Items 1-20 of 1256

    • Journal Article

      Different response of bacteria, archaea and fungi to process parameters in nine full‐scale anaerobic digesters 

      Langer, Susanne G.; Gabris, Christina; Einfalt, Daniel; Wemheuer, Bernd; Kazda, Marian; Bengelsdorf, Frank R.
      Microbial Biotechnology 2019; 12(6) p.1210-1225
      Biogas production is a biotechnological process realized by complex bacterial, archaeal and likely fungal communities. Their composition was assessed in nine full-scale biogas plants with distinctly differing feedstock input and process parameters. This study investigated the actually active microbial community members by using a comprehensive sequencing approach based on ribosomal 16S and 28S rRNA fragments. The prevailing taxonomical units of each respective community were subsequently linked to process parameters. Ribosomal rRNA of bacteria, archaea and fungi, respectively, showed different compositions with respect to process parameters and supplied feedstocks: (i) bacterial communities were affected by the key factors temperature and ammonium concentration; (ii) composition of archaea was mainly related to process temperature; and (iii) relative abundance of fungi was linked to feedstocks supplied to the digesters. Anaerobic digesters with a high methane yield showed remarkably similar bacterial communities regarding identified taxonomic families. Although archaeal communities differed strongly on genus level from each other, the respective digesters still showed high methane yields. Functional redundancy of the archaeal communities may explain this effect. 28S rRNA sequences of fungi in all nine full-scale anaerobic digesters were primarily classified as facultative anaerobic Ascomycota and Basidiomycota. Since the presence of ribosomal 28S rRNA indicates that fungi may be active in the biogas digesters, further research should be carried out to examine to which extent they are important players in anaerobic digestion processes.
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      Contribution to the knowledge of the oribatid mite genus Kalloia (Acari, Oribatida, Carabodidae), with description of a new species from Indonesia 

      Ermilov, Sergey G.; Sandmann, Dorothee; Scheu, Stefan
      Acarologia 2019; 59(3) p.323-334
      The genus Kalloia (Oribatida, Carabodidae) is recorded in the Oriental region for the first time. A new species — Kalloia gerdweigmanni n. sp. — is described from litter of oil palm plantations and jungle rubber agroforests from Sumatra, Indonesia. It differs from Kalloia simpliseta Mahunka, 1985 by the presence of a transverse ridge in the mediodistal part of the lamellae, translamella and two thick, diagonal, convergent ridges forming a triangular structure in the medioanterior part of the notogaster, and by the localization of notogastral setae da, dm, la, lm, lp and h1. The generic status of Kalloia is discussed and supported. Kalloia mahunkai Pérez-Íñigo and Baggio, 1989 and Machadocepheus foveolatus Mahunka, 1978, which were considered representatives of Kalloia, are removed from this genus and combined preliminarily in Gibbicepheus. Revised generic diagnosis and data on ecology and distribution of known species of Kalloia are presented.
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      "The dead shall be raised": Multidisciplinary analysis of human skeletons reveals complexity in 19th century immigrant socioeconomic history and identity in New Haven, Connecticut 

      Aronsen, Gary P.; Fehren-Schmitz, Lars; Krigbaum, John; Kamenov, George D.; Conlogue, Gerald J.; Warinner, Christina; Ozga, Andrew T.; Sankaranarayanan, Krithivasan; Griego, Anthony; DeLuca, Daniel W.; et al.
      Eckels, Howard T.Byczkiewicz, Romuald K.Grgurich, TaniaPelletier, Natalie A.Brownlee, Sarah A.Marichal, AnaWilliamson, KylieTonoike, YukikoBellantoni, Nicholas F.
      PLOS ONE 2019; 14(9): Art. e0219279
      n July 2011, renovations to Yale-New Haven Hospital inadvertently exposed the cemetery of Christ Church, New Haven, Connecticut's first Catholic cemetery. While this cemetery was active between 1833 and 1851, both the church and its cemetery disappeared from public records, making the discovery serendipitous. Four relatively well-preserved adult skeletons were recovered with few artifacts. All four individuals show indicators of manual labor, health and disease stressors, and dental health issues. Two show indicators of trauma, with the possibility of judicial hanging in one individual. Musculoskeletal markings are consistent with physical stress, and two individuals have arthritic indicators of repetitive movement/specialized activities. Radiographic analyses show osteopenia, healed trauma, and other pathologies in several individuals. Dental calculus analysis did not identify any tuberculosis indicators, despite osteological markers. Isotopic analyses of teeth indicate that all four were likely recent immigrants to the Northeastern United States. Nuclear and mitochondrial DNA were recovered from three individuals, and these analyses identified ancestry, hair/eye color, and relatedness. Genetic and isotopic results upended our initial ancestry assessment based on burial context alone. These individuals provide biocultural evidence of New Haven's Industrial Revolution and the plasticity of ethnic and religious identity in the immigrant experience. Their recovery and the multifaceted analyses described here illuminate a previously undescribed part of the city's rich history. The collective expertise of biological, geochemical, archaeological, and historical researchers interprets socioeconomic and cultural identity better than any one could alone. Our combined efforts changed our initial assumptions of a poor urban Catholic cemetery's membership, and provide a template for future discoveries and analyses.
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      Associations between cognitive performance and sigma power during sleep in children with attention-deficit/hyperactivity disorder, healthy children, and healthy adults 

