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    Word-object and action-object association learning across early development 

    Eiteljoerge, Sarah F. V.; Adam, Maurits; Elsner, Birgit; Mani, Nivedita
    PLOS ONE 2019; 14(8): Art. e0220317
    Successful communication often involves comprehension of both spoken language and observed actions with and without objects. Even very young infants can learn associations between actions and objects as well as between words and objects. However, in daily life, children are usually confronted with both kinds of input simultaneously. Choosing the critical information to attend to in such situations might help children structure the input, and thereby, allow for successful learning. In the current study, we therefore, investigated the developmental time course of children's and adults' word and action learning when given the opportunity to learn both word-object and action-object associations for the same object. All participants went through a learning phase and a test phase. In the learning phase, they were presented with two novel objects which were associated with a distinct novel name (e.g., "Look, a Tanu") and a distinct novel action (e.g., moving up and down while tilting sideways). In the test phase, participants were presented with both objects on screen in a baseline phase, then either heard one of the two labels or saw one of the two actions in a prime phase, and then saw the two objects again on screen in a recognition phase. Throughout the trial, participants' target looking was recorded to investigate whether participants looked at the target object upon hearing its label or seeing its action, and thus, would show learning of the word-object and action-object associations. Growth curve analyses revealed that 12-month-olds showed modest learning of action-object associations, 36-month-olds learned word-object associations, and adults learned word-object and action-object associations. These results highlight how children attend to the different information types from the two modalities through which communication is addressed to them. Over time, with increased exposure to systematic word-object mappings, children attend less to action-object mappings, with the latter potentially being mediated by word-object learning even in adulthood. Thus, choosing between different kinds of input that may be more relevant in their rich environment encompassing different modalities might help learning at different points in development.
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    CCDC42 Localizes to Manchette, HTCA and Tail and Interacts With ODF1 and ODF2 in the Formation of the Male Germ Cell Cytoskeleton 

    Tapia Contreras, Constanza; Hoyer-Fender, Sigrid
    Frontiers in Cell and Developmental Biology 2019; 7: Art. 151
    Terminal differentiation of male germ cells into functional spermatozoa requires shaping and condensation of the nucleus as well as the formation of sperm-specific structures. A transient microtubular structure, the manchette, is mandatory for sperm head shaping and the development of the connecting piece and the sperm tail. The connecting piece or head-to-tail coupling apparatus (HTCA) mediates the tight linkage of sperm head and tail causing decapitation and infertility when faulty. Using mice as the experimental model, several proteins have already been identified affecting the linkage complex, manchette or tail formation when missing. However, our current knowledge is far too rudimentary to even draft an interacting protein network. Depletion of the major outer dense fiber protein 1 (ODF1) mainly caused decapitation and male infertility but validated binding partners collaborating in the formation of sperm-specific structures are largely unknown. Amongst all candidate proteins affecting the HTCA when missing, the structural protein CCDC42 attracted our attention. The coiled-coil domain containing 42 (CCDC42) is important for HTCA and sperm tail formation but is otherwise largely uncharacterized. We show here that CCDC42 is expressed in spermatids and localizes to the manchette, the connecting piece and the tail. Beyond that, we show that CCDC42 is not restricted to male germ cells but is also expressed in somatic cells in which it localizes to the centrosome. Although centrosomal and sperm tail location seems to be irrespective of ODF1 we asked whether both proteins may form an interacting network in the male germ cell.We additionally considered ODF2, a prevalent protein involved in the formation of spermatid-specific cytoskeletal structures, as a putative binding partner. Our data depict for the first time the subcellular location of CCDC42 in spermatids and deepen our knowledge about the composition of the spermatid/sperm-specific structures. The presence of CCDC42 in the centrosome of somatic cells together with the obvious restricted male-specific phenotype when missing strongly argues for a compensatory function by other still unknown proteins most likely of the same family.
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    Small Neotropical primates promote the natural regeneration of anthropogenically disturbed areas 

