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opencc-zeroJan 2024View details →

Data from: A zebrafish model to elucidate the impact of host genes on the microbiota

Every host species and organism provide a unique environmental niche contributing to the overall diversity of microbial ecosystems from the intestine of an animal to the oceans and forests of our planet. The study of host-microbiota interactions has long focused on the well-established effects the microbiota has on its host. In contrast, little focus has been allocated to the role of the host in these intricate interactions. However, understanding the role of the host may well be an essential key to understanding the complexity of the relationship between the host and its microbiota. In this study, we present a model in which the effects of host genes on the microbiota can be elucidated and how such genetic effects may shape host-associated microbiota. We demonstrate a hologenomic approach implementing the CRISPR/Cas system in the zebrafish model to combine the effects of a host gene with 16S metabarcoding and metabolomics data. We show that knocking out the gene coding for the rate-limiting enzyme in melanogenesis, tyrosinase (tyr), correlates with changes in the intestinal microbiota of zebrafish and differences in the abundance of specific metabolites illustrating the value of our model for studying the impact of host genes on the composition and function of the intestinal microbiota.

opencc-zeroJan 2024View details →

PFOS negatively impacts prey capture in larval zebrafish

Per- and polyfluoroalkyl substances (PFAS) are widely used in many industrial and domestic applications. The wide range use of PFAS has resulted in unintentional human exposures and bioaccumulation in blood and other organs. Perfluorooctanesulfonate (PFOS) is among the most prevalent PFAS in the environment and has been postulated to affect brain functions in exposed organisms. However, the impacts of PFOS on early neural development have not been well-described. Here, we used zebrafish larvae to assess the effects of PFOS on two fundamental complex behaviors, prey capture and learning. Zebrafish exposed to PFOS concentrations ranging from 2 – 20 µM for differing 48-hour periods were viable through early larval stages. In addition, PFOS uptake was unaffected by the presence of a chorion. We employed two different experimental paradigms; we first assessed the impacts of increasing organismal PFOS bioaccumulation on prey capture and learning, and second, we probed stage-specific sensitivity to PFOS by exposing zebrafish at different developmental stages (0-2 vs 3-5 days post fertilization). Following both assays we measured the amount of PFOS present in each larva. PFOS levels varied in larvae from different groups within each experimental paradigm. Significant negative correlations were observed between larval PFOS accumulation and the percentage of captured prey, while non-significant negative correlations were observed between PFOS accumulation and experienced-induced prey capture learning. These findings suggest that PFOS accumulation negatively affects larval zebrafish's ability to perform complicated multisensory behaviors and highlight potential risks of PFOS exposure to animals in the wild, with implications for human health.

opencc-by-4.0Feb 2024View details →

Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled scRNAseq

During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the relative contributions of mRNA transcription and degradation to shaping those profiles remains challenging, especially within embryos with diverse cellular identities. Here, we combine single-cell RNA-Seq and metabolic labeling to capture temporal cellular transcriptomes of zebrafish embryos where newly-transcribed (zygotic) and pre-existing (maternal) mRNA can be distinguished. We then introduce kinetic models to quantify mRNA transcription and degradation rates within individual cell types during their specification. These models reveal highly varied regulatory rates across thousands of genes, coordinated transcription and destruction rates for many transcripts, and link differences in degradation to specific sequence elements. They also identify cell-type-specific differences in degradation, namely selective retention of maternal transcripts within primordial germ cells and enveloping layer cells, two of the earliest specified cell-types. Our study provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response.   This repository contains the raw microscopy data that is analyzed in Figures 6F-I and Supplementary Figure S4 B-D.

Zebrafish embryos time-course, 5'UTR nup43

This Zenodo file contains data for the 5′ UTR-nup43-sfGFP mRNA reporter. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 2 of Reimão-Pinto et al., Dev Cell, 2024. Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications. Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.

Zebrafish embryos time-course, 5'UTRs hnrnpl and egfl6

This Zenodo file contains data for the 5′ UTR-hnrnpl-sfGFP and 5′ UTR-egfl6-sfGFP mRNA reporters. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 2 of Reimão-Pinto et al., Dev Cell, 2024. Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications. Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.

Zebrafish embryos time-course, M&Z 5'UTRs scarb2c

This Zenodo file contains data for the maternal and zygotic 5′ UTR-scarb2c-sfGFP mRNA reporters. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 7 of Reimão-Pinto et al., Dev Cell, 2024. Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications. Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.

