Biology subjects

Kubo, F.

Publications and source records attributed to Kubo, F..

3 recordsLinked to original sources

bioRxiv2025

Tracking Satb2-positive retinal ganglion cells in zebrafish unveils developmental functional reorganization

Retinal ganglion cells (RGCs) relay visual information to the brain, and their functional properties are crucial for visually guided behavior. However, functional maturation of RGCs across development remains elusive. Here, we investigated the developmental maturation of a genetically defined RGC subtype expressing Satb2 in zebrafish, which allowed single-layer-resolved analysis of the tectal neuropil. Using in vivo calcium imaging, we characterized visual response properties of Satb2-positive RGC axon terminals at two developmental stages. At the early stage, responses segregated into seven functional clusters with diverse tuning profiles. By later stage, these responses reorganized into five clusters, indicating developmental restructuring of functional identities. Longitudinal imaging of individual RGC axons revealed that while some response types remain stable across development, others exhibit pronounced plasticity. In particular, certain RGC cluster acquired additional tuning features and converged into motion-sensitive cluster, coinciding with a marked expansion of motion-responsive cluster and reflecting progressive functional specialization. Visual deprivation experiments revealed that core visual tuning is genetically determined, whereas visual experience is crucial for fine-tuning of the particular functional subtype. Together, our findings provide a single-cell-resolved view of retinal circuit maturation and reveal how stable and flexible responses are integrated during the development of vertebrate vision.

neuroscience↗

bioRxiv2025

Molecular and functional dissection using CaMPARI-seq reveals the neuronal organization for dissociating optic flow-dependent behaviors

Optic flow processing is critical for the visual control of body and eye movements in many animals. Rotational and translational binocular optic flow patterns need to be clearly distinguished to induce different behavior outputs. However, the specific neuron types and their connectivity involved in this computation remain unclear. Here, we developed a method to link the functional labeling using a photoconvertible calcium indicator called CaMPARI2 and single-cell RNA-sequencing (CaMPARI-seq) to investigate the transcriptional profile of the pretectum, a center for processing optic flow in larval zebrafish. Using this technique, we identified a pretectal cluster expressing tcf7l2, which can be further classified into molecularly distinct subclusters. In vivo calcium imaging and cell ablation revealed that nkx1.2lb-positive pretectal neurons are commissural inhibitory neurons required for the optomotor response but not for the optokinetic response. Our genetic and functional dissection using CaMPARI-seq uncovered the neuronal organization essential for dissociating different optic flow-dependent behaviors.

neuroscience↗

bioRxiv2020

A calibrated optogenetic toolbox of stable zebrafish opsin lines

Optogenetic actuators with diverse spectral tuning, ion selectivity and kinetics are constantly being engineered providing powerful tools for controlling neural activity with subcellular resolution and millisecond precision. Achieving reliable and interpretable in vivo optogenetic manipulations requires reproducible actuator expression and calibration of photocurrents in target neurons. Here, we developed nine transgenic zebrafish lines for stable opsin expression and calibrated their efficacy in vivo. We first used high-throughput behavioural assays to compare opsin ability to elicit or silence neural activity. Next, we performed in vivo whole-cell electrophysiological recordings to quantify the amplitude and kinetics of photocurrents and test opsin ability to precisely control spiking. We observed substantial variation in efficacy, associated with differences in both opsin expression level and photocurrent characteristics, and identified conditions for optimal use of the most efficient opsins. Overall, our calibrated optogenetic toolkit will facilitate the design of controlled optogenetic circuit manipulations.

neuroscience↗