@misc{ZurellKoenigMalchowetal.2021,
  author    = {Zurell, Damaris and K{\"o}nig, Christian and Malchow, Anne-Kathleen and Kapitza, Simon and Bocedi, Greta and Travis, Justin M. J. and Fandos, Guillermo},
  title     = {Spatially explicit models for decision-making in animal conservation and restoration},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  volume    = {2022},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  edition   = {4},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-54991},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-549915},
  pages     = {1 -- 16},
  year      = {2021},
  abstract  = {Models are useful tools for understanding and predicting ecological patterns and processes. Under ongoing climate and biodiversity change, they can greatly facilitate decision-making in conservation and restoration and help designing adequate management strategies for an uncertain future. Here, we review the use of spatially explicit models for decision support and to identify key gaps in current modelling in conservation and restoration. Of 650 reviewed publications, 217 publications had a clear management application and were included in our quantitative analyses. Overall, modelling studies were biased towards static models (79\%), towards the species and population level (80\%) and towards conservation (rather than restoration) applications (71\%). Correlative niche models were the most widely used model type. Dynamic models as well as the gene-to-individual level and the community-to-ecosystem level were underrepresented, and explicit cost optimisation approaches were only used in 10\% of the studies. We present a new model typology for selecting models for animal conservation and restoration, characterising model types according to organisational levels, biological processes of interest and desired management applications. This typology will help to more closely link models to management goals. Additionally, future efforts need to overcome important challenges related to data integration, model integration and decision-making. We conclude with five key recommendations, suggesting that wider usage of spatially explicit models for decision support can be achieved by 1) developing a toolbox with multiple, easier-to-use methods, 2) improving calibration and validation of dynamic modelling approaches and 3) developing best-practise guidelines for applying these models. Further, more robust decision-making can be achieved by 4) combining multiple modelling approaches to assess uncertainty, and 5) placing models at the core of adaptive management. These efforts must be accompanied by long-term funding for modelling and monitoring, and improved communication between research and practise to ensure optimal conservation and restoration outcomes.},
  language  = {en}
}
@article{ZimmermannStoofLeichsenringKruseetal.2021,
  author    = {Zimmermann, Heike and Stoof-Leichsenring, Kathleen R. and Kruse, Stefan and N{\"u}rnberg, Dirk and Tiedemann, Ralf and Herzschuh, Ulrike},
  title     = {Sedimentary ancient DNA from the subarctic North Pacific},
  series = {Paleoceanography and paleoclimatology},
  volume    = {36},
  journal   = {Paleoceanography and paleoclimatology},
  number    = {4},
  publisher = {Wiley},
  address   = {Hoboken, NJ},
  issn      = {2572-4525},
  doi       = {10.1029/2020PA004091},
  pages     = {18},
  year      = {2021},
  abstract  = {We traced diatom composition and diversity through time using diatom-derived sedimentary ancient DNA (sedaDNA) from eastern continental slope sediments off Kamchatka (North Pacific) by applying a short, diatom-specific marker on 63 samples in a DNA metabarcoding approach. The sequences were assigned to diatoms that are common in the area and characteristic of cold water. SedaDNA allowed us to observe shifts of potential lineages from species of the genus Chaetoceros that can be related to different climatic phases, suggesting that pre-adapted ecotypes might have played a role in the long-term success of species in areas of changing environmental conditions. These sedaDNA results complement our understanding of the long-term history of diatom assemblages and their general relationship to environmental conditions of the past. Sea-ice diatoms (Pauliella taeniata [Grunow] Round \& Basson, Attheya septentrionalis [ostrup] R. M. Crawford and Nitzschia frigida [Grunow]) detected during the late glacial and Younger Dryas are in agreement with previous sea-ice reconstructions. A positive correlation between pennate diatom richness and the sea-ice proxy IP25 suggests that sea ice fosters pennate diatom richness, whereas a negative correlation with June insolation and temperature points to unfavorable conditions during the Holocene. A sharp increase in proportions of freshwater diatoms at similar to 11.1 cal kyr BP implies the influence of terrestrial runoff and coincides with the loss of 42\% of diatom sequence variants. We assume that reduced salinity at this time stabilized vertical stratification which limited the replenishment of nutrients in the euphotic zone.},
  language  = {en}
}
@article{ZhangCasertaYarmanetal.2021,
  author    = {Zhang, Xiaorong and Caserta, Giorgio and Yarman, Aysu and Supala, Eszter and Tadjoung Waffo, Armel Franklin and Wollenberger, Ulla and Gyurcsanyi, Robert E. and Zebger, Ingo and Scheller, Frieder W.},
  title     = {"Out of Pocket" protein binding},
  series = {Chemosensors},
  volume    = {9},
  journal   = {Chemosensors},
  number    = {6},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2227-9040},
  doi       = {10.3390/chemosensors9060128},
  pages     = {13},
  year      = {2021},
