Ontology highlight
ABSTRACT:
PROVIDER: PRJNA783562 | ENA |
REPOSITORIES: ENA
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Project description:Vanee2010 - Genome-scale metabolic model of
Cryptosporidium hominis (iNV213)
This model is described in the article:
A genome-scale metabolic
model of Cryptosporidium hominis.
Vanee N, Roberts SB, Fong SS, Manque
P, Buck GA.
Chem. Biodivers. 2010 May; 7(5):
1026-1039
Abstract:
The apicomplexan Cryptosporidium is a protozoan parasite of
humans and other mammals. Cryptosporidium species cause acute
gastroenteritis and diarrheal disease in healthy humans and
animals, and cause life-threatening infection in
immunocompromised individuals such as people with AIDS. The
parasite has a one-host life cycle and commonly invades
intestinal epithelial cells. The current genome annotation of
C. hominis, the most serious human pathogen, predicts 3884
genes of which ca. 1581 have predicted functional annotations.
Using a combination of bioinformatics analysis, biochemical
evidence, and high-throughput data, we have constructed a
genome-scale metabolic model of C. hominis. The model is
comprised of 213 gene-associated enzymes involved in 540
reactions among the major metabolic pathways and provides a
link between the genotype and the phenotype of the organism,
making it possible to study and predict behavior based upon
genome content. This model was also used to analyze the two
life stages of the parasite by integrating the stage-specific
proteomic data for oocyst and sporozoite stages. Overall, this
model provides a computational framework to systematically
study and analyze various functional behaviors of C. hominis
with respect to its life cycle and pathogenicity.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180071.
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2015-07-30 | MODEL1507180071 | BioModels
Project description:Kelp are the largest photosynthetic organisms in the ocean with tissue differentiation and complex life cycles. Other multicellular organisms with similar complexity such as plants and animals are well known to posses epigenetic mechanisms such as DNA methylation to control development and morphogenesis. Despite plant-like body plans and the presence of different life-cycle stages, the kelp species Saccharina japonica has only a very low level of DNA methylation, yet we have found strong evidence for differential methylation of regulatory elements and protein-coding genes which seem to contribute to the formation of life-cycle stages, tissue differentiation, growth and halogen metabolism. Thus, DNA methylation seems to play an important role in kelp, which has not been reported before.
2018-07-17 | GSE117191 | GEO
Project description:The life cycle of schistosomes is complex, being characterised by a series of distinct parasitic and free-living phases involving an invertebrate snail host, water and a mammalian host. A custom designed oligonucleotide microarray was utilized to profile developmental gene expression in the Asian blood fluke, Schistosoma japonicum during these parasitic and free-living transitions. Total RNAs were isolated from lung schistosomula, juvenile females and males (paired but little or no egg production), adult males and females (paired with full scale egg production), eggs, miracidia, sporocysts and cercariae. We focused on the three distinct environmental phases of the lifecycle - aquatic/snail (eggs, miracidia, sporocysts, cercariae), juvenile (lung schistosomula and paired pre-egg laying adults) and adult (paired males and females, both examined separately) stages. Single colour schistosome life cycle with technical replicates in triplicate: Separate adult female and male worms at 4, 6, 6.5 and 7 weeks; cercariae; eggs; miracidia; schistosomula; and sporocysts. This study includes 6 adult male biological replicates.
2010-06-19 | E-GEOD-12704 | biostudies-arrayexpress
Project description:Genetic Evidence for Parasexual Life Cycle in Cochliopodium (Amoebozoa)
| PRJNA394890 | ENA
Project description:Brugia malayi transcriptomics at different life cycle stages
| PRJEB2709 | ENA
Project description:Hepatitis B virus (HBV) is a hepatotropic virus that can regulate many host cellular gene expressions participating in the HBV life cycle, liver inflammation and hepatocellular injury. However, the underlying mechanism of differential gene expression is not understood. We report here a genome-wide analysis of histone methylation on two histone H3 lysine residues (H3K4me3 and H3K27me3) and gene expression profiles in HepG2 and HepG2.2.15 cells. We found that specific correlation exists between gene expression and the amounts of H3K4me3 (positive correlation) and H3K27me3 (negative correlation) across the gene body. These correlations displayed three distinct modes (repressive, active and poised), reflecting different functions of these genes in the HBV life cycle, liver inflammation and hepatocellular injury. Furthermore, a permissive chromatin state of each gene was established by a combination of different histone modifications. Our findings reveal a complex regulation by histone methylation in differential gene expression and suggest that histone methylation may be responsible for the HBV life cycle, liver inflammation and hepatocellular injury induced by HBV. Examination of 2 different histone modifications (H3K4me3, H3K27me3) in 2 cell types (HepG2, HepG2.2.15).
2012-08-01 | E-GEOD-35462 | biostudies-arrayexpress
Project description:Hepatitis B virus (HBV) is a hepatotropic virus that can regulate many host cellular gene expressions participating in the HBV life cycle, liver inflammation and hepatocellular injury. However, the underlying mechanism of differential gene expression is not understood. We report here a genome-wide analysis of histone methylation on two histone H3 lysine residues (H3K4me3 and H3K27me3) and gene expression profiles in HepG2 and HepG2.2.15 cells. We found that specific correlation exists between gene expression and the amounts of H3K4me3 (positive correlation) and H3K27me3 (negative correlation) across the gene body. These correlations displayed three distinct modes (repressive, active and poised), reflecting different functions of these genes in the HBV life cycle, liver inflammation and hepatocellular injury. Furthermore, a permissive chromatin state of each gene was established by a combination of different histone modifications. Our findings reveal a complex regulation by histone methylation in differential gene expression and suggest that histone methylation may be responsible for the HBV life cycle, liver inflammation and hepatocellular injury induced by HBV. A large-scale analysis of gene expression of 2 different cell types (HepG2, HepG2.2.15) using a digital gene expression (DGE) tag profiling approach.
2012-08-01 | E-GEOD-35464 | biostudies-arrayexpress
Project description:Nematostella vectensis is a venomous organism with a complex life cycle. We harness different approaches to study venom composition dynamics along its life cycle. Our methods include but not limited to transcriptomica and proteomics. Here we perform semi quantitative analysis of Nematostella proteom at 4 developmental stages to compare abundance of different toxins.
2018-02-14 | PXD008218 | Pride
Project description:the growth of the mosquito population is directly related to the spread of malaria, the Four Stage Life Cycle is incorporated to model the effects of climate change and interspecies competition within the mosquito life cycle stages of Egg, Larvae, and Pupae.
2024-09-02 | BIOMD0000000922 | BioModels