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Genome-scale metabolic models are mathematical representations of all known reactions occurring in a cell. Combined with constraints based on physiological measurements, these models have been used to accurately predict metabolic fluxes and effects of perturbations (e.g. knock-outs) and to inform metabolic engineering strategies. Recently, protein-constrained models have been shown to increase predictive potential (especially in overflow metabolism), while alleviating the need for measurement of nutrient uptake rates. The resulting modelling frameworks quantify the upkeep cost of a certain metabolic flux as the minimum amount of enzyme required for catalysis. These improvements are based on the use of in vitro turnover numbers or in vivo apparent catalytic rates of enzymes for model parameterization. In this thesis several tools for the estimation and refinement of these parameters based on in vivo proteomics data of Escherichia coli, Saccharomyces cerevisiae, and Chlamydomonas reinhardtii have been developed and applied. The difference between in vitro and in vivo catalytic rate measures for the three microorganisms was systematically analyzed. The results for the facultatively heterotrophic microalga C. reinhardtii considerably expanded the apparent catalytic rate estimates for photosynthetic organisms. Our general finding pointed at a global reduction of enzyme efficiency in heterotrophy compared to other growth scenarios. Independent of the modelled organism, in vivo estimates were shown to improve accuracy of predictions of protein abundances compared to in vitro values for turnover numbers. To further improve the protein abundance predictions, machine learning models were trained that integrate features derived from protein-constrained modelling and codon usage. Combining the two types of features outperformed single feature models and yielded good prediction results without relying on experimental transcriptomic data. The presented work reports valuable advances in the prediction of enzyme allocation in unseen scenarios using protein constrained metabolic models. It marks the first successful application of this modelling framework in the biotechnological important taxon of green microalgae, substantially increasing our knowledge of the enzyme catalytic landscape of phototrophic microorganisms.
We analyze how conventional emissions trading schemes (ETS) can be modified by introducing “clean-up certificates” to allow for a phase of net-negative emissions. Clean-up certificates bundle the permission to emit CO2 with the obligation for its removal. We show that demand for such certificates is determined by cost-saving technological progress, the discount rate and the length of the compliance period. Introducing extra clean-up certificates into an existing ETS reduces near-term carbon prices and mitigation efforts. In contrast, substituting ETS allowances with clean-up certificates reduces cumulative emissions without depressing carbon prices or mitigation in the near term. We calibrate our model to the EU ETS and identify reforms where simultaneously (i) ambition levels rise, (ii) climate damages fall, (iii) revenues from carbon prices rise and (iv) carbon prices and aggregate mitigation cost fall. For reducing climate damages, roughly half of the issued clean-up certificates should replace conventional ETS allowances. In the context of the EU ETS, a European Carbon Central Bank could manage the implementation of cleanup certificates and could serve as an enforcement mechanism.
Zum dreißigjährigen Bestehen des Kommunalwissenschaftlichen Instituts an der Universität Potsdam vereint dieser Jubiläumsband kurze Aufsätze von ehemaligen und aktuellen Vorstandsmitgliedern, von Ehrenmitgliedern des Vorstands, langjährigen wissenschaftlichen Mitarbeitern des Instituts und aktuellen wissenschaftlichen Kooperationspartnern. Die insgesamt zwölf Beiträge befassen sich mit den Kommunalwissenschaften und der Geschichte des Kommunalwissenschaftlichen Instituts, mit aktuellen kommunalwissenschaftlichen Fragestellungen und wissenschaftlichen Kooperationen des KWI. Der vom KWI-Vorstand herausgegebene Band soll einen breiten Blick auf 30 Jahre Kommunalwissenschaften in Brandenburg und an der Universität Potsdam werfen und einen Ausblick auf zukünftige kommunalwissenschaftliche Forschung geben.
The Jewish museums established in the fin-de-siècle Habsburg Empire postulated the unity of “the Jewish people,” with custodians constructing an “us” (Jews) in distinction to the “other” (non-Jews). In the difference-oriented frenzy of the time, Jewish identity was predominantly presented as Central European, enlightened, not overly religious, and middle-class. Then, when the Viennese Jewish Museum opened its doors in 1895, the painters Isidor Kaufmann and David Kohn created an installation called “Die Gute Stube” (The Parlor). This exhibit housed books, furniture, as well as decorative and ritual objects of the kind that were thought to be found in typical Eastern European Jewish households. However, as this article argues, this attempted visualization of the essence of Judaism and the range of Jewish life worlds promoted a paradigmatic stereotype with which Jewish museums would have to struggle for decades to come.
