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Institute
- Institut für Biochemie und Biologie (32)
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‘The Territorialities of U.S. Imperialisms’ sets into relation U.S. imperial and Indigenous conceptions of territoriality as articulated in U.S. legal texts and Indigenous life writing in the 19th century. It analyzes the ways in which U.S. legal texts as “legal fictions” narratively press to affirm the United States’ territorial sovereignty and coherence in spite of its reliance on a variety of imperial practices that flexibly disconnect and (re)connect U.S. sovereignty, jurisdiction and territory.
At the same time, the book acknowledges Indigenous life writing as legal texts in their own right and with full juridical force, which aim to highlight the heterogeneity of U.S. national territory both from their individual perspectives and in conversation with these legal fictions. Through this, the book’s analysis contributes to a more nuanced understanding of the coloniality of U.S. legal fictions, while highlighting territoriality as a key concept in the fashioning of the narrative of U.S. imperialism.
To meet the demands of a growing world population while reducing carbon dioxide (CO2) emissions, it is necessary to capture CO2 and convert it into value-added compounds. In recent years, metabolic engineering of microbes has gained strong momentum as a strategy for the production of valuable chemicals. As common microbial feedstocks like glucose directly compete with human consumption, the one carbon (C1) compound formate was suggested as an alternative feedstock. Formate can be easily produced by various means including electrochemical reduction of CO2 and could serve as a feedstock for microbial production, hence presenting a novel entry point for CO2 to the biosphere and a storage option for excess electricity. Compared to the gaseous molecule CO2, formate is a highly soluble compound that can be easily handled and stored. It can serve as a carbon and energy source for natural formatotrophs, but these microbes are difficult to cultivate and engineer. In this work, I present the results of several projects that aim to establish efficient formatotrophic growth of E. coli – which cannot naturally grow on formate – via synthetic formate assimilation pathways. In the first study, I establish a workflow for growth-coupled metabolic engineering of E. coli. I demonstrate this approach by presenting an engineering scheme for the PFL-threonine cycle, a synthetic pathway for anaerobic formate assimilation in E. coli. The described methods are intended to create a standardized toolbox for engineers that aim to establish novel metabolic routes in E. coli and related organisms. The second chapter presents a study on the catalytic efficiency of C1-oxidizing enzymes in vivo. As formatotrophic growth requires generation of both energy and biomass from formate, the engineered E. coli strains need to be equipped with a highly efficient formate dehydrogenase, which provides reduction equivalents and ATP for formate assimilation. I engineered a strain that cannot generate reducing power and energy for cellular growth, when fed on acetate. Under this condition, the strain depends on the introduction of an enzymatic system for NADH regeneration, which could further produce ATP via oxidative phosphorylation. I show that the strain presents a valuable testing platform for C1-oxidizing enzymes by testing different NAD-dependent formate and methanol dehydrogenases in the energy auxotroph strain. Using this platform, several candidate enzymes with high in vivo activity, were identified and characterized as potential energy-generating systems for synthetic formatotrophic or methylotrophic growth in E. coli. In the third chapter, I present the establishment of the serine threonine cycle (STC) – a synthetic formate assimilation pathway – in E. coli. In this pathway, formate is assimilated via formate tetrahydrofolate ligase (FtfL) from Methylobacterium extorquens (M. extorquens). The carbon from formate is attached to glycine to produce serine, which is converted into pyruvate entering central metabolism. Via the natural threonine synthesis and cleavage route, glycine is regenerated and acetyl-CoA is produced as the pathway product. I engineered several selection strains that depend on different STC modules for growth and determined key enzymes that enable high flux through threonine synthesis and cleavage. I could show that expression of an auxiliary formate dehydrogenase was required to achieve growth via threonine synthesis and cleavage on pyruvate. By overexpressing most of the pathway enzymes from the genome, and applying adaptive laboratory evolution, growth on glycine and formate was achieved, indicating the activity of the complete cycle. The fourth chapter shows the establishment of the reductive glycine pathway (rGP) – a short, linear formate assimilation route – in E. coli. As in the STC, formate is assimilated via M. extorquens FtfL. The C1 from formate is condensed with CO2 via the reverse reaction of the glycine cleavage system to produce glycine. Another carbon from formate is attached to glycine to form serine, which is assimilated into central metabolism via pyruvate. The engineered E. coli strain, expressing most of the pathway genes from the genome, can grow via the rGP with formate or methanol as a sole carbon and energy source.
