Danio rerio
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ABSTRACT:
PROVIDER: PRJNA97745 | ENA |
REPOSITORIES: ENA
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Project description:Sexual differentiation in vertebrates is initiated during embryogenesis and leads to the development of individuals into phenotypic males or females. The molecular pathways showing sexual dimorphic patterns have been principally investigated in the gonads. In other organs, much less is known about the gender-associated pattern of gene expression. The brain plays a coordinating role on sexual function in both genders including regulation of reproductive development and maturation through the synthesis of neuropeptide hormones and the regulation of sexual behavior in both males and females. In this study, we aimed at identifying molecular pathways regulated in a gender specific manner in breeding zebrafish in order to generate a greater understanding of the gender specific physiology of the brain. To do so, we measured the gene expression profiles of individual brains of 6 males and 5 females using a 17k oligonucleotide microarray, and interrogated the dataset for genes showing a gender-specific gene expression profile. 42 genes were found to be differentially expressed between males and females from which 18 genes were over-expressed in males and 24 genes were over-expressed in females. Keywords: gender specific gene expression in the zebrafish brain
2008-01-01 | GSE6853 | GEO
Project description:Sexual differentiation in vertebrates is initiated during embryogenesis and leads to the development of individuals into phenotypic males or females. The molecular pathways showing sexual dimorphic patterns have been principally investigated in the gonads. In other organs, much less is known about the gender-associated pattern of gene expression. The brain plays a coordinating role on sexual function in both genders including regulation of reproductive development and maturation through the synthesis of neuropeptide hormones and the regulation of sexual behavior in both males and females. In this study, we aimed at identifying molecular pathways regulated in a gender specific manner in breeding zebrafish in order to generate a greater understanding of the gender specific physiology of the brain. To do so, we measured the gene expression profiles of individual brains of 6 males and 5 females using a 17k oligonucleotide microarray, and interrogated the dataset for genes showing a gender-specific gene expression profile. 42 genes were found to be differentially expressed between males and females from which 18 genes were over-expressed in males and 24 genes were over-expressed in females. Sexually mature fish (6 males and 6 females) were kept in a 15L tank and allowed to breed naturally. After a 20-day period, fish were sacrificed humanly and the brain was extracted, fixed in RNAlater (Ambion) and stored at -20oC until required for microarray analysis. RNA was extracted using the TRI reagent method followed by a LiCl precipitation (Sigma) according to the manufacturer's instructions. Total RNA was amplified and labeled using the Amino Allyl MessageAmp aRNA amplification kit (Ambion). A reference design was used for the array hybridizations. Array analysis was performed according to established protocols (described in Santos et al., 2007) and the data was extracted and queried for differences in gene expression profiles between genders.
2010-05-27 | E-GEOD-6853 | biostudies-arrayexpress
Project description:This study sought to evaluate the effects of dietary MeHg exposure on adult female yellow perch (Perca flavescens) and zebrafish (Danio rerio) reproduction by relating controlled exposures with subsequent reproductive effects. Yellow perch were used in the study for their socioeconomic and ecological importance within the Great Lakes basin, and the use of zebrafish allowed for a detailed analysis of the molecular effects of MeHg. MeHg exposures at environmentally relevant levels were done in zebrafish for a full life cycle, mimicking a realistic exposure scenario, and in adult yellow perch for twenty weeks, capturing early seasonal ovarian development. In zebrafish, several genes involved in reproductive processes were shown to be dysregulated by RNA-seq and QPCR, but no significant phenotypic or physiological changes were observed with ovarian staging, fecundity, or embryo mortality. Yellow perch did not appear to be affected by MeHg, either at a molecular level, as assessed by QPCR of eight genes in the pituitary, liver, and ovary tissue, or a physiological level, as seen with ovarian somatic index, circulating estradiol, and ovarian staging. Lack of impact in yellow perch limits the usefulness of zebrafish as a model and suggests that the reproductive sensitivity to environmentally relevant levels of MeHg differs between yellow perch and zebrafish.
2018-01-01 | GSE73615 | GEO
Project description:Gender specific comparisons of gene expression during Zebrafish pectoral fin regeneration
| PRJNA145067 | ENA
Project description:Molecular Conservation of Zebrafish and Human Liver Tumors.
| PRJNA93567 | ENA
Project description:Olsen et al (2010) have shown that induced Diabetes mellitus (DM) in adult Zebrafish results in an impairment of tissue regeneration as monitored by caudal fin regeneration. In those studies, streptozocin was used to induce hyperglycemia in adult zebrafish, and then, following streptozocin withdrawal, a recovery phase was allowed to re-establish euglycemia, due to pancreatic b-cell regeneration. DM-associated impaired fin regeneration continued indefinitely in the metabolic memory state (MM); allowing for subsequent molecular analysis of the underlying mechanisms of MM. This study focuses on elucidating the molecular basis explaining DM-associated impaired fin regeneration and why it persists into the MM state. The analysis of microarray data indicated that of the 14,900 transcripts analyzed, aberrant expression of 71 genes relating to tissue developmental and regeneration processes were identified in DM fish and the aberrant expression of these 71 genes persisted into the MM state. Key regulatory genes of major signal transduction pathways were identified among this group of 71; and therefore, these findings provide a possible explanation for how hyperglycemia induces impaired fin regeneration and why it continues into the MM state. Total RNA was extracted from caudal fin at 0, 12, 24 and 48 hours post amputation from untreated controls and metabolic memory zebrafish.