  abstract  = {The epitope imprinting approach applies exposed peptides as templates to synthesize Molecularly Imprinted Polymers (MIPs) for the recognition of the parent protein. While generally the template protein binding to such MIPs is considered to occur via the epitope-shaped cavities, unspecific interactions of the analyte with non-imprinted polymer as well as the detection method used may add to the complexity and interpretation of the target rebinding. To get new insights on the effects governing the rebinding of analytes, we electrosynthesized two epitope-imprinted polymers using the N-terminal pentapeptide VHLTP-amide of human hemoglobin (HbA) as the template. MIPs were prepared either by single-step electrosynthesis of scopoletin/pentapeptide mixtures or electropolymerization was performed after chemisorption of the cysteine extended VHLTP peptide. Rebinding of the target peptide and the parent HbA protein to the MIP nanofilms was quantified by square wave voltammetry using a redox probe gating, surface enhanced infrared absorption spectroscopy, and atomic force microscopy. While binding of the pentapeptide shows large influence of the amino acid sequence, all three methods revealed strong non-specific binding of HbA to both polyscopoletin-based MIPs with even higher affinities than the target peptides.},
  language  = {en}
}
@article{YildizLeimkuehler2021,
  author    = {Yildiz, Tugba and Leimk{\"u}hler, Silke},
  title     = {TusA is a versatile protein that links translation efficiency to cell division in Escherichia coli},
  series = {Journal of bacteriology},
  volume    = {203},
  journal   = {Journal of bacteriology},
  number    = {7},
  publisher = {American Society for Microbiology},
  address   = {Washington},
  issn      = {1098-5530},
  doi       = {10.1128/JB.00659-20},
  pages     = {20},
  year      = {2021},
  abstract  = {To enable accurate and efficient translation, sulfur modifications are introduced posttranscriptionally into nucleosides in tRNAs. The biosynthesis of tRNA sulfur modifications involves unique sulfur trafficking systems for the incorporation of sulfur atoms in different nucleosides of tRNA. One of the proteins that is involved in inserting the sulfur for 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U34) modifications in tRNAs is the TusA protein. TusA, however, is a versatile protein that is also involved in numerous other cellular pathways. Despite its role as a sulfur transfer protein for the 2-thiouridine formation in tRNA, a fundamental role of TusA in the general physiology of Escherichia coli has also been discovered. Poor viability, a defect in cell division, and a filamentous cell morphology have been described previously for tusA-deficient cells. In this report, we aimed to dissect the role of TusA for cell viability. We were able to show that the lack of the thiolation status of wobble uridine (U-34) nucleotides present on Lys, Gln, or Glu in tRNAs has a major consequence on the translation efficiency of proteins; among the affected targets are the proteins RpoS and Fis. Both proteins are major regulatory factors, and the deregulation of their abundance consequently has a major effect on the cellular regulatory network, with one consequence being a defect in cell division by regulating the FtsZ ring formation. <br /> IMPORTANCE More than 100 different modifications are found in RNAs. One of these modifications is the mnm(5)s(2)U modification at the wobble position 34 of tRNAs for Lys, Gln, and Glu. The functional significance of U34 modifications is substantial since it restricts the conformational flexibility of the anticodon, thus providing translational fidelity. We show that in an Escherichia coli TusA mutant strain, involved in sulfur transfer for the mnm(5)s(2)U34 thio modifications, the translation efficiency of RpoS and Fis, two major cellular regulatory proteins, is altered. Therefore, in addition to the transcriptional regulation and the factors that influence protein stability, tRNA modifications that ensure the translational efficiency provide an additional crucial regulatory factor for protein synthesis.},
  language  = {en}
}
@article{YarmanKurbanoğluZebgeretal.2021,
  author    = {Yarman, Aysu and Kurbanoğlu, Sevin{\c{c}} and Zebger, Ingo and Scheller, Frieder W.},
  title     = {Simple and robust},
  series = {Sensors and actuators : B, Chemical : an international journal devoted to research and development of chemical transducers},
  volume    = {330},
  journal   = {Sensors and actuators : B, Chemical : an international journal devoted to research and development of chemical transducers},
  publisher = {Elsevier Science},
  address   = {Amsterdam [u.a.]},
  issn      = {0925-4005},
  doi       = {10.1016/j.snb.2020.129369},
  pages     = {12},
  year      = {2021},
  abstract  = {A spectrum of 7562 publications on Molecularly Imprinted Polymers (MIPs) has been presented in literature within the last ten years (Scopus, September 7, 2020). Around 10 \% of the papers published on MIPs describe the recognition of proteins. The straightforward synthesis of MIPs is a significant advantage as compared with the preparation of enzymes or antibodies. MIPs have been synthesized from only one up to six functional monomers while proteins are made up of 20 natural amino acids. Furthermore, they can be synthesized against structures of low immunogenicity and allow multi-analyte measurements via multi-target synthesis. Electrochemical methods allow simple polymer synthesis, removal of the template and readout. Among the different sensor configurations electrochemical MIP-sensors provide the broadest spectrum of protein analytes. The sensitivity of MIP-sensors is sufficiently high for biomarkers in the sub-nanomolar region, nevertheless the cross-reactivity of highly abundant proteins in human serum is still a challenge. MIPs for proteins offer innovative tools not only for clinical and environmental analysis, but also for bioimaging, therapy and protein engineering.},
  language  = {en}
}
@article{YanFrokjarEngelbrektetal.2021,
  author    = {Yan, Jiawei and Fr{\o}kj{\ae}r, Emil Egede and Engelbrekt, Christian and Leimk{\"u}hler, Silke and Ulstrup, Jens and Wollenberger, Ulla and Xiao, Xinxin and Zhang, Jingdong},
