Duck reovirus SY isolate:DRV-SY | breed:Cherry Valley ducks
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA541784 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9046000.fastq.gz | Fastqsanger.gz | |||
| SRR9046001.fastq.gz | Fastqsanger.gz | |||
| SRR9046002.fastq.gz | Fastqsanger.gz | |||
| SRR9046003.fastq.gz | Fastqsanger.gz | |||
| SRR9045994.fastq.gz | Fastqsanger.gz |
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Project description:Muscle development and lipid deposition are complex processes regulated by a coordinated expression profile of genes. Pekin ducks displayed a significant difference from Cherry Valley duck in muscle fiber development and IMF contents. Genetic comparisons between these two breeds would contribute to the exploration of mechanisms underlying the phenotypic differences. In the present study, breast tissues of Pekin (BD) and Cherry Valley (CD) ducks were used for RNA-seq in two different time points (3 and 6-week) to investigate the transcriptome basis. A total of 16705 genes from duck breast muscle were detected as positively expressed genes (RPKM>0.1) and 2273 genes were regarded as novel genes. Differentially expressed genes (DEGs) in BD3 VS CD3 were regarded as muscle development-related genes as CD3 grown faster than BD3 in muscle fibers. DEGs in BD6 VS CD6 were regarded as lipid-related genes as a much higher IMF contents in BD6 than CD6 while no differences observed in 3-week. DEGs obtained from BD3 VS BD6 and CD3 VS CD6 were also analyzed as relative genes here. In all, 9 genes (MAT1A, KAZALD1, SHROOM3, KLHL6, MYH13, ALDOA, TNNT2, PDLIM3 and PFKM) were validated as muscle development correlated candidate genes, and another 11 genes (DHCR24, CNTFR, ANGPTL4, BCL6, HIP1, TRIB1, ADORA1, C1QTNF2, CD36, PRKAG2 and ACSL1) were regarded as lipid correlated genes in duck. What’s more, functional analysis confirmed that the immune reaction, ECM and energy metabolism also correlated with muscle development and lipid deposition closely. The present study not only enlarged the duck genetic information pool but also provided a dozen of candidate genes related to muscle development and lipid deposition, which laid a firm foundation for the further studies on molecular mechanisms in duck.
2016-12-27 | GSE92920 | GEO
Project description:Duck reovirus (DRV) is an typical aquatic bird pathogen belonging to the Orthoreovirus genus of the Reoviridae family. Reovirus causes a fatal disease resulting to huge economic losses to the duck industry. Although DRV has been identified and isolated long ago, the responses of Cairna moschata to classical/novel duck reovirus (CDRV/NDRV) infections are largely unknown. Using an integrated approach involving TMT labeling and LC-MS/MS analysis, proteomes of C. moschata liver cells under C/NDRV infections were analyzed. In total, 5571 proteins were identified, among which 5015 proteins were quantified. The differential expressed proteins (DEPs) between the control and infected liver cells displayed various biological functions and diverse subcellular localizations. Among the DEPs, most of the metabolism-related proteins were down-regulated, suggesting a decrease in the basal metabolisms under C/NDRV infections. Several important factors in the complement, coagulation and fibrinolytic systems were significantly up-regulated by C/NDRV infections, indicating that the serine protease-mediated innate immune system may play roles in the responses to C/NDRV infections. Moreover, a number of molecular chaperones were identified, and no significantly changes in their abundances were observed in the liver cells. Our data may give a comprehensive resource for investigating the regulation mechanism involved in the responses to C/NDRV infections in C. moschata.
2018-10-22 | PXD008623 | Pride
Project description:The novel duck reovirus (NDRV) can cause hemorrhage and necrosis on the spleen of Pekin ducks, this disease has resulted in great economic losses to the duck industry. However, the molecular pathogenesis of NDRV remains poorly understood. In the current study, the quantitative proteomic analysis of NDRV-infected duck embryo fibroblasts was performed to explore the cellular protein changes in response to viral infection through iTRAQ coupled with the LC–MS/MS method. A total of 6,137 proteins were obtained in cell samples at 24 hours post infection. Of these, 179 differentially expressed proteins (DEPs) were identified (cutoff set to 1.5-fold change), including 89 upregulated and 90 downregulated proteins. Bioinformatic analysis showed that DEPs can be divided into the cellular component, molecular function, and biological process, they were mainly involved in the signal transduction, infectious diseases, cell growth and death, and the immune system. The subcellular localization of most proteins was cytoplasm. Importantly, the expression of signal transducer and activator of transcription 1 (STAT1) and various interferon-stimulated genes (ISGs) were upregulated after NDRV infection. The mRNA transcripts of some ISGs were consistent with proteomic data, showing an increased trend. Results of our study suggested that NDRV infection can elicit the strong expression changes of cellular proteins, and activate the expression of ISGs from the point of quantitative proteomic analysis. The study provides a new insight into the understanding of NDRV pathogenesis.
