Histone Acetylation Dynamics during In Vivo and In Vitro Oocyte Aging in Common Carp Cyprinus carpio.
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ABSTRACT:
SUBMITTER: Waghmare SG
PROVIDER: S-EPMC8199789 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The purpose of the current study was to analyze phenotypic and functional characteristics of common carp (Cyprinus carpio) spermatozoa during in vitro aging and to investigate whether global DNA methylation is affected by sperm aging. Milt was collected from five individual males, stored in vitro on ice in a refrigerator for up to 96 h post stripping (HPS) and used to fertilize eggs with intervals of 1, 24 and 96 h. Computer-assisted sperm analysis and a S3e Cell Sorter was employed to determine the spermatozoa phenotypic characteristics (motility, velocity, concentration and viability). In addition, pH and osmolality of the seminal fluid and the capacity of the spermatozoa to fertilize, hatching rate and health of the resulting embryos were examined at different aging times. Whole-genome bisulfite sequencing was used to compare the global and gene-specific DNA methylation in fresh and aged spermatozoa. The results demonstrated that spermatozoa aging in common carp significantly affects their performance and thus the success of artificial fertilization. The methylation level at the cytosine-phosphate-guanine (CpG) sites increased significantly with 24 HPS spermatozoa compared to the fresh group at 1 HPS and then decreased significantly at 96 HPS. A more detailed investigation of gene specific differences in the DNA methylation was hindered by incomplete annotation of the C. carpio genome in the public databases.
| S-EPMC8198300 | biostudies-literature
Project description:TLR5 is responsible for the recognition of bacterial flagellin in vertebrates. In this study, we cloned the TLR5M gene of common carp using the rapid amplification of cDNA ends (RACE) method. The TLR5M cDNA was 3182?bp in length and contained a 2658-bp open reading frame, which encoded a protein of 885 amino acids (aa). The entire coding region of the TLR5M gene was successfully amplified from genomic DNA and contained a single exon. The aa sequence of carp TLR5M showed the highest similarity (84.46%) to Cirrhinus mrigala. Tissue-specific expression analysis of the TLR5M gene by quantitative real-time polymerase chain reaction revealed its broad distribution in various organs and tissues; however, the highest level of TLR5M expression was noted in the liver. TLR5M gene expression was examined after flagellin stimulation and showed highly significant (p<0.01) induction in the spleen, heart, liver and kidney. The induction of TLR5M was analyzed in various organs infected with Aeromonas hydrophila. TLR5M gene expression in the kidney and spleen was significantly (p<0.01) increased. Concurrently, modulation of TLR5M gene expression and the induction of IFN-?, IL-1?, IL-10 and TNF-?4 were analyzed in peripheral blood leucocytes after lipopolysaccharide, concanavalin A, and flagellin stimulation. In the treated group, significant induction of these genes was noted, although the intensity varied between the tissues. These findings may indicate a crucial role for TLR5M in the innate immunity of common carp in response to pathogenic invasion.
| S-EPMC3785217 | biostudies-literature
Project description:Water from wastewater treatment plants contains concentrations of pharmaceutically active compounds as high as micrograms per liter, which can adversely affect fish health and behavior, and contaminate the food chain. Here, we tested the ability of the common carp hepatic S9 fraction to produce the main metabolites from citalopram, metoprolol, sertraline, and venlafaxine. Metabolism in fish S9 fractions was compared to that in sheep. The metabolism of citalopram was further studied in fish. Our results suggest a large difference in the rate of metabolites formation between fish and sheep. Fish hepatic S9 fractions do not show an ability to form metabolites from venlafaxine, which was also the case for sheep. Citalopram, metoprolol, and sertraline were metabolized by both fish and sheep S9. Citalopram showed concentration-dependent N-desmethylcitalopram formation with Vmax = 1781 pmol/min/mg and Km = 29.7 ?M. The presence of ellipticine, a specific CYP1A inhibitor, in the incubations reduced the formation of N-desmethylcitalopram by 30-100% depending on the applied concentration. These findings suggest that CYP1A is the major enzyme contributing to the formation of N-desmethylcitalopram. In summary, the results from the present in vitro study suggest that common carp can form the major metabolites of citalopram, metoprolol, and sertraline.
