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1,138 results for “Toxin”
San Francisco Estuary Institute Phytoplankton eDNA and Toxin Monitoring, San Francisco Bay, CA, 2014-2023
From late 2014-present, San Francisco Estuary Institute has conducted molecular monitoring of phytoplankton in partnership with the US Geological Survey from several stations stretching from Rio Vista in the North Delta to the Lower South Bay, past the Dumbarton Bridge. These samples have been analyzed for 18S eDNA data in partnership with Timothy Otten at Bend Genetics, targeting the V7 region. The included dataset covers the 2014-2023 period, including data up to 2022, conducted with an Illumina MISEQ platform, and from 2022-2023 using a NEXTSEQ platform, which enabled much greater sampling depth. Two sets of taxonomic assignments are included in this data release, one using the Silva database, and the other using the PR2 database, two of the leading sources of phytoplankton taxonomic data aiding in assignments of OTUs to taxa. Raw sequence data will also be uploaded to NCBI for comparison. Data collection continues and this release will be updated as new time periods are added.
Inter-Chemical Correlation results for the study: HHEARx2018-2532 (Environmental Toxins in Early Life: Shaping Health and Disease in Childhood)
Title: Environmental Toxins in Early Life: Shaping Health and Disease in Childhood <br>Species: Homo sapiens <br>Number of samples: 1147 <br>Number of named analytes: 48 <br>Datasource url: https://hheardatacenter.mssm.edu/PublicFile/ViewPublicFile?projectid=69 <br>
S40 | ALGALTOX | Algal toxins list from CompTox
<p>This is the collection associated with list S40 ALGALTOX on the NORMAN Suspect List Exchange.</p> <p><a href="https://www.norman-network.com/?q=suspect-list-exchange">https://www.norman-network.com/?q=suspect-list-exchange</a></p> <p>S40</p> <p>ALGALTOX</p> <p><strong>Algal toxins list from CompTox</strong></p> <p>ALGALTOX <a href="https://www.norman-network.com/sites/default/files/files/suspectListExchange/120219Update/ALGALTOX_14022019.xlsx">XLSX</a>, <a href="https://www.norman-network.com/sites/default/files/files/suspectListExchange/120219Update/ALGALTOX_14022019.csv">CSV</a> (14/02/2019)<br> CompTox <a href="https://comptox.epa.gov/dashboard/chemical_lists/algaltox">ALGALTOX List</a></p> <p>ALGALTOX <a href="https://www.norman-network.com/sites/default/files/files/suspectListExchange/120219Update/ALGALTOX_InChIKeys_14022019.txt">InChIKeys </a>(14/02/2019)</p> <p>List of algal toxins (generated during blooms) from the CompTox Chemicals Dashboard.</p>
Data and analysis code for a toxin induction study on two species of Dinophysis dinoflagellates
<h3>General description</h3> <p>This repository contains the datasets, analysis code and output generated and used in the manuscript "Effects of copepod chemical cues on intra- and extracellular toxins in two species of <em>Dinophysis</em>", which has been published as a research article in Harmful Algae (https://doi.org/10.1016/j.hal.2024.102793).</p> <h3>Files</h3> <p><strong>HRMS_data_Dinophysis_induction_experiment.zip </strong>contains the source high-resolution mass-spectroscopy endometabolomics data in open file formats.</p> <p><strong>Put_annot_sign_affect_feat_metabol_data.xlsx</strong> (corresponds to <strong>Supplementary spreadsheet 1</strong> in the main manuscript) contains putative annotations of significantly affected features from the metabolomics data, for each <em>Dinophysis </em>species (<em>D.</em> <em>sacculus </em>and <em>D. acuminata</em>) and each mode of ionization. Notably, results obtained from GNPS (Global Natural Products Social Molecular Networking, <a href="https://gnps.ucsd.edu/" target="_blank" rel="noopener noreferrer">https://gnps.ucsd.edu/</a>), and SIRIUS (<a href="https://bio.informatik.uni-jena.de/sirius/" target="_blank" rel="noopener noreferrer">https://bio.informatik.uni-jena.de/sirius/</a>) were mentionned. When available, MS/MS spectra were also provided. </p> <p><strong>Tabl_sign_affect_feat.xlsx</strong> (corresponds to <strong>Supplementary spreadsheet 3</strong> in the main manuscript) contains tables of significantly affected features (ANOVA, Tukey’s post hoc test, adjusted p-value cut-offs of 0.001 or 0.01) from the metabolomics data, for each <em>Dinophysis </em>species (<em>sacculus </em>and <em>acuminata</em>) and each mode of ionization. A visual representation (heatmaps) of these significant fetures are available as Figs S3-S6 in the supplementary information of the main mauscript. </p> <p><strong>Toxin_analysis_code_output.Rmd</strong> is the R-markdown file that produces the interactive analysis output output (<strong>Toxin_analysis_code_output.html</strong>, corresponds to <strong>Supplementary code & output </strong>in the main manuscript) of the toxin analysis, and uses the datasets <strong>Toxin_analysis_data.csv</strong>,<strong> pca_score_sacculus.csv</strong>,<strong> </strong>and<strong> pca_score_acuminata.csv</strong> source datasets to perform the statistical analyses and generate figures (details for each dataset below).