@article{ZhengToenjesPikovskij2021,
  author    = {Zheng, Chunming and Toenjes, Ralf and Pikovskij, Arkadij},
  title     = {Transition to synchrony in a three-dimensional swarming model with helical trajectories},
  series = {Physical review : E, Statistical, nonlinear and soft matter physics},
  volume    = {104},
  journal   = {Physical review : E, Statistical, nonlinear and soft matter physics},
  number    = {1},
  publisher = {American Physical Society},
  address   = {College Park},
  issn      = {2470-0045},
  doi       = {10.1103/PhysRevE.104.014216},
  pages     = {7},
  year      = {2021},
  abstract  = {We investigate the transition from incoherence to global collective motion in a three-dimensional swarming model of agents with helical trajectories, subject to noise and global coupling. Without noise this model was recently proposed as a generalization of the Kuramoto model and it was found that alignment of the velocities occurs discontinuously for arbitrarily small attractive coupling. Adding noise to the system resolves this singular limit and leads to a continuous transition, either to a directed collective motion or to center-of-mass rotations.},
  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{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}
}
@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}
}
@article{WitteLinnemannstoensHonemannCapitoetal.2021,
  author    = {Witte, Leonie and Linnemannstoens, Karen and Honemann-Capito, Mona and Groß, Julia Christina},
  title     = {Visualization and quantitation of Wg trafficking in the Drosophila wing imaginal epithelium},
  series = {Bio-protocol},
  volume    = {11},
  journal   = {Bio-protocol},
  number    = {11},
  publisher = {bio-protocol.org},
  address   = {Sunnyvale, CA},
  issn      = {2331-8325},
  doi       = {10.21769/BioProtoc.4040},
  pages     = {16},
  year      = {2021},
  abstract  = {Secretory Wnt trafficking can be studied in the polarized epithelial monolayer of Drosophila wing imaginal discs (WID). In this tissue, Wg (Drosophila Wnt-I) is presented on the apical surface of its source cells before being internalized into the endosomal pathway. Long-range Wg secretion and spread depend on secondary secretion from endosomal compartments, but the exact post-endocytic fate of Wg is poorly understood. Here, we summarize and present three protocols for the immunofluorescencebased visualization and quantitation of different pools of intracellular and extracellular Wg in WID: (1) steady-state extracellular Wg; (2) dynamic Wg trafficking inside endosomal compartments; and (3) dynamic Wg release to the cell surface. Using a genetic driver system for gene manipulation specifically at the posterior part of the WID (EnGal4) provides a robust internal control that allows for direct comparison of signal intensities of control and manipulated compartments of the same WID. Therefore, it also circumvents the high degree of staining variability usually associated with whole-tissue samples. In combination with the genetic manipulation of Wg pathway components that is easily feasible in Drosophila, these methods provide a tool-set for the dissection of secretory Wg trafficking and can help us to understand how Wnt proteins travel along endosomal compartments for short-and long-range signal secretion.},
  language  = {en}
}
@article{WittStibollerRaschkeetal.2021,
  author    = {Witt, Barbara and Stiboller, Michael and Raschke, Stefanie and Friese, Sharleen and Ebert, Franziska and Schwerdtle, Tanja},
  title     = {Characterizing effects of excess copper levels in a human astrocytic cell line with focus on oxidative stress markers},
  series = {Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements, GMS},
  volume    = {65},
  journal   = {Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements, GMS},
  publisher = {Elsevier},
  address   = {M{\"u}nchen},
  issn      = {1878-3252},
  doi       = {10.1016/j.jtemb.2021.126711},
  pages     = {9},
  year      = {2021},
  abstract  = {Background: Being an essential trace element, copper is involved in diverse physiological processes. However, excess levels might lead to adverse effects. Disrupted copper homeostasis, particularly in the brain, has been associated with human diseases including the neurodegenerative disorders Wilson and Alzheimer?s disease. In this context, astrocytes play an important role in the regulation of the copper homeostasis in the brain and likely in the prevention against neuronal toxicity, consequently pointing them out as a potential target for the neurotoxicity of copper. Major toxic mechanisms are discussed to be directed against mitochondria probably via oxidative stress. However, the toxic potential and mode of action of copper in astrocytes is poorly understood, so far. Methods: In this study, excess copper levels affecting human astrocytic cell model and their involvement in the neurotoxic mode of action of copper, as well as, effects on the homeostasis of other trace elements (Mn, Fe, Ca and Mg) were investigated. Results: Copper induced substantial cytotoxic effects in the human astrocytic cell line following 48 h incubation (EC30: 250 ?M) and affected mitochondrial function, as observed via reduction of mitochondrial membrane potential and increased ROS production, likely originating from mitochondria. Moreover, cellular GSH metabolism was altered as well. Interestingly, not only cellular copper levels were affected, but also the homeostasis of other elements (Ca, Fe and Mn) were disrupted. Conclusion: One potential toxic mode of action of copper seems to be effects on the mitochondria along with induction of oxidative stress in the human astrocytic cell model. Moreover, excess copper levels seem to interact with the homeostasis of other essential elements such as Ca, Fe and Mn. Disrupted element homeostasis might also contribute to the induction of oxidative stress, likely involved in the onset and progression of neurodegenerative disorders. These insights in the toxic mechanisms will help to develop ideas and approaches for therapeutic strategies against copper-mediated diseases.},
  language  = {en}
}
@article{WiggerSchumacherSchneiderSchauliesetal.2021,
  author    = {Wigger, Dominik and Schumacher, Fabian and Schneider-Schaulies, Sibylle and Kleuser, Burkhard},
  title     = {Sphingosine 1-phosphate metabolism and insulin signaling},
  series = {Cellular signalling},
  volume    = {82},
  journal   = {Cellular signalling},
  publisher = {Elsevier Science},
  address   = {Amsterdam [u.a.]},
  issn      = {0898-6568},
  doi       = {10.1016/j.cellsig.2021.109959},
  pages     = {16},
  year      = {2021},
  abstract  = {Insulin is the main anabolic hormone secreted by 13-cells of the pancreas stimulating the assimilation and storage of glucose in muscle and fat cells. It modulates the postprandial balance of carbohydrates, lipids and proteins via enhancing lipogenesis, glycogen and protein synthesis and suppressing glucose generation and its release from the liver. Resistance to insulin is a severe metabolic disorder related to a diminished response of peripheral tissues to the insulin action and signaling. This leads to a disturbed glucose homeostasis that precedes the onset of type 2 diabetes (T2D), a disease reaching epidemic proportions. A large number of studies reported an association between elevated circulating fatty acids and the development of insulin resistance. The increased fatty acid lipid flux results in the accumulation of lipid droplets in a variety of tissues. However, lipid intermediates such as diacylglycerols and ceramides are also formed in response to elevated fatty acid levels. These bioactive lipids have been associated with the pathogenesis of insulin resistance. More recently, sphingosine 1-phosphate (S1P), another bioactive sphingolipid derivative, has also been shown to increase in T2D and obesity. Although many studies propose a protective role of S1P metabolism on insulin signaling in peripheral tissues, other studies suggest a causal role of S1P on insulin resistance. In this review, we critically summarize the current state of knowledge of S1P metabolism and its modulating role on insulin resistance. A particular emphasis is placed on S1P and insulin signaling in hepatocytes, skeletal muscle cells, adipocytes and pancreatic 13-cells. In particular, modulation of receptors and enzymes that regulate S1P metabolism can be considered as a new therapeutic option for the treatment of insulin resistance and T2D.},
  language  = {en}
}
@article{WetzelScholtkaSchumacheretal.2021,
  author    = {Wetzel, Alexandra Nicole and Scholtka, Bettina and Schumacher, Fabian and Rawel, Harshadrai Manilal and Geisend{\"o}rfer, Birte and Kleuser, Burkhard},
  title     = {Epigenetic DNA methylation of EBI3 modulates human interleukin-35 formation via NFkB signaling},
  series = {International journal of molecular sciences},
  volume    = {22},
  journal   = {International journal of molecular sciences},
  number    = {10},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {1422-0067},
  doi       = {10.3390/ijms22105329},
  pages     = {21},
  year      = {2021},
  abstract  = {Ulcerative colitis (UC), a severe chronic disease with unclear etiology that is associated with increased risk for colorectal cancer, is accompanied by dysregulation of cytokines. Epstein-Barr virus-induced gene 3 (EBI3) encodes a subunit in the unique heterodimeric IL-12 cytokine family of either pro- or anti-inflammatory function. After having recently demonstrated that upregulation of EBI3 by histone acetylation alleviates disease symptoms in a dextran sulfate sodium (DSS)-treated mouse model of chronic colitis, we now aimed to examine a possible further epigenetic regulation of EBI3 by DNA methylation under inflammatory conditions. Treatment with the DNA methyltransferase inhibitor (DNMTi) decitabine (DAC) and TNF alpha led to synergistic upregulation of EBI3 in human colon epithelial cells (HCEC). Use of different signaling pathway inhibitors indicated NF kappa B signaling was necessary and proportional to the synergistic EBI3 induction. MALDI-TOF/MS and HPLC-ESIMS/MS analysis of DAC/TNF alpha-treated HCEC identified IL-12p35 as the most probable binding partner to form a functional protein. EBI3/IL-12p35 heterodimers (IL-35) induce their own gene upregulation, something that was indeed observed in HCEC cultured with media from previously DAC/TNF alpha-treated HCEC. These results suggest that under inflammatory and demethylating conditions the upregulation of EBI3 results in the formation of anti-inflammatory IL-35, which might be considered as a therapeutic target in colitis.},
  language  = {en}
}
@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{WehrhanPuppeKaczoreketal.2021,
  author    = {Wehrhan, Marc and Puppe, Daniel and Kaczorek, Danuta and Sommer, Michael},
  title     = {Spatial patterns of aboveground phytogenic Si stocks in a grass-dominated catchment},
  series = {Biogeosciences : BG},
  volume    = {18},
  journal   = {Biogeosciences : BG},
  number    = {18},
  publisher = {Copernicus},
  address   = {G{\"o}ttingen},
  issn      = {1726-4170},
  doi       = {10.5194/bg-18-5163-2021},
  pages     = {5163 -- 5183},
  year      = {2021},
  abstract  = {Various studies have been performed to quantify silicon (Si) stocks in plant biomass and related Si fluxes in terrestrial biogeosystems. Most studies are deliberately designed on the plot scale to ensure low heterogeneity in soils and plant composition, hence similar environmental conditions. Due to the immanent spatial soil variability, the transferability of results to larger areas, such as catchments, is therefore limited. However, the emergence of new technical features and increasing knowledge on details in Si cycling lead to a more complex picture at landscape and catchment scales. Dynamic and static soil properties change along the soil continuum and might influence not only the species composition of natural vegetation but also its biomass distribution and related Si stocks. Maximum likelihood (ML) classification was applied to multispectral imagery captured by an unmanned aerial system (UAS) aiming at the identification of land cover classes (LCCs). Subsequently, the normalized difference vegetation index (NDVI) and ground-based measurements of biomass were used to quantify aboveground Si stocks in two Si-accumulating plants (Calamagrostis epige-jos and Phragmites australis) in a heterogeneous catchment and related corresponding spatial patterns of these stocks to soil properties. We found aboveground Si stocks of C. epige-jos and P. australis to be surprisingly high (maxima of Si stocks reach values up to 98 g Sim(-2)), i.e. comparable to or markedly exceeding reported values for the Si storage in aboveground vegetation of various terrestrial ecosystems. We further found spatial patterns of plant aboveground Si stocks to reflect spatial heterogeneities in soil properties. From our results, we concluded that (i) aboveground biomass of plants seems to be the main factor of corresponding phytogenic Si stock quantities, and (ii) a detection of biomass heterogeneities via UAS-based remote sensing represents a promising tool for the quantification of lifelike phytogenic Si pools at landscape scales.},
  language  = {en}
}
@article{WardelmannRathCastroetal.2021,
  author    = {Wardelmann, Kristina and Rath, Michaela and Castro, Jos{\´e} Pedro and Bl{\"u}mel, Sabine and Schell, Mareike and Hauffe, Robert and Schumacher, Fabian and Flore, Tanina and Ritter, Katrin and Wernitz, Andreas and Hosoi, Toru and Ozawa, Koichiro and Kleuser, Burkhard and Weiß, J{\"u}rgen and Sch{\"u}rmann, Annette and Kleinridders, Andr{\´e}},
  title     = {Central acting Hsp10 regulates mitochondrial function, fatty acid metabolism and insulin sensitivity in the hypothalamus},
  series = {Antioxidants},
  volume    = {10},
  journal   = {Antioxidants},
  number    = {5},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2076-3921},
  doi       = {10.3390/antiox10050711},
  pages     = {22},
  year      = {2021},
  abstract  = {Mitochondria are critical for hypothalamic function and regulators of metabolism. Hypothalamic mitochondrial dysfunction with decreased mitochondrial chaperone expression is present in type 2 diabetes (T2D). Recently, we demonstrated that a dysregulated mitochondrial stress response (MSR) with reduced chaperone expression in the hypothalamus is an early event in obesity development due to insufficient insulin signaling. Although insulin activates this response and improves metabolism, the metabolic impact of one of its members, the mitochondrial chaperone heat shock protein 10 (Hsp10), is unknown. Thus, we hypothesized that a reduction of Hsp10 in hypothalamic neurons will impair mitochondrial function and impact brain insulin action. Therefore, we investigated the role of chaperone Hsp10 by introducing a lentiviral-mediated Hsp10 knockdown (KD) in the hypothalamic cell line CLU-183 and in the arcuate nucleus (ARC) of C57BL/6N male mice. We analyzed mitochondrial function and insulin signaling utilizing qPCR, Western blot, XF96 Analyzer, immunohistochemistry, and microscopy techniques. We show that Hsp10 expression is reduced in T2D mice brains and regulated by leptin in vitro. Hsp10 KD in hypothalamic cells induced mitochondrial dysfunction with altered fatty acid metabolism and increased mitochondria-specific oxidative stress resulting in neuronal insulin resistance. Consequently, the reduction of Hsp10 in the ARC of C57BL/6N mice caused hypothalamic insulin resistance with acute liver insulin resistance.},
  language  = {en}
}
@article{WangCherstvyKantzetal.2021,
  author    = {Wang, Wei and Cherstvy, Andrey G. and Kantz, Holger and Metzler, Ralf and Sokolov, Igor M.},
  title     = {Time averaging and emerging nonergodicity upon resetting of fractional Brownian motion and heterogeneous diffusion processes},
  series = {Physical review : E, Statistical, nonlinear and soft matter physics},
  volume    = {104},
  journal   = {Physical review : E, Statistical, nonlinear and soft matter physics},
  number    = {2},
  publisher = {American Institute of Physics},
  address   = {Woodbury, NY},
  issn      = {2470-0045},
  doi       = {10.1103/PhysRevE.104.024105},
  pages     = {27},
  year      = {2021},
  abstract  = {How different are the results of constant-rate resetting of anomalous-diffusion processes in terms of their ensemble-averaged versus time-averaged mean-squared displacements (MSDs versus TAMSDs) and how does stochastic resetting impact nonergodicity? We examine, both analytically and by simulations, the implications of resetting on the MSD- and TAMSD-based spreading dynamics of particles executing fractional Brownian motion (FBM) with a long-time memory, heterogeneous diffusion processes (HDPs) with a power-law space-dependent diffusivity D(x) = D0|x|gamma and their "combined" process of HDP-FBM. We find, inter alia, that the resetting dynamics of originally ergodic FBM for superdiffusive Hurst exponents develops disparities in scaling and magnitudes of the MSDs and mean TAMSDs indicating weak ergodicity breaking. For subdiffusive HDPs we also quantify the nonequivalence of the MSD and TAMSD and observe a new trimodal form of the probability density function. For reset FBM, HDPs and HDP-FBM we compute analytically and verify by simulations the short-time MSD and TAMSD asymptotes and long-time plateaus reminiscent of those for processes under confinement. We show that certain characteristics of these reset processes are functionally similar despite a different stochastic nature of their nonreset variants. Importantly, we discover nonmonotonicity of the ergodicitybreaking parameter EB as a function of the resetting rate r. For all reset processes studied we unveil a pronounced resetting-induced nonergodicity with a maximum of EB at intermediate r and EB similar to(1/r )-decay at large r. Alongside the emerging MSD-versus-TAMSD disparity, this r-dependence of EB can be an experimentally testable prediction. We conclude by discussing some implications to experimental systems featuring resetting dynamics.},
  language  = {en}
}
@article{WangDanielsConnellyetal.2021,
  author    = {Wang, Ningzhen and Daniels, Robert and Connelly, Liam and Sotzing, Michael and Wu, Chao and Gerhard, Reimund and Sotzing, Gregory A. and Cao, Yang},
  title     = {All-organic flexible ferroelectret nanogenerator with fabric-based electrodes for self-powered body area networks},
  series = {Small : nano micro},
  volume    = {17},
  journal   = {Small : nano micro},
  number    = {33},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {1613-6810},
  doi       = {10.1002/smll.202103161},
  pages     = {11},
  year      = {2021},
  abstract  = {Due to their electrically polarized air-filled internal pores, optimized ferroelectrets exhibit a remarkable piezoelectric response, making them suitable for energy harvesting. Expanded polytetrafluoroethylene (ePTFE) ferroelectret films are laminated with two fluorinated-ethylene-propylene (FEP) copolymer films and internally polarized by corona discharge. Poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS)-coated spandex fabric is employed for the electrodes to assemble an all-organic ferroelectret nanogenerator (FENG). The outer electret-plus-electrode double layers form active device layers with deformable electric dipoles that strongly contribute to the overall piezoelectric response in the proposed concept of wearable nanogenerators. Thus, the FENG with spandex electrodes generates a short-circuit current which is twice as high as that with aluminum electrodes. The stacking sequence spandex/FEP/ePTFE/FEP/ePTFE/FEP/spandex with an average pore size of 3 mu m in the ePTFE films yields the best overall performance, which is also demonstrated by the displacement-versus-electric-field loop results. The all-organic FENGs are stable up to 90 degrees C and still perform well 9 months after being polarized. An optimized FENG makes three light emitting diodes (LEDs) blink twice with the energy generated during a single footstep. The new all-organic FENG can thus continuously power wearable electronic devices and is easily integrated, for example, with clothing, other textiles, or shoe insoles.},
  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}
}
@phdthesis{Tung2021,
  author    = {Tung, Wing Tai},
  title     = {Polymeric fibrous scaffold on macro/microscale towards tissue regeneration},
  school      = {Universit{\"a}t Potsdam},
  year      = {2021},
  language  = {en}
}
@article{TongKuekenRazaghiMoghadametal.2021,
  author    = {Tong, Hao and K{\"u}ken, Anika and Razaghi-Moghadam, Zahra and Nikoloski, Zoran},
  title     = {Characterization of effects of genetic variants via genome-scale metabolic modelling},
  series = {Cellular and molecular life sciences : CMLS},
  volume    = {78},
  journal   = {Cellular and molecular life sciences : CMLS},
  number    = {12},
  publisher = {Springer International Publishing AG},
  address   = {Cham},
  issn      = {1420-682X},
  doi       = {10.1007/s00018-021-03844-4},
  pages     = {5123 -- 5138},
  year      = {2021},
  abstract  = {Genome-scale metabolic networks for model plants and crops in combination with approaches from the constraint-based modelling framework have been used to predict metabolic traits and design metabolic engineering strategies for their manipulation. With the advances in technologies to generate large-scale genotyping data from natural diversity panels and other populations, genome-wide association and genomic selection have emerged as statistical approaches to determine genetic variants associated with and predictive of traits. Here, we review recent advances in constraint-based approaches that integrate genetic variants in genome-scale metabolic models to characterize their effects on reaction fluxes. Since some of these approaches have been applied in organisms other than plants, we provide a critical assessment of their applicability particularly in crops. In addition, we further dissect the inferred effects of genetic variants with respect to reaction rate constants, abundances of enzymes, and concentrations of metabolites, as main determinants of reaction fluxes and relate them with their combined effects on complex traits, like growth. Through this systematic review, we also provide a roadmap for future research to increase the predictive power of statistical approaches by coupling them with mechanistic models of metabolism.},
