TY - THES A1 - Józefczuk, Szymon T1 - "Escherichia coli" stress response on the level of transcriptome and metabolome Y1 - 2009 ER - TY - JOUR A1 - Zhang, Xiaorong A1 - Caserta, Giorgio A1 - Yarman, Aysu A1 - Supala, Eszter A1 - Tadjoung Waffo, Armel Franklin A1 - Wollenberger, Ulla A1 - Gyurcsanyi, Robert E. A1 - Zebger, Ingo A1 - Scheller, Frieder W. T1 - "Out of Pocket" protein binding BT - a dilemma of epitope imprinted polymers revealed for human hemoglobin JF - Chemosensors N2 - The epitope imprinting approach applies exposed peptides as templates to synthesize Molecularly Imprinted Polymers (MIPs) for the recognition of the parent protein. While generally the template protein binding to such MIPs is considered to occur via the epitope-shaped cavities, unspecific interactions of the analyte with non-imprinted polymer as well as the detection method used may add to the complexity and interpretation of the target rebinding. To get new insights on the effects governing the rebinding of analytes, we electrosynthesized two epitope-imprinted polymers using the N-terminal pentapeptide VHLTP-amide of human hemoglobin (HbA) as the template. MIPs were prepared either by single-step electrosynthesis of scopoletin/pentapeptide mixtures or electropolymerization was performed after chemisorption of the cysteine extended VHLTP peptide. Rebinding of the target peptide and the parent HbA protein to the MIP nanofilms was quantified by square wave voltammetry using a redox probe gating, surface enhanced infrared absorption spectroscopy, and atomic force microscopy. While binding of the pentapeptide shows large influence of the amino acid sequence, all three methods revealed strong non-specific binding of HbA to both polyscopoletin-based MIPs with even higher affinities than the target peptides. KW - Molecularly Imprinted Polymers KW - epitope imprinting KW - non-specific KW - binding KW - redox gating KW - SEIRA spectroelectrochemistry Y1 - 2021 U6 - https://doi.org/10.3390/chemosensors9060128 SN - 2227-9040 VL - 9 IS - 6 PB - MDPI CY - Basel ER - TY - JOUR A1 - Schrapers, Peer A1 - Hartmann, Tobias A1 - Kositzki, Ramona A1 - Dau, Holger A1 - Reschke, Stefan A1 - Schulzke, Carola A1 - Leimkühler, Silke A1 - Haumann, Michael T1 - 'Sulfido and Cysteine Ligation Changes at the Molybdenum Cofactor during Substrate Conversion by Formate Dehydrogenase (FDH) from Rhodobacter capsulatus JF - Inorganic chemistry N2 - Formate dehydrogenase (FDH) enzymes are attractive catalysts for potential carbon dioxide conversion applications. The FDH from Rhodobacter capsulatus (RcFDH) binds a bis-molybdopterin-guanine-dinucleotide (bis-MGD) cofactor, facilitating reversible formate (HCOO-) to CO2 oxidation. We characterized the molecular structure of the active site of wildtype RcFDH and protein variants using X-ray absorption spectroscopy (XAS) at the Mo K-edge. This approach has revealed concomitant binding of a sulfido ligand (Mo=S) and a conserved cysteine residue (S(Cys386)) to Mo(VI) in the active oxidized molybdenum cofactor (Moco), retention of such a coordination motif at Mo(V) in a chemically reduced enzyme, and replacement of only the S(Cys386) ligand by an oxygen of formate upon Mo(IV) formation. The lack of a Mo=S bond in RcFDH expressed in the absence of FdsC implies specific metal sulfuration by this bis-MGD binding chaperone. This process still functioned in the Cys386Ser variant, showing no Mo-S(Cys386) ligand, but retaining a Mo=S bond. The C386S variant and the protein expressed without FdsC were inactive in formate oxidation, supporting that both Moligands are essential for catalysis. Low-pH inhibition of RcFDH was attributed to protonation at the conserved His387, supported by the enhanced activity of the His387Met variant at low pH, whereas inactive cofactor species showed sulfido-to-oxo group exchange at the Mo ion. Our results support that the sulfido and S(Cys386) ligands at Mo and a hydrogen-bonded network including His387 are crucial for positioning, deprotonation, and oxidation of formate during the reaction cycle of RcFDH. Y1 - 2015 U6 - https://doi.org/10.1021/ic502880y SN - 0020-1669 SN - 1520-510X VL - 54 IS - 7 SP - 3260 EP - 3271 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Uhlig, Katja A1 - Madaboosi, Narayanan A1 - Schmidt, Stephan A1 - Jäger, Magnus S. A1 - Rose, Jürgen A1 - Duschl, Claus A1 - Volodkin, Dmitry V. T1 - 3d localization and diffusion of proteins in polyelectrolyte multilayers JF - Soft matter N2 - The interaction of diverse biomaterials with surfaces is more crucial than ever for biomedical applications to ensure efficiency and reproducibility. Very interesting surface materials are micrometer-thick polyelectrolyte multilayers. Not only their surface but also the bulk can be loaded with biomaterials like proteins or DNA for various purposes. Therefore, we established a method to analyze the lateral and vertical distribution of fluorescently labelled proteins of various size and charge in polyelectrolyte films composed of poly(L-lysine) and hyaluronic acid by confocal laser scanning microscopy. This approach enables us to measure the diffusion coefficients of the proteins via fluorescence recovery after photobleaching as a function of their vertical position in the film and facilitates the understanding of molecular interactions in the film with a high resolution in both space and time. As a result, we confirm that protein loading in the film is driven by electrostatic interactions - uncharged dextran molecules of 10 and 500 kDa do not diffuse into the film. Proteins of different sizes (3-11 nm) can diffuse relatively fast (D = 2-4 mm(2) s(-1)) independent of their net charge, indicating complex interpolymer interactions. This approach is a new powerful experimental tool to design the polyelectrolyte multilayers for bio-applications by finding a relationship between intermolecular interactions and mobility and availability of biomolecules to biological samples (e.g. cells) or detection units (e.g. biosensors). Y1 - 2012 U6 - https://doi.org/10.1039/c2sm26500a SN - 1744-683X VL - 8 IS - 47 SP - 11786 EP - 11789 PB - Royal Society of Chemistry CY - Cambridge ER - TY - THES A1 - Balk, Maria T1 - 3D structured shape-memory hydrogels with enzymatically-induced shape shifting Y1 - 2015 ER - TY - JOUR A1 - Schwarzer, Christian A1 - Huamani, Fatima Cßceres A1 - Cano, Asunción A1 - La Torre, María I. La A1 - Weigend, Maximilian T1 - 400 years for long-distance dispersal and divergence in the northern atacama desert : insights from the Huaynaputina pumice slopes of Moquegua, Peru N2 - The Huaynaputina eruption (1600 AD, Moquegua, S Peru) in the northern Atacama Desert denuded the Ornate area of all vegetation and deposited deep pumice layers. Data on the flora, climate and soil characteristics of these slopes near Ornate at 1600-2600 m a.s.l. are provided. Fifty-nine angiosperm species established themselves on the pumice slopes in the past ca. 400 years, with the bulk of the small and herbaceous species and several species new records for Peru. Three Ornate sites were sampled in both a dry and a wet year and species numbers differed widely (14 versus 45 spp.). Among areas compared floristic composition is most similar to the Lomas de Tacna, and has less in common with geographically closer Lomas or Sierra formations. Nine species represent highly disjunct populations (200->700 km) from their nearest known living populations in central Peru, Chile, or Argentina/Bolivia and appear to have reached the area via long-distance dispersal. Abiotic conditions may have played an important role in limiting the establishment of species from the neighboring vegetation. Four taxa on the pumice slopes show clear morphological differences to populations elsewhere, two of them may represent neoendemics of the Ornate pumice, indicating rapid morphological divergence. (C) 2010 Elsevier Ltd. All rights reserved. Y1 - 2010 U6 - https://doi.org/10.1016/j.jaridenv.2010.05.034 SN - 0140-1963 ER - TY - JOUR A1 - Gruden, Kristina A1 - Hren, Matjaz A1 - Herman, Ana A1 - Blejec, Andrej A1 - Albrecht, Tanja A1 - Selbig, Joachim A1 - Bauer, Christian G. A1 - Schuchardt, Johannes A1 - Or-Guil, Michal A1 - Zupancic, Klemen A1 - Svajger, Urban A1 - Stabuc, Borut A1 - Ihan, Alojz A1 - Kopitar, Andreja Natasa A1 - Ravnikar, Maja A1 - Knezevic, Miomir A1 - Rozman, Primoz A1 - Jeras, Matjaz T1 - A "Crossomics" study analysing variability of different components in peripheral blood of healthy caucasoid individuals JF - PLoS one N2 - Background: Different immunotherapy approaches for the treatment of cancer and autoimmune diseases are being developed and tested in clinical studies worldwide. Their resulting complex experimental data should be properly evaluated, therefore reliable normal healthy control baseline values are indispensable. Methodology/Principal Findings: To assess intra- and inter-individual variability of various biomarkers, peripheral blood of 16 age and gender equilibrated healthy volunteers was sampled on 3 different days within a period of one month. Complex "crossomics'' analyses of plasma metabolite profiles, antibody concentrations and lymphocyte subset counts as well as whole genome expression profiling in CD4(+)T and NK cells were performed. Some of the observed age, gender and BMI dependences are in agreement with the existing knowledge, like negative correlation between sex hormone levels and age or BMI related increase in lipids and soluble sugars. Thus we can assume that the distribution of all 39.743 analysed markers is well representing the normal Caucasoid population. All lymphocyte subsets, 20% of metabolites and less than 10% of genes, were identified as highly variable in our dataset. Conclusions/Significance: Our study shows that the intra- individual variability was at least two-fold lower compared to the inter-individual one at all investigated levels, showing the importance of personalised medicine approach from yet another perspective. Y1 - 2012 U6 - https://doi.org/10.1371/journal.pone.0028761 SN - 1932-6203 VL - 7 IS - 1 PB - PLoS CY - San Fransisco ER - TY - GEN A1 - Brechun, Katherine E. A1 - Woolley, Andrew A1 - Arndt, Katja Maren T1 - A Bacterial Bandpass Assay for Protein-Protein Interactions T2 - Protein science : a publication of the Protein