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39 results for “ecotoxicology”
Optimizing laboratory cultures of <i>Gammarus fossarum</i> (Crustacea: Amphipoda) as a study organism in environmental sciences and ecotoxicology
<p>Supplemental code and data for Alther, Krähenbühl, Bucher & Altermatt (2022) 'Optimizing laboratory cultures of <em>Gammarus fossarum</em> (Crustacea: Amphipoda) as a study organism in environmental sciences and ecotoxicology' (DOI: 10.1016/j.scitotenv.2022.158730). The repository folder contains three text files and a corresponding R script.</p> <p>Rerunning the analysis and producing figures requires two raw data files: LabdataAK_v6_210616_Daylength_input.txt and Nutrition_Exp_KaplanMeier_v1_input.txt. In order to reproduce the analysis and figures, run 'AmphipodHusbandry_20220919.R'. Make sure that your working directory is the folder containing all data files, easily achieved by (re)starting R (or R Studio) by double-clicking the R script file in the folder. The analysis script will produce all the figures from the paper, organized in a folder 'Results' and a subfolder 'Supplement'. Figures are prepared as pixel graphics (PNG).</p> <p>The R script was tested in R ver. 4.1.1 (Windows 10, version 21H1), 4.1.3 (macOS 11.6), and 4.2.0 (Ubuntu 22.04. Required packages are survival (version 3.2-13 worked), survminer (version 0.4.9 worked), and vioplot (version 0.3.7 worked).</p>
Predicted and experimental chemical and ecotoxicological properties for the toxic unit based hazard assessment
<p><strong>Description</strong></p> <p>This dataset contains ecotoxicity data of 1585 chemicals of environmental concern (CECs) and chemical identifiers. The ecotoxicity data was retrieved from <a href="https://cfpub.epa.gov/ecotox">US EPA ECOTOX Knowlegdebase</a> in ASCII file format and was aggregated for the ecotoxicity groups algae, crustaceans, and fish based on the ideas of <a href="https://dx.doi.org/10.1002/etc.3460">Busch et al. 2016</a>. The dataset includes the 5-percentile, the mean and the geomean of all retrieved ecotoxicity for each compound. Missing ecotoxicity data was estimated with ECOSAR 1.0 algorithms for green algae, daphnids, and fish using <a href="https://www.ufz.de/index.php?en=34593">ChemProp 6.8</a>. The main purpose of this dataset is the <a href="http://doi.org/10.1016/0043-1354(70)90018-7">toxic unit</a> (TU) based hazard assessment of environmental water samples. Chemical properties were estimated using <a href="https://github.com/kmansouri/OPERA">OPERA 2.7</a>, <a href="https://chemaxon.com/products/instant-jchem">Instant JChem</a>, and ACD Percepta 2015 based on QSAR-ready SMILES derived from OPERA 2.7. All data aggregated from EcoTox Knowledgebase (e.g., raw values, species, etc.) is available in the dataset in the detailed sheets. REcoTox, the processing script written in R is available on <a href="https://github.com/tsufz/REcoTox/releases/latest">GitHub</a>.</p> <p><strong>CAUTION</strong></p> <p>It needs to be emphasized that quantitative-structure activity relationship data is just an estimate, which does not necessarily reflect the real property and behaviour of a modelled compound. The calculated data needs to be reviewed in deep. Especially for non-polar or very polar compounds, the QSAR predictions might fail. If a compound ranks high in the TU ranking, it is required to search for literature or regulative data evidences to underpin the finding to avoid false positive prioritizations.</p> <p><strong>RELEASE NOTE</strong></p> <p>Version 210714_v1 was created with <a href="https://github.com/tsufz/REcoTox/releases/tag/v0.1.0">REcoTox version v0.1.0</a>.</p>
Pesticide ecotoxicology Tier 1 endpoints database
<p>The database was developed under the contract CT/EFSA/PPR/2010/03 with the purpose to provide a compilation in IUCLID 5.2 of ecotoxicological endpoints of the active substances and plant protection products (PPPs). It was developed to support the revision of guidance documents on aquatic and terrestrial ecotoxicology. The database for all Tier 1 studies where higher tier studies we also available in the dossier submitted under Directive 91/414/EEC for aquatic organisms, bees, non target arthropods, non target plants and soil organisms. The variables include report metadata, active substance, species tested, description of the experimental conditions and endpoint values (e.g LC50, NOEC, EC50, ER50) according to OECD harmonised templates for Effects on biotic systems. The database includes data extraction for 5745 ecotoxicological endpoint and 1625 risk assessment endpoints.</p> <p>The Format XML export from IUCLID 5.2. with author names removed. XSD is included. The study was outsourced after a procurement procedure.</p>
Figure 3. Limnocoris submontandoni testis with clomazone 162 in Ecotoxicological effects of commercial herbicides on the reproductive system of aquatic arthropod Limnocoris submontandoni (Hemiptera: Naucoridae)
Figure 3. Limnocoris submontandoni testis with clomazone 162 mg / L, (A) Apparent enlargement of the testicular interstice and degeneration of some spermatoids (SPTI), with normal concentrations of spermatozoa (SPTZ) in the outer regions, (B) spermatocytes (SPTO) with normal appearance and sperm (SPTZ) with slight alteration of spermatids (SPTI), C) profusion of sperm (SPTZ) with a high degree of compaction, indicating high rates of spermatogenesis and integrity of tubular cells (arrowhead). Dye: Toluidine Blue.
