Marine metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA396231 | ENA |
REPOSITORIES: ENA
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Project description:Increasing seawater’s calcium concentration has shown to increase reef building (scleractinian) coral’s calcification rates. In this way the expression of the genes that are associated with the calcification process also altered and, thus can be identified. Needless to say that the overall gene repertoire that participate in the coral calcification process and its molecular mechanisms have not yet been revealed, although sporadic genes that are related to the process have been discovered and investigated. In this study, nubbins of the Red Sea scleractinian coral, Stylophora pistillata were treated with increased calcium concentrations seawater (addition of 100 gm/L) and the genes that have been up-regulated were compared to the genes expression profile of corals with natural seawater calcium concentration. Measurements of AT were taken at mid-day (11:00) and in nighttime (23:00), to record the calcification rates of coral individuals under normal and increased calcium seawater concentrations. In order to reveal the gene involved in the calcification process, S. pistillata fragments of normal and of increased calcium concentrations were sampled for microarray RNA transcriptional profiling at two time-points (mid-day and nighttime).Results of this study have revealed that Smad genes may play a role in the coral skeletal growth apparatus. This study show that the calcification molecular mechanism is conserved Among identified genes are large group of genes that are characterized in the TGF-b/BMP signal transduction pathways which have been revealed in other organisms to participate in bone and cartilage tissue development molecular processes.
2017-06-29 | GSE87159 | GEO
Project description:On going efforts are directed at understanding the mutualism between the gut microbiota and the host in breast-fed versus formula-fed infants. Due to the lack of tissue biopsies, no investigators have performed a global transcriptional (gene expression) analysis of the developing human intestine in healthy infants. As a result, the crosstalk between the microbiome and the host transcriptome in the developing mucosal-commensal environment has not been determined. In this study, we examined the host intestinal mRNA gene expression and microbial DNA profiles in full term 3 month-old infants exclusively formula fed (FF) (n=6) or breast fed (BF) (n=6) from birth to 3 months. Host mRNA microarray measurements were performed using isolated intact sloughed epithelial cells in stool samples collected at 3 months. Microbial composition from the same stool samples was assessed by metagenomic pyrosequencing. Both the host mRNA expression and bacterial microbiome phylogenetic profiles provided strong feature sets that clearly classified the two groups of babies (FF and BF). To determine the relationship between host epithelial cell gene expression and the bacterial colony profiles, the host transcriptome and functionally profiled microbiome data were analyzed in a multivariate manner. From a functional perspective, analysis of the gut microbiota's metagenome revealed that characteristics associated with virulence differed between the FF and BF babies. Using canonical correlation analysis, evidence of multivariate structure relating eleven host immunity / mucosal defense-related genes and microbiome virulence characteristics was observed. These results, for the first time, provide insight into the integrated responses of the host and microbiome to dietary substrates in the early neonatal period. Our data suggest that systems biology and computational modeling approaches that integrate “-omic” information from the host and the microbiome can identify important mechanistic pathways of intestinal development affecting the gut microbiome in the first few months of life. KEYWORDS: infant, breast-feeding, infant formula, exfoliated cells, transcriptome, metagenome, multivariate analysis, canonical correlation analysis 12 samples, 2 groups
2012-03-19 | E-GEOD-31075 | biostudies-arrayexpress
Project description:Global survey of coral (Stylophora pistillata and Pocillopora verrucosa) and seawater bacteria
| PRJNA280923 | ENA