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Dataset results
23 results for “environmental degradation”
Enrichment and characterisation of a mixed-source ethanologenic community degrading the organic fraction of municipal solid waste under minimal environmental control
<p>The spread sheets in this workbook correspond to the datasets evaluating different inocula sources for ethanol (EtOH) production from the organic fraction of municipal solid waste (OMSW) at initially acid and neutral pH, and initially aerobic and anaerobic conditions.</p>
Data supporting: Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions
<p>Although the use and development of molecular biomonitoring tools based on environmental nucleic acids (eDNA and eRNA; collectively known as eNAs) have gained broad interest for the quantification of biodiversity in natural ecosystems, studies investigating the impact of site-specific physicochemical parameters on eNA-based detection methods (particularly eRNA) remain scarce. Here, we used a controlled laboratory microcosm experiment to comparatively assess the environmental degradation of eDNA and eRNA across an acid-base gradient following complete removal of the progenitor organism (<em>Daphnia pulex</em>). Using water samples collected over a 30-day period, eDNA and eRNA copy numbers were quantified using a droplet digital PCR (ddPCR) assay targeting the mitochondrial <em>cytochrome c oxidase</em> subunit I (COI) gene of <em>D. pulex</em>. We found that eRNA decayed more rapidly than eDNA at all pH conditions tested, with detectability—predicted by an exponential decay model—for up to 57 hours (eRNA; neutral pH) and 143 days (eDNA; acidic pH) post organismal removal. Decay rates for eDNA were significantly higher in neutral and alkaline conditions than in acidic conditions, while decay rates for eRNA did not differ significantly among pH levels. Collectively, our findings provide the basis for a predictive framework assessing the persistence and degradation dynamics of eRNA and eDNA across a range of ecologically relevant pH conditions, establish the potential for eRNA to be used in spatially and temporally sensitive biomonitoring studies (as it is detectable across a range of pH levels), and may be used to inform future sampling strategies in aquatic habitats.</p>
Data: Approaching a population level assessment of body size in pinnipeds using drones, an early warning of environmental degradation.
<p>Data and R sctipts for measuring harbour seal body sizes and estimating mass based on .shp files containing outlines. Associated with the manusctipt currently titled "Approaching a population level assessment of body size in pinnipeds using drones, an early warning of environmental degradation."</p> <p>1_Seal_Volume_Function.R: A function for the estimation of length, width, and ellipsoid volume of harbour seals from georeferenced polygons representing individual outlines 2_Polygon_Process.R: This script uses the curved_length_vol function (1_Seal_Volume_Function.R) to process a folder full of .shp file subfolders containing georeferenced polygons representing individual outlines and outputs a .csv with estimates of length, width, and ellipsoid volume for each individual. 3_Calibration.R: This script processes and calibrates summarized harbor seal measurements based on reference to known individuals</p> <p>CSV_Files: Folder containing data files</p> <p>Known_Seals.csv: True measurments of length and mass for known seals with derived estimates of 'true' width and volume. Drone based estimates of length, width, simple and complex volume for the same individuals, information on pose.</p> <p>measurments.csv: Drone based estimates of length, width, simple and complex volume for all individuals.</p> <p>Pup_growth.csv: Data on pup mass by age from Harding et al. 2005 (<a href="https://doi.org/10.1111/j.0269-8463.2005.00945.x" rel="nofollow">https://doi.org/10.1111/j.0269-8463.2005.00945.x</a>).</p> <p>Slottsskogen_Data.csv: True and drone based measurments for individual captive harbour seals taken on two seperate occasions.</p> <p>Summarised_Weights.csv: True measurments of length, girth, and mass for harbour seals.</p>
Fastq sequence files supporting: Assessing the degradation of environmental DNA and RNA based on genomic origin in a metabarcoding context
<p>Molecular tools of species identification based on eNAs (environmental nucleic acids; eDNA and eRNA) have the potential to greatly transform biodiversity science. However, the ability of eNAs to obtain "real-time" biodiversity estimates may be complicated by the differential persistence and degradation dynamics of the molecular template (eDNA or eRNA) and the barcode marker used. Here, we collected water samples over a 28-day period to comparatively assess species detection using eDNA and eRNA metabarcoding of two distinct barcode markers—a mitochondrial mRNA marker (COI) and a nuclear rRNA marker (18S)—following complete removal of <em>Arthropoda </em>taxa in a semi-natural freshwater system. Our findings demonstrate that <em>Arthropoda </em>community composition was largely influenced by marker choice, rather than molecular template, individual microcosm, or sampling time point. Further, although eRNA may capture similar species diversity as the established eDNA method, this finding may be marker dependent. Although we found little to no difference in decay rates observed among sample groups (COI eDNA, COI eRNA, 18S eDNA, 18S eRNA), this result is likely due to limitations in the ability of eNA-based metabarcoding to provide a strong correlation between true eNA copy numbers present in the environment and final read counts obtained (following the metabarcoding workflow). Collectively, our findings provide further support for the use of multi-marker assessments in metabarcoding surveys to unravel the broadest taxonomic diversity possible, highlight the limitations of eNA metabarcoding methods in providing accurate decay rate estimates, as well as establish the need for further comparative studies using both metabarcoding and single-species detection methods to assess the persistence and degradation dynamics of eNAs for a diverse range of taxa.</p>
