Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1124178 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In this work, we used a functional gene microarray approach (GeoChip) to assess the soil microbial community functional potential related to the different wine quality. In order to minimize the soil variability, this work was conducted at a “within-vineyard” scale, comparing two similar soils (BRO11 and BRO12) previously identified with respect to pedological and hydrological properties within a single vineyard in Central Tuscany and that yielded highly contrasting wine quality upon cultivation of the same Sangiovese cultivar
2020-03-04 | GSE146289 | GEO
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
Project description:Background: Bacterial spores can remain dormant for decades, yet harbor the exceptional capacity to rapidly resume metabolic activity and recommence life. Although germinants and their corresponding receptors have been known for more than 30 years, the molecular events underlying this remarkable cellular transition from dormancy to full metabolic activity are only partially defined. Results: Here, we examined whether protein phospho-modifications occur during germination, the first step of exiting dormancy, thereby facilitating spore revival. Utilizing Bacillus subtilis as a model organism, we performed phosphoproteomic analysis to define the Ser/Thr/Tyr phosphoproteome of a reviving spore. The phosphoproteome was found to chiefly comprise newly identified phosphorylation sites located within proteins involved in basic biological functions, such as transcription, translation, carbon metabolism and spore-specific determinants. Quantitative comparison of dormant and germinating spore phosphoproteomes revealed phosphorylation dynamics, indicating that phospho-modifications could modulate protein activity during this cellular transition. Furthermore, by mutating select phosphorylation sites located within proteins representative of key biological processes, we established a functional connection between phosphorylation and the progression of spore revival. Conclusions: In this study we provide for the first time a phosphoproteomic view of a germinating bacterial spore. We show that the spore phosphoproteome is dynamic and present evidence that phosphorylation events play an integral role in facilitating spore revival.
2015-08-27 | PXD002559 | Pride
Project description:Summary
To facilitate more accurate spore proteomic analysis, the current study focuses on inducing homogeneous sporulation by overexpressing kinA and assesses the effect of sporulation synchronization on spore resistance, structures, the germination behavior at single-spore level and the proteome. The results indicate that, in our set up, the synchronized sporulation by overexpressing kinA can generate a spore yield of 70% within 8 hours. The procedure increases spore wet heat resistance and thickness of the spore coat and cortex layers, whilst delaying the time to spore phase-darkening and burst after addition of germinant. The proteome analysis reveals that the upregulated proteins in the kinA induced spores, compared to spores without kinA induction as well as the wildtype spores, are mostly involved in spore formation. The downregulated proteins mostly belong to the categories of coping with stress, carbon and nitrogen metabolism, as well as regulation of sporulation. Thus, while kinA overexpression enhances sporulation synchronicity it also has profound effects on the central equilibrium of spore formation and spore germination through modulation of the spore molecular composition and stress resistance physiology.
2020-04-28 | MSV000085346 | MassIVE
Project description:The application of sensors in viticulture is a fast and efficient method to monitor grapevine vegetative, yield, and quality parameters and determine spatial intra-vineyard variability. Molecular analysis at the gene expression level can further contribute to the understanding of the observed variability by elucidating how pathways contributing to different grape quality traits behave in zones diverging on any of these parameters. The intra-vineyard variability of a Cabernet Sauvignon vineyard was evaluated through a Normalized Difference Vegetation Index (NDVI) map calculated from a multispectral image and detailed ground-truthing (e.g., vegetative, yield, and berry ripening compositional parameters). The relationships between NDVI and ground measurements were explored by correlation analysis. Moreover, berries were investigated by microarray gene expression analysis performed at five time points from fruit set to full ripening. Comparison between the transcriptomes of samples taken from locations with the highest and lowest NDVI values identified 968 differentially expressed genes. Spatial variability maps of the expression level of key berry ripening genes showed consistent patterns aligned with the vineyard vigor map. These insights indicate that berries from different vigor zones present distinct molecular maturation programs and suggest that transcriptome analysis may be a valuable tool for the management of vineyard variability.
2024-02-27 | GSE254304 | GEO
Project description:The transcriptome profiles of sporulating vs non-sporulating cells, within an isogenic culture were compared. RNA was isolated from endospore containing cells which were separated from non-spore forming cells using buoyant density gradient centrifugation within an isogenic culture (details in Veening et al, submitted).
2010-05-25 | E-GEOD-9266 | biostudies-arrayexpress