Dataset connected to the project "Cross-species bioanalytical assessment of the oxidative stress and xenobiotic metabolism modes of action for environmental water samples – a multi-layered approach to testing and modelling"
https://doi.org/10.5878/zwnq-qb88
Please refer to the README file for additional information.
The dataset comprises raw data, metadata, additional analyses, and a supplementary manuscript that links to three publications: the main article and two Data in Brief co-submissions.
Main article: Cross-species bioanalytical assessment of the oxidative stress and xenobiotic metabolism modes of action for environmental water samples – a multi-layered approach to testing and modelling
Data in Brief: A dataset on the multi-species and multi-endpoint bioanalytical assessment of environmental samples derived from Swedish wastewater treatment plants
Data in Brief: Human and zebrafish cross-species comparison on ligand affinity towards the aryl hydrocarbon receptor and Keap1 oxidative stress sensor: a molecular docking dataset
Subject: Earth and Environmental Sciences; Interdisciplinary: Environmental Chemistry; Health, Toxicology, and Mutagenesis; Water Science and Technology; Computational Biology
Specific subject area: Environmental Toxicology, Bioanalytical assessment of environmental samples, Molecular docking
Type of data: Table, Chart, Figure, Image, Graph, Molecular docking illustrations, Gene and Protein sequence files, Text
Data format: Raw – within supplementary files; Analysed – within the articles and supplementary files; Illustrative – within the articles and supplementary files
Data source location: Swedish University of Agricultural Sciences (SLU), Uppsala, Uppland, Sweden.
Background & Aim: New approach methods (NAMs), particularly effect-based in vitro assays such as embryo tests and cellular reporter systems, are approaching regulatory acceptance for high-throughput environmental monitoring, yet are predominantly derived from mammalian or bacterial models, limiting their representativeness for aquatic protection goals. This study evaluates the suitability of mammalian reporter assays as surrogates for aquatic vertebrates in effect-based assessments of environmental water samples through integrated biological, chemical, and computational analyses.
Data collection & description: environmental water samples were collected and analysed using a modified zebrafish embryo test, multispecies reporter gene assays targeting oxidative stress and xenobiotic metabolism, and cellular viability assays. Molecular docking and sequence alignment were conducted in silico using publicly available ligand, protein, and sequence databases, with structures processed and analysed using standard computational tools.
Location: Water sampling was conducted at three southern and western Swedish WWTPs (precise location disclosed due to confidentiality) and their respective catchments. All WWTPs are located in close proximity to waterbodies of primary anthropogenic and ecological concern. Chemical analyses and bioanalytics were conducted at SLU, Uppsala, Sweden. Molecular docking modelling and in silico-mediated effect-directed analysis were conducted at RECETOX, Masaryk University, Brno, Czech Republic.
Time period: Chemical analyses: 2018-2019. Bioanalytics: 2019-2022. Computational analyses: 2022-2024
Data organisation: please refer to the README file for a tabular summary.
Documentation files
Documentation files
Citation and access
Citation and access
Data access level:
Creator/Principal investigator(s):
- Sara Alsayfi
Research principal:
Principal's reference number:
- SLU.hbio.2026.IÄ-5
Data contains personal data:
No
Citation:
Language:
Method and outcome
Method and outcome
Unit of analysis:
Population:
cells, zebrafish embryos, in silico generated receptor-ligand models
Time method:
Description of sampling:
Recipient samples were collected as grab samples. Influent and effluent samples as 1-7 day composites. Zebrafish wild-type strains were kept in a state-of-the-art aquatic facility. Embryo tests were conducted in accordance with international guidelines and published literature. Reporter lines were cultured in a state-of-the-art cell culture laboratory. Mode-of-action-specific reporter assays were conducted in accordance with international guidelines and published literature.
The molecular docking dataset was entirely generated in silico. All generated and utilised PDBQT and FASTA-type files are given in the supplementary information (SI10). The following data sources were utilised: PubChem (https://pubchem.ncbi.nlm.nih.gov); UniProt (https://www.uniprot.org); RCSB Protein Data Bank (https://www.rcsb.org); National Center for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov). All acquired crystal and cryo-EM partial structures are mentioned in DIB_B, section 4, and the SM.