  title     = {Voltammetry and single-molecule in situ scanning tunnelling microscopy of the redox metalloenzyme human sulfite oxidase},
  series = {ChemElectroChem},
  volume    = {8},
  journal   = {ChemElectroChem},
  number    = {1},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {2196-0216},
  doi       = {10.1002/celc.202001258},
  pages     = {164 -- 171},
  year      = {2021},
  abstract  = {Human sulfite oxidase (hSO) is a homodimeric two-domain enzyme central in the biological sulfur cycle. A pyranopterin molybdenum cofactor (Moco) is the catalytic site and a heme b(5) group located in the N-terminal domain. The two domains are connected by a flexible linker region. Electrons produced at the Moco in sulfite oxidation, are relayed via heme b(5) to electron acceptors or an electrode surface. Inter-domain conformational changes between an open and a closed enzyme conformation, allowing "gated" electron transfer has been suggested. We first recorded cyclic voltammetry (CV) of hSO on single-crystal Au(111)-electrode surfaces modified by self-assembled monolayers (SAMs) both of a short rigid thiol, cysteamine and of a longer structurally flexible thiol, omega-amino-octanethiol (AOT). hSO on cysteamine SAMs displays a well-defined pair of voltammetric peaks around -0.207 V vs. SCE in the absence of sulfite substrate, but no electrocatalysis. hSO on AOT SAMs displays well-defined electrocatalysis, but only "fair" quality voltammetry in the absence of sulfite. We recorded next in situ scanning tunnelling spectroscopy (STS) of hSO on AOT modified Au(111)-electrodes, disclosing, a 2-5 \% surface coverage of strong molecular scale contrasts, assigned to single hSO molecules, notably with no contrast difference in the absence and presence of sulfite. In situ STS corroborated this observation with a sigmoidal tunnelling current/overpotential correlation.},
  language  = {en}
}
@article{XuNieWangetal.2021,
  author    = {Xu, Xun and Nie, Yan and Wang, Weiwei and Ullah, Imran and Tung, Wing Tai and Ma, Nan and Lendlein, Andreas},
  title     = {Generation of 2.5D lung bud organoids from human induced pluripotent stem cells},
  series = {Clinical hemorheology and microcirculation : blood flow and vessels},
  volume    = {79},
  journal   = {Clinical hemorheology and microcirculation : blood flow and vessels},
  number    = {1},
  publisher = {IOS Press},
  address   = {Amsterdam},
  issn      = {1386-0291},
  doi       = {10.3233/CH-219111},
  pages     = {217 -- 230},
  year      = {2021},
  abstract  = {Human induced pluripotent stem cells (hiPSCs) are a promising cell source to generate the patient-specific lung organoid given their superior differentiation potential. However, the current 3D cell culture approach is tedious and time-consuming with a low success rate and high batch-to-batch variability. Here, we explored the establishment of lung bud organoids by systematically adjusting the initial confluence levels and homogeneity of cell distribution. The efficiency of single cell seeding and clump seeding was compared. Instead of the traditional 3D culture, we established a 2.5D organoid culture to enable the direct monitoring of the internal structure via microscopy. It was found that the cell confluence and distribution prior to induction were two key parameters, which strongly affected hiPSC differentiation trajectories. Lung bud organoids with positive expression of NKX 2.1, in a single-cell seeding group with homogeneously distributed hiPSCs at 70\% confluence (SC 70\% hom) or a clump seeding group with heterogeneously distributed cells at 90\% confluence (CL 90\% het), can be observed as early as 9 days post induction. These results suggest that a successful lung bud organoid formation with single-cell seeding of hiPSCs requires a moderate confluence and homogeneous distribution of cells, while high confluence would be a prominent factor to promote the lung organoid formation when seeding hiPSCs as clumps. 2.5D organoids generated with defined culture conditions could become a simple, efficient, and valuable tool facilitating drug screening, disease modeling and personalized medicine.},
  language  = {en}
}
@article{XuRazaghiMoghadamNikoloski2021,
  author    = {Xu, Rudan and Razaghi-Moghadam, Zahra and Nikoloski, Zoran},
  title     = {Maximization of non-idle enzymes improves the coverage of the estimated maximal in vivo enzyme catalytic rates in Escherichia coli},
  series = {Bioinformatics},
  volume    = {37},
  journal   = {Bioinformatics},
  number    = {21},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1367-4803},
  doi       = {10.1093/bioinformatics/btab575},
  pages     = {3848 -- 3855},
  year      = {2021},
  abstract  = {Motivation: Constraint-based modeling approaches allow the estimation of maximal in vivo enzyme catalytic rates that can serve as proxies for enzyme turnover numbers. Yet, genome-scale flux profiling remains a challenge in deploying these approaches to catalogue proxies for enzyme catalytic rates across organisms. Results: Here, we formulate a constraint-based approach, termed NIDLE-flux, to estimate fluxes at a genome-scale level by using the principle of efficient usage of expressed enzymes. Using proteomics data from Escherichia coli, we show that the fluxes estimated by NIDLE-flux and the existing approaches are in excellent qualitative agreement (Pearson correlation > 0.9). We also find that the maximal in vivo catalytic rates estimated by NIDLE-flux exhibits a Pearson correlation of 0.74 with in vitro enzyme turnover numbers. However, NIDLE-flux results in a 1.4-fold increase in the size of the estimated maximal in vivo catalytic rates in comparison to the contenders. Integration of the maximum in vivo catalytic rates with publically available proteomics and metabolomics data provide a better match to fluxes estimated by NIDLE-flux. Therefore, NIDLE-flux facilitates more effective usage of proteomics data to estimate proxies for kcatomes.},
