@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}
}
@article{GluecklerHerzschuhKruseetal.2021,
  author    = {Gl{\"u}ckler, Ramesh and Herzschuh, Ulrike and Kruse, Stefan and Andreev, Andrei and Vyse, Stuart Andrew and Winkler, Bettina and Biskaborn, Boris and Pestryakova, Luidmila Agafyevna and Dietze, Elisabeth},
  title     = {Wildfire history of the boreal forest of south-western Yakutia (Siberia) over the last two millennia documented by a lake-sediment charcoal record},
  series = {Biogeosciences : BG / European Geosciences Union},
  volume    = {18},
  journal   = {Biogeosciences : BG / European Geosciences Union},
  number    = {13},
  publisher = {Copernicus},
  address   = {G{\"o}ttingen},
  issn      = {1726-4170},
  doi       = {10.5194/bg-18-4185-2021},
  pages     = {4185 -- 4209},
  year      = {2021},
  abstract  = {Wildfires, as a key disturbance in forest ecosystems, are shaping the world's boreal landscapes. Changes in fire regimes are closely linked to a wide array of environmental factors, such as vegetation composition, climate change, and human activity. Arctic and boreal regions and, in particular, Siberian boreal forests are experiencing rising air and ground temperatures with the subsequent degradation of permafrost soils leading to shifts in tree cover and species composition. Compared to the boreal zones of North America or Europe, little is known about how such environmental changes might influence long-term fire regimes in Russia. The larch-dominated eastern Siberian deciduous boreal forests differ markedly from the composition of other boreal forests, yet data about past fire regimes remain sparse. Here, we present a high-resolution macroscopic charcoal record from lacustrine sediments of Lake Khamra (southwest Yakutia, Siberia) spanning the last ca. 2200 years, including information about charcoal particle sizes and morphotypes. Our results reveal a phase of increased charcoal accumulation between 600 and 900 CE, indicative of relatively high amounts of burnt biomass and high fire frequencies. This is followed by an almost 900-year-long period of low charcoal accumulation without significant peaks likely corresponding to cooler climate conditions. After 1750 CE fire frequencies and the relative amount of biomass burnt start to increase again, coinciding with a warming climate and increased anthropogenic land development after Russian colonization. In the 20th century, total charcoal accumulation decreases again to very low levels despite higher fire frequency, potentially reflecting a change in fire management strategies and/or a shift of the fire regime towards more frequent but smaller fires. A similar pattern for different charcoal morphotypes and comparison to a pollen and non-pollen palynomorph (NPP) record from the same sediment core indicate that broad-scale changes in vegetation composition were probably not a major driver of recorded fire regime changes. Instead, the fire regime of the last two millennia at Lake Khamra seems to be controlled mainly by a combination of short-term climate variability and anthropogenic fire ignition and suppression.},
  language  = {en}
}
@article{CourtinAndreevRaschkeetal.2021,
  author    = {Courtin, J{\´e}r{\´e}my and Andreev, Andrei and Raschke, Elena and Bala, Sarah and Biskaborn, Boris and Liu, Sisi and Zimmermann, Heike and Diekmann, Bernhard and Stoof-Leichsenring, Kathleen R. and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike},
  title     = {Vegetation changes in Southeastern Siberia during the late pleistocene and the holocene},
  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.2021.625096},
  pages     = {18},
  year      = {2021},
  abstract  = {Relationships between climate, species composition, and species richness are of particular importance for understanding how boreal ecosystems will respond to ongoing climate change. This study aims to reconstruct changes in terrestrial vegetation composition and taxa richness during the glacial Late Pleistocene and the interglacial Holocene in the sparsely studied southeastern Yakutia (Siberia) by using pollen and sedimentary ancient DNA (sedaDNA) records. Pollen and sedaDNA metabarcoding data using the trnL g and h markers were obtained from a sediment core from Lake Bolshoe Toko. Both proxies were used to reconstruct the vegetation composition, while metabarcoding data were also used to investigate changes in plant taxa richness. The combination of pollen and sedaDNA approaches allows a robust estimation of regional and local past terrestrial vegetation composition around Bolshoe Toko during the last similar to 35,000 years. Both proxies suggest that during the Late Pleistocene, southeastern Siberia was covered by open steppe-tundra dominated by graminoids and forbs with patches of shrubs, confirming that steppe-tundra extended far south in Siberia. Both proxies show disturbance at the transition between the Late Pleistocene and the Holocene suggesting a period with scarce vegetation, changes in the hydrochemical conditions in the lake, and in sedimentation rates. Both proxies document drastic changes in vegetation composition in the early Holocene with an increased number of trees and shrubs and the appearance of new tree taxa in the lake's vicinity. The sedaDNA method suggests that the Late Pleistocene steppe-tundra vegetation supported a higher number of terrestrial plant taxa than the forested Holocene. This could be explained, for example, by the "keystone herbivore" hypothesis, which suggests that Late Pleistocene megaherbivores were able to maintain a high plant diversity. This is discussed in the light of the data with the broadly accepted species-area hypothesis as steppe-tundra covered such an extensive area during the Late Pleistocene.},
  language  = {en}
}
@article{CalderanRodriguesLuzarowskiMonteBelloetal.2021,
  author    = {Calderan-Rodrigues, Maria Juliana and Luzarowski, Marcin and Monte-Bello, Carolina Cassano and Minen, Romina Ines and Z{\"u}hlke, Boris M. and Nikoloski, Zoran and Skirycz, Aleksandra and Caldana, Camila},
  title     = {Proteogenic dipeptides are characterized by diel fluctuations and target of rapamycin complex-signaling dependency in the model plant Arabidopsis thaliana},
  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.2021.758933},
  pages     = {15},
  year      = {2021},
  abstract  = {As autotrophic organisms, plants capture light energy to convert carbon dioxide into ATP, nicotinamide adenine dinucleotide phosphate (NADPH), and sugars, which are essential for the biosynthesis of building blocks, storage, and growth. At night, metabolism and growth can be sustained by mobilizing carbon (C) reserves. In response to changing environmental conditions, such as light-dark cycles, the small-molecule regulation of enzymatic activities is critical for reprogramming cellular metabolism. We have recently demonstrated that proteogenic dipeptides, protein degradation products, act as metabolic switches at the interface of proteostasis and central metabolism in both plants and yeast. Dipeptides accumulate in response to the environmental changes and act via direct binding and regulation of critical enzymatic activities, enabling C flux distribution. Here, we provide evidence pointing to the involvement of dipeptides in the metabolic rewiring characteristics for the day-night cycle in plants. Specifically, we measured the abundance of 13 amino acids and 179 dipeptides over short- (SD) and long-day (LD) diel cycles, each with different light intensities. Of the measured dipeptides, 38 and eight were characterized by day-night oscillation in SD and LD, respectively, reaching maximum accumulation at the end of the day and then gradually falling in the night. Not only the number of dipeptides, but also the amplitude of the oscillation was higher in SD compared with LD conditions. Notably, rhythmic dipeptides were enriched in the glucogenic amino acids that can be converted into glucose. Considering the known role of Target of Rapamycin (TOR) signaling in regulating both autophagy and metabolism, we subsequently investigated whether diurnal fluctuations of dipeptides levels are dependent on the TOR Complex (TORC). The Raptor1b mutant (raptor1b), known for the substantial reduction of TOR kinase activity, was characterized by the augmented accumulation of dipeptides, which is especially pronounced under LD conditions. We were particularly intrigued by the group of 16 dipeptides, which, based on their oscillation under SD conditions and accumulation in raptor1b, can be associated with limited C availability or photoperiod. By mining existing protein-metabolite interaction data, we delineated putative protein interactors for a representative dipeptide Pro-Gln. The obtained list included enzymes of C and amino acid metabolism, which are also linked to the TORC-mediated metabolic network. Based on the obtained results, we speculate that the diurnal accumulation of dipeptides contributes to its metabolic adaptation in response to changes in C availability. We hypothesize that dipeptides would act as alternative respiratory substrates and by directly modulating the activity of the focal enzymes.},
  language  = {en}
}
@article{FriedrichOberkoflerTrindadeetal.2021,
  author    = {Friedrich, Thomas and Oberkofler, Vicky and Trindade, In{\^e}s and Altmann, Simone and Brzezinka, Krzysztof and L{\"a}mke, J{\"o}rn S. and Gorka, Michal and Kappel, Christian and Sokolowska, Ewelina and Skirycz, Aleksandra and Graf, Alexander and B{\"a}urle, Isabel},
  title     = {Heteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis},
  series = {Nature Communications},
  volume    = {12},
  journal   = {Nature Communications},
  number    = {1},
  publisher = {Nature Publishing Group UK},
  address   = {[London]},
  issn      = {2041-1723},
  doi       = {10.1038/s41467-021-23786-6},
  pages     = {15},
  year      = {2021},
  abstract  = {Adaptive plasticity in stress responses is a key element of plant survival strategies. For instance, moderate heat stress (HS) primes a plant to acquire thermotolerance, which allows subsequent survival of more severe HS conditions. Acquired thermotolerance is actively maintained over several days (HS memory) and involves the sustained induction of memory-related genes. Here we show that FORGETTER3/ HEAT SHOCK TRANSCRIPTION FACTOR A3 (FGT3/HSFA3) is specifically required for physiological HS memory and maintaining high memory-gene expression during the days following a HS exposure. HSFA3 mediates HS memory by direct transcriptional activation of memory-related genes after return to normal growth temperatures. HSFA3 binds HSFA2, and in vivo both proteins form heteromeric complexes with additional HSFs. Our results indicate that only complexes containing both HSFA2 and HSFA3 efficiently promote transcriptional memory by positively influencing histone H3 lysine 4 (H3K4) hyper-methylation. In summary, our work defines the major HSF complex controlling transcriptional memory and elucidates the in vivo dynamics of HSF complexes during somatic stress memory. Moderate heat stress primes plants to acquire tolerance to subsequent, more severe heat stress. Here the authors show that the HSFA3 transcription factor forms a heteromeric complex with HSFA2 to sustain activated transcription of genes required for acquired thermotolerance by promoting H3K4 hyper-methylation.},
  language  = {en}
}
@article{CarpioAriasAriasMogrovejoNicolaldeCifuentesetal.2021,
  author    = {Carpio Arias, Tannia Valeria and Arias Mogrovejo, Diana Carolina and Nicolalde Cifuentes, Tom{\´a}s Marcelo and Tapia Veloz, Estephany Carolina and Zeeuw, Chris I. de and Vinueza Veloz, Maria Fernanda},
  title     = {Sleep quality does not mediate the negative effects of chronodisruption on body composition and metabolic syndrome in healthcare workers in Ecuador},
  series = {Diabetes \& metabolic syndrome : clinical research \& reviews ; the official journal of DiabetesIndia},
  volume    = {15},
  journal   = {Diabetes \& metabolic syndrome : clinical research \& reviews ; the official journal of DiabetesIndia},
  number    = {1},
  publisher = {Elsevier},
  address   = {Amsterdam [u.a.]},
  issn      = {1871-4021},
  doi       = {10.1016/j.dsx.2021.01.017},
  pages     = {397 -- 402},
  year      = {2021},
  abstract  = {Background and aims: The objective of the present work was to determine to what extent sleep quality may mediate the association between chronodisruption (CD) and metabolic syndrome (MS), and between CD and body composition (BC). Methodology: Cross-sectional study which included 300 adult health workers, 150 of whom were night shift workers and thereby exposed to CD. Diagnosis of MS was made based on Adult Treatment Panel III criteria. Sleep quality was measured using the Pittsburgh Sleep Quality Index. Body mass index (BMI), fat mass percentage, and visceral fat percentage were measured as indicators of body composition (BC). Data were analyzed using logistic, linear regression and structural equation models. Results: The odds of health workers exposed to CD to suffer MS was 22.13 (IC95 8.68-66.07) when the model was adjusted for age, gender, physical activity and energy consumption. CD was also significantly associated with an increase in fat mass and visceral fat percentages, but not to BMI. Surprisingly, there was not enough evidence supporting the hypothesis that sleep quality contributes to the association between CD and MS or between CD and BC. Conclusions: Sleep quality does not mediate the negative effects of CD on MS nor on BC.},
  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{NwosuRoeserYangetal.2021,
  author    = {Nwosu, Ebuka Canisius and Roeser, Patricia Angelika and Yang, Sizhong and Pinkerneil, Sylvia and Ganzert, Lars and Dittmann, Elke and Brauer, Achim and Wagner, Dirk and Liebner, Susanne},
  title     = {Species-level spatio-temporal dynamics of cyanobacteria in a hard-water temperate lake in the Southern Baltics},
  series = {Frontiers in microbiology},
  volume    = {12},
  journal   = {Frontiers in microbiology},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {1664-302X},
  doi       = {10.3389/fmicb.2021.761259},
  pages     = {17},
  year      = {2021},
  abstract  = {Cyanobacteria are important primary producers in temperate freshwater ecosystems. However, studies on the seasonal and spatial distribution of cyanobacteria in deep lakes based on high-throughput DNA sequencing are still rare. In this study, we combined monthly water sampling and monitoring in 2019, amplicon sequence variants analysis (ASVs; a proxy for different species) and quantitative PCR targeting overall cyanobacteria abundance to describe the seasonal and spatial dynamics of cyanobacteria in the deep hard-water oligo-mesotrophic Lake Tiefer See, NE Germany. We observed significant seasonal variation in the cyanobacterial community composition (p < 0.05) in the epi- and metalimnion layers, but not in the hypolimnion. In winter-when the water column is mixed-picocyanobacteria (Synechococcus and Cyanobium) were dominant. With the onset of stratification in late spring, we observed potential niche specialization and coexistence among the cyanobacteria taxa driven mainly by light and nutrient dynamics. Specifically, ASVs assigned to picocyanobacteria and the genus Planktothrix were the main contributors to the formation of deep chlorophyll maxima along a light gradient. While Synechococcus and different Cyanobium ASVs were abundant in the epilimnion up to the base of the euphotic zone from spring to fall, Planktothrix mainly occurred in the metalimnetic layer below the euphotic zone where also overall cyanobacteria abundance was highest in summer. Our data revealed two potentially psychrotolerant (cold-adapted) Cyanobium species that appear to cope well under conditions of lower hypolimnetic water temperature and light as well as increasing sediment-released phosphate in the deeper waters in summer. The potential cold-adapted Cyanobium species were also dominant throughout the water column in fall and winter. Furthermore, Snowella and Microcystis-related ASVs were abundant in the water column during the onset of fall turnover. Altogether, these findings suggest previously unascertained and considerable spatiotemporal changes in the community of cyanobacteria on the species level especially within the genus Cyanobium in deep hard-water temperate lakes.},