With populations growing worldwide and climate change threatening food production there is an urgent need to find ways to ensure food security. Increasing carbon fixation rate in plants is a promising approach to boost crop yields. The carbon-fixing enzyme Rubisco catalyzes, beside the carboxylation reaction, also an oxygenation reaction that generates glycolate-2P, which needs to be recycled via a metabolic route termed photorespiration. Photorespiration dissipates energy and most importantly releases previously fixed CO2, thus significantly lowering carbon fixation rate and yield. Engineering plants to omit photorespiratory CO2 release is the goal of the FutureAgriculture consortium and this thesis is part of this collaboration. The consortium aims to establish alternative glycolate-2P recycling routes that do not release CO2. Ultimately, they are expected to increase carbon fixation rates and crop yields. Natural and novel reactions, which require enzyme engineering, were considered in the pathway design process. Here I describe the engineering of two pathways, the arabinose-5P and the erythrulose shunt. They were designed to recycle glycolate-2P via glycolaldehyde into a sugar phosphate and thereby reassimilate glycolate-2P to the Calvin cycle. I used Escherichia coli gene deletion strains to validate and characterize the activity of both synthetic shunts. The strains’ auxotrophies can be alleviated by the activity of the synthetic route, thus providing a direct way to select for pathway activity. I introduced all pathway components to these dedicated selection strains and discovered inhibitions, limitations and metabolic cross talk interfering with pathway activity. After resolving these issues, I was able to show the in vivo activity of all pathway components and combine them into functional modules.. Specifically, I demonstrate the activity of a new-to-nature module of glycolate reduction to glycolaldehyde. Also, I successfully show a new glycolaldehyde assimilation route via arabinose-5P to ribulose-5P. In addition, all necessary enzymes for glycolaldehyde assimilation via L-erythrulose were shown to be active and an L-threitol assimilation route via L-erythrulose was established in E. coli. On their own, these findings demonstrate the power of using an easily engineerable microbe to test novel pathways; combined, they will form the basis for implementing photorespiration bypasses in plants.
TrainTrap
(2020)
Due to continuously intensifying human usage of the marine environment worldwide ranging cetaceans face an increasing number of threats. Besides whaling, overfishing and by-catch, new technical developments increase the water and noise pollution, which can negatively affect marine species. Cetaceans are especially prone to these influences, being at the top of the food chain and therefore accumulating toxins and contaminants. Furthermore, they are extremely noise sensitive due to their highly developed hearing sense and echolocation ability. As a result, several cetacean species were brought to extinction during the last century or are now classified as critically endangered. This work focuses on two odontocetes. It applies and compares different molecular methods for inference of population status and adaptation, with implications for conservation. The worldwide distributed sperm whale (Physeter macrocephalus) shows a matrilineal population structure with predominant male dispersal. A recently stranded group of male sperm whales provided a unique opportunity to investigate male grouping for the first time. Based on the mitochondrial control region, I was able to infer that male bachelor groups comprise multiple matrilines, hence derive from different social groups, and that they represent the genetic variability of the entire North Atlantic. The harbor porpoise (Phocoena phocoena) occurs only in the northern hemisphere. By being small and occurring mostly in coastal habitats it is especially prone to human disturbance. Since some subspecies and subpopulations are critically endangered, it is important to generate and provide genetic markers with high resolution to facilitate population assignment and subsequent protection measurements. Here, I provide the first harbour porpoise whole genome, in high quality and including a draft annotation. Using it for mapping ddRAD seq data, I identify genome wide SNPs and, together with a fragment of the mitochondrial control region, inferred the population structure of its North Atlantic distribution range. The Belt Sea harbors a distinct subpopulation oppose to the North Atlantic, with a transition zone in the Kattegat. Within the North Atlantic I could detect subtle genetic differentiation between western (Canada-Iceland) and eastern (North Sea) regions, with support for a German North Sea breading ground around the Isle of Sylt. Further, I was able to detect six outlier loci which show isolation by distance across the investigated sampling areas. In employing different markers, I could show that single maker systems as well as genome wide data can unravel new information about population affinities of odontocetes. Genome wide data can facilitate investigation of adaptations and evolutionary history of the species and its populations. Moreover, they facilitate population genetic investigations, providing a high resolution, and hence allowing for detection of subtle population structuring especially important for highly mobile cetaceans.
With rising complexity of today's software and hardware systems and the hypothesized increase in autonomous, intelligent, and self-* systems, developing correct systems remains an important challenge. Testing, although an important part of the development and maintainance process, cannot usually establish the definite correctness of a software or hardware system - especially when systems have arbitrarily large or infinite state spaces or an infinite number of initial states. This is where formal verification comes in: given a representation of the system in question in a formal framework, verification approaches and tools can be used to establish the system's adherence to its similarly formalized specification, and to complement testing.
One such formal framework is the field of graphs and graph transformation systems. Both are powerful formalisms with well-established foundations and ongoing research that can be used to describe complex hardware or software systems with varying degrees of abstraction. Since their inception in the 1970s, graph transformation systems have continuously evolved; related research spans extensions of expressive power, graph algorithms, and their implementation, application scenarios, or verification approaches, to name just a few topics.
