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opencc-by-4.0Jul 2020View details →

Volcano plot of Sigma B-dependent differential gene expression of Clostridioides difficile

A customized whole-genome DNA microarray of Clostridioides difficile 630∆erm was used (8x15K format, Agilent). Quadruplicate samples were analysed for the DNA microarray. Using the ULS fluorescent labelling kit for Agilent arrays (Kreatech), 1 µg of total RNA was used for labelling with either Cy3 (Ptet-sigB) or Cy5 (Ptet-sLucopt). After pooling and fragmentation, 300 ng of labelled RNA per sample was hybridized according to the two-color microarray protocol from Agilent. DNA microarrays were scanned with an Agilent C scanner and analysed. CDS_ID=GenBank identifier, gene_name=annotated gene name (when available), locus_tag= locus tag, protein=annotation of protein function (when available), log2FC= log 2 of the fold change (sigB overproduction/control), adj_Pvalue = adjusted P-value, significance = -10log(adj_Pvalue).

opencc-zeroFeb 2020View details →

Data from: A quantitative review of density-dependent growth and survival in salmonids: biological mechanisms, methodological biases, and management implications

Understanding the complex variation in patterns of density-dependent individual growth and survival across populations is critical to adaptive fisheries management, but the extent to which this variation is caused by biological or methodological differences is unclear. Consequently, we conducted a correlational meta-analysis of published literature to investigate the relative importance of methodological and biological predictors on the shape and strength of density-dependent individual growth and survival in salmonids. We obtained 160 effect sizes from 75 studies of 12 species conducted between 1977-2019 that differed in experimental approach (sensu Hurlbert, 1984; 65 laboratory experiments, 60 observational field studies, and 35 field experiments). The experimental approach was the strongest factor influencing the strength of density-dependence across studies: density-dependent survival was stronger than growth in field observational studies, whereas laboratory experiments detected stronger density-dependent growth than survival. The difference between density-dependent growth and survival was minimal in field experiments, and between lotic and lentic habitats. The shape of density-dependence (logarithmic, linear, exponential, or density-independent) could be predicted with 66.7% accuracy based solely on the experimental approach and the density gradient (highest/lowest*100) of the study. Overall, the strength and shape of density-dependence were primarily influenced by methodological predictors, while biological factors (predator presence, food abundance, and species) had predictable but modest effects. For both empirical studies and adaptive fisheries management, we recommend using field experiments with a density gradient of at least 460% to detect the proper shape of the density-dependent response, or accounting for potential biases if observational or laboratory studies are conducted.

opencc-zeroJun 2020View details →

Data from: Prevalence of pelagic dependence among coral reef predators across an atoll seascape.

1) Coral reef food webs are complex, vary spatially and remain poorly understood. Certain large predators, notably sharks, are subsidised by pelagic production on outer reef slopes, but how widespread this dependence is across all teleost fishery target species and within atolls is unclear. 2) North Malé Atoll (Maldives) includes oceanic barrier as well as lagoonal reefs. Nine fishery target predators constituting ca. 55% of the local fishery target species biomass at assumed trophic levels 3-5 were selected for analysis. Data were derived from carbon (δ13C), nitrogen (δ15N) and sulfur (δ34S) stable isotopes from predator white dorsal muscle samples, and primary consumer species representing production source end-members. 3) Three-source Bayesian stable isotope mixing models showed that uptake of pelagic production extends throughout the atoll, with predatory fishes showing equal planktonic reliance between inner and outer edge reefs. Median plankton contribution was 65-80% for all groupers and 68-88% for an emperor, a jack and snappers. 4) Lagoonal and atoll edge predators are equally at risk from anthropogenic and climate-induced changes which may impact the linkages they construct, highlighting the need for management plans that transcend the boundaries of this threatened ecosystem.