Society Y1 - 2017 SN - 0961-8368 SN - 1469-896X VL - 26 SP - 198 EP - 198 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Ruzanski, Christian A1 - Smirnova, Julia A1 - Rejzek, Martin A1 - Cockburn, Darrell A1 - Pedersen, Henriette L. A1 - Pike, Marilyn A1 - Willats, William G. T. A1 - Svensson, Birte A1 - Steup, Martin A1 - Ebenhöh, Oliver A1 - Smith, Alison M. A1 - Field, Robert A. T1 - A bacterial glucanotransferase can replace the complex maltose metabolism required for starch to sucrose conversion in leaves at night JF - The journal of biological chemistry N2 - Controlled conversion of leaf starch to sucrose at night is essential for the normal growth of Arabidopsis. The conversion involves the cytosolic metabolism of maltose to hexose phosphates via an unusual, multidomain protein with 4-glucanotransferase activity, DPE2, believed to transfer glucosyl moieties to a complex heteroglycan prior to their conversion to hexose phosphate via a cytosolic phosphorylase. The significance of this complex pathway is unclear; conversion of maltose to hexose phosphate in bacteria proceeds via a more typical 4-glucanotransferase that does not require a heteroglycan acceptor. It has recently been suggested that DPE2 generates a heterogeneous series of terminal glucan chains on the heteroglycan that acts as a glucosyl buffer to ensure a constant rate of sucrose synthesis in the leaf at night. Alternatively, DPE2 and/or the heteroglycan may have specific properties important for their function in the plant. To distinguish between these ideas, we compared the properties of DPE2 with those of the Escherichia coli glucanotransferase MalQ. We found that MalQ cannot use the plant heteroglycan as an acceptor for glucosyl transfer. However, experimental and modeling approaches suggested that it can potentially generate a glucosyl buffer between maltose and hexose phosphate because, unlike DPE2, it can generate polydisperse malto-oligosaccharides from maltose. Consistent with this suggestion, MalQ is capable of restoring an essentially wild-type phenotype when expressed in mutant Arabidopsis plants lacking DPE2. In light of these findings, we discuss the possible evolutionary origins of the complex DPE2-heteroglycan pathway. KW - Carbohydrate Metabolism KW - Computer Modeling KW - Metabolic Regulation KW - Oligosaccharide KW - Plant Biochemistry KW - Glucanotransferase KW - Leaf Cell KW - Maltose Metabolism KW - Starch Degradation Y1 - 2013 U6 - https://doi.org/10.1074/jbc.M113.497867 SN - 0021-9258 SN - 1083-351X VL - 288 IS - 40 SP - 28581 EP - 28598 PB - American Society for Biochemistry and Molecular Biology CY - Bethesda ER - TY - THES A1 - Stephan, Mareike Sophia T1 - A bacterial mimetic system to study bacterial inactivation and infection N2 - The emerging threat of antibiotic-resistant bacteria has become a global challenge in the last decades, leading to a rising demand for alternative treatments for bacterial infections. One approach is to target the bacterial cell envelope, making understanding its biophysical properties crucial. Specifically, bacteriophages use the bacterial envelope as an entry point to initiate infection, and they are considered important building blocks of new antibiotic strategies against drug-resistant bacteria.. Depending on the structure of the cell wall, bacteria are classified as Gram-negative and Gram-positive. Gram-negative bacteria are equipped with a complex cell envelope composed of two lipid membranes enclosing a rigid peptidoglycan layer. The synthesis machinery of the Gram-negative cell envelope is the target of antimicrobial agents, including new physical sanitizing procedures addressing the outer membrane (OM). It is therefore very important to study the biophysical properties of the Gram-negative bacterial cell envelope. The high complexity of the Gram-negative OM sets the demand for a model system in which the contribution of individual components can be evaluated separately. In this respect, giant unilamellar vesicles (GUVs) are promising membrane systems to study membrane properties while controlling parameters such as membrane composition and surrounding medium conditions. The aim of this work was to develop methods and approaches for the preparation and characterization of a GUV-based membrane model that mimics the OM of the Gram-negative cell envelope. A major component of the OM is the lipopolysaccharide (LPS) on the outside of the OM heterobilayer. The vesicle model was designed to contain LPS in the outer leaflet and lipids in the inner leaflet. Furthermore, the interaction of the prepared LPS-GUVs with bacteriophages was tested. LPS containing GUVs were prepared by adapting the inverted emulsion technique to meet the challenging properties of LPS, namely their high self-aggregation rate in aqueous solutions. Notably, an additional emulsification step together with the adaption of solution conditions was employed to asymmetrically incorporate LPS containing long polysaccharide chains into the artificial membranes. GUV membrane asymmetry was verified with a fluorescence quenching assay. Since the necessary precautions for handling the quenching agent sodium dithionite are often underestimated and poorly described, important parameters were tested and identified to obtain a stable and reproducible assay. In the context of varied LPS incorporation, a microscopy-based technique was introduced to determine the LPS content on individual GUVs and to directly compare vesicle properties and LPS coverage. Diffusion coefficient measurements in the obtained GUVs showed that increasing LPS concentrations in the membranes resulted in decreased diffusivity. Employing LPS-GUVs we could demonstrate that a Salmonella bacteriophage bound with high specificity to its LPS receptor when presented at the GUV surface, and that the number of bound bacteriophages scaled with the amount of presented LPS receptor. In addition to binding, the bacteriophages were able to eject their DNA into the vesicle lumen. LPS-GUVs thus provide a starting platform for bottom-up approaches for the generation of more complex membranes, in which the effects of individual components on the membrane properties and the interaction with antimicrobial agents such as bacteriophages could be explored. N2 - Die wachsende Bedrohung durch antibiotikaresistente Bakterien ist in den letzten Jahrzehnten zu einer globalen Herausforderung geworden, was zu einer steigenden Nachfrage nach alternativen Behandlungsmethoden für bakterielle Infektionen geführt hat. Ein Ansatz besteht darin, die bakterielle Zellhülle anzugreifen, weshalb das Verständnis ihrer biophysikalischen Eigenschaften entscheidend ist. Insbesondere Bakteriophagen, Viren, die Bakterien infizieren, nutzen die Bakterienhülle als ersten Angriffspunkt für die Infektion und gelten als wichtige Bausteine für neue Antibiotikastrategien gegen arzneimittelresistente Bakterien. Je nach Struktur der Zellwand werden Bakterien in gramnegative und grampositive Bakterien eingeteilt. Gramnegative Bakterien sind mit einer komplexen Zellhülle ausgestattet. Daher ist es sehr wichtig, ihre biophysikalischen Eigenschaften zu untersuchen. Die hohe Komplexität der äußeren Zellhülle, auch äußere Membran genannt, erfordert ein Modellsystem, in dem der Beitrag jeder einzelnen Komponente separat bewertet werden kann. In dieser Hinsicht sind Vesikel-basierte Modellsysteme sehr vielversprechend, da sie wichtige Eigenschaften der äußeren Membran simulieren können, aber in ihrer Komplexität stark reduziert und kontrollierbar sind. Ziel dieser Arbeit war es, Methoden und Ansätze für die Herstellung und Charakterisierung eines Vesikel-basierten Modells zu entwickeln, das die äußere Membran der gramnegativen bakteriellen Zellhülle nachahmt. Ein Hauptbestandteil der äußeren Membran ist Lipopolysaccharid (LPS), das asymmetrisch auf der Außenseite der äußeren Membran vorhanden ist. Das Vesikelmodell wurde so konzipiert, dass es außen LPS und innen Phospholipide enthält. Die Herstellung des beschriebenen Modellsystems erforderte einige Anpassungen, da die Hüllkomponente LPS eine hohe Tendenz zur Bildung von Selbstaggregaten aufweist. Durch die Einführung eines zusätzlichen Schrittes in das Standardprotokoll konnten Vesikel mit LPS-Inkorporation erzeugt werden. Es wurde sowohl die Menge als auch die asymmetrische Verteilung des LPS-Einbaus bestimmt. Mit Hilfe von Bakteriophagen sollte die biologische Wirkung des Modellsystems getestet werden. Es wurde gezeigt, dass Bakteriophagen, die spezifisch LPS erkennen und binden, nach Zugabe zum Modellsystem die Vesikel binden und ihr genetisches Material in das Vesikel-Innere injizieren. Die hier beschriebenen LPS-haltigen Vesikel können als Ausgangsplattform für Bottom-up-Ansätze zur Herstellung komplexerer Membranen verwendet werden. Mit diesen komplexeren, aber kontrollierbaren Systemen lassen sich die Auswirkungen einzelner Komponenten der bakteriellen Zellhülle auf die Eigenschaften der Zellhülle sowie ihre Wechselwirkung mit antimikrobiellen Wirkstoffen wie Bakteriophagen untersuchen. KW - Bakterien KW - Bakteriophagen KW - Zellmembran KW - Vesikel KW - Konfokale Mikroskopie KW - Lipopolysaccharid KW - gramnegativ KW - bacteria KW - bacteriophage KW - cell membrane KW - vesicle KW - confocal microscopy KW - lipopolysaccharide KW - gram-negative Y1 - 2023 ER - TY - GEN A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd T1 - A balance to death T2 - Nature plants N2 - Leaf senescence plays a crucial role in nutrient recovery in late-stage plant development and requires vast transcriptional reprogramming by transcription factors such as ORESARA1 (ORE1). A proteolytic mechanism is now found to control ORE1 degradation, and thus senescence, during nitrogen starvation. Y1 - 2018 U6 - https://doi.org/10.1038/s41477-018-0279-6 SN - 2055-026X SN - 2055-0278 VL - 4 IS - 11 SP - 863 EP - 864 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Mulder, Christian A1 - Boit, Alice A1 - Bonkowski, Michael A1 - De Ruiter, Peter C. A1 - Mancinelli, Giorgio A1 - Van der Heijden, Marcel G. A. A1 - Van Wijnen, Harm J. A1 - Vonk, J. Arie A1 - Rutgers, Michiel ED - Woodward, G T1 - A belowground perspective on dutch agroecosystems how soil organisms interact to support ecosystem services JF - Advances in ecological research JF - Advances in Ecological Research N2 - 1. New patterns and trends in land use are becoming increasingly evident in Europe's heavily modified landscape and else whereas sustainable agriculture and nature restoration are developed as viable long-term alternatives to intensively farmed arable land. The success of these changes depends on how soil biodiversity and processes respond to changes in management. To improve our understanding of the community structure and ecosystem functioning of the soil biota, we analyzed abiotic variables across 200 sites, and biological variables across 170 sites in The Netherlands, one of the most intensively farmed countries. The data were derived from the Dutch Soil Quality Network (DSQN), a long-term monitoring framework designed to obtain ecological insight into soil types (STs) and ecosystem types (ETs). 