Recent Submissions

  • Journal Article

    Review of the mite genus Krantzolaspina Datta & Bhattacharjee (Mesostigmata, Parholaspididae) with re-description of K. angustatus comb. nov. (Ishikawa) from Indonesia 

    Quintero-Gutiérrez, Edwin Javier; Sandmann, Dorothee; Cómbita-Heredia, Orlando; Klarner, Bernhard; Widyastuti, Rahayu; Scheu, Stefan
    ZooKeys 2020; 997 p.47-68
    Herein, we update the diagnosis and description of the genus Krantzolaspina Datta & Bhattacharjee and provide a list of the three valid species including new combinations and synonyms, as follows: 1) Krant-zolaspina angustatus (Ishikawa, 1987) comb. nov. (= Indutolaelaps jiroftensis Hajizadeh et al., 2017 syn. nov.),2) K. rebatii Datta & Bhattacharjee, 1989 and 3) K. solimani (Metwali, 1983) comb. nov.Finally, we re-describe K. angustatus (Ishikawa, 1987) comb. nov. based on the holotype from Japan, voucher specimens from Iran and additional females that we found in soil samples from oil palm planta-tions in Sumatra, Indonesia.
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  • Journal Article

    Camostat Mesylate May Reduce Severity of Coronavirus Disease 2019 Sepsis: A First Observation 

    Hofmann-Winkler, Heike; Moerer, Onnen; Alt-Epping, Sabine; Bräuer, Anselm; Büttner, Benedikt; Müller, Martin; Fricke, Torben; Grundmann, Julian; Harnisch, Lars-Olav; Heise, Daniel; et al.
    Kernchen, AndreaPressler, MeikeStephani, CasparTampe, BjörnKaul, ArturGärtner, SabineKramer, StefaniePöhlmann, StefanWinkler, Martin Sebastian
    Critical Care Explorations 2020; 2(11) p.1-5: Art. e0284
    Objectives: Severe acute respiratory syndrome coronavirus 2 cell entry depends on angiotensin-converting enzyme 2 and transmembrane serine protease 2 and is blocked in cell culture by camostat mesylate, a clinically proven protease inhibitor. Whether camostat mesylate is able to lower disease burden in coronavirus disease 2019 sepsis is currently unknown. Design: Retrospective observational case series. Setting: Patient treated in ICU of University hospital Göttingen, Germany. Patients: Eleven critical ill coronavirus disease 2019 patients with organ failure were treated in ICU. Interventions: Compassionate use of camostat mesylate (six patients, camostat group) or hydroxychloroquine (five patients, hydroxychloroquine group). Measurements and Main Results: Clinical courses were assessed by Sepsis-related Organ Failure Assessment score at days 1, 3, and 8. Further, viral load, oxygenation, and inflammatory markers were determined. Sepsis-related Organ Failure Assessment score was comparable between camostat and hydroxychloroquine groups upon ICU admission. During observation, the Sepsis-related Organ Failure Assessment score decreased in the camostat group but remained elevated in the hydroxychloroquine group. The decline in disease severity in camostat mesylate treated patients was paralleled by a decline in inflammatory markers and improvement of oxygenation. Conclusions: The severity of coronavirus disease 2019 decreased upon camostat mesylate treatment within a period of 8 days and a similar effect was not observed in patients receiving hydroxychloroquine. Camostat mesylate thus warrants further evaluation within randomized clinical trials.
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  • Journal Article

    New insights into the morphology and evolution of the ventral pharynx and jaws in Histriobdellidae (Eunicida, Annelida) 