      Bestmann, Arnika; Conzelmann, Annette; Baving, Lioba; Prehn-Kristensen, Alexander
      PLOS ONE 2019; 14(10): Art. e0224166
      Sigma power during sleep is associated with cognitive abilities in healthy humans. We examined the relationship between sigma power in sleep EEG and intelligence and alertness in schoolchildren with ADHD (n = 17) in comparison to mentally healthy children (n = 16) and adults (n = 23). We observed a positive correlation between sigma power in sleep stage 2 and IQ in healthy adults but a negative correlation in children with ADHD. Furthermore, children with ADHD showed slower reaction times in alertness testing than both control groups. In contrast, only healthy children displayed a positive correlation between sigma power and reaction times. These data suggest that the associations between sigma power and cognitive performance underlie distinct developmental processes. A negative association between IQ and sigma power indicates a disturbed function of sleep in cognitive functions in ADHD, whereas the function of sleep appears to be matured early in case of motor-related alertness performance.
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      Shift in trophic niches of soil microarthropods with conversion of tropical rainforest into plantations as indicated by stable isotopes (15N, 13C) 

      Krause, Alena; Sandmann, Dorothee; Bluhm, Sarah L.; Ermilov, Sergey; Widyastuti, Rahayu; Haneda, Noor Farikhah; Scheu, Stefan; Maraun, Mark
      PLOS ONE 2019; 14(10): Art. e0224520
      Land-use change is threatening biodiversity worldwide, affecting above and below ground animal communities by altering their trophic niches. However, shifts in trophic niches with changes in land use are little studied and this applies in particular to belowground animals. Oribatid mites are among the most abundant soil animals, involved in decomposition processes and nutrient cycling. We analyzed shifts in trophic niches of six soil-living oribatid mite species with the conversion of lowland secondary rainforest into plantation systems of different land-use intensity (jungle rubber, rubber and oil palm monoculture plantation) in two regions of southwest Sumatra, Indonesia. We measured stable isotope ratios (13C/12C and 15N/14N) of single oribatid mite individuals and calculated shifts in stable isotope niches with changes in land use. Significant changes in stable isotope ratios in three of the six studied oribatid mite species indicated that these species shift their trophic niches with changes in land use. The trophic shift was either due to changes in trophic level (δ15N values), to changes in the use of basal resources (δ13C values) or to changes in both. The trophic shift generally was most pronounced between more natural systems (rainforest and jungle rubber) on one side and monoculture plantations systems (rubber and oil palm plantations) on the other, reflecting that the shifts were related to land-use intensity. Although trophic niches of the other three studied species did not differ significantly between land-use systems they followed a similar trend. Overall, the results suggest that colonization of very different ecosystems such as rainforest and intensively managed monoculture plantations by oribatid mite species likely is related to their ability to shift their trophic niches, i.e. to trophic plasticity.
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    • Journal Article

      Role of rhesus macaque IFITM3(2) in simian immunodeficiency virus infection of macaques 

