Transcription profiling of Strongyloides ratti to host immunity
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ABSTRACT:
ORGANISM(S): Strongyloides ratti
SUBMITTER: unknown unknown
PROVIDER: E-MAXD-53 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Strongyloides ratti is a parasitic nematode of rats and a laboratory model for nematode infection more generally. The aim of this experiment was to determine the gene expression response of parasitic females to abiotic factors in its environment ex vivo that may be relevant to its natural environment in the gut in vivo. Thus, we used cDNA arrays to assay transcriptional responses to high and low salt, to RPMI versus PBS media and to 37C versus 40C. A moderate number of gene expression changes were observed.
2009-09-03 | E-MAXD-52 | biostudies-arrayexpress
Project description:This experiment exploits the life-cycle of Strongyloides ratti, which is a parasitic nematode of brown rats that exhibits three adult stages within its life-cycle - parasitic females, freeliving females and free-living males. We use a cDNA microarray to examine patterns of (i) gender-biased gene expression by contrasting free-living females against free-living males, and (ii) parasitic-biased expression by contrasting parasitic females against free-living females. Of the 3688 distinct transcripts represented on our array, 20% exhibited male-biased expression 19% exhibit female-biased expression, 11% exhibit parasitic-biased expression and 8% exhibit free-living-biased expression. Among the top responding genes, an orthologue of major sperm protein is upregulated in males, distinct aspartic protease orthologues are upregulated in either parasitic or in free-living females, and orthologues of hsp-17 chaperone are upregulated in parasitic females. Upon a global analysis of gene expression, we find that female-biased expression is associated with genes involved in reproductive processes and larval development, that male-biased expression is associated with genes involved in metabolism, and that free-living biased expression is associated with genes involved in regulation of body fluids and response to external stimulus. The association of gene ontology with parasite-biased expression is less clear. Our results provide an initial gene expression analysis of gender- and parasite-biased expression in S. ratti, may be more generally applicable to other parasitic nematodes, and may help to refine the search for novel drug or vaccine targets against parasitic nematodes.
2008-01-17 | E-MAXD-37 | biostudies-arrayexpress
Project description:Strongyloides ratti is a parasitic nematode of rats and a laboratory model for nematode infection more generally. Selected lines were generated over the course of 20 - 30 generations such that eggs were harvested either at the beginning or towards the end of an infection, termed 'fast' and 'slow' lines, respectively. Phenotypic differences in these lines in their fecundity and response to host immunity were observed. The gene expression response of these lines in both permissive and restrictive immune environments were assayed using cDNA microarrays. Large numbers of responding genes were found (but with modest fold changes) and clusters of co-expressed genes identified. Genes exhibiting female-biased expression responded to host immunity, consistent with increased investment into transmission in restrictive immune environments.
2009-09-03 | E-MAXD-54 | biostudies-arrayexpress
Project description:In previous studies we have shown that the two adult females morphs of S. ratti have very different lifespans. This experiment was designed to try to identify differentially expressed genes in these two adult morphs that may account for these differing lifespans. The genes expressed by S. ratti parasitic females at day 6 p.i. were compared to the genes expressed by S. ratti free living females at 3 days 19 degrees C. This comparison was done using a microarray chip that is spotted with PCR fragments from the libraries that were generated from parasitic females extracted at day 6 and day 15 p.i., and a microarray chip that is spotted with PCR fragments from the libraries that were generated from free-living larval stages L1, L2 and infective L3s and from free-living males and females.
2008-05-24 | E-TABM-236 | biostudies-arrayexpress
Project description:We wished to determine the changes in gene expression that occurred in S. ratti parasitic females as an infection progressed and thus as these stages are exposed to an anti-S. ratti immune response. To do this we compared gene expression in parasitic females recovered 6 days p.i. (i.e. no or very low immune response) with those recovered at 15 days p.i. (i.e. high immune response); for convenience, we refer to these as parasitic females subject to "low immune pressure" and "high immune pressure", respectively. These days were chosen because previous analyses of S. ratti parasitic females have shown significant differences in the size, appearance etc. of worms at these time points. The experimental design used, was to have at least three biological replicates for each sample (i.e. three independent preparations of the relevant worm samples and their RNA) and to have at least three technical replicates (i.e. independent, separate cDNA synthesis, amplification and hybridization etc.) for each biological replicate. For each hybridisation (below) a dye-swap was used i.e. each sample to be used in a hybridisation was labelled, separately, with each of the two dyes (below).<br> <br> 21,085 ESTs were sequenced from various S. ratti stage-specific libraries, of which 14,761 resulted in sequence data above a quality threshold that were then submitted to public databases. 11,551 clones were derived from the S. ratti parasitic libraries of which 7,385 produced sequence data (above a quality threshold); all of these 7,385 clones were arrayed together with a random sample of 1,619 of clones for which no sequence data were available. These 7,385 ESTs are highly redundant since they represent 2,963 contigs and 2,125 clusters, both including 1,220 singletons (i.e. clusters or contigs containing only one EST). Notwithstanding this redundancy, they were used in the microarray construction for two reasons: (i) this approach was less error-prone than attempting to select a unique clone set and (ii) this in-built redundancy provides many replicates of individual contigs and clusters, which can be exploited in quality-control analyses. In addition to these 9,004 S. ratti clones, the following controls were included: 281 EST clones from the mixed iL3/free-living adult library (representing 173 contigs and 167 clusters, 67 of which are singletons) to ensure that gene expression in the parasitic and free-living stages could be differentiated; 230 commercially available controls (Amersham Biosciences UK, Ltd.). 12 poly-A and 457 spotting buffer-only controls. Thus, in total 9,984 spots were arrayed.