  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{SchefflerBoginHermanussen2021,
  author    = {Scheffler, Christiane and Bogin, Barry and Hermanussen, Michael},
  title     = {Catch-up growth is a better indicator of undernutrition than thresholds for stunting},
  series = {Public health nutrition : PHN / The Nutrition Society},
  volume    = {24},
  journal   = {Public health nutrition : PHN / The Nutrition Society},
  number    = {1},
  publisher = {Cambridge University Press},
  address   = {Cambridge ; New York, NY},
  issn      = {1475-2727},
  doi       = {10.1017/S1368980020003067},
  pages     = {52 -- 61},
  year      = {2021},
  abstract  = {Objective: Stunting (height-for-age < -2 SD) is one of the forms of undernutrition and is frequent among children of low- and middle-income countries. But stunting perSe is not a synonym of undernutrition. We investigated association between body height and indicators of energetic undernutrition at three critical thresholds for thinness used in public health: (1) BMI SDS < -2; (2) mid-upper arm circumference divided by height (MUAC (mm) × 10/height (cm) < 1·36) and (3) mean skinfold thickness (SF) < 7 mm and to question the reliability of thresholds as indicators of undernutrition. Design: Cross-sectional study; breakpoint analysis. Setting: Rural and urban regions of Indonesia and Guatemala - different socio-economic status (SES). Participants: 1716 Indonesian children (6·0-13·2 years) and 3838 Guatemalan children (4·0-18·9 years) with up to 50 \% stunted children. Results: When separating the regression of BMI, MUAC or SF, on height into distinguishable segments (breakpoint analysis), we failed to detect relevant associations between height, and BMI, MUAC or SF, even in the thinnest and shortest children. For BMI and SF, the breakpoint analysis either failed to reach statistical significance or distinguished at breakpoints above critical thresholds. For MUAC, the breakpoint analysis yielded negative associations between MUAC/h and height in thin individuals. Only in high SES Guatemalan children, SF and height appeared mildly associated with R2 = 0·017. Conclusions: Currently used lower thresholds of height-for-age (stunting) do not show relevant associations with anthropometric indicators of energetic undernutrition. We recommend using the catch-up growth spurt during early re-feeding instead as immediate and sensitive indicator of past undernourishment. We discuss the primacy of education and social-economic-political-emotional circumstances as responsible factors for stunting.},
  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{HampfNendelStreyetal.2021,
  author    = {Hampf, Anna and Nendel, Claas and Strey, Simone and Strey, Robert},
  title     = {Biotic yield losses in the Southern Amazon, Brazil},
  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.2021.621168},
  pages     = {16},
  year      = {2021},
  abstract  = {Pathogens and animal pests (P\&A) are a major threat to global food security as they directly affect the quantity and quality of food. The Southern Amazon, Brazil's largest domestic region for soybean, maize and cotton production, is particularly vulnerable to the outbreak of P\&A due to its (sub)tropical climate and intensive farming systems. However, little is known about the spatial distribution of P\&A and the related yield losses. Machine learning approaches for the automated recognition of plant diseases can help to overcome this research gap. The main objectives of this study are to (1) evaluate the performance of Convolutional Neural Networks (ConvNets) in classifying P\&A, (2) map the spatial distribution of P\&A in the Southern Amazon, and (3) quantify perceived yield and economic losses for the main soybean and maize P\&A. The objectives were addressed by making use of data collected with the smartphone application Plantix. The core of the app's functioning is the automated recognition of plant diseases via ConvNets. Data on expected yield losses were gathered through a short survey included in an "expert" version of the application, which was distributed among agronomists. Between 2016 and 2020, Plantix users collected approximately 78,000 georeferenced P\&A images in the Southern Amazon. The study results indicate a high performance of the trained ConvNets in classifying 420 different crop-disease combinations. Spatial distribution maps and expert-based yield loss estimates indicate that maize rust, bacterial stalk rot and the fall armyworm are among the most severe maize P\&A, whereas soybean is mainly affected by P\&A like anthracnose, downy mildew, frogeye leaf spot, stink bugs and brown spot. Perceived soybean and maize yield losses amount to 12 and 16\%, respectively, resulting in annual yield losses of approximately 3.75 million tonnes for each crop and economic losses of US\$2 billion for both crops together. The high level of accuracy of the trained ConvNets, when paired with widespread use from following a citizen-science approach, results in a data source that will shed new light on yield loss estimates, e.g., for the analysis of yield gaps and the development of measures to minimise them.},
  language  = {en}
}
@article{CasertaZhangYarmanetal.2021,
  author    = {Caserta, Giorgio and Zhang, Xiaorong and Yarman, Aysu and Supala, Eszter and Wollenberger, Ulla and Gyurcs{\´a}nyi, R{\´o}bert E. and Zebger, Ingo and Scheller, Frieder W.},
  title     = {Insights in electrosynthesis, target binding, and stability of peptide-imprinted polymer nanofilms},
  series = {Electrochimica acta : the journal of the International Society of Electrochemistry (ISE)},
  volume    = {381},
  journal   = {Electrochimica acta : the journal of the International Society of Electrochemistry (ISE)},
  publisher = {Elsevier},
  address   = {New York, NY [u.a.]},
  issn      = {0013-4686},
  doi       = {10.1016/j.electacta.2021.138236},
  pages     = {8},
  year      = {2021},
  abstract  = {Molecularly imprinted polymer (MIP) nanofilms have been successfully implemented for the recognition of different target molecules: however, the underlying mechanistic details remained vague. This paper provides new insights in the preparation and binding mechanism of electrosynthesized peptide-imprinted polymer nanofilms for selective recognition of the terminal pentapeptides of the beta-chains of human adult hemoglobin, HbA, and its glycated form HbA1c. To differentiate between peptides differing solely in a glucose adduct MIP nanofilms were prepared by a two-step hierarchical electrosynthesis that involves first the chemisorption of a cysteinyl derivative of the pentapeptide followed by electropolymerization of scopoletin. This approach was compared with a random single-step electrosynthesis using scopo-letin/pentapeptide mixtures. Electrochemical monitoring of the peptide binding to the MIP nanofilms by means of redox probe gating revealed a superior affinity of the hierarchical approach with a Kd value of 64.6 nM towards the related target. Changes in the electrosynthesized non-imprinted polymer and MIP nanofilms during chemical, electrochemical template removal and rebinding were substantiated in situ by monitoring the characteristic bands of both target peptides and polymer with surface enhanced infrared absorption spectroscopy. This rational approach led to MIPs with excellent selectivity and provided key mechanistic insights with respect to electrosynthesis, rebinding and stability of the formed MIPs.},
  language  = {en}
}
@article{YarmanKurbanoğluZebgeretal.2021,
  author    = {Yarman, Aysu and Kurbanoğlu, Sevin{\c{c}} and Zebger, Ingo and Scheller, Frieder W.},
  title     = {Simple and robust},
  series = {Sensors and actuators : B, Chemical : an international journal devoted to research and development of chemical transducers},
  volume    = {330},
  journal   = {Sensors and actuators : B, Chemical : an international journal devoted to research and development of chemical transducers},
  publisher = {Elsevier Science},
  address   = {Amsterdam [u.a.]},
  issn      = {0925-4005},
  doi       = {10.1016/j.snb.2020.129369},
  pages     = {12},
  year      = {2021},
  abstract  = {A spectrum of 7562 publications on Molecularly Imprinted Polymers (MIPs) has been presented in literature within the last ten years (Scopus, September 7, 2020). Around 10 \% of the papers published on MIPs describe the recognition of proteins. The straightforward synthesis of MIPs is a significant advantage as compared with the preparation of enzymes or antibodies. MIPs have been synthesized from only one up to six functional monomers while proteins are made up of 20 natural amino acids. Furthermore, they can be synthesized against structures of low immunogenicity and allow multi-analyte measurements via multi-target synthesis. Electrochemical methods allow simple polymer synthesis, removal of the template and readout. Among the different sensor configurations electrochemical MIP-sensors provide the broadest spectrum of protein analytes. The sensitivity of MIP-sensors is sufficiently high for biomarkers in the sub-nanomolar region, nevertheless the cross-reactivity of highly abundant proteins in human serum is still a challenge. MIPs for proteins offer innovative tools not only for clinical and environmental analysis, but also for bioimaging, therapy and protein engineering.},
  language  = {en}
}
@article{TranTamuraPhametal.2021,
  author    = {Tran, V. Phuong and Tamura, Yui and Pham, Van-Cuong and Elhussiny, Mohamed Z. and Han, Guofeng and Sur Chowdhury, Vishwajit and Furuse, Mitsuhiro},
  title     = {Neuropeptide Y modifies a part of diencephalic catecholamine but not indolamine metabolism in chicks depending on feeding status},
  series = {Neuropeptides},
  volume    = {89},
  journal   = {Neuropeptides},
  publisher = {Elsevier},
  address   = {New York, NY},
  issn      = {0143-4179},
  doi       = {10.1016/j.npep.2021.102169},
  pages     = {9},
  year      = {2021},
  abstract  = {The role of the monoaminergic system in the feeding behavior of neonatal chicks has been reported, but the functional relationship between the metabolism of monoamines and appetite-related neuropeptides is still unclear. This study aimed to investigate the changes in catecholamine and indolamine metabolism in response to the central action of neuropeptide Y (NPY) in different feeding statuses and the underlying mechanisms. In Experiment 1, the diencephalic concentrations of amino acids and monoamines following the intracerebroventricular (ICV) injection of NPY (375 pmol/10 mu l/chick), saline solution under ad libitum, and fasting conditions for 30 min were determined. Central NPY significantly decreased L-tyrosine concentration, the precursor of catecholamines under feeding condition, but not under fasting condition. Central NPY significantly increased dopamine metabolites, including 3,4-dihydroxyphenylacetic acid and homovanillic acid (HVA). The concentration of 3-methoxy-4-hydroxyphenylglycol was significantly reduced under feeding condition, but did not change under fasting condition by NPY. However, no effects of NPY on indolamine metabolism were found in either feeding status. Therefore, the mechanism of action of catecholamines with central NPY under feeding condition was elucidated in Experiment 2. Central NPY significantly attenuated diencephalic gene expression of catecholaminergic synthetic enzymes, such as tyrosine hydroxylase, L-aromatic amino acid decarboxylase, and GTP cyclohydrolase I after 30 min of feeding. In Experiment 3, co-injection of alpha-methyl-L-tyrosine, an inhibitor of tyrosine hydroxylase with NPY, moderately attenuated the orexigenic effect of NPY, accompanied by a significant positive correlation between food intake and HVA levels. In Experiment 4, there was a significant interaction between NPY and clorgyline, an inhibitor of monoamine oxidase A with ICV co-injection which implies that co-existence of NPY and clorgyline enhances the orexigenic effect of NPY. In conclusion, central NPY modifies a part of catecholamine metabolism, which is illustrated by the involvement of dopamine transmission and metabolism under feeding but not fasting conditions.},
  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{KaechDennisVorburger2021,
  author    = {Kaech, Heidi and Dennis, Alice B. and Vorburger, Christoph},
  title     = {Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa},
  series = {BMC genomics},
  volume    = {22},
  journal   = {BMC genomics},
  number    = {1},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1471-2164},
  doi       = {10.1186/s12864-021-07742-8},
  pages     = {21},
  year      = {2021},
  abstract  = {Background Secondary endosymbionts of aphids provide benefits to their hosts, but also impose costs such as reduced lifespan and reproductive output. The aphid Aphis fabae is host to different strains of the secondary endosymbiont Hamiltonella defensa, which encode different putative toxins. These strains have very different phenotypes: They reach different densities in the host, and the costs and benefits (protection against parasitoid wasps) they confer to the host vary strongly. Results We used RNA-Seq to generate hypotheses on why four of these strains inflict such different costs to A. fabae. We found different H. defensa strains to cause strain-specific changes in aphid gene expression, but little effect of H. defensa on gene expression of the primary endosymbiont, Buchnera aphidicola. The highly costly and over-replicating H. defensa strain H85 was associated with strongly reduced aphid expression of hemocytin, a marker of hemocytes in Drosophila. The closely related strain H15 was associated with downregulation of ubiquitin-related modifier 1, which is related to nutrient-sensing and oxidative stress in other organisms. Strain H402 was associated with strong differential regulation of a set of hypothetical proteins, the majority of which were only differentially regulated in presence of H402. Conclusions Overall, our results suggest that costs of different strains of H. defensa are likely caused by different mechanisms, and that these costs are imposed by interacting with the host rather than the host's obligatory endosymbiont B. aphidicola.},
  language  = {en}
}
@article{KorniienkoNguyenBaumgartneretal.2021,
