Find research datasets worth reusing

opencc-by-4.0Sep 2020View details →

Targeted Disruption of Mouse Dip2B Leads to Abnormal Lung Development and Prenatal Lethality

Supplementary Figures Figure S1. Picro-sirius red stained sections of lung at E18.5. Figure S2. Cell apoptosis assay by TUNEL staining. A. Immunofluorescent TUNEL staining of E18.5 lungs. Scale bar: 66.2μm. B. Quantitative analysis by counting of multiple sections from 3 independent samples per group. NS= not significant by student’s t- test. Table S1. Summary of RNA-Seq mapping results. The raw reads were mapped to the Mus Musculus genome (GRCm38) using TopHat2. Table S2. List of DEG (Differentially Expressed Gene) from RNA-Seq analysis results. Differentail expression analysis was carried out using DESeq2. Table S3. List of DEGs annotated under Gene Ontology (GO) terms cell cycle and immune system process. Table S4. List of DEGs annotated under KEGG Pathway oxidative phosphorylation and hematopoietic cell lineage pathways.

opencc-zeroDec 2016View details →

Data from: Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity

Host-associated microbiomes perform many beneficial functions including resisting pathogens and training the immune system. Here, we show that amphibians developing in captivity lose substantial skin bacterial diversity, primarily due to reduced ongoing input from environmental sources. We combined studies of wild and captive amphibians with a database of over 1 000 strains that allows us to examine antifungal function of the skin microbiome. We tracked skin bacterial communities of 62 endangered boreal toads, Anaxyrus boreas, across 18 time points, four probiotic treatments, and two exposures to the lethal fungal pathogen Batrachochytrium dendrobatidis (Bd) in captivity, and compared these to 33 samples collected from wild populations at the same life stage. As the amphibians in captivity lost the Bd-inhibitory bacteria through time, the proportion of individuals exposed to Bd that became infected rose from 33% to 100% in subsequent exposures. Inoculations of the Bd-inhibitory probiotic Janthinobacterium lividum resulted in a 40% increase in survival during the second Bd challenge, indicating that the effect of microbiome depletion was reversible by restoring Bd-inhibitory bacteria. Taken together, this study highlights the functional role of ongoing environmental inputs of skin-associated bacteria in mitigating a devastating amphibian pathogen, and that long-term captivity decreases this defensive function.

opencc-by-4.0Oct 2016View details →

Dataset 1: All homozygous mutant embryo phenotypes from lethal and sub-viable lines scored by DMDD to date (Nov 2016)

The table lists the annotation data from homozygous mutant embryos that is the basis of the study. For every annotation the gene symbol, MGI_ID, allele symbol, DMDD_ID, MP term, ID and name is listed. In some cases the same MP term is listed more than once for a specific embryo (DMDD_ID), indicating the phenotypic abnormality was observed more than once in that embryo.

opencc-by-4.0Feb 2017View details →

Dataset 2: All wild type embryo phenotypes from lethal and sub-viable lines scored by DMDD to date (Nov 2016)

The table lists the annotation data from wild type embryos that is the basis of the study. For every annotation the gene symbol, MGI_ID, allele symbol, DMDD_ID, MP term, ID and name is listed. In some cases the same MP term is listed more than once for a specific embryo (DMDD_ID), indicating the phenotypic abnormality was observed more than once in that embryo.

opencc-by-nd-4.0Jun 2017View details →

Data-set of studies on mortality, sub-lethal and reproductive effect on amphibians and reptiles

