Recent Submissions

  • Journal Article

    Perspective review of optical imaging in welfare assessment in animal-based research 

    Pereira, Carina Barbosa; Kunczik, Janosch; Bleich, André; Haeger, Christine; Kiessling, Fabian; Thum, Thomas; Tolba, René; Lindauer, Ute; Treue, Stefan; Czaplik, Michael
    Journal of Biomedical Optics 2019; 24: Art. 070601
    To refine animal research, vital signs, activity, stress, and pain must be monitored. In chronic studies, some measures can be assessed using telemetry sensors. Although this methodology provides high-precision data, an initial surgery for device implantation is necessary, potentially leading to stress, wound infections, and restriction of motion. Recently, camera systems have been adapted for animal research. We give an overview of parameters that can be assessed using imaging in the visible, near-infrared, and thermal spectrum of light. It focuses on heart activity, respiration, oxygen saturation, and motion, as well as on wound analysis. For each parameter, we offer recommendations on the minimum technical requirements of appropriate systems, regions of interest, and light conditions, among others. In general, these systems demonstrate great performance. For heart and respiratory rate, the error was <4  beats  /  min and 5 breaths/min. Furthermore, the systems are capable of tracking animals during different behavioral tasks. Finally, studies indicate that inhomogeneous temperature distribution around wounds might be an indicator of (pending) infections. In sum, camera-based techniques have several applications in animal research. As vital parameters are currently only assessed in sedated animals, the next step should be the integration of these modalities in home-cage monitoring.
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  • Journal Article

    Highly variable lifespan in an annual reptile, Labord’s chameleon (Furcifer labordi) 

    Eckhardt, Falk; Kappeler, Peter M.; Kraus, Cornelia
    Scientific Reports 2017; 7(1)
    Among tetrapods, the current record holder for shortest lifespan is Labord's chameleon, Furcifer labordi. These reptiles from the arid southwest of Madagascar have a reported lifespan of 4-5 months during the annual rainy season and spend the majority of their life (8-9 months) as a developing embryo. This semelparous, annual life history is unique among tetrapods, but only one population (Ranobe) in the southernmost distribution range has been studied. We therefore investigated the potential for environmentally-dependent variability in lifespan in a population in Kirindy Forest, which has a much longer warm rainy season. While no adults were found after March in Ranobe, the disappearance of adults was delayed by several months in Kirindy. Our data also revealed sex-biased mortality, suggesting that females have a longevity advantage. Furthermore, we found that, after an unusually long previous rainy season, one female was capable of surviving until a second breeding season. Keeping F. labordi in cages under ambient conditions demonstrated that also males can also survive until the next season of activity under these conditions. Our study therefore revealed considerable variability in the extreme life history of this tetrapod that is linked to variation in ecological factors.
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  • Journal Article

    Biodiversity effects on ecosystem functioning in a 15-year grassland experiment: Patterns, mechanisms, and open questions 

