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#zebrafish

2 posts2 participants0 posts today
Public
preLights

#spotLights hits episode 10! 🙌

Jonathan Townson talks to Helena Crellin (#BuckleyLab) about her #preprint introducing an optogenetic approach to study "how forces are propagated through complex tissues during development" in #zebrafish 🧠🐟

Listen below! 🎧
🎙️ youtu.be/6uce4whDt2M

youtu.be- YouTubeEnjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on YouTube.
#biologists100#optogenetics#OpenScience
Public
Amelia Cervera 🧬

Environmentally induced variation in sperm sRNAs is linked to gene expression and transposable elements in zebrafish offspring.

#Transposons #sRNAs #miRNAs #piRNAs #Sperm #Competition #Zebrafish

nature.com/articles/s41437-025

NatureEnvironmentally induced variation in sperm sRNAs is linked to gene expression and transposable elements in zebrafish offspring - HeredityEnvironmental factors affect not only paternal condition but may translate into the following generations where sperm-mediated small RNAs (sRNAs) can contribute to the transmission of paternal effects. sRNAs play a key role in the male germ line in genome maintenance and repair, and particularly in response to environmental stress and the resulting increase in transposable element (TE) activity. Here, we investigated how the social environment (high competition, low competition) of male zebrafish Danio rerio affects sRNAs in sperm and how these are linked to gene expression and TE activity in their offspring. In a first experiment, we collected sperm samples after exposing males to each social environment for 2 weeks to test for differentially expressed sperm micro- (miRNA) and piwi-interacting RNAs (piRNA). In a separate experiment, we performed in vitro fertilisations after one 2-week period using a split-clutch design to control for maternal effects and collected embryos at 24 h to test for differentially expressed genes and TEs. We developed new computational prediction tools to link sperm sRNAs with differentially expressed TEs and genes in the embryos. Our results support the idea that the molecular stress response in the male germ line has significant down-stream effects on the molecular pathways, and we provide a direct link between sRNAs, TEs and gene expression.
Public
Amelia Cervera 🧬

A recombinase-activated ribozyme to knock down endogenous gene expression in zebrafish.

#Ribozymes #Recombinase #KnockDown #Zebrafish #RNA

journals.plos.org/plosgenetics

journals.plos.orgA recombinase-activated ribozyme to knock down endogenous gene expression in zebrafishAuthor summary Understanding mRNA and protein function requires tools to module gene expression. Current tools in vertebrates include site-directed recombinases and endonucleases, which display variable efficiency depending on the genomic context. Here, we introduce a complementary tool to knock down gene expression in zebrafish, one based on the T3H48 self-cleaving ribozyme. We first show that the T3H48 ribozyme can reduce the expression of a reporter transgene, as well as that of an endogenous gene. Using a base-editing strategy to inactivate the ribozyme, we show that this knock down is specific and reversible. We then created a Flippase- and Cre-activatable T3H48 ribozyme called RiboFlip. We find that the induction of RiboFlip recapitulates the mutant phenotype when inserted in the albino gene. Moreover, we show that a Cre- and Dre-controllable Gal4/UAS reporter in the RiboFlip cassette can label knocked-down cells independently of the expression of the target gene. Altogether, these data show that the RiboFlip can serve as a flexible knockdown tool, thereby complementing existing strategies to control gene expression.
Public
Albert Cardona

"Forecasting Whole-Brain Neuronal Activity from Volumetric Video", Immer et al. 2025 (with Florian Engert, Jeff Lichtman, Misha Ahrens, Viren Jain and Michal Januszewski)
arxiv.org/abs/2503.00073

"ZAPBench: a benchmark for whole-brain activity prediction in zebrafish", Lueckmann et al. 2025
openreview.net/pdf?id=oCHsDpya

arXiv logo
arXiv.orgForecasting Whole-Brain Neuronal Activity from Volumetric VideoLarge-scale neuronal activity recordings with fluorescent calcium indicators are increasingly common, yielding high-resolution 2D or 3D videos. Traditional analysis pipelines reduce this data to 1D traces by segmenting regions of interest, leading to inevitable information loss. Inspired by the success of deep learning on minimally processed data in other domains, we investigate the potential of forecasting neuronal activity directly from volumetric videos. To capture long-range dependencies in high-resolution volumetric whole-brain recordings, we design a model with large receptive fields, which allow it to integrate information from distant regions within the brain. We explore the effects of pre-training and perform extensive model selection, analyzing spatio-temporal trade-offs for generating accurate forecasts. Our model outperforms trace-based forecasting approaches on ZAPBench, a recently proposed benchmark on whole-brain activity prediction in zebrafish, demonstrating the advantages of preserving the spatial structure of neuronal activity.
#ZAPBench#neuroscience#zebrafish
Public
Albert Cardona

Parallels between the head direction neuron circuits and the central complex:

"we asked if and how the recently identified HD [head direction] cells in the larval zebrafish ... incorporate visual information."

"zebrafish HD cells can reliably track the orientation of multiple visual scenes, exploiting both landmark and optic flow cues. The mapping between landmark cues and the heading estimates is idiosyncratic across fish, and experience-dependent."

"The physiological and morphological parallels suggest that a Hebbian mechanism similar to the fly ring neuron is at work in the habenula axons."

From: "Mechanisms for plastic landmark anchoring in zebrafish compass neurons" by Tanaka and Portugues, 2024
biorxiv.org/content/10.1101/20

bioRxiv · Mechanisms for plastic landmark anchoring in zebrafish compass neuronsVision is a sensory modality particularly important for navigation, as it can inform animals of their current heading (i.e. visual landmarks) as well as its changes (i.e. optic flow). It has been shown that head direction (HD) neurons in various species incorporate the visual cues into their heading estimates. However, circuit mechanisms underlying this process remain still elusive in vertebrates. Here, we asked if and how the recently identified HD cells in the larval zebrafish – one of the smallest vertebrate models – incorporate visual information. By combining two-photon microscopy with a panoramic virtual reality setup, we demonstrate that the zebrafish HD cells can reliably track the orientation of multiple visual scenes, exploiting both landmark and optic flow cues. The mapping between landmark cues and the heading estimates is idiosyncratic across fish, and experience-dependent. Furthermore, we show that the landmark tracking requires the lateralized projection from the habenula to the interpeduncular nucleus (IPN), where the HD neuron processes innervate. The physiological and morphological parallels suggest that a Hebbian mechanism similar to the fly ring neuron is at work in the habenula axons. Overall, the observations that the hindbrain HD cells of the larval zebrafish lacking an elaborate visual telencephalon shed new light on the evolution of the navigation circuitry in vertebrates. ### Competing Interest Statement The authors have declared no competing interest.
#neuroscience#CentralComplex
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