</p> <p><strong>Toxin_analysis_data.csv</strong> (corresponds to <strong>Supplementary spreadsheet 2</strong> in the main manuscript) contains the main data used to statistically analyse the toxin and growth dynamics of both <em>Dinophysis</em> species in response to different grazer treatments, and to produce the majority of the figures in the main manuscript (Figs. 2-6) and supplementary information (Figs. S1-S2). </p> <p><strong>pca_score_sacculus.csv</strong> & <strong>pca_score_acuminata.csv</strong> contain the scores of the first two principal components of the PCA performed on LC-HRMS derived metabolomic profiles of <em>D. sacculus </em>and <em>D. acuminata</em> respectively, in both positive and negative ion mode. These are used to produce PCA score plots (Fig. 6 in the main manuscript and Fig. S2 in the supplementary information).</p> <p><strong>custom.css</strong> is a custom html style sheet file that formats the <strong>Toxin_analysis_code_output.html</strong> to display scrollable tables correctly. It is used by <strong>Toxin_analysis_code_output.Rmd </strong>and is necessary for true reproduction of the output (<strong>.html</strong>) file.</p>
Toxins: Toxic (985) DwCA
Various datasets about toxicity of organisms.<p></p>Various datasets about toxicity of organisms, literature sources.
Supplementary phylogenetic data for Rouïl et. al. 2020 "The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals"
<p>Supplementary phylogenetic data for Rouïl <em>et. al.</em> 2020 "The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals"</p> <p> </p> <p>The data set consists of the following sub-directories:</p> <p>1) "APSE_conserved_proteins_alns": Single-copy conserved genes codon sequences and alignments in FASTA format.</p> <p>2) "APSE_phylogeny": Files used for APSE phylogenetic and recombination analyses.</p> <p>3) "APSE_reannotations": GenBank-formatted files of the assemblies and re-annotations of APSE phages. Newly-sequenced phages deposited at the European nucleotide Archive are also included. ***New in this version***</p> <p>4) "APSE_toxin_lyzozyme": Files used for APSE toxin-cassette and lyzozyme-related gene phylogenies.</p> <p>5) "Arsenophonus_PHASTER": PHASTER phage annotation output files organised by organisim and contig/scaffold.</p> <p>6) "Hamiltonella_drafts": Newly-sequenced low-coverage draft <em>Hamiltonella</em> genomes in FASTA format.</p> <p>7) "Hamiltonella_phylogeny": files used for <em>Hamiltonella</em> phylogenetic analysis.</p> <p> </p> <p>See enclosed README.txt file for more details.</p> <p> </p> <p>* ver. 1.1.1: Updated annotations for APSE genomes including inteins missing in previous annotation files.</p>
The functions of cholera toxin subunit B as a modulator of silica nanoparticle endocytosis
<p>The gastrointestinal tract is the main target of orally ingested nanoparticles (NPs) and at 9 the same time exposed to noxious substances, such as bacterial components. We investigated the 10 interaction of 59 nm silica (SiO2) NPs with differentiated Caco-2 intestinal epithelial cells in the pres-11 ence of cholera toxin subunit B (CTxB) and compared the effects to J774A.1 macrophages. CTxB can 12 affect cellular functions and modulate endocytosis via binding to the monosialoganglioside (GM1) 13 receptor, expressed on both cell lines. After stimulating macrophages with CTxB, we observed no-14 table changes in the membrane structure but not in Caco-2 cells and no secretion of the pro-inflam-15 matory cytokine TNF-α was detected. Cells were then exposed to 59 nm SiO2 NPs and CtxB sequen-16 tially and simultaneously, resulting in a high NPs uptake in J774A.1 cells but no uptake in Caco-2 17 cells was detected. Flow cytometry analysis revealed that exposure of J774A.1 cells to CTxB resulted 18 in a significant reduction in the uptake of SiO2 NPs. In contrast, the uptake of NPs by highly selective 19 Caco-2 cells remained unaffected following CTxB exposure. Based on colocalization studies, CTxB 20 and NPs might enter cells via shared endocytic pathways, followed by their sorting into different 21 intracellular compartments. Our findings provide new insights into the CTxB function to modulate 22 SiO2 NPs uptake in phagocytic but not in differentiated intestine cells.</p>
S64 | NATOXAQ | NaToxAq: Natural Toxins and Drinking Water Quality - From Source to Tap