Amphibians and reptiles have not been considered in environmental risk assessments of chemicals, which has generated some debate about whether risk posed by some pollutants like pesticides on these animals are covered by surrogates in the groups of fish, mammals and birds. In order to develop a scientifically sound and robust risk assessment scheme it is necessary to have enough information available on the biological relevance of effects observed in laboratory studies in view of population level effects, to identify sensitive life stages and to compare sensitivity of our target study groups with that of their surrogates. With these objectives, a systematic review of toxicological literature on amphibians and reptiles a comprehensive search of relevant literature on toxicity data related to amphibians and reptiles was conducted, using the appropriate search strings and combinations, in six different source types: multidisciplinary databases of scientific literature (i.e. Web of Science and Scopus), literature included in general amphibian and reptile ecotoxicology compilations, literature compiled in technical reports previously prepared for EFSA, literature sources used for creating amphibian or reptile records in the ecotoxicological database created by De Zwart (see references for details), literature sources used for creating amphibian or reptile records in toxicological online databases (United States Environmental Protection Agency’s Ecotoxicology Knowledgebase–ECOTOX, and National Library of Medicine’s Hazardous Substances Data Bank–HSDB), and indexes of herpetological scientific journals of local scope not included in Web of Science or Scopus. Data extraction consisted of the retrieval of relevant information, including among other fields: species, age, sex, chemical substance, exposure route and duration, type of recorded endpoint, type of response, exposure concentration, mean effect value of the control and exposed groups and the reported variability measures of these mean effects, and statistical significance of the comparison. <ul> <li>Data category 1: Reporting endpoints. Endpoints are defined here as benchmark values obtained from the integration of responses measured at different concentrations (e.g. LC50, EC50, NOEC, for which calculation it is necessary to make a regression with the percentage of effect at different exposure concentrations).</li> <li>Data category 2: Reporting responses for each tested level. These are studies in which different replicates of experimental units are exposed to different levels (doses, concentrations), including a control treatment, and a magnitude of effect is recorded at each level. For some of these studies it was possible to calculate an endpoint (e.g. LC50, EC50, NOEC) and for others it was not (e.g. if only one concentration was tested or if a statistically significant adjustment between exposure level and effect cannot be achieved).</li> </ul>   Three objectives corresponding to the review of the effects of chemicals on amphibians and reptiles, the main results of the study were: <ol> <li>Identification of the most sensitive life stage.</li> <li>Extrapolation from laboratory data to mesocosm and field situations</li> <li>Comparison with surrogate taxa</li> </ol> The review was conducted on 3642 full-text records for chemical exposure effects and 556 for life history traits, out of which 1332 and 204, respectively, were finally used for data extraction. The datasets comprised 23152 values corresponding to effects of chemicals and 1854 values corresponding to life history traits.

opencc-zeroNov 2023View details →

Characterizing a lethal mitonuclear incompatibility in naturally hybridizing Xiphophorus swordtails

The evolution of reproductive barriers is the first step in the formation of new species and can help us understand the diversification of life on Earth. These reproductive barriers often take the form of "hybrid incompatibilities," where alleles derived from two different species no longer interact properly in hybrids. Theory predicts that hybrid incompatibilities may be more likely to arise at rapidly evolving genes and that incompatibilities involving multiple genes should be common, but there has been sparse empirical data to evaluate these predictions. Here, we describe a mitonuclear incompatibility involving three genes in physical contact within respiratory Complex I of naturally hybridizing swordtail fish species. Individuals homozygous for mismatched protein combinations fail to complete embryonic development or die as juveniles, while those heterozygous for the incompatibility have reduced Complex I function and unbalanced representation of parental alleles in the mitochondrial proteome. We find that the impacts of different genetic interactions on survival are non-additive, highlighting subtle complexity in the genetic architecture of hybrid incompatibilities. Finally, we document the evolutionary history of the genes involved, showing signals of accelerated evolution and the first case of an incompatibility transferred between species via hybridization.

opencc-by-4.0Oct 2021View details →

Co-formulant in a commercial fungicide product causes lethal and sub-lethal effects in bumble bees

