Similar Datasets
Project description:Perfluorooctane sulfonate (PFOS) has been manufactured for over 50 years in increasing quantities and has been used for several industrial and commercial aims. Due to the persistence and the bioaccumulation of this pollutant, it can be found worldwide in wildlife and humans. Biochemical effects of PFOS exposure are mainly studied in mammalian model species and information about effects on fish species remain largely scarce. This lack of toxicity data points out that there is an urgent need for the mechanistic molecular understanding of the mode of action of this pollutant. In the present study, common carp (Cyprinus carpio) was exposed through water for 14 days at concentrations of 0.1; 0.5 and 1 mg/l PFOS. Liver was selected as target tissue. Custom microarrays were constructed from cDNA libraries obtained with Suppression Subtractive Hybridization-Polymerase chain reaction (SSH-PCR) experiments. Microarray data revealed that the expression of several genes in the liver was influenced by PFOS exposure and real-time PCR was used to confirm these gene expression changes. The affected genes were mainly involved in energy metabolism, reproduction and stress response. Furthermore, the relative condition factor and the hepatosomatic index of the exposed fish were significantly lower after 14 days of exposure as well as the available glycogen reserves. At all levels of biological organization, indications of a trade-off between the metabolic cost of toxicant exposure on one hand and processes vital to the survival of the organism on the other hand were seen. Our results support the prediction that increases in energy expenditure negatively affects processes vital to the survival of an organism, such as growth. Keywords: PFOS, common carp, microarray, condition factor, energy reserves, metabolic cost There were 3 biological replicates for each exposure concentration. For each biological replicate control versus exposed hybridizations were carried out. The mean of the biological replicates was calculated for the differentially expressed genes.
2008-08-15 | E-GEOD-10980 | biostudies-arrayexpress
Project description:Common carp is one of the main commercial fishes captured and cultured worldwide. Although common carp genome is not finished yet, this study provides a first large scale cloning and characterization of common carp miRNAs and their potential targets. These miRNAs add to the growing database of new miRNA and lay the foundation for further understanding of miRNA function in gene regulation of common carp.
2012-07-16 | GSE35131 | GEO
Project description:Common carp is one of the main commercial fishes captured and cultured worldwide. Although common carp genome is not finished yet, this study provides a first large scale cloning and characterization of common carp miRNAs and their potential targets. These miRNAs add to the growing database of new miRNA and lay the foundation for further understanding of miRNA function in gene regulation of common carp. We constructed a small RNA library from 17 Cyprinus carpio samples.
2012-07-16 | E-GEOD-35131 | biostudies-arrayexpress
Project description:Perfluorooctane sulfonate (PFOS) has been manufactured for over 50 years in increasing quantities and has been used for several industrial and commercial aims. Due to the persistence and the bioaccumulation of this pollutant, it can be found worldwide in wildlife and humans. Biochemical effects of PFOS exposure are mainly studied in mammalian model species and information about effects on fish species remain largely scarce. This lack of toxicity data points out that there is an urgent need for the mechanistic molecular understanding of the mode of action of this pollutant. In the present study, common carp (Cyprinus carpio) was exposed through water for 14 days at concentrations of 0.1; 0.5 and 1 mg/l PFOS. Liver was selected as target tissue. Custom microarrays were constructed from cDNA libraries obtained with Suppression Subtractive Hybridization-Polymerase chain reaction (SSH-PCR) experiments. Microarray data revealed that the expression of several genes in the liver was influenced by PFOS exposure and real-time PCR was used to confirm these gene expression changes. The affected genes were mainly involved in energy metabolism, reproduction and stress response. Furthermore, the relative condition factor and the hepatosomatic index of the exposed fish were significantly lower after 14 days of exposure as well as the available glycogen reserves. At all levels of biological organization, indications of a trade-off between the metabolic cost of toxicant exposure on one hand and processes vital to the survival of the organism on the other hand were seen. Our results support the prediction that increases in energy expenditure negatively affects processes vital to the survival of an organism, such as growth. Keywords: PFOS, common carp, microarray, condition factor, energy reserves, metabolic cost
2008-08-15 | GSE10980 | GEO
Project description:purpose?To elucidate the relationship of utilization different type of diets in fish method?enzyme activity determination and transcriptome sequencing were performed in common carp fed with single animal diet group (group AD), plant diet group (group PD) and mix diets group (group MD). Group MD as control group results? 916 and 1296 differentially expressed genes were identified between group AD vs MD and PD vs MD. Protein digestion and absorption, bile secretion, hematopoietic cell lineage and intestinal immune network for IgA production pathways were significantly differentially expressed between common carp fed with single type of diet and mix diets. Conclusion?common carp fed with mix diets had stronger immunity than common carp fed with single type of diets.
2019-01-19 | GSE125366 | GEO
Project description:Genome-wide analysis of skin color-related lncRNA and mRNA expression in Koi carp, Cyprinus carpio L. LncRNAs information linked to fish skin color regulation is over-limited. In this study, Illumina sequencing and bioinformatics were primarily conducted on black, white and red skin colors of Koi carp. A total of 590,415,050 clean reads, 446,614 putative transcripts, 4,252 known and 72,907 novel lncRNAs were simultaneously obtained, respectively. Out of these genes, 92 significant differentially expressed lncRNAs and 722 mRNAs were excavated. Ccr_lnc5622441, Ccr_lnc765201 were found up-regulated in black and red skins; Ccr_lnc14074601 were up-regulated in white skin; and premelanosome proteins a (Pmela), tyrosinase (Tyr) were up-regulated in black skin, etc. Quantitative real-time PCR (qRT-PCR) further validated 12 differentially expressed genes were consistent with RNA-seq. Moreover, 70 lncRNAs on 107 target mRNAs in cis and 79 lncRNAs on 41,625 target mRNAs in trans were investigated, the networks revealed one lncRNAs can connected with numerous mRNAs, vice versa. These findings broadened the lncRNAs landscape of skin colors and provided new insights into the mechanisms underlying lncRNAs mediated pigmentation and differentiation in Koi carp.
2019-01-15 | GSE125039 | GEO
Project description:Bulk transcriptomes of common carp during embryogenesis and under thermal stress
| PRJNA824204 | ENA
Project description:Cyprinid herpesvirus 3 (CyHV-3), also known as koi herpesvirus (KHV), is the aetiological agent of an emerging and lethal disease in common and koi carp. In this work we studied the immune response of two genetically different lines of common carp (Polish K and Polish R3) infected with CyHV-3 by immersion. The two carp lines presented a 20% difference in survival rate and, furthermore, significant difference in virus loads measured at day 3 post infection (p.i.). Microarray analysis revealed that 581 genes in line K (330 up-regulated, 251 down-regulated) and 107 genes in line R3 (77 up-regulated, 30 down-regulated), were at least 2-fold differentially expressed at day 3 p.i. compared to day 0. Genes which were at least 4-fold differentially expressed in both lines were selected as potential markers of an infection of common carp by CyHV-3. This group includes 17 up-regulated and only 1 down-regulated genes. In addition, microarray analysis revealed no significant differences in gene expression between line K and R3 at day 0. At day 3 p.i. there were, however, 76 genes that were at least 2-fold differentially expressed between the two lines. The kinetics of expression of T cell markers and selected cytokines indicate for higher activation of immune response in more resistant R3 line. Thus, our study revealed that differences in resistance to CyHV-3 between two carp lines can be correlated with differentially expressed immune-related genes. The experiment included four biological replicates with no dye swaps for (i) each strain (K and R3) and (ii) each condition (day 0 and day 3).
2012-01-05 | E-GEOD-30426 | biostudies-arrayexpress