  language  = {en}
}
@phdthesis{Ting2021,
  author    = {Ting, Michael Kien Yin},
  title     = {Circadian-regulated dynamics of translation in Arabidopsis thaliana},
  school      = {Universit{\"a}t Potsdam},
  pages     = {130},
  year      = {2021},
  language  = {en}
}
@article{TchewonpiSaguLandgraeberHenkeletal.2021,
  author    = {Tchewonpi Sagu, Sorel and Landgr{\"a}ber, Eva and Henkel, Ina M. and Huschek, Gerd and Homann, Thomas and Bußler, Sara and Schl{\"u}ter, Oliver K. and Rawel, Harshadrai Manilal},
  title     = {Effect of cereal α-amylase/trypsin inhibitors on developmental characteristics and abundance of digestive enzymes of mealworm larvae (Tenebrio molitor L.)},
  series = {Insects},
  volume    = {12},
  journal   = {Insects},
  number    = {5},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2075-4450},
  doi       = {10.3390/insects12050454},
  pages     = {16},
  year      = {2021},
  abstract  = {The objective of this work was to investigate the potential effect of cereal α-amylase/trypsin inhibitors (ATIs) on growth parameters and selective digestive enzymes of Tenebrio molitor L. larvae. The approach consisted of feeding the larvae with wheat, sorghum and rice meals containing different levels and composition of α-amylase/trypsin inhibitors. The developmental and biochemical characteristics of the larvae were assessed over feeding periods of 5 h, 5 days and 10 days, and the relative abundance of α-amylase and selected proteases in larvae were determined using liquid chromatography tandem mass spectrometry. Overall, weight gains ranged from 21\% to 42\% after five days of feeding. The larval death rate significantly increased in all groups after 10 days of feeding (p < 0.05), whereas the pupation rate was about 25\% among larvae fed with rice (Oryza sativa L.) and Siyazan/Esperya wheat meals, and only 8\% and 14\% among those fed with Damougari and S35 sorghum meals. As determined using the Lowry method, the protein contents of the sodium phosphate extracts ranged from 7.80 ± 0.09 to 9.42 ± 0.19 mg/mL and those of the ammonium bicarbonate/urea reached 19.78 ± 0.16 to 37.47 ± 1.38 mg/mL. The total protein contents of the larvae according to the Kjeldahl method ranged from 44.0 and 49.9 g/100 g. The relative abundance of α-amylase, CLIP domain-containing serine protease, modular serine protease zymogen and C1 family cathepsin significantly decreased in the larvae, whereas dipeptidylpeptidase I and chymotrypsin increased within the first hours after feeding (p < 0.05). Trypsin content was found to be constant independently of time or feed material. Finally, based on the results we obtained, it was difficult to substantively draw conclusions on the likely effects of meal ATI composition on larval developmental characteristics, but their effects on the digestive enzyme expression remain relevant.},
  language  = {en}
}
@article{TadjoungWaffoMitrovaTiedemannetal.2021,
  author    = {Tadjoung Waffo, Armel Franklin and Mitrova, Biljana and Tiedemann, Kim and Iobbi-Nivol, Chantal and Leimk{\"u}hler, Silke and Wollenberger, Ulla},
  title     = {Electrochemical trimethylamine n-oxide biosensor with enzyme-based oxygen-scavenging membrane for long-term operation under ambient air},
  series = {Biosensors : open access journal},
  volume    = {11},
  journal   = {Biosensors : open access journal},
  number    = {4},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2079-6374},
  doi       = {10.3390/bios11040098},
  pages     = {17},
  year      = {2021},
  abstract  = {An amperometric trimethylamine N-oxide (TMAO) biosensor is reported, where TMAO reductase (TorA) and glucose oxidase (GOD) and catalase (Cat) were immobilized on the electrode surface, enabling measurements of mediated enzymatic TMAO reduction at low potential under ambient air conditions. The oxygen anti-interference membrane composed of GOD, Cat and polyvinyl alcohol (PVA) hydrogel, together with glucose concentration, was optimized until the O-2 reduction current of a Clark-type electrode was completely suppressed for at least 3 h. For the preparation of the TMAO biosensor, Escherichia coli TorA was purified under anaerobic conditions and immobilized on the surface of a carbon electrode and covered by the optimized O-2 scavenging membrane. The TMAO sensor operates at a potential of -0.8 V vs. Ag/AgCl (1 M KCl), where the reduction of methylviologen (MV) is recorded. The sensor signal depends linearly on TMAO concentrations between 2 mu M and 15 mM, with a sensitivity of 2.75 +/- 1.7 mu A/mM. The developed biosensor is characterized by a response time of about 33 s and an operational stability over 3 weeks. Furthermore, measurements of TMAO concentration were performed in 10\% human serum, where the lowest detectable concentration is of 10 mu M TMAO.},
  language  = {en}
}
@article{StieglerKiemelEccardetal.2021,
  author    = {Stiegler, Jonas and Kiemel, Katrin and Eccard, Jana and Fischer, Christina and Hering, Robert and Ortmann, Sylvia and Strigl, Lea and Tiedemann, Ralph and Ullmann, Wiebke and Blaum, Niels},
  title     = {Seed traits matter},
  series = {Ecology and evolution},
  volume    = {11},
  journal   = {Ecology and evolution},
  number    = {24},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.8440},
  pages     = {18477 -- 18491},
  year      = {2021},
  abstract  = {Although many plants are dispersed by wind and seeds can travel long distances across unsuitable matrix areas, a large proportion relies on co-evolved zoochorous seed dispersal to connect populations in isolated habitat islands. Particularly in agricultural landscapes, where remaining habitat patches are often very small and highly isolated, mobile linkers as zoochorous seed dispersers are critical for the population dynamics of numerous plant species. However, knowledge about the quali- or quantification of such mobile link processes, especially in agricultural landscapes, is still limited. In a controlled feeding experiment, we recorded the seed intake and germination success after complete digestion by the European brown hare (Lepus europaeus) and explored its mobile link potential as an endozoochoric seed disperser. Utilizing a suite of common, rare, and potentially invasive plant species, we disentangled the effects of seed morphological traits on germination success while controlling for phylogenetic relatedness. Further, we measured the landscape connectivity via hares in two contrasting agricultural landscapes (simple: few natural and semi-natural structures, large fields; complex: high amount of natural and semi-natural structures, small fields) using GPS-based movement data. With 34,710 seeds of 44 plant species fed, one of 200 seeds (0.51\%) with seedlings of 33 species germinated from feces. Germination after complete digestion was positively related to denser seeds with comparatively small surface area and a relatively slender and elongated shape, suggesting that, for hares, the most critical seed characteristics for successful endozoochorous seed dispersal minimize exposure of the seed to the stomach and the associated digestive system. Furthermore, we could show that a hare's retention time is long enough to interconnect different habitats, especially grasslands and fields. Thus, besides other seed dispersal mechanisms, this most likely allows hares to act as effective mobile linkers contributing to ecosystem stability in times of agricultural intensification, not only in complex but also in simple landscapes.},
  language  = {en}
}
@article{StieglerKiemelEccardetal.2021,
  author    = {Stiegler, Jonas and Kiemel, Katrin and Eccard, Jana and Fischer, Christina and Hering, Robert and Ortmann, Sylvia and Strigl, Lea and Tiedemann, Ralph},
  title     = {Seed traits matter},
  series = {Ecology and Evolution},
  volume    = {11},
  journal   = {Ecology and Evolution},
  number    = {24},
  publisher = {John Wiley \& Sons, Inc.},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.8440},
  pages     = {18477 -- 18491},
  year      = {2021},
  abstract  = {Although many plants are dispersed by wind and seeds can travel long distances across unsuitable matrix areas, a large proportion relies on co-evolved zoochorous seed dispersal to connect populations in isolated habitat islands. Particularly in agricultural landscapes, where remaining habitat patches are often very small and highly isolated, mobile linkers as zoochorous seed dispersers are critical for the population dynamics of numerous plant species. However, knowledge about the quali- or quantification of such mobile link processes, especially in agricultural landscapes, is still limited. In a controlled feeding experiment, we recorded the seed intake and germination success after complete digestion by the European brown hare (Lepus europaeus) and explored its mobile link potential as an endozoochoric seed disperser. Utilizing a suite of common, rare, and potentially invasive plant species, we disentangled the effects of seed morphological traits on germination success while controlling for phylogenetic relatedness. Further, we measured the landscape connectivity via hares in two contrasting agricultural landscapes (simple: few natural and semi-natural structures, large fields; complex: high amount of natural and semi-natural structures, small fields) using GPS-based movement data. With 34,710 seeds of 44 plant species fed, one of 200 seeds (0.51\%) with seedlings of 33 species germinated from feces. Germination after complete digestion was positively related to denser seeds with comparatively small surface area and a relatively slender and elongated shape, suggesting that, for hares, the most critical seed characteristics for successful endozoochorous seed dispersal minimize exposure of the seed to the stomach and the associated digestive system. Furthermore, we could show that a hare's retention time is long enough to interconnect different habitats, especially grasslands and fields. Thus, besides other seed dispersal mechanisms, this most likely allows hares to act as effective mobile linkers contributing to ecosystem stability in times of agricultural intensification, not only in complex but also in simple landscapes.},
  language  = {en}
}
@article{SteppertSchoenfelderSchultzetal.2021,
  author    = {Steppert, Isabel and Sch{\"o}nfelder, Jessy and Schultz, Carolyn and Kuhlmeier, Dirk},
  title     = {Rapid in vitro differentiation of bacteria by ion mobility spectrometry},
  series = {Applied Microbiology and Biotechnology},
  volume    = {105},
  journal   = {Applied Microbiology and Biotechnology},
  number    = {10},
  publisher = {Springer},
  address   = {New York},
  issn      = {0175-7598},
  doi       = {10.1007/s00253-021-11315-w},
  pages     = {4297 -- 4307},
  year      = {2021},
  abstract  = {Rapid screening of infected people plays a crucial role in interrupting infection chains. However, the current methods for identification of bacteria are very tedious and labor intense. Fast on-site screening for pathogens based on volatile organic compounds (VOCs) by ion mobility spectrometry (IMS) could help to differentiate between healthy and potentially infected subjects. As a first step towards this, the feasibility of differentiating between seven different bacteria including resistant strains was assessed using IMS coupled to multicapillary columns (MCC-IMS). The headspace above bacterial cultures was directly drawn and analyzed by MCC-IMS after 90 min of incubation. A cluster analysis software and statistical methods were applied to select discriminative VOC clusters. As a result, 63 VOC clusters were identified, enabling the differentiation between all investigated bacterial strains using canonical discriminant analysis. These 63 clusters were reduced to 7 discriminative VOC clusters by constructing a hierarchical classification tree. Using this tree, all bacteria including resistant strains could be classified with an AUC of 1.0 by receiver-operating characteristic analysis. In conclusion, MCC-IMS is able to differentiate the tested bacterial species, even the non-resistant and their corresponding resistant strains, based on VOC patterns after 90 min of cultivation. Although this result is very promising, in vivo studies need to be performed to investigate if this technology is able to also classify clinical samples. With a short analysis time of 5 min, MCC-IMS is quite attractive for a rapid screening for possible infections in various locations from hospitals to airports. Key Points center dot Differentiation of bacteria by MCC-IMS is shown after 90-min cultivation. center dot Non-resistant and resistant strains can be distinguished. center dot Classification of bacteria is possible based on metabolic features.},
  language  = {en}
}
@inproceedings{StephanBarbirzRobinsonetal.2021,
  author    = {Stephan, Mareike Sophia and Barbirz, Stefanie and Robinson, Tom and Yandrapalli, Naresh and Dimova, Rumiana},
  title     = {Bacterial mimetic systems for studying bacterial inactivation and infection},
  series = {Biophysical journal : BJ / ed. by the Biophysical Society},
  volume    = {120},
  booktitle = {Biophysical journal : BJ / ed. by the Biophysical Society},
  number    = {3},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {0006-3495},
  doi       = {10.1016/j.bpj.2020.11.1087},
  pages     = {148A -- 148A},
  year      = {2021},
  language  = {en}
}
@article{StarkBachGuill2021,
  author    = {Stark, Markus and Bach, Moritz and Guill, Christian},
  title     = {Patch isolation and periodic environmental disturbances have idiosyncratic effects on local and regional population variabilities in meta-food chains},
  series = {Theoretical ecology},
  volume    = {14},
  journal   = {Theoretical ecology},
  number    = {3},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {1874-1738},
  doi       = {10.1007/s12080-021-00510-0},
  pages     = {489 -- 500},
  year      = {2021},
  abstract  = {While habitat loss is a known key driver of biodiversity decline, the impact of other landscape properties, such as patch isolation, is far less clear. When patch isolation is low, species may benefit from a broader range of foraging opportunities, but are at the same time adversely affected by higher predation pressure from mobile predators. Although previous approaches have successfully linked such effects to biodiversity, their impact on local and metapopulation dynamics has largely been ignored. Since population dynamics may also be affected by environmental disturbances that temporally change the degree of patch isolation, such as periodic changes in habitat availability, accurate assessment of its link with isolation is highly challenging. To analyze the effect of patch isolation on the population dynamics on different spatial scales, we simulate a three-species meta-food chain on complex networks of habitat patches and assess the average variability of local populations and metapopulations, as well as the level of synchronization among patches. To evaluate the impact of periodic environmental disturbances, we contrast simulations of static landscapes with simulations of dynamic landscapes in which 30 percent of the patches periodically become unavailable as habitat. We find that increasing mean patch isolation often leads to more asynchronous population dynamics, depending on the parameterization of the food chain. However, local population variability also increases due to indirect effects of increased dispersal mortality at high mean patch isolation, consequently destabilizing metapopulation dynamics and increasing extinction risk. In dynamic landscapes, periodic changes of patch availability on a timescale much slower than ecological interactions often fully synchronize the dynamics. Further, these changes not only increase the variability of local populations and metapopulations, but also mostly overrule the effects of mean patch isolation. This may explain the often small and inconclusive impact of mean patch isolation in natural ecosystems.},
  language  = {en}
}
@article{SpikesRodriguezSilvaBennettetal.2021,
  author    = {Spikes, Montrai and Rodr{\´i}guez-Silva, Rodet and Bennett, Kerri-Ann and Br{\"a}ger, Stefan and Josaphat, James and Torres-Pineda, Patricia and Ernst, Anja and Havenstein, Katja and Schlupp, Ingo and Tiedemann, Ralph},
  title     = {A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario},
  series = {BMC Research Notes},
  volume    = {14},
  journal   = {BMC Research Notes},
  publisher = {BMC Research Notes / Biomed Central},
  address   = {London},
  issn      = {1756-0500},
  doi       = {10.1186/s13104-021-05843-x},
  pages     = {1 -- 8},
  year      = {2021},
  abstract  = {Objective The Caribbean is an important global biodiversity hotspot. Adaptive radiations there lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. A prime example are freshwater fish of the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Mirago{\^a}ne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Mirago{\^a}ne, relative to their congeners throughout the Caribbean. Results For 12 Limia species, we obtained almost complete sequences of the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships. We included sequences of six further Limia species from GenBank (total N  = 18 species). Our phylogenies are in concordance with other published phylogenies of Limia. There is strong support that the species found in Lake Mirago{\^a}ne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Mirago{\^a}ne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies using multiple unlinked genetic markers are needed to disentangle the relationships within the Lake Mirago{\^a}ne clade.},
  language  = {en}
}
@article{SoeriyadiOngleyKehretal.2021,
  author    = {Soeriyadi, Angela H. and Ongley, Sarah E. and Kehr, Jan-Christoph and Pickford, Russel and Dittmann, Elke and Neilan, Brett A.},
  title     = {Tailoring enzyme stringency masks the multispecificity of a lyngbyatoxin (indolactam alkaloid) nonribosomal peptide synthetase},
  series = {ChemBioChem},
  volume    = {23},
  journal   = {ChemBioChem},
  number    = {3},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {1439-4227},
  doi       = {10.1002/cbic.202100574},
  pages     = {6},
  year      = {2021},
  abstract  = {Indolactam alkaloids are activators of protein kinase C (PKC) and are of pharmacological interest for the treatment of pathologies involving PKC dysregulation. The marine cyanobacterial nonribosomal peptide synthetase (NRPS) pathway for lyngbyatoxin biosynthesis, which we previously expressed in E. coli, was studied for its amenability towards the biosynthesis of indolactam variants. Modification of culture conditions for our E. coli heterologous expression host and analysis of pathway products suggested the native lyngbyatoxin pathway NRPS does possess a degree of relaxed specificity. Site-directed mutagenesis of two positions within the adenylation domain (A-domain) substrate-binding pocket was performed, resulting in an alteration of substrate preference between valine, isoleucine, and leucine. We observed relative congruence of in vitro substrate activation by the LtxA NRPS to in vivo product formation. While there was a preference for isoleucine over leucine, the substitution of alternative tailoring domains may unveil the true in vivo effects of the mutations introduced herein.},
  language  = {en}
}
@article{SmithRheinwaltBookhagen2021,
  author    = {Smith, Taylor and Rheinwalt, Aljoscha and Bookhagen, Bodo},
  title     = {Topography and climate in the upper Indus Basin},
  series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  volume    = {786},
  journal   = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0048-9697},
  doi       = {10.1016/j.scitotenv.2021.147363},
  pages     = {11},
  year      = {2021},
  abstract  = {The Upper Indus Basin (UIB), which covers a wide range of climatic and topographic settings, provides an ideal venue to explore the relationship between climate and topography. While the distribution of snow and glaciers is spatially and temporally heterogeneous, there exist regions with similar elevation-snow relationships. In this work, we construct elevation-binned snow-cover statistics to analyze 3415 watersheds and 7357 glaciers in the UIB region. We group both glaciers and watersheds using a hierarchical clustering approach and find that (1) watershed clusters mirror large-scale moisture transport patterns and (2) are highly dependent on median watershed elevation. (3) Glacier clusters are spatially heterogeneous and are less strongly controlled by elevation, but rather by local topographic parameters that modify solar insolation. Our clustering approach allows us to clearly define self-similar snow-topographic regions. Eastern watersheds in the UIB show a steep snow cover-elevation relationship whereas watersheds in the central and western UIB have moderately sloped relationships, but cluster in distinct groups. We highlight this snow-cover-topographic transition zone and argue that these watersheds have different hydrologic responses than other regions. Our hierarchical clustering approach provides a potential new framework to use in defining climatic zones in the cyrosphere based on empirical data.},
  language  = {en}
}
@article{SmirnovBolotovOsipovetal.2021,
  author    = {Smirnov, Lev A. and Bolotov, Maxim I. and Osipov, Grigorij V. and Pikovskij, Arkadij},
  title     = {Disorder fosters chimera in an array of motile particles},
  series = {Physical review : E, Statistical, nonlinear and soft matter physics},
  volume    = {104},
  journal   = {Physical review : E, Statistical, nonlinear and soft matter physics},
  number    = {3},
  publisher = {American Physical Society},
  address   = {Melville, NY},
