@article{DreymannWuenscheSabrowskietal.2022,
  author    = {Dreymann, Nico and Wuensche, Julia and Sabrowski, Wiebke and Moeller, Anja and Czepluch, Denise and Vu Van, Dana and F{\"u}ssel, Susanne and Menger, Marcus M.},
  title     = {Inhibition of Human Urokinase-Type Plasminogen Activator (uPA) Enzyme Activity and Receptor Binding by DNA Aptamers as Potential Therapeutics through Binding to the Different Forms of uPA},
  series = {International journal of molecular sciences},
  volume    = {23},
  journal   = {International journal of molecular sciences},
  number    = {9},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {1661-6596},
  doi       = {10.3390/ijms23094890},
  pages     = {22},
  year      = {2022},
  abstract  = {Urokinase-type plasminogen activator is widely discussed as a marker for cancer prognosis and diagnosis and as a target for cancer therapies. Together with its receptor, uPA plays an important role in tumorigenesis, tumor progression and metastasis. In the present study, systematic evolution of ligands by exponential enrichment (SELEX) was used to select single-stranded DNA aptamers targeting different forms of human uPA. Selected aptamers allowed the distinction between HMW-uPA and LMW-uPA, and therefore, presumably, have different binding regions. Here, uPAapt-02-FR showed highly affine binding with a K-D of 0.7 nM for HMW-uPA and 21 nM for LMW-uPA and was also able to bind to pro-uPA with a K-D of 14 nM. Furthermore, no cross-reactivity to mouse uPA or tissue-type plasminogen activator (tPA) was measured, demonstrating high specificity. Suppression of the catalytic activity of uPA and inhibition of uPAR-binding could be demonstrated through binding with different aptamers and several of their truncated variants. Since RNA aptamers are already known to inhibit uPA-uPAR binding and other pathological functions of the uPA system, these aptamers represent a novel, promising tool not only for detection of uPA but also for interfering with the pathological functions of the uPA system by additionally inhibiting uPA activity.},
  language  = {en}
}
@article{ZhangHuYangetal.2022,
  author    = {Zhang, Kai and Hu, Jiege and Yang, Shuai and Xu, Wei and Wang, Zhichao and Zhuang, Peiwen and Grossart, Hans-Peter and Luo, Zhuhua},
  title     = {Biodegradation of polyester polyurethane by the marine fungus Cladosporium halotolerans 6UPA1},
  series = {Journal of hazardous materials},
  volume    = {437},
  journal   = {Journal of hazardous materials},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0304-3894},
  doi       = {10.1016/j.jhazmat.2022.129406},
  pages     = {10},
  year      = {2022},
  abstract  = {Lack of degradability and the accumulation of polymeric wastes increase the risk for the health of the environment. Recently, recycling of polymeric waste materials becomes increasingly important as raw materials for polymer synthesis are in short supply due to the rise in price and supply chain disruptions. As an important polymer, polyurethane (PU) is widely used in modern life, therefore, PU biodegradation is desirable to avoid its accumulation in the environment. In this study, we isolated a fungal strain Cladosporium halotolerans from the deep sea which can grow in mineral medium with a polyester PU (Impranil DLN) as a sole carbon source. Further, we demonstrate that it can degrade up to 80\% of Impranil PU after 3 days of incubation at 28 celcius by breaking the carbonyl groups (1732 cm(-1)) and C-N-H bonds (1532 cm(-1) and 1247 cm(-1)) as confirmed by Fourier-transform infrared (FTIR) spectroscopy analysis. Gas chromatography-mass spectrometry (GC-MS) analysis revealed polyols and alkanes as PU degradation intermediates, indicating the hydrolysis of ester and urethane bonds. Esterase and urease activities were detected in 7 days-old cultures with PU as a carbon source. Transcriptome analysis showed a number of extracellular protein genes coding for enzymes such as cutinase, lipase, peroxidase and hydrophobic surface binding proteins A (HsbA) were expressed when cultivated on Impranil PU. The yeast two-hybrid assay revealed that the hydrophobic surface binding protein ChHsbA1 directly interacts with inducible esterases, ChLip1 (lipase) and ChCut1 (cutinase). Further, the KEGG pathway for "fatty acid degradation " was significantly enriched in Impranil PU inducible genes, indicating that the fungus may use the degradation intermediates to generate energy via this pathway. Taken together, our data indicates secretion of both esterase and hydrophobic surface binding proteins by C. halotolerans plays an important role in Impranil PU absorption and subsequent degradation. Our study provides a mechanistic insight into Impranil PU biodegradation by deep sea fungi and provides the basis for future development of biotechnological PU recycling.},
  language  = {en}
}
@article{RaffeinerUestuenGuerraetal.2022,
  author    = {Raffeiner, Margot and {\"U}st{\"u}n, Suayib and Guerra, Tiziana and Spinti, Daniela and Fitzner, Maria and Sonnewald, Sophia and Baldermann, Susanne and B{\"o}rnke, Frederik},
  title     = {The Xanthomonas type-III effector XopS stabilizes CaWRKY40a to regulate defense responses and stomatal immunity in pepper (Capsicum annuum)},
  series = {The plant cell},
  volume    = {34},
  journal   = {The plant cell},
  number    = {5},
  publisher = {Oxford Univ. Press},
  address   = {Cary},
  issn      = {1040-4651},
  doi       = {10.1093/plcell/koac032},
  pages     = {1684 -- 1708},
  year      = {2022},
  abstract  = {As a critical part of plant immunity, cells that are attacked by pathogens undergo rapid transcriptional reprogramming to minimize virulence. Many bacterial phytopathogens use type III effector (T3E) proteins to interfere with plant defense responses, including this transcriptional reprogramming. Here, we show that Xanthomonas outer protein S (XopS), a T3E of Xanthomonas campestris pv. vesicatoria (Xcv), interacts with and inhibits proteasomal degradation of WRKY40, a transcriptional regulator of defense gene expression. Virus-induced gene silencing of WRKY40 in pepper (Capsicum annuum) enhanced plant tolerance to Xcv infection, indicating that WRKY40 represses immunity. Stabilization of WRKY40 by XopS reduces the expression of its targets, which include salicylic acid-responsive genes and the jasmonic acid signaling repressor JAZ8. Xcv bacteria lacking XopS display significantly reduced virulence when surface inoculated onto susceptible pepper leaves. XopS delivery by Xcv, as well as ectopic expression of XopS in Arabidopsis thaliana or Nicotiana benthamiana, prevented stomatal closure in response to bacteria and biotic elicitors. Silencing WRKY40 in pepper or N. benthamiana abolished XopS's ability to prevent stomatal closure. This suggests that XopS interferes with both preinvasion and apoplastic defense by manipulating WRKY40 stability and downstream gene expression, eventually altering phytohormone crosstalk to promote pathogen proliferation.},
  language  = {en}
}
@article{HanniganNendelKrull2022,
  author    = {Hannigan, Sara and Nendel, Claas and Krull, Marcos},
  title     = {Effects of temperature on the movement and feeding behaviour of the large lupine beetle, Sitona gressorius},
  series = {Journal of pest science},
  journal   = {Journal of pest science},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {1612-4758},
  doi       = {10.1007/s10340-022-01510-7},
  pages     = {389 -- 402},
  year      = {2022},
  abstract  = {Even though the effects of insect pests on global agricultural productivity are well recognised, little is known about movement and dispersal of many species, especially in the context of global warming. This work evaluates how temperature and light conditions affect different movement metrics and the feeding rate of the large lupine beetle, an agricultural pest responsible for widespread damage in leguminous crops. By using video recordings, the movement of 384 beetles was digitally analysed under six different temperatures and light conditions in the laboratory. Bayesian linear mixed-effect models were used to analyse the data. Furthermore, the effects of temperature on the daily diffusion coefficient of beetles were estimated by using hidden Markov models and random walk simulations. Results of this work show that temperature, light conditions, and beetles' weight were the main factors affecting the flight probability, displacement, time being active and the speed of beetles. Significant variations were also observed in all evaluated metrics. On average, beetles exposed to light conditions and higher temperatures had higher mean speed and flight probability. However, beetles tended to stay more active at higher temperatures and less active at intermediate temperatures, around 20 degrees C. Therefore, both the diffusion coefficient and displacement of beetles were lower at intermediate temperatures. These results show that the movement behaviour and feeding rates of beetles can present different relationships in the function of temperature. It also shows that using a single diffusion coefficient for insects in spatially explicit models may lead to over- or underestimation of pest spread.},
  language  = {en}
}
@article{HilgersHartmannPfaenderetal.2022,
  author    = {Hilgers, Leon and Hartmann, Stefanie and Pfaender, Jobst and Lentge-Maass, Nora and Marwoto, Ristiyanti M. and von Rintelen, Thomas and Hofreiter, Michael},
  title     = {Evolutionary divergence and radula diversification in two ecomorphs from an adaptive radiation of freshwater snails},
  series = {Genes},
  volume    = {13},
  journal   = {Genes},
  number    = {6},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2073-4425},
  doi       = {10.3390/genes13061029},
  pages     = {16},
  year      = {2022},
  abstract  = {(1) Background: Adaptive diversification of complex traits plays a pivotal role in the evolution of organismal diversity. In the freshwater snail genus Tylomelania, adaptive radiations were likely promoted by trophic specialization via diversification of their key foraging organ, the radula. (2) Methods: To investigate the molecular basis of radula diversification and its contribution to lineage divergence, we used tissue-specific transcriptomes of two sympatric Tylomelania sarasinorum ecomorphs. (3) Results: We show that ecomorphs are genetically divergent lineages with habitat-correlated abundances. Sequence divergence and the proportion of highly differentially expressed genes are significantly higher between radula transcriptomes compared to the mantle and foot. However, the same is not true when all differentially expressed genes or only non-synonymous SNPs are considered. Finally, putative homologs of some candidate genes for radula diversification (hh, arx, gbb) were also found to contribute to trophic specialization in cichlids and Darwin's finches. (4) Conclusions: Our results are in line with diversifying selection on the radula driving Tylomelania ecomorph divergence and indicate that some molecular pathways may be especially prone to adaptive diversification, even across phylogenetically distant animal groups.},
  language  = {en}
}
@article{PerkinsSantosRoseetal.2022,
  author    = {Perkins, Anita K. and Santos, Isaac R. and Rose, Andrew L. and Schulz, Kai G. and Grossart, Hans-Peter and Eyre, Bradley D. and Kelaher, Brendan P. and Oakes, Joanne M.},
  title     = {Production of dissolved carbon and alkalinity during macroalgal wrack degradation on beaches},
  series = {Biogeochemistry},
  volume    = {160},
  journal   = {Biogeochemistry},
  number    = {2},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {0168-2563},
  doi       = {10.1007/s10533-022-00946-4},
  pages     = {159 -- 175},
  year      = {2022},
  abstract  = {Marine macroalgae are a key primary producer in coastal ecosystems, but are often overlooked in blue carbon inventories. Large quantities of macroalgal detritus deposit on beaches, but the fate of wrack carbon (C) is little understood. If most of the wrack carbon is respired back to CO2, there would be no net carbon sequestration. However, if most of the wrack carbon is converted to bicarbonate (alkalinity) or refractory DOC, wrack deposition would represent net carbon sequestration if at least part of the metabolic products (e.g., reduced Fe and S) are permanently removed (i.e., long-term burial) and the DOC is not remineralised. To investigate the release of macroalgal C via porewater and its potential to contribute to C sequestration (blue carbon), we monitored the degradation of Ecklonia radiata in flow-through mesocosms simulating tidal flushing on sandy beaches. Over 60 days, 81\% of added E. radiata organic matter (OM) decomposed. Per 1 mol of detritus C, the degradation produced 0.48 +/- 0.34 mol C of dissolved organic carbon (DOC) (59\%) and 0.25 +/- 0.07 mol C of dissolved inorganic carbon (DIC) (31\%) in porewater, and a small amount of CO2 (0.3 +/- 0.0 mol C; ca. 3\%) which was emitted to the atmosphere. A significant amount of carbonate alkalinity was found in porewater, equating to 33\% (0.27 +/- 0.05 mol C) of the total degraded C. The degradation occurred in two phases. In the first phase (days 0-3), 27\% of the OM degraded, releasing highly reactive DOC. In the second phase (days 4-60), the labile DOC was converted to DIC. The mechanisms underlying E. radiata degradation were sulphate reduction and ammonification. It is likely that the carbonate alkalinity was primarily produced through sulphate reduction. The formation of carbonate alkalinity and semi-labile or refractory DOC from beach wrack has the potential to play an overlooked role in coastal carbon cycling and contribute to marine carbon sequestration.},
  language  = {en}
}
@article{TeraoGarattiniRomaoetal.2020,
  author    = {Terao, Mineko and Garattini, Enrico and Rom{\~a}o, Maria Jo{\~a}o and Leimk{\"u}hler, Silke},
  title     = {Evolution, expression, and substrate specificities of aldehyde oxidase enzymes in eukaryotes},
  series = {The journal of biological chemistry},
  volume    = {295},
  journal   = {The journal of biological chemistry},
  number    = {16},
  publisher = {American Society for Biochemistry and Molecular Biology},
  address   = {Rockville},
  issn      = {0021-9258},
  doi       = {10.1074/jbc.REV119.007741},
  pages     = {5377 -- 5389},
  year      = {2020},
  abstract  = {Aldehyde oxidases (AOXs) are a small group of enzymes belonging to the larger family of molybdo-flavoenzymes, along with the well-characterized xanthine oxidoreductase. The two major types of reactions that are catalyzed by AOXs are the hydroxylation of heterocycles and the oxidation of aldehydes to their corresponding carboxylic acids. Different animal species have different complements of AOX genes. The two extremes are represented in humans and rodents; whereas the human genome contains a single active gene (AOX1), those of rodents, such as mice, are endowed with four genes (Aox1-4), clustering on the same chromosome, each encoding a functionally distinct AOX enzyme. It still remains enigmatic why some species have numerous AOX enzymes, whereas others harbor only one functional enzyme. At present, little is known about the physiological relevance of AOX enzymes in humans and their additional forms in other mammals. These enzymes are expressed in the liver and play an important role in the metabolisms of drugs and other xenobiotics. In this review, we discuss the expression, tissue-specific roles, and substrate specificities of the different mammalian AOX enzymes and highlight insights into their physiological roles.},
  language  = {en}
}
@article{KunstmannEngstroemWehleetal.2020,
  author    = {Kunstmann, Ruth Sonja and Engstr{\"o}m, Olof and Wehle, Marko and Widmalm, G{\"o}ran and Santer, Mark and Barbirz, Stefanie},
  title     = {Increasing the affinity of an O-Antigen polysaccharide binding site in Shigella flexneri bacteriophage Sf6 tailspike protein},
  series = {Chemistry - A European Journal},
  volume    = {26},
  journal   = {Chemistry - A European Journal},
  number    = {32},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {0947-6539},
  doi       = {10.1002/chem.202000495},
  pages     = {7263 -- 7273},
  year      = {2020},
  abstract  = {Broad and unspecific use of antibiotics accelerates spread of resistances. Sensitive and robust pathogen detection is thus important for a more targeted application. Bacteriophages contain a large repertoire of pathogen-binding proteins. These tailspike proteins (TSP) often bind surface glycans and represent a promising design platform for specific pathogen sensors. We analysed bacteriophage Sf6 TSP that recognizes the O-polysaccharide of dysentery-causing Shigella flexneri to develop variants with increased sensitivity for sensor applications. Ligand polyrhamnose backbone conformations were obtained from 2D H-1,H-1-trNOESY NMR utilizing methine-methine and methine-methyl correlations. They agreed well with conformations obtained from molecular dynamics (MD), validating the method for further predictions. In a set of mutants, MD predicted ligand flexibilities that were in good correlation with binding strength as confirmed on immobilized S. flexneri O-polysaccharide (PS) with surface plasmon resonance. In silico approaches combined with rapid screening on PS surfaces hence provide valuable strategies for TSP-based pathogen sensor design.},
  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{ThirumalaikumarGorkaSchulzetal.2020,
  author    = {Thirumalaikumar, Venkatesh P. and Gorka, Michal and Schulz, Karina and Masclaux-Daubresse, Celine and Sampathkumar, Arun and Skirycz, Aleksandra and Vierstra, Richard D. and Balazadeh, Salma},
  title     = {Selective autophagy regulates heat stress memory in Arabidopsis by NBR1-mediated targeting of HSP90.1 and ROF1},
  series = {Autophagy},
  volume    = {17},
  journal   = {Autophagy},
  number    = {9},
  publisher = {Taylor \& Francis},
  address   = {Abingdon},
  issn      = {1554-8635},
  doi       = {10.1080/15548627.2020.1820778},
  pages     = {2184 -- 2199},
  year      = {2020},