2. At the outset we describe STs and biota, and we estimate the contribution of various groups to the provision of ecosystem services. We focused on interactive effects of soil properties on community patterns and ecosystem functioning using food web models. Ecologists analyze soil food webs by means of mechanistic and statistical modelling, linking network structure to energy flow and elemental dynamics commonly based on allometric scaling. 3. We also explored how predatory and metabolic processes are constrained by body size, diet and metabolic type, and how these constraints govern the interactions within and between trophic groups. In particular, we focused on how elemental fluxes determine the strengths of ecological interactions, and the resulting ecosystem services, in terms of sustenance of soil fertility. 4. We discuss data mining, food web visualizations, and an appropriate categorical way to capture subtle interrelationships within the DSQN dataset. Sampled metazoans were used to provide an overview of below-ground processes and influences of land use. Unlike most studies to date we used data from the entire size spectrum, across 15 orders of magnitude, using body size as a continuous trait crucial for understanding ecological services. 5. Multimodality in the frequency distributions of body size represents a performance filter that acts as a buffer to environmental change. Large differences in the body-size distributions across ETs and STs were evident. Most observed trends support the hypothesis that the direct influence of ecological stoichiometry on the soil biota as an independent predictor (e.g. in the form of nutrient to carbon ratios), and consequently on the allometric scaling, is more dominant than either ET or ST. This provides opportunities to develop a mechanistic and physiologically oriented model for the distribution of species' body sizes, where responses of invertebrates can be predicted. 6. Our results highlight the different roles that organisms play in a number of key ecosystem services. Such a trait-based research has unique strengths in its rigorous formulation of fundamental scaling rules, as well as in its verifiability by empirical data. Nonetheless, it still has weaknesses that remain to be addressed, like the consequences of intraspecific size variation, the high degree of omnivory, and a possibly inaccurate assignment to trophic groups. 7. Studying the extent to which nutrient levels influence multitrophic interactions and how different land-use regimes affect soil biodiversity is clearly a fruitful area for future research to develop predictive models for soil ecosystem services under different management regimes. No similar efforts have been attempted previously for soil food webs, and our dataset has the potential to test and further verify its usefulness at an unprecedented space scale. Y1 - 2011 SN - 978-0-12-374794-5 U6 - https://doi.org/10.1016/B978-0-12-374794-5.00005-5 SN - 0065-2504 VL - 44 IS - 2 SP - 277 EP - 357 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Wolff, Martin A1 - Zhang-Haagen, Bo A1 - Decker, Christina A1 - Barz, Bogdan A1 - Schneider, Mario A1 - Biehl, Ralf A1 - Radulescu, Aurel A1 - Strodel, Birgit A1 - Willbold, Dieter A1 - Nagel-Steger, Luitgard T1 - A beta 42 pentamers/hexamers are the smallest detectable oligomers in solution JF - Scientific reports Y1 - 2017 U6 - https://doi.org/10.1038/s41598-017-02370-3 SN - 2045-2322 VL - 7 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Klauschies, Toni A1 - Coutinho, Renato Mendes A1 - Gaedke, Ursula T1 - A beta distribution-based moment closure enhances the reliability of trait-based aggregate models for natural populations and communities JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - Ecological communities are complex adaptive systems that exhibit remarkable feedbacks between their biomass and trait dynamics. Trait-based aggregate models cope with this complexity by focusing on the temporal development of the community’s aggregate properties such as its total biomass, mean trait and trait variance. They are based on particular assumptions about the shape of the underlying trait distribution, which is commonly assumed to be normal. However, ecologically important traits are usually restricted to a finite range, and empirical trait distributions are often skewed or multimodal. As a result, normal distribution-based aggregate models may fail to adequately represent the biomass and trait dynamics of natural communities. We resolve this mismatch by developing a new moment closure approach assuming the trait values to be beta-distributed. We show that the beta distribution captures important shape properties of both observed and simulated trait distributions, which cannot be captured by a Gaussian. We further demonstrate that a beta distribution-based moment closure can strongly enhance the reliability of trait-based aggregate models. We compare the biomass, mean trait and variance dynamics of a full trait distribution (FD) model to the ones of beta (BA) and normal (NA) distribution-based aggregate models, under different selection regimes. This way, we demonstrate under which general conditions (stabilizing, fluctuating or disruptive selection) different aggregate models are reliable tools. All three models predicted very similar biomass and trait dynamics under stabilizing selection yielding unimodal trait distributions with small standing trait variation. We also obtained an almost perfect match between the results of the FD and BA models under fluctuating selection, promoting skewed trait distributions and ongoing oscillations in the biomass and trait dynamics. In contrast, the NA model showed unrealistic trait dynamics and exhibited different alternative stable states, and thus a high sensitivity to initial conditions under fluctuating selection. Under disruptive selection, both aggregate models failed to reproduce the results of the FD model with the mean trait values remaining within their ecologically feasible ranges in the BA model but not in the NA model. Overall, a beta distribution-based moment closure strongly improved the realism of trait-based aggregate models. KW - Moment closure KW - Normal and beta distribution KW - Skewed and peaked trait distributions KW - Fitness landscape and frequency-dependent selection KW - Eco-evolutionary dynamics KW - Modelling functional diversity Y1 - 2018 U6 - https://doi.org/10.1016/j.ecolmodel.2018.02.001 SN - 0304-3800 SN - 1872-7026 VL - 381 SP - 46 EP - 77 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Huang, T. A1 - Warsinke, Axel A1 - Koroljova-Skorobogatko, O. V. A1 - Makower, Alexander A1 - Kuwana, T. A1 - Scheller, Frieder W. T1 - A bienzyme carbon paste electrode for the sensitive detection of NADPH and the measurement of glucose-6- phosphate dehydrogenase Y1 - 1999 ER - TY - JOUR A1 - Gajovic, Nenad A1 - Warsinke, Axel A1 - Scheller, Frieder W. T1 - A bienzyme electrode for L-malate based on a novel and general design Y1 - 1998 ER - TY - JOUR A1 - Eremenko, A. V. A1 - Makower, Alexander A1 - Bauer, Christian G. A1 - Kurochkin, I. N. A1 - Scheller, Frieder W. T1 - A bienzyme electrode for tyrosine containing peptides determination Y1 - 1997 ER - TY - JOUR A1 - Lettau, Kristian A1 - Warsinke, Axel A1 - Katterle, Martin A1 - Danielsson, Bengt A1 - Scheller, Frieder W. T1 - A bifunctional molecularly imprinted polymer (MIP): analysis of binding and catalysis by a thermistor N2 - Binding or catalysis? Both can be distinguished with a molecularly imprinted polymer (MIP) by the different patterns of heat generation. The catalytically active sites, like in the corresponding enzyme, generate a steady-state temperature increase. Thus, enzyme-like catalysis and antibody-analogue binding are analyzed simultaneously in a bifunctional MIP for the first time (see scheme). Y1 - 2006 UR - http://www3.interscience.wiley.com/cgi-bin/jhome/26737/ U6 - https://doi.org/10.1002/anie.200601796 ER - TY - JOUR A1 - Zhang, Shuhao A1 - Bramski, Julia A1 - Tutus, Murat A1 - Pietruszka, Jörg A1 - Böker, Alexander A1 - Reinicke, Stefan T1 - A Biocatalytically Active Membrane Obtained from Immobilization of 2-Deoxy-D-ribose-5-phosphate Aldolase on a Porous Support JF - ACS applied materials & interfaces N2 - Aldol reactions play an important role in organic synthesis, as they belong to the class of highly beneficial C-C-linking reactions. Aldol-type reactions can be efficiently and stereoselectively catalyzed by the enzyme 2-deoxy-D-ribose-5-phosphate aldolase (DERA) to gain key intermediates for pharmaceuticals such as atorvastatin. The immobilization of DERA would open the opportunity for a continuous operation mode which gives access to an efficient, large-scale production of respective organic intermediates. In this contribution, we synthesize and utilize DERA/polymer conjugates for the generation and fixation of a DERA bearing thin film on a polymeric membrane support. The conjugation strongly increases the tolerance of the enzyme toward the industrial relevant substrate acetaldehyde while UV-cross-linkable groups along the conjugated polymer chains provide the opportunity for covalent binding to the support. First, we provide a thorough characterization of the conjugates followed by immobilization tests on representative, nonporous cycloolefinic copolymer supports. Finally, immobilization on the target supports constituted of polyacrylonitrile (PAN) membranes is performed, and