@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} } @article{TofeldeBufeTurowski2022, author = {Tofelde, Stefanie and Bufe, Aaron and Turowski, Jens M.}, title = {Hillslope Sediment Supply Limits Alluvial Valley Width}, series = {AGU Advances}, journal = {AGU Advances}, publisher = {American Geophysical Union (AGU); Wiley}, address = {Hoboken, New Jersey, USA}, issn = {2576-604X}, doi = {10.1029/2021AV000641}, pages = {20}, year = {2022}, abstract = {River-valley morphology preserves information on tectonic and climatic conditions that shape landscapes. Observations suggest that river discharge and valley-wall lithology are the main controls on valley width. Yet, current models based on these observations fail to explain the full range of cross-sectional valley shapes in nature, suggesting hitherto unquantified controls on valley width. In particular, current models cannot explain the existence of paired terrace sequences that form under cyclic climate forcing. Paired river terraces are staircases of abandoned floodplains on both valley sides, and hence preserve past valley widths. Their formation requires alternating phases of predominantly river incision and predominantly lateral planation, plus progressive valley narrowing. While cyclic Quaternary climate changes can explain shifts between incision and lateral erosion, the driving mechanism of valley narrowing is unknown. Here, we extract valley geometries from climatically formed, alluvial river-terrace sequences and show that across our dataset, the total cumulative terrace height (here: total valley height) explains 90\%-99\% of the variance in valley width at the terrace sites. This finding suggests that valley height, or a parameter that scales linearly with valley height, controls valley width in addition to river discharge and lithology. To explain this valley-width-height relationship, we reformulate existing valley-width models and suggest that, when adjusting to new boundary conditions, alluvial valleys evolve to a width at which sediment removal from valley walls matches lateral sediment supply from hillslope erosion. Such a hillslope-channel coupling is not captured in current valley-evolution models. Our model can explain the existence of paired terrace sequences under cyclic climate forcing and relates valley width to measurable field parameters. Therefore, it facilitates the reconstruction of past climatic and tectonic conditions from valley topography.}, language = {en} } @article{MiklashevskyFischerLindemann2022, author = {Miklashevsky, Alex and Fischer, Martin H. and Lindemann, Oliver}, title = {Spatial-numerical associations without a motor response? Grip force says 'Yes'}, series = {Acta Psychologica}, volume = {231}, journal = {Acta Psychologica}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1873-6297}, doi = {10.1016/j.actpsy.2022.103791}, pages = {1 -- 17}, year = {2022}, abstract = {In numerical processing, the functional role of Spatial-Numerical Associations (SNAs, such as the association of smaller numbers with left space and larger numbers with right space, the Mental Number Line hypothesis) is debated. Most studies demonstrate SNAs with lateralized responses, and there is little evidence that SNAs appear when no response is required. We recorded passive holding grip forces in no-go trials during number processing. In Experiment 1, participants performed a surface numerical decision task ("Is it a number or a letter?"). In Experiment 2, we used a deeper semantic task ("Is this number larger or smaller than five?"). Despite instruction to keep their grip force constant, participants' spontaneous grip force changed in both experiments: Smaller numbers led to larger force increase in the left than in the right hand in the numerical decision task (500-700 ms after stimulus onset). In the semantic task, smaller numbers again led to larger force increase in the left hand, and larger numbers increased the right-hand holding force. This effect appeared earlier (180 ms) and lasted longer (until 580 ms after stimulus onset). This is the first demonstration of SNAs with passive holding force. Our result suggests that (1) explicit motor response is not a prerequisite for SNAs to appear, and (2) the timing and strength of SNAs are task-dependent. (216 words).}, language = {en} } @article{LindnerMoellerHildebrandtetal.2022, author = {Lindner, Nadja and Moeller, Korbinian and Hildebrandt, Frauke and Hasselhorn, Marcus and Lonnemann, Jan}, title = {Children's use of egocentric reference frames in spatial language is related to their numerical magnitude understanding}, series = {Frontiers in Psychology}, journal = {Frontiers in Psychology}, publisher = {Frontiers}, address = {Lausanne, Schweiz}, issn = {1664-1078}, doi = {10.3389/fpsyg.2022.943191}, pages = {1 -- 13}, year = {2022}, abstract = {Numerical magnitude information is assumed to be spatially represented in the form of a mental number line defined with respect to a body-centred, egocentric frame of reference. In this context, spatial language skills such as mastery of verbal descriptions of spatial position (e.g., in front of, behind, to the right/left) have been proposed to be relevant for grasping spatial relations between numerical magnitudes on the mental number line. We examined 4- to 5-year-old's spatial language skills in tasks that allow responses in egocentric and allocentric frames of reference, as well as their relative understanding of numerical magnitude (assessed by a number word comparison task). In addition, we evaluated influences of children's absolute understanding of numerical magnitude assessed by their number word comprehension (montring different numbers using their fingers) and of their knowledge on numerical sequences (determining predecessors and successors as well as identifying missing dice patterns of a series). Results indicated that when considering responses that corresponded to the egocentric perspective, children's spatial language was associated significantly with their relative numerical magnitude understanding, even after controlling for covariates, such as children's SES, mental rotation skills, and also absolute magnitude understanding or knowledge on numerical sequences. This suggests that the use of egocentric reference frames in spatial language may facilitate spatial representation of numbers along a mental number line and thus seem important for preschoolers' relative understanding of numerical magnitude.}, language = {en} } @inproceedings{CurzonKalasSchubertetal.2015, author = {Curzon, Paul and Kalas, Ivan and Schubert, Sigrid and Schaper, Niclas and Barnes, Jan and Kennewell, Steve and Br{\"o}ker, Kathrin and Kastens, Uwe and Magenheim, Johannes and Dagiene, Valentina and Stupuriene, Gabriele and Ellis, Jason Brent and Abreu-Ellis, Carla Reis and Grillenberger, Andreas and Romeike, Ralf and Haugsbakken, Halvdan and Jones, Anthony and Lewin, Cathy and McNicol, Sarah and Nelles, Wolfgang and Neugebauer, Jonas and Ohrndorf, Laura and Schaper, Niclas and Schubert, Sigrid and Opel, Simone and Kramer, Matthias and Trommen, Michael and Pottb{\"a}cker, Florian and Ilaghef, Youssef and Passig, David and Tzuriel, David and Kedmi, Ganit Eshel and Saito, Toshinori and Webb, Mary and Weigend, Michael and Bottino, Rosa and Chioccariello, Augusto and Christensen, Rhonda and Knezek, Gerald and Gioko, Anthony Maina and Angondi, Enos Kiforo and Waga, Rosemary and Ohrndorf, Laura and Or-Bach, Rachel and Preston, Christina and Younie, Sarah and Przybylla, Mareen and Romeike, Ralf and Reynolds, Nicholas and Swainston, Andrew and Bendrups, Faye and Sysło, Maciej M. and Kwiatkowska, Anna Beata and Zieris, Holger and Gerstberger, Herbert and M{\"u}ller, Wolfgang and B{\"u}chner, Steffen and Opel, Simone and Schiller, Thomas and Wegner, Christian and Zender, Raphael and Lucke, Ulrike and Diethelm, Ira and Syrbe, J{\"o}rn and Lai, Kwok-Wing and Davis, Niki and Eickelmann, Birgit and Erstad, Ola and Fisser, Petra and Gibson, David and Khaddage, Ferial and Knezek, Gerald and Micheuz, Peter and Kloos, Carlos Delgado}, title = {KEYCIT 2014}, editor = {Brinda, Torsten and Reynolds, Nicholas and Romeike, Ralf and Schwill, Andreas}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-292-6}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-70325}, pages = {438}, year = {2015}, abstract = {In our rapidly changing world it is increasingly important not only to be an expert in a chosen field of study but also to be able to respond to developments, master new approaches to solving problems, and fulfil changing requirements in the modern world and in the job market. In response to these needs key competencies in understanding, developing and using new digital technologies are being brought into focus in school and university programmes. The IFIP TC3 conference "KEYCIT - Key Competences in Informatics and ICT (KEYCIT 2014)" was held at the University of Potsdam in Germany from July 1st to 4th, 2014 and addressed the combination of key competencies, Informatics and ICT in detail. The conference was organized into strands focusing on secondary education, university education and teacher education (organized by IFIP WGs 3.1 and 3.3) and provided a forum to present and to discuss research, case studies, positions, and national perspectives in this field.}, language = {en} } @article{OgunkolaGuiraudieCaprazFeronetal.2023, author = {Ogunkola, Moses Olalekan and Guiraudie-Capraz, Gaelle and F{\´e}ron, Fran{\c{c}}ois and Leimk{\"u}hler, Silke}, title = {The Human Mercaptopyruvate Sulfurtransferase TUM1 Is Involved in Moco Biosynthesis, Cytosolic tRNA Thiolation and Cellular Bioenergetics in Human Embryonic Kidney Cells}, series = {Biomolecules}, volume = {13}, journal = {Biomolecules}, edition = {1}, publisher = {MDPI}, address = {Basel, Schweiz}, issn = {2218-273X}, doi = {10.3390/biom13010144}, pages = {1 -- 23}, year = {2023}, abstract = {Sulfur is an important element that is incorporated into many biomolecules in humans. The incorporation and transfer of sulfur into biomolecules is, however, facilitated by a series of different sulfurtransferases. Among these sulfurtransferases is the human mercaptopyruvate sulfurtransferase (MPST) also designated as tRNA thiouridine modification protein (TUM1). The role of the human TUM1 protein has been suggested in a wide range of physiological processes in the cell among which are but not limited to involvement in Molybdenum cofactor (Moco) biosynthesis, cytosolic tRNA thiolation and generation of H2S as signaling molecule both in mitochondria and the cytosol. Previous interaction studies showed that TUM1 interacts with the L-cysteine desulfurase NFS1 and the Molybdenum cofactor biosynthesis protein 3 (MOCS3). Here, we show the roles of TUM1 in human cells using CRISPR/Cas9 genetically modified Human Embryonic Kidney cells. Here, we show that TUM1 is involved in the sulfur transfer for Molybdenum cofactor synthesis and tRNA thiomodification by spectrophotometric measurement of the activity of sulfite oxidase and liquid chromatography quantification of the level of sulfur-modified tRNA. Further, we show that TUM1 has a role in hydrogen sulfide production and cellular bioenergetics.}, language = {en} } @article{MarggrafLindeckeVoigtetal.2023, author = {Marggraf, Lara Christin and Lindecke, Oliver and Voigt, Christian C. and Pētersons, Gunārs and Voigt-Heucke, Silke Luise}, title = {Nathusius' bats, Pipistrellus nathusii, bypass mating opportunities of their own species, but respond to foraging heterospecifics on migratory transit flights}, series = {Frontiers in Ecology and Evolution}, journal = {Frontiers in Ecology and Evolution}, publisher = {Frontiers}, address = {Lausanne, Schweiz}, issn = {2296-701X}, doi = {10.3389/fevo.2022.908560}, pages = {1 -- 10}, year = {2023}, abstract = {In late summer, migratory bats of the temperate zone face the challenge of accomplishing two energy-demanding tasks almost at the same time: migration and mating. Both require information and involve search efforts, such as localizing prey or finding potential mates. In non-migrating bat species, playback studies showed that listening to vocalizations of other bats, both con-and heterospecifics, may help a recipient bat to find foraging patches and mating sites. However, we are still unaware of the degree to which migrating bats depend on con-or heterospecific vocalizations for identifying potential feeding or mating opportunities during nightly transit flights. Here, we investigated the vocal responses of Nathusius' pipistrelle bats, Pipistrellus nathusii, to simulated feeding and courtship aggregations at a coastal migration corridor. We presented migrating bats either feeding buzzes or courtship calls of their own or a heterospecific migratory species, the common noctule, Nyctalus noctula. We expected that during migratory transit flights, simulated feeding opportunities would be particularly attractive to bats, as well as simulated mating opportunities which may indicate suitable roosts for a stopover. However, we found that when compared to the natural silence of both pre-and post-playback phases, bats called indifferently during the playback of conspecific feeding sounds, whereas P. nathusii echolocation call activity increased during simulated feeding of N. noctula. In contrast, the call activity of P. nathusii decreased during the playback of conspecific courtship calls, while no response could be detected when heterospecific call types were broadcasted. Our results suggest that while on migratory transits, P. nathusii circumnavigate conspecific mating aggregations, possibly to save time or to reduce the risks associated with social interactions where aggression due to territoriality might be expected. This avoidance behavior could be a result of optimization strategies by P. nathusii when performing long-distance migratory flights, and it could also explain the lack of a response to simulated conspecific feeding. However, the observed increase of activity in response to simulated feeding of N. noctula, suggests that P. nathusii individuals may be eavesdropping on other aerial hawking insectivorous species during migration, especially if these occupy a slightly different foraging niche.