  author    = {Korniienko, Yevheniia and Nguyen, Linh and Baumgartner, Stephanie and Vater, Marianne and Tiedemann, Ralph and Kirschbaum, Frank},
  title     = {Correction to: Intragenus F1-hybrids of African weakly electric fish (Mormyridae: Campylomormyrus tamandua male x C. compressirostris female) are fertile (vol 206, pg 571, 2020)},
  series = {Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology},
  volume    = {207},
  journal   = {Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology},
  number    = {6},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {0340-7594},
  doi       = {10.1007/s00359-021-01513-2},
  pages     = {773 -- 773},
  year      = {2021},
  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{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{AngeleskaOmranianNikoloski2021,
  author    = {Angeleska, Angela and Omranian, Sara and Nikoloski, Zoran},
  title     = {Coherent network partitions},
  series = {Theoretical computer science : the journal of the EATCS},
  volume    = {894},
  journal   = {Theoretical computer science : the journal of the EATCS},
  publisher = {Elsevier},
  address   = {Amsterdam [u.a.]},
  issn      = {0304-3975},
  doi       = {10.1016/j.tcs.2021.10.002},
  pages     = {3 -- 11},
  year      = {2021},
  abstract  = {We continue to study coherent partitions of graphs whereby the vertex set is partitioned into subsets that induce biclique spanned subgraphs. The problem of identifying the minimum number of edges to obtain biclique spanned connected components (CNP), called the coherence number, is NP-hard even on bipartite graphs. Here, we propose a graph transformation geared towards obtaining an O (log n)-approximation algorithm for the CNP on a bipartite graph with n vertices. The transformation is inspired by a new characterization of biclique spanned subgraphs. In addition, we study coherent partitions on prime graphs, and show that finding coherent partitions reduces to the problem of finding coherent partitions in a prime graph. Therefore, these results provide future directions for approximation algorithms for the coherence number of a given graph.},
  language  = {en}
}
@article{YanFrokjarEngelbrektetal.2021,
  author    = {Yan, Jiawei and Fr{\o}kj{\ae}r, Emil Egede and Engelbrekt, Christian and Leimk{\"u}hler, Silke and Ulstrup, Jens and Wollenberger, Ulla and Xiao, Xinxin and Zhang, Jingdong},
  title     = {Voltammetry and single-molecule in situ scanning tunnelling microscopy of the redox metalloenzyme human sulfite oxidase},
  series = {ChemElectroChem},
  volume    = {8},
  journal   = {ChemElectroChem},
  number    = {1},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {2196-0216},
  doi       = {10.1002/celc.202001258},
  pages     = {164 -- 171},
  year      = {2021},
  abstract  = {Human sulfite oxidase (hSO) is a homodimeric two-domain enzyme central in the biological sulfur cycle. A pyranopterin molybdenum cofactor (Moco) is the catalytic site and a heme b(5) group located in the N-terminal domain. The two domains are connected by a flexible linker region. Electrons produced at the Moco in sulfite oxidation, are relayed via heme b(5) to electron acceptors or an electrode surface. Inter-domain conformational changes between an open and a closed enzyme conformation, allowing "gated" electron transfer has been suggested. We first recorded cyclic voltammetry (CV) of hSO on single-crystal Au(111)-electrode surfaces modified by self-assembled monolayers (SAMs) both of a short rigid thiol, cysteamine and of a longer structurally flexible thiol, omega-amino-octanethiol (AOT). hSO on cysteamine SAMs displays a well-defined pair of voltammetric peaks around -0.207 V vs. SCE in the absence of sulfite substrate, but no electrocatalysis. hSO on AOT SAMs displays well-defined electrocatalysis, but only "fair" quality voltammetry in the absence of sulfite. We recorded next in situ scanning tunnelling spectroscopy (STS) of hSO on AOT modified Au(111)-electrodes, disclosing, a 2-5 \% surface coverage of strong molecular scale contrasts, assigned to single hSO molecules, notably with no contrast difference in the absence and presence of sulfite. In situ STS corroborated this observation with a sigmoidal tunnelling current/overpotential correlation.},
  language  = {en}
}
@article{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{SchefflerHermanussenRogol2021,
  author    = {Scheffler, Christiane and Hermanussen, Michael and Rogol, Alan D.},
  title     = {Stunting},
  series = {Archives of disease in childhood : a peer review journal for health professionals and researchers covering conception to adolescence},
  volume    = {106},
  journal   = {Archives of disease in childhood : a peer review journal for health professionals and researchers covering conception to adolescence},
  number    = {8},
  publisher = {BMJ Publishing Group},
  address   = {London},
  issn      = {0003-9888},
  doi       = {10.1136/archdischild-2020-319240},
  pages     = {819 -- 820},
  year      = {2021},
  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{KindermannDoblerNiedeggenetal.2021,
  author    = {Kindermann, Liana and Dobler, Magnus and Niedeggen, Daniela and Linst{\"a}dter, Anja},
  title     = {A new protocol for estimation of woody aboveground biomass in disturbance-prone ecosystems},
  series = {Ecological indicators : integrating monitoring, assessment and management},
  volume    = {135},
  journal   = {Ecological indicators : integrating monitoring, assessment and management},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {1470-160X},
  doi       = {10.1016/j.ecolind.2021.108466},
  pages     = {16},
  year      = {2021},
  abstract  = {Almost one third of global drylands are open forests and savannas, which are typically shaped by frequent natural disturbances such as wildfire and herbivory. Studies on ecosystem functions and services of woody vegetation require robust estimates of aboveground biomass (AGB). However, most methods have been developed for comparatively undisturbed forest ecosystems. As they are not tailored to accurately quantify AGB of small and irregular growth forms, their application on these growth forms may lead to unreliable or even biased AGB estimates in disturbance-prone dryland ecosystems. Moreover, these methods cannot quantify AGB losses caused by disturbance agents. Here we propose a methodology to estimate individual-and stand-level woody AGB in disturbance-prone ecosystems. It consists of flexible field sampling routines and estimation workflows for six growth classes, delineated by size and damage criteria. It also comprises a detailed damage assessment, harnessing the ecological archive of woody growth for past disturbances. Based on large inventories collected along steep gradients of elephant disturbances in African dryland ecosystems, we compared the AGB estimates generated with our proposed method against estimates from a less adapted forest inventory method. We evaluated the necessary stepwise procedures of method adaptation and analyzed each step's effect on stand-level AGB estimation. We further explored additional advantages of our proposed method with regard to disturbance impact quantification. Results indicate that a majority of growth forms and individuals in savanna vegetation could only be assessed if methods of AGB estimation were adapted to the conditions of a disturbance-prone ecosystem. Furthermore, our damage assessment demonstrated that one third to half of all woody AGB was lost to disturbances. Consequently, less adapted methods may be insufficient and are likely to render inaccurate AGB estimations. Our proposed method has the potential to accurately quantify woody AGB in disturbance-prone ecosystems, as well as AGB losses. Our method is more time consuming than conventional allometric approaches, yet it can cover sufficient areas within reasonable timespans, and can also be easily adapted to alternative sampling schemes.},
  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{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{ZhangCasertaYarmanetal.2021,
  author    = {Zhang, Xiaorong and Caserta, Giorgio and Yarman, Aysu and Supala, Eszter and Tadjoung Waffo, Armel Franklin and Wollenberger, Ulla and Gyurcsanyi, Robert E. and Zebger, Ingo and Scheller, Frieder W.},
  title     = {"Out of Pocket" protein binding},
  series = {Chemosensors},
  volume    = {9},
  journal   = {Chemosensors},
  number    = {6},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2227-9040},
  doi       = {10.3390/chemosensors9060128},
  pages     = {13},
  year      = {2021},
  abstract  = {The epitope imprinting approach applies exposed peptides as templates to synthesize Molecularly Imprinted Polymers (MIPs) for the recognition of the parent protein. While generally the template protein binding to such MIPs is considered to occur via the epitope-shaped cavities, unspecific interactions of the analyte with non-imprinted polymer as well as the detection method used may add to the complexity and interpretation of the target rebinding. To get new insights on the effects governing the rebinding of analytes, we electrosynthesized two epitope-imprinted polymers using the N-terminal pentapeptide VHLTP-amide of human hemoglobin (HbA) as the template. MIPs were prepared either by single-step electrosynthesis of scopoletin/pentapeptide mixtures or electropolymerization was performed after chemisorption of the cysteine extended VHLTP peptide. Rebinding of the target peptide and the parent HbA protein to the MIP nanofilms was quantified by square wave voltammetry using a redox probe gating, surface enhanced infrared absorption spectroscopy, and atomic force microscopy. While binding of the pentapeptide shows large influence of the amino acid sequence, all three methods revealed strong non-specific binding of HbA to both polyscopoletin-based MIPs with even higher affinities than the target peptides.},
  language  = {en}
}
@inproceedings{DennisInaebnit2021,
  author    = {Dennis, Alice B. and In{\"a}bnit, Thomas},
  title     = {Physiological and genomic variation among cryptic species of a marsh snail (Melampus bidentatus)},
  series = {Integrative and comparative biology / Society of Integrative and Comparative Biology},
  volume    = {61},
  booktitle = {Integrative and comparative biology / Society of Integrative and Comparative Biology},
  publisher = {Oxford University Press},
  address   = {Oxford},
  issn      = {1540-7063},
  doi       = {10.1093/icb/icab001},
  pages     = {E195 -- E196},
  year      = {2021},
  language  = {en}
}
@article{QiuZhangBicketal.2021,
  author    = {Qiu, Liang and Zhang, Haoran and Bick, Thomas and Martin, Johannes and Wendler, Petra and B{\"o}ker, Alexander and Glebe, Ulrich and Xing, Chengfen},
  title     = {Construction of highly ordered glyco-inside nano-assemblies through RAFT dispersion polymerization of galactose-decorated monomer},
  series = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition},
  volume    = {60},
  journal   = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition},
  number    = {20},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {1433-7851},
  doi       = {10.1002/anie.202015692},
  pages     = {11098 -- 11103},
  year      = {2021},
  abstract  = {Glyco-assemblies derived from amphiphilic sugar-decorated block copolymers (ASBCs) have emerged prominently due to their wide application, for example, in biomedicine and as drug carriers. However, to efficiently construct these glyco-assemblies is still a challenge. Herein, we report an efficient technology for the synthesis of glyco-inside nano-assemblies by utilizing RAFT polymerization of a galactose-decorated methacrylate for polymerization-induced self-assembly (PISA). Using this approach, a series of highly ordered glyco-inside nano-assemblies containing intermediate morphologies were fabricated by adjusting the length of the hydrophobic glycoblock and the polymerization solids content. A specific morphology of complex vesicles was captured during the PISA process and the formation mechanism is explained by the morphology of its precursor and intermediate. Thus, this method establishes a powerful route to fabricate glyco-assemblies with tunable morphologies and variable sizes, which is significant to enable the large-scale fabrication and wide application of glyco-assemblies.},
  language  = {en}
}
@article{DeSousaMotaDinizCoelhoetal.2021,
  author    = {De Sousa Mota, Cristiano and Diniz, Ana and Coelho, Catarina and Santos-Silva, Teresa and Esmaeeli Moghaddam Tabalvandani, Mariam and Leimk{\"u}hler, Silke and Cabrita, Eurico J. and Marcelo, Filipa and Rom{\~a}o, Maria Jo{\~a}o},
  title     = {Interrogating the inhibition mechanisms of human aldehyde oxidase by X-ray crystallography and NMR spectroscopy},
  series = {Journal of medicinal chemistry / American Chemical Society},
  volume    = {64},
  journal   = {Journal of medicinal chemistry / American Chemical Society},
  number    = {17},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {0022-2623},
  doi       = {10.1021/acs.jmedchem.1c01125},
  pages     = {13025 -- 13037},
  year      = {2021},
  abstract  = {Human aldehyde oxidase (hAOX1) is mainly present in the liver and has an emerging role in drug metabolism, since it accepts a wide range of molecules as substrates and inhibitors. Herein, we employed an integrative approach by combining NMR, X-ray crystallography, and enzyme inhibition kinetics to understand the inhibition modes of three hAOX1 inhibitors-thioridazine, benzamidine, and raloxifene. These integrative data indicate that thioridazine is a noncompetitive inhibitor, while benzamidine presents a mixed type of inhibition. Additionally, we describe the first crystal structure of hAOX1 in complex with raloxifene. Raloxifene binds tightly at the entrance of the substrate tunnel, stabilizing the flexible entrance gates and elucidating an unusual substrate-dependent mechanism of inhibition with potential impact on drug-drug interactions. This study can be considered as a proof-of-concept for an efficient experimental screening of prospective substrates and inhibitors of hAOX1 relevant in drug discovery.},
  language  = {en}
}
@article{BrandesSicksBerger2021,
  author    = {Brandes, Stefanie and Sicks, Florian and Berger, Anne},
  title     = {Behaviour classification on giraffes (Giraffa camelopardalis) using machine learning algorithms on triaxial acceleration data of two commonly used GPS devices and its possible application for their management and conservation},
  series = {Sensors},
  volume    = {21},
  journal   = {Sensors},
  number    = {6},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {1424-8220},
  doi       = {10.3390/s21062229},
  pages     = {22},
  year      = {2021},