| S-EPMC7321103 | biostudies-literature
Project description:Oocyte ageing is the most important factor affecting egg quality of several fish species after ovulation. Oxidative stress has been proposed as the initiator of the oocyte ageing process in other vertebrates. To identify the role of oxidative stress and apoptosis on the progress of oocyte ageing in the common carp Cyprinus carpio, changes in the relative mRNA abundance of selected transcripts were examined. The possible alteration in the oxidation status of the oocytes during ageing was also studied. In addition, the activity of antioxidant enzymes during oocyte ageing was evaluated. Oocytes from 6 females were incubated in vivo for 14 hours post-ovulation (HPO) and in vitro for 10 hours post-stripping (HPS) at 20°C before fertilization. Hatching rates were over 65% up to 4-6 HPO, finally dropping to 1.3% at 12-14 HPO.Hatching rates were over 65% up to 4-6 HPO, finally dropping to 1.3% at 12-14 HPO. Hatching rates were more than 70% for the eggs stored in vitro up to 6 HPS and then decreased to 21.3% at 10 HPS. The results demonstrated no significant changes in the relative mRNA levels of oxidative stress-related genes or genes involved in the cell cycle during the progress of oocyte ageing in common carp. Additionally, the amount of TBARS and carbonyls did not change as time elapsed following ovulation. The apoptosis-related genes however, were significantly altered following the prolonged time interval between ovulation and fertilization. The lack of response of both activities of antioxidant enzymes and oxidation products during oocyte ageing strengthens the conclusion that oxidative stress is unlikely to be a main factor determining the progress of oocyte ageing in common carp. However, an increase in the mRNA abundance of apoptosis-related genes demonstrates that apoptotic pathway might be involved in the progress of oocyte ageing.
| S-EPMC6386366 | biostudies-literature
Project description:BACKGROUND: MicroRNAs (miRNAs) exist pervasively across viruses, plants and animals and play important roles in the post-transcriptional regulation of genes. In the common carp, miRNA targets have not been investigated. In model species, single-nucleotide polymorphisms (SNPs) have been reported to impair or enhance miRNA regulation as well as to alter miRNA biogenesis. SNPs are often associated with diseases or traits. To date, no studies into the effects of SNPs on miRNA biogenesis and regulation in the common carp have been reported. RESULTS: Using homology-based prediction combined with small RNA sequencing, we have identified 113 common carp mature miRNAs, including 92 conserved miRNAs and 21 common carp specific miRNAs. The conserved miRNAs had significantly higher expression levels than the specific miRNAs. The miRNAs were clustered into three phylogenetic groups. Totally 394 potential miRNA binding sites in 206 target mRNAs were predicted for 83 miRNAs. We identified 13 SNPs in the miRNA precursors. Among them, nine SNPs had the potential to either increase or decrease the energy of the predicted secondary structures of the precursors. Further, two SNPs in the 3' untranslated regions of target genes were predicted to either disturb or create miRNA-target interactions. CONCLUSIONS: The common carp miRNAs and their target genes reported here will help further our understanding of the role of miRNAs in gene regulation. The analysis of the miRNA-related SNPs and their effects provided insights into the effects of SNPs on miRNA biogenesis and function. The resource data generated in this study will help advance the study of miRNA function and phenotype-associated miRNA identification.
| S-EPMC3478155 | biostudies-literature
Project description:Juvenile common carp (Cyprinus carpio) were used as a model to investigate acute toxicity and oxidative stress caused by silver nanoparticles (Ag-NPs). The fish were exposed to different concentrations of Ag-NPs for 48 h and 96 h. After exposure, antioxidant enzyme levels were measured, including glutathione-S-transferase (GST), superoxidase dismutase, and catalase (CAT). Other biochemical parameters and histological abnormalities in different tissues (i.e., the liver, gills, and brain) were also examined. The results showed that Ag-NPs agglomerated in freshwater used during the exposure experiments, with particle size remaining <100 nm. Ag-NPs had no lethal effect on fish after 4 days of exposure. Biochemical analysis showed that enzymatic activities in the brain of the fish exposed to 200 μg/L of Ag-NPs were significantly reduced. Varied antioxidant enzyme activity was recorded in the liver and gills. Varied antioxidant enzyme activity was recorded for CAT in the liver and GST in the gills of the fish. However, the recovery rate of fish exposed to 200 μg/L of Ag-NPs was slower than when lower particle concentrations were used. Other biochemical indices showed no significant difference, except for NH(3) and blood urea nitrogen concentrations in fish exposed to 50 μg/L of Ag-NPs. This study provides new evidence about the effects of nanoparticles on aquatic organisms.
