@article{KnoxBrownRindfleischGuentheretal.2020, author = {Knox-Brown, Patrick and Rindfleisch, Tobias and G{\"u}nther, Anne and Balow, Kim and Bremer, Anne and Walther, Dirk and Miettinen, Markus S. and Hincha, Dirk K. and Thalhammer, Anja}, title = {Similar Yet Different}, series = {International Journal of Molecular Sciences}, volume = {21}, journal = {International Journal of Molecular Sciences}, number = {8}, publisher = {Molecular Diversity Preservation International}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms21082794}, pages = {25}, year = {2020}, abstract = {The importance of intrinsically disordered late embryogenesis abundant (LEA) proteins in the tolerance to abiotic stresses involving cellular dehydration is undisputed. While structural transitions of LEA proteins in response to changes in water availability are commonly observed and several molecular functions have been suggested, a systematic, comprehensive and comparative study of possible underlying sequence-structure-function relationships is still lacking. We performed molecular dynamics (MD) simulations as well as spectroscopic and light scattering experiments to characterize six members of two distinct, lowly homologous clades of LEA_4 family proteins from Arabidopsis thaliana. We compared structural and functional characteristics to elucidate to what degree structure and function are encoded in LEA protein sequences and complemented these findings with physicochemical properties identified in a systematic bioinformatics study of the entire Arabidopsis thaliana LEA_4 family. Our results demonstrate that although the six experimentally characterized LEA_4 proteins have similar structural and functional characteristics, differences concerning their folding propensity and membrane stabilization capacity during a freeze/thaw cycle are obvious. These differences cannot be easily attributed to sequence conservation, simple physicochemical characteristics or the abundance of sequence motifs. Moreover, the folding propensity does not appear to be correlated with membrane stabilization capacity. Therefore, the refinement of LEA_4 structural and functional properties is likely encoded in specific patterns of their physicochemical characteristics.}, language = {en} } @article{Schenck2020, author = {Schenck, Marcia C.}, title = {Small Strangers at the School of Friendship: Memories of Mozambican School Students of The German Democratic Republic}, series = {German Historical Institute Washington Bulletin / Supplement}, journal = {German Historical Institute Washington Bulletin / Supplement}, number = {15}, publisher = {Max Weber Stiftung - Deutsche Geisteswissenschaftliche Institute im Ausland}, pages = {41 -- 59}, year = {2020}, language = {en} } @book{TaylorNanzTaylor2020, author = {Taylor, Charles and Nanz, Patrizia and Taylor, Madeleine Beaubien}, title = {Reconstructing democracy}, publisher = {Harvard University Press}, address = {Cambridge}, isbn = {978-0-674-24462-7}, pages = {107}, year = {2020}, abstract = {Across the world, democracies are suffering from a disconnect between the people and political elites. In communities where jobs and industry are scarce, many feel the government is incapable of understanding their needs or addressing their problems. The resulting frustration has fueled the success of destabilizing demagogues. To reverse this pattern and restore responsible government, we need to reinvigorate democracy at the local level. But what does that mean? Drawing on examples of successful community building in cities large and small, from a shrinking village in rural Austria to a neglected section of San Diego, Reconstructing Democracy makes a powerful case for re-engaging citizens. It highlights innovative grassroots projects and shows how local activists can form alliances and discover their own power to solve problems.}, language = {en} } @book{OPUS4-50028, title = {The First World War as a Caesura?}, series = {Gewaltpolitik und Menschenrechte ; 3}, journal = {Gewaltpolitik und Menschenrechte ; 3}, editor = {Pschichholz, Christin}, publisher = {Duncker \& Humblot}, address = {Berlin}, isbn = {978-3-428-18146-9}, pages = {247}, year = {2020}, abstract = {During the phases of mobile warfare, the ethnically and religiously very heterogeneous population in the border regions of the multi-ethnic empires suffered in particular. Even if the real military situation in the course of the war hardly gave cause for concern, the image of disloyal ethnic and national minorities was widespread. This was particularly the case when ethnic groups lived on both sides of the border and social and political tensions had already established themselves along ethnic or religious lines of conflict before the war. Displacements, deportations and mass violence were the result. The genocide of the Armenian population is the most extreme example of this development. This anthology examines the border regions of the Ottoman, Russian and Habsburg empires during the First World War with regard to radical population policy and genocidal violence from a comparative perspective in order to draw a more precise picture of escalating and deescalating factors.