@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} }