the resulting enzymatically active membranes are implemented in a simple membrane module setup for the first assessment of biocatalytic performance in the continuous operation mode using the combination hexanal/acetaldehyde as the substrate. KW - 2-deoxy-D-ribose-5-phoshphate aldolase KW - enzyme immobilization KW - enzymatically active membrane KW - enzyme/polymer conjugate KW - self-assembly Y1 - 2019 U6 - https://doi.org/10.1021/acsami.9b12029 SN - 1944-8244 SN - 1944-8252 VL - 11 IS - 37 SP - 34441 EP - 34453 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Boëchat, Iola G. A1 - Weithoff, Guntram A1 - Krüger, Angela A1 - Gücker, Björn A1 - Adrian, Rita T1 - A biochemical explanation for the success of the mixotrophy in the flagellate Ochromonas sp. N2 - We report the influence of different nutritional modes-autotrophy, mixotrophy, and heterotrophy-on the fatty acid and sterol composition of the freshwater flagellate Ochromonas sp. and discuss the ecological significance of our results with respect to the resource competition theory (rct). Polyunsaturated fatty acids (PUFAs) are the most efficient biochemical variable distinguishing between nutritional modes of Ochromonas sp. Decreasing concentrations of PUFAs were observed in the order autotrophs, mixotrophs, heterotrophs. In mixotrophs and heterotrophs, concentrations of saturated fatty acids were higher than those of monounsaturated fatty acids and PUFAs as a result of bacterivory. Stigmasterol was the main sterol in Ochromonas sp., regardless of nutritional mode. Mixotrophs showed higher growth rates than heterotrophs, which could not be explained by rct. Heterotrophs, in turn, exhibited higher growth rates than autotrophs, which were cultured under the same light conditions as mixotrophs. Mixotrophs can synthesize PUFAs, which are important for many physiological functions such as membrane permeability and growth. Thus, mixotrophy facilitated efficient growth as well as the ability to synthesize complex and essential biomolecules. These strong synergetic effects are due to the combination of biochemical benefits of heterotrophic and autotrophic metabolic pathways and cannot be predicted by rct. Y1 - 2007 UR - http://www.aslo.org/lo/ U6 - https://doi.org/10.4319/lo.2007.52.4.1624 SN - 0024-3590 ER - TY - JOUR A1 - Badalyan, Artavazd A1 - Neumann-Schaal, Meina A1 - Leimkühler, Silke A1 - Wollenberger, Ursula T1 - A Biosensor for aromatic aldehydes comprising the mediator dependent PaoABC-Aldehyde oxidoreductase JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - A novel aldehyde oxidoreductase (PaoABC) from Escherichia coli was utilized for the development of an oxygen insensitive biosensor for benzaldehyde. The enzyme was immobilized in polyvinyl alcohol and currents were measured for aldehyde oxidation with different one and two electron mediators with the highest sensitivity for benzaldehyde in the presence of hexacyanoferrate(III). The benzaldehyde biosensor was optimized with respect to mediator concentration, enzyme loading and pH using potassium hexacyanoferrate(III). The linear measuring range is between 0.5200 mu M benzaldehyde. In correspondence with the substrate selectivity of the enzyme in solution the biosensor revealed a preference for aromatic aldehydes and less effective conversion of aliphatic aldehydes. The biosensor is oxygen independent, which is a particularly attractive feature for application. The biosensor can be applied to detect contaminations with benzaldehyde in solvents such as benzyl alcohol, where traces of benzaldehyde in benzyl alcohol down to 0.0042?% can be detected. KW - Aldehyde oxidoreductase KW - Benzaldehyde KW - Biosensor KW - Aromatic aldehydes KW - Molybdenum cofactor Y1 - 2013 U6 - https://doi.org/10.1002/elan.201200362 SN - 1040-0397 VL - 25 IS - 1 SP - 101 EP - 108 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Berg-Mohnicke, Michael A1 - Nendel, Claas T1 - A case for object capabilities as the foundation of a distributed environmental model and simulation infrastructure JF - Environmental modelling & software with environment data news N2 - 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. KW - Cap'n proto KW - Scientific collaboration KW - Co -development KW - Communication KW - protocol KW - Object capability Y1 - 2022 U6 - https://doi.org/10.1016/j.envsoft.2022.105471 SN - 1364-8152 SN - 1873-6726 VL - 156 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Benina, Maria A1 - Ribeiro, Dimas Mendes A1 - Gechev, Tsanko S. A1 - Müller-Röber, Bernd A1 - Schippers, Jos H. M. T1 - A cell type-specific view on the translation of mRNAs from ROS-responsive genes upon paraquat treatment of Arabidopsis thaliana leaves JF - Plant, cell & environment : cell physiology, whole-plant physiology, community physiology N2 - Oxidative stress causes dramatic changes in the expression levels of many genes. The formation of a functional protein through successful mRNA translation is central to a coordinated cellular response. To what extent the response towards reactive oxygen species (ROS) is regulated at the translational level is poorly understood. Here we analysed leaf- and tissue-specific translatomes using a set of transgenic Arabidopsis thaliana lines expressing a FLAG-tagged ribosomal protein to immunopurify polysome-bound mRNAs before and after oxidative stress. We determined transcript levels of 171 ROS-responsive genes upon paraquat treatment, which causes formation of superoxide radicals, at the whole-organ level. Furthermore, the translation of mRNAs was determined for five cell types: mesophyll, bundle sheath, phloem companion, epidermal and guard cells. Mesophyll and bundle sheath cells showed the strongest response to paraquat treatment. Interestingly, several ROS-responsive transcription factors displayed cell type-specific translation patterns, while others were translated in all cell types. In part, cell type-specific translation could be explained by the length of the 5-untranslated region (5-UTR) and the presence of upstream open reading frames (uORFs). Our analysis reveals insights into the translational regulation of ROS-responsive genes, which is important to understanding cell-specific responses and functions during oxidative stress. The study illustrates the response of different Arabidopsis thaliana leaf cells and tissues to oxidative stress at the translational level, an aspect of reactive oxygen species (ROS) biology that has been little studied in the past. Our data reveal insights into how translational regulation of ROS-responsive genes is fine-tuned at the cellular level, a phenomenon contributing to the integrated physiological response of leaves to stresses involving changes in ROS levels. KW - Arabidopsis KW - gene regulation KW - oxidative stress KW - tissue-specific KW - translation Y1 - 2015 U6 - https://doi.org/10.1111/pce.12355 SN - 0140-7791 SN - 1365-3040 VL - 38 IS - 2 SP - 349 EP - 363 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Haueis, Lisa A1 - Stech, Marlitt A1 - Kubick, Stefan T1 - A Cell-free Expression Pipeline for the Generation and Functional Characterization of Nanobodies JF - Frontiers in Bioengineering and Biotechnology N2 - 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. KW - cell-free protein synthesis KW - In vitro transcription KW - translation KW - nanobody KW - VHH KW - camelid KW - CHO cell lysate Y1 - 2022 U6 - https://doi.org/10.3389/fbioe.2022.896763 SN - 2296-4185 VL - 10 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Çabuk, Uğur A1 - Ünlü, Ercan Selçuk T1 - A combined de novo assembly approach increases the quality of prokaryotic draft genomes JF - Folia microbiologica : international journal for general, environmental and applied microbiology, and immunology N2 - 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. KW - De novo assembly KW - Prokaryotes KW - Bacteria KW - NGS KW - Short reads KW - Draft genome Y1 - 2022 U6 - https://doi.org/10.1007/s12223-022-00980-7 SN - 0015-5632 SN - 1874-9356 VL - 67 SP - 801 EP - 810 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Bernhardt, Nadine A1 - Pestryakova, Luidmila Agafyevna A1 - Epp, Laura Saskia A1 - Herzschuh, Ulrike A1 - Tiedemann, Ralph T1 - A combined paleolimnological/genetic analysis of diatoms reveals divergent evolutionary lineages of Staurosira and Staurosirella (Bacillariophyta) in Siberian lake sediments along a latitudinal transect JF - Journal of paleolimnolog N2 - Diatom diversity in lakes of northwest Yakutia (Siberia) was investigated by microscopic and genetic analysis of surface and cored lake sediments, to evaluate the use of sedimentary DNA for paleolimnological diatom studies and to identify obscure genetic diversity that cannot be detected by microscopic methods. Two short (76 and 73 bp) and one longer (577 bp) fragments of the ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL) gene, encoding the large subunit of the rbcL, were used as genetic markers. Diverse morphological assemblages of diatoms, dominated by small benthic fragilarioid taxa, were retrieved from the sediments of each lake. These minute fragilarioid taxa were examined by scanning electron microscopy, revealing diverse morphotypes in Staurosira and Staurosirella from the different lakes. Genetic analyses indicated a dominance of haplotypes that were assigned to fragilarioid taxa and less genetic diversity in other diatom taxa. The long rbcL_577 amplicon identified considerable diversification among haplotypes clustering within the Staurosira/Staurosirella genera, revealing 19 different haplotypes whose spatial distribution appears to be primarily related to the latitude of the lakes, which corresponds to a vegetation and climate gradient. Our rbcL markers are valuable tools for tracking differences between diatom lineages that are not visible in their morphologies. These markers revealed putatively high genetic diversity within the Staurosira/Staurosirella species complex, at a finer scale than is possible to resolve by microscopic determination. The rbcL markers may provide additional reliable information on the diversity of barely distinguishable minute benthic fragilarioids. Environmental sequencing may thus allow the tracking of spatial and temporal diversification in Siberian lakes, especially in the context of diatom