}, language = {en} } @article{KuehneFauthDestinaSevdeetal.2021, author = {K{\"u}hne, Franziska and Fauth, Henriette and Destina Sevde, Ay-Bryson and Visser, Leonie N.C. and Weck, Florian}, title = {Communicating the diagnosis of cancer or depression: Results of a randomized controlled online study using video vignettes}, series = {Cancer Medicine}, volume = {10}, journal = {Cancer Medicine}, edition = {24}, publisher = {Wiley}, address = {Hoboken, New Jersey, USA}, issn = {2045-7634}, doi = {10.1002/cam4.4396}, pages = {9012 -- 9021}, year = {2021}, abstract = {Background Communicating a diagnosis is highly important, yet complex, especially in the context of cancer and mental disorders. The aim was to explore the communication style of an oncologist vs. psychotherapist in an online study. Methods Patients (N = 136: 65 cancer, 71 depression) were randomly assigned to watch a standardized video vignette with one of two communication styles (empathic vs. unempathic). Outcome measures of affectivity, information recall, communication skills, empathy and trust were applied. Results Regardless of diagnosis, empathic communication was associated with the perception of a significantly more empathic (p < 0.001, η2partial = 0.08) and trustworthy practitioner (p = 0.014, η2partial = 0.04) with better communication skills (p = 0.013, η2partial = 0.05). Cancer patients reported a larger decrease in positive affect (p < 0.001, η2partial = 0.15) and a larger increase in negative affect (p < 0.001, η2partial = 0.14) from pre- to post-video than depressive patients. Highly relevant information was recalled better in both groups (p < 0.001, d = 0.61-1.06). Conclusions The results highlight the importance of empathy while communicating both a diagnosis of cancer and a mental disorder. Further research should focus on the communication of a mental disorder in association with cancer.}, language = {en} } @article{ReegStriglJeltsch2022, author = {Reeg, Jette and Strigl, Lea and Jeltsch, Florian}, title = {Agricultural buffer zone thresholds to safeguard functional bee diversity}, series = {Ecology and Evolution}, volume = {12}, journal = {Ecology and Evolution}, edition = {3}, publisher = {Wiley Online Library}, address = {Hoboken, New Jersey, USA}, issn = {2045-7758}, doi = {10.1002/ece3.8748}, pages = {1 -- 17}, year = {2022}, abstract = {Wild bee species are important pollinators in agricultural landscapes. However, population decline was reported over the last decades and is still ongoing. While agricultural intensification is a major driver of the rapid loss of pollinating species, transition zones between arable fields and forest or grassland patches, i.e., agricultural buffer zones, are frequently mentioned as suitable mitigation measures to support wild bee populations and other pollinator species. Despite the reported general positive effect, it remains unclear which amount of buffer zones is needed to ensure a sustainable and permanent impact for enhancing bee diversity and abundance. To address this question at a pollinator community level, we implemented a process-based, spatially explicit simulation model of functional bee diversity dynamics in an agricultural landscape. More specifically, we introduced a variable amount of agricultural buffer zones (ABZs) at the transition of arable to grassland, or arable to forest patches to analyze the impact on bee functional diversity and functional richness. We focused our study on solitary bees in a typical agricultural area in the Northeast of Germany. Our results showed positive effects with at least 25\% of virtually implemented agricultural buffer zones. However, higher amounts of ABZs of at least 75\% should be considered to ensure a sufficient increase in Shannon diversity and decrease in quasi-extinction risks. These high amounts of ABZs represent effective conservation measures to safeguard the stability of pollination services provided by solitary bee species. As the model structure can be easily adapted to other mobile species in agricultural landscapes, our community approach offers the chance to compare the effectiveness of conservation measures also for other pollinator communities in future.}, language = {en} } @article{LiebeDordevicKaufmannetal.2022, author = {Liebe, Thomas and Dordevic, Milos and Kaufmann, J{\"o}rn and Avetisyan, Araks and Skalej, Martin and M{\"u}ller, Notger Germar}, title = {Investigation of the functional pathogenesis of mild cognitive impairment by localisation-based locus coeruleus resting-state fMRI}, series = {Human Brain Mapping}, volume = {43}, journal = {Human Brain Mapping}, edition = {18}, publisher = {Wiley}, address = {New York, NY, USA}, issn = {1097-0193}, doi = {10.1002/hbm.26039}, pages = {5630 -- 5642}, year = {2022}, abstract = {Dementia as one of the most prevalent diseases urges for a better understanding of the central mechanisms responsible for clinical symptoms, and necessitates improvement of actual diagnostic capabilities. The brainstem nucleus locus coeruleus (LC) is a promising target for early diagnosis because of its early structural alterations and its relationship to the functional disturbances in the patients. In this study, we applied our improved method of localisation-based LC resting-state fMRI to investigate the differences in central sensory signal processing when comparing functional connectivity (fc) of a patient group with mild cognitive impairment (MCI, n = 28) and an age-matched healthy control group (n = 29). MCI and control participants could be differentiated in their Mini-Mental-State-Examination (MMSE) scores (p < .001) and LC intensity ratio (p = .010). In the fMRI, LC fc to anterior cingulate cortex (FDR p < .001) and left anterior insula (FDR p = .012) was elevated, and LC fc to right temporoparietal junction (rTPJ, FDR p = .012) and posterior cingulate cortex (PCC, FDR p = .021) was decreased in the patient group. Importantly, LC to rTPJ connectivity was also positively correlated to MMSE scores in MCI patients (p = .017). Furthermore, we found a hyperactivation of the left-insula salience network in the MCI patients. Our results and our proposed disease model shed new light on the functional pathogenesis of MCI by directing to attentional network disturbances, which could aid new therapeutic strategies and provide a marker for diagnosis and prediction of disease progression.}, language = {en} } @article{HauffeRathAgyapongetal.2022, author = {Hauffe, Robert and Rath, Michaela and Agyapong, Wilson and Jonas, Wenke and Vogel, Heike and Schulz, Tim Julius and Schwarz, Maria and Kipp, Anna Patricia and Bl{\"u}her, Matthias and Kleinridders, Andr{\´e}}, title = {Obesity Hinders the Protective Effect of Selenite Supplementation on Insulin Signaling}, series = {Antioxidants}, volume = {11}, journal = {Antioxidants}, edition = {5}, publisher = {MDPI}, address = {Basel, Schweiz}, issn = {2076-3921}, doi = {10.3390/antiox11050862}, pages = {1 -- 16}, year = {2022}, abstract = {The intake of high-fat diets (HFDs) containing large amounts of saturated long-chain fatty acids leads to obesity, oxidative stress, inflammation, and insulin resistance. The trace element selenium, as a crucial part of antioxidative selenoproteins, can protect against the development of diet-induced insulin resistance in white adipose tissue (WAT) by increasing glutathione peroxidase 3 (GPx3) and insulin receptor (IR) expression. Whether selenite (Se) can attenuate insulin resistance in established lipotoxic and obese conditions is unclear. We confirm that GPX3 mRNA expression in adipose tissue correlates with BMI in humans. Cultivating 3T3-L1 pre-adipocytes in palmitate-containing medium followed by Se treatment attenuates insulin resistance with enhanced GPx3 and IR expression and adipocyte differentiation. However, feeding obese mice a selenium-enriched high-fat diet (SRHFD) only resulted in a modest increase in overall selenoprotein gene expression in WAT in mice with unaltered body weight development, glucose tolerance, and insulin resistance. While Se supplementation improved adipocyte morphology, it did not alter WAT insulin sensitivity. However, mice fed a SRHFD exhibited increased insulin content in the pancreas. Overall, while selenite protects against palmitate-induced insulin resistance in vitro, obesity impedes the effect of selenite on insulin action and adipose tissue metabolism in vivo.}, language = {en} } @article{KayhanMatthesMarriottHaresignetal.2022, author = {Kayhan, Ezgi and Matthes, Daniel and Marriott Haresign, Ira and B{\´a}nki, Anna and Michel, Christine and Langeloh, Miriam and Wass, Sam and Hoehl, Stefanie}, title = {DEEP: A dual EEG pipeline for developmental hyperscanning studies}, series = {Developmental Cognitive Neuroscience}, volume = {54}, journal = {Developmental Cognitive Neuroscience}, publisher = {Elsevier}, address = {Amsterdam, Niederlande}, issn = {1878-9307}, doi = {10.1016/j.dcn.2022.101104}, pages = {1 -- 11}, year = {2022}, abstract = {Cutting-edge hyperscanning methods led to a paradigm shift in social neuroscience. It allowed researchers to measure dynamic mutual alignment of neural processes between two or more individuals in naturalistic contexts. The ever-growing interest in hyperscanning research calls for the development of transparent and validated data analysis methods to further advance the field. We have developed and tested a dual electroencephalography (EEG) analysis pipeline, namely DEEP. Following the preprocessing of the data, DEEP allows users to calculate Phase Locking Values (PLVs) and cross-frequency PLVs as indices of inter-brain phase alignment of dyads as well as time-frequency responses and EEG power for each participant. The pipeline also includes scripts to control for spurious correlations. Our goal is to contribute to open and reproducible science practices by making DEEP publicly available together with an example mother-infant EEG hyperscanning dataset.}, language = {en} } @article{TiedemannIobbiNivolLeimkuehler2022, author = {Tiedemann, Kim and Iobbi-Nivol, Chantal and Leimk{\"u}hler, Silke}, title = {The Role of the Nucleotides in the Insertion of the bis-Molybdopterin Guanine Dinucleotide Cofactor into apo-Molybdoenzymes}, series = {Molecules}, volume = {27}, journal = {Molecules}, edition = {9}, publisher = {MDPI}, address = {Basel, Schweiz}, issn = {1420-3049}, doi = {10.3390/molecules27092993}, pages = {1 -- 15}, year = {2022}, abstract = {The role of the GMP nucleotides of the bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor of the DMSO reductase family has long been a subject of discussion. The recent characterization of the bis-molybdopterin (bis-Mo-MPT) cofactor present in the E. coli YdhV protein, which differs from bis-MGD solely by the absence of the nucleotides, now enables studying the role of the nucleotides of bis-MGD and bis-MPT cofactors in Moco insertion and the activity of molybdoenzymes in direct comparison. Using the well-known E. coli TMAO reductase TorA as a model enzyme for cofactor insertion, we were able to show that the GMP nucleotides of bis-MGD are crucial for the insertion of the bis-MGD cofactor into apo-TorA.}, language = {en} } @article{WeithoffBell2022, author = {Weithoff, Guntram and Bell, Elanor Margaret}, title = {Complex Trophic Interactions in an Acidophilic Microbial Community}, series = {Microorganisms}, volume = {10}, journal = {Microorganisms}, edition = {7}, publisher = {MDPI}, address = {Basel, Schweiz}, issn = {2076-2607}, doi = {10.3390/microorganisms10071340}, pages = {1 -- 10}, year = {2022}, abstract = {Extreme habitats often harbor specific communities that differ substantially from non-extreme habitats. In many cases, these communities are characterized by archaea, bacteria and protists, whereas the number of species of metazoa and higher plants is relatively low. In extremely acidic habitats, mostly prokaryotes and protists thrive, and only very few metazoa thrive, for example, rotifers. Since many studies have investigated the physiology and ecology of individual species, there is still a gap in research on direct, trophic interactions among extremophiles. To fill this gap, we experimentally studied the trophic interactions between a predatory protist (Actinophrys sol, Heliozoa) and its prey, the rotifers Elosa woralli and Cephalodella sp., the ciliate Urosomoida sp. and the mixotrophic protist Chlamydomonas acidophila (a green phytoflagellate, Chlorophyta). We found substantial predation pressure on all animal prey. High densities of Chlamydomonas acidophila reduced the predation impact on the rotifers by interfering with the feeding behaviour of A. sol. These trophic relations represent a natural case of intraguild predation, with Chlamydomonas acidophila being the common prey and the rotifers/ciliate and A. sol being the intraguild prey and predator, respectively. We further studied this intraguild predation along a resource gradient using Cephalodella sp. as the intraguild prey. The interactions among the three species led to an increase in relative rotifer abundance with increasing resource (Chlamydomonas) densities. By applying a series of laboratory experiments, we revealed the complexity of trophic interactions within a natural extremophilic community.}, language = {en} } @book{WeissVerlaanVasquezCarruthersetal.2022, author = {Weiß, Norman and Verlaan, Stephanie and Vasquez Carruthers, Juan Francisco and Mair, Theresa and Conner, Sean and Maaser, Lucas and R{\"o}thlisberger, Livia}, title = {Transitional Justice}, series = {Potsdamer Studien zu Staat, Recht und Politik}, journal = {Potsdamer Studien zu Staat, Recht und Politik}, number = {7}, editor = {Weiß, Norman}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-473-9}, issn = {1869-2443}, doi = {10.25932/publishup-43171}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431711}, publisher = {Universit{\"a}t Potsdam}, pages = {194}, year = {2022}, abstract = {This publication deals with the topic of transitional justice. In six case studies, the authors link theoretical and practical implications in order to develop some innovative approaches. Their proposals might help to deal more effectively with the transition of societies, legal orders and political systems. Young academics from various backgrounds provide fresh insights and demonstrate the relevance of the topic. The chapters analyse transitions and conflicts in Sierra Leone, Argentina, Nicaragua, Nepal, and South Sudan as well as Germany's colonial genocide in Namibia. Thus, the book provides the reader with new insights and contributes to the ongoing debate about transitional justice.}, language = {en} } @article{PrasseIversenLienhardetal.2022, author = {Prasse, Paul and Iversen, Pascal and Lienhard, Matthias and Thedinga, Kristina and Herwig, Ralf and Scheffer, Tobias}, title = {Pre-Training on In Vitro and Fine-Tuning on Patient-Derived Data Improves Deep Neural Networks for Anti-Cancer Drug-Sensitivity Prediction}, series = {MDPI}, volume = {14}, journal = {MDPI}, edition = {16}, publisher = {MDPI}, address = {Basel, Schweiz}, issn = {2072-6694}, doi = {10.3390/cancers14163950}, pages = {1 -- 14}, year = {2022}, abstract = {Large-scale databases that report the inhibitory capacities of many combinations of candidate drug compounds and cultivated cancer cell lines have driven the development of preclinical drug-sensitivity models based on machine learning. However, cultivated cell lines have devolved from human cancer cells over years or even decades under selective pressure in culture conditions. Moreover, models that have been trained on in vitro data cannot account for interactions with other types of cells. Drug-response data that are based on patient-derived cell cultures, xenografts, and organoids, on the other hand, are not available in the quantities that are needed to train high-capacity machine-learning models. We found that pre-training deep neural network models of drug sensitivity on in vitro drug-sensitivity databases before fine-tuning the model parameters on patient-derived data improves the models' accuracy and improves the biological plausibility of the features, compared to training only on patient-derived data. From our experiments, we can conclude that pre-trained models outperform models that have been trained on the target domains in the vast majority of cases.