Interaction between microbiota and development of the olfactory system in Zebrafish
Ontology highlight
ABSTRACT: Olfactory systems are one of the most conserved and ancient sensory systems in vertebrates. The vertebrate olfactory epithelium is colonized by complex communities of commensal microorganisms, but their impact on olfactory epithelial development and function remains unknown. Using germ-free zebrafish model, we aim to understand the transcriptional responses that colonization with a microbiota induces in olfactory organs. This study was aimed to understand the changes in gene expression in the olfactory organ of Germ Free (GF) zebrafish compared to conventionalized (ConvD) zebrafish. This experiment is related to E-MTAB-5046 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5046)
Project description:Olfactory systems are one of the most conserved and ancient sensory systems in vertebrates. The vertebrate olfactory epithelium is colonized by complex communities of commensal microorganisms, but their impact on olfactory epithelial development and function remains unknown. Using germ-free mouse model, we aim to understand the transcriptional responses that colonization with a microbiota induces in olfactory organs. This study was aimed to understand the changes in gene expression in the nose of Germ Free (GF) mice compared to conventionalized (ConvD) mice. This experiment is related to E-MTAB-5045 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5045)
Project description:Sorafenib is associated with cardiac adverse effects, including left ventricular dysfunction. However, the precise mechanism remains unclear. Here, we aimed to establish the genes responsible for this cardiotoxicity using zebrafish. A pigmentless zebrafish line expressing green fluorescent protein in the heart were treated with or without sorafenib. In vivo fluorescent cardiac imaging revealed that the ventricular dimension of the longitudinal axis in zebrafish treated with sorafenib was significantly lower than in those without sorafenib. Transcriptome analysis of zebrafish hearts revealed that expression of stanniocalcin1 (stc1) in zebrafish treated with sorafenib was significantly lower than that without sorafenib treatment. We were able to demonstrate that the ventricular dimension of the longitudinal axis in stc1 morphant was significantly smaller than that of control zebrafish and that forced expression of stc1 normalized the decrease in ventricular diameter in stc1 morphant and zebrafish treated with sorafenib. These data suggest that stc1 is the gene responsible for sorafenib-induced cardiotoxicity. Gene expression regulated by sorafenib in zebrafish at 4 dpf was measured. Four independent experiments were performed for each group.
Project description:To investigate the patterns of global gene expression profiles modulated by the different sized AgNPs and to differentiate their modes of toxicity, zebrafish (Danio rerio) will be exposed to the AgNPs (50, and 150nm) and used for microarray analysis by Agilent Zebrafish Oligo Microarray system. 334 genes overlaped between AgNPs and Ag+ treatments in a total of 7,538 differential expressed genes. Immune response, antigen processing and presentation, response to estradiol stimulus and regulation of RNA metabolic process are most significant GO terms enriched in genes up regulated by four treatments. Neuroactive ligand-receptor interaction pathway was enriched among AgNP 50nm and AgNP 150nm activated genes, and specifically induced by AgNP 50nm include cell cycle and Toll-like receptor signaling pathways. The zebrafish larvae (72hpf) was exposed to AgNPs for 96hour. And then after total RNA extration from the each samples, the AgNPs related gene expression profiles identified using Agilent Zebrafish Oligo Microarray. Significant alterations in gene expression were found for all treatments and many of the gene pathways connected.
Project description:A convergence of technological breakthroughs in the past decade has facilitated the development of rapid screening tools for biomarkers of toxicant exposure and effect. Platforms using the whole adult organism to evaluate the genome-wide response to toxicants are especially attractive. Recent work demonstrates the feasibility of this approach in vertebrates using the experimentally robust zebrafish model. In the present study, we evaluated gene expression changes in whole adult zebrafish following an acute 24 hour exposure to three metals with known human health risks. Male adult zebrafish were exposed to nickel chloride, cobalt chloride, and sodium dichromate concentrations corresponding to their respective 96 hr LC20, LC40 and LC60. Histopathology was performed on a subset of metal-exposed zebrafish to phenotypically anchor transcriptional changes associated with each metal. Comparative analysis identified subsets of differentially expressed transcripts both overlapping and unique to each metal. Application of gene ontology (GO) and transcription factor enrichment algorithms revealed a number of key biological processes perturbed by metal exposures and the master transcriptional regulators mediating gene expression changes. Metal exposures differentially activated biological processes associated with ribosome biogenesis, proteosomal degradation and p53 signaling cascades, while repressing oxygen-generating pathways associated with amino acid and lipid metabolism. Despite appreciable effects on gene regulation, nickel exposures did not induce any morphological alterations in zebrafish organs and tissues. Histopathological effects of cobalt remained confined to the olfactory system, while chromium targeted the gills, pharynx and intestinal mucosa. A number of enriched transcription factors mediate the observed gene response to metal exposure, including known targets such as p53, HIF1M-oM-^AM-! and the myc oncogene and novel regulatory factors such as XBP1, GATA6 and HNF3M-oM-^AM-". This work uses an experimentally innovative approach to capture global responses to metal exposures and provides mechanistic insights into metal toxicity mechanisms. Metal induced changes in gene expression in zebrafish were measured after 24 h exposures to each of three metals (nickel, chromium or cobalt). A total of 48 arrays were processed - 16 arrays per metal with 4 replicates for each exposure condition (control, low, mid, and high).
