TY - JOUR A1 - Coloma, Sebastian A1 - Gaedke, Ursula A1 - Sivonen, Kaarina A1 - Hiltunen, Teppo T1 - Frequency of virus-resistant hosts determines experimental community dynamics JF - Ecology : a publication of the Ecological Society of America N2 - Parasites, such as bacterial viruses (phages), can have large effects on host populations both at the ecological and evolutionary levels. In the case of cyanobacteria, phages can reduce primary production and infected hosts release intracellular nutrients influencing planktonic food web structure, community dynamics, and biogeochemical cycles. Cyanophages may be of great importance in aquatic food webs during large cyanobacterial blooms unless the host population becomes resistant to phage infection. The consequences on plankton community dynamics of the evolution of phage resistance in bloom forming cyanobacterial populations are still poorly studied. Here, we examined the effect of different frequencies of a phage-resistant genotype within a filamentous nitrogen-fixing Nodularia spumigena population on an experimental plankton community. Three Nodularia populations with different initial frequencies (0%, 5%, and 50%) of phage-resistant genotypes were inoculated in separate treatments with the phage 2AV2, the green alga Chlorella vulgaris, and the rotifer Brachionus plicatilis, which formed the experimental plankton community subjected to either nitrogen-limited or nitrogen-rich conditions. We found that the frequency of the phage-resistant Nodularia genotype determined experimental community dynamics. Cyanobacterial populations with a high frequency (50%) of the phage-resistant genotype dominated the cultures despite the presence of phages, retaining most of the intracellular nitrogen in the plankton community. In contrast, populations with low frequencies (0% and 5%) of the phage-resistant genotype were lysed and reduced to extinction by the phage, transferring the intracellular nitrogen held by Nodularia to Chlorella and rotifers, and allowing Chlorella to dominate the communities and rotifers to survive. This study shows that even though phages represent minuscule biomass, they can have key effects on community composition and eco-evolutionary feedbacks in plankton communities. KW - cyanobacteria KW - eco-evolutionary feedbacks KW - experimental evolution KW - host-parasite interaction KW - phage resistance KW - predator-prey interaction Y1 - 2018 U6 - https://doi.org/10.1002/ecy.2554 SN - 0012-9658 SN - 1939-9170 VL - 100 IS - 1 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Wendler, Petra A1 - Enenkel, Cordula T1 - Nuclear Transport of Yeast Proteasomes JF - Frontiers in molecular biosciences N2 - Proteasomes are key proteases in regulating protein homeostasis. Their holo-enzymes are composed of 40 different subunits which are arranged in a proteolytic core (CP) flanked by one to two regulatory particles (RP). Proteasomal proteolysis is essential for the degradation of proteins which control time-sensitive processes like cell cycle progression and stress response. In dividing yeast and human cells, proteasomes are primarily nuclear suggesting that proteasomal proteolysis is mainly required in the nucleus during cell proliferation. In yeast, which have a closed mitosis, proteasomes are imported into the nucleus as immature precursors via the classical import pathway. During quiescence, the reversible absence of proliferation induced by nutrient depletion or growth factor deprivation, proteasomes move from the nucleus into the cytoplasm. In the cytoplasm of quiescent yeast, proteasomes are dissociated into CP and RP and stored in membrane-less cytoplasmic foci, named proteasome storage granules (PSGs). With the resumption of growth, PSGs clear and mature proteasomes are transported into the nucleus by Blm10, a conserved 240 kDa protein and proteasome-intrinsic import receptor. How proteasomes are exported from the nucleus into the cytoplasm is unknown. KW - proteasome KW - nuclear transport KW - importin KW - karyopherin KW - Blm10 KW - proteasome storage granules Y1 - 2019 U6 - https://doi.org/10.3389/fmolb.2019.00034 SN - 2296-889X VL - 6 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Sperber, Hannah Sabeth A1 - Welke, Robert-William A1 - Petazzi, Roberto Arturo A1 - Bergmann, Ronny A1 - Schade, Matthias A1 - Shai, Yechiel A1 - Chiantia, Salvatore A1 - Herrmann, Andreas A1 - Schwarzer, Roland T1 - Self-association and subcellular localization of Puumala hantavirus envelope proteins JF - Scientific reports N2 - Hantavirus assembly and budding are governed by the surface glycoproteins Gn and Gc. In this study, we investigated the glycoproteins of Puumala, the most abundant Hantavirus species in Europe, using fluorescently labeled wild-type constructs and cytoplasmic tail (CT) mutants. We analyzed their intracellular distribution, co-localization and oligomerization, applying comprehensive live, single-cell fluorescence techniques, including confocal microscopy, imaging flow cytometry, anisotropy imaging and Number&Brightness analysis. We demonstrate that Gc is significantly enriched in the Golgi apparatus in absence of other viral components, while Gn is mainly restricted to the endoplasmic reticulum (ER). Importantly, upon co-expression both glycoproteins were found in the Golgi apparatus. Furthermore, we show that an intact CT of Gc is necessary for efficient Golgi localization, while the CT of Gn influences protein stability. Finally, we found that Gn assembles into higher-order homo-oligomers, mainly dimers and tetramers, in the ER while Gc was present as mixture of monomers and dimers within the Golgi apparatus. Our findings suggest that PUUV Gc is the driving factor of the targeting of Gc and Gn to the Golgi region, while Gn possesses a significantly stronger self-association potential. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-018-36879-y SN - 2045-2322 VL - 9 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Diekmann, Martin A1 - Andres, Christian A1 - Becker, Thomas A1 - Bennie, Jonathan A1 - Blueml, Volker A1 - Bullock, James M. A1 - Culmsee, Heike A1 - Fanigliulo, Miriam A1 - Hahn, Annett A1 - Heinken, Thilo A1 - Leuschner, Christoph A1 - Luka, Stefanie A1 - Meissner, Justus A1 - Müller, Josef A1 - Newton, Adrian A1 - Peppler-Lisbach, Cord A1 - Rosenthal, Gert A1 - van den Berg, Leon J. L. A1 - Vergeer, Philippine A1 - Wesche, Karsten T1 - Patterns of long-term vegetation change vary between different types of semi-natural grasslands in Western and Central Europe JF - Journal of vegetation science N2 - Questions Has plant species richness in semi-natural grasslands changed over recent decades? Do the temporal trends of habitat specialists differ from those of habitat generalists? Has there been a homogenization of the grassland vegetation? Location Different regions in Germany and the UK. Methods We conducted a formal meta-analysis of re-survey vegetation studies of semi-natural grasslands. In total, 23 data sets were compiled, spanning up to 75 years between the surveys, including 13 data sets from wet grasslands, six from dry grasslands and four from other grassland types. Edaphic conditions were assessed using mean Ellenberg indicator values for soil moisture, nitrogen and pH. Changes in species richness and environmental variables were evaluated using response ratios. Results In most wet grasslands, total species richness declined over time, while habitat specialists almost completely vanished. The number of species losses increased with increasing time between the surveys and were associated with a strong decrease in soil moisture and higher soil nutrient contents. Wet grasslands in nature reserves showed no such changes or even opposite trends. In dry grasslands and other grassland types, total species richness did not consistently change, but the number or proportions of habitat specialists declined. There were also considerable changes in species composition, especially in wet grasslands that often have been converted into intensively managed, highly productive meadows or pastures. We did not find a general homogenization of the vegetation in any of the grassland types. Conclusions The results document the widespread deterioration of semi-natural grasslands, especially of those types that can easily be transformed to high production grasslands. The main causes for the loss of grassland specialists are changed management in combination with increased fertilization and nitrogen deposition. Dry grasslands are most resistant to change, but also show a long-term trend towards an increase in more mesotrophic species. KW - dry grasslands KW - fragmentation KW - homogenization KW - management KW - meta-analysis KW - nitrogen deposition KW - quasi-permanent plot KW - re-survey KW - species richness KW - wet grasslands Y1 - 2019 U6 - https://doi.org/10.1111/jvs.12727 SN - 1100-9233 SN - 1654-1103 VL - 30 IS - 2 SP - 187 EP - 202 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Tanabe, Tomohisa Sebastian A1 - Leimkühler, Silke A1 - Dahl, Christiane ED - Poole, RK T1 - The functional diversity of the prokaryotic sulfur carrier protein TusA JF - Advances in microbial physiology N2 - Persulfide groups participate in a wide array of biochemical pathways and are chemically very versatile. The TusA protein has been identified as a central element supplying and transferring sulfur as persulfide to a number of important biosynthetic pathways, like molybdenum cofactor biosynthesis or thiomodifications in nucleosides of tRNAs. In recent years, it has furthermore become obvious that this protein is indispensable for the oxidation of sulfur compounds in the cytoplasm. Phylogenetic analyses revealed that different TusA protein variants exists in certain organisms, that have evolved to pursue specific roles in cellular pathways. The specific TusA-like proteins thereby cannot replace each other in their specific roles and are rather specific to one sulfur transfer pathway or shared between two pathways. While certain bacteria like Escherichia coli contain several copies of TusA-like proteins, in other bacteria like Allochromatium vinosum a single copy of TusA is present with an essential role for this organism. Here, we give an overview on the multiple roles of the various TusA-like proteins in sulfur transfer pathways in different organisms to shed light on the remaining mysteries of this versatile protein. Y1 - 2019 SN - 978-0-12-817715-0 SN - 978-0-12-817714-3 U6 - https://doi.org/10.1016/bs.ampbs.2019.07.004 SN - 0065-2911 VL - 75 SP - 233 EP - 277 PB - Elsevier Acad. Press CY - Amsterdam ER - TY - JOUR A1 - Rosenbaum, Benjamin A1 - Raatz, Michael A1 - Weithoff, Guntram A1 - Fussmann, Gregor F. A1 - Gaedke, Ursula T1 - Estimating parameters from multiple time series of population dynamics using bayesian inference JF - Frontiers in ecology and evolution N2 - Empirical time series of interacting entities, e.g., species abundances, are highly useful to study ecological mechanisms. Mathematical models are valuable tools to further elucidate those mechanisms and underlying processes. However, obtaining an agreement between model predictions and experimental observations remains a demanding task. As models always abstract from reality one parameter often summarizes several properties. Parameter measurements are performed in additional experiments independent of the ones delivering the time series. Transferring these parameter values to different settings may result in incorrect parametrizations. On top of that, the properties of organisms and thus the respective parameter values may vary considerably. These issues limit the use of a priori model parametrizations. In this study, we present a method suited for a direct estimation of model parameters and their variability from experimental time series data. We combine numerical simulations of a continuous-time dynamical population model with Bayesian inference, using a hierarchical framework that allows for variability of individual parameters. The method is applied to a comprehensive set of time series from a laboratory predator-prey system that features both steady states and cyclic population dynamics. Our model predictions are able to reproduce both steady states and cyclic dynamics of the data. Additionally to the direct estimates of the parameter values, the Bayesian approach also provides their uncertainties. We found that fitting cyclic population dynamics, which contain more information on the process rates than steady states, yields more precise parameter estimates. We detected significant variability among parameters of different time series and identified the variation in the maximum growth rate of the prey as a source for the transition from steady states to cyclic dynamics. By lending more flexibility to the model, our approach facilitates parametrizations and shows more easily which patterns in time series can be explained also by simple models. Applying Bayesian inference and dynamical population models in conjunction may help to quantify the profound variability in organismal properties in nature. KW - Bayesian inference KW - chemostat experiments KW - ordinary differential equation KW - parameter estimation KW - population dynamics KW - predator prey KW - time series analysis KW - trait variability Y1 - 2019 U6 - https://doi.org/10.3389/fevo.2018.00234 SN - 2296-701X VL - 6 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Perkins, Daniel M. A1 - Perna, Andrea A1 - Adrian, Rita A1 - Cermeno, Pedro A1 - Gaedke, Ursula A1 - Huete-Ortega, Maria A1 - White, Ethan P. A1 - Yvon-Durocher, Gabriel T1 - Energetic equivalence underpins the size structure of tree and phytoplankton communities JF - Nature Communications N2 - The size structure of autotroph communities - the relative abundance of small vs. large individuals - shapes the functioning of ecosystems. Whether common mechanisms underpin the size structure of unicellular and multicellular autotrophs is, however, unknown. Using a global data compilation, we show that individual body masses in tree and phytoplankton communities follow power-law distributions and that the average exponents of these individual size distributions (ISD) differ. Phytoplankton communities are characterized by an average ISD exponent consistent with three-quarter-power scaling of metabolism with body mass and equivalence in energy use among mass classes. Tree communities deviate from this pattern in a manner consistent with equivalence in energy use among diameter size classes. Our findings suggest that whilst universal metabolic constraints ultimately underlie the emergent size structure of autotroph communities, divergent aspects of body size (volumetric vs. linear dimensions) shape the ecological outcome of metabolic scaling in forest vs. pelagic ecosystems. Y1 - 2019 U6 - https://doi.org/10.1038/s41467-018-08039-3 SN - 2041-1723 VL - 10 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Parfenteva, Olga A1 - Groth, Detlef A1 - Scheffler, Christiane A1 - Zaharova, Maria F. T1 - Influence of the A/T polymorphism of the FTO gene and sport specializations on the body composition of young Russian athletes JF - Journal of biological and clinical anthropology : Anthropologischer Anzeiger ; Mitteilungsorgan der Gesellschaft für Anthropologie N2 - Background: The polymorphism in FTO gene (rs9939609) is known to be associated with higher BMI and body fat mass content. However, environmental factors can modify this effect. The purpose of the present study was to investigate an association between sport specialization and the rs9939609 SNP in FTO gene in the cohort of professional and amateur young athletes. Methods: A total number of 250 young individuals 8-18 years old living in Moscow or Moscow district participated in the study. Individuals were divided into 3 groups in accordance with their physical activity level: control group (n = 49), amateurs (n = 67) and professionals (n = 137). Amateur and professional athletes were subdivided into groups according to their sport specialization. Quantile regression was used as a regression model, where the dependent (outcome) variable was BMI, along with percentage of body fat mass, and the independent variables (predictors) were the rs9939609 SNP in FTO gene, physical activity (active versus inactive), sport specialization (aerobic, intermittent sports and martial arts), nationality, level of sport experience (in years), gender and percentage of free fat mass content. Results: The regression analysis revealed that physical activity and sport specialization had greater impact compared to FTO allele in the group of physically active individuals. Physical activity, in particular aerobic, had negative associations with body fat mass and BMI. The rs9939609 SNP in FTO gene is associated with physical activity and aerobic activity. The magnitude of association becomes significantly larger at the upper quantiles of the body fat mass distribution. Conclusion: Physical activity and sport specialization explained more variance in body composition of physically active young individuals compared to the FTO polymorphism. Effect of interaction of physical activity, in particular aerobic, with the FTO polymorphism on body composition of young athletes was found. KW - physical activity KW - professional and amateur athletes KW - children and adolescents KW - BMI KW - percentage of fat mass KW - FTO KW - aerobic sports activity KW - quantile regression Y1 - 2019 U6 - https://doi.org/10.1127/anthranz/2019/0943 SN - 0003-5548 VL - 76 IS - 5 SP - 401 EP - 408 PB - Schweizerbart CY - Stuttgart ER - TY - JOUR A1 - Werchmeister, Rebecka Maria Larsen A1 - Tang, Jing A1 - Xiao, Xinxin A1 - Wollenberger, Ulla A1 - Hjuler, Hans Aage A1 - Ulstrup, Jens A1 - Zhang, Jingdong T1 - Three-Dimensional Bioelectrodes Utilizing Graphene Based Bioink JF - Journal of The Electrochemical Society N2 - Enzyme immobilization using nanomaterials offers new approaches to enhanced bioelectrochemical performance and is essential for the preparation of bioelectrodes with high reproducibility and low cost. In this report, we describe the development of new three-dimensional (3D) bioelectrodes by immobilizing a "bioink" of glucose oxidase (GOD) in a matrix of reduced graphene oxides (RGOs), polyethylenimine (PEI), and ferrocene carboxylic acid (FcCOOH) on carbon paper (CP). CP with 3D interwoven carbon fibers serves as a solid porous and electronically conducting skeleton, providing large surface areas and space for loading the bioink and diffusion of substrate molecules, respectively. RGO enhances contact between the GOD-matrix and CP, maintaining high conductivity. The composition of the bioink has been systematically optimized. The GOD bioelectrodes show linearly increasing electrocatalytic oxidation current toward glucose concentration up to 48 mM. A hybrid enzymatic biofuel cell equipped with the GOD bioelectrode as a bioanode and a platinum cathode furthermore registers a maximum power density of 5.1 mu W cm(-2) and an open circuit voltage of 0.40 V at 25 degrees C. The new method reported of preparing a bioelectrode by drop-casting the bioink onto the substrate electrode is facile and versatile, with the potential of application also for other enzymatic bioelectrodes. Y1 - 2019 U6 - https://doi.org/10.1149/2.0261916jes SN - 0013-4651 SN - 1945-7111 VL - 166 IS - 16 SP - G170 EP - G177 PB - The Electrochemical Society CY - Pennington ER - TY - JOUR A1 - Thomas, Jessica E. A1 - Carvalho, Gary R. A1 - Haile, James A1 - Rawlence, Nicolas J. A1 - Martin, Michael D. A1 - Ho, Simon Y. W. A1 - Sigfusson, Arnor P. A1 - Josefsson, Vigfus A. A1 - Frederiksen, Morten A1 - Linnebjerg, Jannie F. A1 - Castruita, Jose A. Samaniego A1 - Niemann, Jonas A1 - Sinding, Mikkel-Holger S. A1 - Sandoval-Velasco, Marcela A1 - Soares, Andre E. R. A1 - Lacy, Robert A1 - Barilaro, Christina A1 - Best, Juila A1 - Brandis, Dirk A1 - Cavallo, Chiara A1 - Elorza, Mikelo A1 - Garrett, Kimball L. A1 - Groot, Maaike A1 - Johansson, Friederike A1 - Lifjeld, Jan T. A1 - Nilson, Goran A1 - Serjeanston, Dale A1 - Sweet, Paul A1 - Fuller, Errol A1 - Hufthammer, Anne Karin A1 - Meldgaard, Morten A1 - Fjeldsa, Jon A1 - Shapiro, Beth A1 - Hofreiter, Michael A1 - Stewart, John R. A1 - Gilbert, M. Thomas P. A1 - Knapp, Michael T1 - Demographic reconstruction from ancient DNA supports rapid extinction of the great auk JF - eLife N2 - The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation. Y1 - 2019 U6 - https://doi.org/10.7554/eLife.47509 SN - 2050-084X VL - 8 PB - eLife Sciences Publications CY - Cambridge ER - TY - JOUR A1 - Bröker, Katharine A1 - Sinelnikov, Evgeny A1 - Gustavus, Dirk A1 - Schumacher, Udo A1 - Pörtner, Ralf A1 - Hoffmeister, Hans A1 - Lüth, Stefan A1 - Dammermann, Werner T1 - Mass Production of Highly Active NK Cells for Cancer Immunotherapy in a GMP Conform Perfusion Bioreactor JF - Frontiers in Bioengineering and Biotechnology N2 - NK cells have emerged as promising candidates for cancer immunotherapy, especially due to their ability to fight circulating tumor cells thereby preventing metastases formation. Hence several studies have been performed to generate and expand highly cytotoxic NK cells ex vivo, e.g., by using specific cytokines to upregulate both their proliferation and surface expression of distinct activating receptors. Apart from an enhanced activity, application of NK cells as immunotherapeutic agent further requires sufficient cell numbers and a high purity. All these parameters depend on a variety of different factors including the starting material, additives like cytokines as well as the culture system. Here we analyzed PBMC-derived NK cells of five anonymized healthy donors expanded under specific conditions in an innovative perfusion bioreactor system with respect to their phenotype, IFN gamma production, and cytotoxicity in vitro. Important features of the meander type bioreactors used here are a directed laminar flow of medium and control of relevant process parameters. Cells are cultivated under "steady state" conditions in perfusion mode. Our data demonstrate that expansion of CD3(+) T cell depleted PBMCs in our standardized system generates massive amounts of highly pure (>85%) and potent anticancer active NK cells. These cells express a variety of important receptors driving NK cell recruitment, adhesion as well as activation. More specifically, they express the chemokine receptors CXCR3, CXCR4, and CCR7, the adhesion molecules L-selectin, LFA-1, and VLA-4, the activating receptors NKp30, NKp44, NKp46, NKG2D, DNAM1, and CD16 as well as the death ligands TRAIL and Fas-L. Moreover, the generated NK cells show a strong IFN gamma expression upon cultivation with K562 tumor cells and demonstrate a high cytotoxicity toward leukemic as well as solid tumor cell lines in vitro. Altogether, these characteristics promise a high clinical potency of thus produced NK cells awaiting further evaluation. KW - natural killer cells (NK cells) KW - cytotoxicity KW - tumor immunity KW - immunotherapy KW - perfusion bioreactor KW - GMP KW - mass production process Y1 - 2019 U6 - https://doi.org/10.3389/fbioe.2019.00194 SN - 2296-4185 VL - 7 PB - Frontiers Research Foundation CY - Lausanne ER - TY - GEN A1 - Rodriguez-Sillke, Yasmina A1 - Steinhoff, U. A1 - Bojarski, Christian A1 - Lissner, Donata A1 - Schumann, Michael A1 - Branchi, F. A1 - Siegmund, Britta A1 - Glauben, Rainer T1 - Deep immune profiling of human Peyer´s Patches in patients of inflammatory bowel diseases T2 - European journal of immunology Y1 - 2019 U6 - https://doi.org/10.1002/eji.201970300 SN - 0014-2980 SN - 1521-4141 VL - 49 SP - 203 EP - 204 PB - Wiley CY - Weinheim ER - TY - JOUR A1 - Miele, Vincent A1 - Guill, Christian A1 - Ramos-Jiliberto, Rodrigo A1 - Kéfi, Sonia T1 - Non-trophic interactions strengthen the diversity-functioning relationship in an ecological bioenergetic network model JF - PLoS Computational Biology : a new community journal N2 - Ecological communities are undeniably diverse, both in terms of the species that compose them as well as the type of interactions that link species to each other. Despite this long recognition of the coexistence of multiple interaction types in nature, little is known about the consequences of this diversity for community functioning. In the ongoing context of global change and increasing species extinction rates, it seems crucial to improve our understanding of the drivers of the relationship between species diversity and ecosystem functioning. Here, using a multispecies dynamical model of ecological communities including various interaction types (e.g. competition for space, predator interference, recruitment facilitation in addition to feeding), we studied the role of the presence and the intensity of these interactions for species diversity, community functioning (biomass and production) and the relationship between diversity and functioning. Taken jointly, the diverse interactions have significant effects on species diversity, whose amplitude and sign depend on the type of interactions involved and their relative abundance. They however consistently increase the slope of the relationship between diversity and functioning, suggesting that species losses might have stronger effects on community functioning than expected when ignoring the diversity of interaction types and focusing on feeding interactions only. Y1 - 2020 U6 - https://doi.org/10.1371/journal.pcbi.1007269 SN - 1553-7358 VL - 15 IS - 8 PB - PLoS CY - San Fransisco ER - TY - GEN A1 - Höfer, Chris Tina A1 - Di Lella, Santiago A1 - Dahmani, Ismail A1 - Jungnick, Nadine A1 - Bordag, Natalie A1 - Bobone, Sara A1 - Huan, Q. A1 - Keller, S. A1 - Herrmann, A. A1 - Chiantia, Salvatore T1 - Corrigendum to: Structural determinants of the interaction between influenza A virus matrix protein M1 and lipid membranes (Biochimica et Biophysica Acta (BBA) - Biomembranes. - 1861, (2019), pg 1123-1134) T2 - Biochimica et biophysica acta : Biomembranes Y1 - 2019 U6 - https://doi.org/10.1016/j.bbamem.2019.07.002 SN - 0005-2736 SN - 1879-2642 VL - 1861 IS - 10 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Alker, Wiebke A1 - Schwerdtle, Tanja A1 - Schomburg, Lutz A1 - Haase, Hajo T1 - A Zinpyr-1-based Fluorimetric Microassay for Free Zinc in Human Serum JF - International journal of molecular sciences N2 - Zinc is an essential trace element, making it crucial to have a reliable biomarker for evaluating an individual’s zinc status. The total serum zinc concentration, which is presently the most commonly used biomarker, is not ideal for this purpose, but a superior alternative is still missing. The free zinc concentration, which describes the fraction of zinc that is only loosely bound and easily exchangeable, has been proposed for this purpose, as it reflects the highly bioavailable part of serum zinc. This report presents a fluorescence-based method for determining the free zinc concentration in human serum samples, using the fluorescent probe Zinpyr-1. The assay has been applied on 154 commercially obtained human serum samples. Measured free zinc concentrations ranged from 0.09 to 0.42 nM with a mean of 0.22 ± 0.05 nM. It did not correlate with age or the total serum concentrations of zinc, manganese, iron or selenium. A negative correlation between the concentration of free zinc and total copper has been seen for sera from females. In addition, the free zinc concentration in sera from females (0.21 ± 0.05 nM) was significantly lower than in males (0.23 ± 0.06 nM). The assay uses a sample volume of less than 10 µL, is rapid and cost-effective and allows us to address questions regarding factors influencing the free serum zinc concentration, its connection with the body’s zinc status, and its suitability as a future biomarker for an individual’s zinc status. KW - zinc KW - free zinc KW - serum KW - biomarker KW - fluorescent probe KW - Zinypr-1 Y1 - 2019 U6 - https://doi.org/10.3390/ijms20164006 SN - 1661-6596 SN - 1422-0067 VL - 20 IS - 16 PB - MDPI CY - Basel ER - TY - JOUR A1 - Neiber, Marco Thomas A1 - Kahl, Sandra M. A1 - Wiggering, Benedikt A1 - Glaubrecht, Matthias T1 - Adding the West-African riverine component BT - Revision of the Recent freshwater snails belonging to Pseudocleopatra Thiele, 1928 (Caenogastropoda, Cerithioidea, Paludomidae) JF - Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists N2 - While Africa’s lacustrine gastropod fauna, in particular of Lake Tanganyika, has received much attention, the continent’s riverine malacofauna has long been neglected. Pseudocleopatra is a relatively poorly known paludomid gastropod genus with species found throughout the lower reaches of the West African Volta and Congo rivers. In the course of ongoing systematic revisions of African paludomids, we present here a morphometric analysis and revision of the recent species assigned to the genus, i.e., P. togoensis, P. voltana, P. dartevellei and P. bennikei, to improve taxonomic acuity for this group. We use available museum material for geometric morphometrics, multivariate ratio analysis and comparisons of radular and opercular characters. Our results demonstrate that the four recent species of Pseudocleopatra are clearly distinguishable on the basis of ratios of shell measurements as well as radular and opercular characters. Pseudocleopatra has generic-level synapomorphies including: concentric opercula with relatively large paucispiral nuclei, and rachidian radular teeth with usually 13–20 cusps. On the basis of this characterisation, the nominal species Cleopatra broecki is transferred to Pseudocleopatra. Additionally, the nominal taxon P. bennikei is synonymized with P. broecki n. comb. The phylogenetic relationships of Pseudocleopatra are currently unknown, but the observed tendency of some fossil taxa assigned to Pseudocleopatra towards thalassoidism, i.e., the resemblance to marine gastropods, has led to the hypothesis that some of the thalassoid endemics in Lake Tanganyika may have originated from or be related to Pseudocleopatra. Should this hypothesis be correct, which is in need of testing by molecular genetic methods when suitable samples become available, Pseudocleopatra may play a crucial role in understanding of the evolution of thalassoidism in African Paludomidae. KW - Africa KW - Congo River KW - Volta River KW - thalassoidism KW - geometric morphometrics KW - multivariate ratio analysis Y1 - 2019 U6 - https://doi.org/10.11646/zootaxa.4674.3.1 SN - 1175-5326 SN - 1175-5334 VL - 4674 IS - 3 SP - 301 EP - 328 PB - Magnolia Press CY - Auckland ER - TY - JOUR A1 - Chen, Shun-Gang A1 - Li, Ji A1 - Zhang, Fan A1 - Xiao, Bo A1 - Hu, Jia-Ming A1 - Cui, Yin-Qiu A1 - Hofreiter, Michael A1 - Hou, Xin-Dong A1 - Sheng, Gui-Lian A1 - Lai, Xu-Long A1 - Yuan, Jun-Xia T1 - Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China JF - Mitochondrial DNA Part A N2 - Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290-1180 cal. Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95% credibility interval 117-222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis a slow increase in female effective population size of C. bactrianus from 5000 years ago, which to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road. KW - Camelus bactrianus KW - mitochondrial genome KW - ancient DNA KW - phylogeny KW - maternal lineages Y1 - 2019 U6 - https://doi.org/10.1080/24701394.2019.1659250 SN - 2470-1394 SN - 2470-1408 VL - 30 IS - 7 SP - 786 EP - 793 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Adem, Fozia A. A1 - Kuete, Victor A1 - Mbaveng, Armelle T. A1 - Heydenreich, Matthias A1 - Koch, Andreas A1 - Ndakala, Albert A1 - Irungu, Beatrice A1 - Yenesew, Abiy A1 - Efferth, Thomas T1 - Cytotoxic flavonoids from two Lonchocarpus species JF - Natural Product Research N2 - A new isoflavone, 4′-prenyloxyvigvexin A (1) and a new pterocarpan, (6aR,11aR)-3,8-dimethoxybitucarpin B (2) were isolated from the leaves of Lonchocarpus bussei and the stem bark of Lonchocarpus eriocalyx, respectively. The extract of L. bussei also gave four known isoflavones, maximaisoflavone H, 7,2′-dimethoxy-3′,4′-methylenedioxyisoflavone, 6,7,3′-trimethoxy-4′,5′-methylenedioxyisoflavone, durmillone; a chalcone, 4-hydroxylonchocarpin; a geranylated phenylpropanol, colenemol; and two known pterocarpans, (6aR,11aR)-maackiain and (6aR,11aR)-edunol. (6aR,11aR)-Edunol was also isolated from the stem bark of L. eriocalyx. The structures of the isolated compounds were elucidated by spectroscopy. The cytotoxicity of the compounds was tested by resazurin assay using drug-sensitive and multidrug-resistant cancer cell lines. Significant antiproliferative effects with IC50 values below 10 μM were observed for the isoflavones 6,7,3′-trimethoxy-4′,5′-methylenedioxyisoflavone and durmillone against leukemia CCRF-CEM cells; for the chalcone, 4-hydroxylonchocarpin and durmillone against its resistant counterpart CEM/ADR5000 cells; as well as for durmillone against the resistant breast adenocarcinoma MDA-MB231/BCRP cells and resistant gliobastoma U87MG.ΔEGFR cells. KW - Lonchocarpus bussei KW - Lonchocarpus eriocalyx KW - Leguminosae KW - isoflavone KW - pterocarpan KW - cytotoxicity Y1 - 2019 U6 - https://doi.org/10.1080/14786419.2018.1462179 SN - 1478-6419 SN - 1478-6427 VL - 33 IS - 18 SP - 2609 EP - 2617 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Rieck, Christoph Paul Kurt A1 - Geiger, Daniel A1 - Munkert, Jennifer A1 - Messerschmidt, Katrin A1 - Petersen, Jan A1 - Strasser, Juliane A1 - Meitinger, Nadine A1 - Kreis, Wolfgang T1 - Biosynthetic approach to combine the first steps of cardenolide formation in Saccharomyces cerevisiae JF - Microbiologyopen N2 - A yeast expression plasmid was constructed containing a cardenolide biosynthetic module, referred to as CARD II, using the AssemblX toolkit, which enables the assembly of large DNA constructs. The genes cloned into the vector were (a) a Δ5‐3β‐hydroxysteroid dehydrogenase gene from Digitalis lanata, (b) a steroid Δ5‐isomerase gene from Comamonas testosteronii, (c) a mutated steroid‐5β‐reductase gene from Arabidopsis thaliana, and (d) a steroid 21‐hydroxylase gene from Mus musculus. A second plasmid bearing an ADR/ADX fusion gene from Bos taurus was also constructed. A Saccharomyces cerevisiae strain bearing these two plasmids was generated. This strain, termed “CARD II yeast”, was capable of producing 5β‐pregnane‐3β,21‐diol‐20‐one, a central intermediate in 5β‐cardenolide biosynthesis, starting from pregnenolone which was added to the culture medium. Using this approach, five consecutive steps in cardenolide biosynthesis were realized in baker's yeast. Y1 - 2019 U6 - https://doi.org/10.1002/mbo3.925 SN - 2045-8827 VL - 8 IS - 12 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Scherer, Cedric A1 - Radchuk, Viktoriia A1 - Staubach, Christoph A1 - Mueller, Sophie A1 - Blaum, Niels A1 - Thulke, Hans-Hermann A1 - Kramer-Schadt, Stephanie T1 - Seasonal host life-history processes fuel disease dynamics at different spatial scales JF - Journal of animal ecology : a journal of the British Ecological Society N2 - Understanding the drivers underlying disease dynamics is still a major challenge in disease ecology, especially in the case of long-term disease persistence. Even though there is a strong consensus that density-dependent factors play an important role for the spread of diseases, the main drivers are still discussed and, more importantly, might differ between invasion and persistence periods. Here, we analysed long-term outbreak data of classical swine fever, an important disease in both wild boar and livestock, prevalent in the wild boar population from 1993 to 2000 in Mecklenburg-Vorpommern, Germany. We report outbreak characteristics and results from generalized linear mixed models to reveal what factors affected infection risk on both the landscape and the individual level. Spatiotemporal outbreak dynamics showed an initial wave-like spread with high incidence during the invasion period followed by a drop of incidence and an increase in seroprevalence during the persistence period. Velocity of spread increased with time during the first year of outbreak and decreased linearly afterwards, being on average 7.6 km per quarter. Landscape- and individual-level analyses of infection risk indicate contrasting seasonal patterns. During the persistence period, infection risk on the landscape level was highest during autumn and winter seasons, probably related to spatial behaviour such as increased long-distance movements and contacts induced by rutting and escaping movements. In contrast, individual-level infection risk peaked in spring, probably related to the concurrent birth season leading to higher densities, and was significantly higher in piglets than in reproductive animals. Our findings highlight that it is important to investigate both individual- and landscape-level patterns of infection risk to understand long-term persistence of wildlife diseases and to guide respective management actions. Furthermore, we highlight that exploring different temporal aggregation of the data helps to reveal important seasonal patterns, which might be masked otherwise. KW - classical swine fever KW - disease invasion KW - infection risk KW - pathogen persistence KW - seasonality KW - Sus scrofa KW - wild boar KW - wildlife disease Y1 - 2019 U6 - https://doi.org/10.1111/1365-2656.13070 SN - 0021-8790 SN - 1365-2656 VL - 88 IS - 11 SP - 1812 EP - 1824 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Eugenia Tietze, Hedwig Selma A1 - Joshi, Jasmin Radha A1 - Pugnaire, Francisco Ignacio A1 - Dechoum, Michele de Sa T1 - Seed germination and seedling establishment of an invasive tropical tree species under different climate change scenarios JF - Austral ecology N2 - Increasing air temperature and atmospheric CO2 levels may affect the distribution of invasive species. Whereas there is wide knowledge on the effect of global change on temperate species, responses of tropical invasive species to these two global change drivers are largely unknown. We conducted a greenhouse experiment on Terminalia catappa L. (Combretaceae), an invasive tree species on Brazilian coastal areas, to evaluate the effects of increased air temperature and CO2 concentration on seed germination and seedling growth on the island of Santa Catarina (Florianopolis, Brazil). Seeds of the invasive tree were subjected to two temperature levels (ambient and +1.6 degrees C) and two CO2 levels (ambient and 650 ppmv) with a factorial design. Increased temperature enhanced germination rate and shortened germination time of T. catappa seeds. It also increased plant height, number of leaves and above-ground biomass. By contrast, increased atmospheric CO2 concentration had no significant effects, and the interaction between temperature and CO2 concentration did not affect any of the measured traits. Terminalia catappa adapts to a relatively broad range of environmental conditions, being able to tolerate cooler temperatures in its invasive range. As T. catappa is native to tropical areas, global warming might favour its establishment along the coast of subtropical South America, while increased CO2 levels seem not to have significant effects on seed germination or seedling growth. KW - CO2 concentration KW - coastal dunes KW - establishment KW - invasive plant KW - plant invasion KW - temperature KW - Terminalia catappa Y1 - 2019 U6 - https://doi.org/10.1111/aec.12809 SN - 1442-9985 SN - 1442-9993 VL - 44 IS - 8 SP - 1351 EP - 1358 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Hansen, Dominique A1 - Abreu, Ana A1 - Doherty, Patrick A1 - Völler, Heinz T1 - Dynamic strength training intensity in cardiovascular rehabilitation: is it time to reconsider clinical practice? A systematic review JF - European journal of preventive cardiology : the official ESC journal for primary & secondary cardiovascular prevention, rehabilitation and sports cardiology N2 - When added to endurance training, dynamic strength training leads to significantly greater improvements in peripheral muscle strength and power output in patients with cardiovascular disease, which may be relevant to enhance the patient’s prognosis. As a result, dynamic strength training is recommended in the rehabilitative treatment of many different cardiovascular diseases. However, what strength training intensity should be selected remains under intense debate. Evidence is nonetheless emerging that high-intensity strength training (≥70% of one-repetition maximum) is more effective to increase acutely myofibrillar protein synthesis, cause neural adaptations and, in the long term, increase muscle strength, when compared to low-intensity strength training. Moreover, multiple studies report that high-intensity strength training causes fewer increments in (intra-)arterial blood pressure and cardiac output, as opposed to low-intensity strength training, thus potentially pointing towards sufficient medical safety for the cardiovascular system. The aim of this systematic review is therefore to discuss this line of evidence, which is in contrast to current clinical practice, and to re-open the debate as to what dynamic strength training intensities should actually be applied. KW - Cardiovascular rehabilitation KW - strength training KW - guidelines Y1 - 2019 U6 - https://doi.org/10.1177/2047487319847003 SN - 2047-4873 SN - 2047-4881 VL - 26 IS - 14 SP - 1483 EP - 1492 PB - Sage Publ. CY - London ER - TY - JOUR A1 - Schöpke, Benito A1 - Heinze, Johannes A1 - Pätzig, Marlene A1 - Heinken, Thilo T1 - Do dispersal traits of wetland plant species explain tolerance against isolation effects in naturally fragmented habitats? JF - Plant ecology : an international journal N2 - The effects of habitat fragmentation and isolation on plant species richness have been verified for a wide range of anthropogenically fragmented habitats, but there is currently little information about their effects in naturally small and isolated habitats. We tested whether habitat area, heterogeneity, and isolation affect the richness of wetland vascular plant species in kettle holes, i.e., small glacially created wetlands, in an agricultural landscape of 1 km(2) in NE Germany. We compared fragmentation effects with those of forest fragments in the same landscape window. Since wetland and forest species might differ in their tolerance to isolation, and because isolation effects on plant species may be trait dependent, we asked which key life history traits might foster differences in isolation tolerance between wetland and forest plants. We recorded the flora and vegetation types in 83 isolated sites that contained 81 kettle holes and 25 forest fragments. Overall, the number of wetland species increased with increasing area and heterogeneity, i.e., the number of vegetation types, while area was not a surrogate for heterogeneity in these naturally fragmented systems. Isolation did not influence the number of wetland species but decreased the number of forest species. We also found that seeds of wetland species were on average lighter, more persistent and better adapted to epizoochory, e.g., by waterfowl, than seeds of forest species. Therefore, we suggest that wetland species are more tolerant to isolation than forest species due to their higher dispersal potential in space and time, which may counterbalance the negative effects of isolation. KW - Forest species KW - Habitat fragmentation KW - Isolation KW - Kettle holes KW - Life history traits KW - Wetland species Y1 - 2019 U6 - https://doi.org/10.1007/s11258-019-00955-8 SN - 1385-0237 SN - 1573-5052 VL - 220 IS - 9 SP - 801 EP - 815 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Zupok, Arkadiusz A1 - Górka, Michał Jakub A1 - Siemiatkowska, Beata A1 - Skirycz, Aleksandra A1 - Leimkühler, Silke T1 - Iron-Dependent Regulation of Molybdenum Cofactor Biosynthesis Genes in Escherichia coli JF - Journal of bacteriology N2 - Molybdenum cofactor (Moco) biosynthesis is a complex process that involves the coordinated function of several proteins. In recent years it has become obvious that the availability of iron plays an important role in the biosynthesis of Moco. First, the MoaA protein binds two (4Fe-4S] clusters per monomer. Second, the expression of the moaABCDE and moeAB operons is regulated by FNR, which senses the availability of oxygen via a functional NFe-4S) cluster. Finally, the conversion of cyclic pyranopterin monophosphate to molybdopterin requires the availability of the L-cysteine desulfurase IscS, which is a shared protein with a main role in the assembly of Fe-S clusters. In this report, we investigated the transcriptional regulation of the moaABCDE operon by focusing on its dependence on cellular iron availability. While the abundance of selected molybdoenzymes is largely decreased under iron-limiting conditions, our data show that the regulation of the moaABCDE operon at the level of transcription is only marginally influenced by the availability of iron. Nevertheless, intracellular levels of Moco were decreased under iron-limiting conditions, likely based on an inactive MoaA protein in addition to lower levels of the L-cysteine desulfurase IscS, which simultaneously reduces the sulfur availability for Moco production. IMPORTANCE FNR is a very important transcriptional factor that represents the master switch for the expression of target genes in response to anaerobiosis. Among the FNR-regulated operons in Escherichia coli is the moaABCDE operon, involved in Moco biosynthesis. Molybdoenzymes have essential roles in eukaryotic and prokaryotic organisms. In bacteria, molybdoenzymes are crucial for anaerobic respiration using alternative electron acceptors. This work investigates the connection of iron availability to the biosynthesis of Moco and the production of active molybdoenzymes. KW - Escherichia coli KW - FNR KW - iron regulation KW - iron-sulfur cluster KW - anaerobic respiration KW - molybdenum cofactor Y1 - 2019 U6 - https://doi.org/10.1128/JB.00382-19 SN - 0021-9193 SN - 1098-5530 VL - 201 IS - 17 PB - American Society for Microbiology CY - Washington ER - TY - JOUR A1 - Pehlivanoglu, Tuna A1 - Würtz-Kozak, Karin A1 - Heider, Franziska A1 - Sauer, Daniel A1 - Wanke-Jellinek, Lorenz A1 - Mayer, Michael A1 - Mehren, Christoph T1 - Clinical and Radiographic Outcome of Patients With Cervical Spondylotic Myelopathy Undergoing Total Disc Replacement JF - SPINE N2 - Study Design. A nonrandomized, prospective, and single-center clinical trial. Objective. The aim of this study was to investigate the clinical and radiographic efficacy of ProDisc Vivo cervical total disc replacement (cTDR) in patients with clinical and radiographic documented cervical spondylotic myelopathy (CSM), due to degenerative changes at the index level. Summary of Background Data. Decompression and fusion is still the gold standard in patients with cervical myelopathy. Very limited data are available regarding the application of cTDR in patients with clinical and radiological documented CSM in context of clinical and radiographic outcomes. Methods. Clinical outcome scores included the Neck Disability Index (NDI), Visual Analogue Scale (VAS), arm and neck pain self-assessment questionnaires as well as the Nurick grade and the Japanese Orthopaedic Association (JOA) score. The radiological outcome included the range of motion (ROM), the segmental and global (C2-C7) lordosis, and the occurrence of heterotopic ossifications. Results. Eighteen consecutive patients (10 males, 8 females) with documented clinical and radiological signs of myelopathy were included in this investigation. The study population had a mean age of 52.4 years and a follow-up period of 20.3 months in average (range 3-48 months). The mean range ROM of the index level stayed consistent with 6.8 degrees preoperatively and 7.2 degrees (P = 0.578) at the last follow-up; the global lordosis in neutral position changed from 3.5 degrees to 14.2 degrees significantly (P = 0.005) in mean. The JOA score improved from 11.3 to 16.6 (P < 0.001) as well as the NDI 36.7 to 10.3 (P < 0.001) and the VAS score from 5.7/6.1 (arm/neck) to 1.3/2.0 (P P < 0.001). The mean Nurick grade was 1.33 preoperatively and dropped down in all cases to Nurick grade of 0 (P < 0.001). Conclusion. cTDR (with ProDisc Vivio) in patients with CSM yielded good clinical and radiographic outcomes and found as a reliable, safe, and motion-preserving surgical treatment option, although its indication is very limited due to numerous exclusion criteria. KW - cervical myelopathy KW - cervical total disc replacement KW - disc arthroplasty KW - ProDisc Vivo Y1 - 2019 U6 - https://doi.org/10.1097/BRS.0000000000003079 SN - 0362-2436 SN - 1528-1159 VL - 44 IS - 20 SP - 1403 EP - 1411 PB - Lippincott Williams & Wilkins CY - Philadelphia ER - TY - JOUR A1 - Schiro, Gabriele A1 - Colangeli, Pierluigi A1 - Müller, Marina E. H. T1 - A Metabarcoding Analysis of the Mycobiome of Wheat Ears Across a Topographically Heterogeneous Field JF - Frontiers in microbiology KW - Fusarium KW - microclimate KW - canopy KW - fungal community KW - Alternaria KW - spatially induced variance Y1 - 2019 U6 - https://doi.org/10.3389/fmicb.2019.02095 SN - 1664-302X VL - 10 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Schwarzer, Christian A1 - Joshi, Jasmin Radha T1 - Ecotypic differentiation, hybridization and clonality facilitate the persistence of a cold-adapted sedge in European bogs JF - Biological journal of the Linnean Society : a journal of evolution N2 - Recent research has shown that many cold-adapted species survived the last glacial maximum (LGM) in northern refugia. Whether this evolutionary history has had consequences for their genetic diversity and adaptive potential remains unknown. We sampled 14 populations of Carex limosa, a sedge specialized to bog ecosystems, along a latitudinal gradient from its Scandinavian core to the southern lowland range-margin in Germany. Using microsatellite and experimental common-garden data, we evaluated the impacts of global climate change along this gradient and assessed the conservation status of the southern marginal populations. Microsatellite data revealed two highly distinct genetic groups and hybrid individuals. In our common-garden experiment, the two groups showed divergent responses to increased nitrogen/phosphorus (N/P) availability, suggesting ecotypic differentiation. Each group formed genetically uniform populations at both northern and southern sampling areas. Mixed populations occurred throughout our sampling area, an area that was entirely glaciated during the LGM. The fragmented distribution implies allopatric divergence at geographically separated refugia that putatively differed in N/P availability. Molecular data and an observed low hybrid fecundity indicate the importance of clonal reproduction for hybrid populations. At the southern range-margin, however, all populations showed effects of clonality, lowered fecundity and low competitiveness, suggesting abiotic and biotic constraints to population persistence. KW - biogeography KW - bog/mire plants KW - Carex limosa KW - climate change KW - glacial divergence KW - global change KW - leading/trailing edge KW - population differentiation KW - sexual/asexual reproduction Y1 - 2019 U6 - https://doi.org/10.1093/biolinnean/blz141 SN - 0024-4066 SN - 1095-8312 VL - 128 IS - 4 SP - 909 EP - 925 