  issn      = {2470-0045},
  doi       = {10.1103/PhysRevE.104.034205},
  pages     = {8},
  year      = {2021},
  abstract  = {We consider an array of nonlocally coupled oscillators on a ring, which for equally spaced units possesses a Kuramoto-Battogtokh chimera regime and a synchronous state. We demonstrate that disorder in oscillators positions leads to a transition from the synchronous to the chimera state. For a static (quenched) disorder we find that the probability of synchrony survival depends on the number of particles, from nearly zero at small populations to one in the thermodynamic limit. Furthermore, we demonstrate how the synchrony gets destroyed for randomly (ballistically or diffusively) moving oscillators. We show that, depending on the number of oscillators, there are different scalings of the transition time with this number and the velocity of the units.},
  language  = {en}
}
@misc{SenBoginMondaletal.2021,
  author    = {Sen, Jaydip and Bogin, Barry and Mondal, Nitish and Dey, Sima and Roy, Shreysai},
  title     = {Groundwater arsenic contamination in the Bengal Delta Plain is an important public health issue},
  series = {Human Biology and Public Health},
  volume    = {2021},
  journal   = {Human Biology and Public Health},
  number    = {1},
  editor    = {Scheffler, Christiane and Koziel, Slawomir and Hermanussen, Michael and Bogin, Barry},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  issn      = {2748-9957},
  doi       = {10.52905/hbph.v1.7},
  pages     = {1 -- 31},
  year      = {2021},
  abstract  = {There is a close association between human biology, epidemiology and public health. Exposure to toxic elements is one area of such associations and global concerns. The Bengal Delta Plain (BDP) is a region where contamination of ground water by arsenic has assumed epidemic proportions. Apart from dermatological manifestations, chronic exposure to arsenic causes a heavy toll through several carcinogenic and non-carcinogenic disorders. This article provides a global overview of groundwater arsenic contamination in the BDP region, especially the sources, speciation, and mobility of arsenic, and critically reviews the effects of arsenic on human health. The present review also provides a summary of comprehensive knowledge on various measures required for mitigation and social consequences of the problem of arsenic contaminated groundwater in the BDP region.},
  language  = {en}
}
@article{SchoenemannKocKarthaeuseretal.2021,
  author    = {Sch{\"o}nemann, Eric and Koc, Julian and Karth{\"a}user, Jana and {\"O}zcan, Onur and Schanzenbach, Dirk and Schardt, Lisa and Rosenhahn, Axel and Laschewsky, Andr{\´e}},
  title     = {Sulfobetaine methacrylate polymers of unconventional polyzwitterion architecture and their antifouling properties},
  series = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences},
  volume    = {22},
  journal   = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences},
  number    = {4},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1525-7797},
  doi       = {10.1021/acs.biomac.0c01705},
  pages     = {1494 -- 1508},
  year      = {2021},
  abstract  = {Combining high hydrophilicity with charge neutrality, polyzwitterions are intensely explored for their high biocompatibility and low-fouling properties. Recent reports indicated that in addition to charge neutrality, the zwitterion's segmental dipole orientation is an important factor for interacting with the environment. Accordingly, a series of polysulfobetaines with a novel architecture was designed, in which the cationic and anionic groups of the zwitterionic moiety are placed at equal distances from the backbone. They were investigated by in vitro biofouling assays, covering proteins of different charges and model marine organisms. All polyzwitterion coatings reduced the fouling effectively compared to model polymer surfaces of poly(butyl methacrylate), with a nearly equally good performance as the reference polybetaine poly(3-(N-(2-(methacryloyloxy)ethyl)-N,N-dimethylammonio)propanesulfonate). The specific fouling resistance depended on the detailed chemical structure of the polyzwitterions. Still, while clearly affecting the performance, the precise dipole orientation of the sulfobetaine group in the polyzwitterions seems overall to be only of secondary importance for their antifouling behavior.},
  language  = {en}
}
@article{SchneebergerSchulzeScheffleretal.2021,
  author    = {Schneeberger, Karin and Schulze, Michael and Scheffler, Ingo and Caspers, Barbara A.},
  title     = {Evidence of female preference for odor of distant over local males in a bat with female dispersal},
  series = {Behavioral ecology : the official journal of the International Society for Behavioral Ecology},
  volume    = {32},
  journal   = {Behavioral ecology : the official journal of the International Society for Behavioral Ecology},
  number    = {4},
  publisher = {Oxford University Press},
  address   = {Oxford},
  issn      = {1045-2249},
  doi       = {10.1093/beheco/arab003},
  pages     = {657 -- 661},
  year      = {2021},
  abstract  = {Geographic variation of sexually selected male traits is common in animals. Female choice also varies geographically and several studies found female preference for local males, which is assumed to lead to local adaptation and, therefore, increases fitness. As females are the nondispersing sex in most mammalian taxa, this preference for local males might be explained by the learning of male characteristics. Studies on the preference of females in female-dispersing species are lacking so far. To find out whether such females would also show preferences for local males, we conducted a study on greater sac-winged bats (Saccopteryx bilineata), a species where females disperse and males stay in their natal colony. Male greater sac-winged bats possess a wing pouch that is filled with odoriferous secretion and fanned toward females during courtship display. In a combination of chemical analysis and behavioral preference tests, we analyzed whether the composition of wing sac secretion varies between two geographically distinct populations (300 km), and whether females show a preference for local or distant male scent. Using gas chromatography, we found significant differences in the composition of the wing sac odors between the two geographically distinct populations. In addition, the behavioral preference experiments revealed that females of both populations preferred the scent of geographically distant males over local males. The wing sac odor might thus be used to guarantee optimal outbreeding when dispersing to a new colony. This is-to our knowledge-the first study on odor preference of females of a species with female-biased dispersal.},
  language  = {en}
}
@article{SchirrmannLandwehrGiebeletal.2021,
  author    = {Schirrmann, Michael and Landwehr, Niels and Giebel, Antje and Garz, Andreas and Dammer, Karl-Heinz},
  title     = {Early detection of stripe rust in winter wheat using deep residual neural networks},
  series = {Frontiers in plant science : FPLS},
  volume    = {12},
  journal   = {Frontiers in plant science : FPLS},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {1664-462X},
  doi       = {10.3389/fpls.2021.469689},
  pages     = {14},
  year      = {2021},
  abstract  = {Stripe rust (Pst) is a major disease of wheat crops leading untreated to severe yield losses. The use of fungicides is often essential to control Pst when sudden outbreaks are imminent. Sensors capable of detecting Pst in wheat crops could optimize the use of fungicides and improve disease monitoring in high-throughput field phenotyping. Now, deep learning provides new tools for image recognition and may pave the way for new camera based sensors that can identify symptoms in early stages of a disease outbreak within the field. The aim of this study was to teach an image classifier to detect Pst symptoms in winter wheat canopies based on a deep residual neural network (ResNet). For this purpose, a large annotation database was created from images taken by a standard RGB camera that was mounted on a platform at a height of 2 m. Images were acquired while the platform was moved over a randomized field experiment with Pst-inoculated and Pst-free plots of winter wheat. The image classifier was trained with 224 x 224 px patches tiled from the original, unprocessed camera images. The image classifier was tested on different stages of the disease outbreak. At patch level the image classifier reached a total accuracy of 90\%. To test the image classifier on image level, the image classifier was evaluated with a sliding window using a large striding length of 224 px allowing for fast test performance. At image level, the image classifier reached a total accuracy of 77\%. Even in a stage with very low disease spreading (0.5\%) at the very beginning of the Pst outbreak, a detection accuracy of 57\% was obtained. Still in the initial phase of the Pst outbreak with 2 to 4\% of Pst disease spreading, detection accuracy with 76\% could be attained. With further optimizations, the image classifier could be implemented in embedded systems and deployed on drones, vehicles or scanning systems for fast mapping of Pst outbreaks.},
  language  = {en}
}
@article{SchindlerMoldenhawerStangeetal.2021,
  author    = {Schindler, Daniel and Moldenhawer, Ted and Stange, Maike and Lepro, Valentino and Beta, Carsten and Holschneider, Matthias and Huisinga, Wilhelm},
  title     = {Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows},
  series = {PLoS Computational Biology : a new community journal},
  volume    = {17},
  journal   = {PLoS Computational Biology : a new community journal},
  number    = {8},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1553-734X},
  doi       = {10.1371/journal.pcbi.1009268},
  pages     = {33},
  year      = {2021},
  abstract  = {Amoeboid cell motility is essential for a wide range of biological processes including wound healing, embryonic morphogenesis, and cancer metastasis. It relies on complex dynamical patterns of cell shape changes that pose long-standing challenges to mathematical modeling and raise a need for automated and reproducible approaches to extract quantitative morphological features from image sequences. Here, we introduce a theoretical framework and a computational method for obtaining smooth representations of the spatiotemporal contour dynamics from stacks of segmented microscopy images. Based on a Gaussian process regression we propose a one-parameter family of regularized contour flows that allows us to continuously track reference points (virtual markers) between successive cell contours. We use this approach to define a coordinate system on the moving cell boundary and to represent different local geometric quantities in this frame of reference. In particular, we introduce the local marker dispersion as a measure to identify localized membrane expansions and provide a fully automated way to extract the properties of such expansions, including their area and growth time. The methods are available as an open-source software package called AmoePy, a Python-based toolbox for analyzing amoeboid cell motility (based on time-lapse microscopy data), including a graphical user interface and detailed documentation. Due to the mathematical rigor of our framework, we envision it to be of use for the development of novel cell motility models. We mainly use experimental data of the social amoeba Dictyostelium discoideum to illustrate and validate our approach. <br /> Author summary Amoeboid motion is a crawling-like cell migration that plays an important key role in multiple biological processes such as wound healing and cancer metastasis. This type of cell motility results from expanding and simultaneously contracting parts of the cell membrane. From fluorescence images, we obtain a sequence of points, representing the cell membrane, for each time step. By using regression analysis on these sequences, we derive smooth representations, so-called contours, of the membrane. Since the number of measurements is discrete and often limited, the question is raised of how to link consecutive contours with each other. In this work, we present a novel mathematical framework in which these links are described by regularized flows allowing a certain degree of concentration or stretching of neighboring reference points on the same contour. This stretching rate, the so-called local dispersion, is used to identify expansions and contractions of the cell membrane providing a fully automated way of extracting properties of these cell shape changes. We applied our methods to time-lapse microscopy data of the social amoeba Dictyostelium discoideum.},
  language  = {en}
}
@article{ScharnweberChaguacedaEkloev2021,
  author    = {Scharnweber, Inga Kristin and Chaguaceda, Fernando and Ekl{\"o}v, Peter},
  title     = {Fatty acid accumulation in feeding types of a natural freshwater fish population},
  series = {Oecologia / in cooperation with the International Association for Ecology, Intecol},
  volume    = {196},
  journal   = {Oecologia / in cooperation with the International Association for Ecology, Intecol},
  number    = {1},
  publisher = {Springer},
  address   = {Berlin ; Heidelberg [u.a.]},
  issn      = {0029-8549},
  doi       = {10.1007/s00442-021-04913-y},
  pages     = {53 -- 63},
  year      = {2021},
  abstract  = {Fatty acids are widely used to study trophic interactions in food web assemblages. Generally, it is assumed that there is a very small modification of fatty acids from one trophic step to another, making them suitable as trophic biomarkers. However, recent literature provides evidence that many fishes possess genes encoding enzymes with a role in bioconversion, thus the capability for bioconversion might be more widespread than previously assumed. Nonetheless, empirical evidence for biosynthesis occurring in natural populations remains scarce. In this study, we investigated different feeding types of perch (Perca fluviatilis) that are specialized on specific resources with different levels of highly unsaturated fatty acids (HUFAs), and analyzed the change between HUFA proportions in perch muscle tissue compared to their resources. Perch showed matching levels to their resources for EPA, but ARA and especially DHA were accumulated. Compound-specific stable isotope analyses helped us to identify the origin of HUFA carbon. Our results suggest that perch obtain a substantial amount of DHA via bioconversion when feeding on DHA-poor benthic resources. Thus, our data indicate the capability of bioconversion of HUFAs in a natural freshwater fish population.},
  language  = {en}
}
@article{ScharnweberAnderssonChaguacedaetal.2021,
  author    = {Scharnweber, Inga Kristin and Andersson, Matilda L. and Chaguaceda, Fernando and Ekl{\"o}v, Peter},
  title     = {Intraspecific differences in metabolic rates shape carbon stable isotope trophic discrimination factors of muscle tissue in the common teleost Eurasian perch (Perca fluviatilis)},
  series = {Ecology and evolution},
  volume    = {11},
  journal   = {Ecology and evolution},
  number    = {14},
  publisher = {John Wiley \& Sons, Inc.},
  address   = {New Jersey},
  issn      = {2045-7758},
  pages     = {9804 -- 9814},
  year      = {2021},
  abstract  = {Stable isotopes represent a unique approach to provide insights into the ecology of organisms. δ13C and δ15N have specifically been used to obtain information on the trophic ecology and food-web interactions. Trophic discrimination factors (TDF, Δ13C and Δ15N) describe the isotopic fractionation occurring from diet to consumer tissue, and these factors are critical for obtaining precise estimates within any application of δ13C and δ15N values. It is widely acknowledged that metabolism influences TDF, being responsible for different TDF between tissues of variable metabolic activity (e.g., liver vs. muscle tissue) or species body size (small vs. large). However, the connection between the variation of metabolism occurring within a single species during its ontogeny and TDF has rarely been considered. Here, we conducted a 9-month feeding experiment to report Δ13C and Δ15N of muscle and liver tissues for several weight classes of Eurasian perch (Perca fluviatilis), a widespread teleost often studied using stable isotopes, but without established TDF for feeding on a natural diet. In addition, we assessed the relationship between the standard metabolic rate (SMR) and TDF by measuring the oxygen consumption of the individuals. Our results showed a significant negative relationship of SMR with Δ13C, and a significant positive relationship of SMR with Δ15N of muscle tissue, but not with TDF of liver tissue. SMR varies inversely with size, which translated into a significantly different TDF of muscle tissue between size classes. In summary, our results emphasize the role of metabolism in shaping-specific TDF (i.e., Δ13C and Δ15N of muscle tissue) and especially highlight the substantial differences between individuals of different ontogenetic stages within a species. Our findings thus have direct implications for the use of stable isotope data and the applications of stable isotopes in food-web studies.},
  language  = {en}
}
@article{SauerGrebe2021,
  author    = {Sauer, Michael and Grebe, Markus},
  title     = {Plant cell biology},
  series = {Current biology : CB},
  volume    = {31},
  journal   = {Current biology : CB},
  number    = {9},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {0960-9822},
  doi       = {10.1016/j.cub.2021.03.070},
  pages     = {R449 -- R451},
  year      = {2021},
  abstract  = {PIN-FORMED (PIN) polar protein localization directs transport of the growth and developmental regulator auxin in plants. Once established after cytokinesis, PIN polarity requires maintenance. Now, direct interactions between PIN, MAB4/MEL and PID proteins suggest self-reinforced maintenance of PIN polarity through limiting lateral diffusion.},
  language  = {en}
}
@article{SantamansCordobaFrancoetal.2021,
  author    = {Santamans, Carla Daniela and Cordoba, Francisco E. and Franco, Mar{\´i}a G. and Vignoni, Paula and Lupo, Liliana C.},
  title     = {Hydro-climatological variability in Lagunas de Vilama System, Argentinean Altiplano-Puna Plateau, Southern Tropical Andes (22 degrees S) and its response to large-scale climate forcings},
  series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  volume    = {767},
  journal   = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0048-9697},
  doi       = {10.1016/j.scitotenv.2020.144926},
  pages     = {19},
  year      = {2021},
  abstract  = {The Altiplano-Puna Plateau holds several shallow lakes, which are very sensitive to climate changes. This work is focused on a high-altitude lake system called Lagunas de Vilama (LVS), located in a complex climatic transition area with scarcity of continuous and homogeneous instrumental records. The objective of this study is to determine the regional spatial-temporal variability of precipitation and evaluate the seasonal and interannual lake responses. We use a lake-surfaces record derived from Landsat images to investigate links with regional precipitations and different climatic forcings. The results reveal that austral summer and autumn precipitations control the variability of the annual lake-surfaces. Also, we found intra-annual and interannual lags in the lake responses to precipitations, and identified several wet and dry stages. Our results show negative trends in precipitations and lake-surfaces, whose were strengthened by a shift to a warm phase of the Atlantic Multidecadal Oscillation in the 1990s. The El Nino Southern Oscillation, Pacific Decadal Oscillation, and Southern Annular Mode also exert a strong influence in the region. This study demonstrates that the variability of LVS lakes is strongly related to the South American Monsoon System dynamics and large-scale climate fordngs from the Pacific and Atlantic Oceans. This work provides novel indices which demonstrated to be good indicators of regional hydroclimatological variability for this region of South America.},
  language  = {en}
}
@article{SandhageHofmannLinstaedterKindermannetal.2021,
  author    = {Sandhage-Hofmann, Alexandra and Linst{\"a}dter, Anja and Kindermann, Liana and Angombe, Simon and Amelung, Wulf},
  title     = {Conservation with elevated elephant densities sequesters carbon in soils despite losses of woody biomass},
  series = {Global change biology},
  volume    = {27},
  journal   = {Global change biology},
  number    = {19},
  publisher = {Blackwell Science},
  address   = {Oxford [u.a.]},
  issn      = {1354-1013},
  doi       = {10.1111/gcb.15779},
  pages     = {4601 -- 4614},
  year      = {2021},
  abstract  = {Nature conservation and restoration in terrestrial ecosystems is often focused on increasing the numbers of megafauna, expecting them to have positive impacts on ecological self-regulation processes and biodiversity. In sub-Saharan Africa, conservation efforts also aspire to protect and enhance biodiversity with particular focus on elephants. However, elephant browsing carries the risk of woody biomass losses. In this context, little is known about how increasing elephant numbers affects carbon stocks in soils, including the subsoils. We hypothesized that (1) increasing numbers of elephants reduce tree biomass, and thus the amount of C stored therein, resulting (2) in a loss of soil organic carbon (SOC). If true, a negative carbon footprint could limit the sustainability of elephant conservation from a global carbon perspective. To test these hypotheses, we selected plots of low, medium, and high elephant densities in two national parks and adjacent conservancies in the Namibian component of the Kavango Zambezi Transfrontier Area (KAZA), and quantified carbon storage in both woody vegetation and soils (1 m). Analyses were supplemented by the assessment of soil carbon isotopic composition. We found that increasing elephant densities resulted in a loss of tree carbon storage by 6.4 t ha(-1). However, and in contrast to our second hypothesis, SOC stocks increased by 4.7 t ha(-1) with increasing elephant densities. These higher SOC stocks were mainly found in the topsoil (0-30 cm) and were largely due to the formation of SOC from woody biomass. A second carbon input source into the soils was megaherbivore dung, which contributed with 0.02-0.323 t C ha(-1) year(-1) to ecosystem carbon storage in the low and high elephant density plots, respectively. Consequently, increasing elephant density does not necessarily lead to a negative C footprint, as soil carbon sequestration and transient C storage in dung almost compensate for losses in tree biomass.},