    Weisser, Wolfgang W.; Roscher, Christiane; Meyer, Sebastian T.; Ebeling, Anne; Luo, Guangjuan; Allan, Eric; Beßler, Holger; Barnard, Romain L.; Buchmann, Nina; Buscot, François; et al.
    Engels, ChristofFischer, ChristineFischer, MarkusGessler, ArthurGleixner, GerdHalle, StefanHildebrandt, AnkeHillebrand, Helmutde Kroon, HansLange, MarkusLeimer, SophiaLe Roux, XavierMilcu, AlexandruMommer, LiesjeNiklaus, Pascal A.Oelmann, YvonneProulx, RaphaelRoy, JacquesScherber, ChristophScherer-Lorenzen, MichaelScheu, StefanTscharntke, TejaWachendorf, MichaelWagg, CameronWeigelt, AlexandraWilcke, WolfgangWirth, ChristianSchulze, Ernst-DetlefSchmid, BernhardEisenhauer, Nico
    Basic and Applied Ecology 2017; 23 p.1-73
    In the past two decades, a large number of studies have investigated the relationship between biodiversity and ecosystemfunctioning, most of which focussed on a limited set of ecosystem variables. The Jena Experiment was set up in 2002 toinvestigate the effects of plant diversity on element cycling and trophic interactions, using a multi-disciplinary approach. Here,we review the results of 15 years of research in the Jena Experiment, focussing on the effects of manipulating plant speciesrichness and plant functional richness. With more than 85,000 measures taken from the plant diversity plots, the Jena Experimenthas allowed answering fundamental questions important for functional biodiversity research.First, the question was how general the effect of plant species richness is, regarding the many different processes that take placein an ecosystem. About 45% of different types of ecosystem processes measured in the ‘main experiment’, where plant speciesrichness ranged from 1 to 60 species, were significantly affected by plant species richness, providing strong support for the viewthat biodiversity is a significant driver of ecosystem functioning. Many measures were not saturating at the 60-species level,but increased linearly with the logarithm of species richness. There was, however, great variability in the strength of responseamong different processes. One striking pattern was that many processes, in particular belowground processes, took severalyears to respond to the manipulation of plant species richness, showing that biodiversity experiments have to be long-term,to distinguish trends from transitory patterns. In addition, the results from the Jena Experiment provide further evidence thatdiversity begets stability, for example stability against invasion of plant species, but unexpectedly some results also suggestedthe opposite, e.g. when plant communities experience severe perturbations or elevated resource availability. This highlights theneed to revisit diversity–stability theory.Second, we explored whether individual plant species or individual plant functional groups, or biodiversity itself is moreimportant for ecosystem functioning, in particular biomass production. We found strong effects of individual species and plantfunctional groups on biomass production, yet these effects mostly occurred in addition to, but not instead of, effects of plantspecies richness.Third, the Jena Experiment assessed the effect of diversity on multitrophic interactions. The diversity of most organismsresponded positively to increases in plant species richness, and the effect was stronger for above- than for belowground organisms,and stronger for herbivores than for carnivores or detritivores. Thus, diversity begets diversity. In addition, the effect on organismicdiversity was stronger than the effect on species abundances.Fourth, the Jena Experiment aimed to assess the effect of diversity on N, P and C cycling and the water balance of theplots, separating between element input into the ecosystem, element turnover, element stocks, and output from the ecosystem. While inputs were generally less affected by plant species richness, measures of element stocks, turnover and output were oftenpositively affected by plant diversity, e.g. carbon storage strongly increased with increasing plant species richness. Variables ofthe N cycle responded less strongly to plant species richness than variables of the C cycle.Fifth, plant traits are often used to unravel mechanisms underlying the biodiversity–ecosystem functioning relationship. Inthe Jena Experiment, most investigated plant traits, both above- and belowground, were plastic and trait expression dependedon plant diversity in a complex way, suggesting limitation to using database traits for linking plant traits to particular functions.Sixth, plant diversity effects on ecosystem processes are often caused by plant diversity effects on species interactions.Analyses in the Jena Experiment including structural equation modelling suggest complex interactions that changed withdiversity, e.g. soil carbon storage and greenhouse gas emission were affected by changes in the composition and activity of thebelowground microbial community. Manipulation experiments, in which particular organisms, e.g. belowground invertebrates,were excluded from plots in split-plot experiments, supported the important role of the biotic component for element and waterfluxes.Seventh, the Jena Experiment aimed to put the results into the context of agricultural practices in managed grasslands. Theeffect of increasing plant species richness from 1 to 16 species on plant biomass was, in absolute terms, as strong as the effect ofa more intensive grassland management, using fertiliser and increasing mowing frequency. Potential bioenergy production fromhigh-diversity plots was similar to that of conventionally used energy crops. These results suggest that diverse ‘High NatureValue Grasslands’ are multifunctional and can deliver a range of ecosystem services including production-related services.A final task was to assess the importance of potential artefacts in biodiversity–ecosystem functioning relationships, causedby the weeding of the plant community to maintain plant species composition. While the effort (in hours) needed to weed aplot was often negatively related to plant species richness, species richness still affected the majority of ecosystem variables.Weeding also did not negatively affect monoculture performance; rather, monocultures deteriorated over time for a number ofbiological reasons, as shown in plant-soil feedback experiments.To summarize, the Jena Experiment has allowed for a comprehensive analysis of the functional role of biodiversity in anecosystem. A main challenge for future biodiversity research is to increase our mechanistic understanding of why the magnitudeof biodiversity effects differs among processes and contexts. It is likely that there will be no simple answer. For example, amongthe multitude of mechanisms suggested to underlie the positive plant species richness effect on biomass, some have receivedlimited support in the Jena Experiment, such as vertical root niche partitioning. However, others could not be rejected in targetedanalyses. Thus, from the current results in the Jena Experiment, it seems likely that the positive biodiversity effect results fromseveral mechanisms acting simultaneously in more diverse communities, such as reduced pathogen attack, the presence of moreplant growth promoting organisms, less seed limitation, and increased trait differences leading to complementarity in resourceuptake. Distinguishing between different mechanisms requires careful testing of competing hypotheses. Biodiversity researchhas matured such that predictive approaches testing particular mechanisms are now possible.
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  • Journal Article