2021-09-07 | PXD020171 | Pride
Project description:BackgroundAlthough several studies have revealed that the sensitivity of ducklings to duck Tembusu virus (DTMUV) was related to age, however, DTMUV was originally isolated from egg-laying ducks, and the ovary was the target organ of this virus. Cherry Valley breeding ducks aged 15- and 55-week-old (they are reserve breeding ducks and the normal egg-laying breeding ducks, respectively) were infected with DTMUV, using intramuscular injection, to study the effect of age-related difference on the pathogenicity of DTMUV in breeding ducks.ResultsExaminations of clinical symptoms, gross and microscopic lesions, viral loads, cytokines and serum neutralizing antibodies were performed. Results showed that obvious clinical symptoms, such as depression, ruffled feathers, ataxia and egg-laying drop were observed in the 55-week-old laying ducks, with five ducks dying at 5-7 days post infection (dpi). The 15-week-old ducks showed slight symptoms during infection. Gross lesions were severe and characterized by the congestion, hemorrhage and swelling of some organs in the 55-week-old ducks, including the hemorrhage of endocardium, hepatomegaly, splenomegaly, oviduct hemorrhage, hyperemia and deformation of the ovary. Mild endocardial hemorrhage and hepatosplenomegaly were observed in the 15-week-old ducks. Similarly, there was a significant difference in microscopic lesions between the two groups. The older ducks displayed severe microscopic lesions, specifically in the hemorrhage, interstitial inflammatory cell infiltration of the endocardium, typical viral encephalitis and hemorrhage in the ovary. But on the whole, the 15-week-old ducks showed milder lesions. Viral loads in tissues of the older group were significantly higher than those of the younger group. The levels of interferon (IFN)-γ, interleukin (IL)-2 and neutralizing antibody in the 15-week-old ducks were higher than in the 55-week-old ducks at the early stage of the DTMUV infection, suggesting the immune response in the younger ducks to DTMUV was stronger than in the older ducks.ConclusionsThese results demonstrated that age-related differences in susceptibility to DTMUV in breeding ducks was significant, with 55-week-old egg-laying ducks being more susceptible to DTMUV than 15-week-old reserve breeding ducks.
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Project description:Duck plague caused by duck plague virus (DPV) is an acute and contagious disease. To better understand the pathogenic mechanism of duck plague virus in ducklings, an infection experiment was performed. Our results showed that typical symptoms were observed in the infected ducklings. DPV could replicate quickly in many tissues, leading to pathological lesions, especially on the spleen. Real-time quantitative PCR demonstrated that expression of many innate immune-related genes was mostly up-regulated in the brain, and the antiviral innate immune response was established, but not sufficient to restrict viral replication. In contrast, although the expression of many major pattern recognition receptors (PRRs) increased in the spleen, the expression of most cytokines was declined. Our study indicates that DPV is a pantropic virus that can replicate rapidly in tissues, causing serious pathological lesions but the immune responses are different in the spleen and brain. To our knowledge, this is the first report to systematically explore the expression profiles of the immune genes in the DPV-infected ducks. Our data provide a foundation for further study of the pathogenicity of duck plague.
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Project description:Anas platyrhynchos isolate:PD, CD | breed:Pekin duck | cultivar:Native and Cherry Valley Pekin duck Genome sequencing and assembly
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Project description:Duck reovirus (DRV), a member of the genus Orthoreovirus in the family Reoviridae, was first isolated from Muscovy ducks. The disease associated with DRV causes great economic losses to the duck industry. However, the responses of duck (Cairna moschata) to the classical/novel DRV (C/NDRV) infections are largely unknown. To reveal the relationship of pathogenesis and immune response, the proteomes of duck spleen cells under the control and C/NDRV infections were compared. In total, 5986 proteins were identified, of which 5389 proteins were quantified. The different expressed proteins (DEPs) under the C/NDRV infections showed displayed various biological functions and diverse subcellular localizations. The proteins related to the serine protease system were siginificantly changed, suggesting that the activated serine protease system may play an important role under the C/NDRV infections. Furthermore, the differences in the responses to the C/NRDV infections between the duck liver and spleen cells were compared. Only a small number of common DEPs were identified in both liver and spleen cells, suggesting diversified pattern involved in the responses to the C/NRDV infections. However, the changes in the proteins involved in the serine protease systems were similar in both liver and spleen cells. Our data may give a comprehensive resource for investigating the responses to C/NDRV infections in ducks.