    Tzetlin, Alexander; Budaeva, Nataliya; Vortsepneva, Elena; Helm, Conrad
    Zoological Letters 2020; 6(1) p.1-19: Art. 14
    The jaw apparatus in several annelid families represents a powerful tool for systematic approaches and evolutionary investigations. Nevertheless, for several taxa, this character complex has scarcely been investigated, and complete comparative analyses of all annelid jaws are lacking. In our comprehensive study, we described the fine structure of the jaw apparatus and the ventral pharyngeal organ (VPO) in Histriobdella homari – a minute ectocommensal of lobsters putatively belonging to the Eunicida – using different comparative morphological approaches, including SEM, TEM, CLSM and subsequent 3D reconstruction. The H. homari jaw apparatus is composed of ventral paired mandibles and dorsal symmetrical maxillae consisting of numerous dental plates, ventral carriers and an unpaired dorsal rod, and the general assemblage and arrangement of the different parts are highly comparable to those of other eunicid families. The jaw ultrastructure of histriobdellids resembles that of the families Dorvilleidae and (juvenile) Onuphidae. Furthermore, our data reveal that in the process of development of the jaw apparatus, the mandibles, maxillae II and unpaired dorsal rod are formed first, and the remaining maxillae and ventral carriers appear later. Notably, the muscular apparatus differs from that in Dorvilleidae and Onuphidae in terms of the number and arrangement of muscle fibers encompassing the jaws – not only because of the very small size of Histriobdella but also because histriobdellid maxillary protraction occurs due to straightening of the dorsal rod and thus requires a different muscular scaffold. Based on our investigations, the arrangement of the muscular apparatus of the jaws, the presence of paired ventral carriers and the dorsal rod, and the morphology of the ventral pharyngeal organ represent a histriobdellid autapomorphy. Our datasets form a basis for further comparative analyses to elucidate the evolution of Eunicida and jaw-bearing Annelida.
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  • Journal Article

    The relation of meiotic behaviour to hybridity, polyploidy and apomixis in the Ranunculus auricomus complex (Ranunculaceae) 

    Barke, Birthe H; Karbstein, Kevin; Daubert, Mareike; Hörandl, Elvira
    BMC Plant Biology 2020; 20(1) p.1-14: Art. 523
    Background Hybridization and polyploidization are powerful evolutionary factors that are associated with manifold developmental changes in plants such as irregular progression of meiosis and sporogenesis. The emergence of apomixis, which is asexual reproduction via seeds, is supposed to be connected to these factors and was often regarded as an escape from hybrid sterility. However, the functional trigger of apomixis is still unclear. Recently formed di- and polyploid Ranunculus hybrids, as well as their parental species were analysed for their modes of mega- and microsporogenesis by microscopy. Chromosomal configurations during male meiosis were screened for abnormalities. Meiotic and developmental abnormalities were documented qualitatively and collected quantitatively for statistical evaluations. Results Allopolyploids showed significantly higher frequencies of erroneous microsporogenesis than homoploid hybrid plants. Among diploids, F2 hybrids had significantly more disturbed meiosis than F1 hybrids and parental plants. Chromosomal aberrations included laggard chromosomes, chromatin bridges and disoriented spindle activities. Failure of megasporogenesis appeared to be much more frequent in than of microsporogenesis is correlated to apomixis onset. Conclusions Results suggest diverging selective pressures on female and male sporogenesis, with only minor effects of hybridity on microsporogenesis, but fatal effects on the course of megasporogenesis. Hence, pollen development continues without major alterations, while selection will favour apomixis as alternative to the female meiotic pathway. Relation of investigated errors of megasporogenesis with the observed occurrence of apospory in Ranunculus hybrids identifies disturbed female meiosis as potential elicitor of apomixis in order to rescue these plants from hybrid sterility. Male meiotic disturbance appears to be stronger in neopolyploids than in homoploid hybrids, while disturbances of megasporogenesis were not ploidy-dependent.
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  • Journal Article

    Sequence heterochrony led to a gain of functionality in an immature stage of the central complex: A fly–beetle insight 

    Farnworth, Max S.; Eckermann, Kolja N.; Bucher, Gregor
    PLOS Biology 2020; 18(10) p.1-32: Art. e3000881
    Animal behavior is guided by the brain. Therefore, adaptations of brain structure and function are essential for animal survival, and each species differs in such adaptations. The brain of one individual may even differ between life stages, for instance, as adaptation to the divergent needs of larval and adult life of holometabolous insects. All such differences emerge during development, but the cellular mechanisms behind the diversification of brains between taxa and life stages remain enigmatic. In this study, we investigated holometabolous insects in which larvae differ dramatically from the adult in both behavior and morphology. As a consequence, the central complex, mainly responsible for spatial orientation, is conserved between species at the adult stage but differs between larvae and adults of one species as well as between larvae of different taxa. We used genome editing and established transgenic lines to visualize cells expressing the conserved transcription factor retinal homeobox, thereby marking homologous genetic neural lineages in both the fly Drosophila melanogaster and the beetle Tribolium castaneum. This approach allowed us for the first time to compare the development of homologous neural cells between taxa from embryo to the adult. We found complex heterochronic changes including shifts of developmental events between embryonic and pupal stages. Further, we provide, to our knowledge, the first example of sequence heterochrony in brain development, where certain developmental steps changed their position within the ontogenetic progression. We show that through this sequence heterochrony, an immature developmental stage of the central complex gains functionality in Tribolium larvae.
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  • Journal Article