2007-04-07 | E-MEXP-1010 | biostudies-arrayexpress
Project description:Isofemale line ED321 Heterogonic was used. Fresh faeces were collected from S. ratti-infected rats at days 5, 6, 7 and 8 p.i. and L1s prepared with a Baermann funnel held for 6 h at 19oC. The larvae were concentrated by centrifugation and then cleaned by flotation on 60% v/v sucrose. Infective L3s were harvested from 14 day-old faecal cultures that had been maintained at 19oC. The iL3s were cleaned by sucrose flotation as for the L1s, above. In excess of 150,000 larvae of either stage were routinely isolated from 6 infected hosts. The experimental design used, was to have at least three biological replicates for each sample (i.e. three independent preparations of the relevant worm samples and their RNA) and to have at least three technical replicates (i.e. independent, separate cDNA synthesis, amplification and hybridization etc.) for each biological replicate. For each hybridisation a dye-swap was used i.e. each sample to be used in a hybridisation was labelled, separately, with each of the two dyes.
2022-11-21 | E-MEXP-697 | biostudies-arrayexpress
Project description:The genus Strongyloides spp. include important human parasites. There is also a well studied rodent model, S. ratti. Uniquely among parasitic nematodes, the Strongyloides life-cycle includes both a parasitic female stage and a genetically identical free-living female stage. Differences between these two female forms must be epigenetic, presumably controlled by altered transcription and translation. This is a project to compare the proteome and transcriptome of the parasitic and free-living females of S. ratti. From this we will define the genes and gene products of the parasitic female stage. This approach exploits the currently advanced S. ratti genome sequencing project. This work will give an understanding of the molecular basis of nematode parasitism, and so define new potential drug targets. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2013-06-11 | E-ERAD-151 | biostudies-arrayexpress
Project description:S. ratti Isofemale line ED321 Heterogonic predominantly undergoes indirect development; isofemale line ED5 Homogonic predominantly undergoes direct development. Therefore, L2 stages of ED321 Heterogonic and of ED5 Homogonic are destined for indirect (i.e. L2 indirect) and direct (i.e. L2 direct) development, respectively; these sources of material were used in this comparison. To do this, for both isofemale lines, rats were infected with ED321 Heterogonic or ED5 Homogonic and faeces collected on days 5, 6, 7 and 8 p.i. and cultured for 24 h at 19oC, after which larvae were prepared with a Baermann funnel held for 6 h at 19oC, larvae were concentrated and cleaned by sucrose flotation, as above. In excess of 75,000 worms were routinely isolated from three infected hosts. The experimental design used, was to have at least three biological replicates for each sample (i.e. three independent preparations of the relevant worm samples and their RNA) and to have at least three technical replicates (i.e. independent, separate cDNA synthesis, amplification and hybridization etc.) for each biological replicate. For each hybridisation a dye-swap was used i.e. each sample to be used in a hybridisation was labelled, separately, with each of the two dyes.
2022-11-22 | E-MEXP-709 | biostudies-arrayexpress
Project description:Tissue resident memory T cells (TRM) provide superior protection against infection localised to extra-lymphoid compartments in the body. Here we show that CD103+CD8+ TRM cells develop in skin from killer cell lectin-like receptor (KLR)G1-negative precursors that selectively infiltrate the epithelial layer. In the skin, a combination of chemokine-guided epithelial entry, local interleukin (IL)-15 and transforming growth factor (TGF)-β signalling is required for formation and survival of these long-lived memory cells. Importantly, TRM differentiation results in the gradual acquisition of a unique transcriptional profile that differs from that expressed by memory cells in the circulation and other types of skin-resident intra-epithelial T cells, such as the dendritic epidermal T cells (DETC). We provide a comprehensive molecular and developmental framework for the local differentiation of a distinct type of peripheral memory T cell that contributes to an important first-line of immune defence in barrier tissues such as skin and mucosa. 24 samples were analyzed: 3 replicates of memory gB-T CD8+. CD103+ T cells isolated from the skin of C57/BL6 mice on day 30 p.i. with HSV KOS. 3 replicates of memory P14 CD8+ T cells isolated from gut of mice on day 60 p.i. with LCMV Armstrong. 3 replicates of memory gB-T CD8+ T cells from the lung of mice on day 30 p.i. with influenza WSN. 3 replicates of memory CD62L high CD8+ T cells from the spleen of mice on day 30 p.i. with HSV KOS. 3 replicates of memory CD62L low CD8+ T cells from the spleen of mice of day 30 p.i. with HSV KOS. 3 replicates of γδ-DETC isolated from the skin of C57/BL6 mice on day 30 p.i. with HSV KOS. 3 replicates of αβ-DETC from naive TCRδ-/- mice; and 3 replicates of naive gB-T CD8+ T cells from the spleen of naive gB-T transgenic mice.
2013-10-01 | E-GEOD-47045 | biostudies-arrayexpress
Project description:Gene expression profiles were examined in whole lung tissue collected from male and female Long-Evans rats at different time points after inoculation with Seoul virus (i.e., the species-specific hantavirus that infects Norway rats); We used microarray analyses to analyze global gene expression differences between the sexes during hantavirus infection Experiment Overall Design: Gonadally-intact male and female rats were inoculated with 10^4 pfu of Seoul virus (strain SR-11) and lung samples were collected 0, 3, 15, and 40 days post-inoculation (p.i.) to assess gene expression patterns during the acute (i.e., days 3-15 p.i.) and persistent (i.e., day 40 p.i.) phases of infection
2008-06-15 | E-GEOD-7271 | biostudies-arrayexpress