}, language = {en} } @article{OmaneHoehle2020, author = {Omane, Paul Okyere and H{\"o}hle, Barbara}, title = {Acquiring syntactic variability}, series = {Frontiers in communication}, volume = {2021}, journal = {Frontiers in communication}, publisher = {Frontiers Media}, address = {Lausanne, Schweiz}, issn = {2297-900X}, doi = {10.3389/fcomm.2021.604951}, pages = {15}, year = {2020}, abstract = {This paper investigates the predictions of the Derivational Complexity Hypothesis by studying the acquisition of wh-questions in 4- and 5-year-old Akan-speaking children in an experimental approach using an elicited production and an elicited imitation task. Akan has two types of wh-question structures (wh-in-situ and wh-ex-situ questions), which allows an investigation of children's acquisition of these two question structures and their preferences for one or the other. Our results show that adults prefer to use wh-ex-situ questions over wh-in-situ questions. The results from the children show that both age groups have the two question structures in their linguistic repertoire. However, they differ in their preferences in usage in the elicited production task: while the 5-year-olds preferred the wh-in-situ structure over the wh-ex-situ structure, the 4-year-olds showed a selective preference for the wh-in-situ structure in who-questions. These findings suggest a developmental change in wh-question preferences in Akan-learning children between 4 and 5 years of age with a so far unobserved u-shaped developmental pattern. In the elicited imitation task, all groups showed a strong tendency to maintain the structure of in-situ and ex-situ questions in repeating grammatical questions. When repairing ungrammatical ex-situ questions, structural changes to grammatical in-situ questions were hardly observed but the insertion of missing morphemes while keeping the ex-situ structure. Together, our findings provide only partial support for the Derivational Complexity Hypothesis.}, language = {en} } @phdthesis{Mueller2008, author = {M{\"u}ller, Melanie J. I.}, title = {Bidirectional transport by molecular motors}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-18715}, school = {Universit{\"a}t Potsdam}, year = {2008}, abstract = {In biological cells, the long-range intracellular traffic is powered by molecular motors which transport various cargos along microtubule filaments. The microtubules possess an intrinsic direction, having a 'plus' and a 'minus' end. Some molecular motors such as cytoplasmic dynein walk to the minus end, while others such as conventional kinesin walk to the plus end. Cells typically have an isopolar microtubule network. This is most pronounced in neuronal axons or fungal hyphae. In these long and thin tubular protrusions, the microtubules are arranged parallel to the tube axis with the minus ends pointing to the cell body and the plus ends pointing to the tip. In such a tubular compartment, transport by only one motor type leads to 'motor traffic jams'. Kinesin-driven cargos accumulate at the tip, while dynein-driven cargos accumulate near the cell body. We identify the relevant length scales and characterize the jamming behaviour in these tube geometries by using both Monte Carlo simulations and analytical calculations. A possible solution to this jamming problem is to transport cargos with a team of plus and a team of minus motors simultaneously, so that they can travel bidirectionally, as observed in cells. The presumably simplest mechanism for such bidirectional transport is provided by a 'tug-of-war' between the two motor teams which is governed by mechanical motor interactions only. We develop a stochastic tug-of-war model and study it with numerical and analytical calculations. We find a surprisingly complex cooperative motility behaviour. We compare our results to the available experimental data, which we reproduce qualitatively and quantitatively.}, language = {en} } @article{RoseGroegerHoelzle2021, author = {Rose, Robert and Groeger, Lars and H{\"o}lzle, Katharina}, title = {The Emergence of Shared Leadership in Innovation Labs}, series = {Frontiers in Psychology}, volume = {12}, journal = {Frontiers in Psychology}, publisher = {Frontiers in psychology}, address = {Lausanne, Schweiz}, issn = {1664-1078}, doi = {10.3389/fpsyg.2021.685167}, pages = {1 -- 13}, year = {2021}, abstract = {Implementing innovation laboratories to leverage intrapreneurship are an increasingly popular organizational practice. A typical feature in these creative environments are semi-autonomous teams in which multiple members collectively exert leadership influence, thereby challenging traditional command-and-control conceptions of leadership. An extensive body of research on the team-centric concept of shared leadership has recognized the potential for pluralized leadership structures in enhancing team effectiveness; however, little empirical work has been conducted in organizational contexts in which creativity is key. This study set out to explore antecedents of shared leadership and its influence on team creativity in an innovation lab. Building on extant shared leadership and innovation research, we propose antecedents customary to creative teamwork, that is, experimental culture, task reflexivity, and voice. Multisource data were collected from 104 team members and 49 evaluations of 29 coaches nested in 21 teams working in a prototypical innovation lab. We identify factors specific to creative teamwork that facilitate the emergence of shared leadership by providing room for experimentation, encouraging team members to speak up in the creative process, and cultivating a reflective application of entrepreneurial thinking. We provide specific exemplary activities for innovation lab teams to increase levels of shared leadership.}, language = {en} } @article{DordevicHoelzerRussoetal.2022, author = {Dordevic, Milos and H{\"o}lzer, Sonja and Russo, Augusta and Garc{\´i}a Alanis, Jos{\´e} Carlos and M{\"u}ller, Notger Germar}, title = {The Role of the Precuneus in Human Spatial Updating in a Real Environment Setting—A cTBS Study}, series = {Life}, volume = {12}, journal = {Life}, edition = {8}, publisher = {MDPI}, address = {Basel, Schweiz}, issn = {2075-1729}, doi = {10.3390/life12081239}, pages = {1 -- 13}, year = {2022}, abstract = {As we move through an environment, we update positions of our body relative to other objects, even when some objects temporarily or permanently leave our field of view—this ability is termed egocentric spatial updating and plays an important role in everyday life. Still, our knowledge about its representation in the brain is still scarce, with previous studies using virtual movements in virtual environments or patients with brain lesions suggesting that the precuneus might play an important role. However, whether this assumption is also true when healthy humans move in real environments where full body-based cues are available in addition to the visual cues typically used in many VR studies is unclear. Therefore, in this study we investigated the role of the precuneus in egocentric spatial updating in a real environment setting in 20 healthy young participants who underwent two conditions in a cross-over design: (a) stimulation, achieved through applying continuous theta-burst stimulation (cTBS) to inhibit the precuneus and (b) sham condition (activated coil turned upside down). In both conditions, participants had to walk back with blindfolded eyes to objects they had previously memorized while walking with open eyes. Simplified trials (without spatial updating) were used as control condition, to make sure the participants were not affected by factors such as walking blindfolded, vestibular or working memory deficits. A significant interaction was found, with participants performing better in the sham condition compared to real stimulation, showing smaller errors both in distance and angle. The results of our study reveal evidence of an important role of the precuneus in a real-environment egocentric spatial updating; studies on larger samples are necessary to confirm and further investigate this finding.}, language = {en} } @article{WestphalKalinowskiHoferichteretal.2022, author = {Westphal, Andrea and Kalinowski, Eva and Hoferichter, Clara Josepha and Vock, Miriam}, title = {K-12 teachers' stress and burnout during the COVID-19 pandemic: A systematic review}, series = {Frontiers in Psychology}, journal = {Frontiers in Psychology}, publisher = {Frontiers}, address = {Lausanne, Schweiz}, issn = {1664-1078}, doi = {10.3389/fpsyg.2022.920326}, pages = {1 -- 29}, year = {2022}, abstract = {We present the first systematic literature review on stress and burnout in K-12 teachers during the COVID-19 pandemic. Based on a systematic literature search, we identified 17 studies that included 9,874 K-12 teachers from around the world. These studies showed some indication that burnout did increase during the COVID-19 pandemic. There were, however, almost no differences in the levels of stress and burnout experienced by K-12 teachers compared to individuals employed in other occupational fields. School principals' leadership styles emerged as an organizational characteristic that is highly relevant for K-12 teachers' levels of stress and burnout. Individual teacher characteristics associated with burnout were K-12 teachers' personality, self-efficacy in online teaching, and perceived vulnerability to COVID-19. In order to reduce stress, there was an indication that stress-management training in combination with training in technology use for teaching may be superior to stress-management training alone. Future research needs to adopt more longitudinal designs and examine the interplay between individual and organizational characteristics in the development of teacher stress and burnout during the COVID-19 pandemic and beyond.}, language = {en} } @article{SpikesRodriguezSilvaBennettetal.2021, author = {Spikes, Montrai and Rodr{\´i}guez-Silva, Rodet and Bennett, Kerri-Ann and Br{\"a}ger, Stefan and Josaphat, James and Torres-Pineda, Patricia and Ernst, Anja and Havenstein, Katja and Schlupp, Ingo and Tiedemann, Ralph}, title = {A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario}, series = {BMC Research Notes}, volume = {14}, journal = {BMC Research Notes}, publisher = {BMC Research Notes / Biomed Central}, address = {London}, issn = {1756-0500}, doi = {10.1186/s13104-021-05843-x}, pages = {1 -- 8}, year = {2021}, abstract = {Objective The Caribbean is an important global biodiversity hotspot. Adaptive radiations there lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. A prime example are freshwater fish of the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Mirago{\^a}ne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Mirago{\^a}ne, relative to their congeners throughout the Caribbean. Results For 12 Limia species, we obtained almost complete sequences of the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships. We included sequences of six further Limia species from GenBank (total N  = 18 species). Our phylogenies are in concordance with other published phylogenies of Limia. There is strong support that the species found in Lake Mirago{\^a}ne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Mirago{\^a}ne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies using multiple unlinked genetic markers are needed to disentangle the relationships within the Lake Mirago{\^a}ne clade.}, language = {en} } @article{KruegerFoersterTrauthetal.2021, author = {Kr{\"u}ger, Johanna and Foerster, Verena Elisabeth and Trauth, Martin H. and Hofreiter, Michael and Tiedemann, Ralph}, title = {Exploring the Past Biosphere of Chew Bahir/Southern Ethiopia: Cross-Species Hybridization Capture of Ancient Sedimentary DNA from a Deep Drill Core}, series = {Frontiers in Earth Science}, journal = {Frontiers in Earth Science}, publisher = {Frontiers in Earth Science}, address = {Lausanne, Schweiz}, issn = {2296-6463}, doi = {10.3389/feart.2021.683010}, pages = {1 -- 20}, year = {2021}, abstract = {Eastern Africa has been a prime target for scientific drilling because it is rich in key paleoanthropological sites as well as in paleolakes, containing valuable paleoclimatic information on evolutionary time scales. The Hominin Sites and Paleolakes Drilling Project (HSPDP) explores these paleolakes with the aim of reconstructing environmental conditions around critical episodes of hominin evolution. Identification of biological taxa based on their sedimentary ancient DNA (sedaDNA) traces can contribute to understand past ecological and climatological conditions of the living environment of our ancestors. However, sedaDNA recovery from tropical environments is challenging because high temperatures, UV irradiation, and desiccation result in highly degraded DNA. Consequently, most of the DNA fragments in tropical sediments are too short for PCR amplification. We analyzed sedaDNA in the upper 70 m of the composite sediment core of the HSPDP drill site at Chew Bahir for eukaryotic remnants. We first tested shotgun high throughput sequencing which leads to metagenomes dominated by bacterial DNA of the deep biosphere, while only a small fraction was derived from eukaryotic, and thus probably ancient, DNA. Subsequently, we performed cross-species hybridization capture of sedaDNA to enrich ancient DNA (aDNA) from eukaryotic remnants for paleoenvironmental analysis, using established barcoding genes (cox1 and rbcL for animals and plants, respectively) from 199 species that may have had relatives in the past biosphere at Chew Bahir. Metagenomes yielded after hybridization capture are richer in reads with similarity to cox1 and rbcL in comparison to metagenomes without prior hybridization capture. Taxonomic assignments of the reads from these hybridization capture metagenomes also yielded larger fractions of the eukaryotic domain. For reads assigned to cox1, inferred wet periods were associated with high inferred relative abundances of putative limnic organisms (gastropods, green algae), while inferred dry periods showed increased relative abundances for insects. These findings indicate that cross-species hybridization capture can be an effective approach to enhance the information content of sedaDNA in order to explore biosphere changes associated with past environmental conditions, enabling such analyses even under tropical conditions.