responses to recent environmental changes, which remains a matter of controversy. KW - Arctic lake sediments KW - Diatoms KW - Environmental DNA KW - Intraspecific variation KW - RbcL Y1 - 2014 U6 - https://doi.org/10.1007/s10933-014-9779-1 SN - 0921-2728 SN - 1573-0417 VL - 52 IS - 1-2 SP - 77 EP - 93 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Zor, K. A1 - Heiskanen, A. A1 - Caviglia, Claudia A1 - Vergani, M. A1 - Landini, E. A1 - Shah, F. A1 - Carminati, Marco A1 - Martinez-Serrano, A. A1 - Ramos Moreno, T. A1 - Kokaia, M. A1 - Benayahu, Dafna A1 - Keresztes, Zs. A1 - Papkovsky, D. A1 - Wollenberger, Ursula A1 - Svendsen, W. E. A1 - Dimaki, M. A1 - Ferrari, G. A1 - Raiteri, R. A1 - Sampietro, M. A1 - Dufva, M. A1 - Emneus, Jenny T1 - A compact multifunctional microfluidic platform for exploring cellular dynamics in real-time using electrochemical detection JF - RSC Advances N2 - Downscaling of microfluidic cell culture and detection devices for electrochemical monitoring has mostly focused on miniaturization of the microfluidic chips which are often designed for specific applications and therefore lack functional flexibility. We present a compact microfluidic cell culture and electrochemical analysis platform with in-built fluid handling and detection, enabling complete cell based assays comprising on-line electrode cleaning, sterilization, surface functionalization, cell seeding, cultivation and electrochemical real-time monitoring of cellular dynamics. To demonstrate the versatility and multifunctionality of the platform, we explored amperometric monitoring of intracellular redox activity in yeast (Saccharomyces cerevisiae) and detection of exocytotically released dopamine from rat pheochromocytoma cells (PC12). Electrochemical impedance spectroscopy was used in both applications for monitoring cell sedimentation and adhesion as well as proliferation in the case of PC12 cells. The influence of flow rate on the signal amplitude in the detection of redox metabolism as well as the effect of mechanical stimulation on dopamine release were demonstrated using the programmable fluid handling capability. The here presented platform is aimed at applications utilizing cell based assays, ranging from e.g. monitoring of drug effects in pharmacological studies, characterization of neural stem cell differentiation, and screening of genetically modified microorganisms to environmental monitoring. Y1 - 2014 U6 - https://doi.org/10.1039/c4ra12632g SN - 2046-2069 VL - 4 IS - 109 SP - 63761 EP - 63771 PB - Royal Society of Chemistry CY - Cambridge ER - TY - GEN A1 - Zór, K. A1 - Heiskanen, A. A1 - Caviglia, Claudia A1 - Vergani, M. A1 - Landini, E. A1 - Shah, F. A1 - Carminati, Marco A1 - Martínez-Serrano, A. A1 - Ramos Moreno, T. A1 - Kokaia, M. A1 - Benayahu, Dafna A1 - Keresztes, Zs. A1 - Papkovsky, D. A1 - Wollenberger, Ursula A1 - Svendsen, W. E. A1 - Dimaki, M. A1 - Ferrari, G. A1 - Raiteri, R. A1 - Sampietro, M. A1 - Dufva, M. A1 - Emnéus, J. T1 - A compact multifunctional microfluidic platform for exploring cellular dynamics in real-time using electrochemical detection N2 - Downscaling of microfluidic cell culture and detection devices for electrochemical monitoring has mostly focused on miniaturization of the microfluidic chips which are often designed for specific applications and therefore lack functional flexibility. We present a compact microfluidic cell culture and electrochemical analysis platform with in-built fluid handling and detection, enabling complete cell based assays comprising on-line electrode cleaning, sterilization, surface functionalization, cell seeding, cultivation and electrochemical real-time monitoring of cellular dynamics. To demonstrate the versatility and multifunctionality of the platform, we explored amperometric monitoring of intracellular redox activity in yeast (Saccharomyces cerevisiae) and detection of exocytotically released dopamine from rat pheochromocytoma cells (PC12). Electrochemical impedance spectroscopy was used in both applications for monitoring cell sedimentation and adhesion as well as proliferation in the case of PC12 cells. The influence of flow rate on the signal amplitude in the detection of redox metabolism as well as the effect of mechanical stimulation on dopamine release were demonstrated using the programmable fluid handling capability. The here presented platform is aimed at applications utilizing cell based assays, ranging from e.g. monitoring of drug effects in pharmacological studies, characterization of neural stem cell differentiation, and screening of genetically modified microorganisms to environmental monitoring. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 289 Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-99492 ER - TY - JOUR A1 - Niemeyer, Bastian A1 - Epp, Laura Saskia A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Pestryakova, Luidmila Agafyevna A1 - Herzschuh, Ulrike T1 - A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline JF - Molecular ecology resources N2 - Reliable information on past and present vegetation is important to project future changes, especially for rapidly transitioning areas such as the boreal treeline. To study past vegetation, pollen analysis is common, while current vegetation is usually assessed by field surveys. Application of detailed sedimentary DNA (sedDNA) records has the potential to enhance our understanding of vegetation changes, but studies systematically investigating the power of this proxy are rare to date. This study compares sedDNA metabarcoding and pollen records from surface sediments of 31 lakes along a north-south gradient of increasing forest cover in northern Siberia (Taymyr peninsula) with data from field surveys in the surroundings of the lakes. sedDNA metabarcoding recorded 114 plant taxa, about half of them to species level, while pollen analyses identified 43 taxa, both exceeding the 31 taxa found by vegetation field surveys. Increasing Larix percentages from north to south were consistently recorded by all three methods and principal component analyses based on percentage data of vegetation surveys and DNA sequences separated tundra from forested sites. Comparisons of the ordinations using procrustes and protest analyses show a significant fit among all compared pairs of records. Despite similarities of sedDNA and pollen records, certain idiosyncrasies, such as high percentages of Alnus and Betula in all pollen and high percentages of Salix in all sedDNA spectra, are observable. Our results from the tundra to single-tree tundra transition zone show that sedDNA analyses perform better than pollen in recording site-specific richness (i.e., presence/absence of taxa in the vicinity of the lake) and perform as well as pollen in tracing vegetation composition. KW - environmental DNA KW - metabarcoding KW - pollen KW - Siberia KW - trnL marker KW - vegetation Y1 - 2017 U6 - https://doi.org/10.1111/1755-0998.12689 SN - 1755-098X SN - 1755-0998 VL - 17 SP - e46 EP - e62 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Allan, Eric A1 - Weisser, Wolfgang W. A1 - Fischer, Markus A1 - Schulze, Ernst-Detlef A1 - Weigelt, Alexandra A1 - Roscher, Christiane A1 - Baade, Jussi A1 - Barnard, Romain L. A1 - Bessler, Holger A1 - Buchmann, Nina A1 - Ebeling, Anne A1 - Eisenhauer, Nico A1 - Engels, Christof A1 - Fergus, Alexander J. F. A1 - Gleixner, Gerd A1 - Gubsch, Marlen A1 - Halle, Stefan A1 - Klein, Alexandra Maria A1 - Kertscher, Ilona A1 - Kuu, Annely A1 - Lange, Markus A1 - Le Roux, Xavier A1 - Meyer, Sebastian T. A1 - Migunova, Varvara D. A1 - Milcu, Alexandru A1 - Niklaus, Pascal A. A1 - Oelmann, Yvonne A1 - Pasalic, Esther A1 - Petermann, Jana S. A1 - Poly, Franck A1 - Rottstock, Tanja A1 - Sabais, Alexander C. W. A1 - Scherber, Christoph A1 - Scherer-Lorenzen, Michael A1 - Scheu, Stefan A1 - Steinbeiss, Sibylle A1 - Schwichtenberg, Guido A1 - Temperton, Vicky A1 - Tscharntke, Teja A1 - Voigt, Winfried A1 - Wilcke, Wolfgang A1 - Wirth, Christian A1 - Schmid, Bernhard T1 - A comparison of the strength of biodiversity effects across multiple functions JF - Oecologia N2 - In order to predict which ecosystem functions are most at risk from biodiversity loss, meta-analyses have generalised results from biodiversity experiments over different sites and ecosystem types. In contrast, comparing the strength of biodiversity effects across a large number of ecosystem processes measured in a single experiment permits more direct comparisons. Here, we present an analysis of 418 separate measures of 38 ecosystem processes. Overall, 45 % of processes were significantly affected by plant species richness, suggesting that, while diversity affects a large number of processes not all respond to biodiversity. We therefore compared the strength of plant diversity effects between different categories of ecosystem processes, grouping processes according to the year of measurement, their biogeochemical cycle, trophic level and compartment (above- or belowground) and according to whether they were measures of biodiversity or other ecosystem processes, biotic or abiotic and static or dynamic. Overall, and for several individual processes, we found that biodiversity effects became stronger over time. Measures of the carbon cycle were also affected more strongly by plant species richness than were the measures associated with the nitrogen cycle. Further, we found greater plant species richness effects on measures of biodiversity than on other processes. The differential effects of plant diversity on the various types of ecosystem processes indicate that future research and political effort should shift from a general debate about whether biodiversity loss impairs ecosystem functions to focussing on the specific functions of interest and ways to preserve them individually or in combination. KW - Bottom-up effects KW - Carbon cycling KW - Ecological synthesis KW - Ecosystem processes KW - Grasslands KW - Jena experiment KW - Nitrogen cycling Y1 - 2013 U6 - https://doi.org/10.1007/s00442-012-2589-0 SN - 0029-8549 VL - 173 IS - 1 SP - 223 EP - 237 PB - Springer CY - New York ER - TY - JOUR A1 - Ziege, Madlen A1 - Hennige-Schulz, Carmen A1 - Muecksch, Frauke A1 - Bierbach, David A1 - Tiedemann, Ralph A1 - Streit, Bruno A1 - Plath, Martin T1 - A comparison of two