Figure 1 in Ecotoxicological effects of commercial herbicides on the reproductive system of aquatic arthropod Limnocoris submontandoni (Hemiptera: Naucoridae)
Figure 1. Photomicrographs of the control group of Limnocoris submontandoni, (A) helical distribution of the seminiferous tubule with germ cells, spermatogonia (SPGO), spermatocytes (SPTO), spermatids (SPTI), sperms (SPTZ), (B) spermatocytes (SPTO) and spermatids (SPTI) in different degrees of maturation, (C) spermatocytes (SPTO) with slightly colored areas (*) displaced to one of the cell poles, spermatids (SPTI) with different degrees of maturation, acrosome vesicle (arrows), elongation of slightly colored structures (**), elongated cells forming the tubular wall (arrowhead), core (n), (D) Spermatids (SPTI) in different degrees of maturation, spermatozoa (SPTZ) forming compact bundles and very elongated nucleus, nucleus (n) and acrosome vesicles (arrows) of some spermatoids and (E) Compact sperm bundles (SPTZ), sperm nuclei (n), tubular wall cells (arrowhead) and tracheole (tr). Dye: Toluidine Blue.
Figure 5 in Ecotoxicological investigation of cyanobacterial crude extracts to Daphnia magna under subchronic test conditions
Figure 5. Filtration (A) and ingestion (B) rates of Daphnia magna after exposing to cyanobacterial crude extracts. Asterisks indicate significant differences by the Kruskal-Wallis test, followed by the Wilcoxon rank-sum test for multiple comparison (*P ≤.05).
Figure 2 in Ecotoxicological investigation of cyanobacterial crude extracts to Daphnia magna under subchronic test conditions
Figure 2. The degradation of eggs and neonates (red arrows) of the Daphnia magna gravid females exposed to cyanobacterial crude extracts. A: dead eggs, B: dead neonate, C: malformation of the tail, and D: normal tail of control Daphnia magna.
Figure 1 in Ecotoxicological investigation of cyanobacterial crude extracts to Daphnia magna under subchronic test conditions
Figure 1. The effects of cyanobacterial crude extracts on the brood size. A: the first brood, B: the second brood. Asterisks indicate significant differences by the Kruskal-Wallis test, followed by the Wilcoxon rank-sum test for multiple comparison (*P <.05, **P <.01, ***P <.001).
Figure 3 in Ecotoxicological investigation of cyanobacterial crude extracts to Daphnia magna under subchronic test conditions
Figure 3. Regression equations and correlation coefficients (R2) describing the highest correlations between the number of neonates per female (as mean) and CCE concentrations. The red color indicates the microcystin-containing crude extract and the green color indicates the microcystin-free crude extract.
Figure 4 in Ecotoxicological investigation of cyanobacterial crude extracts to Daphnia magna under subchronic test conditions
Figure 4. The effects of cyanobacterial crude extracts on somatic growth of Daphnia magna. Asterisks indicate significant differences by the Kruskal-Wallis test, followed by the Wilcoxon rank-sum test for multiple comparison (*P <.05, **P <.01, ***P <.001).
Combining time-resolved transcriptomics and proteomics data for Adverse Outcome Pathway refinement in ecotoxicology
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The zebra mussel (Dreissena polymorpha) as a model organism for ecotoxicological studies: a prior 1H NMR spectrum interpretation of a whole body extract for metabolism monitoring.
