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Development of gene expression profile for a seasonal variation study in a natural population of Riba-Roja, in the Ebro River, Spain

ABSTRACT: To analyze the impact of seasonal and environmental variations on the physiology and metabolism of zebramussel, we use a custom microarray developed in our laboratory, using 4057 publicly availabe DNA sequences from Dreissena and other realted genera. Transcriptome profiles were analyszed using half-body samples captured in Riba Roja (low Ebro River), a location considered relatively free of chemical pollution, at three different stages of the vital cycle. The results showed a clear separation on transcriptome profiles between samples collected in February and June (pre- and spawning, respectively) and samples collected during gonad resorption (September). A total of 753 transcripts changed significantly their mRNA levels during these three months (ANOVA p<0.01, fc ±1.5). These changes could be considered as response to variations of temperature, reproductive stages, as well as food availability. Genes involved in oxidative stress were overrepresented in September, whereas genes related to reproductive functions were overrrepresented in the spawning and pre-spawning period.

ORGANISM(S): Dreissena polymorpha

PROVIDER: GSE35353 | GEO | 2012/01/27

SECONDARY ACCESSION(S): PRJNA152733

REPOSITORIES: GEO

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Development of gene expression profile for a seasonal variation study in a natural population of Riba-Roja, in the Ebro River, Spain

Project description:To analyze the impact of seasonal and environmental variations on the physiology and metabolism of zebramussel, we use a custom microarray developed in our laboratory, using 4057 publicly availabe DNA sequences from Dreissena and other realted genera. Transcriptome profiles were analyszed using half-body samples captured in Riba Roja (low Ebro River), a location considered relatively free of chemical pollution, at three different stages of the vital cycle. The results showed a clear separation on transcriptome profiles between samples collected in February and June (pre- and spawning, respectively) and samples collected during gonad resorption (September). A total of 753 transcripts changed significantly their mRNA levels during these three months (ANOVA p<0.01, fc ±1.5). These changes could be considered as response to variations of temperature, reproductive stages, as well as food availability. Genes involved in oxidative stress were overrepresented in September, whereas genes related to reproductive functions were overrrepresented in the spawning and pre-spawning period. For each season (February: pre-spawning; June: Spawning; September: gonad resorption) it was used 2 biological replicates using the half body as a target tissue to analyze .

2012-01-27 | E-GEOD-35353 | biostudies-arrayexpress

Development of gene expression profile in different tissues of zebra mussel and larvae

Project description:To analyze the different pattern of expression among tissues in D. polymorpha it was used acustom microarray designed in our laboratory using 4057 publicly availabe DNA sequences from Dreissena and other realted genera. Transcriptome profiles were analyszed using gills, digestive gland, gonad and half a body of adult zebra mussel and larvae 24 h pf. The samples analyzed in the microarray were not treated in order to detect the normal pattern of expression in each tissue. A total of 221 transcripts changed significantly their mRNA levels in the different tissues (ANOVA p<0.01, fc ±1.5). The results showed a clear separation on transcriptome profiles between samples with the main changes in gills, larvae and half a body.

2012-01-27 | GSE35352 | GEO

Development of gene expression profile in different tissues of zebra mussel and larvae

2012-01-27 | E-GEOD-35352 | biostudies-arrayexpress

Factorial Microarray Analysis of Zebra Mussel Adhesion Process under the Impact of Multiple Environmental Factors

Project description:Factorial Microarray Analysis of Zebra Mussel (Dreissena polymorpha) Adhesion Process under the Impact of Multiple Environmental Factors The expression profiles of the zebra mussel byssus unique genes in our cDNA microarray can be influenced by multiple factors. Three environmental factors plus adhesion status were considered as four main factors in this study.

