@article{XiaoLiuWangetal.2020, author = {Xiao, Shangbin and Liu, Liu and Wang, Wei and Lorke, Andreas and Woodhouse, Jason Nicholas and Grossart, Hans-Peter}, title = {A Fast-Response Automated Gas Equilibrator (FaRAGE) for continuous in situ measurement of CH4 and CO2 dissolved in water}, series = {Hydrology and earth system sciences : HESS}, volume = {24}, journal = {Hydrology and earth system sciences : HESS}, number = {7}, publisher = {European Geosciences Union (EGU) ; Copernicus}, address = {Munich}, issn = {1027-5606}, doi = {10.5194/hess-24-3871-2020}, pages = {3871 -- 3880}, year = {2020}, abstract = {Biogenic greenhouse gas emissions, e.g., of methane (CH4) and carbon dioxide (CO2) from inland waters, contribute substantially to global warming. In aquatic systems, dissolved greenhouse gases are highly heterogeneous in both space and time. To better understand the biological and physical processes that affect sources and sinks of both CH4 and CO2, their dissolved concentrations need to be measured with high spatial and temporal resolution. To achieve this goal, we developed the Fast-Response Automated Gas Equilibrator (FaRAGE) for real-time in situ measurement of dissolved CH4 and CO2 concentrations at the water surface and in the water column. FaRAGE can achieve an exceptionally short response time (t(95\%) = 12 s when including the response time of the gas analyzer) while retaining an equilibration ratio of 62.6\% and a measurement accuracy of 0.5\% for CH4. A similar performance was observed for dissolved CO2 (t(95\%) = 10 s, equilibration ratio 67.1 \%). An equilibration ratio as high as 91.8\% can be reached at the cost of a slightly increased response time (16 s). The FaRAGE is capable of continuously measuring dissolved CO2 and CH4 concentrations in the nM-to-submM (10(-9)-10(-3) mol L-1) range with a detection limit of subnM (10(-10) mol L-1), when coupling with a cavity ring-down greenhouse gas analyzer (Picarro GasScouter). FaRAGE allows for the possibility of mapping dissolved concentration in a "quasi" three-dimensional manner in lakes and provides an inexpensive alternative to other commercial gas equilibrators. It is simple to operate and suitable for continuous monitoring with a strong tolerance for suspended particles. While the FaRAGE is developed for inland waters, it can be also applied to ocean waters by tuning the gas-water mixing ratio. The FaRAGE is easily adapted to suit other gas analyzers expanding the range of potential applications, including nitrous oxide and isotopic composition of the gases.}, language = {en} } @article{ReegHeineMihanetal.2020, author = {Reeg, Jette and Heine, Simon and Mihan, Christine and McGee, Sean and Preuss, Thomas G. and Jeltsch, Florian}, title = {A graphical user interface for the plant community model IBC-grass}, series = {Plos One}, volume = {15}, journal = {Plos One}, number = {3}, publisher = {Plos 1}, address = {San Francisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0230012}, pages = {18}, year = {2020}, abstract = {Plants located adjacent to agricultural fields are important for maintaining biodiversity in semi-natural landscapes. To avoid undesired impacts on these plants due to herbicide application on the arable fields, regulatory risk assessments are conducted prior to registration to ensure proposed uses of plant protection products do not present an unacceptable risk. The current risk assessment approach for these non-target terrestrial plants (NTTPs) examines impacts at the individual-level as a surrogate approach for protecting the plant community due to the inherent difficulties of directly assessing population or community level impacts. However, modelling approaches are suitable higher tier tools to upscale individual-level effects to community level. IBC-grass is a sophisticated plant community model, which has already been applied in several studies. However, as it is a console application software, it was not deemed sufficiently user-friendly for risk managers and assessors to be conveniently operated without prior expertise in ecological models. Here, we present a user-friendly and open source graphical user interface (GUI) for the application of IBC-grass in regulatory herbicide risk assessment. It facilitates the use of the plant community model for predicting long-term impacts of herbicide applications on NTTP communities. The GUI offers two options to integrate herbicide impacts: (1) dose responses based on current standard experiments (acc. to testing guidelines) and (2) based on specific effect intensities. Both options represent suitable higher tier options for future risk assessments of NTTPs as well as for research on the ecological relevance of effects.