Project description:To understand the effects of Hsp60 deficiency in developing vertebrates, we generated CRISPR/Cas9-mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the proteome changes in zebrafish larvae at 5 days post fertilization (DPF). Wildtype control and hspd1-/- larvae at 5dpf, were analyzed by TMT and nanoLC-MS/MS based proteomcis. For this purpose, we studied five pools from each genotype, and each pool consisted of five larvae.
Project description:To understand the effects of Hsp60 deficiency in developing vertebrates, we generated CRISPR/Cas9-mediated hspd1 knockout zebrafish lines by targeting exon 2 to induce a frameshift mutation. We selected an allele with a 56 base pair deletion inducing a frameshift mutation leading to loss of protein functions. We examined the transcriptome changes in zebrafish larvae at 5 dpf .
Project description:Precise regulation of RNA polymerase II (RNAPII) is fundamental to transcriptional fidelity in eukaryotes. The Integrator complex, a conserved multi-subunit assembly, safeguards transcriptional integrity through its interaction with RNAPII, mediating transcription initiation, nascent RNA cleavage, and 3′ end processing. INTS1, the largest subunit of the Integrator complex, is critical for its function, and its mutations are linked to human neurodevelopmental disorders, yet, the underlying transcriptional effects remain poorly defined. Here, we characterize the global transcriptional effects of INTS1 deficiency in zebrafish. INTS1 loss leads to widespread gene expression changes, including of genes linked to hyperactivity and pathways associated with Attention-Deficit/Hyperactivity Disorder. We observe mutant-specific first intron retentions and transcript extensions. These findings underscore a central role for INTS1 in coordinating transcriptional regulation, and highlight the essential function of the Integrator complex in maintaining transcriptome integrity. Together, they offer insights into how INTS1 disruption may contribute to behavioral and physiological abnormalities.
Project description:The Liver X Receptors (LXRs) play important roles in multiple metabolic pathways, including fatty acid, cholesterol, carbohydrate and energy metabolism. To expand the knowledge of the functions of LXR signaling during embryonic development, we performed a whole-genome microarray analysis of Lxr target genes in zebrafish larvae treated with either one of the synthetic LXR ligands T0901317 or GW3965. Assessment of the biological processes enriched by differentially expressed genes revealed a prime role for Lxr in regulating lipid metabolic processes, similarly to the function of LXR in mammals. In addition, exposure to the Lxr ligands induced changes in expression of genes in the neural retina and lens of the zebrafish eye, including the photoreceptor guanylate cyclase activators and lens gamma crystallins, suggesting a potential novel role for Lxr in modulating the transcription of genes associated with visual function in zebrafish. The regulation of expression of metabolic genes was phenotypically reflected in an increased absorption of yolk in the zebrafish larvae, and changes in the expression of genes involved in visual perception were associated with morphological alterations in the retina and lens of the developing zebrafish eye. The regulation of expression of both lipid metabolic and eye specific genes was sustained in 1 month old fish. The transcriptional networks demonstrated several conserved effects of LXR activation between zebrafish and mammals, and also identified potential novel functions of Lxr, supporting zebrafish as a promising model for investigating the role of Lxr during development.
Project description:To investigate the effects of glucocorticoids on the gene expression profiles in zebrafish, we performed a microarray-based transcriptomic study using larvae exposed to three representative glucocoriticoids at environmentally relevant high and low concentrations. Transcriptiomic profiel of developing zebrafish larvae exposed to dexamethasone, prednisolone or triamcinolone at 50 pM to 50 nM from 3 hours post-fertilisation to 5 days post-fertilisation were analyzed using G2519F Agilent Zebrafish Whole Genome Oligo Microarray Ver3.0, 4x44K.
Project description:Genome-wide microarray analysis of the effects of swim-training on caudal fin development in zebrafish larvae. Zebrafish were subjected to swim-training from 5 days post fertilization (dpf) until 10 dpf. Subsequently, we performed a genome-wide microarray analysis on the caudal fins of control and trained fish at 10 dpf. The goal of the project was to investigate the effects of swim-training on the gene expression level during caudal fin development in zebrafish larvae.
Project description:Transcriptional profiling of 3dpf wild type zebrafish larvae treated with 20mM PTZ for 30 and 90 minutes compared with 3dpf wild type control untreated zebrafish larvae.
Project description:In this work we investigated how the brain proteome of the larval zebrafish is modified by behavioral adaptation to the environmental challenge of a water vortex. We monitored the behavior of larvae and observed that they behaviorally adapted to the presence of a water vortex. We obtained the larval zebrafish brain proteome by extracting brains from zebrafish larvae and analyzing them using and LFQ-based LC-MS/MS-approach. In total we identified 5929 proteins in the larval brain. Within this proteome, we identified 57 proteins that were significantly regulated following experience of the water vortex: 41 proteins were up regulated and 16 were down regulated. Of these, 29 proteins are known to have neuronal functions, 17 proteins are known to have other cellular functions, and 11 proteins are still uncharacterized.