| S-EPMC3470888 | biostudies-literature
Project description:With the steady growth of the human population, food security becomes a prime challenge. Aquaculture is the fastest growing sector providing proteins from an animal source, but outbreaks of infectious diseases repeatedly hamper the production and further development of this sector. Breeding of disease-resistant strains is a desired sustainable solution to this problem. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus damaging production of common carp, an important food and ornamental fish. Previously, we have demonstrated successful introgression of CyHV-3 resistance from a feral strain to commercial strains. Here, we used genotyping by sequencing to identify two novel quantitative trait loci (QTLs) for disease survival that map to different linkage groups than two other QTLs that we previously identified. Effects of these four QTLs were validated and further studied in 14 families with various levels of disease resistance. CyHV-3 survival was found to be a quantitative trait conditioned by mild additive QTL effects and by intricate dominant allelic and epistatic QTL-QTL interactions. Both rare feral alleles and alleles common to feral and cultured strains contributed to survival. This and other advantages of feral alleles introgression were demonstrated. These QTLs, which affected survival of individuals within families, had no significant effect on variation in cumulative family % survival, suggesting that more between family variation remains to be explored. Unraveling the underlying genetics of survival is important for enhancing the breeding of resistant strains and our knowledge of disease resistance mechanisms.
| S-EPMC6972736 | biostudies-literature
Project description:Head size is important economic trait for many aquaculture fish which is directly linked to their carcass yield. The genetic basis of head size trait remains unclear in many widely cultured fish species. Common carp (Cyprinus carpio) is one of the most widely studied fish due to its importance on both economic and environmental aspects. In this study, we performed genome-wide association study using 433 Yellow River carp individuals from multiple families to identify loci and genes potentially associated with head size related traits including head length (HL), head length/body length ratio (HBR), eye diameter (ED), and eye cross (EC). QTL mapping was utilized to filter the effects of population stratification and improve power for the candidates identification in the largest surveyed family with a published genetic linkage map. Twelve SNPs showed significant for head size traits in GWAS and 18 QTLs were identified in QTL mapping. Our study combining both GWAS and QTL mapping could compensate the deficiency from each other and advance our understanding of head size traits in common carp. To acquire a better understanding of the correlation between head size and body growth, we also performed comparisons between QTLs of head size traits and growth-related traits. Candidate genes underlying head size traits were identified surrounding the significant SNPs, including parvalbumin, srpk2, fsrp5, igf1, igf3, grb10, igf1r, notch2, sfrp2. Many of these genes have been identified with potential functions on bone formation and growth. Igf1 was a putative gene associated with both head size and body growth in Yellow River carp. The teleost-specific igf3 was a candidate head size related gene, related to both HL and HBR. Our study also indicated the importance of Igf signaling pathway for both growth and head size determination in common carp, which could be potentially used in future selective breeding in common carp as well as other species.
| S-EPMC6190898 | biostudies-literature
Project description:The Cyprinus carpio is one of the most important food fish with over hundred varieties in the world. It shows many morphological and genetic variations after selection breeding. It is also considered an alternative vertebrate fish model to zebrafish. MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been suggested to have a crucial role in embryonic development. However, systemic research on the lncRNAs and miRNAs during embryonic development of C. carpio has not been reported yet. In this study, we investigated the miRNA, lncRNA and mRNA expression profiles during six main embryonic development stages (cleavage (2 hours post-fertilization hpf)), blastocyst (6 hpf), gastrulation (12 hpf), organ formation (20 hpf), hatching (64 hpf) and 1 day post-hatching). A total of 9,888,123 clean reads were obtained frommiRNA library. After filtering, 2886 miRNAs were identified. The results would open the way for future genetic, genomic, and evolutionary studies and enable better understanding of gene regulation during embryonic development of C. carpio.
2019-03-26 | GSE128806 | GEO
Project description:Research on common carp, Cyprinus carpio, is beneficial for zebrafish research because of resources available owing to its large body size, such as the availability of sufficient organ material for transcriptomics, proteomics, and metabolomics. Here we describe the shot gun sequencing of a clonal double-haploid common carp line. The assembly consists of 511891 scaffolds with an N50 of 17?kb, predicting a total genome size of 1.4-1.5?Gb. A detailed analysis of the ten largest scaffolds indicates that the carp genome has a considerably lower repeat coverage than zebrafish, whilst the average intron size is significantly smaller, making it comparable to the fugu genome. The quality of the scaffolding was confirmed by comparisons with RNA deep sequencing data sets and a manual analysis for synteny with the zebrafish, especially the Hox gene clusters. In the ten largest scaffolds analyzed, the synteny of genes is almost complete. Comparisons of predicted exons of common carp with those of the zebrafish revealed only few genes specific for either zebrafish or carp, most of these being of unknown function. This supports the hypothesis of an additional genome duplication event in the carp evolutionary history, which--due to a higher degree of compactness--did not result in a genome larger than that of zebrafish.
| S-EPMC3371262 | biostudies-literature