Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31093309_1.fastq.gz | Fastqsanger.gz | |||
| SRR31093309_2.fastq.gz | Fastqsanger.gz | |||
| SRR31093310_1.fastq.gz | Fastqsanger.gz | |||
| SRR31093310_2.fastq.gz | Fastqsanger.gz | |||
| SRR31093311_1.fastq.gz | Fastqsanger.gz |
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Project description:World aquaculture production of the Pacific white shrimp (Litopenaeus vannamei) is estimated to account for 80% of the total shrimp produce worldwide. The global demand for shrimp has driven the industry to utilize and rely on semi-intensive and intensive shrimp systems. In the United States, Pacific white shrimp production can take place in semi-intensive earthen ponds, recirculating aquaculture systems (RAS), biofloc technology and green water. In this study, the effects of lowering dissolved oxygen conditions in outdoor green water tanks on global gene expression is examined. Tissue samples from the gill and intestine were collected for gene expression analysis via RNA sequencing. Among all comparisons, RNA sequencing revealed the up-regulation of a single gene: hydroxyacid oxidase 1 gene. The HOA1 gene was found to be 7-fold higher in the intestine sample at the medium aeration level compare to that of the high (control) level. The HAO1 gene, also known as glycolate oxidase 1 (GOX1) is a gene related to the 2-hydroxyacid oxidase enzyme that is part of the oxidoreductase family and plays a role in glyoxylate and dicarboxylate metabolism. The identification of a single differentially expressed gene across all analyzed samples suggests that Pacific white shrimp exposed to lowering dissolved oxygen set points does not induce global changes in gene expression at these levels.
2025-07-17 | GSE281217 | GEO
Project description:The phenomenon of trained immunity, which facilitates vaccine development for disease control, has been identified in shrimp; however, the mechanism remains elusive. In the present study, we found that histone H3K27 acetylation (H3K27ac) mediated by the lysine acetyltransferase KAT8 plays an important role in preventing white spot syndrome virus (WSSV) infection in the shrimp Marsupenaeus japonicus. We then successfully established a model of trained immunity via the use of UV-inactivated WSSV to explore the underlying mechanism(s) in shrimp. In UV-WSSV-trained shrimp, the glycolysis and tricarboxylic acid (TCA) cycle metabolic pathways were enhanced and acetyl-CoA concentrations were increased. As the acetyl group donor, acetyl-CoA promotes KAT8 activity to increase H3K27 acetylation. H3K27ac is deposited at the promoter region of the transcription factor Dorsal to facilitate its expression and then Dorsal promotes the expression of an interferon-like cytokine, Vago5, and antimicrobial peptides that act against WSSV infection. H3K27ac is also deposited at the promoter region of hexokinase 2 and isocitrate dehydrogenase, which positively regulates glycolysis and the TCA cycle in a feedforward manner. Our results reveal a novel mechanism of trained immunity induced by UV-WSSV in shrimp and provide a theoretical basis for the development of antiviral vaccines for disease control in shrimp aquaculture.
2025-08-01 | GSE273689 | GEO
Project description:The primary goal of this project is to monitor host global gene expression patterns in response to viral infection in the shrimp, Litopenaeus stylirostris. Specific Pathogen Free (SPF) L. stylirostris were obtained from High Health Aquaculture (Honolulu, Hawaii) and kept in environmentally controlled tanks. For control, animals were injected with saline (30 ul) between the second and third tergal plates of the lateral side of the tail using a 1 ml tuberculin syringe. Infected individuals were inoculated with homogenate created from IHHNV infected shrimp tissue. After 24 hours, the shrimp were sacrificed and tissue was collected from the ventral and flash frozen in liquid nitrogen and stored in the -80 ºC freezer. Libraries of sequence tags were generated via the Long-SAGE kit (Invitrogen®, Carlsbad, CA) until the ditag PCR preparation step and directly pyrosequenced by 454 Roche.
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Project description:Microbial community of shrimp aquaculture
| PRJNA429671 | ENA