Transcription profiling of migratory vs sedentary brown trout (Salmo trutta) and wild vs hatchery Atlantic salmon (Salmo salar)
ABSTRACT: A total of 55 individuals were analysed: 15 migratory brown trout (Salmo trutta) individuals from the Redon river, 15 sedentary brown trout (S. trutta) individuals from the Redon river, 15 sedentary brown trout (S. trutta) individuals from the Chevenne river, and 10 Atlantic salmon (S. salar) individuals of a hatchery strain. For each individual, RNA was isolated twice from different parts of the same tissue, independently reverse transcribed into Cy3-labeled cDNA and then probed on two different slides, which leads to total of 110 single slide experiments.
SUBMITTER: Michael HansenLaurent ExcoffierRichard PowellThomas GigerCarlo LargiaderAlexis ChampigneullePhilip Day
Project description:The main purpose of the experiment is to look for changes in the transcriptome of LNCaP cells during neuroendocrine differentiation induced by incubation in steroid stripped serum (charcoal treated fetal bovine serum) for four days.
Project description:1. effect of radiation on transcription in normal and radiation sensitive primary human fibroblasts. 2. comparison of the basal transcription levels in normal and radiation sensitive primary human fibroblasts.
Project description:To identify epigenetically silenced genes in multiple myeloma (MM) cell lines and to determine the effects of 5-aza-2-deoxycytidine and trichostatin A on gene expression. We treated 3 multiple myeloma cell lines (MM1, NCI-H929, U266) with 5-aza-2-deoxycytidine and/or trichostatin A.
Project description:Oral immunization of trout against infectious pancreatic necrosis virus (IPNV) have been recently reported by using a DNA vector coding the viral capsid VP2 gene encapsulated in alginate microspheres. We report here an study of the transcripts in head kidney and pyloric ceca 7 days after oral vaccination of rainbow trout by using a newly designed rainbow trout 60-mer oligo microarray focused in their immune-related genes. Trout were obtained from 4 different farms, one group of trout was defined as belonging to one of the farms. Each of the trout 4 groups were divided into two subgroups of 6 trout for each subgroup. Subgroup I was orally vaccinated with 10 µl of suspension of the vaccine microspheres each containing 10 µg of pcDNA-VP2 diluted in 10µl of PBS, while subgroup II received similar microspheres suspension but pcDNA. Head kidney and pyloric ceca were collected from each subgroup and RNA was extracted.
Project description:The Infectious Hematopoietic Necrosic Virus (IHNV) DNA vaccine is based on the viral glycoprotein gene (G gene) and induces a non-specific anti-viral immune response and long-term specific immunity against IHNV in salmonid fishes. This study characterized gene expression responses associated with the early anti-viral response. Homozygous rainbow trout were injected intra-muscularly (I.M.) with vector DNA or the IHNV DNA vaccine. Gene expression at the I.M. site was evaluated using a 16,000 feature salmon cDNA microarray. Eighty different transcripts were significantly modulated in the vector DNA group while 910 transcripts were modulated in the IHNV DNA vaccinated group relative to control group. Quantitative reverse transcriptase PCR was used to examine expression of selected genes at the I.M. site and in other secondary tissues. In the localized response (I.M. site), the magnitudes of gene expression changes were higher in the vaccinate group relative to the vector DNA group for the majority of genes analyzed. At secondary systemic sites (e.g. gill, kidney and spleen) evaluated with RT-PCR of specific genes, the main difference was the up-regulation of the type I IFN-related genes in only the IHNV DNA vaccinated group. Keywords: disease vaccine response Gene expression at the site of I.M injection was evaluated 7 days post-injection in clonal rainbow trout. Gene expression was compared across three treatments, with replicate clonal rainbow trout individuals (Hot Creek strain) within each treatment. Treatments included injection with 1X PBS (control group), plasmid vector only (without IHNV G gene; hereafter referred to as vector group), and the pIHNV vaccine (vaccine group). Three clonal individuals from the control, three individuals from the vector group, and four individuals from the vaccine group were labeled with Cy3 and used for individual hybridizations to ten slides, comparing hybridization of each individual to a major reference RNA pool. The major reference pool consisted of three unhandled clonal rainbow trout and constituted a pool of RNA from the anterior kidney, spleen, liver and muscle and was labelled with Cy5. Total RNA was extracted from samples, amplified, and hybridized to 16,000 feature Atlantic salmon cDNA arrays developed by the Genomic Research for Atlantic Salmon project. Differential expression was compared among control, vector, and vaccine groups.
Project description:The aim of this project was to search for the new factors engaged in mitochondrial nucleic acids metabolism under stress conditions. To this end we treated human 293 cells with mitochondrial replication/transcription inhibitor ethidium bromide and we compared proteomes of untreated vs treated cells. We were looking for the proteins whose level would be differentially regulated in response to disturbed mitochondrial gene expression. In our studies we utilized a stable 293 cell line that inducible expresses a fusion of EGFP with mitochondria targeting sequence. This approach enabled us to control mitochondrial import by analysis of the abundance of mitochondrial EGFP marker. We isolated highly purified mitochondria from the cells, lysed them and subjected protein extracts to labelling with iTRAQ reagents. We performed quantitative analysis of stress- induced changes of human mitochondrial proteome with the use of MaxQuant software.
Project description:Investigation of transcriptome variability in neurospheres originating from separate isolations (individuals), different passages and parallel cultures. As a control neurospheres were also compared to neurospheres induced to differentiate by adding serum and plating onto solid support.
Project description:We describe here transcripts induced after intraperitoneal injection of rainbow trout with 2 different viruses, both belonging to strain 23.75 of viral hemorrhagic septicemia virus (VHSV): a deleted Nv gene (dNV) virus and a wild type (wt) virus. Two days after infection, differentially expressed transcript levels from selected immune-related trout genes were studied in internal organs (spleen and head kidney). Fishes were divided in two groups (3 fishes per group). The first group was intraperitoneally injected with 100000 pfu per trout of dNV VHSV, while the second group was injected with 100000 pfu/trout of wt VHSV. All fishes were sacrificed two days post infection.