}, language = {en} } @article{ZhangChenSiemiatkowskaetal.2020, author = {Zhang, Youjun and Chen, Moxian and Siemiatkowska, Beata and Toleco, Mitchell Rey and Jing, Yue and Strotmann, Vivien and Zhang, Jianghua and Stahl, Yvonne and Fernie, Alisdair R.}, title = {A highly efficient agrobacterium-mediated method for transient gene expression and functional studies in multiple plant species}, series = {Plant Communications}, volume = {1}, journal = {Plant Communications}, number = {5}, publisher = {Science Direct}, address = {New York}, issn = {2590-3462}, pages = {12}, year = {2020}, abstract = {Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis.}, language = {en} } @article{SchittkoBernardVerdierHegeretal.2020, author = {Schittko, Conrad and Bernard-Verdier, Maud and Heger, Tina and Buchholz, Sascha and Kowarik, Ingo and von der Lippe, Moritz and Seitz, Birgit and Joshi, Jasmin Radha and Jeschke, Jonathan M.}, title = {A multidimensional framework for measuring biotic novelty: How novel is a community?}, series = {Global Change Biology}, volume = {26}, journal = {Global Change Biology}, number = {8}, publisher = {John Wiley \& Sons, Inc.}, address = {New Jersey}, pages = {17}, year = {2020}, abstract = {Anthropogenic changes in climate, land use, and disturbance regimes, as well as introductions of non-native species can lead to the transformation of many ecosystems. The resulting novel ecosystems are usually characterized by species assemblages that have not occurred previously in a given area. Quantifying the ecological novelty of communities (i.e., biotic novelty) would enhance the understanding of environmental change. However, quantification remains challenging since current novelty metrics, such as the number and/or proportion of non-native species in a community, fall short of considering both functional and evolutionary aspects of biotic novelty. Here, we propose the Biotic Novelty Index (BNI), an intuitive and flexible multidimensional measure that combines (a) functional differences between native and non-native introduced species with (b) temporal dynamics of species introductions. We show that the BNI is an additive partition of Rao's quadratic entropy, capturing the novel interaction component of the community's functional diversity. Simulations show that the index varies predictably with the relative amount of functional novelty added by recently arrived species, and they illustrate the need to provide an additional standardized version of the index. We present a detailed R code and two applications of the BNI by (a) measuring changes of biotic novelty of dry grassland plant communities along an urbanization gradient in a metropolitan region and (b) determining the biotic novelty of plant species assemblages at a national scale. The results illustrate the applicability of the index across scales and its flexibility in the use of data of different quality. Both case studies revealed strong connections between biotic novelty and increasing urbanization, a measure of abiotic novelty. We conclude that the BNI framework may help building a basis for better understanding the ecological and evolutionary consequences of global change.}, 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{Trindade2020, author = {Trindade, Ines}, title = {A shelter for the future}, series = {Molecular plant}, volume = {13}, journal = {Molecular plant}, number = {12}, publisher = {Cell Press}, address = {Cambridge}, issn = {1674-2052}, doi = {10.1016/j.molp.2020.11.009}, pages = {1675 -- 1675}, year = {2020}, abstract = {Plant development in its majority occurs post-embryonically through the activity of local meristems that provide daughter cells for the development of new organs. It has long been acknowledged that the shoot apical meristem (SAM), which holds the stem cells that will form above-ground organs, is recalcitrant to infection by multiple pathogens, a crucial strategy to safeguard normal devel- opment and subsequent generations. However, the molecular mechanisms underlying SAM immunity remain largely unknown.