  abstract  = {Averting today's loss of biodiversity and ecosystem services can be achieved through conservation efforts, especially of keystone species. Giraffes (Giraffa camelopardalis) play an important role in sustaining Africa's ecosystems, but are 'vulnerable' according to the IUCN Red List since 2016. Monitoring an animal's behavior in the wild helps to develop and assess their conservation management. One mechanism for remote tracking of wildlife behavior is to attach accelerometers to animals to record their body movement. We tested two different commercially available high-resolution accelerometers, e-obs and Africa Wildlife Tracking (AWT), attached to the top of the heads of three captive giraffes and analyzed the accuracy of automatic behavior classifications, focused on the Random Forests algorithm. For both accelerometers, behaviors of lower variety in head and neck movements could be better predicted (i.e., feeding above eye level, mean prediction accuracy e-obs/AWT: 97.6\%/99.7\%; drinking: 96.7\%/97.0\%) than those with a higher variety of body postures (such as standing: 90.7-91.0\%/75.2-76.7\%; rumination: 89.6-91.6\%/53.5-86.5\%). Nonetheless both devices come with limitations and especially the AWT needs technological adaptations before applying it on animals in the wild. Nevertheless, looking at the prediction results, both are promising accelerometers for behavioral classification of giraffes. Therefore, these devices when applied to free-ranging animals, in combination with GPS tracking, can contribute greatly to the conservation of giraffes.},
  language  = {en}
}
@inproceedings{BoginHermanussenScheffler2021,
  author    = {Bogin, Barry and Hermanussen, Michael and Scheffler, Christiane},
  title     = {Fear, violence, inequality and stunting in Guatemala},
  series = {American journal of human biology : the official journal of the Human Biology Association},
  volume    = {33},
  booktitle = {American journal of human biology : the official journal of the Human Biology Association},
  publisher = {Wiley Interscience},
  address   = {New York, NY [u.a.]},
  issn      = {1520-6300},
  doi       = {10.1002/ajhb.23593},
  pages     = {1},
  year      = {2021},
  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}
}
@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{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{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{deOliveiraSilvaPiratelliZurelletal.2021,
  author    = {de Oliveira-Silva, Anna Elizabeth and Piratelli, Augusto Jo{\~a}o and Zurell, Damaris and da Silva, Fernando Rodrigues},
  title     = {Vegetation cover restricts habitat suitability predictions of endemic Brazilian Atlantic Forest birds},
  series = {Perspectives in Ecology and Conservation},
  volume    = {20},
  journal   = {Perspectives in Ecology and Conservation},
  number    = {1},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {2530-0644},
  doi       = {10.1016/j.pecon.2021.09.002},
  pages     = {1 -- 8},
  year      = {2021},
  abstract  = {Ecological niche models (ENMs) are often used to investigate how climatic variables from known occurrence records can estimate potential species range distribution. Although climate-based ENMs provide critical baseline information, the inclusion of non-climatic predictors related to vegetation cover might generate more realistic scenarios. This assumption is particularly relevant for species with life-history traits related to forest habitats and sensitive to habitat loss and fragmentation. Here, we developed ENMs for 36 Atlantic Forest endemic birds considering two sets of predictor variables: (i) climatic variables only and (ii) climatic variables combined with the percentage of remaining native vegetation. We hypothesized that the inclusion of native vegetation data would decrease the potential range distribution of forest-dependent species by limiting their occurrence in regions harboring small areas of native vegetation habitats, despite otherwise favorable climatic conditions. We also expected that habitat restriction in the climate-vegetation models would be more pronounced for highly forest-dependent birds. The inclusion of vegetation data in the modeling procedures restricted the final distribution ranges of 22 out of 36 modeled species, while the 14 remaining presented an expansion of their ranges. We observed that species with high and medium forest dependency showed higher restriction in range size predictions between predictor sets than species with low forest dependency, which showed no alteration or range expansion. Overall, our results suggest that ENMs based on climatic and landscape variables may be a useful tool for conservationists to better understand the dynamic of bird species distributions in threatened and highly fragmented regions such as the Atlantic Forest hotspot.(c) 2021 Associacao Brasileira de Cie circumflex accent ncia Ecol ogica e Conservacao. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/ ).},
  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{GuentherSchmidtQuittetal.2021,
  author    = {G{\"u}nther, Kerstin and Schmidt, Marcus and Quitt, Heinz and Heinken, Thilo},
  title     = {Ver{\"a}nderungen der Waldvegetation im Elbe-Havelwinkel von 1960 bis 2015},
  series = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft},
  journal   = {Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft},
  number    = {41},
  publisher = {Floristisch-Soziologische Arbeitsgemeinschaft},
  address   = {G{\"o}ttingen},
  issn      = {0722-494X},
  doi       = {10.14471/2021.41.005},
  pages     = {53 -- 85},
  year      = {2021},
  abstract  = {Forest ecosystems are subject to a variety of influences such as forest management, nitrogen deposition, changes in the groundwater level or the immigration of invasive species. The repetition of historical releves is an important means of documenting the resulting changes in plant communities and determining their main drivers. In 2015, we examined the vegetation change in 140 semi-permanent plots in managed forests in the Elbe valley in the NE German lowlands (Saxony-Anhalt, Brandenburg). The first survey took place from 1956 to 1963. The releves cover an almost uniquely broad spectrum of different site conditions, ranging from wet forests (alluvial, swamp and bog forests of Alnion incanae, Alnion glutinosae and Betulion pubescentis) to acidic mixed oak forests (Quercion roboris) up to acidic, mostly dry pine forests with different nutrient status (Dicrano-Pinion). We analyzed the changes in the vegetation with the help of forest stand data, winner and loser species, alpha- and beta-diversity as well as the Ellenberg indicator values for nitrogen, reaction, moisture and light. In contrast to previous resurvey studies, areas were also taken into account on which a complete change of forest stand had taken place before the second survey. Particularly in the wet forests and acidic forests with a moderately good nutrient supply, changes in the main tree species have been recorded, and many pine stands have been newly established in the meantime. The species richness has decreased overall and in almost all forest types, but the beta-diversity has remained unchanged or has increased. The Ellenberg values indicate a decrease in soil moisture in the wet forests, while the acidic pine forests in particular have become darker, richer in nutrients and more humid. The number of loser species is more than twice as high as that of the winner species, but with different developments in the individual forest types. In particular, the wet forests, the acidic mixed oak forests and the lichen-pine forests have lost most of their characteristic species. The resurvey after more than 50 years shows a different development of the individual forest types. Vegetation changes in the wet forests are mainly due to local groundwater level drawdown and the resulting increased availability of nutrients. The alluvial forests were also strongly influenced by forest interventions. The reasons for the trend towards more humid and more nutrient-rich conditions in formerly dry acidic pine and oak forests are nitrogen depositions and a succession after the abandonment of historical forms of forest use (litter raking, forest pasture). Although the individual forest types have developed differently, eutrophication, falling groundwater levels and silviculture are the most important causes for the changes in vegetation. Silvicultural interventions such as clear cutting and stand conversion with a change of tree species are at the same time the main reason why the vegetation has not been homogenized despite the leveling of the site gradient as measured by the beta-diversity.},
  language  = {de}
}
@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{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}
}
@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{KimLeifheitMaassetal.2021,
  author    = {Kim, Shin Woong and Leifheit, Eva F. and Maaß, Stefanie and Rillig, Matthias C.},
  title     = {Time-dependent toxicity of tire particles on soil nematodes},
  series = {Frontiers in Environmental Science},
  volume    = {9},
  journal   = {Frontiers in Environmental Science},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {2296-665X},
  doi       = {10.3389/fenvs.2021.744668},
  pages     = {9},
  year      = {2021},
  abstract  = {Tire-wear particles (TWPs) are being released into the environment by wearing down during car driving, and are considered an important microplastic pollution source. The chemical additive leaching from these polymer-based materials and its potential effects are likely temporally dynamic, since amounts of potentially toxic compounds can gradually increase with contact time of plastic particles with surrounding media. In the present study, we conducted soil toxicity tests using the soil nematode Caenorhabditis elegans with different soil pre-incubation (30 and 75 days) and exposure (short-term exposure, 2 days; lifetime exposure, 10 days) times. Soil pre-incubation increased toxicity of TWPs, and the effective concentrations after the pre-incubation were much lower than environmentally relevant concentrations. The lifetime of C. elegans was reduced faster in the TWP treatment groups, and the effective concentration for lifetime exposure tests were 100- to 1,000-fold lower than those of short-term exposure tests. Water-extractable metal concentrations (Cr, Cu, Ni, Pb, and Zn) in the TWP-soils showed no correlation with nominal TWP concentrations or pre-incubation times, and the incorporated metals in the TWPs may be not the main reason of toxicity in this study. Our results show that toxic effects of TWPs can be time-dependent, both in terms of the microplastic particles themselves and their interactions in the soil matrix, but also because of susceptibility of target organisms depending on developmental stage. It is vital that future works consider these aspects, since otherwise effects of microplastics and TWPs could be underestimated.},
  language  = {en}
}
@article{OuedraogoZareKorbeogoetal.2021,
  author    = {Ou{\´e}draogo, Karim and Zar{\´e}, Alhassane and Korb{\´e}ogo, Gabin and Ou{\´e}draogo, Oumarou and Linst{\"a}dter, Anja},
  title     = {Resilience strategies of West African pastoralists in response to scarce forage resources},
  series = {Pastoralism : research, policy and practice},
  volume    = {11},
  journal   = {Pastoralism : research, policy and practice},
  number    = {1},
  publisher = {SpringerOpen},
  address   = {Heidelberg},
  issn      = {2041-7136},
  doi       = {10.1186/s13570-021-00210-8},
  pages     = {14},
  year      = {2021},
  abstract  = {Finding sufficient natural fodder resources to feed livestock has become a challenge for herders in the Sahel zone of Burkina Faso. Despite the existence of pastoral reserves, the issue of fodder shortage remains unsolved. This article highlights the changes in behaviour and the evolution of pastoral practices caused by the scarcity of forage resources. These changes are defined and classified as resilience strategies. Thus, this paper aims to analyse these strategies using new semantics that calls for other forms of perceptions or approach to the questions of pastoralists' resilience strategies. Interviews (semi-structured and casual conversations), ethnographic observations and ethnobotanical surveys were used to collect data. In rangelands, such high value fodder species as Andropogon gayanus, Pennisetum pedicellatum and Dactyloctenium aegyptium that were abundant herbaceous plants during the last decades are disappearing. Concomitantly, species with lower forage value, such as Senna obtusifolia, which are more resilient to ecological disturbance factors, are colonizing rangelands. Faced with these ecological changes, pastoralists are trying to redefine and reconfigure their practices, and this implies a redefinition of their identity. They use resilience strategies such as mowing grasses, building up fodder bundles, conserving crop residues, exploiting Senna obtusifolia (a previously neglected species), using woody fodder and adapting the type of livestock and the size of the herds to the ability of pastoralists to feed them. Strategies that are older than these are the integration of agriculture with livestock and decollectivized transhumance. It is these resilience strategies that this article exposes and analyses as defence mechanisms of Sahelian pastoralists in the face of the depletion of forage resources in their environments.},
  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{JohnOlasMuellerRoeber2021,
  author    = {John, Sheeba and Olas, Justyna Jadwiga and M{\"u}ller-R{\"o}ber, Bernd},
  title     = {Regulation of alternative splicing in response to temperature variation in plants},
  series = {Journal of experimental botany},
  volume    = {72},
  journal   = {Journal of experimental botany},
  number    = {18},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0022-0957},
  doi       = {10.1093/jxb/erab232},
  pages     = {6150 -- 6163},
  year      = {2021},
  abstract  = {Plants have evolved numerous molecular strategies to cope with perturbations in environmental temperature, and to adjust growth and physiology to limit the negative effects of extreme temperature. One of the strategies involves alternative splicing of primary transcripts to encode alternative protein products or transcript variants destined for degradation by nonsense-mediated decay. Here, we review how changes in environmental temperature-cold, heat, and moderate alterations in temperature-affect alternative splicing in plants, including crops. We present examples of the mode of action of various temperature-induced splice variants and discuss how these alternative splicing events enable favourable plant responses to altered temperatures. Finally, we point out unanswered questions that should be addressed to fully utilize the endogenous mechanisms in plants to adjust their growth to environmental temperature. We also indicate how this knowledge might be used to enhance crop productivity in the future.},
  language  = {en}
}
@article{MazzaGuenther2021,
  author    = {Mazza, Valeria and G{\"u}nther, Anja},
  title     = {City mice and country mice},
  series = {Animal behaviour},
  volume    = {172},
  journal   = {Animal behaviour},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0003-3472},
  doi       = {10.1016/j.anbehav.2020.12.007},
  pages     = {197 -- 210},
  year      = {2021},