    The Orphan Cytokine Receptor CRLF3 Emerged With the Origin of the Nervous System and Is a Neuroprotective Erythropoietin Receptor in Locusts 

    Hahn, Nina; Büschgens, Luca; Schwedhelm-Domeyer, Nicola; Bank, Sarah; Geurten, Bart R. H.; Neugebauer, Pia; Massih, Bita; Göpfert, Martin C.; Heinrich, Ralf
    Frontiers in Molecular Neuroscience 2019; 12: Art. 251
    The orphan cytokine receptor-like factor 3 (CRLF3) was identified as a neuroprotective erythropoietin receptor in locust neurons and emerged with the evolution of the eumetazoan nervous system. Human CRLF3 belongs to class I helical cytokine receptors that mediate pleiotropic cellular reactions to injury and diverse physiological challenges. It is expressed in various tissues including the central nervous system but its ligand remains unidentified. A CRLF3 ortholog in the holometabolous beetle Tribolium castaneum was recently shown to induce anti-apoptotic mechanisms upon stimulation with human recombinant erythropoietin. To test the hypothesis that CRLF3 represents an ancient cell-protective receptor for erythropoietin-like cytokines, we investigated its presence across metazoan species. Furthermore, we examined CRLF3 expression and function in the hemimetabolous insect Locusta migratoria. Phylogenetic analysis of CRLF3 sequences indicated that CRLF3 is absent in Porifera, Placozoa and Ctenophora, all lacking the traditional nervous system. However, it is present in all major eumetazoan groups ranging from cnidarians over protostomians to mammals. The CRLF3 sequence is highly conserved and abundant amongst vertebrates. In contrast, relatively few invertebrates express CRLF3 and these sequences show greater variability, suggesting frequent loss due to low functional importance. In L. migratoria, we identified the transcript Lm-crlf3 by RACE-PCR and detected its expression in locust brain, skeletal muscle and hemocytes. These findings correspond to the ubiquitous expression of crlf3 in mammalian tissues. We demonstrate that the sole addition of double-stranded RNA to the culture medium (called soaking RNA interference) specifically interferes with protein expression in locust primary brain cell cultures. This technique was used to knock down Lm-crlf3 expression and to abolish its physiological function. We confirmed that recombinant human erythropoietin rescues locust brain neurons from hypoxia-induced apoptosis and showed that this neuroprotective effect is absent after knocking down Lm-crlf3. Our results affirm the erythropoietin-induced neuroprotective function of CRLF3 in a second insect species from a different taxonomic group. They suggest that the phylogenetically conserved CRLF3 receptor may function as a cell protective receptor for erythropoietin or a structurally related cytokine also in other animals including vertebrate and mammalian species.
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  • Journal Article

    Variants of the Bacillus subtilis LysR-Type Regulator GltC With Altered Activator and Repressor Function 

    Dormeyer, Miriam; Lentes, Sabine; Richts, Björn; Heermann, Ralf; Ischebeck, Till; Commichau, Fabian M.
    Frontiers in Microbiology 2019; 10: Art. 2321
    The Gram-positive soil bacterium Bacillus subtilis relies on the glutamine synthetase and the glutamate synthase for glutamate biosynthesis from ammonium and 2-oxoglutarate. During growth with the carbon source glucose, the LysR-type transcriptional regulator GltC activates the expression of the gltAB glutamate synthase genes. With excess of intracellular glutamate, the gltAB genes are not transcribed because the glutamate-degrading glutamate dehydrogenases (GDHs) inhibit GltC. Previous in vitro studies revealed that 2-oxoglutarate and glutamate stimulate the activator and repressor function, respectively, of GltC. Here, we have isolated GltC variants with enhanced activator or repressor function. The majority of the GltC variants with enhanced activator function differentially responded to the GDHs and to glutamate. The GltC variants with enhanced repressor function were still capable of activating the PgltA promoter in the absence of a GDH. Using PgltA promoter variants (PgltA∗) that are active independent of GltC, we show that the wild type GltC and the GltC variants with enhanced repressor function inactivate PgltA∗ promoters in the presence of the native GDHs. These findings suggest that GltC may also act as a repressor of the gltAB genes in vivo. We discuss a model combining previous models that were derived from in vivo and in vitro experiments.
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  • Journal Article

