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Environment Sample

ABSTRACT: Unraveling the effect of the combination of modified atmosphere packaging and Epsilon Poly L Lysine on the physicochemical properties and bacterial community of greater amberjack

PROVIDER: PRJNA887851 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR21835152_subreads.fastq.gz	Fastqsanger.gz
	SRR21835153_subreads.fastq.gz	Fastqsanger.gz
	SRR21835154_subreads.fastq.gz	Fastqsanger.gz
	SRR21835155_subreads.fastq.gz	Fastqsanger.gz
	SRR21835156_subreads.fastq.gz	Fastqsanger.gz

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Molecular Adaptation to Ambient Salinity Oscillations in Greater Amberjack (Seriola dumerili): Implications to Aquaculture

Project description:Ambient salinity is one of the crucial abiotic factors that poses substantial impacts on fish growth, development and reproduction. Greater amberjack (Seriola dumerili) is of high economic value because, and its reproduction and survival are sensitive to water salinity. To better understand the molecular adaptive mechanism to salinity fluctuations in greater amberjack, we performed comparative transcriptome analysis for gill and kidney between the optimum salinity (30 ppt, CK) and undesired regimes (10 and 40 ppt). For the gill, the skeletal development was provoked upon either hypo- or hyper-salinity stimuli, and the development of pronephros, as well as vascular endothelial cells and cortisol-mediated mitochondria-rich cell, was activated in response to the salinity alterations in kidney. These enhancements may encourage the maintenance of the gill and kidney structures and alleviate the salinity-induced damage. Ion channels NKCC1 and CFTR and the transporters for ammonium and other substances were highly upregulated in the gills and kidney, respectively, which act important roles in the osmoregulation of greater amberjack. More important, undesirable alterations of ambient salinity were found to pose adverse impacts on the immune function of greater amberjack, which may increase the risk of pathogen infection and reduce the security and yield of aquaculture of greater amberjack. In addition, deviation from the optimum salinity condition may result in undesirable uptake and accumulation of environmental toxins in greater amberjack, which attracts further attention to the food safety. Collectively, these novel findings advance our knowledge on adaptative mechanisms to ambient salinity oscillations in greater amberjack and provide a theoretical guidance for the optimal breeding mode for the aquaculture of greater amberjack.

2023-06-24 | GSE220485 | GEO

RNA sequencing analysis of 5637 cells with D-xyl@epsilonPLCDs

Project description:We designed D-xylose-modified, epsilon-poly-L-lysine-based carbon dots (D-xyl@epsilonPLCDs) to effectively inhibit intracellular UPEC. D-xyl@εPLCDs effectively entered cells, reduced bacterial adhesion and promoted intracellular UPEC clearance. To investigate the regulation of immune responses in bladder epithelial 5637 cells after treatment with D-xyl@epsilonPLCDs, RNA sequencing analysis were performed.

2024-07-23 | GSE236507 | GEO

RNA sequencing analysis of bladder tissue from CFT073-infected C57B/6J mice with or without treatments of D-xyl@epsilonPLCDs and epsilonPLCDs

Project description:We designed D-xylose-modified, epsilon-poly-L-lysine-based carbon dots (D-xyl@epsilonPLCDs) to effectively inhibit intracellular UPEC. Treatment with D-xyl@epsilonPLCDs ultimately resulted in a reduction of UPEC in the bladders of mouse UTIs model. To investigate the regulation of immune responses in bladders of CFT073-infected mice post-D-xyl@epsilonPLCDs treatment, RNA sequencing analysis were performed.

2024-07-23 | GSE236506 | GEO

An RNA sequencing data set revealing differentially expressed transcripts during ε-poly-L-lysine production in Streptomyces albulus.

Project description:Purpose: Streptomyces albulus is an industrial producer of ε-poly-L-lysine, an antimicrobial cationic homo poly-amino acid used practically as a natural food preservative. Here, we present RNA sequencing data set unveiling differentially expressed transcripts during ε-poly-L-lysine production in the most extensively studied poly-L-Lys producer, S. albulus NBRC14147. Methods: During the poly-L-Lys fermentation, cells grown for 8 hours and 35 hours were harvested as growth phase cells and production phase cells, respectively, and total RNA were extracted individually. A 100-bp paired-end mRNA sequencing was performed for each sample on the Illumina HiSeq 2500 system. Result: Using an optimized data analysis workflow, we were able to map more than 44 million sequence reads per sample to the reference genome (GenBank accession number ASM385166v1). Differential gene expression analysis was performed using the edgeR. The RNA-seq data revealed that a total of 2449 genes were considered to be differentially expressed during poly-L-Lys production using a fold change cutoff of log2 less than -1 and greater than 1 (equivalent to a ±2-fold change). Conclusion: Our data will serve as a primary source for investigating the regulatory mechanism which govern poly-L-Lys production in S. albulus NBRC14147.

2022-01-19 | GSE192684 | GEO

Project description:Greater amberjack genetic variants

| PRJEB24756 | ENA

Project description:Greater amberjack larvae microbiome

| PRJNA875121 | ENA

Listeria monocytogenes J0161 shows altered resistance characteristics when grown at low temperature and under anaerobic conditions.

Project description:Listeria monocytogenes is a food-borne pathogen and the causative agent of listeriosis, an infection which typically arises through the consumption of contaminated foodstuffs. L. monocytogenes is a psychotrophic and facultatively anaerobic; properties which permit growth under refrigeration conditions and within modified atmosphere packaging. Through transcriptional changes L. monocytogenes is able to mount adaptive responses against stressors. Such responses typically cross protect against subsequent stresses.

2016-12-30 | GSE84879 | GEO

Transcriptional analysis of THP-1 cells stimulated by bacterial extracellular vesicles enriched by ultracentrifugation and an ε-poly- L-lysine-based method

Project description:We propose an isolation strategy based on a broad-spectrum antimicrobial epsilon-poly-L–lysine (ε-PL) to precipitate bacterial extracellular vesicles (BEVs) at a relatively low centrifugal speed (10,000 × g). Compared to the standard ultracentrifugation (UC) strategy, our method can enrich BEVs from large volumes of media inexpensively and rapidly. The precipitated BEVs can be recovered by adjusting pH and ionic strength of the media, followed by ultrafiltration step to remove ε-PL and achieve buffer exchange. To address whether BEVs isolated by these two methods lead to different host responses, we isolated Escherichia coli (E. coli) and Staphylococcus aureus BEVs from bacterial culture media using ultracentrifugation and our ε-poly- L-lysine-based method, respectively. Then we stimulated THP-1 cells with the isolated BEVs and the global transcript profiles were evaluated by the RNA-seq technique. Compared with the unstimulated THP-1 cells, BEV isolated by both methods could trigger a striking alteration in the gene expression pattern. Among the functions significantly enriched by these DEGs were immune response and leucocyte chemotaxis. The results indicated that the BEVs isolated by the ε-PL-based method also retained the in vitro biological activity as the commonly used ultracentrifugation.

2022-08-02 | GSE207009 | GEO

Seriola dumerili

Project description:Greater amberjack (Seriola dumerili) EST analysis

| PRJDB5896 | ENA

Seriola dumerili

Project description:Greater amberjack (Seriola dumerili) whole genome resequencing

| PRJDB6634 | ENA