<p>This is the collection associated with list S64 NaToxAq on the NORMAN Suspect List Exchange.</p> <p><a href="https://www.norman-network.com/nds/SLE/">https://www.norman-network.com/nds/SLE/</a></p> <p><strong>NaToxAq: Natural Toxins and Drinking Water Quality - From Source to Tap</strong></p> <p>NaToxAq (<a href="https://natoxaq.ku.dk">https://natoxaq.ku.dk</a>) is a European Training Network (ETN) funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 722493, to produce knowledge about natural toxins in aquatic environments. This is a list of all NaToxAq chemicals registered in MassBank within the project, provided by Tobias Schulze, UFZ and hosted on the NORMAN Suspect List Exchange (<a href="https://www.norman-network.com/nds/SLE/">https://www.norman-network.com/nds/SLE/</a>). DOI: 10.5281/zenodo.3695174</p> <p> </p>
Portimine A toxin causes skin pathology through ZAKα-dependent NLRP1 inflammasome activation: LC-MS/MS raw data for Figure 1. C
<p>This dataset pertains to the LC-MS/MS analyses conducted as part of a study on microalgal toxins present in samples from Senegal, published in the paper entitled <em>"Portimine A toxin causes skin pathology through ZAK</em><em>α</em><em>-dependent NLRP1 inflammasome activation."</em> The data correspond to the quantification results of environmental samples presented in Figure 1C.</p> <p>The raw data were acquired using Analyst software (Applied Biosystems proprietary software). The materials and methods used to generate these data are detailed in the associated publication in <em>EMBO Molecular Medicine</em> (ISSN: 1757-4676, 2024).</p>
Salmonella, Shiga toxin-producing Escherichia coli O157:H7 and Listeria monocytogenes numbers during dry-aging of beef loins
<p>This dataset contains bacterial count data and loin characteristics from an experimental study assessing the survival/growth of <em>Salmonella</em>, <em>Escherichia coli</em> O157:H7 and <em>Listeria monocytogenes</em> during dry-aging of beef loins, after artificial inoculation. </p> <p>Four different csv files are provided with tabular data. A detailed description of the data is provided in the readme file.</p> <p> </p>
Data and code from: Seasonal variation in the response to a toxin-producing cyanobacteria in Daphnia
<p>Data and code accompanying: </p> <p>Hegg, Radersma & Uller. 2022. Seasonal variation in the response to a toxin-producing cyanobacteria in Daphnia. Freshwater Biology, accepted.</p> <p><strong>Abstract</strong></p> <ol> <li>Many populations of water fleas (<em>Daphnia</em>) are exposed to algal blooms dominated by microcystin-producing cyanobacteria. However, the severity of these effects on <em>Daphnia</em> fitness remain poorly understood in natural populations. </li> <li>We investigated seasonal changes in body size, reproduction and survival of <em>Daphnia</em> <em>longispina</em> individuals from five eutrophic lakes in southern Sweden. We tested whether individuals collected before, during or following algal blooms differed in their reproduction and survival when experimentally exposed to microcystin-producing cyanobacteria. </li> <li>The concentration of microcystin in the lakes was significantly higher during summer and autumn compared to spring, but there were substantial differences between lakes. The reproductive output of individuals declined consistently over the season, and this decline was stronger for <em>Daphnia</em> collected during periods of, or lakes from, high microcystin concentration. There was little evidence that individuals adapted to the toxin over the season. </li> <li>The strong seasonal changes in body size, reproduction and survival in these <em>Daphnia</em> <em>longispina</em> appears to be partly caused by variation in the abundance of toxin-producing cyanobacteria. Populations were unable to adapt sufficiently quickly during summer and autumn to recover from the negative effects of microcystin. We therefore suggest that seasonal increases in tolerance to microcystin-producing cyanobacteria have limited effects on the eco-evolutionary dynamics between <em>Daphnia</em> and phytoplankton.</li> </ol>
Data file: Amino acid sequence Cm28; a scorpion toxin
<p>The Data set contains the amino acid sequence of Cm28, a peptide toxin found in the venom of <em>Centruroides margaritatus</em>. The peptide sequence and functional data are reported in an article in the Journal of General Physiology (JGP) under this DOI 10.1085/jgp.202213146 and this data will appear in the UniProt Knowledgebase under the accession<br> number C0HM22.</p>
Fig. 4 in The dual impact of Ostreopsis cf. ovata on Mytilus galloprovincialis and Paracentrotus lividus: Toxin accumulation and pathological aspects Abstract
Fig. 4: Health status of sea urchins (avg±SDV, n = 4 animals) exposed to Ostreopsis cf. ovata (strain D483) for five days at different cell densities. Health index 1 corresponds to all four sea urchins alive after five days of exposure, 0 to all sea urchins dead in four days, intermediate values to different degrees of damage such as spine folded, partial and total spine loss and death in five days.
