Zebrafish Information Network, the knowledgebase for <i>Danio rerio</i> research

Bradford, Yvonne M.; Slyke, Ceri E. Van; Singer, Amy; Paddock, Holly; Eagle, Anne; Fashena, David; Howe, Douglas G.; Frazer, Ken; Martin, R. D.; Pich, Christian; Ramachandran, Sridhar; Ruzicka, Leyla; Westerfield, Monte

doi:10.1101/2021.09.22.461443

Cited by 11 publications

(13 citation statements)

References 24 publications

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“…In order to identify gene products that may be contributing to the mechanotransduction process, we conducted a survey of previously published lateral line neuromast scRNA-seq data 26 . A MATLAB script (Mathworks, R2020B) was written that performed the following steps: cells that express the hair cell marker tmc2b were selected, the transcripts expressed by each selected cell were filtered to include genes annotated with a relevant list of ontology terms (“ion transport”, “ion channel activity”, “gpcr activity”, “chemical synaptic transmission”, “hormone activity”, “neuropeptide hormone” for Danio rerio in AmiGo2 27 and a manually curated listed of similar genes not captured in the gene ontology database (based on searches of zfin.org 28 ), and the resulting list was then reviewed to identify genes with known anion efflux activity. This analysis was performed exclusively for hypothesis generation.…”

Section: Methodsmentioning

confidence: 99%

Anion efflux mediates transduction in hair cells of zebrafish lateral line

Lunsford

Bobkov

Ray

et al. 2022

Preprint

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Hair cells are the principal sensory receptors of the vertebrate auditory system, and transduce sounds with mechanically-gated ion channels that permit cations to flow from the surrounding endolymph into the cells. The lateral line of zebrafish has served as a key model system for understanding hair cell physiology and development, and it has often been speculated that these hair cells employ a similar transduction mechanism. In this study, we demonstrate that the hair cells are exposed to an unregulated external environment with cation concentrations that are too low to support transduction. Instead, our results indicate that hair cell excitation is mediated by a fundamentally different mechanism involving the outward flow of anions.

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Section: Methodsmentioning

confidence: 99%

Anion efflux mediates transduction in hair cells of zebrafish lateral line

Lunsford

Bobkov

Ray

et al. 2022

Preprint

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“…In addition, the zebrafish community has exceptionally valuable resources, including the web platform ZFIN, which aggregates genomic data, publications, gene expression profiles, and information about mutants, transgenics, antibodies, and other reagents. 37 Some zebrafish lines, including several wild-type strains, can be requested from the Zebrafish International Resource Center or the European Zebrafish Resource Center. These include the original AB line from the University of Oregon and the TU line from Tübingen, which was later used for sequencing the genome.…”

Section: Advantages and Disadvantages Of The Zebrafish As A Model For...mentioning

confidence: 99%

Zebrafish Models of Cardiac Disease: From Fortuitous Mutants to Precision Medicine

González‐Rosa

2022

Circulation Research

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Heart disease is the leading cause of death worldwide. Despite decades of research, most heart pathologies have limited treatments, and often the only curative approach is heart transplantation. Thus, there is an urgent need to develop new therapeutic approaches for treating cardiac diseases. Animal models that reproduce the human pathophysiology are essential to uncovering the biology of diseases and discovering therapies. Traditionally, mammals have been used as models of cardiac disease, but the cost of generating and maintaining new models is exorbitant, and the studies have very low throughput. In the last decade, the zebrafish has emerged as a tractable model for cardiac diseases, owing to several characteristics that made this animal popular among developmental biologists. Zebrafish fertilization and development are external; embryos can be obtained in high numbers, are cheap and easy to maintain, and can be manipulated to create new genetic models. Moreover, zebrafish exhibit an exceptional ability to regenerate their heart after injury. This review summarizes 25 years of research using the zebrafish to study the heart, from the classical forward screenings to the contemporary methods to model mutations found in patients with cardiac disease. We discuss the advantages and limitations of this model organism and introduce the experimental approaches exploited in zebrafish, including forward and reverse genetics and chemical screenings. Last, we review the models used to induce cardiac injury and essential ideas derived from studying natural regeneration. Studies using zebrafish have the potential to accelerate the discovery of new strategies to treat cardiac diseases.

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“…To further explore the data, we transformed read numbers into fragments per kilobase per million reads (FPKM) (Supplementary Data 01) and developed custom routines in Python for plotting. We subselected transcription factors by selecting genes identified with "DNA-binding transcription factor activity" in ZFIN (80) and repeated principal component and differential expression analyses (Supplementary Data 02 and 03). Transcription factors were considered as significantly expressed if at least 20% (i.e., 7 out of 35) of the samples had positive reads.…”

Section: Rna-seq Data Analysismentioning

confidence: 99%

Identification of transcription factors involved in the specification of photoreceptor subtypes

Angueyra

Kunze

Patak

et al. 2021

Preprint

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During development, retinal progenitors navigate a complex landscape of fate decisions that culminates with an array of unique cell types that are required for proper vision. Here, we aim to identify factors that are required for fate decisions in photoreceptors. These factors help create a diversity of photoreceptor subtypes that sustain vision in day and night, enable the detection of colors, of prey and predators, and other aspects of vision. To identify these factors, we generate a high-quality and deep transcriptomic profile of each photoreceptor subtype in zebrafish. From these profiles, we focus on transcription factors—key players in cell-fate decisions. We apply CRISPR-FØ screening as a versatile platform to explore the involvement of transcription factors in photoreceptor subtype-specification. We find that three differentially-expressed transcription factors (Foxq2, Tbx2a and Tbx2b) play unique roles in controling the identity of photoreceptor subtypes within the retina. Our results provide novel insights into the function of these factors and how photoreceptors acquire their final identities. Furthermore, we have made our transcriptomic dataset openly available and easy to explore. This dataset and the screening method will be valuable to the scientific community and will enable the exploration of genes involved in many essential aspects of photoreceptor biology.

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Zebrafish Information Network, the knowledgebase for Danio rerio research

Cited by 11 publications

References 24 publications

Anion efflux mediates transduction in hair cells of zebrafish lateral line

Anion efflux mediates transduction in hair cells of zebrafish lateral line

Zebrafish Models of Cardiac Disease: From Fortuitous Mutants to Precision Medicine

Identification of transcription factors involved in the specification of photoreceptor subtypes

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