  language  = {en}
}
@misc{WolffGastEversetal.2021,
  author    = {Wolff, Martin and Gast, Klaus and Evers, Andreas and Kurz, Michael and Pfeiffer-Marek, Stefania and Sch{\"u}ler, Anja and Seckler, Robert and Thalhammer, Anja},
  title     = {A Conserved Hydrophobic Moiety and Helix-Helix Interactions Drive the Self-Assembly of the Incretin Analog Exendin-4},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {9},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-52208},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-522081},
  pages     = {22},
  year      = {2021},
  abstract  = {Exendin-4 is a pharmaceutical peptide used in the control of insulin secretion. Structural information on exendin-4 and related peptides especially on the level of quaternary structure is scarce. We present the first published association equilibria of exendin-4 directly measured by static and dynamic light scattering. We show that exendin-4 oligomerization is pH dependent and that these oligomers are of low compactness. We relate our experimental results to a structural hypothesis to describe molecular details of exendin-4 oligomers. Discussion of the validity of this hypothesis is based on NMR, circular dichroism and fluorescence spectroscopy, and light scattering data on exendin-4 and a set of exendin-4 derived peptides. The essential forces driving oligomerization of exendin-4 are helix-helix interactions and interactions of a conserved hydrophobic moiety. Our structural hypothesis suggests that key interactions of exendin-4 monomers in the experimentally supported trimer take place between a defined helical segment and a hydrophobic triangle constituted by the Phe22 residues of the three monomeric subunits. Our data rationalize that Val19 might function as an anchor in the N-terminus of the interacting helix-region and that Trp25 is partially shielded in the oligomer by C-terminal amino acids of the same monomer. Our structural hypothesis suggests that the Trp25 residues do not interact with each other, but with C-terminal Pro residues of their own monomers.},
  language  = {en}
}
@article{WolffGastEversetal.2021,
  author    = {Wolff, Martin and Gast, Klaus and Evers, Andreas and Kurz, Michael and Pfeiffer-Marek, Stefania and Sch{\"u}ler, Anja and Seckler, Robert and Thalhammer, Anja},
  title     = {A Conserved Hydrophobic Moiety and Helix-Helix Interactions Drive the Self-Assembly of the Incretin Analog Exendin-4},
  series = {Biomolecules},
  volume    = {11},
  journal   = {Biomolecules},
  number    = {9},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2218-273X},
  doi       = {10.3390/biom11091305},
  pages     = {20},
  year      = {2021},
  abstract  = {Exendin-4 is a pharmaceutical peptide used in the control of insulin secretion. Structural information on exendin-4 and related peptides especially on the level of quaternary structure is scarce. We present the first published association equilibria of exendin-4 directly measured by static and dynamic light scattering. We show that exendin-4 oligomerization is pH dependent and that these oligomers are of low compactness. We relate our experimental results to a structural hypothesis to describe molecular details of exendin-4 oligomers. Discussion of the validity of this hypothesis is based on NMR, circular dichroism and fluorescence spectroscopy, and light scattering data on exendin-4 and a set of exendin-4 derived peptides. The essential forces driving oligomerization of exendin-4 are helix-helix interactions and interactions of a conserved hydrophobic moiety. Our structural hypothesis suggests that key interactions of exendin-4 monomers in the experimentally supported trimer take place between a defined helical segment and a hydrophobic triangle constituted by the Phe22 residues of the three monomeric subunits. Our data rationalize that Val19 might function as an anchor in the N-terminus of the interacting helix-region and that Trp25 is partially shielded in the oligomer by C-terminal amino acids of the same monomer. Our structural hypothesis suggests that the Trp25 residues do not interact with each other, but with C-terminal Pro residues of their own monomers.},
  language  = {en}
}
@article{WojcikCeulemansGaedke2021,
  author    = {Wojcik, Laurie Anne and Ceulemans, Ruben and Gaedke, Ursula},
  title     = {Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs},
  series = {Ecology and Evolution},
  volume    = {11},
  journal   = {Ecology and Evolution},
  number    = {22},
  publisher = {John Wiley \& Sons, Inc.},
  address   = {Hoboken (New Jersey)},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.8214},
  pages     = {15639 -- 15663},
  year      = {2021},
  abstract  = {Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: This loss may hamper ecosystems' ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. We investigated the effects of functional diversity on the robustness, that is, resistance, resilience, and elasticity, using a tritrophic—and thus more realistic—plankton food web model. We compared a non-adaptive food chain with no diversity within the individual trophic levels to a more diverse food web with three adaptive trophic levels. The species fitness differences were balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience, and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occurred. Importantly, we found that a more diverse food web was generally more resistant and resilient but its elasticity was context-dependent. Particularly, functional diversity reduced the probability of a regime shift toward a non-desirable alternative state. The basal-intermediate interaction consistently determined the robustness against a nutrient pulse despite the complex influence of the shape and type of the dynamical attractors. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience, and potentially elasticity as functional diversity declines.},