This thesis focuses on a verification approach for graph transformation systems called k-inductive invariant checking, which is an extension of previous work on 1-inductive invariant checking. Instead of exhaustively computing a system's state space, which is a common approach in model checking, 1-inductive invariant checking symbolically analyzes graph transformation rules - i.e. system behavior - in order to draw conclusions with respect to the validity of graph constraints in the system's state space. The approach is based on an inductive argument: if a system's initial state satisfies a graph constraint and if all rules preserve that constraint's validity, we can conclude the constraint's validity in the system's entire state space - without having to compute it.
However, inductive invariant checking also comes with a specific drawback: the locality of graph transformation rules leads to a lack of context information during the symbolic analysis of potential rule applications. This thesis argues that this lack of context can be partly addressed by using k-induction instead of 1-induction. A k-inductive invariant is a graph constraint whose validity in a path of k-1 rule applications implies its validity after any subsequent rule application - as opposed to a 1-inductive invariant where only one rule application is taken into account. Considering a path of transformations then accumulates more context of the graph rules' applications.
As such, this thesis extends existing research and implementation on 1-inductive invariant checking for graph transformation systems to k-induction. In addition, it proposes a technique to perform the base case of the inductive argument in a symbolic fashion, which allows verification of systems with an infinite set of initial states. Both k-inductive invariant checking and its base case are described in formal terms. Based on that, this thesis formulates theorems and constructions to apply this general verification approach for typed graph transformation systems and nested graph constraints - and to formally prove the approach's correctness.
Since unrestricted graph constraints may lead to non-termination or impracticably high execution times given a hypothetical implementation, this thesis also presents a restricted verification approach, which limits the form of graph transformation systems and graph constraints. It is formalized, proven correct, and its procedures terminate by construction. This restricted approach has been implemented in an automated tool and has been evaluated with respect to its applicability to test cases, its performance, and its degree of completeness.
"How Wenzel and Cassie were wrong" – this was the eye-catching title of an article published by Lichao Gao and Thomas McCarthy in 2007, in which fundamental interpretations of wetting behavior were put into question. The authors initiated a discussion on a subject, which had been generally accepted a long time ago and they showed that wetting phenomena were not as fully understood as imagined. Similarly, this thesis tries to put a focus on certain aspects of liquid wetting, which so far have been widely neglected in terms of interpretation and experimental proof. While the effect of surface roughness on the macroscopically observed wetting behavior is commonly and reliably interpreted according to the well-known models of Wenzel and Cassie/Baxter, the size-scale of the structures responsible for the surface's rough texture has not been of further interest. Analogously, the limits of these models have not been described and exploited. Thus, the question arises, what will happen when the size of surface structures is reduced to the size of the contacting liquid molecules itself? Are common methods still valid or can deviations from macroscopic behavior be observed?
This thesis wants to create a starting point regarding these questions. In order to investigate the effect of smallest-scale surface structures on liquid wetting, a suitable model system is developed by means of self-assembled monolayer (SAM) formation from (fluoro)organic thiols of differing lengths of the alkyl chain. Surface topographies are created which rely on size differences of several Ångströms and exhibit surprising wetting behavior depending on the choice of the individual precursor system. Thus, contact angles are experimentally detected, which deviate considerably from theoretical calculations based on Wenzel and Cassie/Baxter models and confirm that sub-nm surface topographies affect wetting. Moreover, experimentally determined wetting properties are found to correlate well to an assumed scale-dependent surface tension of the contacting liquid. This behavior has already been described for scattering experiments taking into account capillary waves on the liquid surface induced by temperature and had been predicted earlier by theoretical calculations.
However, the investigation of model surfaces requires the provision of suitable precursor molecules, which are not commercially available and opens up a door to the exotic chemistry of fluoro-organic materials. During the course of this work, the synthesis of long-chain precursors is examined with a particular focus put on oligomerically pure semi-fluorinated n-alkyl thiols and n-alkyl trichlorosilanes. For this, general protocols for the syntheses of the desired compounds are developed and product mixtures are assayed to be separated into fractions of individual chain lengths by fluorous-phase high-performance liquid chromatography (F-HPLC).
The transition from model systems to technically more relevant surfaces and applications is initiated through the deposition of SAMs from long-chain fluorinated n-alkyl trichlorosilanes. Depositions are accomplished by a vapor-phase deposition process conducted on a pilot-scale set-up, which enables the exact control of relevant process parameters. Thus, the influence of varying deposition conditions on the properties of the final coating is examined and analyzed for the most important parameters. The strongest effect is observed for the partial pressure of reactive water vapor, which directly controls the extent of precursor hydrolysis during the deposition process. Experimental results propose that the formation of ordered monolayers rely on the amount of hydrolyzed silanol species present in the deposition system irrespective of the exact grade of hydrolysis. However, at increased amounts of species which are able to form cross-linked molecules due to condensation reactions, films deteriorate in quality. This effect is assumed to be caused by the introduction of defects within the film and the adsorption of cross linked agglomerates. Deposition conditions are also investigated for chain extended precursor species and reveal distinct differences caused by chain elongation.