    Strategic deployment of feature-based attentional gain in primate visual cortex 

    Kozyrev, Vladislav; Daliri, Mohammad Reza; Schwedhelm, Philipp; Treue, Stefan
    PLOS Biology 2019; 17(8): Art. e3000387
    Attending to visual stimuli enhances the gain of those neurons in primate visual cortex that preferentially respond to the matching locations and features (on-target gain). Although this is well suited to enhance the neuronal representation of attended stimuli, it is nonoptimal under difficult discrimination conditions, as in the presence of similar distractors. In such cases, directing attention to neighboring neuronal populations (off-target gain) has been shown to be the most efficient strategy, but although such a strategic deployment of attention has been shown behaviorally, its underlying neural mechanisms are unknown. Here, we investigated how attention affects the population responses of neurons in the middle temporal (MT) visual area of rhesus monkeys to bidirectional movement inside the neurons' receptive field (RF). The monkeys were trained to focus their attention onto the fixation spot or to detect a direction or speed change in one of the motion directions (the "target"), ignoring the distractor motion. Population activity profiles were determined by systematically varying the patterns' directions while maintaining a constant angle between them. As expected, the response profiles show a peak for each of the 2 motion directions. Switching spatial attention from the fixation spot into the RF enhanced the peak representing the attended stimulus and suppressed the distractor representation. Importantly, the population data show a direction-dependent attentional modulation that does not peak at the target feature but rather along the slopes of the activity profile representing the target direction. Our results show that attentional gains are strategically deployed to optimize the discriminability of target stimuli, in line with an optimal gain mechanism proposed by Navalpakkam and Itti.
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  • Journal Article

    Modulation of HIV-1 Gag/Gag-Pol frameshifting by tRNA abundance 

    Korniy, Natalia; Goyal, Akanksha; Hoffmann, Markus; Samatova, Ekaterina; Peske, Frank; Pöhlmann, Stefan; Rodnina, Marina V.
    Nucleic Acids Research 2019; 47(10) p.5210-5222
    A hallmark of translation in human immunodeficiency virus type 1 (HIV-1) is a -1 programmed ribosome frameshifting event that produces the Gag-Pol fusion polyprotein. The constant Gag to Gag-Pol ratio is essential for the virion structure and infectivity. Here we show that the frameshifting efficiency is modulated by Leu-tRNALeu that reads the UUA codon at the mRNA slippery site. This tRNALeu isoacceptor is particularly rare in human cell lines derived from T-lymphocytes, the cells that are targeted by HIV-1. When UUA decoding is delayed, the frameshifting follows an alternative route, which maintains the Gag to Gag-Pol ratio constant. A second potential slippery site downstream of the first one is normally inefficient but can also support -1-frameshifting when altered by a compensatory resistance mutation in response to current antiviral drug therapy. Together these different regimes allow the virus to maintain a constant -1-frameshifting efficiency to ensure successful virus propagation.
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  • Journal Article

    Long-tailed macaques extract statistical information from repeated types of events to make rational decisions under uncertainty 

    Placì, Sarah; Padberg, Marie; Rakoczy, Hannes; Fischer, Julia
    Scientific Reports 2019; 9(1): Art. 12107
    Human children and apes seem to be intuitive statisticians when making predictions from populations of objects to randomly drawn samples, whereas monkeys seem not to be. Statistical reasoning can also be investigated in tasks in which the probabilities of different possibilities must be inferred from relative frequencies of events, but little is known about the performance of nonhuman primates in such tasks. In the current study, we investigated whether long-tailed macaques extract statistical information from repeated types of events to make predictions under uncertainty. In each experiment, monkeys first experienced the probability of rewards associated with different factors separately. In a subsequent test trial, monkeys could then choose between the different factors presented simultaneously. In Experiment 1, we tested whether long-tailed macaques relied on probabilities and not on a comparison of absolute quantities to make predictions. In Experiment 2 and 3 we varied the nature of the predictive factors and the complexity of the covariation structure between rewards and factors. Results indicate that long-tailed macaques extract statistical information from repeated types of events to make predictions and rational decisions under uncertainty, in more or less complex scenarios. These findings suggest that the presentation format affects the monkeys' statistical reasoning abilities.
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  • Journal Article