  abstract  = {In nature, plants are constantly exposed to many transient, but recurring, stresses. Thus, to complete their life cycles, plants require a dynamic balance between capacities to recover following cessation of stress and maintenance of stress memory. Recently, we uncovered a new functional role for macroautophagy/autophagy in regulating recovery from heat stress (HS) and resetting cellular memory of HS inArabidopsis thaliana. Here, we demonstrated that NBR1 (next to BRCA1 gene 1) plays a crucial role as a receptor for selective autophagy during recovery from HS. Immunoblot analysis and confocal microscopy revealed that levels of the NBR1 protein, NBR1-labeled puncta, and NBR1 activity are all higher during the HS recovery phase than before. Co-immunoprecipitation analysis of proteins interacting with NBR1 and comparative proteomic analysis of annbr1-null mutant and wild-type plants identified 58 proteins as potential novel targets of NBR1. Cellular, biochemical and functional genetic studies confirmed that NBR1 interacts with HSP90.1 (heat shock protein 90.1) and ROF1 (rotamase FKBP 1), a member of the FKBP family, and mediates their degradation by autophagy, which represses the response to HS by attenuating the expression ofHSPgenes regulated by the HSFA2 transcription factor. Accordingly, loss-of-function mutation ofNBR1resulted in a stronger HS memory phenotype. Together, our results provide new insights into the mechanistic principles by which autophagy regulates plant response to recurrent HS.},
  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{HussJuddKoperetal.2022,
  author    = {Huß, Sebastian and Judd, Rika Siedah and Koper, Kaan and Maeda, Hiroshi A. and Nikoloski, Zoran},
  title     = {An automated workflow that generates atom mappings for large-scale metabolic models and its application to Arabidopsis thaliana},
  series = {The plant journal},
  volume    = {111},
  journal   = {The plant journal},
  number    = {5},
  publisher = {Wiley-Blackwell},
  address   = {Oxford [u.a.]},
  issn      = {0960-7412},
  doi       = {10.1111/tpj.15903},
  pages     = {1486 -- 1500},
  year      = {2022},
  abstract  = {Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determines cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA), which relies on the patterns of isotope labeling of metabolites in the network. The application of MFA also requires a stoichiometric model with atom mappings that are currently not available for the majority of large-scale metabolic network models, particularly of plants. While automated approaches such as the Reaction Decoder Toolkit (RDT) can produce atom mappings for individual reactions, tracing the flow of individual atoms of the entire reactions across a metabolic model remains challenging. Here we establish an automated workflow to obtain reliable atom mappings for large-scale metabolic models by refining the outcome of RDT, and apply the workflow to metabolic models of Arabidopsis thaliana. We demonstrate the accuracy of RDT through a comparative analysis with atom mappings from a large database of biochemical reactions, MetaCyc. We further show the utility of our automated workflow by simulating N-15 isotope enrichment and identifying nitrogen (N)-containing metabolites which show enrichment patterns that are informative for flux estimation in future N-15-MFA studies of A. thaliana. The automated workflow established in this study can be readily expanded to other species for which metabolic models have been established and the resulting atom mappings will facilitate MFA and graph-theoretic structural analyses with large-scale metabolic networks.},
  language  = {en}
}
@article{OstermannMiyashitaKoenigPernatetal.2022,
  author    = {Ostermann-Miyashita, Emu-Felicitas and K{\"o}nig, Hannes J. and Pernat, Nadja and Bellingrath-Kimura, Sonoko Dorothea and Hibler, Sophia and Kiffner, Christian},
  title     = {Knowledge of returning wildlife species and willingness to participate in citizen science projects among wildlife park visitors in Germany},
  series = {People and nature},
  volume    = {4},
  journal   = {People and nature},
  number    = {5},
  publisher = {British Ecological Society; Wiley},
  address   = {London; Hoboken, NJ},
  issn      = {2575-8314},
  doi       = {10.1002/pan3.10379},
  pages     = {1201 -- 1215},
  year      = {2022},
  abstract  = {Successful conservation efforts have led to recent increases of large mammals such as European bison Bison bonasus, moose Alces alces and grey wolf Canis lupus and their return to former habitats in central Europe. While embraced by some, the recovery of these species is a controversial topic and holds potential for human-wildlife conflicts. Involving the public has been suggested to be an effective method for monitoring wildlife and mitigating associated conflicts. To assess two interrelated prerequisites for engaging people in Citizen Science (CS)-knowledge of returning species and respondents' readiness to participate in CS activities for monitoring and managing these species-we conducted a survey (questionnaire) in two wildlife parks located in different states of Germany. Based on 472 complete questionnaires, we developed generalized linear models to understand how sociodemographic variables and exposure to the species affected visitors' knowledge of each species, and to investigate if sociodemographic variables and knowledge influenced the likelihood of visitors to participate in CS activities. Almost all visitors were aware of the returning wolf population, while knowledge and awareness about bison and moose were significantly lower. Knowledge of the two herbivores differed geographically (higher knowledge of moose in the north-eastern state), possibly indicating a positive association between exposure to the species and knowledge. However, models generally performed poorly in predicting knowledge about wildlife, suggesting that such specific knowledge is insufficiently explained by sociodemographic variables. Our model, which explained stated willingness in CS indicated that younger participants and those with higher knowledge scores in the survey were more willing to engage in CS activities. Overall, our analyses highlight how exposure to large mammals, knowledge about wildlife and human demographics are interrelated-insights that are helpful for effectively recruiting citizen scientists for wildlife conservation. Read the free Plain Language Summary for this article on the Journal blog.},
  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{LeinsBanitzGrimmetal.2020,
  author    = {Leins, Johannes A. and Banitz, Thomas and Grimm, Volker and Drechsler, Martin},
  title     = {High-resolution PVA along large environmental gradients to model the combined effects of climate change and land use timing},
  series = {Ecological modelling : international journal on ecological modelling and systems ecology},
  volume    = {440},
  journal   = {Ecological modelling : international journal on ecological modelling and systems ecology},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0304-3800},
  doi       = {10.1016/j.ecolmodel.2020.109355},
  pages     = {15},
  year      = {2020},
  abstract  = {Both climate change and land use regimes affect the viability of populations, but they are often studied separately. Moreover, population viability analyses (PVAs) often ignore the effects of large environmental gradients and use temporal resolutions that are too coarse to take into account that different stages of a population's life cycle may be affected differently by climate change. Here, we present the High-resolution Large Environmental Gradient (HiLEG) model and apply it in a PVA with daily resolution based on daily climate projections for Northwest Germany. We used the large marsh grasshopper (LMG) as the target species and investigated (1) the effects of climate change on the viability and spatial distribution of the species, (2) the influence of the timing of grassland mowing on the species and (3) the interaction between the effects of climate change and grassland mowing. The stageand cohort-based model was run for the spatially differentiated environmental conditions temperature and soil moisture across the whole study region. We implemented three climate change scenarios and analyzed the population dynamics for four consecutive 20-year periods. Climate change alone would lead to an expansion of the regions suitable for the LMG, as warming accelerates development and due to reduced drought stress. However, in combination with land use, the timing of mowing was crucial, as this disturbance causes a high mortality rate in the aboveground life stages. Assuming the same date of mowing throughout the region, the impact on viability varied greatly between regions due to the different climate conditions. The regional negative effects of the mowing date can be divided into five phases: (1) In early spring, the populations were largely unaffected in all the regions; (2) between late spring and early summer, they were severely affected only in warm regions; (3) in summer, all the populations were severely affected so that they could hardly survive; (4) between late summer and early autumn, they were severely affected in cold regions; and (5) in autumn, the populations were equally affected across all regions. The duration and start of each phase differed slightly depending on the climate change scenario and simulation period, but overall, they showed the same pattern. Our model can be used to identify regions of concern and devise management recommendations. The model can be adapted to the life cycle of different target species, climate projections and disturbance regimes. We show with our adaption of the HiLEG model that high-resolution PVAs and applications on large environmental gradients can be reconciled to develop conservation strategies capable of dealing with multiple stressors.},
  language  = {en}
}
@article{PotenteLeveilleBourretYousefietal.2022,
  author    = {Potente, Giacomo and L{\´e}veill{\´e}-Bourret, {\´E}tienne and Yousefi, Narjes and Choudhury, Rimjhim Roy and Keller, Barbara and Diop, Seydina Issa and Duijsings, Dani{\"e}l and Pirovano, Walter and Lenhard, Michael and Sz{\"o}v{\´e}nyi, P{\´e}ter and Conti, Elena},
  title     = {Comparative genomics elucidates the origin of a supergene controlling floral heteromorphism},
  series = {Molecular biology and evolution : MBE},
  volume    = {39},
  journal   = {Molecular biology and evolution : MBE},
  number    = {2},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0737-4038},
  doi       = {10.1093/molbev/msac035},
  pages     = {16},
  year      = {2022},
  abstract  = {Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite the importance of supergenes in adaptation, little is known on how they originate. A classic example of supergene is the S locus controlling heterostyly, a floral heteromorphism occurring in 28 angiosperm families. In Primula, heterostyly is characterized by the cooccurrence of two complementary, self-incompatible floral morphs and is controlled by five genes clustered in the hemizygous, ca. 300-kb S locus. Here, we present the first chromosome-scale genome assembly of any heterostylous species, that of Primula veris (cowslip). By leveraging the high contiguity of the P. veris assembly and comparative genomic analyses, we demonstrated that the S-locus evolved via multiple, asynchronous gene duplications and independent gene translocations. Furthermore, we discovered a new whole-genome duplication in Ericales that is specific to the Primula lineage. We also propose a mechanism for the origin of S-locus hemizygosity via nonhomologous recombination involving the newly discovered two pairs of CFB genes flanking the S locus. Finally, we detected only weak signatures of degeneration in the S locus, as predicted for hemizygous supergenes. The present study provides a useful resource for future research addressing key questions on the evolution of supergenes in general and the S locus in particular: How do supergenes arise? What is the role of genome architecture in the evolution of complex adaptations? Is the molecular architecture of heterostyly supergenes across angiosperms similar to that of Primula?},
  language  = {en}
}
@article{LucenaPerezBazzicalupoPaijmansetal.2022,
  author    = {Lucena-Perez, Mar{\´i}a and Bazzicalupo, Enrico and Paijmans, Johanna and Kleinman-Ruiz, Daniel and Dal{\´e}n, Love and Hofreiter, Michael and Delibes, Miguel and Clavero, Miguel and Godoy, Jos{\´e} A.},
  title     = {Ancient genome provides insights into the history of Eurasian lynx in Iberia and Western Europe},
  series = {Quaternary science reviews : the international multidisciplinary research and review journal},
  volume    = {285},
  journal   = {Quaternary science reviews : the international multidisciplinary research and review journal},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0277-3791},
  doi       = {10.1016/j.quascirev.2022.107518},
  pages     = {9},
  year      = {2022},
  abstract  = {The Eurasian lynx (Lynx lynx) is one of the most widely distributed felids in the world. However, most of its populations started to decline a few millennia ago. Historical declines have been especially severe in Europe, and particularly in Western Europe, from where the species disappeared in the last few centuries. Here, we analyze the genome of an Eurasian lynx inhabiting the Iberian Peninsula 2500 ya, to gain insights into the phylogeographic position and genetic status of this extinct population. Also, we contextualize previous ancient data in the light of new phylogeographic studies of the species. Our results suggest that the Iberian population is part of an extinct European lineage closely related to the current Carpathian-Baltic lineages. Also, this sample holds the lowest diversity reported for the species so far, and similar to that of the highly endangered Iberian lynx. A combination of historical factors, such as a founder effect while colonizing the peninsula, together with intensified human impacts during the Holocene in the Cantabrian strip, could have led to a genetic impoverishment of the population and precipitated its extinction. Mitogenomic lineages distribution in space and time support the long-term coexistence of several lineages of Eurasian lynx in Western Europe with fluctuating ranges. While mitochondrial sequences related to the lineages currently found in Balkans and Caucasus were predominant during the Pleistocene, those more closely related to the lineage currently distributed in Central Europe prevailed during the Holocene. The use of ancient genomics has proven to be a useful tool to understand the biogeographic pattern of the Eurasian lynx in the past.},
  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{EscalanteDominguezGomezRuizetal.2022,
  author    = {Escalante, Ignacio and Dominguez, Marisol and Gomez-Ruiz, Daisy Alejandra and Machado, Glauco},
  title     = {Benefits and costs of mixed-species aggregations in Harvestmen (Arachnida: Opiliones)},
  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.2021.766323},
  pages     = {24},
  year      = {2022},
  abstract  = {Many animals form aggregations with individuals of the same species (single-species aggregations, SSA). Less frequently, individuals may also aggregate with individuals of other species (mixed-species aggregations, MSA). Although the benefits and costs of SSA have been intensively studied, the same is not true for MSA. Here, we first review the cases of MSA in harvestmen, an arachnid order in which the records of MSA are more frequent than other arthropod orders. We then propose several benefits and costs of MSA in harvestmen, and contrast them with those of SSA. Second, using field-gathered data we describe gregariousness in seven species of Prionostemma harvestmen from Costa Rica. These species form MSA, but individuals are also found solitarily or in SSA. We tested one possible benefit and one possible cost of gregariousness in Prionostemma harvestmen. Regarding the benefit, we hypothesized that individuals missing legs would be more exposed to predation than eight-legged individuals and thus they should be found preferentially in aggregations, where they would be more protected from predators. Our data, however, do not support this hypothesis. Regarding the cost, we hypothesized that gregariousness increases the chances of parasitism. We found no support for this hypothesis either because both mite prevalence and infestation intensity did not differ between solitary or aggregated individuals. Additionally, the type of aggregation (SSA or MSA) was not associated with the benefit or the cost we explored. This lack of effect may be explained by the fluid membership of the aggregations, as we found high turnover over time in the number of individuals and species composition of the aggregations. In conclusion, we hope our review and empirical data stimulate further studies on MSA, which remains one of the most elusive forms of group living in animals.},
  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{KrumbholzIshidaBaunachetal.2022,
  author    = {Krumbholz, Julia and Ishida, Keishi and Baunach, Martin and Teikari, Jonna and Rose, Magdalena M. and Sasso, Severin and Hertweck, Christian and Dittmann, Elke},
  title     = {Deciphering chemical mediators regulating specialized metabolism in a symbiotic cyanobacterium},
  series = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker. International edition},
  journal   = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker. International edition},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {1433-7851},
  doi       = {10.1002/anie.202204545},
  pages     = {10},
  year      = {2022},
  abstract  = {Genomes of cyanobacteria feature a variety of cryptic biosynthetic pathways for complex natural products, but the peculiarities limiting the discovery and exploitation of the metabolic dark matter are not well understood. Here we describe the discovery of two cell density-dependent chemical mediators, nostoclide and nostovalerolactone, in the symbiotic model strain Nostoc punctiforme, and demonstrate their pronounced impact on the regulation of specialized metabolism. Through transcriptional, bioinformatic and labeling studies we assigned two adjacent biosynthetic gene clusters to the biosynthesis of the two polyketide mediators. Our findings provide insight into the orchestration of specialized metabolite production and give lessons for the genomic mining and high-titer production of cyanobacterial bioactive compounds.},
