Entamoeba dispar SAW760
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA12914 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR9417920.fastq.gz | Fastqsanger.gz | |||
| SRR9417917.fastq.gz | Fastqsanger.gz | |||
| SRR9417918.fastq.gz | Fastqsanger.gz | |||
| SRR9417919.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
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Project description:Little is known about the extent of genetic variability among Entamoeba strains and potential genotypic associations with virulence. Variable phenotypes have been identified for Entamoeba strains. E. histolytica is invasive and causes colitis and liver abscesses, but only in 10% of infected individuals; 90% of subjects remain asymptomatically colonized. E. dispar, a closely related species, appears to be incapable of causing invasive disease. In order to determine the extent of genetic diversity among Entamoeba strains we have developed an E. histolytica genomic DNA microarray and used it to genotype strains of E. dispar and E. histolytica. Based on the identification of divergent genetic loci, all six strains (four EH and two ED) had unique genetic fingerprints. Genomic regions with unusually high levels of divergence were identified indicating that structural or evolutionary pressures are molding selective regions of the Entamoeba genome. Comparison of divergent genetic regions allowed us to readily distinguish between EH and ED, identify novel genetic regions that may be used for strain and species typing, and identity a number of novel potential virulence determinants. Among these are Androgen Inducible Gene1, a CXXC receptor kinase, a peroxiredoxin 1-related gene, a Ras family member gene, a Rab geranylgeranyltransferase, and a gene with a UPF0034 domain. Among the four EH strains, an avirulent strain EH (Rahman) was the most divergent and phylogenetically distinct raising the intriguing possibility that genetic subtypes of E. histolytica may be at least partially responsible for the observed variability in clinical outcomes. Our approach shows the utility of a microarray-based genotyping assay to identify genetic variability between Entamoeba isolates and can readily be applied to the study of clinical isolates. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Keywords: genotyping_design
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Project description:Entamoeba histolytica is a protozoan parasite which causes colitis and liver abscesses. Using a genomic DNA microarray consisting of 1.6 - 2.0 kb genomic inserts we have generated a transcriptional profile of 1,971 unique parasite transcripts. The arrays in this experiment set were used to (1) estimate relative transcript abundance for Entamoeba histolytica (HM-1:IMSS) trophozoites in mid-logarithmic growth and (2) to examine changes in the transcriptional profile of Entamoeba histolytica when the parasite interacts with colonic epithelial cells (Caco-2). A time course was used such that RNA was isolated from ameba alone and ameba + Caco-2 cells at 3hrs, 6hrs and 9hrs corresponding to 10%, 50% and 90% cell monolayer destruction. At least two biological experiments and three replicates were used for each time point. Groups of assays that are related as part of a time series. Keywords: time_series_design
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2005-08-23 | E-SMDB-2766 | biostudies-arrayexpress
Project description:Little is known about the extent of genetic variability among Entamoeba strains and potential genotypic associations with virulence. Variable phenotypes have been identified for Entamoeba strains. E. histolytica is invasive and causes colitis and liver abscesses, but only in 10% of infected individuals; 90% of subjects remain asymptomatically colonized. E. dispar, a closely related species, appears to be incapable of causing invasive disease. In order to determine the extent of genetic diversity among Entamoeba strains we have developed an E. histolytica genomic DNA microarray and used it to genotype strains of E. dispar and E. histolytica. Based on the identification of divergent genetic loci, all six strains (four EH and two ED) had unique genetic fingerprints. Genomic regions with unusually high levels of divergence were identified indicating that structural or evolutionary pressures are molding selective regions of the Entamoeba genome. Comparison of divergent genetic regions allowed us to readily distinguish between EH and ED, identify novel genetic regions that may be used for strain and species typing, and identity a number of novel potential virulence determinants. Among these are Androgen Inducible Gene1, a CXXC receptor kinase, a peroxiredoxin 1-related gene, a Ras family member gene, a Rab geranylgeranyltransferase, and a gene with a UPF0034 domain. Among the four EH strains, an avirulent strain EH (Rahman) was the most divergent and phylogenetically distinct raising the intriguing possibility that genetic subtypes of E. histolytica may be at least partially responsible for the observed variability in clinical outcomes. Our approach shows the utility of a microarray-based genotyping assay to identify genetic variability between Entamoeba isolates and can readily be applied to the study of clinical isolates. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. User Defined
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Project description:Entamoeba histolytica is a protozoan parasite that causes colitis and liver abscesses. Several Entamoeba species and strains with differing levels of virulence have been identified. E. histolytica HM-1:IMSS is a virulent strain, E. histolytica Rahman is a nonvirulent strain, and Entamoeba dispar is a nonvirulent species. We used an E. histolytica DNA microarray consisting of 2,110 genes to assess the transcriptional differences between these species/strains with the goal of identifying genes whose expression correlated with a virulence phenotype. We found 415 genes expressed at lower levels in E. dispar and 32 genes with lower expression in E. histolytica Rahman than in E. histolytica HM-1:IMSS. Overall, 29 genes had decreased expression in both the nonvirulent species/strains than the virulent E. histolytica HM-1:IMSS. Interestingly, a number of genes with potential roles in stress response and virulence had decreased expression in either one or both nonvirulent Entamoeba species/strains. These included genes encoding Fe hydrogenase (9.m00419), peroxiredoxin (176.m00112), type A flavoprotein (6.m00467), lysozyme (6.m00454), sphingomyelinase C (29.m00231), and a hypothetical protein with homology to both a Plasmodium sporozoite threonine-asparagine-rich protein (STARP) and a streptococcal hemagglutinin (238.m00054). The function of these genes in Entamoeba and their specific roles in parasite virulence need to be determined. We also found that a number of the non-long-terminal-repeat retrotransposons (EhLINEs and EhSINEs), which have been shown to modulate gene expression and genomic evolution, had lower expression in the nonvirulent species/strains than in E. histolytica HM-1:IMSS. Our results, identifying expression profiles and patterns indicative of a virulence phenotype, may be useful in characterizing the transcriptional framework of virulence. A species experiment design type assays differences between distinct species. Keywords: species_design
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