    Slow presynaptic mechanisms that mediate adaptation in the olfactory pathway of Drosophila 

    Martelli, Carlotta; Fiala, André
    eLife 2019; 8: Art. e43735
    The olfactory system encodes odor stimuli as combinatorial activity of populations of neurons whose response depends on stimulus history. How and on which timescales previous stimuli affect these combinatorial representations remains unclear. We use in vivo optical imaging in Drosophila to analyze sensory adaptation at the first synaptic step along the olfactory pathway. We show that calcium signals in the axon terminals of olfactory receptor neurons (ORNs) do not follow the same adaptive properties as the firing activity measured at the antenna. While ORNs calcium responses are sustained on long timescales, calcium signals in the postsynaptic projection neurons (PNs) adapt within tens of seconds. We propose that this slow component of the postsynaptic response is mediated by a slow presynaptic depression of vesicle release and enables the combinatorial population activity of PNs to adjust to the mean and variance of fluctuating odor stimuli.
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  • Journal Article

    Nuclear Pre-snRNA Export Is an Essential Quality Assurance Mechanism for Functional Spliceosomes 

    Becker, Daniel; Hirsch, Anna Greta; Bender, Lysann; Lingner, Thomas; Salinas, Gabriela; Krebber, Heike
    Cell Reports 2019; 27(11) p.3199-3214.e3
    Removal of introns from pre-mRNAs is an essential step in eukaryotic gene expression, mediated by spliceosomes that contain snRNAs as key components. Although snRNAs are transcribed in the nucleus and function in the same compartment, all except U6 shuttle to the cytoplasm. Surprisingly, the physiological relevance for shuttling is unclear, in particular because the snRNAs in Saccharomyces cerevisiae were reported to remain nuclear. Here, we show that all yeast pre-snRNAs including U6 undergo a stepwise maturation process after nuclear export by Mex67 and Xpo1. Sm- and Lsm-ring attachment occurs in the cytoplasm and is important for the snRNA re-import, mediated by Cse1 and Mtr10. Finally, nuclear pre-snRNA cleavage and trimethylation of the 5'-cap finalizes shuttling. Importantly, preventing pre-snRNAs from being exported or processed results in faulty spliceosome assembly and subsequent genome-wide splicing defects. Thus, pre-snRNA export is obligatory for functional splicing and resembles an essential evolutionarily conserved quality assurance step
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  • Journal Article

    Land Use Change and Water Quality Use for Irrigation Alters Drylands Soil Fungal Community in the Mezquital Valley, Mexico. 

    Lüneberg, Kathia; Schneider, Dominik; Brinkmann, Nicole; Siebe, Christina; Daniel, Rolf
    Frontiers in Microbiology 2019; 10: Art. 1220
    Soil fungal communities provide important ecosystem services, however, some soil borne representatives damage agricultural productivity. Composition under land-use change scenarios, especially in drylands, is rarely studied. Here, the soil fungal community composition and diversity of natural shrubland was analyzed and compared with agricultural systems irrigated with different water quality, namely rain, fresh water, dam-stored, and untreated wastewater. Superficial soil samples were collected during the dry and rainy seasons. Amplicon-based sequencing of the ITS2 region was performed on total DNA extractions and used the amplicon sequence variants to predict specific fungal trophic modes with FUNGuild. Additionally, we screened for potential pathogens of crops and humans and assessed potential risks. Fungal diversity and richness were highest in shrubland and least in the wastewater-irrigated soil. Soil moisture together with soil pH and exchangeable sodium were the strongest drivers of the fungal community. The abundance of saprophytic fungi remained constant among the land use systems, while symbiotic and pathogenic fungi of plants and animals had the lowest abundance in soil irrigated with untreated wastewater. We found lineage-specific adaptations to each land use system: fungal families associated to shrubland, rainfed and part of the freshwater were adapted to drought, hence sensitive to exchangeable sodium content and most of them to N and P content. Taxa associated to freshwater, dam wastewater and untreated wastewater irrigated systems show the opposite trend. Additionally, we identified potentially harmful human pathogens that might be a health risk for the population.
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  • Journal Article

    Routing information flow by separate neural synchrony frequencies allows for “functionally labeled lines” in higher primate cortex 