  language  = {en}
}
@misc{WojcikCeulemansGaedke2021,
  author    = {Wojcik, Laurie Anne and Ceulemans, Ruben and Gaedke, Ursula},
  title     = {Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1251},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-55373},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-553730},
  pages     = {25},
  year      = {2021},
  abstract  = {Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: This loss may hamper ecosystems' ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. We investigated the effects of functional diversity on the robustness, that is, resistance, resilience, and elasticity, using a tritrophic—and thus more realistic—plankton food web model. We compared a non-adaptive food chain with no diversity within the individual trophic levels to a more diverse food web with three adaptive trophic levels. The species fitness differences were balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience, and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occurred. Importantly, we found that a more diverse food web was generally more resistant and resilient but its elasticity was context-dependent. Particularly, functional diversity reduced the probability of a regime shift toward a non-desirable alternative state. The basal-intermediate interaction consistently determined the robustness against a nutrient pulse despite the complex influence of the shape and type of the dynamical attractors. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience, and potentially elasticity as functional diversity declines.},
  language  = {en}
}
@phdthesis{Woehlecke2021,
  author    = {Woehlecke, Sandra},
  title     = {Das erweiterte Fachwissen f{\"u}r den schulischen Kontext als Leitlinie f{\"u}r eine additive fachliche Lehrveranstaltung im Lehramtsstudium Biologie},
  doi       = {10.25932/publishup-52120},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-521209},
  school      = {Universit{\"a}t Potsdam},
  pages     = {304},
  year      = {2021},
  abstract  = {Das Fachwissen von Lehrkr{\"a}ften weist f{\"u}r die Auspr{\"a}gung fachdidaktischer Expertise eine hohe Bedeutung auf. Welche Merkmale universit{\"a}re Lehrveranstaltungen aufweisen sollten, um Lehramtsstudierenden ein berufsspezifisches Fachwissen zu vermitteln, ist jedoch {\"u}berwiegend noch unklar. Innerhalb des Projekts PSI-Potsdam wurde auf theoretischer Grundlage das fach{\"u}bergreifende Modell des erweiterten Fachwissens f{\"u}r den schulischen Kontext entwickelt. Als Ansatz zur Verbesserung des Biologie-Lehramtsstudiums diente dieses Modell als Konzeptionsgrundlage f{\"u}r eine additive Lehrveranstaltung. Hierbei werden Lerngelegenheiten geboten, um das universit{\"a}r erworbene Fachwissen {\"u}ber zellbiologische Inhalte auf schulische Kontexte anzuwenden, z.B. durch die Dekonstruktion und anschließende Rekonstruktion von schulischen Lerntexten. Die Wirkung des Seminars wurde in mehreren Zyklen im Forschungsformat der Fachdidaktischen Entwicklungsforschung beforscht. Eine der zentralen Forschungsfragen lautet dabei: Wie kann eine Lerngelegenheit f{\"u}r Lehramtsstudierende der Biologie gestaltet sein, um ein erweitertes Fachwissen f{\"u}r den schulischen Kontext f{\"u}r den zellbiologischen Themenbereich „Struktur und Funktion der Biomembran" zu f{\"o}rdern? Anhand fall{\"u}bergreifender Analysen (n = 29) wird im empirischen Teil aufgezeigt, welche Einstellungen zum Lehramtsstudium in der Stichprobe bestehen. Als ein wichtiges Ergebnis kann hierbei herausgestellt werden, dass sich das Fachinteresse hinsichtlich schulisch und universit{\"a}r vermittelter Inhalte bei den untersuchten Studierenden auffallend unterscheidet, wobei dem Schulwissen ein deutlich h{\"o}heres Interesse entgegengebracht wird. Die Berufsrelevanz fachlicher Inhalte wird seitens der Studierenden h{\"a}ufig am Schulwissen festgemacht. Innerhalb konkreter Einzelfallanalysen (n = 6) wird anhand von Lernpfaden dargestellt, wie sich {\"u}ber mehrere Design-Experimente hinweg fachliche Konzepte entwickelt haben. Bei der Beschreibung wird vor allem auf Schl{\"u}sselstellen und H{\"u}rden im Lernprozess fokussiert. Aus diesen Ergebnissen folgend werden vorgenommene Iterationen f{\"u}r die einzelnen Zyklen beschrieben, die ebenfalls anhand der iterativen Entwicklung der Design-Prinzipien dargelegt werden. Es konnte gezeigt werden, dass die Schl{\"u}sselstellen sehr individuell aufgrund der subjektiv fokussierten Inhalte zu Tage treten. Meist treten sie jedoch im Zusammenhang mit der Verkn{\"u}pfung verschiedener fachlicher Konzepte oder durch kooperative Aufschl{\"u}sselungen von Konzepten auf. Fachliche H{\"u}rden konnten hingegen in Form von fachlich unangemessenen Vorstellungen fall{\"u}bergreifend identifiziert werden. Dies betrifft unter anderem die Vorstellung der Biomembran als Wand, die mit den Vorstellungen einer Schutzfunktion und einer formgebenden Funktion der Biomembran einhergeht. Weiterhin wird beleuchtet, wie das erweiterte Fachwissen f{\"u}r den schulischen Kontext zur Bearbeitung der Lernaufgaben angewendet wurde. Es hat sich gezeigt, dass sich bestimmte Lerngelegenheiten eigenen, um bestimmte Facetten des erweiterten Fachwissens zu f{\"o}rdern. Insgesamt scheint das Modell des erweiterten Fachwissens f{\"u}r den schulischen Kontext {\"a}ußerst geeignet zu sein, um anhand der Facetten und deren Beschreibungen Lerngelegenheiten oder Gestaltungsprinzipien f{\"u}r diese zu konzipieren. F{\"u}r das untersuchte Lehr-Lernarrangement haben sich kleinere Adaptationen des Modells als sinnvoll erwiesen. Hinsichtlich der Methodologie konnten Ableitungen f{\"u}r die Anwendung der fachdidaktischen Entwicklungsforschung f{\"u}r additive fachliche Lehrveranstaltungen dieser Art herausgestellt werden. Um den Professionsbezug der fachwissenschaftlichen Anteile im Lehramtsstudium zu verbessern, ist der weitere Einbezug des erweiterten Fachwissens f{\"u}r den schulischen Kontext in die fachwissenschaftlichen Studienanteile {\"u}beraus w{\"u}nschenswert.},