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Lemaire, Olivier N. A1 - Honore, Flora A. A1 - Tempel, Sebastien A1 - Fortier, Emma M. A1 - Leimkühler, Silke A1 - Mejean, Vincent A1 - Iobbi-Nivol, Chantal T1 - Shewanella decolorationis LDS1 Chromate Resistance JF - Applied and environmental microbiology N2 - The genus Shewanella is well known for its genetic diversity, its outstanding respiratory capacity, and its high potential for bioremediation. Here, a novel strain isolated from sediments of the Indian Ocean was characterized. A 16S rRNA analysis indicated that it belongs to the species Shewanella decolorationis. It was named Shewanella decolorationis LDS1. This strain presented an unusual ability to grow efficiently at temperatures from 24 degrees C to 40 degrees C without apparent modifications of its metabolism, as shown by testing respiratory activities or carbon assimilation, and in a wide range of salt concentrations. Moreover, S. decolorationis LDS1 tolerates high chromate concentrations. Indeed, it was able to grow in the presence of 4 mM chromate at 28 degrees C and 3 mM chromate at 40 degrees C. Interestingly, whatever the temperature, when the culture reached the stationary phase, the strain reduced the chromate present in the growth medium. In addition, S. decolorationis LDS1 degrades different toxic dyes, including anthraquinone, triarylmethane, and azo dyes. Thus, compared to Shewanella oneidensis, this strain presented better capacity to cope with various abiotic stresses, particularly at high temperatures. The analysis of genome sequence preliminary data indicated that, in contrast to S. oneidensis and S. decolorationis S12, S. decolorationis LDS1 possesses the phosphorothioate modification machinery that has been described as participating in survival against various abiotic stresses by protecting DNA. We demonstrate that its heterologous production in S. oneidensis allows it to resist higher concentrations of chromate. IMPORTANCE Shewanella species have long been described as interesting microorganisms in regard to their ability to reduce many organic and inorganic compounds, including metals. However, members of the Shewanella genus are often depicted as cold-water microorganisms, although their optimal growth temperature usually ranges from 25 to 28 degrees C under laboratory growth conditions. Shewanella decolorationis LDS1 is highly attractive, since its metabolism allows it to develop efficiently at temperatures from 24 to 40 degrees C, conserving its ability to respire alternative substrates and to reduce toxic compounds such as chromate or toxic dyes. Our results clearly indicate that this novel strain has the potential to be a powerful tool for bioremediation and unveil one of the mechanisms involved in its chromate resistance. KW - Shewanella KW - bioremediation KW - chromium KW - decolorization KW - dndBCDE KW - dyes KW - temperature Y1 - 2019 U6 - https://doi.org/10.1128/AEM.00777-19 SN - 0099-2240 SN - 1098-5336 VL - 85 IS - 18 PB - American Society for Microbiology CY - Washington ER - TY - THES A1 - Dammhahn, Melanie T1 - From individual variation to community structure : paterns, determinants and consequences of within- and between-species variation in behaviour, life-history and ecology Y1 - 2019 ER - TY - JOUR A1 - Albers, Philip A1 - Üstün, Suayib A1 - Witzel, Katja A1 - Kraner, Max Erdmund A1 - Börnke, Frederik T1 - A Remorin from Nicotiana benthamiana Interacts with the Pseudomonas Type-III Effector Protein HopZ1a and is Phosphorylated by the Immune-Related Kinase PBS1 JF - Molecular Plant-Microbe Interactions N2 - The plasma membrane (PM) is at the interface of plant-pathogen interactions and, thus, many bacterial type-III effector (T3E) proteins target membrane-associated processes to interfere with immunity. The Pseudomonas syringae T3E HopZ1a is a host cell PM-localized effector protein that has several immunity-associated host targets but also activates effector-triggered immunity in resistant backgrounds. Although HopZ1a has been shown to interfere with early defense signaling at the PM, no dedicated PM-associated HopZ1a target protein has been identified until now. Here, we show that HopZ1a interacts with the PM-associated remorin protein NbREM4 from Nicotiana benthamiana in several independent assays. NbREM4 relocalizes to membrane nanodomains after treatment with the bacterial elicitor flg22 and transient overexpression of NbREM4 in N. benthamiana induces the expression of a subset of defense-related genes. We can further show that NbREM4 interacts with the immune-related receptor-like cytoplasmic kinase avrPphB-susceptible 1 (PBS1) and is phosphorylated by PBS1 on several residues in vitro. Thus, we conclude that NbREM4 is associated with early defense signaling at the PM. The possible relevance of the HopZ1a-NbREM4 interaction for HopZ1a virulence and avirulence functions is discussed. KW - bacterial pathogenesis KW - defense signaling pathways KW - effectors KW - elicitors KW - HopZ1a KW - MAMPs KW - PAMPs KW - PBS1 KW - Pseudomonas syringae KW - remorin KW - type-3 secretion Y1 - 2019 U6 - https://doi.org/10.1094/MPMI-04-19-0105-R SN - 0894-0282 SN - 1943-7706 VL - 32 IS - 9 SP - 1229 EP - 1242 PB - Amer phytopathological SOC CY - ST Paul ER - TY - JOUR A1 - Ozcelikay, Goksu A1 - Kurbanoglu, Sevinc A1 - Zhang, Xiaorong A1 - Söz, Çağla Kosak A1 - Wollenberger, Ulla A1 - Ozkan, Sibel A. A1 - Yarman, Aysu A1 - Scheller, Frieder W. T1 - Electrochemical MIP Sensor for Butyrylcholinesterase JF - Polymers N2 - Molecularly imprinted polymers (MIPs) mimic the binding sites of antibodies by substituting the amino acid-scaffold of proteins by synthetic polymers. In this work, the first MIP for the recognition of the diagnostically relevant enzyme butyrylcholinesterase (BuChE) is presented. The MIP was prepared using electropolymerization of the functional monomer o-phenylenediamine and was deposited as a thin film on a glassy carbon electrode by oxidative potentiodynamic polymerization. Rebinding and removal of the template were detected by cyclic voltammetry using ferricyanide as a redox marker. Furthermore, the enzymatic activity of BuChE rebound to the MIP was measured via the anodic oxidation of thiocholine, the reaction product of butyrylthiocholine. The response was linear between 50 pM and 2 nM concentrations of BuChE with a detection limit of 14.7 pM. In addition to the high sensitivity for BuChE, the sensor responded towards pseudo-irreversible inhibitors in the lower mM range. KW - molecularly imprinted polymers KW - biomimetic sensors KW - butyrylcholinesterase KW - o-phenylenediamine KW - rivastigmine Y1 - 2019 U6 - https://doi.org/10.3390/polym11121970 SN - 2073-4360 VL - 11 IS - 12 PB - MDPI CY - Basel ER - TY - JOUR A1 - Horreo, J. L. A1 - Breedveld, Merel Cathelijne A1 - Lindtke, D. A1 - Heulin, B. A1 - Surget-Groba, Yann A1 - Fitze, Patrick S. T1 - Genetic introgression among differentiated clades is lower among clades exhibiting different parity modes JF - Heredity N2 - Mechanisms leading to sympatric speciation are diverse and may build up reproductive isolation. Reproductive isolation among differentiated clades may exist due to genetic incompatibilities, sexual selection, differences in parity mode, reduced post-zygotic survival or reproductive success of hybrids. Here, we test whether differences in parity mode lead to reproductive isolation by investigating introgression in Zootoca vivipara, a lizard species exhibiting oviparous and viviparous reproduction. We measured introgression in transects spanning different viviparous clades, different oviparous subclades, transects containing oviparous and viviparous clades, and transects within the same subclade (control transects). Introgression in transects spanning oviparous and viviparous clades was one order of magnitude smaller than transects spanning the same reproductive mode and no statistical differences existed between transects spanning the same reproductive mode and control transects. Among types of transects, no significant differences existed in genetic and geographic distances, nor number of detected alleles. Moreover, hybrids were detected in all types of transects, showing that parity mode alone does not necessarily lead to complete reproductive isolation, which suggests that reinforcement may play an important role. The evolution of different parity modes together with reinforcement may thus promote reproductive isolation and rapid speciation, potentially explaining why only six of the almost 40,000 vertebrates belonging to groups consisting of viviparous and oviparous species exhibit bimodal reproduction. Y1 - 2019 U6 - https://doi.org/10.1038/s41437-019-0201-7 SN - 0018-067X SN - 1365-2540 VL - 123 IS - 2 SP - 264 EP - 272 PB - Nature Publ. Group CY - London ER - TY - GEN A1 - Horreo, J. L. A1 - Breedveld, Merel Cathelijne A1 - Lindtke, D. A1 - Heulin, B. A1 - Surget-Groba, Yann A1 - Fitze, Patrick S. T1 - Correction: Genetic introgression among differentiated clades is lower among clades exhibiting different parity modes. - (Heredity. - 123, (2019) pg 264) T2 - Heredity N2 - The original version of this Article contained an error in the spelling of the author Y. Surget-Groba, which was incorrectly given as J. Surget-Groba. This has now been corrected in both the PDF and HTML versions of the Article. Y1 - 2019 U6 - https://doi.org/10.1038/s41437-019-0223-1 SN - 0018-067X SN - 1365-2540 VL - 123 IS - 2 SP - 285 EP - 285 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Sauer, Michael A1 - Kleine-Vehn, Jürgen T1 - PIN-FORMED and PIN-LIKES auxin transport facilitators JF - Development : Company of Biologists N2 - The phytohormone auxin influences virtually all aspects of plant growth and development. Auxin transport across membranes is facilitated by, among other proteins, members of the PIN-FORMED (PIN) and the structurally similar PIN-LIKES (PILS) families, which together govern directional cell-to-cell transport and intracellular accumulation of auxin. Canonical PIN proteins, which exhibit a polar localization in the plasma membrane, determine many patterning and directional growth responses. Conversely, the less-studied noncanonical PINs and PILS proteins, which mostly localize to the endoplasmic reticulum, attenuate cellular auxin responses. Here, and in the accompanying poster, we provide a brief summary of current knowledge of the structure, evolution, function and regulation of these auxin transport facilitators. KW - Auxin KW - Auxin transport KW - Phytohormone Y1 - 2019 U6 - https://doi.org/10.1242/dev.168088 SN - 0950-1991 SN - 1477-9129 VL - 146 IS - 15 PB - Company biologists ltd CY - Cambridge ER - TY - JOUR A1 - Dunsing, Valentin A1 - Irmscher, Tobias A1 - Barbirz, Stefanie A1 - Chiantia, Salvatore T1 - Purely Polysaccharide-Based Biofilm Matrix Provides Size-Selective Diffusion Barriers for Nanoparticles and Bacteriophages JF - Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences N2 - Biofilms are complex mixtures of proteins, DNA, and polysaccharides surrounding bacterial communities as protective barriers that can be biochemically modified during the bacterial life cycle. However, their compositional heterogeneity impedes a precise analysis of the contributions of individual matrix components to the biofilm structural organization. To investigate the structural properties of glycan-based biofilms, we analyzed the diffusion dynamics of nanometer-sized objects in matrices of the megadalton-sized anionic polysaccharide, stewartan, the major biofilm component of the plant pathogen, Pantoea stewartii. Fluorescence correlation spectroscopy and single-particle tracking of nanobeads and bacteriophages indicated notable subdiffusive dynamics dependent on probe size and stewartan concentration, in contrast to free diffusion of small molecules. Stewartan enzymatic depolymerization by bacteriophage tailspike proteins rapidly restored unhindered diffusion. We, thus, hypothesize that the glycan polymer stewartan determines the major physicochemical properties of the biofilm, which acts as a selective diffusion barrier for nanometer-sized objects and can be controlled by enzymes. Y1 - 2019 U6 - https://doi.org/10.1021/acs.biomac.9b00938 SN - 1525-7797 SN - 1526-4602 VL - 20 IS - 10 SP - 3842 EP - 3854 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Zupok, Arkadiusz A1 - Iobbi-Nivol, Chantal A1 - Mejean, Vincent A1 - Leimkühler, Silke T1 - The regulation of Moco biosynthesis and molybdoenzyme gene expression by molybdenum and iron in bacteria JF - Metallomics : integrated biometal science N2 - Bacterial molybdoenzymes are key enzymes involved in the global sulphur, nitrogen and carbon cycles. These enzymes require the insertion of the molybdenum cofactor (Moco) into their active sites and are able to catalyse a large range of redox-reactions. Escherichia coli harbours nineteen different molybdoenzymes that require a tight regulation of their synthesis according to substrate availability, oxygen availability and the cellular concentration of molybdenum and iron. The synthesis and assembly of active molybdoenzymes are regulated at the level of transcription of the structural genes and of translation in addition to the genes involved in Moco biosynthesis. The action of global transcriptional regulators like FNR, NarXL/QP, Fur and ArcA and their roles on the expression of these genes is described in detail. In this review we focus on what is known about the molybdenum- and iron-dependent regulation of molybdoenzyme and Moco biosynthesis genes in the model organism E. coli. The gene regulation in E. coli is compared to two other well studied model organisms Rhodobacter capsulatus and Shewanella oneidensis. Y1 - 2019 U6 - https://doi.org/10.1039/c9mt00186g SN - 1756-5901 SN - 1756-591X VL - 11 IS - 10 SP - 1602 EP - 1624 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Heim, Olga A1 - Puisto, Anna I. E. A1 - Fukui, Dai A1 - Vesterinen, Eero J. T1 - Molecular evidence of bird-eating behavior in Nyctalus aviator JF - Acta ethologica N2 - Insectivorous bats consume a large variety of food items. Previous observations of feathers found in feces led to the hypothesis that the birdlike noctule (Nyctalus aviator, Vespertilionidae) could prey on birds. To test the hypothesis, we analyzed fecal samples from six species (Barbastella pacifica, Murina hilgendorfi, Myotis frater, N. aviator, Plecotus sacrimontis, and Vespertilio sinensis) collected from central Hokkaido, Japan, via DNA barcoding. We identified the presence of the Middendorff’s grasshopper warbler (Locustella ochotensis) in the diet of a pregnant individual of N. aviator. All the other samples proved negative regarding bird prey DNA. This is the first time that the consumption of a bird by N. aviator is confirmed with molecular evidence. Our findings add invaluable insight into the diet of this bat and its potentially opportunistic foraging behavior. KW - Nyctalus aviator KW - Locustella ochotensis KW - Bird prey KW - DNA barcoding KW - Sanger sequencing Y1 - 2019 U6 - https://doi.org/10.1007/s10211-019-00319-5 SN - 0873-9749 SN - 1437-9546 VL - 22 IS - 3 SP - 223 EP - 226 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Rossberg, Axel G. A1 - Gaedke, Ursula A1 - Kratina, Pavel T1 - Dome patterns in pelagic size spectra reveal strong trophic cascades JF - Nature Communications N2 - In ecological communities, especially the pelagic zones of aquatic ecosystems, certain bodysize ranges are often over-represented compared to others. Community size spectra, the distributions of community biomass over the logarithmic body-mass axis, tend to exhibit regularly spaced local maxima, called "domes", separated by steep troughs. Contrasting established theory, we explain these dome patterns as manifestations of top-down trophic cascades along aquatic food chains. Compiling high quality size-spectrum data and comparing these with a size-spectrum model introduced in this study, we test this theory and develop a detailed picture of the mechanisms by which bottom-up and top-down effects interact to generate dome patterns. Results imply that strong top-down trophic cascades are common in freshwater communities, much more than hitherto demonstrated, and may arise in nutrient rich marine systems as well. Transferring insights from the general theory of nonlinear pattern formation to domes patterns, we provide new interpretations of past lake-manipulation experiments. Y1 - 2019 U6 - https://doi.org/10.1038/s41467-019-12289-0 SN - 2041-1723 VL - 10 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Staszek, Pawel A1 - Krasuska, Urszula A1 - Otulak-Koziel, Katarzyna A1 - Fettke, Jörg A1 - Gniazdowska, Agnieszka T1 - Canavanine-Induced Decrease in Nitric Oxide Synthesis Alters Activity of Antioxidant System but Does Not Impact S-Nitrosoglutathione Catabolism in Tomato Roots JF - Frontiers in plant science N2 - Canavanine (CAN) is a nonproteinogenic amino acid synthesized in legumes. In mammalians, as arginine analogue, it is an inhibitor of nitric oxide synthase (NOS) activity. The aim of this study was to investigate the impact of CAN-induced nitric oxide level limitation on the antioxidant system and S-nitrosoglutathione (GSNO) metabolism in roots of tomato seedlings. Treatment with CAN (10 or 50 mu M) for 24-72 h led to restriction in root growth. Arginine-dependent NOS-like activity was almost completely inhibited, demonstrating direct effect of CAN action. CAN increased total antioxidant capacity and the level of sulphydryl groups. Catalase (CAT) and superoxide dismutase (SOD) activity decreased in CAN exposed roots. CAN supplementation resulted in the decrease of transcript levels of genes coding CAT (with the exception of CAT1). Genes coding SOD (except MnSOD and CuSOD) were upregulated by CAN short treatment; prolonged exposition to 50-mu M CAN resulted in downregulation of FeSOD, CuSOD, and SODP-2. Activity of glutathione reductase dropped down after short-term (10-mu M CAN) supplementation, while glutathione peroxidase activity was not affected. Transcript levels of glutathione reductase genes declined in response to CAN. Genes coding glutathione peroxidase were upregulated by 50-mu M CAN, while 10-mu M CAN downregulated GSHPx1. Inhibition of NOS-like activity by CAN resulted in lower GSNO accumulation in root tips. Activity of GSNO reductase was decreased by short-term supplementation with CAN. In contrast, GSNO reductase protein abundance was higher, while transcript levels were slightly altered in roots exposed to CAN. This is the first report on identification of differentially nitrated proteins in response to supplementation with nonproteinogenic amino acid. Among nitrated proteins differentially modified by CAN, seed storage proteins (after short-term CAN treatment) and components of the cellular redox system (after prolonged CAN supplementation) were identified. The findings demonstrate that due to inhibition of NOS-like activity, CAN leads to modification in antioxidant system. Limitation in GSNO level is due to lower nitric oxide formation, while GSNO catabolism is less affected. We demonstrated that monodehydroascorbate reductase, activity of which is inhibited in roots of CAN-treated plants, is the protein preferentially modified by tyrosine nitration. KW - canavanine KW - cellular antioxidant system KW - GSNOR-GSNO reductase KW - nitrated proteins KW - nitric oxide-NO KW - nonproteinogenic amino acid KW - NOS-like activity KW - reactive nitrogen species (RNS) Y1 - 2019 U6 - https://doi.org/10.3389/fpls.2019.01077 SN - 1664-462X VL - 10 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Matthey-Doret, Cyril A1 - van der Kooi, Casper J. A1 - Jeffries, Daniel L. A1 - Bast, Jens A1 - Dennis, Alice B. A1 - Vorburger, Christoph A1 - Schwander, Tanja T1 - Mapping of Multiple Complementary Sex Determination Loci in a Parasitoid Wasp JF - Genome biology and evolution N2 - Sex determination has evolved in a variety of ways and can depend on environmental and genetic signals. A widespread form of genetic sex determination is haplodiploidy, where unfertilized, haploid eggs develop into males and fertilized diploid eggs into females. One of the molecular mechanisms underlying haplodiploidy in Hymenoptera, the large insect order comprising ants, bees, and wasps, is complementary sex determination (CSD). In species with CSD, heterozygosity at one or several loci induces female development. Here, we identify the genomic regions putatively underlying multilocus CSD in the parasitoid wasp Lysiphlebus fabarum using restriction -site associated DNA sequencing. By analyzing segregation patterns at polymorphic sites among 331 diploid males and females, we identify up to four CSD candidate regions, all on different chromosomes. None of the candidate regions feature evidence for homology with the csd gene from the honey bee, the only species in which CSD has been characterized, suggesting that CSD in L. fabarum is regulated via a novel molecular mechanism. Moreover, no homology is shared between the candidate loci, in contrast to the idea that multilocus CSD should emerge from duplications of an ancestral single -locus system. Taken together, our results suggest that the molecular mechanisms underlying CSD in Hymenoptera are not conserved between species, raising the question as to whether CSD may have evolved multiple times independently in the group. KW - hymenoptera KW - sex determination KW - Lysiphlebus fabarum KW - CSD Y1 - 2019 U6 - https://doi.org/10.1093/gbe/evz219 SN - 1759-6653 VL - 11 IS - 10 SP - 2954 EP - 2962 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Rühl, Martin A1 - Pietzner, Verena A1 - Vilcinskas, Andreas A1 - Zorn, Holger T1 - Insects and molds as bio-resources: food biotechnology JF - Chemie in unserer Zeit N2 - Microorganisms are used for the production of foodstuffs since thousands of years. By now, these biotechnological processes are not restricted to some of the known microorganisms. The possibility to produce enzymes independently from their host organisms extended their range of application. Since then, exploration of new bioresources leads to novel enzymes and peptides applicable for a diverse set of food production processes: peptidases of grain pest beetles are able to hydrolyse gluten and antimicrobial active peptides of insects maybe of use for preservation of food. Examples of our own work depict strategies to identify novel biocatalysts for food biotechnology. N2 - Mikroorganismen werden seit Jahrtausenden zur Herstellung von Lebensmitteln genutzt. Mittlerweile sind diese biotechnologischen Verfahren nicht mehr auf die Verwendung einiger Organismen beschränkt. Die Möglichkeit, Enzyme unabhängig von ihrem Wirtsorganismus zu produzieren, erweiterte den Einsatzbereich dieser technischen Hilfsmittel ungemein. Seither werden vermehrt neue Bioressourcen erschlossen, um neuartige Enzyme und Peptide für die Lebensmittelproduktion verfügbar zu machen: Peptidasen aus Getreideschädlingen vermögen Gluten zu hydrolysieren und antimikrobiell wirksame Peptide aus Insekten könnten zur Haltbarmachung von Lebensmitteln eingesetzt werden. Aber wie findet man solche Katalysatoren? Beispiele aus eigenen Arbeiten zeigen es. T2 - Insekten und Schimmelpilze als Bioressource KW - Gelbe Biotechnologie KW - Insekten KW - Ascomyceten KW - antimikrobielle Peptide Y1 - 2019 U6 - https://doi.org/10.1002/ciuz.201900833 SN - 0009-2851 SN - 1521-3781 VL - 53 IS - 5 SP - 342 EP - 348 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Toulouse, Charlotte Marguerite A1 - Schmucker, Sonja A1 - Metesch, Kristina A1 - Pfannstiel, Jens A1 - Michel, Bernd A1 - Starke, Ines A1 - Möller, Heiko Michael A1 - Stefanski, Volker A1 - Steuber, Julia T1 - Mechanism and impact of catecholamine conversion by Vibrio cholerae JF - Biochimica et biophysica acta : Bioenergetics N2 - Bacterial pathogens are influenced by signaling molecules including the catecholamines adrenaline and noradrenaline which are host-derived hormones and neurotransmitters. Adrenaline and noradrenaline modulate growth, motility and virulence of bacteria. We show that adrenaline is converted by the pathogen Vibrio cholerae to adrenochrome in the course of respiration, and demonstrate that superoxide produced by the respiratory, Na+ - translocating NADH:quinone oxidoreductase (NQR) acts as electron acceptor in the oxidative conversion of adrenaline to adrenochrome. Adrenochrome stimulates growth of V. cholerae, and triggers specific responses in V. cholerae and in immune cells. We performed a quantitative proteome analysis of V. cholerae grown in minimal medium with glucose as carbon source without catecholamines, or with adrenaline, noradrenaline or adrenochrome. Significant regulation of proteins participating in iron transport and iron homeostasis, in energy metabolism, and in signaling was observed upon exposure to adrenaline, noradrenaline or adrenochrome. On the host side, adrenochrome inhibited lipopolysaccharide-triggered formation of TNF-alpha by THP-1 monocytes, though to a lesser extent than adrenaline. It is proposed that adrenochrome produced from adrenaline by respiring V. cholerae functions as effector molecule in pathogen-host interaction. KW - Vibrio cholerae KW - Na+ - NADH:quinone oxidoreductase KW - NQR KW - Superoxide KW - Adrenaline KW - Adrenochrome Y1 - 2019 U6 - https://doi.org/10.1016/j.bbabio.2019.04.003 SN - 0005-2728 SN - 1879-2650 VL - 1860 IS - 6 SP - 478 EP - 487 PB - Elsevier CY - Amsterdam ER - TY - GEN A1 - Dahmani, Ismail A1 - Ludwig, Kai A1 - Chiantia, Salvatore T1 - Influenza A matrix protein M1 induces lipid membrane deformation via protein multimerization T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - The matrix protein M1 of the Influenza A virus (IAV) is supposed to mediate viral assembly and budding at the plasma membrane (PM) of infected cells. In order for a new viral particle to form, the PM lipid bilayer has to bend into a vesicle toward the extracellular side. Studies in cellular models have proposed that different viral proteins might be responsible for inducing membrane curvature in this context (including M1), but a clear consensus has not been reached. In the present study, we use a combination of fluorescence microscopy, cryogenic transmission electron microscopy (cryo-TEM), cryo-electron tomography (cryo-ET) and scanning fluorescence correlation spectroscopy (sFCS) to investigate M1-induced membrane deformation in biophysical models of the PM. Our results indicate that M1 is indeed able to cause membrane curvature in lipid bilayers containing negatively charged lipids, in the absence of other viral components. Furthermore, we prove that protein binding is not sufficient to induce membrane restructuring. Rather, it appears that stable M1–M1 interactions and multimer formation are required in order to alter the bilayer three-dimensional structure, through the formation of a protein scaffold. Finally, our results suggest that, in a physiological context,M1-induced membrane deformation might be modulated by the initial bilayer curvature and the lateral organization of membrane components (i.e. the presence of lipid domains). T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 768 KW - confocal microscopy KW - influenza KW - lipid membranes KW - membranes KW - protein-protein interactions KW - viral matrix proteins Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-438689 SN - 1866-8372 IS - 768 ER - TY - GEN A1 - Ceulemans, Ruben A1 - Gaedke, Ursula A1 - Klauschies, Toni A1 - Guill, Christian T1 - The effects of functional diversity on biomass production, variability, and resilience of ecosystem functions in a tritrophic system T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Diverse communities can adjust their trait composition to altered environmental conditions, which may strongly influence their dynamics. Previous studies of trait-based models mainly considered only one or two trophic levels, whereas most natural system are at least tritrophic. Therefore, we investigated how the addition of trait variation to each trophic level influences population and community dynamics in a tritrophic model. Examining the phase relationships between species of adjacent trophic levels informs about the strength of top-down or bottom-up control in non-steadystate situations. Phase relationships within a trophic level highlight compensatory dynamical patterns between functionally different species, which are responsible for dampening the community temporal variability. Furthermore, even without trait variation, our tritrophic model always exhibits regions with two alternative states with either weak or strong nutrient exploitation, and correspondingly low or high biomass production at the top level. However, adding trait variation increased the basin of attraction of the high-production state, and decreased the likelihood of a critical transition from the high- to the lowproduction state with no apparent early warning signals. Hence, our study shows that trait variation enhances resource use efficiency, production, stability, and resilience of entire food webs. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 744 KW - early-warning signals KW - top-down control KW - community ecology KW - regime shifts KW - food webs KW - compensatory dynamics KW - consumer diversity KW - metabolic theory KW - rapid evolution KW - stable states Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-435439 SN - 1866-8372 IS - 744 ER - TY - GEN A1 - Porada, Philipp A1 - Tamm, Alexandra A1 - Raggio, Jose A1 - Yafang, Cheng A1 - Kleidon, Axel A1 - Pöschl, Ulrich A1 - Weber, Bettina T1 - Global NO and HONO emissions of biological soil crusts estimated by a process-based non-vascular vegetation model T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - The reactive trace gases nitric oxide (NO) and nitrous acid (HONO) are crucial for chemical processes in the atmosphere, including the formation of ozone and OH radicals, oxidation of pollutants, and atmospheric self-cleaning. Recently, empirical studies have shown that biological soil crusts are able to emit large amounts of NO and HONO, and they may therefore play an important role in the global budget of these trace gases. However, the upscaling of local estimates to the global scale is subject to large uncertainties, due to unknown spatial distribution of crust types and their dynamic metabolic activity. Here, we perform an alternative estimate of global NO and HONO emissions by biological soil crusts, using a process-based modelling approach to these organisms, combined with global data sets of climate and land cover. We thereby consider that NO and HONO are emitted in strongly different proportions, depending on the type of crust and their dynamic activity, and we provide a first estimate of the global distribution of four different crust types. Based on this, we estimate global total values of 1.04 Tg yr⁻¹ NO–N and 0.69 Tg yr⁻¹ HONO–N released by biological soil crusts. This corresponds to around 20% of global emissions of these trace gases from natural ecosystems. Due to the low number of observations on NO and HONO emissions suitable to validate the model, our estimates are still relatively uncertain. However, they are consistent with the amount estimated by the empirical approach, which confirms that biological soil crusts are likely to have a strong impact on global atmospheric chemistry via emissions of NO and HONO. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 746 KW - net primary productivity KW - hilly loes plateau KW - mojave desert KW - spatial-distribution KW - nitrous-oxide KW - succulent karoo KW - inner-mongolia KW - carbon KW - lichens KW - bryophytes Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-435682 SN - 1866-8372 IS - 746 SP - 2003 EP - 2031 ER - TY - GEN A1 - Riedel, Simona A1 - Siemiatkowska, Beata A1 - Watanabe, Mutsumi A1 - Müller, Christina S. A1 - Schünemann, Volker A1 - Hoefgen, Rainer A1 - Leimkühler, Silke T1 - The ABCB7-Like Transporter PexA in Rhodobacter capsulatus Is Involved in the Translocation of Reactive Sulfur Species T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - The mitochondrial ATP-binding cassette (ABC) transporters ABCB7 in humans, Atm1 in yeast and ATM3 in plants, are highly conserved in their overall architecture and particularly in their glutathione binding pocket located within the transmembrane spanning domains. These transporters have attracted interest in the last two decades based on their proposed role in connecting the mitochondrial iron sulfur (Fe–S) cluster assembly with its cytosolic Fe–S cluster assembly (CIA) counterpart. So far, the specific compound that is transported across the membrane remains unknown. In this report we characterized the ABCB7-like transporter Rcc02305 in Rhodobacter capsulatus, which shares 47% amino acid sequence identity with its mitochondrial counterpart. The constructed interposon mutant strain in R. capsulatus displayed increased levels of intracellular reactive oxygen species without a simultaneous accumulation of the cellular iron levels. The inhibition of endogenous glutathione biosynthesis resulted in an increase of total glutathione levels in the mutant strain. Bioinformatic analysis of the amino acid sequence motifs revealed a potential aminotransferase class-V pyridoxal-50-phosphate (PLP) binding site that overlaps with the Walker A motif within the nucleotide binding domains of the transporter. PLP is a well characterized cofactor of L-cysteine desulfurases like IscS and NFS1 which has a role in the formation of a protein-bound persulfide group within these proteins. We therefore suggest renaming the ABCB7-like transporter Rcc02305 in R. capsulatus to PexA for PLP binding exporter. We further suggest that this ABC-transporter in R. capsulatus is involved in the formation and export of polysulfide species to the periplasm. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 740 KW - ABCB7 KW - persulfide KW - polysulfide KW - glutathione KW - ABC transporter KW - Walker A motif KW - pyridoxal-50-phosphate Y1 - 1019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-434975 SN - 1866-8372 IS - 740 ER - TY - JOUR A1 - Colangeli, Pierluigi A1 - Schlägel, Ulrike E. A1 - Obertegger, Ulrike A1 - Petermann, Jana S. A1 - Tiedemann, Ralph A1 - Weithoff, Guntram T1 - Negative phototactic response to UVR in three cosmopolitan rotifers: a video analysis approach JF - Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica KW - Risk avoidance behavior KW - Brachionus calyciflorus KW - Keratella cochlearis KW - BEMOVI KW - Movement ecology Y1 - 2018 U6 - https://doi.org/10.1007/s10750-018-3801-y SN - 0018-8158 SN - 1573-5117 VL - 844 IS - 1 SP - 43 EP - 54 PB - Springer CY - Dordrecht ER - TY - THES A1 - Canitz, Julia T1 - Genome and karyotype evolution underlying speciation and diversification of electric organ discharges in African weakly electric fish (Campylomormyrus, Mormyridae, Teleostei) N2 - The African weakly electric fish genus Campylomormyrus is a well-investigated fish group of the species-rich family Mormyridae. They are able to generate species-specific electric organ discharges (EODs) which vary in their waveform characteristics including polarity, phase umber and duration. In mormyrid species EODs are used for communication, species discrimination and mate recognition, and it is thought hat they serve as pre-zygotic isolation mechanism driving sympatric speciation by promoting assortative mating. The EOD diversification, its volutionary effects and the link to species divergence have been examined histologically, behaviorally, and genetically. Molecular analyses are a major tool to identify species and their phenotypic traits by studying the underlying genes. The genetic variability between species further provides information from which evolutionary processes, such as speciation, can be deduced. Hence, the ultimate aim of this study is the investigation of genetic variability within the African weakly electric fish genus Campylomormyrus to better understand their sympatric speciation and comprehend their evolutionary drivers. In order to extend the current knowledge and gain more insights into its species history, karyological and genomic approaches are being pursued considering species differences. Previous studies have shown that species with different EOD duration have specific gene expression patterns and single nucleotide polymorphisms (SNPs). As EODs play a crucial role during the evolution of Campylomormyrus species, the identification of its underlying genes may suggest how the EOD diversity evolved and whether this trait is based on a complex network of genetic processes or is regulated by only a few genes. The results obtained in this study suggest that genes with non-synonymous SNPs, which are exclusive to C. tshokwe with an elongated EOD, have frequent functions ssociated with tissue morphogenesis and transcriptional regulation. Therefore, it is proposed that these processes likely co-determine EOD characteristics of Campylomormyrus species. Furthermore, genome-wide analyses confirm the genetic difference among most Campylomormyrus species. In contrast, the same analyses reveal genetic similarity among individuals of the alces-complex showing different EOD waveforms. It is therefore hypothesized that the low genetic variability and high EOD diversity represents incipient sympatric speciation. The karyological description of a Campylomormyrus species provides crucial information about chromosome number and shapes. Its diploid chromosome number of 2n=48 supports the conservation of this trait within Mormyridae. Differences have been detected in the number of bi-armed chromosomes which is unusually high compared to other mormyrid species. This high amount can be due to chromosome rearrangements which could cause genetic incompatibility and reproductive isolation. Hence an alternative hypothesis regarding processes which cause sympatric speciation is that chromosome differences are involved in the speciation process of Campylomormyrus by acting as postzygotic isolation mechanism. In summary, the karyological and genomic investigations conducted in this study contributed to the increase of knowledge about Campylomormyrus species, to the solution of some existing ambiguities like phylogenetic relationships and to the raising of new hypothesis explaining the sympatric speciation of those African weakly electric fish. This study provides a basis for future genomic research to obtain a complete picture for causes and results of evolutionary processes in Campylomormyrus. Y1 - 2019 ER - TY - JOUR A1 - Romero-Mujalli, Daniel A1 - Jeltsch, Florian A1 - Tiedemann, Ralph T1 - Elevated mutation rates are unlikely to evolve in sexual species, not even under rapid environmental change JF - BMC Evolutionary Biology N2 - Background Organisms are expected to respond to changing environmental conditions through local adaptation, range shift or local extinction. The process of local adaptation can occur by genetic changes or phenotypic plasticity, and becomes especially relevant when dispersal abilities or possibilities are somehow constrained. For genetic changes to occur, mutations are the ultimate source of variation and the mutation rate in terms of a mutator locus can be subject to evolutionary change. Recent findings suggest that the evolution of the mutation rate in a sexual species can advance invasion speed and promote adaptation to novel environmental conditions. Following this idea, this work uses an individual-based model approach to investigate if the mutation rate can also evolve in a sexual species experiencing different conditions of directional climate change, under different scenarios of colored stochastic environmental noise, probability of recombination and of beneficial mutations. The color of the noise mimicked investigating the evolutionary dynamics of the mutation rate in different habitats. Results The results suggest that the mutation rate in a sexual species experiencing directional climate change scenarios can evolve and reach relatively high values mainly under conditions of complete linkage of the mutator locus and the adaptation locus. In contrast, when they are unlinked, the mutation rate can slightly increase only under scenarios where at least 50% of arising mutations are beneficial and the rate of environmental change is relatively fast. This result is robust under different scenarios of stochastic environmental noise, which supports the observation of no systematic variation in the mutation rate among organisms experiencing different habitats. Conclusions Given that 50% beneficial mutations may be an unrealistic assumption, and that recombination is ubiquitous in sexual species, the evolution of an elevated mutation rate in a sexual species experiencing directional climate change might be rather unlikely. Furthermore, when the percentage of beneficial mutations and the population size are small, sexual species (especially multicellular ones) producing few offspring may be expected to react to changing environments not by adaptive genetic change, but mainly through plasticity. Without the ability for a plastic response, such species may become – at least locally – extinct. KW - Individual-based models KW - sexual species KW - Beneficial mutations KW - Recombination KW - Directional climate change KW - Mutator locus KW - Mutation rate Y1 - 2019 U6 - https://doi.org/10.1186/s12862-019-1494-0 SN - 1471-2148 VL - 19 PB - BioMed Central CY - London ER - TY - JOUR A1 - De Cahsan, Binia A1 - Westbury, Michael V. A1 - Drews, Hauke A1 - Tiedemann, Ralph T1 - The complete mitochondrial genome of a European fire-bellied toad (Bombina bombina) from Germany JF - Mitochondrial DNA Part B N2 - The European fire-bellied toad, Bombina bombina, is a small aquatic toad belonging to the family Bombinatoridae. The species is native to the lowlands of Central and Eastern Europe, where population numbers have been in decline in recent past decades. Here, we present the first complete mitochondrial genome of the endangered European fire-bellied toad from Northern Germany recovered using iterative mapping. Phylogenetic analyses including other representatives of the Bombinatoridae placed our German specimen as sister to a Polish B. bombina sequence with high support. This finding is congruent with the postulated Pleistocene history of the species. Our complete mitochondrial genome represents an important resource for further population analysis of the European fire-bellied toad, especially those found within Germany. KW - Bombina bombina KW - Fire-bellied toad KW - mitogenome KW - conservation genetics KW - population delimitation Y1 - 2019 U6 - https://doi.org/10.1080/23802359.2018.1547143 SN - 2380-2359 VL - 4 IS - 1 SP - 498 EP - 500 PB - Taylor & Francis Group CY - London ER - TY - THES A1 - Romero Mujalli, Daniel T1 - Ecological modeling of adaptive evolutionary responses to rapid climate change T1 - Ökologische Modellierung anpassungsfähiger evolutionärer Reaktionen auf schnellen Klimawandel N2 - A contemporary challenge in Ecology and Evolutionary Biology is to anticipate the fate of populations of organisms in the context of a changing world. Climate change and landscape changes due to anthropic activities have been of major concern in the contemporary history. Organisms facing these threats are expected to respond by local adaptation (i.e., genetic changes or phenotypic plasticity) or by shifting their distributional range (migration). However, there are limits to their responses. For example, isolated populations will have more difficulties in developing adaptive innovations by means of genetic changes than interconnected metapopulations. Similarly, the topography of the environment can limit dispersal opportunities for crawling organisms as compared to those that rely on wind. Thus, populations of species with different life history strategy may differ in their ability to cope with changing environmental conditions. However, depending on the taxon, empirical studies investigating organisms’ responses to environmental change may become too complex, long and expensive; plus, complications arising from dealing with endangered species. In consequence, eco-evolutionary modeling offers an opportunity to overcome these limitations and complement empirical studies, understand the action and limitations of underlying mechanisms, and project into possible future scenarios. In this work I take a modeling approach and investigate the effect and relative importance of evolutionary mechanisms (including phenotypic plasticity) on the ability for local adaptation of populations with different life strategy experiencing climate change scenarios. For this, I performed a review on the state of the art of eco-evolutionary Individual-Based Models (IBMs) and identify gaps for future research. Then, I used the results from the review to develop an eco-evolutionary individual-based modeling tool to study the role of genetic and plastic mechanisms in promoting local adaption of populations of organisms with different life strategies experiencing scenarios of climate change and environmental stochasticity. The environment was simulated through a climate variable (e.g., temperature) defining a phenotypic optimum moving at a given rate of change. The rate of change was changed to simulate different scenarios of climate change (no change, slow, medium, rapid climate change). Several scenarios of stochastic noise color resembling different climatic conditions were explored. Results show that populations of sexual species will rely mainly on standing genetic variation and phenotypic plasticity for local adaptation. Population of species with relatively slow growth rate (e.g., large mammals) – especially those of small size – are the most vulnerable, particularly if their plasticity is limited (i.e., specialist species). In addition, whenever organisms from these populations are capable of adaptive plasticity, they can buffer fitness losses in reddish climatic conditions. Likewise, whenever they can adjust their plastic response (e.g., bed-hedging strategy) they will cope with bluish environmental conditions as well. In contrast, life strategies of high fecundity can rely on non-adaptive plasticity for their local adaptation to novel environmental conditions, unless the rate of change is too rapid. A recommended management measure is to guarantee interconnection of isolated populations into metapopulations, such that the supply of useful genetic variation can be increased, and, at the same time, provide them with movement opportunities to follow their preferred niche, when local adaptation becomes problematic. This is particularly important for bluish and reddish climatic conditions, when the rate of change is slow, or for any climatic condition when the level of stress (rate of change) is relatively high. N2 - Eine aktuelle Herausforderung in der Ökologie und Evolutionsbiologie besteht darin, das Schicksal von Populationen verschiedener Lebewesen im Kontext einer sich verändernden Welt zu antizipieren. Der Klimawandel und die durch anthropologische Aktivitäten verursachten Landschaftsveränderungen sind im Laufe der Geschichte von großer Bedeutung geworden. Von den Organismen, die sich diesen Veränderungen stellen, wird erwartet, dass sie durch lokale Anpassung (d.h. genetische Veränderungen oder phänotypische Plastizität) oder durch Verschiebung ihres Verbreitungsgebietes (Migration) darauf reagieren. Allerdings sind diese Reaktionen begrenzt. So werden beispielsweise isolierte Populationen mehr Schwierigkeiten bei der Entwicklung adaptiver Neuheiten mittels genetischer Variation haben als vernetzte Metapopulationen. Ebenso kann die Topographie der Umgebung die Ausbreitungsmöglichkeiten für zum Beispiel kriechende Organismen im Vergleich zu denen, die auf Wind angewiesen sind, einschränken. So können Populationen von Arten mit unterschiedlichen Lebensstrategien verschiedene Fähigkeiten haben, mit den sich ändernden Umweltbedingungen umzugehen. Empirische Studien, die die Reaktionen von Organismen auf Umweltveränderungen untersuchen, können jedoch, je nach Taxon, zu komplex, langwierig und teuer werden. Ebenso sollten Komplikationen im Umgang mit gefährdeten Arten nicht außer Acht gelassen werden. Die ökoevolutionäre Modellierung bietet jedoch die Möglichkeit, diese Einschränkungen zu überwinden und empirische Studien zu ergänzen, die Wirkung und Grenzen der zugrunde liegenden Mechanismen zu verstehen und mögliche Zukunftsszenarien zu erstellen. In dieser Arbeit untersuche ich mittels einer Modellierungsmethode die Wirkung und relative Bedeutung evolutionärer Mechanismen (einschließlich phänotypischer Plastizität) auf die Fähigkeit zur lokalen Anpassung von Populationen mit unterschiedlichen Lebensstrategien, die Szenarien des Klimawandels durchleben. Dazu habe ich in einem Review den Stand der Technik ökoevolutionärer individuenbasierender Modelle (Individual-Based Models; IBMs) zusammengefasst und Ansätze für eine zukünftige Forschung identifiziert. Die Erkenntnisse des Reviews nutzte ich, um ein ökoevolutionäres, individuelles Modellierungsprogramm zu entwickeln. Dieses analysiert die Rolle genetischer und plastischer Mechanismen zur Förderung der lokalen Anpassung organismischer Populationen mit unterschiedlichen Lebensstrategien, welche Szenarien des Klimawandels und der ökologischen Stochastik erfahren. Die Umweltbedingungen wurden durch eine klimatische Variable (z.B. Temperatur) simuliert, die ein phänotypisches Optimum definiert, das sich mit einer bestimmten Änderungsrate bewegt. Verschiedene Änderungsraten wurden angewandt, um unterschiedliche Szenarien des Klimawandels darzustellen (keine Veränderung, langsamer, mittlerer, schneller Klimawandel). Es wurden mehrere Szenarien stochastischen Farbrauschens untersucht, die verschiedene klimatische Bedingungen widerspiegeln. Die Ergebnisse zeigen, dass Populationen sexueller Arten hauptsächlich auf genetische Variation und phänotypische Plastizität hinsichtlich lokalen Anpassung angewiesen sind. Populationen von Arten mit relativ langsamer Wachstumsrate (z.B. große Säugetiere), und insbesondere die mit kleiner Populationsgröße, sind am anfälligsten, vor allem wenn ihre Plastizität begrenzt ist (d.h. spezialisierte Arten). Wenn Individuen dieser Populationen zu adaptiver Plastizität fähig sind, können sie Fitnessverluste unter „rötlichen“ Klimabedingungen ausgleichen. Zugleich können diese Populationen durch Anpassung der Plastizität auch unter bläulichen Umweltbedingungen zurecht kommen (z.B. Bed-Hedging-Strategie). Im Gegensatz dazu können sich Lebensstrategen mit hoher Reproduktionszahl auf nicht-adaptive Plastizität zur lokalen Anpassung an neue Umweltbedingungen verlassen, es sei denn, die Änderungsrate ist zu schnell. Eine empfohlene Handlungsmaßnahme ist es, die Eingliederung von isolierten Populationen in Metapopulationen zu gewährleisten, so dass die genetische Variation erhöht werden kann. Wenn eine lokale Anpassung problematisch wird, sollte ihnen gleichzeitig Migrationsfreiraum gegeben werden, um ihrer bevorzugten Nische zu folgen. Dies ist besonders wichtig für „bläuliche“ und „rötliche“ Klimabedingungen, bei denen die Änderungsrate langsam ist, oder für jede klimatische Bedingung, wenn die Belastung (Änderungsrate) relativ hoch ist. KW - climate change KW - local adaptation KW - plasticity KW - evolution KW - individual-based model KW - Klimawandel KW - lokale Anpassung KW - Plastizität KW - Evolution KW - Individuen-basierende Modelle Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-430627 ER - TY - GEN A1 - De Cahsan, Binia A1 - Westbury, Michael V. A1 - Drews, Hauke A1 - Tiedemann, Ralph T1 - The complete mitochondrial genome of a European fire-bellied toad (Bombina bombina) from Germany T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - The European fire-bellied toad, Bombina bombina, is a small aquatic toad belonging to the family Bombinatoridae. The species is native to the lowlands of Central and Eastern Europe, where population numbers have been in decline in recent past decades. Here, we present the first complete mitochondrial genome of the endangered European fire-bellied toad from Northern Germany recovered using iterative mapping. Phylogenetic analyses including other representatives of the Bombinatoridae placed our German specimen as sister to a Polish B. bombina sequence with high support. This finding is congruent with the postulated Pleistocene history of the species. Our complete mitochondrial genome represents an important resource for further population analysis of the European fire-bellied toad, especially those found within Germany. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 532 KW - Bombina bombina KW - Fire-bellied toad KW - mitogenome KW - conservation genetics KW - population delimitation Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-423222 SN - 1866-8372 IS - 532 ER - TY - GEN A1 - Romero-Mujalli, Daniel A1 - Jeltsch, Florian A1 - Tiedemann, Ralph T1 - Elevated mutation rates are unlikely to evolve in sexual species, not even under rapid environmental change T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Background Organisms are expected to respond to changing environmental conditions through local adaptation, range shift or local extinction. The process of local adaptation can occur by genetic changes or phenotypic plasticity, and becomes especially relevant when dispersal abilities or possibilities are somehow constrained. For genetic changes to occur, mutations are the ultimate source of variation and the mutation rate in terms of a mutator locus can be subject to evolutionary change. Recent findings suggest that the evolution of the mutation rate in a sexual species can advance invasion speed and promote adaptation to novel environmental conditions. Following this idea, this work uses an individual-based model approach to investigate if the mutation rate can also evolve in a sexual species experiencing different conditions of directional climate change, under different scenarios of colored stochastic environmental noise, probability of recombination and of beneficial mutations. The color of the noise mimicked investigating the evolutionary dynamics of the mutation rate in different habitats. Results The results suggest that the mutation rate in a sexual species experiencing directional climate change scenarios can evolve and reach relatively high values mainly under conditions of complete linkage of the mutator locus and the adaptation locus. In contrast, when they are unlinked, the mutation rate can slightly increase only under scenarios where at least 50% of arising mutations are beneficial and the rate of environmental change is relatively fast. This result is robust under different scenarios of stochastic environmental noise, which supports the observation of no systematic variation in the mutation rate among organisms experiencing different habitats. Conclusions Given that 50% beneficial mutations may be an unrealistic assumption, and that recombination is ubiquitous in sexual species, the evolution of an elevated mutation rate in a sexual species experiencing directional climate change might be rather unlikely. Furthermore, when the percentage of beneficial mutations and the population size are small, sexual species (especially multicellular ones) producing few offspring may be expected to react to changing environments not by adaptive genetic change, but mainly through plasticity. Without the ability for a plastic response, such species may become – at least locally – extinct. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 776 KW - Individual-based models KW - sexual species KW - Beneficial mutations KW - Mutation rate KW - Mutator locus KW - Directional climate change KW - Recombination Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-439058 SN - 1866-8372 IS - 776 ER - TY - CHAP A1 - Duffus, Benjamin R. A1 - Hartmann, Tobias A1 - Teutloff, Christian A1 - Leimkühler, Silke T1 - Refining catalytic insights toward the chemical mechanism of R. capsulatus formate dehydrogenase via EPR spectroscopy T2 - Abstracts of papers : joint conference / The Chemical Institute of Cananda, CIC, American Chemical Society, ACS Y1 - 2019 SN - 0065-7727 VL - 257 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Liu, Junzhong A1 - Feng, Lili A1 - Gu, Xueting A1 - Deng, Xian A1 - Qiu, Qi A1 - Li, Qun A1 - Zhang, Yingying A1 - Wang, Muyang A1 - Deng, Yiwen A1 - Wang, Ertao A1 - He, Yuke A1 - Bäurle, Isabel A1 - Li, Jianming A1 - Cao, Xiaofeng A1 - He, Zuhua T1 - An H3K27me3 demethylase-HSFA2 regulatory loop orchestrates transgenerational thermomemory in Arabidopsis JF - Cell research N2 - Global warming has profound effects on plant growth and fitness. Plants have evolved sophisticated epigenetic machinery to respond quickly to heat, and exhibit transgenerational memory of the heat-induced release of post-transcriptional gene silencing (PTGS). However, how thermomemory is transmitted to progeny and the physiological relevance are elusive. Here we show that heat-induced HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2) directly activates the H3K27me3 demethylase RELATIVE OF EARLY FLOWERING 6 (REF6), which in turn derepresses HSFA2. REF6 and HSFA2 establish a heritable feedback loop, and activate an E3 ubiquitin ligase, SUPPRESSOR OF GENE SILENCING 3 (SGS3)-INTERACTING PROTEIN 1 (SGIP1). SGIP1-mediated SGS3 degradation leads to inhibited biosynthesis of trans-acting siRNA (tasiRNA). The REF6-HSFA2 loop and reduced tasiRNA converge to release HEAT-INDUCED TAS1 TARGET 5 (HTT5), which drives early flowering but attenuates immunity. Thus, heat induces transmitted phenotypes via a coordinated epigenetic network involving histone demethylases, transcription factors, and tasiRNAs, ensuring reproductive success and transgenerational stress adaptation. KW - Chromatin KW - Epigenetic memory KW - Epigenetics KW - Innate immunity KW - Plant signalling Y1 - 2019 U6 - https://doi.org/10.1038/s41422-019-0145-8 SN - 1001-0602 SN - 1748-7838 VL - 29 IS - 5 SP - 379 EP - 390 PB - Nature Publ. Group CY - London ER - TY - THES A1 - Petrovic, Nevena T1 - Analysis of the role of Forgetter2 in thermotolerance responses in Arabidopsis thaliana Y1 - 2019 ER - TY - JOUR A1 - Bontrup, Carolin A1 - Taylor, William R. A1 - Fliesser, Michael A1 - Visscher, Rosa A1 - Green, Tamara A1 - Wippert, Pia-Maria A1 - Zemp, Roland T1 - Low back pain and its relationship with sitting behaviour among sedentary office workers JF - Applied ergonomics : human factors in technology and society N2 - The relationships between sedentary lifestyle, sitting behaviour, and low back pain (LBP) remain controversial. In this study, we investigated the relationship between back pain and occupational sitting habits in 64 call-centre employees. A textile pressure mat was used to evaluate and parameterise sitting behaviour over a total of 400 h, while pain questionnaires evaluated acute and chronic LBP. Seventy-five percent of the participants reported some level of either chronic or acute back pain. Individuals with chronic LBP demonstrated a possible trend (t-test not significant) towards more static sitting behaviour compared to their pain-free counterparts. Furthermore, a greater association was found between sitting behaviour and chronic LBP than for acute pain/disability, which is plausibly due to a greater awareness of pain-free sitting positions in individuals with chronic pain compared to those affected by acute pain. KW - Office chair KW - Pressure distribution KW - Low back pain KW - Sitting behaviour KW - Dynamic sitting Y1 - 2019 U6 - https://doi.org/10.1016/j.apergo.2019.102894 SN - 0003-6870 SN - 1872-9126 VL - 81 PB - Elsevier CY - Oxford ER - TY - THES A1 - Guislain, Alexis T1 - Eco-physiological consequences of fluctuating light on phytoplankton T1 - Ökophysiologische Konsequenzen von fluktuierendem Licht auf das Phytoplankton N2 - Phytoplankton growth depends not only on the mean intensity but also on the dynamics of the light supply. The nonlinear light-dependency of growth is characterized by a small number of basic parameters: the compensation light intensity PARcompμ, where production and losses are balanced, the growth efficiency at sub-saturating light αµ, and the maximum growth rate at saturating light µmax. In surface mixed layers, phytoplankton may rapidly move between high light intensities and almost darkness. Because of the different frequency distribution of light and/or acclimation processes, the light-dependency of growth may differ between constant and fluctuating light. Very few studies measured growth under fluctuating light at a sufficient number of mean light intensities to estimate the parameters of the growth-irradiance relationship. Hence, the influence of light dynamics on µmax, αµ and PARcompμ are still largely unknown. By extension, accurate modelling predictions of phytoplankton development under fluctuating light exposure remain difficult to make. This PhD thesis does not intend to directly extrapolate few experimental results to aquatic systems – but rather improving the mechanistic understanding of the variation of the light-dependency of growth under light fluctuations and effects on phytoplankton development. In Lake TaiHu and at the Three Gorges Reservoir (China), we incubated phytoplankton communities in bottles placed either at fixed depths or moved vertically through the water column to mimic vertical mixing. Phytoplankton at fixed depths received only the diurnal changes in light (defined as constant light regime), while phytoplankton received rapidly fluctuating light by superimposing the vertical light gradient on the natural sinusoidal diurnal sunlight. The vertically moved samples followed a circular movement with 20 min per revolution, replicating to some extent the full overturn of typical Langmuir cells. Growth, photosynthesis, oxygen production and respiration of communities (at Lake TaiHu) were measured. To complete these investigations, a physiological experiment was performed in the laboratory on a toxic strain of Microcystis aeruginosa (FACBH 1322) incubated under 20 min period fluctuating light. Here, we measured electron transport rates and net oxygen production at a much higher time resolution (single minute timescale). The present PhD thesis provides evidence for substantial effects of fluctuating light on the eco-physiology of phytoplankton. Both experiments performed under semi-natural conditions in Lake TaiHu and at the Three Gorges Reservoir gave similar results. The significant decline in community growth efficiencies αµ under fluctuating light was caused for a great share by different frequency distribution of light intensities that shortened the effective daylength for production. The remaining gap in community αµ was attributed to species-specific photoacclimation mechanisms and to light-dependent respiratory losses. In contrast, community maximal growth rates µmax were similar between incubations at constant and fluctuating light. At daily growth saturating light supply, differences in losses for biosynthesis between the two light regimes were observed. Phytoplankton experiencing constant light suffered photo-inhibition - leading to photosynthesis foregone and additional respiratory costs for photosystems repair. On the contrary, intermittent exposure to low and high light intensities prevented photo-inhibition of mixed algae but forced them to develop alternative light strategy. They better harvested and exploited surface irradiance by enhancing their photosynthesis. In the laboratory, we showed that Microcystis aeruginosa increased its oxygen consumption by dark respiration in the light few minutes only after exposure to increasing light intensities. More, we proved that within a simulated Langmuir cell, the net production at saturating light and the compensation light intensity for production at limiting light are positively related. These results are best explained by an accumulation of photosynthetic products at increasing irradiance and mobilization of these fresh resources by rapid enhancement of dark respiration for maintenance and biosynthesis at decreasing irradiance. At the daily timescale, we showed that the enhancement of photosynthesis at high irradiance for biosynthesis of species increased their maintenance respiratory costs at limiting light. Species-specific growth at saturating light µmax and compensation light intensity for growth PARcompμ of species incubated in Lake TaiHu were positively related. Because of this species-specific physiological tradeoff, species displayed different light affinities to limiting and saturating light - thereby exhibiting a gleaner-opportunist tradeoff. In Lake TaiHu, we showed that inter-specific differences in light acquisition traits (µmax and PARcompμ) allowed coexis¬tence of species on a gradient of constant light while avoiding competitive exclusion. More interestingly we demonstrated for the first time that vertical mixing (inducing fluctuating light supply for phytoplankton) may alter or even reverse the light utilization strategies of species within couple of days. The intra-specific variation in traits under fluctuating light increased the niche space for acclimated species, precluding competitive exclusion. Overall, this PhD thesis contributes to a better understanding of phytoplankton eco-physiology under fluctuating light supply. This work could enhance the quality of predictions of phytoplankton development under certain weather conditions or climate change scenarios. N2 - Das Wachstum von Phytoplankton hängt ab nicht nur von der mittleren Intensität, sondern auch von der Dynamik des verfügbaren Lichts. Die nicht-lineare Lichtabhängigkeit des Wachstums kann durch drei Parameter beschrieben werden: die Kompensationslichtintensität PARcompµ, bei der Bruttoproduktion und Verluste gleich sind, die Wachstumseffizienz bei Lichtlimitation αµ und die maximale Wachstumsrate bei sättigendem Licht µmax. In durchmischten Schichten nahe der Gewässeroberfläche kann das Phytoplankton innerhalb weniger Minuten zwischen Starklicht und nahezu völliger Dunkelheit bewegt werden. Durch die unterschiedliche Häufigkeitsverteilung der Lichtintensitäten und/oder unterschiedliche Anpassungen kann die Lichtabhängigkeit des Wachstums sich bei fluktuierendem Licht von dem bei konstantem Licht unterscheiden. Bislang wurde die Lichtabhängigkeit des Wachstums bei fluktuierendem Licht nur in sehr wenigen Studien für genügend viele Lichtintensitäten gemessen, um die genannten Parameter bestimmen zu können. Entsprechend ist der Einfluss der Lichtdynamik auf die Parameter der Wachstums-Licht-Beziehung noch weitgehend unbekannt. Dies beeinträchtigt auch die Zuverlässigkeit von Modellaussagen zur Phytoplanktondynamik unter Durchmischungsbedingungen. In dieser Dissertation sollen die experimentell gewonnenen Ergebnisse nicht auf ganze Ökosysteme extrapoliert werden; Ziel ist vielmehr ein verbessertes Verständnis der Prozesse, die die Lichtabhängigkeit des Phytoplanktonwachstums unter dynamischen Lichtbedingungen steuern. Hierzu wurden im Tai-See und im Dreischluchten-Stausee (China) Experimente mit Phytoplanktongemeinschaften durchgeführt. Es wurden Proben entweder in konstanten Tiefen exponiert oder mit Liften vertikal zwischen Wasseroberfläche und verschiedenen Tiefen bewegt. Während das Lichtangebot in konstanten Tiefen nur dem Tagesgang der Globalstrahlung folgte (hier als konstantes Licht bezeichnet), war das Phytoplankton in den bewegten Proben zusätzlich raschen Lichtfluktuationen ausgesetzt. Mit der Liftbewegung wurden mittlere Bedingungen in den Außenbahnen von Langmuir-Zellen simuliert, wobei eine Umlaufzeit von 20 Minuten gewählt wurde. Es wurden Wachstum, Photosynthese und (im Tai-See) Respiration gemessen. Zusätzlich wurde in Laborversuchen mit einem toxischen Stamm des Cyanobakteriums Microcystis aeruginosa (FACBH 1322) unter fluktuierendem und konstantem Licht Elektronentransportraten sowie Produktion und Verbrauch von Sauerstoff mit höherer zeitlicher Auflösung (1 min) gemessen. Die Ergebnisse der vorliegenden Dissertation demonstrieren bedeutsame Effekte von Lichtfluktuationen auf die Ökophysiologie von Phytoplankton. Die Experimente unter halb-natürlichen Bedingungen im Tai-See und im Dreischluchten-Stausee zeigten ähnliche Muster. Die Wachstumseffizienz der Gemeinschaften nahm durch fluktuierendes Licht deutlich ab, überwiegend durch die veränderte Häufigkeitsverteilung der Lichtintensitäten, die zu verkürzten effektiven Taglängen führte. Zudem verringerten artspezifische Anpassungsmechanismen und lichtabhängige Verluste durch Respiration die Wachstumseffizienz bei fluktuierendem Licht. Die maximalen Wachstumsraten der Gemeinschaft unterschieden sich hingegen nicht zwischen den Ansätzen mit konstantem und fluktuierendem Licht. Bei Lichtsättigung des Wachstums unterschieden sich die Aufwendungen für die Biosynthese zwischen den beiden Lichtregimen. Unter konstantem Starklicht wurden die Photosynthese gehemmt und die Respiration zur Reparatur der Photosysteme erhöht. Fluktuierendes Licht hingegen vermied Lichthemmung, zwang die vertikal bewegten Algen aber zu alternativen Strategien der Lichtnutzung. Durch eine erhöhte Photosynthesekapazität konnten sie Starklicht nahe der Wasseroberfläche besser nutzen. Microcystis aeruginosa verbrauchte im Labor mehr Sauerstoff durch Respiration bei abnehmenden Lichtintensitäten kurz nach Starklicht. Innerhalb eines Lichtzyklus von 20 min stieg die Kompensationslichtintensität mit steigender Nettoproduktion bei Lichtsättigung. Diese Beobachtungen sind am besten durch eine Anreicherung von Photosyntheseprodukten bei ansteigender Lichtintensität und deren sofortige verstärkte Respiration für Erhaltungsumsatz und Biosynthese bei abnehmender Lichtintensität erklärbar. Im Tagesmittel führte eine verstärkte Photosynthese bei Lichtsättigung zu erhöhter Respiration bei Schwachlicht. Die Kompensationslichtintensitäten dominanter Arten im Tai-See stiegen mit deren artspezifischen maximalen Wachstumsraten. Durch diesen artspezifischen physiologischen Kompromiss unterschieden sich die dominanten Arten im See bezüglich ihrer Lichtoptima. Unterschiedliche Strategien der Lichtnutzung (höhere maximale Wachstumsraten oder niedrigere Lichtansprüche) ermöglichten die Koexistenz verschiedener Arten entlang eines Gradienten der Intensität konstanten Lichts im Tai-See. Durch vertikale Durchmischung änderten sich die Strategien der Lichtnutzung innerhalb weniger Tage komplett. Die unterschiedlichen Anpassungsstrategien an fluktuierendes Licht vergrößerten die ökologischen Nischen der dominanten Arten und verhinderten ihre gegenseitige Verdrängung. Insgesamt trägt diese Dissertation zum besseren Verständnis der Ökophysiologie von Phytoplankton unter Durchmischungsbedingungen bei. Dadurch werden verlässlichere Prognosen der Phytoplanktonentwicklung möglich, kurzzeitig in Kombination mit Wettervorhersagen und über lange Zeiträume durch Kopplung mit Klimaszenarien. KW - Lake TaiHu KW - Three Gorges reservoir KW - functional traits KW - tradeoff KW - fluctuating light KW - pPhytoplankton photoacclimation KW - effective daylength KW - photosynthesis KW - respiration KW - niche partitioning KW - non-equilibrium coexistence KW - TaiHu KW - Dreischluchten-Stausee KW - funktionelle Eigenschaften KW - Zielkonflikte KW - fluktuierendes Licht KW - Lichtanpassung KW - Photosynthese KW - Respiration KW - Nischen-Aufteilung KW - Koexistenz unter wechselnden Bedingungen Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-469272 ER - TY - THES A1 - He, Hai T1 - Exploring and engineering formaldehyde assimilation N2 - Increasing concerns regarding the environmental impact of our chemical production have shifted attention towards possibilities for sustainable biotechnology. One-carbon (C1) compounds, including methane, methanol, formate and CO, are promising feedstocks for future bioindustry. CO2 is another interesting feedstock, as it can also be transformed using renewable energy to other C1 feedstocks for use. While formaldehyde is not suitable as a feedstock due to its high toxicity, it is a central intermediate in the process of C1 assimilation. This thesis explores formaldehyde metabolism and aims to engineer formaldehyde assimilation in the model organism Escherichia coli for the future C1-based bioindustry. The first chapter of the thesis aims to establish growth of E. coli on formaldehyde via the most efficient naturally occurring route, the ribulose monophosphate pathway. Linear variants of the pathway were constructed in multiple-gene knockouts strains, coupling E. coli growth to the activities of the key enzymes of the pathway. Formaldehyde-dependent growth was achieved in rationally designed strains. In the final strain, the synthetic pathway provides the cell with almost all biomass and energy requirements. In the second chapter, taking advantage of the unique feature of its reactivity, formaldehyde assimilation via condensation with glycine and pyruvate by two promiscuous aldolases was explored. Facilitated by these two reactions, the newly designed homoserine cycle is expected to support higher yields of a wide array of products than its counterparts. By dividing the pathway into segments and coupling them to the growth of dedicated strains, all pathway reactions were demonstrated to be sufficiently active. The work paves a way for future implementation of a highly efficient route for C1 feedstocks into commodity chemicals. In the third chapter, the in vivo rate of the spontaneous formaldehyde tetrahydrofolate condensation to methylene-tetrahydrofolate was assessed in order to evaluate its applicability as a biotechnological process. Tested within an E. coli strain deleted in essential genes for native methylene-tetrahydrofolate biosynthesis, the reaction was shown to support the production of this essential intermediate. However, only low growth rates were observed and only at high formaldehyde concentrations. Computational analysis dependent on in vivo evidence from this strain deduced the slow rate of this spontaneous reaction, thus ruling out its substantial contribution to growth on C1 feedstocks. The reactivity of formaldehyde makes it highly toxic. In the last chapter, the formation of thioproline, the condensation product of cysteine and formaldehyde, was confirmed to contribute this toxicity effect. Xaa-Pro aminopeptidase (PepP), which genetically links with folate metabolism, was shown to hydrolyze thioproline-containing peptides. Deleting pepP increased strain sensitivity to formaldehyde, pointing towards the toxicity of thioproline-containing peptides and the importance of their removal. The characterization in this study could be useful in handling this toxic intermediate. Overall, this thesis identified challenges related to formaldehyde metabolism and provided novel solutions towards a future bioindustry based on sustainable C1 feedstocks in which formaldehyde serves as a key intermediate. N2 - Die zunehmende Besorgnis über die Auswirkungen der chemischen Produktion auf die Umwelt hat den Fokus auf die Vorzüge der nachhaltigen Biotechnologie gelenkt. Ein-Kohlenstoff-Verbindungen (C1), wie Methan, Methanol, Formiat und CO, sind vielversprechende Ausgangsstoffe für eine künftige biobasierte Industrie. Darüber hinaus ist CO2 ein weiterer interessanter Rohstoff, da es ebenfalls mit erneuerbarer Energie in andere C1-Verbindungen umgewandelt werden kann. Formaldehyd ist zwar aufgrund seiner Toxizität und Reaktivität nicht als Kohlestoffquelle geeignet, stellt aber ein zentrales Intermediat der C1-Assimilation dar. In dieser Arbeit wurde der Formaldehyd-Stoffwechsel untersucht, um Formaldehyd-Assimilations-Wege im Modellorganismus Escherichia coli für die zukünftige C1-basierte Bioindustrie zu entwickeln. Das erste Kapitel dieser Arbeit zielt darauf ab, das Wachstum von E. coli auf Formaldehyd über den energetisch effizientesten natürlich vorkommenden Weg, den Ribulose-Monophosphat-Weg (RuMP-Weg), zu etablieren. Durch Gendeletionen wurden lineare Varianten des RuMPWeges in E. coli Stämmen konstruiert, um das Wachstum mit der Aktivität der Schlüsselenzyme der Formaldehyd-Assimiliation zu verbinden. So konnte auf Formaldehydabhängiges Wachstum in diesen Stämmen getestet werden. Im finalen Stamm wurde nahezu die gesamte Biomasse und der Energiebedarf der E. coli Zellen über den RuMP-Weg bereitgestellt. Im zweiten Kapitel wurde unter Ausnutzung der einzigartigen Reaktivität des Formaldehyds die Aktivitäten zweier promiskuitiver Aldolasen für die Kondensation von Formaldehyd mit Glycin oder Pyruvat in vivo untersucht. Diese beiden Reaktionen dienen als Schlüsselreaktionen des neu gestalteten Homoserin-Zyklus, der verglichen mit anderen bekannten Assimilierungswegen höhere Ausbeuten einer breiten Palette von Produkten ermöglichen kann. Durch die Unterteilung des Stoffwechselweges in Segmente und deren Selektion in auxotrophen E. coli Stämmen wurde gezeigt, dass alle Reaktionen des Pfades ausreichend aktiv