<p>NMR data of the zebra mussel <em>Dreissena polymorpha</em> whole body polar extract metabolome</p> <p>- 1D <sup>1</sup>H annotated spectrum - 600 MHz</p> <p>- 2D <sup>1</sup>H-<sup>1</sup>H JRES spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>1</sup>H COSY spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>1</sup>H TOCSY spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>13</sup>C HSQC spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>13</sup>C HSQC spectrum - 800 MHz</p> <p>- 2D<sup>1</sup>H-<sup>31</sup>P HSQC spectrum - 800 MHz</p> <p>- <sup>1</sup>H annotated spectrum description tables (.xlsx)</p> <p>- Instructions for data visualization in Topspin</p>
Soil ecotoxicology needs robust biomarkers – a meta-analysis approach to test the robustness of gene expression-based biomarkers for measuring chemical exposure effects in soil invertebrates
<p>Gene expression-based biomarkers are regularly proposed as rapid, sensitive and mechanistically informative tools to identify whether soil invertebrates are experiencing adverse effects due to chemical exposure. However, before biomarkers could be deployed within diagnostic studies, systematic evidence of the robustness of such biomarkers to detect effects is needed. Here, we present an approach for conducting a systematic meta-analysis of the robustness of gene expression-based biomarkers in soil invertebrates.</p> <p>The approach was developed and trialled for two measurements of gene expression commonly proposed as biomarkers in soil ecotoxicology: metallothionein (MT) gene expression in earthworms for metals and heat shock protein 70 (HSP70) gene expression in earthworms for organic chemicals. From a systematic analysis of the published literature, we collected 294 unique gene expression data points and used linear mixed-effect models to assess concentration, exposure duration and species effects on the quantified response.</p> <p>This database provided contains gene-expression data from publications that have used gene expression-based biomakers to study effects of chemical pollutants on soil invertebrates. R scripts are provided that were used to study the patterns of gene expression as reported in accompanying publication. </p> <p>We encourage colleagues in the field to apply this approach to other biomarkers, as such quantitative assessment is a prerequisite to ensuring that the suitability and limitations of proposed biomarkers are known and stated.</p>
SYNTHESIS, CHARACTERIZATION AND ECOTOXICOLOGICAL EVALUATION OF Ag3VO4/Ag NANOCOMPOSITE
<p>Historically, the development of new methods of synthesizing materials has been linked to the development of societies, mainly due to the ability to promote changes in materials and enable new types of technological applications. Although there is quite sophisticated content about pulsed lasers in femtoseconds, there is still a need to understand the mechanisms of formation and transformation of semiconductor materials, as well as to verify the changes provided, in a more appropriate way, when synthesized by this technique. However, such development must always be combined with the need to minimize and verify environmental effects. This study had as its main objectives to synthesize Ag<sub>3</sub>VO<sub>4</sub> via the microwave-assisted hydrothermal method, in different synthesis times (t: 2, 4, 8, 16, 32, 64 min); irradiate the Ag3VO4 samples using a pulsed laser in femtoseconds to form the composite; characterize particulate composites; as well as to evaluate the ecotoxicity of the composite on the floating aquatic macrophyte species <em>Ricciocarpus natans</em>. The powders obtained from the composites were structurally characterized by the techniques of X-ray diffraction, Raman scattering spectroscopy and UV-Vis electronic spectroscopy, and had the surface characterized by scanning and transmission electron microscopy techniques, allowing the identification of structural alterations and surface. Theoretical calculations were used to understand the geometric, vibrational, electronic and charge distribution structures at the atomic level and the nature of chemical interactions present in semiconductor structures. In addition, toxicity bioassays were carried out until the 42nd day in order to obtain an analysis of the ecotoxicological effects, with the aid of mathematical modeling, of these particles on the bioindicator <em>Ricciocarpus natans</em>.