Transcriptional response of trematode-infected Biomphalaria glabrata during development of S. mansoni and E. paraensei
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ABSTRACT: Time series analysis of the transcriptional responses of Biomphalaria glabrata throughout the course of intramolluscan development of Schistosoma mansoni and Echinostoma paraensei. Time series transcriptional profiling of Biompharlia glabrata comparing control uninfected M line B.glabrata with trematdoe infected groups. The experimental groups are: Echinostoma paraensei infected and Schistoma mansoni infected at 12 hours(0.5day), 1 day, 2 days, 4 days, 8 days, 16 days adn 32 days post infection. Samples: control and two trematode infected B.glabrata in a time series: 0.5, 1, 2, 4, 8, 16 and 32 days post exposure were analyzed in triplicate Stress and immune response
Project description:Differential transcriptomic responses of Biomphalaria glabrata (Gastropoda, Mollusca) to bacteria and metazoan parasites Schistosoma mansoni and Echinostoma paraensei (Digenea, Platyhelminthes). Transcriptional profiling of Biomphalaria glabrata comparing control uninfected M-line B. glabrata with five experimental groups. The experimental groups are: wounded but not infected M-line, Escherichia coli infected, Micrococcus luteus infected, Echinostoma paraensei infected and Schistosoma mansoni infected at 12 hours time point post infection. Seven groups of samples: two controls, wounded, two bacterial- and two trematode-infected B. glabrata were analyzed in triplicate, using universal RNA reference.
Project description:Transcriptional profile of snails exposed to irradiated E. paraensei miricidia and four days later challenged with S. mansoni miricidia. Compared to snails exposed to only irradiated E. paraensei miricidia. Each replicate is comprised of 1 individual snail from the specified treatment group. Six replicates of each treatment were analyzed on the Snail oligo array.
Project description:Transcriptional profiles of snails sized 12-20mm exposed to E. paraensei and unexposed controls Keywords: Dose response Five individual snails from the treatment group were analyzed at 12hours, 1, 2, 4, 8, and 16 days. Five unexposed control snails were also analyzed.
Project description:Transcriptional profiles ofBS-90 snails sized 8-12mm exposed to E. paraensei (BS-90 are susceptible) and S. mansoni (BS-90 are resistant) and unexposed controls Keywords: Dose response Five individual snails from the treatment group were pooled to make up 3 repliactes. After exposure to the indicated parasite snails were collected and RNA was isolated at 12hours, 1, 2, 4, 8, 16, and 32 days. Three unexposed control groups were also analyzed.
Project description:Transcriptional profile of snails with induced acquired resistance (exposed first to irradiated E. paraensei miricidia) after secondary challenge with viable miricidia. Compared to snails exposed to irradiated miricidia only or to viable miricidia only. Experiments were done over the course of 16 days, with 8 day intervals between sensitization and secondary challenge. Keywords: Dose response Each replicate is comprised of 5 individual snails from the specified treatment group. Three replicates of each treatment were analyzed on the Snail oligo array.
Project description:The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5'-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. Examination of dimethylsufate reactivity of Xist lncRNA and 18S rRNA in cells using targeted reverse transcription to determine reactivity, and comparisons with untreated control samples.
Project description:Gene regulation in response to intracellular calcium is mediated by the calcineurin-activated transcription factor Prz1 in the fission yeast Schizosaccharomyces pombe. Genome-wide studies of the Crz1 and CrzA fungal orthologs have uncovered numerous target genes involved in conserved and species-specific cellular processes. In contrast, very few target genes of Prz1 have been published. This paper identified an extensive list of genes using transcriptome and ChIP-chip analyses under inducing conditions of Prz1, including CaCl2, and tunicamycin treatment, as well as a â??pmr1 genetic background. We identified 165 upregulated putative target genes of Prz1 in which the majority contained a calcium-dependent response element in their promoters, similar to that of the Saccharomyces cerevisiae ortholog Crz1. These genes were functionally enriched for Crz1-conserved processes such as cell wall biosynthesis. Overexpression of prz1+ increased resistance to the cell wall degradation enzyme zymolyase, likely from upregulation of the O-mannosyltransferase encoding gene omh1+. Loss of omh1+ abrogates this phenotype. We uncovered a novel inhibitory role in flocculation for Prz1. Loss of prz1+ resulted in constitutive flocculation and upregulation of genes encoding the flocculins Gsf2 and Pfl3, as well as the transcription factor Cbf12. The constitutive flocculation of the â??prz1 strain was abrogated by the loss of gsf2+ or cbf12+. This study reveals that Prz1 functions as a positive and negative transcriptional regulator of genes involved in cell wall biosynthesis and flocculation, respectively. Moreover, comparison of target genes between Crz1/CrzA and Prz1 indicate some conservation in DNA-binding specificity, but also substantial rewiring of the calcineurin-mediated transcriptional-regulatory network. We generated 2 ChIP-chip experiments, each with a biological replicate performed as a dye swap.
Project description:Sponges (Porifera) are early-branching Metazoa who do not possess muscles or neurons, however are able to undergo a whole-body movement that involves the closure of their canal system and collapse of an epithelial tent. In this study we profile the proteomic responses of the freshwater sponge Spongilla lacustris during nitric oxide (NO) and agitation induced movements to elucidate the early evolution of coordination in animals. Specifically, we used tandem mass tag (TMT) labeling-based quantification of enriched phosphopeptides to systematically measure quantitative differences in protein phosphorylation. We identified and quantified 12165 unique phosphopeptides in the sponge. NO treatment resulted in quantitative changes of phosphorylation levels on 390 unique phosphopeptides mapping to 270 unique proteins. In turn, agitation led to quantitative changes of phosphorylation levels on 303 unique phosphopeptides (229 proteins).