Large parts of the Earth’s interior are inaccessible to direct observation, yet global geodynamic processes are governed by the physical material properties under extreme pressure and temperature conditions. It is therefore essential to investigate the deep Earth’s physical properties through in-situ laboratory experiments. With this goal in mind, the optical properties of mantle minerals at high pressure offer a unique way to determine a variety of physical properties, in a straight-forward, reproducible, and time-effective manner, thus providing valuable insights into the physical processes of the deep Earth. This thesis focusses on the system Mg-Fe-O, specifically on the optical properties of periclase (MgO) and its iron-bearing variant ferropericlase ((Mg,Fe)O), forming a major planetary building block. The primary objective is to establish links between physical material properties and optical properties. In particular the spin transition in ferropericlase, the second-most abundant phase of the lower mantle, is known to change the physical material properties. Although the spin transition region likely extends down to the core-mantle boundary, the ef-fects of the mixed-spin state, where both high- and low-spin state are present, remains poorly constrained.
In the studies presented herein, we show how optical properties are linked to physical properties such as electrical conductivity, radiative thermal conductivity and viscosity. We also show how the optical properties reveal changes in the chemical bonding. Furthermore, we unveil how the chemical bonding, the optical and other physical properties are affected by the iron spin transition. We find opposing trends in the pres-sure dependence of the refractive index of MgO and (Mg,Fe)O. From 1 atm to ~140 GPa, the refractive index of MgO decreases by ~2.4% from 1.737 to 1.696 (±0.017). In contrast, the refractive index of (Mg0.87Fe0.13)O (Fp13) and (Mg0.76Fe0.24)O (Fp24) ferropericlase increases with pressure, likely because Fe Fe interactions between adjacent iron sites hinder a strong decrease of polarizability, as it is observed with increasing density in the case of pure MgO. An analysis of the index dispersion in MgO (decreasing by ~23% from 1 atm to ~103 GPa) reflects a widening of the band gap from ~7.4 eV at 1 atm to ~8.5 (±0.6) eV at ~103 GPa. The index dispersion (between 550 and 870 nm) of Fp13 reveals a decrease by a factor of ~3 over the spin transition range (~44–100 GPa). We show that the electrical band gap of ferropericlase significantly widens up to ~4.7 eV in the mixed spin region, equivalent to an increase by a factor of ~1.7. We propose that this is due to a lower electron mobility between adjacent Fe2+ sites of opposite spin, explaining the previously observed low electrical conductivity in the mixed spin region. From the study of absorbance spectra in Fp13, we show an increasing covalency of the Fe-O bond with pressure for high-spin ferropericlase, whereas in the low-spin state a trend to a more ionic nature of the Fe-O bond is observed, indicating a bond weakening effect of the spin transition. We found that the spin transition is ultimately caused by both an increase of the ligand field-splitting energy and a decreasing spin-pairing energy of high-spin Fe2+.
During the last decades, therapeutical proteins have risen to great significance in the pharmaceutical industry. As non-human proteins that are introduced into the human body cause a distinct immune system reaction that triggers their rapid clearance, most newly approved protein pharmaceuticals are shielded by modification with synthetic polymers to significantly improve their blood circulation time. All such clinically approved protein-polymer conjugates contain polyethylene glycol (PEG) and its conjugation is denoted as PEGylation. However, many patients develop anti-PEG antibodies which cause a rapid clearance of PEGylated molecules upon repeated administration. Therefore, the search for alternative polymers that can replace PEG in therapeutic applications has become important. In addition, although the blood circulation time is significantly prolonged, the therapeutic activity of some conjugates is decreased compared to the unmodified protein. The reason is that these conjugates are formed by the traditional conjugation method that addresses the protein's lysine side chains. As proteins have many solvent exposed lysines, this results in a somewhat uncontrolled attachment of polymer chains, leading to a mixture of regioisomers, with some of them eventually affecting the therapeutic performance.
This thesis investigates a novel method for ligating macromolecules in a site-specific manner, using enzymatic catalysis. Sortase A is used as the enzyme: It is a well-studied transpeptidase which is able to catalyze the intermolecular ligation of two peptides. This process is commonly referred to as sortase-mediated ligation (SML). SML constitutes an equilibrium reaction, which limits product yield. Two previously reported methods to overcome this major limitation were tested with polymers without using an excessive amount of one reactant.
Specific C- or N-terminal peptide sequences (recognition sequence and nucleophile) as part of the protein are required for SML. The complementary peptide was located at the polymer chain end. Grafting-to was used to avoid damaging the protein during polymerization. To be able to investigate all possible combinations (protein-recognition sequence and nucleophile-protein as well as polymer-recognition sequence and nucleophile-polymer) all necessary building blocks were synthesized. Polymerization via reversible deactivation radical polymerization (RDRP) was used to achieve a narrow molecular weight distribution of the polymers, which is required for therapeutic use.