Data from: Habitat-dependent occupancy and movement in a migrant songbird highlights the importance of mangroves and forested lagoons in Panama and Colombia

Climate change is predicted to impact tropical mangrove forests due to decreased rainfall, sea-level rise, and increased seasonality of flooding. Such changes are likely to influence habitat quality for migratory songbirds occupying mangrove wetlands during the tropical dry season. Overwintering habitat quality is known to be associated with fitness in migratory songbirds, yet studies have focused primarily on territorial species. Little is known about the ecology of non-territorial species that may display more complex movement patterns within and among habitats of differing quality. In this study, we assess within season survival and movement at two spatio-temporal scales of a non-territorial overwintering bird, the prothonotary warbler (Protonotaria citrea), that depends on mangroves and tropical lowland forests. Specifically, we (1) estimated within-patch survival and persistence over a six-week period using radio-tagged birds in central Panama and (2) modelled abundance and occupancy dynamics at survey points throughout eastern Panama and northern Colombia as the dry season progressed. We found that site persistence was highest in mangroves; however, the probability of survival did not differ among habitats. The probability of warbler occupancy increased with canopy cover, and wet habitats were least likely to experience local extinction as the dry season progressed. We also found that warbler abundance is highest in forests with the tallest canopies. This study is one of the first to demonstrate habitat-dependent occupancy and movement in a non-territorial overwintering migrant songbird, and our findings highlight the need to conserve intact, mature mangrove and lowland forests.

Data from: Depth dependent dive kinematics suggest cost-efficient foraging strategies by tiger sharks

Tiger sharks Galeocerdo cuvier are a keystone, top-order predator that are assumed to engage in cost-efficient movement and foraging patterns. To investigate the extent to which patterns of oscillatory diving by these animals conform to these patterns, we used a biologging approach to model their cost of transport. High-resolution biologging tags with tri-axial sensors were deployed on 21 tiger sharks at Ningaloo Reef for durations of 5-48 hours. Using overall dynamic body acceleration (ODBA) as a proxy for energy expenditure, we modelled the cost of transport of oscillatory movements of varying geometries in both horizontal and vertical planes for tiger sharks. The cost of horizontal transport was minimized by descending at the lowest possible angle and ascending at an angle of 5-14°, meaning that vertical oscillations conserved energy compared to swimming at a level depth. Reduction of vertical travel costs occurred at steeper angles. The absolute dive angles of tiger sharks increased between inshore and offshore zones, presumably to reduce the cost of transport while continuously hunting for prey in both benthic and surface habitats. Oscillatory movements of tiger sharks conform to strategies of cost-efficient foraging, and shallow inshore habitats appear to be an important habitat for both hunting prey and conserving energy while travelling.

The brains of elite soccer players are subject to experience-dependent alterations in white matter connectivity