    Heymann, Eckhard W.; Culot, Laurence; Knogge, Christoph; Smith, Andrew C.; Tirado Herrera, Emérita R.; Müller, Britta; Stojan-Dolar, Mojca; Lledo Ferrer, Yvan; Kubisch, Petra; Kupsch, Denis; et al.
    Slana, DarjaKoopmann, Mareike LenaZiegenhagen, BirgitBialozyt, RonaldMengel, ChristinaHambuckers, JulienHeer, Katrin
    Scientific Reports 2019; 9(1): Art. 10356
    Increasingly large proportions of tropical forests are anthropogenically disturbed. Where natural regeneration is possible at all, it requires the input of plant seeds through seed dispersal from the forest matrix. Zoochorous seed dispersal - the major seed dispersal mode for woody plants in tropical forests - is particularly important for natural regeneration. In this study, covering a period of more than 20 years, we show that small New World primates, the tamarins Saguinus mystax and Leontocebus nigrifrons, increase their use of an anthropogenically disturbed area over time and disperse seeds from primary forest tree species into this area. Through monitoring the fate of seeds and through parentage analyses of seedlings of the legume Parkia panurensis from the disturbed area and candidate parents from the primary forest matrix, we show that tamarin seed dispersal is effective and contributes to the natural regeneration of the disturbed area.
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    Consistency of co-occurring actions influences young children’s word learning 

    Eiteljoerge, Sarah F. V.; Adam, Maurits; Elsner, Birgit; Mani, Nivedita
    Royal Society Open Science 2019; 6(8): Art. 190097
    Communication with young children is often multimodal in nature, involving, for example, language and actions. The simultaneous presentation of information from both domains may boost language learning by highlighting the connection between an object and a word, owing to temporal overlap in the presentation of multimodal input. However, the overlap is not merely temporal but can also covary in the extent to which particular actions co-occur with particular words and objects, e.g. carers typically produce a hopping action when talking about rabbits and a snapping action for crocodiles. The frequency with which actions and words co-occurs in the presence of the referents of these words may also impact young children’s word learning. We, therefore, examined the extent to which consistency in the co-occurrence of particular actions and words impacted children’s learning of novel word–object associations. Children (18 months, 30 months and 36–48 months) and adults were presented with two novel objects and heard their novel labels while different actions were performed on these objects, such that the particular actions and word–object pairings always co-occurred (Consistent group) or varied across trials (Inconsistent group). At test, participants saw both objects and heard one of the labels to examine whether participants recognized the target object upon hearing its label. Growth curve models revealed that 18-month-olds did not learn words for objects in either condition, and 30-month-old and 36- to 48-month-old children learned words for objects only in the Consistent condition, in contrast to adults who learned words for objects independent of the actions presented. Thus, consistency in the multimodal input influenced word learning in early childhood but not in adulthood. In terms of a dynamic systems account of word learning, our study shows how multimodal learning settings interact with the child’s perceptual abilities to shape the learning experience.
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    Origin and Consequences of Chromosomal Inversions in the virilis Group of Drosophila 

    Reis, Micael; Vieira, Cristina P.; Lata, Rodrigo; Posnien, Nico; Vieira, Jorge
    Genome Biology and Evolution 2018; 10(12) p.3152-3166
    In Drosophila, large variations in rearrangement rate have been reported among different lineages and among Muller's elements. Nevertheless, the mechanisms that are involved in the generation of inversions, their increase in frequency, as well as their impact on the genome are not completely understood. This is in part due to the lack of comparative studies on species distantly related to Drosophila melanogaster. Therefore, we sequenced and assembled the genomes of two species of the virilis phylad (Drosophila novamexicana [15010-1031.00] and Drosophila americana [SF12]), which are diverging from D. melanogaster for more than 40 Myr. Based on these data, we identified the precise location of six novel inversion breakpoints. A molecular characterization provided clear evidence that DAIBAM (a miniature inverted-repeat transposable element) was involved in the generation of eight out of the nine inversions identified. In contrast to what has been previously reported for D. melanogaster and close relatives, ectopic recombination is thus the prevalent mechanism of generating inversions in species of the virilis phylad. Using pool-sequencing data for three populations of D. americana, we also show that common polymorphic inversions create a high degree of genetic differentiation between populations for chromosomes X, 4, and 5 over large physical distances. We did not find statistically significant differences in expression levels between D. americana (SF12) and D. novamexicana (15010-1031.00) strains for the three genes surveyed (CG9588, Fig 4, and fab1) flanking three inversion breakpoints.
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    Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies 