    Khamechian, Mohammad Bagher; Kozyrev, Vladislav; Treue, Stefan; Esghaei, Moein; Daliri, Mohammad Reza
    Proceedings of the National Academy of Sciences 2019; 116(25) p.12506-12515
    Efficient transfer of sensory information to higher (motor or associative) areas in primate visual cortical areas is crucial for transforming sensory input into behavioral actions. Dynamically increasing the level of coordination between single neurons has been suggested as an important contributor to this efficiency. We propose that differences between the functional coordination in different visual pathways might be used to unambiguously identify the source of input to the higher areas, ensuring a proper routing of the information flow. Here we determined the level of coordination between neurons in area MT in macaque visual cortex in a visual attention task via the strength of synchronization between the neurons' spike timing relative to the phase of oscillatory activities in local field potentials. In contrast to reports on the ventral visual pathway, we observed the synchrony of spikes only in the range of high gamma (180 to 220 Hz), rather than gamma (40 to 70 Hz) (as reported previously) to predict the animal's reaction speed. This supports a mechanistic role of the phase of high-gamma oscillatory activity in dynamically modulating the efficiency of neuronal information transfer. In addition, for inputs to higher cortical areas converging from the dorsal and ventral pathway, the distinct frequency bands of these inputs can be leveraged to preserve the identity of the input source. In this way source-specific oscillatory activity in primate cortex can serve to establish and maintain "functionally labeled lines" for dynamically adjusting cortical information transfer and multiplexing converging sensory signals.
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  • Journal Article

    Algal-fungal symbiosis leads to photosynthetic mycelium 

    Du, Zhi-Yan; Zienkiewicz, Krzysztof; Vande Pol, Natalie; Ostrom, Nathaniel E; Benning, Christoph; Bonito, Gregory M
    eLife 2019; 8
    Mutualistic interactions between free-living algae and fungi are widespread in nature and are hypothesized to have facilitated the evolution of land plants and lichens. In all known algal-fungal mutualisms, including lichens, algal cells remain external to fungal cells. Here, we report on an algal-fungal interaction in which Nannochloropsis oceanica algal cells become internalized within the hyphae of the fungus Mortierella elongata. This apparent symbiosis begins with close physical contact and nutrient exchange, including carbon and nitrogen transfer between fungal and algal cells as demonstrated by isotope tracer experiments. This mutualism appears to be stable, as both partners remain physiologically active over months of co-cultivation, leading to the eventual internalization of photosynthetic algal cells, which persist to function, grow and divide within fungal hyphae. Nannochloropsis and Mortierella are biotechnologically important species for lipids and biofuel production, with available genomes and molecular tool kits. Based on the current observations, they provide unique opportunities for studying fungal-algal mutualisms including mechanisms leading to endosymbiosis.
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  • Journal Article

    A framework of most effective practices in protecting human assets from predators 

    Khorozyan, Igor; Waltert, Matthias
    Human Dimensions of Wildlife 2019; 24(4) p.380-394
    Widespread damage by large mammalian predators to human assets (e.g., livestock, crops, neighborhood safety) requires the application of non-invasive (i.e., without direct contact with predators) and targeted interventions to promote predator conservation and local livelihoods. We compiled 117 cases from 23 countries describing the effectiveness of 12 interventions designed to protect human assets from 21 predators. We found: (a) the most effective interventions were electric fences, guarding animals, calving control, and physical deterrents (protective collars and shocking devices); (b) the most effectively protected asset was livestock; and (c) the most effective interventions being used were to protect assets from cheetahs (Acinonyx jubatus), Eurasian lynx (Lynx lynx), gray wolves (Canis lupus), and lions (Panthera leo). In all of these cases, the relative risk of damage was reduced by 50–100%. We combined these outcomes into a novel framework of most effective practices and discussed its structure, practicality, and future applications.
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  • Journal Article

    Marshland restoration benefits Collembola recruitment: a long-term chronosequence study in Sanjiang mire marshland, China 

