Plasmodium vivax UK traveller study
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB44419 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR5740710_1.fastq.gz | Fastqsanger.gz | |||
| ERR5740710_2.fastq.gz | Fastqsanger.gz | |||
| ERR5740720_1.fastq.gz | Fastqsanger.gz | |||
| ERR5740720_2.fastq.gz | Fastqsanger.gz | |||
| ERR5740730_1.fastq.gz | Fastqsanger.gz |
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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.
2014-01-16 | E-GEOD-45165 | biostudies-arrayexpress
Project description:Transcription profile of the Plasmodium vivax intraerythrocytic cycle Total RNA in Plasmodium vivax strain at every 6 hour of intraerythrocytic cycle using RNA-seq
2016-02-11 | E-GEOD-61252 | biostudies-arrayexpress
Project description:Malaria parasites transmitted by mosquito bite are remarkably efficient in establishing human infections. The infection process requires ~30 minutes and is highly complex as quiescent sporozoites injected with mosquito saliva must be rapidly activated in the skin, migrate through the body, and infect the liver. This process is poorly understood for Plasmodium vivax due to low infectivity in the in vitro models. To study this skin-to-liver stage of malaria, we developed quantitative bioassays coupled with transcriptomics to evaluate parasite changes linked with mammalian microenvironmental factors. Our in vitro phenotype and RNA-seq analyses revealedkey microenvironmental relationships with distinct biological functions. M ost notable, preservation of sporozoite quiescence by exposure to insect-like factors coupled with strategic activation limits untimely activation of invasion-associated genes to dramatically increase hepatocyte invasion rates. We also report the first transcriptomic analysis of the P. vivax sporozoite interaction in salivary glands identifying 118 infection-related differentially-regulated Anopheles dirus genes. These results provide important new insights in malaria parasite biology and identify priority targets for antimalarial therapeutic interventions to block P. vivax infection.
2018-08-16 | GSE117538 | GEO
Project description:This project contains RNA-sequencing reads of Plasmodium vivax derived directly from clinical patients. Here, we aim to characterize the gene expression patterns in patients with various parasite compositions. Patients (n=10) were recruited from two malaria endemic areas in Thailand. Ten RNA samples were treated with DNase, followed by Epicentre Globin-Zero Gold kit to deplete rRNA and globin transcript. The RNA-seq libraries were sequenced on an Illumina HiSeq4000 platform to generate approximately 60 million paired-end reads of 150 bp for each sample.
2019-06-30 | E-MTAB-6753 | biostudies-arrayexpress
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
2010-10-02 | E-GEOD-23982 | biostudies-arrayexpress
Project description:Background: Malaria is a public health problem in parts of Thailand, where Plasmodium falciparum and Plasmodium vivax are the main causes of infection. In the northwestern border province of Tak parasite prevalence is now estimated to be less than 1% by microscopy. Nonetheless, microscopy is insensitive at low-level parasitaemia. The objective of this study was to assess the current epidemiology of falciparum and vivax malaria in Tak using molecular methods to detect exposure to and infection with parasites; in particular, the prevalence of asymptomatic infections and infections with submicroscopic parasite levels. Methods: Three-hundred microlitres of whole blood from finger-prick were collected into capillary tubes from residents of a sentinel village and from patients at a malaria clinic. Pelleted cellular fractions were screened by quantitative PCR to determine parasite prevalence, while plasma was probed on a protein microarray displaying hundreds of P. falciparum and P. vivax proteins to obtain antibody response profiles in those individuals. Results: Of 219 samples from the village, qPCR detected 25 (11.4%) Plasmodium sp. infections, of which 92% were asymptomatic and 100% were submicroscopic. Of 61 samples from the clinic patients, 27 (44.3%) were positive by qPCR, of which 25.9% had submicroscopic parasite levels. Cryptic mixed infections, misdiagnosed as single-species infections by microscopy, were found in 7 (25.9%) malaria patients. All sample donors, parasitaemic and non-parasitaemic alike, had serological evidence of parasite exposure, with 100% seropositivity to at least 54 antigens. Antigens significantly associated with asymptomatic infections were P. falciparum MSP2, DnaJ protein, putative E1E2 ATPase, and three others.
2014-06-22 | GSE55265 | GEO
Project description:The global impact of Plasmodium vivax has been largely underestimated for several decades due to lower mortality rates compared to P. falciparum. However, in recent times, the parasite has become a serious threat to public health due to its ability to cause severe malaria with fatal outcomes. Its unique biology makes it resilient to control measures and poses a challenge to available diagnostic methods. Diagnosis by RDTs is further restricted due to inadequate P. vivax specific antigens for species identification. Therefore, there is an urgent need to develop tests that employ antigens unique to the parasite. This study represents the first in-depth proteomics analysis of human plasma and parasite isolates to identify P. vivax protein biomarkers that can be tested for use in RDTs while developing diagnostics for malaria. Here we report 39 P. vivax proteins in human plasma and 103 highly expressed P. vivax proteins from parasite isolates with high confidence. Interestingly, five proteins, found to be unique to P. vivax were detected in both sources, representing the best candidates for evaluation as diagnostic markers. Moreover, targeted proteomics assays were used to validate some of these proteins. This study represents the first step in the development of new diagnostic assays for P. vivax malaria.
2020-01-30 | PXD015165 | Pride
Project description:Severe thrombocytopenia can be a determinant factor in the morbidity of Plasmodium vivax (Pv), the most widespread human malaria. Although immune mechanisms may drive Pv-induced severe thrombocytopenia (PvST), the current data on the cytokine landscape in PvST is scarce, and often conflicting. The analysis of the bidirectional circuit of inflammatory mediators and miRNAs would lead to a better understanding of the mechanisms underlying PvST.
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Project description:Transcription profile of the Plasmodium vivax intraerythrocytic cycle
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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.
2014-01-16 | GSE45165 | GEO