    Buchberger; Reis; Lu; Posnien
    Genes 2019; 10(7): Art. 492
    Research in various fields of evolutionary biology has shown that divergence in gene expression is a key driver for phenotypic evolution. An exceptional contribution of cis-regulatory divergence has been found to contribute to morphological diversification. In the light of these findings, the analysis of genome-wide expression data has become one of the central tools to link genotype and phenotype information on a more mechanistic level. However, in many studies, especially if general conclusions are drawn from such data, a key feature of gene regulation is often neglected. With our article, we want to raise awareness that gene regulation and thus gene expression is highly context dependent. Genes show tissue- and stage-specific expression. We argue that the regulatory context must be considered in comparative expression studies.
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    Prokaryotic Diversity and Community Patterns in Antarctic Continental Shelf Sponges 

    Steinert, Georg; Wemheuer, Bernd; Janussen, Dorte; Erpenbeck, Dirk; Daniel, Rolf; Simon, Meinhard; Brinkhoff, Thorsten; Schupp, Peter J.
    Frontiers in Marine Science 2019; 6: Art. 297
    Marine sponges (Phylum Porifera) are globally distributed within marine and freshwater ecosystems. In addition, sponges host dense and diverse prokaryotic communities, which are potential sources of novel bioactive metabolites and other complex compounds. Those sponge-derived natural products can span a broad spectrum of bioactivities, from antibacterial and antifungal to antitumor and antiviral compounds. However, most analyses concerning sponge-associated prokaryotes have mainly focused on conveniently accessible relatively shallow sampling locations for sponges. Hence, knowledge of community composition, host-relatedness and biotechnological potential of prokaryotic associations in temperate and cold-water sponges from greater depths (mesophotic to mesopelagic zones) is still scarce. Therefore, we analyzed the prokaryotic community diversity of four phylogenetically divergent sponge taxa from mesophotic to mesopelagic depths of Antarctic shelf at different depths and locations in the region of the South Shetland Islands using 16S rRNA gene ampliconbased sequencing. In addition, we predicted functional profiles applying Tax4Fun from metagenomic 16S rRNA gene data to estimate their biotechnological capability and possible roles as sources of novel bioactive compounds. We found indications that cold and deep-water sponges exhibit host-specific prokaryotic communities, despite different sampling sites and depths. Functional prediction analysis suggests that the associated prokaryotes may enhance the roles of sponges in biodegradation processes of xenobiotics and their involvement in the biosynthesis of secondary metabolites.
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    Isotomidae of Japan and Asiatic part of Russia. II. The genus Tetracanthella of the Far East 

    Potapov, Mikhail; Brinev, Alexey; Sun, Xin
    ZooKeys 2019; 855 p.31-54: Art.
    The paper considers new and little-known species of the genus Tetracanthella distributed in the Far East of Russia and in Japan. Sensillar chaetotaxy and labial palp, two less known morphological characters for the genus, are discussed. Two new species T.annulata sp. nov. and T.tardoki sp. nov. are described; T.manschurica Kutyreva, 1980 and T czernovae Kutyreva, 1980 are redescribed. For the latter species a lectotype and paralectotypes are designated. Remarks are provided for T.sylvatica Yosii, 1939. A second undescribed species is recorded for Japan. New records for T.orientalis Martynova, 1977 and T.sibirica Deharveng, 1987 are listed.
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    Effects of root and leaf litter identity and diversity on oribatid mite abundance, species richness and community composition 