}, language = {en} } @article{SalzwedelHeidlerMengetal.2020, author = {Salzwedel, Annett and Heidler, Maria-Dorothea and Meng, Karin and Schikora, Martin and Wegscheider, Karl and Reibis, Rona Katharina and V{\"o}ller, Heinz}, title = {Impact of cognitive performance on disease-related knowledge six months after multi-component rehabilitation in patients after an acute cardiac event}, series = {European journal of preventive cardiology : the official ESC journal for primary \& secondary cardiovascular prevention, rehabilitation and sports cardiology}, volume = {26}, journal = {European journal of preventive cardiology : the official ESC journal for primary \& secondary cardiovascular prevention, rehabilitation and sports cardiology}, number = {1}, publisher = {Sage Publ.}, address = {London}, issn = {2047-4873}, doi = {10.1177/2047487318791609}, pages = {46 -- 55}, year = {2020}, abstract = {Background Although associations between cardiovascular diseases and cognitive impairment are well known, the impact of cognitive performance on the success of patient education as a core component of cardiac rehabilitation remains insufficiently investigated so far. Design Prospective observational study in two inpatient cardiac rehabilitation centres between September 2014 and August 2015 with a follow-up six months after cardiac rehabilitation. Method At admission to and discharge from cardiac rehabilitation, the cognitive performance of 401 patients (54.5 ± 6.3 years, 80\% men) following an acute coronary syndrome and/or coronary artery bypass graft was tested using the Montreal Cognitive Assessment. Patients' disease-related knowledge was determined using a quiz (22 items for medical knowledge and 12 items for healthy lifestyle and behaviour) at both times and at follow-up. The change in knowledge after cardiac rehabilitation was analysed in multivariable regression models. Potentially influencing parameters (e.g. level of education, medication, cardiovascular risk factors, coronary artery bypass graft, comorbidities, exercise capacity) were considered. Results During cardiac rehabilitation, disease-related knowledge was significantly enhanced in both scales. At follow-up, the average level of medical knowledge was significantly reduced, while lifestyle knowledge remained at a stable level. The maintenance of knowledge after cardiac rehabilitation was predominantly predicted by prior knowledge, cognitive performance at discharge from cardiac rehabilitation and, in the case of medical knowledge, by coronary artery bypass graft. Conclusion Patient education in cardiac rehabilitation led to enhanced disease-related knowledge, but the maintenance of this essentially depended on patients' cognitive performance, especially after coronary artery bypass graft. Therefore, patient education concepts in cardiac rehabilitation should be reconsidered and adjusted as needed.}, language = {en} } @phdthesis{Jing2020, author = {Jing, Yue}, title = {Characterization of Serine Carboxypeptidase-like (SCPL) gene family in Brassicaceae}, school = {Universit{\"a}t Potsdam}, year = {2020}, language = {en} } @article{RyoJeschkeRilligetal.2020, author = {Ryo, Masahiro and Jeschke, Jonathan M. and Rillig, Matthias C. and Heger, Tina}, title = {Machine learning with the hierarchy-of-hypotheses (HoH) approach discovers novel pattern in studies on biological invasions}, series = {Research synthesis methods}, volume = {11}, journal = {Research synthesis methods}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {1759-2879}, doi = {10.1002/jrsm.1363}, pages = {66 -- 73}, year = {2020}, abstract = {Research synthesis on simple yet general hypotheses and ideas is challenging in scientific disciplines studying highly context-dependent systems such as medical, social, and biological sciences. This study shows that machine learning, equation-free statistical modeling of artificial intelligence, is a promising synthesis tool for discovering novel patterns and the source of controversy in a general hypothesis. We apply a decision tree algorithm, assuming that evidence from various contexts can be adequately integrated in a hierarchically nested structure. As a case study, we analyzed 163 articles that studied a prominent hypothesis in invasion biology, the enemy release hypothesis. We explored if any of the nine attributes that classify each study can differentiate conclusions as classification problem. Results corroborated that machine learning can be useful for research synthesis, as the algorithm could detect patterns that had been already focused in previous narrative reviews. Compared with the previous synthesis study that assessed the same evidence collection based on experts' judgement, the algorithm has newly proposed that the studies focusing on Asian regions mostly supported the hypothesis, suggesting that more detailed investigations in these regions can enhance our understanding of the hypothesis. We suggest that machine learning algorithms can be a promising synthesis tool especially where studies (a) reformulate a general hypothesis from different perspectives, (b) use different methods or variables, or (c) report insufficient information for conducting meta-analyses.