2020-08-24 | PXD009703 | Pride
Project description:Duck reovirus (DRV) is a fatal member of the genus Orthoreovirus in the family Reoviridae. The disease caused by DRV leads to huge economic losses to the duck industry. Post-translational modification is an efficient strategy to enhance the immune responses to virus infection. However, the roles of protein phosphorylation in the responses of ducklings to Classic/Novel DRV (C/NDRV) infections are largely unknown. Using a high-resolution LC-MS/MS integrated to highly sensitive immune-affinity antibody method, phosphoproteomes of Cairna moschata spleen tissues under the C/NDRV infections were analyzed, producing a total of 8,504 phosphorylation sites on 2,853 proteins. After normalization with proteomic data, 392 sites on 288 proteins and 484 sites on 342 proteins were significantly changed under the C/NDRV infections, respectively. To characterize the differentially phosphorylated proteins (DPPs), a systematic bioinformatics analyses including Gene Ontology annotation, domain annotation, subcellular localization, and Kyoto Encyclopedia of Genes and Genomes pathway annotation were performed. Two important serine protease system-related proteins, coagulation factor X and fibrinogen α-chain, were identified as phosphorylated proteins, suggesting an involvement of blood coagulation under the C/NDRV infections. Furthermore, 16 proteins involving the intracellular signaling pathways of pattern-recognition receptors were identified as phosphorylated proteins. Changes in the phosphorylation levels of MyD88, NF-κB, RIP1, MDA5 and IRF7 suggested a crucial role of protein phosphorylation in host immune responses of C. moschata. Our study provides new insights into the responses of ducklings to the C/NDRV infections at PTM level.
2021-09-09 | PXD016423 | Pride
Project description:Interferon regulatory factor 8 (IRF8) is also known as interferon (IFN) consensus sequence binding protein (ICSBP), which plays an important role in IFN signal transduction. In this study, we cloned the full-length coding sequence of Cherry Valley duck IRF8 (duIRF8) and analyzed its structure. In addition, we tested the distribution of IRF8 in the tissues of healthy Cherry Valley ducks, and the changes in IRF8 expression levels in the tissues after virus infection. The results show that the open reading frame (ORF) of IRF8 is 1293 bp, encodes 430 amino acids, and have 3 conserved domains: the N-terminal DBD domain, the C-terminal IAD domain, and the NLS domain. Besides, from the analysis of the phylogenetic tree, it can be known that the duIRF8 has the highest homology with the anser cygnoides, and has less homology with the fish. Analyzing the distribution level of IRF8 in the tissues, it is found that the expression level of IRF8 in the liver of Cherry Valley duck is the highest. However, after infection with duck Tambusu virus, novel duck reovirus, and duck plague virus, the expression of IRF8 in the spleen and brain all showed up-regulation. These data indicate that IRF8 is involved in the host's innate immune response against virus in Cherry Valley duck.
| S-EPMC8703080 | biostudies-literature
Project description:Interferon regulatory factor 4 (IRF4) is a multifunctional transcription factor that plays an important regulatory role in the interferon (IFN) signaling. IRF4 participates in the process of antivirus, Th cell differentiation and B cell maturation by regulating the expression of IFN and some lymphokines. In this study, Cherry Valley duck IRF4 (duIRF4) was cloned and its cDNA was analyzed. Expression of duIRF4 in a wide variety of tissues and changes in duIRF4 expression due to viral infection also was detected by quantitative real-time PCR. The results show that duIRF4 contains 1,341 bp of ORF encoding a protein with 446 amino acids and contains 3 domains: DNA-binding domain (DBD), IRF-association domain (IAD) and nuclear localization signal (NLS). Quantitative real-time PCR analysis showed that duIRF4 was evenly expressed in all tissues examined, with the highest expression in the spleen, followed by the bursa of Fabricius, and lower in the skin and brain. In addition, expression of duIRF4 in the brain and spleen was significantly upregulated after being infected by duck plague virus, duck Tembusu virus, and novel duck reovirus. These data suggest that duIRF4 may be involved in innate immune response.
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