High-content screening (HCS) workflows for FAIR image data management with OMERO.

High-content screening (HCS) for bioimaging is a powerful approach to studying biological processes, enabling the acquisition of large amounts of images from biological samples. However, it generates massive amounts of metadata, making HCS experiments a unique data management challenge. This data includes images, reagents, protocols, analytic outputs, and phenotypes, all of which must be stored, linked, and made accessible to users, scientists, collaborators, and the broader community to ensure sharable results.

Leveraging Zebrafish Embryo Phenotypic Observations to Advance Data-Driven Analyses in Toxicology.

Zebrafish have emerged as a central model organism in toxicological research. Zebrafish embryos are exempt from certain animal testing regulations, which facilitates their use in toxicological testing. Next to the zebrafish embryo acute toxicity test (ZFET) according to the OECD TG 236, fish embryos are used in mechanistic investigations, chemical screenings, ecotoxicology, and drug development.

Dynamics in zebrafish development define transcriptomic specificity after angiogenesis inhibitor exposure.

Testing for developmental toxicity is an integral part of chemical regulations. The applied tests are laborious and costly and require a large number of vertebrate test animals. To reduce animal numbers and associated costs, the zebrafish embryo was proposed as an alternative model.

Integrating Time-Resolved Gene-Expression Data into a Full GUTS Model as a Proxy for Toxicodynamic Damage in Zebrafish Embryo.

The immense production of the chemical industry requires an improved predictive risk assessment that can handle constantly evolving challenges while reducing the dependency of risk assessment on animal testing. Integrating omics data into mechanistic models offers a promising solution by linking cellular processes triggered after chemical exposure with observed effects in the organism. With the emerging availability of time-resolved RNA data, the goal of integrating gene expression data into mechanistic models can be approached.

Investigation of Peroxisome Proliferator-Activated Receptor Genes as Requirements for Visual Startle Response Hyperactivity in Larval Zebrafish Exposed to Structurally Similar Per- and Polyfluoroalkyl Substances (PFAS).

Background: Per- and polyfluoroalkyl Substances (PFAS) are synthetic chemicals widely detected in humans and the environment. Exposure to perfluorooctanesulfonic acid (PFOS) or perfluorohexanesulfonic acid (PFHxS) was previously shown to cause dark-phase hyperactivity in larval zebrafish.

Objectives: The objective of this study was to elucidate the mechanism by which PFOS or PFHxS exposure caused hyperactivity in larval zebrafish.

Curated mode-of-action data and effect concentrations for chemicals relevant for the aquatic environment.

Chemicals in the aquatic environment can be harmful to organisms and ecosystems. Knowledge on effect concentrations as well as on mechanisms and modes of interaction with biological molecules and signaling pathways is necessary to perform chemical risk assessment and identify toxic compounds. To this end, we developed criteria and a pipeline for harvesting and summarizing effect concentrations from the US ECOTOX database for the three aquatic species groups algae, crustaceans, and fish and researched the modes of action of more than 3,300 environmentally relevant chemicals in literature and databases.

Analysis of vascular disruption in zebrafish embryos as an endpoint to predict developmental toxicity.

Inhibition of angiogenesis is an important mode of action for the teratogenic effect of chemicals and drugs. There is a gap in the availability of simple, experimental screening models for the detection of angiogenesis inhibition. The zebrafish embryo represents an alternative test system which offers the complexity of developmental differentiation of an entire organism while allowing for small-scale and high-throughput screening.

A data-derived reference mixture representative of European wastewater treatment plant effluents to complement mixture assessment.

Aquatic environments are polluted with a multitude of organic micropollutants, which challenges risk assessment due the complexity and diversity of pollutant mixtures. The recognition that certain source-specific background pollution occurs ubiquitously in the aquatic environment might be one way forward to approach mixture risk assessment. To investigate this hypothesis, we prepared one typical and representative WWTP effluent mixture of organic micropollutants (EWERBmix) comprised of 81 compounds selected according to their high frequency of occurrence and toxic potential.

New approach methodologies in human regulatory toxicology - Not if, but how and when!

The predominantly animal-centric approach of chemical safety assessment has increasingly come under pressure. Society is questioning overall performance, sustainability, continued relevance for human health risk assessment and ethics of this system, demanding a change of paradigm. At the same time, the scientific toolbox used for risk assessment is continuously enriched by the development of "New Approach Methodologies" (NAMs).

A metabolomics approach to reveal the mechanism of developmental toxicity in zebrafish embryos exposed to 6-propyl-2-thiouracil.

A crucial component of a substance registration and regulation is the evaluation of human prenatal developmental toxicity. Current toxicological tests are based on mammalian models, but these are costly, time consuming and may pose ethical concerns. The zebrafish embryo has evolved as a promising alternative model to study developmental toxicity.

AI for predicting chemical-effect associations at the chemical universe level-deepFPlearn.

Many chemicals are present in our environment, and all living species are exposed to them. However, numerous chemicals pose risks, such as developing severe diseases, if they occur at the wrong time in the wrong place. For the majority of the chemicals, these risks are not known.

A risk based assessment approach for chemical mixtures from wastewater treatment plant effluents.

