Zebrafish, from breeding to multiscale functional phenotyping

At IERP, it benefits from both the aquaculture facility and the functional phenotyping platform, combining animal production, experimentation, imaging and analysis.

Line production and maintenance

IERP produces and maintains zebrafish lines for experimental projects.

Models may include genetically modified lines.

The zebrafish facility maintains more than 20 transgenic lines.

Germ-free and gnotobiotic zebrafish and controlled microbiota

IERP has a dedicated SPF area supporting the production of germ-free or gnotobiotic zebrafish and projects involving controlled microbiota. This capability allows controlled studies of interactions between the host and defined microbial communities, according to project requirements.

Controlled breeding conditions

The facility includes two breeding rooms equipped with racks, a quarantine area with two racks and production capacity of approximately 50,000 eggs per year.

Animals are maintained in controlled aquaculture systems that regulate the main environmental parameters required by the model.

Depending on the scientific question, studies can involve adult fish, embryos or larvae.

Using early developmental stages

The transparency and small size of zebrafish embryos and larvae allow observation and analysis at different scales.

Integrating the zebrafish facility and functional phenotyping platform within IERP helps incorporate imaging or high-throughput analysis methods into the experimental design.

Screening and analysis of complex organisms

The platform has a COPAS FP-1000 for high-throughput analysis and sorting of complex biological objects, particularly zebrafish larvae and organoids.

For zebrafish larvae, COPAS can measure optical density and fluorescence signals, characterise their distribution along the organism and sort or dispense larvae into multiwell plates for further monitoring or analysis.

→ Discuss a screening strategy

Multiscale imaging

IERP offers several imaging approaches for zebrafish phenotyping:

• fluorescence microscopy
• confocal and two-photon microscopy
• light-sheet imaging
• histology and 3D reconstruction
• image analysis

The platform has a Benchtop mesoSPIM for 3D light-sheet imaging of cleared samples, complementing fluorescence, confocal and two-photon microscopy.

Infectious diseases, the host and the environment

Zebrafish can be used to explore interactions between the host, microorganisms and the environment.

Subject to project feasibility, containment and functional phenotyping capabilities can support model monitoring and link exposure, host response and phenotype.

Projects involving biological agents or GMOs are assessed during feasibility review before any experimental work is scheduled. The team can help the project lead identify biosafety constraints, define technical requirements and prepare information for regulatory scoping, while respecting the project’s scientific responsibilities.

Behaviour and welfare

Developing non-invasive monitoring methods is another focus of the platform.

Fish behavioural monitoring is being developed using video and movement analysis, with AI approaches investigated through R&D projects or collaborations.