The synthesis of the polymeric building blocks was started by synthesizing the peptide via automated solid-phase peptide synthesis (SPPS) to avoid post-polymerization attachment and to enable easy adaptation of changes in the peptide sequence. To account for the different functionalities (free N- or C-terminus) required for SML, different linker molecules between resin and peptide were used.
To facilitate purification, the chain transfer agent (CTA) for reversible addition-fragmentation chain-transfer (RAFT) polymerization was coupled to the resin-immobilized recognition sequence peptide. The acrylamide and acrylate-based monomers used in this thesis were chosen for their potential to replace PEG.
Following that, surface-initiated (SI) ATRP and RAFT polymerization were attempted, but failed. As a result, the newly developed method of xanthate-supported photo-iniferter (XPI) RAFT polymerization in solution was used successfully to obtain a library of various peptide-polymer conjugates with different chain lengths and narrow molar mass distributions.
After peptide side chain deprotection, these constructs were used first to ligate two polymers via SML, which was successful but revealed a limit in polymer chain length (max. 100 repeat units). When utilizing equimolar amounts of reactants, the use of Ni2+ ions in combination with a histidine after the recognition sequence to remove the cleaved peptide from the equilibrium maximized product formation with conversions of up to 70 %.
Finally, a model protein and a nanobody with promising properties for therapeutical use were biotechnologically modified to contain the peptide sequences required for SML. Using the model protein for C- or N-terminal SML with various polymers did not result in protein-polymer conjugates. The reason is most likely the lack of accessibility of the protein termini to the enzyme. Using the nanobody for C-terminal SML, on the other hand, was successful. However, a similar polymer chain length limit was observed as in polymer-polymer SML. Furthermore, in case of the synthesis of protein-polymer conjugates, it was more effective to shift the SML equilibrium by using an excess of polymer than by employing the Ni2+ ion strategy.
Overall, the experimental data from this work provides a good foundation for future research in this promising field; however, more research is required to fully understand the potential and limitations of using SML for protein-polymer synthesis. In future, the method explored in this dissertation could prove to be a very versatile pathway to obtain therapeutic protein-polymer conjugates that exhibit high activities and long blood circulation times.
Die bedarfsgerechte Versorgung im Alter zukünftig sicherzustellen, gehört zu den entscheidenden Aufgaben unserer Zeit. Der in Deutschland bestehende Fachkräftemangel sowie der demografische Wandel belasten das Pflegesystem in mehrfacher Hinsicht: In einer alternden Gesellschaft sind immer mehr Menschen auf eine anhaltende Unterstützung angewiesen. Niedrige Geburtenraten und damit verbunden ein sinkender Bevölkerungs-anteil von Menschen im erwerbsfähigen Alter bringen einen bereits heute spürbaren Mangel an beruflich Pflegenden mit sich.
Um eine menschenwürdige Pflege anhaltend zu gewährleisten, müssen vorhandene Ressourcen gezielter eingesetzt und zusätzliche Reserven freigelegt werden. Viele Hoffnungen liegen hier auf technologischen Innovationen. Die Digitalisierung soll das Gesundheitswesen effizienter gestalten und beispielsweise durch Künstliche Intelligenz zeitraubende Prozesse vereinfachen oder sogar automatisieren. Im Kontext der Pflege wird der Einsatz von robotischen Assistenzsystemen diskutiert.
Aus diesem Grund wurde die die Potsdamer Bürger:innenkonferenz „Robotik in der Altenpflege?“ initiiert. Um die Zukunft der Pflege gemeinsam zu gestalten, wurden 3.500 Potsdamer Bürgerinnen und Bürger kontaktiert und schließlich fünfundzwanzig Teilnehmende ausgewählt. Im Frühjahr 2024 kamen sie zusammen, um den verantwortlichen Einsatz von Robotik in der Pflege zu diskutieren.
Die hier vorliegende Erklärung ist das Ergebnis der Bürger:innenkonferenz. Sie enthält die zentralen Positionen der Teilnehmenden.
Die Bürger:innenkonferenz ist Teil des Projekts E-cARE („Ethics Guidelines for Socially Assistive Robots in Elderly Care: An Empirical-Participatory Approach“), welches die Juniorprofessur für Medizinische Ethik mit Schwerpunkt auf Digitalisierung der Fakultät für Gesundheitswissenschaften Brandenburg, Universität Potsdam, durchgeführt hat.