2012-11-01 | E-GEOD-37163 | biostudies-arrayexpress
Project description:Domesticated animal populations often show profound reductions in predator avoidance and fear-related behavior compared to wild populations. These reductions are remarkably consistent and have been observed in a diverse array of taxa including fish, birds, and mammals. Experiments conducted in common environments indicate that these behavioral differences have a genetic basis. In this study, we quantified differences in fear-related behavior between wild and domesticated zebrafish strains and used microarray analysis to identify genes that may be associated with this variation. Compared to wild zebrafish, domesticated zebrafish spent more time near the water surface and were more likely to occupy the front of the aquarium nearest a human observer. Microarray analysis of the brain transcriptome identified high levels of population variation in gene expression, with 1,749 genes significantly differentially expressed among populations. Genes that varied among populations belonged to functional categories that included DNA repair, DNA photolyase activity, response to light stimulus, neuron development and axon guidance, cell death, iron-binding, chromatin reorganization, and homeobox genes. Comparatively fewer genes (112) differed between domesticated and wild strains with notable genes including gpr177 (wntless), selenoprotein P1a, synaptophysin and synaptoporin, and acyl-CoA binding domain containing proteins (acbd3 and acbd4). Microarray analysis identified a large number of genes that differed among zebrafish populations and may underlie behavioral domestication. Comparisons with similar microarray studies of domestication in rainbow trout and canids identified sixteen evolutionarily or functionally related genes that may represent components of shared molecular mechanisms underlying convergent behavioral evolution during vertebrate domestication. However, this conclusion must be tempered by limitations associated with comparisons among microarray studies and the low level of population-level replication inherent to these studies. RNA was extracted from the brains of fish from four behaviorally distinct strains of zebrafish and hybridized on Affymetrix microarrays. Brains from 2-5 individual fish of the same sex were pooled and homogenized together, for a total of two biological replicate pools per sex per strain (16 microarrays total).
2012-06-14 | E-GEOD-38729 | biostudies-arrayexpress
Project description:Effects of maternal Cd on the female reproductive functions, gametes development and genes expression of zebrafish
| PRJNA124363 | ENA
Project description:Domesticated animal populations often show profound reductions in predator avoidance and fear-related behavior compared to wild populations. These reductions are remarkably consistent and have been observed in a diverse array of taxa including fish, birds, and mammals. Experiments conducted in common environments indicate that these behavioral differences have a genetic basis. In this study, we quantified differences in fear-related behavior between wild and domesticated zebrafish strains and used microarray analysis to identify genes that may be associated with this variation. Compared to wild zebrafish, domesticated zebrafish spent more time near the water surface and were more likely to occupy the front of the aquarium nearest a human observer. Microarray analysis of the brain transcriptome identified high levels of population variation in gene expression, with 1,749 genes significantly differentially expressed among populations. Genes that varied among populations belonged to functional categories that included DNA repair, DNA photolyase activity, response to light stimulus, neuron development and axon guidance, cell death, iron-binding, chromatin reorganization, and homeobox genes. Comparatively fewer genes (112) differed between domesticated and wild strains with notable genes including gpr177 (wntless), selenoprotein P1a, synaptophysin and synaptoporin, and acyl-CoA binding domain containing proteins (acbd3 and acbd4). Microarray analysis identified a large number of genes that differed among zebrafish populations and may underlie behavioral domestication. Comparisons with similar microarray studies of domestication in rainbow trout and canids identified sixteen evolutionarily or functionally related genes that may represent components of shared molecular mechanisms underlying convergent behavioral evolution during vertebrate domestication. However, this conclusion must be tempered by limitations associated with comparisons among microarray studies and the low level of population-level replication inherent to these studies.
2012-06-15 | GSE38729 | GEO
Project description:Perfluorooctanoic acid (PFOA) is one of the most used perfluorinated compounds in numerous applications and can be detected in environmental samples from around the globe. The aquatic environment is an important site for PFOA deposit. Nevertheless, the exact mode of action and its resulting toxicological effects on aquatic organisms remain largely unknown. To gain a more extensive understanding of the mode of action of teleost PFOA toxicity, transcriptomics, proteomics, biochemical parameters and reproduction were integrated in the present study. Male and female zebrafish were exposed to nominal concentrations of 0.1; 0.5 and 1 mg/l PFOA for 4 and 28 days resulting in an accumulation which was higher in males compared to females. These gender-related differences were likely caused by different elimination rates due to distinct hormone levels and differences in transport activity by solute carriers. The general mode of action of PFOA was believed to be an increase of the mitochondrial membrane permeability which caused effects on the electron transport system at the biochemical level and resulted in alterations of the oxidative phosphorylation, oxidative stress and apoptosis at the gene transcript and protein level. As a consequence, evidence for the replacement of the affected cells and organelles to sustain tissue homeostasis was found at the molecular level. The higher energy demand, due to these adverse effects, was provided by lowering the glycogen stores. Despite this increase in metabolic expenditure, no effects on reproduction were found indicating that the fish seemed to cope with exposure to the tested concentrations of PFOA. Adult zebrafish (Danio rerio) were exposed to nominal concentrations of 0mg/l; 0.1mg/l; 1mg/l PFOA (perfluorooctanoic acid) for 28 days. Three different 25 litre aquaria per exposure concentration were used resulting in 3 biological replicates with each aquarium containing 8 male and 8 female zebrafish. The livers of 6 male fish and 6 female fish were pooled separately and snap frozen in liquid nitrogen. A reference sample was made by pooling equal amounts of RNA from all samples. A carriage wheel design was used in which all samples were connected to the reference sample and the main contrasts of interest were made directly on the same microarrays as frequently as possible. This design resulted in technical triplicates of each sample.
2013-07-20 | E-GEOD-19908 | biostudies-arrayexpress