Ontology highlight
ABSTRACT:
PROVIDER: PRJNA879307 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR21529620_1.fastq.gz | Fastqsanger.gz | |||
| SRR21529620_2.fastq.gz | Fastqsanger.gz | |||
| SRR21529621_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR21529622_subreads.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 56 |
Similar Datasets
Project description:Giardiasis, caused by the protozoan parasite Giardia duodenalis, is an intestinal diarrheal disease affecting almost one billion people worldwide. A small endosymbiotic dsRNA viruses, G. lamblia virus (GLV), genus Giardiavirus, family Totiviridae, might inhabit human and animal isolates of G. duodenalis. Three GLV genomes have been sequenced so far, and only one was intensively studied, moreover a positive correlation between GLV and parasite virulence is yet to be proved. To understand the biological significance of GLV infection in Giardia, the characterization of several GLV strains from naturally infected G. duodenalis isolates is necessary. In the contest of high-throughput sequencing of four GLVs strains, from Giardia isolates of human and animal origin, we report on a new, unclassified viral sequence (designed GdRV-2), unrelated to Giardiavirus, encoding and expressing for a single large protein with a RdRp domain homologous to Totiviridae and Botybirnaviridae. We have analyzed the sequence of the GLV capsid protein (CP) and RNA-dependent RNA polymerase (RdRp) by LC-MS/MS analysis using different enzymatic strategies.
2021-07-05 | PXD025785 | 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.
2012-04-07 | E-GEOD-35920 | biostudies-arrayexpress
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:Homeostatic interactions between the host and its resident microbiota is important for normal physiological functions and if altered, it could lead to dysbiosis, a change in the structure and function of the microbiota, and as a result to various pathophysiologies. Altered structure in bacterial community is associated with various pathophysiologies, but we are just beginning to understand how these structural changes translate into functional changes. Environmental factors including pathogenic infections can lead to altered interactions between the host and its resident microbiota. We used microarray analysis and a C. elegans model system to gain insights on the mechanisms of functional changes in host-commensal bacteria interaction in the presence or absence of G. duodenalis and identified expression pattern in commensal bacteria that are characteristic of homeostatic and dysbiotic interactions. E. coli HB101 exposed to C. elegans in the presence or absence of G. duodenalis conditioned S-basal complete media for 24 hours were used for RNA extraction and hybridization on Affymetrix microarrays. We collected expression data for E. coli HB101, E. coli HB101 exposed to C. elegans, E. coli HB101 exposed to Giardia conditioned media, and E. coli HB101 exposed to both C. elegans and Giardia conditioned media.
2015-04-02 | E-GEOD-61092 | biostudies-arrayexpress
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: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.
2014-10-14 | PXD000452 | Pride