    Quantitative Hormone Signaling Output Analyses of Arabidopsis thaliana Interactions With Virulent and Avirulent Hyaloperonospora arabidopsidis Isolates at Single-Cell Resolution 

    Ghareeb, Hassan; El-Sayed, Mohamed; Pound, Michael; Tetyuk, Olena; Hanika, Katharina; Herrfurth, Cornelia; Feussner, Ivo; Lipka, Volker
    Frontiers in Plant Science 2020; 11 p.1-15: Art. 603693
    The phytohormones salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) are central regulators of biotic and abiotic stress responses in Arabidopsis thaliana. Here, we generated modular fluorescent protein-based reporter lines termed COLORFUL-PR1pro, -VSP2pro, and -PDF1.2apro. These feature hormone-controlled nucleus-targeted transcriptional output sensors and the simultaneous constitutive expression of spectrally separated nuclear reference and plasma membrane-localized reporters. This set-up allowed the study of cell-type specific hormone activities, cellular viability and microbial invasion. Moreover, we developed a software-supported high-throughput confocal microscopy imaging protocol for output quantification to resolve the spatio-temporal dynamics of respective hormonal signaling activities at single-cell resolution. Proof-of-principle analyses in A. thaliana leaves revealed distinguished hormone sensitivities in mesophyll, epidermal pavement and stomatal guard cells, suggesting cell type-specific regulatory protein activities. In plant-microbe interaction studies, we found that virulent and avirulent Hyaloperonospora arabidopsidis (Hpa) isolates exhibit different invasion dynamics and induce spatio-temporally distinct hormonal activity signatures. On the cellular level, these hormone-controlled reporter signatures demarcate the nascent sites of Hpa entry and progression, and highlight initiation, transduction and local containment of immune signals.
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  • Journal Article

    A 3D Printed Device for Easy and Reliable Quantification of Fungal Chemotropic Growth 

    Schunke, Carolin; Pöggeler, Stefanie; Nordzieke, Daniela Elisabeth
    Frontiers in Microbiology 2020; 11 p.1-10: Art. 584525
    Chemical gradients are surrounding living organisms in all habitats of life. Microorganisms, plants and animals have developed specific mechanisms to sense such gradients. Upon perception, chemical gradients can be categorized either as favorable, like nutrients or hormones, or as disadvantageous, resulting in a clear orientation toward the gradient and avoiding strategies, respectively. Being sessile organisms, fungi use chemical gradients for their orientation in the environment. Integration of this data enables them to successfully explore nutrient sources, identify probable plant or animal hosts, and to communicate during sexual reproduction or early colony development. We have developed a 3D printed device allowing a highly standardized, rapid and low-cost investigation of chemotropic growth processes in fungi. Since the 3D printed device is placed on a microscope slide, detailed microscopic investigations and documentation of the chemotropic process is possible. Using this device, we provide evidence that germlings derived from oval conidia of the hemibiotrophic plant pathogen Colletotrichum graminicola can sense gradients of glucose and reorient their growth toward the nutrient source. We describe in detail the method establishment, probable pitfalls, and provide the original program files for 3D printing to enable broad application of the 3D device in basic, agricultural, medical, and applied fungal science.
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  • Journal Article