    Bluhm, Christian; Butenschoen, Olaf; Maraun, Mark; Scheu, Stefan
    PLOS ONE 2019; 14(7): Art. e0219166
    Habitat heterogeneity is an important driver of aboveground species diversity but few studies have investigated effects on soil communities. Trees shape their surrounding by both leaf litter and roots generating small scale heterogeneity and potentially governing community patterns of soil organisms. To assess the role of vegetation for the soil fauna, we studied whether tree species (Fagus sylvatica L., Acer pseudoplatanus L., Fraxinus excelsior L., Tilia cordata Mill.), markedly differing in leaf litter quality and root associated mycorrhizal symbionts, affect oribatid mite communities by shaping below- and aboveground resources and habitat complexity and availability. Oribatid mite abundance, species richness, community structure and the proportion of litter living and parthenogenetic individuals were analyzed and related to microbial biomass and the amount of remaining litter mass. Although leaf litter species with higher nutritional values decomposed considerably faster, microbial biomass only slightly differed between leaf litter species. Neither root species nor leaf litter species affected abundance, species richness or community structure of oribatid mites. However, root species had an effect on the proportion of parthenogenetic individuals with increased proportions in the presence of beech roots. Overall, the results suggest that identity and diversity of vegetation via leaf litter or roots are of minor importance for structuring oribatid mite communities of a temperate forest ecosystem.
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    First Insights Into Bacterial Gastrointestinal Tract Communities of the Eurasian Beaver (Castor fiber) 

    Pratama, Rahadian; Schneider, Dominik; Böer, Tim; Daniel, Rolf
    Frontiers in Microbiology 2019; 10: Art. 1646
    The Eurasian or European beaver (Castor fiber) is the second-largest living rodent after the capybara. It is a semi-aquatic animal known for building dams and lodges. They strictly feed on lignocellulose-rich plants and correspondingly harbor cellulolytic microbial communities in their digestive tract. In this study, the bacterial community composition, diversity, and functional profile of different gut compartments ranging from stomach to colon have been explored. A total of 277 bacterial operational taxonomic units (OTUs) at species level were obtained from the gut systems of two males (juvenile and subadult) and one subadult female beaver. In general, cecum and colon are dominated by Firmicutes and Actinobacteria. High abundance of Bacteroidetes was observed only in male juvenile beaver cecum and colon, suggesting that the bacterial composition changes with age. Within the cecum and colon, members of known cellulase-producing bacterial taxa including the families Ruminococcaceae, Lachnospiraceae, and Clostridiaceae 1 were detected. The presence of putative genes encoding cellulolytic and carbohydrate-degrading enzymes indicated also the degradation of recalcitrant plant material in both gut compartments. The bacterial community in the gut systems of the Eurasian beaver differed from that of the North American beaver. Higher abundance of Actinobacteria and lower abundances of Bacteroidetes were recorded in the Eurasian beaver. Similar differences were obtained to bacterial communities of termites and herbivorous animals such as bovine. The data presented in this study provides the first insight into bacterial communities in the gut system of the Eurasian beaver.
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    Honest Signals of Status: Facial and Bodily Dominance Are Related to Success in Physical but Not Nonphysical Competition 