}, 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{SchellerSchmid2020, author = {Scheller, Frieder W. and Schmid, Rolf}, title = {A tribute to Isao Karube (1942-2020) and his influence on sensor science}, series = {Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry, Analusis and Quimica analitica}, volume = {412}, journal = {Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry, Analusis and Quimica analitica}, number = {28}, publisher = {Springer}, address = {Berlin}, issn = {1618-2642}, doi = {10.1007/s00216-020-02946-5}, pages = {7709 -- 7711}, year = {2020}, language = {en} } @article{LauxWengerBieretal.2020, author = {Laux, Eva-Maria and Wenger, Christian and Bier, Frank Fabian and Hoelzel, Ralph}, title = {AC electrokinetic immobilization of organic dye molecules}, series = {Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry and Analusis}, volume = {412}, journal = {Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry and Analusis}, number = {16}, publisher = {Springer}, address = {Berlin}, issn = {1618-2642}, doi = {10.1007/s00216-020-02480-4}, pages = {3859 -- 3870}, year = {2020}, abstract = {The application of inhomogeneous AC electric fields for molecular immobilization is a very fast and simple method that does not require any adaptions to the molecule's functional groups or charges. Here, the method is applied to a completely new category of molecules: small organic fluorescence dyes, whose dimensions amount to only 1 nm or even less. The presented setup and the electric field parameters used allow immobilization of dye molecules on the whole electrode surface as opposed to pure dielectrophoretic applications, where molecules are attracted only to regions of high electric field gradients, i.e., to the electrode tips and edges. In addition to dielectrophoresis and AC electrokinetic flow, molecular scale interactions and electrophoresis at short time scales are discussed as further mechanisms leading to migration and immobilization of the molecules.}, language = {en} } @article{OlasFichtnerApelt2020, author = {Olas, Justyna Jadwiga and Fichtner, Franziska and Apelt, Federico}, title = {All roads lead to growth}, series = {Journal of experimental botany}, volume = {71}, journal = {Journal of experimental botany}, number = {1}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/erz406}, pages = {11 -- 21}, year = {2020}, abstract = {Plant growth is a highly complex biological process that involves innumerable interconnected biochemical and signalling pathways. Many different techniques have been developed to measure growth, unravel the various processes that contribute to plant growth, and understand how a complex interaction between genotype and environment determines the growth phenotype. Despite this complexity, the term 'growth' is often simplified by researchers; depending on the method used for quantification, growth is viewed as an increase in plant or organ size, a change in cell architecture, or an increase in structural biomass. In this review, we summarise the cellular and molecular mechanisms underlying plant growth, highlight state-of-the-art imaging and non-imaging-based techniques to quantitatively measure growth, including a discussion of their advantages and drawbacks, and suggest a terminology for growth rates depending on the type of technique used.}, language = {en} } @article{EccardLiesenjohannDammhahn2020, author = {Eccard, Jana and Liesenjohann, Thilo and Dammhahn, Melanie}, title = {Among-individual differences in foraging modulate resource exploitation under perceived predation risk}, series = {Oecologia}, volume = {194}, journal = {Oecologia}, number = {4}, publisher = {Springer}, address = {Berlin}, issn = {0029-8549}, doi = {10.1007/s00442-020-04773-y}, pages = {621 -- 634}, year = {2020}, abstract = {Foraging is risky and involves balancing the benefits of resource acquisition with costs of predation. Optimal foraging theory predicts where, when and how long to forage in a given spatiotemporal distribution of risks and resources. However, significant variation in foraging behaviour and resource exploitation remain unexplained. Using single foragers in artificial landscapes of perceived risks and resources with diminishing returns, we aimed to test whether foraging behaviour and resource exploitation are adjusted to risk level, vary with risk during different components of foraging, and (co)vary among individuals. We quantified foraging behaviour and resource exploitation for 21 common voles (Microtus arvalis). By manipulating ground cover, we created simple landscapes of two food patches varying in perceived risk during feeding in a patch and/or while travelling between patches. Foraging of individuals was variable and adjusted to risk level and type. High risk during feeding reduced feeding duration and food consumption more strongly than risk while travelling. Risk during travelling modified the risk effects of feeding for changes between patches and resulting evenness of resource exploitation. Across risk conditions individuals differed consistently in when and how long they exploited resources and exposed themselves to risk. These among-individual differences in foraging behaviour were associated with consistent patterns of resource exploitation. Thus, different strategies in foraging-under-risk ultimately lead to unequal payoffs and might affect lower trophic levels in food webs. Inter-individual differences in foraging behaviour, i.e. foraging personalities, are an integral part of foraging behaviour and need to be fully integrated into optimal foraging theory.}, language = {en} } @article{OthmanWollenberger2020, author = {Othman, Abdelmageed M. and Wollenberger, Ulla}, title = {Amperometric biosensor based on coupling aminated laccase to functionalized carbon nanotubes for phenolics detection}, series = {International journal of biological macromolecules}, volume = {153}, journal = {International journal of biological macromolecules}, publisher = {Elsevier}, address = {New York, NY [u.a.]}, issn = {0141-8130}, doi = {10.1016/j.ijbiomac.2020.03.049}, pages = {855 -- 864}, year = {2020}, abstract = {A biosensor for phenolic compounds based on a chemically modified laccase from Coriolus hirsula immobilized on functionalized screen-printed carbon electrodes (SPCEs) was achieved. Different enzyme modifications and immobilization strategies were analyzed. The electrochemical response of the immobilized laccase on SPCEs modified with carboxyl functionalized multi-walled carbon nanotubes (COOH-MWCNT) was the highest when laccase was aminated prior to the adsorption onto the working electrode. The developed lactase biosensor sensitivity toward different phenolic compounds was assessed to determine the biosensor response with several phenolic compounds. The highest response was obtained for ABTS with a saturation value of I-max = 27.94 mu A. The electrocatalytic efficiency (I-max/K-m(app)) was the highest for ABTS (5588 mu A mu M-1) followed by syringaldazine (3014 mu A.mu M-1). The sensors were considerably stable, whereby 99.5, 82 and 77\% of the catalytic response using catechol as substrate was retained after 4, 8 and 10 successive cycles of reuse respectively, with response time average of 5 s for 12 cycles. No loss of activity was observed after 20 days of storage.}, language = {en} } @article{HeHoeperDodenhoeftetal.2020, author = {He, Hai and H{\"o}per, Rune and Dodenh{\"o}ft, Moritz and Marli{\`e}re, Philippe and Bar-Even, Arren}, title = {An optimized methanol assimilation pathway relying on promiscuous formaldehyde-condensing aldolases in E. coli}, series = {Metabolic Engineering}, volume = {60}, journal = {Metabolic Engineering}, publisher = {Elsevier}, address = {Amsterdam [u.a.]}, issn = {1096-7176}, doi = {10.1016/j.ymben.2020.03.002}, pages = {1 -- 13}, year = {2020}, abstract = {Engineering biotechnological microorganisms to use methanol as a feedstock for bioproduction is a major goal for the synthetic metabolism community. Here, we aim to redesign the natural serine cycle for implementation in E. coli. We propose the homoserine cycle, relying on two promiscuous formaldehyde aldolase reactions, as a superior pathway design. The homoserine cycle is expected to outperform the serine cycle and its variants with respect to biomass yield, thermodynamic favorability, and integration with host endogenous metabolism. Even as compared to the RuMP cycle, the most efficient naturally occurring methanol assimilation route, the homoserine cycle is expected to support higher yields of a wide array of products. We test the in vivo feasibility of the homoserine cycle by constructing several E. coli gene deletion strains whose growth is coupled to the activity of different pathway segments. Using this approach, we demonstrate that all required promiscuous enzymes are active enough to enable growth of the auxotrophic strains. Our findings thus identify a novel metabolic solution that opens the way to an optimized methylotrophic platform.