}, language = {en} } @phdthesis{Lenz2016, author = {Lenz, Josefine}, title = {Thermokarst dynamics in central-eastern Beringia}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-101364}, school = {Universit{\"a}t Potsdam}, pages = {XII, 128, A-47}, year = {2016}, abstract = {Widespread landscape changes are presently observed in the Arctic and are most likely to accelerate in the future, in particular in permafrost regions which are sensitive to climate warming. To assess current and future developments, it is crucial to understand past environmental dynamics in these landscapes. Causes and interactions of environmental variability can hardly be resolved by instrumental records covering modern time scales. However, long-term environmental variability is recorded in paleoenvironmental archives. Lake sediments are important archives that allow reconstruction of local limnogeological processes as well as past environmental changes driven directly or indirectly by climate dynamics. This study aims at reconstructing Late Quaternary permafrost and thermokarst dynamics in central-eastern Beringia, the terrestrial land mass connecting Eurasia and North America during glacial sea-level low stands. In order to investigate development, processes and influence of thermokarst dynamics, several sediment cores from extant lakes and drained lake basins were analyzed to answer the following research questions: 1. When did permafrost degradation and thermokarst lake development take place and what were enhancing and inhibiting environmental factors? 2. What are the dominant processes during thermokarst lake development and how are they reflected in proxy records? 3. How did, and still do, thermokarst dynamics contribute to the inventory and properties of organic matter in sediments and the carbon cycle? Methods applied in this study are based upon a multi-proxy approach combining sedimentological, geochemical, geochronological, and micropaleontological analyses, as well as analyses of stable isotopes and hydrochemistry of pore-water and ice. Modern field observations of water quality and basin morphometrics complete the environmental investigations. The investigated sediment cores reveal permafrost degradation and thermokarst dynamics on different time scales. The analysis of a sediment core from GG basin on the northern Seward Peninsula (Alaska) shows prevalent terrestrial accumulation of yedoma throughout the Early to Mid Wisconsin with intermediate wet conditions at around 44.5 to 41.5 ka BP. This first wetland development was terminated by the accumulation of a 1-meter-thick airfall tephra most likely originating from the South Killeak Maar eruption at 42 ka BP. A depositional hiatus between 22.5 and 0.23 ka BP may indicate thermokarst lake formation in the surrounding of the site which forms a yedoma upland till today. The thermokarst lake forming GG basin initiated 230 ± 30 cal a BP and drained in Spring 2005 AD. Four years after drainage the lake talik was still unfrozen below 268 cm depth. A permafrost core from Mama Rhonda basin on the northern Seward Peninsula preserved a full lacustrine record including several lake phases. The first lake generation developed at 11.8 cal ka BP during the Lateglacial-Early Holocene transition; its old basin (Grandma Rhonda) is still partially preserved at the southern margin of the study basin. Around 9.0 cal ka BP a shallow and more dynamic thermokarst lake developed with actively eroding shorelines and potentially intermediate shallow water or wetland phases (Mama Rhonda). Mama Rhonda lake drainage at 1.1 cal ka BP was followed by gradual accumulation of terrestrial peat and top-down refreezing of the lake talik. A significant lower organic carbon content was measured in Grandma Rhonda deposits (mean TOC of 2.5 wt\%) than in Mama Rhonda deposits (mean TOC of 7.9 wt\%) highlighting the impact of thermokarst dynamics on biogeochemical cycling in different lake generations by thawing and mobilization of organic carbon into the lake system. Proximal and distal sediment cores from Peatball Lake on the Arctic Coastal Plain of Alaska revealed young thermokarst dynamics since about 1,400 years along a depositional gradient based on reconstructions from shoreline expansion rates and absolute dating results. After its initiation as a remnant pond of a previous drained lake basin, a rapidly deepening lake with increasing oxygenation of the water column is evident from laminated sediments, and higher Fe/Ti and Fe/S ratios in the sediment. The sediment record archived characterizing shifts in depositional regimes and sediment sources from upland deposits and re-deposited sediments from drained thaw lake basins depending on the gradually changing shoreline configuration. These changes are evident from alternating organic inputs into the lake system which highlights the potential for thermokarst lakes to recycle old carbon from degrading permafrost deposits of its catchment. The lake sediment record from Herschel Island in the Yukon (Canada) covers the full Holocene period. After its initiation as a thermokarst lake at 11.7 cal ka BP and intense thermokarst activity until 10.0 cal ka BP, the steady sedimentation was interrupted by a depositional hiatus at 1.6 cal ka BP which likely resulted from lake drainage or allochthonous slumping due to collapsing shore lines. The specific setting of the lake on a push moraine composed of marine deposits is reflected in the sedimentary record. Freshening of the maturing lake is indicated by decreasing electrical conductivity in pore-water. Alternation of marine to freshwater ostracods and foraminifera confirms decreasing salinity as well but also reflects episodical re-deposition of allochthonous marine sediments. Based on permafrost and lacustrine sediment records, this thesis shows examples of the Late Quaternary evolution of typical Arctic permafrost landscapes in central-eastern Beringia and the complex interaction of local disturbance processes, regional environmental dynamics and global climate patterns. This study confirms that thermokarst lakes are important agents of organic matter recycling in complex and continuously changing landscapes.}, language = {en} } @book{SmirnovReijersNugterenetal.2010, author = {Smirnov, Sergey and Reijers, Hajo A. and Nugteren, Thijs and Weske, Mathias}, title = {Business process model abstraction : theory and practice}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-86956-054-0}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-41782}, publisher = {Universit{\"a}t Potsdam}, pages = {17}, year = {2010}, abstract = {Business process management aims at capturing, understanding, and improving work in organizations. The central artifacts are process models, which serve different purposes. Detailed process models are used to analyze concrete working procedures, while high-level models show, for instance, handovers between departments. To provide different views on process models, business process model abstraction has emerged. While several approaches have been proposed, a number of abstraction use case that are both relevant for industry and scientifically challenging are yet to be addressed. In this paper we systematically develop, classify, and consolidate different use cases for business process model abstraction. The reported work is based on a study with BPM users in the health insurance sector and validated with a BPM consultancy company and a large BPM vendor. The identified fifteen abstraction use cases reflect the industry demand. The related work on business process model abstraction is evaluated against the use cases, which leads to a research agenda.}, language = {en} } @phdthesis{Loeffler2005, author = {L{\"o}ffler, Frank}, title = {Numerical simulations of neutron star - black hole mergers}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7743}, school = {Universit{\"a}t Potsdam}, year = {2005}, abstract = {Collisions of black holes and neutron stars, named mixed binaries in the following, are interesting because of at least two reasons. Firstly, it is expected that they emit a large amount of energy as gravitational waves, which could be measured by new detectors. The form of those waves is expected to carry information about the internal structure of such systems. Secondly, collisions of such objects are the prime suspects of short gamma ray bursts. The exact mechanism for the energy emission is unknown so far. In the past, Newtonian theory of gravitation and modifications to it were often used for numerical simulations of collisions of mixed binary systems. However, near to such objects, the gravitational forces are so strong, that the use of General Relativity is necessary for accurate predictions. There are a lot of problems in general relativistic simulations. However, systems of two neutron stars and systems of two black holes have been studies extensively in the past and a lot of those problems have been solved. One of the remaining problems so far has been the use of hydrodynamic on excision boundaries. Inside excision regions, no evolution is carried out. Such regions are often used inside black holes to circumvent instabilities of the numerical methods near the singularity. Methods to handle hydrodynamics at such boundaries have been described and tests are shown in this work. One important test and the first application of those methods has been the simulation of a collapsing neutron star to a black hole. The success of these simulations and in particular the performance of the excision methods was an important step towards simulations of mixed binaries. Initial data are necessary for every numerical simulation. However, the creation of such initial data for general relativistic situations is in general very complicated. In this work it is shown how to obtain initial data for mixed binary systems using an already existing method for initial data of two black holes. These initial data have been used for evolutions of such systems and problems encountered are discussed in this work. One of the problems are instabilities due to different methods, which could be solved by dissipation of appropriate strength. Another problem is the expected drift of the black hole towards the neutron star. It is shown, that this can be solved by using special gauge conditions, which prevent the black hole from moving on the computational grid. The methods and simulations shown in this work are only the starting step for a much more detailed study of mixed binary system. Better methods, models and simulations with higher resolution and even better gauge conditions will be focus of future work. It is expected that such detailed studies can give information about the emitted gravitational waves, which is important in view of the newly built gravitational wave detectors. In addition, these simulations could give insight into the processes responsible for short gamma ray bursts.}, subject = {Relativistische Astrophysik}, language = {en} } @phdthesis{Schauer2006, author = {Schauer, Nicolas}, title = {Quantitative trait loci (QTL) for metabolite accumulation and metabolic regulation : metabolite profiling of interspecific crosses of tomato}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7643}, school = {Universit{\"a}t Potsdam}, year = {2006}, abstract = {The advent of large-scale and high-throughput technologies has recently caused a shift in focus in contemporary biology from decades of reductionism towards a more systemic view. Alongside the availability of genome sequences the exploration of organisms utilizing such approach should give rise to a more comprehensive understanding of complex systems. Domestication and intensive breeding of crop plants has led to a parallel narrowing of their genetic basis. The potential to improve crops by conventional breeding using elite cultivars is therefore rather limited and molecular technologies, such as marker assisted selection (MAS) are currently being exploited to re-introduce allelic variance from wild species. Molecular breeding strategies have mostly focused on the introduction of yield or resistance related traits to date. However given that medical research has highlighted the importance of crop compositional quality in the human diet this research field is rapidly becoming more important. Chemical composition of biological tissues can be efficiently assessed by metabolite profiling techniques, which allow the multivariate detection of metabolites of a given biological sample. Here, a GC/MS metabolite profiling approach has been applied to investigate natural variation of tomatoes with respect to the chemical composition of their fruits. The establishment of a mass spectral and retention index (MSRI) library was a prerequisite for this work in order to establish a framework for the identification of metabolites from a complex mixture. As mass spectral and retention index information is highly important for the metabolomics community this library was made publicly available. Metabolite profiling of tomato wild species revealed large differences in the chemical composition, especially of amino and organic acids, as well as on the sugar composition and secondary metabolites. Intriguingly, the analysis of a set of S. pennellii introgression lines (IL) identified 889 quantitative trait loci of compositional quality and 326 yield-associated traits. These traits are characterized by increases/decreases not only of single metabolites but also of entire metabolic pathways, thus highlighting the potential of this approach in uncovering novel aspects of metabolic regulation. Finally the biosynthetic pathway of the phenylalanine-derived fruit volatiles phenylethanol and phenylacetaldehyde was elucidated via a combination of metabolic profiling of natural variation, stable isotope tracer experiments and reverse genetic experimentation.}, subject = {Tomate}, language = {en} } @unpublished{RoellyFradon2006, author = {Roelly, Sylvie and Fradon, Myriam}, title = {Infinite system of Brownian balls : equilibrium measures are canonical Gibbs}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-6720}, year = {2006}, abstract = {We consider a system of infinitely many hard balls in Rd undergoing Brownian motions and submitted to a smooth pair potential. It is modelized by an infinite-dimensional stochastic differential equation with a local time term. We prove that the set of all equilibrium measures, solution of a detailed balance equation, coincides with the set of canonical Gibbs measures associated to the hard core potential added to the smooth interaction potential.