sind. Diese Arbeit ebnet den Weg für die zukünftige Nutzung des Homoserin-Zyklus als hocheffiziente Route für die Umwandlung von C1-Rohstoffen in grundlegende Chemikalien. Im dritten Kapitel wurde die in vivo-Rate der spontanen Kondensation von Formaldehyd mit Tetrahydrofolat zu Methylen-Tetrahydrofolat untersucht, um ihr Potential als Formaldehyd Assimilierungs-Reaktion in einem biotechnologischen Prozess zu bewerten. Die Reaktion wurde in einem E. coli-Stamm getestet, in welchem essentielle Gene für die native Methylen-Tetrahydrofolat-Biosynthese entfernt wurden. Es konnte gezeigt werden, dass die spontane Reaktion die Produktion dieses wesentlichen Zwischenprodukts ermöglicht. Die erreichten Wachstumsraten waren jedoch gering und nur bei hohen Formaldehydkonzentrationen zu beobachten. Eine Computer-gestützte Analyse basierend auf in vivo-Erkenntnissen über diesen Stamm ergab eine langsame Reaktionsgeschwindigkeit dieser spontanen Reaktion und schloss somit ihren wesentlichen Beitrag zum Wachstum auf C1-Einsatzmaterial aus. Seine Reaktivität macht Formaldehyd hochtoxisch. Im letzten Kapitel wurde bestätigt, dass die Bildung von Thioprolin, dem Kondensationsprodukt von Cystein und Formaldehyd, zu dieser Toxizitätswirkung beiträgt. Es wurde gezeigt, dass die Xaa-Pro-Aminopeptidase (PepP), die genetisch mit dem Folat-Stoffwechsel verbunden ist, thioprolinhaltige Peptide hydrolysiert. Die Deletion von PepP erhöhte die Empfindlichkeit des Stammes gegenüber Formaldehyd, was auf die Toxizität der Thioprolin-haltigen Peptide und die Bedeutung ihrer Entfernung hinweist. Diese Studie kann für den Umgang mit der Toxizität von Formaldehyd nützlich sein. Insgesamt identifizierte diese Arbeit Herausforderungen im Zusammenhang mit dem Formaldehyd-Stoffwechsel und lieferte neue Lösungen für eine C1-basierte Bioindustrie, in der Formaldehyd als wichtiges Zwischenprodukt dient. T2 - Erforschung und Entwicklung der Formaldehyd-Assimilierung KW - formaldehyde assimilation KW - ribulose monophosphate pathway KW - metabolic engineering KW - serine cycle KW - auxotrophy KW - methylotrophy KW - Auxotrophie KW - Serin-Zyklus KW - Ribulose-Monophosphat-Weg KW - Methylotrophie KW - metabolisches Engineering KW - Formaldehyd-Assimilierung Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-473867 ER - TY - JOUR A1 - Neukranz, Yannika A1 - Kotter, Annika A1 - Beilschmidt, Lena A1 - Marelja, Zvonimir A1 - Helm, Mark A1 - Graf, Ralph A1 - Leimkühler, Silke T1 - Analysis of the Cellular Roles of MOCS3 Identifies a MOCS3-Independent Localization of NFS1 at the Tips of the Centrosome JF - Biochemistry N2 - The deficiency of the molybdenum cofactor (Moco) is an autosomal recessive disease, which leads to the loss of activity of all molybdoenzymes in humans with sulfite oxidase being the essential protein. Moco deficiency generally results in death in early childhood. Moco is a sulfur-containing cofactor synthesized in the cytosol with the sulfur being provided by a sulfur relay system composed of the L-cysteine desulfurase NFS1, MOCS3, and MOCS2A. Human MOCS3 is a dual-function protein that was shown to play an important role in Moco biosynthesis and in the mcm(5)s(2) U thio modifications of nucleosides in cytosolic tRNAs for Lys, Gln, and Glu. In this study, we constructed a homozygous MOCS3 knockout in HEK293T cells using the CRISPR/Cas9 system. The effects caused by the absence of MOCS3 were analyzed in detail. We show that sulfite oxidase activity was almost completely abolished, on the basis of the absence of Moco in these cells. In addition, mcm(5)s(2)U thio-modified tRNAs were not detectable. Because the L-cysteine desulfurase NFS1 was shown to act as a sulfur donor for MOCS3 in the cytosol, we additionally investigated the impact of a MOCS3 knockout on the cellular localization of NFS1. By different methods, we identified a MOCS3-independent novel localization of NFS1 at the centrosome. Y1 - 2019 U6 - https://doi.org/10.1021/acs.biochem.8b01160 SN - 0006-2960 VL - 58 IS - 13 SP - 1786 EP - 1798 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Batsios, Petros A1 - Gräf, Ralph A1 - Koonce, Michael P. A1 - Larochelle, Denis A. A1 - Meyer, Irene T1 - Nuclear envelope organization in Dictyostelium discoideum JF - The international journal of developmental biology N2 - The nuclear envelope consists of the outer and the inner nuclear membrane, the nuclear lamina and the nuclear pore complexes, which regulate nuclear import and export.The major constituent of the nuclear lamina of Dictyostelium is the lamin NE81. It can form filaments like B-type lamins and it interacts with Sun 1, as well as with the LEM/HeH-family protein Src1. Sun 1 and Src1 are nuclear envelope transmembrane proteins involved in the centrosome-nucleus connection and nuclear envelope stability at the nucleolar regions, respectively. In conjunction with a KASH-domain protein, Sun 1 usually forms a so-called LINC complex.Two proteins with functions reminiscent of KASH-domain proteins at the outer nuclear membrane of Dictyostelium are known; interaptin which serves as an actin connector and the kinesin Kif9 which plays a role in the microtubule-centrosome connector. However, both of these lack the conserved KASH-domain. The link of the centrosome to the nuclear envelope is essential for the insertion of the centrosome into the nuclear envelope and the appropriate spindle formation. Moreover, centrosome insertion is involved in perm eabilization of the mitotic nucleus, which ensures access of tubulin dimers and spindle assembly factors. Our recent progress in identifying key molecular players at the nuclear envelope of Dictyostelium promises further insights into the mechanisms of nuclear envelope dynamics. KW - nuclear envelop KW - Dictyostelium KW - lamin KW - NET KW - centrosome KW - centromere Y1 - 2019 U6 - https://doi.org/10.1387/ijdb.190184rg SN - 0214-6282 SN - 1696-3547 VL - 63 IS - 8-10 SP - 509 EP - 519 PB - UBC Pr CY - Bilbao ER - TY - THES A1 - Neukranz, Yannika T1 - MOCS3 and its role in molybdenum cofactor biosynthesis, tRNA thiolation and other cellular pathways in humans Y1 - 2019 ER - TY - GEN A1 - Sowemimo, Oluwakemi T. A1 - Knox-Brown, Patrick A1 - Borcherds, Wade A1 - Rindfleisch, Tobias A1 - Thalhammer, Anja A1 - Daughdrill, Gary W. T1 - Conserved glycines control disorder and function in the cold-regulated protein, COR15A T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Cold-regulated (COR) 15A is an intrinsically disordered protein (IDP) from Arabidopsis thaliana important for freezing tolerance. During freezing-induced cellular dehydration, COR15A transitions from a disordered to mostly alpha-helical structure. We tested whether mutations that increase the helicity of COR15A also increase its protective function. Conserved glycine residues were identified and mutated to alanine. Nuclear magnetic resonance (NMR) spectroscopy was used to identify residue-specific changes in helicity for wildtype (WT) COR15A and the mutants. Circular dichroism (CD) spectroscopy was used to monitor the coil-helix transition in response to increasing concentrations of trifluoroethanol (TFE) and ethylene glycol. The impact of the COR15A mutants on the stability of model membranes during a freeze-thaw cycle was investigated by fluorescence spectroscopy. The results of these experiments showed the mutants had a higher content of alpha-helical structure and the increased alpha-helicity improved membrane stabilization during freezing. Comparison of the TFE- and ethylene glycol-induced coil-helix transitions support our conclusion that increasing the transient helicity of COR15A in aqueous solution increases its ability to stabilize membranes during freezing. Altogether, our results suggest the conserved glycine residues are important for maintaining the disordered structure of COR15A but are also compatible with the formation of alpha-helical structure during freezing induced dehydration. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1089 KW - COR15A KW - late embryogenesis abundant KW - intrinsically disordered proteins KW - trifluoroethanol KW - nuclear magnetic resonance Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-472217 SN - 1866-8372 IS - 1089 ER - TY - GEN A1 - Schieferdecker, Anne A1 - Wendler, Petra T1 - Structural mapping of missense mutations in the Pex1/Pex6 complex T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Peroxisome biogenesis disorders (PBDs) are nontreatable hereditary diseases with a broad range of severity. Approximately 65% of patients are affected by mutations in the peroxins Pex1 and Pex6. The proteins form the heteromeric Pex1/Pex6 complex, which is important for protein import into peroxisomes. To date, no structural data are available for this AAA+ ATPase complex. However, a wealth of information can be transferred from low-resolution structures of the yeast scPex1/scPex6 complex and homologous, well-characterized AAA+ ATPases. We review the abundant records of missense mutations described in PBD patients with the aim to classify and rationalize them by mapping them onto a homology model of the human Pex1/Pex6 complex. Several mutations concern functionally conserved residues that are implied in ATP hydrolysis and substrate processing. Contrary to fold destabilizing mutations, patients suffering from function-impairing mutations may not benefit from stabilizing agents, which have been reported as potential therapeutics for PBD patients. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1072 KW - Zellweger syndrome spectrum disorder (ZSSD) KW - Zellweger KW - structure KW - Pex1 KW - Pex6 KW - mutation Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-472843 SN - 1866-8372 IS - 1072 ER - TY - GEN A1 - Schwarz, Maria A1 - Lossow, Kristina A1 - Kopp, Johannes F. A1 - Schwerdtle, Tanja A1 - Kipp, Anna Patricia T1 - Crosstalk of Nrf2 with the Trace Elements Selenium, Iron, Zinc, and Copper T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Trace elements, like Cu, Zn, Fe, or Se, are important for the proper functioning of antioxidant enzymes. However, in excessive amounts, they can also act as pro-oxidants. Accordingly, trace elements influence redox-modulated signaling pathways, such as the Nrf2 pathway. Vice versa, Nrf2 target genes belong to the group of transport and metal binding proteins. In order to investigate whether Nrf2 directly regulates the systemic trace element status, we used mice to study the effect of a constitutive, whole-body Nrf2 knockout on the systemic status of Cu, Zn, Fe, and Se. As the loss of selenoproteins under Se-deprived conditions has been described to further enhance Nrf2 activity, we additionally analyzed the combination of Nrf2 knockout with feeding diets that provide either suboptimal, adequate, or supplemented amounts of Se. Experiments revealed that the Nrf2 knockout partially affected the trace element concentrations of Cu, Zn, Fe, or Se in the intestine, liver, and/or plasma. However, aside from Fe, the other three trace elements were only marginally modulated in an Nrf2-dependent manner. Selenium deficiency mainly resulted in increased plasma Zn levels. One putative mediator could be the metal regulatory transcription factor 1, which was up-regulated with an increasing Se supply and downregulated in Se-supplemented Nrf2 knockout mice. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1081 KW - Nrf2 KW - selenium KW - iron KW - copper KW - zinc KW - homeostasis Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-472873 SN - 1866-8372 IS - 1081 ER - TY - GEN A1 - Geißler, Katja A1 - Heblack, Jessica A1 - Uugulu, Shoopala A1 - Wanke, Heike A1 - Blaum, Niels T1 - Partitioning of Water Between Differently Sized Shrubs and Potential Groundwater Recharge in a Semiarid Savanna in Namibia T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Introduction: Many semiarid regions around the world are presently experiencing significant changes in both climatic conditions and vegetation. This includes a disturbed coexistence between grasses and bushes also known as bush encroachment, and altered precipitation patterns with larger rain events. Fewer, more intense precipitation events might promote groundwater recharge, but depending on the structure of the vegetation also encourage further woody encroachment. Materials and Methods: In this study, we investigated how patterns and sources of water uptake of Acacia mellifera (blackthorn), an important encroaching woody plant in southern African savannas, are associated with the intensity of rain events and the size of individual shrubs. The study was conducted at a commercial cattle farm in the semiarid Kalahari in Namibia (MAP 250 mm/a). We used soil moisture dynamics in different depths and natural stable isotopes as markers of water sources. Xylem water of fifteen differently sized individuals during eight rain events was extracted using a Scholander pressure bomb. Results and Discussion: Results suggest the main rooting activity zone of A. mellifera in 50 and 75 cm soil depth but a reasonable water uptake from 10 and 25 cm. Any apparent uptake pattern seems to be driven by water availability, not time in the season. Bushes prefer the deeper soil layers after heavier rain events, indicating some evidence for the classical Walter’s two-layer hypothesis. However, rain events up to a threshold of 6 mm/day cause shallower depths of use and suggest several phases of intense competition with perennial grasses. The temporal uptake pattern does not depend on shrub size, suggesting a fast upwards water flow inside. d2H and d18O values in xylem water indicate that larger shrubs rely less on upper and very deep soil water than smaller shrubs. It supports the hypothesis that in environments where soil moisture is highly variable in the upper soil layers, the early investment in a deep tap-root to exploit deeper, more reliable water sources could reduce the probability of mortality during the establishment phase. Nevertheless, independent of size and time in the season, bushes do not compete with potential groundwater recharge. In a savanna encroached by A. mellifera, groundwater will most likely be affected indirectly. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 798 KW - bush encroachment KW - groundwater recharge KW - rooting depth KW - Savannas KW - stable isotopes KW - shrub size KW - Acacia mellifera KW - rain event depth Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-441110 SN - 1866-8372 IS - 798 ER - TY - THES A1 - Hoang, Yen T1 - De novo binning strategy to analyze and visualize multi-dimensional cytometric data T1 - De novo Binning-Ansatz zur Untersuchung und Visualisierung von multidimensionalen Zytrometriedaten BT - engineering of combinatorial variables for supervised learning approaches N2 - Since half a century, cytometry has been a major scientific discipline in the field of cytomics - the study of system’s biology at single cell level. It enables the investigation of physiological processes, functional characteristics and rare events with proteins by analysing multiple parameters on an individual cell basis. In the last decade, mass cytometry has been established which increased the parallel measurement to up to 50 proteins. This has shifted the analysis strategy from conventional consecutive manual gates towards multi-dimensional data processing. Novel algorithms have been developed to tackle these high-dimensional protein combinations in the data. They are mainly based on clustering or non-linear dimension reduction techniques, or both, often combined with an upstream downsampling procedure. However, these tools have obstacles either in comprehensible interpretability, reproducibility, computational complexity or in comparability between samples and groups. To address this bottleneck, a reproducible, semi-automated cytometric data mining workflow PRI (pattern recognition of immune cells) is proposed which combines three main steps: i) data preparation and storage; ii) bin-based combinatorial variable engineering of three protein markers, the so called triploTs, and subsequent sectioning of these triploTs in four parts; and iii) deployment of a data-driven supervised learning algorithm, the cross-validated elastic-net regularized logistic regression, with these triploT sections as input variables. As a result, the selected variables from the models are ranked by their prevalence, which potentially have discriminative value. The purpose is to significantly facilitate the identification of meaningful subpopulations, which are most distinguish between two groups. The proposed workflow PRI is exemplified by a recently published public mass cytometry data set. The authors found a T cell subpopulation which is discriminative between effective and ineffective treatment of breast carcinomas in mice. With PRI, that subpopulation was not only validated, but was further narrowed down as a particular Th1 cell population. Moreover, additional insights of combinatorial protein expressions are revealed in a traceable manner. An essential element in the workflow is the reproducible variable engineering. These variables serve as basis for a clearly interpretable visualization, for a structured variable exploration and as input layers in neural network constructs. PRI facilitates the determination of marker levels in a semi-continuous manner. Jointly with the combinatorial display, it allows a straightforward observation of correlating patterns, and thus, the dominant expressed markers and cell hierarchies. Furthermore, it enables the identification and complex characterization of discriminating subpopulations due to its reproducible and pseudo-multi-parametric pattern presentation. This endorses its applicability as a tool for unbiased investigations on cell subsets within multi-dimensional cytometric data sets. N2 - Massen- und Durchflusszytometrie-Messungen ermöglichen die detaillierte Einteilung von Zellgruppen nach Eigenschaften vor allem in der Diagnostik und in der Grundlagenforschung anhand der Erfassung von biologischen Informationen auf Einzelzellebene. Sie unterstützen die detaillierte Analyse von komplexen, zellulären Zusammenhängen, um physiologische und pathophysiologische Prozesse zu erkennen, und funktionelle oder krankheitsspezifische Characteristika und rare Zellgruppen genauer zu spezifizieren und zu extrahieren. In den letzten Jahren haben zytometrische Technologien einen enormen Innovationssprung erfahren, sodass heutzutage bis zu 50 Proteine pro Zelle parallel gemessen werden können. Und das mit einem Durchsatz von Hunderttausenden bis mehreren Millionen von Zellen aus einer Probe. Bei der Zunahme der Messparameter steigen jedoch die Dimensionen der kombinierten Parameter exponentiell, sodass eine komplexe Kombinatorik entsteht, die mit konventionellen, manuellen Untersuchungen von bi-axialen Diagrammen nicht mehr durchführbar sind. Derzeit gibt es schon viele neue Datenanalyse-Ansätze, die vorranging auf Cluster- bzw. Dimensionsreduktionstechniken basieren und meist mit einem vorgeschalteten Downsampling in Kombination eingesetzt werden. Diese Tools produzieren aber komplexe Ergebnisse, die größtenteils nicht reproduzierbar sind oder Proben- und Gruppenvergleiche erschweren. Um dieses Problem anzugehen wurde in dieser Dissertation ein reproduzierbarer, halbautomatisierter Datenanalyse-Workflow namens PRI entwickelt, was für pattern recognition of immune cells (Mustererkennung von Immunzellen) steht. Dieser Workflow ist in drei Hauptteile untergliedert: die Datenvorbereitung und -Ablage; die Entwicklung innovativer, bin-basierter Merkmale von drei kombinierten Parametern namens TriploTs und dessen weiterführende Einteilung in vier gleich große TriploT-Areale; und die Anwendung von einem maschinellen Lernansatz basierend auf der Information von diesen Arealen. Als Ergebnis bekommt man eine Selektion der Areale, die am häufigsten von den überwachten Modellen ausgewählt wurden. Dies soll dem Wissenschaftler entscheidend dabei helfen, Zellpopulationen zu identifizieren, die am besten zwischen zwei Gruppen unterscheiden. Der vorgestellte Workflow PRI ist exemplarisch an einem kürzlich veröffentlichten Massenzytometrie-Datensatz validiert worden. Die von den Originalautoren hervorgehobene Zellpopulation konnte nicht nur identifiziert werden, sondern sogar wesentlich weiter spezifiziert werden. Außerdem wurden weitere Erkenntnisse von relevanten, kombinatorischen Proteinexpressionen festgestellt. Die Entwicklung der reproduzierbaren TriploTs führt dazu, dass sie als Basis für verständliche und leicht interpretierbare Visualisierungen, für eine strukturierte Erforschung der Daten mithilfe der Selektion der Areale, und für neuronale Netzwerkkonstrukte genutzt werden können. PRI ermöglicht eine optimierte, semi-kontinuierliche Bestimmung der Expressionsstufen, die die Identifizierung von dominant vorherrschenden und diskriminierenden Proteinen in Zellsubpopulationen wesentlich erleichtert. Darüberhinaus erlaubt es die intuitive Erfassung von korrelierenden Mustern durch die innovative, reproduzierbare Darstellung der Proteinkombinationen und hilft bei der Erforschung von Zellsubpopulationen. KW - machine learning KW - feature engineering KW - machinelles Lernen KW - Feature Engineering Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-443078 ER - TY - JOUR A1 - Scheller, Frieder W. A1 - Zhang, Xiaorong A1 - Yarman, Aysu A1 - Wollenberger, Ulla A1 - Gyurcsányi, Róbert E. T1 - Molecularly imprinted polymer-based electrochemical sensors for biopolymers JF - Current opinion in electrochemistry N2 - Electrochemical synthesis and signal generation dominate among the almost 1200 articles published annually on protein-imprinted polymers. Such polymers can be easily prepared directly on the electrode surface, and the polymer thickness can be precisely adjusted to the size of the target to enable its free exchange. In this architecture, the molecularly imprinted polymer (MIP) layer represents only one ‘separation plate’; thus, the selectivity does not reach the values of ‘bulk’ measurements. The binding of target proteins can be detected straightforwardly by their modulating effect on the diffusional permeability of a redox marker through the thin MIP films. However, this generates an ‘overall apparent’ signal, which may include nonspecific interactions in the polymer layer and at the electrode surface. Certain targets, such as enzymes or redox active proteins, enables a more specific direct quantification of their binding to MIPs by in situ determination of the enzyme activity or direct electron transfer, respectively. KW - Electropolymerization KW - Direct electron transfer KW - Redox marker KW - Epitope imprinting KW - Biomarker Y1 - 2018 U6 - https://doi.org/10.1016/j.coelec.2018.12.005 SN - 2451-9103 VL - 14 SP - 53 EP - 59 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Tang, Jing A1 - Werchmeister, Rebecka Maria Larsen A1 - Preda, Loredana A1 - Huang, Wei A1 - Zheng, Zhiyong A1 - Leimkühler, Silke A1 - Wollenberger, Ulla A1 - Xiao, Xinxin A1 - Engelbrekt, Christian A1 - Ulstrup, Jens A1 - Zhang, Jingdong T1 - Three-dimensional sulfite oxidase bioanodes based on graphene functionalized carbon paper for sulfite/O-2 biofuel cells JF - ACS catalysis N2 - We have developed a three-dimensional (3D) graphene electrode suitable for the immobilization of human sulfite oxidase (hSO), which catalyzes the electrochemical oxidation of sulfite via direct electron transfer (DET). The electrode is fabricated by drop-casting graphene-polyethylenimine (G-P) composites on carbon papers (CPs) precoated with graphene oxide (GO). The negatively charged hSO can be adsorbed electrostatically on the positively charged matrix (G-P) on CP electrodes coated with GO (CPG), with a proper orientation for accelerated DET. Notably, further electrochemical reduction of G-P on CPG electrodes leads to a 9-fold increase of the saturation catalytic current density (j(m)) for sulfite oxidation reaching 24.4 +/- 0.3 mu A to cm(-2), the highest value among reported DET-based hSO bioelectrodes. The increased electron transfer rate plays a dominating role in the enhancement of direct enzymatic current because of the improved electric contact of hSO with the electrode, The optimized hSO bioelectrode shows a significant catalytic rate (k(cat): 25.6 +/- 0.3 s(-1)) and efficiency (k(cat)/K-m: 0.231 +/- 0.003 s(-1) mu M-1) compared to the reported hSO bioelectrodes. The assembly of the hSO bioanode and a commercial platinum biocathode allows the construction of sulfite/O-2 enzymatic biofuel cells (EBFCs) with flowing fuels. The optimized EBFC displays an open-circuit voltage (OCV) of 0.64 +/- 0.01 V and a maximum power density of 61 +/- 6 mu W cm(-2) (122 +/- 12 mW m(-3)) at 30 degrees C, which exceeds the best reported value by more than 6 times. KW - enzymatic biofuel cell KW - reduced graphene oxide KW - sulfite oxidase KW - carbon paper KW - direct electron transfer Y1 - 2019 U6 - https://doi.org/10.1021/acscatal.9b01715 SN - 2155-5435 VL - 9 IS - 7 SP - 6543 EP - 6554 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Dehm, Daniel A1 - Krumbholz, Julia A1 - Baunach, Martin A1 - Wiebach, Vincent A1 - Hinrichs, Katrin A1 - Guljamow, Arthur A1 - Tabuchi, Takeshi A1 - Jenke-Kodama, Holger A1 - Süssmuth, Roderich D. A1 - Dittmann-Thünemann, Elke T1 - Unlocking the spatial control of secondary metabolism uncovers hidden natural product diversity in nostoc punctiforme JF - ACS chemical biology N2 - Filamentous cyanobacteria belong to the most prolific producers of structurally unique and biologically active natural products, yet the majority of biosynthetic gene clusters predicted for these multicellular collectives are currently orphan. Here, we