Trypanosoma vivax Y486 bloodstream stage RNAseq
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ABSTRACT:
ORGANISM(S): Trypanosoma vivax
SUBMITTER: Lin Quan
PROVIDER: E-MTAB-475 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Plasmodium vivax causes 25-40% of malaria cases worldwide, yet research on this human malaria parasite has been neglected. Nevertheless, the recent publication of the P. vivax reference genome now allows genomics and systems biology approaches to be applied to this pathogen. We show here that whole genome analysis of the parasite can be achieved directly from ex vivo-isolated parasites, without the need for in vitro propagation. A single isolate of P. vivax obtained from a febrile patient with clinical malaria from Peru was subjected to whole genome sequencing (30X coverage). This analysis revealed over 18,261 single nucleotide polymorphisms (SNPs), 6,257 of which were further validated using a tiling microarray. Within core chromosomal genes we find that one SNP per every 985 bases of coding sequence distinguishes this recent Peruvian isolate, designated IQ07, from the reference Sal1 strain obtained in 1970. This full-genome sequence of a P. vivax isolate, the second overall and first of an uncultured patient isolate, shows that the same regions with low numbers of aligned sequencing reads are also highly variable by genomic microarray analysis. Finally, we show that the genes containing the largest ratio of nonsynonymous to synonymous SNPs encode two AP2 transcription factors and the P. vivax multidrug resistance-associated protein (PvMRP1), an ABC transporter shown to be associated with quinoline and antifolate tolerance in P. falciparum. This analysis provides a new data set for comparative analysis with important potential for identifying markers for global parasite diversity and drug resistance mapping studies. Genome DNA from Peruvian P. vivax Isolate IQ07 vs. Reference Sal1
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Project description:Plasmodium vivax is the most geographically widespread human malaria parasite causing approximately 130-435 million infections annually. It is an economic burden in many parts of the world and poses a public health challenge along with the other Plasmodium sp. The biology of this parasite is very little understood. Emerging evidences of severe complications due to infections by this parasite provides an impetus to focus research on the same. Investigating this parasite directly from the infected patients is the most feasible way to study its biology and any pathogenic mechanisms which may exist. Gene expression studies of this parasite directly obtained from the patients has provided evidence of gene regulation resulting in varying amount of transcript levels in the different blood stages. However, the mechanisms regulating gene expression in malaria parasites are not well understood. Discovery of natural antisense transcripts (NATs) in P. falciparum has suggested that these might play an important role in regulating gene expression. We report here the genome-wide occurrence of NATs in P. vivax parasites from patients with differing clinical symptoms. A total of 1348 NATs against annotated gene loci have been detected using a custom designed strand specific microarray. Majority of NATs identified from this study shows positive correlation with the expression pattern of the sense transcript. Our data also shows condition specific expression patterns of varying S and AS transcript levels. Genes with AS transcripts enrich to various biological processes. This is the first report detailing the presence of NATs from clinical isolates of P. vivax. The data suggests differential regulation of gene expression in diverse clinical conditions and would lead to future detailed investigations of genome regulation. Plasmodium vivax isolates were collected from patients (n = 8) with differing clinical conditions.The patients exhibited symptoms categorized as un-complicated (n =1) or complicated malaria (n = 7). Criteria for determination of complicated disease were based on World Health Organization year 2010 guidelines. Microarray array based transcriptional profiling was carried out to detect prevalence of natural antisense transcripts.
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Project description:Deep sequencing of the transcriptome of P. vivax parasite populations from vivax malaria patients with scarce parasitemia from the low transmission Brazilian Amazonian endemic region we the aim of better understanding the molecular mechanisms behind this cytoadherence and rosetting phenotypes by identifying proteins, especially parasitic ligands, which might be important for the P. vivax adhesion capacity within the human host. We used RNA-seq coupled with parasite enrichment from field samples and cytoadherence and rosetting assays to privilege the sequence of the whole transcriptome of parasite populations with distinct adhesive characteristics and, also assess the human host immune-related expression profile in the context of vivax malaria disease.
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Project description:Extracellular vesicles are major components of circulating plasma holding insights into pathological processes. Here, we demonstrate high levels of EVs in plasma from patients with Plasmodium vivax (PvEVs), the most widely distributed human malaria parasite. Moreover, mass spectrometry analysis identified parasite proteins in PvEVs and their in vivo distribution demonstrated major spleen tropism. PvEVs were preferentially taken up by human spleen fibroblasts (hSFs) and this uptake induced specific and dose-dependent upregulation of ICAM-1 associated with the translocation of NF-kB to the nucleus. After activation of hSFs by PvEVs, P. vivax-infected reticulocytes from patients showed specific adhesion properties reversed by inhibiting NF-kB translocation to the nucleus. Together, these data provide novel physiological EV-based insights into the mechanisms of human malaria pathology and support the existence of P. vivax-adherent parasite subpopulations in the microvasculature of the human spleen
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