}, language = {en} } @book{OPUS4-721, title = {Interdisciplinary studies on information structure : ISIS ; working papers of the SFB 632. - Vol. 1}, editor = {Ishihara, Shinichiro and Schmitz, Michaela and Schwarz, Anne}, issn = {1866-4725}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-8237}, publisher = {Universit{\"a}t Potsdam}, year = {2004}, abstract = {Contents: A1: Phonology and syntax of focussing and topicalisation: Gisbert Fanselow: Cyclic Phonology-Syntax-Interaction: Movement to First Position in German Caroline F{\´e}ry and Laura Herbst: German Sentence Accent Revisited Shinichiro Ishihara: Prosody by Phase: Evidence from Focus Intonation-Wh-scope Correspondence in Japanese A2: Quantification and information structure: Cornelia Endriss and Stefan Hinterwimmer: The Influence of Tense in Adverbial Quantification A3: Rhetorical Structure in Spoken Language: Modeling of Global Prosodic Parameters: Ekaterina Jasinskaja, J{\"o}rg Mayer and David Schlangen: Discourse Structure and Information Structure: Interfaces and Prosodic Realization B2: Focussing in African Tchadic languages: Katharina Hartmann and Malte Zimmermann: Focus Strategies in Chadic: The Case of Tangale Revisited D1: Linguistic database for information structure: Annotation and retrieval: Stefanie Dipper, Michael G{\"o}tze, Manfred Stede and Tillmann Wegst: ANNIS: A Linguistic Database for Exploring Information Structure}, language = {en} } @book{OPUS4-723, title = {Heterogeneity in focus : creating and using linguistic databases}, editor = {Dipper, Stefanie and G{\"o}tze, Michael and Stede, Manfred}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-937786-48-3}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-8244}, publisher = {Universit{\"a}t Potsdam}, pages = {145}, year = {2005}, abstract = {The papers in this volume were presented at the workshop Heterogeneity in Linguistic Databases', which took place on July 9, 2004 at the University of Potsdam. The workshop was organized by project D1: Linguistic Database for Information Structure: Annotation and Retrieval', a member project of the SFB 632, a collaborative research center entitled Information Structure: the Linguistic Means for Structuring Utterances, Sentences and Texts'. The workshop brought together both developers and users of linguistic databases from a number of research projects which work on an empirical basis, all of which have to cope with different sorts of heterogeneity: primary linguistic data and annotated information may be heterogeneous, as well as the data structures representing them. The first four papers (by Wagner, Schmidt, L{\"u}deling, and Witt) address aspects of heterogeneous data from the point of view of database developers; the remaining three papers (by Meyer, Smith, and Teich/Fankhauser) focus on data exploitation by the users.}, language = {en} } @phdthesis{Andersen2005, author = {Andersen, Audr{\´e}e}, title = {Surfactant dynamics at interfaces : a series of second harmonic generation experiments}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-6553}, school = {Universit{\"a}t Potsdam}, year = {2005}, abstract = {Adsorption layers of soluble surfactants enable and govern a variety of phenomena in surface and colloidal sciences, such as foams. The ability of a surfactant solution to form wet foam lamellae is governed by the surface dilatational rheology. Only systems having a non-vanishing imaginary part in their surface dilatational modulus, E, are able to form wet foams. The aim of this thesis is to illuminate the dissipative processes that give rise to the imaginary part of the modulus. There are two controversial models discussed in the literature. The reorientation model assumes that the surfactants adsorb in two distinct states, differing in their orientation. This model is able to describe the frequency dependence of the modulus E. However, it assumes reorientation dynamics in the millisecond time regime. In order to assess this model, we designed a SHG pump-probe experiment that addresses the orientation dynamics. Results obtained reveal that the orientation dynamics occur in the picosecond time regime, being in strong contradiction with the two states model. The second model regards the interface as an interphase. The adsorption layer consists of a topmost monolayer and an adjacent sublayer. The dissipative process is due to the molecular exchange between both layers. The assessment of this model required the design of an experiment that discriminates between the surface compositional term and the sublayer contribution. Such an experiment has been successfully designed and results on elastic and viscoelastic surfactant provided evidence for the correctness of the model. Because of its inherent surface specificity, surface SHG is a powerful analytical tool that can be used to gain information on molecular dynamics and reorganization of soluble surfactants. They are central elements of both experiments. However, they impose several structural elements of the model system. During the course of this thesis, a proper model system has been identified and characterized. The combination of several linear and nonlinear optical techniques, allowed for a detailed picture of the interfacial architecture of these surfactants.}, subject = {Tensid}, language = {en} } @book{GabbertWeikard1998, author = {Gabbert, Silke and Weikard, Hans-Peter}, title = {Food deficits, food security and food aid : concepts and measurement}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-8589}, publisher = {Universit{\"a}t Potsdam}, year = {1998}, abstract = {The concepts of food deficit, hunger, undernourishment and food security are discussed. Axioms and indices for the assessment of nutrition of individuals and groups are suggested. Furthermore a measure for food aid donor performance is developed and applied to a sample of bilateral and multilateral donors providing food aid for African countries.}, language = {en} } @book{Hans2004, author = {Hans, Silke}, title = {Migrants in Germany, Sweden and the United Kingdom}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-11248}, publisher = {Universit{\"a}t Potsdam}, year = {2004}, abstract = {Contents: 1. Introduction 2. Migration and Assimilation - Theoretical Approaches 2.1 Meaning and Definition of the Terms Migration and Migrant 2.2 Milton M. Gordon - Sub Processes of Assimilation 2.3 Hartmut Esser - Acculturation, Integration, and Assimilation 2.4 The Concept of Integration and Assimilation 2.5 Straight-line Assimilation and its Implications 2.6 Segmented Assimilation and its Implications 3. Social Inequality and Welfare - Theoretical Approaches 3.1 Dimensions of Inequality 3.2 Welfare Regimes and Social Inequality 3.3 Migration, Assimilation and Inequality 4. Research Design 4.1 Research Question and General Proceeding 4.2 Sample and Data Base 4.3 Operationalisation and Indicators 5. Migration, Welfare and Inequality in Three European Countries 6. Empirical Results 6.1 Performance of Migrants Compared With Natives 6.2 Different Trajectories of Assimilation 6.3 Trajectories of Segmented Assimilation and their Determinants 6.4 Policies, Attitudes and Assimilation - An Aggregate Analysis 6.5 Summary - What Determines the Performance of Migrants? 7. Discussion of Empirical Results in Terms of Theoretical Approaches 7.1 The Situation of Migrants in Three European Countries 7.2 Assessment of the Trajectories of Assimilation 8. Conclusion - Future Prospects of Migration in Europe}, language = {en} } @phdthesis{Hoffmann2007, author = {Hoffmann, Toni}, title = {Cloning and characterisation of the HMA3 gene and its promoter from Arabidopsis halleri (L.) O'Kane and Al'Shehbaz and Arabidopsis thaliana (L.) Heynhold}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-15259}, school = {Universit{\"a}t Potsdam}, year = {2007}, abstract = {Being living systems unable to adjust their location to changing environmental conditions, plants display homeostatic networks that have evolved to maintain transition metal levels in a very narrow concentration range in order to avoid either deficiency or toxicity. Hence, plants possess a broad repertoire of mechanisms for the cellular uptake, compartmentation and efflux, as well as for the chelation of transition metal ions. A small number of plants are hypertolerant to one or a few specific transition metals. Some metal tolerant plants are also able to hyperaccumulate metal ions. The Brassicaceae family member Arabidopis halleri ssp. halleri (L.) O´KANE and AL´SHEHBAZ is a hyperaccumulator of zinc (Zn), and it is closely related to the non-hypertolerant and non-hyperaccumulating model plant Arabidopsis thaliana (L.) HEYNHOLD. The close relationship renders A. halleri a promising emerging model plant for the comparative investigation of the molecular mechanisms behind hypertolerance and hyperaccumulation. Among several potential candidate genes that are probably involved in mediating the zinc-hypertolerant and zinc-hyperaccumulating trait is AhHMA3. The AhHMA3 gene is highly similar to AtHMA3 (AGI number: At4g30120) in A. thaliana, and its encoded protein belongs to the P-type IB ATPase family of integral membrane transporter proteins that transport transition metals. In contrast to the low AtHMA3 transcript levels in A. thaliana, the gene was found to be constitutively highly expressed across different Zn treatments in A. halleri, especially in shoots. In this study, the cloning and characterisation of the HMA3 gene and its promoter from Arabidopsis halleri (L.) O´KANE and AL´SHEHBAZ and Arabidopsis thaliana (L.) HEYNHOLD is described. Heterologously expressed AhHMA3 mediated enhanced tolerance to Zn and to a much lesser degree to cadmium (Cd) but not to cobalt (Co) in metal-sensitive mutant strains of budding yeast. It is demonstrated that the genome of A. halleri contains at least four copies of AhHMA3, AhHMA3-1 to AhHMA3-4. A copy-specific real-time RT-PCR indicated that an AhHMA3-1 related gene copy is the source of the constitutively high transcript level in A. halleri and not a gene copy similar to AhHMA3-2 or AhHMA3-4. In accordance with the enhanced AtHMA3mRNA transcript level in A. thaliana roots, an AtHMA3 promoter-GUS gene construct mediated GUS activity predominantly in the vascular tissues of roots and not in shoots. However, the observed AhHMA3-1 and AhHMA3-2 promoter-mediated GUS activity in A. thaliana or A. halleri plants did not reflect the constitutively high expression of AhHMA3 in shoots of A. halleri. It is suggested that other factors e. g. characteristic sequence inserts within the first intron of AhHMA3-1 might enable a constitutively high expression. Moreover, the unknown promoter of the AhHMA3-3 gene copy could be the source of the constitutively high AhHMA3 transcript levels in A. halleri. In that case, the AhHMA3-3 sequence is predicted to be highly homologous to AhHMA3-1. The lack of solid localisation data for the AhHMA3 protein prevents a clear functional assignment. The provided data suggest several possible functions of the AhHMA3 protein: Like AtHMA2 and AtHMA4 it might be localised to the plasma membrane and could contribute to the efficient translocation of Zn from root to shoot and/or to the cell-to-cell distribution of Zn in the shoot. If localised to the vacuolar membrane, then a role in maintaining a low cytoplasmic zinc concentration by vacuolar zinc sequestration is possible. In addition, AhHMA3 might be involved in the delivery of zinc ions to trichomes and mesophyll leaf cells that are major zinc storage sites in A. halleri.}, language = {en} } @misc{Koechert2007, type = {Master Thesis}, author = {K{\"o}chert, Karl}, title = {Development of a method to assess EAAT1 transcription levels in Alzheimer's disease}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-15965}, school = {Universit{\"a}t Potsdam}, year = {2007}, abstract = {Zur Zeit leiden ca. 24 Millionen Menschen auf der ganzen Welt unter Demenz, Alzheimer macht dabei 50-60\% aller Demenzf{\"a}lle aus. Da der Anteil der Bev{\"o}lkerung, der an Demenz leidet, proportional zum Alter zunimmt und der Anteil {\"a}lterer Menschen in der Gesellschaft von Jahr zu Jahr steigt, wird Alzheimer immer mehr zu einem ernstzunehmenden, gesellschaftlichen Problem. Zum Stand der heutigen Forschung ist es etabliert, dass die Aminos{\"a}ure Glutamat - quantitativ einer der wichtigsten Neurotransmitter im Zentralen Nervensystem (ZNS) - toxische Konzentrationen erreichen kann wenn sie - im Zuge der {\"U}bertragung von Aktionspotentialen - nach ihrer Freisetzung nicht aus dem Synaptischen Spalt entfernt wird. Viele Studien haben gezeigt, dass in der Alzheimerschen Krankheit die Glutamataufnahme beeintr{\"a}chtigt ist, was zu toxischen Konzentrationen von Glutamat und dem daraus folgenden Absterben von Neuronen f{\"u}hrt. Der exitatorische Aminos{\"a}uretransporter 1 (EAAT1) geh{\"o}rt zu der Familie der Na+-abh{\"a}ngigen Glutamattransporter und stellt nach EAAT2 den quantitativ wichtigsten Glutamattransporter im ZNS dar. In diesem Projekt wurde eine bis dahin f{\"u}r den Menschen nicht bekannte EAAT1 Spleißvariante, in der Exon 3 ausgeschnitten wird, nachgewiesen. Diese Variante wurde EAAT1Δ3 genannt und stellt damit mit EAAT1Δ9 die zweite f{\"u}r EAAT1 nachgewiesene Spleißvariante dar. Eine auf real-time RT-PCR basierende Methode wurde entwickelt, um die Transkripte von EAAT1 wildtyp (EAAT1 wt), EAAT1Δ3 und EAAT1Δ9 zu quantifizieren. Proben aus verschiedenen Hirnarealen wurden aus einem Set von Kontrollen und Alzheimerf{\"a}llen bei der Quantifizierung verwendet. Die gew{\"a}hlten Areale sind von der Alzheimerschen Krankheit unterschiedlich stark betroffen. Dies diente als interne Kontrolle f{\"u}r die durchgef{\"u}hrten Experimente und erm{\"o}glichte so die Differenzierung zwischen beobachteten Effekten: Nur Effekte die alleinig in von Alzheimer betroffenen Gehirnarealen auftreten, k{\"o}nnen als spezifisch f{\"u}r die Krankheit angesehen werden. Die Resultate diese Projektes zeigen, dass EAAT1Δ3 in sehr geringer Anzahl transkribiert wird, die nur 0.15\% der EAAT1 wt Transkription entspricht. Dahingegen entspricht das EAAT1 Δ9 Transkript im Durchschnitt 26.6\% des EAAT1 wt Transkripts. Es wurde nachgewiesen, dass die Transkriptionsrate aller EAAT1 Varianten in Alzheimerf{\"a}llen signifikant reduziert ist (P<0.0001). Dies unterst{\"u}tzt die Theorie, dass bei Alzheimerf{\"a}llen die EAAT1 Proteinexpression stark reduziert und der Glutamattransport, der normalerweise durch diesen Transporter gew{\"a}hrleistet wird, stark eingeschr{\"a}nkt ist. Dies wiederum resultiert in toxisch hohen Glutamatkonzentrationen und damit dem Absterben von Neuronen. Die gefundene Reduktion der EAAT1Transkription ist nicht spezifisch f{\"u}r Gehirnareale die von Alzheimer betroffen sind, sondern tritt in selbem Maße in nicht von Alzheimer betroffenen Gehirnarealen auf. Daraus l{\"a}sst sich schließen, dass die Reduktion der EAAT1 Transkription eher ein Resultat eines in der Alzheimerschen Krankheit pr{\"a}senten, grundlegenden Krankheitsmechanismus ist als deren Ursache.}, language = {en} } @phdthesis{Imranulhaq2008, author = {Imran ul-haq, Muhammad}, title = {Synthesis of fluorinated polymers in supercritical carbon dioxide (scCO₂)}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-19868}, school = {Universit{\"a}t Potsdam}, year = {2008}, abstract = {For the first time stabilizer-free vinylidene fluoride (VDF) polymerizations were carried out in homogeneous phase with supercritical CO₂. Polymerizations were carried out at 140°C, 1500 bar and were initiated with di-tert-butyl peroxide (DTBP). In-line FT-NIR (Fourier Transform- Near Infrared) spectroscopy showed that complete monomer conversion may be obtained. Molecular weights were determined via size-exclusion chromatography (SEC) and polymer end group analysis by 1H-NMR spectroscopy. The number average molecular weights were below 104 g∙mol-1 and polydispersities ranged from 3.1 to 5.7 depending on DTBP and VDF concentration. To allow for isothermal reactions high CO₂ contents ranging from 61 to 83 wt.