present a systems analysis of secondary metabolite gene expression in the model strain Nostoc punctiforme PCC73102 using RNA-seq and fluorescence reporter analysis. Our data demonstrate that the majority of the cryptic gene clusters are not silent but are expressed with regular or sporadic pattern. Cultivation of N. punctiforme using high-density fermentation overrules the spatial control and leads to a pronounced upregulation of more than 50% of biosynthetic gene clusters. Our data suggest that a combination of autocrine factors, a high CO2 level, and high light account for the upregulation of individual pathways. Our overarching study not only sheds light on the strategies of filamentous cyanobacteria to share the enormous metabolic burden connected with the production of specialized molecules but provides an avenue for the genome-based discovery of natural products in multicellular cyanobacteria as exemplified by the discovery of highly unusual variants of the tricyclic peptide microviridin. Y1 - 2019 U6 - https://doi.org/10.1021/acschembio.9b00240 SN - 1554-8929 SN - 1554-8937 VL - 14 IS - 6 SP - 1271 EP - 1279 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Hassan, Rabeay Y. A. A1 - Wollenberger, Ulla T1 - Direct determination of bacterial cell viability using carbon nanotubes modified screen-printed electrodes JF - Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis N2 - For the early detection of bacterial infection, there is a need for rapid, sensitive, and label-free assays. Thus, in this study, nanostrucured microbial electrochemical platform is designed to monitor the viability and cell growth of S. aureus. Using multi-walled carbon nanotube modified screen-printed electrodes (MWCNTs/SPE), the cyclic voltammetric measurements showed only one irreversible oxidation peak at 600 mV vs Ag/AgCl that accounts for the viable and metabolically active bacterial cells. The assay was optimized and the secreted metabolites, in the extracellular matrix, were directly detected. The peak current showed a positive correlation with viable cell numbers ranging from OD600 nm of 0.1 to 1.1, indicating that the activity of live cells can be quantified. Consequently, responses of viable and non-viable cells of S. aureus to the effects of antibiotic and respiratory chain inhibitors were determined. Thus, the proposed nanostructure-based bacterial sensor provides a reasonable and reliable way for real-time monitoring of live-dead cell functions, and antibacterial profiling. KW - Bacterial biosensor KW - cell viability assay KW - screen printed electrodes (SPEs) KW - carbon nanotubes (CNTs) Y1 - 2019 U6 - https://doi.org/10.1002/elan.201900047 SN - 1040-0397 SN - 1521-4109 VL - 31 IS - 6 SP - 1112 EP - 1117 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Höfer, C. T. A1 - Di Lella, S. A1 - Dahmani, Ismail A1 - Jungnick, N. A1 - Bordag, N. A1 - Bobone, Sara A1 - Huang, Q. A1 - Keller, S. A1 - Herrmann, A. A1 - Chiantia, Salvatore T1 - Structural determinants of the interaction between influenza A virus matrix protein M1 and lipid membranes JF - Biochimica et biophysica acta : Biomembranes N2 - Influenza A virus is a pathogen responsible for severe seasonal epidemics threatening human and animal populations every year. One of the ten major proteins encoded by the viral genome, the matrix protein M1, is abundantly produced in infected cells and plays a structural role in determining the morphology of the virus. During assembly of new viral particles, M1 is recruited to the host cell membrane where it associates with lipids and other viral proteins. The structure of M1 is only partially known. In particular, structural details of M1 interactions with the cellular plasma membrane as well as M1 protein interactions and multimerization have not been clarified, yet. In this work, we employed a set of complementary experimental and theoretical tools to tackle these issues. Using raster image correlation, surface plasmon resonance and circular dichroism spectroscopies, we quantified membrane association and oligomerization of full-length M1 and of different genetically engineered M1 constructs (i.e., N- and C-terminally truncated constructs and a mutant of the polybasic region, residues 95-105). Furthermore, we report novel information on structural changes in M1 occurring upon binding to membranes. Our experimental results are corroborated by an all-atom model of the full-length M1 protein bound to a negatively charged lipid bilayer. KW - Virus assembly KW - Protein-lipid interaction KW - Fluorescence microscopy KW - SPR KW - CD spectroscopy KW - Influenza A virus Y1 - 2019 U6 - https://doi.org/10.1016/j.bbamem.2019.03.013 SN - 0005-2736 SN - 1879-2642 VL - 1861 IS - 6 SP - 1123 EP - 1134 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Bolius, Sarah A1 - Wiedner, Claudia A1 - Weithoff, Guntram T1 - Low invasion success of an invasive cyanobacterium in a chlorophyte dominated lake JF - Scientific reports Y1 - 2019 SN - 2045-2322 VL - 9 PB - Macmillan Publishers Limited CY - London ER - TY - JOUR A1 - Tanner, Norman A1 - Lichtenberg-Kraag, Birgit T1 - Identification and Quantification of Single and Multi-Adulteration of Beeswax by FTIR-ATR Spectroscopy JF - European journal of lipid science and technology N2 - Marketing of adulterated beeswax foundation has recently become a major economic problem for beekeepers. Paraffin contamination leads to collapse of combs, and stearic acid has a negative influence on the development of bee brood. The quality of beeswax for beekeeping has not been standardized in EU regulations. Recently, it was shown that attenuated total reflectance Fourier-transform infrared spectroscopy (FTIR-ATR) can be used to determine beeswax adulteration. Differences in the IR spectra of authentic beeswax can be identified and calculated through comparison with authentic beeswax. In this study, the method is further validated by employing a high number of samples of authentic beeswax from different origins. Low quantification and detection limits are achieved for paraffin, stearic acid, tallow, carnauba wax, and candelilla wax. Furthermore, the FTIR-ATR analytical conditions are verified by analyzing 358 samples of commercial and beekeeper-produced beeswax foundations. Multi-adulterated samples with as many as five different additives in beeswax mixtures are identified with the same accuracy as single substances. Additionally, the spectra of a further 14 different natural and synthetic waxes and hardened fats are analyzed and are compared with beeswax. Finally, a spectral library is established that can be used for further studies. Practical Applications: FTIR-ATR is a fast and cost-efficient tool in beeswax analysis for accurately monitoring a high sample volume. Analysis of 358 beeswax foundations showed an adulteration of 21.8% of the samples with paraffin, stearic acid, tallow, and combinations. Based on the results of this study, it is possible to detect beeswax adulteration of less than 3% of these adulterants and their combinations by FTIR-ATR spectroscopy. This method can be used for monitoring beeswax foundations to identify adulterated materials, exclude these materials from the recycling process, and produce high-quality beeswax, which is essential for bee health. KW - beeswax KW - beeswax substitutes KW - candelilla wax KW - carnauba wax KW - FTIR-ATR KW - multi-adulteration KW - paraffin KW - stearic acid KW - tallow Y1 - 2019 U6 - https://doi.org/10.1002/ejlt.201900245 SN - 1438-7697 SN - 1438-9312 VL - 121 IS - 12 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Feiner, Rebecca Christine A1 - Teschner, Julian A1 - Teschner, Kathrin E. A1 - Radukic, Marco T. A1 - Baumann, Tobias A1 - Hagen, Sven A1 - Hannappel, Yvonne A1 - Biere, Niklas A1 - Anselmetti, Dario A1 - Arndt, Katja Maren A1 - Müller, Kristian Mark T1 - rAAV Engineering for Capsid-Protein Enzyme Insertions and Mosaicism Reveals Resilience to Mutational, Structural and Thermal Perturbations JF - International journal of molecular sciences N2 - Recombinant adeno-associated viruses (rAAV) provide outstanding options for customization and superior capabilities for gene therapy. To access their full potential, facile genetic manipulation is pivotal, including capsid loop modifications. Therefore, we assessed capsid tolerance to modifications of the structural VP proteins in terms of stability and plasticity. Flexible glycine-serine linkers of increasing sizes were, at the genetic level, introduced into the 587 loop region of the VP proteins of serotype 2, the best studied AAV representative. Analyses of biological function and thermal stability with respect to genome release of viral particles revealed structural plasticity. In addition, insertion of the 29 kDa enzyme beta-lactamase into the loop region was tested with a complete or a mosaic modification setting. For the mosaic approach, investigation of VP2 trans expression revealed that a Kozak sequence was required to prevent leaky scanning. Surprisingly, even the full capsid modification with beta-lactamase allowed for the assembly of capsids with a concomitant increase in size. Enzyme activity assays revealed lactamase functionality for both rAAV variants, which demonstrates the structural robustness of this platform technology. KW - adeno-associated-virus KW - beta-lactamase KW - inverted terminal repeat (ITR) KW - loop modification KW - capsid stability Y1 - 2019 U6 - https://doi.org/10.3390/ijms20225702 SN - 1422-0067 VL - 20 IS - 22 PB - MDPI CY - Basel ER - TY - JOUR A1 - Lechthaler, Silvia A1 - Colangeli, Pierluigi A1 - Gazzabin, Moira A1 - Anfodillo, Tommaso T1 - Axial anatomy of the leaf midrib provides new insights into the hydraulic architecture and cavitation patterns of Acer pseudoplatanus leaves JF - Journal of experimental botany N2 - The structure of leaf veins is typically described by a hierarchical scheme (e.g. midrib, 1(st) order, 2nd order), which is used to predict variation in conduit diameter from one order to another whilst overlooking possible variation within the same order. We examined whether xylem conduit diameter changes within the same vein order, with resulting consequences for resistance to embolism. We measured the hydraulic diameter (D-h), and number of vessels (V-N) along the midrib and petioles of leaves of Acer pseudoplatanus, and estimated the leaf area supplied (A(leaf-sup)) at different points of the midrib and how variation in anatomical traits affected embolism resistance. We found that D-h scales with distance from the midrib tip (path length, L) with a power of 0.42, and that V-N scales with A(leaf-sup) with a power of 0.66. Total conductive area scales isometrically with A(leaf-sup). Embolism events along the midrib occurred first in the basipetal part and then at the leaf tip where vessels are narrower. The distance from the midrib tip is a good predictor of the variation in vessel diameter along the 1st order veins in A. pseudoplatanus leaves and this anatomical pattern seems to have an effect on hydraulic integrity since wider vessels at the leaf base embolize first. KW - Acer pseudoplatanus KW - Leaf cavitation KW - leaf hydraulic architecture KW - leaf midrib KW - total conductive area KW - sycamore maple KW - vessel diameter KW - vessel number Y1 - 2019 U6 - https://doi.org/10.1093/jxb/erz347 SN - 0022-0957 SN - 1460-2431 VL - 70 IS - 21 SP - 6195 EP - 6201 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Wu, Hao A1 - Han, Yijie A1 - Rodriguez Sillke, Yasmina A1 - Deng, Hongzhang A1 - Siddiqui, Sophiya A1 - Treese, Christoph A1 - Schmidt, Franziska A1 - Friedrich, Marie A1 - Keye, Jacqueline A1 - Wan, Jiajia A1 - Qin, Yue A1 - Kühl, Anja A. A1 - Qin, Zhihai A1 - Siegmund, Britta A1 - Glauben, Rainer T1 - Lipid droplet-dependent fatty acid metabolism controls the immune suppressive phenotype of tumor-associated macrophages JF - EMBO molecular medicine N2 - Tumor-associated macrophages (TAMs) promote tumor growth and metastasis by suppressing tumor immune surveillance. Herein, we provide evidence that the immunosuppressive phenotype of TAMs is controlled by long-chain fatty acid metabolism, specifically unsaturated fatty acids, here exemplified by oleate. Consequently, en-route enriched lipid droplets were identified as essential organelles, which represent effective targets for chemical inhibitors to block in vitro polarization of TAMs and tumor growth in vivo. In line, analysis of human tumors revealed that myeloid cells infiltrating colon cancer but not gastric cancer tissue indeed accumulate lipid droplets. Mechanistically, our data indicate that oleate-induced polarization of myeloid cells depends on the mammalian target of the rapamycin pathway. Thus, our findings reveal an alternative therapeutic strategy by targeting the pro-tumoral myeloid cells on a metabolic level. KW - cancer immunotherapy KW - lipid droplets KW - lipid metabolism KW - tumor microenvironment KW - tumor-associated macrophage Y1 - 2019 U6 - https://doi.org/10.15252/emmm.201910698 SN - 1757-4676 SN - 1757-4684 VL - 11 IS - 11 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Mehren, Christoph A1 - Wuertz-Kozak, Karin A1 - Sauer, Daniel A1 - Hitzl, Wolfgang A1 - Pehlivanoglu, Tuna A1 - Heider, Franziska T1 - Implant Design and the Anchoring Mechanism Influence the Incidence of Heterotopic Ossification in Cervical Total Disc Replacement at 2-year Follow-up JF - Spine N2 - Study Design. A nonrandomized, prospective, and single-center clinical trial. Objective. The aim of this study was to determine whether the prosthesis design, and especially changes in the primary anchoring mechanism between the keel-based ProDisc C and the spike-based ProDisc Vivo, affects the frequency of heterotopic ossification (HO) formation over time. Summary of Background Data. The occurrence of motion-restricting HO as well as underlying risk factors has so far been a widely discussed, but not well understand phenomenon. The anchoring mechanism and the opening of the anterior cortex may be possible causes of this unwanted complication. Methods. Forty consecutive patients treated with the ProDisc C and 42 consecutive patients treated with the ProDisc Vivo were compared with respect to radiological and clinical outcome, with 2 years of follow-up. Clinical outcome scores included the Neck Disability Index (NDI), Visual Analogue Scale (VAS), and arm and neck pain self-assessment questionnaires. Radiological outcomes included the segmental lordosis and range of motion (ROM) of the index-segment as well as the occurrence of HO. Results. The clinical outcome parameters improved in both groups significantly. [ProDisc C: VAS arm and neck pain from 6.3 and 6.2 preoperatively to 0.7 and 1.3; NDI from 23.0 to 3.7; ProDisc Vivo: VAS arm and neck pain from 6.3 and 4.9 to 1.4 and 1.6, NDI from 34.1 to 8.7; 2-year follow-up (FU)]. The ProDisc Vivo cohort demonstrated a significantly lower incidence of HO than the ProDisc C group at 1-year FU (P = 0.0005) and 2-year FU (P = 0.005). Specifically, high-grade HO occurred in 9% versus 31%. Conclusion. These findings demonstrate that prosthesis designs that allow primary anchoring without violation of the cortical surface help to reduce the incidence of severe ossification, possibly affecting the functionality and mobility of the artificial disc device over of time. KW - anchoring mechanism KW - cervical artificial disc replacement KW - heterotopic ossification (HO) KW - implant design KW - ProDisc C KW - ProDisc Vivo KW - total disc replacement Y1 - 2019 U6 - https://doi.org/10.1097/BRS.0000000000003098 SN - 0362-2436 SN - 1528-1159 VL - 44 IS - 21 SP - 1471 EP - 1480 PB - Lippincott Williams & Wilkins CY - Philadelphia ER - TY - JOUR A1 - Kielar, Charlotte A1 - Xin, Yang A1 - Xu, Xiaodan A1 - Zhu, Siqi A1 - Gorin, Nelli A1 - Grundmeier, Guido A1 - Möser, Christin A1 - Smith, David M. A1 - Keller, Adrian T1 - Effect of staple age on DNA origami nanostructure assembly and stability JF - Molecules N2 - DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions. Furthermore, in the context of DNA origami mass production, the long-term storage of DNA origami nanostructures or their pre-assembled components also becomes an issue of high relevance, especially regarding the possible negative effects on DNA origami structural integrity. Thus, we investigated the effect of staple age on the self-assembly and stability of DNA origami nanostructures using atomic force microscopy. Different harsh processing conditions were simulated by applying different sample preparation protocols. Our results show that staple solutions may be stored at -20 degrees C for several years without impeding DNA origami self-assembly. Depending on DNA origami shape and superstructure, however, staple age may have negative effects on DNA origami stability under harsh treatment conditions. Mass spectrometry analysis of the aged staple mixtures revealed no signs of staple fragmentation. We, therefore, attribute the increased DNA origami sensitivity toward environmental conditions to an accumulation of damaged nucleobases, which undergo weaker base-pairing interactions and thus lead to reduced duplex stability. KW - DNA origami KW - atomic force microscopy KW - stability KW - storage Y1 - 2019 U6 - https://doi.org/10.3390/molecules24142577 SN - 1420-3049 VL - 24 IS - 14 PB - MDPI CY - Basel ER - TY - JOUR A1 - Reschke, Stefan A1 - Duffus, Benjamin R. A1 - Schrapers, Peer A1 - Mebs, Stefan A1 - Teutloff, Christian A1 - Dau, Holger A1 - Haumann, Michael A1 - Leimkühler, Silke T1 - Identification of YdhV as the First Molybdoenzyme Binding a Bis-Mo-MPT Cofactor in Escherichia coli JF - Biochemistry N2 - The oxidoreductase YdhV in Escherichia coli has been predicted to belong to the family of molybdenum/tungsten cofactor (Moco/Wco)-containing enzymes. In this study, we characterized the YdhV protein in detail, which shares amino acid sequence homology with a tungsten-containing benzoyl-CoA reductase binding the bis-W-MPT (for metal-binding pterin) cofactor. The cofactor was identified to be of a bis-Mo-MPT type with no guanine nucleotides present, which represents a form of Moco that has not been found previously in any molybdoenzyme. Our studies showed that YdhV has a preference for bis-Mo-MPT over bis-W-MPT to be inserted into the enzyme. In-depth characterization of YdhV by X-ray absorption and electron paramagnetic resonance spectroscopies revealed that the bis-Mo-MPT cofactor in YdhV is redox active. The bis-Mo-MPT and bis-W-MPT cofactors include metal centers that bind the four sulfurs from the two dithiolene groups in addition to a cysteine and likely a sulfido ligand. The unexpected presence of a bis-Mo-MPT cofactor opens an additional route for cofactor biosynthesis in E. coli and expands the canon of the structurally highly versatile molybdenum and tungsten cofactors. Y1 - 2019 U6 - https://doi.org/10.1021/acs.biochem.9b00078 SN - 0006-2960 VL - 58 IS - 17 SP - 2228 EP - 2242 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Heim, Ramona J. A1 - Hölzel, Norbert A1 - Heinken, Thilo A1 - Kamp, Johannes A1 - Thomas, Alexander A1 - Darman, Galina F. A1 - Smirenski, Sergei M. A1 - Heim, Wieland T1 - Post-burn and long-term fire effects on plants and birds in floodplain wetlands of the Russian Far East JF - Biodiversity and conservation N2 - Wildfires affect biodiversity at multiple levels. While vegetation is directly changed by fire events, animals are often indirectly affected through changes in habitat and food availability. Globally, fire frequency and the extent of fires are predicted to increase in the future. The impact of fire on the biodiversity of temperate wetlands has gained little attention so far. We compared species richness and abundance of plants and birds in burnt and unburnt areas in the Amur floodplain/Russian Far East in the year of fire and 1 year after. We also analysed vegetation recovery in relation to time since fire over a period of 18 years. Plant species richness was higher in burnt compared to unburnt plots in the year of the fire, but not in the year after. This suggests that fire has a positive short-term effect on plant diversity. Bird species richness and abundance were lower on burnt compared to unburnt plots in the year of the fire, but not in the year after. Over a period of 18 years, high fire frequency led to an increase in herb cover and a decrease in grass cover. We show that the effects on biodiversity are taxon- and species-specific. Fire management strategies in temperate wetlands should consider fire frequency as a key driving force of vegetation structure, with carry-over effects on higher trophic levels. Designing fire refuges, i.e., areas that do not burn annually, might locally be necessary to maintain high species richness. KW - Disturbance KW - Bird species richness KW - Vegetation structure KW - Fire frequency KW - Amur River Y1 - 2019 U6 - https://doi.org/10.1007/s10531-019-01746-3 SN - 0960-3115 SN - 1572-9710 VL - 28 IS - 6 SP - 1611 EP - 1628 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Yan, Wenhao A1 - Chen, Dijun A1 - Schumacher, Julia A1 - Durantini, Diego A1 - Engelhorn, Julia A1 - Chen, Ming A1 - Carles, Cristel C. A1 - Kaufmann, Kerstin T1 - Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis JF - Nature Communications N2 - Enhancers are critical for developmental stage-specific gene expression, but their dynamic regulation in plants remains poorly understood. Here we compare genome-wide localization of H3K27ac, chromatin accessibility and transcriptomic changes during flower development in Arabidopsis. H3K27ac prevalently marks promoter-proximal regions, suggesting that H3K27ac is not a hallmark for enhancers in Arabidopsis. We provide computational and experimental evidence to confirm that distal DNase. hypersensitive sites are predictive of enhancers. The predicted enhancers are highly stage-specific across flower development, significantly associated with SNPs for flowering-related phenotypes, and conserved across crucifer species. Through the integration of genome-wide transcription factor (TF) binding datasets, we find that floral master regulators and stage-specific TFs are largely enriched at developmentally dynamic enhancers. Finally, we show that enhancer clusters and intronic enhancers significantly associate with stage-specific gene regulation by floral master TFs. Our study provides insights into the functional flexibility of enhancers during plant development, as well as hints to annotate plant enhancers. Y1 - 2019 U6 - https://doi.org/10.1038/s41467-019-09513-2 SN - 2041-1723 VL - 10 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Guislain, Alexis A1 - Beisner, Beatrix E. A1 - Köhler, Jan T1 - Variation in species light acquisition traits under fluctuating light regimes BT - implications for non-equilibrium coexistence JF - Oikos N2 - Resource distribution heterogeneity offers niche opportunities for species with different functional traits to develop and potentially coexist. Available light (photosynthetically active radiation or PAR) for suspended algae (phytoplankton) may fluctuate greatly over time and space. Species-specific light acquisition traits capture important aspects of the ecophysiology of phytoplankton and characterize species growth at either limiting or saturating daily PAR supply. Efforts have been made to explain phytoplankton coexistence using species-specific light acquisition traits under constant light conditions, but not under fluctuating light regimes that should facilitate non-equilibrium coexistence. In the well-mixed, hypertrophic Lake TaiHu (China), we incubated the phytoplankton community in bottles placed either at fixed depths or moved vertically through the water column to mimic vertical mixing. Incubations at constant depths received only the diurnal changes in light, while the moving bottles received rapidly fluctuating light. Species-specific light acquisition traits of dominant cyanobacteria (Anabaena flos-aquae, Microcystis spp.) and diatom (Aulacoseira granulata, Cyclotella pseudostelligera) species were characterized from their growth-light relationships that could explain relative biomasses along the daily PAR gradient under both constant and fluctuating light. Our study demonstrates the importance of interspecific differences in affinities to limiting and saturating light for the coexistence of phytoplankton species in spatially heterogeneous light conditions. Furthermore, we observed strong intraspecific differences in light acquisition traits between incubation under constant and fluctuating light - leading to the reversal of light utilization strategies of species. This increased the niche space for acclimated species, precluding competitive exclusion. These observations could enhance our understanding of the mechanisms behind the Paradox of the Plankton. KW - niche partitioning KW - phytoplankton photoacclimation Y1 - 2018 U6 - https://doi.org/10.1111/oik.05297 SN - 0030-1299 SN - 1600-0706 VL - 128 IS - 5 SP - 716 EP - 728 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - de la Cruz, Jorge Gonzalez A1 - Machens, Fabian A1 - Messerschmidt, Katrin A1 - Bar-Even, Arren T1 - Core Catalysis of the Reductive Glycine Pathway Demonstrated in Yeast JF - ACS synthetic biology N2 - One-carbon (C1) compounds are attractive microbial feedstocks as they can be efficiently produced from widely available resources. Formate, in particular, represents a promising growth substrate, as it can be generated from electrochemical reduction of CO2 and fed to microorganisms in a soluble form. We previously identified the synthetic reductive glycine pathway as the most efficient route for aerobic growth on formate. We further