Project description:96 hpf zebrafish larvae were exposed to cold (16 degrees C) or heat (34 degrees C) stress for 2, 12, 24 and 48h. Time-matched controls were maintained at 28 degrees C. The transcriptional responses elicited by temperature stress in larval zebrafish were investigated by microarray.
Project description:Infectious hematopoietic necrosis virus (IHNV) is a virus of the genus Novirhabdovirus and the causative agent of infectious hematopoietic necrosis (IHN), one of the most serious threats to salmonid fishes. IHN outbreaks can cause more than 80% mortality rates in certain cases. Studying the transcriptional responses to the secondary immunization with a live attenuated IHNV vaccine will help us understand how fish previously immunized respond when they encounter again the same pathogen and how effective this type of vaccination is.This experiment was aimed at understanding the transcriptomic response of rainbow trout to an IHNV secondary nasal vaccination.
Project description:96 hpf zebrafish larvae were exposed to cold (16 C) or heat (34 C) stress for 2 and 48h. Time-matched controls were maintained at 28 C. The transcriptional responses elicited by temperature stress in larval zebrafish were investigated by microarray.
Project description:This experiment was aimed at understanding transcriptional response to a plant protein diet in multiple tissues of Atlantic salmon. Agilent-based microarray platform with 4 x 44 K probes per slide (Salar_2; Agilent Design ID:025520) oligo microarray was used in this experiment. A dual-labelled experimental design was employed for the microarray hybridisations. aRNA from each experimental sample (Cy3 labelled) was competitively hybridised against a common pooled-reference sample (Cy5 labelled), which comprised equal amounts of aRNA from each of the samples used in the study. This design permits valid statistical comparisons across all treatments to be made. The entire experiment comprised 24 hybridisations - 3 tissues (mid intestine, liver, muscle) x 2 treatments (MP diet / PP diet) x 4 biological replicates.
Project description:Fever implies a significant increase in corporal temperature that aids toward the resolution of infective processes such as viral disease. The majority of vertebrate species are not homeothermic therefore must rely upon the environment for temperature regulation. Here we show that in the zebrafish an artificial viral infection, induced by poly (I:C), induces a fever response regulated by the behavioral choice of temperature. We recorded 12 h of the diurnal cycle in zebrafish previously treated (first 12 hours dark cycle) with the pyrogen, poly (I:C) [10 μg⋅kg-1]. Fish, n=10, were held in a thermal gradient (36-180C) separated into 7 interconnected chambers. Presence or absence of individuals in each chamber was recorded each 15 minutes throughout the 12 hour period. After the experimental period we dissected whole brains for microarray analysis. In monitored zebrafish intraperitoneal treatment with poly (I:C) induced a febrile behaviour with significantly elevated temperature preference (T of about 32ºC) in stark contrast with the observed frequency for saline-injected fish (28ºC). Microarray analyses uncovered significant shifts in transcriptional activity that were highly directed in the poly (I:C)-treated fish housed in the thermal gradient. When compared to gene expression profiles from poly (I:C)-treated fish deprived of a thermal gradient we observed a less intense specific to the poly (I:C) challenge and interestingly observed a scattered generalised stress response. Our results highlight the influence of temperature preference in the development of the immune response in zebrafish. Fever induced gene expression in zebrafish brain was measured at 24 after intra peritoneal injection with 1mg*Kg-1 of Poly (I:C) in zebrafish. Four independent experiments were performed to explore the transcriptomic profile induced by animals injected by Poly (I:C) with/whithout thermal gradient, saline solution (PBS), or control using different animals for each experiment.