methods to assess audience-induced changes in male mate choice JF - Current zoology N2 - Multidirectional communicative interactions in social networks can have a profound effect on mate choice behavior. Male Atlantic molly Poecilia mexicana exhibit weaker mating preferences when an audience male is presented. This could be a male strategy to reduce sperm competition risk: interacting more equally with different females may be advantageous because rivals might copy mate choice decisions. In line with this hypothesis, a previous study found males to show a strong audience effect when being observed while exercising mate choice, but not when the rival was presented only before the choice tests. Audience effects on mate choice decisions have been quantified in poeciliid fishes using association preference designs, but it remains unknown if patterns found from measuring association times translate into actual mating behavior. Thus, we created five audience treatments simulating different forms of perceived sperm competition risk and determined focal males' mating preferences by scoring pre-mating (nipping) and mating behavior (gonopodial thrusting). Nipping did not reflect the pattern that was found when association preferences were measured, while a very similar pattern was uncovered in thrusting behavior. The strongest response was observed when the audience could eavesdrop on the focal male's behavior. A reduction in the strength of focal males' preferences was also seen after the rival male had an opportunity to mate with the focal male's preferred mate. In comparison, the reduction of mating preferences in response to an audience was greater when measuring association times than actual mating behavior. While measuring direct sexual interactions between the focal male and both stimulus females not only the male's motivational state is reflected but also females' behavior such as avoidance of male sexual harassment. KW - Communication networks KW - Male mate choice KW - Non-independent mate choice KW - Sexual selection KW - Sperm competition risk KW - Audience effect Y1 - 2012 SN - 1674-5507 VL - 58 IS - 1 SP - 84 EP - 94 PB - Current Zoology CY - Beijing ER - TY - JOUR A1 - Sellrie, Frank A1 - Schenk, Jörg A. A1 - Behrsing, Olaf A1 - Bottger, Volker A1 - Micheel, Burkhard T1 - A competitive immunoassay to detect a hapten using an enzyme-labelled peptide mimotope as tracer N2 - Mimotope peptides-peptides which mimic the binding of a hapten to its corresponding monoclonal antibody-were conjugated to peroxidase and used in competitive immunoassay. The established immunoassay was used to quantitatively determine the concentration of hapten. As model system in all the experiments described here, we used the binding of the monoclonal antibody B13-DE1 to fluorescein and the corresponding peptide mimotope. Y1 - 2002 UR - http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T2Y-44MGNDF- 1&_coverDate=03%2F01%2F2002&_alid=268992656&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=4931&_sort=d&view=c&_acct=C000053886&_v e ER - TY - JOUR A1 - Noonan, Michael J. A1 - Tucker, Marlee A. A1 - Fleming, Christen H. A1 - Akre, Thomas S. A1 - Alberts, Susan C. A1 - Ali, Abdullahi H. A1 - Altmann, Jeanne A1 - Antunes, Pamela Castro A1 - Belant, Jerrold L. A1 - Beyer, Dean A1 - Blaum, Niels A1 - Boehning-Gaese, Katrin A1 - Cullen Jr, Laury A1 - de Paula, Rogerio Cunha A1 - Dekker, Jasja A1 - Drescher-Lehman, Jonathan A1 - Farwig, Nina A1 - Fichtel, Claudia A1 - Fischer, Christina A1 - Ford, Adam T. A1 - Goheen, Jacob R. A1 - Janssen, Rene A1 - Jeltsch, Florian A1 - Kauffman, Matthew A1 - Kappeler, Peter M. A1 - Koch, Flavia A1 - LaPoint, Scott A1 - Markham, A. Catherine A1 - Medici, Emilia Patricia A1 - Morato, Ronaldo G. A1 - Nathan, Ran A1 - Oliveira-Santos, Luiz Gustavo R. A1 - Olson, Kirk A. A1 - Patterson, Bruce D. A1 - Paviolo, Agustin A1 - Ramalho, Emiliano Estero A1 - Rosner, Sascha A1 - Schabo, Dana G. A1 - Selva, Nuria A1 - Sergiel, Agnieszka A1 - da Silva, Marina Xavier A1 - Spiegel, Orr A1 - Thompson, Peter A1 - Ullmann, Wiebke A1 - Zieba, Filip A1 - Zwijacz-Kozica, Tomasz A1 - Fagan, William F. A1 - Mueller, Thomas A1 - Calabrese, Justin M. T1 - A comprehensive analysis of autocorrelation and bias in home range estimation JF - Ecological monographs : a publication of the Ecological Society of America. N2 - Home range estimation is routine practice in ecological research. While advances in animal tracking technology have increased our capacity to collect data to support home range analysis, these same advances have also resulted in increasingly autocorrelated data. Consequently, the question of which home range estimator to use on modern, highly autocorrelated tracking data remains open. This question is particularly relevant given that most estimators assume independently sampled data. Here, we provide a comprehensive evaluation of the effects of autocorrelation on home range estimation. We base our study on an extensive data set of GPS locations from 369 individuals representing 27 species distributed across five continents. We first assemble a broad array of home range estimators, including Kernel Density Estimation (KDE) with four bandwidth optimizers (Gaussian reference function, autocorrelated‐Gaussian reference function [AKDE], Silverman's rule of thumb, and least squares cross‐validation), Minimum Convex Polygon, and Local Convex Hull methods. Notably, all of these estimators except AKDE assume independent and identically distributed (IID) data. We then employ half‐sample cross‐validation to objectively quantify estimator performance, and the recently introduced effective sample size for home range area estimation ( N̂ area ) to quantify the information content of each data set. We found that AKDE 95% area estimates were larger than conventional IID‐based estimates by a mean factor of 2. The median number of cross‐validated locations included in the hold‐out sets by AKDE 95% (or 50%) estimates was 95.3% (or 50.1%), confirming the larger AKDE ranges were appropriately selective at the specified quantile. Conversely, conventional estimates exhibited negative bias that increased with decreasing N̂ area. To contextualize our empirical results, we performed a detailed simulation study to tease apart how sampling frequency, sampling duration, and the focal animal's movement conspire to affect range estimates. Paralleling our empirical results, the simulation study demonstrated that AKDE was generally more accurate than conventional methods, particularly for small N̂ area. While 72% of the 369 empirical data sets had >1,000 total observations, only 4% had an N̂ area >1,000, where 30% had an N̂ area <30. In this frequently encountered scenario of small N̂ area, AKDE was the only estimator capable of producing an accurate home range estimate on autocorrelated data. KW - animal movement KW - kernel density estimation KW - local convex hull KW - minimum convex polygon KW - range distribution KW - space use KW - telemetry KW - tracking data Y1 - 2018 U6 - https://doi.org/10.1002/ecm.1344 SN - 0012-9615 SN - 1557-7015 VL - 89 IS - 2 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Palkopoulou, Eleftheria A1 - Lipson, Mark A1 - Mallick, Swapan A1 - Nielsen, Svend A1 - Rohland, Nadin A1 - Baleka, Sina Isabelle A1 - Karpinski, Emil A1 - Ivancevici, Atma M. A1 - Thu-Hien To, A1 - Kortschak, Daniel A1 - Raison, Joy M. A1 - Qu, Zhipeng A1 - Chin, Tat-Jun A1 - Alt, Kurt W. A1 - Claesson, Stefan A1 - Dalen, Love A1 - MacPhee, Ross D. E. A1 - Meller, Harald A1 - Rocar, Alfred L. A1 - Ryder, Oliver A. A1 - Heiman, David A1 - Young, Sarah A1 - Breen, Matthew A1 - Williams, Christina A1 - Aken, Bronwen L. A1 - Ruffier, Magali A1 - Karlsson, Elinor A1 - Johnson, Jeremy A1 - Di Palma, Federica A1 - Alfoldi, Jessica A1 - Adelsoni, David L. A1 - Mailund, Thomas A1 - Munch, Kasper A1 - Lindblad-Toh, Kerstin A1 - Hofreiter, Michael A1 - Poinar, Hendrik A1 - Reich, David T1 - A comprehensive genomic history of extinct and living elephants JF - Proceedings of the National Academy of Sciences of the United States of America KW - paleogenomics KW - elephantid evolution KW - mammoth KW - admixture KW - species divergence Y1 - 2018 U6 - https://doi.org/10.1073/pnas.1720554115 SN - 0027-8424 VL - 115 IS - 11 SP - E2566 EP - E2574 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Schurr, Frank Martin A1 - Dean, W. R. J. A1 - Milton, Sue J. A1 - Jeltsch, Florian T1 - A conceptual model linking demography of the shrub species Grewia flava to the dynamics of Kalahari savannas N2 - Environmental heterogeneity is a major determinant of plant population dynamics. In semi-arid Kalahari savannas, heterogeneity is created by savanna structure, i.e. by the spatial arrangement and temporal dynamics of woody plant and open grassland microsites. We formulate a conceptual model describing the effects of savanna dynamics on the population dynamics of the animal-dispersed shrub Grewia flava. From empirical results we derive model rules describing effects of savanna structure on several processes in Grewia's life cycle. By formulating the model, we summarise existing information on Grewia demography and identify gaps in this knowledge. Despite a number of such gaps, the model can be used to make certain quantitative predictions. As an example, we apply the model to investigate the role of seed dispersal in Grewia encroachment on rangelands. Model results show that cattle promote encroachment by depositing substantial numbers of seeds in open areas, where Grewia is otherwise dispersal-limited. Finally, we draw some general conclusions about Grewia's life history and population dynamics. Under natural conditions, concentrated seed deposition under woody plants appears to be a key process causing the observed association between Grewia and other woody plants. Furthermore, low rates of recruitment and high adult survival result in slow-motion dynamics of Grewia populations. As a consequence, Grewia populations interact with savanna dynamics on long temporal and short to intermediate spatial scales. Y1 - 2004 ER - TY - JOUR A1 - Chapman, Eric M. A1 - Lant, Benjamin A1 - Ohashi, Yota A1 - Yu, Bin A1 - Schertzberg, Michael A1 - Go, Christopher A1 - Dogra, Deepika A1 - Koskimaki, Janne A1 - Girard, Romuald A1 - Li, Yan