    Kordsmeyer, Tobias L.; Freund, Daniel; Vugt, Mark van; Penke, Lars
    Evolutionary Psychology 2019; 17(3)
    Recent studies suggest that both facial and bodily dominance promote high status positions and predict status-seeking behaviors such as aggression and social dominance. An evolutionarily relevant context in which associations between these dominance signals and status outcomes may be prevalent are face-to-face status contests. The present study examined whether facial and bodily dominance predicted success in dyadic competitions (one physical discipline, arm wrestling, and three nonphysical disciplines) in men (N ¼ 125) in a controlled laboratory setting. Men’s bodies and faces were independently rated for physical dominance, and associations of these ratings with contest outcomes as well as mediating and moderating variables (such as physical strength, body height, trait dominance, baseline and reactive testosterone) were examined. Both facial and bodily dominance positively predicted success in the physical discipline, mediated by physical strength, but not in the three nonphysical disciplines. Our findings demonstrate that facial and bodily physical dominance may be honest signals for men’s formidability and hence status potential, at least in a physically competitive context.
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    Translation termination depends on the sequential ribosomal entry of eRF1 and eRF3 

    Beißel, Christian; Neumann, Bettina; Uhse, Simon; Hampe, Irene; Karki, Prajwal; Krebber, Heike
    Nucleic Acids Research 2019; 47(9) p.4798-4813
    Translation termination requires eRF1 and eRF3 for polypeptide- and tRNA-release on stop codons. Additionally, Dbp5/DDX19 and Rli1/ABCE1 are required; however, their function in this process is currently unknown. Using a combination of in vivo and in vitro experiments, we show that they regulate a stepwise assembly of the termination complex. Rli1 and eRF3-GDP associate with the ribosome first. Subsequently, Dbp5-ATP delivers eRF1 to the stop codon and in this way prevents a premature access of eRF3. Dbp5 dissociates upon placing eRF1 through ATP-hydrolysis. This in turn enables eRF1 to contact eRF3, as the binding of Dbp5 and eRF3 to eRF1 is mutually exclusive. Defects in the Dbp5-guided eRF1 delivery lead to premature contact and premature dissociation of eRF1 and eRF3 from the ribosome and to subsequent stop codon readthrough. Thus, the stepwise Dbp5-controlled termination complex assembly is essential for regular translation termination events. Our data furthermore suggest a possible role of Dbp5/DDX19 in alternative translation termination events, such as during stress response or in developmental processes, which classifies the helicase as a potential drug target for nonsense suppression therapy to treat cancer and neurodegenerative diseases.
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    Action priming is linked to visual perception in continuous flash suppression 

    Valuch, Christian; Mattler, Uwe
    Journal of Vision 2019; 19(7) p.1-25: Art. 13
    Visual prime stimuli can affect the processing of following target stimuli even if their visibility is reduced due to visual masking. Prime visibility depends on the stimulus parameters of the prime and those of the mask. Here we explored the effects of prime stimuli and modulated their visibility by continuous flash suppression (CFS). CFS reduces the visibility of a stimulus presented to one eye by simultaneously presenting a series of high-contrast masking stimuli to the other eye. We manipulated the strength of CFS effects on perception and examined how action priming effects of the masked stimuli varied under the same conditions. Prime visibility was modulated by the contrast of the primes (Experiments 1 and 2), the contrast of the masks (Experiments 2 and 3), and by the stimulus onset asynchrony between prime and target stimuli (all experiments). Surprisingly, action priming effects were modulated by these experimental variables in a parallel way. In addition, individual differences between participants in prime visibility correlated with individual differences in action priming. Our findings suggest that action priming and prime perception depend in similar ways on prime contrast, mask contrast, stimulus onset asynchrony, and individual dispositions in CFS. These findings distinguish CFS from other perceptual suppression techniques, such as backward masking, that allow reducing prime visibility without parallel effects on action priming. Our results corroborate the view that CFS interferes with visual processing at early stages in the cortical hierarchy with similar effects on later processing for perception and action.
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    The Effects of Road Access on Income Generation. Evidence from An Integrated Conservation and Development Project in Cameroon 