}, language = {en} } @misc{vanderKroefKoszinskiGrinatetal.2020, author = {van der Kroef, Ilona and Koszinski, Sylvia and Grinat, Michael and van der Meij, Marijn W. and Hierold, Wilfried and S{\"u}dekum, Wolfgang and Sommer, Michael}, title = {Digital mapping of buried soil horizons using 2D and pseudo-3D geoelectrical measurements in a ground moraine landscape}, series = {European journal of soil science : EJSS}, volume = {71}, journal = {European journal of soil science : EJSS}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {1351-0754}, pages = {10 -- 26}, year = {2020}, abstract = {The identification of buried soil horizons in agricultural landscapes helps to quantify sediment budgets and erosion-related carbon dynamics. High-resolution mapping of buried horizons using conventional soil surveys is destructive and time consuming. Geoelectrical sensors can offer a fast and non-destructive alternative for determining horizon positions and properties. In this paper, we compare the suitability of several geoelectrical methods for measuring the depth to buried horizons (Apb, Ahb and Hab) in the hummocky ground moraine landscape of northeastern Germany. Soil profile descriptions were developed for 269 locations within a 6-ha experimental field "CarboZALF-D". A stepwise linear discriminant analysis (LDA) estimated the lateral position of the buried horizons using electromagnetic induction data and terrain attributes. To predict the depth of a buried horizon, multiple linear regression (MLR) was used for both a 120-m transect and a 0.2-ha pseudo-three-dimensional (3D) area. At these scales, apparent electrical conductivity (ECa), electrical resistivity (ER) and terrain attributes were used as independent variables. The LDA accurately predicted Apb- and Ahb-horizons (a correct classification of 93\%). The LDA of the Hab-horizon had a misclassification of 24\%, which was probably related to the smaller test set and the higher depth of this horizon. The MLR predicted the depth of the Apb-, Ahb- and Hab-horizons with relative root mean square errors (RMSEs) of 7, 3 and 13\%, respectively, in the pseudo-3D area. MLR had a lower accuracy for the 2D transect compared to the pseudo-3D area. Overall, the use of LDA and MLR has been an efficient methodological approach for predicting buried horizon positions. Highlights The suitability of geoelectrical measurements for digital modelling of diagnostic buried soil horizons was determined. LDA and MLR were used to detect multiple horizons with geoelectrical devices and terrain attributes. Geoelectrical variables were significant predictors of the position of the target soil horizons. The use of these tested digital technologies gives an opportunity to develop high-resolution soil mapping procedures.}, language = {en} } @article{SchaubKlaassenBoutenetal.2020, author = {Schaub, Tonio and Klaassen, Raymond H. G. and Bouten, Willem and Schlaich, Almut E. and Koks, Ben J.}, title = {Collision risk of Montagu's Harriers Circus pygargus with wind turbines derived from high-resolution GPS tracking}, series = {Ibis : the international journal of avian science ; the journal of the British Ornithologists' Union}, volume = {162}, journal = {Ibis : the international journal of avian science ; the journal of the British Ornithologists' Union}, number = {2}, publisher = {Wiley}, address = {Hoboken}, issn = {0019-1019}, doi = {10.1111/ibi.12788}, pages = {520 -- 534}, year = {2020}, abstract = {Flight behaviour characteristics such as flight altitude and avoidance behaviour determine the species-specific collision risk of birds with wind turbines. However, traditional observational methods exhibit limited positional accuracy. High-resolution GPS telemetry represents a promising method to overcome this drawback. In this study, we used three-dimensional GPS tracking data including high-accuracy tracks recorded at 3-s intervals to investigate the collision risk of breeding male Montagu's Harriers Circus pygargus in the Dutch-German border region. Avoidance of wind turbines was quantified by a novel approach comparing observed flights to a null model of random flight behaviour. On average, Montagu's Harriers spent as much as 8.2 h per day in flight. Most flights were at low altitude, with only 7.1\% within the average rotor height range (RHR; 45-125 m). Montagu's Harriers showed significant avoidance behaviour, approaching turbines less often than expected, particularly when flying within the RHR (avoidance rate of 93.5\%). For the present state, with wind farms situated on the fringes of the regional nesting range, collision risk models