  language  = {en}
}
@article{RutschmannChenZhouetal.2021,
  author    = {Rutschmann, Sereina and Chen, Ping and Zhou, Changfa and Monaghan, Michael T.},
  title     = {Three mitochondrial genomes of early-winged insects (Ephemeroptera: Baetidae and Leptophlebiidae)},
  series = {Mitochondrial DNA Part B},
  volume    = {6},
  journal   = {Mitochondrial DNA Part B},
  number    = {10},
  publisher = {Routledge, Taylor \& Francis Group},
  address   = {Abingdon},
  issn      = {2380-2359},
  doi       = {10.1080/23802359.2021.1974966},
  pages     = {2969 -- 2971},
  year      = {2021},
  abstract  = {Mayflies (Ephemeroptera) are a semi-aquatic insect order with comparatively few genomic data available despite their phylogenetic position at the root of the winged-insects and possession of ancestral traits. Here, we provide three mitochondrial genomes (mtgenomes) from representatives of the two most species-rich families, Baetis rutilocylindratus and Cloeon dipterum (Baetidae), and Habrophlebiodes zijinensis (Leptophlebiidae). All mtgenomes had a complete set of 13 protein-coding genes and a conserved orientation except for two inverted tRNAs in H. zijinensis. Phylogenetic reconstructions using 21 mayfly mtgenomes and representatives of seven additional orders recovered both Baetidae and Leptophlebiidae as well supported monophyletic clades, with Ephemeroptera as the sister-taxon to all other winged insects (i.e. Odonata and Neoptera).},
  language  = {en}
}
@article{RottlerVormoorFranckeetal.2021,
  author    = {Rottler, Erwin and Vormoor, Klaus Josef and Francke, Till and Bronstert, Axel},
  title     = {Hydro Explorer},
  series = {River research and applications},
  volume    = {37},
  journal   = {River research and applications},
  number    = {4},
  publisher = {Wiley},
  address   = {New York},
  issn      = {1535-1459},
  doi       = {10.1002/rra.3772},
  pages     = {544 -- 554},
  year      = {2021},
  abstract  = {Climatic changes and anthropogenic modifications of the river basin or river network have the potential to fundamentally alter river runoff. In the framework of this study, we aim to analyze and present historic changes in runoff timing and runoff seasonality observed at river gauges all over the world. In this regard, we develop the Hydro Explorer, an interactive web app, which enables the investigation of >7,000 daily resolution discharge time series from the Global Runoff Data Centre (GRDC). The interactive nature of the developed web app allows for a quick comparison of gauges, regions, methods, and time frames. We illustrate the available analytical tools by investigating changes in runoff timing and runoff seasonality in the Rhine River Basin. Since we provide the source code of the application, existing analytical approaches can be modified, new methods added, and the tool framework can be re-used to visualize other data sets.},
  language  = {en}
}
@article{RomeroMujalliRochowKahletal.2021,
  author    = {Romero-Mujalli, Daniel and Rochow, Markus and Kahl, Sandra M. and Paraskevopoulou, Sofia and Folkertsma, Remco and Jeltsch, Florian and Tiedemann, Ralph},
  title     = {Adaptive and nonadaptive plasticity in changing environments: Implications for sexual species with different life history strategies},
  series = {Ecology and Evolution},
  volume    = {11},
  journal   = {Ecology and Evolution},
  number    = {11},
  publisher = {John Wiley \& Sons, Inc.},
  address   = {New Jersey},
  issn      = {2045-7758},
  pages     = {17},
  year      = {2021},
  abstract  = {Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses under variable conditions. Plasticity is typically modeled as random noise and linear reaction norms that assume simple one-to- one genotype-phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual-based model and study the relative importance of adaptive and nonadaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directiona climate change. Nonadaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, saturating, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (a) smaller phenotypic than genotypic variance in the population (many-to- one genotype-phenotype map) and the coexistence of polymorphisms, and (b) the maintenance of higher genetic variation—compared to linear reaction norms and genetic determinism—even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red environmental noise and was particularly important for life histories with low fecundity. Populations produing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast.},
  language  = {en}
}
@misc{Rogol2021,
  author    = {Rogol, Alan D.},
  title     = {Settings Perspective},
  series = {Human Biology and Public Health},
  volume    = {2021},
  journal   = {Human Biology and Public Health},
  number    = {1},
  editor    = {Scheffler, Christiane and Koziel, Slawomir and Hermanussen, Michael and Bogin, Barry},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  issn      = {2748-9957},
  doi       = {10.52905/hbph.v1.2},
  pages     = {1 -- 2},
  year      = {2021},
  language  = {en}
}
@article{RoeStreckBeachetal.2021,
  author    = {Roe, Stephanie and Streck, Charlotte and Beach, Robert and Busch, Jonah and Chapman, Melissa and Daioglou, Vassilis and Deppermann, Andre and Doelman, Jonathan and Emmet-Booth, Jeremy and Engelmann, Jens and Fricko, Oliver and Frischmann, Chad and Funk, Jason and Grassi, Giacomo and Griscom, Bronson and Havlik, Petr and Hanssen, Steef and Humpen{\"o}der, Florian and Landholm, David and Lomax, Guy and Lehmann, Johannes and Mesnildrey, Leah and Nabuurs, Gert-Jan and Popp, Alexander and Rivard, Charlotte and Sanderman, Jonathan and Sohngen, Brent and Smith, Pete and Stehfest, Elke and Woolf, Dominic and Lawrence, Deborah},
  title     = {Land-based measures to mitigate climate change},
  series = {Global change biology},
  volume    = {27},
  journal   = {Global change biology},
  number    = {23},
  publisher = {Wiley-Blackwell},
  address   = {Oxford},
  issn      = {1365-2486},
  doi       = {10.1111/gcb.15873},
  pages     = {6025 -- 6058},
  year      = {2021},
  abstract  = {Land-based climate mitigation measures have gained significant attention and importance in public and private sector climate policies. Building on previous studies, we refine and update the mitigation potentials for 20 land-based measures in >200 countries and five regions, comparing "bottom-up" sectoral estimates with integrated assessment models (IAMs). We also assess implementation feasibility at the country level. Cost-effective (available up to \$100/tCO2eq) land-based mitigation is 8-13.8 GtCO2eq yr-1 between 2020 and 2050, with the bottom end of this range representing the IAM median and the upper end representing the sectoral estimate. The cost-effective sectoral estimate is about 40\% of available technical potential and is in line with achieving a 1.5°C pathway in 2050. Compared to technical potentials, cost-effective estimates represent a more realistic and actionable target for policy. The cost-effective potential is approximately 50\% from forests and other ecosystems, 35\% from agriculture, and 15\% from demand-side measures. The potential varies sixfold across the five regions assessed (0.75-4.8 GtCO2eq yr-1) and the top 15 countries account for about 60\% of the global potential. Protection of forests and other ecosystems and demand-side measures present particularly high mitigation efficiency, high provision of co-benefits, and relatively lower costs. The feasibility assessment suggests that governance, economic investment, and socio-cultural conditions influence the likelihood that land-based mitigation potentials are realized. A substantial portion of potential (80\%) is in developing countries and LDCs, where feasibility barriers are of greatest concern. Assisting countries to overcome barriers may result in significant quantities of near-term, low-cost mitigation while locally achieving important climate adaptation and development benefits. Opportunities among countries vary widely depending on types of land-based measures available, their potential co-benefits and risks, and their feasibility. Enhanced investments and country-specific plans that accommodate this complexity are urgently needed to realize the large global potential from improved land stewardship.},
  language  = {en}
}
@misc{RobinKatharinaEmilyetal.2021,
  author    = {Robin, Koger and Katharina, Syb{\"o}ck and Emily, Weinelt and Beda, Hartmann and Kirchengast, Sylvia},
  title     = {Advanced maternal age and nicotine consumption during pregnancy},
  series = {Human Biology and Public Health},
  volume    = {2021},
  journal   = {Human Biology and Public Health},
  number    = {1},
  editor    = {Scheffler, Christiane and Koziel, Slawomir and Hermanussen, Michael and Bogin, Barry},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  issn      = {2748-9957},
  doi       = {10.52905/hbph.v1.6},
  pages     = {1 -- 19},
  year      = {2021},
  abstract  = {Background Nicotine consumption during pregnancy and advanced maternal age are well known independent risk factors for poor pregnancy outcome and therefore serious public health problems. Objectives Considering the ongoing trend of delaying childbirth in our society, this study investigates potential additive effects of nicotine consumption during pregnancy and advanced maternal age on foetal growth. Sample and Methods In a medical record-based study, we analysed the impact of maternal age and smoking behaviour before and during pregnancy on newborn size among 4142 singleton births that took place in Vienna, Austria between 1990 and 1995. Results Birth weight (H=82.176, p<0.001), birth length (H=91.525, p<0.001) and head circumference (H=42.097, p<0.001) differed significantly according to maternal smoking behaviour. For birth weight, the adjusted mean differences between smokers and non-smokers increased from 101.8g for the < 18-year-old mothers to 254.8g for >35 year olds, with the respective values for birth length being 0.6 cm to 0.7cm, for head circumference from 0.3 cm to 0.6 cm. Conclusion Increasing maternal age amplified the negative effects of smoking during pregnancy on newborn parameters. Our findings identify older smoking mothers as a high-risk group which should be of special interest for public health systems.},
  language  = {en}
}
@misc{RebekkaMummReimannScheffler2021,
  author    = {Rebekka Mumm, and Reimann, Anna and Scheffler, Christiane},
  title     = {Estimation of percentage of body fat in field studies - a method based on relative elbow breadth (Frame Index) and BMI},
  series = {Human Biology and Public Health},
  volume    = {2021},
  journal   = {Human Biology and Public Health},
  number    = {1},
  editor    = {Scheffler, Christiane and Koziel, Slawomir and Hermanussen, Michael and Bogin, Barry},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  issn      = {2748-9957},
  doi       = {10.52905/hbph.v1.3},
  pages     = {1 -- 12},
  year      = {2021},
  abstract  = {Background Over the last 20 years, a decreasing trend in external skeletal robusticity and an increasing trend in overweight and obesity was observed worldwide in adults and children as modern lifestyles in nutritional and activity behavior have changed. However, body mass index (BMI) as a measure for overweight is not an ideal predictor of \% body fat (\%BF) either in children and adolescents or in adults. On the contrary, it disguises a phenomenon called "hidden obesity". Objectives We aim to approximate \%BF by combining skeletal robusticity and BMI and develop an estimation-based tool to identify normal weight obese children and adolescents. Sample and Methods We analyzed cross-sectional data on height, weight, elbow breadth, and skinfold thickness (triceps and subscapular) of German children aged 6 to 18 years (N=15,034). We used modified Hattori charts and multiple linear regression to develop a tool, the "\%BF estimator", to estimate \%BF by using BMI and skeletal robusticity measured as Frame Index. Results Independent of sex and age an increase in BMI is associated with an increase in \%BF, an increase in Frame Index is associated with a decrease in \%BF. The developed tool "\%BF estimator" allows the estimation of \%BF per sex and age group after calculation of BMI and Frame Index. Conclusion The "\%BF estimator" is an easily applicable tool for the estimation of \%BF in respect of body composition for clinical practice, screening, and public health research. It is non-invasive and has high accuracy. Further, it allows the identification of normal weight obese children and adolescents.},
  language  = {en}
}
@article{RauschBrockmeyerSchwerdtle2021,
  author    = {Rausch, Ann-Kristin and Brockmeyer, Robert and Schwerdtle, Tanja},
  title     = {Development, validation, and application of a multi-method for the determination of mycotoxins, plant growth regulators, tropane alkaloids, and pesticides in cereals by two-dimensional liquid chromatography tandem mass spectrometry},
  series = {Analytical \& bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry, Analusis and Quimica analitica},
  volume    = {413},
  journal   = {Analytical \& bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry, Analusis and Quimica analitica},
  number    = {11},
  publisher = {Springer},
  address   = {Berlin},
  issn      = {1618-2650},
  doi       = {10.1007/s00216-021-03239-1},
  pages     = {3041 -- 3054},
  year      = {2021},
  abstract  = {Mycotoxins and pesticides regularly co-occur in agricultural products worldwide. Thus, humans can be exposed to both toxic contaminants and pesticides simultaneously, and multi-methods assessing the occurrence of various food contaminants and residues in a single method are necessary. A two-dimensional high performance liquid chromatography tandem mass spectrometry method for the analysis of 40 (modified) mycotoxins, two plant growth regulators, two tropane alkaloids, and 334 pesticides in cereals was developed. After an acetonitrile/water/formic acid (79:20:1, v/v/v) multi-analyte extraction procedure, extracts were injected into the two-dimensional setup, and an online clean-up was performed. The method was validated according to Commission Decision (EC) no. 657/2002 and document N° SANTE/12682/2019. Good linearity (R2 > 0.96), recovery data between 70-120\%, repeatability and reproducibility values < 20\%, and expanded measurement uncertainties < 50\% were obtained for a wide range of analytes, including very polar substances like deoxynivalenol-3-glucoside and methamidophos. However, results for fumonisins, zearalenone-14,16-disulfate, acid-labile pesticides, and carbamates were unsatisfying. Limits of quantification meeting maximum (residue) limits were achieved for most analytes. Matrix effects varied highly (-85 to +1574\%) and were mainly observed for analytes eluting in the first dimension and early-eluting analytes in the second dimension. The application of the method demonstrated the co-occurrence of different types of cereals with 28 toxins and pesticides. Overall, 86\% of the samples showed positive findings with at least one mycotoxin, plant growth regulator, or pesticide.},
  language  = {en}
}
@article{Ranisch2021,
  author    = {Ranisch, Robert},
  title     = {Consultation with Doctor Twitter},
  series = {The American journal of bioethics : ajob},
  volume    = {21},
  journal   = {The American journal of bioethics : ajob},
  number    = {7},
  publisher = {Routledge, Taylor \& Francis Group},
  address   = {Philadelphia, Pa.},
  issn      = {1526-5161},
  doi       = {10.1080/15265161.2021.1926595},
  pages     = {24 -- 25},
  year      = {2021},
  language  = {en}
}
@inproceedings{RamadanGuerreroNedielkovetal.2021,
  author    = {Ramadan, Shahenda and Guerrero, Paula and Nedielkov, Ruslan and Klishin, Nikolai and Dimova, Rumiana and Silva, Daniel V. and M{\"o}ller, Heiko},
  title     = {Building a mimetic system for unraveling protein-protein interactions on membranes},
  series = {European biophysics journal : with biophysics letters ; an international journal of biophysics},
  volume    = {50},
  booktitle = {European biophysics journal : with biophysics letters ; an international journal of biophysics},
  number    = {SUPPL 1},
  publisher = {Springer},
  address   = {Berlin ; Heidelberg ; New York},
  issn      = {0175-7571},
  doi       = {10.1007/s00249-021-01558-w},
  pages     = {S153 -- S153},
  year      = {2021},
  language  = {en}
}
@article{RajuKoetz2021,
  author    = {Raju, Rajarshi Roy and Koetz, Joachim},
  title     = {Inner rotation of Pickering Janus emulsions},
  series = {Nanomaterials : open access journal},
  volume    = {11},
  journal   = {Nanomaterials : open access journal},
  number    = {12},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2079-4991},
  doi       = {10.3390/nano11123312},
  pages     = {6},
  year      = {2021},
  abstract  = {Janus droplets were prepared by vortex mixing of three non-mixable liquids, i.e., olive oil, silicone oil and water, in the presence of gold nanoparticles (AuNPs) in the aqueous phase and magnetite nanoparticles (MNPs) in the olive oil. The resulting Pickering emulsions were stabilized by a red-colored AuNP layer at the olive oil/water interface and MNPs at the oil/oil interface. The core-shell droplets can be stimulated by an external magnetic field. Surprisingly, an inner rotation of the silicon droplet is observed when MNPs are fixed at the inner silicon droplet interface. This is the first example of a controlled movement of the inner parts of complex double emulsions by magnetic manipulation via interfacially confined magnetic nanoparticles.},
  language  = {en}
}
@article{RainerSeppeyHammeretal.2021,
  author    = {Rainer, Edda M. and Seppey, Christophe Victor William and Hammer, Caroline and Svenning, Mette M. and Tveit, Alexander Tosdal},
  title     = {The influence of above-ground herbivory on the response of Arctic soil methanotrophs to increasing CH4 concentrations and temperatures},
  series = {Microorganisms : open access journal},
  volume    = {9},
  journal   = {Microorganisms : open access journal},
  number    = {10},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2076-2607},
  doi       = {10.3390/microorganisms9102080},
  pages     = {20},
  year      = {2021},
  abstract  = {Rising temperatures in the Arctic affect soil microorganisms, herbivores, and peatland vegetation, thus directly and indirectly influencing microbial CH4 production. It is not currently known how methanotrophs in Arctic peat respond to combined changes in temperature, CH4 concentration, and vegetation. We studied methanotroph responses to temperature and CH4 concentration in peat exposed to herbivory and protected by exclosures. The methanotroph activity was assessed by CH4 oxidation rate measurements using peat soil microcosms and a pure culture of Methylobacter tundripaludum SV96, qPCR, and sequencing of pmoA transcripts. Elevated CH4 concentrations led to higher CH4 oxidation rates both in grazed and exclosed peat soils, but the strongest response was observed in grazed peat soils. Furthermore, the relative transcriptional activities of different methanotroph community members were affected by the CH4 concentrations. While transcriptional responses to low CH4 concentrations were more prevalent in grazed peat soils, responses to high CH4 concentrations were more prevalent in exclosed peat soils. We observed no significant methanotroph responses to increasing temperatures. We conclude that methanotroph communities in these peat soils respond to changes in the CH4 concentration depending on their previous exposure to grazing. This "conditioning " influences which strains will thrive and, therefore, determines the function of the methanotroph community.},
  language  = {en}
}
@article{RaatzPirhoferWalzlMuelleretal.2021,
  author    = {Raatz, Larissa and Pirhofer-Walzl, Karin and M{\"u}ller, Marina E.H. and Scherber, Christoph and Joshi, Jasmin Radha},
  title     = {Who is the culprit: Is pest infestation responsible for crop yield losses close to semi-natural habitats?},
  series = {Ecology and Evolution},
  volume    = {11},
  journal   = {Ecology and Evolution},
  edition   = {19},
  publisher = {Wiley-Blackwell},
  address   = {Oxford},
  issn      = {1467-6435},
  doi       = {10.1002/ece3.8046},
  pages     = {13232 -- 13246},
  year      = {2021},
  abstract  = {Semi-natural habitats (SNHs) are becoming increasingly scarce in modern agricultural landscapes. This may reduce natural ecosystem services such as pest control with its putatively positive effect on crop production. In agreement with other studies, we recently reported wheat yield reductions at field borders which were linked to the type of SNH and the distance to the border. In this experimental landscape-wide study, we asked whether these yield losses have a biotic origin while analyzing fungal seed and fungal leaf pathogens, herbivory of cereal leaf beetles, and weed cover as hypothesized mediators between SNHs and yield. We established experimental winter wheat plots of a single variety within conventionally managed wheat fields at fixed distances either to a hedgerow or to an in-field kettle hole. For each plot, we recorded the fungal infection rate on seeds, fungal infection and herbivory rates on leaves, and weed cover. Using several generalized linear mixed-effects models as well as a structural equation model, we tested the effects of SNHs at a field scale (SNH type and distance to SNH) and at a landscape scale (percentage and diversity of SNHs within a 1000-m radius). In the dry year of 2016, we detected one putative biotic culprit: Weed cover was negatively associated with yield values at a 1-m and 5-m distance from the field border with a SNH. None of the fungal and insect pests, however, significantly affected yield, neither solely nor depending on type of or distance to a SNH. However, the pest groups themselves responded differently to SNH at the field scale and at the landscape scale. Our findings highlight that crop losses at field borders may be caused by biotic culprits; however, their negative impact seems weak and is putatively reduced by conventional farming practices.},
