Project description:Up until now, the existence of Dnmt2-mediated DNA methylation has mostly been supported by focal analyses in organisms that contain Dnmt2, but no Dnmt1 or Dnmt3 DNA methyltransferase. In these organisms, several independent studies have also provided support for a biologically important function of Dnmt2-dependent DNA methylation. For example, Dnmt2-dependent methylation in Entamoeba histolytica, the causative agent of amebic dysentery, has been connected to the parasite s virulence. However, global DNA methylation levels in Entamoeba have been found to be very low. In addition, no specific features, such as CpG-specificity and specificity for certain genetic subcompartments have been described. This distinguishes Dnmt2-dependent methylation patterns from all other known methylomes and has raised questions about the validity of the underlying results. We have used whole-genome bisulfite sequencing for an unbiased characterization of the Entamoeba histolytica methylome at single-base resolution in a E.histolytica strain HM-1:IMSS devoid of significant level of EhDnmt2 (Ehmeth) expression. Paired-end BS-sequencing was performed on an Illumina Genome Analyzer with read lengths of 105 base pairs and an average insert size of 200 bp.
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
Project description:This dataset contains RNA-seq data from Entamoeba histolytica strains, including a KERP2-knockdown strain (psAP-KERP2gs) and a control strain (psAP-mock). To investigate the functional role of KERP2 (EHI_065630), the knockdown strain was generated using small interfering RNAs with the psAP-2-Gunma plasmid. RNA-Seq analysis revealed distinct transcriptional profiles between KERP2gs and psAP-mock strains. GO and KEGG pathway enrichment analyses identified upregulation of genes involved in proteolysis regulation, sulfur amino acid metabolism, and amoebiasis in the KERP2-knockdown strain. Notably, cysteine synthases (EHI_024230, EHI_160930), methionine γ-lyase (EHI_057550), cysteine protease (EHI_010850), and pore-forming peptides (EHI_169350, EHI_194540, EHI_15940) were significantly upregulated. These findings suggest a potential role for KERP2 in regulating parasitic activities, possibly through chromatin binding. This dataset provides a valuable resource for studying KERP2-associated gene expression changes in E. histolytica.
Project description:Up until now, the existence of Dnmt2-mediated DNA methylation has mostly been supported by focal analyses in organisms that contain Dnmt2, but no Dnmt1 or Dnmt3 DNA methyltransferase. In these organisms, several independent studies have also provided support for a biologically important function of Dnmt2-dependent DNA methylation. For example, Dnmt2-dependent methylation in Entamoeba histolytica, the causative agent of amebic dysentery, has been connected to the parasite s virulence. However, global DNA methylation levels in Entamoeba have been found to be very low. In addition, no specific features, such as CpG-specificity and specificity for certain genetic subcompartments have been described. This distinguishes Dnmt2-dependent methylation patterns from all other known methylomes and has raised questions about the validity of the underlying results. We have used whole-genome bisulfite sequencing for an unbiased characterization of the Entamoeba histolytica methylome at single-base resolution in a E.histolytica strain HM-1:IMSS devoid of significant level of EhDnmt2 (Ehmeth) expression.
Project description:The bacteria Cobetia marina is globally distributed in different oceanic ecosystems and is able to grow in a wide range of temperatures from 0°C to 41°C, with an optimal growth temperature close to 35°C. Its remarkable characteristics include its ability to form biofilm, produce biosurfactants, and use petroleum-derived hydrocarbons as energy and carbon source. In this context, Cobetia marina is a model for biofilm production and the production of diverse biomolecules of relevance for human and animal health, as well as for environmental protection and recovery. This dataset shows the differential expression of genes and gene regulatory circuits that explain the adaptation of Cobetia marina to different temperatures, serving as a model of evolution in response to selection pressures such as temperature changes in the marine environment. In this study, Cobetia marina was grown at 16°C, 35°C, 38°C, and 41°C to establish differential gene expression using high-throughput RNA sequencing.
Project description:This dataset contains the transcriptome sequence of Zostera marina as produced by Illumina sequencing. Four tissues were sequenced, female flower in late and early stages of development, the male flower, the root and leaf tissue.
Project description:we used high-throughput Illumina Genome Analyzer IIx (GAIIx) technology to sequence the small RNA transcriptomes of the mangrove species, Avicennia marina. Based on sequence similarity or the secondary structure of precursors, we have identified 193 conserved miRNAs and 26 novel miRNAs in the small RNA transcriptome of Avicennia marina.
Project description:This dataset contains the transcriptome sequence of Zostera marina as produced by Illumina sequencing. Four tissues were sequenced, female flower in late and early stages of development, the male flower, the root and leaf tissue. Full transcriptome sequencing of four tissues, including female flower at two time points in development