based on our new insights on flight behaviour indicated 0.6-2.0 yearly collisions of adult males (as compared with a population size of c. 40 pairs). However, the erection of a new wind farm inside the core breeding area could markedly increase mortality (up to 9.7 yearly collisions). If repowering of the wind farms was carried out using low-reaching modern turbines (RHR 36-150 m), mortality would more than double, whereas it would stay approximately constant if higher turbines (RHR 86-200 m) were used. Our study demonstrates the great potential of high-resolution GPS tracking for collision risk assessments. The resulting information on collision-related flight behaviour allows for performing detailed scenario analyses on wind farm siting and turbine design, in contrast to current environmental assessment practices. With regard to Montagu's Harriers, we conclude that although the deployment of higher wind turbines represents an opportunity to reduce collision risk for this species, precluding wind energy developments in core breeding areas remains the most important mitigation measure.}, language = {en} } @article{EngelsMedeirosAxfordetal.2020, author = {Engels, Stefan and Medeiros, Andrew S. and Axford, Yarrow and Brooks, Steve and Heiri, Oliver and Luoto, Tomi P. and Nazarova, Larisa B. and Porinchu, David F. and Quinlan, Roberto and Self, Angela E.}, title = {Temperature change as a driver of spatial patterns and long-term trends in chironomid (Insecta: Diptera) diversity}, series = {Global change biology}, volume = {26}, journal = {Global change biology}, number = {3}, publisher = {Wiley}, address = {Hoboken}, issn = {1354-1013}, doi = {10.1111/gcb.14862}, pages = {1155 -- 1169}, year = {2020}, abstract = {Anthropogenic activities have led to a global decline in biodiversity, and monitoring studies indicate that both insect communities and wetland ecosystems are particularly affected. However, there is a need for long-term data (over centennial or millennial timescales) to better understand natural community dynamics and the processes that govern the observed trends. Chironomids (Insecta: Diptera: Chironomidae) are often the most abundant insects in lake ecosystems, sensitive to environmental change, and, because their larval exoskeleton head capsules preserve well in lake sediments, they provide a unique record of insect community dynamics through time. Here, we provide the results of a metadata analysis of chironomid diversity across a range of spatial and temporal scales. First, we analyse spatial trends in chironomid diversity using Northern Hemispheric data sets overall consisting of 837 lakes. Our results indicate that in most of our data sets, summer temperature (T-jul) is strongly associated with spatial trends in modern-day chironomid diversity. We observe a strong increase in chironomid alpha diversity with increasing T-jul in regions with present-day T-jul between 2.5 and 14 degrees C. In some areas with T-jul > 14 degrees C, chironomid diversity stabilizes or declines. Second, we demonstrate that the direction and amplitude of change in alpha diversity in a compilation of subfossil chironomid records spanning the last glacial-interglacial transition (similar to 15,000-11,000 years ago) are similar to those observed in our modern data. A compilation of Holocene records shows that during phases when the amplitude of temperature change was small, site-specific factors had a greater influence on the chironomid fauna obscuring the chironomid diversity-temperature relationship. Our results imply expected overall chironomid diversity increases in colder regions such as the Arctic under sustained global warming, but with complex and not necessarily predictable responses for individual sites.}, language = {en} } @article{StonesTurner2020, author = {Stones, Rob and Turner, Bryan S.}, title = {Successful societies}, series = {The British journal of sociology : BJS online}, volume = {71}, journal = {The British journal of sociology : BJS online}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {0007-1315}, doi = {10.1111/1468-4446.12724}, pages = {183 -- 199}, year = {2020}, abstract = {Combining moral philosophy with sociological theory to build on themes introduced in Hall and Lamont's Successful Societies (2009), the paper outlines a distinctive perspective. It holds that a necessary condition of successful societies is that decision-makers base their decisions on a high level of attentiveness (concern and comprehension) towards subjectively valued and morally legitimate forms of life. Late modern societies consist of a plurality of forms of life, each providing grounds for what Alasdair MacIntyre has called internal goods—valued and morally valuable practices. The status of such goods is examined, and distinctions are drawn between their manifest and latent, and transposable and situationally specific, characteristics. We integrate this refined idea of internal goods into a developed conception of habitus that is both morally