\% were used. The high-temperature, high-pressure conditions were required for homogeneous phase polymerization. These conditions did not alter the amount of defects in VDF chaining. Scanning electron microscopy (SEM) indicated that regular stack-type particles were obtained upon expansion of the homogeneous polymerization mixture. To reduce the required amount of initiator, further VDF polymerizations using chain transfer agents (CTAs) to control molecular weights were carried out in homogeneous phase with supercritical carbon dioxide (scCO₂) at 120 °C and 1500 bar. Using perfluorinated hexyl iodide as CTA, polymers of low polydispersity ranging from 1.5 to 1.2 at the highest iodide concentration of 0.25 mol·L-1 were obtained. Electrospray ionization- mass spectroscopy (ESI-MS) indicates the absence of initiator derived end groups, supporting livingness of the system. The "livingness" is based on the labile C-I bond. However, due to the weakness of the C-I bond perfluorinated hexyl iodide also contributes to initiation. To allow for kinetic analyses of VDF polymerizations the CTA should not contribute to initiation. Therefore, additional CTAs were applied: BrCCl3, C6F13Br and C6F13H. It was found that C6F13H does not contribute to initiation. At 120°C and 1500 bar kp/kt0.5~ 0.64 (L·mol-1·s-1)0.5 was derived. The chain transfer constant (CT) at 120°C has been determined to be 8·10-1, 9·10-2 and 2·10-4 for C6F13I, C6F13Br and C6F13H, respectively. These CT values are associated with the bond energy of the C-X bond. Moreover, the labile C-I bond allows for functionalization of the polymer to triazole end groups applying click reactions. After substitution of the iodide end group by an azide group 1,3 dipolar cycloadditions with alkynes yield polymers with 1,2,3 triazole end groups. Using symmetrical alkynes the reactions may be carried out in the absence of any catalyst. This end-functionalized poly (vinylidene fluoride) (PVDF) has higher thermal stability as compared to the normal PVDF. PVDF samples from homogeneous phase polymerizations in supercritical CO₂ and subsequent expansion to ambient conditions were analyzed with respect to polymer end groups, crystallinity, type of polymorphs and morphology. Upon expansion the polymer was obtained as white powder. Scanning electron microscopy (SEM) showed that DTBP derived polymer end groups led to stack-type particles whereas sponge- or rose-type particles were obtained in case of CTA fragments as end groups. Fourier-Transform Infrared spectroscopy and wide angle X-ray diffraction indicated that the type of polymorph, α or β crystal phase was significantly affected by the type of end group. The content of β-phase material, which is responsible for piezoelectricity of PVDF, is the highest for polymer with DTBP-derived end groups. In addition, the crystallinity of the material, as determined via differential scanning calorimetry is affected by the end groups and polymer molecular weights. For example, crystallinity ranges from around 26 \% for DTBP-derived end groups to a maximum of 62 \% for end groups originating from perfluorinated hexyl iodide for polymers with Mn ~2200 g·mol-1. Expansion of the homogeneous polymerization mixture results in particle formation by a non-optimized RESS (Rapid Expansion from Supercritical Solution) process. Thus, it was tested how polymer end groups affect the particles size distribution obtained from RESS process under controlled conditions (T = 50°C and P = 200 bar). In all RESS experiments, small primary PVDF with diameters less than 100 nm without the use of liquid solvents, surfactants, or other additives were produced. A strong correlation between particle size and particle size distribution with polymer end groups and molecular weight of the original material was observed. The smallest particles were found for RESS of PVDF with Mn~ 4000 g·mol-1 and PFHI (C6F13I) - derived end groups.}, language = {en} } @phdthesis{Miteva2007, author = {Miteva, Rositsa Stoycheva}, title = {Electron acceleration at localized wave structures in the solar corona}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-14775}, school = {Universit{\"a}t Potsdam}, year = {2007}, abstract = {Our dynamic Sun manifests its activity by different phenomena: from the 11-year cyclic sunspot pattern to the unpredictable and violent explosions in the case of solar flares. During flares, a huge amount of the stored magnetic energy is suddenly released and a substantial part of this energy is carried by the energetic electrons, considered to be the source of the nonthermal radio and X-ray radiation. One of the most important and still open question in solar physics is how the electrons are accelerated up to high energies within (the observed in the radio emission) short time scales. Because the acceleration site is extremely small in spatial extent as well (compared to the solar radius), the electron acceleration is regarded as a local process. The search for localized wave structures in the solar corona that are able to accelerate electrons together with the theoretical and numerical description of the conditions and requirements for this process, is the aim of the dissertation. Two models of electron acceleration in the solar corona are proposed in the dissertation: I. Electron acceleration due to the solar jet interaction with the background coronal plasma (the jet--plasma interaction) A jet is formed when the newly reconnected and highly curved magnetic field lines are relaxed by shooting plasma away from the reconnection site. Such jets, as observed in soft X-rays with the Yohkoh satellite, are spatially and temporally associated with beams of nonthermal electrons (in terms of the so-called type III metric radio bursts) propagating through the corona. A model that attempts to give an explanation for such observational facts is developed here. Initially, the interaction of such jets with the background plasma leads to an (ion-acoustic) instability associated with growing of electrostatic fluctuations in time for certain range of the jet initial velocity. During this process, any test electron that happen to feel this electrostatic wave field is drawn to co-move with the wave, gaining energy from it. When the jet speed has a value greater or lower than the one, required by the instability range, such wave excitation cannot be sustained and the process of electron energization (acceleration and/or heating) ceases. Hence, the electrons can propagate further in the corona and be detected as type III radio burst, for example. II. Electron acceleration due to attached whistler waves in the upstream region of coronal shocks (the electron--whistler--shock interaction) Coronal shocks are also able to accelerate electrons, as observed by the so-called type II metric radio bursts (the radio signature of a shock wave in the corona). From in-situ observations in space, e.g., at shocks related to co-rotating interaction regions, it is known that nonthermal electrons are produced preferably at shocks with attached whistler wave packets in their upstream regions. Motivated by these observations and assuming that the physical processes at shocks are the same in the corona as in the interplanetary medium, a new model of electron acceleration at coronal shocks is presented in the dissertation, where the electrons are accelerated by their interaction with such whistlers. The protons inflowing toward the shock are reflected there by nearly conserving their magnetic moment, so that they get a substantial velocity gain in the case of a quasi-perpendicular shock geometry, i.e, the angle between the shock normal and the upstream magnetic field is in the range 50--80 degrees. The so-accelerated protons are able to excite whistler waves in a certain frequency range in the upstream region. When these whistlers (comprising the localized wave structure in this case) are formed, only the incoming electrons are now able to interact resonantly with them. But only a part of these electrons fulfill the the electron--whistler wave resonance condition. Due to such resonant interaction (i.e., of these electrons with the whistlers), the electrons are accelerated in the electric and magnetic wave field within just several whistler periods. While gaining energy from the whistler wave field, the electrons reach the shock front and, subsequently, a major part of them are reflected back into the upstream region, since the shock accompanied with a jump of the magnetic field acts as a magnetic mirror. Co-moving with the whistlers now, the reflected electrons are out of resonance and hence can propagate undisturbed into the far upstream region, where they are detected in terms of type II metric radio bursts. In summary, the kinetic energy of protons is transfered into electrons by the action of localized wave structures in both cases, i.e., at jets outflowing from the magnetic reconnection site and at shock waves in the corona.}, language = {en} } @phdthesis{Kellermann2011, author = {Kellermann, Thorsten}, title = {Accurate numerical relativity simulations of non-vacuumspace-times in two dimensions and applications to critical collapse}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-59578}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {This Thesis puts its focus on the physics of neutron stars and its description with methods of numerical relativity. In the first step, a new numerical framework the Whisky2D code will be developed, which solves the relativistic equations of hydrodynamics in axisymmetry. Therefore we consider an improved formulation of the conserved form of these equations. The second part will use the new code to investigate the critical behaviour of two colliding neutron stars. Considering the analogy to phase transitions in statistical physics, we will investigate the evolution of the entropy of the neutron stars during the whole process. A better understanding of the evolution of thermodynamical quantities, like the entropy in critical process, should provide deeper understanding of thermodynamics in relativity. More specifically, we have written the Whisky2D code, which solves the general-relativistic hydrodynamics equations in a flux-conservative form and in cylindrical coordinates. This of course brings in 1/r singular terms, where r is the radial cylindrical coordinate, which must be dealt with appropriately. In the above-referenced works, the flux operator is expanded and the 1/r terms, not containing derivatives, are moved to the right-hand-side of the equation (the source term), so that the left hand side assumes a form identical to the one of the three-dimensional (3D) Cartesian formulation. We call this the standard formulation. Another possibility is not to split the flux operator and to redefine the conserved variables, via a multiplication by r. We call this the new formulation. The new equations are solved with the same methods as in the Cartesian case. From a mathematical point of view, one would not expect differences between the two ways of writing the differential operator, but, of course, a difference is present at the numerical level. Our tests show that the new formulation yields results with a global truncation error which is one or more orders of magnitude smaller than those of alternative and commonly used formulations. The second part of the Thesis uses the new code for investigations of critical phenomena in general relativity. In particular, we consider the head-on-collision of two neutron stars in a region of the parameter space where two final states a new stable neutron star or a black hole, lay close to each other. In 1993, Choptuik considered one-parameter families of solutions, S[P], of the Einstein-Klein-Gordon equations for a massless scalar field in spherical symmetry, such that for every P > P⋆, S[P] contains a black hole and for every P < P⋆, S[P] is a solution not containing singularities. He studied numerically the behavior of S[P] as P → P⋆ and found that the critical solution, S[P⋆], is universal, in the sense that it is approached by all nearly-critical solutions regardless of the particular family of initial data considered. All these phenomena have the common property that, as P approaches P⋆, S[P] approaches a universal solution S[P⋆] and that all the physical quantities of S[P] depend only on |P - P⋆|. The first study of critical phenomena concerning the head-on collision of NSs was carried out by Jin and Suen in 2007. In particular, they considered a series of families of equal-mass NSs, modeled with an ideal-gas EOS, boosted towards each other and varied the mass of the stars, their separation, velocity and the polytropic index in the EOS. In this way they could observe a critical phenomenon of type I near the threshold of black-hole formation, with the putative solution being a nonlinearly oscillating star. In a successive work, they performed similar simulations but considering the head-on collision of Gaussian distributions of matter. Also in this case they found the appearance of type-I critical behaviour, but also performed a perturbative analysis of the initial distributions of matter and of the merged object. Because of the considerable difference found in the eigenfrequencies in the two cases, they concluded that the critical solution does not represent a system near equilibrium and in particular not a perturbed Tolmann-Oppenheimer-Volkoff (TOV) solution. In this Thesis we study the dynamics of the head-on collision of two equal-mass NSs using a setup which is as similar as possible to the one considered above. While we confirm that the merged object exhibits a type-I critical behaviour, we also argue against the conclusion that the critical solution cannot be described in terms of equilibrium solution. Indeed, we show that, in analogy with what is found in, the critical solution is effectively a perturbed unstable solution of the TOV equations. Our analysis also considers fine-structure of the scaling relation of type-I critical phenomena and we show that it exhibits oscillations in a similar way to the one studied in the context of scalar-field critical collapse.