  language  = {de}
}
@article{WendtSenftlebenGrosetal.2021,
  author    = {Wendt, Martin and Senftleben, Nele and Gros, Patrick and Schmitt, Thomas},
  title     = {Coping with environmental extremes},
  series = {Insects : open access journal},
  volume    = {12},
  journal   = {Insects : open access journal},
  number    = {10},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2075-4450},
  doi       = {10.3390/insects12100896},
  pages     = {12},
  year      = {2021},
  abstract  = {Simple Summary:\& nbsp;High alpine meadows are home to numerous endemic butterfly species. A combination of climate change and changes in agricultural practices has led to a severe decline in many species. A seemingly unaffected representative of this habitat is Erebia pronoe. We studied the behaviour, resource use and population structure of this species to explain its resilience and estimate its future survival potential. This species shows pronounced protandry in combination with serial eclosion. Males were significantly more active and mobile and were also caught significantly more often than females, resulting in a pronounced shift in sex ratio in the predicted population structure. The adults use a wide range of nectar plants and establish homeranges in areas of high habitat quality. Thus, Erebia pronoe adults use a wide array of resources combined with a slight specialisation to avoid niche overlap with closely related species. The resulting ecological flexibility seems to be an adaptation to unpredictable environmental conditions, which should be the result of a long-lasting adaptation process. Moreover, the combination of opportunism and modest specialisation should also be a good basis for coping with future changes caused by climate and land-use change.</p> <br /> <br></p> <br /> A mark-recapture study of the nominotypical Erebia pronoe in the Alps was conducted to survey its ecological demands and characteristics. Population structure analysis revealed a combination of protandry (one-week earlier eclosion of males) and serial eclosion. Significant differences between both sexes were found in population density (males: 580/ha \& PLUSMN; 37 SE; females: 241/ha \& PLUSMN; 66 SE), sex-ratio (2.4) and behaviour (57.7 vs. 11.9\% flying). Both sexes used a wide range of nectar plants (Asteraceae, 77.3\%; Dipsacaceae, 12.3\%; Gentianaceae, 9.7\%). The use of nectar plants shows a non-specific spectrum, which, however, completely avoids overlap with the locally co-occurring species Erebia nivalis. Movement patterns show the establishment of homeranges, which significantly limits the migration potential. Due to its broad ecological niche, E. pronoe will probably be able to react plastically to the consequences of climate change. The formation of high population densities, the unconcerned endangerment status, the unspecific resource spectrum and the sedentary character of the species make E. pronoe a potential indicator of the quality and general resource occurrence of alpine rupicolous grasslands.},
  language  = {en}
}
@article{WarmtFenzelHenkeletal.2021,
  author    = {Warmt, Christian and Fenzel, Carolin Kornelia and Henkel, J{\"o}rg and Bier, Frank Fabian},
  title     = {Using Cy5-dUTP labelling of RPA-amplicons with downstream microarray analysis for the detection of antibiotic resistance genes},
  series = {Scientific reports},
  volume    = {11},
  journal   = {Scientific reports},
  number    = {1},
  publisher = {Macmillan Publishers Limited, part of Springer Nature},
  address   = {[London]},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-021-99774-z},
  pages     = {9},
  year      = {2021},
  abstract  = {In this report we describe Cy5-dUTP labelling of recombinase-polymerase-amplification (RPA) products directly during the amplification process for the first time. Nucleic acid amplification techniques, especially polymerase-chain-reaction as well as various isothermal amplification methods such as RPA, becomes a promising tool in the detection of pathogens and target specific genes. Actually, RPA even provides more advantages. This isothermal method got popular in point of care diagnostics because of its speed and sensitivity but requires pre-labelled primer or probes for a following detection of the amplicons. To overcome this disadvantages, we performed an labelling of RPA-amplicons with Cy5-dUTP without the need of pre-labelled primers. The amplification results of various multiple antibiotic resistance genes indicating great potential as a flexible and promising tool with high specific and sensitive detection capabilities of the target genes. After the determination of an appropriate rate of 1\% Cy5-dUTP and 99\% unlabelled dTTP we were able to detect the bla(CTX-M15) gene in less than 1.6E-03 ng genomic DNA corresponding to approximately 200 cfu of Escherichia coli cells in only 40 min amplification time.},
  language  = {en}
}
@article{WangLiMaetal.2021,
  author    = {Wang, Meng and Li, Panpan and Ma, Yao and Nie, Xiang and Grebe, Markus and Men, Shuzhen},
  title     = {Membrane sterol composition in Arabidopsis thaliana affects root elongation via auxin biosynthesis},
  series = {International journal of molecular sciences},
  volume    = {22},
  journal   = {International journal of molecular sciences},
  number    = {1},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {1422-0067},
  doi       = {10.3390/ijms22010437},
  pages     = {20},
  year      = {2021},