Soccer is the only major sport with voluntary unprotected head-to-ball contact. It is crucial to determine if head impact through regular soccer sports training is manifested in brain structure and connectivity, and whether such alterations are due to sustained training per se. Using diffusion tensor imaging, we documented a comprehensive view of soccer players' brains in a sample of twenty-five right-handed male elite soccer players aged from 18 to 22 years and twenty-five non-athletic controls aged 19 to 24 years. Importantly, none had recalled a history of concussion. We performed a whole-brain tract-based spatial statistical analysis, and a tract-specific probabilistic tractography method to measure differences of white matter properties between groups. Whole-brain integrity analysis showed increased microstructural integrity within the corpus callosum tract in soccer players compared to controls. Further, tract-specific probabilistic tractography revealed that the anterior part of corpus callosum may be the brain structure most relevant to training experience, which may put into perspective prior evidence showing corpus callosum alteration in retired or concussed athletes practicing contact sports. Intriguingly, experience-related alterations showed left hemispheric lateralization of potential early signs of concussion-like effects. This is the first study to-date providing a definitive characterization of soccer-specific experience-related structural alterations. In sum, we concluded that the observed gains and losses may be due to a consequence of engagement in protracted soccer training that incurs prognostic hallmarks associated with minor injury-induced neural inflammation. Soccer is the only major sport with voluntary unprotected head-to-ball contact. It is crucial to determine if head impact through regular soccer sports training is manifested in brain structure and connectivity, and whether such alterations are due to sustained training per se. Using diffusion tensor imaging, we documented a comprehensive view of soccer players' brains in a sample of twenty-five right-handed male elite soccer players aged from 18 to 22 years and twenty-five non-athletic controls aged 19 to 24 years. Importantly, none had recalled a history of concussion. We performed a whole-brain tract-based spatial statistical analysis, and a tract-specific probabilistic tractography method to measure differences of white matter properties between groups. Whole-brain integrity analysis showed increased microstructural integrity within the corpus callosum tract in soccer players compared to controls. Further, tract-specific probabilistic tractography revealed that the anterior part of corpus callosum may be the brain structure most relevant to training experience, which may put into perspective prior evidence showing corpus callosum alteration in retired or concussed athletes practicing contact sports. Intriguingly, experience-related alterations showed left hemispheric lateralization of potential early signs of concussion-like effects. This is the first study to-date providing a definitive characterization of soccer-specific experience-related structural alterations. In sum, we concluded that the observed gains and losses may be due to a consequence of engagement in protracted soccer training that incurs prognostic hallmarks associated with minor injury-induced neural inflammation. Soccer is the only major sport with voluntary unprotected head-to-ball contact. It is crucial to determine if head impact through regular soccer sports training is manifested in brain structure and connectivity, and whether such alterations are due to sustained training per se. Using diffusion tensor imaging, we documented a comprehensive view of soccer players' brains in a sample of twenty-five right-handed male elite soccer players aged from 18 to 22 years and twenty-five non-athletic controls aged 19 to 24 years. Importantly, none had recalled a history of concussion. We performed a whole-brain tract-based spatial statistical analysis, and a tract-specific probabilistic tractography method to measure differences of white matter properties between groups. Whole-brain integrity analysis showed increased microstructural integrity within the corpus callosum tract in soccer players compared to controls. Further, tract-specific probabilistic tractography revealed that the anterior part of corpus callosum may be the brain structure most relevant to training experience, which may put into perspective prior evidence showing corpus callosum alteration in retired or concussed athletes practicing contact sports. Intriguingly, experience-related alterations showed left hemispheric lateralization of potential early signs of concussion-like effects. This is the first study to-date providing a definitive characterization of soccer-specific experience-related structural alterations. In sum, we concluded that the observed gains and losses may be due to a consequence of engagement in protracted soccer training that incurs prognostic hallmarks associated with minor injury-induced neural inflammation.

Escape from natural enemies depends on the enemies, the invader, and competition

The enemy release hypothesis (ERH) attributes the success of some exotic plant species to reduced top-down effects of natural enemies in the non-native range relative to the native range. Many studies have tested this idea, but very few have considered the simultaneous effects of multiple kinds of enemies on more than one invasive species in both the native and non-native ranges. Here, we examined the effects of two important groups of natural enemies – insect herbivores and soil biota – on the performance of Tanacetum vulgare (native to Europe but invasive in the USA) and Solidago canadensis (native to the USA but invasive in Europe) in their native and non-native ranges, and in the presence and absence of competition. In the field, we replicated full-factorial experiments that crossed insecticide, T. vulgare-S. canadensis competition, and biogeographic range (Europe vs. USA) treatments. In greenhouses, we replicated full-factorial experiments that crossed soil sterilization, plant-soil feedback, and biogeographic range treatments. We evaluated the effects of experimental treatments on T. vulgare and S. canadensis biomass. The effects of natural enemies were idiosyncratic. In the non-native range and relative to populations in the native range, T. vulgare escaped the negative effects of insect herbivores but not soil biota, depending upon the presence of S. canadensis; and S. canadensis escaped the negative effects of soil biota but not insect herbivores, regardless of competition. Thus, biogeographic escape from natural enemies depended upon the enemies, the invader, and competition. By explicitly testing the ERH in terms of more than one kind of enemy, more than one invader, and more than one continent, this study enhances our nuanced perspective of how natural enemies can influence the performance of invasive species in their native and non-native ranges.