      Winkler, Michael; Gärtner, Sabine; Markus, Lara; Hoffmann, Markus; Nehlmeier, Inga; Krawczak, Michael; Sauermann, Ulrike; Pöhlmann, Stefan
      PLOS ONE 2019; 14(11): Art. e0224082
      The experimental infection of rhesus macaques (rh) with simian immunodeficiency virus (SIV) is an important model for human immunodeficiency virus (HIV) infection of humans. The interferon-induced transmembrane protein 3 (IFITM3) inhibits HIV and SIV infection at the stage of host cell entry. However, it is still unclear to what extent the antiviral activity of IFITM3 observed in cell culture translates into inhibition of HIV/SIV spread in the infected host. We have shown previously that although rhIFITM3 inhibits SIV entry into cultured cells, polymorphisms in the rhIFITM3 gene are not strongly associated with viral load or disease progression in SIV infected macaques. Here, we examined whether rhIFITM3(2), which is closely related to rhIFITM3 at the sequence level, exerts antiviral activity and whether polymorphisms in the rhIFITM3(2) gene impact the course of SIV infection. We show that expression of rhIFITM3(2) is interferon-inducible and inhibits SIV entry into cells, although with reduced efficiency as compared to rhIFITM3. We further report the identification of 19 polymorphisms in the rhIFITM3(2) gene. However, analysis of a well characterized cohort of SIV infected macaques revealed that none of the polymorphisms had a significant impact upon the course of SIV infection. These results and our previous work suggest that polymorphisms in the rhIFITM3 and rhIFITM3(2) genes do not strongly modulate the course of SIV infection in macaques.
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    • Journal Article

      Correction: S1PR1 drives a feedforward signalling loop to regulate BATF3 and the transcriptional programme of Hodgkin lymphoma cells 

      Vrzalikova, K; Ibrahim, M; Vockerodt, M; Perry, T; Margielewska, S; Lupino, L; Nagy, E; Soilleux, E; Liebelt, D; Hollows, R; et al.
      Last, AReynolds, GAbdullah, MCurley, HCare, MKrappmann, DTooze, RAllegood, JSpiegel, SWei, WWoodman, C B JMurray, P G
      Leukemia 2019; 33(8) p.2126-2126
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      Parthenogenetic vs. sexual reproduction in oribatid mite communities 

      Maraun, Mark; Caruso, Tancredi; Hense, Jonathan; Lehmitz, Ricarda; Mumladze, Levan; Murvanidze, Maka; Nae, Ioana; Schulz, Julia; Seniczak, Anna; Scheu, Stefan
      Ecology and Evolution 2019; 9(12) p.7324-7332
      The dominance of sex in Metazoa is enigmatic. Sexual species allocate resources to the production of males, while potentially facing negative effects such as the loss of well-adapted genotypes due to recombination, and exposure to diseases and predators during mating. Two major hypotheses have been put forward to explain the advantages of parthenogenetic versus sexual reproduction in animals, that is, the Red Queen hypothesis and the Tangled Bank/Structured Resource Theory of Sex. The Red Queen hypothesis assumes that antagonistic predator-prey/ parasite-host interactions favor sex. The Structured Resource Theory of Sex predicts sexual reproduction to be favored if resources are in short supply and aggregated in space. In soil, a remarkable number of invertebrates reproduce by parthenogenesis, and this pattern is most pronounced in oribatid mites (Oribatida, Acari). Oribatid mites are abundant in virtually any soil across very different habitats, and include many sexual and parthenogenetic (thelytokous) species. Thereby, they represent an ideal model group to investigate the role of sexual versus parthenogenetic reproduction across different ecosystems and habitats. Here, we compiled data on oribatid mite communities from different ecosystems and habitats across biomes, including tropical rainforests, temperate forests, grasslands, arable fields, salt marshes, bogs, caves, and deadwood. Based on the compiled dataset, we analyzed if the percentage of parthenogenetic species and the percentage of individuals of parthenogenetic species are related to total oribatid mite density, species number, and other potential driving factors of the reproductive mode including altitude and latitude. We then interpret the results in support of either the Red Queen hypothesis or the Structured Resource Theory of Sex. Overall, the data showed that low density of oribatid mites due to harsh environmental conditions is associated with high frequency of parthenogenesis supporting predictions of the Structured Resource Theory of Sex rather than the Red Queen hypothesis.
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      Leaf and Crown Optical Properties of Five Early-, Mid- and Late-Successional Temperate Tree Species and Their Relation to Sapling Light Demand 