  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{HornBecherJohstetal.2020,
  author    = {Horn, Juliane and Becher, Matthias A. and Johst, Karin and Kennedy, Peter J. and Osborne, Juliet L. and Radchuk, Viktoriia and Grimm, Volker},
  title     = {Honey bee colony performance affected by crop diversity and farmland structure},
  series = {Ecological applications},
  volume    = {31},
  journal   = {Ecological applications},
  number    = {1},
  publisher = {Wiley Periodicals LLC},
  address   = {Washington DC},
  issn      = {1939-5582},
  doi       = {10.1002/eap.2216},
  pages     = {1 -- 22},
  year      = {2020},
  abstract  = {Forage availability has been suggested as one driver of the observed decline in honey bees. However, little is known about the effects of its spatiotemporal variation on colony success. We present a modeling framework for assessing honey bee colony viability in cropping systems. Based on two real farmland structures, we developed a landscape generator to design cropping systems varying in crop species identity, diversity, and relative abundance. The landscape scenarios generated were evaluated using the existing honey bee colony model BEEHAVE, which links foraging to in-hive dynamics. We thereby explored how different cropping systems determine spatiotemporal forage availability and, in turn, honey bee colony viability (e.g., time to extinction, TTE) and resilience (indicated by, e.g., brood mortality). To assess overall colony viability, we developed metrics,P(H)andP(P,)which quantified how much nectar and pollen provided by a cropping system per year was converted into a colony's adult worker population. Both crop species identity and diversity determined the temporal continuity in nectar and pollen supply and thus colony viability. Overall farmland structure and relative crop abundance were less important, but details mattered. For monocultures and for four-crop species systems composed of cereals, oilseed rape, maize, and sunflower,P(H)andP(P)were below the viability threshold. Such cropping systems showed frequent, badly timed, and prolonged forage gaps leading to detrimental cascading effects on life stages and in-hive work force, which critically reduced colony resilience. Four-crop systems composed of rye-grass-dandelion pasture, trefoil-grass pasture, sunflower, and phacelia ensured continuous nectar and pollen supply resulting in TTE > 5 yr, andP(H)(269.5 kg) andP(P)(108 kg) being above viability thresholds for 5 yr. Overall, trefoil-grass pasture, oilseed rape, buckwheat, and phacelia improved the temporal continuity in forage supply and colony's viability. Our results are hypothetical as they are obtained from simplified landscape settings, but they nevertheless match empirical observations, in particular the viability threshold. Our framework can be used to assess the effects of cropping systems on honey bee viability and to develop land-use strategies that help maintain pollination services by avoiding prolonged and badly timed forage gaps.},
  language  = {en}
}
@article{LiPostlBoehmeretal.2022,
  author    = {Li, Chenzhi and Postl, Alexander K. and B{\"o}hmer, Thomas and Cao, Xianyong and Dolman, Andrew M. and Herzschuh, Ulrike},
  title     = {Harmonized chronologies of a global late Quaternary pollen dataset (LegacyAge 1.0)},
  series = {Earth system science data : ESSD},
  volume    = {14},
  journal   = {Earth system science data : ESSD},
  number    = {3},
  publisher = {Copernics Publications},
  address   = {Katlenburg-Lindau},
  issn      = {1866-3508},
  doi       = {10.5194/essd-14-1331-2022},
  pages     = {1331 -- 1343},
  year      = {2022},
  abstract  = {We present a chronology framework named LegacyAge 1.0 containing harmonized chronologies for 2831 pollen records (downloaded from the Neotoma Paleoecology Database and the supplementary Asian datasets) together with their age control points and metadata in machine-readable data formats. All chronologies use the Bayesian framework implemented in Bacon version 2.5.3. Optimal parameter settings of priors (accumulation.shape, memory.strength, memory.mean, accumulation.rate, and thickness) were identified based on information in the original publication or iteratively after preliminary model inspection. The most common control points for the chronologies are radiocarbon dates (86.1 \%), calibrated by the latest calibration curves (IntCal20 and SHCal20 for the terrestrial radiocarbon dates in the Northern Hemisphere and Southern Hemisphere and Marine20 for marine materials). The original publications were consulted when dealing with outliers and inconsistencies. Several major challenges when setting up the chronologies included the waterline issue (18.8\% of records), reservoir effect (4.9 \%), and sediment deposition discontinuity (4.4 \%). Finally, we numerically compare the LegacyAge 1.0 chronologies to those published in the original publications and show that the reliability of the chronologies of 95.4\% of records could be improved according to our assessment. Our chronology framework and revised chronologies provide the opportunity to make use of the ages and age uncertainties in synthesis studies of, for example, pollen-based vegetation and climate change. The LegacyAge 1.0 dataset, including metadata, datings, harmonized chronologies, and R code used, is openaccess and available at PANGAEA (https://doi.org/10.1594/PANGAEA.933132; Li et al., 2021) and Zenodo (https://doi.org/10.5281/zenodo.5815192; Li et al., 2022), respectively.},
  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{IrobBlaumBaldaufetal.2022,
  author    = {Irob, Katja and Blaum, Niels and Baldauf, Selina and Kerger, Leon and Strohbach, Ben and Kanduvarisa, Angelina and Lohmann, Dirk and Tietjen, Britta},
  title     = {Browsing herbivores improve the state and functioning of savannas},
  series = {Ecology and evolution},
  volume    = {12},
  journal   = {Ecology and evolution},
  number    = {3},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.8715},
  pages     = {19},
  year      = {2022},
  abstract  = {Changing climatic conditions and unsustainable land use are major threats to savannas worldwide. Historically, many African savannas were used intensively for livestock grazing, which contributed to widespread patterns of bush encroachment across savanna systems. To reverse bush encroachment, it has been proposed to change the cattle-dominated land use to one dominated by comparatively specialized browsers and usually native herbivores. However, the consequences for ecosystem properties and processes remain largely unclear. We used the ecohydrological, spatially explicit model EcoHyD to assess the impacts of two contrasting, herbivore land-use strategies on a Namibian savanna: grazer- versus browser-dominated herbivore communities. We varied the densities of grazers and browsers and determined the resulting composition and diversity of the plant community, total vegetation cover, soil moisture, and water use by plants. Our results showed that plant types that are less palatable to herbivores were best adapted to grazing or browsing animals in all simulated densities. Also, plant types that had a competitive advantage under limited water availability were among the dominant ones irrespective of land-use scenario. Overall, the results were in line with our expectations: under high grazer densities, we found heavy bush encroachment and the loss of the perennial grass matrix. Importantly, regardless of the density of browsers, grass cover and plant functional diversity were significantly higher in browsing scenarios. Browsing herbivores increased grass cover, and the higher total cover in turn improved water uptake by plants overall. We concluded that, in contrast to grazing-dominated land-use strategies, land-use strategies dominated by browsing herbivores, even at high herbivore densities, sustain diverse vegetation communities with high cover of perennial grasses, resulting in lower erosion risk and bolstering ecosystem services.},
  language  = {en}
}
@article{GhafarianWielandLuettschwageretal.2022,
  author    = {Ghafarian, Fatemeh and Wieland, Ralf and L{\"u}ttschwager, Dietmar and Nendel, Claas},
  title     = {Application of extreme gradient boosting and Shapley Additive explanations to predict temperature regimes inside forests from standard open-field meteorological data},
  series = {Environmental modelling \& software with environment data news},
  volume    = {156},
  journal   = {Environmental modelling \& software with environment data news},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {1364-8152},
  doi       = {10.1016/j.envsoft.2022.105466},
  pages     = {11},
  year      = {2022},
  abstract  = {Forest microclimate can buffer biotic responses to summer heat waves, which are expected to become more extreme under climate warming. Prediction of forest microclimate is limited because meteorological observation standards seldom include situations inside forests. We use eXtreme Gradient Boosting - a Machine Learning technique - to predict the microclimate of forest sites in Brandenburg, Germany, using seasonal data comprising weather features. The analysis was amended by applying a SHapley Additive explanation to show the interaction effect of variables and individualised feature attributions. We evaluate model performance in comparison to artificial neural networks, random forest, support vector machine, and multi-linear regression. After implementing a feature selection, an ensemble approach was applied to combine individual models for each forest and improve robustness over a given single prediction model. The resulting model can be applied to translate climate change scenarios into temperatures inside forests to assess temperature-related ecosystem services provided by forests.},
  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{MitzscherlingMacLeanLipusetal.2022,
  author    = {Mitzscherling, Julia and MacLean, Joana and Lipus, Daniel and Bartholom{\"a}us, Alexander and Mangelsdorf, Kai and Lipski, Andr{\´e} and Roddatis, Vladimir and Liebner, Susanne and Wagner, Dirk},
  title     = {Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste},
  series = {International journal of systematic and evolutionary microbiology},
  volume    = {72},
  journal   = {International journal of systematic and evolutionary microbiology},
  number    = {4},
  publisher = {Microbiology Society},
  address   = {London},
  issn      = {1466-5026},
  doi       = {10.1099/ijsem.0.005319},
  pages     = {11},
  year      = {2022},
  abstract  = {Strain NGK65(T), a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. Strain NGK65(T) hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 degrees C. in 0-1\% NaCl and at pH 7.5-8.0. Glycerol, D-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate. sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources. The predominant membrane fatty acids were iso-C-16:0 followed by iso-C(17:)0 and C-18:1 omega 9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol. The cell-wall peptidoglycan type was A3 gamma, with LL-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H-4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65(T) belongs to the genus Nocardioides (phylum Actinobacteria). appearing most closely related to Nocardioides daejeonensis MJ31(T) (98.6\%) and Nocardioides dubius KSL-104(T) (98.3\%). The genomic DNA G+C content of strain NGK65(T) was 68.2\%. Strain NGK65(T) and the type strains of species involved in the analysis had average nucleotide identity values of 78.3-71.9\% as well as digital DNA-DNA hybridization values between 22.5 and 19.7\%, which clearly indicated that the isolate represents a novel species within the genus Nocardioides. Based on phenotypic and molecular characterization, strain NGK65(T) can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed. The type strain is NGK65(T) (=DSM 113112(T)=NCCB 100846(T)).},
  language  = {en}
}
@article{HiltGrossartMcGinnisetal.2022,
  author    = {Hilt, Sabine and Grossart, Hans-Peter and McGinnis, Daniel F. and Keppler, Frank},
  title     = {Potential role of submerged macrophytes for oxic methane production in aquatic ecosystems},
  series = {Limnology and oceanography},
  journal   = {Limnology and oceanography},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0024-3590},
  doi       = {10.1002/lno.12095},
  pages     = {13},
  year      = {2022},
  abstract  = {Methane (CH4) from aquatic ecosystems contributes to about half of total global CH4 emissions to the atmosphere. Until recently, aquatic biogenic CH4 production was exclusively attributed to methanogenic archaea living under anoxic or suboxic conditions in sediments, bottom waters, and wetlands. However, evidence for oxic CH4 production (OMP) in freshwater, brackish, and marine habitats is increasing. Possible sources were found to be driven by various planktonic organisms supporting different OMP mechanisms. Surprisingly, submerged macrophytes have been fully ignored in studies on OMP, yet they are key components of littoral zones of ponds, lakes, and coastal systems. High CH4 concentrations in these zones have been attributed to organic substrate production promoting classic methanogenesis in the absence of oxygen. Here, we review existing studies and argue that, similar to terrestrial plants and phytoplankton, macroalgae and submerged macrophytes may directly or indirectly contribute to CH4 formation in oxic waters. We propose several potential direct and indirect mechanisms: (1) direct production of CH4; (2) production of CH4 precursors and facilitation of their bacterial breakdown or chemical conversion; (3) facilitation of classic methanogenesis; and (4) facilitation of CH4 ebullition. As submerged macrophytes occur in many freshwater and marine habitats, they are important in global carbon budgets and can strongly vary in their abundance due to seasonal and boom-bust dynamics. Knowledge on their contribution to OMP is therefore essential to gain a better understanding of spatial and temporal dynamics of CH4 emissions and thus to substantially reduce current uncertainties when estimating global CH4 emissions from aquatic ecosystems.},
  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{PanSarhanKochovskietal.2022,
  author    = {Pan, Xuefeng and Sarhan, Radwan Mohamed and Kochovski, Zdravko and Chen, Guosong and Taubert, Andreas and Mei, Shilin and Lu, Yan},
  title     = {Template synthesis of dual-functional porous MoS2 nanoparticles with photothermal conversion and catalytic properties},
  series = {Nanoscale},
  volume    = {14},
  journal   = {Nanoscale},
  number    = {18},
  publisher = {RSC Publ. (Royal Society of Chemistry)},
  address   = {Cambridge},
  issn      = {2040-3372},
  doi       = {10.1039/d2nr01040b},
  pages     = {6888 -- 6901},
  year      = {2022},
  abstract  = {Advanced catalysis triggered by photothermal conversion effects has aroused increasing interest due to its huge potential in environmental purification. In this work, we developed a novel approach to the fast degradation of 4-nitrophenol (4-Nip) using porous MoS2 nanoparticles as catalysts, which integrate the intrinsic catalytic property of MoS2 with its photothermal conversion capability. Using assembled polystyrene-b-poly(2-vinylpyridine) block copolymers as soft templates, various MoS 2 particles were prepared, which exhibited tailored morphologies (e.g., pomegranate-like, hollow, and open porous structures). The photothermal conversion performance of these featured particles was compared under near-infrared (NIR) light irradiation. Intriguingly, when these porous MoS2 particles were further employed as catalysts for the reduction of 4-Nip, the reaction rate constant was increased by a factor of 1.5 under NIR illumination. We attribute this catalytic enhancement to the open porous architecture and light-to-heat conversion performance of the MoS2 particles. This contribution offers new opportunities for efficient photothermal-assisted catalysis.},
  language  = {en}
}
@article{HagemannConejeroStillfriedetal.2022,
  author    = {Hagemann, Justus and Conejero, Carles and Stillfried, Milena and Mentaberre, Gregorio and Castillo-Contreras, Raquel and Fickel, J{\"o}rns and Lopez-Olvera, Jorge Ram{\´o}n},
  title     = {Genetic population structure defines wild boar as an urban exploiter species in Barcelona, Spain},
  series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  volume    = {833},
  journal   = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man},
  publisher = {Elsevier Science},
  address   = {Amsterdam [u.a.]},
  issn      = {0048-9697},
  doi       = {10.1016/j.scitotenv.2022.155126},
  pages     = {10},
  year      = {2022},
  abstract  = {Urban wildlife ecology is gaining relevance as metropolitan areas grow throughout the world, reducing natural habitats and creating new ecological niches. However, knowledge is still scarce about the colonisation processes of such urban niches, the establishment of new communities, populations and/or species, and the related changes in behaviour and life histories of urban wildlife. Wild boar (Sus scrofa) has successfully colonised urban niches throughout Europe. The aim of this study is to unveil the processes driving the establishment and maintenance of an urban wild boar population by analysing its genetic structure. A set of 19 microsatellite loci was used to test whether urban wild boars in Barcelona, Spain, are an isolated population or if gene flow prevents genetic differentiation between rural and urban wild boars. This knowledge will contribute to the understanding of the effects of synurbisation and the associated management measures on the genetic change of large mammals in urban ecosystems. Despite the unidirectional gene flow from rural to urban areas, the urban wild boars in Barcelona form an island population genotypically differentiated from the surrounding rural ones. The comparison with previous genetic studies of urban wild boar populations suggests that forest patches act as suitable islands for wild boar genetic differentiation. Previous results and the genetic structure of the urban wild boar population in Barcelona classify wild boar as an urban exploiter species. These wild boar peri-urban island populations are responsible for conflict with humans and thus should be managed by reducing the attractiveness of urban areas. The management of peri-urban wild boar populations should aim at reducing migration into urban areas and preventing phenotypic changes (either genetic or plastic) causing habituation of wild boars to humans and urban environments.},
