Zebrafish Biomedical Research Applications

An accessible microfluidic perfusion platform for time-restricted control of zebrafish embryonic patterning

This paper introduces a microfluidic platform for controlled drug delivery to zebrafish embryos, enabling the study of developmental patterning through periodic pharmacological perturbations.

Zebrafish facility report on implementation of artificial plants as structural enrichment

Across six zebrafish lines over one year, artificial home-tank plants left sex ratio, fertility and microbial counts unchanged, while fish avoided plant areas.

An optogenetic toolkit for robust activation of FGF, BMP, and Nodal signaling in zebrafish

The paper introduces an optogenetic toolkit for activating FGF, BMP, and Nodal signaling in zebrafish embryos using light-controlled receptor domains.

Pdgfrβ signaling orchestrates meningeal repair via the mobilization of arachnoid cells.

This study identifies PDGFRβ signaling as critical for meningeal cell recruitment and tissue remodeling during zebrafish CNS injury repair.

Tunable gene expression in zebrafish using RiboSCALE

This paper develops an RNA-based chemogenetic method to induce tunable gene expression in zebrafish embryos and larvae, demonstrating time- and concentration-dependent control.

Cp36 serine recombinase as a new tool for zebrafish transgenesis

The paper demonstrates that Cp36 serine recombinase is a viable alternative to Tol2 for zebrafish transgenesis, with comparable efficiency for small constructs but reduced performance for larger ones.

Genetic depletion in zebrafish uncovers requirement for septins in haematopoiesis

This study shows that septins are required for haematopoiesis in zebrafish, as septin-deficient larvae have increased HSPCs and myeloid bias, with implications for blood disorders.

Visual - Acoustic Thigmotaxis in Zebrafish Larvae: A High throughput NAM for Neurotoxicity Assessment

A 96-well square plate zebrafish larva thigmotaxis assay with visual and acoustic stimuli matched 24-well round plates and detected neuroactive chemicals more sensitively than locomotion.

Dolutegravir Developmental Toxicity is Mitigated by Magnesium and Folate in Zebrafish Embryos

This study shows magnesium and folate reduce dolutegravir toxicity in zebrafish embryos, with magnesium acting through both folate receptor-dependent and -independent mechanisms.

Virtual reality exposes fine-scale alterations in behaviour following loss of the ADHD-linked gene adgrl3.1 in zebrafish

The paper uses virtual reality to assess behavioural changes in ADHD-linked adgrl3.1 mutant zebrafish, revealing heightened excitability and lower motor threshold.

CaMPARI2 Enables Stimulus-Locked Whole-Brain Activity Mapping at Cellular Resolution in Unrestrained Larval Zebrafish

The paper introduces CaMPARI2, a method to map whole-brain neural activity in unrestrained larval zebrafish with high temporal precision during behavior.

EmbryoTempoFormer: clip-based developmental tempo inference from zebrafish brightfield time-lapse microscopy

This paper introduces EmbryoTempoFormer, a model that infers developmental tempo from zebrafish time-lapse microscopy, showing that temperature changes alter developmental progression through tempo rather than time offset.

3-Minute Hematoxylin and Oil Red O (H-ORO) Staining Protocol for Frozen Sections of Zebrafish

This paper introduces a rapid H-ORO staining protocol for zebrafish frozen sections that preserves tissue integrity and reduces artifacts compared to traditional methods.

A Novel Zebrafish Luminescent Biosensor for Kidney Tubulopathy, Metal Toxicity, and Drug Screening

The paper introduces a zebrafish biosensor for detecting kidney tubule dysfunction and uses it to study metal toxicity and drug screening.

StrIPETrack: a real-time, ROI-flexible tracking platform for high-throughput zebrafish behavior

StrIPETrack is a Python-based tracking software for zebrafish behavior that supports flexible ROI definitions and complex assays, providing accurate and detailed behavioral phenotyping.

CellCousin2: An Optimized System for Partial Ablation and Tracing of Regenerative Lineages

CellCousin2 improves lineage tracing in zebrafish by reducing background recombination and enhancing ablation efficiency with a new system.

Fentanyl and Alcohol Co-Exposure Induce Robust, Sustained Hyperlocomotion and Neural Circuit Disruption in Larval Zebrafish

This study investigates the combined effects of fentanyl and alcohol in larval zebrafish, finding robust hyperlocomotion and neural circuit disruption.

Aging compromises Zebrafish caudal fin regeneration by disrupting Regenerative gene networks and Cellular metabolism

This study shows that aging impairs zebrafish caudal fin regeneration by disrupting gene networks and cellular metabolism, with mitochondrial dysfunction playing a key role.

TALE and Hox Transcription Factors Control Adult Behaviors in Zebrafish

This study examines the behavioral effects of TALE and Hox TF mutations in zebrafish, finding shared stress responses and TF-specific behavioral dysregulation.

Rescuing functional defects in a zebrafish model of CDKL5 deficiency disorder: Contribution to the identification of new therapeutic compounds

This study identifies potential therapeutic compounds for CDKL5 deficiency disorder using a zebrafish model, finding that fisetin and others partially restore locomotor and craniofacial defects.

Multimodal reference brain atlas of adult Danionella cerebrum

The paper creates a multimodal reference brain atlas for adult Danionella cerebrum, integrating anatomical, molecular, and functional data to study brain structure and sexual dimorphism.

Control of wildtype zebrafish optomotor response with a photoswitchable drug

This study uses Carbadiazocine to modulate optomotor responses in zebrafish larvae, showing reduced accuracy and altered movement patterns when activated by light.

Histo-anatomical atlas and thermal tolerance of Garra rufa: A novel small teleost model adaptable to human body temperature

This paper provides a histo-anatomical atlas of Garra rufa, highlighting its unique morphological features and thermal tolerance, establishing it as a potential novel experimental model.

Optimization of an automated system (ZEG) for rapid cellular extraction from live zebrafish

This paper optimizes an automated system (ZEG) for rapid cellular extraction from live zebrafish embryos, improving DNA collection efficiency and embryo survival beyond 95%.

Characterizing trajectories of innate immune cells in larval zebrafish

This study tracks innate immune cell dynamics in larval zebrafish to show that gut structure, not microbial stimuli, primarily shapes immune cell movement patterns.

Library transgenesis in zebrafish through delayed site-specific mosaic integration for in vivo pooled screening of transgenes

This paper introduces a zebrafish transgenesis method for in vivo pooled screening of transgenes, enabling single-transgene precision in a physiological context.

Local control of cellular proliferation underlies neuromast regeneration in zebrafish

This study uses a computational model to show that local cell proliferation control through a delayed switch enables neuromast regeneration in zebrafish.

High-throughput multi-camera array microscope platform for automated 3D behavioral analysis of swimming zebrafish larvae

This paper introduces a high-throughput 24-camera array microscope for automated 3D behavioral analysis of zebrafish larvae, enabling accurate tracking and morphological dynamics at high frame rates.

A Scalable, High-Throughput Optomotor Response Pipeline for Quantitative Analysis of Vision Using Infinity-Pools

This paper introduces a high-throughput optomotor response platform for analyzing vision in medaka and zebrafish, finding that albino medaka show heightened sensitivity to visual stimuli.

Linking Brain and Behavior States in Zebrafish Larvae Locomotion using Hidden Markov Models

This study uses Hidden Markov Models to link neural activity and behavior in zebrafish larvae, revealing state-based correlations between swimming patterns and circuit activation.