Project description:The Thioacetamide-treated rat was first identified as a model of hepatotoxicity by Gupta in 1956 and is now well-established, not least because the histopathogical output closely mimics that seen in humans with chronic liver disease. Acute treatment of rats with Thioacetamide causes pronounced necrosis and inflammation. Animals received intraperitoneal (ip) doses of vehicle-only (0.9% (v/v) saline) (n=3), or 100 mg/kg Thioacetamide (n=3) and were sacrificed after 24 hours. Blood was withdrawn via the descending vena cava and immediately transferred into potassium/EDTA tubes. Following centrifugation (16,100g, 4M-BM-0C, 5 min) the plasma was collected and stored at -80M-BM-0C. miRNA microarray profiling of RNA extracted from the plasma of rats treated with Thioacetamide revealed that a subset of miRNAs were differentially expressed following treatment. These miRNAs appeared to mediate pathways involved in hepatic fibrosis and stellate cell activation, suggesting that they might function as predictive biomarkers following compound-induced hepatotoxicity. The changes correlated well with increases in ALT levels, which are the current gold standard method for determining the extent of liver injury. Furthermore, it is hypothesised that particular aetiologies of liver damage might cause differing expression profiles of miRNAs, thus certain miRNAs could be implemented in a panel-type expression study to distinguish between different types of hepatic injury. Single channel miRNA microarrays were performed on n= 3 samples, 2 treatment groups; control and test. Control animals received vehicle-only (0.9% (v/v) saline) via the ip route. Test animals received 100 mg/kg Thioacetamide dissolved in 0.9% (v/v) saline, via the ip route. 24 h after dosing animals were sacrificed using decapitation under terminal anaesthesia.
Project description:The aim of this experiment was to explore transcriptomic changes in the distal gut of Altantic salmon fed five experimental and two control diets. The experimental diets were isonitrogenous, isolipidic and isocaloric. They had similar content of fish meal (~22%) and similar total plant protein content (~45%), but differed in the contents of soya protein concentrate (SPC) and bean protein concentrate (BPC). These two ingredients were used to replace each other (either partially or fully) at the levels of incorporation ranging from 0 to 45%, with ~11% increments. As a result, the experimental diets contained either 45% SPC and 0% BPC (S45), 34% SPC and 11% BPC (S34B11), 22% SPC and 22% BPC (S22B22), 11% SPC and 34% BPC (S11B34) or 0% SPC and 45% BPC (B45). The S45 and B45 diets were single plant protein diets, while the others (S34B11, S22B22 and S11B34) were mixed plant protein diets. The control diets were enriched with fish meal (FM diet) or soybean meal (SBM diet) to provide negative and positive controls for gut inflammation (enteritis), respectively. The study was conducted at EWOS Innovation Research Facility in Dirdal (Norway) Atlantic salmon (Salmo salar L.) of the SalmoBreed strain were supplied as fertilized eggs and hatched on site. Mixed-sex juvenile salmon in groups of ~150 fish were transferred to 26 indoor tanks (0.6 x 0.6 x 0.6 m), with ~60 L of freshwater flowing at a rate of 3.9 L/min and continuous aeration. The temperature of water was regulated at 13°C and all animals were exposed to a constant light regime (24 h light/day). Fish were fed a commercial EWOS Start 1 diet and acclimated to the experimental conditions for 2 weeks, after which (at body mass ~1.5 g) they were subjected to a 56-day feeding trial. Tanks were randomly assigned to the dietary treatments, with 4 replicate tanks per each experimental diet (S45, S34B11, S22B22, S11B34 and B45) and 3 replicate tanks per each control diet (FM and SBM diets). Fish were fed to satiation prior to the feeding trial and during the dietary manipulation using automatic band feeders (Holland Technology, Norway). During the feeding trial, all fish in each tank had their biomass recorded on days 0 (start of experiment), 14, 28, 42 and 56 (end of experiment) for evaluation of growth performance.
Project description:Transcriptional profiles of a chlorhexidine tolerant Salmonella Typhimurium were compared to its, chlorhexidine sensitive, isogenic progenitor isolate. RNA was extracted from mid-log phase cells from both isolates, without chlorhexidine exposure and following exposure to 1 µg/ ml of chlorhexidine for 30 minutes. Transcriptional profiles of the tolerant isolate were compared to the sensitive isolate, with and without chlorhexidine exposure. Carried out using 3 biological replicates for each sample; each sample hybridised in a two-channel hybridization against Salmonella genomic DNA as the comparator/reference
Project description:We performed microarray experiments on gastric tissue samples to identify the differential expression patterns between tumor and normal condition. 40 gastric tumor tissue samples, 12 normal gastric tissue samples
Project description:During early stages of development, juvenile fish must rely on their innate immune system to defend against pathogens. At these early stages, the immune system is immature and is unlikely to express the full repertoire of genes that control defences. Although vulnerable, these larval fish can still fight of infections, indicating there are active defence mechanisms. Using rainbow trout as a model, we have taken a transcriptomics approach to determine the antibacterial (Aeromonas salmonicida) and antiviral (VHSV) responses to infection at four early life history stages, eyed egg, post-hatch, first feeding and three weeks post-first feeding. We performed microarray analysis using an Agilent 4x44K custom designed array, using a common RNA reference hybridization design. We show that all stages of the developing fish respond to the disease challenge at 3 days post-challenge, but the number and complexity of the response increases with developmental stage. Specifically, the response to virus at eyed egg and hatch stages does not show the full interferon response as is found at first feeding and 3 weeks post-first feeding. The experiments were carried out with a custom-designed Agilent (Agilent design ID: 028918) oligonucleotide microarray (A-MEXP-2315) named Trout_imm_v1. In total, 46 hybridisations were performed on individual animals, with 4 biological replicates per sampling point (apart from Bacteria infected eyed eggs for which two hybridizations were not used). This work was funded by the European Community’s seventh framework programme (FP7/2007-2013), under grant agreement no. 222719 (LIFECYCLE).
Project description:Evaluation of two commercial microarray platforms (Amersham CodeLink UniSet Human 10K I BioArray and Affymetrix GeneChip HG-U133A). Both platforms have been tested on gene expression profiling of MDA-MB-231 human metastatic breast cancer cells, cultured for 48 h in the absence (control) or presence (treated) of 32 µM resveratrol.
Project description:Gene expression profiling was carried out to compare labeled cRNA derived from 3 experimental groups. Group 1 was mRNA extracted from wild type dorsal root ganglia (DRG) taken from mice 10-12 weeks of age, Group 2 was mRNA extracted from DRG taken from NT-4 -/- mice of 4-5 weeks of age. Group 3 was mRNA extracted from DRGs taken from NT-4 -/- mice of 12 weeks of age. In all cases mRNA was extracted from 6-10 mice per group. The experiment was carried out a total of three times.
Project description:We describe PolyA-Seq, a strand-specific method for high-throughput sequencing of the 3' ends of polyadenylated transcripts. PolyA-Seq is as accurate for digital gene expression as existing RNA sequencing approaches, and superior to microarrays. We used the approach to map polyadenylation (polyA) sites in 24 samples from normal tissues in human, rhesus, dog, mouse, and rat. Detection of polyA sites in a mixture of 24 tissues in human, mouse, rat, dog and rhesus. Samples included two replicates each of MAQC Human Brain Reference and MAQC Universal Human Reference. Two additional human sets of reads are included that were used to distinguish true polyA sites from internal priming sites.
Project description:Comparison of the transcriptome of nrpd1a-4_nrpd1b-11 mutant and the wild type. Experiments were done using two independent biological replicates.<br><br>