  language  = {en}
}
@article{RalevskiApeltOlasetal.2022,
  author    = {Ralevski, Alexandra and Apelt, Federico and Olas, Justyna Jadwiga and M{\"u}ller-R{\"o}ber, Bernd and Rugarli, Elena I. and Kragler, Friedrich and Horvath, Tamas L.},
  title     = {Plant mitochondrial FMT and its mammalian homolog CLUH controls development and behavior in Arabidopsis and locomotion in mice},
  series = {Cellular and molecular life sciences},
  volume    = {79},
  journal   = {Cellular and molecular life sciences},
  number    = {6},
  publisher = {Springer International Publishing AG},
  address   = {Cham (ZG)},
  issn      = {1420-682X},
  doi       = {10.1007/s00018-022-04382-3},
  pages     = {17},
  year      = {2022},
  abstract  = {Mitochondria in animals are associated with development, as well as physiological and pathological behaviors. Several conserved mitochondrial genes exist between plants and higher eukaryotes. Yet, the similarities in mitochondrial function between plant and animal species is poorly understood. Here, we show that FMT (FRIENDLY MITOCHONDRIA) from Arabidopsis thaliana, a highly conserved homolog of the mammalian CLUH (CLUSTERED MITOCHONDRIA) gene family encoding mitochondrial proteins associated with developmental alterations and adult physiological and pathological behaviors, affects whole plant morphology and development under both stressed and normal growth conditions. FMT was found to regulate mitochondrial morphology and dynamics, germination, and flowering time. It also affects leaf expansion growth, salt stress responses and hyponastic behavior, including changes in speed of hyponastic movements. Strikingly, Cluh(+/-) heterozygous knockout mice also displayed altered locomotive movements, traveling for shorter distances and had slower average and maximum speeds in the open field test. These observations indicate that homologous mitochondrial genes may play similar roles and affect homologous functions in both plants and animals.},
  language  = {en}
}
@article{WitzelAbuRishaAlbersetal.2020,
  author    = {Witzel, Katja and Abu Risha, Marua and Albers, Philip and B{\"o}rnke, Frederik and Hanschen, Franziska S.},
  title     = {Corrigendum : Identification and characterization of three epithiospecifier protein isoforms in Brassica oleracea / Witzel, Katja; Abu Risha, Marua; Albers, Philip; B{\"o}rnke, Frederike; Hanschen, Franziska S. - Lausanne: Frontiers Media, 2019. - Frontiers in plant science : FPLS. - 10 (2019) art. 1552. - doi: 10.3389/fpls.2019.01552},
  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.2020.00523},
  pages     = {2},
  year      = {2020},
  language  = {en}
}
@article{SchornSalmanCarvalhoLittmannetal.2019,
  author    = {Schorn, Sina and Salman-Carvalho, Verena and Littmann, Sten and Ionescu, Danny and Grossart, Hans-Peter and Cypionka, Heribert},
  title     = {Cell architecture of the giant sulfur bacterium achromatium oxaliferum},
  series = {FEMS Microbiology Ecology},
  volume    = {96},
  journal   = {FEMS Microbiology Ecology},
  number    = {2},
  publisher = {Oxford University Press},
  address   = {Oxford},
  issn      = {1574-6941},
  doi       = {10.1093/femsec/fiz200},
  pages     = {1 -- 8},
  year      = {2019},
  abstract  = {Achromatium oxaliferum is a large sulfur bacterium easily recognized by large intracellular calcium carbonate bodies. Although these bodies often fill major parts of the cells' volume, their role and specific intracellular location are unclear. In this study, we used various microscopy and staining techniques to identify the cell compartment harboring the calcium carbonate bodies. We observed that Achromatium cells often lost their calcium carbonate bodies, either naturally or induced by treatments with diluted acids, ethanol, sodium bicarbonate and UV radiation which did not visibly affect the overall shape and motility of the cells (except for UV radiation). The water-soluble fluorescent dye fluorescein easily diffused into empty cavities remaining after calcium carbonate loss. Membranes (stained with Nile Red) formed a network stretching throughout the cell and surrounding empty or filled calcium carbonate cavities. The cytoplasm (stained with FITC and SYBR Green for nucleic acids) appeared highly condensed and showed spots of dissolved Ca2+ (stained with Fura-2). From our observations, we conclude that the calcium carbonate bodies are located in the periplasm, in extra-cytoplasmic pockets of the cytoplasmic membrane and are thus kept separate from the cell's cytoplasm. This periplasmic localization of the carbonate bodies might explain their dynamic formation and release upon environmental changes.},
  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{LeinsGrimmDrechsler2022,
  author    = {Leins, Johannes A. and Grimm, Volker and Drechsler, Martin},
  title     = {Large-scale PVA modeling of insects in cultivated grasslands},
  series = {Ecology and evolution},
  volume    = {12},
  journal   = {Ecology and evolution},
  number    = {7},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.9063},
  pages     = {17},
  year      = {2022},
  abstract  = {In many species, dispersal is decisive for survival in a changing climate. Simulation models for population dynamics under climate change thus need to account for this factor. Moreover, large numbers of species inhabiting agricultural landscapes are subject to disturbances induced by human land use. We included dispersal in the HiLEG model that we previously developed to study the interaction between climate change and agricultural land use in single populations. Here, the model was parameterized for the large marsh grasshopper (LMG) in cultivated grasslands of North Germany to analyze (1) the species development and dispersal success depending on the severity of climate change in subregions, (2) the additional effect of grassland cover on dispersal success, and (3) the role of dispersal in compensating for detrimental grassland mowing. Our model simulated population dynamics in 60-year periods (2020-2079) on a fine temporal (daily) and high spatial (250 x 250 m(2)) scale in 107 subregions, altogether encompassing a range of different grassland cover, climate change projections, and mowing schedules. We show that climate change alone would allow the LMG to thrive and expand, while grassland cover played a minor role. Some mowing schedules that were harmful to the LMG nevertheless allowed the species to moderately expand its range. Especially under minor climate change, in many subregions dispersal allowed for mowing early in the year, which is economically beneficial for farmers. More severe climate change could facilitate LMG expansion to uninhabited regions but would require suitable mowing schedules along the path. These insights can be transferred to other species, given that the LMG is considered a representative of grassland communities. For more specific predictions on the dynamics of other species affected by climate change and land use, the publicly available HiLEG model can be easily adapted to the characteristics of their life cycle.},
  language  = {en}
}
@article{GhafarianWielandNendel2022,
  author    = {Ghafarian, Fatemeh and Wieland, Ralf and Nendel, Claas},
  title     = {Estimating the Evaporative Cooling Effect of Irrigation within and above Soybean Canopy},
  series = {Water},
  volume    = {14},
  journal   = {Water},
  number    = {3},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2073-4441},
  doi       = {10.3390/w14030319},
  pages     = {16},
  year      = {2022},
  abstract  = {Vegetation with an adequate supply of water might contribute to cooling the land surface around it through the latent heat flux of transpiration. This study investigates the potential estimation of evaporative cooling at plot scale, using soybean as example. Some of the plants' physiological parameters were monitored and sampled at weekly intervals. A physics-based model was then applied to estimate the irrigation-induced cooling effect within and above the canopy during the middle and late season of the soybean growth period. We then examined the results of the temperature changes at a temporal resolution of ten minutes between every two irrigation rounds. During the middle and late season of growth, the cooling effects caused by evapotranspiration within and above the canopy were, on average, 4.4 K and 2.9 K, respectively. We used quality indicators such as R-squared (R-2) and mean absolute error (MAE) to evaluate the performance of the model simulation. The performance of the model in this study was better above the canopy (R-2 = 0.98, MAE = 0.3 K) than below (R-2 = 0.87, MAE = 0.9 K) due to the predefined thermodynamic condition used to estimate evaporative cooling. Moreover, the study revealed that canopy cooling contributes to mitigating heat stress conditions during the middle and late seasons of crop growth.},
  language  = {en}
}
@article{MillesDammhahnJeltschetal.2022,
  author    = {Milles, Alexander Benedikt and Dammhahn, Melanie and Jeltsch, Florian and Schl{\"a}gel, Ulrike and Grimm, Volker},
  title     = {Fluctuations in density-dependent selection drive the evolution of a pace-of-life syndrome within and between populations},
  series = {The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences},
  volume    = {199},
  journal   = {The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences},
  number    = {4},
  publisher = {Univ. of Chicago Press},
  address   = {Chicago},
  issn      = {0003-0147},
  doi       = {10.1086/718473},
  pages     = {E124 -- E139},
  year      = {2022},
  abstract  = {The pace-of-life syndrome (POLS) hypothesis posits that suites of traits are correlated along a slow-fast continuum owing to life history trade-offs. Despite widespread adoption, environmental conditions driving the emergence of POLS remain unclear. A recently proposed conceptual framework of POLS suggests that a slow-fast continuum should align to fluctuations in density-dependent selection. We tested three key predictions made by this framework with an ecoevolutionary agent-based population model. Selection acted on responsiveness (behavioral trait) to interpatch resource differences and the reproductive investment threshold (life history trait). Across environments with density fluctuations of different magnitudes, we observed the emergence of a common axis of trait covariation between and within populations (i.e., the evolution of a POLS). Slow-type (fast-type) populations with high (low) responsiveness and low (high) reproductive investment threshold were selected at high (low) population densities and less (more) intense and frequent density fluctuations. In support of the predictions, fast-type populations contained a higher degree of variation in traits and were associated with higher intrinsic reproductive rate (r(0)) and higher sensitivity to intraspecific competition (gamma), pointing to a universal trade-off. While our findings support that POLS aligns with density-dependent selection, we discuss possible mechanisms that may lead to alternative evolutionary pathways.},
  language  = {en}
}
@article{MasigolKhodaparastMostowfizadehGhalamfarsaetal.2020,
  author    = {Masigol, Hossein and Khodaparast, Seyed Akbar and Mostowfizadeh-Ghalamfarsa, Reza and Rojas-Jimenez, Keilor and Woodhouse, Jason Nicholas and Neubauer, Darshan and Grossart, Hans-Peter},
  title     = {Taxonomical and functional diversity of Saprolegniales in Anzali lagoon, Iran},
  series = {Aquatic Ecology},
  volume    = {54},
  journal   = {Aquatic Ecology},
  number    = {1},
  publisher = {Springer Science},
  address   = {Dordrecht},
  issn      = {1573-5125},
  doi       = {10.1007/s10452-019-09745-w},
  pages     = {323 -- 336},
  year      = {2020},
  abstract  = {Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran, as well as Achlya strains, which were closely related to A. bisexualis, A. debaryana and A. intricata. Evaluation of the ligno-, cellulo- and chitinolytic activities was performed using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn, and nearly 50\% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar, but functionally different aquatic fungi in freshwater ecosystems.},
  language  = {en}
}
@article{StankeWengerBieretal.2022,
  author    = {Stanke, Sandra and Wenger, Christian and Bier, Frank Fabian and H{\"o}lzel, Ralph},
  title     = {AC electrokinetic immobilization of influenza virus},
  series = {Electrophoresis : microfluids \& proteomics},
  volume    = {43},
  journal   = {Electrophoresis : microfluids \& proteomics},
  number    = {12},
  publisher = {Wiley-Blackwell},
  address   = {Weinheim},
  issn      = {0173-0835},
  doi       = {10.1002/elps.202100324},
  pages     = {1309 -- 1321},
  year      = {2022},
  abstract  = {The use of alternating current (AC) electrokinetic forces, like dielectrophoresis and AC electroosmosis, as a simple and fast method to immobilize sub-micrometer objects onto nanoelectrode arrays is presented. Due to its medical relevance, the influenza virus is chosen as a model organism. One of the outstanding features is that the immobilization of viral material to the electrodes can be achieved permanently, allowing subsequent handling independently from the electrical setup. Thus, by using merely electric fields, we demonstrate that the need of prior chemical surface modification could become obsolete. The accumulation of viral material over time is observed by fluorescence microscopy. The influences of side effects like electrothermal fluid flow, causing a fluid motion above the electrodes and causing an intensity gradient within the electrode array, are discussed. Due to the improved resolution by combining fluorescence microscopy with deconvolution, it is shown that the viral material is mainly drawn to the electrode edge and to a lesser extent to the electrode surface. Finally, areas of application for this functionalization technique are presented.},
  language  = {en}
}
@article{TongNankarLiuetal.2022,
  author    = {Tong, Hao and Nankar, Amol N. and Liu, Jintao and Todorova, Velichka and Ganeva, Daniela and Grozeva, Stanislava and Tringovska, Ivanka and Pasev, Gancho and Radeva-Ivanova, Vesela and Gechev, Tsanko and Kostova, Dimitrina and Nikoloski, Zoran},
  title     = {Genomic prediction of morphometric and colorimetric traits in Solanaceous fruits},
  series = {Horticulture research},
  volume    = {9},
  journal   = {Horticulture research},
  publisher = {Oxford Univ. Press},
  address   = {Cary},
  issn      = {2052-7276},
  doi       = {10.1093/hr/uhac072},
  pages     = {11},
  year      = {2022},
  abstract  = {Selection of high-performance lines with respect to traits of interest is a key step in plant breeding. Genomic prediction allows to determine the genomic estimated breeding values of unseen lines for trait of interest using genetic markers, e.g. single-nucleotide polymorphisms (SNPs), and machine learning approaches, which can therefore shorten breeding cycles, referring to genomic selection (GS). Here, we applied GS approaches in two populations of Solanaceous crops, i.e. tomato and pepper, to predict morphometric and colorimetric traits. The traits were measured by using scoring-based conventional descriptors (CDs) as well as by Tomato Analyzer (TA) tool using the longitudinally and latitudinally cut fruit images. The GS performance was assessed in cross-validations of classification-based and regression-based machine learning models for CD and TA traits, respectively. The results showed the usage of TA traits and tag SNPs provide a powerful combination to predict morphology and color-related traits of Solanaceous fruits. The highest predictability of 0.89 was achieved for fruit width in pepper, with an average predictability of 0.69 over all traits. The multi-trait GS models are of slightly better predictability than single-trait models for some colorimetric traits in pepper. While model validation performs poorly on wild tomato accessions, the usage as many as one accession per wild species in the training set can increase the transferability of models to unseen populations for some traits (e.g. fruit shape for which predictability in unseen scenario increased from zero to 0.6). Overall, GS approaches can assist the selection of high-performance Solanaceous fruits in crop breeding.},
  language  = {en}
}
@article{MoradianRochLendleinetal.2020,
  author    = {Moradian, Hanieh and Roch, Toralf and Lendlein, Andreas and Gossen, Manfred},
  title     = {mRNA transfection-induced activation of primary human monocytes and macrophages},
  series = {Scientific reports},
  volume    = {10},
  journal   = {Scientific reports},
  number    = {1},
  publisher = {Springer Nature},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-020-60506-4},
  pages     = {1 -- 15},
  year      = {2020},
  abstract  = {Monocytes and macrophages are key players in maintaining immune homeostasis. Identifying strategies to manipulate their functions via gene delivery is thus of great interest for immunological research and biomedical applications. We set out to establish conditions for mRNA transfection in hard-to-transfect primary human monocytes and monocyte-derived macrophages due to the great potential of gene expression from in vitro transcribed mRNA for modulating cell phenotypes. mRNA doses, nucleotide modifications, and different carriers were systematically explored in order to optimize high mRNA transfer rates while minimizing cell stress and immune activation. We selected three commercially available mRNA transfection reagents including liposome and polymer-based formulations, covering different application spectra. Our results demonstrate that liposomal reagents can particularly combine high gene transfer rates with only moderate immune cell activation. For the latter, use of specific nucleotide modifications proved essential. In addition to improving efficacy of gene transfer, our findings address discrete aspects of innate immune activation using cytokine and surface marker expression, as well as cell viability as key readouts to judge overall transfection efficiency. The impact of this study goes beyond optimizing transfection conditions for immune cells, by providing a framework for assessing new gene carrier systems for monocyte and macrophage, tailored to specific applications.},