Zebrafish embryos time-course, M&Z 5'UTRs cfl1l

This Zenodo file contains data for the maternal and zygotic 5′ UTR-cfl1l-sfGFP mRNA reporters. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 7 of Reimão-Pinto et al., Dev Cell, 2024. Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications. Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.

opencc-by-4.0Nov 2024View details →

THE HYBRID HISTORY OF ZEBRAFISH

This repository contains files associated with the manuscript titled "The Hybrid History of Zebrafish" by Braedan M. McCluskey, Peter Batzel, and<a href="http://orcid.org/0000-0002-5476-2137" target="_blank" rel="noopener"> </a>John H. Postlethwait.  In addition to code used during the analysis, this repository contains the multiple sequence alignment used for phylogenetic inference (geno.phy), the resulting phylogeny inferred by RAxML (RAxML_bipartitionsBranchLabels.geno), the genotypes called for each species (geno.vcf.gz), and the genotypes called for 12 zebrafish samples from previous studies (DrerioRAD_12Samples.vcf.gz).

opencc-zeroDec 2021View details →

Zebrafish larvae exploration and aversive chemotaxis dataset

This dataset contains recordings of larval zebrafish behavior. The full details are described in the paper "A lexical approach for identifying behavioral action sequences". The experiment investigates zebrafish larvae behavior in free swimming and aversive chemotaxis conditions. In each experiment, 12 larvae (7 dpf) are placed in 12 rectangular wells. Ten min-long videos were recorded at 160 Hz with an exposure time of 1 ms, and a pixel size of 70 µm using a ViewWorks camera (Basler acA2040-180km) controlled by the Hiris software (R&D Vision, Nogent sur Marne, http://www.rd-vision.com/r-d-vision-eng). The fish are tracked using a custom-made software, Zebrazoom (https://zebrazoom.org/). The algorithm begins by locating all the wells and by extracting the background of the video. ZebraZoom first applies a series of actions to detect the animal in each well: i) contours of head and entire body are detected using active contours, ii) the center of the head is identified as the center of mass of the head contour and the tip of the tail is detected using both the curvature along the body contour and distance to the center of the head. The midline is then identified between the left and right borders of the body contour. For each animal, the difference in pixel intensity between subsequent frames enables the automated detection of bout start and end. Then, for each bout, the algorithm calculates the head position, head direction and the tail angle from which kinematic parameters are subsequently estimated: number of oscillations, instantaneous tail beat frequency, maximum amplitude for each tail bend, bout speed, bout duration, and bout distance. Tunable parameters in the tracking algorithm were optimized to detect small amplitude forward bouts occurring frequently during exploration. In order to validate our algorithm, we manually inspected validation videos where the head direction and tail position were superimposed on the raw image when a bout is detected, allowing to check both the tracking and bout detection quality. The dataset contains MATLAB files which can be read using the Python code uploaded along with the dataset. The codebase also includes a Cython implementation of the BASS algorithm. The ReadMe for using the Python code to analyze the larval zebrafish dataset and for using BASS is included with the code.

opencc-by-4.0Dec 2021View details →

Growth orientations, rather than heterogeneous growth rates, dominate jaw joint morphogenesis in the larval zebrafish

Supplementary material for paper entitled "Growth orientations, rather than heterogeneous growth rates, dominate jaw joint morphogenesis in the larval zebrafish". Raw data, scripts, models and results are made available along with supplementary figures.

opencc-by-4.0Jan 2022View details →

Data_Sheet_2_Management of Hypercholesterolemia Through Dietary ß-glucans–Insights From a Zebrafish Model

Supplementary tables for Management of Hypercholesterolemia Through Dietary ß-glucans–Insights From a Zebrafish Model

opencc-by-4.0Jan 2022View details →

Data_Sheet_1_Management of Hypercholesterolemia Through Dietary ß-glucans–Insights From a Zebrafish Model

Supplementary figures for Management of Hypercholesterolemia Through Dietary ß-glucans–Insights From a Zebrafish Model

opencc-by-4.0Jan 2022View details →

Zebrafish Brain Registration Utility Archive

Sample brain images, atlases and scripts for larval zebrafish whole brain imaging and registration.

opencc-by-4.0Feb 2022View details →

Zebrafish 2-photon imaging data during seizures; Original data

This is imaging data in .tiff format from the publication "Seizures initiate in zones of relative hyperexcitation in a zebrafish epilepsy model"

opencc-by-4.0Apr 2022View details →

Investigation the cytotoxicity of newly synthesized quinazo-line–sulfonamide derivatives in human leukemia cell lines and hematopoietic activity in zebrafish embryos.

These videos contain the time lapse imaging of the wild type  zebrafish embryos showing the circulation, control (mock 0.5% V/V DMSO) and compound 4a treated embryos at 72 hours post fertilization. The compound 4a specifically blocked the formation of blood and no circulation was seen in these embryos.

opencc-zeroMay 2022View details →

Exposure to 3, 3', 4, 4', 5-pentachlorobiphenyl (PCB 126) causes widespread DNA hypomethylation in adult zebrafish testis