    Dou, Yongjing; Zhang, Bing; Sun, Xin; Chang, Liang; Wu, Donghui
    PeerJ 2019; 7: Art. e7198
    To examine the biodiversity restoration of marshlands after human-induced disturbances, a long-term chronosequence study of Collembola communities was completed that included cultivated treatment (marshes with 15 years of soybean cultivation; CU15), two restored treatments (with 6 and 12 years of agricultural abandonment; RE06 and RE12, respectively), and an intact marshland (IM) as a reference in the Sanjiang Plain, Northeastern China. Changes in the soil properties and Collembola communities under different treatments were analyzed. Soil parameters (i.e., soil organic carbon, available N, P and K, soil moisture) significantly increased from the cultivated treatment to the 6-year agricultural abandoned, and then 12-year agricultural abandoned treatment, indicating that the degraded soil began to recover after agricultural abandonment. The density, species richness and diversity of Collembola in RE12 were significantly higher than in RE06 and CU15, and even surpass the IM, indicating marshland restoration (after 12 years of agricultural abandonment) benefited recruitment and reconstruction of Collembola community. We found soil surface-dwelling Collembola recovered faster than eu-edaphic species, that is probably due to some common traits (i.e., parthenogenesis and fast dispersal) between epi- and hemi-edaphic species. The changes in the vegetation and soil properties during long-term soybean cultivation and agricultural abandonment were the key factors affecting the composition, density, and species richness of soil
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  • Journal Article

    Membrane Lipids, Waxes and Oxylipins in the Moss Model Organism Physcomitrella patens 

    Resemann, Hanno C.; Lewandowska, Milena; Gömann, Jasmin; Feussner, Ivo
    Plant and Cell Physiology 2019; 60(6) p.1166-1175
    The moss Physcomitrella patens receives increased scientific interest since its genome was sequenced a decade ago. As a bryophyte, it represents the first group of plants that evolved in a terrestrial habitat still without a vascular system that developed later in tracheophytes. It is easily transformable via homologous recombination, which enables the formation of targeted loss-of-function mutants. Even though genetics, development and life cycle in Physcomitrella are well studied nowadays, research on lipids in Physcomitrella is still underdeveloped. This review aims on presenting an overview on the state of the art of lipid research with a focus on membrane lipids, surface lipids and oxylipins. We discuss in this review that Physcomitrella possesses very interesting features regarding its membrane lipids. Here, the presence of very-long-chain polyunsaturated fatty acids (VLC-PUFA) still shows a closer similarity to marine microalgae than to vascular plants. Unlike algae, Physcomitrella has a cuticle comparable to vascular plants composed of cutin and waxes. The presence of VLC-PUFA in Physcomitrella also leads to a greater variability of signaling lipids even though the phytohormone jasmonic acid is not present in this organism, which is different to vascular plants. In summary, the research on lipids in Physcomitrella is still in its infancy, especially considering membrane lipids. We hope that this review will help to promote the further advancement of lipid research in this important model organism in the future, so we can better understand how lipids are involved in the evolution of land plants.
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  • Journal Article

    Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors 

    Yus, Eva; Lloréns-Rico, Verónica; Martínez, Sira; Gallo, Carolina; Eilers, Hinnerk; Blötz, Cedric; Stülke, Jörg; Lluch-Senar, Maria; Serrano, Luis
    Cell Systems 2019; 9(2) p.143-145: Art. 158.e13
    Here, we determined the relative importance of different transcriptional mechanisms in the genome-reduced bacterium Mycoplasma pneumoniae, by employing an array of experimental techniques under multiple genetic and environmental perturbations. Of the 143 genes tested (21% of the bacterium's annotated proteins), only 55% showed an altered phenotype, highlighting the robustness of biological systems. We identified nine transcription factors (TFs) and their targets, representing 43% of the genome, and 16 regulators that indirectly affect transcription. Only 20% of transcriptional regulation is mediated by canonical TFs when responding to perturbations. Using a Random Forest, we quantified the non-redundant contribution of different mechanisms such as supercoiling, metabolic control, RNA degradation, and chromosome topology to transcriptional changes. Model-predicted gene changes correlate well with experimental data in 95% of the tested perturbations, explaining up to 70% of the total variance when also considering noise. This analysis highlights the importance of considering non-TF-mediated regulation when engineering bacteria.
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  • Journal Article

    One size fits all? Relationships among group size, health, and ecology indicate a lack of an optimal group size in a wild lemur population 

