Analysis of the transcriptome of the protozoan Theileria parva using MPSS reveals that the majority of genes are transcriptionally active in the schizont stage

Bishop, Richard P.; Shah, Trushar; Pellé, Roger; Hoyle, David C.; Pearson, Terry W.; Haines, Lee R.; Brass, Andy; Hulme, Helen; Graham, Simon P.; Taracha, Evans; Kang'a, S.; Lu, Charles; Hass, Brian; Wortman, Jennifer; White, Owen; Gardner, Malcolm J.; Nene, Vishvanath; Villiers, Etienne P. de

doi:10.1093/nar/gki818

Cited by 48 publications

(32 citation statements)

References 39 publications

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“…2C). Transcriptome analysis of T. parva using massively parallel signature sequencing indicated that Tp2 is expressed at a relatively high level (1069 tpm) in the schizont stage [17]. The cDNA clone was isolated from the schizont cDNA library contains a 1026 bp insert with 105 and 396 bp 5' and 3' UTR's, respectively.…”

Section: Resultsmentioning

confidence: 99%

Untitled

et al. 2007

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BackgroundImmunity against the bovine protozoan parasite Theileria parva has previously been shown to be mediated through lysis of parasite-infected cells by MHC class I restricted CD8+ cytotoxic T lymphocytes. It is hypothesized that identification of CTL target schizont antigens will aid the development of a sub-unit vaccine. We exploited the availability of the complete genome sequence data and bioinformatics tools to identify genes encoding secreted or membrane anchored proteins that may be processed and presented by the MHC class I molecules of infected cells to CTL.ResultsOf the 986 predicted open reading frames (ORFs) encoded by chromosome 1 of the T. parva genome, 55 were selected based on the presence of a signal peptide and/or a transmembrane helix domain. Thirty six selected ORFs were successfully cloned into a eukaryotic expression vector, transiently transfected into immortalized bovine skin fibroblasts and screened in vitro using T. parva-specific CTL. Recognition of gene products by CTL was assessed using an IFN-γ ELISpot assay. A 525 base pair ORF encoding a 174 amino acid protein, designated Tp2, was identified by T. parva-specific CTL from 4 animals. These CTL recognized and lysed Tp2 transfected skin fibroblasts and recognized 4 distinct epitopes. Significantly, Tp2 specific CD8+ T cell responses were observed during the protective immune response against sporozoite challenge.ConclusionThe identification of an antigen containing multiple CTL epitopes and its apparent immunodominance during a protective anti-parasite response makes Tp2 an attractive candidate for evaluation of its vaccine potential.

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Section: Resultsmentioning

confidence: 99%

Untitled

et al. 2007

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“…Thus, the seven anther and pollen transcriptomes include transcripts of 44% (18,267/41,046) of the rice genes. This percentage should be higher in actuality, because we excluded transcripts with less than five TPM as possible background noises and also tags that hit identical genome sequences as mixed-pool noises (Bishop et al, 2005;Peiffer et al, 2008). Had we included transcripts having two to four TPM, we would have an additional 3,159 transcripts.…”

Section: High-quality Sbs Transcriptomes Of Anthers and Mature Pollenmentioning

confidence: 99%

Analyses of Advanced Rice Anther Transcriptomes Reveal Global Tapetum Secretory Functions and Potential Proteins for Lipid Exine Formation

Huang

Wei

et al. 2008

Plant Physiology

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The anthers in flowers perform important functions in sexual reproduction. Several recent studies used microarrays to study anther transcriptomes to explore genes controlling anther development. To analyze the secretion and other functions of the tapetum, we produced transcriptomes of anthers of rice (Oryza sativa subsp. japonica) at six progressive developmental stages and pollen with sequencing-by-synthesis technology. The transcriptomes included at least 18,000 unique transcripts, about 25% of which had antisense transcripts. In silico anther-minus-pollen subtraction produced transcripts largely unique to the tapetum; these transcripts include all the reported tapetum-specific transcripts of orthologs in other species. The differential developmental profiles of the transcripts and their antisense transcripts signify extensive regulation of gene expression in the anther, especially the tapetum, during development. The transcriptomes were used to dissect two major cell/biochemical functions of the tapetum. First, we categorized and charted the developmental profiles of all transcripts encoding secretory proteins present in the cellular exterior; these transcripts represent about 12% and 30% of the those transcripts having more than 100 and 1,000 transcripts per million, respectively. Second, we successfully selected from hundreds of transcripts several transcripts encoding potential proteins for lipid exine synthesis during early anther development. These proteins include cytochrome P450, acyltransferases, and lipid transfer proteins in our hypothesized mechanism of exine synthesis in and export from the tapetum. Putative functioning of these proteins in exine formation is consistent with proteins and metabolites detected in the anther locule fluid obtained by micropipetting.

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“…The authors briefly present the by then known characteristics of T. parva genome and previewed significant insights on vaccine development and disease control through the combination of genome annotation, microarray technology and comparative genomics. T. parva transcriptome was analyzed using massively parallel signature sequencing (MPSS) [82]. The authors have established that transcripts were widely distributed throughout the genome and that there was a significant concordance between transcription and protein expression for heat shock proteins, particularly over-expressed in the schizont stage.…”

Section: 1mentioning

confidence: 99%