  abstract  = {Plant membrane sterol composition has been reported to affect growth and gravitropism via polar auxin transport and auxin signaling. However, as to whether sterols influence auxin biosynthesis has received little attention. Here, by using the sterol biosynthesis mutant cyclopropylsterol isomerase1-1 (cpi1-1) and sterol application, we reveal that cycloeucalenol, a CPI1 substrate, and sitosterol, an end-product of sterol biosynthesis, antagonistically affect auxin biosynthesis. The short root phenotype of cpi1-1 was associated with a markedly enhanced auxin response in the root tip. Both were neither suppressed by mutations in polar auxin transport (PAT) proteins nor by treatment with a PAT inhibitor and responded to an auxin signaling inhibitor. However, expression of several auxin biosynthesis genes TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 (TAA1) was upregulated in cpi1-1. Functionally, TAA1 mutation reduced the auxin response in cpi1-1 and partially rescued its short root phenotype. In support of this genetic evidence, application of cycloeucalenol upregulated expression of the auxin responsive reporter DR5:GUS (beta-glucuronidase) and of several auxin biosynthesis genes, while sitosterol repressed their expression. Hence, our combined genetic, pharmacological, and sterol application studies reveal a hitherto unexplored sterol-dependent modulation of auxin biosynthesis during Arabidopsis root elongation.},
  language  = {en}
}
@article{WandtWinkelbeinerBornhorstetal.2021,
  author    = {Wandt, Viktoria Klara Veronika and Winkelbeiner, Nicola Lisa and Bornhorst, Julia and Witt, Barbara and Raschke, Stefanie and Simon, Luise and Ebert, Franziska and Kipp, Anna Patricia and Schwerdtle, Tanja},
  title     = {A matter of concern},
  series = {Redox Biology},
  volume    = {41},
  journal   = {Redox Biology},
  publisher = {Elsevier},
  address   = {Amsterdam},
  doi       = {10.1016/j.redox.2021.101877},
  pages     = {13},
  year      = {2021},
  abstract  = {Neurons are post-mitotic cells in the brain and their integrity is of central importance to avoid neurodegeneration. Yet, the inability of self-replenishment of post-mitotic cells results in the need to withstand challenges from numerous stressors during life. Neurons are exposed to oxidative stress due to high oxygen consumption during metabolic activity in the brain. Accordingly, DNA damage can occur and accumulate, resulting in genome instability. In this context, imbalances in brain trace element homeostasis are a matter of concern, especially regarding iron, copper, manganese, zinc, and selenium. Although trace elements are essential for brain physiology, excess and deficient conditions are considered to impair neuronal maintenance. Besides increasing oxidative stress, DNA damage response and repair of oxidative DNA damage are affected by trace elements. Hence, a balanced trace element homeostasis is of particular importance to safeguard neuronal genome integrity and prevent neuronal loss. This review summarises the current state of knowledge on the impact of deficient, as well as excessive iron, copper, manganese, zinc, and selenium levels on neuronal genome stability},
  language  = {en}
}
@phdthesis{Verbancic2021,
  author    = {Verbancic, Jana},
  title     = {Carbon supply and the regulation of primary cell wall synthesis in Arabidopsis thaliana},
  school      = {Universit{\"a}t Potsdam},
  pages     = {x, 179},
  year      = {2021},
  abstract  = {Cellulose is the most abundant biopolymer on Earth and cell wall (CW) synthesis is one of the major carbon consumers in the plant cell. Structure and several interaction partners of plasma membrane (PM)-bound cellulose synthase (CESA) complexes, CSCs, have been studied extensively, but much less is understood about the signals that activate and translocate CESAs to the PM and how exactly cellulose synthesis is being regulated during the diel cycle. The literature describes CSC regulation possibilities through interactions with accessory proteins upon stress conditions (e.g. CC1), post-translational modifications that regulate CSC speed and their possible anchoring in the PM (e.g. with phosphorylation and S-acylation, respectively). In this thesis, 13CO2 labeling and imaging techniques were employed in the same Arabidopsis seedling growth system to elucidate how and when new carbon is incorporated into cell wall (CW) sugars and UDP-glucose, and to follow CSC behavior during the diel cycle. Additionally, an ubiquitination analysis was performed to investigate a possible mechanism to affect CSC trafficking to and/or from the PM. Carbon is being incorporated into CW glucose at a 3-fold higher rate during the light period in comparison to the night in wild-type seedlings. Furthermore, CSC density at the PM, as an indication of active cellulose synthesizing machinery, is increasing in the light and falling during the night, showing that CW biosynthesis is more active in the light. Therefore, CW synthesis might be regulated by the carbon status of the cell. This regulation is broken in the starchless pgm mutant where light and dark carbon incorporation rates into CW glucose are similar, possibly due to the high soluble sugar content in pgm during the first part of the night. Strikingly, pgm CSC abundance at the PM is constantly low during the whole diel cycle, indicating little or no cellulose synthesis, but can be restored with exogenous sucrose or a longer photoperiod. Ubiquitination was explored as a possible regulating mechanism for translocation of primary CW CSCs from the PM and several potential ubiquitination sites have been identified.. The approach in this thesis enabled to study cellulose/CW synthesis from different angles but in the same growth system, allowing direct comparison of those methodologies, which could help understand the relationship between the amount of available carbon in a plant cell and the cells capacity to synthesize cellulose/CW. Understanding which factors contribute to cellulose synthesis regulation and addressing those fundamental questions can provide essential knowledge to manage the need for increased crop production.},
  language  = {en}
}
@phdthesis{Uflewski2021,