Data from: Phytoplankton growth and stoichiometric responses to warming, nutrient addition and grazing depend on lake productivity and cell size

Global change involves shifts in multiple environmental factors that act in concert to shape ecological systems in ways that depend on local biotic and abiotic conditions. Little is known about the effects of combined global change stressors on phytoplankton communities, and particularly how these are mediated by distinct community properties such as productivity, grazing pressure and size distribution. Here, we tested for the effects of warming and eutrophication on phytoplankton net growth rate and C:N:P stoichiometry in two phytoplankton cell size fractions (<30 μm and >30 μm) in the presence and absence of grazing in microcosm experiments. Because effects may also depend on lake productivity, we used phytoplankton communities from three Dutch lakes spanning a trophic gradient. We measured the response of each community to multifactorial combinations of temperature, nutrient, and grazing treatments and found that nutrients elevated net growth rates and reduced carbon:nutrient ratios of all three phytoplankton communities. Warming effects on growth and stoichiometry depended on nutrient supply and lake productivity, with enhanced growth in the most productive community dominated by cyanobacteria, and strongest stoichiometric responses in the most oligotrophic community at ambient nutrient levels. Grazing effects were also most evident in the most oligotrophic community, with reduced net growth rates and phytoplankton C:P stoichiometry that suggests consumer‐driven nutrient recycling. Our experiments indicate that stoichiometric responses to warming and interactions with nutrient addition and grazing are not universal but depend on lake productivity and cell size distribution.

Functional redundancy in natural pico-phytoplankton communities depends on temperature and biogeography

Biodiversity affects ecosystem function, and how this relationship will change in a warming world is a major and well-examined question in ecology. Yet, it remains understudied for pico-phytoplankton communities, which contribute to carbon cycles and aquatic food webs year-round. Observational studies show a link between phytoplankton community diversity and ecosystem stability, but there is only scarce causal or empirical evidence. Here, we sampled phytoplankton communities from two geographically related regions with distinct thermal and biological properties in the Southern Baltic Sea, and carried out a series of dilution/regrowth experiments across three assay temperatures. This allowed us to investigate the effects of loss of rare taxa and establish causal links in natural communities between species richness and several ecologically relevant traits (e.g. size, biomass production, and oxygen production), depending on sampling location and assay temperature. We found that the samples' bio-geographical origin determined whether and how functional redundancy changed as a function of temperature for all traits under investigation. Samples obtained from the slightly warmer and more thermally variable regions showed overall high functional redundancy. Samples from the slightly cooler, less variable, stations showed little functional redundancy, i.e. function decreased when species were lost from the community. The differences between regions were more pronounced at elevated assay temperatures. Our results imply that the importance of rare species and the amount of species required to maintain ecosystem function even under short-term warming may differ drastically even within geographically closely related regions of the same ecosystem.

Supplemental tables from: Antifibrogenic activities of CYP11A1-derived vitamin D3-hydroxyderivatives are dependent on RORγ

Previous studies showed that non-calcemic 20(OH)D3, a product of CYP11A1 action on vitamin D3, has antifibrotic activity in human dermal fibroblasts and in a bleomycin mouse model of scleroderma. In this study we tested the role of RORγ, which is expressed in skin, in the action of CYP11A1-derived secosteroids using murine fibroblasts isolated from the skin of wild type (RORg+/+), knock out (RORg-/-) and heterozygote (RORg+/-) mice. CYP11A1-derived 20(OH)D3, 20,23(OH)2D3, 1,20(OH)2D3, and 1,20,23(OH)3D3 inhibited proliferation of RORγ+/+ fibroblasts in a dose-dependent manner with a similar potency to 1,25(OH)2D3. Surprisingly, this effect was reversed in RORγ+/- and RORγ-/- fibroblasts with the most pronounced stimulatory effect seen in RORγ-/- fibroblasts. All of the analogs tested inhibited TGF-β1-induced collagen synthesis in RORγ+/+ fibroblasts and the expression of other fibrosis-related genes. This effect was curtailed or reversed in RORγ-/- fibroblasts. These results show that the antiproliferative and antifibrotic activities of the vitamin D hydroxy-derivatives are dependent on a functional RORγ. The dramatic changes in the transcriptomes of fibroblasts of RORg-/- versus wild type mice following treatment with 20(OH)D3 or 1,20(OH)2D3 provide a molecular basis to explain, at least in part, the observed phenotypic differences

opencc-by-4.0Aug 2020View details →

The Brokers in a Dependency Ecosystem: An Empirical Study on using Package Managers

