Genomic surveillance of Vibrio sp
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB68309 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genomic surveillance of Vibrio cholerae infections in Austria
| PRJEB68166 | ENA
Project description:Genomic surveillance of Vibrio cholerae infections
| PRJEB61542 | ENA
Project description:Proteomes of Vibrio sp. 1A01 exponentially growing on various carbon sources as well as on chitin. Chitin samples contain planktonic cells, particle-associated proteins and excreted proteins.
2022-05-19 | MSV000089499 | MassIVE
Project description:Brown macroalgae holds an enormous potential as a future feedstock because it rapidly forms large biomasses and has high carbohydrate content (35% of its dry weight consists of alginate and mannitol). However, utilization of brown macroalgae by conventional microbial platforms (e.g., Escherichia coli and Saccharomyces cerevisiae) has been limited due to the inability of these platforms to metabolize alginate. Although recent studies engineered them to utilize alginate, their growth rates and metabolic activities are still too low for industrial applications, likely due to the unoptimized expression of multiple xenogeneic genes. Here, we isolated Vibrio sp. dhg, a novel, fast-growing bacterium that has been naturally evolved for efficient alginate assimilation (growth rate = 0.98 h-1). Especially, both the growth rate and sugar uptake rate of V. sp. dhg are substantially higher than the rates of E. coli for most biomass-derivable sugars. Based on our systematic characterization of its metabolism and gene expression architecture, we were able to develop a genetic toolbox for its engineering. By using this microorganism, we successfully demonstrated its ability to produce a broad spectrum of chemicals from alginate-mannitol mixtures with high productivities (1.1 g ethanol/L/h, 1.3 g 2,3-butanediol and acetoin/L/h, and 0.69 mg lycopene/L/h). Collectively, the V. sp. dhg strain is a powerful platform for the conversion of brown macroalgae sugars whose usage will dramatically accelerate the production of value-added biochemicals in the future.
2019-05-02 | GSE119357 | GEO
Project description:Genomic surveillance of Salmonella Typhi using ONT platform
| PRJEB60768 | ENA
Project description:Macrophages play fundamental roles in regulation of inflammatory responses to pathogens, resolution of inflammation and tissue repair, and maintenance of tissue homeostasis. The long (L) and short (S) isoforms of SP-R210/MYO18A, a macrophage receptor for surfactant protein A (SP-A) and C1q, regulate basal and inflammatory macrophage phenotype at multiple gene expression, translational, and subcellular levels in addition to their SP-A and C1q-mediated functions; disruption of L renders macrophages hyper-inflammatory, although the underlying mechanism had previously been unexplored. We questioned whether disruption of the L isoform would alter the global genomic responses. RNA sequencing analysis of SP-R210L(DN) macrophages revealed basal and influenza induced upregulation of genes associated with inflammatory pathways, including TLR, RIG-I, NOD, and cytoplasmic DNA signaling, whereas knockdown of both SP-R210 isoforms (L and S) only resulted in increased RIG-I and NOD signaling. Chromatin immunoprecipitation sequencing (ChIP-seq) analysis showed increased genome-wide deposition of the pioneer transcription factor PU.1 in SP-R210L(DN) compared to WT cells. ChIP-seq analysis of histone H3 methylation showed alterations in both repressive (H3K9me3 and H3K27me3) and transcriptionally active (H3K9me3) histone marks. Influenza A virus (IAV) infection, which stimulates an array of cytosolic and TLR-mediated antiviral mechanisms, resulted in differential redistribution between proximal promoter and distal sites and decoupling of PU.1 binding from Toll-like receptor regulated gene promoters in SP-R210L(DN) cells. Our findings suggest that SP-R210L-deficient macrophages are poised with an open PU.1-primed chromatin conformation to rapidly respond to inflammatory and metabolic stimuli.
2020-12-31 | GSE164034 | GEO
Project description:SARS-CoV-2 Genomic Surveillance in Greece
| PRJEB43435 | ENA
Project description:We used the bioluminescent squid symbiont, Vibrio fischeri, to identify essential regulatory factors that control expression and function of a strain-specific T6SS encoded within a genomic island. Random transposon mutagenesis revealed that three genes located on the T6SS2-encoding genomic island are necessary to activate expression of a T6SS reporter. We used a proteomics approach to identify proteins that were differentially abundant in mutant strains compared to the wild type when cells were grown in a high-viscosity media.
2021-08-24 | PXD017722 | Pride