2009-07-10 | GSE16397 | GEO

Blood plasma proteomic profiles of pink salmon Oncorhynchus gorbuscha Walbaum, 1792 during spawning migration

Project description:The pink salmon (Oncorhynchus gorbuscha) is a commercial anadromous fish species of the family Salmonidae. The species has a peculiar life cycle that includes spawning migration from marine to freshwater environments, which is accompanied by significant adaptive changes in the body, both the physiological and biochemical. This study described and revealed the variability of blood plasma proteomes of female and male pink salmon collected from three different biotopes - marine, estuarine and riverine - that the fish pass through spawning migration. Identification and comparative analysis of pink salmon blood plasma protein profiles were performed using proteomic and bioinformatic approaches. Blood proteomes of female and male spawners collected from different biotopes were qualitatively and quantitatively distinguished. Females differed primarily by proteins associated with reproductive system development (certain vitellogenin and choriogenin), lipid transport (fatty acid binding protein) and energy production (fructose 1,6-bisphosphatase), and males - by proteins involved in blood coagulation (fibrinogen), immune response (lectins) and reproductive processes (vitellogenin). Differentially expressed sex-specific proteins were implicated in proteolysis (aminopeptidases), platelet activation (β- and γ-chain fibrinogen), cell growth and differentiation (a protein containing the TGF_BETA_2 domain) and lipid transport processes (vitellogenin and apolipoprotein). The results obtained are of fundamental and practical importance, providing to the existing knowledge of biochemical adaptations to spawning of pink salmon, representative of the economically important migratory fish species.

2023-06-07 | PXD042278 | Pride

Transcriptome analysis of a PRRSV-infected and control PAMs

Project description:Transcriptomes analysis of long noncoding RNA (lncRNA) and mRNA expression profiles of the porcine alveolar macrophages (PAMs) after porcine reproductive and respiratory syndrome virus (PRRSV) infection in vitro. We obtained 105,627,026 clean reads from 109,443,286 raw reads. A total of 951 annotated and 751 novel lncRNAs were identified. PAMs showed distinct transcriptome profiles after PRRSV infection. It was observed that 126 lncRNAs and 753 mRNAs were differentially expressed between PRRSV-infected and control group PAMs.

2019-06-20 | GSE132735 | GEO

Pacific salmon gill samples: fate tracking at spawning grounds

Project description:The long-term viability of Pacific salmon stocks and the fisheries they support are threatened if large numbers die prematurely en-route to spawning grounds. Physiological profiles that were correlated with the fate of wild sockeye salmon during river migration were discovered using functional genomics studies on biopsied tissues. Three independent biotelemetry studies tracked the biopsied fish after tagging in the marine environment over 200 km from the Fraser River, in the lower river 69 km from the river mouth and at the spawning grounds. Salmon carrying the poor performance (unhealthy) profile in the ocean exhibited a 4-times lower probability of arriving to spawning grounds than those with a healthy genomic signature, although generally migrated into the river and to the spawning grounds faster. A related unhealthy signature observed in the river was associated with a 30% reduction in survival to spawning grounds in one of the three stocks tested. At spawning grounds, the same poor performance signature was associated with twice the pre-spawning mortality compared with healthy fish. Functional analysis revealed that the unhealthy signature, which intensified during migration to spawning grounds, was consistent with an intracellular pathogenic infection, likely a virus. These results are the first to suggest a pathogen present in salmon in the marine environment could be a major source of mortality during migration and spawning in the river. This series are gill expression profiles from the study of fish at the Weaver creek spawning grounds, and were observed for pre-spawning mortality or successful spawning.

2010-12-31 | GSE22347 | GEO

Comparison of male and female floral organs

Project description:We conducted micro-array analysis to quantify the global transcriptome variations in floral organs of a male and female tree allowing for identification of sex-linked transcripts. We used RNA samples from male floral buds in August and female floral buds in September. Bud scale were removed. While the sampling time differed, the developmental stage of the floral organs was similar between the male and female. Five independent samples of floral bud tissues with bud scales removes were collected from the upper crown of a sexually mature male tree and female tree. RNA was extracted from tissues and hybridized on Affymetrix Genechip Poplar Genome Array.

2011-12-29 | E-GEOD-29336 | biostudies-arrayexpress