A package manager (PM) is crucial to most technology stacks, acting as a broker to ensure that a verified dependency package is correctly installed, configured, or removed from an application. Diversity in technology stacks has led to dozens of PMs with various features. While recent studies have shown that developers struggle to migrate their dependencies, the common assumption is that PMs broker dependencies without any issues. In this paper, we would like to explore issues faced by developers when using PMs through an empirical study of content on Stack Overflow (SO). Through a quantitative analysis of 470,806 posts related to 16 PMs, we first determine the importance of PM-related posts and extract topics contained in these posts. We then carry out a qualitative analysis of 1,131 posts related to the Maven, npm, and NuGet dependency ecosystems to analyze questions, underlying causes and their resolutions. Our results confirm that developers tend to struggle with PMs. The choice of PM affects their user experience, as questions are likely to arise from lack of instructions and error messages. We find that PM-related posts are not likely to get resolved, with only 40% to 50% having an accepted answer. Our work further lays out a road-map to investigate the trade-off between design features to understand what an ideal PM would look like.

opencc-by-4.0Aug 2020View details →

Data production of ''Lunar Titanium and Frequency‐Dependent Microwave Loss Tangent ... LRO Diviner Lunar Radiometers"

These are the image data of "Lunar Titanium and Frequency‐Dependent Microwave Loss Tangent as Constrained by the Chang'E‐2 MRM and LRO Diviner Lunar Radiometers".

Dispersal evolution diminishes the negative density dependence in dispersal

In many organisms, dispersal varies with the local population density. Such patterns of density-dependent dispersal (DDD) are expected to shape the dynamics, spatial spread and invasiveness of populations. Despite their ecological importance, empirical evidence for the evolution of DDD patterns remains extremely scarce. This is especially relevant because rapid evolution of dispersal traits has now been empirically confirmed in several taxa. Changes in DDD of dispersing populations could help clarify not only the role of DDD in dispersal evolution, but also the possible pattern of subsequent range expansion. Here, we investigate the relationship between dispersal evolution and DDD using a long-term experimental evolution study on Drosophila melanogaster. We compared the DDD patterns of four dispersal-selected populations and their non-selected controls. The control populations showed negative DDD, which was stronger in females than in males. In contrast, the dispersal-selected populations showed density-independent dispersal, where neither males nor females exhibited DDD. We compare our results with previous evolutionary predictions that focused largely on positive DDD, and highlight how the direction of evolutionary change depends on the initial DDD pattern of a population. Finally, we discuss the implications of DDD evolution for spatial ecology and evolution.

Alzheimer's disease risk gene BIN1 induces Tau-dependent network hyperexcitability — MEA Axion Biosciences Maestro Recordings, Figure 6

Genome-wide association studies identified the BIN1 locus as a leading modulator of genetic risk in Alzheimer's disease (AD). One limitation in understanding BIN1's contribution to AD is its unknown function in the brain. AD-associated BIN1 variants are generally noncoding and likely change expression. Here, we determined the effects of increasing expression of the major neuronal isoform of human BIN1 in cultured rat hippocampal neurons. Higher BIN1 induced network hyperexcitability on multielectrode arrays, increased frequency of synaptic transmission, and elevated calcium transients, indicating that increasing BIN1 drives greater neuronal activity. In exploring the mechanism of these effects on neuronal physiology, we found that BIN1 interacted with L-type voltage-gated calcium channels (LVGCCs) and that BIN1–LVGCC interactions were modulated by Tau in rat hippocampal neurons and mouse brain. Finally, Tau reduction prevented BIN1-induced network hyperexcitability. These data shed light on BIN1's neuronal function and suggest that it may contribute to Tau-dependent hyperexcitability in AD.

Model output data for "Negative density-dependent dispersal emerges from the joint evolution of density- and body condition-dependent dispersal strategies"

Empirical studies have documented both positive and negative density-dependent dispersal, yet most theoretical models predict positive density dependence as a mechanism to avoid competition. Several hypotheses have been proposed to explain the occurrence of negative density-dependent dispersal, but few of these have been formally modeled. Here, we developed an individual based model of the evolution of density-dependent dispersal. This model is novel in that it considers the effects of density on dispersal directly, and indirectly through effects on individual condition. Body condition is determined mechanistically, by having juveniles compete for resources in their natal patch. We found that the evolved dispersal strategy was a steep, increasing function of both density and condition. Interestingly, although populations evolved a positive density-dependent dispersal strategy, the simulated metapopulations exhibited negative density-dependent dispersal. This occurred because of the negative relationship between density and body condition: high density sites produced low condition individuals that lacked the resources required for dispersal. Our model therefore generates the novel hypothesis that observed negative density-dependent dispersal can occur when high density limits the ability of organisms to disperse. We suggest that future studies consider how phenotype is linked to the environment when investigating the evolution of dispersal.

