasma Mass-Spectrometry from a series of hydrothermal copper sulphides and their alteration products. Copper and lead isotope ratios were measured in coexisting phases of chalcopyrite and malachite and also coexisting malachite and azurite. No significant fractionation was observed in malachite-azurite phases, but in chalcopyrite-malachite coexisting phases, malachite always shows a positive fractionation to heavier isotope values. Zhu et al. and Larson et al. showed that isotopic variations in copper principally reflect mass fractionation in response to low temperature processes rather than source heterogeneity. The low temperature ore formation processes are mostly represented by weathering of primary sulphide ores to produce secondary carbonate phases and therefore are usually observed on the surface of ore deposits, which were probably removed during the early Bronze Age. Using this concept, copper isotope ratios were measured in some Early Bronze Age copper alloys and Roman copper alloys. However, no large copper isotope fractionation has been observed. Lead and copper isotope ratios were measured on samples from the Kupferschiefer. Two profiles were investigated; 1) Sangerhausen, which was not directly influenced by the oxidizing brines of Rote Fäule and 2) Oberkatz, where both Rote Fäule-controlled and structure-controlled mineralization were observed. Results from maturation studies of organic matter suggest the maximum temperature affecting the Kupferschiefer did not exceed 130°C. delta-65-Cu ranges between -0.78-+0.58‰, shows a positive correlation with copper concentration. Maximum temperature in the Kupferschiefer profile from Oberkatz is supposed to be around 150°C. delta-65Cu in this profile ranges between -0.71-+0.68‰. The pattern of copper isotope fractionation and copper concentration is same as the for profile of Sangerhausen. Origina lead isotope ratios are strongly overprinted by high concentrations of uranium in bottom of both profiles causing more radiogenic lead.
Ubiquitination regulates nearly all cellular processes by coordinated activity of ubiquitin writers (E1, E2, and E3 enzymes), erasers (deubiquitinating enzymes) and readers (proteins that recognize ubiquitinated proteins by their ubiquitin-binding domains). By differentially modifying cellular proteome and by recognizing these ubiquitin modifications, ubiquitination machinery tightly regulates execution of specific cellular events in space and time. Dynamic and complex ubiquitin architecture, ranging from monoubiquitination, multiple monoubiquitination, eight different modes of homotypic and numerous types of heterogeneous polyubiquitin linkages, enables highly dynamic and complex regulation of cellular processes. We discuss available tools and approaches to study ubiquitin networks, including methods for the identification and quantification of ubiquitin-modified substrates, as well as approaches to quantify the length, abundance, linkage type and architecture of different ubiquitin chains. Furthermore, we also summarize the available approaches for the discovery of novel ubiquitin readers and ubiquitin-binding domains, as well as approaches to monitor and visualize activity of ubiquitin conjugation and deconjugation machineries. We also discuss benefits, drawbacks and limitations of available techniques, as well as what is still needed for detailed spatiotemporal dissection of cellular ubiquitination networks
SUMOylation is a reversible posttranslational modification pathway catalyzing the conjugation of small ubiquitin-related modifier (SUMO) proteins to lysine residues of distinct target proteins. SUMOylation modifies a wide variety of cellular regulators thereby affecting a multitude of key processes in a highly dynamic manner. The SUMOylation pathway displays a hallmark in cellular stress-adaption, such as heat or redox stress. It has been proposed that enhanced cellular SUMOylation protects the brain during ischemia, however, little is known about the specific regulation of the SUMO system and the potential target proteins during cardiac ischemia and reperfusion injury (I/R). By applying left anterior descending (LAD) coronary artery ligation and reperfusion in mice, we detect dynamic changes in the overall cellular SUMOylation pattern correlating with decreased SUMO deconjugase activity during I/R injury. Further, unbiased system-wide quantitative SUMO-proteomics identified a sub-group of SUMO targets exhibiting significant alterations in response to cardiac I/R. Notably, transcription factors that control hypoxia- and angiogenesis-related gene expression programs, exhibit altered SUMOylation during ischemic stress adaptation. Moreover, several components of the ubiquitin proteasome system undergo dynamic changes in SUMO conjugation during cardiac I/R suggesting an involvement of SUMO signaling in protein quality control and proteostasis in the ischemic heart. Altogether, our study reveals regulated candidate SUMO target proteins in the mouse heart, which might be important in coping with hypoxic/proteotoxic stress during cardiac I/R injury.
