Project description:High-throughput sequencing to profile the transcriptome of the human filarial nematode Brugia malayi, the causative agent of lymphatic filariasis, across multiple life-cycle stages.
Project description:Recent advances in high throughput sequencing methodologies allow the opportunity to probe in depth the transcriptomes of organisms including N. caninum. In this project, we are using Illumina sequencing technology to analyze the transcriptome (RNA-Seq) of experimentally accessible stages (e.g. tachyzoites at different times points) of N. caninum NCLiv. The aim is to make transcriptional landscape maps at different time points at different life cycle stages of N. caninum and compare it with equivalent datasets from the closely related parasite Toxoplasma gondii
Project description:Recent advances in high throughput sequencing methodologies allow the opportunity to probe in depth the transcriptomes of organisms including N. caninum and Toxoplasma gondii. In this project, we are using Illumina sequencing technology to analyze the transcriptome (RNA-Seq) of experimentally accessible stages (e.g. tachyzoites at different times points) of T. gondii VEG strain. The aim is to make comparative transcriptional landscape maps of Neospora and Toxoplasma at different time points at different life cycle stages and compare levels of expression of orthologous genes in these two organisms.
Project description:The Mouse Genomes Project ( http://www.sanger.ac.uk/science/data/mouse-genomes-project ) uses using next-generation sequencing technologies to catalogue molecular variation in the common laboratory mouse strains, and a selected set of wild-derived inbred strains. Access to complete sequence of multiple inbred strains will add to these resources and will become a permanent foundation for a systems biology approach to phenotypic variation in the mouse. In this particular study, we have sequenced the transcriptome of whole-brain tissue from 16 laboratory mouse strains to examine differences in gene expression levels, differential RNA-editing, and for use in de novo gene prediction.
Project description:Plasmodium yoelii YM asexual blood stage parasites express multiple members of the py235 gene family, part of the super-family of genes including those coding for Plasmodium vivax reticulocyte binding proteins and Plasmodium falciparum RH proteins. Dr Tony Holder's laboratory (NIMR, London) has been successful in deleting one of the RH family genes (Py01365) by transfection and insertion of the TgDHFR gene, and cloned the resulting parasite in YM background. The gene expression patterns of the mutant parasite line were compared to that of the wild type YM parasite.
Project description:To further understand immune mechanims involved in regulating intestinal inflammation, we employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential of regulating inflammation in the absence of IL-10. Whole colon tissue from IL-10-deficient and C57BL/6 (wild-type) mice was collected 2 weeks after Citrobacter rodentium infection and from uninfected controls. Consistent with the histological and cellular analysis, expression levels of many chemokines and cytokines involved in recruiting leukocytes and promoting inflammation were, on average, lower in IL-10 deficient compared to wild-type mice after infection. An exception to this general trend was IL-27, a cytokine with both pro- and anti-inflammatory properties. Two weeks after Citrobacter rodentium challenge, total RNA was extracted and analyzed from whole colon tissue of infected IL-10-deficient and wild-type mice, and compared to uninfected controls. Each sample contained equal amounts of total RNA from 4-5 female mice which were pooled and used in the experiment.
Project description:Identification of the targets of RegA with and without bicarbonate stimulation by comparing RegA knockout to multicopy RegA transgenics. RegA is an AraC like transcription factor identified in a mutational screen for virulence genes in Citrobacter rodentium, an attaching and effacing pathogen that causes transmissible colonic hyperplasia in mice. This experiment compares the RegA null strain with a multicopy plasmid rescue of this null strain in the presence and absence of bicarbonate with the aim of identifying pathogenesis related genes related to the early and late stages of attachment and effacement. Keywords: genetic modification, transcription factor, induction A strain of Citrobacter rodentium with a knockout of RegA was compared to the same strain rescued with a multicopy plasmid containing the wildtype RegA gene. These strains were analyzed with and without bicarbonate in an unconnected two factor design with dye balanced biological replicates.
Project description:An experiment to test the equivalence of the Citrobacter rodentium RegA and E.Coli SMS 3-5 homologue 8 Conditions (4 Genotypes by 2 treatments) in duplicate. Reference design without dye swaps.
Project description:We compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor C. grandiflora. There is a clear shift in the expression of genes associated with flowering phenotypes; a similar shift is seen in the related genus Arabidopsis, where self-fertilization evolved about 1 million years ago. This is a two group comparison of gene expression between the self-compatible Capsella Rubella and out-crossing Capsella Grandiflora mixed stage flowerbuds. Leaf expression is also provided as an annotation reference dataset.