  abstract  = {The ability to produce innovative behaviour is a key determinant in the successful coping with environmental challenges and changes. The expansion of human-altered environments presents wildlife with multiple novel situations in which innovativeness could be beneficial. A better understanding of the drivers of within-species variation in innovation propensity and its consequences will provide insights into the traits enabling animals to thrive in the face of human-induced rapid environmental change. We compared problem-solving performance of 31 striped field mice, Apodemus agrarius, originating from rural or urban environments in a battery of eight foraging extraction tasks. We tested whether differences in problem-solving performance were mediated by the extent and duration of the animal's exploration of the experimental set-ups, the time required to solve the tasks, and their persistence. In addition, we tested the influence of the diversity of motor responses, as well as of behavioural traits boldness and activity on problem-solving performance. Urban individuals were better problem solvers despite rural individuals approaching faster and interacting longer with the test set-ups. Participation rates and time required to solve a task did not differ between rural and urban individuals. However, in case of failure to solve a task, rural mice were more persistent. The best predictors of solving success, aside from the area of origin, were the time spent exploring the set-ups and boldness, while activity and diversity of motor responses did not explain it. Problem-solving ability could thus be a contributing factor to the successful coping with the rapid and recent expansion of human-altered environments.},
  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{WarmtFenzelHenkeletal.2021,
  author    = {Warmt, Christian and Fenzel, Carolin Kornelia and Henkel, J{\"o}rg and Bier, Frank Fabian},
  title     = {Using Cy5-dUTP labelling of RPA-amplicons with downstream microarray analysis for the detection of antibiotic resistance genes},
  series = {Scientific reports},
  volume    = {11},
  journal   = {Scientific reports},
  number    = {1},
  publisher = {Macmillan Publishers Limited, part of Springer Nature},
  address   = {[London]},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-021-99774-z},
  pages     = {9},
  year      = {2021},
  abstract  = {In this report we describe Cy5-dUTP labelling of recombinase-polymerase-amplification (RPA) products directly during the amplification process for the first time. Nucleic acid amplification techniques, especially polymerase-chain-reaction as well as various isothermal amplification methods such as RPA, becomes a promising tool in the detection of pathogens and target specific genes. Actually, RPA even provides more advantages. This isothermal method got popular in point of care diagnostics because of its speed and sensitivity but requires pre-labelled primer or probes for a following detection of the amplicons. To overcome this disadvantages, we performed an labelling of RPA-amplicons with Cy5-dUTP without the need of pre-labelled primers. The amplification results of various multiple antibiotic resistance genes indicating great potential as a flexible and promising tool with high specific and sensitive detection capabilities of the target genes. After the determination of an appropriate rate of 1\% Cy5-dUTP and 99\% unlabelled dTTP we were able to detect the bla(CTX-M15) gene in less than 1.6E-03 ng genomic DNA corresponding to approximately 200 cfu of Escherichia coli cells in only 40 min amplification time.},
  language  = {en}
}
@article{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{RuthsatzScherzVences2021,
  author    = {Ruthsatz, Katharina and Scherz, Mark D. and Vences, Miguel},
  title     = {Dissecting the tree of life},
  series = {Zootaxa : an international journal of zootaxonomy ;},
  volume    = {5016},
  journal   = {Zootaxa : an international journal of zootaxonomy ;},
  number    = {3},
  publisher = {Magnolia Press},
  address   = {Auckland},
  issn      = {1175-5326},
  doi       = {10.11646/zootaxa.5016.3.10},
  pages     = {448 -- 450},
  year      = {2021},
  language  = {en}
}
@article{BaunachChowdhuryStallforthetal.2021,
  author    = {Baunach, Martin and Chowdhury, Somak and Stallforth, Pierre and Dittmann-Th{\"u}nemann, Elke},
  title     = {The landscape of recombination events that create nonribosomal peptide diversity},
  series = {Molecular biology and evolution : MBE},
  volume    = {38},
  journal   = {Molecular biology and evolution : MBE},
  number    = {5},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0737-4038},
  doi       = {10.1093/molbev/msab015},
  pages     = {2116 -- 2130},
  year      = {2021},
  abstract  = {Nonribosomal peptides (NRP) are crucial molecular mediators in microbial ecology and provide indispensable drugs. Nevertheless, the evolution of the flexible biosynthetic machineries that correlates with the stunning structural diversity of NRPs is poorly understood. Here, we show that recombination is a key driver in the evolution of bacterial NRP synthetase (NRPS) genes across distant bacterial phyla, which has guided structural diversification in a plethora of NRP families by extensive mixing andmatching of biosynthesis genes. The systematic dissection of a large number of individual recombination events did not only unveil a striking plurality in the nature and origin of the exchange units but allowed the deduction of overarching principles that enable the efficient exchange of adenylation (A) domain substrates while keeping the functionality of the dynamic multienzyme complexes. In the majority of cases, recombination events have targeted variable portions of the A(core) domains, yet domain interfaces and the flexible A(sub) domain remained untapped. Our results strongly contradict the widespread assumption that adenylation and condensation (C) domains coevolve and significantly challenge the attributed role of C domains as stringent selectivity filter during NRP synthesis. Moreover, they teach valuable lessons on the choice of natural exchange units in the evolution of NRPS diversity, which may guide future engineering approaches.},
  language  = {en}
}
@inproceedings{LeBehrsingRothschildetal.2021,
  author    = {Le, Dinh To and Behrsing, Olaf and Rothschild, Claire and Radukic, Marco T. and Arndt, Katja and M{\"u}ller, Kristian M.},
  title     = {AAV capsid proteins fused with SARS-CoV-2 RBD or RBM: Expression in E. coli, in-vitro assembly, and characterization},
  series = {Molecular therapy : the journal of the American Society of Gene Therapy},
  volume    = {29},
  booktitle = {Molecular therapy : the journal of the American Society of Gene Therapy},
  number    = {4, Suppl. 1},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {1525-0016},
  doi       = {10.1016/j.ymthe.2021.04.019},
  pages     = {357 -- 357},
  year      = {2021},
  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{PriesRazaghiMoghadamKopkaetal.2021,
  author    = {Pries, Christopher and Razaghi-Moghadam, Zahra and Kopka, Joachim and Nikoloski, Zoran},
  title     = {Integration of relative metabolomics and transcriptomics time-course data in a metabolic model pinpoints effects of ribosome biogenesis defects on Arabidopsis thaliana metabolism},
  series = {Scientific reports},
  volume    = {11},
  journal   = {Scientific reports},
  number    = {1},
  publisher = {Macmillan Publishers Limited, part of Springer Nature},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-021-84114-y},
  pages     = {12},
  year      = {2021},
  abstract  = {Ribosome biogenesis is tightly associated to plant metabolism due to the usage of ribosomes in the synthesis of proteins necessary to drive metabolic pathways. Given the central role of ribosome biogenesis in cell physiology, it is important to characterize the impact of different components involved in this process on plant metabolism. Double mutants of the Arabidopsis thaliana cytosolic 60S maturation factors REIL1 and REIL2 do not resume growth after shift to moderate 10 degrees C chilling conditions. To gain mechanistic insights into the metabolic effects of this ribosome biogenesis defect on metabolism, we developed TC-iReMet2, a constraint-based modelling approach that integrates relative metabolomics and transcriptomics time-course data to predict differential fluxes on a genome-scale level. We employed TC-iReMet2 with metabolomics and transcriptomics data from the Arabidopsis Columbia 0 wild type and the reil1-1 reil2-1 double mutant before and after cold shift. We identified reactions and pathways that are highly altered in a mutant relative to the wild type. These pathways include the Calvin-Benson cycle, photorespiration, gluconeogenesis, and glycolysis. Our findings also indicated differential NAD(P)/NAD(P)H ratios after cold shift. TC-iReMet2 allows for mechanistic hypothesis generation and interpretation of system biology experiments related to metabolic fluxes on a genome-scale level.},
  language  = {en}
}
@article{RoedelAbdelilahSeyfried2021,
  author    = {R{\"o}del, Claudia Jasmin and Abdelilah-Seyfried, Salim},
  title     = {A zebrafish toolbox for biomechanical signaling in cardiovascular development and disease},
  series = {Current opinion in hematology},
  volume    = {28},
  journal   = {Current opinion in hematology},
  number    = {3},
  publisher = {Lippincott Williams \& Wilkins},
  address   = {Philadelphia},
  issn      = {1065-6251},
  doi       = {10.1097/MOH.0000000000000648},
  pages     = {198 -- 207},
  year      = {2021},
  abstract  = {Purpose of review The zebrafish embryo has emerged as a powerful model organism to investigate the mechanisms by which biophysical forces regulate vascular and cardiac cell biology during development and disease. A versatile arsenal of methods and tools is available to manipulate and analyze biomechanical signaling. This review aims to provide an overview of the experimental strategies and tools that have been utilized to study biomechanical signaling in cardiovascular developmental processes and different vascular disease models in the zebrafish embryo. Within the scope of this review, we focus on work published during the last two years. Recent findings Genetic and pharmacological tools for the manipulation of cardiac function allow alterations of hemodynamic flow patterns in the zebrafish embryo and various types of transgenic lines are available to report endothelial cell responses to biophysical forces. These tools have not only revealed the impact of biophysical forces on cardiovascular development but also helped to establish more accurate models for cardiovascular diseases including cerebral cavernous malformations, hereditary hemorrhagic telangiectasias, arteriovenous malformations, and lymphangiopathies. Summary The zebrafish embryo is a valuable vertebrate model in which in-vivo manipulations of biophysical forces due to cardiac contractility and blood flow can be performed. These analyses give important insights into biomechanical signaling pathways that control endothelial and endocardial cell behaviors. The technical advances using this vertebrate model will advance our understanding of the impact of biophysical forces in cardiovascular pathologies.},
  language  = {en}
}
@article{FloederYongKlauschiesetal.2021,
  author    = {Fl{\"o}der, Sabine and Yong, Joanne and Klauschies, Toni and Gaedke, Ursula and Poprick, Tobias and Brinkhoff, Thorsten and Moorthi, Stefanie},
  title     = {Intraspecific trait variation alters the outcome of competition in freshwater ciliates},
  series = {Ecology and evolution},
  volume    = {11},
  journal   = {Ecology and evolution},
  number    = {15},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.7828},
  pages     = {10225 -- 10243},
  year      = {2021},
  abstract  = {Trait variation among heterospecific and conspecific organisms may substantially affect community and food web dynamics. While the relevance of competition and feeding traits have been widely studied for different consumer species, studies on intraspecific differences are more scarce, partly owing to difficulties in distinguishing different clones of the same species. Here, we investigate how intraspecific trait variation affects the competition between the freshwater ciliates Euplotes octocarinatus and Coleps hirtus in a nitrogen-limited chemostat system. The ciliates competed for the microalgae Cryptomonas sp. (Cry) and Navicula pelliculosa (Nav), and the bacteria present in the cultures over a period of 33 days. We used monoclonal Euplotes and three different Coleps clones (Col 1, Col 2, and Col 3) in the experiment that could be distinguished by a newly developed rDNA-based molecular assay based on the internal transcribed spacer (ITS) regions. While Euplotes feeds on Cry and on bacteria, the Coleps clones cannot survive on bacteria alone but feed on both Cry and Nav with clone-specific rates. Experimental treatments comprised two-species mixtures of Euplotes and one or all of the three different Coleps clones, respectively. We found intraspecific variation in the traits "selectivity" and "maximum ingestion rate" for the different algae to significantly affect the competitive outcome between the two ciliate species. As Nav quickly escaped top-down control and likely reached a state of low food quality, ciliate competition was strongly determined by the preference of different Coleps clones for Cry as opposed to feeding on Nav. In addition, the ability of Euplotes to use bacteria as an alternative food source strengthened its persistence once Cry was depleted. Hence, trait variation at both trophic levels codetermined the population dynamics and the outcome of species competition.},
  language  = {en}
}
@article{SchneebergerEccard2021,
  author    = {Schneeberger, Karin and Eccard, Jana},
  title     = {Experience of social density during early life is associated with attraction to conspecific odour in the common vole (Microtus arvalis)},
  series = {Ethology : international journal of behavioural biology},
  volume    = {127},
  journal   = {Ethology : international journal of behavioural biology},
  number    = {10},
  publisher = {Wiley-Blackwell},
  address   = {Berlin},
  issn      = {0179-1613},
  doi       = {10.1111/eth.13211},
  pages     = {908 -- 913},
  year      = {2021},
  abstract  = {Social organisation in species with fluctuating population sizes can change with density. Therefore, information on (future) density obtained during early life stages may be associated with social behaviour. Olfactory cues may carry important social information. We investigated whether early life experience of different experimental densities was subsequently associated with differences in attraction to adult conspecific odours. We used common voles (Microtus arvalis), a rodent species undergoing extreme density fluctuations. We found that individuals originating from high experimental density populations kept in large outdoor enclosures invested more time in inspecting conspecific olfactory cues than individuals from low-density populations. Generally, voles from both treatments spent more time with the olfactory cues than expected by chance and did not differ in their latency to approach the odour samples. Our findings indicate either that early experience affects odour sensitivity or that animals evaluate the social information contained in conspecific odours differently, depending on their early life experience of conspecific density.},
  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{KuekenWenderingLangaryetal.2021,
  author    = {K{\"u}ken, Anika and Wendering, Philipp and Langary, Damoun and Nikoloski, Zoran},
  title     = {A structural property for reduction of biochemical networks},
  series = {Scientific reports},