The dataset and code behind an experimental paper in Scientific Reports.  Paper DOI: https://doi.org/10.1038/s41598-021-00919-x Pollinators, particularly wild bees, are suffering declines across the globe, and pesticides are thought to be drivers of these declines. Research into, and regulation of pesticides has focused on the active ingredients, and their impact on bee health. In contrast, the additional components in pesticide formulations have been overlooked as potential threats. By testing an acute oral dose of the fungicide product Amistar, and equivalent doses of each individual co-formulant, we were able to measure the toxicity of the formulation and identify the ingredient responsible. We found that a co-formulant, alcohol ethoxylates, caused a range of damage to bumble bee health. Exposure to alcohol ethoxylates caused 30% mortality and a range of sublethal effects. Alcohol ethoxylates treated bees consumed half as much sucrose as negative control bees over the course of the experiment and lost weight. Alcohol ethoxylates treated bees had significant melanisation of their midguts, evidence of gut damage. We suggest that this gut damage explains the reduction in appetite, weight loss and mortality, with bees dying from energy depletion. Our results demonstrate that sublethal impacts of pesticide formulations need to be considered during regulatory consideration, and that co-formulants can be more toxic than active ingredients.

opencc-zeroOct 2021View details →

Evaluation of lethal control of introduced sugar gliders

Lethal control of invasive mammalian predators can be controversial and is rarely a 'silver bullet' for conservation problems. Evaluating the efficacy of lethal control is important for demonstrating the benefits to threatened species are real and detecting unexpected perverse outcomes. We implemented a pilot study to evaluate if lethal control of introduced sugar gliders Petaurus breviceps can reduce the rate of nest predation on Tasmanian hollow nesting birds including swift parrots (Lathamus discolor). Using a before-after-control-impact design, we implemented a lethal control treatment whereby we attempted to remove sugar gliders from three treatment sites. In each time period across sites we monitored quail eggs in nest boxes to record predation, and used cameras to detect sugar gliders.We caught nine sugar gliders over three treatment sites. The model best supported by the data indicated an effect of site x time period on both egg survival and the rate of glider detection on cameras. There was no support for an effect of treatment on our data. We also recorded predation of a real swift parrot nest by sugar gliders at a treatment site where we recorded no predation of quail eggs. Our pilot study shows that at small scales, intensive lethal control of gliders yields low capture rates and no discernible effect on the metrics we measured. We conclude that alternative approaches to controlling the impact of sugar gliders, such as habitat protection, are critical in this study system before lethal control is widely implemented as a management tool.

opencc-zeroJun 2022View details →

Stable dingo population structure and purity over 11 years of lethal management

Interactions between predators and humans are a key driver of human-wildlife conflicts and can underpin the management of predator populations. Management of the impacts of dingoes (Canis familiaris) on livestock and native species is a prime example of a persistent and contentious predator management issue with potential impacts on the integrity of dingo populations. To manage the potential impacts of dingoes and their control, it is imperative to understand the effects of control approaches on their populations in the short and long term. Hybridisation of dingoes with domestic dogs (C. familiaris) threatens the genetic integrity of pure dingoes. It has been hypothesised that lethal control of dingoes can facilitate hybridisation by disrupting pack social structures leading to increased dingo-domestic dog interactions. Here we use dingo genetic samples from three distinct sampling periods: 2009, 2014, and 2020, within the Murchison Regional Vermin Cell (MRVC) area in Western Australia (WA). At the time of the study, the MRVC was a large, partially-fenced area in which dingo control has been performed for many decades. We assess dingo purity, population clustering, gene flow, and individual relatedness in the context of ongoing control. We identified three genetically distinct populations in the study area, consistent with previous genetic studies of WA, but did not find any evidence of change in dingo purity or population characteristics, however barrier fencing may be influencing recent gene flow. Policy implications: The metapopulation of dingoes in the southern rangelands of WA appears to be stable over the 11 years assessed here and there is no evidence that lethal control to reduce losses to livestock production and for conservation of native wildlife is putting dingo purity at risk. Fencing appears to be an effective management tool as there is some evidence it is separating dingo populations in areas where the fences are well maintained.

opencc-zeroMay 2024View details →

Quantifying intraspecific variation in host resistance and tolerance to a lethal pathogen