  language  = {en}
}
@article{ObbardShiRobertsetal.2020,
  author    = {Obbard, Darren J. and Shi, Mang and Roberts, Katherine E. and Longdon, Ben and Dennis, Alice B.},
  title     = {A new lineage of segmented RNA viruses infecting animals},
  series = {Virus Evolution},
  volume    = {6},
  journal   = {Virus Evolution},
  number    = {1},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {2057-1577},
  doi       = {10.1093/ve/vez061},
  pages     = {1 -- 10},
  year      = {2020},
  abstract  = {Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called 'dark' virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose 'dark' virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.},
  language  = {en}
}
@article{ZwaagHorstBlaženovićetal.2020,
  author    = {Zwaag, Jelle and Horst, Rob ter and Blaženović, Ivana and St{\"o}ßel, Daniel and Ratter, Jacqueline and Worseck, Josephine M. and Schauer, Nicolas and Stienstra, Rinke and Netea, Mihai G. and Jahn, Dieter and Pickkers, Peter and Kox, Matthijs},
  title     = {Involvement of lactate and pyruvate in the anti-inflammatory effects exerted by voluntary activation of the sympathetic nervous system},
  series = {Metabolites},
  volume    = {10},
  journal   = {Metabolites},
  number    = {4},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2218-1989},
  doi       = {10.3390/metabo10040148},
  pages     = {1 -- 18},
  year      = {2020},
  abstract  = {We recently demonstrated that the sympathetic nervous system can be voluntarily activated following a training program consisting of cold exposure, breathing exercises, and meditation. This resulted in profound attenuation of the systemic inflammatory response elicited by lipopolysaccharide (LPS) administration. Herein, we assessed whether this training program affects the plasma metabolome and if these changes are linked to the immunomodulatory effects observed. A total of 224 metabolites were identified in plasma obtained from 24 healthy male volunteers at six timepoints, of which 98 were significantly altered following LPS administration. Effects of the training program were most prominent shortly after initiation of the acquired breathing exercises but prior to LPS administration, and point towards increased activation of the Cori cycle. Elevated concentrations of lactate and pyruvate in trained individuals correlated with enhanced levels of anti-inflammatory interleukin (IL)-10. In vitro validation experiments revealed that co-incubation with lactate and pyruvate enhances IL-10 production and attenuates the release of pro-inflammatory IL-1 beta and IL-6 by LPS-stimulated leukocytes. Our results demonstrate that practicing the breathing exercises acquired during the training program results in increased activity of the Cori cycle. Furthermore, this work uncovers an important role of lactate and pyruvate in the anti-inflammatory phenotype observed in trained subjects.},
  language  = {en}
}
@article{AmenNagelHedtetal.2020,
  author    = {Amen, Rahma and Nagel, Rebecca and Hedt, Maximilian and Kirschbaum, Frank and Tiedemann, Ralph},
  title     = {Morphological differentiation in African weakly electric fish (genus Campylomormyrus) relates to substrate preferences},
  series = {Evolutionary Ecology},
  volume    = {34},
  journal   = {Evolutionary Ecology},
  number    = {3},
  publisher = {Springer Science},
  address   = {Dordrecht},
  issn      = {0269-7653},
  doi       = {10.1007/s10682-020-10043-3},
  pages     = {427 -- 437},
  year      = {2020},
  abstract  = {Under an ecological speciation scenario, the radiation of African weakly electric fish (genus Campylomormyrus) is caused by an adaptation to different food sources, associated with diversification of the electric organ discharge (EOD). This study experimentally investigates a phenotype-environment correlation to further support this scenario. Our behavioural experiments showed that three sympatric Campylomormyrus species with significantly divergent snout morphology differentially react to variation in substrate structure. While the short snout species (C. tamandua) exhibits preference to sandy substrate, the long snout species (C. rhynchophorus) significantly prefers a stone substrate for feeding. A third species with intermediate snout size (C. compressirostris) does not exhibit any substrate preference. This preference is matched with the observation that long-snouted specimens probe deeper into the stone substrate, presumably enabling them to reach prey more distant to the substrate surface. These findings suggest that the diverse feeding apparatus in the genus Campylomormyrus may have evolved in adaptation to specific microhabitats, i.e., substrate structures where these fish forage. Whether the parallel divergence in EOD is functionally related to this adaptation or solely serves as a prezygotic isolation mechanism remains to be elucidated.},
  language  = {en}
}
@article{SabrowskiDreymannMoelleretal.2022,
  author    = {Sabrowski, Wiebke and Dreymann, Nico and M{\"o}ller, Anja and Czepluch, Denise and Albani, Patricia P. and Theodoridis, Dimitrios and Menger, Marcus M.},
  title     = {The use of high-affinity polyhistidine binders as masking probes for the selection of an NDM-1 specific aptamer},
  series = {Scientific reports},
  volume    = {12},
  journal   = {Scientific reports},
  number    = {1},
  publisher = {Macmillan Publishers Limited, part of Springer Nature},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-022-12062-2},
  pages     = {11},
  year      = {2022},
  abstract  = {The emergence of carbapenemase-producing multi-drug resistant Enterobacteriaceae poses a dramatic, world-wide health risk. Limited treatment options and a lack of easy-to-use methods for the detection of infections with multi-drug resistant bacteria leave the health-care system with a fast-growing challenge. Aptamers are single stranded DNA or RNA molecules that bind to their targets with high affinity and specificity and can therefore serve as outstanding detection probes. However, an effective aptamer selection process is often hampered by non-specific binding. When selections are carried out against recombinant proteins, purification tags (e.g. polyhistidine) serve as attractive side targets, which may impede protein target binding. In this study, aptamer selection was carried out against N-terminally hexa-histidine tagged New Delhi metallo-ss-lactamase 1. After 14 selection rounds binding to polyhistidine was detected rather than to New Delhi metallo-ss-lactamase 1. Hence, the selection strategy was changed. As one aptamer candidate showed remarkable binding affinity to polyhistidine, it was used as a masking probe and selection was restarted from selection round 10. Finally, after three consecutive selection rounds, an aptamer with specific binding properties to New Delhi metallo-ss-lactamase 1 was identified. This aptamer may serve as a much-needed detection probe for New Delhi metallo-ss-lactamase 1 expressing Enterobacteriaceae.},
  language  = {en}
}
@article{MorenoRomeroProbstTrindadeetal.2020,
  author    = {Moreno-Romero, Jordi and Probst, Aline V. and Trindade, In{\^e}s and Kalyanikrishna, and Engelhorn, Julia and Farrona, Sara},
  title     = {Looking At the Past and Heading to the Future},
  series = {Frontiers in Plant Science},
  volume    = {10},
  journal   = {Frontiers in Plant Science},
  number    = {1795},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {1664-462X},
  doi       = {10.3389/fpls.2019.01795},
  pages     = {1 -- 12},
  year      = {2020},
  abstract  = {In June 2019, more than a hundred plant researchers met in Cologne, Germany, for the 6th European Workshop on Plant Chromatin (EWPC). This conference brought together a highly dynamic community of researchers with the common aim to understand how chromatin organization controls gene expression, development, and plant responses to the environment. New evidence showing how epigenetic states are set, perpetuated, and inherited were presented, and novel data related to the three-dimensional organization of chromatin within the nucleus were discussed. At the level of the nucleosome, its composition by different histone variants and their specialized histone deposition complexes were addressed as well as the mechanisms involved in histone post-translational modifications and their role in gene expression. The keynote lecture on plant DNA methylation by Julie Law (SALK Institute) and the tribute session to Lars Hennig, honoring the memory of one of the founders of the EWPC who contributed to promote the plant chromatin and epigenetic field in Europe, added a very special note to this gathering. In this perspective article we summarize some of the most outstanding data and advances on plant chromatin research presented at this workshop.},
  language  = {en}
}
@article{CaoTianAndreevetal.2020,
  author    = {Cao, Xianyong and Tian, Fang and Andreev, Andrei and Anderson, Patricia M. and Lozhkin, Anatoly V. and Bezrukova, Elena and Ni, Jian and Rudaya, Natalia and Stobbe, Astrid and Wieczorek, Mareike and Herzschuh, Ulrike},
  title     = {A taxonomically harmonized and temporally standardized fossil pollen dataset from Siberia covering the last 40 kyr},
  series = {Earth System Science Data},
  volume    = {12},
  journal   = {Earth System Science Data},
  number    = {1},
  publisher = {Copernics Publications},
  address   = {Katlenburg-Lindau},
  issn      = {1866-3508},
  doi       = {10.5194/essd-12-119-2020},
  pages     = {119 -- 135},
  year      = {2020},
  abstract  = {Pollen records from Siberia are mostly absent in global or Northern Hemisphere synthesis works. Here we present a taxonomically harmonized and temporally standardized pollen dataset that was synthesized using 173 palynological records from Siberia and adjacent areas (northeastern Asia, 42-75 degrees N, 50-180 degrees E). Pollen data were taxonomically harmonized, i.e. the original 437 taxa were assigned to 106 combined pollen taxa. Age-depth models for all records were revised by applying a constant Bayesian age-depth modelling routine. The pollen dataset is available as count data and percentage data in a table format (taxa vs. samples), with age information for each sample. The dataset has relatively few sites covering the last glacial period between 40 and 11.5 ka (calibrated thousands of years before 1950 CE) particularly from the central and western part of the study area. In the Holocene period, the dataset has many sites from most of the area, with the exception of the central part of Siberia. Of the 173 pollen records, 81 \% of pollen counts were downloaded from open databases (GPD, EPD, PANGAEA) and 10 \% were contributions by the original data gatherers, while a few were digitized from publications. Most of the pollen records originate from peatlands (48 \%) and lake sediments (33 \%). Most of the records (83 \%) have >= 3 dates, allowing the establishment of reliable chronologies. The dataset can be used for various purposes, including pollen data mapping (example maps for Larix at selected time slices are shown) as well as quantitative climate and vegetation reconstructions. The datasets for pollen counts and pollen percentages are available at https://doi.org/10.1594/PANGAEA.898616 (Cao et al., 2019a), also including the site information, data source, original publication, dating data, and the plant functional type for each pollen taxa.},
  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{FichtnerOlasFeiletal.2020,
  author    = {Fichtner, Franziska and Olas, Justyna Jadwiga and Feil, Regina and Watanabe, Mutsumi and Krause, Ursula and Hoefgen, Rainer and Stitt, Mark and Lunn, John Edward},
  title     = {Functional features of Trehalose-6-Phosphate Synthase 1},
  series = {The Plant Cell},
  volume    = {32},
  journal   = {The Plant Cell},
  number    = {6},
  publisher = {Oxford University Press},
  address   = {Oxford},
  issn      = {0032-0781},
  doi       = {10.1105/tpc.19.00837},
  pages     = {1949 -- 1972},
  year      = {2020},
  abstract  = {Tre6P synthesis by TPS1 is essential for embryogenesis and postembryonic growth in Arabidopsis, and appropriate Suc signaling by Tre6P is dependent on the noncatalytic domains of TPS1. In Arabidopsis (Arabidopsis thaliana), TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) catalyzes the synthesis of the sucrose-signaling metabolite trehalose 6-phosphate (Tre6P) and is essential for embryogenesis and normal postembryonic growth and development. To understand its molecular functions, we transformed the embryo-lethal tps1-1 null mutant with various forms of TPS1 and with a heterologous TPS (OtsA) from Escherichia coli, under the control of the TPS1 promoter, and tested for complementation. TPS1 protein localized predominantly in the phloem-loading zone and guard cells in leaves, root vasculature, and shoot apical meristem, implicating it in both local and systemic signaling of Suc status. The protein is targeted mainly to the nucleus. Restoring Tre6P synthesis was both necessary and sufficient to rescue the tps1-1 mutant through embryogenesis. However, postembryonic growth and the sucrose-Tre6P relationship were disrupted in some complementation lines. A point mutation (A119W) in the catalytic domain or truncating the C-terminal domain of TPS1 severely compromised growth. Despite having high Tre6P levels, these plants never flowered, possibly because Tre6P signaling was disrupted by two unidentified disaccharide-monophosphates that appeared in these plants. The noncatalytic domains of TPS1 ensure its targeting to the correct subcellular compartment and its catalytic fidelity and are required for appropriate signaling of Suc status by Tre6P.},
  language  = {en}
}
@article{WeiseAugeBaessleretal.2020,
  author    = {Weise, Hanna and Auge, Harald and Baessler, Cornelia and B{\"a}rlund, Ilona and Bennett, Elena M. and Berger, Uta and Bohn, Friedrich and Bonn, Aletta and Borchardt, Dietrich and Brand, Fridolin and Jeltsch, Florian and Joshi, Jasmin Radha and Grimm, Volker},
  title     = {Resilience trinity},
  series = {Oikos},
  volume    = {129},
  journal   = {Oikos},
  number    = {4},
  publisher = {Wiley-Blackwell},
  address   = {Oxford},
  issn      = {0030-1299},
  doi       = {10.1111/oik.07213},
  pages     = {445 -- 456},
  year      = {2020},
  abstract  = {Ensuring ecosystem resilience is an intuitive approach to safeguard the functioning of ecosystems and hence the future provisioning of ecosystem services (ES). However, resilience is a multi-faceted concept that is difficult to operationalize. Focusing on resilience mechanisms, such as diversity, network architectures or adaptive capacity, has recently been suggested as means to operationalize resilience. Still, the focus on mechanisms is not specific enough. We suggest a conceptual framework, resilience trinity, to facilitate management based on resilience mechanisms in three distinctive decision contexts and time-horizons: 1) reactive, when there is an imminent threat to ES resilience and a high pressure to act, 2) adjustive, when the threat is known in general but there is still time to adapt management and 3) provident, when time horizons are very long and the nature of the threats is uncertain, leading to a low willingness to act. Resilience has different interpretations and implications at these different time horizons, which also prevail in different disciplines. Social ecology, ecology and engineering are often implicitly focussing on provident, adjustive or reactive resilience, respectively, but these different notions of resilience and their corresponding social, ecological and economic tradeoffs need to be reconciled. Otherwise, we keep risking unintended consequences of reactive actions, or shying away from provident action because of uncertainties that cannot be reduced. The suggested trinity of time horizons and their decision contexts could help ensuring that longer-term management actions are not missed while urgent threats to ES are given priority.},
  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{HaueisStechKubick2022,
  author    = {Haueis, Lisa and Stech, Marlitt and Kubick, Stefan},
  title     = {A Cell-free Expression Pipeline for the Generation and Functional Characterization of Nanobodies},
  series = {Frontiers in Bioengineering and Biotechnology},
  volume    = {10},
  journal   = {Frontiers in Bioengineering and Biotechnology},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {2296-4185},
  doi       = {10.3389/fbioe.2022.896763},
  pages     = {11},
  year      = {2022},
  abstract  = {Cell-free systems are well-established platforms for the rapid synthesis, screening, engineering and modification of all kinds of recombinant proteins ranging from membrane proteins to soluble proteins, enzymes and even toxins. Also within the antibody field the cell-free technology has gained considerable attention with respect to the clinical research pipeline including antibody discovery and production. Besides the classical full-length monoclonal antibodies (mAbs), so-called "nanobodies" (Nbs) have come into focus. A Nb is the smallest naturally-derived functional antibody fragment known and represents the variable domain (VHH, similar to 15 kDa) of a camelid heavy-chain-only antibody (HCAb). Based on their nanoscale and their special structure, Nbs display striking advantages concerning their production, but also their characteristics as binders, such as high stability, diversity, improved tissue penetration and reaching of cavity-like epitopes. The classical way to produce Nbs depends on the use of living cells as production host. Though cell-based production is well-established, it is still time-consuming, laborious and hardly amenable for high-throughput applications. Here, we present for the first time to our knowledge the synthesis of functional Nbs in a standardized mammalian cell-free system based on Chinese hamster ovary (CHO) cell lysates. Cell-free reactions were shown to be time-efficient and easy-to-handle allowing for the "on demand" synthesis of Nbs. Taken together, we complement available methods and demonstrate a promising new system for Nb selection and validation.},