</p> <p><strong>Electron Charge Density: 2D Map</strong></p> <p>Raw theoretical electron charge density files which are used to create 2D difference maps for Ag<sub>3</sub>VO<sub>4</sub> and AgVO<sub>3</sub> used in the main manuscript</p> <p><strong>Bader Charges</strong></p> <p>Raw theoretical Bader charges files for Ag<sub>3</sub>VO<sub>4</sub> and AgVO<sub>3</sub> used in the main manuscript</p> <p><strong>Band Structure and Density of States</strong></p> <p>Raw band structure and density of states files for Ag<sub>3</sub>VO<sub>4</sub> and AgVO<sub>3</sub> used in the main manuscript</p> <p><strong>Bioassays</strong></p> <p>Raw bioassays files for composite used in the main manuscript</p> <p><strong>Raman</strong></p> <p>Raw Raman files for Ag<sub>3</sub>VO<sub>4</sub> and composite and theoretical raw Raman files for Ag<sub>3</sub>VO<sub>4</sub> and AgVO<sub>3</sub> used in the manuscript</p> <p><strong>Rietveld Refinement</strong></p> <p>Raw Rietveld refinement files for Ag<sub>3</sub>VO<sub>4</sub> used in the manuscript</p> <p><strong>SEM</strong></p> <p>SEM images for Ag<sub>3</sub>VO<sub>4</sub> and composite used in the manuscript</p> <p><strong>TEM</strong></p> <p>TEM and EDX spectres and maps images for Ag<sub>3</sub>VO<sub>4</sub> and composite and nanodiffraction image for composite used in the manuscript</p> <p><strong>Optimized Structure</strong></p> <p>Raw optimized structure files for Ag<sub>3</sub>VO<sub>4</sub> and AgVO<sub>3</sub> used in the manuscript</p> <p><strong>TOPOND</strong></p> <p>Raw TOPOND files for Ag<sub>3</sub>VO<sub>4</sub> and AgVO<sub>3</sub> used in the manuscript</p> <p><strong>UV-Vis Spectroscopy</strong></p> <p>Raw UV-Vis files for Ag<sub>3</sub>VO<sub>4</sub> and AgVO<sub>3</sub> used in the manuscript</p> <p><strong>XRD</strong></p> <p>Raw XRD files for Ag<sub>3</sub>VO<sub>4</sub> and composite used in the manuscript</p> <p>Note: The words "composite" and "2min_irra or 64 min_irra" are used for the same kind of sample. They are synonymous in this work.</p> <p>Funding provided by: grant #2020/11232-3, São Paulo Research Foundation (FAPESP).</p> <p><em>This</em><em> </em><em>study</em><em> </em><em>was</em><em> </em><em>financed in part</em><em> </em><em>by</em><em> </em><em>the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES) – Finance</em><em> Code 001.</em></p>
Table_A2-5-8_Ecotoxicological threshold values soil organisms
<p>Ecotoxicological threshold values soil organisms</p>
Table_A2-5-7_Ecotoxicological threshold values pollinators
<p>Ecotoxicological threshold values pollinators</p>
The interplay between climate warming driven by greenhouse gas emissions and the ecotoxicological effects of microplastics: Insights from a meta-analysis
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FIGURE 2 in The description of Anacroneuria suerre sp. nov. from Costa Rica (Plecoptera: Perlidae) and using nymphs in ecotoxicological studies
FIGURE 2. Anacroneuria suerre sp. n. male-habitus (A) hammer (B), female subgenital plate (C), aedeagus ventral (D), aedeagus lateral (E), aedeagus dorsal (F).
FIGURE 4 in The description of Anacroneuria suerre sp. nov. from Costa Rica (Plecoptera: Perlidae) and using nymphs in ecotoxicological studies
FIGURE 4. Nymph of Anacroneuria suerre sp. n.: Body-dorsal (A), labrum (B), labium(C), right mandible (D) & right maxilla (E).
Data from: A novel real-world ecotoxicological dataset of pelagic microbial community responses to wastewater
<p>Real-world observational datasets that record and quantify pressure-stressor-response linkages between effluent discharges and natural aquatic systems are rare. With global wastewater volumes increasing at unprecedented rates, it is urgent that the present dataset is available to provide the necessary information about microbial community structure and functioning. Field studies were performed at two time-points in the Austral summer. Single-species and microbial community whole effluent toxicity (WET) testing was performed at a complete range of effluent concentrations and two salinities, with accompanying environmental data to provide new insights into nutrient and organic matter cycling, and to identify ecotoxicological tipping points. The two salinity regimes were chosen to investigate future scenarios based on a predicted salinity increase at the study site, typical of coastal regions with rising sea levels globally. Flow cytometry, amplicon sequencing of 16S and 18S rRNA genes and micro-fluidic quantitative polymerase-chain reactions (MFQPCR) were used to determine chlorophyll-a and total bacterial cell numbers and size, as well as taxonomic and functional diversity of pelagic microbial communities. This strong pilot dataset could be replicated in other regions globally and would be of high value to scientists and engineers to support the next advances in microbial ecotoxicology, environmental biomonitoring and estuarine water quality modelling.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.