Testing for intraspecific variation for host tolerance or resistance in wild populations is important for informing conservation decisions about captive breeding, translocation, and disease treatment. Here, we test the importance of tolerance and resistance in multiple populations of boreal toads (Anaxyrus boreas boreas) against Batrachochytrium dendrobatidis (Bd), the amphibian fungal pathogen responsible for the greatest host biodiversity loss due to disease. Boreal toads have severely declined in Colorado (CO) due to Bd, but toad populations challenged with Bd in western Wyoming (WY) appear to be less affected. We used a common garden infection experiment to expose post-metamorphic toads sourced from four populations (2 in CO and 2 in WY) to Bd and monitored changes in mass, pathogen burden, and survival for eight weeks. We used a multi-state modeling approach to estimate weekly survival and transition probabilities between infected and cleared states, reflecting a dynamic infection process that traditional approaches fail to capture. We found that WY boreal toads are more tolerant to Bd infection with higher survival probabilities than those in CO when infected with identical pathogen burdens. WY toads also appeared more resistant to Bd with a higher probability of infection clearance and an average of five days longer to reach peak infection burdens. Our results demonstrate strong intraspecific differences in tolerance and resistance that likely contribute to why population declines vary regionally across this species. Our multi-state framework allowed us to gain inference on typically hidden disease processes when testing for host tolerance or resistance. Our findings demonstrate that describing an entire host species as 'tolerant' or 'resistant' (or lack thereof) is unwise without testing for intraspecific variation.

opencc-zeroMay 2024View details →

Consumption of pollen contaminated with field-realistic concentrations of fungicide cause sub-lethal effects in common eastern bumble bee (Bombus impatiens [Hymenoptera]: [Apidae]) microcolonies

Bumble bees are declining across the globe. Causes of this decline have been attributed to a variety of stressors, including pesticides. Fungicides are a type of pesticide that have been understudied in the context of bumble bee health. As a result, fungicides are often applied to flowering plants without consideration of pollinator exposure. Recent work demonstrates that fungicides have sublethal effects in bumble bees, but little is known about how much fungicide it takes to cause these sublethal effects. To address this gap in the literature, we fed microcolonies of the common eastern bumble bee (Bombus impatiens) pollen contaminated with a range of fungicide concentrations. We chose these concentrations based on the range of fungicide concentrations in pollen and nectar that were reported in the literature. Results revealed that later-stage pupae and newly emerged males are potentially sensitive to fungicide exposure, showing smaller size and reduced fat reserves at intermediate levels of contamination. Compared to the control, intermediated levels of fungicide-contaminated pollen led to increased pupal mortality and delayed male emergence. Contrary to expectations, higher fungicide levels did not exhibit a linear relationship with negative impacts, suggesting nuanced effects. Because body size and emergence timing are important aspects of bumble bee reproductive behavior, results have implications for mating success, potentially disrupting colony development.

opencc-by-4.0Dec 2023View details →

Fig 1 in Sub-lethal toxic effect of cadmium chloride (CdCl ) on freshwater murrel Channa punctata (BLOCH)

Fig 1: Channa punctata

Fig. 4 in Morganella morganii (Enterobacteriales: Enterobacteriaceae) is a lethal pathogen of Mexican fruit fly (Diptera: Tephritidae) larvae

Fig. 4. Mean number ± SE of Mexican fruit fly pupae produced per cup (#).

Fig. 5 in Morganella morganii (Enterobacteriales: Enterobacteriaceae) is a lethal pathogen of Mexican fruit fly (Diptera: Tephritidae) larvae

Fig. 5. Percent adult emergence ± SE and percent flight ability ± SE by treatment type.

Fig. 2 in Morganella morganii (Enterobacteriales: Enterobacteriaceae) is a lethal pathogen of Mexican fruit fly (Diptera: Tephritidae) larvae

Fig. 2. Bio-assay diet cups at sifing: Lef=Control, Right=inoculated with Morganella morganii.

Fig. 6 in Morganella morganii (Enterobacteriales: Enterobacteriaceae) is a lethal pathogen of Mexican fruit fly (Diptera: Tephritidae) larvae

Fig. 6. Adult Mexican fruit fly ± SE produced from 50 g of diet.

Fig. 1 in Morganella morganii (Enterobacteriales: Enterobacteriaceae) is a lethal pathogen of Mexican fruit fly (Diptera: Tephritidae) larvae

Fig. 1. Mean weight ± SE of Mexican fruit fly larvae produced per cup (g).