Zebrafish Biomedical Research Applications

Automated, high-throughput quantification of EGFP-expressing neutrophils in zebrafish by machine learning and a highly-parallelized microscope

This paper develops a high-throughput method to count EGFP-expressing neutrophils in zebrafish larvae using a parallelized microscope and machine learning, validated against manual counts.

Warming affects routine swimming activity and novel odour molecular response in larval zebrafish

This study shows that warming reduces routine swimming in larval zebrafish and alters molecular responses to novel odours, with energy trade-offs in gene expression.

Alk1/Endoglin dependent increases in vein endothelial cell sizes precipitate arteriovenous malformations

This study identifies Alk1/Endoglin signaling as critical for restricting vein endothelial cell sizes and preventing arteriovenous malformations in zebrafish embryos.

Distinct roles of core autophagy-related genes (ATGs) in zebrafish definitive hematopoiesis

The paper investigates the distinct roles of core autophagy-related genes in zebrafish definitive hematopoiesis, revealing gene-specific and synergistic effects on hematopoietic stem cells and myeloid cell types.

All-optical interrogation of brain-wide activity in freely swimming larval zebrafish

The paper introduces an all-optical technique for brain-wide calcium imaging and optogenetic stimulation in larval zebrafish, showing it can trigger behavior and neural activity changes.

Automated staging of zebrafish embryos with deep learning

This paper introduces KimmelNet, a deep learning model that predicts zebrafish embryo age from 2D brightfield images and detects developmental delay between populations.

A robust knock-in approach using a minimal promoter and a minicircle

The paper develops a robust strategy for generating knock-in reporter animals using minicircle technology and an ectopic promoter, improving efficiency and reducing unintended genomic effects.

pi_tailtrack: A compact, inexpensive, and open-source behaviour-tracking system for head-restrained zebrafish

The paper introduces a low-cost, open-source system for tracking larval zebrafish behavior during functional microscopy.

Identification of side effects of COVID-19 drug candidates on embryogenesis using an integrated zebrafish screening platform

The paper evaluates the effects of 162 FDA-approved drugs on zebrafish embryogenesis and immune response to SARS-CoV-2 spike protein, identifying potential developmental side effects.

Molecular logic of neuromodulatory systems in the zebrafish telencephalon

The paper maps neuromodulatory systems in zebrafish telencephalon using transcriptomics, revealing cell type-specific GPCRs and neuropeptide combinations.

adgrl3.1-deficient zebrafish show noradrenaline-mediated externalizing behaviors, and altered expression of externalizing disorder-candidate genes, suggesting functional targets for treatment

This study shows adgrl3.1-deficient zebrafish exhibit externalizing behaviors rescued by atomoxetine, and identifies differentially expressed genes linked to externalizing disorders.

Transgenic tools targeting striatal and pallidal subpopulations revealed evolutionary conservation and specialization of the cortico-basal ganglia circuit in zebrafish

The paper identifies evolutionary conserved and specialized pathways in the zebrafish cortico-basal ganglia circuit using transgenic tools and single-cell RNA sequencing.

Ligament injury in adult zebrafish triggers ECM remodeling and cell dedifferentiation for scar-free regeneration

This study shows adult zebrafish can regenerate jaw joint ligaments without scarring through dedifferentiation of ligamentocytes and ECM remodeling, with legumain playing a key role.

Causal Genetic Loci for a Motivated Behavior Spectrum Harbor Psychiatric Risk Genes

The paper identifies genetic loci associated with motivated behavior in zebrafish and links them to psychiatric risk genes in humans.

Functional coupling of the mesencephalic locomotor region and V2a reticulospinal neurons driving forward locomotion

This study identifies the mesencephalic locomotor region's role in recruiting V2a reticulospinal neurons to control forward locomotion in zebrafish.

Dermomyotome-derived endothelial cells migrate to the dorsal aorta to support hematopoietic stem cell emergence

The paper shows that endothelial cells from the dermomyotome contribute to the dorsal aorta and support hematopoietic stem cell emergence in zebrafish.

Tuning apicobasal polarity and junctional recycling in the hemogenic endothelium orchestrates the morphodynamic complexity of emerging pre-hematopoietic stem cells

The paper investigates the molecular mechanisms governing the emergence of pre-hematopoietic stem cells from the hemogenic endothelium in zebrafish embryos, showing that apicobasal polarity and junctional recycling play key roles in their morphodynamic complexity.

Zebrafish acta1b as a Candidate for Modelling Human Actin Cardiomyopathies

This study identifies acta1b as the most suitable zebrafish gene for modelling human actin cardiomyopathies due to its expression and CRISPR-induced cardiac phenotypes.

A single base pair substitution on Chromosome 25 in zebrafish distinguishes between development and acute regulation of behavioral thresholds.

This study identifies a single base pair substitution in the syt7a gene in zebrafish linked to an acoustic startle threshold phenotype but shows it does not cause the observed behavioral changes.

Acute stress modulates social approach and social maintenance in adult zebrafish

This study investigates how varying acute stressor intensity affects social approach and maintenance in adult zebrafish, showing intensity-dependent reductions in both behaviors with social maintenance affected at lower stress levels.

A 3D-printed and freely available device to measure the zebrafish optokinetic response before and after injury

The paper describes a 3D-printed device to measure the optokinetic response in zebrafish before and after optic nerve injury.

Genetic tools for the study of the mangrove killifish, Kryptolebias marmoratus, an emerging vertebrate model for phenotypic plasticity

The paper develops genetic tools for the mangrove killifish, improving embryo yield and enabling targeted gene knockout studies.

Kita crispants for systematic image-based genetic screens of complex traits in zebrafish larvae

The paper introduces Kita as a target for CRISPR/Cas9 screens in zebrafish larvae to improve the reliability and efficiency of genetic screens for complex traits.

A zebrafish knock-in reporter line for the Foxo1a transcription factor.

This paper develops a zebrafish knock-in reporter line for the Foxo1a transcription factor to enable in vivo imaging of its expression and localization.

A macrophage subpopulation promotes airineme-mediated intercellular communication in a Matrix Metalloproteinase-9-dependent manner

The paper identifies a macrophage subpopulation that mediates airineme-mediated signaling through MMP9-dependent mechanisms in zebrafish.

A non-invasive photoactivatable split-Cre recombinase system for genome engineering in zebrafish.

This paper develops a non-invasive light-inducible split-Cre system for precise genome engineering in zebrafish.

Differential roles of diet on development and spinal cord regeneration in larval zebrafish

This study compares three diets' effects on growth and spinal cord regeneration in larval zebrafish, finding significant differences in length and regeneration rates between live feed and commercial feeds.

OptoPi: An open source flexible platform for the analysis of small animal behaviour

OptoPi is an open-source platform for small animal behaviour analysis with custom illumination and optogenetic stimulation, demonstrating tracking of zebrafish and Drosophila larvae.

otpb functions in a Lef1-dependent transcriptional network required for expression of the stress response inhibitor crhbp in the zebrafish hypothalamus

The paper identifies otpb as a Lef1-dependent gene required for crhbp expression in zebrafish hypothalamic neurons, linking Lef1-mediated neurogenesis to stress response inhibition.

Insulin-like growth factor receptor / mTOR signaling elevates global translation to accelerate zebrafish fin regenerative outgrowth

The paper identifies IGFR/mTOR signaling as a driver of increased translation during zebrafish fin regeneration, accelerating outgrowth through coordinated cell behavior.