}, language = {en} } @article{SchenkeSchjeidePuescheletal.2020, author = {Schenke, Maren and Schjeide, Brit-Maren and P{\"u}schel, Gerhard Paul and Seeger, Bettina}, title = {Analysis of motor neurons differentiated from human induced pluripotent stem cells for the use in cell-based Botulinum neurotoxin activity assays}, series = {Toxins}, volume = {12}, journal = {Toxins}, number = {5}, publisher = {MDPI}, address = {Basel}, issn = {2072-6651}, doi = {10.3390/toxins12050276}, pages = {20}, year = {2020}, abstract = {Botulinum neurotoxins (BoNTs) are potent neurotoxins produced by bacteria, which inhibit neurotransmitter release, specifically in their physiological target known as motor neurons (MNs). For the potency assessment of BoNTs produced for treatment in traditional and aesthetic medicine, the mouse lethality assay is still used by the majority of manufacturers, which is ethically questionable in terms of the 3Rs principle. In this study, MNs were differentiated from human induced pluripotent stem cells based on three published protocols. The resulting cell populations were analyzed for their MN yield and their suitability for the potency assessment of BoNTs. MNs produce specific gangliosides and synaptic proteins, which are bound by BoNTs in order to be taken up by receptor-mediated endocytosis, which is followed by cleavage of specific soluble N-ethylmaleimide-sensitive-factor attachment receptor (SNARE) proteins required for neurotransmitter release. The presence of receptors and substrates for all BoNT serotypes was demonstrated in MNs generated in vitro. In particular, the MN differentiation protocol based on Du et al. yielded high numbers of MNs in a short amount of time with high expression of BoNT receptors and targets. The resulting cells are more sensitive to BoNT/A1 than the commonly used neuroblastoma cell line SiMa. MNs are, therefore, an ideal tool for being combined with already established detection methods.}, language = {en} } @article{PaijmansBarlowHennebergeretal.2020, author = {Paijmans, Johanna L. A. and Barlow, Axel and Henneberger, Kirstin and Fickel, J{\"o}rns and Hofreiter, Michael and Foerste, Daniel W. G.}, title = {Ancestral mitogenome capture of the Southeast Asian banded linsang}, series = {PLoS ONE}, volume = {15}, journal = {PLoS ONE}, number = {6}, publisher = {PLOS}, address = {San Francisco, California, US}, issn = {1932-6203}, doi = {10.1371/journal.pone.0234385}, pages = {12}, year = {2020}, abstract = {Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives.}, language = {en} } @article{DuffusSchrapersSchuthetal.2020, author = {Duffus, Benjamin R. and Schrapers, Peer and Schuth, Nils and Mebs, Stefan and Dau, Holger and Leimk{\"u}hler, Silke and Haumann, Michael}, title = {Anion binding and oxidative modification at the molybdenum cofactor of formate dehydrogenase from Rhodobacter capsulatus studied by X-ray absorption spectroscopy}, series = {Inorganic chemistry}, volume = {59}, journal = {Inorganic chemistry}, number = {1}, publisher = {American Chemical Society}, address = {Washington, DC}, issn = {0020-1669}, doi = {10.1021/acs.inorgchem.9b01613}, pages = {214 -- 225}, year = {2020}, abstract = {Formate dehydrogenase (FDH) enzymes are versatile catalysts for CO2 conversion. The FDH from Rhodobacter capsulatus contains a molybdenum cofactor with the dithiolene functions of two pyranopterin guanine dinucleotide molecules, a conserved cysteine, and a sulfido group bound at Mo(VI). In this study, we focused on metal oxidation state and coordination changes in response to exposure to O-2, inhibitory anions, and redox agents using X-ray absorption spectroscopy (XAS) at the Mo K-edge. Differences in the oxidative modification of the bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor relative to samples prepared aerobically without inhibitor, such as variations in the relative numbers of sulfido (Mo=S) and oxo (Mo=O) bonds, were observed in the presence of azide (N-3(-)) or cyanate (OCN-). Azide provided best protection against O-2, resulting in a quantitatively sulfurated cofactor with a displaced cysteine ligand and optimized formate oxidation activity. Replacement of the cysteine ligand by a formate (HCO2-) ligand at the molybdenum in active enzyme is compatible with our XAS data. Cyanide (CN-) inactivated the enzyme by replacing the sulfido ligand at Mo(VI) with an oxo ligand. Evidence that the sulfido group may become protonated upon molybdenum reduction was obtained. Our results emphasize the role of coordination flexibility at the molybdenum center during inhibitory and catalytic processes of FDH enzymes.