    Actions do not speak louder than words in an interactive false belief task 

    Wenzel, Lisa; Dörrenberg, Sebastian; Proft, Marina; Liszkowski, Ulf; Rakoczy, Hannes
    Royal Society Open Science 2020; 7(10) p.1-23: Art. 191998
    Traditionally, it had been assumed that meta-representational Theory of Mind (ToM) emerges around the age of 4 when children come to master standard false belief (FB) tasks. More recent research with various implicit measures, though, has documented much earlier competence and thus challenged the traditional picture. In interactive FB tasks, for instance, infants have been shown to track an interlocutor's false or true belief when interpreting her ambiguous communicative acts (Southgate et al. 2010 Dev. Sci.13, 907–912. (doi:10.1111/j.1467-7687.2009.00946.x)). However, several replication attempts so far have produced mixed findings (e.g. Dörrenberg et al. 2018 Cogn. Dev.46, 12–30. (doi:10.1016/j.cogdev.2018.01.001); Grosse Wiesmann et al. 2017 Dev. Sci.20, e12445. (doi:10.1111/desc.12445); Király et al. 2018 Proc. Natl Acad. Sci. USA115, 11 477–11 482. (doi:10.1073/pnas.1803505115)). Therefore, we conducted a systematic replication study, across two laboratories, of an influential interactive FB task (the so-called ‘Sefo’ tasks by Southgate et al. 2010 Dev. Sci.13, 907–912. (doi:10.1111/j.1467-7687.2009.00946.x)). First, we implemented close direct replications with the original age group (17-month-olds) and compared their performance to those of 3-year-olds. Second, we designed conceptual replications with modifications and improvements regarding pragmatic ambiguities for 2-year-olds. Third, we validated the task with explicit verbal test versions in older children and adults. Results revealed the following: the original results could not be replicated, and there was no evidence for FB understanding measured by the Sefo task in any age group except for adults. Comparisons to explicit FB tasks suggest that the Sefo task may not be a sensitive measure of FB understanding in children and even underestimate their ToM abilities. The findings add to the growing replication crisis in implicit ToM research and highlight the challenge of developing sensitive, reliable and valid measures of early implicit social cognition.
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  • Journal Article

    The High Osmolarity Glycerol Mitogen-Activated Protein Kinase regulates glucose catabolite repression in filamentous fungi 

    de Assis, Leandro José; Silva, Lilian Pereira; Liu, Li; Schmitt, Kerstin; Valerius, Oliver; Braus, Gerhard H.; Ries, Laure Nicolas Annick; Goldman, Gustavo Henrique
    PLOS Genetics 2020; 16(8) p.1-27: Art. e1008996
    The utilization of different carbon sources in filamentous fungi underlies a complex regulatory network governed by signaling events of different protein kinase pathways, including the high osmolarity glycerol (HOG) and protein kinase A (PKA) pathways. This work unraveled cross-talk events between these pathways in governing the utilization of preferred (glucose) and non-preferred (xylan, xylose) carbon sources in the reference fungus Aspergillus nidulans. An initial screening of a library of 103 non-essential protein kinase (NPK) deletion strains identified several mitogen-activated protein kinases (MAPKs) to be important for carbon catabolite repression (CCR). We selected the MAPKs Ste7, MpkB, and PbsA for further characterization and show that they are pivotal for HOG pathway activation, PKA activity, CCR via regulation of CreA cellular localization and protein accumulation, as well as for hydrolytic enzyme secretion. Protein-protein interaction studies show that Ste7, MpkB, and PbsA are part of the same protein complex that regulates CreA cellular localization in the presence of xylan and that this complex dissociates upon the addition of glucose, thus allowing CCR to proceed. Glycogen synthase kinase (GSK) A was also identified as part of this protein complex and shown to potentially phosphorylate two serine residues of the HOG MAPKK PbsA. This work shows that carbon source utilization is subject to cross-talk regulation by protein kinases of different signaling pathways. Furthermore, this study provides a model where the correct integration of PKA, HOG, and GSK signaling events are required for the utilization of different carbon sources.
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  • Journal Article

    Protists and collembolans alter microbial community composition, C dynamics and soil aggregation in simplified consumer–prey systems 