  language  = {en}
}
@article{QuinzanGoebelWagneretal.2021,
  author    = {Quinzan, Francesco and G{\"o}bel, Andreas and Wagner, Markus and Friedrich, Tobias},
  title     = {Evolutionary algorithms and submodular functions},
  series = {Natural computing : an innovative journal bridging biosciences and computer sciences ; an international journal},
  volume    = {20},
  journal   = {Natural computing : an innovative journal bridging biosciences and computer sciences ; an international journal},
  number    = {3},
  publisher = {Springer Science + Business Media B.V.},
  address   = {Dordrecht},
  issn      = {1572-9796},
  doi       = {10.1007/s11047-021-09841-7},
  pages     = {561 -- 575},
  year      = {2021},
  abstract  = {A core operator of evolutionary algorithms (EAs) is the mutation. Recently, much attention has been devoted to the study of mutation operators with dynamic and non-uniform mutation rates. Following up on this area of work, we propose a new mutation operator and analyze its performance on the (1 + 1) Evolutionary Algorithm (EA). Our analyses show that this mutation operator competes with pre-existing ones, when used by the (1 + 1) EA on classes of problems for which results on the other mutation operators are available. We show that the (1 + 1) EA using our mutation operator finds a (1/3)-approximation ratio on any non-negative submodular function in polynomial time. We also consider the problem of maximizing a symmetric submodular function under a single matroid constraint and show that the (1 + 1) EA using our operator finds a (1/3)-approximation within polynomial time. This performance matches that of combinatorial local search algorithms specifically designed to solve these problems and outperforms them with constant probability. Finally, we evaluate the performance of the (1 + 1) EA using our operator experimentally by considering two applications: (a) the maximum directed cut problem on real-world graphs of different origins, with up to 6.6 million vertices and 56 million edges and (b) the symmetric mutual information problem using a four month period air pollution data set. In comparison with uniform mutation and a recently proposed dynamic scheme, our operator comes out on top on these instances.},
  language  = {en}
}
@article{PitzenSanderBaumannetal.2021,
  author    = {Pitzen, Valentin and Sander, Sophia and Baumann, Otto and Gr{\"a}f, Ralph and Meyer, Irene},
  title     = {Cep192, a novel missing link between the centrosomal core and corona in Dictyostelium amoebae},
  series = {Cells : open access journal},
  volume    = {10},
  journal   = {Cells : open access journal},
  number    = {9},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2073-4409},
  doi       = {10.3390/cells10092384},
  pages     = {19},
  year      = {2021},
  abstract  = {The Dictyostelium centrosome is a nucleus-associated body with a diameter of approx. 500 nm. It contains no centrioles but consists of a cylindrical layered core structure surrounded by a microtubule-nucleating corona. At the onset of mitosis, the corona disassembles and the core structure duplicates through growth, splitting, and reorganization of the outer core layers. During the last decades our research group has characterized the majority of the 42 known centrosomal proteins. In this work we focus on the conserved, previously uncharacterized Cep192 protein. We use superresolution expansion microscopy (ExM) to show that Cep192 is a component of the outer core layers. Furthermore, ExM with centrosomal marker proteins nicely mirrored all ultrastructurally known centrosomal substructures. Furthermore, we improved the proximity-dependent biotin identification assay (BioID) by adapting the biotinylase BioID2 for expression in Dictyostelium and applying a knock-in strategy for the expression of BioID2-tagged centrosomal fusion proteins. Thus, we were able to identify various centrosomal Cep192 interaction partners, including CDK5RAP2, which was previously allocated to the inner corona structure, and several core components. Studies employing overexpression of GFP-Cep192 as well as depletion of endogenous Cep192 revealed that Cep192 is a key protein for the recruitment of corona components during centrosome biogenesis and is required to maintain a stable corona structure.},
  language  = {en}
}
@article{Picconi2021,
  author    = {Picconi, David},
  title     = {Nonadiabatic quantum dynamics of the coherent excited state intramolecular proton transfer of 10-hydroxybenzo[h]quinoline},
  series = {Photochemical \& photobiological sciences},
  volume    = {20},
  journal   = {Photochemical \& photobiological sciences},
  number    = {11},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {1474-905X},
  doi       = {10.1007/s43630-021-00112-z},
  pages     = {1455 -- 1473},
  year      = {2021},
  abstract  = {The photoinduced nonadiabatic dynamics of the enol-keto isomerization of 10-hydroxybenzo[h]quinoline (HBQ) are studied computationally using high-dimensional quantum dynamics. The simulations are based on a diabatic vibronic coupling Hamiltonian, which includes the two lowest pi pi* excited states and a n pi* state, which has high energy in the Franck-Condon zone, but significantly stabilizes upon excited state intramolecular proton transfer. A procedure, applicable to large classes of excited state proton transfer reactions, is presented to parametrize this model using potential energies, forces and force constants, which, in this case, are obtained by time-dependent density functional theory. The wave packet calculations predict a time scale of 10-15 fs for the photoreaction, and reproduce the time constants and the coherent oscillations observed in time- resolved spectroscopic studies performed on HBQ. In contrast to the interpretation given to the most recent experiments, it is found that the reaction initiated by 1 pi pi* <- S-0 photoexcitation proceeds essentially on a single potential energy surface, and the observed coherences bear signatures of Duschinsky mode-mixing along the reaction path. The dynamics after the 2 pi pi* <- S-0 excitation are instead nonadiabatic, and the n pi* state plays a major role in the relaxation process. The simulations suggest a mainly active role of the proton in the isomerization, rather than a passive migration assisted by the vibrations of the benzoquinoline backbone. <br /> [GRAPHICS] <br /> .},
  language  = {en}
}
@article{PetrovićWendler2021,
  author    = {Petrović, Saša and Wendler, Petra},
  title     = {A RADD approach to probing AAA plus protein function},
  series = {Nature structural \& molecular biology},
  volume    = {28},
  journal   = {Nature structural \& molecular biology},
  number    = {4},
  publisher = {Nature Publishing Group},
  address   = {Berlin},
  issn      = {1545-9993},
  doi       = {10.1038/s41594-021-00579-5},
  pages     = {329 -- 330},
  year      = {2021},
  abstract  = {AAA+ proteins (ATPases associated with various cellular activities) catalyze the energy-dependent movement or rearrangement of macromolecules. A new study addresses the important question of how to design a selective chemical inhibitor for specific proteins in this diverse superfamily. The powerful chemical genetics approach adds to a growing toolbox of applications that allow dissection of the functions of distinct AAA+ proteins in vivo, facilitating the first steps toward effective drug development.},
  language  = {en}
}
@article{PetrichDunsingBoboneetal.2021,
  author    = {Petrich, Annett and Dunsing, Valentin and Bobone, Sara and Chiantia, Salvatore},
  title     = {Influenza A M2 recruits M1 to the plasma membrane},
  series = {Biophysical journal : BJ / ed. by the Biophysical Society},
  volume    = {120},
  journal   = {Biophysical journal : BJ / ed. by the Biophysical Society},
  number    = {24},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {0006-3495},
  doi       = {10.1016/j.bpj.2021.11.023},
  pages     = {5478 -- 5490},
  year      = {2021},
  abstract  = {Influenza A virus (IAV) is a respiratory pathogen that causes seasonal epidemics with significant mortality. One of the most abundant proteins in IAV particles is the matrix protein 1 (M1), which is essential for the virus structural stability. M1 organizes virion assembly and budding at the plasma membrane (PM), where it interacts with other viral components. The recruitment of M1 to the PM as well as its interaction with the other viral envelope proteins (hemagglutinin [HA], neuraminidase, matrix protein 2 [M2]) is controversially discussed in previous studies. Therefore, we used fluorescence fluctuation microscopy techniques (i.e., scanning fluorescence cross-correlation spectroscopy and number and brightness) to quantify the oligomeric state of M1 and its interactions with other viral proteins in co-transfected as well as infected cells. Our results indicate that M1 is recruited to the PM by M2, as a consequence of the strong interaction between the two proteins. In contrast, only a weak interaction between M1 and HA was observed. M1-HA interaction occurred only in the event that M1 was already bound to the PM. We therefore conclude that M2 initiates the assembly of IAV by recruiting M1 to the PM, possibly allowing its further interaction with other viral proteins.},
  language  = {en}
}
@article{PetazziKoikkarahAjiTischleretal.2021,
  author    = {Petazzi, Roberto Arturo and Koikkarah Aji, Amit and Tischler, Nicole D. and Chiantia, Salvatore},
  title     = {Detection of envelope glycoprotein assembly from old world hantaviruses in the Golgi apparatus of living cells},
  series = {Journal of virology},
  volume    = {95},
  journal   = {Journal of virology},
  number    = {4},
  publisher = {American Society for Microbiology},
  address   = {Baltimore, Md.},
  issn      = {1098-5514},
  doi       = {10.1128/JVI.01238-20},
  pages     = {18},
  year      = {2021},
  abstract  = {Hantaviruses are emerging pathogens that occasionally cause deadly outbreaks in the human population. While the structure of the viral envelope has been characterized with high precision, protein-protein interactions leading to the formation of new virions in infected cells are not fully understood. We used quantitative fluorescence microscopy (i.e., number and brightness analysis and fluorescence fluctuation spectroscopy) to monitor the interactions that lead to oligomeric spike complex formation in the physiological context of living cells. To this aim, we quantified protein-protein interactions for the glycoproteins Gn and Gc from Puumala and Hantaan orthohantaviruses in several cellular models. The oligomerization of each protein was analyzed in relation to subcellular localization, concentration, and the concentration of its interaction partner. Our results indicate that, when expressed separately, Gn and Gc form, respectively, homo-tetrameric and homo-dimeric complexes, in a concentration-dependent manner. Site-directed mutations or deletion mutants showed the specificity of their homotypic interactions. When both glycoproteins were coexpressed, we observed in the Golgi apparatus clear indication of GnGc interactions and the formation of Gn-Gc multimeric protein complexes of different sizes, while using various labeling schemes to minimize the influence of the fluorescent tags. Such large glycoprotein multimers may be identified as multiple Gn viral spikes interconnected via Gc-Gc contacts. This observation provides the possible first evidence for the initial assembly steps of the viral envelope within this organelle, and does so directly in living cells. <br /> IMPORTANCE In this work, we investigate protein-protein interactions that drive the assembly of the hantavirus envelope. These emerging pathogens have the potential to cause deadly outbreaks in the human population. Therefore, it is important to improve our quantitative understanding of the viral assembly process in infected cells, from a molecular point of view. By applying advanced fluorescence microscopy methods, we monitored the formation of viral spike complexes in different cell types. Our data support a model for hantavirus assembly according to which viral spikes are formed via the clustering of hetero-dimers of the two viral glycoproteins Gn and Gc. Furthermore, the observation of large Gn-Gc hetero-multimers provide the possible first evidence for the initial assembly steps of the viral envelope, directly in the Golgi apparatus of living cells.},
  language  = {en}
}
@article{Perscheid2021,
  author    = {Perscheid, Cindy},
  title     = {Integrative biomarker detection on high-dimensional gene expression data sets},
  series = {Briefings in bioinformatics},
  volume    = {22},
  journal   = {Briefings in bioinformatics},
  number    = {3},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1467-5463},
  doi       = {10.1093/bib/bbaa151},
  pages     = {18},
  year      = {2021},
  abstract  = {Gene expression data provide the expression levels of tens of thousands of genes from several hundred samples. These data are analyzed to detect biomarkers that can be of prognostic or diagnostic use. Traditionally, biomarker detection for gene expression data is the task of gene selection. The vast number of genes is reduced to a few relevant ones that achieve the best performance for the respective use case. Traditional approaches select genes based on their statistical significance in the data set. This results in issues of robustness, redundancy and true biological relevance of the selected genes. Integrative analyses typically address these shortcomings by integrating multiple data artifacts from the same objects, e.g. gene expression and methylation data. When only gene expression data are available, integrative analyses instead use curated information on biological processes from public knowledge bases. With knowledge bases providing an ever-increasing amount of curated biological knowledge, such prior knowledge approaches become more powerful. This paper provides a thorough overview on the status quo of biomarker detection on gene expression data with prior biological knowledge. We discuss current shortcomings of traditional approaches, review recent external knowledge bases, provide a classification and qualitative comparison of existing prior knowledge approaches and discuss open challenges for this kind of gene selection.},
  language  = {en}
}
@article{Perscheid2021,
  author    = {Perscheid, Cindy},
  title     = {Comprior},
  series = {BMC Bioinformatics},
  volume    = {22},
  journal   = {BMC Bioinformatics},
  publisher = {Springer Nature},
  address   = {London},
  issn      = {1471-2105},
  doi       = {10.1186/s12859-021-04308-z},
  pages     = {1 -- 15},
  year      = {2021},
  abstract  = {Background Reproducible benchmarking is important for assessing the effectiveness of novel feature selection approaches applied on gene expression data, especially for prior knowledge approaches that incorporate biological information from online knowledge bases. However, no full-fledged benchmarking system exists that is extensible, provides built-in feature selection approaches, and a comprehensive result assessment encompassing classification performance, robustness, and biological relevance. Moreover, the particular needs of prior knowledge feature selection approaches, i.e. uniform access to knowledge bases, are not addressed. As a consequence, prior knowledge approaches are not evaluated amongst each other, leaving open questions regarding their effectiveness. Results We present the Comprior benchmark tool, which facilitates the rapid development and effortless benchmarking of feature selection approaches, with a special focus on prior knowledge approaches. Comprior is extensible by custom approaches, offers built-in standard feature selection approaches, enables uniform access to multiple knowledge bases, and provides a customizable evaluation infrastructure to compare multiple feature selection approaches regarding their classification performance, robustness, runtime, and biological relevance. Conclusion Comprior allows reproducible benchmarking especially of prior knowledge approaches, which facilitates their applicability and for the first time enables a comprehensive assessment of their effectiveness},
  language  = {en}
}
@article{PerkinsRoseGrossartetal.2021,
  author    = {Perkins, Anita and Rose, Andrew and Grossart, Hans-Peter and Rojas-Jimenez, Keilor Osvaldo and Barroso Prescott, Selva Kiri and Oakes, Joanne M.},
  title     = {Oxic and Anoxic Organic Polymer Degradation Potential of Endophytic Fungi From the Marine Macroalga, Ecklonia radiata},
  series = {Frontiers in Microbiology},
  volume    = {12},
  journal   = {Frontiers in Microbiology},
  publisher = {Frontiers in microbiology},
  address   = {Lausanne, Schweiz},
  issn      = {1664-302X},
  doi       = {10.3389/fmicb.2021.726138},
  pages     = {1 -- 13},
  year      = {2021},
  abstract  = {Cellulose and chitin are the most abundant polymeric, organic carbon source globally. Thus, microbes degrading these polymers significantly influence global carbon cycling and greenhouse gas production. Fungi are recognized as important for cellulose decomposition in terrestrial environments, but are far less studied in marine environments, where bacterial organic matter degradation pathways tend to receive more attention. In this study, we investigated the potential of fungi to degrade kelp detritus, which is a major source of cellulose in marine systems. Given that kelp detritus can be transported considerable distances in the marine environment, we were specifically interested in the capability of endophytic fungi, which are transported with detritus, to ultimately contribute to kelp detritus degradation. We isolated 10 species and two strains of endophytic fungi from the kelp Ecklonia radiata. We then used a dye decolorization assay to assess their ability to degrade organic polymers (lignin, cellulose, and hemicellulose) under both oxic and anoxic conditions and compared their degradation ability with common terrestrial fungi. Under oxic conditions, there was evidence that Ascomycota isolates produced cellulose-degrading extracellular enzymes (associated with manganese peroxidase and sulfur-containing lignin peroxidase), while Mucoromycota isolates appeared to produce both lignin and cellulose-degrading extracellular enzymes, and all Basidiomycota isolates produced lignin-degrading enzymes (associated with laccase and lignin peroxidase). Under anoxic conditions, only three kelp endophytes degraded cellulose. We concluded that kelp fungal endophytes can contribute to cellulose degradation in both oxic and anoxic environments. Thus, endophytic kelp fungi may play a significant role in marine carbon cycling via polymeric organic matter degradation.},
  language  = {en}
}
@article{PaoliniFontanaVanCuongPhametal.2021,
  author    = {Paolini, Alessio and Fontana, Federica and Van-Cuong Pham, and R{\"o}del, Claudia Jasmin and Seyfried, Salim},
  title     = {Mechanosensitive Notch-Dll4 and Klf2-Wnt9 signaling pathways intersect in guiding valvulogenesis in zebrafish},
  series = {Cell reports},
  volume    = {37},
  journal   = {Cell reports},
  number    = {1},
  publisher = {Cell Press},
  address   = {Maryland Heights, MO},
  issn      = {2211-1247},
  doi       = {10.1016/j.celrep.2021.109782},
  pages     = {13},
  year      = {2021},
  abstract  = {In the zebrafish embryo, the onset of blood flow generates fluid shear stress on endocardial cells, which are specialized endothelial cells that line the interior of the heart. High levels of fluid shear stress activate both Notch and Klf2 signaling, which play crucial roles in atrioventricular valvulogenesis. However, it remains unclear why only individual endocardial cells ingress into the cardiac jelly and initiate valvulogenesis. Here, we show that lateral inhibition between endocardial cells, mediated by Notch, singles out Delta-like-4-positive endocardial cells. These cells ingress into the cardiac jelly, where they form an abluminal cell population. Delta-like-4-positive cells ingress in response to Wnt9a, which is produced in parallel through an Erk5Klf2-Wnt9a signaling cascade also activated by blood flow. Hence, mechanical stimulation activates parallel mechanosensitive signaling pathways that produce binary effects by driving endocardial cells toward either luminal or abluminal fates. Ultimately, these cell fate decisions sculpt cardiac valve leaflets.},
  language  = {en}
}
@article{OrzechowskiSitnickaGrabowskaetal.2021,
  author    = {Orzechowski, Slawomir and Sitnicka, Dorota and Grabowska, Agnieszka and Compart, Julia and Fettke, J{\"o}rg and Zdunek-Zastocka, Edyta},
  title     = {Effect of short-term cold treatment on carbohydrate metabolism in potato leaves},
  series = {International journal of molecular sciences},
  volume    = {22},
  journal   = {International journal of molecular sciences},
  number    = {13},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {1422-0067},
  doi       = {10.3390/ijms22137203},
  pages     = {17},
  year      = {2021},