Data from: Cyanobacterial colonization on epilithic mosses in degraded karst ecosystem: The role of moss traits and environmental factors
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Data supporting: Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions
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Fastq sequence files supporting: Assessing the degradation of environmental DNA and RNA based on genomic origin in a metabarcoding context
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Data from: Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities
Environmental degradation may have strong effects on community assembly processes. We examined the assembly of bacterial and fungal communities in anthropogenically altered and near-pristine streams. Using pyrosequencing of bacterial and fungal DNA from decomposed alder Alnus incana leaves, we specifically examined if environmental degradation deterministically decreases or increases the compositional turnover of bacterial and fungal communities. Our results showed that near-pristine streams and anthropogenically altered streams supported distinct fungal and bacterial communities. The mechanisms assembling these communities were different in near-pristine and altered environments. Environmental disturbance homogenized bacterial communities, whereas fungal communities were more dissimilar in disturbed sites than in near-pristine sites. Compositional variation of both bacteria and fungi was related to water chemistry variables in disturbed sites, further implying the influence of environmental degradation on community assembly. Bacterial and fungal communities in near-pristine streams were weakly controlled by environmental factors, suggesting that the relative importance of niche-based versus neutral processes in assembling microbial communities may strongly depend on the spatial scale and local environmental context. Our results thus suggest that environmental degradation may strongly affect the composition and β-diversity of stream microbial communities colonizing leaf litter, and that the direction of the change can be different between bacteria and fungi. A better understanding of the environmental tolerances of microbes and the mechanisms assembling microbial communities in natural environmental settings is needed to predict how environmental alteration is likely to affect microbial communities.
Supplementary Table S1and S2 (raw data) of "Effect of salinity and water dilution on environmental DNA degradation in freshwater environments"
<p>All data, including the raw values for the qPCR experiments</p>
DNA-based assessment of environmental degradation in an unknown fauna: the freshwater macroinvertebrates of the Indo-Burmese hotspot
<p>New methods are required for biomonitoring of poorly known tropical ecosystems, but biological assessments of environmental status are limited by insufficient information on taxonomy, composition, and ecology of local communities. The current work applies DNA-based assessment to establish the impact of various types of anthropogenic disturbances on the freshwater macroinvertebrates in an understudied biodiversity hotspot in South Asia, an area that attracts increasing attention for the loss of aquatic ecosystems.</p> <p>We sampled 16 river systems in the Chittagong Hill Tracts region of Bangladesh and characterised habitat intactness based on a set of 14 environmental parameters associated with habitat quality and human activities. Whole-community metabarcoding was used to investigate the distribution of hypothetical species-level clusters (Operational Taxonomic Units, OTUs) across sites of different impacts.</p> <p>We found >900 DNA clusters of insects, decapods and molluscs, dominated by Diptera, which revealed significant variation (p<0.001) in richness across sites. The presumed sensitive Ephemeroptera-Plecoptera-Trichoptera (EPT) represented 15.6% of total OTU richness. The type and strength of anthropogenic stressors varied greatly across streams but did not affect total OTU diversity. In contrast, EPT richness decreased by ~50% in response to habitat degradation. Partial-network analysis revealed 26 OTUs that may serve as potential indicators for either good or poor ecological status. Overall, our results document high diversity, local endemicity and pronounced responses to disturbance in these largely unexplored but threatened habitats.</p> <p><em>Synthesis and applications</em>: The proposed methodology combines local habitat surveys across sites of various degrees of disturbance with species-level metabarcoding, as a model for biological evaluation of water bodies in poorly known and inaccessible places across the world. Implemented here for the Indo-Burmese hotspot, the approach will have great value for applied conservation management as a step towards building a biomonitoring system in this region where currently little is known about the taxonomy, diversity and endemicity in both intact and disturbed ecosystems.</p>