  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{AnderssonScharnweberEkloev2022,
  author    = {Andersson, Matilda L. and Scharnweber, Inga Kristin and Ekl{\"o}v, Peter},
  title     = {The interaction between metabolic rate, habitat choice, and resource use in a polymorphic freshwater species},
  series = {Ecology and evolution},
  volume    = {12},
  journal   = {Ecology and evolution},
  number    = {8},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.9129},
  pages     = {12},
  year      = {2022},
  abstract  = {Resource polymorphism is common across taxa and can result in alternate ecotypes with specific morphologies, feeding modes, and behaviors that increase performance in a specific habitat. This can result in high intraspecific variation in the expression of specific traits and the extent to which these traits are correlated within a single population. Although metabolic rate influences resource acquisition and the overall pace of life of individuals it is not clear how metabolic rate interacts with the larger suite of traits to ultimately determine individual fitness. We examined the relationship between metabolic rates and the major differences (habitat use, morphology, and resource use) between littoral and pelagic ecotypes of European perch (Perca fluviatilis) from a single lake in Central Sweden. Standard metabolic rate (SMR) was significantly higher in pelagic perch but did not correlate with resource use or morphology. Maximum metabolic rate (MMR) was not correlated with any of our explanatory variables or with SMR. Aerobic scope (AS) showed the same pattern as SMR, differing across habitats, but contrary to expectations, was lower in pelagic perch. This study helps to establish a framework for future experiments further exploring the drivers of intraspecific differences in metabolism. In addition, since metabolic rates scale with temperature and determine predator energy requirements, our observed differences in SMR across habitats will help determine ecotype-specific vulnerabilities to climate change and differences in top-down predation pressure across habitats.},
  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{SchefflerHermanussen2022,
  author    = {Scheffler, Christiane and Hermanussen, Michael},
  title     = {Reply to the letter titled: "Pathologizing normal height or identifying chronic malnutrition: Public health concerns of calling stunting normal" / by Nafis Faizi, Mohd Yasir Zubair and Fazeelah Tasleem'. - New York, NY [u.a.] : Wiley Interscience. - 2022. - (American Journal of Human Biology : the Official Journal of the Human Biology Council, 16 Feb 2022. - 34(2022) 5 ). - https://doi.org/10.1002/ajhb.23735},
  series = {American journal of human biology : the official journal of the Human Biology Association},
  volume    = {34},
  journal   = {American journal of human biology : the official journal of the Human Biology Association},
  number    = {5},
  publisher = {Wiley Interscience},
  address   = {New York, NY [u.a.]},
  issn      = {1520-6300},
  doi       = {10.1002/ajhb.23741},
  pages     = {2},
  year      = {2022},
  language  = {en}
}
@article{BergMohnickeNendel2022,
  author    = {Berg-Mohnicke, Michael and Nendel, Claas},
  title     = {A case for object capabilities as the foundation of a distributed environmental model and simulation infrastructure},
  series = {Environmental modelling \& software with environment data news},
  volume    = {156},
  journal   = {Environmental modelling \& software with environment data news},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {1364-8152},
  doi       = {10.1016/j.envsoft.2022.105471},
  pages     = {12},
  year      = {2022},
  abstract  = {With the advent of increasingly powerful computational architectures, scientists use these possibilities to create simulations of ever-increasing size and complexity. Large-scale simulations of environmental systems require huge amounts of resources. Managing these in an operational way becomes increasingly complex and difficult to handle for individual scientists. State-of-the-art simulation infrastructures usually provide the necessary re-sources in a centralised setup, which often results in an all-or-nothing choice for the user. Here, we outline an alternative approach to handling this complexity, while rendering the use of high-performance hardware and large datasets still possible. It retains a number of desirable properties: (i) a decentralised structure, (ii) easy sharing of resources to promote collaboration and (iii) secure access to everything, including natural delegation of authority across levels and system boundaries. We show that the object capability paradigm will cover these issues, and present the first steps towards developing a simulation infrastructure based on these principles.},
  language  = {en}
}
@article{CabukUenlue2022,
  author    = {{\c{C}}abuk, Uğur and {\"U}nl{\"u}, Ercan Sel{\c{c}}uk},
  title     = {A combined de novo assembly approach increases the quality of prokaryotic draft genomes},
  series = {Folia microbiologica : international journal for general, environmental and applied microbiology, and immunology},
  volume    = {67},
  journal   = {Folia microbiologica : international journal for general, environmental and applied microbiology, and immunology},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {0015-5632},
  doi       = {10.1007/s12223-022-00980-7},
  pages     = {801 -- 810},
  year      = {2022},
  abstract  = {Next-generation sequencing methods provide comprehensive data for the analysis of structural and functional analysis of the genome. The draft genomes with low contig number and high N50 value can give insight into the structure of the genome as well as provide information on the annotation of the genome. In this study, we designed a pipeline that can be used to assemble prokaryotic draft genomes with low number of contigs and high N50 value. We aimed to use combination of two de novo assembly tools (SPAdes and IDBA-Hybrid) and evaluate the impact of this approach on the quality metrics of the assemblies. The followed pipeline was tested with the raw sequence data with short reads (< 300) for a total of 10 species from four different genera. To obtain the final draft genomes, we firstly assembled the sequences using SPAdes to find closely related organism using the extracted 16 s rRNA from it. IDBA-Hybrid assembler was used to obtain the second assembly data using the closely related organism genome. SPAdes assembler tool was implemented using the second assembly, produced by IDBA-hybrid as a hint. The results were evaluated using QUAST and BUSCO. The pipeline was successful for the reduction of the contig numbers and increasing the N50 statistical values in the draft genome assemblies while preserving the coverage of the draft genomes.},
  language  = {en}
}
@article{OlimiKusstatscherWicaksonoetal.2022,
  author    = {Olimi, Expedito and Kusstatscher, Peter and Wicaksono, Wisnu Adi and Abdelfattah, Ahmed and Cernava, Tomislav and Berg, Gabriele},
  title     = {Insights into the microbiome assembly during different growth stages and storage of strawberry plants},
  series = {Environmental microbiome},
  volume    = {17},
  journal   = {Environmental microbiome},
  number    = {1},
  publisher = {BMC},
  address   = {London},
  issn      = {2524-6372},
  doi       = {10.1186/s40793-022-00415-3},
  pages     = {15},
  year      = {2022},
  abstract  = {Background: Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growth stages and storage using amplicon sequencing, qPCR, and microscopic approaches. <br /> Results: Strawberry plants carried a highly diverse microbiome, therein the bacterial families Sphingomonadaceae (25\%), Pseudomonadaceae (17\%), and Burkholderiaceae (11\%); and the fungal family Mycosphaerella (45\%) were most abundant. All compartments were colonized by high number of bacteria and fungi (10(7)-10(10) marker gene copies per g fresh weight), and were characterized by high microbial diversity (6049 and 1501 ASVs); both were higher for the belowground samples than in the phyllosphere. Compartment type was the main driver of microbial diversity, structure, and abundance (bacterial: 45\%; fungal: 61\%) when compared to the cultivar (1.6\%; 2.2\%). Microbiome assembly was strongly divided for belowground habitats and the phyllosphere; only a low proportion of the microbiome was transferred from soil via the rhizosphere to the phyllosphere. During fruit development, we observed the highest rates of microbial transfer from leaves and flowers to ripe fruits, where most of the bacteria occured inside the pulp. In postharvest fruits, microbial diversity decreased while the overall abundance increased. Developing postharvest decay caused by Botrytis cinerea decreased the diversity as well, and induced a reduction of potentially beneficial taxa. <br /> Conclusion: Our findings provide insights into microbiome assembly in strawberry plants and highlight the importance of microbe transfer during fruit development and storage with potential implications for food health and safety.},
  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{WeyrichGuerreroAltamiranoYasaretal.2022,
  author    = {Weyrich, Alexandra and Guerrero-Altamirano, Tania P. and Yasar, Selma and Czirjak, G{\´a}bor-{\´A}rp{\´a}d and Wachter, Bettina and Fickel, J{\"o}rns},
  title     = {First Steps towards the development of epigenetic biomarkers in female cheetahs (Acinonyx jubatus)},
  series = {Life : open access journal},
  volume    = {12},
  journal   = {Life : open access journal},
  number    = {6},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2075-1729},
  doi       = {10.3390/life12060920},
  pages     = {16},
  year      = {2022},
  abstract  = {Free-ranging cheetahs (Acinonyx jubatus) are generally healthy, whereas cheetahs under human care, such as those in zoological gardens, suffer from ill-defined infectious and degenerative pathologies. These differences are only partially explained by husbandry management programs because both groups share low genetic diversity. However, mounting evidence suggests that physiological differences between populations in different environments can be tracked down to differences in epigenetic signatures. Here, we identified differentially methylated regions (DMRs) between free-ranging cheetahs and conspecifics in zoological gardens and prospect putative links to pathways relevant to immunity, energy balance and homeostasis. Comparing epigenomic DNA methylation profiles obtained from peripheral blood mononuclear cells (PBMCs) from eight free-ranging female cheetahs from Namibia and seven female cheetahs living in zoological gardens within Europe, we identified DMRs of which 22 were hypermethylated and 23 hypomethylated. Hypermethylated regions in cheetahs under human care were located in the promoter region of a gene involved in host-pathogen interactions (KLC1) and in an intron of a transcription factor relevant for the development of pancreatic beta-cells, liver, and kidney (GLIS3). The most canonical mechanism of DNA methylation in promoter regions is assumed to repress gene transcription. Taken together, this could indicate that hypermethylation at the promoter region of KLC1 is involved in the reduced immunity in cheetahs under human care. This approach can be generalized to characterize DNA methylation profiles in larger cheetah populations under human care with a more granular longitudinal data collection, which, in the future, could be used to monitor the early onset of pathologies, and ultimately translate into the development of biomarkers with prophylactic and/or therapeutic potential.},
  language  = {en}
}
@article{LischeidWebberSommeretal.2022,
  author    = {Lischeid, Gunnar and Webber, Heidi and Sommer, Michael and Nendel, Claas and Ewert, Frank},
  title     = {Machine learning in crop yield modelling},
  series = {Agricultural and forest meteorology},
  volume    = {312},
  journal   = {Agricultural and forest meteorology},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0168-1923},
  doi       = {10.1016/j.agrformet.2021.108698},
  pages     = {23},
  year      = {2022},
  abstract  = {Provisioning a sufficient stable source of food requires sound knowledge about current and upcoming threats to agricultural production. To that end machine learning approaches were used to identify the prevailing climatic and soil hydrological drivers of spatial and temporal yield variability of four crops, comprising 40 years yield data each from 351 counties in Germany. Effects of progress in agricultural management and breeding were subtracted from the data prior the machine learning modelling by fitting smooth non-linear trends to the 95th percentiles of observed yield data. An extensive feature selection approach was followed then to identify the most relevant predictors out of a large set of candidate predictors, comprising various soil and meteorological data. Particular emphasis was placed on studying the uniqueness of identified key predictors. Random Forest and Support Vector Machine models yielded similar although not identical results, capturing between 50\% and 70\% of the spatial and temporal variance of silage maize, winter barley, winter rapeseed and winter wheat yield. Equally good performance could be achieved with different sets of predictors. Thus identification of the most reliable models could not be based on the outcome of the model study only but required expert's judgement. Relationships between drivers and response often exhibited optimum curves, especially for summer air temperature and precipitation. In contrast, soil moisture clearly proved less relevant compared to meteorological drivers. In view of the expected climate change both excess precipitation and the excess heat effect deserve more attention in breeding as well as in crop modelling.},
  language  = {en}
}
@article{AgarwalWarmtHenkeletal.2022,
  author    = {Agarwal, Saloni and Warmt, Christian and Henkel, J{\"o}rg and Schrick, Livia and Nitsche, Andreas and Bier, Frank Fabian},
  title     = {Lateral flow-based nucleic acid detection of SARS-CoV-2 using enzymatic incorporation of biotin-labeled dUTP for POCT use},
  series = {Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry, Analusis and Quimica analitica},
  volume    = {414},
  journal   = {Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry, Analusis and Quimica analitica},
  number    = {10},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {1618-2642},
  doi       = {10.1007/s00216-022-03880-4},
  pages     = {3177 -- 3186},
  year      = {2022},
  abstract  = {The degree of detrimental effects inflicted on mankind by the COVID-19 pandemic increased the need to develop ASSURED (Affordable, Sensitive, Specific, User-friendly, Rapid and Robust, Equipment-free, and Deliverable) POCT (point of care testing) to overcome the current and any future pandemics. Much effort in research and development is currently advancing the progress to overcome the diagnostic pressure built up by emerging new pathogens. LAMP (loop-mediated isothermal amplification) is a well-researched isothermal technique for specific nucleic acid amplification which can be combined with a highly sensitive immunochromatographic readout via lateral flow assays (LFA). Here we discuss LAMP-LFA robustness, sensitivity, and specificity for SARS-CoV-2 N-gene detection in cDNA and clinical swab-extracted RNA samples. The LFA readout is designed to produce highly specific results by incorporation of biotin and FITC labels to 11-dUTP and LF (loop forming forward) primer, respectively. The LAMP-LFA assay was established using cDNA for N-gene with an accuracy of 95.65\%. To validate the study, 82 SARS-CoV-2-positive RNA samples were tested. Reverse transcriptase (RT)-LAMP-LFA was positive for the RNA samples with an accuracy of 81.66\%; SARS-CoV-2 viral RNA was detected by RT-LAMP-LFA for as low as CT-33. Our method reduced the detection time to 15 min and indicates therefore that RT-LAMP in combination with LFA represents a promising nucleic acid biosensing POCT platform that combines with smartphone based semi-quantitative data analysis.},
  language  = {en}
}
@article{LaunDuffusWahlefeldetal.2022,
  author    = {Laun, Konstantin and Duffus, Benjamin R. and Wahlefeld, Stefan and Katz, Sagie and Belger, Dennis Heinz and Hildebrandt, Peter and Mroginski, Maria Andrea and Leimk{\"u}hler, Silke and Zebger, Ingo},
  title     = {Infrared spectroscopy flucidates the inhibitor binding sites in a metal-dependent formate dehydrogenase},
  series = {Chemistry - a European journal},
  journal   = {Chemistry - a European journal},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {0947-6539},
  doi       = {10.1002/chem.202201091},
  pages     = {8},
  year      = {2022},
  abstract  = {Biological carbon dioxide (CO2) reduction is an important step by which organisms form valuable energy-richer molecules required for further metabolic processes. The Mo-dependent formate dehydrogenase (FDH) from Rhodobacter capsulatus catalyzes reversible formate oxidation to CO2 at a bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor. To elucidate potential substrate binding sites relevant for the mechanism, we studied herein the interaction with the inhibitory molecules azide and cyanate, which are isoelectronic to CO2 and charged as formate. We employed infrared (IR) spectroscopy in combination with density functional theory (DFT) and inhibition kinetics. One distinct inhibitory molecule was found to bind to either a non-competitive or a competitive binding site in the secondary coordination sphere of the active site. Site-directed mutagenesis of key amino acid residues in the vicinity of the bis-MGD cofactor revealed changes in both non-competitive and competitive binding, whereby the inhibitor is in case of the latter interaction presumably bound between the cofactor and the adjacent Arg587.},
