Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Macrobrachium nipponense

PROVIDER: GSE72418 | GEO | 2016/06/01

SECONDARY ACCESSION(S): PRJNA294000

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-06-01 | E-GEOD-72418 | biostudies-arrayexpress

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]

2016-06-01 | GSE72416 | GEO

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]

2016-06-01 | E-GEOD-72416 | biostudies-arrayexpress

Molecular Cloning and Functional Characterization of a Hexokinase from the Oriental River Prawn Macrobrachium nipponense in Response to Hypoxia.

Project description:Metabolic adjustment to hypoxia in Macrobrachium nipponense (oriental river prawn) implies a shift to anaerobic metabolism. Hexokinase (HK) is a key glycolytic enzyme in prawns. The involvement of HK in the hypoxia inducible factors (HIFs) pathway is unclear in prawns. In this study, the full-length cDNA for HK (MnHK) was obtained from M. nipponense, and its properties were characterized. The full-length cDNA (2385 bp) with an open reading frame of 1350 bp, encoded a 450-amino acid protein. MnHK contained highly conserved amino acids in the glucose, glucose-6-phosphate, ATP, and Mg+2 binding sites. Quantitative real-time reverse transcription PCR assays revealed the tissue-specific expression pattern of MnHK, with abundant expression in the muscle, and gills. Kinetic studies validated the hexokinase activity of recombinant HK. Silencing of HIF-1? or HIF-1? subunit genes blocked the induction of HK and its enzyme activities during hypoxia in muscles. The results suggested that MnHK is a key factor that increases the anaerobic rate, and is probably involved in the HIF-1 pathway related to highly active metabolism during hypoxia.

| S-EPMC5486078 | biostudies-literature

Identification and Characterization of the DMRT11E Gene in the Oriental River Prawn Macrobrachium nipponense.

Project description:The doublesex and mab-3 related transcription factor (DMRT) gene family involvement in sex development is widely conserved from invertebrates to humans. In this study, we identified a DM (Doublesex/Mab-3)-domain gene in Macrobrachium nipponense, which we named MniDMRT11E because it has many similarities to and phylogenetically close relationships with the arthropod DMRT11E. Amino acid alignments and structural prediction uncovered conservation and putative active sites of the DM domain. Real-time PCR analysis showed that the MniDMRT11E was highly expressed in the ovary and testis in both males and females. Cellular localization analysis showed that DMRT11E was mainly located in the oocytes of the ovary and the spermatocyte of the testis. During embryogenesis, the expression level of MniDMRT11E was higher at the cleavage stage than at other stages. During the different stages of ovarian development, MniDMRT11E expression gradually increased from OI to OIII and decreased to the lowest level at the end of OIV. The results indicated that MniDMRT11E probably played important roles in embryonic development and sex maturity in M. nipponense. MniDMRT11E dsRNA injection also significantly reduced vitellogenin (VG) expression and significantly increased insulin-like androgenic gland factor (IAG) expression, indicating a close relationship in gonad development.

| S-EPMC6480115 | biostudies-literature

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.

| S-EPMC5900017 | biostudies-literature

A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense.

Project description:BackgroundThe oriental river prawn, Macrobrachium nipponense, is an economically important shrimp in China. Male prawns have higher commercial value than females because the former grow faster and reach larger sizes. It is therefore important to reveal sex-differentiation and development mechanisms of the oriental river prawn to enable genetic improvement.ResultsWe sequenced 293.3 Gb of raw Illumina short reads and 405.7 Gb of Pacific Biosciences long reads. The final whole-genome assembly of the Oriental river prawn was ∼4.5 Gb in size, with predictions of 44,086 protein-coding genes. A total of 49 chromosomes were determined, with an anchor ratio of 94.7% and a scaffold N50 of 86.8 Mb. A whole-genome duplication event was deduced to have happened 109.8 million years ago. By integration of genome and transcriptome data, 21 genes were predicted as sex-related candidate genes.ConclusionThe first high-quality chromosome-level genome assembly of the oriental river prawn was obtained. These genomic data, along with transcriptome sequences, are essential for understanding sex-differentiation and development mechanisms in the oriental river prawn, as well as providing genetic resources for in-depth studies on developmental and evolutionary biology in arthropods.

| S-EPMC7812440 | biostudies-literature

Molecular Cloning and Expression Analysis of Lactate Dehydrogenase from the Oriental River Prawn Macrobrachium nipponense in Response to Hypoxia.

Project description:Metabolic adaption to hypoxic stress in crustaceans implies a shift from aerobic to anaerobic metabolism. Lactate dehydrogenase (LDH) is a key enzyme in glycolysis in prawns. However, very little is known about the role of LDH in hypoxia inducible factor (HIF) pathways of prawns. In this study, full-length cDNA of LDH (MnLDH) was obtained from the oriental river prawn Macrobrachium nipponense, and was characterized. The full-length cDNA is 2267-bp with an open reading frame of 999 bp coding for a protein of 333 amino acids with conserved domains important for function and regulation. Phylogenetic analysis showed that MnLDH is close to LDHs from other invertebrates. Quantitative real-time PCR revealed that MnLDH is expressed in various tissues with the highest expression level in muscle. MnLDH mRNA transcript and protein abundance in muscle, but not in hepatopancreas, were induced by hypoxia. Silencing of hypoxia-inducible factor 1 (HIF-1) α or HIF-1β subunits blocked the hypoxia-dependent increase of LDH expression and enzyme activity in muscle. A series of MnLDH promoter sequences, especially the full-length promoter, generated an increase in luciferase expression relative to promoterless vector; furthermore, the expression of luciferase was induced by hypoxia. These results demonstrate that MnLDH is probably involved a HIF-1-dependent pathway during hypoxia in the highly active metabolism of muscle.

| S-EPMC6073699 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data