Time period(s) investigated:
Data format/data structure:
Data collection - Field observation
Data collection - Field observation
Mode of collection:
Field observation
Description of the mode of collection:
Samples from wastewater treatment plants (WWTPs; influent and effluent) and their recipients (upstream and downstream) were collected using solid-phase extraction (SPE-DEX, Horizon Technology).
Time period(s) for data collection:
2018-06-01 - 2019-12-31
Data collector:
- Swedish University of Agricultural Sciences
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Source of the data:
- Physical objects
Instrument
Instrument
Name:
SPE-DEX
Name:
DIONEX UltiMate 3000 ultra-high pressure liquid chromatography
Data collection - Biological tests
Data collection - Biological tests
Mode of collection:
Biological tests
Description of the mode of collection:
All samples were bioanalytically assessed using a modified zebrafish embryo test, which scored lethal and sublethal endpoints via stereo microscopy (Leica EZ4D) and time-lapse camera recording (Canon EOS 500D). Influent and effluent samples were also analysed using reporter gene assays across three species (zebrafish, human, and mouse) and two modes of action: oxidative stress and xenobiotic metabolism. Cellular viability was assessed via the MTS assay. All endpoints were recorded on a plate reader (Spark, Tecan).
Time period(s) for data collection:
2019-01-01 - 2022-12-31
Data collector:
- Swedish University of Agricultural Sciences
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Source of the data:
- Physical objects
- Biological samples
Instrument
Instrument
Name:
Leica EZ4D
Name:
Canon EOS 500D
Name:
Tecan Spark
Data collection - Simulation
Data collection - Simulation
Mode of collection:
Simulation
Description of the mode of collection:
Ligand 3D structures were downloaded from PubChem and optimised in Avogadro 1.2.0 and RESP ESP charge Derive (R.E.D.) Server Development 2.0. PDBQT working files were generated via MGLTools. Complete AlphaFold-predicted protein structures were acquired via UniProt. Tertiary structures of the PAS-B domain were predicted with AlphaFold2 using ColabFold. Partial crystal and cryo-EM structures were obtained from RCSB-PDB. AutoDock Vina was utilised for molecular docking. The docking predictions were analysed in PyMOL. For sequence alignment, FASTA files were retrieved from NCBI. Alignment was performed in Unipro Ugene using the ClustalW algorithm.
Time period(s) for data collection:
2022-01-01 - 2023-12-31
Data collector:
Source of the data:
- Other
Geographic coverage
Geographic coverage
Geographic location:
Geographic description:
Environmental water samples (wastewater treatment plant (WWTP) influents, effluents, and associated recipients) were collected from three WWTP sites in southern and western Sweden, located near water bodies of anthropogenic and ecological concern. Actual WWTP sites cannot be disclosed due to confidentiality, but the associated larger water body catchments are highlighted on the map.
Administrative information
Administrative information
Responsible department/unit:
Department of Animal Biosciences (HBIO)
Other research principals:
Contributor(s):
Funding
Funding
Funding agency:
- Royal Swedish Academy of Agriculture and Forestry
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Award number:
GFS2020-0056
Funding agency:
- U-share collaboration grant
Funding information:
SLU + UU collaboration grants for postdoctoral fellowships
Funding agency:
- Swedish Environmental Protection Agency
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Award number:
NV-03301-18
Funding agency:
- Ministry of Education Youth and Sports
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Award number:
LM2023069
Funding agency:
- European Union
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Award number:
CETOCOEN (857560)
Funding agency:
- Government of the Czech Republic
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Award number:
Grant Agency of the Czech Republic (25-18233M)
Funding agency:
- e-Infrastructure of the Czech Republic
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Award number:
90254
Funding agency:
- Czech National Infrastructure for Biological Data
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Award number:
LM2023055