informed and situationally embedded. The sociological approach of strong structuration theory (SST) is employed to demonstrate how this conception of habitus can guide the critique of decision-making that damages internal goods. We identify the most pervasive and invidious forms of damaging decision-making in contemporary societies as those involving excessive forms of instrumental reasoning. We argue that our developed conception of habitus, anchored in the collectively valued practices of specific worlds, can be a powerful focus for resistance. Accounts of scholarship in higher education and of the white working class in America illustrate the specificities of singular, particular, social worlds and illuminate critical challenges raised by the perspective we advocate.}, language = {en} } @article{VoigtSchollBaueretal.2020, author = {Voigt, Christian and Scholl, Julia M. and Bauer, Juliane and Teige, Tobias and Yovel, Yossi and Kramer-Schadt, Stephanie and Gras, Pierre}, title = {Movement responses of common noctule bats to the illuminated urban landscape}, series = {Landscape ecology}, volume = {35}, journal = {Landscape ecology}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {0921-2973}, doi = {10.1007/s10980-019-00942-4}, pages = {189 -- 201}, year = {2020}, abstract = {Context Cities are a challenging habitat for obligate nocturnal mammals because of the ubiquitous use of artificial light at night (ALAN). How nocturnal animals move in an urban landscape, particularly in response to ALAN is largely unknown. Objectives We studied the movement responses, foraging and commuting, of common noctules (Nyctalus noctula) to urban landscape features in general and ALAN in particular. Methods We equipped 20 bats with miniaturized GPS loggers in the Berlin metropolitan area and related spatial positions of bats to anthropogenic and natural landscape features and levels of ALAN. Results Common noctules foraged close to ALAN only next to bodies of water or well vegetated areas, probably to exploit swarms of insects lured by street lights. In contrast, they avoided illuminated roads, irrespective of vegetation cover nearby. Predictive maps identified most of the metropolitan area as non-favoured by this species because of high levels of impervious surfaces and ALAN. Dark corridors were used by common noctules for commuting and thus likely improved the permeability of the city landscape. Conclusions We conclude that the spatial use of common noctules, previously considered to be more tolerant to light than other bats, is largely constrained by ALAN. Our study is the first individual-based GPS tracking study to show sensitive responses of nocturnal wildlife to light pollution. Approaches to protect urban biodiversity need to include ALAN to safeguard the larger network of dark habitats for bats and other nocturnal species in cities.}, language = {en} } @article{Wolf2020, author = {Wolf, Hannah}, title = {Permanent liminality?}, publisher = {Routledge}, address = {London}, isbn = {978-0-429262-28-9}, pages = {99 -- 118}, year = {2020}, abstract = {After more than eight years of multifaceted crisis and extreme austerity policies, the programmes of financial assistance to Greece ended in August 2018, only to be replaced by a strict surveillance plan which leaves little room for manoeuvre towards more socially sensitive policies. In this context, the paper focuses on three major issues of argument between the creditors and the Greek government: property ownership and taxation, reduction of pensions, and continued austerity. Based on research in Athens and starting from the premise that behind figures and statistics lie embodied subjects, the paper discusses these issues drawing from particular people's experiences.}, language = {en} } @article{Fitzi2020, author = {Fitzi, Gregor}, title = {Introduction}, publisher = {Routledge}, address = {London}, isbn = {978-0-429-26230-2}, pages = {1 -- 11}, year = {2020}, abstract = {This introduction presents an overview of the key concepts discussed in the subsequent chapters of this book. The book considers the complex process of the criminalisation of squatting alongside and beyond its juridical apparatuses. It provides insights into the ways in which the substance of social citizenship has been rapidly and significantly weakened, so that life has become much more precarious for low-income urbanites as well as large parts of the middle-class. The book reconstructs the history of Berlin's tenant referendum, which induced the passing of a new local Housing Provision Act—one of the most progressive pieces of housing legislation in Germany. It investigates the modes of doing citizenship and social rights in practice, which characterised the creation of Berlin's Medib{\"u}ro, a network of medical offices, where medical activists provide free medical services to residents lacking access to the medical insurance system, especially to illegal migrants. The book concludes by providing a brief outlook on future research on urban citizenship.