    Spey, Ina-Kathrin; Kupsch, Denis; Bobo, Kadiri Serge; Waltert, Matthias; Schwarze, Stefan
    Sustainability 2019; 11(12): Art. 3368
    Many integrated conservation and development projects use road construction to induce a shift in income activities, since road access can reduce both poverty and environmental degradation. There is, however, little empirical evidence on the effects of road access on income patterns. We contribute to existing literature by analyzing the effects of road access on income activity choice in Korup National Park, Cameroon using a difference-in-difference approach. Road access led to a rise in total household income by 38% due to higher household participation in self-employment and wage labor. We neither found an effect on income from crop farming nor on participation in hunting activities. The effects of road access can be diverse and unforeseeable. Road construction in protected areas should thus be carefully considered and planned and only be implemented when other options are not feasible.
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    Oribatid mites reveal that competition for resources and trophic structure combine to regulate the assembly of diverse soil animal communities 

    Magilton, Matthew; Maraun, Mark; Emmerson, Mark; Caruso, Tancredi
    Ecology and Evolution p.1-11
    1. The role of niche partitioning in structuring species‐rich soil animal communities has been debated for decades and generated the “enigma of soil animal diversity.” More recently, resource‐based niche partitioning has been hypothesized to play a very limited role in the assembly of soil animal communities. To test this hypothesis, we applied a novel combination of stable isotopes and null models of species co‐occurrence to quantify the extent of resource niche partitioning on a diverse oribatid mite community sampled from mature oak woodland. 2. We asked whether species aggregate or segregate spatially and how these patterns correlated with the abundance of estimated trophic guilds. We also estimated the effects of environmental variables on community structure. 3. All measured environmental variables accounted for 12% of variance in community structure, including 8% of pure spatial structure unrelated to measured environmental factors and 2% of pure environmental variance unrelated to spatial variation. Co‐occurrence analysis revealed 10 pairs of species that aggregated and six pairs of species that were spatially segregated. Values of δ15N indicated that five out of the 10 pairs of aggregated species occupied the same trophic guild, while values of δ13C indicated that species in these five pairs consumed resources of different quality, supporting a significant role of resource‐based niche partitioning. Also, one of the five pairs of segregated species occupied the same trophic guild but had overlapping δ13C values suggesting that these species do not co‐occur locally and thus minimize competition for shared resources. 4. Partitioning of resources plays an underestimated role in soil microarthropod communities and different local communities consisted of the same trophic guilds with species identity changing from place to place. The sum of resource partitioning, multi‐trophic interactions, and microscale environmental variability in the environment is a viable solution to the enigma of soil animal diversity.
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    Tree Species Shape Soil Bacterial Community Structure and Function in Temperate Deciduous Forests 

    Dukunde, Amélie; Schneider, Dominik; Schmidt, Marcus; Veldkamp, Edzo; Daniel, Rolf
    Frontiers in Microbiology 2019; 10: Art. 1519
    Amplicon-based analysis of 16S rRNA genes and transcripts was used to assess the effect of tree species composition on soil bacterial community structure and function in a temperate deciduous forest. Samples were collected from mono and mixed stands of Fagus sylvatica (beech), Carpinus betulus (hornbeam), Tilia sp. (lime), and Quercus sp. (oak) in spring, summer, and autumn. Soil bacterial community exhibited similar taxonomic composition at total (DNA-based) and potentially active community (RNA-based) level, with fewer taxa present at active community level. Members of Rhizobiales dominated at both total and active bacterial community level, followed by members of Acidobacteriales, Solibacterales, Rhodospirillales, and Xanthomonadales. Bacterial communities at total and active community level showed a significant positive correlation with tree species identity (mono stands) and to a lesser extent with tree species richness (mixed stands). Approximately 58 and 64% of indicator operational taxonomic units (OTUs) showed significant association with only one mono stand at total and active community level, respectively, indicating a strong impact of tree species on soil bacterial community composition. Soil C/N ratio, pH, and P content similarly exhibited a significant positive correlation with soil bacterial communities, which was attributed to direct and indirect effects of forest stands. Seasonality was the strongest driver of predicted metabolic functions related to C fixation and degradation, and N metabolism. Carbon and nitrogen metabolic processes were significantly abundant in spring, while C degradation gene abundances increased from summer to autumn, corresponding to increased litterfall and decomposition. The results revealed that in a spatially homogenous forest soil, tree species diversity and richness are dominant drivers of structure and composition in soil bacterial communities.
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    Is implicit Theory of Mind real but hard to detect? Testing adults with different stimulus materials 