In this study, 56 effluent samples from 52 European wastewater treatment plants (WWTPs) were investigated for the occurrence of 499 emerging chemicals (ECs) and their associated potential risks to the environment. The two main objectives were (i) to extend our knowledge on chemicals occurring in treated wastewater, and (ii) to identify and prioritize compounds of concern based on three different risk assessment approaches for the identification of consensus mixture risk drivers of concern. Approaches include (i) PNEC and EQS-based regulatory risk quotients (RQs), (ii) species sensitivity distribution (SSD)-based hazard units (HUs) and (iii) toxic units (TUs) for three biological quality elements (BQEs) algae, crustacean, and fish.

Disentangling multiple chemical and non-chemical stressors in a lotic ecosystem using a longitudinal approach.

Meeting ecological and water quality standards in lotic ecosystems is often failed due to multiple stressors. However, disentangling stressor effects and identifying relevant stressor-effect-relationships in complex environmental settings remain major challenges. By combining state-of-the-art methods from ecotoxicology and aquatic ecosystem analysis, we aimed here to disentangle the effects of multiple chemical and non-chemical stressors along a longitudinal land use gradient in a third-order river in Germany.

A Self-Organizing Map of the Fathead Minnow Liver Transcriptome to Identify Consistent Toxicogenomic Patterns across Chemical Fingerprints.

Lack of consistent findings in different experimental settings remains a major challenge in toxicogenomics. The present study investigated whether consistency between findings of different microarray experiments can be improved when the analysis is based on a common reference frame ("toxicogenomic universe"), which can be generated using the machine learning algorithm of the self-organizing map (SOM). This algorithm arranges and clusters genes on a 2-dimensional grid according to their similarity in expression across all considered data.

Transcriptome-level effects of the model organic pollutant phenanthrene and its solvent acetone in three amphipod species.

Polyaromatic hydrocarbons (PAH) are common pollutants of water ecosystems originating from incineration processes and contamination with mineral oil. Water solubility of PAHs is generally low; for toxicity tests with aquatic organisms, they are therefore usually dissolved in organic solvents. Here we examined the effects of a typical model PAH, phenanthrene, and a solvent, acetone, on amphipods as relevant aquatic invertebrate models.

Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods.

Background: Lake Baikal is one of the oldest freshwater lakes and has constituted a stable environment for millions of years, in stark contrast to small, transient bodies of water in its immediate vicinity. A highly diverse endemic endemic amphipod fauna is found in one, but not the other habitat. We ask here whether differences in stress response can explain the immiscibility barrier between Lake Baikal and non-Baikal faunas.

Environmental risk or benefit? Comprehensive risk assessment of groundwater treated with nano Fe-based Carbo-Iron®.

Groundwater is essential for the provision of drinking water in many areas around the world. The performance of the groundwater-bearing aquifer relies on the ecosystem services provided by groundwater-related organisms. Therefore, if remediation of contaminated groundwater is necessary, the remediation method has to be carefully selected to avoid risk-risk trade-offs that might impact these ecosystems.

Combined effects of environmental xeno-estrogens within multi-component mixtures: Comparison of in vitro human- and zebrafish-based estrogenicity bioassays.

Some recent studies showed that in vitro bioassays based on fish or human estrogen receptor (ER) activation may have distinct responses to environmental samples, highlighting the need to better understand bioassay-specific ER response to environmental mixtures. For this purpose, we investigated a 12-compound mixture in two mixture ratios (M1 and M2) on zebrafish (zf) liver cells stably expressing zfERα (ZELHα cells) or zfERβ2 (ZELHβ2 cells) and on human ER-reporter gene (MELN) cells. The mixture included the well-known ER ligands bisphenol A (BPA) and genistein (GEN), and other compounds representatives of a freshwater background contamination.

Can Environmentally Relevant Neuroactive Chemicals Specifically Be Detected with the Locomotor Response Test in Zebrafish Embryos?

Chemicals considered as neuroactive (such as certain pesticides, pharmaceuticals, and industrial chemicals) are among the largest groups of bioactive substances recently detected in European rivers. However, the determination of nervous-system-specific effects has been limited using in vitro tests or conventional end points including lethality. Thus, neurobehavioral tests using in vivo models (e.

Mixture effects in samples of multiple contaminants - An inter-laboratory study with manifold bioassays.

Chemicals in the environment occur in mixtures rather than as individual entities. Environmental quality monitoring thus faces the challenge to comprehensively assess a multitude of contaminants and potential adverse effects. Effect-based methods have been suggested as complements to chemical analytical characterisation of complex pollution patterns.

Solid-phase extraction as sample preparation of water samples for cell-based and other in vitro bioassays.

In vitro bioassays are increasingly used for water quality monitoring. Surface water samples often need to be enriched to observe an effect and solid-phase extraction (SPE) is commonly applied for this purpose. The applied methods are typically optimised for the recovery of target chemicals and not for effect recovery for bioassays.

Characterization and risk assessment of seasonal and weather dynamics in organic pollutant mixtures from discharge of a separate sewer system.

Sites of wastewater discharge are hotspots for pollution of freshwaters with organic micropollutants and are often associated with adverse effects to aquatic organisms. The assessment, monitoring and managment of these hotspots is challenged by variations in the pollutant mixture composition due to season, weather conditions and random spills. In this study, we unraveled temporal exposure patterns in organic micropollutant mixtures from wastewater discharge and analyzed respective acute and sublethal risks for aquatic organisms.