  abstract  = {Plants are often challenged by an array of unfavorable environmental conditions. During cold exposure, many changes occur that include, for example, the stabilization of cell membranes, alterations in gene expression and enzyme activities, as well as the accumulation of metabolites. In the presented study, the carbohydrate metabolism was analyzed in the very early response of plants to a low temperature (2 degrees C) in the leaves of 5-week-old potato plants of the Russet Burbank cultivar during the first 12 h of cold treatment (2 h dark and 10 h light). First, some plant stress indicators were examined and it was shown that short-term cold exposure did not significantly affect the relative water content and chlorophyll content (only after 12 h), but caused an increase in malondialdehyde concentration and a decrease in the expression of NDA1, a homolog of the NADH dehydrogenase gene. In addition, it was shown that the content of transitory starch increased transiently in the very early phase of the plant response (3-6 h) to cold treatment, and then its decrease was observed after 12 h. In contrast, soluble sugars such as glucose and fructose were significantly increased only at the end of the light period, where a decrease in sucrose content was observed. The availability of the monosaccharides at constitutively high levels, regardless of the temperature, may delay the response to cold, involving amylolytic starch degradation in chloroplasts. The decrease in starch content, observed in leaves after 12 h of cold exposure, was preceded by a dramatic increase in the transcript levels of the key enzymes of starch degradation initiation, the alpha-glucan, water dikinase (GWD-EC 2.7.9.4) and the phosphoglucan, water dikinase (PWD-EC 2.7.9.5). The gene expression of both dikinases peaked at 9 h of cold exposure, as analyzed by real-time PCR. Moreover, enhanced activities of the acid invertase as well as of both glucan phosphorylases during exposure to a chilling temperature were observed. However, it was also noticed that during the light phase, there was a general increase in glucan phosphorylase activities for both control and cold-stressed plants irrespective of the temperature. In conclusion, a short-term cold treatment alters the carbohydrate metabolism in the leaves of potato, which leads to an increase in the content of soluble sugars.},
  language  = {en}
}
@article{OmranianAngeleskaNikoloski2021,
  author    = {Omranian, Sara and Angeleska, Angela and Nikoloski, Zoran},
  title     = {Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient},
  series = {Computational and structural biotechnology journal},
  volume    = {19},
  journal   = {Computational and structural biotechnology journal},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {2001-0370},
  doi       = {10.1016/j.csbj.2021.09.014},
  pages     = {5255 -- 5263},
  year      = {2021},
  abstract  = {Identification of protein complexes from protein-protein interaction (PPI) networks is a key problem in PPI mining, solved by parameter-dependent approaches that suffer from small recall rates. Here we introduce GCC-v, a family of efficient, parameter-free algorithms to accurately predict protein complexes using the (weighted) clustering coefficient of proteins in PPI networks. Through comparative analyses with gold standards and PPI networks from Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens, we demonstrate that GCC-v outperforms twelve state-of-the-art approaches for identification of protein complexes with respect to twelve performance measures in at least 85.71\% of scenarios. We also show that GCC-v results in the exact recovery of similar to 35\% of protein complexes in a pan-plant PPI network and discover 144 new protein complexes in Arabidopsis thaliana, with high support from GO semantic similarity. Our results indicate that findings from GCC-v are robust to network perturbations, which has direct implications to assess the impact of the PPI network quality on the predicted protein complexes. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.},
  language  = {en}
}
@article{OmranianAngeleskaNikoloski2021,
  author    = {Omranian, Sara and Angeleska, Angela and Nikoloski, Zoran},
  title     = {PC2P},
  series = {Bioinformatics},
  volume    = {37},
  journal   = {Bioinformatics},
  number    = {1},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1367-4811},
  doi       = {10.1093/bioinformatics/btaa1089},
  pages     = {73 -- 81},
  year      = {2021},
  abstract  = {Motivation: Prediction of protein complexes from protein-protein interaction (PPI) networks is an important problem in systems biology, as they control different cellular functions. The existing solutions employ algorithms for network community detection that identify dense subgraphs in PPI networks. However, gold standards in yeast and human indicate that protein complexes can also induce sparse subgraphs, introducing further challenges in protein complex prediction. Results: To address this issue, we formalize protein complexes as biclique spanned subgraphs, which include both sparse and dense subgraphs. We then cast the problem of protein complex prediction as a network partitioning into biclique spanned subgraphs with removal of minimum number of edges, called coherent partition. Since finding a coherent partition is a computationally intractable problem, we devise a parameter-free greedy approximation algorithm, termed Protein Complexes from Coherent Partition (PC2P), based on key properties of biclique spanned subgraphs. Through comparison with nine contenders, we demonstrate that PC2P: (i) successfully identifies modular structure in networks, as a prerequisite for protein complex prediction, (ii) outperforms the existing solutions with respect to a composite score of five performance measures on 75\% and 100\% of the analyzed PPI networks and gold standards in yeast and human, respectively, and (iii,iv) does not compromise GO semantic similarity and enrichment score of the predicted protein complexes. Therefore, our study demonstrates that clustering of networks in terms of biclique spanned subgraphs is a promising framework for detection of complexes in PPI networks.},
  language  = {en}
}
@article{Omel'chenkoOcampoEspindolaKiss2021,
  author    = {Omel'chenko, Oleh and Ocampo-Espindola, Jorge Luis and Kiss, Istv{\´a}n Z.},
  title     = {Asymmetry-induced isolated fully synchronized state in coupled oscillator populations},
  series = {Physical review : E, Statistical, nonlinear and soft matter physics},
  volume    = {104},
  journal   = {Physical review : E, Statistical, nonlinear and soft matter physics},
  number    = {2},
  publisher = {American Physical Society},
  address   = {Melville, NY},
  issn      = {2470-0045},
  doi       = {10.1103/PhysRevE.104.L022202},
  pages     = {6},
  year      = {2021},
  abstract  = {A symmetry-breaking mechanism is investigated that creates bistability between fully and partially synchronized states in oscillator networks. Two populations of oscillators with unimodal frequency distribution and different amplitudes, in the presence of weak global coupling, are shown to simplify to a modular network with asymmetrical coupling. With increasing the coupling strength, a synchronization transition is observed with an isolated fully synchronized state. The results are interpreted theoretically in the thermodynamic limit and confirmed in experiments with chemical oscillators.},
  language  = {en}
}
@article{OlasApeltWatanabeetal.2021,
  author    = {Olas, Justyna Jadwiga and Apelt, Federico and Watanabe, Mutsumi and H{\"o}fgen, Rainer and Wahl, Vanessa},
  title     = {Developmental stage-specific metabolite signatures in Arabidopsis thaliana under optimal and mild nitrogen limitation},
  series = {Plant science : an international journal of experimental plant biology},
  volume    = {303},
  journal   = {Plant science : an international journal of experimental plant biology},
  publisher = {Elsevier Science},
  address   = {Amsterdam [u.a.]},
  issn      = {0168-9452},
  doi       = {10.1016/j.plantsci.2020.110746},
  pages     = {14},
  year      = {2021},
  abstract  = {Metabolites influence flowering time, and thus are among the major determinants of yield. Despite the reported role of trehalose 6-phosphate and nitrate signaling on the transition from the vegetative to the reproductive phase, little is known about other metabolites contributing and responding to developmental phase changes. To increase our understanding which metabolic traits change throughout development in Arabidopsis thaliana and to identify metabolic markers for the vegetative and reproductive phases, especially among individual amino acids (AA), we profiled metabolites of plants grown in optimal (ON) and limited nitrogen (N) (LN) conditions, the latter providing a mild but consistent limitation of N. We found that although LN plants adapt their growth to a decreased level of N, their metabolite profiles are strongly distinct from ON plant profiles, with N as the driving factor for the observed differences. We demonstrate that the vegetative and the reproductive phase are not only marked by growth parameters such as biomass and rosette area, but also by specific metabolite signatures including specific single AA. In summary, we identified N-dependent and -independent indicators manifesting developmental stages, indicating that the plant's metabolic status also reports on the developmental phases.},
  language  = {en}
}
@article{NwosuRoeserYangetal.2021,
  author    = {Nwosu, Ebuka Canisius and Roeser, Patricia Angelika and Yang, Sizhong and Ganzert, Lars and Dellwig, Olaf and Pinkerneil, Sylvia and Brauer, Achim and Dittmann, Elke and Wagner, Dirk and Liebner, Susanne},
  title     = {From water into sediment-tracing freshwater cyanobacteria via DNA analyses},
  series = {Microorganisms : open access journal},
  volume    = {9},
  journal   = {Microorganisms : open access journal},
  number    = {8},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2076-2607},
  doi       = {10.3390/microorganisms9081778},
  pages     = {20},
  year      = {2021},
  abstract  = {Sedimentary ancient DNA-based studies have been used to probe centuries of climate and environmental changes and how they affected cyanobacterial assemblages in temperate lakes. Due to cyanobacteria containing potential bloom-forming and toxin-producing taxa, their approximate reconstruction from sediments is crucial, especially in lakes lacking long-term monitoring data. To extend the resolution of sediment record interpretation, we used high-throughput sequencing, amplicon sequence variant (ASV) analysis, and quantitative PCR to compare pelagic cyanobacterial composition to that in sediment traps (collected monthly) and surface sediments in Lake Tiefer See. Cyanobacterial composition, species richness, and evenness was not significantly different among the pelagic depths, sediment traps and surface sediments (p > 0.05), indicating that the cyanobacteria in the sediments reflected the cyanobacterial assemblage in the water column. However, total cyanobacterial abundances (qPCR) decreased from the metalimnion down the water column. The aggregate-forming (Aphanizomenon) and colony-forming taxa (Snowella) showed pronounced sedimentation. In contrast, Planktothrix was only very poorly represented in sediment traps (meta- and hypolimnion) and surface sediments, despite its highest relative abundance at the thermocline (10 m water depth) during periods of lake stratification (May-October). We conclude that this skewed representation in taxonomic abundances reflects taphonomic processes, which should be considered in future DNA-based paleolimnological investigations.},
  language  = {en}
}
@article{NwosuBrauerKaiseretal.2021,
  author    = {Nwosu, Ebuka Canisius and Brauer, Achim and Kaiser, J{\´e}r{\^o}me and Horn, Fabian and Wagner, Dirk and Liebner, Susanne},
  title     = {Evaluating sedimentary DNA for tracing changes in cyanobacteria dynamics from sediments spanning the last 350 years of Lake Tiefer See, NE Germany},
  series = {Journal of paleolimnology},
  volume    = {66},
  journal   = {Journal of paleolimnology},
  number    = {3},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {0921-2728},
  doi       = {10.1007/s10933-021-00206-9},
  pages     = {279 -- 296},
  year      = {2021},
  abstract  = {Since the beginning of the Anthropocene, lacustrine biodiversity has been influenced by climate change and human activities. These factors advance the spread of harmful cyanobacteria in lakes around the world, which affects water quality and impairs the aquatic food chain. In this study, we assessed changes in cyanobacterial community dynamics via sedimentary DNA (sedaDNA) from well-dated lake sediments of Lake Tiefer See, which is part of the Klocksin Lake Chain spanning the last 350 years. Our diversity and community analysis revealed that cyanobacterial communities form clusters according to the presence or absence of varves. Based on distance-based redundancy and variation partitioning analyses (dbRDA and VPA) we identified that intensified lake circulation inferred from vegetation openness reconstructions, delta C-13 data (a proxy for varve preservation) and total nitrogen content were abiotic factors that significantly explained the variation in the reconstructed cyanobacterial community from Lake Tiefer See sediments. Operational taxonomic units (OTUs) assigned to Microcystis sp. and Aphanizomenon sp. were identified as potential eutrophication-driven taxa of growing importance since circa common era (ca. CE) 1920 till present. This result is corroborated by a cyanobacteria lipid biomarker analysis. Furthermore, we suggest that stronger lake circulation as indicated by non-varved sediments favoured the deposition of the non-photosynthetic cyanobacteria sister clade Sericytochromatia, whereas lake bottom anoxia as indicated by subrecent- and recent varves favoured the Melainabacteria in sediments. Our findings highlight the potential of high-resolution amplicon sequencing in investigating the dynamics of past cyanobacterial communities in lake sediments and show that lake circulation, anoxic conditions, and human-induced eutrophication are main factors explaining variations in the cyanobacteria community in Lake Tiefer See during the last 350 years.},
  language  = {en}
}
@phdthesis{Nieschalke2021,
  author    = {Nieschalke, Kai},
  title     = {Proteinaddukte und Urinmetaboliten des Nagetierkanzerogens Methyleugenol als Biomarker der Exposition},
  school      = {Universit{\"a}t Potsdam},
  pages     = {142, XLIV},
  year      = {2021},
  language  = {de}
}
@article{NeffeLoewenbergJulichGruneretal.2021,
  author    = {Neffe, Axel T. and L{\"o}wenberg, Candy and Julich-Gruner, Konstanze K. and Behl, Marc and Lendlein, Andreas},
  title     = {Thermally-induced shape-memory behavior of degradable gelatin-based networks},
  series = {International journal of molecular sciences},
  volume    = {22},
  journal   = {International journal of molecular sciences},
  number    = {11},
  publisher = {Molecular Diversity Preservation International},
  address   = {Basel},
  issn      = {1422-0067},
  doi       = {10.3390/ijms22115892},
  pages     = {15},
  year      = {2021},
  abstract  = {Shape-memory hydrogels (SMH) are multifunctional, actively-moving polymers of interest in biomedicine. In loosely crosslinked polymer networks, gelatin chains may form triple helices, which can act as temporary net points in SMH, depending on the presence of salts. Here, we show programming and initiation of the shape-memory effect of such networks based on a thermomechanical process compatible with the physiological environment. The SMH were synthesized by reaction of glycidylmethacrylated gelatin with oligo(ethylene glycol) (OEG) alpha,omega-dithiols of varying crosslinker length and amount. Triple helicalization of gelatin chains is shown directly by wide-angle X-ray scattering and indirectly via the mechanical behavior at different temperatures. The ability to form triple helices increased with the molar mass of the crosslinker. Hydrogels had storage moduli of 0.27-23 kPa and Young's moduli of 215-360 kPa at 4 degrees C. The hydrogels were hydrolytically degradable, with full degradation to water-soluble products within one week at 37 degrees C and pH = 7.4. A thermally-induced shape-memory effect is demonstrated in bending as well as in compression tests, in which shape recovery with excellent shape-recovery rates R-r close to 100\% were observed. In the future, the material presented here could be applied, e.g., as self-anchoring devices mechanically resembling the extracellular matrix.},
  language  = {en}
}
@article{NeffeIzraylitHommesSchattmannetal.2021,
  author    = {Neffe, Axel T. and Izraylit, Victor and Hommes-Schattmann, Paul J. and Lendlein, Andreas},
  title     = {Soft, formstable (Co)polyester blend elastomers},
  series = {Nanomaterials : open access journal},
  volume    = {11},
  journal   = {Nanomaterials : open access journal},
  number    = {6},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2079-4991},
  doi       = {10.3390/nano11061472},
  pages     = {18},
  year      = {2021},
  abstract  = {High crystallization rate and thermomechanical stability make polylactide stereocomplexes effective nanosized physical netpoints. Here, we address the need for soft, form-stable degradable elastomers for medical applications by designing such blends from (co)polyesters, whose mechanical properties are ruled by their nanodimensional architecture and which are applied as single components in implants. By careful controlling of the copolymer composition and sequence structure of poly[(L-lactide)-co-(epsilon-caprolactone)], it is possible to prepare hyperelastic polymer blends formed through stereocomplexation by adding poly(D-lactide) (PDLA). Low glass transition temperature T-g <= 0 degrees C of the mixed amorphous phase contributes to the low Young's modulus E. The formation of stereocomplexes is shown in DSC by melting transitions T-m > 190 degrees C and in WAXS by distinct scattering maxima at 2 theta = 12 degrees and 21 degrees. Tensile testing demonstrated that the blends are soft (E = 12-80 MPa) and show an excellent hyperelastic recovery R-rec = 66-85\% while having high elongation at break epsilon(b) up to >1000\%. These properties of the blends are attained only when the copolymer has 56-62 wt\% lactide content, a weight average molar mass >140 kg center dot mol(-1), and number average lactide sequence length >= 4.8, while the blend is formed with a content of 5-10 wt\% of PDLA. The devised strategy to identify a suitable copolymer for stereocomplexation and blend formation is transferable to further polymer systems and will support the development of thermoplastic elastomers suitable for medical applications.},
  language  = {en}
}
@article{NaserKadowSchumacheretal.2021,
  author    = {Naser, Eyad and Kadow, Stephanie and Schumacher, Fabian and Mohamed, Zainelabdeen H. and Kappe, Christian and Hessler, Gabriele and Pollmeier, Barbara and Kleuser, Burkhard and Arenz, Christoph and Becker, Katrin Anne and Gulbins, Erich and Carpinteiro, Alexander},
  title     = {Characterization of the small molecule ARC39},
  series = {Journal of Lipid Research},
  volume    = {61},
  journal   = {Journal of Lipid Research},
  number    = {6},
  publisher = {American Society for Biochemistry and Molecular Biology},
  address   = {Bethesda},
  issn      = {1539-7262},
  doi       = {10.1194/jlr.RA120000682},
  pages     = {896 -- 910},
  year      = {2021},
  abstract  = {Inhibition of acid sphingomyelinase (ASM), a lysosomal enzyme that catalyzes the hydrolysis of sphingomyelin into ceramide and phosphorylcholine, may serve as an investigational tool or a therapeutic intervention to control many diseases. Specific ASM inhibitors are currently not sufficiently characterized. Here, we found that 1-aminodecylidene bis-phosphonic acid (ARC39) specifically and efficiently (>90\%) inhibits both lysosomal and secretory ASM in vitro. Results from investigating sphingomyelin phosphodiesterase 1 (SMPD1/Smpd1) mRNA and ASM protein levels suggested that ARC39 directly inhibits ASM's catalytic activity in cultured cells, a mechanism that differs from that of functional inhibitors of ASM. We further provide evidence that ARC39 dose- and time-dependently inhibits lysosomal ASM in intact cells, and we show that ARC39 also reduces platelet- and ASM-promoted adhesion of tumor cells. The observed toxicity of ARC39 is low at concentrations relevant for ASM inhibition in vitro, and it does not strongly alter the lysosomal compartment or induce phospholipidosis in vitro. When applied intraperitoneally in vivo, even subtoxic high doses administered short-term induced sphingomyelin accumulation only locally in the peritoneal lavage without significant accumulation in plasma, liver, spleen, or brain. These findings require further investigation with other possible chemical modifications. In conclusion, our results indicate that ARC39 potently and selectively inhibits ASM in vitro and highlight the need for developing compounds that can reach tissue concentrations sufficient for ASM inhibition in vivo.},
  language  = {en}
}
@phdthesis{Nacak2021,
  author    = {Nacak, Selma},
  title     = {Synthesis and Characterization of Upconversion Nanaparticles for Applications in Life Sciences},
  school      = {Universit{\"a}t Potsdam},
  year      = {2021},
  language  = {en}
}
@article{MuenchAbdelilahSeyfried2021,
  author    = {M{\"u}nch, Juliane and Abdelilah-Seyfried, Salim},
  title     = {Sensing and responding of cardiomyocytes to changes of tissue stiffness in the diseased heart},
  series = {Frontiers in cell developmental biology},
  volume    = {9},
  journal   = {Frontiers in cell developmental biology},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {2296-634X},
  doi       = {10.3389/fcell.2021.642840},
  pages     = {13},
  year      = {2021},