}, language = {en} } @article{HartmannPreickAbeltetal.2020, author = {Hartmann, Stefanie and Preick, Michaela and Abelt, Silke and Scheffel, Andr{\´e} and Hofreiter, Michael}, title = {Annotated genome sequences of the carnivorous plant Roridula gorgonias and a non-carnivorous relative, Clethra arborea}, series = {BMC Research Notes}, volume = {13}, journal = {BMC Research Notes}, publisher = {Biomed Central}, address = {London}, issn = {1756-0500}, doi = {10.1186/s13104-020-05254-4}, pages = {6}, year = {2020}, abstract = {Objective Plant carnivory is distributed across the tree of life and has evolved at least six times independently, but sequenced and annotated nuclear genomes of carnivorous plants are currently lacking. We have sequenced and structurally annotated the nuclear genome of the carnivorous Roridula gorgonias and that of a non-carnivorous relative, Madeira's lily-of-the-valley-tree, Clethra arborea, both within the Ericales. This data adds an important resource to study the evolutionary genetics of plant carnivory across angiosperm lineages and also for functional and systematic aspects of plants within the Ericales. Results Our assemblies have total lengths of 284 Mbp (R. gorgonias) and 511 Mbp (C. arborea) and show high BUSCO scores of 84.2\% and 89.5\%, respectively. We used their predicted genes together with publicly available data from other Ericales' genomes and transcriptomes to assemble a phylogenomic data set for the inference of a species tree. However, groups of orthologs showed a marked absence of species represented by a transcriptome. We discuss possible reasons and caution against combining predicted genes from genome- and transriptome-based assemblies.}, language = {en} } @article{OzcelikayKurbanogluYarmanetal.2020, author = {Ozcelikay, Goksu and Kurbanoglu, Sevinc and Yarman, Aysu and Scheller, Frieder W. and Ozkan, Sibel A.}, title = {Au-Pt nanoparticles based molecularly imprinted nanosensor for electrochemical detection of the lipopeptide antibiotic drug Daptomycin}, series = {Sensors and actuators : B, Chemical}, volume = {320}, journal = {Sensors and actuators : B, Chemical}, publisher = {Elsevier Science}, address = {Amsterdam}, issn = {0925-4005}, doi = {10.1016/j.snb.2020.128285}, pages = {7}, year = {2020}, abstract = {In this work, a novel electrochemical molecularly imprinted polymer (MIP) sensor for the detection of the lipopeptide antibiotic Daptomycin (DAP) is presented which integrates gold decorated platinum nanoparticles (Au-Pt NPs) into the nanocomposite film. The sensor was prepared by electropolymerization of o-phenylenediamine (o-PD) in the presence of DAP using cyclic voltammetry. Cyclic voltammetry and differential pulse voltammetry were applied to follow the changes in the MIP-layer related to rebinding and removal of the target DAP by using the redox marker [Fe(CN)(6)](3-/4-). Under optimized operational conditions, the MIP/Au-Pt NPs/ GCE nanosensor exhibits a linear response in the range of 1-20 pM towards DAP. The limit of detection and limit of quantification were determined to be 0.161pM +/- 0.012 and 0.489pM +/- 0.012, respectively. The sensitivity towards the antibiotics Vancomycin and Erythromycin and the amino acids glycine and tryptophan was below 7 percent as compared with DAP. Moreover, the nanosensor was also successfully used for the detection of DAP in deproteinated human serum samples.}, language = {en} } @article{DragoPawlakWeithoff2020, author = {Drago, Claudia and Pawlak, Julia and Weithoff, Guntram}, title = {Biogenic aggregation of small microplastics alters their ingestion by a common freshwater micro-invertebrate}, series = {Frontiers in Environmental Science}, volume = {8}, journal = {Frontiers in Environmental Science}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2296-665X}, doi = {10.3389/fenvs.2020.574274}, pages = {11}, year = {2020}, abstract = {In recent years, increasing concerns have been raised about the environmental risk of microplastics in freshwater ecosystems. Small microplastics enter the water either directly or accumulate through disintegration of larger plastic particles. These particles might then be ingested