      Hagemeier, Marc; Leuschner, Christoph
      Forests 2019; 10(10)
      The optical properties of leaves and canopies determine the availability of radiation for photosynthesis and the penetration of light through tree canopies. How leaf absorptance, reflectance and transmittance and radiation transmission through tree canopies change with forest succession is not well understood. We measured the leaf optical properties in the photosynthetically active radiation (PAR) range of five Central European early-, mid- and late-successional temperate broadleaf tree species and studied the minimum light demand of the lowermost shade leaves and of the species’ o spring. Leaf absorptance in the 350–720 nm range varied between c. 70% and 77% in the crown of all five species with only a minor variation from the sun to the shade crown and between species. However, specific absorptance (absorptance normalized by mass per leaf area) increased about threefold from sun to shade leaves with decreasing leaf mass area (LMA) in the late-successional species (Carpinus betulus L., Tilia cordata Mill., Fagus sylvatica L.), while it was generally lower in the early- to mid-successional species (Betula pendula Roth, Quercus petraea (Matt.)Liebl.), where it changed only a little from sun to shade crown. Due to a significant increase in leaf area index, canopy PAR transmittance to the forest floor decreased from early- to late-successional species from ~15% to 1%–3% of incident PAR, linked to a decrease in the minimum light demand of the lowermost shade leaves (from ~20 to 1%–2%) and of the species’ saplings (from ~20 to 3%–4%). The median light intensity on the forest floor under a closed canopy was in all species lower than the saplings’ minimum light demand. We conclude that the optical properties of the sun leaves are very similar among early-, mid- and late-successional tree species, while the shade leaves of these groups di er not only morphologically, but also in terms of the resource investment needed to achieve high PAR absorptance.
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      Old World and New World Phasmatodea: Phylogenomics Resolve the Evolutionary History of Stick and Leaf Insects 

      Simon, Sabrina; Letsch, Harald; Bank, Sarah; Buckley, Thomas R.; Donath, Alexander; Liu, Shanlin; Machida, Ryuichiro; Meusemann, Karen; Misof, Bernhard; Podsiadlowski, Lars; et al.
      Zhou, XinWipfler, BenjaminBradler, Sven
      Frontiers in Ecology and Evolution 2019; 7: Art. 345
      Phasmatodea comprises over 3,000 extant species and stands out as one of the last remaining insect orders for which a robust, higher-level phylogenetic hypothesis is lacking. New research suggests that the extant diversity is the result of a surprisingly recent and rapid radiation that has been difficult to resolve with standard Sanger sequence data. In order to resolve the early branching events of stick and leaf insects, we analyzed transcriptomes from 61 species, including 38 Phasmatodea species comprising all major clades and 23 outgroup taxa, including all other Polyneoptera orders. Using a custom-made ortholog set based on reference genomes from four species, we identified on average 2,274 orthologous genes in the sequenced transcriptomes. We generated various sub-alignments and performed maximum-likelihood analyses on several representative datasets to evaluate the effect of missing data and matrix composition on our phylogenetic estimates. Based on our new data, we are able to reliably resolve the deeper nodes between the principal lineages of extant Phasmatodea. Among Euphasmatodea, we provide strong evidence for a basal dichotomy of Aschiphasmatodea and all remaining euphasmatodeans, the Neophasmatodea. Within the latter clade, we recovered a previously unrecognized major New World and Old World lineage, for which we introduce the new names Oriophasmata tax. nov. (“Eastern phasmids”) and Occidophasmata tax. nov. (“Western phasmids”). Occidophasmata comprise Diapheromerinae, Pseudophasmatinae, and Agathemera, whereas all remaining lineages form the Oriophasmata, including Heteropterygidae, Phylliinae, Bacillus, Lonchodidae (Necrosciinae + Lonchodinae), Clitumninae, Cladomorphinae, and Lanceocercata. We furthermore performed a divergence time analysis and reconstructed the historical biogeography for stick and leaf insects. Phasmatodea either originated in Southeast Asia or in the New World. Our results suggest that the extant distribution of Phasmatodea is largely the result of dispersal events in a recently and rapidly diversified insect lineage rather than the result of vicariant processes.
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      Analysis of Resistance of Ebola Virus Glycoprotein-Driven Entry Against MDL28170, An Inhibitor of Cysteine Cathepsins 

