Calcium Toolkit genes expression in the zebrafish brain
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ABSTRACT:
PROVIDER: PRJNA525447 | ENA |
REPOSITORIES: ENA
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Project description:Zebrafish are well suited for in vivo calcium imaging because the transparency of their larvae and the ability to express calcium probes in various cell subtypes. This model organism has been used extensively to study brain development, neuronal function, and network activity. However, only a few studies have investigated calcium homeostasis and signaling in zebrafish neurons, and little is known about the proteins that are involved in these processes. Using bioinformatics analysis and available databases, the present study identified 491 genes of the zebrafish Calcium Toolkit (CaTK). Using RNA-sequencing, we then evaluated the expression of these genes in the adult zebrafish brain and found 380 hits that belonged to the CaTK. Based on quantitative real-time polymerase chain reaction arrays, we estimated the relative mRNA levels in the brain of CaTK genes at two developmental stages. In both 5 dpf larvae and adult zebrafish, the highest relative expression was observed for tmbim4, which encodes a Golgi membrane protein. The present data on CaTK genes will contribute to future applications of zebrafish as a model for in vivo and in vitro studies of Ca2+ signaling.
2019-03-05 | GSE127335 | GEO
Project description:We report the application of RNA-seq for molecular profiling of cultured, cortical astrocytes. Our data set is based on about 40 million unique reads per sample in four independent mRNA preparations. Cortical astrocytes are a prototypical cell model for investigating calcium signaling. For analysis of calcium fluxes, we performed direct calcium imaging in the endoplasmic reticulum and in the cytosol. We describe in our study the physiological profile of homeostatic and agonist-induced calcium fluxes. Furthermore, we show how ER calcium release shapes the cytosolic calcium signal. This transcriptome dataset was used to profile the calcium toolkit of astrocytes. The data suggest that a small number of calcium signaling-related proteins mediate calcium homeostasis in astrocytes.
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Project description:Homeostatic calcium fluxes, ER calcium release, SOCE, and calcium oscillations in cultured astrocytes are interlinked by a small calcium toolkit
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Project description:Aim of the study was to examine the expression of calsequestrin isoforms in zebrafish adult brain. By quantitative PCR we found three RNA transcripts coding for Casq1a, Casq1b and Casq2. In brain homogenate, two protein isoforms were detected by western blotting and mass spectrometry. Whole brain fractionation experiments revealed that Casq2 isoform was enriched in a heavy fraction containing microsomes and synaptic membranes, while Casq1a was recovered also in a light cytosolic-enriched fraction. By immunofluorescence, we found that calsequestrins show different cellular localization and we confirmed heterogeneous cell expression of Casq1a and Casq2 mRNA by in situ hybridization. Both isoforms were expressed in cerebellum, and cerebellum-like structures of the brain, Casq2 more concentrated in Purkinje cells, and Casq1 equally distributed in granular and Purkinje cells. At sub cellular level, in Purkinje cells, Casq2 was localized in cell bodies, dendrites and axons, while Casq1 was restricted to cell bodies and axons. Data are discussed in relation to the heterogeneous cellular and subcellular distribution of other Calcium store markers of cerebellum and are evaluated with respect to the relevance of calsequestrins in neuron-specific functional activity.
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Project description:Cilia are slender, hair-like structures extending from cell surfaces and playing essential roles in diverse physiological processes. Within the nervous system, primary cilia contribute to signaling and sensory perception, while motile cilia facilitate cerebrospinal fluid flow. Here, we investigated the impact of ciliary loss on neural circuit development using a zebrafish line displaying ciliogenesis defects. We found that cilia defects after neurulation affects neurogenesis and brain morphology, especially in the cerebellum, and lead to altered gene expression profiles. Using whole brain calcium imaging, we measured reduced light-evoked and spontaneous neuronal activity in all brain regions. By shedding light on the intricate role of cilia in neural circuit formation and function in the zebrafish, our work highlights their evolutionary conserved role in the brain and set the stage for future analysis of ciliopathy models.
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Project description:Purpose: Identify zebrafish control and csf1r-mutant brain transcriptomes Methods: RNA sequencing was performed on whole brain of control (3x), csf1ra-/- microglia (3x) and csf1ra-/-;b+/- microglia (3x) and csf1ra-/-;b-/- zebrafish. 10-20 million reads per sample were obtained. Reads were mapped to zebrafish genome GRC10. Results: We identified that microglia gene expression was reduced in csf1ra-/-;b+/- and csf1ra-/-;b-/;- mutant transcriptomes.
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Project description:We used microarray analyses in adult female zebrafish (Danio rerio) to identify metabolic pathways regulated by starvation in two key organs that 1) serve biosynthetic and energy mobilizing functions (liver) and 2) consume energy and direct behavioral responses (brain). Starvation affected the expression of 574 transcripts in the liver, indicating an overall decrease in metabolic activity, reduced lipid metabolism, protein biosynthesis and proteolysis, and cellular respiration, and increased gluconeogenesis. Starvation also regulated expression of many components of the Unfolded Protein Response, the first such report in a species other than yeast (Saccharomyces cerevisiae) and mice (Mus musculus). The response of the zebrafish hepatic transcriptome to starvation was strikingly similar to that of rainbow trout (Oncorhynchus mykiss), but very different from common carp (Cyprinus carpio) and mouse. The transcriptome of zebrafish whole brain was much less affected than the liver, with only two differentially expressed genes, both down-regulated. Down-regulation of one of these genes, matrix metalloproteinase 9 (mmp9), suggests increased inhibition of apoptosis (neuroprotection) and decreased restructuring of the extracellular matrix in the brain of starved zebrafish. The low level of response in the transcriptome of whole zebrafish brain agrees with observations that the brain is metabolically protected compared to the rest of the body. Experiment Overall Design: Brain treatments: Starved (21 days) and Control (Fed). Four microarrays per treatment. Experiment Overall Design: Liver treatments: Starved (21 days) and Control (Fed). Five microarrays per treatment. Experiment Overall Design: Data for brain and liver were normalized and analyzed separately because variances of expression differed considerably between the tissues.
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Project description:Using 2 male and 2 female zebrafish (pool of 6) brain samples, we generated base-resolution DNA methylation maps to document sex-specific epigenetic differences. Here we generated single-nucleotide resoultion DNA methylation map of 4 zebrafish brain samples using Reduced Representation Bisulfite Sequencing (RRBS)
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