    Rudolph, Katja; Fichtel, Claudia; Schneider, Dominik; Heistermann, Michael; Koch, Flávia; Daniel, Rolf; Kappeler, Peter M.
    Behavioral Ecology and Sociobiology 2019; 73(9): Art. 132
    Group size is a key component of sociality and can affect individual health and fitness. However, proximate links explaining this relationship remain poorly understood, partly because previous studies neglected potential confounding effects of ecological factors. Here, we correlated group size with various measures of health while controlling for measures of seasonality and habitat quality, to explore trade-offs related to group living in a mainly folivorous primate—Verreaux’s sifakas (Propithecus verreauxi). Over a course of 2 years, we studied 42 individuals of 7 differently sized groups (range 2–10) and combined measures of faecal glucocorticoid metabolites (n > 2300 samples), parasitism (n > 500 samples), ranging and activity patterns, together with estimates of habitat quality (measures of ~ 7000 feeding trees). None of our measures was correlated with group size, while seasonality, but not habitat quality, impacted almost all examined variables. We conclude that group size alone might be insufficient to explain patterns in the sociality-health nexus or that the small range of group sizes in this species does not induce effects suggested for species living in larger groups. An optimal group size balancing the advantages and disadvantages of living in differently sized groups may not exist for Verreaux’s sifakas. Our results do not support predictions of the ecological constraints hypothesis or the optimal group size hypothesis as they may only account for species limited in group size by ecological factors—a condition that may not apply to the majority of folivorous mammals, which seem to be limited by social factors.
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  • Journal Article

    Self-Efficacy Beliefs of Interdisciplinary Science Teaching (SElf-ST) Instrument: Drafting a Theory-based Measurement 

    Handtke, Kevin; Bögeholz, Susanne
    Education Sciences 2019; 9(4): Art. 247
    Interdisciplinary science teaching is an issue in various countries. One example in Europe is Germany, especially regarding comprehensive schools. At the same time, German teacher education is primarily subject-specific. An examination of data on self-efficacy beliefs is helpful for understanding the qualifications of teachers for interdisciplinary science. Previous measurement instruments for teaching biology, chemistry, physics, and science lack a literature-based, theorybased, or curricular-valid measurement or a systematic obstacle to overcome. Thus, to meet these requirements, this research developed a draft for a new instrument to measure self-efficacy beliefs of interdisciplinary science teaching (SElf-ST). As the theoretical base, the instrument operationalizes a model of pedagogical content knowledge for teaching science and adapts it to selfefficacy beliefs. In a cross-sectional study (N = 114 pre-service and trainee teachers), a ten-factorsolution for self-efficacy beliefs resulted from an exploratory factor analysis (Kaiser–Meyer–Olkincriterion = 0.858, α = 0.70–0.86). Nine factors are linked to the theoretical model. An additional tenth factor emerged: Teaching Ethically Relevant Issues. Nine factors show low and medium correlations with teaching experience. Eight factors show at least low correlations with self-rated content knowledge in no less than one of the three subjects. In general, science-specific factors show rather low or medium correlations, and generic factors (e.g., Applying Media, and Applying Methods of Evaluation) show low or no correlations. This result is in accordance with the context specificity of self-efficacy beliefs. These results meet most of the research expectations and provide initial indications of the concurrent, curricular, and divergent validity of the SElf-ST instrument. The paper argues for the development of a new, theory-based instrument to measure self-efficacy beliefs of interdisciplinary science teaching.
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  • Journal Article

    Bacterial succession along a sediment porewater gradient at Lake Neusiedl in Austria 

    von Hoyningen-Huene, Avril Jean Elisabeth; Schneider, Dominik; Fussmann, Dario; Reimer, Andreas; Arp, Gernot; Daniel, Rolf
    Scientific Data 2019; 6(1): Art. 163
    We provide bacterial 16S rRNA community and hydrochemical data from water and sediments of Lake Neusiedl, Austria. The sediments were retrieved at 5 cm intervals from 30-40 cm push cores. The lake water community was recovered by filtration through a 3.0/0.2 µm filter sandwich. For 16S rRNA gene amplicon-based community profiling, DNA was extracted from the sediment and filters and the bacterial V3-V4 regions were amplified and sequenced using a MiSeq instrument (Illumina). The reads were quality-filtered and processed using open source bioinformatic tools, such as PEAR, cutadapt and VSEARCH. The taxonomy was assigned against the SILVA SSU NR 132 database. The bacterial community structure was visualised in relation to water and porewater chemistry data. The bacterial community in the water column is distinct from the sediment. The most abundant phyla in the sediment shift from Proteobacteria to Chloroflexota (formerly Chloroflexi). Ammonium and total alkalinity increase while sulphate concentrations in the porewater decrease. The provided data are of interest for studies targeting biogeochemical cycling in lake sediments.
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