  volume    = {11},
  journal   = {Scientific reports},
  number    = {1},
  publisher = {Macmillan Publishers Limited, part of Springer Nature},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-021-96835-1},
  pages     = {11},
  year      = {2021},
  abstract  = {Large-scale biochemical models are of increasing sizes due to the consideration of interacting organisms and tissues. Model reduction approaches that preserve the flux phenotypes can simplify the analysis and predictions of steady-state metabolic phenotypes. However, existing approaches either restrict functionality of reduced models or do not lead to significant decreases in the number of modelled metabolites. Here, we introduce an approach for model reduction based on the structural property of balancing of complexes that preserves the steady-state fluxes supported by the network and can be efficiently determined at genome scale. Using two large-scale mass-action kinetic models of Escherichia coli, we show that our approach results in a substantial reduction of 99\% of metabolites. Applications to genome-scale metabolic models across kingdoms of life result in up to 55\% and 85\% reduction in the number of metabolites when arbitrary and mass-action kinetics is assumed, respectively. We also show that predictions of the specific growth rate from the reduced models match those based on the original models. Since steady-state flux phenotypes from the original model are preserved in the reduced, the approach paves the way for analysing other metabolic phenotypes in large-scale biochemical networks.},
  language  = {en}
}
@article{SeepRazaghiMoghadamNikoloski2021,
  author    = {Seep, Lea and Razaghi-Moghadam, Zahra and Nikoloski, Zoran},
  title     = {Reaction lumping in metabolic networks for application with thermodynamic metabolic flux analysis},
  series = {Scientific reports},
  volume    = {11},
  journal   = {Scientific reports},
  number    = {1},
  publisher = {Macmillan Publishers Limited, part of Springer Nature},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-021-87643-8},
  pages     = {11},
  year      = {2021},
  abstract  = {Thermodynamic metabolic flux analysis (TMFA) can narrow down the space of steady-state flux distributions, but requires knowledge of the standard Gibbs free energy for the modelled reactions. The latter are often not available due to unknown Gibbs free energy change of formation ,Delta fG0, of metabolites. To optimize the usage of data on thermodynamics in constraining a model, reaction lumping has been proposed to eliminate metabolites with unknown Delta fG0. However, the lumping procedure has not been formalized nor implemented for systematic identification of lumped reactions. Here, we propose, implement, and test a combined procedure for reaction lumping, applicable to genome-scale metabolic models. It is based on identification of groups of metabolites with unknown Delta fG0 whose elimination can be conducted independently of the others via: (1) group implementation, aiming to eliminate an entire such group, and, if this is infeasible, (2) a sequential implementation to ensure that a maximal number of metabolites with unknown Delta fG0 are eliminated. Our comparative analysis with genome-scale metabolic models of Escherichia coli, Bacillus subtilis, and Homo sapiens shows that the combined procedure provides an efficient means for systematic identification of lumped reactions. We also demonstrate that TMFA applied to models with reactions lumped according to the proposed procedure lead to more precise predictions in comparison to the original models. The provided implementation thus ensures the reproducibility of the findings and their application with standard TMFA.},
  language  = {en}
}
@article{EnzingmuellerPrechtl2021,
  author    = {Enzingm{\"u}ller, Carolin and Prechtl, Helmut},
  title     = {Constructing graphs in biology class},
  series = {International journal of science and mathematics education},
  volume    = {19},
  journal   = {International journal of science and mathematics education},
  number    = {1},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {1571-0068},
  doi       = {10.1007/s10763-019-09975-2},
  pages     = {1 -- 19},
  year      = {2021},
  abstract  = {There has been a growing awareness that graphing is an essential part of the science curriculum. While much research has focused on student conceptions and abilities regarding graphical representations, only few studies have investigated what teachers think about them and how they use graphs in science class. The purpose of this study is to explore educational beliefs, motivation, and teaching practices of German secondary biology teachers regarding graph construction. Via questionnaire surveys, 71 teachers from different regions in Germany rated their beliefs and motivation as well as the frequency of different graph construction activities in biology class. The teachers surveyed in this study were quite motivated in their teaching of graph construction. Furthermore, they tended to believe that graph construction should be practiced explicitly in biology class and that students should learn clear strategies for constructing graphs. We found that teaching subjects and own research experience make a difference in teachers' beliefs and motivation regarding graph construction in biology class. The self-report on classroom practices revealed that participants may provide limited opportunities for students to experience graphing as a social and iterative practice. Implications are drawn for teacher education and professional development as well as for further research in teacher education contexts.},
  language  = {en}
}
@article{SteppertSteppertSterlaccietal.2021,
  author    = {Steppert, Claus and Steppert, Isabel and Sterlacci, William and Bollinger, Thomas},
  title     = {Rapid detection of SARS-CoV-2 infection by multicapillary column coupled ion mobility spectrometry (MCC-IMS) of breath},
  series = {Journal of breath research : volatiles for medical diagnosis ; official journal of the International Association for Breath Research (IABR) and the International Society for Breath Odor Research (ISBOR)},
  volume    = {15},
  journal   = {Journal of breath research : volatiles for medical diagnosis ; official journal of the International Association for Breath Research (IABR) and the International Society for Breath Odor Research (ISBOR)},
  number    = {2},
  publisher = {IOP Publ. Ltd.},
  address   = {Bristol},
  issn      = {1752-7163},
  doi       = {10.1088/1752-7163/abe5ca},
  pages     = {8},
  year      = {2021},
  abstract  = {There is an urgent need for screening of patients with a communicable viral disease to cut infection chains. Recently, we demonstrated that ion mobility spectrometry coupled with a multicapillary column (MCC-IMS) is able to identify influenza-A infections in patients' breath. With a decreasing influenza epidemic and upcoming SARS-CoV-2 infections we proceeded further and analyzed patients with suspected SARS-CoV-2 infections. In this study, the nasal breath of 75 patients (34 male, 41 female, aged 64.4 +/- 15.4 years) was investigated by MCC-IMS for viral infections. Fourteen were positively diagnosed with influenza-A infection and sixteen with SARS-CoV-2 by reverse transcription polymerase chain reaction (RT-PCR) of nasopharyngeal swabs. In one patient RT-PCR was highly suspicious of SARS-CoV-2 but initially inconclusive. The remaining 44 patients served as controls. Breath fingerprints for specific infections were assessed by a combination of cluster analysis and multivariate statistics. There were no significant differences in gender or age according to the groups. In the cross validation of the discriminant analysis 72 of the 74 clearly defined patients could be correctly classified to the respective group. Even the inconclusive patient could be mapped to the SARS-CoV-2 group by applying the discrimination functions. Conclusion: SARS-CoV-2 infection and influenza-A infection can be detected with the help of MCC-IMS in breath in this pilot study. As this method provides a fast non-invasive diagnosis it should be further developed in a larger cohort for screening of communicable viral diseases. A validation study is ongoing during the second wave of COVID-19. Trial registration: ClinicalTrial.gov, NCT04282135 Registered 20 February 2020-Retrospectively registered,},
  language  = {en}
}
@article{EilersKleineEckertetal.2021,
  author    = {Eilers, Elisabeth Johanna and Kleine, Sandra and Eckert, Silvia and Waldherr, Simon and M{\"u}ller, Caroline},
  title     = {Flower production, headspace volatiles, pollen nutrients, and florivory in tanacetum vulgare chemotypes},
  series = {Frontiers in plant science : FPLS},
  volume    = {11},
  journal   = {Frontiers in plant science : FPLS},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {1664-462X},
  doi       = {10.3389/fpls.2020.611877},
  pages     = {17},
  year      = {2021},
  abstract  = {Floral volatiles and reward traits are major drivers for the behavior of mutualistic as well as antagonistic flower visitors, i.e., pollinators and florivores. These floral traits differ tremendously between species, but intraspecific differences and their consequences on organism interactions remain largely unknown. Floral volatile compounds, such as terpenoids, function as cues to advertise rewards to pollinators, but should at the same time also repel florivores. The reward composition, e.g., protein and lipid contents in pollen, differs between individuals of distinct plant families. Whether the nutritional value of rewards within the same plant species is linked to their chemotypes, which differ in their pattern of specialized metabolites, has yet not been investigated. In the present study, we compared Tanacetum vulgare plants of five terpenoid chemotypes with regard to flower production, floral headspace volatiles, pollen macronutrient and terpenoid content, and floral attractiveness to florivorous beetles. Our analyses revealed remarkable differences between the chemotypes in the amount and diameter of flower heads, duration of bloom period, and pollen nutritional quality. The floral headspace composition of pollen-producing mature flowers, but not of premature flowers, was correlated to that of pollen and leaves in the same plant individual. For two chemotypes, florivorous beetles discriminated between the scent of mature and premature flower heads and preferred the latter. In semi-field experiments, the abundance of florivorous beetles and flower tissue miners differed between T. vulgare chemotypes. Moreover, the scent environment affected the choice and beetles were more abundant in homogenous plots composed of one single chemotype than in plots with different neighboring chemotypes. In conclusion, flower production, floral metabolic composition and pollen quality varied to a remarkable extend within the species T. vulgare, and the attractiveness of floral scent differed also intra-individually with floral ontogeny. We found evidence for a trade-off between pollen lipid content and pollen amount on a per-plant-level. Our study highlights that chemotypes which are more susceptible to florivory are less attacked when they grow in the neighborhood of other chemotypes and thus gain a benefit from high overall chemodiversity.},
  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{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{HashemiRazaghiMoghadamNikoloski2021,
  author    = {Hashemi, Seirana and Razaghi-Moghadam, Zahra and Nikoloski, Zoran},
  title     = {Identification of flux trade-offs in metabolic networks},
  series = {Scientific reports},
  volume    = {11},
  journal   = {Scientific reports},
  number    = {1},
  publisher = {Macmillan Publishers Limited, part of Springer Nature},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-021-03224-9},
  pages     = {10},
  year      = {2021},
  abstract  = {Trade-offs are inherent to biochemical networks governing diverse cellular functions, from gene expression to metabolism. Yet, trade-offs between fluxes of biochemical reactions in a metabolic network have not been formally studied. Here, we introduce the concept of absolute flux trade-offs and devise a constraint-based approach, termed FluTO, to identify and enumerate flux trade-offs in a given genome-scale metabolic network. By employing the metabolic networks of Escherichia coli and Saccharomyces cerevisiae, we demonstrate that the flux trade-offs are specific to carbon sources provided but that reactions involved in the cofactor and prosthetic group biosynthesis are present in trade-offs across all carbon sources supporting growth. We also show that absolute flux trade-offs depend on the biomass reaction used to model the growth of Arabidopsis thaliana under different carbon and nitrogen conditions. The identified flux trade-offs reflect the tight coupling between nitrogen, carbon, and sulphur metabolisms in leaves of C-3 plants. Altogether, FluTO provides the means to explore the space of alternative metabolic routes reflecting the constraints imposed by inherent flux trade-offs in large-scale metabolic networks.},
  language  = {en}
}
@article{StrongScherzCaldwell2021,
  author    = {Strong, Catherine R. C. and Scherz, Mark D. and Caldwell, Michael Wayne},
  title     = {Deconstructing the Gestalt},
  series = {The anatomical record : AR ; advances in integrative anatomy and evolutionary biology ; an official publication of the American Association of Anatomists, AAA},
  volume    = {304},
  journal   = {The anatomical record : AR ; advances in integrative anatomy and evolutionary biology ; an official publication of the American Association of Anatomists, AAA},
  number    = {10},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1932-8486},
  doi       = {10.1002/ar.24630},
  pages     = {2303 -- 2351},
  year      = {2021},
  abstract  = {Snakes-a subset of lizards-have traditionally been divided into two major groups based on feeding mechanics: "macrostomy," involving the ingestion of proportionally large prey items; and "microstomy," the lack of this ability. "Microstomy"-considered present in scolecophidian and early-diverging alethinophidian snakes-is generally viewed as a symplesiomorphy shared with non-snake lizards. However, this perspective of "microstomy" as plesiomorphic and morphologically homogenous fails to recognize the complexity of this condition and its evolution across "microstomatan" squamates. To challenge this problematic paradigm, we formalize a new framework for conceptualizing and testing the homology of overall character complexes, or "morphotypes," which underlies our re-assessment of "microstomy." Using micro-computed tomography (micro-CT) scans, we analyze the morphology of the jaws and suspensorium across purported "microstomatan" squamates (scolecophidians, early-diverging alethinophidians, and non-snake lizards) and demonstrate that key components of the jaw complex are not homologous at the level of primary character state identity across these taxa. Therefore, rather than treating "microstomy" as a uniform condition, we instead propose that non-snake lizards, early-diverging alethinophidians, anomalepidids, leptotyphlopids, and typhlopoids each exhibit a unique and nonhomologous jaw morphotype: "minimal-kinesis microstomy," "snout-shifting," "axle-brace maxillary raking," "mandibular raking," and "single-axle maxillary raking," respectively. The lack of synapomorphy among scolecophidians is inconsistent with the notion of scolecophidians representing an ancestral snake condition, and instead reflects a hypothesis of the independent evolution of fossoriality, miniaturization, and "microstomy" in each scolecophidian lineage. We ultimately emphasize that a rigorous approach to comparative anatomy is necessary in constructing evolutionary hypotheses that accurately reflect biological reality.},