Exposure to environmental toxicants during preconception have been shown to affect offspring health and epigenetic mechanisms such as DNA methylation are hypothesized to be involved in adverse outcomes. However, studies addressing the effects of exposure to environmental toxicants during preconception on epigenetic changes in gametes are limited. The objective of this study is to determine the effect of preconceptional exposure to a dioxin-like PCB (PCB126) on DNA methylation and gene expression in testis. Adult zebrafish were exposed to 3 and 10 nM PCB126 for 24 hours and testis tissue was sampled at 7 days post-exposure for histology, DNA methylation and gene expression profiling. Reduced Representation Bisulfite Sequencing revealed 37 and 92 differentially methylated regions (DMRs) in response to 3 and 10nM PCB126 exposures, respectively. Among them 19 DMRs were found to be common between both PCB126 treatment groups. Gene ontology (GO) analysis of DMRs revealed that enrichment of terms such as RNA processing, iron-sulfur cluster assembly and gluconeogenesis. Gene expression profiling showed differential expression of 40 and 1621 genes in response to 3 and 10nM PCB126 exposures, respectively. GO analysis revealed differential expression of genes related to xenobiotic metabolism, oxidative stress and immune function. There is no overlap in the GO terms or individual genes between DNA methylation and RNAseq results, but functionally many of the altered pathways have been shown to cause spermatogenic defects. Our results indicate that exposure to dioxin-like PCBs during preconception could affect testicular function by altering DNA methylation patterns, with significant implications for reproductive health.

opencc-zeroJul 2022View details →

Beyond bold versus shy: Zebrafish exploratory behavior falls into several behavioral clusters and is influenced by strain and sex

Individual differences in exploratory behavior have been found across a range of taxa and are thought to contribute to evolutionary fitness. Animals that explore more of a novel environment and visit areas of high predation risk are considered bold, whereas animals with the opposite behavioral pattern are shy. Here, we determined whether this bimodal characterization of bold versus shy adequately captures the breadth of behavioral variation in zebrafish or if there are more than these two subtypes. To identify behavioral categories, we applied unsupervised machine to three-dimensional swim traces from over 400 adult zebrafish across four strains (AB, TL, TU, and WIK) and both sexes. We found that behavior stratified into four distinct clusters: previously described bold and shy behavior and two new behavioral types we call wall-huggers and active explorers. Clusters were stable across time and influenced by strain and sex where we found that TLs were shy, female TU fish were bold, male TU fish were active explorers, and male ABs were wall-huggers. Our work suggests that zebrafish exploratory behavior has greater complexity than previously recognized and lays the groundwork for the use of zebrafish in understanding the biological basis of individual differences in behavior.

opencc-zeroAug 2022View details →

Pessimistic cognitive bias is associated with enhanced reproductive investment in female zebrafish

Optimistic and pessimistic cognitive biases have been described in many animals and are related to the perceived valence of the environment. We, therefore, hypothesize that such cognitive bias can be adaptive depending on environmental conditions. In reward rich environments an optimistic bias would be favored, whereas in harsh environments a pessimistic one would thrive. Here, we empirically investigated the potential adaptive value of such bias using zebrafish as a model. We first phenotyped female zebrafish in an optimistic/pessimistic axis using a previously validated judgment bias assay. Optimistic and pessimistic females were then exposed to an unpredictable chronic stress protocol for 17 days, after which fish were euthanized and the sectional area of the different ovarian structures was quantified in both undisturbed and stressed groups. Our results show that zebrafish ovarian development responded to chronic stress, and that judgment bias impacted the relative area of the vitellogenic developmental stage in the stress treatment, with pessimists showing higher vitellogenic areas as compared with optimists. These results suggest that pessimism maximize reproductive investment, through increased vitellogenesis, indicating a relationship between cognitive bias and life-history organismal decisions.

opencc-zeroOct 2022View details →

Raw Sanger sequences of the tyr fragment from crispant and control zebrafish embryos

Thanks to the amenability to genetic modifications, the minimal or non-invasive phenotyping possibilities in early embryos and larvae and the presence of a high percentage of genes orthologous to humans, zebrafish is a successful alternative vertebrate to validate new disease genes and variants and to study mechanisms underlying human diseases. We developed an optimized method allowing early and gentle genotype detection to reduce further possible suffering associated with the generation of genetically modified zebrafish and valid to strategize the employment of "surplus" animals (e.g., those needed solely for line generation or without the desired genotype). The method is based on minimally-invasive tissue (fin) scratching (FS) to obtain genomic DNA material and perform genotyping in early zebrafish embryos. We showcase the method's usefulness for various genotyping needs, including screening both F0 and stable CRISPR/Cas9 lines and obtaining genomic material compatible with Sanger sequencing. Here we provide the raw sequences obtained from FS-derived genomic DNA of single mutant F0 embryos carrying mutations in the tyr gene generated with Base editor (BE) CRISPR/Cas9 technology. We compared the sequencing outcome of FS- vs whole embryos (WE)-based genomic DNA preparation (the WE sequencing results are also provided here). Sequences show the successful C>T (G>A) conversion generating crispant tyr mutants that FS-derived genomic DNA can capture. The resulting dataset demonstrates the compatibility of the method developed with sequencing-based genotyping of early crispant embryos.