}, language = {en} } @phdthesis{Berger2012, author = {Berger, Florian}, title = {Different modes of cooperative transport by molecular motors}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-60319}, school = {Universit{\"a}t Potsdam}, year = {2012}, abstract = {Cargo transport by molecular motors is ubiquitous in all eukaryotic cells and is typically driven cooperatively by several molecular motors, which may belong to one or several motor species like kinesin, dynein or myosin. These motor proteins transport cargos such as RNAs, protein complexes or organelles along filaments, from which they unbind after a finite run length. Understanding how these motors interact and how their movements are coordinated and regulated is a central and challenging problem in studies of intracellular transport. In this thesis, we describe a general theoretical framework for the analysis of such transport processes, which enables us to explain the behavior of intracellular cargos based on the transport properties of individual motors and their interactions. Motivated by recent in vitro experiments, we address two different modes of transport: unidirectional transport by two identical motors and cooperative transport by actively walking and passively diffusing motors. The case of cargo transport by two identical motors involves an elastic coupling between the motors that can reduce the motors' velocity and/or the binding time to the filament. We show that this elastic coupling leads, in general, to four distinct transport regimes. In addition to a weak coupling regime, kinesin and dynein motors are found to exhibit a strong coupling and an enhanced unbinding regime, whereas myosin motors are predicted to attain a reduced velocity regime. All of these regimes, which we derive both by analytical calculations and by general time scale arguments, can be explored experimentally by varying the elastic coupling strength. In addition, using the time scale arguments, we explain why previous studies came to different conclusions about the effect and relevance of motor-motor interference. In this way, our theory provides a general and unifying framework for understanding the dynamical behavior of two elastically coupled molecular motors. The second mode of transport studied in this thesis is cargo transport by actively pulling and passively diffusing motors. Although these passive motors do not participate in active transport, they strongly enhance the overall cargo run length. When an active motor unbinds, the cargo is still tethered to the filament by the passive motors, giving the unbound motor the chance to rebind and continue its active walk. We develop a stochastic description for such cooperative behavior and explicitly derive the enhanced run length for a cargo transported by one actively pulling and one passively diffusing motor. We generalize our description to the case of several pulling and diffusing motors and find an exponential increase of the run length with the number of involved motors.}, language = {en} } @phdthesis{Hoffmann2011, author = {Hoffmann, Anne}, title = {Comparative aerosol studies based on multi-wavelength Raman LIDAR at Ny-{\AA}lesund, Spitsbergen}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-52426}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {The Arctic is a particularly sensitive area with respect to climate change due to the high surface albedo of snow and ice and the extreme radiative conditions. Clouds and aerosols as parts of the Arctic atmosphere play an important role in the radiation budget, which is, as yet, poorly quantified and understood. The LIDAR (Light Detection And Ranging) measurements presented in this PhD thesis contribute with continuous altitude resolved aerosol profiles to the understanding of occurrence and characteristics of aerosol layers above Ny-{\AA}lesund, Spitsbergen. The attention was turned to the analysis of periods with high aerosol load. As the Arctic spring troposphere exhibits maximum aerosol optical depths (AODs) each year, March and April of both the years 2007 and 2009 were analyzed. Furthermore, stratospheric aerosol layers of volcanic origin were analyzed for several months, subsequently to the eruptions of the Kasatochi and Sarychev volcanoes in summer 2008 and 2009, respectively. The Koldewey Aerosol Raman LIDAR (KARL) is an instrument for the active remote sensing of atmospheric parameters using pulsed laser radiation. It is operated at the AWIPEV research base and was fundamentally upgraded within the framework of this PhD project. It is now equipped with a new telescope mirror and new detection optics, which facilitate atmospheric profiling from 450m above sea level up to the mid-stratosphere. KARL provides highly resolved profiles of the scattering characteristics of aerosol and cloud particles (backscattering, extinction and depolarization) as well as water vapor profiles within the lower troposphere. Combination of KARL data with data from other instruments on site, namely radiosondes, sun photometer, Micro Pulse LIDAR, and tethersonde system, resulted in a comprehensive data set of scattering phenomena in the Arctic atmosphere. The two spring periods March and April 2007 and 2009 were at first analyzed based on meteorological parameters, like local temperature and relative humidity profiles as well as large scale pressure patterns and air mass origin regions. Here, it was not possible to find a clear correlation between enhanced AOD and air mass origin. However, in a comparison of two cloud free periods in March 2007 and April 2009, large AOD values in 2009 coincided with air mass transport through the central Arctic. This suggests the occurrence of aerosol transformation processes during the aerosol transport to Ny-{\AA}lesund. Measurements on 4 April 2009 revealed maximum AOD values of up to 0.12 and aerosol size distributions changing with altitude. This and other performed case studies suggest the differentiation between three aerosol event types and their origin: Vertically limited aerosol layers in dry air, highly variable hygroscopic boundary layer aerosols and enhanced aerosol load across wide portions of the troposphere. For the spring period 2007, the available KARL data were statistically analyzed using a characterization scheme, which is based on optical characteristics of the scattering particles. The scheme was validated using several case studies. Volcanic eruptions in the northern hemisphere in August 2008 and June 2009 arose the opportunity to analyze volcanic aerosol layers within the stratosphere. The rate of stratospheric AOD change was similar within both years with maximum values above 0.1 about three to five weeks after the respective eruption. In both years, the stratospheric AOD persisted at higher rates than usual until the measurements were stopped in late September due to technical reasons. In 2008, up to three aerosol layers were detected, the layer structure in 2009 was characterized by up to six distinct and thin layers which smeared out to one broad layer after about two months. The lowermost aerosol layer was continuously detected at the tropopause altitude. Three case studies were performed, all revealed rather large indices of refraction of m = (1.53-1.55) - 0.02i, suggesting the presence of an absorbing carbonaceous component. The particle radius, derived with inversion calculations, was also similar in both years with values ranging from 0.16 to 0.19 μm. However, in 2009, a second mode in the size distribution was detected at about 0.5 μm. The long term measurements with the Koldewey Aerosol Raman LIDAR in Ny-{\AA}lesund provide the opportunity to study Arctic aerosols in the troposphere and the stratosphere not only in case studies but on longer time scales. In this PhD thesis, both, tropospheric aerosols in the Arctic spring and stratospheric aerosols following volcanic eruptions have been described qualitatively and quantitatively. Case studies and comparative studies with data of other instruments on site allowed for the analysis of microphysical aerosol characteristics and their temporal evolution.}, language = {en} } @phdthesis{Bierbaum2011, author = {Bierbaum, Veronika}, title = {Chemomechanical coupling and motor cycles of the molecular motor myosin V}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-53614}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {In the living cell, the organization of the complex internal structure relies to a large extent on molecular motors. Molecular motors are proteins that are able to convert chemical energy from the hydrolysis of adenosine triphosphate (ATP) into mechanical work. Being about 10 to 100 nanometers in size, the molecules act on a length scale, for which thermal collisions have a considerable impact onto their motion. In this way, they constitute paradigmatic examples of thermodynamic machines out of equilibrium. This study develops a theoretical description for the energy conversion by the molecular motor myosin V, using many different aspects of theoretical physics. Myosin V has been studied extensively in both bulk and single molecule experiments. Its stepping velocity has been characterized as a function of external control parameters such as nucleotide concentration and applied forces. In addition, numerous kinetic rates involved in the enzymatic reaction of the molecule have been determined. For forces that exceed the stall force of the motor, myosin V exhibits a 'ratcheting' behaviour: For loads in the direction of forward stepping, the velocity depends on the concentration of ATP, while for backward loads there is no such influence. Based on the chemical states of the motor, we construct a general network theory that incorporates experimental observations about the stepping behaviour of myosin V. The motor's motion is captured through the network description supplemented by a Markov process to describe the motor dynamics. This approach has the advantage of directly addressing the chemical kinetics of the molecule, and treating the mechanical and chemical processes on equal grounds. We utilize constraints arising from nonequilibrium thermodynamics to determine motor parameters and demonstrate that the motor behaviour is governed by several chemomechanical motor cycles. In addition, we investigate the functional dependence of stepping rates on force by deducing the motor's response to external loads via an appropriate Fokker-Planck equation. For substall forces, the dominant pathway of the motor network is profoundly different from the one for superstall forces, which leads to a stepping behaviour that is in agreement with the experimental observations. The extension of our analysis to Markov processes with absorbing boundaries allows for the calculation of the motor's dwell time distributions. These reveal aspects of the coordination of the motor's heads and contain direct information about the backsteps of the motor. Our theory provides a unified description for the myosin V motor as studied in single motor experiments.}, language = {en} } @phdthesis{Swierczynski2012, author = {Swierczynski, Tina}, title = {A 7000 yr runoff chronology from varved sediments of Lake Mondsee (Upper Austria)}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-66702}, school = {Universit{\"a}t Potsdam}, year = {2012}, abstract = {The potential increase in frequency and magnitude of extreme floods is currently discussed in terms of global warming and the intensification of the hydrological cycle. The profound knowledge of past natural variability of floods is of utmost importance in order to assess flood risk for the future. Since instrumental flood series cover only the last ~150 years, other approaches to reconstruct historical and pre-historical flood events are needed. Annually laminated (varved) lake sediments are meaningful natural geoarchives because they provide continuous records of environmental changes > 10000 years down to a seasonal resolution. Since lake basins additionally act as natural sediment traps, the riverine sediment supply, which is preserved as detrital event layers in the lake sediments, can be used as a proxy for extreme discharge events. Within my thesis I examined a ~ 8.50 m long sedimentary record from the pre-Alpine Lake Mondsee (Northeast European Alps), which covered the last 7000 years. This sediment record consists of calcite varves and intercalated detrital layers, which range in thickness from 0.05 to 32 mm. Detrital layer deposition was analysed by a combined method of microfacies analysis via thin sections, Scanning Electron Microscopy (SEM), μX-ray fluorescence (μXRF) scanning and magnetic susceptibility. This approach allows characterizing individual detrital event layers and assigning a corresponding input mechanism and catchment. Based on varve counting and controlled by 14C age dates, the main goals of this thesis are (i) to identify seasonal runoff processes, which lead to significant sediment supply from the catchment into the lake basin and (ii) to investigate flood frequency under changing climate boundary conditions. This thesis follows a line of different time slices, presenting an integrative approach linking instrumental and historical flood data from Lake Mondsee in order to evaluate the flood record inferred from Lake Mondsee sediments. The investigation of eleven short cores covering the last 100 years reveals the abundance of 12 detrital layers. Therein, two types of detrital layers are distinguished by grain size, geochemical composition and distribution pattern within the lake basin. Detrital layers, which are enriched in siliciclastic and dolomitic material, reveal sediment supply from the Flysch sediments and Northern Calcareous Alps into the lake basin. These layers are thicker in the northern lake basin (0.1-3.9 mm) and thinner in the southern lake basin (0.05-1.6 mm). Detrital layers, which are enriched in dolomitic components forming graded detrital layers (turbidites), indicate the provenance from the Northern Calcareous Alps. These layers are generally thicker (0.65-32 mm) and are solely recorded within the southern lake basin. In comparison with instrumental data, thicker graded layers result from local debris flow events in summer, whereas thin layers are deposited during regional flood events in spring/summer. Extreme summer floods as reported from flood layer deposition are principally caused by cyclonic activity from the Mediterranean Sea, e.g. July 1954, July 1997 and August 2002. During the last two millennia, Lake Mondsee sediments reveal two significant flood intervals with decadal-scale flood episodes, during the Dark Ages Cold Period (DACP) and the transition from the Medieval Climate Anomaly (MCA) into the Little Ice Age (LIA) suggesting a linkage of transition to climate cooling and summer flood recurrences in the Northeastern Alps. In contrast, intermediate or decreased flood episodes appeared during the MWP and the LIA. This indicates a non-straightforward relationship between temperature and flood recurrence, suggesting higher cyclonic activity during climate transition in the Northeast Alps. The 7000-year flood chronology reveals 47 debris flows and 269 floods, with increased flood activity shifting around 3500 and 1500 varve yr BP (varve yr BP = varve years before present, before present = AD 1950). This significant increase in flood activity shows a coincidence with millennial-scale climate cooling that is reported from main Alpine glacier advances and lower tree lines in the European Alps since about 3300 cal. yr BP (calibrated years before present). Despite relatively low flood occurrence prior to 1500 varve yr BP, floods at Lake Mondsee could have also influenced human life in early Neolithic lake dwellings (5750-4750 cal. yr BP). While the first lake dwellings were constructed on wetlands, the later lake dwellings were built on piles in the water suggesting an early flood risk adaptation of humans and/or a general change of the Late Neolithic Culture of lake-dwellers because of socio-economic reasons. However, a direct relationship between the final abandonment of the lake dwellings and higher flood frequencies is not evidenced.