Fig. 6 in The dual impact of Ostreopsis cf. ovata on Mytilus galloprovincialis and Paracentrotus lividus: Toxin accumulation and pathological aspects Abstract
Fig. 6: Sea-urchin health status (avg±SDV, n = 4) after exposure to whole Ostreopsis cf. ovata cultures (strain 00APS0810-S1) or toxins extracted from cultures of the same cell density.
Fig. 2 in The dual impact of Ostreopsis cf. ovata on Mytilus galloprovincialis and Paracentrotus lividus: Toxin accumulation and pathological aspects Abstract
Fig. 2: Feeding of Mytilus galloprovincialis on Ostreopsis cf. ovata in a 72 h experiment. Weight-normalised ingested cells (avg±SDV) at different time intervals. Fresh microalgal cultures (2.17±0.23·103 cells ml-1) were provided every 24 h. Of the 10 animals of each replicate, 7-8 died at the beginning of the second day while the survivors were toxic (Table 1).
Fig. 5 in The dual impact of Ostreopsis cf. ovata on Mytilus galloprovincialis and Paracentrotus lividus: Toxin accumulation and pathological aspects Abstract
Fig. 5: Sea urchin health status (avg±SDV, n = 4) upon exposure to entire or sonicated Ostreopsis cf. ovata cultures (strain D483) of the same initial cell density.
Fig. 3 in The dual impact of Ostreopsis cf. ovata on Mytilus galloprovincialis and Paracentrotus lividus: Toxin accumulation and pathological aspects Abstract
Fig. 3: Feeding of Paracentrotus lividus (avg±SDV, n = 15) on Ostreopsis cf. ovata epiphytic on the red alga Asparagopsis taxiformis in five experiments lasting five days each. Experiment 4b was performed with the same animals as 4a, which were given a second stock of seaweeds after a two- day interval. Macroalgae (55-131 g) were completely eaten in all cases. Four additional experiments at low epiphytic cell density (<3.4·103 cells g-1) are not represented. Asterisks indicate the experiments in which sea urchins were weakly toxic at the mouse bioassay (Supplementary Material, Table S2).
Fig. 1 in The dual impact of Ostreopsis cf. ovata on Mytilus galloprovincialis and Paracentrotus lividus: Toxin accumulation and pathological aspects Abstract
Fig. 1: Feeding of Mytilus galloprovincialis in six 24 h experiments with animals of different sizes exposed to different Ostreopsis cf. ovata cell concentrations. A) Mussel wet weight (WW) and O. cf. ovata cell density at the beginning of each experiment (avg±SDV). B) Weight-normalised ingested cells (avg±SDV). The asterisks indicate experiments in which some or all replicates were toxic to the mouse bioassay (Supplementary Material, Table S1).
Toxins: Toxic Set
Various datasets about toxicity of organisms.<p></p>
Dataset related to: Shiga Toxin 2 Triggers C3a-Dependent Glomerular and Tubular Injury through Mitochondrial Dysfunction in Hemolytic Uremic Syndrome
<p>The files contain all the dataset included in the manuscript, divided by figure in each tab.</p> <p> </p> <p><strong>Abstract</strong></p> <p>Shiga toxin (Stx)-producing <em>Escherichia coli</em> is the predominant offending agent of post-diarrheal hemolytic uremic syndrome (HUS), a rare disorder of microvascular thrombosis and acute kidney injury possibly leading to long-term renal sequelae. We previously showed that C3a has a critical role in the development of glomerular damage in experimental HUS. Based on the evidence that activation of C3a/C3a receptor (C3aR) signaling induces mitochondrial dysregulation and cell injury, here we investigated whether C3a caused podocyte and tubular injury through induction of mitochondrial dysfunction in a mouse model of HUS. Mice coinjected with Stx2/LPS exhibited glomerular podocyte and tubular C3 deposits and C3aR overexpression associated with cell damage, which were limited by C3aR antagonist treatment. C3a promoted renal injury by affecting mitochondrial wellness as demonstrated by data showing that C3aR blockade reduced mitochondrial ultrastructural abnormalities and preserved mitochondrial mass and energy production. In cultured podocytes and tubular cells, C3a caused altered mitochondrial fragmentation and distribution, and reduced anti-oxidant SOD2 activity. Stx2 potentiated the responsiveness of renal cells to the detrimental effects of C3a through increased C3aR protein expression. These results indicate that C3aR may represent a novel target in Stx-associated HUS for the preservation of renal cell integrity through the maintenance of mitochondrial function.</p>
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Allen Brain Atlas
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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.