  abstract  = {Cardiomyocytes are permanently exposed to mechanical stimulation due to cardiac contractility. Passive myocardial stiffness is a crucial factor, which defines the physiological ventricular compliance and volume of diastolic filling with blood. Heart diseases often present with increased myocardial stiffness, for instance when fibrotic changes modify the composition of the cardiac extracellular matrix (ECM). Consequently, the ventricle loses its compliance, and the diastolic blood volume is reduced. Recent advances in the field of cardiac mechanobiology revealed that disease-related environmental stiffness changes cause severe alterations in cardiomyocyte cellular behavior and function. Here, we review the molecular mechanotransduction pathways that enable cardiomyocytes to sense stiffness changes and translate those into an altered gene expression. We will also summarize current knowledge about when myocardial stiffness increases in the diseased heart. Sophisticated in vitro studies revealed functional changes, when cardiomyocytes faced a stiffer matrix. Finally, we will highlight recent studies that described modulations of cardiac stiffness and thus myocardial performance in vivo. Mechanobiology research is just at the cusp of systematic investigations related to mechanical changes in the diseased heart but what is known already makes way for new therapeutic approaches in regenerative biology.},
  language  = {en}
}
@article{MeridaFettke2021,
  author    = {Merida, Angel and Fettke, J{\"o}rg},
  title     = {Starch granule initiation in Arabidopsis thaliana chloroplasts},
  series = {The plant journal},
  volume    = {107},
  journal   = {The plant journal},
  number    = {3},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0960-7412},
  doi       = {10.1111/tpj.15359},
  pages     = {688 -- 697},
  year      = {2021},
  abstract  = {The initiation of starch granule formation and the mechanism controlling the number of granules per plastid have been some of the most elusive aspects of starch metabolism. This review covers the advances made in the study of these processes. The analyses presented herein depict a scenario in which starch synthase isoform 4 (SS4) provides the elongating activity necessary for the initiation of starch granule formation. However, this protein does not act alone; other polypeptides are required for the initiation of an appropriate number of starch granules per chloroplast. The functions of this group of polypeptides include providing suitable substrates (maltooligosaccharides) to SS4, the localization of the starch initiation machinery to the thylakoid membranes, and facilitating the correct folding of SS4. The number of starch granules per chloroplast is tightly regulated and depends on the developmental stage of the leaves and their metabolic status. Plastidial phosphorylase (PHS1) and other enzymes play an essential role in this process since they are necessary for the synthesis of the substrates used by the initiation machinery. The mechanism of starch granule formation initiation in Arabidopsis seems to be generalizable to other plants and also to the synthesis of long-term storage starch. The latter, however, shows specific features due to the presence of more isoforms, the absence of constantly recurring starch synthesis and degradation, and the metabolic characteristics of the storage sink organs.},
  language  = {en}
}
@article{MbebiTongNikoloski2021,
  author    = {Mbebi, Alain J. and Tong, Hao and Nikoloski, Zoran},
  title     = {L-2,L-1-norm regularized multivariate regression model with applications to genomic prediction},
  series = {Bioinformatics},
  volume    = {37},
  journal   = {Bioinformatics},
  number    = {18},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1367-4803},
  doi       = {10.1093/bioinformatics/btab212},
  pages     = {2896 -- 2904},
  year      = {2021},
  abstract  = {Motivation: Genomic selection (GS) is currently deemed the most effective approach to speed up breeding of agricultural varieties. It has been recognized that consideration of multiple traits in GS can improve accuracy of prediction for traits of low heritability. However, since GS forgoes statistical testing with the idea of improving predictions, it does not facilitate mechanistic understanding of the contribution of particular single nucleotide polymorphisms (SNP). Results: Here, we propose a L-2,L-1-norm regularized multivariate regression model and devise a fast and efficient iterative optimization algorithm, called L-2,L-1-joint, applicable in multi-trait GS. The usage of the L-2,L-1-norm facilitates variable selection in a penalized multivariate regression that considers the relation between individuals, when the number of SNPs is much larger than the number of individuals. The capacity for variable selection allows us to define master regulators that can be used in a multi-trait GS setting to dissect the genetic architecture of the analyzed traits. Our comparative analyses demonstrate that the proposed model is a favorable candidate compared to existing state-of-the-art approaches. Prediction and variable selection with datasets from Brassica napus, wheat and Arabidopsis thaliana diversity panels are conducted to further showcase the performance of the proposed model.},
  language  = {en}
}
@article{MazzaCzyperreckEccardetal.2021,
  author    = {Mazza, Valeria and Czyperreck, Inken and Eccard, Jana and Dammhahn, Melanie},
  title     = {Cross-Context Responses to Novelty in Rural and Urban Small Mammals},
  series = {Frontiers in Ecology and Evolution},
  volume    = {9},
  journal   = {Frontiers in Ecology and Evolution},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {2296-701X},
  doi       = {10.3389/fevo.2021.661971},
  pages     = {16},
  year      = {2021},
  abstract  = {The Anthropocene is the era of urbanization. The accelerating expansion of cities occurs at the expense of natural reservoirs of biodiversity and presents animals with challenges for which their evolutionary past might not have prepared them. Cognitive and behavioral adjustments to novelty could promote animals' persistence under these altered conditions. We investigated the structure of, and covariance between, different aspects of responses to novelty in rural and urban small mammals of two non-commensal rodent species. We ran replicated experiments testing responses to three novelty types (object, food, or space) of 47 individual common voles (Microtus arvalis) and 41 individual striped field mice (Apodemus agrarius). We found partial support for the hypothesis that responses to novelty are structured, clustering (i) speed of responses, (ii) intensity of responses, and (iii) responses to food into separate dimensions. Rural and urban small mammals did not differ in most responses to novelty, suggesting that urban habitats do not reduce neophobia in these species. Further studies investigating whether comparable response patters are found throughout different stages of colonization, and along synurbanization processes of different duration, will help illuminate the dynamics of animals' cognitive adjustments to urban life.},
  language  = {en}
}
@article{MarzetzWacker2021,
  author    = {Marzetz, Vanessa and Wacker, Alexander},
  title     = {Evaluating the relevance of species sorting and physiological plasticity of phytoplankton communities grown in a multifactor environment},
  series = {Freshwater biology / Freshwater Biological Association},
  volume    = {66},
  journal   = {Freshwater biology / Freshwater Biological Association},
  number    = {10},
  publisher = {Wiley-Blackwell},
  address   = {Oxford},
  issn      = {0046-5070},
  doi       = {10.1111/fwb.13810},
  pages     = {1992 -- 2003},
  year      = {2021},
  abstract  = {The two important mechanisms influencing the response of phytoplankton communities to alterations of abiotic factors in their environment are difficult to distinguish: species sorting resulting from a change in interspecific competitive pressure, and phenotypic plasticity (here explicitly physiological plasticity i.e. species-specific physiological adjustment). A shift in species composition as well as physiological adjustments in species can lead to changes in fatty acid composition that determine the food quality for zooplankton consumers. We used phytoplankton communities consisting of five species and exposed them to two different light intensities, two light conditions (constant and variable), and two levels of phosphorus supply. Changes in fatty acid and species composition were analyzed. We compared community pairs differing in one factor by calculating the Bray-Curtis similarity index for the composition of both variables. Comparing the Bray-Curtis similarity index of the species composition with the index of the fatty acid composition was used to estimate the effects of species sorting and physiological plasticity. Changes in nutrient supply influenced fatty acid responses based on species sorting and physiological plasticity the most. On one hand, the relevance of physiological plasticity was highest at cultivation in different nutrient supplies but the same light environment. Conversely with low nutrients species sorting appeared to dominate the response to changes in light, while at high nutrients physiological plasticity appeared to influence the response. Overall, under low phosphorus supply the communities showed a lower total fatty acid content per carbon and had increased proportions of saturated and monounsaturated fatty acids. Instead, communities in low light produced more of eicosapentaenoic acid. Our results suggest that the relevance of species sorting and physiological plasticity in shaping the community response highly depends on the environmental factors that influence the system. Nutrient supply had the largest effect, while light had more limited conditional effects. However, all of these factors are important in shaping the food quality of the phytoplankton community for higher trophic levels.},
  language  = {en}
}
@article{MarotChevalereSpatola2021,
  author    = {Marot, Medhi and Cheval{\`e}re, Johann and Spatola, Nicolas},
  title     = {Depressed mood, a better predictor of social-distancing compliance and candidate for intervention compared to working memory capacity},
  series = {Proceedings of the National Academy of Sciences of the United States of America},
  volume    = {118},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  number    = {8},
  publisher = {National Academy of Sciences},
  address   = {Washington},
  issn      = {0027-8424},
  doi       = {10.1073/pnas.2024017118},
  pages     = {2},
  year      = {2021},
  language  = {en}
}
@article{MalchowBocediPalmeretal.2021,
  author    = {Malchow, Anne-Kathleen and Bocedi, Greta and Palmer, Stephen C. F. and Travis, Justin M. J. and Zurell, Damaris},
  title     = {RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes},
  series = {Ecography},
  volume    = {44},
  journal   = {Ecography},
  number    = {10},
  publisher = {John Wiley \& Sons, Inc.},
  address   = {New Jersey},
  issn      = {1600-0587},
  pages     = {10},
  year      = {2021},
  abstract  = {Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.},
  language  = {en}
}
@article{MalchowBocediPalmeretal.2021,
  author    = {Malchow, Anne-Kathleen and Bocedi, Greta and Palmer, Stephen C. F. and Travis, Justin M. J. and Zurell, Damaris},
  title     = {RangeShiftR},
  series = {Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos},
  volume    = {44},
  journal   = {Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos},
  number    = {10},
  publisher = {Wiley-Blackwell},
  address   = {Oxford [u.a.]},
  issn      = {1600-0587},
  doi       = {10.1111/ecog.05689},
  pages     = {1443 -- 1452},
  year      = {2021},
  abstract  = {Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.},
  language  = {en}
}
@article{LozanoAguilarTriguerosOnandiaetal.2021,
  author    = {Lozano, Yudi M. and Aguilar-Trigueros, Carlos A. and Onandia, Gabriela and Maaß, Stefanie and Zhao, Tingting and Rillig, Matthias C.},
  title     = {Effects of microplastics and drought on soil ecosystem functions and multifunctionality},
  series = {Journal of applied ecology : an official journal of the British Ecological Society},
  volume    = {58},
  journal   = {Journal of applied ecology : an official journal of the British Ecological Society},
  number    = {5},
  publisher = {Wiley-Blackwell},
  address   = {Oxford [u.a.]},
  issn      = {1365-2664},
  doi       = {10.1111/1365-2664.13839},
  pages     = {988 -- 996},
  year      = {2021},
  abstract  = {1. Microplastics in soils have become an important threat for terrestrial systems as they may potentially alter the geochemical/biophysical soil environment and can interact with drought. As microplastics may affect soil water content, this could exacerbate the well-known negative effects of drought on ecosystem functionality. Thus, functions including litter decomposition, soil aggregation or those related with nutrient cycling can be altered. Despite this potential interaction, we know relatively little about how microplastics, under different soil water conditions, affect ecosystem functions and multifunctionality. 2. To address this gap, we performed an experiment using grassland plant communities growing in microcosms. Microplastic fibres (absent, present) and soil water conditions (well-watered, drought) were applied in a fully factorial design. At harvest, we measured soil ecosystem functions related to nutrient cycling (beta-glucosaminidase, beta-D-cellobiosidase, phosphatase, beta-glucosidase enzymes), respiration, nutrient retention, pH, litter decomposition and soil aggregation (water stable aggregates). As terrestrial systems provide these functions simultaneously, we also assessed ecosystem multifunctionality, an index that encompasses the array of ecosystem functions measured here. 3. We found that the interaction between microplastic fibres and drought affected ecosystem functions and multifunctionality. Drought had negatively affected nutrient cycling by decreasing enzymatic activities by up to similar to 39\%, while microplastics increased soil aggregation by similar to 18\%, soil pH by similar to 4\% and nutrient retention by up to similar to 70\% by diminishing nutrient leaching. Microplastic fibres also impacted soil enzymes, respiration and ecosystem multifunctionality, but importantly, the direction of these effects depended on soil water status. That is, under well-watered conditions, these functions decreased with microplastic fibres by up to similar to 34\% while under drought they had similar values irrespective of the microplastic presence, or tended to increase with microplastics. Litter decomposition had a contrary pattern increasing with microplastics by similar to 6\% under well-watered conditions while decreasing to a similar percentage under drought. 4. Synthesis and applications. Single ecosystem functions can be positively or negatively affected by microplastics fibres depending on soil water status. However, our results suggest that microplastic fibres may cause negative effects on ecosystem soil multifunctionality of a similar magnitude as drought. Thus, strategies to counteract this new global change factor are necessary.},
  language  = {en}
}
@article{LozadaGobilardJeltschZhu2021,
  author    = {Lozada-Gobilard, Sissi Donna and Jeltsch, Florian and Zhu, Jinlei},
  title     = {High matrix vegetation decreases mean seed dispersal distance but increases long wind dispersal probability connecting local plant populations in agricultural landscapes},
  series = {Agriculture, ecosystems \& environment : an international journal for scientific research on the relationship of agriculture and food production to the biosphere},
  volume    = {322},
  journal   = {Agriculture, ecosystems \& environment : an international journal for scientific research on the relationship of agriculture and food production to the biosphere},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0167-8809},
  doi       = {10.1016/j.agee.2021.107678},
  pages     = {8},
  year      = {2021},
  abstract  = {Seed dispersal plays an important role in population dynamics in agricultural ecosystems, but the effects of surrounding vegetation height on seed dispersal and population connectivity on the landscape scale have rarely been studied. Understanding the effects of surrounding vegetation height on seed dispersal will provide important information for land-use management in agricultural landscapes to prevent the spread of undesired weeds or enhance functional connectivity. We used two model species, Phragmites australis and Typha latifolia, growing in small natural ponds known as kettle holes, in an agricultural landscape to evaluate the effects of surrounding vegetation height on wind dispersal and population connectivity between kettle holes. Seed dispersal distance and the probability of long-distance dispersal (LDD) were simulated with the mechanistic WALD model under three scenarios of "low", "dynamic" and "high" surrounding vegetation height. Connectivity between the origin and target kettle holes was quantified with a connectivity index adapted from Hanski and Thomas (1994). Our results show that mean seed dispersal distance decreases with the height of surrounding matrix vegetation, but the probability of long-distance dispersal (LDD) increases with vegetation height. This indicates an important vegetation-based trade-off between mean dispersal distance and LDD, which has an impact on connectivity. Matrix vegetation height has a negative effect on mean seed dispersal distance but a positive effect on the probability of LDD. This positive effect and its impact on connectivity provide novel insights into landscape level (meta-)population and community dynamics - a change in matrix vegetation height by land-use or climatic changes could strongly affect the spread and connectivity of wind-dispersed plants. The opposite effect of vegetation height on mean seed dispersal distance and the probability of LDD should therefore be considered in management and analyses of future land-use and climate change effects.},
  language  = {en}
}
@article{LiuLiFettke2021,
  author    = {Liu, Qingting and Li, Xiaoping and Fettke, J{\"o}rg},
  title     = {Starch granules in Arabidopsis thaliana mesophyll and guard cells show similar morphology but differences in size and number},
  series = {International journal of molecular sciences},
  volume    = {22},
  journal   = {International journal of molecular sciences},
  number    = {11},
  publisher = {Molecular Diversity Preservation International},
  address   = {Basel},
  issn      = {1422-0067},
  doi       = {10.3390/ijms22115666},
  pages     = {11},
  year      = {2021},
  abstract  = {Transitory starch granules result from complex carbon turnover and display specific situations during starch synthesis and degradation. The fundamental mechanisms that specify starch granule characteristics, such as granule size, morphology, and the number per chloroplast, are largely unknown. However, transitory starch is found in the various cells of the leaves of Arabidopsis thaliana, but comparative analyses are lacking. Here, we adopted a fast method of laser confocal scanning microscopy to analyze the starch granules in a series of Arabidopsis mutants with altered starch metabolism. This allowed us to separately analyze the starch particles in the mesophyll and in guard cells. In all mutants, the guard cells were always found to contain more but smaller plastidial starch granules than mesophyll cells. The morphological properties of the starch granules, however, were indiscernible or identical in both types of leaf cells.},
  language  = {en}
}
@article{LiYangSunetal.2021,
  author    = {Li, Xiaoxiao and Yang, Wei and Sun, Tao and Gaedke, Ursula},
  title     = {Quantitative food web structure and ecosystem functions in a warm-temperate seagrass bed},
  series = {Marine biology : international journal on life in oceans and coastal waters},
  volume    = {168},
  journal   = {Marine biology : international journal on life in oceans and coastal waters},
  number    = {5},
  publisher = {Springer},
  address   = {Berlin ; Heidelberg},
  issn      = {0025-3162},
  doi       = {10.1007/s00227-021-03878-z},
  pages     = {17},
  year      = {2021},
  abstract  = {Seagrass beds are important habitats in coastal areas but increasingly decline in area and quality, thus conservation measures are urgently needed. Quantitative food webs, describing the biomass distribution and energy fluxes among trophic groups, reveal structural and functional aspects of ecosystems. Their knowledge can improve ecological conservation. For the recently discovered large warm-temperate seagrass (Zostera japonica) habitat in China's Yellow River Delta wetland, we used delta C-13 and delta N-15 measurements and a Bayesian isotope mixing model to construct its food web diagram with quantitative estimations of consumer diet compositions, comprising detritus and 14 living trophic groups from primary producers to fish. We then estimated the quantitative food web fluxes based on biomass measurements and calculated corresponding ecosystem functions. Pelagic producers were significantly C-13-depleted compared to benthic sources. Consumers (except zooplankton) were increasingly C-13-depleted with increasing trophic positions even though the consumed benthic production surpassed the pelagic one. Bivalves dominated consumer biomasses and fluxes and were the first to connect the pelagic and benthic pathways, whereas zooplankton and gastropods were specialized on the two pathways, respectively. We found flat biomass and production pyramids indicating low trophic transfer efficiencies. Generally, the energetic structure of the quantitative food web was consistent with the stable isotope analysis, and the estimated net primary production and most estimated production to biomass ratios of the trophic groups fell within literature ranges. This study provides a systematical understanding of the quantitative trophic ecology of a seagrass bed and facilitates synergistic knowledge on management, conservation, and restoration.},
  language  = {en}
}
@article{LauMaierBrauneetal.2021,
  author    = {Lau, Skadi and Maier, Anna and Braune, Steffen and Gossen, Manfred and Lendlein, Andreas},
  title     = {Effect of endothelial culture medium composition on platelet responses to polymeric biomaterials},
  series = {International journal of molecular sciences},
