Zebrafish Biomedical Research Applications

Two-photon all-optical electrophysiology for the dissection of larval zebrafish brain functional connectivity

The paper develops a two-photon optical system for high-speed volumetric recording and optogenetic stimulation in larval zebrafish to reconstruct functional connectivity of the left habenula.

foxe1 mutant zebrafish show indications of a hypothyroid phenotype and increased sensitivity to ethanol for craniofacial malformations

This study shows foxe1 mutant zebrafish exhibit hypothyroidism and increased ethanol-induced craniofacial malformations, mirroring human FOXE1 mutation phenotypes.

Stable primary brain cell cultures from zebrafish reveal hyperproliferation of non-neuronal cells from scn1lab mutants

This study develops a long-lived zebrafish primary neuron culture protocol and uses it to show that scn1lab mutants exhibit hyperproliferation of non-neuronal cells.

Cadherin 16 promotes sensory gating via the endocrine corpuscles of Stannius

The paper identifies Cadherin 16 as a regulator of sensory gating in zebrafish via the corpuscle of Stannius, showing its role in calcium homeostasis and behavior.

Megabouts: a flexible pipeline for zebrafish locomotion analysis

Megabouts is a software package for zebrafish locomotion analysis that uses a Transformer neural network to classify behaviors flexibly across tracking methods and frame rates.

Heat stress sensitizes zebrafish embryos to neurological and cardiac toxicity.

This study shows that zebrafish embryos are sensitive to heat stress and that certain compounds enhance their neurological and cardiac toxicity under heat stress.

Birth order specified recruitment of motor circuits during spontaneous neural activity in zebrafish embryo

The paper shows that birth order specifies the sequential recruitment of motor circuits in zebrafish embryos through synchronized and distinct neuronal activity patterns.

Machine learning enables high-throughput, low-replicate screening for novel anti-seizure targets and compounds using combined movement and calcium fluorescence in larval zebrafish

This paper develops a machine learning method combining movement and calcium fluorescence data to detect seizure-like activity in zebrafish, enabling high-throughput, low-replicate screening of anti-seizure compounds.

Probabilistic modeling reveals coordinated social interaction states and their multisensory bases

The paper develops a hidden Markov model to analyze social interactions in zebrafish, revealing two interaction states with distinct sensory bases and temporal dynamics.

Complete persistence of the primary somatosensory system in zebrafish

The paper shows that zebrafish retain both primary and secondary somatosensory systems throughout development, challenging the notion that Rohon-Beard neurons are transient.

Larva in the loop, a closed loop machine interface system for Danio rerio larvae

This paper develops a closed-loop system using zebrafish larvae's optokinetic response to control a robot on a linear track.

Rapid generation of single-insertion transgenics by Tol2 transposition in zebrafish

The paper introduces a competitive dilution strategy to rapidly generate single-insertion transgenic zebrafish lines, reducing animal usage and improving reproducibility.

Individual differences in the boldness of female zebrafish are associated with alterations in serotonin function.

The paper investigates sex-specific associations between serotonin function and boldness behavior in female zebrafish, finding that escitalopram alters thigmotaxis differently in bold and shy fish.

pIGLET: Safe harbor landing sites for reproducible and efficient transgenesis in zebrafish

The paper establishes phiC31 integrase-based transgene landing sites in zebrafish, enabling efficient and reproducible transgenesis with 25-50% germline transmission efficiency.

An atlas and database of neuropeptide gene expression in the adult zebrafish forebrain

The paper creates an atlas and database of neuropeptide gene expression in the adult zebrafish forebrain, identifying novel subnuclei and comparing them to mouse hypothalamic regions.

Genetically defined nucleus incertus neurons differ in connectivity and function

The paper identifies two distinct neuronal clusters in the zebrafish nucleus incertus with different connectivity and functional properties using CRISPR/Cas9 and calcium imaging.

Forward genetics combined with unsupervised classifications identified zebrafish mutants affecting biliary system formation.

The paper identifies 24 zebrafish mutants affecting biliary system formation using forward genetics and unsupervised clustering, revealing distinct genetic impacts on network structure.

Single cell sequencing of zebrafish kidney marrows reveals AHR2-dependent endogenous regulation of hematopoiesis

This study uses single-cell sequencing in zebrafish to show AHR2 regulates gene expression in immune cells without altering cell proportions.

Role of the NOS-cGMP pathways in time-dependent sensitization of behavioral responses in zebrafish

This study investigates the role of NOS-cGMP pathways in time-dependent sensitization (TDS) in zebrafish, showing that different NO-related pathways contribute to TDS at distinct time points.

Highly efficient tamoxifen-inducible Cre recombination in embryonic, larval and adult zebrafish

The paper develops a zebrafish CreERT2 driver line with a modified ubiquitin promoter that enables efficient tamoxifen-inducible recombination in embryos, larvae, and adults.

Novel mathematical morphology model identifies dorsal-ventral asymmetry of endothelial cell morphology in dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos

The paper develops a mathematical model to quantify endothelial cell morphology and vessel geometry in zebrafish dorsal aorta, revealing differences in cell shape and vessel diameter between wild-type and Endoglin-deficient embryos.

Multi-species community platform for comparative neuroscience in teleost fish

The paper develops a multi-species brain atlas platform for comparative neuroscience in teleost fish, revealing species-specific neural structures and enabling gene expression and activity comparisons.

Hemodynamics regulate spatiotemporal artery muscularization in the developing circle of Willis

This study shows that blood flow activates endothelial klf2a, which regulates VSMC differentiation on zebrafish brain arteries in a spatiotemporal manner.

Effects of 4 testing arena sizes and 11 types of embryo media on sensorimotor behaviors in wild-type and chd7 mutant zebrafish larvae

This study examines how testing arena size and embryo media affect sensorimotor behaviors in zebrafish larvae, showing significant impacts on startle sensitivity, locomotion, and other behaviors.

Zebrafish live imaging reveals a surprisingly small percentage of spinal cord motor neurons die during early development

The paper uses live imaging in zebrafish to show that only a small percentage of spinal cord motor neurons die during early development, contradicting the common belief of widespread neuronal death in vertebrates.

The Preoptic Area and Dorsal Habenula Jointly Support Homeostatic Navigation in Larval Zebrafish

This study identifies a neural network connecting the preoptic area and habenula in larval zebrafish that supports thermoregulation through movement and spatial navigation.

Characterizing CSNK2A1 Mutant-Induced Morphological Phenotypes in Zebrafish (Danio rerio): Insights into Okur-Chung Neurodevelopmental Syndrome (OCNDS)

This study uses zebrafish to examine the effects of CSNK2A1 mutations on morphology, showing a link between genetic changes and phenotypes, with partial rescue by wild-type mRNA.

Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin

The paper investigates cell lineage relationships in zebrafish fin regeneration using single-cell RNA sequencing and lineage tracing, revealing compartmentalized osteoblast and blastema contributions to bone formation.

Identification of overlapping and distinct mural cell populations during early embryonic development

The paper identifies novel tagln-positive mural cell populations in zebrafish embryos using transgenic markers and reveals their developmental contributions.

Identification of signalling pathways involved in gill regeneration in zebrafish

This study identifies BMP, FGF, Notch, and Shh signaling pathways as critical for gill regeneration in zebrafish following filament resection.