Structural Biology has moved beyond the aim of simply identifying the components of a cellular subsystem towards analysing the dynamics and interactions of multiple players within a cell. This focal shift comes with additional requirements for the analytical tools used to investigate these systems of increased size and complexity, such as Native Mass Spectrometry, which has always been an important tool for structural biology. Scientific advance and recent developments, such as new ways to mimic a cell membrane for a membrane protein, have caused established methods to struggle to keep up with the increased demands. In this review, we summarize the possibilities, which Laser Induced Liquid Bead Ion Desorption (LILBID) mass spectrometry offers with regard to the challenges of modern structural biology, like increasingly complex sample composition, novel membrane mimics and advanced structural analysis, including next neighbor relations and the dynamics of complex formation.
Intact-cell maldi-tof mass spectrometry for the authentication of drug-adapted cancer cell lines
(2019)
The use of cell lines in research can be affected by cell line misidentification. Short tandem repeat (STR) analysis is an effective method, and the gold standard, for the identification of the genetic origin of a cell line, but methods that allow the discrimination between cell lines of the same genetic origin are lacking. Here, we use intact cell MALDI-ToF mass spectrometry analysis, routinely used for the identification of bacteria in clinical diagnostic procedures, for the authentication of a set of cell lines consisting of three parental neuroblastoma cell lines (IMR-5, IMR-32 and UKF-NB-3) and eleven drug-adapted sublines. Principal component analysis (PCA) of intact-cell MALDI-ToF mass spectrometry data revealed clear differences between most, but not all, of the investigated cell lines. Mass spectrometry whole-cell fingerprints enabled the separation of IMR-32 and its clonal subline IMR-5. Sublines that had been adapted to closely related drugs, for example, the cisplatin- and oxaliplatin-resistant UKF-NB-3 sublines and the vincristine- and vinblastine-adapted IMR-5 sublines, also displayed clearly distinctive patterns. In conclusion, intact whole-cell MALDI-ToF mass spectrometry has the potential to be further developed into an authentication method for mammalian cells of a common genetic origin.
Coagulation factor XIII (FXIII) is a plasma-circulating heterotetrameric pro-transglutaminase complex that is composed of two catalytic FXIII-A and two protective/regulatory FXIII-B subunits. FXIII acts by forming covalent cross-links within a preformed fibrin clots to prevent its premature fibrinolysis. The FXIII-A subunit is known to have pleiotropic roles outside coagulation, but the FXIII-B subunit is a relatively unexplored entity, both structurally as well as functionally. Its discovered roles so far are limited to that of the carrier/regulatory protein of its partner FXIII-A subunit. In the present study, we have explored the co-presence of protein excipients in commercial FXIII plasma concentrate FibrogamminP by combination of protein purification and mass spectrometry-based verification. Complement factor H was one of the co-excipients observed in this analysis. This was followed by performing pull down assays from plasma in order to detect the putative novel interacting partners for the FXIII-B subunit. Complement system proteins, like complement C3 and complement C1q, were amongst the proteins that were pulled down. The only protein that was observed in both experimental set ups was alpha-2-macroglobulin, which might therefore be a putative interacting partner of the FXIII/FXIII-B subunit. Future functional investigations will be needed to understand the physiological significance of this association.
High-throughput protein localization studies require multiple strategies. Mass spectrometric analysis of defined cellular fractions is one of the complementary approaches to a diverse array of cell biological methods. In recent years, the protein content of different cellular (sub-)compartments was approached. Despite of all the efforts made, the analysis of membrane fractions remains difficult, in that the dissection of the proteomes of the envelope membranes of chloroplasts or mitochondria is often not reliable because sample purity is not always warranted. Moreover, proteomic studies are often restricted to single (model) species, and therefore limited in respect to differential individual evolution. In this study we analyzed the chloroplast envelope proteomes of different plant species, namely, the individual proteomes of inner and outer envelope (OE) membrane of Pisum sativum and the mixed envelope proteomes of Arabidopsis thaliana and Medicago sativa. The analysis of all three species yielded 341 identified proteins in total, 247 of them being unique. 39 proteins were genuine envelope proteins found in at least two species. Based on this and previous envelope studies we defined the core envelope proteome of chloroplasts. Comparing the general overlap of the available six independent studies (including ours) revealed only a number of 27 envelope proteins. Depending on the stringency of applied selection criteria we found 231 envelope proteins, while less stringent criteria increases this number to 649 putative envelope proteins. Based on the latter we provide a map of the outer and inner envelope core proteome, which includes many yet uncharacterized proteins predicted to be involved in transport, signaling, and response. Furthermore, a foundation for the functional characterization of yet unidentified functions of the inner and OE for further analyses is provided.