    Erktan, Amandine; Rillig, Matthias C.; Carminati, Andrea; Jousset, Alexandre; Scheu, Stefan
    Biogeosciences 2020; 17(20) p.4961-4980
    Microbes play an essential role in soil functioning including biogeochemical cycling and soil aggregate formation. Yet, a major challenge is to link microbes to higher trophic levels and assess consequences for soil functioning. Here, we aimed to assess how microbial consumers modify microbial community composition (PLFA markers), as well as C dynamics (microbial C use, SOC concentration and CO$_2$ emission) and soil aggregation. We rebuilt two simplified soil consumer–prey systems: a bacterial-based system comprising amoebae (Acanthamoeba castellanii) feeding on a microbial community dominated by the free-living bacterium Pseudomonas fluorescens and a fungal-based system comprising collembolans (Heteromurus nitidus) grazing on a microbial community dominated by the saprotrophic fungus Chaetomium globosum. The amoeba A. castellanii did not affect microbial biomass and composition, but it enhanced the formation of soil aggregates and tended to reduce their stability. Presumably, the dominance of P. fluorescens, able to produce antibiotic toxins in response to the attack by A. castellanii, was the main cause of the unchanged microbial community composition, and the release of bacterial extracellular compounds, such as long-chained polymeric substances or proteases, in reaction to predation was responsible for the changes in soil aggregation as a side effect. In the fungal system, collembolans significantly modified microbial community composition via consumptive and non-consumptive effects including the transport of microbes on the body surface. As expected, fungal biomass promoted soil aggregation and was reduced in the presence of H. nitidus. Remarkably, we also found an unexpected contribution of changes in bacterial community composition to soil aggregation. In both the bacterial and fungal systems, bacterial and fungal communities mainly consumed C from soil organic matter (rather than the litter added). Increased fungal biomass was associated with an increased capture of C from added litter, and the presence of collembolans levelled off this effect. Neither amoebae nor collembolans altered SOC concentrations and CO$_2$ production. Overall, the results demonstrated that trophic interactions are important for achieving a mechanistic understanding of biological contributions to soil aggregation and may occur without major changes in C dynamics and with or without changes in the composition of the microbial community.
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  • Journal Article

    Legacy Effects Overshadow Tree Diversity Effects on Soil Fungal Communities in Oil Palm-Enrichment Plantations 

    Ballauff, Johannes; Zemp, Delphine Clara; Schneider, Dominik; Irawan, Bambang; Daniel, Rolf; Polle, Andrea
    Microorganisms 2020; 8(10) p.1-17: Art. 1577
    Financially profitable large-scale cultivation of oil palm monocultures in previously diverse tropical rain forest areas constitutes a major ecological crisis today. Not only is a large proportion of the aboveground diversity lost, but the belowground soil microbiome, which is important for the sustainability of soil function, is massively altered. Intermixing oil palms with native tree species promotes vegetation biodiversity and stand structural complexity in plantations, but the impact on soil fungi remains unknown. Here, we analyzed the diversity and community composition of soil fungi three years after tree diversity enrichment in an oil palm plantation in Sumatra (Indonesia). We tested the effects of tree diversity, stand structural complexity indices, and soil abiotic conditions on the diversity and community composition of soil fungi. We hypothesized that the enrichment experiment alters the taxonomic and functional community composition, promoting soil fungal diversity. Fungal community composition was affected by soil abiotic conditions (pH, N, and P), but not by tree diversity and stand structural complexity indices. These results suggest that intensive land use and abiotic filters are a legacy to fungal communities, overshadowing the structuring effects of the vegetation, at least in the initial years after enrichment plantings.
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  • Journal Article

    Knowledge of Student Teachers on Sustainable Land Use Issues–Knowledge Types Relevant for Teacher Education 

    Richter-Beuschel, Lisa; Bögeholz, Susanne
    Sustainability 2020; 12(20) p.1-20: Art. 8332
    For restructuring educational processes and institutions toward Sustainable Development, teachers’ knowledge and competences are crucial. Due to the high relevance of teachers’ content knowledge, this study aimed to (i) assess Sustainable Development-relevant knowledge by differentiating between situational, conceptual and procedural knowledge, (ii) find out via item response theory modelling how these theoretically distinguished knowledge types can be empirically supported, and (iii) link the knowledge dimension(s) to related constructs. We developed a paper-and-pencil test to assess these three knowledge types (N = 314). A two-dimensional structure that combines situational and conceptual knowledge and that distinguishes situational/conceptual knowledge from procedural knowledge, fits the data best (EAP/PV situational/conceptual: 0.63; EAP/PV procedural: 0.67). Student teachers at master level outperformed bachelor level students in situational/conceptual knowledge but master level students did not differ from students at bachelor level regarding procedural knowledge. We observed only slight correlations between the two knowledge dimensions and the content-related motivational orientations of professional action competence. Student teachers’ deficits in procedural knowledge can be attributed to the small number of Education for Sustainable Development-relevant courses attended. Systematically fostering procedural knowledge in teacher education could promote achieving cognitive learning objectives associated with Sustainable Development Goals in the long term.
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  • Journal Article

