Metabarcoding Costa Rica Neotropical lowland rainforest soil bacteria
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ABSTRACT:
PROVIDER: PRJEB28284 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:La Selva Biological Station (Costa Rica) Neotropical lowland rainforest soil DNA metabarcoding of the fungal ITS2
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Project description:La Selva Biological Station (Costa Rica) Neotropical lowland rainforest soil DNA metabarcoding of the 18S V4 rRNA
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Project description:Costa Rica subduction zone Metagenome
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Project description:Small RNA was sequenced from banked peripheral blood serum from 1,134 asthmatic children aged 6 to 14 years who participated in the Genetics of Asthma in Costa Rica Study (GACRS). We filtered the participants into high and low bronchodilator response (BDR) quartiles and used DeSeq2 to identify miRNAs with differential expression (DE) in high (N= 277) vs low (N= 278) BDR group. The putative target genes of DE miRNAs were identified, and pathway enrichment analysis was performed. Results: We identified 10 down-regulated miRNAs having odds ratios (OR) between 0.37 and 0.76 for a doubling of miRNA counts and one up-regulated miRNA (OR=2.26) between high and low BDR group. Further, functional annotation of 11 DE miRNAs were performed as well as of two replicated miRs. Target genes of these miRs were enriched in regulation of cholesterol biosynthesis by SREBPs, ESR-mediated signaling, G1/S transition, RHO GTPase cycle, and signaling by TGFB family pathways.
2023-10-09 | GSE244573 | GEO
Project description:Costa Rica subduction zone Targeted loci environmental
| PRJNA797441 | ENA
Project description:Bats are hosts of diverse coronaviruses (CoVs) known to potentially cross the host-species barrier. For analysing coronavirus diversity in a bat species-rich country, a total of 421 anal swabs/faecal samples from Costa Rican bats were screened for CoV RNA-dependent RNA polymerase (RdRp) gene sequences by a pancoronavirus PCR. Six families, 24 genera and 41 species of bats were analysed. The detection rate for CoV was 1%. Individuals (n = 4) from four different species of frugivorous (Artibeus jamaicensis, Carollia perspicillata and Carollia castanea) and nectivorous (Glossophaga soricina) bats were positive for coronavirus-derived nucleic acids. Analysis of 440 nt. RdRp sequences allocated all Costa Rican bat CoVs to the α-CoV group. Several CoVs sequences clustered near previously described CoVs from the same species of bat, but were phylogenetically distant from the human CoV sequences identified to date, suggesting no recent spillover events. The Glossophaga soricina CoV sequence is sufficiently dissimilar (26% homology to the closest known bat CoVs) to represent a unique coronavirus not clustering near other CoVs found in the same bat species so far, implying an even higher CoV diversity than previously suspected.
| S-EPMC7165833 | biostudies-literature
Project description:Phytopathogens from Costa Rica Genome sequencing and assembly
| PRJNA898399 | ENA
Project description:Rationale: MicroRNAs have emerged as crucial post-transcriptional and network regulators in inflammatory diseases, including asthma. We hypothesized that peripheral blood miRNA would be associated with airflow obstruction in children with asthma, and that some of these effects would also be observable in adults with COPD. Methods: We analyzed small RNA-Seq data from 365 peripheral blood samples from the Genetics of Asthma in Costa Rica Study (GACRS). GACRS comprised children from the Central Valley of Costa Rica age 6-14 years with physician-diagnosed asthma and ≥2 respiratory symptoms or asthma attacks in the prior year. FEV1/FVC percent-predicted was dichotomized at 100%, splitting the cohort into those with and without evidence of airflow obstruction and used as our primary outcome. Differentially expressed (DE) miRs were identified using the DESeq2 package in R with a 10% FDR and adjustment for age, gender, and inhaled corticosteroid (ICS) use. We attempted to replicate the top airflow obstruction-associated microRNAs from the GACRS study in the COPDGene study, in which blood microRNA data were available in 439 current and former smoking adults with and without airflow obstruction (defined as raw FEV1/FVC < 0.7). Results: After QC, we had 361 samples and 649 miRs for DE analysis. Of the 361 samples, 220 and 141 were from subjects without and with airflow obstruction, respectively. We found 1 upregulated (let-7e-5p p=0.0004) and 2 downregulated (miR-342-3p p=0.0002; miR-671-5p p=0.0001) miRs in subjects with airflow obstruction compared to those without airflow obstruction. These three miRNAs were then tested for association with airflow obstruction in the COPDGene study, in which let-7e-5p was upregulated (p = 0.064) and miR-342-3p (p =0.085) was downregulated in participants with FEV1/FVC < 0.7 (n=196) compared to those with FEV1/FVC > 0.7 (n=243). Differentially expressed miR’s target genes were enriched for PI3K-Akt, Hippo, WNT, MAPK, and focal adhesion signaling pathways. We also separately considered the targets of only the two miRNAs that were also associated with FEV1/FVC in the adult current and former smokers, where PI3K-Akt, MAPK and Hippo signaling pathways were among the top five most enriched pathways. Conclusion: Three DE miRs were linked to airflow obstruction in children with asthma. Two miRs were associated with FEV1/FVC in current and former smoking adults. These miRs were involved in asthma and COPD-related pathways: PI3K-Akt, Hippo, MAPK, and focal adhesion signaling pathways. Together these findings provide important evidence that these two disorders may share genetic regulatory systems that contribute to airflow obstruction.
2023-10-01 | GSE244036 | GEO