Project description:In Staphylococcus aureus, the role of the GGDEF domain containing protein GdpS remains poorly understood. Previous studies reported that gdpS mutant strains had decreased biofilm formation due to changes in icaADBC expression that were independent of cyclic-di-GMP levels. We deleted gdpS in three unrelated S. aureus isolates, and analyzed the resultant mutants for alterations in biofilm formation, metabolism and transcription. Dynamic imaging during biofilm development showed that GdpS inhibited early biofilm formation in only two out of the three strains examined, without affecting bacterial survival. However, quantification of biofilm formation using crystal violet staining revealed that inactivation of gdpS affected biofilm formation in all three studied strains. Extraction of metabolites from S. aureus cells confirmed the absence of cyclic-di-GMP, suggesting that biofilm formation in this species differs from that in other Gram-positive organisms. In addition, targeted mutagenesis demonstrated that the GGDEF domain was not required for GdpS activity. Transcriptomic analysis revealed that the vast majority of GGDEF-regulated genes were involved in virulence, metabolism, cell wall biogenesis and eDNA release. Finally, expression of lrgAB or deletion of cidABC in a strain lacking gdpS confirmed the role of GdpS on regulation of eDNA production that occurred without an increase in cell autolysis. In summary, S. aureus GdpS contributes to cell-to-cell interactions during early biofilm formation by influencing expression of lrgAB and cidABC mediated eDNA release. We conclude that GdpS acts as a negative regulator of eDNA release.

2014-06-30 | GSE48656 | GEO

GdpS contributes to Staphylococcus aureus biofilm formation by regulation of eDNA release

2014-06-30 | E-GEOD-48656 | biostudies-arrayexpress

Affymetrix SNP array data for Non-Smoking Female Lung Cancer in Taiwan

Project description:Genome-Wide Screening of Genomic Alterations and Transcriptional Modulation in Non-Smoking Female Lung Cancer in Taiwan

2012-12-31 | GSE33355 | GEO

Towards functional profiling for eDNA based monitoring in coastal environments: a comparison of three approaches

Project description:Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics.

2024-04-14 | E-MTAB-13075 | biostudies-arrayexpress

Genotyping of PKD2 Arg803* in Taiwan ADPKD Cohort

Project description:PKD2 Arg803* is the most common mutation in Taiwan ADPKD Cohort. Genotyping of 96 PKD2 Arg803* individuals was performed in Axiom Genome-Wide TWB 2.0 Array Plate to study the existence of founder mutation in Taiwan

2022-06-07 | E-MTAB-11846 | biostudies-arrayexpress

Pacific salmon gill samples: fate tracking in river

Project description:The long-term viability of Pacific salmon stocks and the fisheries they support are threatened if large numbers die prematurely en-route to spawning grounds. Physiological profiles that were correlated with the fate of wild sockeye salmon during river migration were discovered using functional genomics studies on biopsied tissues. Three independent biotelemetry studies tracked the biopsied fish after tagging in the marine environment over 200 km from the Fraser River, in the lower river 69 km from the river mouth and at the spawning grounds. Salmon carrying the poor performance (unhealthy) profile in the ocean exhibited a 4-times lower probability of arriving to spawning grounds than those with a healthy genomic signature, although generally migrated into the river and to the spawning grounds faster. A related unhealthy signature observed in the river was associated with a 30% reduction in survival to spawning grounds in one of the three stocks tested. At spawning grounds, the same poor performance signature was associated with twice the pre-spawning mortality compared with healthy fish. Functional analysis revealed that the unhealthy signature, which intensified during migration to spawning grounds, was consistent with an intracellular pathogenic infection, likely a virus. These results are the first to suggest a pathogen present in salmon in the marine environment could be a major source of mortality during migration and spawning in the river. This series are gill expression profiles from the study of fish sampled and tagged in the lower river and tracked as they swam towards the spawning grounds.

2010-12-31 | GSE22177 | GEO

Gene expression profile of hepatocellular carcinomain in Taiwan (subset 2)

Project description:In this study, we used RNA-seqeuncing to develop gene expression profile of HCC patients in Taiwan.

2022-03-01 | GSE141200 | GEO