  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}
}
@article{ApriyantoTambunan2021,
  author    = {Apriyanto, Ardha and Tambunan, Van Basten},
  title     = {Draft genome sequence, annotation, and SSR mining data of Elaeidobius kamerunicus Faust., an essential oil palm pollinating weevil},
  series = {Data in Brief},
  volume    = {34},
  journal   = {Data in Brief},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {2352-3409},
  doi       = {10.1016/j.dib.2021.106745},
  pages     = {7},
  year      = {2021},
  abstract  = {Elaeidobius kamerunicus Faust. (Coleoptera: Curculionidae) is an essential insect pollinator in oil palm plantations. Recently, researches have been undertaken to improve pollination efficiency using this species. A fundamental understanding of the genes related to this pollinator behavior is necessary to achieve this goal. Here, we present the draft genome sequence, annotation, and simple sequence repeat (SSR) marker data for this pollinator. In total, 34.97 Gb of sequence data from one male individual (monoisolate) were obtained using Illumina short-read platform NextSeq 500. The draft genome assembly was found to be 269.79 Mb and about 59.9\% of completeness based on Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment. Functional gene annotation predicted about 26.566 genes. Also, a total of 281.668 putative SSR markers were identified. This draft genome sequence is a valuable resource for understanding the population genetics, phylogenetics, dispersal patterns, and behavior of this species.},
  language  = {en}
}
@article{Leimkuehler2021,
  author    = {Leimk{\"u}hler, Silke},
  title     = {Transition metals in catalysis},
  series = {Inorganics : open access journal},
  volume    = {9},
  journal   = {Inorganics : open access journal},
  number    = {1},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2304-6740},
  doi       = {10.3390/inorganics9010006},
  pages     = {2},
  year      = {2021},
  language  = {en}
}
@article{MichelchenMicheelHanack2021,
  author    = {Michelchen, Sophia and Micheel, Burkhard and Hanack, Katja},
  title     = {In vitro immunization approach to generate specific murine monoclonal IgG antibodies},
  series = {Journal of immunological methods : JIM},
  volume    = {499},
  journal   = {Journal of immunological methods : JIM},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0022-1759},
  doi       = {10.1016/j.jim.2021.113149},
  pages     = {8},
  year      = {2021},
  abstract  = {Generating a monoclonal antibody to date is a time intense process that requires immunization of laboratory animals. The transfer of the humoral immune response into in vitro settings enables a shortening of this process and circumvents the necessity of in vivo immunization. However, to orchestrate the complex interplay of dendritic cells, T and B lymphocytes in vitro is very challenging. We therefore aimed for a simplified approach focusing on the protagonist of antibody production: the B lymphocyte. We activated purified murine B lymphocytes alone in vitro by using combinations of antigen and stimuli. We were able to induce a specific antibody response within ten days of culture against a viral coat protein as model antigen. Antibodies were of both IgM and IgG subclass. The stimulated B lymphocytes were transformed into permanently antibody-producing hybridomas by cell fusion technology. We furthermore used this method to induce a specific antibody response against L. pneumophila in vitro. We thus established a useful and effective in vitro protocol to generate monoclonal antibodies. By overcoming the necessity of in vivo immunization this protocol may be the first step towards a universal strategy to generate antibodies from various species.},
  language  = {en}
}
@article{Trindade2021,
  author    = {Trindade, In{\^e}s},
  title     = {License to flower},
  series = {Molecular plant},
  volume    = {14},
  journal   = {Molecular plant},
  number    = {5},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1674-2052},
  doi       = {10.1016/j.molp.2021.04.007},
  pages     = {719 -- 720},
  year      = {2021},
  language  = {en}
}
@inproceedings{DunsingPetrichChiantia2021,
  author    = {Dunsing, Valentin and Petrich, Annett and Chiantia, Salvatore},
  title     = {Spectral detection enables multi-color fluorescence fluctuation spectroscopy studies in living cells},
  series = {Biophysical journal : BJ / ed. by the Biophysical Society},
  volume    = {120},
  booktitle = {Biophysical journal : BJ / ed. by the Biophysical Society},
  number    = {3, Suppl. 1},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {0006-3495},
  doi       = {10.1016/j.bpj.2020.11.2206},
  pages     = {356A -- 356A},
  year      = {2021},
  language  = {en}
}
@inproceedings{InaebnitDennis2021,
  author    = {In{\"a}bnit, Thomas and Dennis, Alice},
  title     = {The mitochondrial genome of Melampus bidentatus (Panpulmonata, Ellobioidea)},
  series = {Integrative and comparative biology / Society of Integrative and Comparative Biology},
  volume    = {61},
  booktitle = {Integrative and comparative biology / Society of Integrative and Comparative Biology},
  number    = {Supplement 1},
  publisher = {Oxford University Press},
  address   = {Oxford},
  issn      = {1540-7063},
  pages     = {E405 -- E405},
  year      = {2021},
  language  = {en}
}
@article{CeulemansGuillGaedke2021,
  author    = {Ceulemans, Ruben and Guill, Christian and Gaedke, Ursula},
  title     = {Top predators govern multitrophic diversity effects in tritrophic food webs},
  series = {Ecology : a publication of the Ecological Society of America},
  volume    = {102},
  journal   = {Ecology : a publication of the Ecological Society of America},
  number    = {7},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0012-9658},
  doi       = {10.1002/ecy.3379},
  pages     = {16},
  year      = {2021},
  abstract  = {It is well known that functional diversity strongly affects ecosystem functioning. However, even in rather simple model communities consisting of only two or, at best, three trophic levels, the relationship between multitrophic functional diversity and ecosystem functioning appears difficult to generalize, because of its high contextuality. In this study, we considered several differently structured tritrophic food webs, in which the amount of functional diversity was varied independently on each trophic level. To achieve generalizable results, largely independent of parametrization, we examined the outcomes of 128,000 parameter combinations sampled from ecologically plausible intervals, with each tested for 200 randomly sampled initial conditions. Analysis of our data was done by training a random forest model. This method enables the identification of complex patterns in the data through partial dependence graphs, and the comparison of the relative influence of model parameters, including the degree of diversity, on food-web properties. We found that bottom-up and top-down effects cascade simultaneously throughout the food web, intimately linking the effects of functional diversity of any trophic level to the amount of diversity of other trophic levels, which may explain the difficulty in unifying results from previous studies. Strikingly, only with high diversity throughout the whole food web, different interactions synergize to ensure efficient exploitation of the available nutrients and efficient biomass transfer to higher trophic levels, ultimately leading to a high biomass and production on the top level. The temporal variation of biomass showed a more complex pattern with increasing multitrophic diversity: while the system initially became less variable, eventually the temporal variation rose again because of the increasingly complex dynamical patterns. Importantly, top predator diversity and food-web parameters affecting the top trophic level were of highest importance to determine the biomass and temporal variability of any trophic level. Overall, our study reveals that the mechanisms by which diversity influences ecosystem functioning are affected by every part of the food web, hampering the extrapolation of insights from simple monotrophic or bitrophic systems to complex natural food webs.},
  language  = {en}
}
@article{GarridoLeimkuehler2021,
  author    = {Garrido, Claudia and Leimk{\"u}hler, Silke},
  title     = {The inactivation of human aldehyde oxidase 1 by hydrogen peroxide and superoxide},
  series = {Drug metabolism and disposition / American Society for Pharmacology and Experimental Therapeutics},
  volume    = {49},
  journal   = {Drug metabolism and disposition / American Society for Pharmacology and Experimental Therapeutics},
  number    = {9},
  publisher = {American Society for Pharmacology and Experimental Therapeutics},
  address   = {Bethesda},
  issn      = {1521-009X},
  doi       = {10.1124/dmd.121.000549},
  pages     = {729 -- 735},
  year      = {2021},
  abstract  = {Mammalian aldehyde oxidases (AOX) are molybdo-flavoenzymes of pharmacological and pathophysiologic relevance that are involved in phase I drug metabolism and, as a product of their enzymatic activity, are also involved in the generation of reactive oxygen species. So far, the physiologic role of aldehyde oxidase 1 in the human body remains unknown. The human enzyme hAOX1 is characterized by a broad substrate specificity, oxidizing aromatic/aliphatic aldehydes into their corresponding carboxylic acids, and hydroxylating various heteroaromatic rings. The enzyme uses oxygen as terminal electron acceptor to produce hydrogen peroxide and superoxide during turnover. Since hAOX1 and, in particular, some natural variants produce not only H2O2 but also high amounts of superoxide, we investigated the effect of both ROS molecules on the enzymatic activity of hAOX1 in more detail. We compared hAOX1 to the high-O-2(.-)-producing natural variant L438V for their time-dependent inactivation with H2O2/O-2(.-) during substrate turnover. We show that the inactivation of the hAOX1 wild-type enzyme is mainly based on the production of hydrogen peroxide, whereas for the variant L438V, both hydrogen peroxide and superoxide contribute to the time-dependent inactivation of the enzyme during turnover. Further, the level of inactivation was revealed to be substrate-dependent: using substrates with higher turnover numbers resulted in a faster inactivation of the enzymes. Analysis of the inactivation site of the enzyme identified a loss of the terminal sulfido ligand at the molybdenum active site by the produced ROS during turnover.},
  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{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{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{DunsingPetrichChiantia2021,
  author    = {Dunsing, Valentin and Petrich, Annett and Chiantia, Salvatore},
  title     = {Multicolor fluorescence fluctuation spectroscopy in living cells via spectral detection},
  series = {eLife},
  volume    = {10},
  journal   = {eLife},
  publisher = {eLife Sciences Publications},
  address   = {Cambridge},
  issn      = {2050-084X},
  doi       = {10.7554/eLife.69687},
  pages     = {33},
  year      = {2021},
  abstract  = {Signaling pathways in biological systems rely on specific interactions between multiple biomolecules. Fluorescence fluctuation spectroscopy provides a powerful toolbox to quantify such interactions directly in living cells. Cross-correlation analysis of spectrally separated fluctuations provides information about intermolecular interactions but is usually limited to two fluorophore species. Here, we present scanning fluorescence spectral correlation spectroscopy (SFSCS), a versatile approach that can be implemented on commercial confocal microscopes, allowing the investigation of interactions between multiple protein species at the plasma membrane. We demonstrate that SFSCS enables cross-talk-free cross-correlation, diffusion, and oligomerization analysis of up to four protein species labeled with strongly overlapping fluorophores. As an example, we investigate the interactions of influenza A virus (IAV) matrix protein 2 with two cellular host factors simultaneously. We furthermore apply raster spectral image correlation spectroscopy for the simultaneous analysis of up to four species and determine the stoichiometry of ternary IAV polymerase complexes in the cell nucleus.},
  language  = {en}
}
@article{Trindade2021,
  author    = {Trindade, In{\^e}s},
  title     = {A drop of immunity},
  series = {Molecular plant},
  volume    = {14},
  journal   = {Molecular plant},
  number    = {9},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1674-2052},
  doi       = {10.1016/j.molp.2021.07.022},
  pages     = {1437 -- 1438},
  year      = {2021},
  language  = {en}
}
@article{OberkoflerPratxBaeurle2021,
  author    = {Oberkofler, Vicky and Pratx, Loris and B{\"a}urle, Isabel},
  title     = {Epigenetic regulation of abiotic stress memory},
  series = {Current opinion in plant biology},
  volume    = {61},
  journal   = {Current opinion in plant biology},
  publisher = {Elsevier},
  address   = {London},
  issn      = {1369-5266},
  doi       = {10.1016/j.pbi.2021.102007},
  pages     = {7},
  year      = {2021},
  abstract  = {As sessile organisms, plants have evolved sophisticated ways to constantly gauge and adapt to changing environmental conditions including extremes that may be harmful to their growth and development and are thus perceived as stress. In nature, stressful events are often chronic or recurring and thus an initial stress may prime a plant to respond more efficiently to a subsequent stress event. An epigenetic basis of such stress memory was long postulated and in recent years it has been shown that this is indeed the case. High temperature stress has proven an excellent system to unpick the molecular basis of somatic stress memory, which includes histone modifications and nucleosome occupancy. This review discusses recent findings and pinpoints open questions in the field.},
  language  = {en}
}
@article{HasnatZupokOlasApeltetal.2021,
  author    = {Hasnat, Muhammad Abrar and Zupok, Arkadiusz and Olas-Apelt, Justyna Jadwiga and M{\"u}ller-R{\"o}ber, Bernd and Leimk{\"u}hler, Silke},
  title     = {A-type carrier proteins are involved in [4Fe-4S] cluster insertion into the radical S-adenosylmethionine protein MoaA for the synthesis of active molybdoenzymes},
  series = {Journal of bacteriology},
  volume    = {203},
  journal   = {Journal of bacteriology},
  number    = {12},
  publisher = {American Society for Microbiology},
  address   = {Washington},
  issn      = {1098-5530},
  doi       = {10.1128/JB.00086-21},
  pages     = {20},
  year      = {2021},