    Kulke, Louisa; Wübker, Marieke; Rakoczy, Hannes
    Royal Society Open Science 2019; 6(7): Art. 190068
    Recently, Theory of Mind (ToM) research has been revolutionized by new methods. Eye-tracking studies measuring subjects' looking times or anticipatory looking have suggested that implicit and automatic forms of ToM develop much earlier in ontogeny than traditionally assumed and continue to operate outside of subjects’ awareness throughout the lifespan. However, the reliability of these implicit methods has recently been put into question by an increasing number of non-replications. What remains unclear from these accumulating non-replication findings, though, is whether they present true negatives (there is no robust phenomenon of automatic ToM) or false ones (automatic ToM is real but difficult to tap). In order to address these questions, the current study implemented conceptual replications of influential anticipatory looking ToM tasks with a new variation in the stimuli. In two separate preregistered studies, we used increasingly realistic stimuli and controlled for potential confounds. Even with these more realistic stimuli, previous results could not be replicated. Rather, the anticipatory looking pattern found here remained largely compatible with more parsimonious explanations. In conclusion, the reality and robustness of automatic ToM remains controversial.
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    Impact of Nitriles on Bacterial Communities 

    Egelkamp, Richard; Zimmermann, Till; Schneider, Dominik; Hertel, Robert; Daniel, Rolf
    Frontiers in Environmental Science 2019; 7: Art. 103
    Nitriles are organic molecules with –C≡N as functional group and often toxic for living organisms. Detoxification can occur via nitrilases that degrade nitriles directly to carboxylic acids and ammonia, or with nitrile hydratases and amidases that convert nitriles to amides and subsequently to carboxylic acids and ammonia. Despite the knowledge of enzymatic degradation pathways, the influence of these compounds on the composition of bacterial communities is unknown. The tolerances of four phylogenetically different bacterial strains without known nitrile detoxification systems (Agrobacterium tumefaciens, Bacillus subtilis, Corynebacterium glutamicum, and Escherichia coli) to the toxic effects of nine nitriles and the corresponding carboxylic acids were determined. Based on these results, the effect of nitriles on diversity and composition of compost-derived bacterial communities was monitored over time by 16S rRNA gene amplicon-based andmetagenome analyses. Acetone cyanohydrin, 2-phenylpropionitrile, and pyruvonitrile exhibited a lethal, phenylacetonitrile, 4-hydroxybenzonitrile, and cyclohexanecarbonitrile a growth-suppressing and succinonitrile, acetonitrile, and crotononitrile a growth-promoting effect on the studied communities. Furthermore, each nitrile had a specific community-shaping effect, e.g., communities showing growth-suppression exhibited high relative abundance of Paenibacillus. In general, analysis of all data indicated a higher resistance of Gram-positive than Gram-negative bacterial community members and test organisms to growth-suppressing nitriles. More than 70 putative nitrilase-encoding and over 20 potential nitrile hydratase-encoding genes were identified during analysis of metagenomes derived from nitrile-enrichments, underlining the high yet often unexplored abundance of nitrile-degrading enzymes.
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    COP9 Signalosome Interaction with UspA/Usp15 Deubiquitinase Controls VeA-Mediated Fungal Multicellular Development 