  language  = {en}
}
@article{GryzikHoangLischkeetal.2020,
  author    = {Gryzik, Stefanie and Hoang, Yen and Lischke, Timo and Mohr, Elodie and Venzke, Melanie and Kadner, Isabelle and P{\"o}tzsch, Josephine and Groth, Detlef and Radbruch, Andreas and Hutloff, Andreas and Baumgrass, Ria},
  title     = {Identification of a super-functional Tfh-like subpopulation in murine lupus by pattern perception},
  series = {eLife},
  volume    = {9},
  journal   = {eLife},
  publisher = {eLife Sciences Publications},
  address   = {Cambridge},
  issn      = {2050-084X},
  doi       = {10.7554/eLife.53226},
  pages     = {21},
  year      = {2020},
  abstract  = {Dysregulated cytokine expression by T cells plays a pivotal role in the pathogenesis of autoimmune diseases. However, the identification of the corresponding pathogenic subpopulations is a challenge, since a distinction between physiological variation and a new quality in the expression of protein markers requires combinatorial evaluation. Here, we were able to identify a super-functional follicular helper T cell (Tfh)-like subpopulation in lupus-prone NZBxW mice with our binning approach "pattern recognition of immune cells (PRI)". PRI uncovered a subpopulation of IL-21(+) IFN-gamma(high) PD-1(low) CD40L(high) CXCR5(-) Bcl-6(-) T cells specifically expanded in diseased mice. In addition, these cells express high levels of TNF-alpha and IL-2, and provide B cell help for IgG production in an IL-21 and CD40L dependent manner. This super-functional T cell subset might be a superior driver of autoimmune processes due to a polyfunctional and high cytokine expression combined with Tfh-like properties.},
  language  = {en}
}
@article{CordeiroAndradeMonteiroetal.2022,
  author    = {Cordeiro, Andre M. and Andrade, Luis and Monteiro, Catarina C. and Leitao, Guilherme and Wigge, Philip Anthony and Saibo, Nelson J. M.},
  title     = {Phytochrome-interacting factors},
  series = {Journal of experimental botany},
  volume    = {73},
  journal   = {Journal of experimental botany},
  number    = {12},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0022-0957},
  doi       = {10.1093/jxb/erac142},
  pages     = {3881 -- 3897},
  year      = {2022},
  abstract  = {Review exploring the regulation of PHYTOCHROME-INTERACTING FACTORS by light, their role in abiotic stress tolerance and plant architecture, and their influence on crop productivity. Light is a key determinant for plant growth, development, and ultimately yield. Phytochromes, red/far-red photoreceptors, play an important role in plant architecture, stress tolerance, and productivity. In the model plant Arabidopsis, it has been shown that PHYTOCHROME-INTERACTING FACTORS (PIFs; bHLH transcription factors) act as central hubs in the integration of external stimuli to regulate plant development. Recent studies have unveiled the importance of PIFs in crops. They are involved in the modulation of plant architecture and productivity through the regulation of cell division and elongation in response to different environmental cues. These studies show that different PIFs have overlapping but also distinct functions in the regulation of plant growth. Therefore, understanding the molecular mechanisms by which PIFs regulate plant development is crucial to improve crop productivity under both optimal and adverse environmental conditions. In this review, we discuss current knowledge of PIFs acting as integrators of light and other signals in different crops, with particular focus on the role of PIFs in responding to different environmental conditions and how this can be used to improve crop productivity.},
  language  = {en}
}
@article{AichnerDubbertKieletal.2022,
  author    = {Aichner, Bernhard and Dubbert, David and Kiel, Christine and Kohnert, Katrin and Ogashawara, Igor and Jechow, Andreas and Harpenslager, Sarah-Faye and H{\"o}lker, Franz and Nejstgaard, Jens Christian and Grossart, Hans-Peter and Singer, Gabriel and Wollrab, Sabine and Berger, Stella Angela},
  title     = {Spatial and seasonal patterns of water isotopes in northeastern German lakes},
  series = {Earth system science data : ESSD},
  volume    = {14},
  journal   = {Earth system science data : ESSD},
  number    = {4},
  publisher = {Copernicus},
  address   = {G{\"o}ttingen},
  issn      = {1866-3508},
  doi       = {10.5194/essd-14-1857-2022},
  pages     = {1857 -- 1867},
  year      = {2022},
  abstract  = {Water stable isotopes (delta O-18 and delta H-2) were analyzed in samples collected in lakes, associated with riverine systems in northeastern Germany, throughout 2020. The dataset (Aichner et al., 2021; https://doi.org/10.1594/PANGAEA.935633) is derived from water samples collected at (a) lake shores (sampled in March and July 2020), (b) buoys which were temporarily installed in deep parts of the lake (sampled monthly from March to October 2020), (c) multiple spatially distributed spots in four selected lakes (in September 2020), and (d) the outflow of Muggelsee (sampled biweekly from March 2020 to January 2021). At shores, water was sampled with a pipette from 40-60 cm below the water surface and directly transferred into a measurement vial, while at buoys a Limnos water sampler was used to obtain samples from 1 m below the surface. Isotope analysis was conducted at IGB Berlin, using a Picarro L2130-i cavity ring-down spectrometer, with a measurement uncertainty of < 0.15 parts per thousand (delta O-18) and < 0.0 parts per thousand (delta H-2). The data give information about the vegetation period and the full seasonal isotope amplitude in the sampled lakes and about spatial isotope variability in different branches of the associated riverine systems.},
  language  = {en}
}
@article{PrueferWengerBieretal.2022,
  author    = {Pr{\"u}fer, Mareike and Wenger, Christian and Bier, Frank Fabian and Laux, Eva-Maria and H{\"o}lzel, Ralph},
  title     = {Activity of AC electrokinetically immobilized horseradish peroxidase},
  series = {Electrophoresis : microfluidics, nanoanalysis \& proteomics},
  journal   = {Electrophoresis : microfluidics, nanoanalysis \& proteomics},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0173-0835},
  doi       = {10.1002/elps.202200073},
  pages     = {1920 -- 1933},
  year      = {2022},
  abstract  = {Dielectrophoresis (DEP) is an AC electrokinetic effect mainly used to manipulate cells. Smaller particles, like virions, antibodies, enzymes, and even dye molecules can be immobilized by DEP as well. In principle, it was shown that enzymes are active after immobilization by DEP, but no quantification of the retained activity was reported so far. In this study, the activity of the enzyme horseradish peroxidase (HRP) is quantified after immobilization by DEP. For this, HRP is immobilized on regular arrays of titanium nitride ring electrodes of 500 nm diameter and 20 nm widths. The activity of HRP on the electrode chip is measured with a limit of detection of 60 fg HRP by observing the enzymatic turnover of Amplex Red and H2O2 to fluorescent resorufin by fluorescence microscopy. The initial activity of the permanently immobilized HRP equals up to 45\% of the activity that can be expected for an ideal monolayer of HRP molecules on all electrodes of the array. Localization of the immobilizate on the electrodes is accomplished by staining with the fluorescent product of the enzyme reaction. The high residual activity of enzymes after AC field induced immobilization shows the method's suitability for biosensing and research applications.},
  language  = {en}
}
@article{KiemelDeCahsanParaskevopoulouetal.2022,
  author    = {Kiemel, Katrin and De Cahsan, Binia and Paraskevopoulou, Sofia and Weithoff, Guntram and Tiedemann, Ralph},
  title     = {Mitochondrial genomes of the freshwater monogonont rotifer Brachionus fernandoi and of two additional B. calyciflorus sensu stricto lineages from Germany and the USA (Rotifera, Brachionidae)},
  series = {Mitochondrial DNA. Part B-Resources},
  volume    = {7},
  journal   = {Mitochondrial DNA. Part B-Resources},
  number    = {4},
  publisher = {Routledge, Taylor \& Francis Group},
  address   = {Abingdon},
  issn      = {2380-2359},
  doi       = {10.1080/23802359.2022.2060765},
  pages     = {646 -- 648},
  year      = {2022},
  abstract  = {The Brachionus calyciflorus species complex was recently subdivided into four species, but genetic resources to resolve phylogenetic relationships within this complex are still lacking. We provide two complete mitochondrial (mt) genomes from B. calyciflorus sensu stricto (Germany, USA) and the mt coding sequences (cds) from a German B. fernandoi. Phylogenetic analysis placed our B. calyciflorus sensu stricto strains close to the published genomes of B. calyciflorus, forming the putative sister species to B. fernandoi. Global representatives of B. calyciflorus sensu stricto (i.e. Europe, USA, and China) are genetically closer related to each other than to B. fernandoi (average pairwise nucleotide diversity 0.079 intraspecific vs. 0.254 interspecific).},
  language  = {en}
}
@article{KerneckerFienitzNendeletal.2022,
  author    = {Kernecker, Maria and Fienitz, Meike and Nendel, Claas and Paetzig, Marlene and Walzl, Karin Pirhofer and Raatz, Larissa and Schmidt, Martin and Wulf, Monika and Zscheischler, Jana},
  title     = {Transition zones across agricultural field boundaries for integrated landscape research and management of biodiversity and yields},
  series = {Ecological solutions and evidence},
  volume    = {3},
  journal   = {Ecological solutions and evidence},
  number    = {1},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2688-8319},
  doi       = {10.1002/2688-8319.12122},
  pages     = {7},
  year      = {2022},
  abstract  = {Biodiversity conservation and agricultural production have been largely framed as separate goals for landscapes in the discourse on land use. Although there is an increasing tendency to move away from this dichotomy in theory, the tendency is perpetuated by the spatially explicit approaches used in research and management practice. Transition zones (TZ) have previously been defined as areas where two adjacent fields or patches interact, and so they occur abundantly throughout agricultural landscapes. Biodiversity patterns in TZ have been extensively studied, but their relationship to yield patterns and social-ecological dimensions has been largely neglected. Focusing on European, temperate agricultural landscapes, we outline three areas of research and management that together demonstrate how TZ might be used to facilitate an integrated landscape approach: (i) plant and animal species' use and response to boundaries and the resulting effects on yield, for a deeper understanding of how landscape structure shapes quantity and quality of TZ; (ii) local knowledge on field or patch-level management and its interactions with biodiversity and yield in TZ, and (iii) conflict prevention and collaborative management across land-use boundaries.},
  language  = {en}
}
@article{PalmaVeraReyerLanghammeretal.2022,
  author    = {Palma-Vera, Sergio E. and Reyer, Henry and Langhammer, Martina and Reinsch, Norbert and Derezanin, Lorena and Fickel, J{\"o}rns and Qanbari, Saber and Weitzel, Joachim M. and Franzenburg, Soeren and Hemmrich-Stanisak, Georg and Sch{\"o}n, Jennifer},
  title     = {Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits},
  series = {BMC Biology},
  volume    = {20},
  journal   = {BMC Biology},
  number    = {1},
  publisher = {BMC},
  address   = {London},
  issn      = {1741-7007},
  doi       = {10.1186/s12915-022-01248-9},
  pages     = {20},
  year      = {2022},
  abstract  = {Background Long-term selection experiments are a powerful tool to understand the genetic background of complex traits. The longest of such experiments has been conducted in the Research Institute for Farm Animal Biology (FBN), generating extreme mouse lines with increased fertility, body mass, protein mass and endurance. For >140 generations, these lines have been maintained alongside an unselected control line, representing a valuable resource for understanding the genetic basis of polygenic traits. However, their history and genomes have not been reported in a comprehensive manner yet. Therefore, the aim of this study is to provide a summary of the breeding history and phenotypic traits of these lines along with their genomic characteristics. We further attempt to decipher the effects of the observed line-specific patterns of genetic variation on each of the selected traits. Results Over the course of >140 generations, selection on the control line has given rise to two extremely fertile lines (>20 pups per litter each), two giant growth lines (one lean, one obese) and one long-distance running line. Whole genome sequencing analysis on 25 animals per line revealed line-specific patterns of genetic variation among lines, as well as high levels of homozygosity within lines. This high degree of distinctiveness results from the combined effects of long-term continuous selection, genetic drift, population bottleneck and isolation. Detection of line-specific patterns of genetic differentiation and structural variation revealed multiple candidate genes behind the improvement of the selected traits. Conclusions The genomes of the Dummerstorf trait-selected mouse lines display distinct patterns of genomic variation harbouring multiple trait-relevant genes. Low levels of within-line genetic diversity indicate that many of the beneficial alleles have arrived to fixation alongside with neutral alleles. This study represents the first step in deciphering the influence of selection and neutral evolutionary forces on the genomes of these extreme mouse lines and depicts the genetic complexity underlying polygenic traits.},
  language  = {en}
}
@article{Wiebke2019,
  author    = {Wiebke, Ullmann},
  title     = {Warum hat Bayern mehr Feldhasen als Brandenburg?},
  series = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  journal   = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  publisher = {oerding print GmbH},
  address   = {Braunschweig},
  pages     = {46 -- 47},
  year      = {2019},
  language  = {de}
}
@article{Teckentrup2019,
  author    = {Teckentrup, Lisa},
  title     = {Gefahr an jeder Ecke},
  series = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  journal   = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  publisher = {oerding print GmbH},
  address   = {Braunschweig},
  pages     = {54 -- 55},
  year      = {2019},
  language  = {de}
}
@article{Schaefer2019,
  author    = {Sch{\"a}fer, Merlin},
  title     = {Mut macht einsam},
  series = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  journal   = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  publisher = {oerding print GmbH},
  address   = {Braunschweig},
  pages     = {52 -- 53},
  year      = {2019},
  language  = {de}
}
@article{Kowalski2019,
  author    = {Kowalski, Gabriele Joanna},
  title     = {Auf dem Sprung},
  series = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  journal   = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  publisher = {oerding print GmbH},
  address   = {Braunschweig},
  pages     = {41 -- 42},
  year      = {2019},
  language  = {de}
}
@article{Raatz2019,
  author    = {Raatz, Larissa},
  title     = {Wirtschaften in einer reich strukturierten Landschaft - geht das ?},
  series = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  journal   = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  publisher = {oerding print GmbH},
  address   = {Braunschweig},
  pages     = {32 -- 33},
  year      = {2019},
  language  = {de}
}
@article{LozadaGobilard2019,
  author    = {Lozada Gobilard, Sissi Donna},
  title     = {K{\"o}nnen auch Pflanzen zwischen den S{\"o}llen "wandern"},
  series = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  journal   = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  publisher = {oerding print GmbH},
  address   = {Braunschweig},
  pages     = {30 -- 31},
  year      = {2019},
  language  = {de}
}
@article{LitwinColangeli2019,
  author    = {Litwin, Magdalena and Colangeli, Pierluigi},
  title     = {Wie und wohin reisen Wasserfl{\"o}he?},
  series = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  journal   = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  publisher = {oerding print GmbH},
  address   = {Braunschweig},
  pages     = {28 -- 29},
  year      = {2019},
  language  = {de}
}
@article{Maass2019,
  author    = {Maaß, Stefanie},
  title     = {Blick in die Zukunft},
  series = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  journal   = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  publisher = {oerding print GmbH},
  address   = {Braunschweig},
  pages     = {24 -- 25},
  year      = {2019},
  language  = {de}
}
@article{WeissWulff2019,
  author    = {Weiß, Lina and Wulff, Monika},
  title     = {Ver{\"a}nderung der Landnutzung in der nord-westlichen Uckermark von 1780 bis heute},
  series = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  journal   = {Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018},
  publisher = {oerding print GmbH},
  address   = {Braunschweig},
  pages     = {20 -- 21},
  year      = {2019},
  language  = {de}
}
@article{BapolisiKielbBekiretal.2022,
  author    = {Bapolisi, Alain Murhimalika and Kielb, Patrycja and Bekir, Marek and Lehnen, Anne-Catherine and Radon, Christin and Laroque, Sophie and Wendler, Petra and M{\"u}ller-Werkmeister, Henrike and Hartlieb, Matthias},
  title     = {Antimicrobial polymers of linear and bottlebrush architecture},
  series = {Macromolecular rapid communications : publishing the newsletters of the European Polymer Federation},
  volume    = {43},
  journal   = {Macromolecular rapid communications : publishing the newsletters of the European Polymer Federation},
  number    = {19},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {1521-3927},