      Hoffmann, Markus; Kaufmann, Svenja Victoria; Fischer, Carina; Maurer, Wiebke; Moldenhauer, Anna-Sophie; Pöhlmann, Stefan
      Pathogens 2019; 8(4): Art. 192
      Ebola virus (EBOV) infection can cause severe and frequently fatal disease in human patients. The EBOV glycoprotein (GP) mediates viral entry into host cells. For this, GP depends on priming by the pH-dependent endolysosomal cysteine proteases cathepsin B (CatB) and, to a lesser degree, cathepsin L (CatL), at least in most cell culture systems. However, there is limited information on whether and how EBOV-GP can acquire resistance to CatB/L inhibitors. Here, we addressed this question using replication-competent vesicular stomatitis virus bearing EBOV-GP. Five passages of this virus in the presence of the CatB/CatL inhibitor MDL28170 were su cient to select resistant viral variants and sequencing revealed that all GP sequences contained a V37A mutation, which, in the context of native GP, is located in the base of the GP surface unit. In addition, some GP sequences harbored mutation S195R in the receptor-binding domain. Finally, mutational analysis demonstrated that V37A but not S195R conferred resistance against MDL28170 and other CatB/CatL inhibitors. Collectively, a single amino acid substitution in GP is su cient to confer resistance against CatB/CatL inhibitors, suggesting that usage of CatB/CatL inhibitors for antiviral therapy may rapidly select for resistant viral variants.
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      Oribatid mites show that soil food web complexity and close aboveground-belowground linkages emerged in the early Paleozoic 

      Schaefer, Ina; Caruso, Tancredi
      Communications Biology 2019; 2(1): Art. 387
      The early evolution of ecosystems in Palaeozoic soils remains poorly understood because the fossil record is sparse, despite the preservation of soil microarthropods already from the Early Devonian (~410 Mya). The soil food web plays a key role in the functioning of ecosystems and its organisms currently express traits that have evolved over 400 my. Here, we conducted a phylogenetic trait analysis of a major soil animal group (Oribatida) to reveal the deep time story of the soil food web. We conclude that this group, central to the trophic structure of the soil food web, diversified in the early Paleozoic and resulted in functionally complex food webs by the late Devonian. The evolution of body size, form, and an astonishing trophic diversity demonstrates that the soil food web was as structured as current food webs already in the Devonian, facilitating the establishment of higher plants in the late Paleozoic.
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      The German Ethical Culture Scale (GECS): Development and First Construct Testing 

      Tanner, Carmen; Gangl, Katharina; Witt, Nicole
      Frontiers in Psychology 2019; 10: Art. 1667
      Misconduct in organizations (such as fraud, stealing, deception, and harming others) is not only a matter of some "bad apples" but also related to the organizational context ("bad barrels"), which can facilitate either ethical or unethical behaviors. Given the financial crisis and recurring corporate ethics scandals, policymakers, regulators and organizations are interested in how to change their organizational cultures to enhance ethical behavior and to prevent further disasters. For this purpose, organizations need to better understand what strategies and factors of the organizational environment can affect (un)ethical behavior. However, to assess the corporate ethical culture, solid measures are required. Since there is an urgent need to have a German measure to promote research in German-speaking countries, this research developed and tested the German Ethical Culture Scale (GECS). Drawing on a prominent approach that has received much attention from scholars and practitioners alike, the GECS attempts to integrate the notion of compliance- and integrity-based ethics programs (with its focus on how to steer organizations) with the notion of ethical culture (with its focus on what factors inhibit or foster ethical behavior). Three studies with heterogeneous samples of German and Swiss employees and managers were conducted to develop, test and validate the multidimensional scale (total N > 2000). Overall, the studies provide first evidence of the measure's construct, criteria-related and incremental validity. The paper concludes with a discussion of the strengths and weaknesses of the GECS and implications for future research.
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      Implementing a Need-Adapted Stepped-Care Model for Mental Health of Refugees: Preliminary Data of the State-Funded Project “RefuKey” 