    Arguments for Construct Validity of the Self-Efficacy Beliefs of Interdisciplinary Science Teaching (SElf-ST) Instrument 

    Handtke, Kevin
    European Journal of Educational Research 2020; 9(4) p.1435-1453
    Current research on self-efficacy beliefs of interdisciplinary science teaching indicates shortcomings in facing recent teaching challenges in secondary education and corresponding valid instruments. Thus, we designed the Self-Efficacy Beliefs of Interdisciplinary Science Teaching (SElf-ST) instrument based on a pedagogical content knowledge model for science teaching. We ensured the factorial validity of ten factors. To bring construct validity down to a round figure, we examined convergent and divergent validity in this paper. For answering the overall research question regarding arguments for the convergent and divergent validity of the interpretation of the SElf-ST instrument’s test values (and related hypotheses), we analyzed data of pre-service, trainee, and in-service biology, chemistry, and physics teachers (n = 590) in a cross-sectional study. While the strong latent correlations of the ten SElf-ST factors with self-efficacy beliefs of interdisciplinary science teaching in primary education (r = 0.40 – 0.63, p < 0.01) indicate convergent validity, the rather weak correlations with self-efficacy beliefs of general teaching (r = 0.17 – 0.54, p < 0.01), self-rated content knowledge in science (r = 0.13 – 0.40, p < 0.01), and perceived stress (r = -0.13 – -0.19, p < 0.01) support different divergent validity intensities. Thus, assumed relations within the nomological net surrounding the self-efficacy beliefs of interdisciplinary science teaching construct were confirmed for secondary education. In sum, we shed light on a rarely explored aspect of construct validity in science education research regarding self-efficacy beliefs. Doing so, we gained strong arguments that the SElf-ST instrument’s test values can serve as indicators of self-efficacy beliefs of interdisciplinary science teaching in secondary education.
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  • Journal Article

    Phenotypic Responses, Reproduction Mode and Epigenetic Patterns under Temperature Treatments in the Alpine Plant Species Ranunculus kuepferi (Ranunculaceae) 

    Syngelaki, Eleni; Daubert, Mareike; Klatt, Simone; Hörandl, Elvira
    Biology 2020; 9(10) p.1-20: Art. 315
    Plant life in alpine habitats is shaped by harsh abiotic conditions and cold climates. Phenotypic variation of morphological characters and reproduction can be influenced by temperature stress. Nevertheless, little is known about the performance of different cytotypes under cold stress and how epigenetic patterns could relate to phenotypic variation. Ranunculus kuepferi, a perennial alpine plant, served as a model system for testing the effect of cold stress on phenotypic plasticity, reproduction mode, and epigenetic variation. Diploid and autotetraploid individuals were placed in climate growth cabinets under warm and cold conditions. Morphological traits (height, leaves and flowers) and the proportion of well-developed seeds were measured as fitness indicators, while flow cytometric seed screening (FCSS) was utilized to determine the reproduction mode. Subsequently, comparisons with patterns of methylation-sensitive amplified fragment-length polymorphisms (AFLPs) were conducted. Diploids grew better under warm conditions, while tetraploids performed better in cold treatments. Epigenetic patterns were correlated with the expressed morphological traits. Cold stress reduced the reproduction fitness but did not induce apomixis in diploids. Overall, our study underlines the potential of phenotypic plasticity for acclimation under environmental conditions and confirms the different niche preferences of cytotypes in natural populations. Results help to understand the pattern of geographical parthenogenesis in the species.
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  • Journal Article

    Metagenome-Assembled Genome Sequences from an Anoxygenic Photosynthetic Consortium Involved in Sulfur Cycling 

    Winkler, Lucia; Münker, Marc F.; Brunotte, Susanne; Rohlmann, Lina; Diez Alfageme, Alvaro; Poehlein, Anja; Hoppert, Michael; Reitner, Joachim; Nacke, Heiko
    Microbiology Resource Announcements 2020; 9(40) p.1-3: Art. e00819-20
    We sequenced the metagenome of an anoxygenic photosynthetic consortium originating from pond water and reconstructed four metagenome-assembled genomes. These genomes include Desulfocapsa, Paludibacter, Lamprocystis, and Rhodocyclaceae representatives and indicate the presence of genes for dissimilatory sulfate reduction and oxidation of reduced sulfur compounds.
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  • Journal Article

    Can We Use Gene-Editing to Induce Apomixis in Sexual Plants? 