  author    = {Uflewski, Michal},
  title     = {Characterizing the regulation of proton antiport across the thylakoid membrane},
  school      = {Universit{\"a}t Potsdam},
  pages     = {122},
  year      = {2021},
  abstract  = {Die Energie, die zum Antrieb photochemischer Reaktionen ben{\"o}tigt wird, stammt aus der Ladungstrennung an der Thylakoidmembran. Aufrgrund des Unterschieds in der Protonenkonzentration zwischen dem Stroma der Chloroplasten und dem Thylakoidlumen wird eine Protonenmotorische Kraft (pmf) erzeugt. Die pmf setzt sich aus dem Protonengradienten (ΔpH) und dem Membranpotential (ΔΨ) zusammen, die gemeinsam die ATP-Synthese antreiben. In der Natur schwankt die Energiemenge, die die Photosynthese antreibt, aufgrund h{\"a}ufiger {\"A}nderungen der Lichtintensit{\"a}t. Der Thylakoid-Ionentransport kann den Energiefluss durch einen Photosyntheseapparat an die Lichtverf{\"u}gbarkeit anpassen, indem er die pmf-Zusammensetzung ver{\"a}ndert. Die Dissipation von ΔΨ verringert die Ladungsrekombination am Photosystem II, so dass ein Anstieg der ΔpH-Komponente eine R{\"u}ckkopplung zur Herabregulierung der Photosynthese ausl{\"o}sen kann. Der durch den K+-Austausch-Antiporter 3 (KEA3) gesteuerte K+/H+-Antiport reduziert den ΔpH-Anteil von pmf und d{\"a}mpft dadurch das nicht-photochemische Quenching (NPQ). Infolgedessen erh{\"o}ht sich die Photosyntheseeffizienz beim {\"U}bergang zu geringerer Lichtintensit{\"a}t. Ziel dieser Arbeit war es, Antworten auf Fragen zur Regulierung der KEA3-Aktivit{\"a}t und ihrer Rolle in der Pflanzenentwicklung zu finden. Die vorgestellten Daten zeigen, dass KEA3 in Pflanzen, denen der Chloroplasten-ATP-Synthase-Assembly-Faktor CGL160 fehlt und die eine verminderte ATP-Synthase-Aktivit{\"a}t aufweisen, eine zentrale Rolle bei der Regulierung der Photosynthese und des Pflanzenwachstums unter station{\"a}ren Bedingungen spielt. Das Fehlen von KEA3 in der cgl160-Mutante f{\"u}hrt zu einer starken Beeintr{\"a}chtigung des Wachstums, da die Photosynthese aufgrund des erh{\"o}hten pH-abh{\"a}ngigen NPQs und des verringerten Elektronenflusses durch den Cytochrom b6f-Komplex eingeschr{\"a}nkt ist. Die {\"U}berexpression von KEA3 in der cgl160-Mutante erh{\"o}ht die Ladungsrekombination im Photosystem II und f{\"o}rdert die Photosynthese. In Zeiten geringer ATP-Synthase-Aktivit{\"a}t profitieren die Pflanzen also von der KEA3-Aktivit{\"a}t. KEA3 unterliegt einer Dimerisierung {\"u}ber seinen regulatorischen C-Terminus (RCT). Der RCT reagiert auf Ver{\"a}nderungen der Lichtintensit{\"a}t, da die Pflanzen, die KEA3 ohne diese Dom{\"a}ne exprimieren, einen reduzierten Lichtschutzmechanismus bei Lichtintensit{\"a}tsschwankungen aufweisen. Allerdings fixieren diese Pflanzen w{\"a}hrend der Photosynthese-Induktionsphase mehr Kohlenstoff als Gegenleistung f{\"u}r einen langfristigen Photoprotektor, was die regulierende Rolle von KEA3 in der Pflanzenentwicklung zeigt. Der KEA3-RCT ist dem Thylakoidstroma zugewandt, so dass seine Regulierung von lichtinduzierten Ver{\"a}nderungen in der Stroma-Umgebung abh{\"a}ngt. Die Regulierung der KEA3-Aktivit{\"a}t {\"u}berschneidet sich mit den pH-{\"A}nderungen im Stroma, die bei Lichtschwankungen auftreten. Es hat sich gezeigt, dass ATP und ADP eine Affinit{\"a}t zum heterolog exprimierten KEA3 RCT haben. Eine solche Wechselwirkung verursacht Konformations{\"a}nderungen in der RCT-Struktur. Die Faltung der RCT-Liganden-Interaktion h{\"a}ngt vom pH-Wert der Umgebung ab. Mit einer Kombination aus Bioinformatik und In-vitro-Ansatz wurde die ATP-Bindungsstelle am RCT lokalisiert. Das Einf{\"u}gen einer Punktmutation in der KEA3-RCT Bindungsstelle in planta f{\"u}hrte zu einer Deregulierung der Antiporteraktivit{\"a}t beim {\"U}bergang zu wenig Licht. Die in dieser Arbeit vorgestellten Daten erm{\"o}glichten es uns, die Rolle von KEA3 bei der Anpassung der Photosynthese umfassender zu bewerten und Modelle zur Regulierung der KEA3-Aktivit{\"a}t w{\"a}hrend des {\"U}bergangs zwischen verschiedenen Lichtintensit{\"a}ten vorzuschlagen.},
  language  = {en}
}
@article{TungSunWangetal.2021,
  author    = {Tung, Wing Tai and Sun, Xianlei and Wang, Weiwei and Xu, Xun and Ma, Nan and Lendlein, Andreas},
  title     = {Structure, mechanical properties and degradation behavior of electrospun PEEU fiber meshes and films},
  series = {MRS advances : a journal of the Materials Research Society (MRS)},
  volume    = {6},
  journal   = {MRS advances : a journal of the Materials Research Society (MRS)},
  number    = {10},
  publisher = {Springer Nature Switzerland AG},
  address   = {Cham},
  issn      = {2059-8521},
  doi       = {10.1557/s43580-020-00001-0},
  pages     = {276 -- 282},
  year      = {2021},
  abstract  = {The capability of a degradable implant to provide mechanical support depends on its degradation behavior. Hydrolytic degradation was studied for a polyesteretherurethane (PEEU70), which consists of poly(p-dioxanone) (PPDO) and poly(epsilon-caprolactone) (PCL) segments with a weight ratio of 70:30 linked by diurethane junction units. PEEU70 samples prepared in the form of meshes with average fiber diameters of 1.5 mu m (mesh1.5) and 1.2 mu m (mesh1.2), and films were sterilized and incubated in PBS at 37 degrees C with 5 vol\% CO2 supply for 1 to 6 weeks. Degradation features, such as cracks or wrinkles, became apparent from week 4 for all samples. Mass loss was found to be 11 wt\%, 6 wt\%, and 4 wt\% for mesh1.2, mesh1.5, and films at week 6. The elongation at break decreased to under 20\% in two weeks for mesh1.2. In case of the other two samples, this level of degradation was achieved after 4 weeks. The weight average molecular weight of both PEEU70 mesh and film samples decreased to below 30 kg/mol when elongation at break dropped below 20\%. The time period of sustained mechanical stability of PEEU70-based meshes depends on the fiber diameter and molecular weight.},
  language  = {en}
}