}, language = {en} } @misc{Gassner2012, type = {Master Thesis}, author = {Gassner, Alexandra Carina}, title = {The character of the core-mantle boundary : a systematic study using PcP}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-63590}, school = {Universit{\"a}t Potsdam}, year = {2012}, abstract = {Assuming that liquid iron alloy from the outer core interacts with the solid silicate-rich lower mantle the influence on the core-mantle reflected phase PcP is studied. If the core-mantle boundary is not a sharp discontinuity, this becomes apparent in the waveform and amplitude of PcP. Iron-silicate mixing would lead to regions of partial melting with higher density which in turn reduces the velocity of seismic waves. On the basis of the calculation and interpretation of short-period synthetic seismograms, using the reflectivity and Gauss Beam method, a model space is evaluated for these ultra-low velocity zones (ULVZs). The aim of this thesis is to analyse the behaviour of PcP between 10° and 40° source distance for such models using different velocity and density configurations. Furthermore, the resolution limits of seismic data are discussed. The influence of the assumed layer thickness, dominant source frequency and ULVZ topography are analysed. The Gr{\"a}fenberg and NORSAR arrays are then used to investigate PcP from deep earthquakes and nuclear explosions. The seismic resolution of an ULVZ is limited both for velocity and density contrasts and layer thicknesses. Even a very thin global core-mantle transition zone (CMTZ), rather than a discrete boundary and also with strong impedance contrasts, seems possible: If no precursor is observable but the PcP_model /PcP_smooth amplitude reduction amounts to more than 10\%, a very thin ULVZ of 5 km with a first-order discontinuity may exist. Otherwise, if amplitude reductions of less than 10\% are obtained, this could indicate either a moderate, thin ULVZ or a gradient mantle-side CMTZ. Synthetic computations reveal notable amplitude variations as function of the distance and the impedance contrasts. Thereby a primary density effect in the very steep-angle range and a pronounced velocity dependency in the wide-angle region can be predicted. In view of the modelled findings, there is evidence for a 10 to 13.5 km thick ULVZ 600 km south-eastern of Moscow with a NW-SE extension of about 450 km. Here a single specific assumption about the velocity and density anomaly is not possible. This is in agreement with the synthetic results in which several models create similar amplitude-waveform characteristics. For example, a ULVZ model with contrasts of -5\% VP , -15\% VS and +5\% density explain the measured PcP amplitudes. Moreover, below SW Finland and NNW of the Caspian Sea a CMB topography can be assumed. The amplitude measurements indicate a wavelength of 200 km and a height of 1 km topography, previously also shown in the study by Kampfmann and M{\"u}ller (1989). Better constraints might be provided by a joined analysis of seismological data, mineralogical experiments and geodynamic modelling.}, language = {en} } @phdthesis{Oey2008, author = {Oey, Melanie}, title = {Chloroplasts as bioreactors : high-yield production of active bacteriolytic protein antibiotics}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-28950}, school = {Universit{\"a}t Potsdam}, year = {2008}, abstract = {Plants, more precisely their chloroplasts with their bacterial-like expression machinery inherited from their cyanobacterial ancestors, can potentially offer a cheap expression system for proteinaceous pharmaceuticals. This system would be easily scalable and provides appropriate safety due to chloroplasts maternal inheritance. In this work, it was shown that three phage lytic enzymes (Pal, Cpl-1 and PlyGBS) could be successfully expressed at very high levels and with high stability in tobacco chloroplasts. PlyGBS expression reached an amount of foreign protein accumulation (> 70\% TSP) that has never been obtained before. Although the high expression levels of PlyGBS caused a pale green phenotype with retarded growth, presumably due to exhaustion of plastid protein synthesis capacity, development and seed production were not impaired under greenhouse conditions. Since Pal and Cpl-1 showed toxic effects when expressed in E. coli, a special plastid transformation vector (pTox) was constructed to allow DNA amplification in bacteria. The construction of the pTox transformation vector allowing a recombinase-mediated deletion of an E. coli transcription block in the chloroplast, leading to an increase of foreign protein accumulation to up to 40\% of TSP for Pal and 20\% of TSP for Cpl-1. High dose-dependent bactericidal efficiency was shown for all three plant-derived lytic enzymes using their pathogenic target bacteria S. pyogenes and S. pneumoniae. Confirmation of specificity was obtained for the endotoxic proteins Pal and Cpl-1 by application to E. coli cultures. These results establish tobacco chloroplasts as a new cost-efficient and convenient production platform for phage lytic enzymes and address the greatest obstacle for clinical application. The present study is the first report of lysin production in a non-bacterial system. The properties of chloroplast-produced lysins described in this work, their stability, high accumulation rate and biological activity make them highly attractive candidates for future antibiotics.}, language = {en} } @phdthesis{Regel2008, author = {Regel, Stefanie}, title = {The comprehension of figurative language : electrophysiological evidence on the processing of irony}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-33376}, school = {Universit{\"a}t Potsdam}, year = {2008}, abstract = {Diese Dissertation untersucht das Verstehen figurativer Sprache, im Besonderen die zeitliche Verarbeitung von verbaler Ironie. In sechs Experimenten wurde mittels ereignis-korrelierter Potentiale (EKP) die Gehirnaktivit{\"a}t beim Verstehen ironischer {\"A}ußerungen im Vergleich zu entsprechenden nicht-ironischen {\"A}ußerungen gemessen und analysiert. Dar{\"u}berhinaus wurde der Einfluss verschiedener sprachbegleitender Hinweisreize, z.B. von Prosodie oder der Verwendung von Satzzeichen, sowie außersprachlicher Hinweisreize, wie bspw. pragmatischen Wissens, auf das Ironieverstehen untersucht. Auf Grundlage dieser Ergebnisse werden verschiedene psycholinguistische Modelle figurativer Sprachverarbeitung, d.h. 'standard pragmatic model', 'graded salience hypothesis', sowie 'direct access view', diskutiert.}, language = {en} } @phdthesis{Moerbt2010, author = {M{\"o}rbt, Nora}, title = {Differential proteome analysis of human lung epithelial cells following exposure to aromatic volatile organic compounds}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-49257}, school = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {The widespread usage of products containing volatile organic compounds (VOC) has lead to a general human exposure to these chemicals in work places or homes being suspected to contribute to the growing incidence of environmental diseases. Since the causal molecular mechanisms for the development of these disorders are not completely understood, the overall objective of this thesis was to investigate VOC-mediated molecular effects on human lung cells in vitro at VOC concentrations comparable to exposure scenarios below current occupational limits. Although differential expression of single proteins in response to VOCs has been reported, effects on complex protein networks (proteome) have not been investigated. However, this information is indispensable when trying to ascertain a mechanism for VOC action on the cellular level and establishing preventive strategies. For this study, the alveolar epithelial cell line A549 has been used. This cell line, cultured in a two-phase (air/liquid) model allows the most direct exposure and had been successfully applied for the analysis of inflammatory effects in response to VOCs. Mass spectrometric identification of 266 protein spots provided the first proteomic map of A549 cell line to this extent that may foster future work with this frequently used cellular model. The distribution of three typical air contaminants, monochlorobenzene (CB), styrene and 1,2 dichlorobenzene (1,2-DCB), between gas and liquid phase of the exposure model has been analyzed by gas chromatography. The obtained VOC partitioning was in agreement with available literature data. Subsequently the adapted in vitro system has been successfully employed to characterize the effects of the aromatic compound styrene on the proteome of A549 cells (Chapter 4). Initially, the cell toxicity has been assessed in order to ensure that most of the concentrations used in the following proteomic approach were not cytotoxic. Significant changes in abundance and phosphorylation in the total soluble protein fraction of A549 cells have been detected following styrene exposure. All proteins have been identified using mass spectrometry and the main cellular functions have been assigned. Validation experiments on protein and transcript level confirmed the results of the 2-DE experiments. From the results, two main cellular pathways have been identified that were induced by styrene: the cellular oxidative stress response combined with moderate pro-apoptotic signaling. Measurement of cellular reactive oxygen species (ROS) as well as the styrene-mediated induction of oxidative stress marker proteins confirmed the hypothesis of oxidative stress as the main molecular response mechanism. Finally, adducts of cellular proteins with the reactive styrene metabolite styrene 7,8 oxide (SO) have been identified. Especially the SO-adducts observed at both the reactive centers of thioredoxin reductase 1, which is a key element in the control of the cellular redox state, may be involved in styrene-induced ROS formation and apoptosis. A similar proteomic approach has been carried out with the halobenzenes CB and 1,2-DCB (Chapter 5). In accordance with previous findings, cell toxicity assessment showed enhanced toxicity compared to the one caused by styrene. Significant changes in abundance and phosphorylation of total soluble proteins of A549 cells have been detected following exposure to subtoxic concentrations of CB and 1,2-DCB. All proteins have been identified using mass spectrometry and the main cellular functions have been assigned. As for the styrene experiment, the results indicated two main pathways to be affected in the presence of chlorinated benzenes, cell death signaling and oxidative stress response. The strong induction of pro-apoptotic signaling has been confirmed for both treatments by detection of the cleavage of caspase 3. Likewise, the induction of redox-sensitive protein species could be correlated to an increased cellular level of ROS observed following CB treatment. Finally, common mechanisms in the cellular response to aromatic VOCs have been investigated (Chapter 6). A similar number (4.6-6.9\%) of all quantified protein spots showed differential expression (p<0.05) following cell exposure to styrene, CB or 1,2-DCB. However, not more than three protein spots showed significant regulation in the same direction for all three volatile compounds: voltage-dependent anion-selective channel protein 2, peroxiredoxin 1 and elongation factor 2. However, all of these proteins are important molecular targets in stress- and cell death-related signaling pathways.}, language = {en} } @book{PfauSteinbach2006, author = {Pfau, Roland and Steinbach, Markus}, title = {Modality-independent and modality-specific aspects of grammaticalization in sign languages}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-939469-53-7}, issn = {1864-1857}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-10886}, publisher = {Universit{\"a}t Potsdam}, pages = {97}, year = {2006}, abstract = {One type of internal diachronic change that has been extensively studied for spoken languages is grammaticalization whereby lexical elements develop into free or bound grammatical elements. Based on a wealth of spoken languages, a large amount of prototypical grammaticalization pathways has been identified. Moreover, it has been shown that desemanticization, decategorialization, and phonetic erosion are typical characteristics of grammaticalization processes. Not surprisingly, grammaticalization is also responsible for diachronic change in sign languages. Drawing data from a fair number of sign languages, we show that grammaticalization in visual-gestural languages - as far as the development from lexical to grammatical element is concerned - follows the same developmental pathways as in spoken languages. That is, the proposed pathways are modalityindependent. Besides these intriguing parallels, however, sign languages have the possibility of developing grammatical markers from manual and non-manual co-speech gestures. We will discuss various instances of grammaticalized gestures and we will also briefly address the issue of the modality-specificity of this phenomenon.}, language = {en} } @misc{RoellySortais2004, author = {Roelly, Sylvie and Sortais, Michel}, title = {Space-time asymptotics of an infinite-dimensional diffusion having a long- range memory}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-6700}, year = {2004}, abstract = {We develop a cluster expansion in space-time for an infinite-dimensional system of interacting diffusions where the drift term of each diffusion depends on the whole past of the trajectory; these interacting diffusions arise when considering the Langevin dynamics of a ferromagnetic system submitted to a disordered external magnetic field.}, language = {en} } @misc{RoellyThieullen2005, author = {Roelly, Sylvie and Thieullen, Mich{\`e}le}, title = {Duality formula for the bridges of a Brownian diffusion : application to gradient drifts}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-6710}, year = {2005}, abstract = {In this paper, we consider families of time Markov fields (or reciprocal classes) which have the same bridges as a Brownian diffusion. We characterize each class as the set of solutions of an integration by parts formula on the space of continuous paths C[0; 1]; R-d) Our techniques provide a characterization of gradient diffusions by a duality formula and, in case of reversibility, a generalization of a result of Kolmogorov.}, language = {en} } @misc{RoellyDaiPra2004, author = {Roelly, Sylvie and Dai Pra, Paolo}, title = {An existence result for infinite-dimensional Brownian diffusions with non- regular and non Markovian drift}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-6684}, year = {2004}, abstract = {We prove in this paper an existence result for infinite-dimensional stationary interactive Brownian diffusions. The interaction is supposed to be small in the norm ||.||∞ but otherwise is very general, being possibly non-regular and non-Markovian. Our method consists in using the characterization of such diffusions as space-time Gibbs fields so that we construct them by space-time cluster expansions in the small coupling parameter.}, language = {en} }