  volume    = {22},
  journal   = {International journal of molecular sciences},
  number    = {13},
  publisher = {Molecular Diversity Preservation International},
  address   = {Basel},
  issn      = {1422-0067},
  doi       = {10.3390/ijms22137006},
  pages     = {13},
  year      = {2021},
  abstract  = {Near-physiological in vitro thrombogenicity test systems for the evaluation of blood-contacting endothelialized biomaterials requires co-cultivation with platelets (PLT). However, the addition of PLT has led to unphysiological endothelial cell (EC) detachment in such in vitro systems. A possible cause for this phenomenon may be PLT activation triggered by the applied endothelial cell medium, which typically consists of basal medium (BM) and nine different supplements. To verify this hypothesis, the influence of BM and its supplements was systematically analyzed regarding PLT responses. For this, human platelet rich plasma (PRP) was mixed with BM, BM containing one of nine supplements, or with BM containing all supplements together. PLT adherence analysis was carried out in six-channel slides with plasma-treated cyclic olefin copolymer (COC) and poly(tetrafluoro ethylene) (PTFE, as a positive control) substrates as part of the six-channel slides in the absence of EC and under static conditions. PLT activation and aggregation were analyzed using light transmission aggregometry and flow cytometry (CD62P). Medium supplements had no effect on PLT activation and aggregation. In contrast, supplements differentially affected PLT adherence, however, in a polymer- and donor-dependent manner. Thus, the use of standard endothelial growth medium (BM + all supplements) maintains functionality of PLT under EC compatible conditions without masking the differences of PLT adherence on different polymeric substrates. These findings are important prerequisites for the establishment of a near-physiological in vitro thrombogenicity test system assessing polymer-based cardiovascular implant materials in contact with EC and PLT.},
  language  = {en}
}
@article{KuerschnerSchererRadchuketal.2021,
  author    = {K{\"u}rschner, Tobias and Scherer, C{\´e}dric and Radchuk, Viktoriia and Blaum, Niels and Kramer-Schadt, Stephanie},
  title     = {Movement can mediate temporal mismatches between resource availability and biological events in host-pathogen interactions},
  series = {Ecology and evolution},
  volume    = {11},
  journal   = {Ecology and evolution},
  number    = {10},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.7478},
  pages     = {5728 -- 5741},
  year      = {2021},
  abstract  = {Global change is shifting the timing of biological events, leading to temporal mismatches between biological events and resource availability. These temporal mismatches can threaten species' populations. Importantly, temporal mismatches not only exert strong pressures on the population dynamics of the focal species, but can also lead to substantial changes in pairwise species interactions such as host-pathogen systems. We adapted an established individual-based model of host-pathogen dynamics. The model describes a viral agent in a social host, while accounting for the host's explicit movement decisions. We aimed to investigate how temporal mismatches between seasonal resource availability and host life-history events affect host-pathogen coexistence, that is, disease persistence. Seasonal resource fluctuations only increased coexistence probability when in synchrony with the hosts' biological events. However, a temporal mismatch reduced host-pathogen coexistence, but only marginally. In tandem with an increasing temporal mismatch, our model showed a shift in the spatial distribution of infected hosts. It shifted from an even distribution under synchronous conditions toward the formation of disease hotspots, when host life history and resource availability mismatched completely. The spatial restriction of infected hosts to small hotspots in the landscape initially suggested a lower coexistence probability due to the critical loss of susceptible host individuals within those hotspots. However, the surrounding landscape facilitated demographic rescue through habitat-dependent movement. Our work demonstrates that the negative effects of temporal mismatches between host resource availability and host life history on host-pathogen coexistence can be reduced through the formation of temporary disease hotspots and host movement decisions, with implications for disease management under disturbances and global change.},
  language  = {en}
}
@article{KoekerAkcaalanDittmannetal.2021,
  author    = {K{\"o}ker, Latife and Ak{\c{c}}aalan, Reyhan and Dittmann, Elke and Albay, Meri{\c{c}}},
  title     = {Depth profiles of protein-bound microcystin in K{\"u}{\c{c}}{\"u}k{\c{c}}ekmece Lagoon},
  series = {Toxicon : an international journal devoted to the exchange of knowledge on the poisons derived from the tissues of plants and animals ; official journal of the International Society on Toxinology},
  volume    = {198},
  journal   = {Toxicon : an international journal devoted to the exchange of knowledge on the poisons derived from the tissues of plants and animals ; official journal of the International Society on Toxinology},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0041-0101},
  doi       = {10.1016/j.toxicon.2021.05.005},
  pages     = {156 -- 163},
  year      = {2021},
  abstract  = {Microcystis is the most commonly found toxic cyanobacterial genus around the world and has a negative impact on the ecosystem. As a predominant producer of the potent hepatotoxin microcystin (MC), the genus causes outbreaks in freshwaters worldwide. Standard analytical methods that are used for the detection of microcystin variants can only measure the free form of microcystin in cells. Since microcystin was found as free and proteinbound forms in the cells, a significant proportion of microcystin is underestimated with analytical methods. The aim of the study was to measure protein-bound microcystins and determine the environmental factors that affect the binding of microcystin to proteins. Samples were taken at depths of surface, 1 m, 5 m, 10 m, 15 m, and 18 m in Kucukcekmece Lagoon to analyze depth profiles of two different microcystin forms from June to September 2012 at regular monthly intervals. Our findings suggest that the most important parameter affecting proteinbound microcystin at surface water is high light. Due to favorable environmental conditions such as temperature, light, and physicochemical parameters, the higher microcystin contents, both free and protein-bound MCs, were found in summer periods.},
  language  = {en}
}
@article{KrausMathewStephenSchapranow2021,
  author    = {Kraus, Sara Milena and Mathew-Stephen, Mariet and Schapranow, Matthieu-Patrick},
  title     = {Eatomics},
  series = {Journal of proteome research},
  volume    = {20},
  journal   = {Journal of proteome research},
  number    = {1},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1535-3893},
  doi       = {10.1021/acs.jproteome.0c00398},
  pages     = {1070 -- 1078},
  year      = {2021},
  abstract  = {Quantitative proteomics data are becoming increasingly more available, and as a consequence are being analyzed and interpreted by a larger group of users. However, many of these users have less programming experience. Furthermore, experimental designs and setups are getting more complicated, especially when tissue biopsies are analyzed. Luckily, the proteomics community has already established some best practices on how to conduct quality control, differential abundance analysis and enrichment analysis. However, an easy-to-use application that wraps together all steps for the exploration and flexible analysis of quantitative proteomics data is not yet available. For Eatomics, we utilize the R Shiny framework to implement carefully chosen parts of established analysis workflows to (i) make them accessible in a user-friendly way, (ii) add a multitude of interactive exploration possibilities, and (iii) develop a unique experimental design setup module, which interactively translates a given research hypothesis into a differential abundance and enrichment analysis formula. In this, we aim to fulfill the needs of a growing group of inexperienced quantitative proteomics data analysts. Eatomics may be tested with demo data directly online via https://we.analyzegenomes.com/now/eatomics/or with the user's own data by installation from the Github repository at https://github.com/Millchmaedchen/Eatomics.},
  language  = {en}
}
@article{KraheSchusterTomaszewska2021,
  author    = {Krah{\´e}, Barbara and Schuster, Isabell and Tomaszewska, Paulina},
  title     = {Prevalence of sexual aggression victimization and perpetration in a German university student sample},
  series = {Archives of sexual behavior : the official publication of the International Academy of Sex Research},
  volume    = {50},
  journal   = {Archives of sexual behavior : the official publication of the International Academy of Sex Research},
  number    = {5},
  publisher = {Springer},
  address   = {New York},
  issn      = {0004-0002},
  doi       = {10.1007/s10508-021-01963-4},
  pages     = {2109 -- 2121},
  year      = {2021},
  abstract  = {This study examined the prevalence of sexual aggression perpetration and victimization in a sample of 1,172 students (755 female, 417 male) from four universities in Germany. All participants were asked about both victimization by, and perpetration of, sexual aggression since the age of 14 years, using the Sexual Aggression and Victimization Scale (SAV-S). Prevalence rates were established for different coercive strategies, sexual acts, and victim-perpetrator relationships. Both same-sex and opposite-sex victim-perpetrator constellations were examined. The overall victimization rate was 62.1\% for women and 37.5\% for men. The overall perpetration rate was 17.7\% for men and 9.4\% for women. Prevalence rates of both victimization and perpetration were higher for participants who had sexual contacts with both opposite-sex and same-sex partners than for participants with exclusively opposite-sex partners. Significant overlap was found between victim and perpetrator status for men and women as well as for participants with only opposite-sex and both opposite-sex and same-sex partners. A disparity between (higher) victimization and (lower) perpetration reports was found for both men and women, suggesting a general underreporting of perpetration rather than a gendered explanation in terms of social desirability or the perception of consent cues. The findings are placed in the international research literature on the prevalence of sexual aggression before and after the \#metoo campaign, and their implications for prevention efforts are discussed.},
  language  = {en}
}
@phdthesis{KnoxBrown2021,
  author    = {Knox-Brown, Patrick Frank},
  title     = {Towards understanding the sequence-structure-function relationship of intrinsically disordered LEA_4 proteins from Arabidopsis thaliana},
  school      = {Universit{\"a}t Potsdam},
  pages     = {172, XI},
  year      = {2021},
  abstract  = {Water-deficits can cause lethal damage to organisms, which is rooted in cellular dehydration. Many plant species, but also other organisms have developed mechanisms to tolerate such stresses, such as the expression of LEA proteins. Many studies report on physiological protective functions of LEA proteins but lack information about their precise mechanisms on a molecular level. Most LEA proteins are intrinsically disordered in dilute solution but may adopt a distinct secondary structure upon changes in solvent conditions. Understanding the molecular mechanism of how LEA proteins contribute to the counteraction of cellular damage during water-deficits may in the long-term pave the way for breeding crops that are resistant to the effects of global warming. The objective of the work at hand is to improve the biophysical understanding of the sequencestructure-function relationship of LEA proteins as membrane stabilizers, based on the LEA_4 family of the model plant A. thaliana. This is pursued by using a combination of spectroscopic and scattering techniques, supported by bioinformatics and computational analyses. Eight out of the 18 LEA_4 proteins are experimentally assessed revealing that a coil-helix transition in response to water-deficit is a common feature, as predicted for the entire family. In addition, they all stabilize simple membrane models during a freeze/ thaw cycle. Three-dimensional structure prediction of representative members suggests that their completely folded states are represented by a sequential arrangement of alpha-helical segments connected by unstructured linkers, which is experimentally verified for the LEA_4 protein COR15A. The unstructured linker region of COR15A represents a conserved motif among its closest homologs and is, therefore, of particular interest. Facilitating a set of seven designed and investigated COR15A mutants uncovers a complex interplay of transient interactions between the amphipathic alpha-helical segments, mediated by the linker, which fine-tunes folding transitions and structural ensembles upon reduced water-availability. Finally, alpha-helicity is also induced in COR15A upon temperature decrease, which is enhanced in the presence of osmolytes. In addition, high solution osmolarity induced secondary structure is followed by oligomerization of COR15A. Interestingly, the functionality of COR15A, in terms of liposome stabilization, strongly correlates with its alpha-helix ratio in the folded state. The present work significantly improves the understanding of the sequence-structure-function relationship for LEA_4 proteins and offers novel findings on folding mechanisms and oligomerization of COR15A.},
  language  = {en}
}
@article{KlettCherstvyShinetal.2021,
  author    = {Klett, Kolja and Cherstvy, Andrey G. and Shin, Jaeoh and Sokolov, Igor M. and Metzler, Ralf},
  title     = {Non-Gaussian, transiently anomalous, and ergodic self-diffusion of flexible dumbbells in crowded two-dimensional environments},
  series = {Physical review : E, Statistical, nonlinear and soft matter physics},
  volume    = {104},
  journal   = {Physical review : E, Statistical, nonlinear and soft matter physics},
  number    = {6},
  publisher = {American Physical Society},
  address   = {College Park},
  issn      = {2470-0045},
  doi       = {10.1103/PhysRevE.104.064603},
  pages     = {18},
  year      = {2021},
  abstract  = {We employ Langevin-dynamics simulations to unveil non-Brownian and non-Gaussian center-of-mass self-diffusion of massive flexible dumbbell-shaped particles in crowded two-dimensional solutions. We study the intradumbbell dynamics of the relative motion of the two constituent elastically coupled disks. Our main focus is on effects of the crowding fraction phi and of the particle structure on the diffusion characteristics. We evaluate the time-averaged mean-squared displacement (TAMSD), the displacement probability-density function (PDF), and the displacement autocorrelation function (ACF) of the dimers. For the TAMSD at highly crowded conditions of dumbbells, e.g., we observe a transition from the short-time ballistic behavior, via an intermediate subdiffusive regime, to long-time Brownian-like spreading dynamics. The crowded system of dimers exhibits two distinct diffusion regimes distinguished by the scaling exponent of the TAMSD, the dependence of the diffusivity on phi, and the features of the displacement-ACF. We attribute these regimes to a crowding-induced transition from viscous to viscoelastic diffusion upon growing phi. We also analyze the relative motion in the dimers, finding that larger phi suppress their vibrations and yield strongly non-Gaussian PDFs of rotational displacements. For the diffusion coefficients D(phi) of translational and rotational motion of the dumbbells an exponential decay with phi for weak and a power-law variation D(phi) proportional to (phi - phi(star))(2.4) for strong crowding is found. A comparison of simulation results with theoretical predictions for D(phi) is discussed and some relevant experimental systems are overviewed.},
  language  = {en}
}
@article{KlausIgualGilOst2021,
  author    = {Klaus, Susanne and Igual Gil, Carla and Ost, Mario},
  title     = {Regulation of diurnal energy balance by mitokines},
  series = {Cellular and molecular life sciences : CMLS},
  volume    = {78},
  journal   = {Cellular and molecular life sciences : CMLS},
  number    = {7},
  publisher = {Springer International Publishing AG},
  address   = {Cham (ZG)},
  issn      = {1420-682X},
  doi       = {10.1007/s00018-020-03748-9},
  pages     = {3369 -- 3384},
  year      = {2021},
  abstract  = {The mammalian system of energy balance regulation is intrinsically rhythmic with diurnal oscillations of behavioral and metabolic traits according to the 24 h day/night cycle, driven by cellular circadian clocks and synchronized by environmental or internal cues such as metabolites and hormones associated with feeding rhythms. Mitochondria are crucial organelles for cellular energy generation and their biology is largely under the control of the circadian system. Whether mitochondrial status might also feed-back on the circadian system, possibly via mitokines that are induced by mitochondrial stress as endocrine-acting molecules, remains poorly understood. Here, we describe our current understanding of the diurnal regulation of systemic energy balance, with focus on fibroblast growth factor 21 (FGF21) and growth differentiation factor 15 (GDF15), two well-known endocrine-acting metabolic mediators. FGF21 shows a diurnal oscillation and directly affects the output of the brain master clock. Moreover, recent data demonstrated that mitochondrial stress-induced GDF15 promotes a day-time restricted anorexia and systemic metabolic remodeling as shown in UCP1-transgenic mice, where both FGF21 and GDF15 are induced as myomitokines. In this mouse model of slightly uncoupled skeletal muscle mitochondria GDF15 proved responsible for an increased metabolic flexibility and a number of beneficial metabolic adaptations. However, the molecular mechanisms underlying energy balance regulation by mitokines are just starting to emerge, and more data on diurnal patterns in mouse and man are required. This will open new perspectives into the diurnal nature of mitokines and action both in health and disease.},
  language  = {en}
}
@phdthesis{Kaptur2021,
  author    = {Kaptur, Joanna Alexandra},
  title     = {The LEUNIG regulatory complex},
  school      = {Universit{\"a}t Potsdam},
  year      = {2021},
  abstract  = {Patterning along the apical-basal (A-B) axis is a crucial step during the early stages of plant embryogenesis and leads to the establishment of two poles of which each will develop their own stem cell niches. The activity of these meristems is responsible for post-embryonic growth, with the shoot apical meristem (SAM) generating the above-ground organs and the root apical meristem (RAM) producing the subterranean structures of the plant. While several transcriptional regulators governing A-B patterning have been identified, precisely how their regulatory function is orchestrated remains elusive. This study focuses on transcriptional co-regulators LEUNIG (LUG) and closely related LEUNIG_HOMOLOG (LUH) and their role in the formation of A-B patterning during embryogenesis as well as their post-embryonic maintenance. A link between the LUG regulatory complex and SAM formation and maintenance comes from the observation that lug mutants heterozygous for the luh allele (lug luh+/-) often have enlarged SAMs resulting from misregulated cell divisions. A more severe phenotype is observed in lug luh double mutants which are embryonically lethal. In this study, a detailed characterisation of lug luh embryo phenotype reveals that these mutants display aberrant cell divisions along the A-B axis, which correlates with defects in auxin distribution, complete loss of apical identity, and altered expression of transcription factors determining basal fate. Like other co-regulators, LUG and LUH lack intrinsic DNA-binding domains and instead must interact with DNA-binding cofactors to ensure recruitment to regulatory elements of target genes. This either involves direct contact between the co-regulators and transcription factors (TFs) or the formation of higher-order complexes with adaptor proteins such as SEUSS (SEU) or related SEUSS-LIKEs (SLKs), which facilitate binding to specific TFs. Results presented in this study provide insight into the molecular framework for the LUG regulatory complex activity during embryogenesis. Both yeast and in planta assays showed that LUG/LUH and SEU/SLKs physically associate with a variety of WUSCHEL-RELATED HOMEOBOX (WOX) TFs including members of the WOX2-module. Furthermore, genetic interactions between members of the WOX2-module and the LUG regulatory complex, support their mutual action during embryogenesis. Based on the reduced activity of HOMEODOMAIN LEUCINE-ZIPPER CLASS III (HD-ZIPIII) promoters in lug luh embryos, a model is proposed in which the LUG regulatory complex functions together with WOX2-module to promote apical identity and subsequent SAM initiation through regulation of the HD-ZIPIIIs. The activity of the LUG complex in promoting basal embryo identity through positive regulation of microRNA165/166 suggests that this complex also has functions that are independent of the WOX2-module. Preliminary work reported in this study further uncovered the role of the LUG regulatory complex in post-embryonic development. While the fasciated inflorescence meristems of lug luh+/- plants displayed defects in auxin transport and altered activity of stem cell markers, embryonically rescued lug luh mutants formed flat and differentiated SAMs. In addition, rescued lug luh mutants exhibited severely disorganised RAM and defects in quiescent center (QC) specification, supporting the involvement of the LUG complex in post-embryonic RAM maintenance.},
  language  = {en}
}