Context-dependent modulation of natural approach behavior in mice

Specific features of visual objects innately draw approach responses in animals, and provide natural signals of potential reward. However, visual sampling behaviors and the detection of salient, rewarding stimuli are context and behavioral state-dependent. The neural mechanisms underlying how the brain encodes naturally appetitive stimuli and conditionally transforms them into approach behavior remain unclear. To mechanistically understand this process, we probed natural approach behavior in mice by employing a virtual stimulus orienting paradigm based on prey capture to quantify the conditional expression of visual stimulus-evoked innate approach in freely moving mice. We found that specific combinations of stimulus features selectively evoked innate approach versus freezing behavioral responses when stimuli were unexpected. However, we discovered that prey capture experience, and therefore the expectation of prey in the environment, selectively modified a range of visually-evoked appetitive behaviors, as well as altered those visual features that evoked approach. Thus, we found that mice exhibit robust and selective orienting responses to parameterized visual stimuli that can be readily modified via natural experience. This work provides critical insight into how natural appetitive behaviors are driven by both visual motion and internal state.

NMR data in 'Ca2+-dependent release of Synaptotagmin-1 from the SNARE complex on phosphatidylinositol 4,5-bisphosphate-containing membranes' by Voleti, Jaczynska and Rizo, eLife 2020

The Ca2+ sensor synaptotagmin-1 and the SNARE complex cooperate to trigger neurotransmitter release. Structural studies elucidated three distinct synaptotagmin-1-SNARE complex binding modes involving 'polybasic', 'primary' and 'tripartite' interfaces of synaptotagmin-1. We investigated these interactions using NMR and fluorescence spectroscopy. Synaptotagmin-1 binds to the SNARE complex through the polybasic and primary interfaces in solution. Ca2+-free synaptotagmin-1 binds to SNARE complexes anchored on PIP2-containing nanodiscs. R398Q/R399Q and E295A/Y338W mutations at the primary interface, which strongly impair neurotransmitter release, disrupt and enhance synaptotagmin-1-SNARE complex binding, respectively. Ca2+ induces tight binding of synaptotagmin-1 to PIP2-containing nanodiscs, releasing synaptotagmin-1-SNARE interactions. Specific effects of mutations in the polybasic region on Ca2+-dependent synaptotagmin-1-PIP2-membrane interactions correlate with their effects on release. Our data suggest that synaptotagmin-1 binds to the SNARE complex through the primary interface and that Ca2+ releases this interaction, inducing PIP2/membrane binding and allowing cooperation between synaptotagmin-1 and the SNAREs in membrane fusion to trigger release.

Data from: Attention-related modulation of caudate neurons depends on superior colliculus activity

Recent work has implicated the basal ganglia in visual perception and attention, in addition to their traditional role in motor control. The basal ganglia, especially the caudate nucleus "head" (CDh) of the striatum, receive indirect anatomical connections from the superior colliculus (SC), a midbrain structure that is known to play a crucial role in the control of visual attention. To test the possible functional relationship between these subcortical structures, we recorded CDh neuronal activity before and during unilateral SC inactivation in a spatial attention task. SC inactivation significantly altered the attention-related modulation of CDh neurons and strongly impaired the classification of task epochs based on CDh activity. Only inactivation of the same-side of SC as recorded CDh neurons, not the opposite-side, had these effects. These results demonstrate a novel interaction between SC activity and attention-related visual processing in the basal ganglia.

opengpl-3.0-or-laterAug 2020View details →

Data and R code used in Delory et al (2020) Soil chemical legacies trigger species-specific and context-dependent root responses in later arriving plants

This repository contains the data and R markdown files supporting the findings presented in Delory et al (2020) Soil chemical legacies trigger species-specific and context-dependent root responses in later arriving plants.