demonstrated pathway activity in Escherichia coli after expression of both native and foreign genes. Here, we explore whether the reductive glycine pathway could be established in a model microorganism using only native enzymes. We used the yeast Saccharomyces cerevisiae as host and show that overexpression of only endogenous enzymes enables glycine biosynthesis from formate and CO2 in a strain that is otherwise auxotrophic for glycine. We find the pathway to be highly active in this host, where 0.125 mM formate is sufficient to support growth. Notably, the formate-dependent growth rate of the engineered S. cerevisiae strain remained roughly constant over a very wide range of formate concentrations, 1-500 mM, indicating both high affinity for formate use and high tolerance toward elevated concentration of this C1 feedstock. Our results, as well the availability of endogenous NAD-dependent formate dehydrogenase, indicate that yeast might be an especially suitable host for engineering growth on formate. KW - metabolic engineering KW - synthetic biology KW - one-carbon metabolism KW - carbon labeling KW - tetrahydrofolate KW - glycine cleavage system Y1 - 2019 U6 - https://doi.org/10.1021/acssynbio.8b00464 SN - 2161-5063 VL - 8 IS - 5 SP - 911 EP - 917 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Altintas, Zeynep A1 - Takiden, Aref A1 - Utesch, Tillmann A1 - Mroginski, Maria A. A1 - Schmid, Bianca A1 - Scheller, Frieder W. A1 - Süssmuth, Roderich D. T1 - Integrated approaches toward high-affinity artificial protein binders obtained via computationally simulated epitopes for protein recognition JF - Advanced functional materials N2 - Widely used diagnostic tools make use of antibodies recognizing targeted molecules, but additional techniques are required in order to alleviate the disadvantages of antibodies. Herein, molecular dynamic calculations are performed for the design of high affinity artificial protein binding surfaces for the recognition of neuron specific enolase (NSE), a known cancer biomarker. Computational simulations are employed to identify particularly stabile secondary structure elements. These epitopes are used for the subsequent molecular imprinting, where surface imprinting approach is applied. The molecular imprints generated with the calculated epitopes of greater stability (Cys-Ep1) show better binding properties than those of lower stability (Cys-Ep5). The average binding strength of imprints created with stabile epitopes is found to be around twofold and fourfold higher for the NSE derived peptide and NSE protein, respectively. The recognition of NSE is investigated in a wide concentration range, where high sensitivity (limit of detection (LOD) = 0.5 ng mL(-1)) and affinity (dissociation constant (K-d) = 5.3 x 10(-11)m) are achieved using Cys-Ep1 imprints reflecting the stable structure of the template molecules. This integrated approach employing stability calculations for the identification of stabile epitopes is expected to have a major impact on the future development of high affinity protein capturing binders. KW - artificial protein binders KW - cancer markers KW - computationally simulated epitopes KW - molecular imprinting KW - protein recognition Y1 - 2019 U6 - https://doi.org/10.1002/adfm.201807332 SN - 1616-301X SN - 1616-3028 VL - 29 IS - 15 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Schieferdecker, Anne A1 - Wendler, Petra T1 - Structural Mapping of Missense Mutations in the Pex1/Pex6 Complex JF - International journal of molecular sciences N2 - Peroxisome biogenesis disorders (PBDs) are nontreatable hereditary diseases with a broad range of severity. Approximately 65% of patients are affected by mutations in the peroxins Pex1 and Pex6. The proteins form the heteromeric Pex1/Pex6 complex, which is important for protein import into peroxisomes. To date, no structural data are available for this AAA+ ATPase complex. However, a wealth of information can be transferred from low-resolution structures of the yeast scPex1/scPex6 complex and homologous, well-characterized AAA+ ATPases. We review the abundant records of missense mutations described in PBD patients with the aim to classify and rationalize them by mapping them onto a homology model of the human Pex1/Pex6 complex. Several mutations concern functionally conserved residues that are implied in ATP hydrolysis and substrate processing. Contrary to fold destabilizing mutations, patients suffering from function-impairing mutations may not benefit from stabilizing agents, which have been reported as potential therapeutics for PBD patients. KW - Zellweger syndrome spectrum disorder (ZSSD) KW - Zellweger KW - structure KW - Pex1 KW - Pex6 KW - mutation Y1 - 2019 U6 - https://doi.org/10.3390/ijms20153756 SN - 1422-0067 VL - 20 IS - 15 PB - MDPI CY - Basel ER - TY - JOUR A1 - Geißler, Katja A1 - Hahn, Claudia A1 - Joubert, David A1 - Blaum, Niels T1 - Functional responses of the herbaceous plant community explain ecohydrological impacts of savanna shrub encroachment JF - Perspectives in plant ecology, evolution and systematics N2 - Major drivers of savanna shrub encroachment are climatic conditions, CO2 and unsustainable grazing management including fire prevention. Although all drivers affect ecohydrological processes, and given that water is a seasonally scarce resource in savannas, it remains largely unclear how shrub encroachment itself affects hydrological conditions that feed back into water use and community assembly of the remaining plant community. Hence, understanding direct ecohydrological effects of shrubs that may limit the recovery of the perennial herbaceous vegetation in grazed areas and promote the establishment of shrub seedlings facilitates the identification of areas that are most sensitive to further encroachment. In our trait-based approach, we determined relationships among shrub cover, soil and plant trait characteristics sensitive to water limitation in 120 plots along a shrub cover gradient. We focused on two functional response traits indicating immediate drought stress and subsequent water use for drought stress recovery with associated competition for water (midday leaf/xylem water potential and diurnally recovery rate of leaf water potential), and three functional response traits indicating long-term stress adaptation and related resource use strategies (SLA, plant height and seed release height). To understand species assembly and the associated mechanisms of resource use, we calculated community weighted mean traits, intraspecific trait variability as a proxy for the mechanism of coexistence, and mean traits at plant functional type level including 2-year-old Acacia mellifera-saplings. We found a low intraspecific trait variability in drought stress recovery rate and height suggesting that competitive exclusion via active resource acquisition (i.e. water exploitation) played a minor role for community assembly in a shrub encroaching savanna. The dominant community assembly process was passive stress avoidance via resource conservation up to stress tolerance indicated by the high variability in SLA and midday leaf water potential. Correlations of traits with soil moisture suggest a rooting niche differentiation between annual and perennial grasses and that Acacia-shrub saplings within the first 50 cm of soil already escaped the highest drought stress. Interestingly, immediate drought stress for the herbaceous community was lowest on moderately shrub encroached sites and not on grass dominated sites. Since passive stress avoidance accompanied by a distinct stress tolerance in semi-arid savannas is more important than active competition, and assuming that the low drought stress of the herbaceous community at intermediate levels of shrub cover also applies to newly emerging shrub seedlings, these areas are likely to be most sensitive to further encroachment. As such, they should be considered as focal areas for prevention management. KW - Community-weighted means KW - Drought stress KW - Intraspecific variation KW - Soil moisture KW - Stress recovery KW - Plant functional traits Y1 - 2019 U6 - https://doi.org/10.1016/j.ppees.2019.125458 SN - 1433-8319 VL - 39 PB - Elsevier CY - München ER - TY - JOUR A1 - Ryser, Remo A1 - Häussler, Johanna A1 - Stark, Markus A1 - Brose, Ulrich A1 - Rall, Björn C. A1 - Guill, Christian T1 - The biggest losers: habitat isolation deconsructs complex food webs from top to bottom JF - Proceedings of the Royal Society of London : B, Biological sciences N2 - Habitat fragmentation threatens global biodiversity. To date, there is only limited understanding of how the different aspects of habitat fragmentation (habitat loss, number of fragments and isolation) affect species diversity within complex ecological networks such as food webs. Here, we present a dynamic and spatially explicit food web model which integrates complex food web dynamics at the local scale and species-specific dispersal dynamics at the landscape scale, allowing us to study the interplay of local and spatial processes in metacommunities. We here explore how the number of habitat patches, i.e. the number of fragments, and an increase of habitat isolation affect the species diversity patterns of complex food webs (alpha-,beta-,gamma-, diversities). We specifically test whether there is a trophic dependency in the effect of these two factors on species diversity. In our model, habitat isolation is the main driver causing species loss and diversity decline. Our results emphasize that large-bodied consumer species at high trophic positions go extinct faster than smaller species at lower trophic levels, despite being superior dispersers that connect fragmented landscapes better. We attribute the loss of top species to a combined effect of higher biomass loss during dispersal with increasing habitat isolation in general, and the associated energy limitation in highly fragmented landscapes, preventing higher trophic levels to persist. To maintain trophic-complex and species-rich communities calls for effective conservation planning which considers the interdependence of trophic and spatial dynamics as well as the spatial context of a landscape and its energy availability. KW - food webs KW - allometry KW - bioenergetic model KW - metacommunity dynamics KW - dispersal mortality KW - landscape structure Y1 - 2019 U6 - https://doi.org/10.1098/rspb.2019.1177 SN - 0962-8452 SN - 1471-2954 VL - 286 IS - 1908 PB - Royal Society CY - London ER - TY - JOUR A1 - Busch, Verena A1 - Klaus, Valentin Helmut A1 - Schaefer, Deborah A1 - Prati, Daniel A1 - Boch, Steffen A1 - Müller, Jörg A1 - Chiste, Melanie A1 - Mody, Karsten A1 - Blüthgen, Nico A1 - Fischer, Markus A1 - Hölzel, Norbert A1 - Kleinebecker, Till T1 - Will I stay or will I go? Plant species-specific response and tolerance to high land-use intensity in temperate grassland ecosystems JF - Journal of vegetation science KW - community composition KW - ecological strategies KW - Ellenberg indicator values KW - land-use intensity niche KW - plant functional traits KW - species-specific niche breadth KW - species-specific niche optima KW - temperate grasslands KW - vegetation dynamics Y1 - 2019 U6 - https://doi.org/10.1111/jvs.12749 SN - 1100-9233 SN - 1654-1103 VL - 30 IS - 4 SP - 674 EP - 686 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Andrés-Delgado, Laura A1 - Ernst, Alexander A1 - Galardi-Castilla, María A1 - Bazaga, David A1 - Peralta, Marina A1 - Münch, Juliane A1 - Gonzalez-Rosa, Juan M. A1 - Marques, Inês A1 - Tessadori, Federico A1 - de la Pompa, José Luis A1 - Vermot, Julien A1 - Mercader, Nadia T1 - Actin dynamics and the Bmp pathway drive apical extrusion of proepicardial cells JF - Development : Company of Biologists N2 - The epicardium, the outer mesothelial layer enclosing the myocardium, plays key roles in heart development and regeneration. During embryogenesis, the epicardium arises from the proepicardium (PE), a cell cluster that appears in the dorsal pericardium (DP) close to the venous pole of the heart. Little is known about how the PE emerges from the pericardial mesothelium. Using a zebrafish model and a combination of genetic tools, pharmacological agents and quantitative in vivo imaging, we reveal that a coordinated collective movement of DP cells drives PE formation. We found that Bmp signaling and the actomyosin cytoskeleton promote constriction of the DP, which enables PE cells to extrude apically. We provide evidence that cell extrusion, which has been described in the elimination of unfit cells from epithelia and the emergence of hematopoietic stem cells, is also a mechanism for PE cells to exit an organized mesothelium and fulfil their developmental fate to form a new tissue layer, the epicardium. KW - Actomyosin KW - Bmp KW - Cell extrusion KW - Proepicardium KW - Zebrafish KW - Heart development Y1 - 2019 U6 - https://doi.org/10.1242/dev.174961 SN - 0950-1991 SN - 1477-9129 VL - 146 IS - 13 PB - The Company of Biologists Ltd CY - Cambridge ER - TY - JOUR A1 - Holec, Jan A1 - Rybáček, Jiří A1 - Vacek, Jaroslav A1 - Karras, Manfred A1 - Bednárová, Lucie A1 - Budesinsky, Milos A1 - Slusna, Michaela A1 - Holy, Petr A1 - Schmidt, Bernd A1 - Stará, Irena G. A1 - Starý, Ivo T1 - Chirality-Controlled Self-Assembly of Amphiphilic Dibenzo[6]helicenes into Langmuir-Blodgett Thin Films JF - Chemistry - a European journal N2 - Racemic and highly enantioenriched 3-methoxycarbonyl, 3-carboxy, and 3-hydroxymethyl derivatives of dibenzo[6]helicene were prepared. The Langmuir layers of these helicenes were formed at the air-water interface and transferred onto solid substrates to afford Langmuir-Blodgett films, which were then studied by ambient atomic force microscopy and (chir)optical spectroscopy. Significant differences were found in the behaviour of the Langmuir layers as well as in the morphology, UV/Vis, electronic circular dichroism (ECD), and fluorescence spectra of the Langmuir-Blodgett thin films depending on the molecular chirality and nature of the polar group. The experimental results were supported by molecular dynamics simulations. KW - arenes KW - chirality KW - helical structures KW - Langmuir-Blodgett films KW - self-assembly Y1 - 2019 U6 - https://doi.org/10.1002/chem.201901695 SN - 0947-6539 SN - 1521-3765 VL - 25 IS - 49 SP - 11494 EP - 11502 PB - Wiley-VCH CY - Weinheim ER - TY - GEN A1 - Dunsing, Valentin A1 - Irmscher, Tobias A1 - Barbirz, Stefanie A1 - Chiantia, Salvatore T1 - Microviscosity of bacterial biofilm matrix characterized by fluorescence correlation spectroscopy and single particle tracking T2 - European biophysics journal : with biophysics letters ; an international journal of biophysics Y1 - 2019 U6 - https://doi.org/https://doi.org/10.1007/s00249-019-01373-4 SN - 0175-7571 SN - 1432-1017 VL - 48 SP - S115 EP - S115 PB - Springer CY - New York ER - TY - GEN A1 - Luckner, Madlen A1 - Dunsing, Valentin A1 - Drüke, Markus A1 - Zuehlke, B. A1 - Petazzi, Roberto Arturo A1 - Chiantia, Salvatore A1 - Herrmann, A. T1 - Quantifying protein oligomerization directly in living cells BT - a systematic comparison of fluorescent proteins and application to Influenza A virus infection T2 - European biophysics journal : with biophysics letters ; an international journal of biophysics Y1 - 2019 SN - 0175-7571 SN - 1432-1017 VL - 48 SP - S183 EP - S183 PB - Springer CY - New York ER - TY - GEN A1 - Moga, A. A1 - Robinson, T. A1 - Leimkühler, Silke T1 - Towards reconstituting a biosynthetic pathway within compartmentalized GUVs T2 - European biophysics journal : with biophysics letters ; an international journal of biophysics Y1 - 2019 SN - 0175-7571 SN - 1432-1017 VL - 48 SP - S218 EP - S218 PB - Springer CY - New York ER - TY - JOUR A1 - Chaturvedi, Neha A1 - Mehrotra, Bagish A1 - Kumari, Sangeeta A1 - Gupta, Saurabh A1 - Subramanya, Hosahalli A1 - Saberwal, Gayatri T1 - Some data quality issues at ClinicalTrials.gov JF - Trials KW - ClinicalTrials KW - gov KW - Drugs KW - Biologicals KW - Clinical trial KW - Principal Investigator KW - Data quality KW - Database errors Y1 - 2019 U6 - https://doi.org/10.1186/s13063-019-3408-2 SN - 1745-6215 VL - 20 PB - BMC CY - London ER - TY - JOUR A1 - Brechun, Katherine E. A1 - Zhen, Danlin A1 - Jaikaran, Anna A1 - Borisenko, Vitali A1 - Kumauchi, Masato A1 - Hoff, Wouter D. A1 - Arndt, Katja Maren A1 - Woolley, Andrew G T1 - Detection of Incorporation of p-Coumaric Acid into Photoactive Yellow Protein Variants in Vivo JF - Biochemistry N2 - We report the design and characterization of photoactive yellow protein (PYP)-blue fluorescent protein (mTagBFP) fusion constructs that permit the direct assay of reconstitution and function of the PYP domain. These constructs allow for in vivo testing of co-expression systems for enzymatic production of the p-coumaric acid-based PYP chromophore, via the action of tyrosine ammonia lyase and p-coumaroyl-CoA ligase (pCL or 4CL). We find that different 4CL enzymes can function to reconstitute PYP, including 4CL from Arabidopsis thaliana that can produce similar to 100% holo-PYP protein under optimal conditions. mTagBFP fusion constructs additionally enable rapid analysis of effects of mutations on PYP photocycles. We use this mTagBFP fusion strategy to demonstrate in vivo reconstitution of several PYP-based optogenetic tools in Escherichia coli via a biosynthesized chromophore, an important step for the use of these optogenetic tools in vivo in diverse hosts. Y1 - 2019 U6 - https://doi.org/10.1021/acs.biochem.9b00279 SN - 0006-2960 VL - 58 IS - 23 SP - 2682 EP - 2694 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Betke, Alexander A1 - Lokstein, Heiko T1 - Two-photon excitation spectroscopy of photosynthetic light-harvesting complexes and pigments JF - Faraday discussions N2 - In addition to (bacterio)chlorophylls, (B)Chls, light-harvesting complexes (LHCs) bind carotenoids, and/or their oxygen derivatives, xanthophylls. Xanthophylls/carotenoids have pivotal functions in LHCs: in stabilization of the structure, as accessory light-harvesting pigments and, probably most importantly, in photoprotection. Xanthophylls are assumed to be involved in the not yet fully understood mechanism of energy-dependent (qE) non-photochemical quenching of Chl fluorescence (NPQ) in higher plants and algae. The so called "xanthophyll cycle" appears to be crucial in this regard. The molecular mechanism(s) of xanthophyll involvement in qE/NPQ have not been established, yet. Moreover, excitation energy transfer (EET) processes involving carotenoids are also difficult to study, due to the fact that transitions between the ground state (S-0, 1(1)A(g)(-)) and the lowest excited singlet state (S-1, 2(1)A(g)(-)) of carotenoids are optically one-photon forbidden ("dark"). Two-photon excitation spectroscopic techniques have been used for more than two decades to study one-photon forbidden states of carotenoids. In the current study, two-photon excitation profiles of LHCII samples containing different xanthophyll complements were measured in the presumed 1(1)A(g)(-) -> 2(1)A(g)(-) (S-0 -> S-1) transition spectral region of the xanthophylls, as well as for isolated chlorophylls a and b in solution. The results indicate that direct two-photon excitation of Chls in this spectral region is dominant over that by xanthophylls. Implications of the results for proposed mechanism(s) of qE/NPQ will be discussed. Y1 - 2019 U6 - https://doi.org/10.1039/c8fd00198g SN - 1359-6640 SN - 1364-5498 VL - 216 SP - 494 EP - 506 PB - Royal Society of Chemistry CY - Cambridge ER - TY - GEN A1 - Arnold, Patrick T1 - The origin of morphological integration and modularity in the Mammalian Neck T2 - Journal of morphology Y1 - 2019 U6 - https://doi.org/10.1002/jmor.21003 SN - 0362-2525 SN - 1097-4687 VL - 280 SP - S13 EP - S13 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Fages, Antoine A1 - Hanghoj, Kristian A1 - Khan, Naveed A1 - Gaunitz, Charleen A1 - Seguin-Orlando, Andaine A1 - Leonardi, Michela A1 - Constantz, Christian McCrory A1 - Gamba, Cristina A1 - Al-Rasheid, Khaled A. S. A1 - Albizuri, Silvia A1 - Alfarhan, Ahmed H. A1 - Allentoft, Morten A1 - Alquraishi, Saleh A1 - Anthony, David A1 - Baimukhanov, Nurbol A1 - Barrett, James H. A1 - Bayarsaikhan, Jamsranjav A1 - Benecke, Norbert A1 - Bernaldez-Sanchez, Eloisa A1 - Berrocal-Rangel, Luis A1 - Biglari, Fereidoun A1 - Boessenkool, Sanne A1 - Boldgiv, Bazartseren A1 - Brem, Gottfried A1 - Brown, Dorcas A1 - Burger, Joachim A1 - Crubezy, Eric A1 - Daugnora, Linas A1 - Davoudi, Hossein A1 - Damgaard, Peter de Barros A1 - de Chorro y de Villa-Ceballos, Maria de los Angeles A1 - Deschler-Erb, Sabine A1 - Detry, Cleia A1 - Dill, Nadine A1 - Oom, Maria do Mar A1 - Dohr, Anna A1 - Ellingvag, Sturla A1 - Erdenebaatar, Diimaajav A1 - Fathi, Homa A1 - Felkel, Sabine A1 - Fernandez-Rodriguez, Carlos A1 - Garcia-Vinas, Esteban A1 - Germonpre, Mietje A1 - Granado, Jose D. A1 - Hallsson, Jon H. A1 - Hemmer, Helmut A1 - Hofreiter, Michael A1 - Kasparov, Aleksei A1 - Khasanov, Mutalib A1 - Khazaeli, Roya A1 - Kosintsev, Pavel A1 - Kristiansen, Kristian A1 - Kubatbek, Tabaldiev A1 - Kuderna, Lukas A1 - Kuznetsov, Pavel A1 - Laleh, Haeedeh A1 - Leonard, Jennifer A. A1 - Lhuillier, Johanna A1 - von Lettow-Vorbeck, Corina Liesau A1 - Logvin, Andrey A1 - Lougas, Lembi A1 - Ludwig, Arne A1 - Luis, Cristina A1 - Arruda, Ana Margarida A1 - Marques-Bonet, Tomas A1 - Silva, Raquel Matoso A1 - Merz, Victor A1 - Mijiddorj, Enkhbayar A1 - Miller, Bryan K. A1 - Monchalov, Oleg A1 - Mohaseb, Fatemeh A. A1 - Morales, Arturo A1 - Nieto-Espinet, Ariadna A1 - Nistelberger, Heidi A1 - Onar, Vedat A1 - Palsdottir, Albina H. A1 - Pitulko, Vladimir A1 - Pitskhelauri, Konstantin A1 - Pruvost, Melanie A1 - Sikanjic, Petra Rajic A1 - Papesa, Anita Rapan A1 - Roslyakova, Natalia A1 - Sardari, Alireza A1 - Sauer, Eberhard A1 - Schafberg, Renate A1 - Scheu, Amelie A1 - Schibler, Jorg A1 - Schlumbaum, Angela A1 - Serrand, Nathalie A1 - Serres-Armero, Aitor A1 - Shapiro, Beth A1 - Seno, Shiva Sheikhi A1 - Shevnina, Irina A1 - Shidrang, Sonia A1 - Southon, John A1 - Star, Bastiaan A1 - Sykes, Naomi A1 - Taheri, Kamal A1 - Taylor, William A1 - Teegen, Wolf-Rudiger A1 - Vukicevic, Tajana Trbojevic A1 - Trixl, Simon A1 - Tumen, Dashzeveg A1 - Undrakhbold, Sainbileg A1 - Usmanova, Emma A1 - Vahdati, Ali A1 - Valenzuela-Lamas, Silvia A1 - Viegas, Catarina A1 - Wallner, Barbara A1 - Weinstock, Jaco A1 - Zaibert, Victor A1 - Clavel, Benoit A1 - Lepetz, Sebastien A1 - Mashkour, Marjan A1 - Helgason, Agnar A1 - Stefansson, Kari A1 - Barrey, Eric A1 - Willerslev, Eske A1 - Outram, Alan K. A1 - Librado, Pablo A1 - Orlando, Ludovic T1 - Tracking five millennia of horse management with extensive ancient genome time series JF - Cell N2 - Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (>= 1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modem legacy of past equestrian civilisations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modem breeding impacted genetic diversity more dramatically than the previous millennia of human management. Y1 - 2019 U6 - https://doi.org/10.1016/j.cell.2019.03.049 SN - 0092-8674 SN - 1097-4172 VL - 177 IS - 6 SP - 1419 EP - 1435 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Frommhold, Martin A1 - Heim, Arend A1 - Barabanov, Mikhail A1 - Maier, Franziska A1 - Mühle, Ralf-Udo A1 - Smirenski, Sergei M. A1 - Heim, Wieland T1 - Breeding habitat and nest-site selection by an obligatory "nest-cleptoparasite", the Amur Falcon Falco amurensis JF - Ecology and evolution N2 - The selection of a nest site is crucial for successful reproduction of birds. Animals which re-use or occupy nest sites constructed by other species often have limited choice. Little is known about the criteria of nest-stealing species to choose suitable nesting sites and habitats. Here, we analyze breeding-site selection of an obligatory "nest-cleptoparasite", the Amur Falcon Falco amurensis. We collected data on nest sites at Muraviovka Park in the Russian Far East, where the species breeds exclusively in nests of the Eurasian Magpie Pica pica. We sampled 117 Eurasian Magpie nests, 38 of which were occupied by Amur Falcons. Nest-specific variables were assessed, and a recently developed habitat classification map was used to derive landscape metrics. We found that Amur Falcons chose a wide range of nesting sites, but significantly preferred nests with a domed roof. Breeding pairs of Eurasian Hobby Falco subbuteo and Eurasian Magpie were often found to breed near the nest in about the same distance as neighboring Amur Falcon pairs. Additionally, the occurrence of the species was positively associated with bare soil cover, forest cover, and shrub patches within their home range and negatively with the distance to wetlands. Areas of wetlands and fallow land might be used for foraging since Amur Falcons mostly depend on an insect diet. Additionally, we found that rarely burned habitats were preferred. Overall, the effect of landscape variables on the choice of actual nest sites appeared to be rather small. We used different classification methods to predict the probability of occurrence, of which the Random forest method showed the highest accuracy. The areas determined as suitable habitat showed a high concordance with the actual nest locations. We conclude that Amur Falcons prefer to occupy newly built (domed) nests to ensure high nest quality, as well as nests surrounded by available feeding habitats. KW - cleptoparasitism KW - fire KW - habitat use KW - machine learning KW - magpie KW - nest-site selection KW - random forest Y1 - 2019 U6 - https://doi.org/10.1002/ece3.5878 SN - 2045-7758 VL - 9 IS - 24 SP - 14430 EP - 14441 PB - Wiley CY - Hoboken ER -