}, language = {en} } @phdthesis{Temmen2020, author = {Temmen, Jens}, title = {The Territorialities of U.S. Imperialism(s)}, series = {American Studies ; 308}, journal = {American Studies ; 308}, publisher = {Winter}, address = {Heidelberg}, isbn = {978-3-8253-4713-0}, school = {Universit{\"a}t Potsdam}, pages = {x, 259}, year = {2020}, abstract = {'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.}, language = {en} } @article{SchinkoethBrand2020, author = {Schink{\"o}th, Michaela and Brand, Ralf}, title = {Automatic associations and the affective valuation of exercise}, series = {German Journal of Exercise and Sport Research}, volume = {50}, journal = {German Journal of Exercise and Sport Research}, number = {654}, publisher = {Springer}, address = {Berlin ; Heidelberg}, issn = {2509-3150}, doi = {10.1007/s12662-020-00664-9}, pages = {366 -- 376}, year = {2020}, abstract = {The decision to exercise is not only bound to rational considerations but also automatic affective processes. The affective-reflective theory of physical inactivity and exercise (ART) proposes a theoretical framework for explaining how the automatic affective process (type‑1 process) will influence exercise behavior, i.e., through the automatic activation of exercise-related associations and a subsequent affective valuation of exercise. This study aimed to empirically test this assumption of the ART with data from 69 study participants. A single-measurement study, including within-subject experimental variation, was conducted. Automatic associations with exercise were first measured with a single-target implicit association test. The somato-affective core of the participants' automatic valuation of exercise-related pictures was then assessed via heart rate variability (HRV) analysis, and the affective valence of the valuation was tested with a facial expression (FE; smile and frown) task. Exercise behavior was assessed via self-report. Multiple regression (path) analysis revealed that automatic associations predicted HRV reactivity (β = -0.24, p = .044); the signs of the correlation between automatic associations and the smile FE score was in the expected direction but remained nonsignificant (β = -0.21, p = .078). HRV reactivity predicted self-reported exercise behavior (β = -0.28, p = .013) (the same pattern of results was achieved for the frown FE score). The HRV-related results illustrate the potential role of automatic negative affective reactions to the thought of exercise as a restraining force in exercise motivation. For better empirical distinction between the two ART type‑1 process components, automatic associations and the affective valuation should perhaps be measured separately in the future. The results support the notion that automatic and affective processes should be regarded as essential aspects of the motivation to exercise.}, language = {en} } @article{MardoukhiChechkinMetzler2020, author = {Mardoukhi, Yousof and Chechkin, Aleksei V. and Metzler, Ralf}, title = {Spurious ergodicity breaking in normal and fractional Ornstein-Uhlenbeck process}, series = {New Journal of Physics}, volume = {22}, journal = {New Journal of Physics}, publisher = {IOP}, address = {London}, issn = {1367-2630}, doi = {10.1088/1367-2630/ab950b}, pages = {18}, year = {2020}, abstract = {The Ornstein-Uhlenbeck process is a stationary and ergodic Gaussian process, that is fully determined by its covariance function and mean. We show here that the generic definitions of the ensemble- and time-averaged mean squared displacements fail to capture these properties consistently, leading to a spurious ergodicity breaking. We propose to remedy this failure by redefining the mean squared displacements such that they reflect unambiguously the statistical properties of any stochastic process. In particular we study the effect of the initial condition in the Ornstein-Uhlenbeck process and its fractional extension. For the fractional Ornstein-Uhlenbeck process representing typical experimental situations in crowded environments such as living biological cells, we show that the stationarity of the process delicately depends on the initial condition.}, language = {en} } @phdthesis{Moratti2020, author = {Moratti, Fabio Giulio}, title = {Structural analysis of DYW proteins and identification of the mitochondrial DNA-binding proteome of Arabidopsis thaliana}, school = {Universit{\"a}t Potsdam}, pages = {164}, year = {2020}, language = {en} } @phdthesis{Wenk2020, author = {Wenk, Sebastian}, title = {Engineering formatotrophic growth in Escherichia coli}, school = {Universit{\"a}t Potsdam}, pages = {V, 107}, year = {2020}, abstract = {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.}, language = {en} } @phdthesis{Kubis2020, author = {Kubis, Armin}, title = {Synthetic carbon neutral photorespiration bypasses}, school = {Universit{\"a}t Potsdam}, pages = {68}, year = {2020}, abstract = {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.}, language = {en} }