      Trilesnik, Beata; Altunoz, Umut; Wesolowski, Janina; Eckhoff, Leonard; Ozkan, Ibrahim; Loos, Karin; Penteker, Gisela; Graef-Calliess, Iris Tatjana
      Frontiers in Psychiatry 2019; 10: Art. 688
      Introduction: Refugees have been shown to be a rather vulnerable population with increased psychiatric morbidity and lack of access to adequate mental health care. By expanding regional psychosocial and psychiatric-psychotherapeutic care structures and adapting psychiatric routine care to refugees' needs, the state-funded project "refuKey" based in Lower Saxony, Germany, pursues to ease access to mental health care and increase service quality for refugees. A stepped-care treatment model along with intercultural opening of mental health care services is proposed. Methods: The project is subject to a four-part evaluation study. The first part investigates the state of psychiatric routine care for refugees in Lower Saxony by requesting data from all psychiatric clinics, participating and non-participating ones, regarding the numbers of refugee patients, their diagnoses, settings of treatment, etc. The second part explores experiences and work satisfaction of mental health care professionals treating refugees in refuKey cooperation clinics. The third part consists of interviews and focus group discussions with experts regarding challenges in mental health care of refugees and expectations for improvement through refuKey. The fourth part compares mental health parameters like depression, anxiety, traumatization, somatization, psychoticism, quality of life, as well as "pathways-to-care" of refuKey-treated refugees before and after treatment and, in a follow-up, to a non-refuKey-treated refugee control group. Results: RefuKey-treated refugees reported many mental health problems and estimated their mental health burden as high. The symptoms decreased significantly over the course of treatment. Mental health in the refuKey sample was strongly linked to post-migration stressors. Discussion: The state of mental health care for refugees is discussed. Implications for the improvement and the need for adaptation of routine mental health care services are drawn.
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      Physiological and anatomical investigation of the auditory brainstem in the Fat-tailed dunnart (Sminthopsis crassicaudata) 

      Garrett, Andrew; Lannigan, Virginia; Yates, Nathanael J.; Rodger, Jennifer; Mulders, Wilhelmina
      PeerJ 2019; 7: Art. e7773
      The fat-tailed dunnart (Sminthopsis crassicaudata) is a small (10-20 g) native marsupial endemic to the south west of Western Australia. Currently little is known about the auditory capabilities of the dunnart, and of marsupials in general. Consequently, this study sought to investigate several electrophysiological and anatomical properties of the dunnart auditory system. Auditory brainstem responses (ABR) were recorded to brief (5 ms) tone pips at a range of frequencies (4-47.5 kHz) and intensities to determine auditory brainstem thresholds. The dunnart ABR displayed multiple distinct peaks at all test frequencies, similar to other mammalian species. ABR showed the dunnart is most sensitive to higher frequencies increasing up to 47.5 kHz. Morphological observations (Nissl stain) revealed that the auditory structures thought to contribute to the first peaks of the ABR were all distinguishable in the dunnart. Structures identified include the dorsal and ventral subdivisions of the cochlear nucleus, including a cochlear nerve root nucleus as well as several distinct nuclei in the superior olivary complex, such as the medial nucleus of the trapezoid body, lateral superior olive and medial superior olive. This study is the first to show functional and anatomical aspects of the lower part of the auditory system in the Fat-tailed dunnart.
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      The NLRX R package: A next‐generation framework for reproducible NetLogo model analyses 

      Salecker, Jan; Sciaini, Marco; Meyer, Katrin M.; Wiegand, Kerstin
      Methods in Ecology and Evolution
      1. Agent‐based models find wide application in all fields of science where large‐scale patterns emerge from properties of individuals. Due to increasing capacities of computing resources it was possible to improve the level of detail and structural realism of nextgeneration models in recent years. However, this is at the expense of increased model complexity, which requires more efficient tools for model exploration, analysis and documentation that enable reproducibility, repeatability and parallelization. NetLogo is a widely used environment for agent‐based model development, but it does not provide sufficient built‐in tools for extensive model exploration, such as sensitivity analyses. One tool for controlling NetLogo externally is the r‐package RNetLogo. However, this package is not suited for efficient, reproducible research as it has stability and resource allocation issues, is not straightforward to be setup and used on high performance computing clusters and does not provide utilities, such as storing and exchanging metadata, in an easy way. 2. We present the r‐package nlrx, which overcomes stability and resource allocation issues by running NetLogo simulations via dynamically created XML experiment files. Class objects make setting up experiments more convenient and helper functions provide many parameter exploration approaches, such as Latin Hypercube designs, Sobol sensitivity analyses or optimization approaches. Output is automatically collected in user‐friendly formats and can be post‐processed with provided utility functions. nlrx enables reproducibility by storing all relevant information and simulation output of experiments in one r object which can conveniently be archived and shared. 3. We provide a detailed description of the nlrx package functions and the overall workflow. We also present a use case scenario using a NetLogo model, for which we performed a sensitivity analysis and a genetic algorithm optimization. 4. The nlrx package is the first framework for documentation and application of reproducible NetLogo simulation model analysis.
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      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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      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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      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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