Supplementary material 1 from: Ávila MP, Carvalho RN, Casatti L, Simião-Ferreira J, de Morais LF, Teresa FB (2018) Metrics derived from fish assemblages as indicators of environmental degradation in Cerrado streams. Zoologia 35: 1-8. https://doi.org/10.3897/zoologia.35.e12895
Table S1. Species identity, total number of individuals and species classification according to trophic guilds and habitat use. Terins: terrestrial invertivorous; Aquins: aquatic invertivorous; Det-Per: detritivorous/periphytivorous; Pis: piscivorous; Omni: omnivorous; WC: water column; Ben: benthic; Nectb: nectobenthic; Bank: bank-dwelling species; Rheo: rheophilic. Figure S1. Species accumulation (black) and rarefaction curve (gray) based on samples. : Data type: measurement
Dataset for Environmentally Degraded Polyethylene and Polypropylene
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Data from: Next-generation sequencing for rodent barcoding: species identification from fresh, degraded and environmental samples
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A quantitative analysis of vertebrate environmental DNA degradation in soil in response to time, UV light and temperature
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Data from: Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities
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DNA-based assessment of environmental degradation in an unknown fauna: the freshwater macroinvertebrates of the Indo-Burmese hotspot
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Data from: The interrelationship among economic activities, environmental degradation, material consumption, and population health in low-income countries: a longitudinal ecological study
Objectives: The theory of ecological unequal exchange explains how trade and various forms of economic activity create the problem of environmental degradation, and lead to the deterioration of population health. Based on this theory, our study examined the inter-relationship among economic characteristics, ecological footprints, CO2 emissions, infant mortality rates and under-5 mortality rates in low-income countries. Design: A longitudinal ecological study design. Setting: Sixty-six low-income countries from 1980 to 2010 were included in the analyses. Data for each country represented an average of 23 years (N=1497). Data sources: Data were from the World Development Indicators, UN Commodity Trade Statistics Database, Global Footprint Network and Polity IV Project. Analyses: Linear mixed models with a spatial power covariance structure and a correlation that decreased over time were constructed to accommodate the repeated measures. Statistical analyses were conducted separately by sub-Saharan Africa, Latin America and other regions. Results: After controlling for country-level sociodemographic characteristics, debt and manufacturing, economic activities were positively associated with infant mortality rates and under-5 mortality rates in sub-Saharan Africa. By contrast, export intensity and foreign investment were beneficial for reducing infant and under-5 mortality rates in Latin America and other regions. Although the ecological footprints and CO2 emissions did not mediate the relationship between economic characteristics and health outcomes, export intensity increased CO2 emissions, but reduced the ecological footprints in sub-Saharan Africa. By contrast, in Asia, the Middle East and North Africa, although export intensity was positively associated with the ecological footprints and also CO2 emissions, the percentage of exports to high-income countries was negatively associated with the ecological footprints. Conclusions: This study suggested that environmental protection and economic development are important for reducing infant and under-5 mortality rates in low-income countries.
Dataset of paper "Environmental life cycle assessment of UV-C LEDs vs. mercury lamps and oxidant selection for diclofenac degradation"
<p>Dataset of paper "Environmental life cycle assessment of UV-C LEDs vs. mercury lamps and oxidant selection for diclofenac degradation":</p> <ul> <li><span><span>Absolute impact across all categories of the Environmental Footprint (EF) for each treatment and scenario </span></span></li> <li><span><span>Relative impacts as percentages </span></span></li> </ul>
Figure 2 from: Ávila MP, Carvalho RN, Casatti L, Simião-Ferreira J, de Morais LF, Teresa FB (2018) Metrics derived from fish assemblages as indicators of environmental degradation in Cerrado streams. Zoologia 35: 1-8. https://doi.org/10.3897/zoologia.35.e12895
Figure 2 Stream sites grouped by their environmental characteristics by using UPGMA (Unweighted Pair Group Method with Arithmetic Mean). Height at y-axis refers to Euclidean distance.
Figure 3 from: Ávila MP, Carvalho RN, Casatti L, Simião-Ferreira J, de Morais LF, Teresa FB (2018) Metrics derived from fish assemblages as indicators of environmental degradation in Cerrado streams. Zoologia 35: 1-8. https://doi.org/10.3897/zoologia.35.e12895
Figure 3 Box-and-Whisker plots of the three sensitive metrics. Rectangles represent the 1st and 3rd quartiles, small squares are medians, bars are maximum and minimum values. Different letters indicate statistically significant differences.
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.