    Scheben, Armin; Hojsgaard, Diego
    Genes 2020; 11(7) p.1-28: Art. 781
    Apomixis, the asexual formation of seeds, is a potentially valuable agricultural trait. Inducing apomixis in sexual crop plants would, for example, allow breeders to fix heterosis in hybrid seeds and rapidly generate doubled haploid crop lines. Molecular models explain the emergence of functional apomixis, i.e., apomeiosis + parthenogenesis + endosperm development, as resulting from a combination of genetic or epigenetic changes that coordinate altered molecular and developmental steps to form clonal seeds. Apomixis-like features and synthetic clonal seeds have been induced with limited success in the sexual plants rice and maize by using gene editing to mutate genes related to meiosis and fertility or via egg-cell specific expression of embryogenesis genes. Inducing functional apomixis and increasing the penetrance of apomictic seed production will be important for commercial deployment of the trait. Optimizing the induction of apomixis with gene editing strategies that use known targets as well as identifying alternative targets will be possible by better understanding natural genetic variation in apomictic species. With the growing availability of genomic data and precise gene editing tools, we are making substantial progress towards engineering apomictic crops.
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  • Journal Article

    A comparison of common metrics used to quantify the effectiveness of conservation interventions 

    Khorozyan, Igor
    PeerJ 2020; 8 p.1-15: Art. e9873
    Background: Evidence-based conservation is urgently needed to identify, apply and promote effective interventions for mitigation of threats and recovery of the natural environment. Estimation of intervention effectiveness is subject to robust study design and statistical analysis, and much progress is documented in these fields. In contrast, little is understood about the accuracy and biases (underestimation and overestimation) of different effectiveness metrics and how they are affected by sample size. Methods: In this study, a dataset (n = 500 cases) consisting of random, positive, integer numbers was simulated to produce frequency input data for the 2 × 2 contingency table. For each case, three metrics of the relative risk, odds ratio and the magnitude of change were calculated, their disparity was estimated and the characteristics of treatment (with intervention) and control (without intervention) samples significantly affecting this disparity were studied by means of linear regression. Further, four case studies from different conservation interventions are provided to support the results. Results: The study has shown that the relative risk and the magnitude of change produce identical estimates of intervention effectiveness only when treatment and control samples are equal, or when the number of target outcomes (e.g., number of livestock killed by predators) in treatment sample reaches zero. In other situations, the magnitude of change gives overestimates or underestimates, depending on relationships between treatment and control sample sizes. The table summarizing the conditions of equalities and biases between these two metrics is provided. These conditions are valid for both reduction-aimed interventions reducing negative target outcomes (e.g., livestock protection to reduce livestock losses to predators) and for addition-aimed interventions increasing positive target outcomes (e.g., establishment of protected areas to increase species presence). No significant effects on the odds ratio were found. Conclusion: Researchers should set equal treatment and control sample sizes so that to produce identical estimates of intervention effectiveness by the relative risk and the magnitude of change. Otherwise, these estimates are biased if produced by the magnitude of change and the relative risk should be used instead. As setting equal treatment and control samples can be impractical, I encourage researchers and practitioners to use the relative risk in estimation of intervention effectiveness. This will not take additional efforts as both metrics are calculated from the same contingency table. Treatment and control sample sizes, along with their sub-samples affected and not by an intervention, should be explicitly reported by researchers to allow independent evaluation of intervention effectiveness. This approach can help obtain more accurate information on intervention effectiveness for making better decisions in conservation actions.
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  • Journal Article

    Do infants and preschoolers quantify probabilities based on proportions? 