  doi       = {10.1002/marc.202200288},
  pages     = {14},
  year      = {2022},
  abstract  = {Polymeric antimicrobial peptide mimics are a promising alternative for the future management of the daunting problems associated with antimicrobial resistance. However, the development of successful antimicrobial polymers (APs) requires careful control of factors such as amphiphilic balance, molecular weight, dispersity, sequence, and architecture. While most of the earlier developed APs focus on random linear copolymers, the development of APs with advanced architectures proves to be more potent. It is recently developed multivalent bottlebrush APs with improved antibacterial and hemocompatibility profiles, outperforming their linear counterparts. Understanding the rationale behind the outstanding biological activity of these newly developed antimicrobials is vital to further improving their performance. This work investigates the physicochemical properties governing the differences in activity between linear and bottlebrush architectures using various spectroscopic and microscopic techniques. Linear copolymers are more solvated, thermo-responsive, and possess facial amphiphilicity resulting in random aggregations when interacting with liposomes mimicking Escheria coli membranes. The bottlebrush copolymers adopt a more stable secondary conformation in aqueous solution in comparison to linear copolymers, conferring rapid and more specific binding mechanism to membranes. The advantageous physicochemical properties of the bottlebrush topology seem to be a determinant factor in the activity of these promising APs.},
  language  = {en}
}
@article{AzcorraDickinsonMendezDominguezetal.2022,
  author    = {Azcorra, Hugo and Dickinson, Federico and Mendez-Dominguez, Nina and Mumm, Rebekka and Valent{\´i}n, Graciela},
  title     = {Development of birthweight and length for gestational age and sex references in Yucatan, Mexico},
  series = {American journal of human biology : the official journal of the Human Biology Council},
  volume    = {34},
  journal   = {American journal of human biology : the official journal of the Human Biology Council},
  number    = {6},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1042-0533},
  doi       = {10.1002/ajhb.23732},
  pages     = {13},
  year      = {2022},
  abstract  = {Objective To develop sex- and gestational age specific reference percentiles and curves for birth weight and length for Yucatec neonates using data from birth registers of infants born during 2015-2019. Material and methods Observational, descriptive, epidemiologic study in a 5-year period including every registered birth in the state of Yucatan, Mexico using birth registries. A total of 158 432 live, physically healthy singletons (76 442 females and 81 990 males) between 25 and 42 weeks of gestation were included in the analysis. We used the LMS method to construct smoothed reference centiles (3rd, 10th, 25th, 50th, 75th, 95th, and 97th) and curves for males and females separately. Results Mean maternal age was 26 (SD = 6.22) years. Fifty-two percent of births occurred by vaginal delivery, 37\% were firstborn and similar proportions were second (33\%) and third or more (30\%) born. 5.5\% of newborns included in the references corresponds to neonates born before 37 weeks of gestation (5.9\% boys and 5.1\% girls). In both sexes, the percentage of infants with a birthweight less than 2500 g was 6.7\%. The birthweight at the 50th percentile for males and females at 40 weeks of gestation in this cohort was 3256 and 3167 g, respectively, and the corresponding values for birth length were 50.23 and 49.84 cm (mean differences between sexes: 89 g and 0.40 cm, respectively). Conclusion The reference percentile and curves developed in this study are useful for research purposes and can help health practitioners to assess the biological status of infants born in Yucatan.},
  language  = {en}
}
@article{EhrlichThygesenKiorboe2022,
  author    = {Ehrlich, Elias and Thygesen, Uffe H{\o}gsbro and Ki{\o}rboe, Thomas},
  title     = {Evolution of toxins as a public good in phytoplankton},
  series = {Proceedings of the Royal Society of London : B, Biological sciences},
  volume    = {289},
  journal   = {Proceedings of the Royal Society of London : B, Biological sciences},
  number    = {1977},
  publisher = {Royal Society},
  address   = {London},
  issn      = {0962-8452},
  doi       = {10.1098/rspb.2022.0393},
  pages     = {9},
  year      = {2022},
  abstract  = {Toxic phytoplankton blooms have increased in many waterbodies worldwide with well-known negative impacts on human health, fisheries and ecosystems. However, why and how phytoplankton evolved toxin production is still a puzzling question, given that the producer that pays the costs often shares the benefit with other competing algae and thus provides toxins as a 'public good' (e.g. damaging a common competitor or predator). Furthermore, blooming phytoplankton species often show a high intraspecific variation in toxicity and we lack an understanding of what drives the dynamics of coexisting toxic and non-toxic genotypes. Here, by using an individual-based two-dimensional model, we show that small-scale patchiness of phytoplankton strains caused by demography can explain toxin evolution in phytoplankton with low motility and the maintenance of genetic diversity within their blooms. This patchiness vanishes for phytoplankton with high diffusive motility, suggesting different evolutionary pathways for different phytoplankton groups. In conclusion, our study reveals that small-scale spatial heterogeneity, generated by cell division and counteracted by diffusive cell motility and turbulence, can crucially affect toxin evolution and eco-evolutionary dynamics in toxic phytoplankton species. This contributes to a better understanding of conditions favouring toxin production and the evolution of public goods in asexually reproducing organisms in general.},
  language  = {en}
}
@article{EccardMendesFerreiraPeredoArceetal.2022,
  author    = {Eccard, Jana and Mendes Ferreira, Clara and Peredo Arce, Andres and Dammhahn, Melanie},
  title     = {Top-down effects of foraging decisions on local, landscape and regional biodiversity of resources (DivGUD)},
  series = {Ecology letters},
  volume    = {25},
  journal   = {Ecology letters},
  number    = {1},
  publisher = {Wiley-Blackwell},
  address   = {Oxford [u.a.]},
  issn      = {1461-0248},
  doi       = {10.1111/ele.13901},
  pages     = {3 -- 16},
  year      = {2022},
  abstract  = {Foraging by consumers acts as a biotic filtering mechanism for biodiversity at the trophic level of resources. Variation in foraging behaviour has cascading effects on abundance, diversity, and functional trait composition of the community of resource species. Here we propose diversity at giving-up density (DivGUD), i.e. when foragers quit exploiting a patch, as a novel concept and simple measure quantifying cascading effects at multiple spatial scales. In experimental landscapes with an assemblage of plant seeds, patch residency of wild rodents decreased local alpha-DivGUD (via elevated mortality of species with large seeds) and regional gamma-DivGUD, while dissimilarity among patches in a landscape (beta-DivGUD) increased. By linking theories of adaptive foraging behaviour with community ecology, DivGUD allows to investigate cascading indirect predation effects, e.g. the ecology-of-fear framework, feedbacks between functional trait composition of resource species and consumer communities, and effects of inter-individual differences among foragers on the biodiversity of resource communities.},
  language  = {en}
}
@article{PerrellaBaeurlevanZanten2022,
  author    = {Perrella, Giorgio and B{\"a}urle, Isabel and van Zanten, Martijn},
  title     = {Epigenetic regulation of thermomorphogenesis and heat stress tolerance},
  series = {New phytologist : international journal of plant science},
  volume    = {234},
  journal   = {New phytologist : international journal of plant science},
  number    = {4},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0028-646X},
  doi       = {10.1111/nph.17970},
  pages     = {1144 -- 1160},
  year      = {2022},
  abstract  = {Many environmental conditions fluctuate and organisms need to respond effectively. This is especially true for temperature cues that can change in minutes to seasons and often follow a diurnal rhythm. Plants cannot migrate and most cannot regulate their temperature. Therefore, a broad array of responses have evolved to deal with temperature cues from freezing to heat stress. A particular response to mildly elevated temperatures is called thermomorphogenesis, a suite of morphological adaptations that includes thermonasty, formation of thin leaves and elongation growth of petioles and hypocotyl. Thermomorphogenesis allows for optimal performance in suboptimal temperature conditions by enhancing the cooling capacity. When temperatures rise further, heat stress tolerance mechanisms can be induced that enable the plant to survive the stressful temperature, which typically comprises cellular protection mechanisms and memory thereof. Induction of thermomorphogenesis, heat stress tolerance and stress memory depend on gene expression regulation, governed by diverse epigenetic processes. In this Tansley review we update on the current knowledge of epigenetic regulation of heat stress tolerance and elevated temperature signalling and response, with a focus on thermomorphogenesis regulation and heat stress memory. In particular we highlight the emerging role of H3K4 methylation marks in diverse temperature signalling pathways.},
  language  = {en}
}
@article{BergCernava2022,
  author    = {Berg, Gabriele and Cernava, Tomislav},
  title     = {The plant microbiota signature of the Anthropocene as a challenge for microbiome research},
  series = {Microbiome},
  volume    = {10},
  journal   = {Microbiome},
  number    = {1},
  publisher = {BMC},
  address   = {London},
  issn      = {2049-2618},
  doi       = {10.1186/s40168-021-01224-5},
  pages     = {12},
  year      = {2022},
  abstract  = {Background: One promise of the recently presented microbiome definition suggested that, in combination with unifying concepts and standards, microbiome research could be important for solving new challenges associated with anthropogenic-driven changes in various microbiota. With this commentary we want to further elaborate this suggestion, because we noticed specific signatures in microbiota affected by the Anthropocene. Results: Here, we discuss this based on a review of available literature and our own research targeting exemplarily the plant microbiome. It is not only crucial for plants themselves but also linked to planetary health. We suggest that different human activities are commonly linked to a shift of diversity and evenness of the plant microbiota, which is also characterized by a decrease of host specificity, and an increase of r-strategic microbes, pathogens, and hypermutators. The resistome, anchored in the microbiome, follows this shift by an increase of specific antimicrobial resistance (AMR) mechanisms as well as an increase of plasmid-associated resistance genes. This typical microbiome signature of the Anthropocene is often associated with dysbiosis and loss of resilience, and leads to frequent pathogen outbreaks. Although several of these observations are already confirmed by meta-studies, this issue requires more attention in upcoming microbiome studies. Conclusions: Our commentary aims to inspire holistic studies for the development of solutions to restore and save microbial diversity for ecosystem functioning as well as the closely connected planetary health.},
  language  = {en}
}
@article{StrippDuffusFourmondetal.2022,
  author    = {Stripp, Sven T. and Duffus, Benjamin R. and Fourmond, Vincent and Leger, Christophe and Leimk{\"u}hler, Silke and Hirota, Shun and Hu, Yilin and Jasniewski, Andrew and Ogata, Hideaki and Ribbe, Markus W.},
  title     = {Second and outer coordination sphere effects in nitrogenase, hydrogenase, formate dehydrogenase, and CO dehydrogenase},
  series = {Chemical reviews : CR},
  volume    = {122},
  journal   = {Chemical reviews : CR},
  number    = {14},
  publisher = {American Chemical Society},
  address   = {Washington, DC},
  issn      = {0009-2665},
  doi       = {10.1021/acs.chemrev.1c00914},
  pages     = {11900 -- 11973},
  year      = {2022},
  abstract  = {Gases like H-2, N-2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N-2, CO2, and CO and the production of H-2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N-2 fixation by nitrogenase and H-2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.},
  language  = {en}
}
@article{DelkerQuintWigge2022,
  author    = {Delker, Carolin and Quint, Marcel and Wigge, Philip Anthony},
  title     = {Recent advances in understanding thermomorphogenesis signaling},
  series = {Current opinion in plant biology},
  volume    = {68},
  journal   = {Current opinion in plant biology},
  publisher = {Elsevier},
  address   = {London},
  issn      = {1369-5266},
  doi       = {10.1016/j.pbi.2022.102231},
  pages     = {10},
  year      = {2022},
  abstract  = {Plants show remarkable phenotypic plasticity and are able to adjust their morphology and development to diverse environmental stimuli. Morphological acclimation responses to elevated ambient temperatures are collectively termed thermomorphogenesis. In Arabidopsis thaliana, morphological changes are coordinated to a large extent by the transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), which in turn is regulated by several thermosensing mechanisms and modulators. Here, we review recent advances in the identification of factors that regulate thermomorphogenesis of Arabidopsis seedlings by affecting PIF4 expression and PIF4 activity. We summarize newly identified thermosensing mechanisms and highlight work on the emerging topic of organ- and tissue-specificity in the regulation of thermomorphogenesis.},
  language  = {en}
}
@article{RistowPanitsaMeyeretal.2022,
  author    = {Ristow, Michael and Panitsa, Maria and Meyer, Stefan and Bergmeier, Erwin},
  title     = {Factors of detection deficits in vascular plant inventories - an island case study},
  series = {Diversity},
  volume    = {14},
  journal   = {Diversity},
  number    = {4},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {1424-2818},
  doi       = {10.3390/d14040303},
  pages     = {12},
  year      = {2022},
  abstract  = {The degree of completeness of large-scale floristic inventories is often difficult to judge. We compared prior vascular plant species inventories of the Mediterranean island of Limnos (North Aegean, Greece) with 231 recent records from 2016-2021. Together with the recent records, the known number of vascular plant species on the island is 960 native taxa, 63 established neophytes, and 27 species of as yet casual status for a total of 1050 taxa. We looked at a number of traits (plant family, size, flower color, perceptibility, habitat, reproduction period, rarity, and status) to investigate whether they were overrepresented in the dataset of the newly found taxa. Overrepresentation was found in some plant families (e.g., Poaceae and Chenopodiaceae) and for traits such as hydrophytic life form, unobtrusive flower color, coastal as well as agricultural and ruderal habitats, and late (summer/autumn) reproduction period. Apart from the well-known fact of esthetic bias, we found evidence for ecological and perceptibility biases. Plant species inventories based on prior piecemeal collated data should focus on regionally specific species groups and underrepresented and rare habitats.},
  language  = {en}
}
@article{ScharfWeineltSchroederetal.2022,
  author    = {Scharf, Christina and Weinelt, Ferdinand Anton and Schroeder, Ines and Paal, Michael and Weigand, Michael and Zoller, Michael and Irlbeck, Michael and Kloft, Charlotte and Briegel, Josef and Liebchen, Uwe},
  title     = {Does the cytokine adsorber CytoSorb (R) reduce vancomycin exposure in critically ill patients with sepsis or septic shock?},
  series = {Annals of intensive care},
  volume    = {12},
  journal   = {Annals of intensive care},
  number    = {1},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {2110-5820},
  doi       = {10.1186/s13613-022-01017-5},
  pages     = {8},
  year      = {2022},
  abstract  = {Background: Hemadsorption of cytokines is used in critically ill patients with sepsis or septic shock. Concerns have been raised that the cytokine adsorber CytoSorb (R) unintentionally adsorbs vancomycin. This study aimed to quantify vancomycin elimination by CytoSorb (R) . Methods: Critically ill patients with sepsis or septic shock receiving continuous renal replacement therapy and CytoSorb (R) treatment during a prospective observational study were included in the analysis. Vancomycin pharmacokinetics was characterized using population pharmacokinetic modeling. Adsorption of vancomycin by the CytoSorb (R) was investigated as linear or saturable process. The final model was used to derive dosing recommendations based on stochastic simulations. Results: 20 CytoSorb (R) treatments in 7 patients (160 serum samples/24 during CytoSorb (R)-treatment, all continuous infusion) were included in the study. A classical one-compartment model, including effluent flow rate of the continuous hemodialysis as linear covariate on clearance, best described the measured concentrations (without CytoSorb (R)). Significant adsorption with a linear decrease during CytoSorb (R) treatment was identified (p <0.0001) and revealed a maximum increase in vancomycin clearance of 291\% (initially after CytoSorb (R) installation) and a maximum adsorption capacity of 572 mg. For a representative patient of our cohort a reduction of the area under the curve (AUC) by 93 mg/L*24 h during CytoSorb (R) treatment was observed. The additional administration of 500 mg vancomycin over 2 h during CytoSorb (R) attenuated the effect and revealed a negligible reduction of the AUC by 4 mg/L*24h. Conclusion: We recommend the infusion of 500 mg vancomycin over 2 h during CytoSorb (R) treatment to avoid subtherapeutic concentrations.},
  language  = {en}
}