Ontology highlight
ABSTRACT:
PROVIDER: PRJNA885968 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21773975_1.fastq.gz | Fastqsanger.gz | |||
| SRR21773975_2.fastq.gz | Fastqsanger.gz | |||
| SRR21773976_1.fastq.gz | Fastqsanger.gz | |||
| SRR21773976_2.fastq.gz | Fastqsanger.gz | |||
| SRR21773977.fastq.gz | Fastqsanger.gz |
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Project description:Giardia duodenalis is a protozoan parasite responsible for gastroenteritis in vertebrates, including humans. The prevalence of G. duodenalis is partly owed to its direct and simple life cycle, as well as the formation of the environmentally resistant and infective cysts. Several proteomic and transcriptomic studies have previously analysed global changes during the encystation process using the well-characterised laboratory isolate and genome strain, WBC6. To expand current comparative analyses, this study presents the first quantitative global study of encystation using pathogenically relevant and alternative assemblage A strains: the human-derived BRIS/82/HEPU/106 and avian-derived BRIS/95/HEPU/2041. We have utilised tandem MS/MS with a label-free quantitative approach to compare cysts and trophozoite life stages between strains for variation, as well as confirm universal encystation markers of Assemblage A.
2015-06-10 | PXD002002 | Pride
Project description:Giardia duodenalis is a protozoan parasite of a wide range of vertebrates and one of the leading causes of gastroenteritis worldwide. G. duodenalis is a species complex of 8 assemblages with the zoonotic assemblage A as one of two discrete subtypes that is infective for humans. With increasing genomic and transcriptomic data now publicly available through the centralised giardiaDB.org, we have quantitatively analysed the proteomes of 8 G. duodenalis assemblage A strains (7 A1 and 1 A2) to provide a comprehensive proteomic baseline to complement these studies. Protein analysis identified a non-redundant total of 1220 proteins with an average of 764 proteins in each strain. At least 10% of all proteins identified were from the 4 protein families in the G. duodenalis variable genome, and substantial differences in number and abundance profiles in the Variable Surface Protein (VSP) family was observed. We also searched the 8 strains against both assemblage A genomes (subassemblage A1 and A2 genomes) and showed losses in protein identifications, especially for protein identifications associated with Giardia variable gene families which are sub-assemblage specific. We observed two expression profiles of VSPs within Giardia, which was independent to host origin, subassemblage, geographic origin and introduction to axenic culture and may indicate variation in surface antigen switching events and population heterogeneity. We hypothesise this variation may be related to karotype and chromosomal variation, which would indicate an assemblage-independent mechanism of variation in G. duodenalis.
2015-02-26 | PXD001272 | Pride
Project description:Giardia duodenalis is a protozoan parasite of the small intestine in vertebrates, including humans. Assemblage A of G. duodenalis is one of two discrete subtypes that infects humans, and is considered a zoonotic assemblage. Two G. duodenalis Assemblage A strains BRIS/95/HEPU/2041 and BRIS/83/HEPU/106, constituting virulent and control strains respectively, were analysed in one of the first comparative shotgun proteomic studies performed in this parasite. Protein extracts were prepared using a multiplatform approach with both an in-gel and in-solution sample preparation to enable us to assess the complementarity for future Giardia proteomic studies. Protein analysis revealed that BRIS/95/HEPU/2041 possessed a wider and more varied repertoire of variant surface proteins (VSPs), which are hypothesised to be involved in host adaptation, immune evasion and virulence. A total of 38 VSPs were identified, with 3 common to strains, 6 unique to BRIS/83/HEPU/106 and 26 unique to BRIS/95/HEPU/2041. Additionally up to 25.6% of all differentially expressed proteins in BRIS/95/HEPU/2041 belonged to the VSP family, a trend not seen in the control BRIS/83/HEPU/106. Greater antigen variation in BRIS/95/HEPU/2041 may explain aspects of virulence phenotypes in G. duodenalis, with a highly diverse population capable of evading host immune responses.