    Placì, Sarah; Fischer, Julia; Rakoczy, Hannes
    Royal Society Open Science 2020; 7(9) p.1-8: Art. 191751
    Most statistical problems encountered throughout life require the ability to quantify probabilities based on proportions. Recent findings on the early ontogeny of this ability have been mixed: For example, when presented with jars containing preferred and less preferred items, 12-month-olds, but not 3- and 4-years-olds, seem to rely on the proportions of objects in the jars to predict the content of samples randomly drawn out of them. Given these contrasting findings, it remains unclear what the probabilistic reasoning abilities of young children are and how they develop. In our study, we addressed this question and tested, with identical methods across age groups and similar methods to previous studies, whether 12-month-olds and 3- and 4-years-olds rely on proportions of objects to estimate probabilities of random sampling events. Results revealed that neither infants nor preschoolers do. While preschoolers' performance is in line with previous findings, infants' performance is difficult to interpret given their failure in a control condition in which the outcomes happened with certainty rather than a graded probability. More systematic studies are needed to explain why infants succeeded in a previous study but failed in our study.
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  • Journal Article

    The development of early pioneer neurons in the annelid Malacoceros fuliginosus 

    Kumar, Suman; Tumu, Sharat C; Helm, Conrad; Hausen, Harald
    BMC Evolutionary Biology. 2020 Sep 14;20(1):117
    Abstract Background Nervous system development is an interplay of many processes: the formation of individual neurons, which depends on whole-body and local patterning processes, and the coordinated growth of neurites and synapse formation. While knowledge of neural patterning in several animal groups is increasing, data on pioneer neurons that create the early axonal scaffold are scarce. Here we studied the first steps of nervous system development in the annelid Malacoceros fuliginosus. Results We performed a dense expression profiling of a broad set of neural genes. We found that SoxB expression begins at 4 h postfertilization, and shortly later, the neuronal progenitors can be identified at the anterior and the posterior pole by the transient and dynamic expression of proneural genes. At 9 hpf, the first neuronal cells start differentiating, and we provide a detailed description of axonal outgrowth of the pioneer neurons that create the primary neuronal scaffold. Tracing back the clonal origin of the ventral nerve cord pioneer neuron revealed that it is a descendant of the blastomere 2d (2d221), which after 7 cleavages starts expressing Neurogenin, Acheate-Scute and NeuroD. Conclusions We propose that an anterior and posterior origin of the nervous system is ancestral in annelids. We suggest that closer examination of the first pioneer neurons will be valuable in better understanding of nervous system development in spirally cleaving animals, to determine the potential role of cell-intrinsic properties in neuronal specification and to resolve the evolution of nervous systems.
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  • Journal Article

    Studded leather collars are very effective in protecting cattle from leopard (Panthera pardus) attacks 

    Khorozyan, Igor; Ghoddousi, Siavash; Soufi, Mobin; Soofi, Mahmood; Waltert, Matthias
    Ecological Solutions and Evidence 2020; 1(1) p.1-9: Art. e12013
    1. Human‐wildlife conflicts are widespread, particularly with big cats which can kill domestic livestock and create a counteraction between conservation and local livelihoods, especially near protected areas. Minimisation of livestock losses caused by big cats and other predators is essential to mitigate conflicts and promote socially acceptable conservation. As big cats usually kill by throat bites, protective collars represent a potentially effective non‐lethal intervention to prevent livestock depredation, yet the application and effectiveness estimation of these tools are very limited. 2. In this study, for the first time we measured the effectiveness of studded leather collars in protecting cattle from leopard (Panthera pardus) attacks. We conducted a randomised controlled experiment during 14 months to collar 202 heads and leave uncollared 258 heads grazing in forests and belonging to 27 owners from eight villages near three protected areas in Mazandaran Province, northern Iran. 3. Our results show that none of collared cattle and nine uncollared cattle were lost to leopard depredation, meaning that collars caused a zero relative risk of damage and a perfect 100% damage reduction. Most losses occurred in summer and autumn due to lush vegetation attracting more cattle, long daytime allowing movements deep into leopard habitats and dense cover favouring leopard hunts from ambush. Losses were recorded in only six owners and four villages, suggesting local rarity and patchy distribution of leopards. 4. We suggest that collars can be successfully applied to cattle freely grazing in habitats of leopards or other felids for a long time and thus remaining persistently exposed to depredation. As grazing cattle are usually not supervised by shepherds or dogs, collars can be the only practical protection tool. Production and sales of collars can become a sustainable small‐scale business for farmers to further boost conservation and rural livelihoods.
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