    Meister, Cindy; Thieme; Karl G.; Thieme, Sabine; Köhler, Anna M.; Schmitt, Kerstin; Valerius, Oliver; Braus, Gerhard H.
    Biomolecules 2019; 9(6): Art. 238
    COP9 signalosome (CSN) and Den1/A deneddylases physically interact and promote multicellular development in fungi. CSN recognizes Skp1/cullin-1/Fbx E3 cullin-RING ligases (CRLs) without substrate and removes their posttranslational Nedd8 modification from the cullin scaffold. This results in CRL complex disassembly and allows Skp1 adaptor/Fbx receptor exchange for altered substrate specificity. We characterized the novel ubiquitin-specific protease UspA of the mold Aspergillus nidulans, which corresponds to CSN-associated human Usp15 and interacts with six CSN subunits. UspA reduces amounts of ubiquitinated proteins during fungal development, and the uspA gene expression is repressed by an intact CSN. UspA is localized in proximity to nuclei and recruits proteins related to nuclear transport and transcriptional processing, suggesting functions in nuclear entry control. UspA accelerates the formation of asexual conidiospores, sexual development, and supports the repression of secondary metabolite clusters as the derivative of benzaldehyde (dba) genes. UspA reduces protein levels of the fungal NF-kappa B-like velvet domain protein VeA, which coordinates differentiation and secondary metabolism. VeA stability depends on the Fbx23 receptor, which is required for light controlled development. Our data suggest that the interplay between CSN deneddylase, UspA deubiquitinase, and SCF-Fbx23 ensures accurate levels of VeA to support fungal development and an appropriate secondary metabolism.
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    Cold-water corals and hydrocarbon-rich seepage in Pompeia Province (Gulf of Cádiz) – living on the edge 

    Rincón-Tomás, Blanca; Duda, Jan-Peter; Somoza, Luis; González, Francisco Javier; Schneider, Dominik; Medialdea, Teresa; Santofimia, Esther; López-Pamo, Enrique; Madureira, Pedro; Hoppert, Michael; et al.
    Reitner, Joachim
    Biogeosciences 2019; 16(7) p.1607-1627
    Azooxanthellate cold-water corals (CWCs) have a global distribution and have commonly been found in areas of active fluid seepage. The relationship between the CWCs and these fluids, however, is not well understood. This study aims to unravel the relationship between CWC development and hydrocarbon-rich seepage in Pompeia Province (Gulf of Cádiz, Atlantic Ocean). This region is comprised of mud volcanoes (MVs), coral ridges and fields of coral mounds, which are all affected by the tectonically driven seepage of hydrocarbon-rich fluids. These types of seepage, for example, focused, scattered, diffused or eruptive, is tightly controlled by a complex system of faults and diapirs. Early diagenetic carbonates from the currently active Al Gacel MV exhibit δ13C signatures down to −28.77 ‰ Vienna Pee Dee Belemnite (VPDB), which indicate biologically derived methane as the main carbon source. The same samples contain 13C-depleted lipid biomarkers diagnostic for archaea such as crocetane (δ13C down to −101.2 ‰ VPDB) and pentamethylicosane (PMI) (δ13C down to −102.9 ‰ VPDB), which is evidence of microbially mediated anaerobic oxidation of methane (AOM). This is further supported by next generation DNA sequencing data, demonstrating the presence of AOM-related microorganisms (ANMEs, archaea, sulfate-reducing bacteria) in the carbonate. Embedded corals in some of the carbonates and CWC fragments exhibit less negative δ13C values (−8.08 ‰ to −1.39 ‰ VPDB), pointing against the use of methane as the carbon source. Likewise, the absence of DNA from methane- and sulfide-oxidizing microbes in sampled coral does not support the idea of these organisms having a chemosynthetic lifestyle. In light of these findings, it appears that the CWCs benefit rather indirectly from hydrocarbon-rich seepage by using methane-derived authigenic carbonates as a substratum for colonization. At the same time, chemosynthetic organisms at active sites prevent coral dissolution and necrosis by feeding on the seeping fluids (i.e., methane, sulfate, hydrogen sulfide), allowing cold-water corals to colonize carbonates currently affected by hydrocarbon-rich seepage.
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