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Project description:Giardia duodenalis a species-complex of common gastrointestinal protists of major medical and veterinary importance. This complex is currently subclassifed as ‘Assemblages’, with Assemblage A and B infective to humans. To date, post-genomic proteomics are derived exclusively from Assemblage A, biasing understanding of these parasites’ biology. This bias is particularly notable, as Assemble B is the more prevalent cause of human infections. To address this gap, we quantitatively analysed proteomes of the intestinal ‘trophozoite’ stage of three Assemblage B isolates, including the genome reference (GS/M) and two clinical isolates (BRIS/91/HEPU/1279 and BRIS/92/HEPU/1487), during in vitro axenic culture. We used spectrum-to-peptide matching metrics to infer currently unknown intra-assemblage variation. We identified and quantified over 3000 proteins in the GS isolate, but demonstrated significant isolate-dependent losses in peptide and protein identifications in non-reference isolates, suggesting significant intra-assemblage variation. We also explore differential protein expression between in vitro cultured subpopulations enriched for dividing relative to feeding cells. This data is an important proteomic baseline for Assemblage B, and highlights unique differences heretofore avoided in post-genomic Giardia proteomics.
2018-07-03 | PXD007943 | Pride
Project description:Despite of Giardia duodenalis being one of the most commonly found intestinal pathogens in humans and animals, little is known of the host-parasite interactions in natural hosts. Therefore, the objective of this study was to investigate the intestinal response in calves following a G. duodenalis infection, using a bovine high-density oligo microarray to analyze global gene expression in the small intestine. The resulting microarray data suggested a decrease in inflammation, immune response and immune cell migration in infected animals, which was examined in more detail by quantitative real-time PCR on a panel of cytokines combined with histological analyses. The cytokine transcription levels showed a trend of down regulated expression in infected animals compared to the negative controls, best seen in jejunum for IL-6 and IL-8 and statistically significant for IL-17, IL-13 and IFN-?. No increased immune cell recruitment could be seen after infection, as well as no intestinal pathologies, such as villus shortening or increased levels of apoptosis. Key regulators in this intestinal response seem to be the nuclear peroxisome proliferator-activated receptors alpha (PPARA) and gamma (PPARG), for which an up-regulated expression was seen on microarray and qRT-PCR data. The activation of PPARs can exert an anti-inflammatory effect with inhibition of pro-inflammatory cytokines and a decrease in cell recruitment. . How the PPARs are activated during a Giardia infection still needs to be further elucidated. Eight male Holstein calves aged two to four weeks old were used for the trial. Prior to arrival, all animals were screened for the presence of Giardia cysts in their faecal samples. After confirming their negative status for all these pathogens, four of the animals were randomly chosen and placed in a G. duodenalis contaminated environment, whereas the four remaining animals were kept as negative controls in separate G. duodenalis-free stables. All calves in the study received the same commercial milk replacer. After three weeks, the presence or absence of a G. duodenalis infection was confirmed by IFA on faecal samples after which the animals were euthanized. Changes in gene expression profiles induced by Giardia duodenalis infection were compared using a high-density 60mer bovine oligo microarray.
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Project description:Giardia causes more episodes of illness worldwide than any other parasite. It is a flagellated cyst-forming enteric pathogen that inhabits the lumen of the small intestine and although it is clear that more and less virulent strains do occur, pathogenesis and virulence of Giardia remains poorly understood. Identification of Giardia virulence factors is highly desirable since their expression would be the best indicator for determining disease outcome. The advent of quantitative proteomics has been timely in investigating which proteins are likely to be secreted virulence factors. Here we successfully apply such analyses to the whole parasite and to the supernatants derived from the parasite, in order to ascertain a repertoire of secreted proteins. In our initial analysis we compared replicates of Giardia cells and culture supernatants from the two major lineages which cause human disease – assemblage A and assemblage B. The genome of Giardia is believed to contain open reading frames which could encode as many as 6000 proteins. In our study we confirm expression of ~1600 proteins from each assemblage, the vast majority of which being common to both lineages. To look for actual enrichment of secreted proteins, we considered the ratio of proteins in the supernatant compared with the pellet. This simple method defines a small group of enriched proteins, putatively secreted at a steady state by cultured growing Giardia trophozoites of both assemblages. This secretome contains a high proportion annotated to have N’ terminus signal peptides, with some showing evidence of having recently evolved under strong positive selective pressure. The most abundant secreted proteins include known virulence factors such as the Cathepsin B cysteine proteases and members of a Giardia superfamily of Cysteine Rich Proteins which comprises VSPs, HCMPs and a new class of virulence factors, the Giardia Tenascins. Since we also find that physiological function of human enteric epithelial cells can be disrupted by soluble factors even in the absence of the trophozoites we are able to propose a straightforward model of Giardia pathogenesis incorporating key roles for the major Giardia derived soluble mediators.
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