by filter-feeding zooplankton, such as rotifers. Particles released into the water may also interact with the biota through the formation of aggregates, which might alter the uptake by zooplankton. In this study, we tested for size-specific aggregation of polystyrene microspheres and their ingestion by a common freshwater rotifer Brachionus calyciflorus. The ingestion of three sizes of polystyrene microspheres (MS) 1-, 3-, and 6-mu m was investigated. Each MS size was tested in combination with three different treatments: MS as the sole food intake, MS in association with food algae and MS aggregated with biogenic matter. After 72 h incubation in pre-filtered natural river water, the majority of the 1-mu m spheres occurred as aggregates. The larger the particles, the higher the relative number of single particles and the larger the aggregates. All particles were ingested by the rotifer following a Type-II functional response. The presence of algae did not influence the ingestion of the MS for all three sizes. The biogenic aggregation of microspheres led to a significant size-dependent alteration in their ingestion. Rotifers ingested more microspheres (MS) when exposed to aggregated 1- and 3-mu m MS as compared to single spheres, whereas fewer aggregated 6-mu m spheres were ingested. This indicates that the small particles when aggregated were in an effective size range for Brachionus, while the aggregated larger spheres became too large to be efficiently ingested. These observations provide the first evidence of a size- and aggregation-dependent feeding interaction between microplastics and rotifers. Microplastics when aggregated with biogenic particles in a natural environment can rapidly change their size-dependent availability. The aggregation properties of microplastics should be taken into account when performing experiments mimicking the natural environment.}, language = {en} } @article{StieglervonHoermannMuelleretal.2020, author = {Stiegler, Jonas and von Hoermann, Christian and M{\"u}ller, J{\"o}rg and Benbow, Mark Eric and Heurich, Marco}, title = {Carcass provisioning for scavenger conservation in a temperate forest ecosystem}, series = {Ecosphere}, volume = {11}, journal = {Ecosphere}, number = {4}, publisher = {ESA}, address = {Ithaca, NY}, issn = {2150-8925}, doi = {10.1002/ecs2.3063}, pages = {13}, year = {2020}, abstract = {Carrion plays an essential role in shaping the structure and functioning of ecosystems and has far-reaching implications for biodiversity conservation. The change in availability and type of carcasses throughout ecosystems can involve negative effects for scavenging communities. To address this issue, there have been recent conservation management measures of carrion provision in natural systems. However, the optimal conditions under which exposing carcasses to optimize conservation outcomes are still limited. Here, we used camera traps throughout elevational and vegetational gradients to monitor the consumption of 48 deer carcasses over a study period of six years by evaluating 270,279 photographs resulting out of 15,373 trap nights. We detected 17 species visiting carcass deployments, including five endangered species. Our results show that large carcasses, the winter season, and a heterogeneous surrounding habitat enhanced the frequency of carcass visits and the species richness of scavenger assemblages. Contrary to our expectations, carcass species, condition (fresh/frozen), and provision schedule (continuous vs single exposure) did not influence scavenging frequency or diversity. The carcass visitation frequency increased with carcass mass and lower temperatures. The effect of large carcasses was especially pronounced for mesopredators and the Eurasian lynx (Lynx lynx ). Lynx were not too influenced in its carrion acquisition by the season, but exclusively preferred remote habitats containing higher forest cover. Birds of prey, mesopredators, and top predators were also positively influenced by the visiting rate of ravens (Corvus corax ), whereas no biotic or abiotic preferences were found for wild boars (Sus scrofa ). This study provides evidence that any ungulate species of carrion, either in a fresh or in previously frozen condition, attracts a high diversity of scavengers especially during winter, thereby supporting earlier work that carcass provisions may support scavenger communities and endangered species.}, language = {en} }