  abstract  = {Iron sulfur (Fe-S) clusters are important biological cofactors present in proteins with crucial biological functions, from photosynthesis to DNA repair, gene expression, and bioenergetic processes. For the insertion of Fe-S clusters into proteins, A-type carrier proteins have been identified. So far, three of them have been characterized in detail in Escherichia coli, namely, IscA, SufA, and ErpA, which were shown to partially replace each other in their roles in [4Fe-4S] cluster insertion into specific target proteins. To further expand the knowledge of [4Fe-4S] cluster insertion into proteins, we analyzed the complex Fe-S cluster-dependent network for the synthesis of the molybdenum cofactor (Moco) and the expression of genes encoding nitrate reductase in E. coli. Our studies include the identification of the A-type carrier proteins ErpA and IscA, involved in [4Fe-4S] cluster insertion into the radical Sadenosyl-methionine (SAM) enzyme MoaA. We show that ErpA and IscA can partially replace each other in their role to provide [4Fe-4S] clusters for MoaA. Since most genes expressing molybdoenzymes are regulated by the transcriptional regulator for fumarate and nitrate reduction (FNR) under anaerobic conditions, we also identified the proteins that are crucial to obtain an active FNR under conditions of nitrate respiration. We show that ErpA is essential for the FNR-dependent expression of the narGHJI operon, a role that cannot be compensated by IscA under the growth conditions tested. SufA does not appear to have a role in Fe-S cluster insertion into MoaA or FNR under anaerobic growth employing nitrate respiration, based on the low level of gene expression. <br /> IMPORTANCE Understanding the assembly of iron-sulfur (Fe-S) proteins is relevant to many fields, including nitrogen fixation, photosynthesis, bioenergetics, and gene regulation. Remaining critical gaps in our knowledge include how Fe-S clusters are transferred to their target proteins and how the specificity in this process is achieved, since different forms of Fe-S clusters need to be delivered to structurally highly diverse target proteins. Numerous Fe-S carrier proteins have been identified in prokaryotes like Escherichia coli, including ErpA, IscA, SufA, and NfuA. In addition, the diverse Fe-S cluster delivery proteins and their target proteins underlie a complex regulatory network of expression, to ensure that both proteins are synthesized under particular growth conditions.},
  language  = {en}
}
@article{CompartLiFettke2021,
  author    = {Compart, Julia and Li, Xiaoping and Fettke, J{\"o}rg},
  title     = {Starch-A complex and undeciphered biopolymer},
  series = {Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants},
  volume    = {258},
  journal   = {Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants},
  publisher = {Elsevier},
  address   = {M{\"u}nchen},
  issn      = {0176-1617},
  doi       = {10.1016/j.jplph.2021.153389},
  pages     = {258 -- 259},
  year      = {2021},
  abstract  = {Starch is a natural storage carbohydrate in plants and algae. It consists of two relatively simple homo-biopolymers, amylopectin and amylose, with only alpha-1,4 and alpha-1,6 linked glucosyl units. Starch is an essential source of nutrition and animal food, as well as an important raw material for industry. However, despite increasing knowledge, detailed information about its structure and turnover are largely lacking. In the last decades, most data were generated using bulk experiments, a method which obviously presents limitations regarding a deeper understanding of the starch metabolism. Here, we discuss some unavoidable questions arising from the existing data. We focus on a few examples related to starch biosynthesis, degradation, and structure where these limitations strongly emerge. Closing these knowledge gaps will also be extremely important for taking the necessary steps in order to set up starch-providing crops for the challenges of the ongoing climate changes, as well as for increasing the usability of starches for industrial applications by biotechnology.},
  language  = {en}
}
@article{GraefGrafeMeyeretal.2021,
  author    = {Gr{\"a}f, Ralph and Grafe, Marianne and Meyer, Irene and Mitic, Kristina and Pitzen, Valentin},
  title     = {The dictyostelium centrosome},
  series = {Cells : open access journal},
  volume    = {10},
  journal   = {Cells : open access journal},
  number    = {10},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2073-4409},
  doi       = {10.3390/cells10102657},
  pages     = {26},
  year      = {2021},
  abstract  = {The centrosome of Dictyostelium amoebae contains no centrioles and consists of a cylindrical layered core structure surrounded by a corona harboring microtubule-nucleating gamma-tubulin complexes. It is the major centrosomal model beyond animals and yeasts. Proteomics, protein interaction studies by BioID and superresolution microscopy methods led to considerable progress in our understanding of the composition, structure and function of this centrosome type. We discuss all currently known components of the Dictyostelium centrosome in comparison to other centrosomes of animals and yeasts.},
  language  = {en}
}
@article{FudickarRoderListeketal.2021,
  author    = {Fudickar, Werner and Roder, Phillip and Listek, Martin and Hanack, Katja and Linker, Torsten},
  title     = {Pyridinium alkynylanthracenes as sensitizers for photodynamic therapy},
  series = {Photochemistry and photobiology},
  volume    = {98},
  journal   = {Photochemistry and photobiology},
  number    = {1},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0031-8655},
  doi       = {10.1111/php.13554},
  pages     = {193 -- 201},
  year      = {2021},
  abstract  = {Photodynamic therapy (PDT) is a mild but effective method to treat certain types of cancer upon irradiation with visible light. Here, three isomeric methylpyridinium alkynylanthracenes 1op were evaluated as sensitizers for PDT. Upon irradiation with blue or green light, all three compounds show the ability to initiate strand breaks of plasmid DNA. The mayor species responsible for cleavage is singlet oxygen (O-1(2)) as confirmed by scavenging reagents. Only isomers 1m and 1p can be incorporated into HeLa cells, whereas isomer 1o cannot permeate through the membrane. While isomer 1m targets the cell nucleus, isomer 1p assembles in the cellular cytoplasm and impacts the cellular integrity. This is in accordance with a moderate toxicity of 1p in the dark, whereas 1m exhibits no dark toxicity. Both isomers are suitable as PDT reagents, with a CC50 of 3 mu m and 75 nm, for 1p and 1m, respectively. Thus, derivative 1m, which can be easily synthesized, becomes an interesting candidate for cancer therapy.},
  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}
}
@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{GuillHuelsemannKlauschies2021,
  author    = {Guill, Christian and H{\"u}lsemann, Janne and Klauschies, Toni},
  title     = {Self-organised pattern formation increases local diversity in metacommunities},
  series = {Ecology letters},
  volume    = {24},
  journal   = {Ecology letters},
  number    = {12},
  publisher = {Wiley-Blackwell},
  address   = {Oxford},
  issn      = {1461-023X},
  doi       = {10.1111/ele.13880},
  pages     = {2624 -- 2634},
  year      = {2021},
  abstract  = {Self-organised formation of spatial patterns is known from a variety of different ecosystems, yet little is known about how these patterns affect the diversity of communities. Here, we use a food chain model in which autotroph diversity is described by a continuous distribution of a trait that affects both growth and defence against heterotrophs. On isolated patches, diversity is always lost over time due to stabilising selection, and the local communities settle on one of two alternative stable community states that are characterised by a dominance of either defended or undefended species. In a metacommunity context, dispersal can destabilise these states and complex spatio-temporal patterns in the species' abundances emerge. The resulting biomass-trait feedback increases local diversity by an order of magnitude compared to scenarios without self-organised pattern formation, thereby maintaining the ability of communities to adapt to potential future changes in biotic or abiotic environmental conditions.},
  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}
}
@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{WojcikCeulemansGaedke2021,
  author    = {Wojcik, Laurie Anne and Ceulemans, Ruben and Gaedke, Ursula},
  title     = {Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs},
  series = {Ecology and Evolution},
  volume    = {11},
  journal   = {Ecology and Evolution},
  number    = {22},
  publisher = {John Wiley \& Sons, Inc.},
  address   = {Hoboken (New Jersey)},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.8214},
  pages     = {15639 -- 15663},
  year      = {2021},
  abstract  = {Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: This loss may hamper ecosystems' ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. We investigated the effects of functional diversity on the robustness, that is, resistance, resilience, and elasticity, using a tritrophic—and thus more realistic—plankton food web model. We compared a non-adaptive food chain with no diversity within the individual trophic levels to a more diverse food web with three adaptive trophic levels. The species fitness differences were balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience, and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occurred. Importantly, we found that a more diverse food web was generally more resistant and resilient but its elasticity was context-dependent. Particularly, functional diversity reduced the probability of a regime shift toward a non-desirable alternative state. The basal-intermediate interaction consistently determined the robustness against a nutrient pulse despite the complex influence of the shape and type of the dynamical attractors. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience, and potentially elasticity as functional diversity declines.},
  language  = {en}
}
@misc{WojcikCeulemansGaedke2021,
  author    = {Wojcik, Laurie Anne and Ceulemans, Ruben and Gaedke, Ursula},
  title     = {Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1251},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-55373},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-553730},
  pages     = {25},
  year      = {2021},
  abstract  = {Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: This loss may hamper ecosystems' ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. We investigated the effects of functional diversity on the robustness, that is, resistance, resilience, and elasticity, using a tritrophic—and thus more realistic—plankton food web model. We compared a non-adaptive food chain with no diversity within the individual trophic levels to a more diverse food web with three adaptive trophic levels. The species fitness differences were balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience, and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occurred. Importantly, we found that a more diverse food web was generally more resistant and resilient but its elasticity was context-dependent. Particularly, functional diversity reduced the probability of a regime shift toward a non-desirable alternative state. The basal-intermediate interaction consistently determined the robustness against a nutrient pulse despite the complex influence of the shape and type of the dynamical attractors. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience, and potentially elasticity as functional diversity declines.},
  language  = {en}
}
@article{DragoWeithoff2021,
  author    = {Drago, Claudia and Weithoff, Guntram},
  title     = {Variable Fitness Response of Two Rotifer Species Exposed to Microplastics Particles},
  series = {Toxics},
  volume    = {9},
  journal   = {Toxics},
  number    = {11},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2305-6304},
  doi       = {10.3390/toxics9110305},
  pages     = {13},
  year      = {2021},
  abstract  = {Plastic pollution is an increasing environmental problem, but a comprehensive understanding of its effect in the environment is still missing. The wide variety of size, shape, and polymer composition of plastics impedes an adequate risk assessment. We investigated the effect of differently sized polystyrene beads (1-, 3-, 6-µm; PS) and polyamide fragments (5-25 µm, PA) and non-plastics items such as silica beads (3-µm, SiO2) on the population growth, reproduction (egg ratio), and survival of two common aquatic micro invertebrates: the rotifer species Brachionus calyciflorus and Brachionus fernandoi. The MPs were combined with food quantity, limiting and saturating food concentration, and with food of different quality. We found variable fitness responses with a significant effect of 3-µm PS on the population growth rate in both rotifer species with respect to food quantity. An interaction between the food quality and the MPs treatments was found in the reproduction of B. calyciflorus. PA and SiO2 beads had no effect on fitness response. This study provides further evidence of the indirect effect of MPs in planktonic rotifers and the importance of testing different environmental conditions that could influence the effect of MPs.},
  language  = {en}
}
@misc{DragoWeithoff2021,
  author    = {Drago, Claudia and Weithoff, Guntram},
  title     = {Variable Fitness Response of Two Rotifer Species Exposed to Microplastics Particles},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1248},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-55261},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-552615},
  pages     = {13},
  year      = {2021},
  abstract  = {Plastic pollution is an increasing environmental problem, but a comprehensive understanding of its effect in the environment is still missing. The wide variety of size, shape, and polymer composition of plastics impedes an adequate risk assessment. We investigated the effect of differently sized polystyrene beads (1-, 3-, 6-µm; PS) and polyamide fragments (5-25 µm, PA) and non-plastics items such as silica beads (3-µm, SiO2) on the population growth, reproduction (egg ratio), and survival of two common aquatic micro invertebrates: the rotifer species Brachionus calyciflorus and Brachionus fernandoi. The MPs were combined with food quantity, limiting and saturating food concentration, and with food of different quality. We found variable fitness responses with a significant effect of 3-µm PS on the population growth rate in both rotifer species with respect to food quantity. An interaction between the food quality and the MPs treatments was found in the reproduction of B. calyciflorus. PA and SiO2 beads had no effect on fitness response. This study provides further evidence of the indirect effect of MPs in planktonic rotifers and the importance of testing different environmental conditions that could influence the effect of MPs.},
  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}
}
@misc{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 = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  volume    = {12},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-55052},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-550520},
  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}
}