A1 - Fraser, Andrew G. A1 - Awad, Issam A. A1 - Abdelilah-Seyfried, Salim A1 - Gingras, Anne-Claude A1 - Derry, William Brent T1 - A conserved CCM complex promotes apoptosis non-autonomously by regulating zinc homeostasis JF - Nature Communications N2 - Apoptotic death of cells damaged by genotoxic stress requires regulatory input from surrounding tissues. The C. elegans scaffold protein KRI-1, ortholog of mammalian KRIT1/CCM1, permits DNA damage-induced apoptosis of cells in the germline by an unknown cell non-autonomous mechanism. We reveal that KRI-1 exists in a complex with CCM-2 in the intestine to negatively regulate the ERK-5/MAPK pathway. This allows the KLF-3 transcription factor to facilitate expression of the SLC39 zinc transporter gene zipt-2.3, which functions to sequester zinc in the intestine. Ablation of KRI-1 results in reduced zinc sequestration in the intestine, inhibition of IR-induced MPK-1/ERK1 activation, and apoptosis in the germline. Zinc localization is also perturbed in the vasculature of krit1(-/-) zebrafish, and SLC39 zinc transporters are mis-expressed in Cerebral Cavernous Malformations (CCM) patient tissues. This study provides new insights into the regulation of apoptosis by cross-tissue communication, and suggests a link between zinc localization and CCM disease. Y1 - 2019 U6 - https://doi.org/10.1038/s41467-019-09829-z SN - 2041-1723 VL - 10 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Wolff, Martin A1 - Gast, Klaus A1 - Evers, Andreas A1 - Kurz, Michael A1 - Pfeiffer-Marek, Stefania A1 - Schüler, Anja A1 - Seckler, Robert A1 - Thalhammer, Anja T1 - A Conserved Hydrophobic Moiety and Helix-Helix Interactions Drive the Self-Assembly of the Incretin Analog Exendin-4 JF - Biomolecules N2 - Exendin-4 is a pharmaceutical peptide used in the control of insulin secretion. Structural information on exendin-4 and related peptides especially on the level of quaternary structure is scarce. We present the first published association equilibria of exendin-4 directly measured by static and dynamic light scattering. We show that exendin-4 oligomerization is pH dependent and that these oligomers are of low compactness. We relate our experimental results to a structural hypothesis to describe molecular details of exendin-4 oligomers. Discussion of the validity of this hypothesis is based on NMR, circular dichroism and fluorescence spectroscopy, and light scattering data on exendin-4 and a set of exendin-4 derived peptides. The essential forces driving oligomerization of exendin-4 are helix–helix interactions and interactions of a conserved hydrophobic moiety. Our structural hypothesis suggests that key interactions of exendin-4 monomers in the experimentally supported trimer take place between a defined helical segment and a hydrophobic triangle constituted by the Phe22 residues of the three monomeric subunits. Our data rationalize that Val19 might function as an anchor in the N-terminus of the interacting helix-region and that Trp25 is partially shielded in the oligomer by C-terminal amino acids of the same monomer. Our structural hypothesis suggests that the Trp25 residues do not interact with each other, but with C-terminal Pro residues of their own monomers. KW - biophysics KW - diabetes KW - peptides KW - oligomerization KW - conformational change KW - molecular modeling KW - static and dynamic light scattering KW - spectroscopy Y1 - 2021 U6 - https://doi.org/10.3390/biom11091305 SN - 2218-273X VL - 11 IS - 9 PB - MDPI CY - Basel ER - TY - GEN A1 - Wolff, Martin A1 - Gast, Klaus A1 - Evers, Andreas A1 - Kurz, Michael A1 - Pfeiffer-Marek, Stefania A1 - Schüler, Anja A1 - Seckler, Robert A1 - Thalhammer, Anja T1 - A Conserved Hydrophobic Moiety and Helix-Helix Interactions Drive the Self-Assembly of the Incretin Analog Exendin-4 T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Exendin-4 is a pharmaceutical peptide used in the control of insulin secretion. Structural information on exendin-4 and related peptides especially on the level of quaternary structure is scarce. We present the first published association equilibria of exendin-4 directly measured by static and dynamic light scattering. We show that exendin-4 oligomerization is pH dependent and that these oligomers are of low compactness. We relate our experimental results to a structural hypothesis to describe molecular details of exendin-4 oligomers. Discussion of the validity of this hypothesis is based on NMR, circular dichroism and fluorescence spectroscopy, and light scattering data on exendin-4 and a set of exendin-4 derived peptides. The essential forces driving oligomerization of exendin-4 are helix–helix interactions and interactions of a conserved hydrophobic moiety. Our structural hypothesis suggests that key interactions of exendin-4 monomers in the experimentally supported trimer take place between a defined helical segment and a hydrophobic triangle constituted by the Phe22 residues of the three monomeric subunits. Our data rationalize that Val19 might function as an anchor in the N-terminus of the interacting helix-region and that Trp25 is partially shielded in the oligomer by C-terminal amino acids of the same monomer. Our structural hypothesis suggests that the Trp25 residues do not interact with each other, but with C-terminal Pro residues of their own monomers. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1161 KW - biophysics KW - diabetes KW - peptides KW - oligomerization KW - conformational change KW - molecular modeling KW - static and dynamic light scattering KW - spectroscopy Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-522081 SN - 1866-8372 IS - 9 ER - TY - JOUR A1 - Luetkecosmann, Steffi A1 - Faupel, Thomas A1 - Porstmann, Silvia A1 - Porstmann, Tomas A1 - Micheel, Burkhard A1 - Hanack, Katja T1 - A cross-reactive monoclonal antibody as universal detection antibody in autoantibody diagnostic assays JF - Clinica chimica acta N2 - Diagnostics of Autoimmune Diseases involve screening of patient samples for containing autoantibodies against various antigens. To ensure quality of diagnostic assays a calibrator is needed in each assay system. Different calibrators as recombinant human monoclonal antibodies as well as chimeric antibodies against the autoantigens of interest are described. A less cost-intensive and also more representative possibility covering different targets on the antigens is the utilization of polyclonal sera from other species. Nevertheless, the detection of human autoantibodies as well as the calibration reagent containing antibodies from other species in one assay constitutes a challenge in terms of assay calibration. We therefore developed a cross-reactive monoclonal antibody which binds human as well as rabbit sera with similar affinities in the nanomolar range. We tested our monoclonal antibody S38CD11B12 successfully in the commercial Serazym (R) Anti-Cardiolipin-beta 2-GPI IgG/IgM assay and could thereby prove the eligibility of S38CD11B12 as detection antibody in autoimmune diagnostic assays using rabbit derived sera as reference material. KW - Monoclonal antibody KW - Detection KW - Autoimmune diagnostics KW - Cross reactivity KW - Assay calibration Y1 - 2019 U6 - https://doi.org/10.1016/j.cca.2019.09.003 SN - 0009-8981 SN - 1873-3492 VL - 499 SP - 87 EP - 92 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Samuel, Prinson P. A1 - Horn, Sebastian A1 - Döring, Alexander A1 - Havelius, Kajsa G. V. A1 - Reschke, Stefan A1 - Leimkühler, Silke A1 - Haumann, Michael A1 - Schulzke, Carola T1 - A Crystallographic and Mo K-Edge XAS Study of Molybdenum Oxo Bis-,Mono-, and Non-Dithiolene Complexes - First-Sphere Coordination Geometry and Noninnocence of Ligands JF - European journal of inorganic chemistry : a journal of ChemPubSoc Europe N2 - Ten square-based pyramidal molybdenum complexes with different sulfur donor ligands, that is, a variety of dithiolenes and sulfides, were prepared, which mimic coordination motifs of the molybdenum cofactors of molybdenum-dependent oxidoreductases. The model compounds were investigated by Mo K-edge X-ray absorption spectroscopy (XAS) and (with one exception) their molecular structures were analyzed by X-ray diffraction to derive detailed information on bond lengths and geometries of the first coordination shell of molybdenum. Only small variations in Mo=O and Mo-S bond lengths and their respective coordination angles were observed for all complexes including those containing Mo(CO)(2) or Mo(mu-S)(2)Mo motifs. XAS analysis (edge energy) revealed higher relative oxidation levels in the molybdenum ion in compounds with innocent sulfur-based ligands relative to those in dithiolene complexes, which are known to exhibit noninnocence, that is, donation of substantial electron density from ligand to metal. In addition, longer average Mo-S and Mo=O bonds and consequently lower.(Mo=O) stretching frequencies in the IR spectra were observed for complexes with dithiolene-derived ligands. The results emphasize that the noninnocent character of the dithiolene ligand influences the electronic structure of the model compounds, but does not significantly affect their metal coordination geometry, which is largely determined by the Mo(IV) or (V) ion itself. The latter conclusion also holds for the molybdenum site geometries in the oxidized Mo-VI cofactor of DMSO reductase and the reduced Mo-IV cofactor of arsenite oxidase. The innocent behavior of the dithiolene molybdopterin ligands observed in the enzymes is likely to be related to cofactor-protein interactions. KW - Molybdenum KW - Enzyme models KW - X-ray absorption spectroscopy KW - Noninnocence KW - Bioinorganic chemistry Y1 - 2011 U6 - https://doi.org/10.1002/ejic.201100331 SN - 1434-1948 IS - 28 SP - 4387 EP - 4399 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Landau, Alejandra Mabel A1 - Lokstein, Heiko A1 - Scheller, Henrik Vibe A1 - Lainez, Veronica A1 - Maldonado, Sara A1 - Prina, Alberto Raúl T1 - A cytoplasmically inherited barley mutant is defective in photosystem I assembly due to a temperature-sensitive defect in ycf3 splicing N2 - A cytoplasmically inherited chlorophyll-deficient mutant of barley (Hordeum vulgare) termed cytoplasmic line 3 (CL3), displaying a viridis (homogeneously light-green colored) phenotype, has been previously shown to be affected by elevated temperatures. In this article, biochemical, biophysical, and molecular approaches were used to study the CL3 mutant under different temperature and light conditions. The results lead to the conclusion that an impaired assembly of photosystem I (PSI) under higher temperatures and certain light conditions is the primary cause of the CL3 phenotype. Compromised splicing of ycf3 transcripts, particularly at elevated temperature, resulting from a mutation in a noncoding region (intron 1) in the mutant ycf3 gene results in a defective synthesis of Ycf3, which is a chaperone involved in PSI assembly. The defective PSI assembly causes severe photoinhibition and degradation of PSII. Y1 - 2009 UR - http://www.plantphysiol.org/ U6 - https://doi.org/10.1104/pp.109.147843 SN - 0032-0889 ER - TY - JOUR A1 - Chen, Ziping A1 - Warsinke, Axel A1 - Gajovic, Nenad A1 - Große, St. A1 - Hu, J. A1 - Kleber, H.