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Identification and characterization analysis of the Oriental River Prawn (Macrobrachium nipponense) microRNA response to hypoxia using a deep sequencing approach

ABSTRACT: Identification and characterization analysis of the Oriental River Prawn (Macrobrachium nipponense) microRNA response to hypoxia using a deep sequencing approach

PROVIDER: PRJNA294000 | ENA |

REPOSITORIES: ENA

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Identification and characterization analysis of the Oriental River Prawn (Macrobrachium nipponense) microRNA response to hypoxia using a deep sequencing approach [miRNA-Seq]

2016-06-01 | GSE72417 | GEO

Identification and characterization analysis of the Oriental River Prawn (Macrobrachium nipponense) microRNA response to hypoxia using a deep sequencing approach [miRNA microarray analysis]

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Macrobrachium nipponense breed:Oriental river prawn

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Identification and characterization analysis of the Oriental River Prawn (Macrobrachium nipponense) microRNA response to hypoxia using a deep sequencing approach [miRNA-Seq]

Project description:MicroRNAs (miRNAs) function as regulators in a broad range of phenotypes. The Oriental River Prawn (Macrobrachium nipponense) is an important commercial species that is widely distributed in freshwater and low-salinity estuarine regions of China and other Asian countries. To date, there are no reports describing M. nipponense miRNAs. In this study, Solexa deep sequencing technology was used for high-throughput analysis of miRNAs in a small RNA library isolated from four M. nipponense tissues (gill, hepatopancreas, muscle and hemocytes). In total, 9,227,356 reads were obtained, 4,293,155 of which were related to 267 unique miRNAs, including 203 conserved and 64 prawn-specific miRNAs. Furthermore, miRNA features including length distribution and end variations were characterized. Annotation of targets revealed a broad range of biological processes and signal transduction pathways regulated by M. nipponense miRNAs. In addition, 880 co-expressed and 39 specific (25 normoxia-specific and 14 hypoxia-specific) miRNAs of four combined tissues of prawns that may be involved in the response to hypoxia were confirmed using miRNA microarray analysis. Real-time quantitative PCR (qPCR) analysis of eight miRNAs in the normoxia and hypoxia groups showed good concordance between the sequencing and qPCR data. This study provides the first large-scale identification and characterization of M. nipponense miRNAs and their potential targets, and represents a foundation for further characterization of their roles in the regulation of the diversity of hypoxia processes.

2016-06-01 | E-GEOD-72417 | biostudies-arrayexpress

Identification and characterization analysis of the Oriental River Prawn (Macrobrachium nipponense) microRNA response to hypoxia using a deep sequencing approach [miRNA microarray analysis]

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Macrobrachium nipponense isolate:oriental river prawn

Project description:Macrobrachium nipponense isolate:oriental river prawn Raw sequence reads

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Based on the Metabolomic Approach the Energy Metabolism Responses of Oriental River Prawn Macrobrachium nipponense Hepatopancreas to Acute Hypoxia and Reoxygenation

Project description:Hypoxia represents a major physiological challenge for prawns and is a problem in aquaculture. Therefore, an understanding of the metabolic response mechanism of economically important prawn species to hypoxia and re-oxygenation is essential. However, little is known about the intrinsic mechanisms by which the oriental river prawn Macrobrachium nipponense copes with hypoxia at the metabolic level. In this study, we conducted gas chromatography-mass spectrometry-based metabolomics studies and assays of energy metabolism-related parameters to investigate the metabolic mechanisms in the hepatopancreas of M. nipponense in response to 2.0 O2/L hypoxia for 6 and 24 h, and reoxygenation for 6 h following hypoxia for 24 h. Prawns under hypoxic stress displayed higher glycolysis-related enzyme activities and lower mRNA expression levels of aerobic respiratory enzymes than those in the normoxic control group, and those parameters returned to control levels in the reoxygenated group. Our results showed that hypoxia induced significant metabolomic alterations in the prawn hepatopancreas within 24 h. The main metabolic alterations were depletion of amino acids and 2-hydroxybutanoic acid and accumulation of lactate. Further, the findings indicated that hypoxia disturbed energy metabolism and induced antioxidant defense regulation in prawns. Surprisingly, recovery from hypoxia (i.e., reoxygenation) significantly affected 25 metabolites. Some amino acids (valine, leucine, isoleucine, lysine, glutamate, and methionine) were markedly decreased compared to the control group, suggesting that increased degradation of amino acids occurred to provide energy in prawns at reoxygenation conditions. This study describes the acute metabolomic alterations that occur in prawns in response to hypoxia and demonstrates the potential of the altered metabolites as biomarkers of hypoxia.

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Comparative Phosphoproteomics Reveals a Role for AMPK in Hypoxia Signaling in Testes of Oriental River Prawn (Macrobrachium nipponense)

Project description:Hypoxia is one of the major stresses in aquaculture animals. Recently, we reported that hypoxia disrupts the endocrine system and inhibits testicular function of oriental river prawns (Macrobrachium nipponense), but the molecular mechanism of testes responded to hypoxia remains largely unknown. In the present study, we aimed to integrate whole phosphoproteomic profiles of hypoxia-treated testes of the oriental river prawn (Macrobrachium nipponense). We successfully isolated sperm cells, and evaluated mitochondrial morphology and function using laser confocal microscopy, flow cytometry, and biochemical analyses. Quantitative proteomics identified 117 differentially abundant phosphorylated proteins, and these proteins are mainly involved in the pathways related to cellular processes, including autophagy, apoptosis, FoxO signaling pathway. Protein–protein interaction analysis clustered these phosphoproteins into three groups, many of which have been suggested to impact carbohydrate metabolism, autophagy and signal regulation in testes. Western blotting confirmed that phosphorylated proteins including AMPK, ULK1, and TP53 (of the AMPK pathway) may contribute to testicular dysfunction caused by hypoxia. Further, we investigated the potential roles of AMP-activated protein kinase (AMPK)’s in testes mitochondrial autophagy and apoptosis in M. nipponense as induced by hypoxia. Simultaneous knockdown of AMPKα in sperm cells led to a decrease in FOXO3a phosphorylation at Ser413, upregulation of caspase-3 and caspase-9 activities, and an increased apoptosis rate. These results improve our understanding of hypoxia-induced energy metabolism disorders in the testes of M. nipponense.

2021-03-09 | PXD024614 |

Analysis of the transcriptome, proteome, histological, and biochemical profiles of oriental river prawn Macrobrachium nipponense under long-term salinity exposure

Project description:the transcriptome changes in long-term different salinity gradients were determined to investigate the related gene responsible for the molecular involvements to M. nipponense after long-term salinity exposure.

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oriental river prawn intestine

Project description:oriental river prawn intestinal microbial community diversity

| PRJNA542767 | ENA