-P. A1 - Scheller, Frieder W. T1 - A D-carnitine dehydrogenase electrode for the assessment of enantiomeric purity of L-carnitine preparations Y1 - 2000 ER - TY - JOUR A1 - Hentrich, Doreen A1 - Taabache, Soraya A1 - Brezesinski, Gerald A1 - Lange, Nele A1 - Unger, Wolfgang A1 - Kuebel, Christian A1 - Bertin, Annabelle A1 - Taubert, Andreas T1 - A Dendritic Amphiphile for Efficient Control of Biomimetic Calcium Phosphate Mineralization JF - Macromolecular bioscience N2 - The phase behavior of a dendritic amphiphile containing a Newkome-type dendron as the hydrophilic moiety and a cholesterol unit as the hydrophobic segment is investigated at the air-liquid interface. The amphiphile forms stable monomolecular films at the airliquid interface on different subphases. Furthermore, the mineralization of calcium phosphate beneath the monolayer at different calcium and phosphate concentrations versus mineralization time shows that at low calcium and phosphate concentrations needles form, whereas flakes and spheres dominate at higher concentrations. Energy-dispersive X-ray spectroscopy, X-ray photoelectron spectroscopy, and electron diffraction confirm the formation of calcium phosphate. High-resolution transmission electron microscopy and electron diffraction confirm the predominant formation of octacalcium phosphate and hydroxyapatite. The data also indicate that the final products form via a complex multistep reaction, including an association step, where nano-needles aggregate into larger flake-like objects. Y1 - 2017 U6 - https://doi.org/10.1002/mabi.201600524 SN - 1616-5187 SN - 1616-5195 VL - 17 SP - 2541 EP - 2548 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Hlinak, Andreas A1 - Müller, Thomas A1 - Kramer, Matthias A1 - Mühle, Ralf-Udo A1 - Liebherr, Helga A1 - Ziedler, Klaus T1 - A descriptive analysis of the potenrial association between migration patterns of bean and white-fronted geese and the occurence of newcastle disease outbreaks in domestic birds N2 - Sightings and migration patterns of 65 bean and 65 white-fronted geese are reported. These geese were tagged and serologically screened. 19 of the 53 birds sighted had serologic evidence of Newcastle Disease. The migration patterns of the wild geese provided further evidence that the main resting and wintering sites of migratory waterfowl are likely to be important for the inter- and intraspecies transmission of avian diseases. Y1 - 1999 SN - 0005-2086 ER - TY - JOUR A1 - Bukovinszky, Tibor A1 - Helmsing, Nico R. A1 - Grau, R. A. A1 - Bakker, Elisabeth S. A1 - Bezemer, T. Martijn A1 - Vos, Matthijs A1 - Uittenhout, H. A1 - Verschoor, A. M. T1 - A device to study the behavioral responses of zooplankton to food quality and quantity JF - Journal of insect behavior N2 - In order to explore the behavioral mechanisms underlying aggregation of foragers on local resource patches, it is necessary to manipulate the location, quality and quantity of food patches. This requires careful control over the conditions in the foraging arena, which may be a challenging task in the case of aquatic resource-consumer systems, like that of freshwater zooplankton feeding on suspended algal cells. We present an experimental tool designed to aid behavioral ecologists in exploring the consequences of resource characteristics for zooplankton aggregation behavior and movement decisions under conditions where the boundaries and characteristics (quantity and quality) of food patches can be standardized. The aggregation behavior of Daphnia magna and D. galeata x hyalina was tested in relation to i) the presence or absence of food or ii) food quality, where algae of high or low nutrient (phosphorus) content were offered in distinct patches. Individuals of both Daphnia species chose tubes containing food patches and D. galeata x hyalina also showed a preference towards food patches of high nutrient content. We discuss how the described equipment complements other behavioral approaches providing a useful tool to understand animal foraging decisions in environments with heterogeneous resource distributions. KW - Foraging behavior KW - behavioral choice KW - food preference KW - Daphnia KW - flow-through vessel Y1 - 2013 U6 - https://doi.org/10.1007/s10905-012-9366-0 SN - 0892-7553 VL - 26 IS - 4 SP - 453 EP - 465 PB - Springer CY - New York ER - TY - JOUR A1 - Ettlinger, Julia A1 - Schenk, Jörg A. A1 - Micheel, Burkhard A1 - Ehrentreich-Förster, Eva A1 - Gajovic-Eichelmann, Nenad T1 - A direct competitive homogeneous immunoassay for progesterone - the Redox Quenching Immunoassay JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - A direct competitive amperometric immunoassay format for the detection of haptens and proteins was developed. The method is based on the quenching of electroactivity of ferrocenium, which is coupled to the antigen and used as the primary reporter, upon binding to a monoclonal anti-ferrocenium antibody, which is coupled to the detection antibody and used as a secondary reporter. A separation-free progesterone immunoassay with a lower detection limit of 1 ng?mL-1 (3.18 nmol?L-1) in 1?:?2 diluted blood serum was realised by combining two bifunctional conjugates, a ferrocenium-PEG-progesterone tracer and a bioconjugate of one anti-progesterone and one anti-ferrocenium antibody. The immune complex is formed within 30 s upon addition of progesterone, resulting in a total analysis time of 1.5 min. KW - Immunoassay KW - Amperometry KW - Ferrocene KW - Progesterone Y1 - 2012 U6 - https://doi.org/10.1002/elan.201200107 SN - 1040-0397 VL - 24 IS - 7 SP - 1567 EP - 1575 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Fussmann, Gregor F. A1 - Weithoff, Guntram A1 - Yoshida, Takehito T1 - A direct, experimental test of resource versus consumer dependence : reply Y1 - 2007 UR - http://esapubs.org/esapubs/journals/ecology.htm U6 - https://doi.org/10.1890/06-1692 SN - 0012-9658 ER - TY - JOUR A1 - Fussmann, Gregor F. A1 - Weithoff, Guntram A1 - Yoshida, Takehito T1 - A direct, experimental test of resource vs. consumer dependence N2 - The uptake of resources from the environment is a vital process for all organisms. Many experimental studies have revealed that the rate at which this process occurs depends critically on the resource concentration, a relationship called "functional response." However, whether the concentration of the consumer normally affects the functional response has been the subject of a long-standing, predominantly theoretical, debate in ecology. Here we present an experimental test between the alternative hypotheses that food uptake depends either only on the resource concentration or on both the resource and the consumer concentrations. In short-term laboratory experiments, we measured the uptake of radioactively labeled, unicellular green algae (Monoraphidium minutum, resource) by the rotifer Brachionus calyciflorus (a consumer) for varying combinations of resource and consumer concentrations. We found that the food uptake by Brachionus depended on the algal concentration with the relationship best described by a Holling type 3 functional response. We detected significant consumer effects on the functional response only at an extraordinarily high Brachionus density (similar to 125 rotifers/mL), which by far exceeds concentrations normally encountered in the field. We conclude that con sumer-dependent food uptake by planktonic rotifers is a phenomenon that can occur under extreme conditions, but probably plays a minor role in natural environments Y1 - 2005 ER - TY - JOUR A1 - Trindade, Inês T1 - A drop of immunity JF - Molecular plant Y1 - 2021 U6 - https://doi.org/10.1016/j.molp.2021.07.022 SN - 1674-2052 SN - 1752-9867 VL - 14 IS - 9 SP - 1437 EP - 1438 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Demal, Till Joscha A1 - Heise, Melina A1 - Reiz, Benedikt A1 - Dogra, Deepika A1 - Braenne, Ingrid A1 - Reichenspurner, Hermann A1 - Männer, Jörg A1 - Aherrahrou, Zouhair A1 - Schunkert, Heribert A1 - Erdmann, Jeanette A1 - Abdelilah-Seyfried, Salim T1 - A familial congenital heart disease with a possible multigenic origin involving a mutation in BMPR1A JF - Scientific reports N2 - The genetics of many congenital heart diseases (CHDs) can only unsatisfactorily be explained by known chromosomal or Mendelian syndromes. Here, we present sequencing data of a family with a potentially multigenic origin of CHD. Twelve of nineteen family members carry a familial mutation [NM_004329.2:c.1328 G > A (p.R443H)] which encodes a predicted deleterious variant of BMPR1A. This mutation co-segregates with a linkage region on chromosome 1 that associates with the emergence of severe CHDs including Ebstein’s anomaly, atrioventricular septal defect, and others. We show that the continuous overexpression of the zebrafish homologous mutation bmpr1aap.R438H within endocardium causes a reduced AV valve area, a downregulation of Wnt/ß-catenin signalling at the AV canal, and growth of additional tissue mass in adult zebrafish hearts. This finding opens the possibility of testing genetic interactions between BMPR1A and other candidate genes within linkage region 1 which may provide a first step towards unravelling more complex genetic patterns in cardiovascular disease aetiology. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-019-39648-7 SN - 2045-2322 VL - 9 PB - Nature Publ. Group CY - London ER -